The upregulated expression of thyrosine kinase AXL has been reported in several hematologic and solid human tumors including gastric, breast, colorectal, prostate, and ovarian cancers. Thus, AXL can potentially serve as a diagnostic and prognostic biomarker for various cancers. This paper reports the first-ever use of loop-mediated isothermal amplification (LAMP) of the AXL gene as a diagnostic method for ovarian cancer. We demonstrated simple instrumentation toward a point-of-care device to perform LAMP. This paper also reports the first-ever use of core-shell beads as a microreactor to perform LAMP as an attempt to promote environmentally friendly laboratory practices.

The largest gene families in plants were found to be Glutathione transferase (GSTs), which played significant roles in regulating plant growth, development, and stress response. Within the GSTs gene family, members were found to play a crucial role in the low-temperature response process of plants. A comprehensive study identified a total of 70 BraGSTs genes. Cluster analysis results demonstrated that the BraGSTs in Brassica rapa(B.rapa) could be categorized into eight sub-families and were unevenly distributed across ten chromosomes. The 39 BraGSTs genes were found to be organized into 15 tandem gene clusters, with the promoters containing multiple cis-elements associated with low-temperature response. Cold stress was observed to stimulate the expression of 15 genes, with the BraGSTF2 gene exhibiting the highest level of expression, sug-gesting its significant involvement in winter B.rapa's response to low-temperature stress. Sub-cellular localization analysis of the BraGSTF2 protein indicated its potential expression in both the cell membrane and nucleus. The analysis of stress resistance in BraGSTF2 transgenic Arabidopsis thaliana lines emon-strated that the over-expression of this gene resulted in significantly elevated levels of SOD, POD activity, and SP content compared to the wild type following exposure to low temperatures. These levels reached their peak after 24 hours of treatment. Conversely, the MDA content was lower in the transgenic plants compared to the wild type. Additionally, the survival rate of BraGSTF2 transgenic Arabidopsis thaliana was higher than that of the wild type, suggesting that the BraG-STF2 gene may play a crucial role in enhancing the cold stress tolerance of winter B. rapa. This study lay a foundation for further study on the role of BraGSTs gene in the molecular regulation of cold resistance in winter B.rapa.

The Translationally Controlled Tumor Protein (TCTP) is a multifunctional protein found in most eukaryotic taxa. In plants, TCTP regulates cell-cycle progression as well as programmed cell death and is involved in plant regeneration and responses to abiotic and biotic stress, among other functions. Additionally, there is evidence that the transcript and protein are transported over long-distance. Potatoes are a crop of agricultural interest that can reproduce asexually by regeneration from stolons and tubers. Therefore, in this study the effect of transient expression of Solanum tuberosum TCTP (StTCTP) on tuberization was analyzed. StTCTP mRNA was shown to be transported long-distance. Additionally, transient overexpression of StTCTP resulted in tuber bearing shoots with a greater diameter compared to control plants. Furthermore, the early stages of tuberization were induced compared to control plants, in which only mature tubers were observed.

Tourism has increased in prominence as a key industry that generates employment and encourages economic diversity. The coastline region is a major contributor to worldwide tourism. Since then, coastal areas have been in the forefront of tourism infrastructure development. The presence of a large number of visitors has frequently had a negative influence on the efficient use of available resources. Maya Bay in Krabi Province, southern Thailand, is one example of a coastal area that has suffered from the negative effects of over-tourism Because of the Government of India's plan to place Lakshadweep on the world map of tourism destinations that compete with other archipelagos, it was critical that the current state of tourism in Lakshadweep be studied and precautionary measures be reviewed so that tourism growth does not devolve into over-tourism and Lakshadweep does not follow the same path as Maya Bay.

This report gives a comprehensive summary of two problems about graph convolutional networks (GCNs): over-smoothing and heterophily challenges, and outlines future directions to explore.

DNS is a necessary infrastructure for accessing the Internet. Until now, privacy protection in domain name resolution has mainly focused on end user privacy (communication encryption between clients and DNS full-service resolver). For this reason, communication between DNS full-service resolver and authoritative DNS servers is still done in plaintext. A DNS request from a DNS full-service resolver to an authoritative DNS server does not pose a privacy issue because the source IP address that comes from is the DNS full-service resolver. However, in recent years, there have been reports of specific techniques for identifying the privacy of previously unknown institutions by analyzing the logs of authoritative DNS servers. In order to further strengthen privacy in DNS communication, we proposed an architecture to encrypt all DNS communication in DoH, created a prototype environment, and investigated performance evaluation. The main contributions of this paper are threefold. First, we proposed the Full-DoH DNS architecture. This is a domain name resolution framework designed specifically for institutional privacy. Second, we evaluated the proposed architecture through a prototype implementation. Finally, we discussed related issues to the proposed architecture.

In Taiwan, farmers often apply excess compost to ensure adequate crop yield in highly frequent tillage, highly weathered, and lower fertility soils. The potential of biochar (BC) for diminishing soil C mineralization, and improving soil nutrient availability in compost over-fertilized soil is promising, but the study is still under-examined. To test the hypothesis, 434 days in vitro C mineralization kinetics of incubation experiment were conducted. Woody BC 0%, 0.5%, 1.0% and 2.0% (w/w) made of lead tree (Leucaena leucocephala (Lam.) de. Wit) were added to an Oxisols, and two Inceptisols of Taiwan. In each treatment, 5% swine manure compost (2 times recommended amount) was added and served as the over-fertilized soil. The results indicated that soil type strongly influenced the impact of BC addition on soil carbon mineralization potential. Respiration per unit of total organic carbon (total mineralization coefficient, TMC) of three studied soils significantly decreased with BC addition increased. Principal component analysis (PCA) suggested that for retaining more plant nutrients in addition to the effects of carbon sequestration, it is recommended that farmer could use locally produced biochars and composts in highly weathered and highly frequent tillage soil. Adding 0.5%-1% woody BC in soil should be reasonable and appropriate.

In Taiwan, farmers often apply excess compost to ensure adequate crop yield in highly frequent tillage, highly weathered, and lower fertility soils. The potential of biochar (BC) for diminishing soil C mineralization, and improving soil nutrient availability in compost over-fertilized soil is promising, but the study is still under-examined. To test the hypothesis, 434 days in vitro C mineralization kinetics of incubation experiment were conducted. Woody BC 0%, 0.5%, 1.0% and 2.0% (w/w) made of lead tree (Leucaena leucocephala (Lam.) de. Wit) were added to an Oxisols, and two Inceptisols of Taiwan. In each treatment, 5% swine manure compost (2 times recommended amount) was added and served as the over-fertilized soil. The results indicated that soil type strongly influenced the impact of BC addition on soil carbon mineralization potential. Respiration per unit of total organic carbon (total mineralization coefficient, TMC) of three studied soils significantly decreased with BC addition increased. Principal component analysis (PCA) suggested that for retaining more plant nutrients in addition to the effects of carbon sequestration, it is recommended that farmer could use locally produced biochars and composts in highly weathered and highly frequent tillage soil. Adding 0.5%-1% woody BC in soil should be reasonable and appropriate.

Abstract: The baculovirus expression vector (BEV) system is an efficient, cost effective and scalable method to produce recombinant adeno-associated virus (rAAV) gene therapy vectors. Most BEV designs emulate the wild type AAV transcriptome and translate the AAV capsid proteins, VP1, VP2 and VP3 from a single mRNA transcript with three overlapping open reading frames (ORFs). Non-canonical translation initiation codons for VP1 and VP2 reduce their abundances relative to VP3. Changing capsid ratios to improve rAAV vector efficacy requires theoretical modification of translational context. We have made a Lac repressor inducible system to empirically regulate expression of VP1 and VP2 proteins relative to VP3 in the context of the BEV. We demonstrate the use of this system to tune the abundance, titer and potency of a neurospecific rAAV9 serotype derivative. VP1:VP2:VP3 ratios of 1:1:8 gave optimal potency for this rAAV. It was discovered that ratios of capsid proteins expressed were different than ratios that ultimately were in purified capsids. Over expressed VP1 did not become incorporated into capsids while over expressed VP2 did. Overabundance of VP2 correlated with reduced rAAV titers. This work demonstrates a novel technology for controlling production of rAAV in the BEV system and shows a new perspective on the biology of rAAV capsid assembly.

Antibiotic-sparing treatments are required to prevent the further emergence of anti-microbial resistance in Neisseria gonorrhoeae. Commensal Neisseria species have previously been found to inhibit the growth of pathogenic Neisseria species. For example, a previous study found that 3 out of 5 historical isolates of Neisseria mucosa could inhibit the growth of N. gonorrhoeae. In this study, we used agar overlay assays to assess if 24 circulating and historical isolates of Neisseria mucosa could inhibit the growth of 28 circulating and historical isolates of N. gonorrhoeae. Although pitting around each colony of N. mucosa created an optical illusion of decreased growth of N. gonorrhoeae, we found no evidence of inhibition (n=24). In contrast, positive controls of Streptococcus pneumoniae and Escherichia coli demonstrated a strong inhibitory effect against the growth of N. gonorrhoeae.

We propose a 10-Gb/s 64-quadrature amplitude modulation (QAM) signal-based Radio over Fiber (RoF) system for 50 km of standard single mode fiber length which utilizes Reinforcement Learning (RL) SARSA based decision method to indicate an effective decision which mitigates nonlinearity. By utilizing RL-SARSA algorithm, the results demonstrate that significant reduction can be obtained in terms of bit error rate.

Machine learning (ML) methodologies have been looked upon recently as a potential candidate for mitigating nonlinearity issues in optical communications. In this paper, we experimentally demonstrate a 40-Gb/s 256-quadrature amplitude modulation (QAM) signal-based Radio over Fiber (RoF) system for 50 km of standard single mode fiber length which utilizes support vector machine (SVM) decision method to indicate an effective nonlinearity mitigation. The influence of different impairments in the system is evaluated that includes the influences of Mach-Zehnder Modulator nonlinearities, in-phase and quadrature phase skew of the modulator. By utilizing SVM, the results demonstrated in terms of bit error rate and eye linearity suggest that impairments are significantly reduced and licit input signal power span of 5dBs is enlarged to 15 dBs.

L-glutamate is one the most important excitatory neurotransmitter at central nervous system level and it is implicated in several pathologies. So, it is very important to monitor its variations, in real time in animal models’ brain. Amperometric biosensors have been used because of their very high temporal and spatial resolution, and because suitable for a short to mid-term implantation. The present study aimed to develop and characterize a new glutamate biosensor design that exploits the selectivity of Glutamate Oxidase (GluOx) for l-glutamate, and the capability of a small molecule as propylene glycol (PG) to influence and extend the stability and the activity of enzyme. Different designs were evaluated by modifying the main components in their concentrations to find the most suitable design. Moreover, enzyme concentrations from 100 U/ml up to 200 U/ml were verified and different PG concentrations (1%, 0.1% and 0.05%) were tested. The most suitable selected design was Pt_c/PPD/PEI(1%)₂/GlutOx₅/PG(0.1%) and it was compared to the same already described design loading PEDGE, instead of PG, in terms of over-time performances. PG has proved to be capable of determining an over-time stability of the glutamate biosensor in particular in terms of linear region slope (LRS) up to 21 days.

The present study was performed to examine that transforming growth factor beta (TGF-β) in root-surrounding tissues on deciduous teeth during the physiological root resorption regulates the differentiation induction into odontoclast. We prepared root-surrounding tissues with (R) or without (N) physiological root resorption scraped off at three regions (R1-R3 or N1-N3) from the cervical area to the apical area of the tooth and measured both TGF-β and the tartrate-resistant acid phosphatase (TRAP) activities. The TGF-β activity level was increased in N1-N3, whereas the TRAP activity was increased in R2 and R3. In vitro experiments for RANKL-mediated osteoclast differentiation revealed that TGF-β in N1-N3 and R1-R3 enhanced the TRAP activity in RAW264 cells. A genetic study indicated that the mRNA level of TGF-β1 in N1 and N2 was significantly increased, and corresponded with that of osteoprotegerin (OPG). In contrast, the expression level of receptor activator of NF-κB ligand (RANKL) was increased in R2 and R3. Our findings suggest that TGF-β is closely related to the regulation of OPG induction and RANKL-mediated odontoclast differentiation depending on the timing of RANKL and OPG mRNA expression in the root-surrounding tissues of deciduous teeth during physiological root resorption.

The ultimate goal of our review is to draw clinician’s attention, especially of those who are managing pediatric patients with permanent, long-standing, ventriculoperitoneal or, less commonly, ventriculo-atrial shunts. This specific subgroup of patients may eventually suffer from severe, intractable headaches which may negatively impair their quality of daily living. In the absence of any other clinical condition that could be attributed as the cause of the headache, shunt overdrainage should not be overlooked but, on the contrary, should be seriously taken into consideration in the therapeutic armamentarium of such cases, that are difficult to be handled.

Background A body composition monitor (BCM) has a role not only in determining over-hydration (OH) but also as an aid to nutritional assessment. For dialysis patient-specific clinical applications of BCM, it is necessary to clarify the relationship between body composition parameters and OH in healthy Chinese individuals. Methods This cross-sectional study involved 314 healthy individuals with a mean age of 45.7±13.1 years. BCM measurements were performed while the subjects were fasting. Results The mean OH level was 0.379±0.81 L. Lean tissue index (LTI) and Lean tissue mass (LTM) were significantly higher in males (p<0.001), while fat tissue index (FTI) was significantly higher in females (p<0.001). In univariate correlation analysis, FTI, Fat, and ATM had a negative correlation with OH in females and all subjects (p<0.05), while LTM and BCM had a positive correlation in all subjects (p<0.05). There was a significant negative correlation between phase angle (PhA) and OH in males, females, and all subjects (r=-0.634, p<0.001; r=-0.666, p<0.001; r=-0.484, p<0.001, respectively). In multivariate linear regression analysis, PhA (b=-1.266, p<0.001), LTM (b=0.987, p<0.001), age (b=-0.307, p<0.001) were independent predictors of OH. Conclusions This study demonstrated that age, LTM and especially PhA, had important roles in predicting OH in healthy Chinese individuals. In the future, PhA may aid in clinical assessment by helping to titrate dry weight among hemodialysis patients with malnutrition.

Facial expression has lots of applications in human-computer interaction. Although feature extraction and selection have been well studied, the specificity of each expression variation is not fully explored in state-of-the-art works. In this work, the problem of multiclass expression recognition is converted into triplet-wise expression recognition. For each expression triplet, a new feature optimization model based on Action Unit (AU) weighting and patch weight optimization is proposed to represent the specificity of the expression triplet. Sparse representation based approach is then proposed to detect the active AUs of testing sample for better generalization. The algorithm achieved competitive accuracies of 89.67% and 94.09% for Jaffe and CK+ databases, respectively. Better cross-database performance has also been observed.

This research investigates the socio-economic impact of rattan cane processing on the livelihoods of practitioners in Ibadan Metropolis. It comprehensively assesses raw material availability, examines factors influencing demand and supply, and evaluates sales to determine the profitability of rattan processors. With the snowball and total enumeration sampling methods, the study engages with a diverse group of rattan processors. The study reveals a concerning 36% acknowledgement of a decline in the availability of canes attributed to deforestation and over-exploitation. Notably, it emphasizes that rattan product manufacturing in Ibadan Metropolis operates at a craft level, employing tools like saws, hammers, knives, gas cylinders, pinches, and tape rules, impacting production efficiency and product longevity. Additionally, the research underscores the absence of government support and credit facilities reported by all respondents. The Market Margin analysis highlights varying profitability levels across rattan products, with chairs exhibiting notably higher profitability (32.22%) than others. Individual profit margins for specific products, such as chairs (145.00%), underscore the significance of processing costs, production time, and market demand. The study offers strategic recommendations, advocating for district-level service centres for training, technology transfer, and support to enhance skills and technical efficiency. It calls for government intervention through incentives, facilities, tax breaks, and policies to fortify the rattan trade, improving production standards and unlocking export market potential. Furthermore, financial support, technical assistance, and mechanization should be employed to reduce production costs and time, ultimately elevating income generation in the rattan industry. This research contributes valuable insights to the discourse on sustainable livelihoods and economic viability within the rattan sector.

Transit-oriented development (TOD), such as metro depot and over-track building complexes, has expanded rapidly in China. Over-track building construction has the advantage of comprehensive utilization of land resources, ease of commuting to work, and provide funds for subway construction. However, there still has a pending problem, disturbance of railway vibration, for TOD. Excessive noise and vibration seriously affect people’s life. To address this challenge, field measurements are used to obtain the vibration source characteristics and vibration propagation of the ground and the superstructure in this study. And the typical metro depot with over-track building in Wuhan was selected. The effects of vibration on the surrounding ground and adjacent buildings caused by the operation of trains have been measured, and the propagation law of train-induced ground vibration acceleration in the time and frequency domains has been analyzed. The distribution and propagation laws of vibration noise, structural noise and secondary structure noise in sensitive areas such as the throat area, depot area, test section and access section of the over-track buildings and their impact laws on the over-track buildings are obtained. And the effectiveness of the vibration and noise reduction methods used were evaluated. Results show that within 43 m from the train running track, the train running induced vertical vibration acceleration level in the high-rise building peak size of 58.8 dB, the average value of 55.62 dB; vibration frequency components are mainly 40-60 Hz. The findings might provide useful insight for designing vibration mitigation systems in new metro depots with over-track buildings.

Diabetes is a serious health problem throughout the world, including in Indonesia. The International Diabetes Federation (IDF) reports that the number of adults with diabetes is increasing every year. The Behavioral Risk Factor Surveillance System (BRFSS) is a survey conducted by the Centers for Disease Control and Prevention (CDC) in the United States. Classification methods in data mining techniques are used to classify diabetics and non-diabetics. The data mining process is carried out by preprocessing, feature selection, and dataset classification stages. In the preprocessing stage, data cleaning, data formatting, and data oversampling are carried out using the Synthetic Minority Over-sampling Technique (SMOTE). Next, the feature selection stage is carried out using the Particle Swarm Optimization (PSO) algorithm to find the best attributes. The dataset classification stage is carried out using the CART Model Decision Tree algorithm. The results of the performance evaluation of the CART algorithm are calculated using the confusion matrix and the MAE value, the results obtained for the CART algorithm without SMOTE and PSO obtained the best accuracy of 75.34% and the MAE value of 0.2466, while the CART algorithm using SMOTE and PSO can increase accuracy by 10 .94% to 86.28% and an MAE value of 0.1372.

Use of Machine Learning (ML) methodologies in optical communications has paved a new pathway. In this paper, firstly, we discuss the use of ML methodologies for reducing optical fiber nonlinearities, nonlinearity compensation, fault detection and optical performance monitoring. Then we present our recent work where we compare RL-SARSA and SVM based method with conventional method. The results show that RL-SARSA and SVM methods are successful candidates in mitigating the nonlinearities in proposed system as compared to conventional optical communication system.

Extreme overvalued beliefs (EOB) are rigidly-held, shared beliefs that are the motive behind most acts of terrorism and mass shootings. EOBs are differentiated from delusions and obsessions. The concept of overvalued idea was first described by Wernicke and later applied to terrorism by McHugh. Our group of forensic psychiatrists (Rahman, Resnick, Harry) refined the definition as an aid in the differential diagnosis seen in acts of violence. The form and content of EOBs is discussed as well as group effects, conformity and obedience to authority. Religious cults such as: The People’s Temple, Heaven’s Gate, Aum Shinrikyo, Islamic State (ISIS) and conspiracy beliefs such as assassinations, moon-hoax and vaccine-induced autism beliefs are discussed using this construct. Finally, some concluding thoughts on countering violent extremism, including its online presence is discussed utilizing information learned from online eating disorder and consumer experience.

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.

In the context of the French tertiary decree, it is crucial to reduce the energy consumption of buildings by first addressing the design of the electrical architecture. Implementing Direct Current (DC) nanogrids in buildings could offers a promising advantage for energy efficiency, significantly impacting overall energy consumption and sustainability goals. For an insulated area with a subtropical climate, such as La Réunion island, DC nanogrids could also facilitate the insertion of local renewable energy sources, especially solar energy. This article presents the deployment and efficiency evaluation of an end-to-end Low Voltage Direct Current (LVDC) nanogrid, from conception to real-world installation within a company. The nanogrid consists of a photovoltaic power plant, a Lithium-Iron-Phosphate (LFP) battery, and DC end-use equipment such as LED lighting and DC fans for two individual offices. An innovation is provided for the power supply and energy management of terminal equipment using the Power Over Ethernet (PoE) standard IEEE 802.3bt. The efficiency of the nanogrid is measured to be 40% higher than the efficiency of an installation powered by PV and distributed at 230 VAC. These results are obtained under certain deployment conditions, which are discussed in this article, in order to enhance the energy efficiency of buildings by using 48VDC. The nanogrid hardware and software infrastructure, the methodology employed for efficiency quantification and the measurement results are described in the paper.

In the context of partial autonomy, where autonomous vehicles and humans share control of the vehicle, bringing out-of-the-loop drivers back into the loop is a significant challenge. While warning signal design guidelines are commonly used to provide alerts, few studies have examined each signal in depth with an emphasis on the autonomous environment. This study aims to fill this gap by investigating visual, auditory, and tactile stimuli and modifying their sub-attributes to explore variations related to age, gender, and other individual backgrounds. A driving simulator was utilized to create a realistic driving environment and measure participants' reaction times in takeover request situations. Analysis of the data revealed correlations between age and reaction times for auditory and tactile signals, with interaction effects observed between age and sub-attribute intensity. Additionally, participants exhibited varying reaction time patterns in response to different sub-attribute intensities. By evaluating individual differences in perception based on modality characteristics, often overlooked in prior research, this study serves as a foundational contribution to future research in the field.

This article addresses the problem of contact voltage increase caused by the low frequency oscillation of the train-grid system in the phase-separation process of the EMU. The article establishes the EMU-contact line-traction substation model, reveals the mechanism of low-frequency oscillation, and obtains the relationship between the separation phase angle of the pantograph with line and low-frequency oscillations. Methods to suppress the over-voltage during the low-frequency oscillation are proposed. The study shows that when the power phase angle of the pantograph-line separation is within the range of 60°~90° and 240°~270°, the voltage amplitude in the neutral zone is larger, the maximum amplitude can reach 52.2kV, and low-frequency oscillation will occur in the neutral zone. When low frequency oscillation occurs, the contact line voltage in the neutral zone is mainly 1/3 power frequency (16.7Hz). After installing an RC suppression device in the neutral zone, when the EMU enters the neutral zone, the absolute value of the voltage peak drops to below 20 kV. Compared with the situation where the suppression device is not connected, the absolute value of the voltage peak is reduced by nearly 60%. The study provides a basis for the design of the neutral zone of the contact line and the selection of the high-voltage equipment of the EMU.

Thyroid hormones have a catabolic effect on bone homeostasis. Hence, this study aimed to evaluate serum vitamin D, calcium, and phosphate and bone marker levels and bone mineral density (BMD) among patients with different thyroid diseases. This cross-sectional study included patients with underlying thyroid diseases (n=64, hyperthyroid; n=53 euthyroid; and n=18, hypothyroid) and healthy controls (n=64). BMD was assessed using z-score and left hip and lumbar bone density (g/cm2). Results showed that the mean serum vitamin D Levels of all groups was low (<50 nmol/L). Thyroid patients had higher serum vitamin D levels than healthy controls. All groups had normal serum calcium and phosphate levels. The bone marker levels were significantly high in the hyperthyroid group and low in the hypothyroid group. The z-score for hip and spine did not significantly differ between thyroid patients and control groups. The hip bone density was remarkably low in the hyperthyroid group. In all groups, the serum vitamin D levels were below the cutoff value. However, thyroid patients had a higher serum vitamin D level than healthy controls. The carboxy terminal collagen crosslink and procollagen type I N-terminal propeptide levels were high in hyperthyroid patients and low in hypothyroid patients. Further, hyperthyroid patients had a low hip BMD.

Mutations that provide environment dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates and are abundant in both coding and non-coding regions and could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from nine closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5’UTRs and coding regions compared to 3’UTRs and non-coding transcripts among Helianthus spp. Further, allele frequency differences measured by pairwise FST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.

Molecular studies regarding regulatory elements such as small ncRNAs and their mechanisms are poorly understood in infectious diseases. Tuberculosis is one of the oldest infectious diseases of humanity, and it is still a challenge to prevent and treat it. The control of the infection as well as its diagnosis are still complex, and treatments used are linked to several side effects. This study aimed to investigate miRNA’s expression profile to identify possible biomarkers for tuberculosis. We applied NGS techniques to investigate miRNA’s global expression profile from blood samples of infected patients with tuberculosis, their respective healthy physicians, and external healthy individuals as controls. Samples from 22 individuals run through a differential expression, target genes, gene set enrichment, and miRNA-gene network analysis. We observed 153 altered miRNAs, among which, only three DEmiRNAs (hsa-let-7g-5p, hsa-miR-486-3p and hsa-miR-4732-5p) were found between the investigated patients and their respective physicians. These DEmiRNAs are suggested to play an important role in granuloma regulation and their immune physiopathology. Our results propose that miRNAs may be involved in immune modulation, regulating the repertoire of genes expressed in the immune system’s cells. Our findings encourage the application of miRNAs as potential biomarkers for tuberculosis.

In the paper, the author presents explicit and unified expressions for a sequence of improper integrals in terms of the beta functions and the Wallis ratios. Hereafter, the author derives integral representations for the Catalan numbers originating from combinatorics.

Spinal cord injuries (SCI) can result in sensory and motor dysfunctions, which were long-considered permanent. Recent advancement in electrical neuromodulation has been proven to restore sensorimotor function in people with SCI. These stimulation protocols, however, were mostly invasive, expensive, and difficult to implement. In this study, transcutaneous electrical stimulation (tES) was used to restore over-ground walking of an individual with 21 years of chronic paralysis from a cervical SCI. After a total of 66 weeks of rehabilitation training with tES, which included standing, functional reaching, reclined sit-up, treadmill walking and active biking, significant improvement in lower-limb volitional movements and overall light touch sensation were shown by International Standards for Neurological Classification of Spinal Cord Injury (ISNCSCI) score. By the end of the study, the participant could walk in a 4-meter walking test with the aid of a walking frame and ankle foot orthoses. The success in the sensorimotor recovery of our study participant sheds light on the future of non-invasive neuromodulation treatment for SCI paralysis.

Premenstrual syndrome is characterized by pain and symptoms affecting the women´s quality of life. We aimed to evaluate the safety and effectiveness of an oral fixed dose combination containing naproxen 220 mg + paracetamol 300 mg + pamabrom 25 mg tablet (Analgen Fem®) during the routine clinical practice. A prospective, open-label, multicenter, observational post-marketing study was conducted from December 2017 to December 2019 including 270 women older than 18 years. Primary endpoint was the proportion of adverse events, meanwhile the pain intensity, premenstrual syndrome symptoms, and patient proportion with a pain score reduction by at least 50% were secondary endpoints. The mean age of population was 28.9 ± 8.8 years. Among the 270 women, 8 (3%) experienced 10 adverse events. These were headache (5/8), gastritis (2/8) dyspepsia (1/8), diarrhea (1/8) and nausea (1/8). The investigator discontinued the study medication in 3/8 patients because of adverse events. The median of differences between the pain intensity at baseline and at last observation (-4.5, 95%CI; -5, -4) demonstrated that naproxen 220 mg + paracetamol 300 mg + pamabrom 25 mg fixed dose combination reduced pain intensity (p<0.001). In addition, the proportion of patients with pain reduction by at least 50% at the end of the treatment was 70.7%. The study demonstrated that this drug represents a safe and tolerated treatment, reducing pain intensity and premenstrual symptoms.

Fragility scales are intended to help in therapeutic decisions. Here we asked if the fragility as-sessment in MM patients ≥75 years old qualified for treatment by the local physician correlates with the choice of treatment: a 2- or 3-drug regimen. Between 7/2018 to 12/2019 we prospectively enrolled 197 MM patients at the start of treatment from the 13 Polish Myeloma Group centers. The data to assess fragility were prospectively collected, but centrally assessed fragility was not disclosed to the local center. The activity of daily living (ADL) could be assessed in 192 (97.5%) and was independent in 158 (80.2%), moderately impaired in 23 (11.7%), and 11 (5.6%) in com-pletely dependent. Patients with more than 3 comorbidities were 26.9% (53 patients). Thus, ac-cording to the Palumbo calculator, 43 patients were in the intermediate-fitness group (21.8%), and the rest belonged to the frailty group (153, 77.7%). Overall, 79.7% of patients (157) received 3-drug regimens and 20.3% (40) received 2-drug regimens. In each ECOG group, more than 3/4 of patients received 3-drug regimens. According to the ADL scale, 82.3% of the independent 65.2% of moderately impaired, and 81.8% of the dependent received 3-drug regimens. Out of 53 pa-tients with at least 4 comorbidities, 71.7% received 3-drug regimens, and the rest 2-drug regi-mens. Three-drugs regimens received 34 patients from the intermediate-fit group (79.0%), and 123 (79.9%) from the frail group. Early mortality occurred in 25 patients (12.7%). No one discon-tinued treatment due to toxicity. To conclude, MM patients over 75 are mainly treated with tri-ple-drug regimens, not only in reduced doses, regardless of their frailty scores. However, the absence of prospective fragility assessment did not negatively affect early mortality and the number of treatment discontinuations which questions the clinical utility of current fragility scales in everyday practice.

Drivers of L3 automated vehicles (AVs) are not required to continuously monitor the AV system. However, they must be prepared to take over when requested. Therefore, it is necessary to design an in-vehicle environment that allows drivers to adapt their levels of preparedness to the likelihood of control transition. This study evaluates ambient in-vehicle lighting that continuously communicates the current level of AV reliability, specifically on how it could influence drivers' take-over performance and mental workload (MW). We conducted an experiment in a driving simulator with 42 participants who experienced 10 take-over requests (TORs). The experimental group experienced a four-stage ambient light display that communicated the current level of AV reliability, which was not provided to the control group. The experimental group demonstrated better take-over performance, based on lower vehicle jerks. Notably, perceived MW did not differ between the groups, and the EEG indices of MW (frontal theta power, parietal alpha power, Task-Load Index) did not differ between the groups. These findings suggest that communicating the current level of reliability using ambient light might help drivers be better prepared for TORs and perform better without increasing their MW.

A lot of previous research have proposed various frameworks and algorithms to optimize routes to reduce the total transportation cost, which accounts for over 70% of overall logistics cost. However, it is very hard to find the cases applied the mathematical models or algorithms to the practical business environment cases, especially daily operating logistics services like convenient stores. Most of previous research have considered the developing an optimal algorithm which can solve the mathematical problem within the practical time while satisfying all constraints such as the capacity of delivery and pick-up, and time windows. For the daily pick-up and delivery service like supporting several convenient stores, it is required to consider the unit transporting container as well as the demand, capacity of trucks, traveling distance and traffic congestion. Especially, the reusable transporting container, trays, should be regarded as the important asset of logistics center. However, if the mathematical model focuses on only satisfying constraints related delivery and not considering the cost of trays, it is often to leave the empty trays on the pick-up points when there is not enough space in the track. In this research, it has been proposed to build the mathematical model for optimizing pick-up and delivery plans by extending the general vehicle routing problem of simultaneous delivery and pickup with time windows while considering left-over cost. With the numerical experiments, it has been proved that the proposed model may reduce the total delivery cost. It may be possible to apply the proposed approach to the various logistics business which uses the reusable transporting container like shipping containers, refrigerating containers, trays, and pallets.

We construct a real square system related to a given over-determined real system. We prove that the simple real zeros of the over-determined system are the simple real zeros of the related square system and the real zeros of the two systems are one-to-one correspondence with the constraint that the value of the sum of squares of the polynomials in the over-determined system at the real zeros is identically zero. After certifying the simple real zeros of the related square system with the interval methods, we assert that the certified zero is a local minimum of the sum of squares of the input polynomials. If the value of the sum of the squares of the input polynomials at the certified zero is equal to zero, it is a zero of the input system. As an application, we also consider the heuristic verification of the isolated zeros of polynomial systems and their multiplicity structures. Notice that a complex system with complex zeros can be transformed into a real system with real zeros.

We present a first formal analysis of specific and complete local integration. Complete local integration was previously proposed as a criterion for detecting entities or wholes in distributed dynamical systems. Such entities in turn were conceived to form the basis of a theory of emergence of agents within dynamical systems. Here, we give a more thorough account of the underlying formal measures. The main contribution is the disintegration theorem which reveals a special role of completely locally integrated patterns (what we call ι-entities) within the trajectories they occur in. Apart from proving this theorem we introduce the disintegration hierarchy and its refinement-free version as a way to structure the patterns in a trajectory. Furthermore we construct the least upper bound and provide a candidate for the greatest lower bound of specific local integration. Finally, we calculate the i-entities in small example systems as a first sanity check and find that ι-entities largely fulfil simple expectations.

(1) Background: Intracortical microelectrodes (IMEs) are an important part of interfacing with the central nervous system (CNS) and recording neural signals. However, recording electrodes have shown a characteristic steady decline in recording performance owing to chronic neuroinflammation. The topography of implanted devices has been explored to mimic the nanoscale three-dimensional architecture of the extracellular matrix. Our previous work used histology to study the implant sites of non-recording probes and showed that a nanoscale topography at the probe surface mitigated the neuroinflammatory response compared to probes with smooth surfaces. Here, we hypothesized that the improvement in the neuroinflammatory response for probes with nanoscale surface topography would extend to improved recording performance. (2) Methods: A novel design modification was implemented on planar silicon-based neural probes by etching nanopatterned grooves (with a 500 nm pitch) into the probe shank. To assess the hypothesis, two groups of rats were implanted with either nanopatterned (n=6) or smooth control (n=6) probes, and their recording performance was assessed over 4 weeks. Postmortem gene expression analysis was performed to compare the neuroinflammatory response from the two groups. (3) Results: Nanopatterned probes demonstrated increased impedance and noise floor compared to controls. However, the recording performance of the nanopatterned and smooth probes was similar, with active electrode yield for control probes and nanopatterned probes being approximately 50% and 45%, respectively by 4 weeks post-implantation. Gene expression analysis showed 1 gene, Sirt1, differentially expressed out of 152 in the panel. (4) Conclusions: This study provides a foundation for investigating novel nanoscale topographies on neural probes.

In this paper, an analytical form of Rump Function is presented. This seminal function constitutes a fundamental concept of digital signal processing theory and is also involved in many other areas of applied mathematics. In particular, Rump Function is performed in a simple manner as the limit of a sequence of real functions letting ? tend to infinity. This limit is zero for strictly negative values of the real variable ? whereas it coincides with the independent variable ? for strictly positive values of the variable ?. The novelty of this work compared to other research studies concerning analytical expressions of the Ramp Function, is that the proposed formula is not exhibited in terms of miscellaneous special functions, e.g. Gamma Function, Biexponential Function or any other special functions such as Error Function, Hyperbolic Function, Orthogonal polynomials etc. Hence, this formula may be much more practical, flexible and useful in the computational procedures which are inserted into digital signal processing techniques and other engineering practices.

The aim of present study was to link the gene expression profile of selected candidate genes with blood profile, growth performance and carcass traits of Barki lambs. Thirty-eight Barki lambs were divided into 3 groups (fast, intermediate and slow growing) according to growth perfor-mance. Body tissues (muscle, liver and fat) were taken from for RNA isolation and Real-time PCR. The results indicated that, the final body weight hot carcass weight were heavier (P ≤ 0.05) in fast (49.9 Kg and 24.57) than intermediate (40.7 and 19.07 Kg) and slow (30.8 and 15.10 Kg) growing animals. The blood profile of total protein, total lipids, calcium, T3 and T4 hormones did not differ among sheep groups. Genes involved in protein biosynthesis (RPL7), fatty acid oxidation (CPT1) and lipolysis (FABP4) were up regulated in fast and intermediate growing lambs in all studied tissues. While, gene-regulating lipogenesis (ADIPOQ) was expressed simi-larly in fat and liver tissues, but increased its expression in muscle of fast and intermediate growing lambs. Expression of CAPN3 was increased in fast and intermediate growing compared to slow growing lambs. In conclusion, the current study providing an evidence for the im-portance of co-expression of these genes in main body tissues linked with growth performance of Barki lambs.

Cyanobacteria are highly diverse, widely distributed photosynthetic bacteria inhabiting various environments ranging from deserts to the cryosphere. Throughout this range of niches, they have to cope with various stresses and kinds of deprivation which threaten their growth and viability. In order to adapt to these stresses and survive, they have developed several global adaptive responses which modulate the patterns of gene expression and the cellular functions at work. Sigma factors, two-component systems, transcriptional regulators and small regulatory RNAs acting either separately or collectively, for example, induce appropriate cyanobacterial stress responses. The aim of this review is to summarize our current knowledge about the diversity of the sensors and regulators involved in the perception and transduction of light, oxidative and thermal stresses and nutrient starvation responses. The studies discussed here point to the fact that various stresses affecting the photosynthetic capacity are transduced by common mechanisms.

Methylenetetrahydrofolate reductase (MTHFR), an enzyme expressed in mammalian testes exerts direct effect on spermatogenesis; however, its protein characteristics in bovine testes remain unknown. Here, we analysed bovine testicular structure, MTHFR bioinformatics profile, mRNA, and protein expression characteristics in yellow-cattle (y-c) and yak testis using histological procedures, bioinformatics analysis, qRT-PCR, and western blot. Testes from 13 bovines, ≤ 2 years juvenile (y-c, n = 3; yak, n=3) and ≥ 3 years adult (y-c, n = 3; yak, n = 4) were collected and analysed. Anatomical characteristics of testis in y-c and yak were similar except the weight or size for which that of y-c was significantly higher or greater than yak. In y-c, an open reading frame (ORF) for 2600 nucleotides sequence, encoding 655 amino acids showed high homology with zebu cattle (99.51%) and wild yak (98.68%). Secondary and 3D protein structures were similar to that of humans with differences in number of nucleotides, amino acids, and some physico-chemical characteristics. MTHFR mRNA expression in y-c and yak were significantly higher in adult testes compared with juvenile ones. However, its protein expression was higher but not statistically significant in adult y-c and yak compared to the juvenile ones. The highlights and inferences of these and other findings are discussed.

MicroRNA (miRNA) is a typical class of small RNAs that could modulate gene expression in trans at the post-transcriptional level. miRNAs bind to the miRNA binding sites (MBSs) in target mRNAs by sequence complementarity. Alternative splicing (AS) is another commonly occurred process in pre-mRNAs that changes the isoforms of a gene. It is hypothesized that there should be an interaction for gene regulation that involves both AS and miRNA targeting. Studies have verified this hypothesis in the model organism Arabidopsis thaliana. High-throughput sequencing data suggested that in Arabidopsis a considerably large fraction of MBSs are affected by AS events. The overlapping between MBS and AS exceeds the randomly simulated number. Functional experiments have indicated that the AS events are required for the gene expression changes of miRNA targets. Therefore, AS and MBS are mutually favored. The observed expression changes caused by miRNAs could also be contributed by AS events. In the present perspective article, we propose that the AS analysis should be incorporated in the differential-expression analysis of miRNA studies. When defining a differentially-expressed gene, it should be clarified whether the change in gene expression is caused by AS events or solely by miRNA targeting.

Previous studies on the prognostic impact of survivin expression in gastrointestinal (GI) cancer have yielded inconsistent results. This study was initiated to assess the relationship between survivin expression and overall survival (OS) or disease free survival (DFS) in GI cancer patients. We applied system literature searches on EMBASE, PubMed, Web of science, and the Cochrane library to conduct this up-to-date meta-analysis. Thirty studies with totally 3622 GI cancer patients were collected. The prevalence of high survivin expression in GI cancer was 0.57 (95% CI: 0.51-0.63). High survivin expression was significantly associated with shorter OS (HR 1.57, 95% CI: 1.42-1.74) and DFS (HR 1.38, 95% CI: 1.21-1.58). Subgroup analysis also showed significant association between high survivin expression and poorer OS or DFS in gastric cancer or colorectal cancer. In summary, our study indicated that high survivin expression was related to poor prognosis in GI cancer. Well-designed studies with large sample and more convincing data are needed to confirm our conclusion.

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.

Background: The oldest old people (≥ 85 years) represent the fastest growing age group in Western populations. Knowledge on early outcomes of acute ischemic stroke (AIS) in very old female patients remains limited. Methods: We assessed gender differences and female-specific clinical data and in-hospital mortality in very old patients with AIS. Acute cerebral infarction was diagnosed in 506 very old female patients from a total of 4,600 acute cerebrovascular infarctions available in an ongoing 24-year hospital stroke data bank. A comparative analysis of vital status at discharge (alive versus dead) was performed in terms of cardiovascular risk factors, clinical data, and early outcomes. Results: The overall in-hospital mortality rate was 20.4%. In multivariate analysis, sudden onset, altered level of consciousness, and neurological, respiratory, cardiological or hemorrhagic complications, and lacunar infarcts appeared to be independent predictors of in-hospital mortality. Conclusions: Female patients ≥85 years with AIS are an unfavorable subgroup of stroke patients with a high risk of early mortality, which may be due to comorbidity, stroke subtype distribution, and higher frequency of medical complications. However, the presence of lacunar infarcts showed a significant protective effect.

Exploration practices have proven that over mature shale gas exhibits a feature of carbon isotope reversal. The geochemical statistics indicate that the wetness (C2-C5/C1-C5) of shale gas with carbon isotope reversal is less than 1.8%. In addition, the magnitude of carbon isotope reversal (δ13C1- δ13C2) for the over mature shale gas presents a parabolic variation with decreasing wetness. δ13C1-δ13C2 increases with decreasing wetness within a wetness range of 0.9% ~1.8% and then decreases with decreasing wetness at wetness < 0.9%. The CH4 cracking experiment demonstrates that CH4 polymerization occurring in the early stage of CH4 cracking is an important factor involved in isotope reversal of over mature shale gas. Moreover, δ13C1- δ13C2 decreases with an increase in experimental temperature prior to CH4 substantial cracking. The values of δ13C1 and δ13C2 tend to equalize during CH4 substantial cracking. The δ13C1-δ13C2 of mud gas present at different depths during shale gas drilling in Sichuan Basin increases initially, then decreases with further increase in the depth and finally tends to zero, with only a trace hydrocarbon gas being detectable. Statistical data suggests that the shale gas production in Sichuan Basin decreases with the decreasing δ13C1-δ13C2 value and wetness. Thus, δ13C1-δ13C2 and wetness could potentially serve as useful criteria to screen CH4 cracking degree and to determine the largest depth of natural gas exploration. Great care should be taken during shale gas exploration in deeper layers, with wetness and δ13C1-δ13C2 less than 0.2% and 1%, respectively, since very low wetness (<0.2%) and δ13C1-δ13C2 (<1%) might be indicative of CH4 substantial cracking in a geological setting.

The article analyzes existing materials and structures with quadratic-nonlinear optical properties that can be used to generate a difference frequency in the terahertz and sub-terahertz frequency ranges. The principle of constructing a nonlinear optical-radio converter, based on an optical focon (a focusing cone), is proposed. Based on the assumption that this focon can be implemented from the metal-organic framework (MOF), we propose a technique for modeling its parameters. The mathematical model of the process of propagation and nonlinear interaction of waves inside the focon is based on a simplification of the nonlinear wave equation. Within the framework of the developed model, the following parameters are approximately determined: the 3D gradient of the linear refractive index and the function determining the geometric profile of the focon, which provide a few-mode-based generation of the difference frequency.

In this paper, we give explicit asymptotic formulas for some sums over primes involving generalized alternating hyperharmonic numbers of types I, II and III. Analogous results for numbers with $k$-prime factors will also be considered.

This paper presents a study on the influence of the frequency variation of a nonlinear1 control allocation technique execution, developed by the author [1], named by Fast Control2 Allocation (FCA) for the Quadrotor Tilt-Rotor (QTR) aircraft. Then, through Software In The3 Loop (SITL) simulation, the proposed work considers the use of Gazebo, QGroundControl, and4 Matlab applications, where different frequencies of the FCA can be implemented separated in5 Matlab, always analyzing the QTR stability conditions from the virtual environment performed in6 Gazebo. TheresultsshowedthattheFCAneedsatleast200HzoffrequencyfortheQTRsafeflight7 conditions, i. e., 2 times smaller than the main control loop frequency, 400 Hz. Lower frequencies8 than this one would case instability or crashes during the QTR Operation.

The design flood concept (DF) provides for an essential tool in designing the hydraulic works, in defining the reservoir operation programs and for a reliable flood hazard identification. Under a simplified approach, the maximum discharge and the floods volume are statistically processed to reasonably define the DF. Yet, the integral hydrograph provides additional key temporal and quantitative details of important significance for flood management and particularly for the res-ervoirs operation and associated risks of failures. The procedure presented in this paper (as applied on a set of compatibly shaped hydrographs) involves the following key stages: (i) normalize the floods, (ii) define similar flood shape classes and (iii) evaluate the average dimensionless flood (ADF) for each class. The ADFs are finally transformed into a set of (DF)s. Many statistical distributions approximate acceptably the frequent values of the maximum discharges or the flood volumes, yet displaying a significant spread for medium or rare probabilities of exceedance (PE). This scattering, which can be explained by the epistemic uncertainty, defines an area of uncertainty both for measured and extrapolated values. In considering upper and lower values of the uncertainty in-tervals as limits for maximum discharges and flood volumes, then by combining them compatibly, a set of DFs - as completely defined hydrographs, with different shapes - results for each PE. The herein proposed procedure defines both one peak DF and multi-peaks DF. Subsequently, such DFs do assist water managers in examining and establishing tailored approaches for a variety of input hydrographs. Among the DFs that would correspond to a same PE, the most compact floods arise a special interest, for they are basic in defining the set of safe operation rules for hydraulic structures.

Hippocampal neuronal activity generates dendritic and somatic Ca2+ signals, which depending on stimulus intensity, rapidly propagate to the nucleus and induce the expression of transcription factors and genes with crucial roles in cognitive functions. Soluble Amyloid-beta Oligomers (AβOs), the main synaptotoxins engaged in the pathogenesis of Alzheimer's disease, generate aberrant Ca2+ signals in primary hippocampal neurons, increase their oxidative tone and disrupt structural plasticity. Here, we explored the effects of sub-lethal AβOs concentrations on activity-generated nuclear Ca2+ signals and on the Ca2+-dependent expression of neuroprotective genes. To induce neuronal activity, neuron-enriched primary hippocampal cultures were treated with the GABAA receptor blocker gabazine (GBZ), and nuclear Ca2+ signals were measured in AβOs-treated or control neurons transfected with a genetically encoded nuclear Ca2+ sensor. Incubation (6 h) with AβOs significantly reduced the nuclear Ca2+ signals and the enhanced phosphorylation of cyclic AMP response element binding protein (CREB) induced by GBZ. Likewise, incubation (6 h) with AβOs significantly reduced the GBZ-induced increases in the mRNA levels of Neuronal Per Arnt Sim domain protein 4 (Npas4), Brain-derived Neurotrophic Factor (Bdnf), Ryanodine Receptor type-2 (RyR2), and the antioxidant enzyme NADPH-Quinone-Oxidoreductase (Nqo1). Based on these findings we propose that AβOs, by inhibiting the generation of activity induced nuclear Ca2+ signals, disrupt key neuroprotective gene expression pathways required for hippocampal-dependent learning and memory processes.

Purpose: This study aims to analyze the factors that affect the behavior of user-defined avatars in different virtual environments, and compare the differences in public self-awareness, self-expression, and emotional expression among customized avatars in multiple virtual contexts. Methods: Using a between-subjects experimental design, two random groups of participants were asked to customize avatars for themselves in two contexts, a multiplayer online social game (MOSG) and a virtual meeting (VM). i.e. a relaxed and a serious social environment. Results: When subjects perceived a more relaxed environment, the customized avatars had less self-similarity, and the subjects exhibited a stronger self-disclosure willingness and enhanced avatar wishful identification; nevertheless, public self-consciousness was not increased. When subjects perceived a more serious environment, the customized avatars exhibited a higher degree of self-similarity, and the subjects exhibited a greater self-presentation willingness, along with enhanced identification of avatar similarity, and increased public self-consciousness. Conclusions: Participants expressed positive emotions, suggesting that avatars play a positive role in various virtual contexts. The virtual context affects the self-similarity of user-customized avatars, and avatar self-similarity affects self-presentation and self-disclosure willingness, and these factors will affect the behavior of the user-customized avatar. This study contributes suggestions to the Metaverse avatar customization platform design.

Decades of research identified numerous gene biomarkers of cardiac diseases whose restored sequence or/and expression level was hoped to recover the normal cardiac function. However, each human has unique and dynamic pathophysiological characteristics resulting from the unrepeatable combination of favoring factors such are: race, sex, age, medical history, diet, stress, exposure to toxins, habits etc. As such, no treatment fits everybody and finding personalized solutions is a top priority for medicine of 21st century. The Genomic Fabric Paradigm (GFP) provides the most theoretically possible comprehensive characterization of the transcriptome, its alterations in disease and recovery following a treatment. By attaching to each gene the independent average expression level, expression variation and expression coordination with each other gene, GFP delivers thousands times more information than the traditional analysis. This report presents the theoretical bases of the GFP and some applications to our microarray data from mouse models of post ischemic, and constant and intermittent hypoxia-induced heart failure. The GFP analyses revealed novel transcriptomic aspects of the gene expression control and networking under ischemic conditions. Through all-inclusive characterization of the transcriptome and the unrepeatable gene hierarchy in each condition, GFP is an essential avenue towards development of a truly personalized cardiogenomic therapy.

We assessed the use of Evidence-Based Practice (EBP) among pharmacists working in community pharmacies in France, and the factors linked to this practice. During 3 months in 2018 an online survey was sent to over 7,000 active pharmacists, and posted on pharmacist social media sites. The 40-item questionnaire described four clinical cases reflecting typical situations (conventional med-icine and Complementary and Alternative Medicine) encountered daily by community pharma-cists. Multiple-choice responses were proposed and scored according to whether they reflected EBP. A high total score indicated behavior in line with EBP. Univariate and multivariate analyses were used to evaluate factors that might explain adherence to EPB (pharmacy’s characteristics, the pharmacist’s status, mode of continuing education and sources of information). 595 pharmacists completed the questionnaire. The majority relied on pharmaceutical industry and other biased and/or non-evidence-based sources, particularly concerning information on homeopathic products. The consultation of independent reviews, health agency recommendations, and peer-reviewed scientific journals, was associated with evidence-based decisions. In contrast, reliance on phar-maceutical industry documents, personal experience and informal handbooks was linked to lower EBP scores. The level of EBP use by French community pharmacists needs to be improved to ensure that good quality scientifically-based advice is given to customers.

Job satisfaction has a strong impact on the intention to stay which is an important aspect to counter skills shortage in academic medicine. In an interview study combining qualitative and quantitative methods we investigated how the mental representation of working conditions influences job satisfaction and its impact on the intention to stay. In a first study chief physicians participated in interviews about job satisfaction in academic hospitals. Answers were segmented into statements, ordered by topics and rated according to their valence. In a second study assistant physicians (residents) during and after their training period talked about strength, weaknesses and potential improvements of working conditions. Again, answers were segmented, ordered, rated and used to develop a ‘job satisfaction scale’. In a third study, assistant physicians participated in a computer-led repertory grid procedure composing ‘mental maps’ of job satisfaction factors, filled in the job satisfaction scale and rated if they would recommend work and training in their clinic as well as their intention to stay. Comparing the interview results with recommendation rates and intention to stay show that a negative attitude is linked to high workload and poor career perspectives. A positive attitude towards work environment and high intention to stay are linked to sufficient personnel and technical capacities, reliable duty scheduling and fair salaries. The third study using repertory grids showed that the perception of current teamwork and future developments concerning work environment were the main aspects to improve job satisfaction and the intention to stay. The results of the interview studies were used to develop an array of adaptive improvement measure. The results support prior findings that job dissatisfaction is mostly based on generally known “hygiene factors” and whereas job satisfaction is due to individual aspects.

The study of pain requires a balance between subjective methods that rely on self-reports and complementary objective biometrics that ascertain physical signals associated with subjective accounts. There are at present no objective scales that enable the personalized assessment of pain, as most work involving electrophysiology rely on summary statistics from a priori theoretical population assumptions. Along these lines, recent work has provided evidence of differences in pain sensations between participants with Sensory Over Responsivity (SOR) and controls. While these analyses are useful to understand pain across groups, there remains a need to quantify individual differences more precisely in a personalized manner. Here we offer new methods to characterize pain using the moment-by-moment standardized fluctuations in EEG brain activity centrally reflecting the person’s experiencing temperature-based stimulation at the periphery. This type of gross data is often disregarded as noise, yet here we show its utility to characterize the lingering sensation of discomfort raising to the level of pain, individually, for each participant. We show fundamental differences between the SOR group in relation to controls and provide an objective account of pain congruent with the subjective self-reported data. This offers the potential to build a standardized scale useful to profile pain levels in a personalized manner across the general population.

Background: Although rarely indicated, antibiotics are commonly used for acute diarrhoea in China. We conducted a randomized, double blind exploratory clinical trial of loperamide, berberine and turmeric for treatment of acute diarrhoea. Methods: Adults with acute uncomplicated diarrhoea were randomized to 4 groups: (A) loperamide; (B) loperamide and berberine; (C) loperamide and turmeric; (D) loperamide, berberine and turmeric. All participants were given rescue ciprofloxacin for use after 48 hours if symptoms worsened or were unimproved. Primary endpoints were feasibility and ciprofloxacin use during the 2 week follow-up period. Semi-structured interviews were conducted following recruitment. Results: Only 21.5% (278/1295) of patients screened were deemed eligible, and 49% (136/278) of these consented and entered into the final analysis. Most participants had mild symptoms, because most patients with moderate or severe symptoms wanted to be given antibiotics. Follow-up was good (94% at 2 weeks). Only two participants used rescue antibiotics compared to 65% of acute diarrhoea patients in the hospital during the recruitment period. The median symptom duration was: 14 hours in group B (IQR 10-22), 16 hours in group D (IQR 10-22), 18 hours in group A (IQR 10-33), 20 hours in group C (IQR 16-54). Re-consultation rates were low. There were no serious treatment-related adverse events. Most interviewed participants said the treatment was effective. Conclusion: Although recruitment was challenging because of widespread expectations for antibiotics, patients with mild diarrhoea accepted to try an alternative. This therapy requires further evaluation in a fully powered, randomised controlled trial among a broader sample.

Zanthoxylum armatum is an forest tree with apomixis characteristic, and RWP-RKs are plant-specific transcription factors known to regulate nitrogen response and embryonic development. However, the genome-wide analysis of RWP-RK family genes in Z.armatum is unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z.armatum, among which 15 genes were belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed close phylogenetic relationship between Z.armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of embryonic development of Z.armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein-protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z.armatum.

One of the most crucial elements in deeply understanding humans on a psychological level is manifested through facial expressions. The analysis of a human behavior can be informed by their facial expressions, making it essential to employ indicators such as expression (Expr), valence-arousal (VA), and action units (AU). In this paper, we introduce the method proposed in the Challenge of the 6th Workshop and Competition on Affective Behavior Analysis in-the-wild (ABAW) at CVPR 2024. Our proposed method utilizes the multi-modal Aff-wild2 dataset, which is splitted into spatial and audio modalities. For the spatial data, we extract features using a SimMiM model that was pre-trained on a diverse set of facial expression data. For the audio data, we extract features using a WAV2VEC model. To fusion the extracted spatial and audio features, we employed the cascaded cross-attention mechanism of a transformer.

Subclinical inflammation in protocol biopsies relates to tacrolimus exposure and human leukocyte antigen (HLA) matching. We aimed to characterize transcripts associated with rejection and tacrolimus exposure and its association with transplant outcome. We tested whether gene expression is associated with rejection using strictly normal protocol biopsies (n = 17) and biopsies with TCMR or ABMR according to Banff criteria (n = 12). Subsequently, we analyzed these transcripts in a set of 4-month protocol biopsies (n = 137) to assess their association with donor and recipient characteristics, the intensity of immunosuppression, and graft outcome. Differential expression (FDR&gt;3) between normal and rejection biopsies yielded a set of 111 genes. Nineteen out of these 111 genes were correlated with tacrolimus trough levels (TAC-C0) at the time of biopsy in the protocol biopsy cohort (n=137) and allowed us to define 2 clusters of biopsies. The 2 clusters differed in donor age and tacrolimus levels. Subclinical rejection, including borderline lesions, tended to occur in the same cluster. Logistic regression analysis indicated that TAC-C0 at the time of biopsy (OR: 0.83, 95%CI:0.72-0.06, p=0.0117) was associated with cluster 2. In a follow-up averaging 70±30 months, this patient group displayed a significant decline in renal function (p=0.0135). The expression of rejection-associated transcripts in early protocol biopsies is associated with tacrolimus exposure and a faster decline in renal function.

Background: We screened key genes involved in the dedifferentiation process of thyroid cancer by analyzing differentially expressed genes in anaplastic thyroid carcinoma (ATC) using Gene Expression Omnibus (GEO) database. Methods: We analyzed differentially expressed genes in ATC from GEO database and constructed a co-expression network using Weighted Gene Co-expression Network Analysis (WGCNA) . Cytoscape was used to calculate top ten key genes based on their gene scores. DEPDC1 was selected as interest gene for further validation, including examination of its prognostic relationship with thyroid cancer, correlation analysis with thyroid differentiation markers, immune cell infiltration, and tumor microenvironment. The impact of DEPDC1 on cancer cell migration, invasion, and proliferation was validated through downregulation and overexpression of DEPDC1 gene in thyroid cancer cell lines c643 and BCPAP. Results: We identified top 10 key genes in ATC: AURKA, TPX2, RACGAP1, MELK, DLGAP5, DEPDC1, KIF2C, NCAPG, CCNB1, and PBK. DEPDC1 showed a strong correlation with the prognosis of thyroid cancer. The odds ratio (OR) for overall survival was 3.5 (P=0.016) in individuals with high DEPDC1 expression, and the OR for disease-free survival was 2.6 (P=0.003). Additionally, the analysis revealed a significant negative correlation between the expression of DEPDC1 and thyroid differentiation markers. Gene Ontology enrichment analysis demonstrated that DEPDC1 co-expressed genes were enriched in cellular processes, cell cycle pathways, and dynamic protein groups. Matrix and immune scoring indicated tumor microenvironment and immune scores were associated with DEPDC1 expression. TIMER2.0 online analysis revealed a strong correlation between DEPDC1 expression and immune cell infiltration in papillary thyroid carcinoma. After downregulation of DEPDC1 expression, the invasion, migration, and proliferation abilities of tumor cells were significantly reduced. Conversely, overexpression of DEPDC1 exhibited the opposite effect. Conclusion: DEPDC1, a newly identified dedifferentiation gene in thyroid cancer, inversely correlated with the degree of differentiation. High expression of DEPDC1 promotes cancer progression and leads to poor prognosis in thyroid cancer.

Coordination of activities between nuclei and organelles in plant cells involves information exchange, in which phytohormones may play an essential role. Therefore, dissection of the mechanisms of hormone-related integration between phytohormones and mitochondria is an important and challenging task. Here, we found that inputs from multiple hormones may cause changes in transcript accumulation of mitochondrial-encoded genes and nuclear genes encoding mitochondrial (mt) proteins. In particular, treatments with exogenous hormones induced changes in GUS expression in the reporter line possessing a 5'-deletion fragment of the RPOTmp promoter. These changes corresponded in part to up- or downregulation of RPOTmp in wild-type plants, which affected the transcription of mt-encoded genes, implying that promoter fragments of the RPOTmp gene are functionally involved in responses to IAA (indole-3-acetic acid), ACC (1-aminocyclopropane-1-carboxylic acid), and ABA (abscisic acid). Hormone-dependent modulations in the expression of mt-encoded genes can also be mediated through mitochondrial transcription termination factors 15, 17, and 18 of the mTERF family and genes for tetratricopeptide repeat proteins that are coexpressed with mTERF genes, in addition to SWIB5 encoding a mitochondrial SWI/SNF (nucleosome remodelling) complex B protein. These genes specifically responded to hormone treatment, displaying both negative and positive regulation in a context-dependent manner. According to bioinformatic resources, their promoter regions possess putative cis-acting elements involved in responses to phytohormones. Alternatively, hormone-related transcriptional activity of these genes may be modulated indirectly, which is especially relevant for brassinosteroids (BS). In general, the results of the study indicate that hormones are essential mediators that are able to cause alterations in the transcript accumulation of mt-related nuclear genes, which in turn trigger the expression of mt genes.

Autophagy is a highly conserved self-degradation process involving the degradation and recycling of cellular components and organelles. Although the involvement of autophagy in metabolic changes during fruit ripening has been preliminarily demonstrated, the variations in autophagic flux and specific functional roles in fruit ripening remain to be elucidated. In this study, we analyzed the occurrence of autophagy during tomato fruit ripening. The results revealed differential expression of SlATG8 family member during tomato fruit ripening. Transmission electron microscopy observations and dansylcadaverine (MDC) staining confirmed the presence of autophagy at the cellular level in tomato fruits. Furthermore, the overexpression of SlATG8f induced the formation of autophagosomes, increased autophagic flux within tomato fruits, effectively enhanced the expression of ATG8 proteins during the color transition phase of fruit ripening, thereby promoting tomato fruit maturation. This overexpression also led to the accumulation of vitamin C (VC) and soluble solids while reducing acidity in the fruit. Collectively, our findings highlight the pivotal role of SlATG8f in enhancing tomato fruit ripening, providing insights into the mechanistic involvement of autophagy in this process. This research contributes to a better understanding of key factors regulating tomato fruit quality and offers a theoretical basis for tomato variety improvement.

Water deficit greatly affects global crop growth and productivity, particularly in water-limited environments like upland rice cultivation, leading to reduced grain yield. Plants activate various defense mechanisms during water deficit, involving numerous genes and complex metabolic pathways. Exploring orthologous genes, linked to enhanced drought tolerance, can aid functional validation in target species using genomic data from model organisms. Here, we studied the OsCPK5 gene in upland rice, an AtCPK6 ortholog from A. thaliana, by overexpressing it in the BRSMG Curinga cultivar. Transformants were assessed under two conditions: water deficit applied 79 days after seeding, lasting 14 days, followed by 7 days of irrigation at 80% field capacity. Physiological data and samples were collected at R3, R6, and R8 stages. GM plants consistently exhibited higher OsCPK5 gene expression across stages, peaking during grain filling. During this phase, GM plants displayed reduced stomatal conductance, photosynthetic rate, and increased water use efficiency compared to non-GM plants under drought. GM plants also exhibited higher filled grain percentage in both irrigation conditions. Their drought susceptibility index was 0.9 times lower than NGM plants, and they maintained a higher chlorophyll a/b index, indicating sustained photosynthesis. NGM plants under water deficit exhibited more leaf senescence, while OsCPK5-overexpressing plants retained green leaves. Overall, OsCPK5 overexpression induced diverse drought tolerance mechanisms, hinting at potential for future development of more drought-tolerant rice cultivars.

This paper presents ConF, a novel deep learning model designed for accurate and efficient prediction of non-coding RNA families. NcRNAs are essential functional RNA molecules involved in various cellular processes, including replication, transcription, and gene expression. Identifying ncRNA families is crucial for comprehensive RNA research, as ncRNAs within the same family often exhibit similar functionalities. Traditional experimental methods for identifying ncRNA fam-ilies are time-consuming and labor-intensive. Computational approaches relying on annotated secondary structure data face limitations in handling complex structures like pseudoknots and have restricted applicability, resulting in suboptimal prediction performance. To overcome these chal-lenges, ConF integrates mainstream techniques such as residual networks with dilated convolutions and cross multi-head attention mechanisms. By employing a combination of dual-layer convolu-tional networks and BiLSTM, ConF effectively captures intricate features embedded within RNA sequences. This feature extraction process leads to significantly improved prediction accuracy compared to existing methods. Experimental evaluations conducted on a ten-fold publicly available dataset demonstrate the superiority of ConF in terms of accuracy, sensitivity, and other perfor-mance metrics. Overall, ConF represents a promising solution for accurate and efficient ncRNA family prediction, addressing the limitations of traditional experimental and computational methods.

Prostate cancer (PCa) Lung metastases are rarely resected, therefore PCa lung metastases are insufficiently molecularly characterized. We recently identified carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) as a potential driver of pulmonary metastatic spread. Here, we show the biological significance of CEACAM6 in PCa cell proliferation, apoptosis and migration. CEACAM6 was silenced by siRNA in PC3 cells. Functional assessment of apoptosis, cell viability, proliferation and migration were performed in siRNA-CEACAM6 PC3 cells. Non-treated and scrambled (scr) RNA PC3 cells were used as control. Following a specific knockdown of CEACAM6 in PC3 cells, the expression of CEACAM6 protein was significantly decreased in comparison to controls. Cell viability and cell counts decreased in CEACAM6 silent PC3 cells. In contrast, caspase-3 activity was highly elevated in siRNA-CEACAM6 PC3. Furthermore, by performing a cell scratch assay, the migration ratio in siRNA-CEACAM6 PC3 cells were significantly diminished compared with the control group after 48 hours of post transfection incubation. CEACAM6 as a cell adhesion molecule has been implicated in promoting metastatic disease in several solid tumours such as colorectal or gastric cancer. We could show that silencing of CEACAM6 has a significant functional effect on PCa cells. CEACAM6 might play an important role in fostering metastatic spread to the lung of PCa patients via enhancing proliferation and suppressing apoptosis. CEACAM6 might therefore pose an attractive therapeutic target to prevent metastatic disease.

At 2.3 megabases in length, the dystrophin gene is enormous: transcription of a single mRNA requires approximately 16 hours. Principally expressed in skeletal muscle, the dystrophin protein product protects the muscle sarcolemma against contraction-induced injury, and dystrophin deficiency results in the fatal muscle-wasting disease, Duchenne muscular dystrophy. This gene is thus of key clinical interest, and therapeutic strategies aimed at eliciting dystrophin restoration require quantitative analysis of its expression. Approaches for quantifying dystrophin at the protein level are well established, however study at the mRNA level warrants closer scrutiny: measured expression values differ in a sequence-dependent fashion, with significant consequences for data interpretation. In this manuscript we discuss these nuances of expression and present evidence to support a transcriptional model whereby the long transcription time is coupled to a short mature mRNA half-life, with dystrophin transcripts being predominantly nascent as consequence. We explore the effects of such a model on cellular transcriptional dynamics, and then discuss key implications for the study of dystrophin gene expression, focussing both on conventional (qPCR) and next-gen (RNAseq) approaches.

Real-time fluorescent quantitative PCR (RT-qPCR) is the most classic and widely used technology for evaluating the expression level of target gene. In order to select the proper internal reference genes for RT-qPCR analysis in Amorphophallus konjac (Araceae), eight candidate internal reference genes, including 25S ribosomal RNA gene (25S rRNA), 18S ribosomal RNA gene (18S rRNA), actin gene (ACT), glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH), Ubiquitin gene (UBQ), β-tubulin gene (β-TUB), eukaryotic elongation factor 1-αgene(eEF-1α), and eukaryotic translation initiation factor 4α-1 gene (eIF-4α) were selected and tested the corresponding expression level in different tissues at different growing stages. The results showed that 25S rRNA, 18S rRNA, and ACT at the reproductive periods, eEF-1α and eIF-4α at the nutritional periods, and eEF-1α, UBQ, and ACT at different leaf developmental periods had a stable level of gene expression, respectively. These results might be useful for the study of gene function in A. konjac.

Diabetes is a chronic condition that worsens living conditions and causes significant problems, particularly in the vascular system. Many different treatment options are used to prevent these negative effects of diabetes. The most important of these is changing living conditions and exercising regularly.This study aimed todetermining the impacts of a 6-week anaerobic exercise protocol on the blood glucose levels and Glut4 gene expression in the muscle tissues of streptozocin (STZ)-induced diabetic rats. A total of 45 rats were separate control, sedentary, and exercise groups (n=15 each). The STZ used to induce diabetes in rats was applied once with a single intraperitoneal injection. No diabetes was created in the control group, and no exercise was performed, whereas in the sedentary group, diabetes was induced, and no exercise was applied. It was determined that the Glut4 gene expression in the muscle tissue of the exercise group was importantly increased when compared with the sedentary diabetes group.Glut4 gene is an important gene involved in blood glucose regulation and anaerobic exercise significantly increased the expression level of this gene in our study.

Caseous lymphadenitis (CL) is a chronic contagious disease that affects small ruminants and is characterized by the formation of pyogranulomas in lymph nodes and other organs. However, the pathogenesis of this disease and the response of the host genome to infection are not yet fully understood. This study aimed to investigate the whole blood transcriptome and evaluate differential gene expression during the later stages of CL in naturally infected ewes. The study included diseased, serologically positive (EP), exposed, serologically negative (EN) ewes from the same infected flock and healthy ewes (CN) from a different flock. RNA sequencing was performed using the Illumina NextSeq system, and differential gene expression was estimated using DESeq2 and Edge R approaches. The analysis identified 191 annotated differentially expressed genes (DEGs) in the EP group (102 upregulated and 89 downregulated) and 256 DEGs in the EN group (106 upregulated and 150 downregulated). Infection influenced numerous immunoregulatory interactions between lymphoid and nonlymphoid cells in both EP and EN ewes. Immune DEGs were preferentially assigned to antigen presentation through the MHC complex, T-lymphocyte mediated immunity, and extracellular matrix interactions. Furthermore, the EP group showed altered regulation of cytokine and chemokine signalling and activation and recombination of B-cell receptors. Conversely, NF-kappa B signalling, apoptosis, and stress response were the main processes influenced in the EN group. In addition, statistically significant enrichment of the essential immune pathways of Binding and Uptake of Ligands by Scavenger Receptors in EP and p53 signalling in the EN group was found. In conclusion, this study provides new insights into the disease course and host‒pathogen interaction in naturally CL-infected sheep by investigating the blood transcriptome.

This concept paper gives a narrative about intelligence from insects to the human brain, showing where evolution may have been influenced by the structures in these simpler organisms. The ideas also come from the author's own cognitive model, where a number of algorithms have been developed over time and the precursor structures should be codable to some level. Through developing and trying to implement the design, ideas like separating the data from the function have become architecturally appropriate and there have been several opportunities to make the system more orthogonal. Similarly for the human brain, neural structures may work in-sync with the neural functions, or may be slightly separate from them. Each section discusses one of the neural assemblies with a potential functional result, that cover ideas such as timing or scheduling, structural intelligence and neural binding. Another aspect of self-representation or expression is interesting and may help the brain to realise higher-level functionality based on these lower-level processes.

For developmental processes we know most of the gene networks controlling specific cell responses. We still have to determine how these networks cooperate and how signals become integrated. The JNK pathway is one of the key elements modulating cellular responses during development. Yet, we still know little on how the core components of the pathway interact with additional regulators or how this network modulates cellular responses in the whole organism in homeostasis or during tissue morphogenesis. We have performed a promoter analysis searching for potential regulatory sequences of puc and identified different specific enhancers directing gene expression in different tissues and at different developmental times. Remarkably, some of these domains respond to the JNK activity, but not all. Altogether, these analyses show that puc expression regulation is very complex and that JNK activities participate in non-previously known processes during the development of Drosophila.

Background: Hypoxia-inducible factors (HIFs) are transcription factors that get activated and stabilized in the heterodimerized form under hypoxic conditions. The three members of the HIF alpha factors share high structural similarity but have tissue-specific expression patterns. A majority of studies have reported the importance of the HIF1A and HIF2A activity in the survival, proliferation, metastatic potential, and metabolic regulation of hypoxic cancer cells. However, the importance of the expression pattern and activity of HIF3A in a variety of cancers remains unknown. Method and materials: The expression profile of 13 different types of The Cancer Genome Atlas (TCGA) cancer samples were downloaded, normalized and differential gene expression analysis (DGE) was performed to compare the expression pattern of HIF alpha family members in cancer and adjacent normal tissues, as well as at different stages and tumor-sizes. Receiver operating characteristic (ROC) test and survival analysis were carried out to estimate the diagnostic potential of HIF alpha isomers in different cancers, as well as the survival rate of patients with the varying expression levels of HIF alpha factors. Results: The expression status of HIF3A was notably less in all cancer samples in contrast to their adjacent normal tissues. The expression degree of HIF1A varied among distinct types of cancer and the expression degree of HIF2A was lower in nearly all types of cancers. The expression level of HIF alpha isomers did not significantly correlate with different sizes of tumor samples and stages of different tumor tissue samples. HIF3A had very weak diagnostic potential, while HIF2A had better diagnostic potential in most types of cancers compared to HIF1A. Patients who had a higher level of HIF3A had better survival, while the higher expression levels of HIF1A and HIF2A were associated with worse survival in many types of cancers. Conclusion: Our study shows the heterogenous expression pattern of HIF alpha subunits in distinctive kinds of cancers and the influence of HIF3A expression level in the survival of patients with varying types of cancers.

The Brassica family contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB, https://biodb.swu.edu.cn/brassica/) for the research community. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for Brassica crop researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies GO terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g. weakly, moderately or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, SEA and GSEA. These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server https://webfsgor.sysbio.cytogen.ru/ .

MicroRNAs are small non-coding RNAs that are implicated in several physiological processes such as cell development, proliferation, differentiation, apoptosis, immune response and angiogenesis. In the last couple of decades, several studies on miRNA profiling in OSCC have tried to associate miRNAs with clinical characteristics such as relapse, metastasis, and survival, however, the results have been found to vary considerably, sometimes even being contradictory. The main objective of our study was to analyse and verify miRNA expression in oral squamous cell carcinoma in a Spanish population. Second, we attempted to associate the identified deregulated miRNAs with molecular pathways. 8 Oral Squamous Cell Carcinoma patients and 8 healthy control samples were analysed by a microarray Affymetrix® miRNA 4.1 array plate and validated with 8 more cases using RT-qPCR. Deregulated miRNAs were studied using Diana Tools miRPath 3.0 to associate miRNA targets with molecular pathways. Microarray analysis identified 80 deregulated miRNAs (35 over-expressed and 45 under-expressed). Only miR-497-5p and miR-4417 maintained its deregulated expression after validation with qPCR. Among the molecular pathways in which deregulated miRNAs could be implicated, the most statistically significant pathway was ‘proteoglycans in cancer’. No relationship was found between miR-497-5p or miR-4417 expression and clinical or pathological parameters except of nodular affectation (high miR-4417 expression in patients with nodular affectation, p = 0.035) and radiotherapy (diminished miR-497-5p expression in patients who needed radiotherapy, p = 0.05). We have verified the altered expression of miR-497-5p and miR-4417 in Oral Squamous Cell Carcinoma samples and related the deregulated miRNAs with the ‘proteoglycans in cancer’ pathway.

Background: Triple negative breast cancer (TNBC) is the most aggressive form of breast cancer with poor outcomes. The molecular basis of TNBC remains poorly understood. The objective of this study was to explore the relationship between obesity and TNBC in premenopausal and postmenopausal Caucasian women using whole genome transcription profiling. Methods: We compared gene expression levels of tumor samples drawn from normal weight, overweight and obese in pre and postmenopausal women diagnosed with TNBC. We performed hierarchical clustering to assess similarity in patterns of gene expression profiles, and conducted network and pathway analysis to identify molecular networks and biological pathways. Results: We discovered gene signatures distinguishing normal weight from obese, normal weight from overweight and overweight from obese individuals in both premenopausal and postmenopausal women. The analysis revealed molecular networks and biological pathways dysregulated in response to obesity. Among the discovered pathways included the unfolded protein response, endoplasmatic reticulum stress, B cell receptor and the autophagy signaling pathways in obese premenopausal women and the integrin, axonal guidance, ERK/MAPK and Glutathione biosynthesis signaling pathways obese postmenopausal women. Conclusions: The results suggest that both overweight and obesity are associated with TNBC, highlighting the need for conformation of these results in independent studies.

Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants’ growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

Formula feeding, as an alternative to breastfeeding, offers benefits such as convenience and consistent nutrition. Among the drawbacks of formula feeding, however, is potential dilution or concentration errors in the of formula during preparation that may lead to infant health issues. The present study aimed to investigate the accuracy of caregiver measurements as they prepared infant formula under multiple conditions, compared with manufacturer specifications. A diverse sample of caregivers (N = 84) participated in this cross-over experimental study. Participants hand-scooped infant formula powder and poured water to prepare 4oz and 7oz feedings, using both a standardized set of infant formula products and participants’ own products. Linear mixed effects models were used to estimate fixed effects of target amount (4oz versus 7oz) and products (participant versus researcher) on mean absolute percent error (MAPE) of measurement. Across all conditions MAPE was significantly greater for measuring powder than for water (9.0% vs. 4.4%; p&lt;0.001) with a combined powder and water MAPE at 13.0%. Greater measurement error was associated with the odd-sized 7oz preparation and participants’ own products. We observed considerable variability and substantial error during infant formula preparation, particularly for hand-scooping of powder, which tended toward higher values than the theoretical gold standard.

Background and aims: Only one cohort study exists on the incidence of the risk of malnutrition (RM) in older adults, though numerous cross-sectional –and that cohort research– have reported several risk factors associated with the prevalence and incidence of this condition. However, alterations of body composition and impaired physical performance as exposition variables of RM have not been explored. This study assessed the incidence of RM and determined its association with excess fat mass, low total lean tissue, gait speed, and handgrip strength as exposition variables for RM in community-dwelling older adults. Methods: This is a secondary analysis in older adults (≥60 years old) derived from the study “Frailty, dynapenia, and sarcopenia in Mexican adults (FraDySMex)” a prospective cohort project conducted from 2014 to 2019 in Mexico City. At baseline, volunteers underwent body composition analysis and physical performance tests. Several covariates were identified through comprehensive geriatric assessment. At baseline and follow-up, RM was assessed using the long form of the mini nutritional assessment (MNA-LF) scale. Associations between the exposition variables and RM were assessed by multiple logistic regression. Results: The cohort included 241 subjects. Average age was 75.6±7.8 years; 83.4% were women. The mean follow-up period was 4.1 years, during which 28.6% of subjects developed RM. This condition was less likely to occur in subjects with excess fat mass index, even after adjusting for several covariates. RM was also more likely to occur in subjects with low total lean tissue index, according to both an unadjusted model and after adjusting for the corresponding variables. Regarding the association between RM and gait speed, RM was also more likely to occur in subjects with low gait speed according to both the unadjusted and adjusted models. Similar results were found for RM in relation to low handgrip strength; however, after adjusting for the associated covariates, models 1 and 2 no longer reached the level of significance. Conclusion: The risk of malnutrition diagnosed by MNA-LF was significantly less likely to occur among subjects with excess fat mass, but possibility was significantly higher in those with low total lean tissue and low gait speed after 4.1 years of follow-up in community-dwelling older adults. These results highlight that excess fat mass, low total lean tissue, and low gait speed are first than risk of malnutrition and not vice versa.

In this study we propose a semi-parametric, parsimonious Value at Risk forecasting model, based on quantile regression and machine learning methods, combined with readily available market prices of option contracts from the over-the-counter foreign exchange rate interbank market. We aim at improving existing methods for VaR prediction of currency investments using machine learning. We employ two different methods - ensemble methods and neural networks. Explanatory variables are implied volatilities with plausible economic interpretation. The forward-looking nature of the model, achieved by the application of implied volatilities as risk factors, ensures that new information is rapidly reflected in Value at Risk estimates. To the best of our knowledge, this paper is the first to utilize information in the volatility surface, combined with machine learning and quantile regression, for VaR prediction of currency investments. The proposed ensemble models achieve good estimates across all quantiles. The light gra-dient-boosting machine model and the categorical boosting model both yield estimates which are better than, or equal to, those of the benchmark model. The neural network models are in general quite unstable.

Originating in the Mediterranean, B. oleracea is grown all over the world and is highly valued for its nutritional value and variety in cooking. Its susceptibility to pests, diseases, and environmental stressors, however, poses significant challenges to sustaining consistent crop quality and productivity. The BASIC PENTACYSTEINE gene significantly impacts plant growth and responses to abiotic stresses. Nevertheless, little is known about its precise role and the underlying biological processes in B. oleracea. Eleven BPC genes in B. oleracea were identified by a thorough genome-wide investigation and categorized into three categories according to their structural traits and gene motifs. There were eight different chromosomes on which these BoBPCs were located. Comparative synteny analysis was used to reveal the evolutionary traits of potatoes, Arabidopsis, and B. oleracea. The BoBPC family genes in B. oleracea were found to have specific cis-elements linked to growth, stress responses, and hormone regulation when their promoter regions were studied. Cuticular wax synthesis expression revealed that all BoBZR1 genes, from wild to mutant, expressed at varied amounts in distinct types. Moreover, distinctive BoBPC gene expression patterns were found in the seven distinct tissues that were studied. Our thorough analysis shows that the BoBPC family is widely involved in B. oleracea developmental processes. The present findings provide an established theoretical basis for further exploration into the composition and roles of BoBPC in B. oleracea.

: F-box proteins are a large gene family in plants, and play crucial roles in plant growth, development, and stress response. However, a comprehensive investigation of F-box family genes in cultivated peanut (Arachis hypogaea L.), has not been undertaken. In this study, we used a bioinformatics approach to identify and analyze F-box protein family genes in the cultivated peanut genome, and examined their expression profiles. Herein, a total of 95 F-box protein family members on 18 chromosomes were identified in cultivated peanut, which were sequentially designed as AhFBX1-AhFBX95. Phylogenetic analysis classified these AhFBXs into four different groups (Group I - IV), and eight subfamilies based on the structural domains of the C-terminal. Structural analysis revealed the presence of ten unique motifs within these genes. Additionally, the investigation of non-synonymous and synonymous substitution rates (Ka/Ks), and synteny in the F-box proteins, provided valuable insights into the evolutionary and domestication processes of AhFBX genes in peanut. Furthermore, in silico expression profiling of 22 different tissues demonstrated that most genes were predominantly expressed in leaves, pistils, and the aerial gynophore tip, while some members showed tissue-specific expression at the apex of both vegetative and reproductive shoots. Subsequently, we validated the expression of 9 differentially expressed genes (DEGs) using transcriptomeic data of lateral branch development and qRT-PCR analysis. These DEGs may be involved in regulating the development of lateral branches and subsequently affect the architecture of peanut plants.

Abstract: There are a large number of cross-linked chemical bonds such as tight disulfide bonds, hydrogen bonds,and salt bonds in keratin, which makes it difficult to break the structural stability of the protein using conventional methods. The degradation of feather waste using keratinases produced by microorganisms has the advantage of being efficient and environmentally friendly. In this study, 23 strains capable of producing transparent circles were obtained via preliminary screening with skim milk as the sole carbon and nitrogen source, and 9 strains capable of degrading feathers were obtained via rescreening with feathers as the sole carbon and nitrogen source. Finally, through the determination of enzyme activity, the strain CY-A with a high ability to degrade feathers was obtained. The strain was identified as Bacillus tequilensis via morphological observation, physiological and biochemical identification, and 16 S rRNA molecular biology. The keratinase gene (bta) of Bacillus tequila was cloned, and its full-length gene sequence was 1110 bp, containing an open reading frame of 1089, encoding 369 amino acids (GeneBank accession number OR733336). The physicochemical properties, secondary structure, and tertiary structure of the recombinant protein were analyzed using bioinformatics tools such as ProtParm, SOPMA, MEGA, and SWISS-MODELS. It was found that the relative molecular mass was 37.953 kD and that the isoelectric point was 8.48. The protein was a hydrophilic protein. The keratinase bta gene was ligated to the expression vector pET28a(+) using T4 ligase, and the recombination expression plasmid pET28-bta was constructed and transformed into E. coli BL21(DE3) to obtain recombinant engineered bacteria. The expressed keratinase was purified using a Ni2+ affinity chromatography column to obtain recombinant bta keratinase bta with a molecular weight of 37.953 kD. The identification and characterization of this keratinase gene provides some theoretical basis for the further enhancement of keratinase activity by means of genetic engineering.

Several specialized terpenoids that are used as phytoalexins are produced in the plant of tobacco. They play a key role in plant defense against pests and pathogens. Here, we performed genome-wide identification, classification, and expression profiling of the terpene synthase (TPS) genes in the tobacco genome. A total of 186 TPS genes were identified, which is significantly higher than that in wild Nicotiana, Capsicum and Solanum species. Phylogenetic analysis of these TPS genes in tobacco and Solanaceous relatives as well as Arabidopsis showed that a few tobacco-exclusive TPS clades occurred recently through gene duplication events. These clades are likely to be responsible for a range of compounds that separate N. tabacum cultivars from its wild relatives. Transcriptome sequencing of two cultivars of N. tabacum at several developmental stages revealed that some TPS genes from the TPS-a and TPS-b lineages are constitutively expressed and a few duplicated TPS genes are only expressed post anthesis at the time of harvest. Additionally, some TPS genes underwent alternative splicing, further diversifying the gene products of the TPS genes. Our findings provide an important candidate genes for further understanding of the diversity and evolution as well as functionality of TPS genes in the plant of tobacco.

Introduction: Depending on the kind of cancer and neurological disorders, there might be a direct or inverse link between neurodegeneration and cancer. The inverse interaction between cancer and Alzheimer's pathology has garnered substantial interest in medical research. While this inverse interaction between Alzheimer's pathology and cancer presents a fascinating scientific puzzle, there is still limited information and studies on the potential mechanisms involved in this inverse rela-tionship. Aim: This study aims to identify potential genes from Alzheimer's disease that may protect against cancer. Method: The Gene Expression Omnibus (GEO) database provided the Alzheimer's pathology dataset, and GEO 2R was utilized to examine genes that were differentially expressed. The expression of upregulated Alzheimer's pathology genes in breast, colorectal, and prostate cancer was compared using VENN 2.1, colorectal, and prostate cancer was compared using VENN 2.1, and colorectal and prostate cancers were compared using VENN 2.1. Results: Among the upregulated genes associated with Alzheimer's disease, 25 genes are shared among breast cancer, colorectal cancer, and prostate cancer, while 28 of these genes were exclusive to Alzheimer's dis-ease. Gene expression profiling interactive analysis among the shared genes revealed that AQP1, C4A, CSRP2, CRYAB, MACF1, HSPB2, and NEAT1 were downregulated in breast, colorectal, and prostate cancers. These genes have varying roles in cancer progression and suppression. Functional analysis of Alzheimer's disease-related upregulated genes revealed that C1orf56 and HIST1H2AC control cell proliferation, with HIST1H2AC playing a role in necroptosis. Additionally, C1orf56 worked as an oncogenic modifier to support DNMT3B's tumor suppressor properties. Conclusion: Given the role of HIST1H2AC and C1orf56 in the negative control of cell proliferation and their upregulation in Alzheimer's disease, there is a need to further investigate HIST1H2AC and C1orf56 as potential tumor suppressors responsible for Alzheimer's disease and cancer inverse association.

Deeper understanding of biological processes, disease mechanisms, and prospective therapeutic targets can be attained by Gene Expression Network Analysis (GENA), which offers a potent framework for revealing the intricate regulatory mechanisms controlling gene expression. GENA is a computational method used to understand the intricate interactions and relationships between the genes in a biological system. It entails using network theory, statistical analysis, and gene expression data to pinpoint functional modules, regulatory linkages, and important genes or pathways involved in a particular biological process or illness. This chapter broadly outlines the principles and practice of GENA, to an novice reader and outlines a simple method of performing a GENA using online Rice gene expression datasets available in various websites.

Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), has emerged as a significant health concern following the COVID-19 pandemic. Molecular mechanisms underlying the occurrence and progression of long COVID include viral persistence, immune dysregulation, endothelial dysfunction, and neurological involvement, and highlight the need for further research to develop targeted therapies for this condition. While a clearer picture of the clinical symptomatology is shaping, many molecular mechanisms are yet to be unraveled, given their complexity and high level of interaction with other metabolic pathways. This review summarizes some of the most important symptoms and associated molecular mechanisms that occur in long COVID, as well as the most relevant molecular techniques that can be used in understanding the viral pathogen, its affinity towards the host and the possible outcomes of host-pathogen interaction.

Nitrogen (N) is an important mineral nutrient for plant growth, as well as a limiting factor for crop yield, and how to improve the utilization efficiency of N fertilizer by plants is currently a research hotspot. This article uses bioinformatics methods to identify and analyze members of the glutamine synthetase (GS) and glutamate synthase (GOGAT) gene families in pecan. A total of 6 GS genes and 4 GOGAT genes were identified, and their physicochemical properties, gene structures, and homologous evolutionary relationships were analyzed. Analysis of tissue-specific expression of GS and GOGAT genes based on transcriptome data from pecan. The enzyme activities of GS and GOGAT and the gene expression were quantitatively analyzed under different N form ratios in pecan. According to the results, the promoter cis-acting elements of GS and GOGAT genes can be roughly divided into three types: light-responsive elements, hormone-responsive elements, and stress-responsive elements. The results of homologous evolution showed that there was no tandem duplication event for the two gene families, and GS and GOGAT have undergone purification during the evolutionary process. CiGS2s and CiFd-GOGATs were expressed mainly in leaves, and CiNADH-GOGATs were expressed mainly in fruits. The qPCR analysis results showed that T4 treatment significantly increased the expression levels of CiGS and CiGOGAT genes in the leaves. The enzyme activities of GS and GOGAT in pecan were significantly increased under T3, T4, and T5 treatments. In summary, a higher proportion of ammonium nitrogen (NH4+) in the nutrient solution was profit to pecan NH4+ assimilation. This study determined the appropriate nitrogen ratio for pecan, promoting a theoretical basis for reducing environmental pollution caused by nitrogen fertilizer and improving the nitrogen utilization efficiency of pecan. In summary, both CiGSs and CiGOGATs exhibit tissue specificity, and an ammonium-nitrate mixture with a higher proportion of NH4+ is more favorable for NH4+ assimilation in pecan. This study provides a reference basis for further understanding the functions of CiGSs and CiGOGATs in pecan, and offers a theoretical foundation for improving N use efficiency in pecan.

Eimeria tenella rhoptry protein has the properties of a protective antigen. EtROP27 is a pathogenic related gene detected by transcriptome, but its expression pattern, immunogenicity and potency have been unknown. Therefore, a gene segment of EtROP27 was amplified and transplanted to pET28a prokaryotic vector for recombinant protein expression and purified to generate polyclonal antibody. Then, RT-PCR, Western blotting were performed to know the expression pattern of EtROP27. Subsequently, animal experiments were conducted to evaluate the immunoprotective effect of the recombinant protein using different immunizing doses (50, 100, 150 μg). The results showed that the expression of EtROP27 gradually increased with the prolongation of infection time, reaching the highest level after 96 hours and then decreased. And EtROP27 was a natural antigen of coccidia which can stimulate the body to produce high levels of IgY. As recombinant protein vaccines, the immune protection evaluation tests of EtROP27 showed that the average weight gain rate of the immune challenge groups were significantly higher than that of the infection control group. The average lesion scores were significantly lower than that of the control group. The oocyst excretion decreased by 81.25%, 86.21%, 80.01% and the anticoccidial index were 159.45, 171.47, 166.75. EtROP27 is a promising candidate antigen gene for development of coccidiosis vaccine.

Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which N6-Methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as therapeutic approach. In this review, we overview the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.

Background: TP53 alterations have a significant prognostic effect in myeloid neoplasms. Our objective was to investigate the TP53 gene mutation status, p53 protein expression, and their re-lationship in dysplasia-related myeloid neoplasms with varying levels of myeloblast counts. Methods: 76 bone marrow biopsy samples with different blast counts were analyzed. Total and strong (3+) p53 expression was determined. Dual immunohistochemical staining was performed to determine the cell population associated with p53 expression. NGS analysis was performed using the Accel-Amplicon Comprehensive TP53 panel. Results: Both p53 expression and TP53 VAF showed a significant correlation with the myeloblast ratio (p<0.0001), however, p53 expres-sion was present in other cell lineages as well. The VAF value exhibited a significant correlation with p53 expression. A high specificity (0.9800) was observed for TP53 mutation using the ≥10% strong (3+) p53 cut-off value, although the sensitivity (0.4231) was low. Conclusion: Strong (3+) p53 expression using a ≥10% cut-off value accurately predicts TP53 mutation but doesn't reveal the allelic state. The p53 expression is significantly influenced by myeloblast count, and histo-logical interpretation should consider the presence of intermixed non-neoplastic marrow cells with varying physiological p53 expression.

Cell identity is determined by chromatin structure and the profiles of gene expression, which are dependent on chromatin accessibility and DNA methylation of regions critical for gene expression, such as enhancers and promoters. These epigenetic modifications are required for mammalian development and are essential for the establishment and the maintenance of the cellular identity. DNA methylation was once thought to be a permanent repressive epigenetic mark, but systematic analysis in various genomic contexts reveals a more dynamic regulation than previously thought. In fact, both active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation. To link methylation signatures of specific genes to their expression profiles, we have determined the methyl-CpG configurations of the promoters of five genes switched on and off during murine postnatal brain differentiation by bisulfite-targeted sequencing. We report here the structure of significant, dynamic and stable methyl-CpG profiles associated with silencing or activation of expression of genes during neural stem cell and brain postnatal differentiation. Strikingly, these methylation cores mark different mouse brain areas and cell types derived from the same areas during differentiation.

Matrix metalloproteinases (MMPs) are often considered biomarkers of skin fibrosis. At the early stages of the pathological process, an elevation of their enzymatic activity causes significant changes in the composition of the extracellular matrix. MMPs secreted by immune cells facilitate their migration to the site of damage. Then, the immune cells eliminate the affected cells and biomolecules. Moreover, bidirectional changes in the activity of proteolytic enzymes, including MMPs, accompany wound healing. This study aimed to assess changes in the expression of Mmp2, Mmp3, and Mmp9 after treating the mice with laser therapy using the experimental model of bleomycin-induced skin fibrosis. Using immunohistochemistry, we characterized the histological features of scarred skin. We also analyzed changes in the expression of MMPs using real-time polymerase chain reaction before and after the irradiation with laser. We showed that treatment of the mice with CO2 laser partially normalized the histological features of scarred skin. We also noticed a decrease in the expression of Mmp2, Mmp3 (both p &lt; 0.05), and Mmp9 (p = 0.065) during scar healing. The obtained results suggest that normalization of skin homeostasis requires a control of MMPs activities via induction of their genes.

Drought stress on soybean is a research-demanding matter for negative influence that agricultural drought brings about. This study was designated to evaluate the effect of drought stress on some gene expression in flowering and pod elongation stages in soybean. This experiment was carried out in split-plot format with RCBD design with four replicates. Drought stress as the main factor included three levels (irrigation after 50, 100, and 150 millimeters evaporation from the A-class evaporation pot) of which 50 millimeters evaporation is considered as control. The sub-factor included a factorial combination of 3 varieties (DPX, Sari and WE6) and two sampling stages (flowering and pod elongation). The gene expression analysis was carried out by using the QRT-PCR technique. According to our results, all genes have shown overexpression in drought stress despite this result was not the same for all genotypes and stress levels. Some genes have up-regulated in mediate stress (treatment 100) level (like as Gmdreb 2, Gmdreb 5, GmRD20A, GmaxACD2) and other genes up-regulated in serve stress (treatment 150) level. Between genotypes, DPX cultivar and WE6 line were better than of the sari cultivar for all genes up-regulated.

Background Polycystic ovary syndrome (PCOS) is a common hormonal disorder worldwide among women of reproductive age. It is characterized by endocrine, reproductive, and metabolic abnormalities. Insulin resistance (IR) is one of its most important clinical features, associated with metabolic disorders and increased risk of type 2 diabetes (T2D). This study aimed to explore the whole blood gene expression profiling related to IR in PCOS patients compared to controls. Methods Blood RNA was extracted from 5 PCOS and 5 non-PCOS women with matched age and BMI. Homeostasis model assessment (HOMA-IR) was used to estimate the IR. The expression of IR genes was analyzed by Profiler PCR array. Results Both groups have similar levels of HOMA-IR (p>0.05). However, differential expression levels were observed between them. Fourteen genes were upregulated and 26 genes were downregulated in PCOS samples. Among the upregulated genes (>2 fold-change, p-value<0.05) are ADIPOQ, ADIPOR1, OLR, IGF-1, and APOE. Downregulated genes (>-2 fold-change, p-value<0.05) include HK-2, IRS1, and SERPINE1. These genes are involved in insulin and adipokines signaling, commonly dysregulated in T2D. They are also involved in innate immunity and inflammatory processes and are essential for lipid and carbohydrate metabolism. Conclusion Our finding suggests that despite both groups having no difference in IR level, there are differentially expressed genes involved in the IR pathway.

Given the importance of menstrual blood in the pathogenesis of endometriosis and the multifunctional roles of menstrual mesenchymal stem cells (MenSCs) in regenerative medicine, this issue has gained prominence in the scientific community. Moreover, recent reviews highlight how robust the integrated assessment of omics data is for endometriosis. To our knowledge, no study has applied the multi-omics approaches to endometriosis MenSCs. It is a case-control study at a university-affiliated hospital. MenSCs transcriptome and proteome data were obtained by RNA-seq and UHPLC-MS/MS detection. Among the differentially expressed proteins and genes, we emphasize ATF3, ID1, ID3, FOSB, SNAI1, NR4A1, EGR1, LAMC3, and ZFP36 genes and MT2A, TYMP, COL1A1, COL6A2, and NID2 proteins that were already reported in the endometriosis. Our functional enrichment analysis reveals integrated modulating signaling pathways such as epithelial-mesenchymal transition (↑) and PI3K signaling via AKT to mTORC1 (↓in proteome), mTORC1 signaling, TGF beta signaling, TNFA signaling via NFkB, and response to hypoxia via HIF1A targets (↑in transcriptome). Our findings highlight primary changes in the endometriosis MenSCs, suggesting that the chronic inflammatory endometrial microenvironment can modulate these cells, providing opportunities for endometriosis etiopathogenesis. Moreover, they identify challenges for future research leveraging knowledge for regenerative and precision medicine in endometriosis.

Middle East Respiratory Syndrome coronavirus (MERS-CoV) infects dromedary camels and zoonotically infects humans, causing a respiratory disease with severe pneumonia and death. With no approved antiviral or vaccine interventions for MERS, vaccines are being developed for camels to prevent virus transmission into humans. We have previously developed a chimpanzee adenoviral vector-based vaccine for MERS-CoV (ChAdOx1 MERS) and reported its strong humoral immunogenicity in dromedary camels. Here, we looked back at total RNA isolated from three immunised dromedaries pre and post-vaccination during the first day; and performed RNA sequencing and bioinformatic analysis in order to shed light on the molecular immune responses following a ChAdOx1 MERS vaccination. Our finding shows that a number of transcripts were differentially regulated as an effect of the vaccination, including genes that are involved in innate and adaptive immunity, such as type I and II interferon responses. The camel Bcl-3 and Bcl-6 transcripts were significantly upregulated, indicating a strong activation of Tfh cells, B cell, and NF-kB pathways. In conclusion, this study gives an overall view of the first changes in the immune transcriptome of dromedaries after vaccination; it supports the potency of ChAdOx1 MERS as a potential camel vaccine to block transmission and prevent new human cases and outbreaks.

The ability to express and recognize emotion via facial expressions is well known to change with age. The present study investigated the differences in the facial recognition and facial expression of the elderly (n = 57) and the young (n = 115) and measure how each group uses different facial muscles for each emotion with Facial Action Coding System (FACS). In facial recognition task, the elderly did not recognize facial expressions better than young people and reported stronger feelings of fear and sad from photographs. In making facial expression task, the elderly rated all their facial expressions as stronger than the younger, but in fact, they expressed strong expressions in fear and anger. Furthermore, the elderly used more muscles in the lower face when making facial expressions than younger people. These results help to understand better how the facial recognition and expression of the elderly change, and show that the elderly do not effectively execute the top-down processing concerning facial expression.