ARTICLE | doi:10.20944/preprints201808.0084.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: genistein; ∆F508-CF; mouse; survival
Online: 4 August 2018 (11:24:00 CEST)
Genistein is a naturally occurring isoflavone found in soy. Mice homozygous for the ∆F508 mutation are characterized with severe intestinal disease and require constant laxative treatment for survival. This pathology mimics the intestinal obstruction (meconium ileus) seen in some cystic fibrosis (CF) patients. We therefore tested whether dietary supplementation with genistein would reduce the dependence of the ∆F508 CF mouse model on laxatives for survival, thereby improving mortality rates. At weaning (21 days), we maintained homozygous ∆F508 mice on three diet regimens for a period of up to 65 days; normal diet, normal diet + Colyte or genistein diet. Survival rates for males were as follows: standard diet (38%), standard diet plus Colyte (83%) or genistein diet (60%). Survival rates for females were as follows: standard diet (47%), standard diet plus Colyte (71%), or genistein diet (87%). Average weight of male mice fed genistein diet increased by ~2.5 g more compared to those with Colyte treatment. Genistein diet did not change final body weight of females. Expression of SGLT-1 increased 2-fold with genistein diet in females (no change in males). Expression of GLUT2 and GLUT5 was comparable between all diet groups. Genistein diet reduced the number of goblet cells per micometer of crypt depth in female, yet was without effect in males. We conclude that supplementation of diet with genistein for ~45 days increases the survival rate of female ∆F508-CF mice precluding the requirement for laxatives, and only improves weight gain in males.
ARTICLE | doi:10.20944/preprints202010.0025.v1
Online: 1 October 2020 (16:46:42 CEST)
The objective of this study was to evaluate the effects of dietary supplementation with bacteriophage and β-mannanase on health and growth performance in calves. Thirty-six pre-weaning male Holstein calves were randomly allocated to one of four dietary treatments: no supplementation, 0.1% β-mannanase, 0.1% bacteriophage, and both 0.1% bacteriophage and β-mannanase supplementation in a starter. The experiment lasted from 2 weeks before weaning to 8 weeks after weaning. Twenty-two calves survived to the end of the experiment. No interaction was observed between the two methods of supplementation. A 1-kg increase in initial BW resulted in a 1.41-fold increase in the odds ratio of survival (p < 0.01). The bacteriophage supplementation tended to increase the odds ratio of survival (p = 0.09). The number of Escherichia coli in feces significantly decreased one week after weaning. β-mannanase supplementation increased the concentrates intake (p < 0.01) and tended to increase the final BW (p = 0.08). Analysis of repeated measures indicated β-mannanase supplementation increased weekly body weight gain (p = 0.018). We conclude that bacteriophage supplementation may have a positive effect on calf survival rate, while β-mannanase supplementation may increase the growth rate and intake of a starter in calves.
ARTICLE | doi:10.20944/preprints201810.0152.v1
Subject: Medicine & Pharmacology, Other Keywords: video assisted thoracic surgery, open thoracotomy, recurrence-free survival, overall survival, positive margins, postoperative length of stay.
Online: 8 October 2018 (15:23:21 CEST)
Background: Video assisted thoracoscopic surgery (VATS) has become the recommended approach for treatment of resectable lung cancer. However, no large randomized clinical trial has been conducted formally comparing surgical resections completed by VATS to those done by open thoracotomy (OT) in low volume centers. The current study sought to assess differences in recurrence-free survival (RFS), overall survival (OS), positive margins and postoperative length of stay (LOS) between VATS and OT lobectomies in our center. Method: A single institution retrospective chart review from May 2005 through May 2015 was conducted. All patients diagnosed with stage I through III lung cancer who underwent surgical resection were selected. Patient and tumor characteristics recorded included age at diagnosis, sex, tobacco use, tumor location (side and lobe), stage, size and receipt of chemotherapy or radiotherapy. Chis-square and Wilcoxon-Mann-Whitney tests were used to compare demographics, tumor characteristics and LOS. Multiple logistic and Cox regression analyses were used to compute relative risk (RR) for positive margins and mortality hazard ratios along with 95 percent confidence intervals (95%CI), respectively. Results: Of the 235 patients, 101 subjects had VATS while OT was performed in 134 patients. Age at diagnosis, sex, tobacco use, tumor location, and size were comparable for VATS and OT. No significant difference was observed in the relative risk of positive margins for VATS versus OT, RR = 0.56 (95%CI = 0.26, 1.05). However, VATS had shorter median LOS compared to OT (4 vs. 6 days, respectively), p = 0.002. A comparison of VATS versus OT showed no significant difference in the risk of recurrence, HR = 1.21 (95%CI = 0.74, 2.00), or death, HR = 1.34 (95%CI = 0.88, 2.06), in the intent-to-treat population. Similarly, no significant differences in recurrence or mortality risk were observed between VATS versus OT for analyses conducted separately for each cancer stage group or those limited to patients with negative margins. Conclusion: Our study indicates that compared to OT, VATS leads to shorter LOS while achieving comparable margins status, recurrence-free and overall survival regardless of tumor stage at diagnosis.
ARTICLE | doi:10.20944/preprints202209.0246.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: hemoglobin; monocytes; overall survival; prostate cancer; radiotherapy
Online: 16 September 2022 (10:11:15 CEST)
The prognostic value of inflammatory indices such as absolute monocyte count (AMC) has been a subject of interest in recent prostate cancer (PCa) literature, while hemoglobin concentration (HGB) has been recognized as a survival factor in castration-resistant metastatic prostate cancer, but its value remains unclear in localized disease. The aim of this study was to test the prognostic value of these two simple and inexpensive biomarkers for survival based on a cohort of 1016 patients treated with primary radiotherapy and androgen deprivation therapy for localized or locally advanced intermediate- or high-risk PCa. Complete survival data was available for all cases based on the National Cancer Registry with a median observation time of 120 months (IQR 80.9-144.7). Missing blood test data were supplemented using the Nearest Neighbor Imputation, and the Cox proportional hazards regression model was used for analysis. The median age was 68.8 years (IQR 63.3-73.5). The five-year overall survival was 82.8%, and 508 patients were alive at the time of analysis. The median time between blood tests and the first day of radiotherapy was 6 days (IQR 0-19). HGB (p = 0.009) and AMC (p = 0.003) were independent prognostic factors for survival, along with age, ISUP Grade Group, clinical T stage and maximum PSA concentration. The study demonstrated that HGB and AMC can be useful biomarkers for overall survival in patients treated with radiotherapy for localized intermediate- or high-risk PCa.
REVIEW | doi:10.20944/preprints202109.0242.v1
Subject: Life Sciences, Molecular Biology Keywords: PDK1; breast cancer; survival; prognosis; targeted therapy
Online: 14 September 2021 (14:51:06 CEST)
Given that 3-Phosphoinositide-dependent kinase 1 (PDK1) plays a crucial role in malignant biological behaviors of a wide-range of cancers, we further review the influence of PDK1 in breast cancer (BC). First, we describe the power of PDK1 in cellular behaviors and extensively demonstrate the interacting networks of PDK1 via PI3K-dependent/ PI3K-independent pathway. Then we enlighten the roles of PDK1 in carcinogenesis, growth and survival, metastasis, and chemoresistance in BC cells. More important, we sort the current preclinical or clinical trials of PDK1 targeted therapy in BC and find that even though at present no selective PDK1 inhibitor is available for BC therapy, but the combination trials of PDK1 targeted therapy and other agents have demonstrated some benefit. Thus, there is increasing anticipations that PDK1 targeted therapy will have its space in future therapeutic concepts of BC, and we hope to feature PDK1 in BC to the clinic and bring the new promising to patients for targeted therapies.
ARTICLE | doi:10.20944/preprints202108.0135.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Glioblastoma; biomarker; TSPO; single nucleotide polymorphism; survival.
Online: 5 August 2021 (10:22:34 CEST)
Glioblastoma (GBM) is the most common primary brain tumor in adults, with few available therapies and a 5-year survival rate of 7.2%. Hence, strategies for improving GBM prognosis are urgently needed. The translocator protein 18kDa (TSPO) plays crucial roles in essential mito-chondria-based physiological processes and is a validated biomarker of neuroinflammation, which is implicated in GBM progression. The TSPO gene has a germline single nucleotide pol-ymorphism, rs6971, which is the most common SNP in the Caucasian population. High TSPO gene expression is associated with reduced survival in GBM patients; however, the relation between the most frequent TSPO genetic variant and GBM pathogenesis is not known. The present study ret-rospectively analyzed the correlation of the TSPO polymorphic variant rs6971 with overall and progression-free survival in GBM patients using three independent cohorts. TSPO rs6971 poly-morphism was significantly associated with shorter overall survival and progression-free survival in male GBM patients but not in females in one large cohort of 441 patients. We observed similar trends in two other independent cohorts. These observations suggest that the TSPO rs6971 pol-ymorphism could be a significant predictor of poor prognosis in GBM, with a potential for use as a prognosis biomarker in GBM patients. These results reveal for the first time a biological sex-specific relation between rs6971 TSPO polymorphism and GBM.
Subject: Keywords: gender-based violence, coping, abuse, survival, resilient
Online: 2 July 2021 (14:00:57 CEST)
Gender-based violence is considered a serious social and public health problem. Overcoming this situation implies a process that results in the favorable biopsychosocial rehabilitation, the resilient of women. The objective of this study was to analyze the tools, resources and personal and psychosocial mechanisms used by women survivors of gender-based violence. The design was an interpretative phenomenology. It carried out with 22 women who have overcome gender-based violence. Data was collected through personal interviews and narration. The results were grouped into four themes: "Process of violence", "Social resources for coping and overcoming GBV", "Personal tools for coping and overcoming GBV", and "Feelings identified, from the abuse stage to the survival stage". Several studies concluded that overcoming abuse is influenced by the women social network, and it can be the action of these people determining their survival to gender violence. Despite the recognized usefulness of these available resources, it would be desirable to strengthen them in order to be able to drive more women toward survival, assuming a strengthening of coping and overcoming, without forgetting the importance of other support mechanisms such as their family and group therapies.
ARTICLE | doi:10.20944/preprints202005.0057.v2
Subject: Medicine & Pharmacology, General Medical Research Keywords: COVID-19; treatment; drug; survival; antiviral; hydroxychloroquine
Online: 9 May 2020 (04:45:37 CEST)
Background: Although no specific treatment for COVID 19 has been proven effective yet, some drugs with in vitro potential against SARS-CoV-2 virus have been proposed for clinical use. Hydroxychloroquine has in vitro anti-viral and immunomodulatory activity, but there is no current clinical evidence of its effectiveness on the outcome of the disease. Methods: We enrolled all 18-85 years old inpatients from Central Defense Hospital, Madrid, Spain, who were hospitalised due to COVID-19 and had a definitive outcome (either dead or discharged). We used a statistical survival analysis. Results: We analysed 220 medical records. 166 patients met the inclusion criteria. 48,8 % of patients not treated with HCQ died, versus 22% in the group of hydroxychloroquine (p=0,002). According to clinical picture at admission, hydroxychloroquine increased the mean cumulative survival in all groups from 1,4 to 1,8 times. This difference was statistically significant in the mild group. Conclusions: in a cohort of 166 patients between 18 to 85 years hospitalised with COVID-19, hydroxychloroquine treatment with an initial loading dose of 800mg improved patient survival when admitted in early stages of the disease. There was a non-statistically significant trend towards survival in all groups, which will need to be clarified in subsequent studies.
ARTICLE | doi:10.20944/preprints201907.0333.v1
Subject: Biology, Animal Sciences & Zoology Keywords: correlated response; pre-weaning; survival; weight; welfare
Online: 29 July 2019 (09:40:36 CEST)
A divergent selection experiment on environmental sensitivity was performed in rabbits. The aim of this study was to estimate the correlated response in kits’ weight and its survival, and weight distance from birth to weaning. Weight distance was calculated as the absolute values of the differences between the individual value and the mean value of its litter. Also, relationship between probability of survival at 4 d of age and weight at birth was studied. Environmental sensitivity was measured as litter size variability. A total of 2484 kits from 127 does of the low line (selected for reducing litter size variability) and 1916 kits of 114 does of the high line (selected for increasing litter size variability) of the 12th generation were weighed. Bayesian methodology was used to estimate the correlated response to selection, and LOGISTIC procedure of SAS was used to estimate the relationship between weight and probability of survival. Both lines showed similar individual weight at birth and at weaning, and similar survival at birth and at 4 d of age. Survival at weaning was higher in the low line than in the high line (0.67 and 0.62; P= 0.93). Weight distance was higher at birth but lower at weaning in the low line (47.8 g and 54.1 g; P=0.98). Kit’s weight at birth affected its survival. In conclusion, selection for environmental sensitivity showed correlated response in kits survival and in homogeneity of litter weight at weaning.
ARTICLE | doi:10.20944/preprints201805.0427.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: breast cancer; comorbidities; older women; radiotherapy; survival
Online: 29 May 2018 (13:01:28 CEST)
Background: Radiotherapy plays an important role in the management and survival of patients with breast cancer. The aim of this study was to examine the association between age, comorbidities and use of radiotherapy in this population. Methods: Patients diagnosed with breast cancer from 2004–2013 were identified from the American College of Surgeons National Cancer Database (NCDB). Follow-up time was measured from the date of diagnosis (baseline) to the date of death or censoring. Adjusted hazard ratios (aHR) and 95% confidence intervals (95%CI) were used as the measure of association. Results: Independently of comorbidities and other important outcome-related factors, patients >65 years of age who received radiotherapy survived significantly longer than those who did not receive radiotherapy (aHR = 0.53, 95%CI = 0.52–0.54). However, as women aged, those with comorbidities were less likely to receive RT (adjusted P-trend by age <0.0001). Conclusions: The development of decision-making tools to assist clinicians, and older women with breast cancer and comorbidities, are needed to facilitate personalized treatment plans regarding RT. This is particularly relevant as the population ages and the number of women with breast cancer is expected to increase in the near future.
ARTICLE | doi:10.20944/preprints201801.0174.v1
Subject: Life Sciences, Other Keywords: provenances, height, root-collar-diameter, survival, growth
Online: 18 January 2018 (16:39:53 CET)
The aims of the study were to evaluate seedling growth and survival of Prunus africana provenances in awi highland based on ecological requirement of the tree. We measured survival and growth of three P.africana provenances seedlings found in Ethiopia (provenances sources namely: Gedeo, Jibat and Munnessa). Design of experiment with randomized complete block design (RCBD) with three replications. Seedlings planted at 2m, 2.5m and 3m distance between plants, plot, and blocks respectively. A plot size of 10mx10m and 25 plants are found per plot (0.01ha). We used ANOVA to test differences in survival, and growth among provenances over time. Results concluded that, provenances have no significant variation among in establishment rate, plant height and collar diameter growth. Of these provenances, Jibat was the first in establishment (56%), second in height (1.97m) and diameter (2.89cm). Gedeo was stood first in height (2.30m) but second in establishment rate (52%) and thickness(3.45cm), but Munessa with very good growth in diameter(3.59cm) might be prefreed for bark extraction followed by Gedeo, last in height (1.75m),but established second (52%). Contrary to expectations, seedlings were still at substantial risk of mortality ≥3 years after planting. Probably the plants survival rate and growth probably affected by altitude, soil water potential, light exposure, and wild animal presence in the surrounding. In steep slope sites, canopy shade, existing weed vegetation as well as wild animals such as apes is unlikely to enhance seedling survival after planting. Our results suggest that seedling mean growth increased with 0.008mm thickness and 0.41mm per day while 2.8mm thickness and 146.8mm tall increment recorded in 2560meter elevated high land or injibara with mean value of 18.5°C and rain fall is 1300mm.
ARTICLE | doi:10.20944/preprints201611.0028.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: random survival forests; ependymoma; predictors; valproic acid
Online: 3 November 2016 (11:02:12 CET)
Ependymoma is responsible for 8–10% of all pediatric brain tumors and constitutes the third most common brain tumor in children. No robust molecular markers are yet in routine clinical use. Surgical resection and adjuvant radiotherapy cure approximately 40-70% of pediatric patients with ependymoma. In our centre, we have been using prophylactic valproic acid treatment for brain tumor patients. Initial observations indicated that valproate could have a beneficial effect in the survival of patients. Recent observations by other authors have shown that patients with glioblastoma benefited from the treatment with valproic acid, a histone deacetylase inhibitor. We have used random survival forest, a novel ensemble survival modelling method to study a single- center, small number cohort of pediatric patients with ependymoma. This analysis has confirmed surgery resection extent and treatment with radiotherapy as independent predictors of overall survival. Treatment with valproic acid was also a predictor of higher survival in this cohort. These results highlight the potential usefullness of the random survival forest model in gathering information from retrospective data. More data is needed about the possible influence of histone deacetylase inhibition by valproic acid in the survival of patients with ependymoma.
ARTICLE | doi:10.20944/preprints202112.0104.v1
Online: 7 December 2021 (12:55:23 CET)
HLA-G is an immune checkpoint molecule with immunosuppressive and anti-inflammatory activities, and its expression and level of its soluble form (sHLA-G) may play an important role in tumor prognosis. The HLA-G 14 bp ins/del polymorphism and the plasma level of soluble HLA-G (sHLA-G) were investigated by a polymerase chain reaction and ELISA, respectively, in 59 glioma patients. A significantly higher proportion of glioma patients had the 14 nt insert in both homozygous and heterozygous states compared to the control group. Glioma patients had also higher plasma levels of sHLA-G. Patients with methylated MGMT promoter had lower levels of sHLA-G than those with unmethylated MGMT promoter. Level of sHLA-G negatively correlated with the overall survival of patients. Glioblastoma patients who survived more than one year after diagnosis had lower levels of sHLA-G than those surviving less than one year. Patients with sHLA-G levels below the cut off value 40 U/mL survived significantly longer than patients with sHLA-G above 40 U/mL. The levels of sHLA-G also negatively correlated with the level of IL-6 (P=0.0004) and positively with IL-10/IL-6 (P=0.046). Conclusion: The presence of 14 nt insert in both homozygous and heterozygous states of the HLA-G 14 bp ins/del polymorphism is more frequent in glioma patients and the elevated plasma levels of sHLA-G are negatively associated with their survival.
ARTICLE | doi:10.20944/preprints202010.0046.v1
Subject: Life Sciences, Biochemistry Keywords: glioblastoma; master regulators; IGFBP2; survival; tumorigenicity; transcription factors
Online: 2 October 2020 (15:21:34 CEST)
Only 2% of Glioblastoma multiforme (GBM) patients respond to standard care and survive beyond 36 months (long-term survivors, LTS) while the majority survives less than 12 months (short-term survivors, STS). To understand the mechanism leading to poor survival, we analyzed publicly available datasets of 113 STS and 58 LTS. This analysis revealed 198 differentially expressed genes (DEGs) that co-occur with aggressive tumor growth and may be responsible for the poor prognosis. These genes belong largely to the GO-categories “epithelial to mesenchymal transition” and “response to hypoxia”. Promoter and network analysis of the DEGs identified 5 potential master regulators that may explain dysregulation of the DEGs in the STS. The following 5 important master-regulators were identified: IGFBP2, VEGFA, PDGFA, OSMR and AEBP1. It is known that IGFBP2 confers increasing malignancy leading to poor prognosis. However, the molecular mechanism by which IGFBP2 affects disease progression and patient prognosis is unclear. Here we found that IGFBP2 is highly upregulated in short survivors and significantly impact survival. Further investigation of the gene regulatory network revealed that IGFBP2 expression can be regulated by FRA-1 transcription factor via MEK2/RAF/ERK5 pathway. FRA-1 is found to be upregulated and to have significant impact on survival in GBM. It is previously reported that FRA-1 can dysregulate at-least 50 genes involved in tumor invasiveness in tumor xenografts making it a therapeutic target for GBM intervention. We propose that IGFBP2 drives dysregulated gene network responsible for short survival in GBM via FRA-1 transcription factor.
Subject: Biology, Animal Sciences & Zoology Keywords: Cherax quadricarinatus; red claw; substrate; survival; growth; molting
Online: 7 September 2020 (09:53:47 CEST)
The experiment was conducted to determine the effects of different substrate on the survival, growth and total number of moulting in juvenile red claw, Cherax quadricarinatus for aquaculture purposes. In the present study, there is a problem in culturing juvenile stage of C. quadricarinatus especially for survival and growth. Thus, a substrate was used to improve the survival and growth of C. quadricarinatus especially for the intensive system due C. quadricarinatus need a large space to survive. C. quadricarinatus with initial body weight from 1.10 to 2.90 g, total length 2.82 to 4.36 cm were placed in tanks (80 L in volume capacity) with 55L in water and there are eight juveniles in each tank. Treatment tanks were introduced with coral as treatment 2 and pipe as treatment 3. While, tank without shelters was set as control (treatment 1). Black nets were installed on top of each for circumventing foreign objects enter the tank and protect from direct sunlight. Besides, C. quadricarinatus were acclimatized for seven days before started the experiment. The experiment was done in duplicate and conducted for 60 days and C. quadricarinatus were fed twice daily (morning and evening) based on 5% of body weight. From the total of two replications, C. quadricarinatus for treatment 2 (coral) were significantly in survival (81.25±8.84%), weight gain (347.36 ±6.04%), specific growth rate (2.50±0.02%), carapace length (32.93 ± 0.93 %) and total number of moulting (55.00±2.93%) compared to other treatments. Besides, the control treatment (treatment 1) has a lower percentage in survival (37.50±8.84%) weight gain (122.60±20.51%) specific growth rate (1.33±0.15%), carapace length (25.84±0.33 %) and total number of molting (29.00±0.71%). As a conclusion, usage of coral as the substrate in the rearing tank showed improvement in survival, weight gain, specific growth rate, carapace length and total number of molting in C. quadricarinatus. The coral can use in rearing tank for increase the growth and survival for a small scale and not for commercial. In addition, in the environmental aspect, the present study showed the benefit of replacing the use of PVC pipes with the natural structure of dead coral.
ARTICLE | doi:10.20944/preprints202005.0497.v1
Subject: Social Sciences, Organizational Economics & Management Keywords: Product innovation; enterprise survival; competitive intensity; competitive advantage
Online: 31 May 2020 (19:45:30 CEST)
Product innovation is a crucial factor in enterprise survival. Even though there are sources from strategic theory that guides the clear comprehension towards appreciating the nexus between these two variables (product innovation and enterprise survival), there are still many lacunas that should be addressed and filled. Consequently, the need for additional empirical corroboration or support is pertinent. This study aimed at verifying the nexus between product innovation and enterprise survival, and how they are affected by the existence of antecedent variables such as competitive intensity and competitive advantage. In the methodology, this study adopts the conduct of explanatory and cross-sectional investigations through the use of structural equation modelling (SEM) to a sample of selected food and beverages enterprises in Lagos, Nigeria. Regarding the food and beverage enterprises in Lagos, Nigeria, this study discovered that competitive intensity has huge positive implication on product innovation at (0.39; t = 5.69, p < 0.05). This gives numerical evidence that, in the face of more market competition, enterprises will be pressured to adopt the model of costs reduction on products which will enhance the reduction of product prices, and will have significant impact on profit. However, the findings reveal that there is no significance between competitive advantage and product innovation at (0.002; t = 0.203, p > 0.05), and there is no significance between product innovation and enterprise survival at (-0.035; t = -1.583, p > .05). As a result, the food and beverage enterprises should concentrate more on product innovation so that they will be able to stand the intensity of competition. The results emanated from the study is germane as it make significant contribution to literature and the body of knowledge and on strategic management by enlightening that competitive intensity is a necessary inducement for product innovation.
ARTICLE | doi:10.20944/preprints202003.0425.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: cancer; immune checkpoint inhibitors; survival; antibiotic; meta-analysis
Online: 29 March 2020 (06:43:23 CEST)
Antibiotics (ABs) are common medications used for treating infections. In cancer patients treated with immune checkpoint inhibitors (ICIs), concomitant exposure to ABs may impair the efficacy of ICIs and lead to a poorer outcome compared to AB non-users. We report here the results of a meta-analysis evaluating the effects of ABs on the outcome of patients with solid tumors treated with ICIs. PubMed, the Cochrane Library, and Embase were searched from inception until September 2019 for observational or prospective studies reporting prognosis of adult patients with cancer treated with ICIs and with or without ABs. Overall survival (OS) was the primary endpoint, and progression-free survival (PFS) was the secondary endpoint. The effect size was reported as hazard ratios (HRs) with a 95% confidence interval (CI), and an HR > 1 associated with a worse outcome in ABs users compared to no-ABs users. Fifteen publications were retrieved for a total of 2363 patients. In the main analysis (n = 15 studies reporting data), OS was reduced in patients exposed to ABs before or during treatment with ICIs (HR = 2.07, 95%CI 1.51–2.84; P<.01). Similarly, PFS was inferior in ABs users in n = 13 studies with data available (HR = 1.53, 95%CI 1.22–1.93; p<.01). In cancer patients treated with ICIs, AB use significantly reduces OS and PFS. Short duration/course of ABs may be considered in clinical situations in which they are strictly needed.
ARTICLE | doi:10.20944/preprints201911.0094.v1
Subject: Biology, Other Keywords: hPSCs; ROCK inhibitors; fasudil; cell survival; metabolism; differentiation
Online: 8 November 2019 (10:41:13 CET)
Poor survival of human pluripotent stem cells (hPSCs) following freezing, thawing, or passaging hinders maintenance and differentiation in stem cell research. Rho-associated kinases (ROCKs) play a crucial role in hPSC survival. To date, a typical ROCK inhibitor, Y-27632, has been the primary agent used in hPSC research. Here, we report that another ROCK inhibitor, fasudil, can be used as an alternative. Fasudil increased hPSC growth due to survival rather than proliferation following thawing and passaging, similar to Y-27632. It did not affect pluripotency and genetic integrity including mitochondrial genome (mtDNA). Notably, the genes related to metabolism, mTORC1, and TP53 have mainly displayed a faster recovery pattern with ROCK inhibitors than control. Furthermore, fasudil was confirmed as useful for the single dissociation of hPSCs and for aggregation. It also increased retinal pigment epithelium (RPE) differentiation and the survival of neural crest cells during differentiation. These findings suggest that fasudil can replace Y-27632 for use in stem cell research.
ARTICLE | doi:10.20944/preprints201910.0180.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: long term survival; Glioblastoma; IDH; EGFR; Ki67; p53
Online: 16 October 2019 (08:30:25 CEST)
Background: Glioblastomas (GBM) is generally burdened, to date, by a dismal prognosis, although Long Term Survivors have a relatively significant incidence. Our specific aim was to determine the exact impact of many surgery-, patient- and tumor-related variable on Survival parameters. Methods: The surgical, radiological and clinical outcomes of patients have been retrospectively reviewed for the present study. All the patients have been operated on in our Institution and classified according their Overall Survival in LTS (Long Term Survivors) and STS (Short Term Survivors). A thorough Review of our surgical series was conducted to compare the oncologic results of the patients in regards to 1. Surgical , 2. Molecular, and 3.Treatment related features. Results: A total of 177 patients were included in the final cohort. Extensive statistical analysis by means of univariate, multivariate and survival analyses disclosed a survival advantage for patients presenting a younger age, a smaller lesion and a better functional status at presentation. From the Histochemical point of view, Ki67(%) was the strongest predictor of better oncologic outcomes. A stepwise analysis of variance outlines the existence of 8 prognostic subgroups according to the molecular patterns of Ki67 overexpression and EGFR, p53 and IDH mutations. Conclusions: On the ground of our statistical analyses we can affirm that the following factors were significant predictors of survival advantage: KPS, Age, Volume of the lesion, Motor disorder at presentation, a Ki67 overexpression. A fine molecular profiling is feasible to precisely stratify the prognosis of GBM patients.
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: 5-hmC; ELISA; TET; HNSCC; disease-free survival
Online: 22 July 2019 (08:55:04 CEST)
Ten-eleven translocation (TET) enzymes are implicated in DNA demethylation through dioxygenase activity, which converts 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC). However, the specific roles of TET enzymes and 5-hmC levels in head and neck squamous cell carcinoma (HNSCC) have not yet been evaluated. In this study, we analyzed 5-hmC levels and TET mRNA expression in a well-characterized dataset of 117 matched pairs of HNSCC tissues and normal tissues. 5-hmC levels and TET mRNA expression were examined via enzyme-linked immunosorbent assay and quantitative real-time PCR, respectively. 5-hmC levels were evaluated according to various clinical characteristics and prognostic implications. Notably, we found that 5-hmC levels were significantly correlated with tumor stage (P = 0.032) and recurrence (P = 0.018). Univariate analysis revealed that low levels of 5-hmC were correlated with poor disease-free survival (DFS; log-rank test, P = 0.038). The expression of TET family genes was not associated with outcomes. In multivariate analysis, low levels of 5-hmC were evaluated as a significant independent prognostic factor of DFS (hazard ratio: 2.352, 95% confidence interval: 1.136–4.896; P = 0.021). Taken together, our findings showed that reduction of TET family gene expression and subsequent low levels of 5-hmC may affect the development of HNSCC.
ARTICLE | doi:10.20944/preprints201906.0017.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: breast cancer; relative survival; excess hazard; excess mortality
Online: 3 June 2019 (10:08:23 CEST)
Measurement of breast cancer burden and identification of its influencing factors help in the development of public health policy and strategy against the disease. This study aimed to examine the variability of the excess mortality of female breast cancer patients in the North East Region of Peninsular Malaysia. This retrospective cohort study was conducted using breast cancer data from the Kelantan Cancer Registry between 2007 and 2011, and Kelantan general population mortality data. The breast cancer cases were followed up for five years until 2016. Out of 598 cases, 549 cases met the study criteria and were included in the analysis. Modelling of excess mortality was conducted using Poisson regression. Excess mortality of breast cancer varied according to age group (50 years old and below vs above 50 years old, Adj. EHR: 1.47; 95% CI: 1.31, 4.09; P=0.004), ethnicity (Malay vs non-Malay, Adj. EHR: 2.31; 95% CI: 1.11, 1.96; P=0.008), and stage (stage III and IV vs. stage I and II, Adj. EHR: 5.75; 95% CI: 4.24, 7.81; P<0.001). In conclusion, public health policy and strategy aim to improve cancer survival should focus more on patients presented at age below 50 years old, Malay ethnicity, and at a later stage.
ARTICLE | doi:10.20944/preprints201902.0042.v1
Subject: Life Sciences, Molecular Biology Keywords: RNA-Seq; Oncology; DNA repair; Survival; PCNA metagene
Online: 4 February 2019 (16:55:20 CET)
Removal of the proliferation component of gene expression by PCNA adjustment has been addressed in numerous survival prediction studies for breast cancer and all cancers in the TCGA. These studies indicate that widespread co-regulation of proliferation upwardly biases survival prediction when gene selection is performed on a genome-wide basis. In addition, removal of the correlative effects of proliferation does not reduce the random bias associated with survival prediction using random gene selection. Since most cancers become addicted to DNA repair as a result of forced cellular replication, increased oxidation, and repair deficiencies from oncogenic loss or genetic polymorphisms, we pursued an investigation to remove the proliferation component of expression in DNA repair genes to determine survival prediction. This translational hypothesis-driven focus on DNA repair genes is directly amenable to finding new sets of DNA repair genes that could potentially be studied for inhibition therapy. Overall survival (OS) prediction was evaluated in 18 cancers by using normalized RNA-Seq data for 126 DNA repair genes with expression available in TCGA. Transformations for normality and adjustments for age at diagnosis, stage, and PCNA metagene expression were performed for all DNA repair genes. We also analyzed genomic event rates (GER) for somatic mutations, deletions, and amplification in driver genes and DNA repair genes. After performing empirical p-value testing with use of randomly selected gene sets, it was observed that OS could be predicted significantly by sets of DNA repair genes for 61% (11/18) of the cancers. Interestingly, PARP1 was not a significant predictor of survival for any of the 11 cancers. Results from cluster analysis of GERs indicates that the most opportunistic cancers for inhibition therapy may be AML, colorectal, and renal papillary, because of potentially less confounding due to lower GERs for mutations, deletions, and amplifications in DNA repair genes. However, the most opportunistic cancer for inhibition therapy is likely to be AML, since it showed the lowest GERs for mutations, deletions, and amplifications in DNA repair genes. In conclusion, our hypothesis-driven focus to target DNA repair gene expression adjusted for the PCNA metagene as a means of predicting OS in various cancers resulted in statistically significant sets of genes.
ARTICLE | doi:10.20944/preprints201812.0151.v1
Subject: Biology, Ecology Keywords: Peripatidae, conservation status, survival, urban populations, threatened species
Online: 12 December 2018 (14:07:09 CET)
ABSTRACT: Charismatic species, like the panda, play an important role in conservation, and velvet worms arguably are charismatic worms. Thanks to their extraordinary hunting mechanism, they have inspired from a female metal band in Japan, to origami worms in Russia and video game monsters in the USA. Objective: To assess their conservation status in Costa Rica. Methods: we located all collection records of the 29 known species from the Onychophora Database in the map of the Costa Rican Conservation Network. Results: We found that seven species are protected inside forest reserves, five in Protected Zones, four in Wildlife Refuges, two in National Parks and one, Principapillatus hitoyensis, in a strictly pristine Biological Reserve. The largest species in the world, Peripatus solorzanoi, occurs both inside a Forest Reserve and in protected private land. Protection inside Costa Rican nature areas is enforced year round by personnel that includes armed guards, and is supported by educational programs in surrounding communities. Twelve species have not been found in protected areas, but in Costa Rica, all biological species, named and unnamed, are protected by law and cannot be legally collected, or exported, without technically issued permits. Conclusion: Like in the only other country with similar information (New Zealand), the conservation of onychophorans seems to be of least concern for at least two thirds of the known species. Epiperipatus isthmicola, recently rediscovered after a century of absence in collections, can be considered Threatened because nearly all of its natural habitat has now been covered by a city.
ARTICLE | doi:10.20944/preprints201810.0383.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Biologic subtypes; diagnosis; inflammatory breast cancer; pCR; survival
Online: 17 October 2018 (11:08:56 CEST)
The aim of this study was to examine pathologic complete response (pCR) and overall survival (OS) of patients diagnosed with non-metastatic inflammatory breast cancer (IBC). A total of N=8,550 cases undergoing surgery were identified between 2004-2013, using the National Cancer Database (NCDB). Patients were grouped into 4 biologic subtypes (HR+/HER2-, HR+/HER2+, HR-/HER2+, HR-/HER2-). The median age at diagnosis was 56 years. On average, women were followed for 3.7 years [interquartile range=3.0]. The majority were white (80%), had private health insurance (50%), and presented with poorly differentiated tumors (57%). Approximately 46% of the cancers were >5cm. Most patients underwent mastectomy (94%) and received radiotherapy (71%). Differences by biologic subtypes were observed for grade, lymph node invasion, race, and tumor size (p<.0001). Compared with non-pCR (54%), patients experiencing pCR had superior 5-year survival (77%) (p<.0001). Survival was poor for triple-negative (TN) tumors (37%) vs. other biologic subtypes (60%) (p<.0001). On multivariable analysis, TN-IBC, positive margins, and not receiving either chemotherapy, hormonal therapy or radiotherapy were independently associated with poor 5-year survival (p<.0001). In this large multicentric analysis of IBC, categorized by biologic subtypes, we observed significant differential tumor, patient and treatment characteristics, and OS.
ARTICLE | doi:10.20944/preprints201806.0490.v1
Subject: Arts & Humanities, General Humanities Keywords: The Uncanny, Deadly Premonition, Twin Peaks, Survival Horror
Online: 29 June 2018 (15:33:39 CEST)
The influence of the cult television series Twin Peaks (1990-91) can be detected in a wide range of videogames, from adventure, to roleplaying to survival horror titles. While many games variously draw upon the narrative, setting and imagery of the series for inspiration, certain element of the distinctive uncanniness of Twin Peaks are difficult to translate into gameplay, particularly its ability consistently disrupt the expectations and emotional responses of its audience. This paper examines the ways in which the 2010 survival horror title Deadly Premonition attempts to replicate the uncanniness of Twin Peaks in both its narrative and gameplay, noting how it expands upon conceptualisations of the gamerly uncanny (Hoeger and Huber 2007). It contends that Deadly Premonition's awkward and uncanny recombination of seemingly inconsistent and excessive gameplay features mirrors the ways in which David Lynch and Mark Frost draw upon and subvert audience expectations for police procedurals and soap operas in the original Twin Peaks, while also providing a similarly disorienting excess of “realistic” detail. Furthermore its exploration of the theme of possession – a central element of the television series – offers a diegetic exploration of the uncanny relationship between the player and their onscreen avatar.
ARTICLE | doi:10.20944/preprints202105.0093.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Breast neoplasms; neoplasm metastasis; inflammatory breast neoplasms; survival analysis
Online: 6 May 2021 (14:56:00 CEST)
The purpose of this study was to determine the change in overall survival (OS) for patients with de novo metastatic breast cancer (dnMBC) over time. We conducted a retrospective cohort study with 1981 patients with dnMBC diagnosed between January 1995 and December 2017 at The University of Texas MD Anderson Cancer Center. OS was measured from the date of diagnosis of dnMBC. OS was compared between patients diagnosed during different time periods: 5-year periods and periods defined according to when key agents were approved for clinical use. The median OS was 3.4 years. The 5- and 10-year OS rates improved over time across both types of time periods. A subgroup analysis showed that OS improved significantly over time for the estrogen-receptor-positive/HER2-positive (ER+/HER2+) subtype, and exhibited a tendency toward improvement over time for the ER-negative (ER-)/HER2+ subtype. Median OS was significantly longer in patients with non-inflammatory breast cancer (P = .02) and in patients with ER+ disease, progesterone-receptor-positive disease, HER2+ disease, lower nuclear grade, locoregional therapy, and metastasis to a single organ (all P <.0001). These findings showed that OS at 5 and 10 years after diagnosis in patients with dnMBC improved over time. The significant improvements in OS over time for the ER+/HER2+ subtype and the tendency toward improvement for ER-/HER2+ subtype suggest the contribution of HER2-targeted therapy to survival.
ARTICLE | doi:10.20944/preprints202104.0529.v1
Subject: Mathematics & Computer Science, Algebra & Number Theory Keywords: censored data; machine learning; deep learning; DNNSurv; survival analysis
Online: 20 April 2021 (11:15:02 CEST)
As the development of high-throughput technologies, more and more high-dimensional or ultra high-dimensional genomic data are generated. Therefore, how to make effective analysis of such data becomes a challenge. Machine learning (ML) algorithms have been widely applied for modelling nonlinear and complicated interactions in a variety of practical fields such as high-dimensional survival data. Recently, the multilayer deep neural network (DNN) models have made remarkable achievements. Thus, a Cox-based DNN prediction survival model (DNNSurv model) , which was built with Keras and Tensorflow, was developed. However, its results were only evaluated to the survival datasets with high-dimensional or large sample sizes. In this paper, we evaluate the prediction performance of the DNNSurv model using ultra high-dimensional and high-dimensional survival datasets, and compare it with three popular ML survival prediction models (i.e., random survival forest and Cox-based LASSO and Ridge models). For this purpose we also present the optimal setting of several hyper-parameters including selection of tuning parameter. The proposed method demonstrates via data analysis that the DNNSurv model performs overall well as compared with the ML models, in terms of three main evaluation measures (i.e., concordance index, time-dependent Brier score and time-dependent AUC) for survival prediction performance.
ARTICLE | doi:10.20944/preprints202101.0244.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: DPP9; SNPs; Hepatocellular carcinoma; Survival; TCGA; DPP4 gene family
Online: 13 January 2021 (12:13:37 CET)
Dipeptidyl peptidase (DPP) 9, DPP8, DPP4 and fibroblast activation protein (FAP) are the four enzymatically active members of the S9b protease family. Associations of DPP9 with human liver cancer, exonic single nucleotide polymorphisms (SNPs) in DPP9 and loss of function (LoF) variants have not been explored. Human genomic databases including The Cancer Genome Atlas (TCGA) were interrogated to identify DPP9 LoF variants and associated cancers. Survival and gene signature analyses were performed on hepatocellular carcinoma (HCC) data. We found that DPP9 and DPP8 are intolerant to LoF variants. DPP9 LoF variants were most often associated with uterine carcinoma. Two DPP9 intronic SNPs that have been associated with lung fibrosis and COVID-19 were not associated with liver fibrosis or cancer. All four DPP4-like genes were overexpressed in liver tumours and their joint high expression was associated with poor survival in HCC. Increased DPP9 expression was associated with obesity in HCC patients.. High expression of genes that positively correlated with overexpression of DPP4, DPP8, and DPP9 were associated with very poor survival in HCC. Enriched pathways analysis of these positively correlated genes featured Toll-like receptor and SUMOylation pathways. This comprehensive data mining suggests that DPP9 is essential for human survival and the DPP4 protease family is important in cancer pathogenesis.
ARTICLE | doi:10.20944/preprints202012.0476.v1
Subject: Biology, Anatomy & Morphology Keywords: Ovarian cancer; mapping-based; mapping-free; SNVs; survival prognosis
Online: 18 December 2020 (15:15:50 CET)
Ovarian cancer is the most frequent cause of deaths in gynecologic malignancies. Many possible mechanisms have been proposed via RNAseq and DNAseq technique recently. However, the driving factors are still obscure. The possible reasons are attributed to the incomplete human reference. This study integrated the canonical mapping-based and mapping-free protocols to extract reliable variations and novel events. We eventually obtained 450 reliable SNVs from the WES data and novel events from the RNAseq data, including 154 SNVs, 462 intron events, two repeats and six splice events. We identified six differentially expressed genes and six contigs that are significantly related to survival prognosis. The recurrent SNVs in significantly differentially expressed genes can be validated in an independent cohort of 20 Chinese ovarian cancer patients.
ARTICLE | doi:10.20944/preprints202010.0624.v1
Subject: Medicine & Pharmacology, Allergology Keywords: medical record systems; cutaneous malignant melanoma; survival analysis; immunotherapy
Online: 29 October 2020 (16:02:44 CET)
Background: Cutaneous malignant melanoma (CMM) is one of the most aggressive types of skin cancer. Currently, innovative approaches such as target therapies and immunotherapies have been introduced in clinical practice for the treatment of metastatic CMM. Data of clinical trials and real life studies that evaluate the outcomes of these therapeutic associations are necessary to establish their clinical utility. The aim of this study is to investigate the types of oncological treatments employed in the real-life clinical management of patients with advanced CMM in several Italian centers which are part of the Clinical National Melanoma Registry (CNMR), and the oncological outcomes obtained. Methods: CNMR collects data of patients with a histologically confirmed diagnosis of primary CMM treated in one of the 38 Italian institutions (hospitals, research institutes, etc.) participating in the network. Melanoma-specific survival and Overall survival were calculated. Kaplan-Meier curves and medians of OS and 95% CI are presented overall and by immunotherapy and target treatments. The Log-rank test compared curves by treatments. Multivariate Cox regression models were used to estimate the hazard ratios adjusting for confounders and other prognostic factors. Results: The median follow-up time was 36 months (range 1.2-185.1). 787 CMM were included in the analysis with completed information about therapies.Global immunotherapy showed a significant improved survival compared with all other therapies (p=0.001). 75% was the highest reduction of death reached by nivolumab/pembrolizumab immunotherapy (anti-PD1 HR=0.25 95% CI 0.14-0.42), globally immunotherapy was significantly associated with improved survival, either for anti-CTL A4 monotherapy or combined with anti-PD1 (HR=0.47;95% CI 0.33-0.66 and HR=0.26; 95% CI 0.15-0.46, respectively). Conclusions: The nivolumab/pembrolizumab and the combination of ipilimumab can be considered the best therapy to improve survival in a real-world-population. The CNMR can complement clinical registries with the intent of improving cancer management and standardizing cancer treatment.
ARTICLE | doi:10.20944/preprints202007.0277.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: colorectal cancer; survival; KRAS; median; codon; metastasis; sided; tumour
Online: 13 July 2020 (03:03:23 CEST)
Colorectal cancer (CRC) is the third most common cancer, with rising incidence due to lifestyle and diet. 40% of CRC cases are found to have KRAS mutations. In this study, we investigate the survival outcome of metastatic Colorectal cancer mCRC) patients in Brunei Darussalam restrospectively. Chi-squared test was used to compare the survival outcomes of mCRC patients, and Mann-Whitney U test was used to compare the median ages of both groups. Kaplan-Meier survival curves were drawn and logrank test was used to compare the survival outcome between two groups. There was a total of 105 patients with stage IV CRC being treated during the study period. 81.6% (n=62) of mCRC patients were found to have the primary tumours on the left side of the colon. 19 of these 26 (73.1%) mutant KRAS mCRC patients died, while 23 of 50 (46.0%) wild-type KRAS mCRC patients died at the end of the study period, contributing to death rates of 45.2% and 54.8%, correspondingly. 30.3% (n=23) of the study population had a single metastatic site detected (either liver, or lung or any other organs), while 69.7% (n=53) of the 76 mCRC patients had two (double) or more metastatic sites. 69.2% (n=18) and 30.8% (n=8) of the mutant KRAS mCRC patients had mutations within codons 12 and 13, respectively. To our knowledge, this is the first study in Brunei Darussalam to analyse both the survival outcomes of metastatic CRC patients and those of mutant KRAS mCRC patients. Chi-squared analysis showed a significant difference between the survival outcomes of wild-type KRAS and mutant KRAS mCRC patients (p-value = 0.024). There was a significant difference in the survival outcome between the mutant KRAS mCRC patients with RCC and mutant KRAS mCRC with LCC patients. There was no significant difference between the survival outcomes of mutant KRAS patients with mutations in either codon 12 or 13 of the KRAS gene (Table 3). However, there is a significant difference in the median survival periods between the mutant KRAS mCRC patients with mutations in codon 12 and those with mutation in codon 13 of the KRAS gene (p-value = 0.003). In conclusion, we found that mutant KRAS mCRC patients had a significantly poorer OS, which was shown to be worse when the primary tumours were found at the left side of the colon. Mutant KRAS mCRC patients with mutations in codon 12 were found to have shorter survival median periods than those with mutations within codon 13.
ARTICLE | doi:10.20944/preprints202005.0110.v1
Subject: Biology, Other Keywords: COVID-19; intervention; growth curve; survival; doubling time; correlation
Online: 7 May 2020 (08:24:00 CEST)
COVID-19 is fast spreading around the globe in a highly contagious manner. In this article we have described that after prolonged interventions the percentage growth curve for COVID-19 cases showed a flattened nature, after prolonged volatility in number of COVID-19 cases. The stability in the growth curve was continuously maintained from 18 April, 2020 to 29 April, 2020. The significance of this sustained stable curve on survival & doubling time has been discussed. One significant part of the study reflected that the doubling time of COVID-19 cases showed a negative correlation with the percent increase in COVID-19 cases (R=0.301). It is plausible that if such negative correlation is maintained with further flattening of the growth curve at a lower level, it may influence the infective ability of nCoV-19 & ultimately have a positive evolutionary implication on the spread of COVID-19 among the population.
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: glioblastoma; miRNA; MGMT; survival; radiotherapy; chemotherapy; temozolomide; translational medicine
Online: 9 April 2020 (08:27:12 CEST)
Glioblastoma multiforme (GBM) is the most common high-grade intracranial tumor in adults. It is characterized by uncontrolled proliferation, diffuse infiltration due to high invasive and migratory capacities, as well as intense resistance to chemo- and radiotherapy. With a five-year survival of less than 3% and an average survival rate of 12 months after diagnosis, GBM has become a focus of current research to urgently develop new therapeutic approaches in order to prolong survival of GBM patients. The methylation status of the promoter region of the O6-methylguanine–DNA methyltransferase (MGMT) is nowadays routinely analyzed, since a methylated promoter region is beneficial for an effective response to temozolomide-based chemotherapy. Furthermore, several miRNAs were identified regulating MGMT expression, apart from promoter methylation, by degrading MGMT mRNA before protein translation. These miRNAs could be a promising innovative treatment approach to enhance Temozolomide (TMZ) sensitivity in MGMT unmethylated patients and to increase progression-free survival as well as long-term survival. In this review, the relevant miRNAs are systematically reviewed.
REVIEW | doi:10.20944/preprints202207.0251.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: adenovirus infection; adenovirus disease; cidofovir; preemptive therapy; risk factors; survival
Online: 18 July 2022 (08:13:46 CEST)
Human Adenovirus (HAdV) infection occurs in 14-16% of patients in the early months after pediatric hematopoietic cell transplantation (HCT) and this correlates with a higher risk to develop HAdV disease and overall 6-month mortality. The main risk factors for HAdV infection are T-cell depletion of the graft by ex vivo CD34+ selection or in vivo use of alemtuzumab or anti-thymocyte serum, the development of grade III-IV graft versus host disease (GVHD), the type of donor (unrelated donor, cord blood, haploidentical or HLA mismatched parent) and severe lymphopenia (< 0.2 x 109/L). The prevention of HAdV disease is based on early intervention with antivirals in the asymptomatic patient when the permitted viral load threshold on blood (> 102-3 copies/ml) and/or on the stool (109 copies/g stool) is exceeded. Cidofovir, a monophosphate nucleotide analog of cytosine, is the primary drug for preemptive therapy, used at 5 mg/kg/week for 2 weeks followed by 3-5 mg/kg every 2 weeks. The alternative schedule is 1 mg/kg every other day (three times/week). Enhancing virus-specific T-cell immunity in the first months post-HCT by donor-derived or third-party-derived virus-specific T cells represents an innovative and promising way of intervention applicable both in prevention and therapeutic setting.
ARTICLE | doi:10.20944/preprints202202.0051.v1
Subject: Life Sciences, Other Keywords: Glioblastoma; survival prediction; Machine Learning; biomarkers; HumanPSDTM; Long-term survivor
Online: 3 February 2022 (12:00:23 CET)
Glioblastoma (GBM) is a very aggressive malignant brain tumor with the vast majority of patients surviving less than 12 months (Short-term survivors [STS]). Only around 2% of patients survive more than 36 months (Long-term survivors [LTS]). Studying these extreme survival groups might help in better understanding GBM biology. This work aims at exploring application of machine learning methods in predicting survival groups(STS, LTS). We used age and gene expression profiles belonging to 249 samples from publicly available datasets. 10 Machine learning methods have been implemented and compared for their performances. Hyperparameter tuned random forest model performed best with accuracy of 80% (AUC of 74% and F1_score of 85%). The performance of this model is validated on external test data of 16 samples. The model predicted the true survival group for 15 samples achieving an accuracy of 93.75%. This classification model is deployed as a web tool GlioSurvML. The top 1500 features which retained classification efficiency (Accuracy of 80%, AUC of 74%) were studied for enriched pathways and disease-causal biomarker associations using the HumanPSDTM database. We identified 199 genes as possible biomarkers of GBM and/or similar diseases (like Glioma, astrocytoma, and others). 57 of these genes are shown to be differentially expressed across survival groups and/or have impact on survival. This work demonstrates the application of machine learning methods in predicting survival groups of GBM.
ARTICLE | doi:10.20944/preprints202201.0426.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Sinonasal squamous cell carcinoma; Head and neck; HPV; p16; Survival
Online: 28 January 2022 (07:20:10 CET)
Background: Sinonasal squamous cell carcinoma (SNSCC) is rare in the general population. No clear and consistent etiologic correlation between human papillomavirus and SNSCC has yet been delineated in literature. p16 is a tumour suppressor protein used as a surrogate marker for HPV. This study aims to evaluate the relationship between p16 overexpression in SNSCC and its role in prognosis and survival. Methods: A population-based retrospective analysis was performed using prospectively collected data from the Northern Alberta Head and Neck Tumour Board, Alberta Cancer Registry, and Alberta Cancer Research Biobank. p16 overexpression was analyzed from pathologic sample of patients meeting study criteria, and participants were dichotomized by status. Subsequently, nonparametric analysis of demographics, initial staging, and initial treatment were performed, and a Kapan-Meier curve was developed to assess differences in survival. Results: 16 patients were included in analysis. p16 overexpression was seen in 68.8% of patients. p16 positive and negative groups were comparable for age, gender, smoking status, stage, and treatment. A statistically significant five-year survival advantage was observed in patients with p16 positive SNSCC (p = 0.013). Conclusions: This is the first Canadian study to demonstrate a high prevalence of p16 positivity in SNSCC and its presence denoting a statistically significant survival advantage. Results demonstrate a previously unconfirmed role of oncogenic HPV in SNSCC.
ARTICLE | doi:10.20944/preprints202108.0289.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: bortezomib; cMAF; MAFb; multiple myeloma; POMP; prognosis; PFS; survival; OS
Online: 13 August 2021 (08:43:42 CEST)
While multiple myeloma (MM) treatment with proteasome inhibitors and other agents yields encouraging results, primary and secondary resistance remains an emerging problem. An important factor in such treatment resistance is the overexpression of several proteins. The present study comprehensively evaluates the expression of POMP, PSMB5, NRF2, XBP1, cMAF and MAFb proteins in plasma cells isolated from the bone marrow of 39 MM patients treated with bortezomib-based regimens using enzyme-linked immunosorbent assay (ELISA). The proteins were selected on the basis of previous laboratory and clinical studies in bortezomib treated MM patients. It was found that the expression of the investigated proteins did not significantly differ between bortezomib-sensitive and bortezomib-refractory patients. However, the expression of some proteins correlated with overall survival (OS); this was significantly shorter in patients with higher POMP expression (HR 2.8, 95% CI: 1.1-7.0, p = 0.0277) and longer in those with higher MAFB expression (HR 0.32, 95% CI: 0.13-0.80, p = 0.0147). Our results indicate that high expression of POMP and MAFB in MM plasma cells may serve as predictors of OS in MM patients treated with bortezomib-based regimens. However, further studies are needed to determine the role of these factors in effective strategies for improving anti-myeloma therapy.
ARTICLE | doi:10.20944/preprints202106.0330.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Chemotherapy; Radiotherapy; Cognitive dysfunction; Big data; Cohort studies; Survival analysis
Online: 14 June 2021 (07:51:57 CEST)
Background: We aimed to assess the risk of chemotherapy- and radiotherapy-related cognitive impairment in colorectal cancer patients. Methods: We randomly selected 40% of colorectal cancer patients from Korean National Health Insurance Database (NHID), 2004-2018 (N=148,848). Patients with one or more ICD-10 diagnostic codes for dementia or mild cognitive impairment was defined as cognitive impairment cases. Patients who were aged 18 or younger, diagnosed with cognitive impairment before colorectal cancer (N=8,225) and did not receive primary resection (N=45,320) were excluded. The effects of each chemotherapy agent on cognitive impairment were estimated. We additionally estimated the effect of radiotherapy in rectal cancer patients. Time-dependent competing risk Cox regression was conducted to estimate overall and age-specific hazard ratios (HR) separately for colon and rectal cancer. Results: In colon cancer, capecitabine and irinotecan was associated with higher cognitive im-pairment, while 5-fluorouracil was not. In rectal cancer, no chemotherapy agents increased the risk of cognitive impairment, nor did radiotherapy. Hazardous association of irinotecan was estimated larger in elderly patients compared with younger counterparts. Conclusion: Heterogeneous associations between various chemotherapy agents and cognitive impairment were observed. Elderly patients were more vulnerable to possible adverse cognitive effects. Radiotherapy did not increase the risk of cognitive impairment.
ARTICLE | doi:10.20944/preprints202102.0002.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Acute Toxicity, Oropharyngeal Cancer; Proton Beam Therapy; Radiation Therapy; Survival
Online: 1 February 2021 (08:57:08 CET)
Purpose: To report the early clinical outcomes of combining intensity‐modulated radiation therapy (IMRT) and intensity‐modulated proton therapy (IMPT) in comparison with IMRT alone in treating the oropharynx cancer (OPC) patients. Materials and Methods: The medical records of 148 OPC patients were retrospectively reviewed, who underwent definitive radiotherapy (RT) with concurrent systemic therapy, from January 2016 till December 2019 at Samsung Medical Center. During the 5.5 weeks’ RT course, the initial 16 (or 18) fractions were delivered by IMRT in all patients, and the subsequent 12 (or 10) fractions were either by IMRT in 81 patients (IMRT only) or by IMPT in 67 (IMRT/IMPT combination), respectively, based on comparison of adaptive re-plan profiles and availability of equipment. Propensity‐score matching (PSM) was done on 76 patients (38 from each group) for comparative analyses. Results: With the median follow‐up of 24.7 months, there was no significant difference in overall survival and progression free survival between groups, both before and after PSM. Before PSM, IMRT/IMPT combination group experienced grade ≥3 acute toxicities less frequently: mucositis in 37.0% and 13.4% (p<0.001); and analgesic quantification algorithm (AQA) in 37.0% and 19.4% (p=0.019), respectively. The same trends were observed after PSM: mucositis in 39.5% and 15.8% (p=0.021); and AQA in 47.4% and 21.1% (p=0.016), respectively. In multivariate logistic regression, grade ≥3 mucositis was significantly less frequent in IMRT/IMPT combination group, both before and after PSM (p=0.027 and 0.024, respectively). AQA score ≥3 was also less frequent in IMRT/IMPT combination group, both before and after PSM (p=0.085 and 0.018, respectively). Conclusions: In treating the OPC patients, with comparable early oncologic outcomes, more favorable acute toxicity profiles were achieved following IMRT/IMPT combination than IMRT alone.
REVIEW | doi:10.20944/preprints202010.0243.v1
Subject: Social Sciences, Accounting Keywords: distance education; open and distance education; student retention; survival analysis
Online: 12 October 2020 (13:22:55 CEST)
Student retention is one indicator of accountability in the implementation of educational programs. Achievement of student retention rates indicates the performance of the quality objectives of an institution or college. To get an accurate picture of the factors related to retention, we need to do modeling. The retention variable is the time response variable measured in semester units. One of the statistical analyzes that can be used to analyze response data in time is survival analysis. The selection of an accurate analytical method in modeling will produce valid conclusions and impact making policies that are right and on target. This paper presents alternative modeling of student retention in distance education using survival analysis. The method used is a literature review. This paper also briefly describes distance education, open and distance education, distance education students' characteristics, distance education student retention, and survival models for modeling student retention in distance education.
CASE REPORT | doi:10.20944/preprints201908.0278.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: FOLFIRINOX; pancreatic ductal adenocarcinoma; surgery; liver metastases; long term survival
Online: 27 August 2019 (05:16:03 CEST)
Metastatic pancreatic ductal adenocarcinoma pancreatic (PDAC) is characterized by poor prognosis and short survival. Today, the use of new polytherapeutic regimens increases clinical outcome of these patients opening new clinical scenario. A crucial issue related to the actual improvement achieved with these new regimens is represented by the occasional possibility to observe a radiological complete response of metastatic lesions in patients with synchronous primary tumor. What could be the best therapeutic management of these patients? Could surgery represent an indication? Herein we reported a case of a patient with a PDAC of the head with multiple liver metastasis, who underwent first line chemotherapy with mFOLFIRINOX. After 10 cycles, he achieved a complete radiological response of liver metastases and a partial response of pancreatic lesion. A, duodenocephalopancreasectomy was performed. Due to liver a lung metastases after 8 months from surgery, a second line therapy was started with a disease free survival and overall survival of 8 months and 45 months, respectively. Improvement in the molecular characterization of PDAC could help in the selection of patients suitable for multimodal treatments.
ARTICLE | doi:10.20944/preprints201710.0086.v2
Subject: Engineering, Electrical & Electronic Engineering Keywords: cluster head; dead node; random; vicinity; modulation; index; survival; overhead
Online: 23 October 2017 (08:06:47 CEST)
As Heterogeneous Wireless Sensor Network (HWSN) fulfill the requirements of researchers in the design of real life application to resolve the issues of unattended problem. But, the main constraint face by researchers is energy source available with sensor nodes. To prolong the life of sensor nodes and hence HWSN, it is necessary to design energy efficient operational schemes. One of the most suitable routing scheme is clustering approach, which improves stability and hence enhances performance parameters of HWSN. A novel solution proposed in this article is to design energy efficient clustering protocol for HWSN, to enhance performance parameters by EECPEP-HWSN. Propose protocol is designed with three level nodes namely normal, advance and super node respectively. In clustering process, for selection of cluster head we consider three parameters available with sensor node at run time, i.e., initial energy, hop count and residual energy. This protocol enhance the energy efficiency of HWSN, it improves performance parameters in the form of enhance energy remain in the network, force to enhance stability period, prolong lifetime and hence higher throughput. It is been found that proposed protocol outperforms than LEACH, DEEC and SEP with about 188, 150 and 141 percent respectively.
ARTICLE | doi:10.20944/preprints202106.0477.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Infective endocarditis; Kidney Transplantation; Survival analysis; graft failure; transplant infectious diseases
Online: 18 June 2021 (11:17:15 CEST)
Purpose: Kidney Transplant Recipients (KTRs) tend to develop infections with characteristic epidemiology, presentation and outcome. While infective endocarditis (IE) is among such complications in KTRs, literature is scarce. We describe the presentation, epidemiology, and factors associated with IE in KTRs. Methods: We performed a retrospective case/control study which included patients from two centers. First episodes of definite or possible IE (Duke criteria), in adult KTRs from January 2007 to December 2018 were included, as well as two controls per case, and followed until December 31 2019. Clinical, biological, and microbiological data and the outcome were collected. Survival was studied using the Kaplan-Meier method. Finally, we searched for factors associated with the onset of IE in KTRs by the comparison of cases and controls. Results: Seventeen cases and 34 controls were included. IE was diagnosed after a mean delay of 78 months after KT, mostly on native valves of the left heart only. Pathogens of digestive origin were most frequently involved (six Enterococcus spp, three Streptococcus gallolyticus and one Escherichia coli), followed by Staphylococci (three cases of S. aureus and S. epidermidis each). Among the risk factors evaluated only age was significantly associated with the occurrence of IE in our study (63.8 years for cases vs. 55.6 years for controls, P=0.03) Patient and death-censored graft survival were greatly diminished five years after IE compared to controls being 50.3% vs. 80.6% (p<0.003) and 29.7% vs. 87.5% (p<0.002), respectively. Conclusion: IE in KTRs is a disease that carries significant risks both for the survival of the patient and the transplant.
REVIEW | doi:10.20944/preprints202105.0296.v1
Subject: Life Sciences, Biochemistry Keywords: CAD/CAM; dental restoration; ceramic; all-ceramic; survival; fixed dental prosthesis
Online: 13 May 2021 (13:18:51 CEST)
Although CAD/CAM ceramics present a promising alternative to metal-ceramic fixed dental prostheses, little is known about their mid- and long-term clinical performance. This systematic review aims to estimate the survival and success rates and describes the underlying complication characteristics for CAD/CAM tooth-supported fixed dental prostheses (FDPs). We systematically searched MEDLINE and Web of Science to find relevant prospective studies with a follow-up of at least one year. We estimated pooled 1-, 5- and 10-year survival and success rates by combining the collected data in a Poisson regression model. Descriptive statistics were conducted to evaluate the distribution of failures and complications in the included studies. Risk of bias for the included studies was assessed with an adapted checklist for single-arm trials. Pooled estimated 1-, 5-, and 10-year survival rates ranged from 93.80% to 94.66%, 89.67% to 91.1%, and 79.33% to 82.20%, respectively. The corresponding success rates, excluding failures but including any other types of intervention, were 94.53% to 96.77%, 90.89% to 94.62%, and 81.78% to 89.25%. Secondary caries was the most frequent cause of failure, followed by chipping of the veneering. The most common cause of complication, excluding failures but requiring intervention, was chipping of the veneering. Risk of bias was generally acceptable for the included studies, with 7 studies associated with low risk of bias, 8 studies with a moderate risk of bias, and 3 studies with serious risk of bias. The current meta-analysis on CAD/CAM supported FDPs revealed satisfying survival and success rates for up to 10 years of exposure. More prospective studies focusing on long-term performance are needed to strengthen the evidence currently available in the literature.
ARTICLE | doi:10.20944/preprints202102.0365.v1
Subject: Life Sciences, Biochemistry Keywords: Cancer subtype detection; Multi-omics data; Data integration; Autoencoder; Survival analysis
Online: 17 February 2021 (10:09:51 CET)
A heterogeneous disease like cancer is activated through multiple pathways and different perturbations. Depending upon the activated pathway(s), patients’ survival vary significantly and show different efficacy to various drugs. Therefore, cancer subtype detection using genomics level data is a significant research problem. Subtype detection is often a complex problem, and in most cases, needs multi-omics data fusion to achieve accurate subtyping. Different data fusion and subtyping approaches have been proposed, such as kernel-based fusion, matrix factorization, and deep learning autoencoders. In this paper, we compared the performance of different deep learning autoencoders for cancer subtype detection. We performed cancer subtype detection on four different cancer types from The Cancer Genome Atlas (TCGA) datasets using four autoencoder implementations. We also predicted the optimal number of subtypes in a cancer type using the silhouette score. We observed that the detected subtypes exhibit significant differences in survival profiles. Furthermore, we also compared the effect of feature selection and similarity measures for subtype detection. To evaluate the results obtained, we selected the Glioblastoma multiforme (GBM) dataset and identified the differentially expressed genes in each of the subtypes identified by the autoencoders; the obtained results coincide well with other genomic studies and can be corroborated with the involved pathways and biological functions. Thus, it shows that the results from the autoencoders, obtained through the interaction of different datatypes of cancer, can be used for the prediction and characterization of patient subgroups and survival profiles.
ARTICLE | doi:10.20944/preprints202005.0081.v1
Subject: Life Sciences, Genetics Keywords: Lung cancer; biomarker; gene ontology; protein-protein interaction networks; survival analysis
Online: 5 May 2020 (12:28:25 CEST)
Objective: The aim of study is to find key genes and enriched pathways associated with lung cancer. Participants and Methods: Differentially expressed genes (DEGs) data of 54674 genes based on stage, tumor and status of lung cancer was taken from 66 patients of African American (AAs) origin. 2392 DEGs were found based on stage, 13502 DEGs were found based on tumor, 2927 DEGs were found based on status having p value (p<0.05). Results: Total 33 common DEGs were found from stage, tumor and status of lung cancer. Gene ontology (GO) and KEGG pathway enrichment analysis was performed and 49 significant pathways were obtained, out of which 10 pathways were found to be exclusively involved in lung cancer development. Protein-protein interaction (PPI) network analysis found 69 nodes and 324 edges and identified 10 hub genes based on their highest degrees. Module analysis of PPI found that ‘Viral carcinogenesis’, ‘pathways in cancer’, ‘notch signaling pathway’, ‘AMPK signaling pathways’ had a close association with lung cancer. Conclusion: These identified DEGs regulate other genes which play important role in growth of lung cancer. The key genes and enriched pathways identified can thus help in better identification and prediction of lung cancer.
REVIEW | doi:10.20944/preprints201811.0511.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: coeliac disease; Crohn’s disease; dysplasia; histotype; overall survival; tumor infiltrating lymphocyte.
Online: 20 November 2018 (16:43:14 CET)
Small bowel carcinomas (SBC) are uncommon neoplasms, whose predisposing conditions include hereditary syndromes and immune-mediated intestinal disorders, including coeliac disease (CD) and Crohn’s disease (CrD). Although both CD-associated SBC (CD-SBC) and CrD-associated SBC (CrD-SBC) arise from an inflammatory background, they differ substantially in tumour cell phenotype, frequency of microsatellite instability and nuclear β-catenin expression, as well as in prognosis. For these patients, high tumor-infiltrating lymphocyte density and glandular/medullary histotype represent independent positive prognostic factors. Dysplasia adjacent to SBC is rare and characterized by intestinal phenotype and nuclear β-catenin in CD, while it is frequent and typified by gastro-pancreatobiliary marker expression and preserved membranous β-catenin in CrD. Recent evidence suggests that Epstein-Barr virus-positive dysplasia and SBC, albeit exceptional, do exist and are associated with CrD. In this review we summarize the novel pathological and molecular insights of clinical and therapeutic interest to guide the care of CD-SBC and CrD-SBC.
ARTICLE | doi:10.20944/preprints202210.0330.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: megalin; oral squamous cell carcinoma; lymph node metastases; vascular invasion; overall survival
Online: 21 October 2022 (10:17:46 CEST)
Megalin (LRP2) is a rapidly recycling multiligand endocytic receptor, primarily expressed in polarized epithelial cells. Despite megalin could promote tumor growth and invasiveness through several mechanisms, it has been understudied in the field of molecular oncology so far. The present study aimed to evaluate the impact of megalin expression in oral squamous cell carcinoma (OSCC) on disease progression. Megalin expression was evaluated immunohistochemically in 63 OSCC specimens. Data obtained were retrospectively compared with patients’ clinicopathological features and survival. The proportion of megalin-expressing cells in primary OSCC tissue was significantly associated with metastatic spreading to lymph nodes, vascular invasion and lower overall survival rate. Results obtained by the study suggest that megalin can be considered as a novel molecule involved in OSCC pathogenesis, but also useful as a potential biomarker for cancer progression.
REVIEW | doi:10.20944/preprints202210.0008.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: relapsed-refractory multiple myeloma; overall survival; CAR-T; non CAR-T agents
Online: 3 October 2022 (12:16:01 CEST)
In recent years, new treatments have been studied for relapsed-refractory multiple myeloma (RRMM), including two CAR-T products and a variety of non CAR-T agents. Since direct comparisons between these innovative treatments are not available, indirect comparisons can be of interest. Reconstruction of individual patient data from Kaplan-Meier graphs (Shiny method) has been employed in numerous reports that have validated its performance. In the present review, we evaluated six treatments proposed for RRMM including two CAR-T products (ciltacabtagene autoleucel and idecabtagene vicleucel) and four treatments not based on a CAR-T (melflufen plus dexamethasone, isatuximab plus dexamethasone, selinexor, and belantamab). The end-point was overall survival (OS); the Shiny method was used to generate reconstructed survival curves. Our results showed statistically significant differences in OS across these treatments. Compared with pharmacological treatments, CAR-T products significantly prolonged OS with an improvement of remarkable clinical relevance. In particular, ciltacabtagene autoleucel showed better OS than idecabtagene vicleucel. As regards non CAR-T treatments, the ranking in OS was headed by isatuximab plus dexamethasone, followed by belantamab, selinexor, and melflufen plus dexamethasone. In conclusion, while the Shiny method has confirmed its validity in reconstructing individual patient data, our indirect comparisons have offered some original clues to better interpret the information on OS published in these studies.
REVIEW | doi:10.20944/preprints202201.0188.v1
Subject: Biology, Other Keywords: emerging model organisms; tardigrades; Hypsibius exemplaris; evo-devo; survival of extremes; protectants
Online: 13 January 2022 (11:43:29 CET)
Experimentally tractable organisms like C. elegans, Drosophila, zebrafish, and mouse are popular models for addressing diverse questions in biology. In 1997, two of the most valuable invertebrate model organisms to date – C. elegans and Drosophila – were found to be much more closely related to each other than expected. C. elegans and Drosophila belong to the nematodes and arthropods respectively, and these two phyla and six other phyla make up a clade of molting animals referred to as the Ecdysozoa. The other ecdysozoan phyla could be valuable models for comparative biology, taking advantage of the rich and continual sources of research findings as well as tools from both C. elegans and Drosophila. But when the Ecdysozoa was first recognized, few tools were available for laboratory studies in any of these six other ecdysozoan phyla. In 1999 I began an effort to develop tools for studying one such phylum, the tardigrades. Here, I describe how the tardigrade species Hypsibius exemplaris and tardigrades more generally have emerged over the past two decades as valuable new models for answering diverse questions. To date, these questions have included how animal body plans evolve and how biological materials can survive some remarkably extreme conditions.
Subject: Physical Sciences, Acoustics Keywords: Great Filter; Computing Power; Deep Space Missions; Human Landings; Colonization; Humanity; Survival
Online: 20 July 2021 (16:09:23 CEST)
A foundational model has been developed based on trends built from empirical data of space exploration and computing power through the first six plus decades of the Space Age which projects earliest possible launch dates for human-crewed missions from cis-lunar space to selected Solar System and interstellar destinations. The model uses computational power, expressed as transistors per microprocessor, as a key broadly limiting factor for deep space missions’ reach and complexity. The goal of this analysis is to provide a projected timeframe for humanity to become a multi-world species through off-world colonization, and in so doing all but guarantees the long-term survival of the human race from natural and human-caused calamities that could befall life on Earth. Be-ginning with the development and deployment of the first nuclear weapons near the end of World War II, humanity entered a ‘Window of Peril’ which will not be safely closed until robust off-world colonies become a reality. Our findings suggest the first human-crewed missions to land on Mars, selected Asteroid Belt objects, and selected moons of Jupiter and Saturn can occur before the end of the 21st century. Launches of human-crewed interstellar missions to exoplanet destinations within roughly 40 lightyears of the Solar System are seen as possible during the 23rd century and launch of intragalactic missions by the end of the 24th century. An aggressive and sustained space exploration program, which includes colonization, is thus seen as critical to the long-term survival of the human race.
HYPOTHESIS | doi:10.20944/preprints202011.0257.v1
Subject: Life Sciences, Biochemistry Keywords: Listeria monocytogenes; virulence heterogeneity; hypervirulent clones; prolonged in vivo survival; invasive listeriosis
Online: 8 November 2020 (14:49:05 CET)
Although all isolates of the foodborne pathogen Listeria monocytogenes are considered to be pathogenic, epidemiological evidence indicates that certain serovar 4b lineages are more likely to cause severe invasive (neuromeningeal, maternal-fetal) listeriosis. Recently described as L. monocytogenes “hypervirulent” clones, no distinctive bacterial trait has been identified so far that could account for the differential pathogenicity of these strains. Here we discuss some preliminary observations in experimentally infected mice suggesting that serovar 4b hypervirulent strains may have a hitherto unrecognized capacity for prolonged in vivo survival. We propose the hypothesis that protracted survivability in primary infection foci in liver and spleen –first target organs after intestinal translocation– may cause L. monocytogenes serovar 4b hypervirulent clones to have a higher probability of secondary dissemination to brain and placenta.
ARTICLE | doi:10.20944/preprints202003.0108.v1
Subject: Biology, Other Keywords: Taiwan tuna longline fishery; circle hook; tuna hook; catch rate; survival rate
Online: 6 March 2020 (08:57:07 CET)
Taiwan is the world’s leading country regarding tuna longline fisheries; the combined catches with those from Japan account for more than half of the global total. However, the bycatch of sea turtles, seabirds, and dolphins in longline fisheries has attracted international concern. Regarding sea turtle conservation, the use of circle hooks in longline fisheries will inevitably become a trend. Meanwhile, Taiwanese fishermen are concerned whether the use of circle hooks will have a negative impact on the catch efficiency of target species. This study was conducted to compare the catch efficiency of circle and tuna hooks by the Taiwanese commercial tuna longline fishing vessels in the eastern Pacific Ocean. The results indicated that if the effects of immersion time were considered, the catch rates of all groups were the same between 4.2-sun circle and tuna hooks. However, the catch rate of 4.0-sun circle hooks was significantly higher than the two types of 4.2-sun circle and tuna hooks. Regarding survival rates, fish caught with circle hooks showed higher survival rates than tuna hooks for total commercial fish, tunas and yellowfin tuna (Thunnus albacares). However, the survival rate was only determined at haulback; the relationship between survival rate and immersion time still needs further investigation. Regarding catch sizes, there were no significant differences in the sizes of bigeye (Thunnus obesus) and yellowfin tuna between circle and tuna hooks. But based solely on mean weight, the value of yellowfin tuna caught using circle hooks may be higher than those using tuna hooks. In summary, the circle hooks used in this study did not show a negative impact on the catch efficiency of Taiwanese longline fisheries, and could show a superior performance than that of tuna hooks. These results could be actively promoted in the industry through the education and training of fishermen; thus enabling Taiwan to comply with international sea turtle conservation trends.
ARTICLE | doi:10.20944/preprints201810.0518.v1
Subject: Earth Sciences, Environmental Sciences Keywords: Korean fir; hierarchical regression model; climate change; seedling survival; dwarf bamboo; drought
Online: 23 October 2018 (05:00:38 CEST)
Regional declines of the Korean fir (Abies koreana) have been observed since the 1980s on the subalpine region. To explain this decline, it is fundamental to investigate the degree to which environmental factors have contributed to plant distributions on diverse spatial scales. We applied a hierarchical regression model to determine quantitatively the relationship between the abundance of Korean fir (seedlings) and diverse environmental factors across two different ecological scales. We measured Korean fir density and the occurrence of its seedlings in 102 (84) plots nested at five sites and collected a range of environmental factors at the same plots. Our model included hierarchical explanatory variables at both site-level (weather conditions) and plot-level (micro-topographic factors, soil properties, and competing species). The occurrence of Korean fir seedlings was positively associated with moss cover and rock cover but negatively related to dwarf bamboo cover. On site-level, winter precipitation was significantly positively related to the occurrence of seedlings. A hierarchical Poisson regression model revealed that Korean fir density were negatively associated with slope aspect, topographic position index, Quercus mongolica cover, and mean summer temperature. Our results suggest that drought and competition with other species are factors which halt the survival of Korean fir. We can predict that the population of Korean fir will continue to decline on the Korean Peninsula due to rising temperatures and seasonal drought, and only a few Korean fir will survive on northern slopes or valleys where competition with dwarf bamboo and Q. mongolica can be avoided.
ARTICLE | doi:10.20944/preprints201809.0588.v1
Subject: Mathematics & Computer Science, Probability And Statistics Keywords: non-mixture model; Fréchet distribution; right censored survival data; maximum likelihood method
Online: 29 September 2018 (07:55:08 CEST)
This paper considers a non-mixture cure model for right censored data. It utilizes the maximum likelihood method to estimate model parameters in the non-mixture cure model. The simulation study is based on Fréchet susceptible distribution to evaluate the performance of the method. Comparing with Weibull and exponentiated exponential distributions, the non-mixture Fréchet distribution is shown to be the best in modeling a real data on allogeneic marrow HLA-matched donors and ECOG phase III clinical trial e1684 data.
ARTICLE | doi:10.20944/preprints201804.0008.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: SNP; multiple analysis pipeline; pharmacogenomics; overall survival curves; data mining: statistical analysis
Online: 2 April 2018 (07:53:23 CEST)
Personalized medicine is an aspect of the P4 medicine (predictive, preventive, personalized and participatory) based precisely on the customization of all medical characters of each subject. In personalized medicine, the development of medical treatments and drugs is tailored to the individual characteristics and needs of each subject, according to the study of diseases at different scales from genotype to phenotype scale. To make concrete the goal of personalized medicine, it is necessary to employ high-throughput methodologies such as Next Generation Sequencing (NGS), Genome-Wide Association Studies (GWAS), Mass Spectrometry or Microarrays, that are able to investigate a single disease from a broader perspective. For example, by using genotyping microarrays (e.g. collections of Single Nucleotide Polymorphism - SNP) it is possible to uncover the reasons (i.e. mutation in genes) because a treatment works properly in some patients (for example absence of mutated genes), but it does not work (presence of mutated genes) in others. A side effect of high-throughput methodologies is the massive amount of data produced for each single experiment, that poses several challenges (e.g. high execution time and required memory) to bioinformatic software. Thus a main requirement of modern bioinformatic software is the use of good software engineering methods and efficient programming techniques, able to face those challenges, that include the use of parallel programming and efficient and compact data structures. Thus, to exploit all the potential of this massive amount of data in the short possible time (before that data becomes obsolete), the necessity to develop parallel software tools for efficient data collection and analysis arise. Moreover, due to the heterogeneity of the data produced by the different kinds of experimental platforms, it is necessary to automatize in a comprehensive software pipeline, the various steps that compose a bioinformatic analysis, such as: the preprocessing of raw data to remove noise or corrupted data; the annotation of data with external knowledge (e.g. Gene Ontology), and the integration of molecular data with clinical data. It should be noted that such steps are necessary to make statistical or data mining analysis more effective. This paper presents the design and the experimentation of a comprehensive software pipeline, named microPipe, for the preprocessing, annotation and analysis of microarray-based SNP genotyping data. A case study in pharmacogenomics is presented. The main advantages of using microPipe are: the reduction of errors that may happen when trying to make data compatible among different tools; the possibility to analyze in parallel huge datasets; the easy annotation and integration of data.
ARTICLE | doi:10.20944/preprints201803.0143.v1
Subject: Medicine & Pharmacology, Other Keywords: counting process; censoring; Cox proportional-hazard regression; Kaplan-Meier; imputation; survival analysis
Online: 19 March 2018 (07:42:49 CET)
Censoring occurs when complete follow-up time information is unavailable for patients enrolled in a clinical study. The process is considered to be informative (nonignorable) if the likelihood function for the censoring model cannot be partitioned into a set of response parameters that are independent of the censoring parameters. In such cases, estimated survival time probabilities may be biased, prompting the need for special statistical methods to remedy the situation. The problem is especially salient when censoring is skewed toward the early phase of a study. In this paper, we describe a method to impute censored follow-up times using a counting process method.
ARTICLE | doi:10.20944/preprints202111.0257.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: metastatic melanoma; targeted therapy; immune checkpoint inhibitor therapy; survival; statutory health insurance data
Online: 15 November 2021 (11:50:07 CET)
(1) Background: Targeted (TT) and immune checkpoint inhibitor (ICI) therapies have become available in the routine care of metastatic melanoma in recent years. (2) Objective: We compared mortality in patients with metastatic melanoma and different systemic therapies. (3) Methods: A retrospective cohort study, based on pseudonymized health insurance data of about 2 million individuals from Saxony, Germany, was conducted for the years 2010 to 2020. Only patients with an advanced stage, i.e. distant metastases were considered for the main analysis. Relative survival since metastasis and predicted survivor curves derived from a Cox model were used to assess potential differences in mortality. (4) Results: Relative survival was highest in the subgroup with sequential use of ICI and TT. All treatments except interferon had significant hazard ratios (HR) in the Cox model with time-dependent effects indicating a protective effect after treatment initiation (HR 0.01-0.146) but decreasing over time (HR 1.351-2.310). The predicted survivor curves revealed best survival under ICI-TT treatment and worst survival under TT treatment alone. (5) Conclusions: We found real-world evidence for survival benefits of patients with metastatic melanoma who received sequential ICI and TT treatment. It is conceivable that the observed high survival differences were overestimated due to bias, such as confounding by indication.
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Meta-analysis; p53 wild type antibodies; p53 mutant antibodies; cancer survival prognostic factor.
Online: 24 September 2021 (12:46:26 CEST)
Importance: p53 is an unequivocal tumor suppressor altered in half cancers. The immune system produces systemic p53 autoantibodies (p53 Abs) in many cancer patients. Objective: The focus of this systemic review and meta-analysis is on the prognostic value of p53 Abs expressed in the serum of patients with solid tumors. Data Sources: All the clinical investigations were searched on PubMed, MBase and Cochrane from 1993 reporting the first study until May 2021. Study Selection: Studies were included that met the following criteria: 1) participants with cancer; 2) outcome results expressed in relation to the presence of a p53 antibody; 3) a primary outcome (disease free survival, overall survival or progression free survival) expressed as hazard ratio (HR). The following exclusion criteria were used: 1) insufficient data available to evaluate outcomes; 2) animal studies; 3) studies with less than 10 participants. 1333 potentially relevant articles; studies as duplicates, non-patients studies or reviews were excluded. After viewing the titles and abstracts of the 52 remaining studies, the full texts of 34 studies were retrieved and 12 studies were included in the analysis. Data Extraction and Synthesis: PRISMA guidelines were used for abstracting and assessing data quality and validity by three independent observers. The summary estimates were generated using a fixed-effect model (Mantel–Haenszel method) or a random-effect model (DerSimonian–Laird-method) depending on the absence or presence of heterogeneity (I2). Main Outcome(s) and Measure(s): The primary study outcome was to determine the prognostic value of p53 Abs from a large population size of patients with solid tumors, as determined before data collection. Results: In total 12 clinical studies and of which 2094 patients were included and it was determined that p53-wt Abs expression in the serum significantly correlated with a worse survival of cancer patients (95% CI 1.48 [1.24, 1.77]; p<0.00001). On the contrary, data from literature indicated that there was a potential association between p53-mut Abs antibodies with better survival. Conclusions and Relevance: This is the first meta-analysis proving the diagnostic utility of p53-Abs for cancer patients, predicting a worse outcome. The serum-p53 value (s-p53-value) could be useful for future theranostics.
ARTICLE | doi:10.20944/preprints202109.0289.v1
Subject: Medicine & Pharmacology, Urology Keywords: BRD9; Prostate Cancer; SWI/SNF; Survival; pathways; signal transduction; human cohorts; targeted therapy
Online: 16 September 2021 (13:51:57 CEST)
Background and aims: Despite recent advances in advanced prostate cancer treatments, there are no clinically useful biomarkers or treatments for men with such cancers. Targeted therapies have shown promise, but there remain fewer actionable targets in prostate cancer than in other cancers. This work aims to characterize BRD9, currently understudied in prostate cancer, and investigate its co-expression with other genes to assess its potential as a biomarker and therapeutic target in human prostate cancer. Materials and methods: Omics data from a total of 2053 prostate cancer patients across 11 independent datasets were accessed via Cancertool and cBioPortal. mRNA expression and co-expression, mutations, amplifications, and deletions were assessed with respect to key clinical parameters including survival, Gleason grade, stage, progression and treatment. Network and pathway analysis was carried out using Genemania, and heatmaps were constructed using Morpheus. Results: BRD9 is overexpressed in prostate cancer patients, especially those with metastatic disease. BRD9 expression did not differ in patients treated with second generation antiandrogens versus those who were not. BRD9 is co-expressed with many genes in the SWI/SNF and BET complexes, as well as those in common signaling pathways in prostate cancer. Summary and conclusions: BRD9 has potential as a diagnostic and prognostic biomarker in prostate cancer. BRD9 also shows promise as a therapeutic target, particularly in advanced prostate cancer, and as a co-target alongside other genes in the SWI/SNF and BET complexes, and those in common prostate cancer signalling pathways. These promising results highlight the need for wider experimental inhibition and co-targeted inhibition of BRD9 in vitro and in vivo, to build on the limited inhibition data available.
ARTICLE | doi:10.20944/preprints202109.0106.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: mechanical circulatory support; heart transplantation; survival curve; ventricular assist device; extracorporeal membrane oxygenation
Online: 6 September 2021 (14:39:13 CEST)
BACKGROUND: The number of waitlisted patients requiring mechanical circulatory support (MCS) as a bridge to heart transplantation is increasing. The data concerning the results of double-bridge strategy are limited. We sought to investigate the post-transplant outcomes across the different bridge strategies. METHODS: We retrospectively reviewed a heart transplantation database from Jan 2009 to Jan 2019. Intra-aortic balloon pump (IABP), extracorporeal membrane oxygenation (ECMO), and ventricular assist devices (VAD) were the MCS that we investigated. The pre- and post-transplant characteristics and variables of patients bridged with the different types of MCS were collected. The post-transplant survival was compared using Kaplan-Meier survival analysis. RESULTS: A total of 251 heart transplants were reviewed; 115 without MCS and 136 with MCS. The patients were divided to five groups: Group 1 (no MCS): n=115; Group 2 (IABP): n=15; Group 3 (ECMO): n=33; Group 4 (ECMO-VAD): double-bridge (n=59); Group 5 (VAD): n=29. Survival analysis demonstrated that the 3-year post-transplant survival rates were significantly different among the groups (Log-rank p < 0.001). There was no difference in survival between group 4(ECMO-VAD) and group 1(no MCS)1 (p = 0.136), or between group 4(ECMO-VAD) and group 5(VAD) (p = 0.994). Group 3(ECMO) had significantly inferior 3-year survival than group 4(ECMO-VAD) and group 5(VAD). CONCLUSION: Double bridge may not lead to worse mid-term results in patients who could receive a transplantation. Initial stabilization with ECMO for critical patients before implantation of VAD might be considered as a strategy for obtaining an optimal post-transplant outcome.
REVIEW | doi:10.20944/preprints202106.0504.v1
Subject: Biology, Anatomy & Morphology Keywords: Microbiota; Microbiome; Mosquitoes; Behavior; Oviposition; Larval habitat; Life History Traits; Nutrition; Development; Survival
Online: 21 June 2021 (11:22:15 CEST)
Mosquitoes are considered one of the most important threats worldwide due to their ability to vector pathogens. They are responsible for the transmission of major pathogens such as Malaria, dengue, Zika or Chikungunya. Due to the lack of treatments or prophylaxis against many of the transmitted pathogens and an increasing prevalence of mosquito resistance to insecticides and drugs available, alternative strategies are now being explored. Some of these involve the use of microorganisms as promising agent to limit the fitness of mosquitoes, attract or repel them and decrease the replication and transmission of pathogenic agents. In recent years, the importance of microorganisms colonizing the habitat of mosquitoes has particularly been investigated since they appeared to play major roles in their development and diseases transmission. In this issue we will synthesize researches investigating how microorganisms present within water habitats may influence breeding site selection and oviposition strategy of gravid mosquito females. We will also highlight the impact, effect of such microbes on the fate of females’ progeny during their immature stages with a specific focus on egg hatching, development rate and larvae of pupae survival.
ARTICLE | doi:10.20944/preprints202103.0747.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Leptospirosis; Leptospira; water; random; metagenomic; epidemiology; soil; environment; survival; climate; zones; serial sampling
Online: 30 March 2021 (14:17:24 CEST)
Human leptospirosis cannot be investigated without studying zoonotic and environmental as-pects of the disease. The objectives of this study are to explore the abundance of Leptospira in dif-ferent climate zones of Sri Lanka and to describe the presence of Leptospira in same water source at different time points. First, water and soil samples were collected from whole-island, secondly, water sampling continued only in dry-zone, finally serial sampling of water from ten open wells was performed at five different time points. Quantitative PCR for water and metagenomic se-quencing for soil were used to detect Leptospira. In first component, 2 out of 12 water sites were positive and both are situated in wet-zone. Very small quantities of Genus Leptospira was detect-ed by metagenomic analysis of soil. Only 5 out of 26 samples were positive in the second compo-nent. Six, five, four, five, six wells were positive respectively in serial measurements of third component. All wells were positive at least one measurement while only one well was positive in all measurements. Closer to tank and higher distance from main road were significant risk fac-tors associated with well positivity. Presence of Leptospira seems not consistent indicating ran-dom abundance of Leptospira in natural environment.
ARTICLE | doi:10.20944/preprints202008.0322.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: TAP1; transcriptional expression; methylation analysis; survival analysis; co-expression; pathway analysis; health informatics
Online: 14 August 2020 (11:17:29 CEST)
Transporter associated with antigen processing 1 (TAP1) gene codes for a transporter protein, which is responsible for tumor antigen presentation in the MHC I or HLA complex. A defect in the gene results in an inadequate tumor tracking. TAP1 may also influence multi drug resistance, which is an extreme threat in providing treatment by drugs which are chemotherapeutic. The gene of TAP1 was analyzed bioinformatically. It gave us prognostic data as a confirmation of whether it should be used as a biomarker. The expression level and pattern analysis were conducted using ONCOMINE, GENT2 and GEPIA2 online platforms. Samples with different clinical outcomes were investigated for expression and promoter methylation analysis was done in cancer vs normal tissues using UALCAN. The copy number alteration and mutation frequency and expression in different cancer studies were analyzed using cBioPortal. The PrognoScan and KM plotter survival analysis of significant data (p-value<0.05) was representing graphically. Pathway and Gene ontology analysis of gene correlated to TAP1 gene was presented using bar charts. After arranging the data in a single panel and correlating expression to prognosis, understanding mutational and alterations and comparing pathways, TAP1 may be a potential novel target to evade a threat against chemotherapy and the study gives new aspects to consider for immunotherapy in human breast, lung, liver and ovarian cancer.
ARTICLE | doi:10.20944/preprints202008.0180.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: biliary atresia; Kasai portoenterostomy; cholangitis; portal hypertension; bile ducts dilatations; native liver survival
Online: 7 August 2020 (09:27:14 CEST)
The prospective study enrolled 144 patients after surgical treatment of biliary atresia in early infancy. We analyze the immediate effectiveness of the surgery and the age-related structure of complications in the up to 16-year follow-up. The immediate 2-year survival rate after the surgery constituted 49.5%. At the time of this writing, 17 of the patients have celebrated their 10th birthdays with good quality of life and no indications for LT. The obtained results underscore the critical importance of surgical correction of BA by Kasai surgery during the first 60 days of life and subsequent dynamic follow-up of the patients for the purpose of the early detection and timely correction of possible complications.
REVIEW | doi:10.20944/preprints201906.0269.v1
Subject: Behavioral Sciences, Behavioral Neuroscience Keywords: subjective paranormal experience, homeostasis, trauma, dissociation, depersonalisation, compartmentalisation, fantasy proneness, safety, control, survival
Online: 26 June 2019 (13:59:44 CEST)
Subjective paranormal experience (SPE) has been a notable part of the human historical narrative. Alleged miracles, telepathy, clairvoyance, precognition, witchcraft, spiritualism, monsters and ghosts have received a supernatural interpretation. The incidence and prevalence of reported SPE remains at high levels in all populations investigated to date. Previous research on SPE has focused on the cognitive and social factors that facilitate paranormal beliefs and experiences. I consider here developmental factors in the brain’s responses to trauma that appear to predispose certain individuals towards SPE. The theory draws upon the established mechanisms of dissociation and fantasy generation to describe and explain the origins of paranormal experience. The theory hypothesizes that childhood abuse and victimization trigger autonomic responses of dissociation, depersonalization and compartmentalization. Freezing and associated releases of fantasy serve as a survival strategy in the homeostatic regaining of safety and control. The predictions from the homeostasis theory are consistent with the findings of multiple studies and falsifying evidence has yet to be identified.
ARTICLE | doi:10.20944/preprints202008.0172.v2
Subject: Engineering, Automotive Engineering Keywords: Sustainable Urban Drainage Systems; green roofs; analytical probabilistic approach; pre-filling volume; vegetation survival
Online: 7 December 2020 (08:07:00 CET)
The implementation of green roofs as sustainable urban drainage systems provides benefits for stormwater control and the environment and is always more encouraged. In this paper, the estimation of the probability of vegetation survival without irrigation has been proposed as a guide to choose the proper values for the design parameters; in particular the growing medium thickness has been related to the average return interval of the water content at the end of the dry period. Moreover the study represents an improvement of the analytical probabilistic approach since a chain of consecutive rainfall events has been considered, in order to take into account the possibility that the storage capacity is not completely available at the beginning of each event because of the pre-filling from more than one previous rainfall as typically happens for green roofs. Finally, developed equations have been validated by means of their application to two case studies, respectively in northern and southern Italy.
ARTICLE | doi:10.20944/preprints201911.0329.v1
Subject: Medicine & Pharmacology, Other Keywords: Vibrio cholerae cytotoxin; VCC; MAPKs; p38; ERK; pro-inflammatory; innate immune response; survival response
Online: 27 November 2019 (04:33:42 CET)
The human innate immune response to the pore-forming toxin of Vibrio cholerae VCC, is currently under study. Here, in vitro studies on a human macrophage cell line (THP-1), helped explore the activated pathways involved on the onset the innate immune response towards the cytotoxin. The secreted monomeric 65 KDa form interacts with mature macrophages in pg/ml concentrations, determined by dose response experiments after treatments under 1 h. Non vacuolating concentrations (pg/ml) were applied to the cells; immunoblots revealed activation of MAPKs: early overexpression of p38 and ERK. Cell lysis by release of lactate dehydrogenase (LDH) was not apparent in the first hour, nonetheless it was positive after 24 h. Finally, to discern whether the VCC stimulates transcriptional activators via MAPKs pathway, NF-κB and AP-1 were studied by real time quantitation. Increased expression of p50 (NF-κB), cJun and cFos (AP-1) was observed. Given that NF-κB is the transcription factor initiating inflammation of innate immune response and in turn, AP-1 is responsible for cell surviving response, results from this study lead us to conclude that VCC in vitro treatments, induce a pro-inflammatory and a surviving response, in less than one hour on activated macrophages.
ARTICLE | doi:10.20944/preprints202209.0242.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: pancreatic cancer (PC); abdominal ultrasonography (US); surveillance; prognosis; medical checkup; 5-year survival; cancer screening
Online: 16 September 2022 (08:08:33 CEST)
Recent advancements in surgical and anti-cancer therapies have provided significant hope of long survival in patients with pancreatic cancer (PC). To realize this hope, routine medical checkups of asymptomatic people should be performed to identify operable PCs. In this study, we evaluated the efficacy of medical checkups using abdominal ultrasonography (US). We retrospectively analyzed 374 patients with PC at our institute between 2010 and 2021. We divided these patients into several groups according to the diagnostic approach and compared their background and prognosis. These groups comprised PCs diagnosed through (a) symptoms, 242 cases; (b) US during medical checkup for asymptomatic individuals, 17; and other means. Of the 375 patients, 192 were men (51.3%), and the median age was 74 years (34–105). Tumors were located in the pancreatic tail in 67 patients (17.9%). Excision ratio and 5-year survival rate were significantly better in group (b) than in (a) (58.8% vs. 23.1%, P<0.01 and 42.2% vs. 9.4%, P<0.001, respectively). The prognosis of patients diagnosed using US during medical checkup was better than that of patients identified through symptomatic presentation of PC. US for asymptomatic individuals with PC might be useful for promoting better prognosis of PCs.
ARTICLE | doi:10.20944/preprints201808.0548.v1
Subject: Biology, Plant Sciences Keywords: Origanum vulgare; Spodoptera littoralis; terpenoid biosynthesis; larval survival; antioxidant enzyme activity and gene expression; toxicity
Online: 31 August 2018 (13:28:51 CEST)
Terpenoids are toxic compounds produced by plants as a defense strategy against insect herbivores. We tested the effect of Origanum vulgare terpenoids on the generalist herbivore Spodoptera littoralis and the response of the plant to herbivory. Terpenoids were analyzed by GC-FID and GC-MS and quantitative gene expression (qPCR) was evaluated on selected plant genes involved in both terpene biosynthesis. The insect detoxification response to terpenes was evaluated by monitoring antioxidant enzymes activity and expression of insect genes involved in terpene detoxification. O. vulgare terpenoid biosynthesis and gene expression was modulated by S. littoralis feeding. The herbivore-induced increased level of terpenoids (particularly carvacrol and p-cymene) interacted with the herbivore by decreasing larval survival and growth rate. The assimilation by S. littoralis of more than 50% of ingested terpenes correlated with the possible toxic effects of O. vulgare terpenoids. In choice test experiments, carvacrol and γ-terpinene mediated the larval feeding preferences, wherease the prolonged feeding on O. vulgare terpenoids (particularly on γ-terpinene) exerted relevant antinutritional effects on larvae. S. littoralis was found to react to O. vulgare terpenoids by increasing its antioxidant enzymes activities and gene expression, although this was not sufficient to sustain the toxicity of O. vulgare terpenoids.
ARTICLE | doi:10.20944/preprints201809.0540.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Modified FOLFIRINOX; Severe neutropenia; Overall survival; Overall response rate; Time to treatment failure; Advanced pancreatic cancer
Online: 27 September 2018 (10:12:08 CEST)
Modified FOLFIRINOX is effective for advanced pancreatic cancer but frequently causes severe neutropenia. The present study was designed to investigate the influence of severe neutropenia on clinical outcomes in advanced pancreatic cancer patients receiving modified FOLFIRINOX. Fifty-one advanced pancreatic cancer patients who received modified FOLFIRINOX during January 2014 and May 2018 were subjects of the present study. Adverse events, including neutropenia, were graded according to the Common Terminology Criteria for Adverse Events, version 4.0. Median overall survival (OS) was determined as the primary endpoint, while median time to treatment failure (TTF), overall response rate (ORR), and the incidence of other adverse events were measured as secondary endpoints. Severe neutropenia (grade≥3) occurred in 39 patients (76.4%), in which high level of total bilirubin (>0.6mg/dL) was a significant risk as assessed by a multivariate logistic regression analysis. Median duration of OS was significantly longer in patients with severe neutropenia than in those without it (15.2 months versus 7.2 months, P=0.032). Moreover, there was a significant correlation between OS and the grade of neutropenia (R=0.306, P=0.029). ORR tended to be higher, though not significantly, in patients with severe neutropenia. In contrast, the incidence rates of other adverse events were not different between the two groups. Severe neutropenia is an independent predictor of prognosis in advanced pancreatic cancer patients received modified FOLFIRNOX therapy.
REVIEW | doi:10.20944/preprints202112.0278.v1
Subject: Medicine & Pharmacology, Nutrition Keywords: systematic review; meta-analysis; dietary pattern; prospective cohort; randomized controlled trial; cancer prognosis; cancer survival; dietary intervention
Online: 16 December 2021 (15:06:33 CET)
Cancer survival continues to improve in high-income countries, partly explained by advances in screening and treatment. Previous studies have mainly examined the relationship between individual dietary components and cancer prognosis in tumours with good therapeutic response (breast, colon and prostate cancers). The aim of this review was to assess qualitatively (and quantitatively where appropriate) the associations of dietary patterns and cancer prognosis from published prospective cohort studies, as well as the effect of diet interventions by means of randomized controlled trials (RCT). A systematic search was conducted in PubMed, and a total of 35 prospective cohort studies and 14 RCT published between 2011 and 2021 were selected. Better overall diet quality was associated with improved survival among breast and colorectal cancer survivors; adherence to the Mediterranean diet was associated to lower risk of mortality in colorectal and prostate cancer survivors. A meta-analysis using a random-effects model showed that higher versus lower diet quality was associated with a 23% reduction in overall mortality in breast cancer survivors. There was evidence that dietary interventions, generally combined with physical activity, improved overall quality of life, though most studies were in breast cancer survivors. Further cohort and intervention studies in other cancers are needed to make more specific recommendations.
CONCEPT PAPER | doi:10.20944/preprints202111.0118.v1
Subject: Social Sciences, Accounting Keywords: Disruptive Technologies; Operational Breakeven; Altman’s Z-score; Enyi’s RSR; Going Concern; Market Induced Survival Ratio; Disruptive Technology Gains Index
Online: 5 November 2021 (11:31:53 CET)
Disruptive technologies (DT) have featured prominently in almost every human activity since the advent of computerization. The likely effects of DT on economic processes and human professions have and continue to generate fears and debates which spurred this investigation. To break away from the traditional approach the operational breakeven theory and the discriminant analysis techniques of Altman’s Z-score, and Enyi’s Relative Solvency Ratio were used to examine the relationship between firms’ market-induced-survival-ratio (MISR) and the disruptive technology gains index (DTGI) of seventy-three firms drawn from Nigeria and India. Descriptive and inferential statistics were used to analyze the data generated. The results showed that a sizeable number of firms has profited from the introduction of disruptive technologies with MISR and DTGI returning a 10% significant relationship while others are still struggling to measure up to the requirements of disruptive technologies in their chosen economic fields. The implication of this is that businesses must brace up and embrace digital transformation if they must stay afloat in this era of disruptive technologies. This study recommends a revolutionary approach to digital transformation in view of the fast pace of global integration while managers and business owners should adopt more pragmatic approach in appraising the operations and finances of a firm for effective results and timely responses to potential business challenges.
Subject: Biology, Other Keywords: stress granules; G3BP1; G3BP2; Caprin-1; USP10; TIA1; TIAR; cancer prognosis; biomarker; metastasis; resistance; cell death; pro-survival properties
Online: 7 April 2020 (01:56:12 CEST)
Stress Granules formation is a pro-survival mechanism helping cells to cope with environmental challenges. Stress Granules have been studied for two decades in fundamental research, and are now being examined in the context of human pathogenesis. Here, we review studies highlighting stress granules’ involvement in cancer development through translational pattern modification.
ARTICLE | doi:10.20944/preprints202211.0200.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: neutropenia; neutropenic fever; chemotherapy; kidney function impairment; mild kidney disease; eGFR; CKD-EPI; G-CSF; Kaplan-Meier curves; survival analysis
Online: 10 November 2022 (11:11:40 CET)
Neutropenia is a common adverse event during myelosuppressive oncological chemotherapy, predisposing to febrile neutropenia (FN). Patients with coexisting moderate-to-severe chronic kidney disease (CKD) have an increased risk of FN, included in the guidelines for the primary prophylaxis of FN. However, this does not include mild kidney function impairment with esti-mated glomerular filtration rate (eGFR) 60–89 ml/min/1.73m2. This prospective study analyzed the risk of neutropenia in patients on chemotherapy without indication for the primary prophy-laxis of FN. The study enrolled 38 patients starting chemotherapy, including 26 (68.4%) patients aged 65 years or more. The median duration of follow-up was 76 days. The methodology of cre-atinine assessment enabled the use of the newly recommended CKD-EPI formula for identifying patients with a mild reduction of glomerular filtration. Sixteen (42.1%) patients developed at least G2 neutropenia without episodes of FN. Only five (13.1%) patients had eGFR<60ml/min/1.73m2, while 15 (62.5%) eGFR< 90ml/min/1.73m2. The relative risk of neutro-penia in patients with impaired eGFR was over six times higher than in patients with eGFR>90 ml/min/1.73m2 (RR=6.08; 95%CI:1.45–27.29; p< 0.01). Our observation indicates that even a mild reduction in eGFR is a risk factor for the development of neutropenia and a potential risk factor for FN.
ARTICLE | doi:10.20944/preprints202111.0229.v1
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: Total metabolic tumor volume; bone marrow to liver ratio; PET/CT; overall survival; immunotherapy; immune checkpoint inhibitor; standardized uptake value; response prediction
Online: 12 November 2021 (14:59:35 CET)
Quantitative biomarkers derived from positron-emission tomography/computed tomography (PET/CT) have been suggested as prognostic variables in immune-checkpoint inhibitor (ICI) treated non-small cell lung cancer (NSCLC). As such data for first-line ICI therapy and especially for chemotherapy-ICI combinations are still scarce, we retrospectively evaluated baseline 18F-FDG-PET/CT of 85 consecutive patients receiving first-line pembrolizumab with chemotherapy (n=70) or as monotherapy (n=15). Maximum and mean standardized uptake value, metabolic tumor volume (MTV), total lesion glycolysis and bone marrow-/ spleen to liver ratio (BLR/SLR) were calculated. Kaplan-Meier analyses and Cox-regression models were used to assess progression-free/overall survival (PFS/OS) and their determinant variables. Multivariate selection for PFS/OS revealed MTV as most relevant PET/CT biomarker (p<0.001). Median PFS/OS were significantly longer in patients with MTV≤70mL versus >70mL (PFS: 10 months (M; 95% confidence interval 4-16) vs. 4M (3-5), p=0.001; OS: not reached vs. 10M (5-15), p=0.004). Disease control rate was 81% vs. 53% for MTV≤/>70mL (p=0.007). BLR ≤1.06 versus >1.06 was associated with better outcomes (PFS: 8M (4-13) vs. 4M (3-6), p=0.034; OS: 19M (12-/) vs. 6M (4-12), p=0.005). In patients with MTV>70mL, concomitant BLR≤1.06 indicated a better prognosis. Higher MTV is associated with inferior PFS/OS in first-line ICI treated NSCLC, with BLR allowing additional risk stratification.
ARTICLE | doi:10.20944/preprints202001.0122.v1
Subject: Physical Sciences, Astronomy & Astrophysics Keywords: cervical adenocarcinoma; immune-checkpoint inhibitor; programmed cell death-1(PD-1); programmed cell death-ligand 1(PD-L1); CD8 expression; lymphocyte; survival analysis
Online: 12 January 2020 (15:01:23 CET)
The effectiveness of immunotherapy for cervical adenocarcinoma (CA) has not been demonstrated yet. It may be possible for us to use programmed cell death 1 (PD-1), programmed cell death-ligand 1 (PD-L1), and CD8 as biomarkers of response to immune therapy in CA patients. In the present study, we aimed to investigate whether the expression levels of PD-1, PD-L1, and CD8 can predict the prognosis of CA patients and their response to ICI therapy. The levels of the PD-1, PD-L1, and CD8 proteins were analyzed by immunohistochemical analysis from formalin-fixed, paraffin-embedded tumor samples. The correlation between the expression levels and patient prognosis was analyzed by the Kaplan–Meier method and univariate and multivariate Cox proportional hazard regression model. We observed a significant inverse-correlation between the PD-1 and CD8 expression (p=0.001, chi square test). We also found a significant inverse-correlation between the PD-L1 and CD8 expression (p=0.027). The overall survival was significantly worse in patients with positive PD-1 expression (p=0.027). Similarly, the progression-free survival was also worse (p=0.087). Our results demonstrate that a high level of PD-1 expression is associated with a poor prognosis in CA patients. Further research is necessary to identify the molecular mechanisms that mediate this association.
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: SARS-CoV-2; COVID-19; public health intervention; disease severity; personal survival strategy; randomized control trials; epidemiological model; junk science; mind and body; reductionist
Online: 24 August 2020 (03:11:34 CEST)
To predict how the COVID-19 pandemic progresses, we developed a systematic method for predicting disease outcomes. In the method, we evaluate how personal disease outcomes are mainly affected by viral concentration and exposure time and four defense mechanisms: human innate immunity/host response, acquired immune response, inflammation resolution and micro circulation, and the available space in the thorax cage. By considering how pandemic measures affect viral exposure and those mechanisms, we found many pandemic measures are misused or abused to deliver long-term adverse impacts. We noted that lifestyles have been changed as a result of movement restriction measures. By using the method, we found that altered lifestyles are predicted to raise infection rate, disability and death risks in the future. We show that a person can use personal, environmental, emotional factors to reduce infection rate and death risk. To prove the validity of this finding, we extensively examined medical research models, holistic and reductionist models, epidemiological models, disease risk factors, etc, and found that population methods are unfit for studying holistic health, statistical population does not exist in most clinical trials, mathematical models were misused for studying disease properties for a population, mathematical equations for modeling personal diseases are beyond human ability to solve, statistical models are misused, population-derived treatments are inherently dangerous to patients, vaccines have limited benefits due to unique lung structure and rapid RNA mutation, and immune system damage is caused by fast viral replication rate. We found that altering biological properties to improve the defense mechanisms could prevent a super majority of deaths and prevent the virus from reaching a point to damage the immune system. For vulnerable persons, such measure is a viable strategy for surviving from the pandemic. As a whole, holistic personalized medicine is more powerful than population-based reductionist treatment by one to several orders of magnitudes. We urge people do their parts to force the medical establishment to abandon population treatment models that are responsible for failure of medicine and dissemination of misleading and factually wrong information on the effectiveness of medical treatments.
ARTICLE | doi:10.20944/preprints202108.0210.v1
Subject: Medicine & Pharmacology, Other Keywords: microscopic polyangiitis; granulomatosis with poliangiitis; eosinophilic granulomatosis with poliangiitis; kidney biopsy; pauci-immune focal and segmental necrotizing and crescentic glomerulonephritis; tubular atrophy and interstitial fibrosis; kidney survival
Online: 10 August 2021 (07:59:00 CEST)
ANCA-associated vasculitis (AAV) pose a significant risk of kidney failure, kidney biopsy remains a key prognostic tool. Pathology classification of the AAV glomerulonephritis (GN) developed by Berden et al showed correlation between GN classes and kidney outcomes; ANCA Renal Risk Score (ARRS) included tubular atrophy and interstitial fibrosis (TA/IF) as an additional parameter for risk assessment. We aimed to evaluate kidney survival across AAV GN classes and ARRS groups. A single-center retrospective study included 85 adult patients with biopsy-proven AAV kidney disease followed in 2000-2020. Primary outcome was kidney survival at the end of 18 [5; 66] months follow-up, kidney death considered as CKD stage 5. We found significant difference in the kidney survival for sclerotic, mixed, crescentic and focal AAV GN classes: 19%, 76.2%, 91.7% and 100% respectively (p=0.009). Kidney survival was 0%, 75.6% and 100% for the high, median and low risk ARRS groups respectively (p<0.001); TA/IF analysis showed kidney survival 49.6% vs 87.7% for widespread and mild TA/IF respectively (р=0.003). Kidney survival was significantly lower in anti-MPO-ANCA versus anti-PR3-ANCA carriers (50.3% and 78.1% respectively, р=0.045). We conclude that unfavorable AAV kidney outcomes associated with sclerotic GN class by Berden’s classification, ARRS high risk group, and anti-MPO-ANCA subtype.
ARTICLE | doi:10.20944/preprints201806.0479.v1
Subject: Mathematics & Computer Science, Analysis Keywords: Wearable Healthcare kit; Composite IoT sensors; Trauma Scoring; TRISS; Prediction of Survival PoS; NEWS; RTS; HL7 FHIR; SNOMED-CT; Location Aware Healthcare kit; GIS GPS Healthcare kit
Online: 28 June 2018 (15:44:00 CEST)
With the availability of wearable health monitoring sensor modules like 3-Lead Electrocardiogram (ECG), Pulse Oximeter (SpO2), Galvanic Skin Response (GSR), Hall effect sensor (for measuring Respiratory Rate), Blood Pressure and Temperature measuring and sensing elements, it has now become possible to device a composite health status monitoring kit that can measure vital signs and other physiological parameters pertaining to human health in real time. Traditionally, the physiological parameters along with vital signs related examination was possible only in a hospitalized or ambulatory environment, however due to advances in sensing and embedded system technology and miniaturization of data acquisition and processing elements health monitoring has become possible even when individuals remain engaged in their day to day activities at the convenience of space and location. The patients or individuals subject to monitoring may suffer from a traumatic experience due to their medical condition and may need emergent incidence response and the critical care team may have to prepare for the treatment only after the patient arrives, which often is too late, as in case of cardiac arrests or severe injuries. The research focused on real-time health status monitoring and trauma scoring using standard physiological parameters along with standard telemetry protocols to make the critical care team aware of an emergent situation and prepare for a medical emergency. Vital signs and physiological parameters (heart rate, temperature, respiratory rate, and blood pressure, SpO2) were measured in real time from human subjects non-invasively. In order to enable monitoring of the patients engaged in day to day activities, errors due to the motion were removed using stationary wavelet transform correction (correlation coefficient of 0.9 after correction) and signals from various sensors were denoised, filtered and were encoded in a format suitable for further data analysis. A composite sensor kit capable of monitoring vital signs and physiological parameters can be very useful in incident response when an individual undergoes a traumatic experience related to stroke, cardiac arrest, fits or even injury, as along with monitoring information the kit can calculate scores related to trauma like the Injury Severity Score (ISS), National Early Warning Signs (NEWS), Revised Trauma Score (RTS). Trauma Injury Severity Score (TRISS), Probability of Survival (Ps) score. An open access database of vital signs and physiological parameters from Physionet, MIMIC 2 Numerics (mimicdb/numerics) database was used to calculate NEWS and RTS and to generate correlation and regression models using the vital signs/physiological parameters for a clinical class of patients with respiratory failure and admitted to Intensive Care Unit (ICU). NEWS and RTS scores showed no significant correlation (r = 0.25, p<0.001) amongst themselves, however together NEWS and RTS showed significant correlation with Ps (blunt) (r = 0.70, p<0.001). RTS and Ps (blunt) scores showed some correlation (r = 0.63, p<0.001) and NEWS score showed significant correlation (r = 0.79, p<0.001) with Ps (blunt) scores. Furthermore, since individuals have to be monitored regardless of location, these kits have to have a built-in capability to locate the individual so that the incident response team can locate the individual based on Global Positioning System coordinates (GPS). A Quantum GIS (Geographical Information System) application using real-time GPS coordinates (OpenStreetMap coordinates) was used to calculate the shortest path using QGIS Network Analysis tool to demonstrate the calculation of shortest path and direction to locate the nearest service provider in shortest time. Along with locating the nearest healthcare service provider, it would help if the critical care team could be made aware of the physiological parameters and trauma scores using standard protocols accepted across the globe. The physiological parameters from the sensors along with the calculated trauma scores were encoded according to a standard Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT) coding system and International Code of Diseases (ICD) codes and the trauma information was logged to Electronic Health Records (EHR) using Fast Health Interoperability Resources (FHIR) servers. FHIR servers provided interoperable web services to log the event information in real time. It could be concluded that analytical models trained on existing datasets can help in analyzing a traumatic experience or an injury and the information can be logged using a standard telemetry protocol as a telemedicine initiative. These scores enable the healthcare service providers to estimate the extent of trauma and prepare for medical emergency procedures and find applications in general and military healthcare.
Subject: Life Sciences, Biochemistry Keywords: Head and Neck Squamous Cell Carcinoma (HNSCC); the Cancer Genome Atlas (TCGA); Survival Analysis; Optimal Cutoff; Surgical Margin; Holistic Cancer Care; Therapeutic Relationship; Mindfulness Meditation; Transcriptomic Analysis; Effect Size; CAMK2N1; CALML5; FCGBP
Online: 7 July 2021 (08:48:26 CEST)
The survival analysis of the Cancer Genome Atlas (TCGA) dataset is a well-known method to discover the gene expression-based prognostic biomarkers of head and neck squamous cell carcinoma (HNSCC). A cutoff point is usually used in survival analysis for the patients' dichotomization in the continuous gene expression. There is some optimization software for cutoff determination. However, the software's predetermined cutoffs are usually set at the median or quantiles of gene expression value to perform the analyses. There are also few clinicopathological features available on their pre-processed data sets. We applied an in-house workflow, including data retrieving and pre-processing, feature selection, sliding-window cutoff selection, Kaplan-Meier survival analysis, and Cox proportional hazard modeling for biomarker discovery. In our approach for the TCGA HNSCC cohort, we scanned human protein-coding genes to find optimal cutoff values. After adjustment with confounders, the clinical tumor stage and the surgical margin involvement are independent risk factors for patients' prognosis. According to the resulting tables with Bonferroni-adjusted P value under the optimal cutoff and the hazard ratio, three biomarker candidates, CAMK2N1, CALML5, and FCGBP, are significantly associated with the patients' overall survival. We validated this discovery by using the other independent HNSCC dataset (GSE65858). Thus, we suggest the transcriptomic analysis could help for biomarker discovery.
REVIEW | doi:10.20944/preprints202210.0248.v1
Subject: Biology, Other Keywords: Trade-off of survival for reproduction; natural selection of aging; regulatory redundancy; aging’s individual benefit; regulatory molecular biology; Darwin’s dilemma; aging-reproduction trade-off; aging declines force of selection; master gene; holistic regulatory mechanism
Online: 18 October 2022 (04:36:09 CEST)
There is scientific consensus that organismal aging did not evolve by natural selection (NS) because it lacks individual benefit. Nonetheless it exists, leading to much speculation about its origins, and when the diminishing force of selection begins. Both concepts are based upon two misconceptions; that aging occurs in and of itself and is caused by the declining strength of NS during the reproductive lifespan. Although lacking individual benefit, aging evolved by NS as a tradeoff of survival for reproduction. Based upon regulatory dynamics that participate in this tradeoff, aging begins once reproductive success has been achieved through offspring nurturing. Thereafter, the strength of NS wanes to exponentially accelerate aging, leading to death. Assumptions of the theory are that: (1) a life-long, “holistic” regulatory mechanism whose genic expression is modified epigenetically, originates in ontogenesis; (2) the regulatory mechanism of the last developmental stage becomes redundantly expressed during “morphostasis”, a non-aging, life interval of peak vitality to ensure completion of reproduction through nurturing, and (3) thereafter, loss of regulatory redundancy causes aging which reduces the strength of natural selection and allows accumulation of randomly occurring somatic damage.