ARTICLE | doi:10.20944/preprints201806.0247.v1
Subject: Computer Science And Mathematics, Analysis Keywords: data mining; association rule learning; policyholder lapse; auto insurance; market inefficiency
Online: 15 June 2018 (09:01:03 CEST)
For automobile insurance, it has long been implied that when a policyholder made at least one claim in the prior year, the subsequent premium is likely to increase. When this happens, the policyholder may seek to switch to another insurance company to possibly avoid paying for a higher premium. In such situations, insurers may be faced with the challenges of policyholder retention by keeping premiums low in the face of competition. In this paper, we seek to find empirical evidence of possible association between policyholder switching after a claim and the associated change in premium. In accomplishing this goal, we employ the method of association rule learning, a data mining technique that has its origins in marketing for analyzing and understanding consumer purchase behavior. We apply this unique technique in two stages. In the first stage, we identify policyholder and vehicle characteristics that affect the size of the claim and resulting change in premium regardless of policy switch. In the second stage, together with policyholder and vehicle characteristics, we identify the association among the size of the claim, the level of premium increase and policy switch. This empirical process is often challenging to insurers because they are unable to observe the new premium for those policyholders who switched. However, we used a 9-year claims data for the entire Singapore automobile insurance market that allowed us to track information before and after the switch. Our results provide evidence of a strong association among the size of the claim, the level of premium increase and policy switch. We attribute this to the possible inefficiency of the insurance market because of the lack of sharing and exchange of claims history among the companies.
ARTICLE | doi:10.20944/preprints202201.0331.v1
Subject: Environmental And Earth Sciences, Geochemistry And Petrology Keywords: Concentration field; Spatial auto-correlation; Association rules; Apriori algorithm; Element co-occurrence
Online: 21 January 2022 (13:42:44 CET)
The spatial distribution of elements can be regarded as a numerical field of concentration values with a continuous spatial coverage. An active area of research is to discover geologically meaningful relationships among elements from their spatial distribution. To solve this problem, we propose an association rule mining method based on clustered events of spatial auto-correlation and applied it to the polymetallic deposits of the Chahanwusu River area, Qinghai Province, China. The elemental data for stream sediments were first clustered into HH (high-high), LL (low-low), HL (high-low), and LH (low-high) groups by using local Moran’s I clustering map (LMIC). Then the Apriori algorithm was used to mine the association rules among different elements in these clusters. More than 86% of the mined rule points are located within 1000 m of faults and near known ore occurrences, and occur in the upper reaches of the stream and catchment areas. In addition, we found that the Indosinian granodiorite is enriched in sulfophile elements, e.g., Zn, Ag and Cd, and the Variscan granite quartz diorite (P1γδο) coexists with Cu and associated elements. Therefore, the proposed algorithm is an effective method for mining co-existence patterns of elements and provides an insight into their enrichment mechanisms.
ARTICLE | doi:10.20944/preprints202307.1185.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: microRNA; isomiR; genetic association
Online: 18 July 2023 (07:52:22 CEST)
MicroRNA plays a critical role in regulating gene expression post-transcriptionally. Variations in mature microRNA sequences, known as isomiRs, arise from imprecise cleavage and nucleotide substitution or addition. These isomiRs can target different mRNAs or compete with their canonical counterparts, thereby expanding the scope of miRNA post-transcriptional regulation. Our study investigated the relationship between cis-acting single nucleotide polymorphisms (SNPs) in precursor miRNA regions and isomiR composition, represented by the ratio of a specific 5’-isomiR subtype to all isomiRs identified for a particular mature miRNA. Significant associations between 95 SNP-isomiR pairs were identified. Of note, rs6505162 was significantly associated with both 5’-extension of hsa-miR-423-3p and 5’-trimming of hsa-miR-423-5p. Comparison of breast cancer and normal samples revealed that expression of both isomiRs was significantly higher in tumors than in normal tissues. This study sheds light on the genetic regulation of isomiR maturation and advances our understanding of post-transcriptional regulation by microRNA.
ARTICLE | doi:10.20944/preprints202305.2204.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Linked; marker association; annotation; Genes
Online: 31 May 2023 (08:41:16 CEST)
Shea tree (Vitellaria paradoxa) is an important fruit tree crop because of its oil used for cooking and industrial manufacture of cosmetics. Despite its many benefits, quantitative trait loci linked to the economic traits have not yet been studied. In this study, we performed association mapping on a panel of 374 shea tree accessions using 7,530 single-nucleotide polymorphisms (SNPs) markers for oil yield and seed related traits. Twenty three markers that were significantly (–log10 (p) = 4.87) associated to kernel oil content, kernel length; width and weight were identified. The kernel dry matter oil content and kernel width had the most significant Marker Trait Association (MTA) on chromosomes 1 and 8 respectively. Sixteen candidate genes that condition early induction of flower buds and somatic embryos, seed growth and development, substrate binding, transport, lipid biosynthesis, metabolic processes during seed germination and disease resistance and abiotic stress adaptation were identified. The presence of these genes suggest their role in promoting shea bioactive functions that condition high oil synthesis. This study provides insights into the important marker-linked seed traits with genes controlling them, useful for molecular breeding for improving oil yield in the species.
ARTICLE | doi:10.20944/preprints202305.1720.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Trebouxia; lichen; symbiosis; association; coevolution
Online: 25 May 2023 (03:09:53 CEST)
Biotic and abiotic factors influence the formation of fungal-algal pairings in lichen symbiosis. It is poorly known which factors determine the specific associations, especially when distantly related fungi are considered. Here, we investigated the effect of different drivers on the association patterns of taxonomically diverse lichenized fungi and their trebouxioid symbiotic partners. In 200 samples collected across three biomes, we found 41 species of lichenized fungi, associating with 16 species of trebouxioid green algae, of which 62% were previously unreported. Species identity of the fungal and algal partner had the greatest effect on the outcome of the symbiosis compared with abiotic factors such as climatic variables and geographic distance. Partner specificity was found to be higher in tropical regions than in temperate and arctic regions. Co-phylogenetic analyses indicated congruent phylogenies of trebouxioid algae and associated fungi, rejecting their random associations. Evolutionary mechanisms contributing most to the observed phylogenetic patterns were ‘loss’ and ‘failure to diverge’ of the algal partners. This study broadens our knowledge of fungi-algae symbiotic patterns in view of Trebouxia-associated fungi.
ARTICLE | doi:10.20944/preprints202305.1612.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: rapeseed; glucosinolate; phenolics; GBS; association study
Online: 23 May 2023 (08:09:23 CEST)
The phenolics concentrations of rapeseed are important because they are antinutritional com-pound or directly positive related to antioxidant actives. In this study, single nucleotide poly-morphisms (SNPs) identified from genotyping-by-sequencing (GBS), and genome-wide associa-tion study of phenolic contents were investigated in 95 rapeseed mutant lines derived from gamma rays and their original cultivar. A total of 3,196,318 SNPs were detected, identifying a set of 70,208 union SNPs used to perform association studies. Six phenolics and glucosinolate (pro-goitrin) were identified, sinapine was the major phenolic compound (91.2–99.2%) in all geno-types. The association study was conducted for six phenolic compounds, progoitrin, total sinap-ine content (TSC), total phenolic content (TPC) and seed yield. The association study identified 241 SNPs that were significantly associated with six phenolic compounds, progoitrin, TSC and TPC. Based on the detected SNP markers, BnaA06g31740D, a gene associated progoitrin, BnaC-nng39930D, a gene associated trans-sinapine 1, BnaA07g31720D, a gene associated trans-sinapine 2, BnaC03g31950D and BnaA06g09180D, a gene associated TSC, and BnaAnng27700D, a gene associ-ated TPC, were selected as candidate genes. The SNP makers associated major phenolic com-pounds identified and could be used as targets for breeding programs aimed at improving anti-oxidant contents and reducing antinutritional components.
ARTICLE | doi:10.20944/preprints202301.0229.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: psoriasis; psoriatic arthropathy; psoriasis and association
Online: 13 January 2023 (01:52:05 CET)
Objective. The aim of this study was to determine the incidence and prevalence of psoriatic arthropathy and to point out the problem of their occurrence in a sample of patients diagnosed with psoriasis. Methods. 109 patients with diagnosed psoriasis and psoriatic arthropathy, took part in the survey. The average age of patients was 48,85±10,11. We analyzed the incidence and prevalence of the psoriatic arthropathy occurrence for the patients with psoriasis. Results. Psoriatic arthropathy registered with patients wer those with arthritic changes on: sacroiliac joints with 24 (22,02%) patients, 19 (79,17%) male and 5 (20,83%) female (p<0,001); spine with 11 (10,09%) patients, 6 (54,56%) male and 5 (45,45%) female (p=0,578); peripheral joints with 74 (67,89%) patients, 33 (44,59%) male and 41 (55,41%) female (p<0,01). When comparing the symptoms, most of the patients (63,30%) skin changes were represented before arthritis, for 27,52% patients arthritis preceded the skin changes, and for 9,17% patients the changes were simultaneous, Conclusion. Psoriatic arthropathy occurs more often in median age (31 to 50 years old) and it is more common for men than women. For most patients psoriatic skin changes preceded joints affection, with the most common ones being polyarthritis.
ARTICLE | doi:10.20944/preprints202209.0087.v1
Subject: Medicine And Pharmacology, Pediatrics, Perinatology And Child Health Keywords: Malnutrition; association; feeding; practice; infants; Pakistan
Online: 6 September 2022 (10:13:18 CEST)
Breastmilk is the only recommended source of nutrition for infants below six-months of age. However, a significant proportion of children are either on supplemental breastfeeding(SBF) or weaned due to the early introduction of solid/semi-solid/soft food and liquids(SSF) before 6 months of age. There is good evidence that Exclusive Breastfeeding(EBF) in infants below six-months of age protects them from preventable illnesses, including malnutrition. The relationship between infant feeding practices and coexisting forms of malnutrition(CFM) has not yet been explored. This study examined the association of different feeding indicators(continuation of breastfeeding, predominant feeding, and SSF) and feeding practices(EBF, SBF, and complete weaning) with CFM in infants aged below six-months of age in Pakistan. National and regional datasets of Pakistan from the last ten years were retrieved from the Demographic Health Surveys(DHS) and UNICEF data repositories. In Pakistan, 34.5%(n=6131) of infants have some form of malnutrition. Among malnourished infants, 44.7%(~15.4% of the total sample) had a CFM. Continuation of breastfeeding was observed in more than 85% of infants, but less than a quarter were on EBF, and the rest were either SBF(65.4%) or weaned infants(13.7%). Compared to EBF, complete weaning increased the odds of coexistence of underweight with wasting and underweight with both wasting and stunting by 1.96(1.12-3.47) and 2.25(1.16-4.36), respectively. Overall, breastfed children had lower odds of various forms of CFM (compared to non-breastfed), except for the coexistence of stunting with overweight/obesity. Continuation of any breastfeeding protects infants in Pakistan from various types of CFM during the first six months of life.
ARTICLE | doi:10.20944/preprints202208.0537.v1
Subject: Biology And Life Sciences, Horticulture Keywords: Pepino; Metabolome; Soil nutrients; Association analysis
Online: 31 August 2022 (08:18:32 CEST)
Different soil nutrients affect plant metabolites accumulation characteristics. The main soil nutrients and their correlation with Pepino metabolites were investigated in this study to evaluate differences between greenhouses on the Loess Plateau in northwest China. A total of 269 Pepino metabolites in the fruits were identified using a UPLC-QTOF-MS approach from plants grown in three major Pepino growing regions. Their differential distribution characteristics were analyzed. 99 metabolites differed among the Pepino fruits in the three regions. The main classes of the differentially accumulated metabolites were ranked as Amino acids and derivatives, Nucleotides and derivatives, Organic acids, Alkaloids, Vitamins, Saccharides and Alcohols, Phenolic acids, Lipids, and others. Environmental factor analysis indicated that soil nutrients were the primary differentiating factor. Five soil nutrient indicators: TN（total nitrogen）, TP（total phosphorus）, AP（available phosphorus）, AK（available potassium）, and OM（organic matter）, exhibited significant differences in three growing sites. Metabolite and soil nutrient association analysis using redundancy analysis (RDA) and Mantel test indicated that TNand OM contributed to the accumulation of amino acids and derivatives, nucleotides and derivatives, and alkaloids while inhibiting organic acids, vitamins coagulation biosynthesis. Moreover, AP and TP were associated with the highest accumulation of saccharides and, alcohols, phenolic acids. Consequently, differences in soil nutrients were reflected in Pepino metabolites variability. This study clarified the metabolite variability and the relationship between Pepino and soil nutrients in the main planting areas of northwest China. It provides a theoretical basis for the subsequent development of Pepino's nutritional value and cultivation management.
ARTICLE | doi:10.20944/preprints202009.0012.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Rattlesnake; Crotalus; Sistrurus; Venom; Toxin; Association
Online: 1 September 2020 (11:42:14 CEST)
The specificity and potency of venom components gives them a unique advantage in development of various pharmaceutical drugs. Though venom is a cocktail of proteins rarely is the synergy and association between various venom components studied. Understanding the relationship between various components is critical in medical research. Using meta-analysis, we found underlying patterns and associations in the appearance of the toxin families. For Crotalus, Dis has the most associations with the following toxins: PDE; BPP; CRL; CRiSP; LAAO; SVMP P-I & LAAO; SVMP P-III and LAAO. In Sistrurus venom CTL and NGF had most associations. These associations can be used to predict presence of proteins in novel venom and to understand synergies between venom components for enhanced bioactivity. Using this approach, the need to revisit classification of proteins as major components or minor components is highlighted. The revised classification of venom components needs to be based on ubiquity, bioactivity, number of associations and synergies. The revised classification will help in increased research on venom components such as NGF which have high medical importance.
ARTICLE | doi:10.20944/preprints201909.0040.v1
Subject: Business, Economics And Management, Business And Management Keywords: data mining; security; association rule; ECLAT
Online: 4 September 2019 (03:48:58 CEST)
The purpose of this paper is to develop WebSecuDMiner algorithm to discover unusual web access patterns based on analysing the potential rules hidden in web server log and user navigation history. Design/methodology/approach: WebSecuDMiner uses equivalence class transformation (ECLAT) algorithm to extract user access patterns from the web log data, which will be used to identify the user access behaviours pattern and detect unusual one. Data extracted from the web serve log and user browsing behaviour is exploited to retrieve the web access pattern that is produced by the same user. Findings: WebSecuDMiner is used to detect whether any unauthorized access have been posed and take appropriate decisions regarding the review of the original rights of suspicious user. Research limitations/implications: The present work uses the database which is extracted from web serve log file and user browsing behaviour. Although the page is viewed by the user, the visit is not recorded in the server log file, since it can be access from the browser's cache.
ARTICLE | doi:10.20944/preprints202111.0386.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome-wide association study; transcriptome-wide association study; meta-analysis; expression quantitative trait loci; nicotine addiction
Online: 22 November 2021 (11:46:13 CET)
Genome-wide association studies (GWAS) have identified and reproduced thousands of diseases associated loci but many of them are not directly interpretable due to the strong linkage disequilibrium among variants. Transcriptome-wide association studies (TWAS) incorporated expression quantitative trait loci (eQTL) cohorts as reference panel to detect associations with the phenotype at the gene level and were gaining popularity in recent years. For nicotine addiction, several important susceptible genetic variants were identified by GWAS, but TWAS that detected genes associated with nicotine addiction and unveiled the underlying molecular mechanism were still lacking. In this study, we used eQTL data from the Genotype-Tissue Expression (GTEx) consortium as reference panel to conduct tissue specific TWAS on cigarettes per day (CPD) over 13 brain tissues in two large cohorts: UK Biobank (UKBB; N=142,202) and the GWAS & Sequencing Consortium of Alcohol and Nicotine use (GSCAN; N=143,210), and then meta-analyzed the results across tissues while considering the heterogeneity across tissues. We identified three major clusters of genes with different meta-patterns across tissues consistent in both cohorts, including homogenous genes associated with CPD in all brain tissues, partially homogeneous genes associated with CPD in cortex, cerebellum and hippocampus tissues, and lastly the tissue-specific genes associated with CPD in only few specific brain tissues. Downstream enrichment analyses on each gene cluster identified unique biological pathways associated with CPD and provided important biological insights into the regulatory mechanism of nicotine dependence in the brain.
REVIEW | doi:10.20944/preprints202311.1819.v1
Subject: Biology And Life Sciences, Other Keywords: genome‐wide association; human genetics; machine learning
Online: 28 November 2023 (15:41:32 CET)
Machine learning, including deep learning, reinforcement learning, and generative artificial intelligence are revolutionising every area of our lives when data is made available. With the help of these methods, we can decipher information from larger datasets while addressing the complex nature of biological systems in a more efficient way. Although machine learning methods have been introduced to human genetic epidemiological research as early as 2004, those were never used to their full capacity. In this review, we outline some of the main applications of machine learning to assigning human genetic loci to health outcomes. We summarise widely used methods and discuss their advantages and challenges. We also identify several tools, such as Combi, GenNet and GMSTool, specifically designed to integrate these methods for hypothesis-free analysis of genetic variation data. We elaborate on the additional value and limitations of these tools from a geneticist’s perspective. Finally, we discuss the fast-moving field of foundation models and large multi-modal omics biobank initiatives.
ARTICLE | doi:10.20944/preprints202308.0902.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: ecosystems; conservation; vegetation; phytocoenoses; association; ecological characterization
Online: 11 August 2023 (07:58:00 CEST)
The purpose of this paper is to develop a phytosociological, ecological, cytogenetic, eco-protective and economic study of the vegetation of the wetland ecosystems in the Vlădeasa Massif built by the phytocoenoses of the association Carici echinatae-Sphagnetum (Balázs 1942) Soó 1955. In order to attain the aim and objectives put forward we carried out 10 phytocoenological surveys (surveys) in the phytocoenoses of the ecosystems during the optimal vegetation periods related to the summer-serotinal season in the timeframe 2020-2021. The taxonomically inventoried species were included in an association table by the criteria of their belonging to the basic coenotaxa of the association, alliance, order, vegetation class. The outcomes of the phytocoenosis research of the vegetation of the wetland ecosystems were processed, analysed, interpreted based on tables, histograms, diagrams, regarding the numerical and percentage weight of the species in the ecological categories of bioforms, phytogeographic elements (geoelements) and cytogenetic elements. The ecological behaviour of the species confined in ecosystems was also analysed by their relationship with ecological factors, edaphic soil moisture, air temperature and chemical reaction of the soil. The current state of ecosystems, potential threats, sustainable conservation of biodiversity, dynamics of phytocenoses, economic and scientific relevance were also subjected to research. The results obtained in the surveyed territory were analysed and compared numerically and as percentage with the data provided by two reference scientific works belonging to authors who independently carried out research with a similar topic in two different geographical regions of the Western Carpathians.
ARTICLE | doi:10.20944/preprints201906.0144.v1
Subject: Computer Science And Mathematics, Security Systems Keywords: data mining; network security; association rules; DDoS
Online: 16 June 2019 (02:42:59 CEST)
Typical modern information systems are required to process copious data. Conventional manual approaches can no longer effectively analyze such massive amounts of data, and thus humans resort to smart techniques and tools to complement human effort. Currently, network security events occur frequently, and generate abundant log and alert files. Processing such vast quantities of data particularly requires smart techniques. This study reviewed several crucial developments of existent data mining algorithms, including those that compile alerts generated by heterogeneous IDSs into scenarios and employ various HMMs to detect complex network attacks. Moreover, sequential pattern mining algorithms were examined to develop multi-step intrusion detection. These studies can focus on applying these algorithms in practical settings to effectively reduce the occurrence of false alerts. This article researched the application of data mining algorithms in network security. The academic community has recently generated numerous studies on this topic.
ARTICLE | doi:10.20944/preprints202310.0066.v1
Subject: Engineering, Telecommunications Keywords: Convergence; multi-agent; reinforcement learning; reward; user association
Online: 3 October 2023 (08:50:12 CEST)
Machine learning offers advanced tools for efficient management of radio resources in modern wireless networks. In this study, we leverage a multi-agent deep reinforcement learning (DRL) approach, specifically the Parameterized Deep Q-Network (DQN), to address the challenging problem of power allocation and user association in massive multiple-input multiple-output (M-MIMO) communication networks. Our approach tackles a multi-objective optimization problem aiming to maximize network utility while meeting stringent quality of service requirements in M-MIMO networks. To address the non-convex and nonlinear nature of this problem, we introduce a novel multi-agent DQN framework. This framework defines a large action space, state space, and reward functions, enabling us to learn a near-optimal policy. Simulation results demonstrate the superiority of our Parameterized Deep DQN (PD-DQN) approach when compared to traditional DQN and RL methods. Specifically, we show that our approach outperforms traditional DQN methods in terms of convergence speed and final performance. Additionally, our approach shows 72.2 % and 108.5 % improvement over DQN methods and RL method respectively in handling large-scale multi-agent problems in M-MIMO networks.
ARTICLE | doi:10.20944/preprints202306.0016.v1
Subject: Medicine And Pharmacology, Dermatology Keywords: psoriasis; psoriatic arthritis; IFIH1; MDA5; polymorphism; genetic association
Online: 1 June 2023 (03:40:11 CEST)
The melanoma differentiation-associated protein 5 (MDA5; encoded by the IFIH1 gene) mediates the activation of the interferon pathway in response to viral infection. This protein is also upregulated in autoimmune diseases and psoriasis skin lesions. IFIH1 gene variants that increased the MDA5 activity have been associated with increased risk for immune mediated diseases, including psoriasis. Our aim was to determine the association between three IFIH1 variants (rs35337543, intron8 +1G>C; rs35744605, Glu627Stop; and rs1990760, Ala946Thr) and the main clinical findings in a cohort of Spanish patients with psoriatic disease (N=572; 77% early-onset). Early-onset psoriasis (EOPs) had a significant higher frequency of severe disease and Cw6+. Carriers of the 946Thr variant were more common in EOPs (p<0.001), and the effect was more pronounced among Cw6-negatives. This variant was also associated with an increased risk of psoriatic arthritis (PsA) independently of other factors (OR=1.62, 95%CI=1.11-2.37). The rs3533754 and rs35744605 have been reported as risk factors for viral infection and protective for autoimmune diseases, but we did not find significant differences between the two onset age or PsA groups. However, due to the reduced frequency of the two variants (<0.02) the size of our cohort was too low to conclude a significant effect. In conclusion, the common IFIH1 rs1990760 T allele that has been linked to increased gene expression was significantly more frequent in EOPs patients. This variant was also an independent risk factor for PsA in our cohort. This risk allele was in linkage disequilibrium with other variants previously associated with the risk of psoriasis and PsA. Our study reinforces the widely reported role of IFIH1 gene variants on psoriatic disease and other immune mediated diseases.
ARTICLE | doi:10.20944/preprints202111.0326.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: SNP; calpaincalpastatin system genes; genomic association; tenderization; ageing
Online: 18 November 2021 (13:48:09 CET)
The most important factor that determines beef tenderness is its proteolytic activity and the balance between calpain1 protease activity and calpastatin inhibition is especially important, while contributions could arise from calpain2 and possibly calpain3. These processes are however affected by the meat aging process itself. To determine whether genotypes in the calpaincalpastatin system can enhance tenderness throughout a 20 day aging period, South African purebred beef bulls (n=166) were genotyped using the Illumina BovineHD SNP BeadChip, through genebased association analysis targeting the cast, capn3, capn2 and capn1 genes. The WarnerBratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 d 20 of aging, with protease enzyme activity in the first 20 h postmortem. Although several of the 134 SNP associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to agingassociated increases in tenderness for at least three of the four aging periods. While most genomic associations were relatively stable over time, some genotypes within SNP responded differently to aging, resulting in altered genomic effects over time. The level of aging at which genomic associations are performed is an important factor that determines whether SNP affect tenderness phenotypes.
ARTICLE | doi:10.20944/preprints202010.0001.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Association mapping; chromosomes; drought tolerance; markers, structure; traits
Online: 1 October 2020 (08:40:47 CEST)
The objective of this study were to conduct association mapping for drought tolerance at the seedling stage and yield-related traits. 60 cowpea accessions were used in the study. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Association mapping was conducted using single-marker regression (SMR) in Q Gene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. The population of the cowpea accessions were analysed using STRUCTURE 2.3.4 and the peak of delta K in the greenhouse showed seven population types, whereas the peak of delta K in the glasshouse indicated the presence of six population types. One SNP marker, 14083649|F|0-9 was associated with NP with a p value <0.001. Fifty SNP markers were associated with PWT at p <0.001. Four SNP markers, 14074781|F|0-16, 100047392|F|0-36, 14083801|F|0-28 and 100051488|F|0-49 were associated with AVSPD at p <0.001. SNP markers, 14074781|F|0-16, 14083801|F|0-28 and 100051488|F|0-49 were associated with PL at P <0.001. Five SNP markers, 100047392|F|0-36, 14083801|F|0-28, 100072738|F|0-34, 14076881|F|0-49 and 14076881|F|0-49 were associated with PWDTH at p <0.001. The 65 SNP markers identified can be used in cowpea molecular breeding to select for AVSPD, NP, PL, PWDTH, PWT, and RR through marker assisted selection (MAS).
REVIEW | doi:10.20944/preprints202007.0583.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genetic association studies; extreme phenotype; genetic epidemiology; tinnitus
Online: 24 July 2020 (13:43:00 CEST)
Exome sequencing has been commonly used in rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) to search for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to heritability in complex clinical traits. We have conducted a systematic review to find evidence supporting the use of EP strategies to search for rare variants in genetic studies of complex diseases, to highlight the contribution of rare variation to the genetic structure of multiallelic conditions. After performing the quality assessment of the retrieved records, we selected 19 genetic studies considering EP to demonstrate genetic association. All the studies successfully identified several rare variants, de novo mutations and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach in patients with an early onset of the disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.
DATASET | doi:10.20944/preprints202006.0226.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: candidate-gene association; estimation; bias; confounding; case study
Online: 18 June 2020 (07:50:33 CEST)
Estimation of the reality can easily be flawed, hence, in order to result in accurate and useful estimates the process has to be protected from bias and confounding and should follow other methodological milestones inherent to different types of empirical observations. Candidate-gene association studies are a specific form of observations that have been rather extensively applied in psychiatry yielding valuable information on various aspects – when methodologically adequate and used in appropriate settings. However, certain flaws that may occur in such studies might not be bluntly obvious, at least not at first glance, and may pass unnoticed by researchers and reviewers. This case study uses two recent published candidate-gene association reports suggesting involvement of cannabinoid receptor type 1 and of heat shock protein single nucleotide polymorphisms in development of neurocognitive performance and psychopathology in a cohort of adult first episode psychosis patients to point-out the types of flaws inevitably resulting in inaccurate and useless estimates.
ARTICLE | doi:10.20944/preprints202305.1433.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Japanese apricot; scab; resistance; genome-wide association study (GWAS)
Online: 19 May 2023 (10:46:02 CEST)
Japanese apricot (Prunus mume) is a culturally and economically important fruit tree in East Asia. ‘Nanko’, the primary cultivar of the Japanese apricot well known in Japan, usually suffers from scab, a disease caused by Venturia carpophila. Scab results in the development of black spots on the fruit surface, which considerably reduces its commercial value. Despite being an economic concern for Japanese apricot, there have been few reports on the phenotypic variation in scab resistance/susceptibility, the underlying genetic factors, and the development of DNA markers. Therefore, in this study, we performed a comprehensive trait analysis for scab resistance and susceptibility for four years and conducted a genome-wide association study (GWAS) to identify the associated loci. The results showed that significant GWAS peaks were detected in 2017 and 2018. Promising candidate gene encoding domains associated with disease resistance were found at the nine single-nucleotide polymorphisms (SNPs) identified in 2017 and 2018. These SNPs were thought to be associated with scab susceptibility of ‘Nanko’ lineages. These findings shed light on the mechanisms of scab resistance in P. mume and will assist future breeding programs to improve scab resistance in ‘Nanko’ lineages.
ARTICLE | doi:10.20944/preprints202305.0043.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Genome-Wide Association Study; Genomic Selection, Marker-Assisted Selection
Online: 2 May 2023 (02:33:16 CEST)
Advancement in biotechnology and genomics research have promoted access to DNA markers and their use in breeding programs. Genome-wide association study (GWAS), Genomic selection (GS) and Marker-Assisted Selection (MAS) are some of the applications of DNA markers in plant breeding. Researchers have suggested combining these individual applications for better selection accuracies. This study examines the potential advantages of incorporating GWAS-results into MAS and GS as well as the validity of the different methods for combining these approaches. From this study, it was concluded that number of QTNs have greater effects on prediction accuracies compared to heritability estimates. Also, the increase in prediction accuracy from the invalid method of incorporating GWAS results into GS and MAS model is similar to results recorded with using the valid approach. However, greater difference may be observed in another scenario which can lead to spurious results when used to make breeding decisions.
ARTICLE | doi:10.20944/preprints202204.0256.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: tea intake; fracture; Mendelian randomization; genome-wide association studies
Online: 27 April 2022 (10:40:34 CEST)
Fracture is a global public health disease. Bone health and fracture risk have become the focus of public and scientific attention. Observational studies have reported that tea consumption is associated with fracture risk, but the results are inconsistent. The present study was conducted to evaluate whether tea consumption was causally associated with the risk of bone fracture through two-sample Mendelian Randomization (MR) analysis. We included a large genome-wide association study (GWAS) associated with tea consumption of 447,485 individuals and analyzed the effects of genetic instruments on fractures using fracture cases from the UK Biobank dataset (n=361,194). Inverse variance weighted (IVW) indicated no causal effects of tea consumption on fractures of the skull and face, shoulder and upper arm, hand and wrist, femur, calf, and ankle (odds ratio=1.000, P=0.881; OR=1.000, P=0.857; OR=1.002, P=0.339; OR=0.997, P=0.054; OR=0.998, P=0.569, respectively). Consistent results were also found in MR-Egger, weighted median, and weighted mode. Our research provided evidence that tea consumption is unlikely to affect the incidence of fractures.
REVIEW | doi:10.20944/preprints202009.0348.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: DNA methylation; epialleles; epiRILs; epigenetics; Epigenome-Wide Association Studies.
Online: 26 September 2020 (08:08:27 CEST)
Plant breeding conventionally depends on genetic variability available in a species to improve a particular trait in the crop. However, epigenetic diversity may provide an additional tier of variation. The recent advent of epigenome technologies has elucidated the role of epigenetic variation in shaping phenotype. Further, the development of epigenetic recombinant inbred lines (epi-RILs) in the model species such as Arabidopsis has enabled accurate genetic analysis of epigenetic variation. Subsequently, mapping of epigenetic quantitative trait loci (epiQTL) allowed association between epialleles and phenotypic traits. Thus, quantitative epigenetics provides ample opportunities to dissect the role of epigenetic variation in trait regulation, which can be eventually utilized in crop improvement programs. Moreover, locus-specific manipulation of DNA methylation by epigenome-editing tools such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) can facilitate epigenetic based molecular breeding of important crop plants.
ARTICLE | doi:10.20944/preprints201803.0093.v1
Subject: Engineering, Control And Systems Engineering Keywords: linear regression; covariance matrix; data association; sensor fusing; SLAM
Online: 13 March 2018 (04:06:56 CET)
Linear regression is a basic tool in mobile robotics, since it enables accurate estimation of straight lines from range-bearing scans or in digital images, which is a prerequisite for reliable data association and sensor fusing in the context of feature-based SLAM. This paper discusses, extends and compares existing algorithms for line fitting applicable also in case of strong covariances between the coordinates at each single data point, which must not be neglected if range-bearing sensors are used. Besides, particularly the determination of the covariance matrix is considered, which is required for stochastic modeling. The main contribution is a new error model of straight lines in closed form for calculating fast and reliably the covariance matrix dependent on just a few comprehensible and easily obtainable parameters. The model can be applied widely in any case when a line is fitted from a number of distinct points also without a-priori knowledge of the specific measurement noise. By means of extensive simulations the performance and robustness of the new model in comparison to existing approaches is shown.
TECHNICAL NOTE | doi:10.20944/preprints201901.0126.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: flax; association mapping; genome-wide association study (GWAS); simple sequence repeat (SSR); single nucleotide polymorphism (SNP); quantitative trait loci (QTL); chromosome-scale pseudomolecules
Online: 14 January 2019 (07:19:08 CET)
Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits in a population. To date, a total of 267 QTL for 29 quantitative traits have been reported in 13 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, scaffold sequences, or pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but were mainly based on simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. This article provides methods with software tools and database files to uniquely map SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules. Using these methods, 195 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters. Mapping of QTL from different studies to the same reference enables comparisons and facilitates genome-wide QTL analysis, candidate gene scanning, and breeding applications.
CASE REPORT | doi:10.20944/preprints202309.0638.v1
Subject: Medicine And Pharmacology, Internal Medicine Keywords: Polymyositis; Cytomegalovirus infection; Hashimoto`s thyroiditis, association, coexistence, autoimmune diseases
Online: 11 September 2023 (09:31:53 CEST)
Polymyositis is a rare condition with an unknown etiology occurring more frequently in adult women. There is a lack of evidence on the coexistence of PM and CMV infection in a patient with Hashimoto Thyroiditis hypothyroidism. However, the increasing incidence of CMV infection and autoimmune diseases overlapping points out a relationship, while the association direction remains unclear. Case outline: A 32-year-old woman recently treated for HT hypothyroidism was admitted to the hospital two weeks after being treated for common flu by the family doctor, complaining about a worsening condition with muscle pain, weakness, frequent falls, and fatigue. The first tests showed a normalized thyroid function, with elevated values of troponin and serum creatinine kinase (KC). The immunological tests revealed the presence of a high titer of CMV IgG antibodies and raised levels of CMV DNA. Pelvis MRI images demonstrated markedly elevated signals on the STIR sequences in the pelvis, thighs, and calves, indicating active and severe multifocal myositis. The diagnosis of PM was confirmed with the muscle biopsy on day 7 of hospitalization. The patient showed significant improvements within two weeks after the medical therapy and physiotherapy.
ARTICLE | doi:10.20944/preprints202305.1102.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Alfalfa; Plant Growth Vigor; Alphafold; Protein 3D Structure; Association Study
Online: 16 May 2023 (05:32:22 CEST)
Plant breeding aims to develop elite crop varieties appropriate for various environments with higher quality and quantity of production. Researchers use quantitative trait loci (QTL) mapping and association studies to identify regions in the genome responsible for the variation of the quantitative traits of interest. However, mapped regions do not always translate to functional proteins, which makes it challenging to identify genes associated with traits of interest. The biological functions of proteins are strongly dependent on their 3D structure. Alternatively, if proteins can be directly linked with the phenotypes, the effect of mutations on phenotypic changes can be assessed. Innovation of deep learning models in biology opens new avenues of exploration. AlphaFold is an AI system that predicts the 3D structure of a protein from its amino acid sequence with near experimental accuracy and was used in this study. Point mutations with a significant influence on the 3D structure of a protein can capture the effect on phenotypes through association study, and this provides insights into the regions that are of functional importance. In the current study, 534 plants were selected based on plant vigor, and 154 missense variants that change amino acid sequences, including 5 significant hits from previous study, were included. The changes in protein 3D structure were assessed by association with the phenotype. The analysis identified five significant associations, four of which were also identified in previous study of SNPs GWAS, however, a new fifth association was also identified which was annotated as disease resistance gene in Medicago truncatula. This study helps to associate SNPs that could be missed by GWAS due to stringent Bonferroni corrected p-values by providing a more robust filter for SNPs using features from predicted protein 3D structures.
ARTICLE | doi:10.20944/preprints202305.0989.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: genome-wide association study; carcass length; meat color; genetic parameter
Online: 15 May 2023 (07:25:43 CEST)
Ningxiang pig is renowned breed for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 minutes and 24 hours) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30 ~ 0.80) for carcass traits and from low to high (0.11 ~ 0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the HMGA1 gene emerged as a pleiotropic gene correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs.
ARTICLE | doi:10.20944/preprints202105.0102.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: Market basket analysis; association rule mining; buying pattern; data mining
Online: 6 May 2021 (15:14:25 CEST)
Buyer practices have changed as individuals are figuring out how to live with the new truth of COVID-19. Take-out and conveyance orders have expanded, and our customer has added new items to their menu because of new client inclinations. With every one of the continuous changes, the customer had numerous unanswered inquiries, for example, Smartbridge has broad involvement with café innovation development Café TECHNOLOGY CAPABILITIES :Are the most famous items as yet unchanged after COVID? :Which are the most sold item blends now? :What is the acknowledgment of new things? :What are clients purchasing alongside new things? :How have liquor deals changed? The customer previously had reports that followed item deals and operational measurements, notwithstanding, there was a need to get a more profound knowledge into item examination. The customer expected to recognize what items and introductions were being sold all the more frequently, measure the acknowledgment of new items, and figure out what items clients buy together to improve advertising efforts, advancements, and deals. he E-business industry is filling immensely in the Indian market. The modest 4G web bundles in India clearly gives a push to these ventures. Thus, as Covid19 first hit in Quite a while, individuals got terrified to go out from their homes in light of the fact that, in their mind, it's a dread of Covid. They even wonder whether or not to go out to purchase fundamental (FMCG) products. Frenzy purchasing additionally has seen and to stay away from this dread of COVID-19, individuals are offering inclinations to the E-Commerce destinations to purchase fundamental products and a few clients are new which joined to purchase fundamental merchandise during this Pandemic Lockdown period. Numerous clients are moving their purchasing conduct from disconnected retail locations to online stores. This paper examines the customer buying pattern during lockdown.
ARTICLE | doi:10.20944/preprints202001.0384.v1
Subject: Business, Economics And Management, Business And Management Keywords: Mixed reality; Interactivity; Vividness; Brand loyalty; Brand awareness; Brand association
Online: 31 January 2020 (11:35:28 CET)
Mixed reality technology is being increasingly used in cultural heritage attractions to enhance visitors’ experience. However, how the characteristics of mixed reality affect satisfaction and brand loyalty has not been explored in previous research. The purpose of this study is to identify factors affecting satisfaction with mixed reality experiences at cultural and artistic visitor attractions and their influence on brand loyalty, which is connected with management performance. We propose a theoretical model based on brand equity theory in the context of mixed reality experience. Survey data were gathered from 251 respondents visiting a cultural and artistic visitor attraction in Seoul, Korea using a stratified sampling method. PLS-SEM was employed for the data analysis. The results suggest that the characteristics of mixed reality (interactivity, vividness) not only influence the affective aspects (perceived immersion, perceived enjoyment) of visitors’ experience, but also positively affect brand awareness, brand association, and brand loyalty.
ARTICLE | doi:10.20944/preprints201911.0117.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: malignant mesothelioma; epidemiology; association rule mining; Apriori method; imbalanced dataset
Online: 10 November 2019 (16:15:14 CET)
Malignant mesothelioma is a rare proliferative cancer that develops in the thin layer of tissues surrounding the lungs. Malignant mesothelioma is associated with an extremely poor prognosis and the majority of patients do not show symptoms. The epidemiology of mesothelioma is important for the identification of disease. The primary aim of this study is to explore the risk factors associated with mesothelioma. The dataset consists of healthy and mesothelioma patients but only mesothelioma patients were selected for the identification of symptoms. The raw data set has been pre-processed and then the Apriori method was utilized for association rules with various configurations. The pre-processing task involved the removal of duplicated and irrelevant attributes, balanced the dataset, numerical to the nominal conversion of attributes in the dataset and creating the association rules in the dataset. Strong associations of disease’s factors; asbestos exposure, duration of asbestos exposure, duration of symptoms, erythrocyte sedimentation rate and Pleural to serum LDH ratio determined via Apriori algorithm. The identification of risk factors associated with mesothelioma may prevent patients from going into the high danger of the disease. This will also help to control the comorbidities associated with mesothelioma which are cardiovascular diseases, cancer-related emotional distress, diabetes, anemia, and hypothyroidism.
ARTICLE | doi:10.20944/preprints201807.0238.v1
Subject: Computer Science And Mathematics, Hardware And Architecture Keywords: Multiple object tracking; Airborne video; Tracklet confidence; Hierarchical association framework
Online: 13 July 2018 (14:27:22 CEST)
Multi-object tracking (MOT) in airborne videos is a challenging problem due to the uncertain airborne vehicle motion, vibrations of the mounted camera, unreliable detections, size, appearance and motion of the moving objects as well as occlusions due to the interaction between the moving objects and with other static objects in the scene.To deal with these problems, this work proposes a four-stage Hierarchical Association framework for multiple object Tracking in Airborne video (HATA). The proposed framework combines data association-based tracking (DAT) methods and target tracking using a Compressive Tracking approach, to robustly track objects in complex airborne surveillance scenes. In each association stage, different sets of tracklets and detections are associated to efficiently handle local tracklet generation, local trajectory construction, global drifting tracklet correction and global fragmented tracklet linking. Experiments with challenging airborne video datasets show significant tracking improvement compared to existing state-of-art methods.
ARTICLE | doi:10.20944/preprints201801.0231.v1
Subject: Engineering, Control And Systems Engineering Keywords: Data mining; Association rules; Previous Cause; Type of Accident; Overexertion
Online: 24 January 2018 (19:40:52 CET)
An analysis of workplace accidents in the mining sector has been done using the database from the Spanish administration between the period 2005-2015 and applying data mining techniques. Data has been processed by means of the software Weka. Two scenarios were chosen regarding the accidents database, surface and underground mining. The most important variables involved in occupation accidents and their association rules have been determined. These rules are formed by several predictor variables that cause an accident, defining its characteristics and context. This study exposes the 20 most important association rules of the sector, either surface or underground mining, based on statistical confidence levels of each rule obtained by Weka. The outcomes display the most typical immediate causes with the percentage of accident basis of each association rule. The most typical immediate cause is body movement with physical effort or overexertion and type of accident is physical effort or overexertion. On the other hand, the second most important immediate cause and type of accident change in both scenarios. Data mining techniques have been proved as a very powerful tool to find out the root of the accidents, apply corrective measures and verify their effectiveness, either for public or private companies.
ARTICLE | doi:10.20944/preprints202311.1133.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: glutathione; tripeptides; ultrasonic relaxation spectroscopy; molecular docking; self-association; proton-transfer
Online: 17 November 2023 (04:32:02 CET)
We report a detailed investigation of vibrational modes, structure, and dynamics of glutathione (GSH) solutions using ultrasonic relaxation spectroscopy, FT-IR vibrational spectroscopy and electronic absorption measurements. The experimental data were analyzed in view of density functional theory (DFT) and molecular docking calculations. Three distinct Debye-type relaxation processes are resolved in the acoustic spectra, which are assigned to conformational changes between GSH conformers, self-association of GSH, and protonation processes. The standard volume changes for each process were estimated both experimentally and theoretically revealing a close resemblance among them. The higher the effect of the relaxation process in the structure, the greater the induced volume changes. From the temperature dependence of specific acoustic parameters, the thermodynamic characteristics of each process were determined. The experimental FT-IR spectra were compared with the corresponding theoretically predicted vibrational spectra revealing that the GSH dimers and extended conformers dominate the structure of GSH solutions in the high concentration region. The absorption spectra in the ultraviolet region confirmed the gradual aggregation mechanism that takes place in the aqueous GSH solutions. The results of the present study were discussed and analyzed in the framework of the current phenomenological status of the field.
ARTICLE | doi:10.20944/preprints202306.1504.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Atopic Dermatitis; Meta-analysis; Eczema; Association study; polymorphism; SNP; candidate gene
Online: 21 June 2023 (08:29:58 CEST)
Atopic dermatitis (AD) has been extensively investigated for genetic associations utilizing both candidate gene approaches and genome-wide scans. Here, we comprehensively evaluated the available literature to determine the association of candidate genes in AD to gain additional insight in the etiopathogenesis of the disease. We systematically screened all studies that explored the association between polymorphisms and AD risks in cases of European and Asian ancestry and synthesized the available evidence through random-effects meta-analysis. We identified 97 studies that met our inclusion/exclusion criteria that examined 17 candidate loci in Europeans and 14 candidate genes in Asians. We confirmed the significant associations between FLG variants in both European and Asian populations and AD risk, while additional synthesis of available data revealed novel loci mapped to IL18 and TGFB1 genes in Europeans and IL12RB1 and MIF in Asians, that have not yet been identified by genome-wide association studies. Our findings provide comprehensive evidence for AD risk loci in cases of both European and Asian ancestries, validating previous associations as well as revealing novel loci that could imply previously unexplored biological pathways.
ARTICLE | doi:10.20944/preprints202304.0813.v1
Subject: Engineering, Transportation Science And Technology Keywords: shield subway tunnel; surface defects; 3D laser scanning; defect association analysis
Online: 24 April 2023 (03:53:13 CEST)
The surface defects of shield subway tunnel can significantly affect the serviceability of the tunnel structure and may compromise the operation safety. To effectively detect the multiple surface defects, this research employs a tunnel inspection trolley (TIT) based on the mobile laser scanning technique. By conducting the inspection of the shield tunnel on a metro line section, various surface defects are identified by the TIT, including water leakage defect, dislocation, spalling, cross-section deformation, etc. To explore the root causes of the surface defects, the association rules between different defects are calculated via an improved Apriori algorithm. Results show that: i) there are significant differences in different association rules of various surface defects of the shield tunnel; ii) the average confidence of the association rule “dislocation & spalling → water leakage” is as high as 57.78%, indicating that most of the water leakage defects are caused by dislocation and spalling of the shield tunnel in the sections being inspected; iii) the weakest rule appears at “water leakage → spalling”, with the average confidence of 13%. The association analysis can be used in predicting the critical defects influencing the structural reliability and operation safety, such as water leakage, and optimizing the construction and maintenance work for the shield subway tunnel.
ARTICLE | doi:10.20944/preprints202304.0233.v1
Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: thermoreversible gelation; gelation time; relaxation time; multiple cross-links; stepwise association
Online: 12 April 2023 (03:35:41 CEST)
The gelation time tg necessary for a solution of functional (associating) molecules to reach its gel point after a temperature jump, or a sudden concentration change, is theoretically calculated as a function of the concentration and temperature for the molecules carrying the number f of functional groups. Quite generally, tg is given by the product of the relaxation time tR and a thermodynamic factor Q. For pairwise cross-linking, and cross-linking with a fixed multiplicity k, precise values of tg are derived. For cross-linking with variable multiplicity, kinetic equation of stepwise association is derived for the reactivity pk of the functional groups, on the basis of which tg and tR are estimated. The thermodynamic factor Q is shown to generate a singularity of logarithmic divergence as the temperature (concentration) approaches the equilibrium gel point, while the relaxation time tR changes continuously across it. The retardation effect on the gelation time due to the reversibility of the cross-linking is explicitly calculated for some specific models of cross-linking. For a micellar cross-linking covering a wide range of the multiplicity, as seen in hydrophobically-modified water-soluble polymers, tR is shown to obey a formula similar to the Aniansson-Wall law.
ARTICLE | doi:10.20944/preprints202301.0341.v1
Subject: Medicine And Pharmacology, Other Keywords: Deep Learning; COVID-19; Clinical Informatics; Machine Learning; Transformer; Association Mining
Online: 19 January 2023 (02:00:16 CET)
Predicting Length of Stay (LoS) and understanding its underlying factors is essential to minimize the risk of hospital-acquired conditions, improve financial, operational, and clinical outcomes, and to better manage future pandemics. The purpose of this study is to forecast patients’ LoS using a deep learning model and analyze cohorts of risk factors minimizing or maximizing LoS. We employed various pre-processing techniques, SMOTE-N to balance data, and Tab-Transformer model to forecast LoS. Finally, Apriori algorithm was applied to analyze cohorts of risk factors influencing LoS at hospital. The Tab-Transformer outperformed the base Machine Learning models with an F1-score (.92), precision (.83), recall (.93), and accuracy (.73) for discharge dataset, and F1-score (.84), precision (.75), recall (.98), and accuracy (.77) for deceased dataset. The association mining algorithm was able to identify significant risk factors/indicators belonging to lab, X-Ray, and clinical data such as elevated LDH, and D-Dimer, lymphocytes count, and comorbidities such as hypertension and diabetes responsible for extending patients LoS. It also reveals what treatments has reduced the symptoms of COVID-19 patients leading to reduction in LoS particularly when no vaccines or medication such as Paxlovid were available.
ARTICLE | doi:10.20944/preprints202208.0178.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: alcohol dependence; comorbidity; gene network; genome-wide association study; sex differences
Online: 9 August 2022 (10:35:29 CEST)
At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in male and female patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33×10^-8 calculated with the Yates-corrected Chi-square test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWAS of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network. This study indicates that a number of genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The results also suggest the genetic basis of sex-specific psychiatric comorbidities of AD.
ARTICLE | doi:10.20944/preprints202206.0360.v1
Subject: Business, Economics And Management, Business And Management Keywords: tourism and related; SMEs; small particulate matters; association rules; data mining
Online: 27 June 2022 (10:24:27 CEST)
In northern Thailand, the problem of small particulate matter happens every year, with the pri-mary source being agricultural weed burning and wildfire. The tourism industry is strongly impacted and has been the spotlight for the past few years. Thus, the study aims to investigate the effect of small particulate matter on tourism and related SMEs in Chiang Mai, Thailand. The data was collected from 286 entrepreneurs in the tourism and related SMEs sectors. The data was analyzed using data mining and association rule techniques. The study revealed that small particulate matter has a considerable impact on customer factors, especially the number of customers has decreased. Operational factors and prod-uct/service factors are also affected by the dust in the form of adjustments to keep the business running and the protection of the health of employees and customers. Certainly, financial factors are affected by the small particulate matter situation, both lower revenues and higher costs.
ARTICLE | doi:10.20944/preprints202205.0258.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Mendelian randomisation; Alcohol Consumption; UK Biobank; Phenome wide association studies; Biomarker
Online: 19 May 2022 (09:09:35 CEST)
Background: Alcohol consumption is associated with the development of cardiovascular diseases, cancer, and liver disease. The biological mechanisms are still largely unclear. Here, we aimed to use an agnostic approach to identify phenotypes mediating the effect of alcohol on various diseases. Methods: We performed an agnostic association analysis between alcohol consumption (red, and white wine, beer/cider, fortified wine, and spirits) with over 7,800 phenotypes from the UK biobank comprising 223,728 participants. We performed Mendelian randomisation analysis to infer causality. We additionally performed a Phenome-wide association analysis and a mediation analysis between alcohol consumption as exposure, traits in causal relationship with alcohol consumption as mediators, and various diseases as outcome. Results: Of 45 traits in association with alcohol consumption, 20 were in causal relationship with alcohol consumption. Gamma glutamyltransferase (GGT; β=9.44; CI,5.94-12.93; Pfdr=9.04×10-7), mean sphered cell volume (β=0.189; CI,0.11-0.27; Pfdr=1.00×10-4), mean corpuscular volume (β=0.271; CI,0.19-0.35; Pfdr=7.09×10-10) and mean corpuscular haemoglobin (β=0.278; CI,0.19-0.36; Pfdr=1.60×10-6) showed the strongest causal relationships. We also identified GGT and physical activity as mediators causing liver cirrhosis and alcohol dependence. Conclusion: Our study provides evidence of causality between alcohol consumption and 20 traits and a mediation effect for physical activity on health consequences of alcohol consumption.
Subject: Engineering, Chemical Engineering Keywords: membrane theory; Association-Induction Hypothesis; ion transport, ion adsorption; membrane potential
Online: 13 August 2021 (08:53:04 CEST)
Accurate prediction of the membrane potential by membrane theory is possible on the basis that the plasma membrane is selectively permeable to ions and that permeability determines the characteristics of the membrane potential. However, an experimental and artificial cell system with an impermeable membrane serving as a model plasma membrane has a non-zero membrane potential, and this potential generated across the membrane is somehow consistent with the potential characteristics predicted by the membrane theory, despite the impermeability of the membrane to ions. A long-forgotten theory, called the association-induction hypothesis (AIH), has emerged as a more plausible mechanism for generating the membrane potential than the membrane theory to explain this unexpected behavior. The AIH asserts that ion-selective membrane permeability is not necessary for the generation of the membrane potential, which is contrary to the membrane theory. Although such an idea is not easy to accept, the experimental results clearly suggest the correctness of the AIH.
REVIEW | doi:10.20944/preprints202103.0066.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: GRAS protein, DELLA, Intrinsically Disordered Proteins, Arbuscular Mycorrhizal association, abiotic stress
Online: 2 March 2021 (10:01:42 CET)
The GAI‐RGA ‐ and ‐SCR (GRAS) proteins belong to the plant-specific transcription factor gene family and involved in several developmental processes, phytohormone and phytochrome signaling, symbiosis, stress responses etc. GRAS proteins have a conserved GRAS domain at C-terminal and hypervariable N-terminal. The C-terminal conserved domain directly affects the function of the GRAS proteins. For instance, in Arabidopsis, mutations in this domain in Slender rice 1 (SLR1) and Repressor of GA (RGA) proteins cause significant phenotypic changes. GRAS proteins have been reported in more than 30 plant species and till now it has been divided into 17 subfamilies. This review highlighted GRAS protein's importance during several biological processes in plants, structural features of GRAS proteins, their expansion and diversification in the plants, GRAS-interacting proteins complexes and their role in biological processes. We also summarized available recent research that utilized CRISPR-Cas9 technology to manipulate GRAS genes in a plant for different traits. Further, the exploitation of GRAS genes in crop improvement programs has also been discussed
ARTICLE | doi:10.20944/preprints202007.0077.v1
Subject: Social Sciences, Cognitive Science Keywords: Second Language Learning; Word Learning; Cognate Effect; Synonymy; Picture Word Association
Online: 5 July 2020 (15:00:57 CEST)
The effects of cognate synonymy in L2 word learning are explored. Participants learned the names of well-known concrete concepts in a new fictional language following a picture-word association paradigm. Half of the concepts (set A) had two possible translations in the new language (i.e., both words were synonyms): one was a cognate in participants’ L1 and the other one was not. The other half of the concepts (set B) had only one possible translation in the new language, a non-cognate word. After learning the new words, participants’ memory was tested in a picture-word matching task and a translation recognition task. In line with previous findings, our results clearly indicate that cognates are much easier to learn, as we found that the cognate translation was remembered much better than both its non-cognate synonym and the non-cognate from set B. Our results also seem to suggest that non-cognates without cognate synonyms (set B) are better learned than non-cognates with cognate synonyms (set A). This suggests that, at early stages of L2 acquisition, learning a cognate would produce a poorer acquisition of its non-cognate synonym, as compared to a solely learned non-cognate. These results are discussed under the light of different theories and models of bilingual mental lexicon.
ARTICLE | doi:10.20944/preprints201906.0235.v1
Subject: Computer Science And Mathematics, Probability And Statistics Keywords: bivariate Copula; measures of association; dependence modeling; Kendall’s t; Blomqvist’s P
Online: 24 June 2019 (08:58:06 CEST)
Copulas are useful tools for modeling the dependence structure between two or more variables. Copulas are becoming a quite flexible tool in modeling dependence among the components of a multivariate vector, in particular to predict losses in insurance and finance. In this article, we study the dependence structure of some well-known real life insurance data (with two components mainly) and subsequently identify the best bivariate copula to model such a scenario via VineCopula package in R. Associated structural properties of these bivariate copulas are also discussed.
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Genome-wide association studies (GWAS); post-GWAS; sheep; tail fat deposition
Online: 11 June 2019 (10:04:39 CEST)
The type of tail of sheep is an important economic trait. However, the candidate genes associated with the tail type are uncertain. The objective of this study was to identify the genetic region and genotype responsible for the tail type phenotype. Here we perform a genome-wide association study (GWAS) in 40 large tailed Han sheep and 40 Altay sheep as case and 40 Tibetan sheep as control. The results indicated that a total 31 genome-wide significant SNPs associated with type of tail traits were detected. For significant SNPS loci, determine its physical location, and screening of candidate genes within section. By combining information of previously reported and annotated biological functional genes, we identified SPAG17, Tbx15, VRTN, NPC2, BMP2 and PDGFD as the most promising candidate genes for type of tail traits. Based on the above identified candidate genes on type of tail traits, we selected BMP2 and PDGFD to conduct the genetic effect analysis in a large Altay sheep and Tibetan sheep population. Rs119 T>C in the exon1 of BMP2 gene and 1 SNPs in the exon4 (rs69 C>A) of PDGFD gene were detected, rs119 that located on exon1 of BMP2 gene was TT genotype in Altay sheep, while with CC genotype in Tibetan sheep. On rs69 of PDGFD gene, Altay sheep with CC genotype, however, Tibetan sheep with AA genotype. These results indicated that the significant associations of SNPs detected in GWAS were indirectly caused by the genetic effects of BMP2 and PDGFD on sheep tail fat deposition.
ARTICLE | doi:10.20944/preprints201804.0227.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Ensemble clustering; cluster stability; F-measure; co-association matrix; genetic algorithm
Online: 17 April 2018 (15:58:22 CEST)
Nowadays, we live in a world in which people are facing with a lot of data that should be stored or displayed. One of the key methods to control and manage this data refers to grouping and classifying them in clusters. Today, clustering has a critical role in information retrieval methods for organizing large collections inside a few significant clusters. One of the main motivations for the use of clustering is to determine and reveal the hidden and inherent structure of a set of data. Ensemble clustering algorithms combine multiple clustering algorithms to finally reach an overall clustering system. Ensemble clustering methods by lack of information fusing utilize several primary partitions of data to find better ways. Since various clustering algorithms look at the different data points, they can produce various partitions from such data. It is possible to create a partition with high performance by combining the partitions obtained from different algorithms, even if the clusters to be very dense from each other. Most studies in this area have examined all the initial clusters. In this study, a new method is used in which the most sustainable clusters are utilized instead of all primary produced clusters. Consensus function based on co-association matrixes used to select more stable clusters. The most stable clusters selection method is done by cluster stability criterion based on F-measure. Optimization functions are used to optimize the obtained final clusters. The genetic algorithm is the optimizer used in this article to find the ultimate clusters participated in a consensus. Experimental results on several datasets show that the output of proposed method is various clusters with high stability.
ARTICLE | doi:10.20944/preprints202310.1379.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: maize; Gibberella ear rot; Fusarium graminearum; genome-wide association study; kernel bioassay
Online: 23 October 2023 (09:43:00 CEST)
Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most destructive diseases in maize that severely reduces grain yield and contaminates several potential mycotoxins. However, few efforts had been devoted to dissect the genetic basis of maize GER resistance. In the present study, a genome-wide association study (GWAS) was conducted in a maize association panel consisting of 303 diverse inbred lines. The phenotypes of GER severity were evaluated using kernel bioassay across multiple time points in the laboratory. Then, three models including fixed and random model circulating probability unification model (FarmCPU), general linear model (GLM) and mixed linear model (MLM), were conducted simultaneously in GWAS to identify single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance. A total of four individual significant association SNPs with the phenotypic variation explained (PVE) ranging from 3.51 to 6.42% were obtained. Interestingly, the peak SNP (PUT-163a-71443302-3341) with the greatest PVE value, was co-localized in all models. Subsequently, 12 putative genes were captured from the peak SNP that several of these genes were directly or indirectly involved in disease resistance. Overall, these findings contribute to understand the complex plant-pathogen interactions in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the kernel bioassay that can be used for evaluating and selecting elite germplasm resources with GER resistance in maize.
ARTICLE | doi:10.20944/preprints202305.1636.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: Multiple extended targets; Data association; Tracklets; Min-cost network flow; Intermittent measurements
Online: 23 May 2023 (10:17:47 CEST)
The main problem in pursuing multiple extended targets tracking is distinguishing the origins of the measurements. The association of measurements to the possible origins within the target’s extent is difficult, especially for the occlusions or the detection blind zone which cause the intermittent measurements. To solve the problem, a hierarchical network-based tracklets data association algorithm is proposed. At the low level, the min cost network flow model is used to extract possible tracklets from the divided measurement set. At the high-level, the trajectories are estimated from the tracks produced by the previous low level network. The experimental results show that the hierarchical network-based tracklets data association algorithm outperforms the JPDA and RFS-based method when the measurement is intermittently unavailable.
ARTICLE | doi:10.20944/preprints202202.0164.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: rare variants; genome-wide association study; validation test; SNP chip; genomic selection
Online: 11 February 2022 (15:59:26 CET)
The experiments described in this research article were designed to test the effect of rare variants into genomic prediction in dairy cattle. Common polymorphisms are able to explain only a small proportion of the underlying genetic variation of complex phenotypes. Variants representing functional mutations with large effects on complex phenotypes are expected to be rare due to natural (humans) or artificial (livestock) selection pressure. Therefore, it is important to check whether the use of rare variants could increase the accuracy of ranking of animals by providing the tool for more precise differentiation among the bulls with high additive genetic merit. The goal of our study was to verify whether including rare variants in a genomic selection model allows for a more accurate description of the additive genetic background of traits under selection in dairy cattle. We used the linear mixed model for comparison SNP estimates for Holstein-Friesian cattle of the two data sets – a set containing only single nucleotide polymorphisms defined by minor allele frequency ≥ 0.01, which is routinely used in the Polish genomic evaluation system (46,216 SNPs), and a set containing SNPs selected based only on the call rate (54,378 SNPs). Based on the SNP estimates we also calculated DGV and GEBV and compared them between both data sets. In all the analyses we used production, fertility, conformation and udder health traits. We also assessed the time required for the two most computationally demanding components of genomic selection: preparing genotype data, and estimation of SNP effects between those two data sets. The results of our study indicated that the analysis including rare variants resulted in changes in the individual ranking of the top 100 male and female candidates, but had no effect on the outcome of the quality of EBV prediction as expressed by the Interbull validation test.
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: feeding and eating disorder; genome-wide association study; methylation quantitative trait loci
Online: 8 October 2021 (14:23:39 CEST)
Eating disorders (ED) are characterized by alterations in eating behavior. The genetic factors shared between ED diagnoses have been underexplored. The present study aimed to perform a genome-wide association study on individuals with disordered eating behaviors in the Mexican population, blood methylation quantitative trait loci (blood-meQTL) analysis, and in silico function prediction by different algorithms. The analysis included a total of 1803 individuals. Genome-wide association study and blood-meQTL analysis were performed by logistic and linear regression. In silico functional variant prediction, phenome-wide, and transcriptome-wide association studies by different algorithms were analyzed. In the genome-wide association study, we identified 44 single-nucleotide polymorphisms (SNP) associated at a nominal value and 7 blood-meQTL at a genome-wide umbral. The SNPs were enriched in genome-wide associations of the metabolic and immunologic domains. In the in silico analysis, the SNP rs10419198 located on an enhancer mark could change the expression of PRR12 on blood, adipocytes, and brain areas that regulate food intake. The present study supports the previous associations of genetic variation in the metabolic domain with ED.
REVIEW | doi:10.20944/preprints202107.0045.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: genome wide association studies (GWAS); single nucleotide polymorphism (SNP); oestrogen; ESR1; HOXA10
Online: 2 July 2021 (09:59:27 CEST)
Endometriosis is a chronic neuro-inflammatory disorder the defining feature of which is the growth of tissue (lesions) that resembles the endometrium in sites outside the uterus. Estimates of prevalence typically quote rates of ~10% of women of reproductive age, equating to ~190 million women world-wide. Three subtypes of endometriosis are usually considered when discussing the aetiology of the disorder - superficial peritoneal, ovarian (endometrioma cysts), and deep (infiltrating). Genetic, hormonal and immunological factors have all been proposed as contributing to risk factors associated with the development of lesions. Twin studies report the heritable component of endometriosis as ~50%. Genome wide association studies (GWAS) have been conducted allowing unbiased scanning of the genome for single nucleotide polymorphisms (SNPs) in many thousands of individuals. These studies have identified SNPs that appear over-represented in patients with endometriosis, particularly those with more extensive disease (stage III/IV). Amongst the larger scale GWAS there has been replication of SNPs near genes involved in oestrogen and other signalling pathways including ESR1 (oestrogen receptor alpha), GREB1, HOXA10, WNT4 and MAPK kinase signalling. The results from patients with endometriosis have also provided an opportunity to make comparisons with GWAS conducted on other patient cohorts including those with reproductive traits (age at menarche) and disorders (fibroids, endometrial and ovarian cancer) and conditions that are reported by women with endometriosis (migraine, depression). These comparative studies have highlighted some shared genetically-controlled biological mechanisms, including hormone-regulated pathways which might explain the co-occurrence of endometriosis with these disorders. In summary, unbiased genetic analysis has provided new insights into the genetic factors that may contribute to increased risk of developing endometriosis. New studies are needed to broaden the range of patients contributing to these datasets and to improve integration with non-genomic and tissue expression data before their full potential for diagnosis and improvements in patient care can be fully realised.
ARTICLE | doi:10.20944/preprints202008.0268.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: Authentication; Password Authentication; Password Strength; Password Memorability; Association Password Technique; Computer Security
Online: 11 August 2020 (15:08:21 CEST)
The Study proposes possible solution to enhance Password Authentication using Association Technique based on the Ecological theory of memory and data at the Presbyterian university College Ghana. The study used a deductive research approach and employed two empirical Studies using the non-probability sampling technique where few respondents were selected in categories out of the populace by means of openness in other to get similar categories of respondents with different age groups and education background. The two Empirical study also used a quasi-experimental approach which structure incorporate observation, experimental treatment and timing. The First empirical study carried out an investigation to identify existing Password authentication Technique used by End Users, as well as their behavior in password utilization through a self-completed questionnaires which was analyzed using SPSS version 21 . The Second empirical study was an experiment to compared three kinds of password constructions that is own set, modified dictionary, and association against one another to see which of them would be best meet the ecological theory of memory and data which aims at creating a secured password that is easy to recall. The computation and evaluation of password construction was done using My1login Password meter whiles Levenshtein Distance String Edit Software was also used to compute the memorability of all given password. Across-tabulation was then employed out of the experiment using SPSS version 21. The result from the analysis revealed that the majority of the respondents do have weak passwords and also have few passwords which they even end up sharing with families and friends and reuse it. This confirms statements made by researchers that human being is the weakest connection in information system securities. To maintain Confidentiality, Availability and Integrity of data, the study therefore recommended the use of the Association Password technique which makes it easier to develop a much secured password that is difficult to crack but easy remember.
ARTICLE | doi:10.20944/preprints202002.0202.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Napier grass; elephant grass; EMBRAPA; forage yield; feed quality; marker trait association
Online: 15 February 2020 (15:01:37 CET)
The evaluation of forage crops for adaptability and performance across production systems and environments is one of the main strategies used to improve forage production. To enhance the genetic resource base and identify traits responsible for increased feed potential of Napier grass, forty-five genotypes from EMBRAPA, Brazil, were evaluated for forage biomass yield and feed nutritional quality in a replicated trial under wet and dry season conditions in Ethiopia. The results revealed significant variation in forage yield and feed nutritional qualities among the genotypes and between the wet and dry seasons. Feed fibre components were lower in the dry season while crude protein, in vitro organic matter digestibility and metabolizable energy were higher. Based on the cumulative biomass yield and metabolizable energy yield, top performing genotypes were identified that are candidates for future forage improvement studies. Furthermore, the marker-trait association study identified diagnostic SNP and SilicoDArT markers and potential candidate genes that could differentiate high biomass yielding and high metabolizable energy genotypes in the collection.
ARTICLE | doi:10.20944/preprints201907.0166.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: DArTseq; Groundnut; Linkage disequilibrium; Marker assisted selection; Marker trait association; Physiological traits
Online: 12 July 2019 (11:42:33 CEST)
In order to integrate genomics in breeding and development of drought tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used SNP markers for a genetic analysis of the ICRISAT groundnut minicore collection for genome wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD) present in the genetic resources. The LD analysis showed that about 36% of loci pairs were in significant LD (P < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. There was rapid decline in LD with distance and the LD was <0.2 at a distance of 41635 bp. The marker trait association (MTAs) studies revealed 20 significant MTAs (p <0.001) with 11 markers for leaf area index (4), canopy temperature (13), chlorophyll content (1) and NDVI (2). The markers explained 2 to 21% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. The duplications of effect observed could be due to common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes seen in the current study. The present study identified a total of 20 highly significant marker trait associations with 11 markers for four physiological traits of importance in groundnut; LAI, CT, SCMR and NDVI. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance. The identified markers in this study may be useful for marker assisted selection after further validation.
ARTICLE | doi:10.20944/preprints201806.0491.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: epidemiology, causality, association, smoking, lung cancer, vitamin D, sun exposure, multiple sclerosis
Online: 29 June 2018 (15:42:02 CEST)
If environmental exposures are shown to cause an adverse health outcome, reducing exposure should reduce the disease risk. Links between exposures and outcomes are typically based on ‘associations’ derived from observational studies, and causality may not be clear. Randomised controlled trials to ‘prove’ causality are often not feasible or ethical. Here the history of evidence that tobacco smoking causes lung cancer – in observational studies – is compared to that of low sun exposure and/or low vitamin D status as causal risk factors for the autoimmune disease, multiple sclerosis. Evidence derives from in vitro and animal studies, as well as ecological, case-control and cohort studies, in order of increasing strength. For smoking and lung cancer, the associations are strong, consistent, and biologically plausible – the evidence is coherent or ‘in harmony’. For low sun exposure/vitamin D as risk factors for MS, the evidence is weaker, with smaller effect sizes, but coherent across a range of sources of evidence, and biologically plausible. The association is less direct – smoking is directly toxic and carcinogenic to the lung, but sun exposure/vitamin D modulate the immune system, which in turn may reduce the risk of immune attack on self-proteins in the central nervous system. Opinion about whether there is sufficient evidence to conclude that low sun exposure/vitamin D increase the risk of multiple sclerosis, is divided. General public health advice to receive sufficient sun exposure to avoid vitamin D deficiency (<50nmol/L) should also ensure any benefits for multiple sclerosis.
ARTICLE | doi:10.20944/preprints202008.0210.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: Textual Entailment by Generality; Asymmetric Word Similarities; Asymmetric Association Measure; Informative Asymmetric Measure
Online: 8 August 2020 (17:45:18 CEST)
In this work we present a new unsupervised and language-independent methodology to detect relations of textual generality, for this, we introduce a particular case of textual entailment (TE), namely Textual Entailment by Generality (TEG). TE aims to capture primary semantic inference needs across applications in Natural Language Processing (NLP). Since 2005, in the TE recognition (RTE) task, systems are asked to automatically judge whether the meaning of a portion of the text, the Text - T, entails the meaning of another text, the Hypothesis - H. Several novel approaches and improvements in TE technologies demonstrated in RTE Challenges are signalling of renewed interest towards a more in-depth and better understanding of the core phenomena involved in TE. In line with this direction, in this work, we focus on a particular case of entailment, entailment by generality, to detect relations of textual generality. In-text, there are different kinds of entailment, yielded from different types of implicative reasoning (lexical, syntactical, common sense based), but here we focus just on TEG, which can be defined as an entailment from a specific statement towards a relatively more general one. Therefore, we have T→GH whenever the premise T entails the hypothesis H, being it also more general than the premise. We propose an unsupervised and language-independent method to recognize TEGs, from a pair 〈T,H〉 having an entailment relation. To this end, we introduce an Informative Asymmetric Measure (IAM) called Simplified Asymmetric InfoSimba (AISs), which we combine with different Asymmetric Association Measures (AAM). In this work, we hypothesize the existence of a particular mode of TE, namely TEG. Thus, the main contribution of our study is to highlight the importance of this inference mechanism. Consequently, the new annotation data seems to be a valuable resource for the community.
REVIEW | doi:10.20944/preprints202007.0516.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Megakaryocyte, IFITM3, VWF, ADAMTS13, emperipolesis, self-association, unfractionated heparin (UFH), histone, NETs, Thrombin
Online: 22 July 2020 (11:03:08 CEST)
COVID-19 thromboembolic disease has brought all of us back to the drawing board. In COVID-19, pre-existing activated endothelium with increased Von Willebrand factor (VWF), low density lipoprotein (LDL) promoting “self-association” and “sticking” of long VWF strings to the vascular endothelial wall, suppressed ADAMTS13 cleavage of VWF, hypoxia induced upregulation and activation of VWF, fibrous network from neutrophil extracellular traps (NETs) with free DNA and histone, all appear to be initiating the thrombogenesis. Worsening complement activation, cytokine storm and resulting endothelial destruction, unregulated thrombogenesis leads to vascular occlusions and hypoxia. At this stage, the presence of abundant extracellular DNA, histone and -defensins appears worse than the SARS-CoV-2 itself. Previously observed in vitro mechanisms like histone “auto-activating” prothrombin, histone activated platelets generating thrombin without FXII, thrombin and plasmin cleaving complement C5 appears highly likely in COVID-19. Megakaryocytes are actively producing platelets in the lungs and appear to play a major role in thrombogenesis of COVID-19 raising suspicion of emperipolesis. This focused review is a compilation of my observations in relation to the pathophysiology of the intravascular environment, mainly in COVID-19 lungs. Pathophysiology based clinical trials are paramount in reducing morbidity and mortality in COVID-19.
ARTICLE | doi:10.20944/preprints201810.0221.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: Smart Cities; Internet of things; Bicycle sharing systems; Machine learning; Association rule mining
Online: 10 October 2018 (14:24:32 CEST)
Bike sharing systems are a key element of a smart city as they have the potential for reducing pollutant emissions and traffic congestion thus substantially improving citizens’ quality of life. In these systems, bicycles are made available for shared use to individuals on a very short-term basis. They are rented in a station and returned in any other station with free docks. However, to achieve a satisfactory user experience, all the stations in the system must be neither overloaded nor empty. The occupancy level of the stations can be constantly monitored through IoT-based services. The goal of this work is to analyze occupancy level data acquired from real systems to discover situations of dock overload in multiple stations which could lead to service disruption. The proposed methodology relies on a pattern mining approach. A new pattern type, called Occupancy Monitoring Pattern (OMPs), is proposed to characterize situations of dock overload in multiple stations. Since stations are geo-referenced and their occupancy levels are periodically monitored, OMPs can be filtered and evaluated by considering also the spatial and temporal correlation of the acquired measurements. The results achieved on real Smart City data highlight the potential of these techniques in supporting domain experts in maintenance activities, such as periodic re-balancing of the occupancy levels of the stations, as well as in improving the user experience, such as suggesting alternative stations in the neighborhood.
ARTICLE | doi:10.20944/preprints201803.0107.v2
Subject: Environmental And Earth Sciences, Environmental Science Keywords: fire management; human activities; participation; firewood; charcoal; grazing; water; honey; farming; community forest association
Online: 12 June 2018 (11:20:43 CEST)
This paper proposes an Integrated Fire Management (IFM) framework that can be used to support communities and resource managers in finding effective and efficient approaches to prevent damaging fires, as well as maintain desirable fire regimes in Kenya. Designing and implementing an IFM approach in Kenya calls for a systematic understanding of the various uses of fire and the underlying perceptions and traditional ecological knowledge of the local people. The here proposed IFM framework allows an evaluation of the risks posed by fires, while balancing them with their beneficial ecological and economic effects, and thus developing effective fire management approaches. A case study of the proposed IFM framework was conducted in Gathiuru Forest that is part of the larger Mt. Kenya Forest Ecosystem. Focus group discussions were held with key resource persons, primary and secondary data on socio-economic activities were studied, fire and weather records were analyzed and the current fire management plans were consulted. Questionnaires were used to assess how the IFM is implemented in the Gathiuru Forest Station. The results show that the proposed IFM framework is scalable and can be applied in places with fire-dependent ecosystems as well as in places with fire-sensitive ecosystems in Kenya. The effectiveness is dependent on the active participation, formulation and implementation of the IFM activities by the main stakeholder groups (Kenya Forest Service (KFS), Kenya Wildlife Service (KWS), and the Community Forest Associations (CFA)). The proposed IFM framework helps in implementing cost-effective approaches to prevent damaging fires and maintain desirable fire regimes in Kenya.
ARTICLE | doi:10.20944/preprints201801.0136.v1
Subject: Chemistry And Materials Science, Nanotechnology Keywords: polymer-drug association; inclusion nano-complex; an amphiphilic polymer; polysoaps; antibiotic resistance; ampicillin trihydrate
Online: 16 January 2018 (07:56:15 CET)
Biocompatible polymeric materials with potential to form functional structures in association with different therapeutic molecules have a high potential for biological, medical and pharmaceutical applications. Therefore, the protective capability of the inclusion nano-Complex formed between the sodium salt of poly(maleic acid-alt-octadecene) and a β-lactam drug (ampicillin trihydrate) on the chemical, enzymatic and biological degradation was evaluated. PAM-18Na was produced and characterized as reported previously. The formation of polymeric hydrophobic aggregates in aqueous solution was determined, using pyrene as a fluorescent probe. Furthermore, the formation of polymer-drug nano-complexes was characterized by Differential Scanning Calorimetry-DSC, viscometric, ultrafiltration/centrifugation assays, zeta potential and size measurements by dynamic light scattering-DLS. The PAM-18Na capacity to avoid the chemical degradation was studied through stress stability tests. The enzymatic degradation was evaluated from a pure β-lactamase, while the biological degradation was determined by different β-lactamase producing Staphylococcus aureus strains. When ampicillin was associated with PAM-18Na, the half-life time in acidic conditions increased, whereas both the enzymatic degradation and the minimum inhibitory concentration decreased to a 90 and 75%, respectively. These results suggest a promissory capability of this polymer to protect the β-lactam drugs against chemical, enzymatic and biological degradation.
REVIEW | doi:10.20944/preprints202111.0253.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: Cell therapy; chronic limb-threating ischemia; peripheral artery disease; diabetes; atherosclerosis obliterans; thromboangiitis obliterans; personalized medicine; artificial intelligence; machine learning; genome-wide association studies; transcriptome-wide association studies; clonal hematopoiesis of indeterminate potential.
Online: 15 November 2021 (11:18:43 CET)
Stem/progenitor cell transplantation is a potential novel therapeutic strategy to induce angiogenesis in ischemic tissue, which can prevent major amputation in patients with advanced peripheral artery disease (PAD). Thus, clinicians can use cell therapies worldwide to treat PAD. However, some cell therapy studies did not report beneficial outcomes. Clinical researchers suggested that classical risk factors and comorbidities may adversely affect the efficacy of cell therapy. Some studies have indicated that the response to stem cell therapy varies among patients even in those harboring limited risk factors. This suggested the role of undetermined risk factors, including genetic alterations, somatic mutations, and clonal hematopoiesis. Personalized stem cell-based therapy can be developed by analyzing individual risk factors. These approaches must consider several clinical biomarkers and perform studies (such as genome-wide association studies (GWAS)) on disease-related genetic traits and integrate the findings with those of transcriptome-wide association studies (TWAS) and whole-genome sequencing in PAD. Additional unbiased analyses with state-of-the-art computational methods, such as machine learning-based patient stratification, are suited for predictions in clinical investigations. The integration of these complex approaches into a unified analysis procedure for the identification of responders and non-responders before stem cell therapy, which can decrease treatment expenditure, is a major challenge to increase the efficacy of therapies.
ARTICLE | doi:10.20944/preprints202308.0881.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: blood type; COVID-19; coronavirus; immunology; association; severity; infection A; O; B; AB; Rh factor
Online: 11 August 2023 (12:58:06 CEST)
Introduction: The objectives of this study were to (1) investigate the association between human blood type and COVID-19 infection in both inpatient and longitudinal populations at our institution in South Florida and (2) identify the association between blood type and severity of COVID-19 infection via presence of cellular biomarkers of severe infection in hospitalized individuals. Methods: This study consists of (1) a single-center retrospective analysis of 669 of 2,741 COVID-19 positive screened patients seen from January 1, 2020 until March 31, 2021 at the University of Miami Emergency Department (ED) who tested positive for COVID-19 infection and had a documented ABO blood type and (2) a longitudinal SARS-CoV-2 immunity study (“CITY”) at the University of Miami Miller School of Medicine consisting of 185 survey participants. COVID-19 outcome rates and 95% confidence intervals were calculated for each ABO blood type and Rh group using Chi-squared tests for categorical and ANOVA for continuous variables in the inpatient cohort and Chi-squared tests for the longitudinal cohort, all executed in R studio. Results: Our inpatient cohort had a mean age of 53.6 (± 17.9) years with 48% males and 52% females. When compared to patients with other blood types, those with O- demonstrated less risk of developing COVID-19 pneumonia (26.7% for O- vs. 69.2% for type A-, 56.5% for A+, 71.4% for AB+, 53.7% for B+, 51.5% for O+, p-value= 0.003 via Chi-squared test) and decreased mortality due to COVID-19 infection (17.0% mortality for O vs. 26.3% for A, 29.2% for B, p-value= 0.012 via Chi-squared test). Blood type O- demonstrated less elevated levels of LDH than did other blood types (p-value= 0.001, ANOVA) and a higher frequency of clinically accepted baseline levels of troponin (0.04 ng/mL) (p-value= 0.026, ANOVA) (Figure 1). Most of the longitudinal cohort was ABO blood grouping type O (47% (87/185)), with 33.5% type A, 14.1% B, and 5.4% AB. Most individuals were Rh positive (85.9%). There was no significant association found between COVID status (infection vs. non-infection) and ABO (Chi-squared test (3, N = 185) = 1.8, p = 0.6) or Rh (Chi-squared test (1, N = 185) = 0.16, p = 0.7) blood typing. Nearly all participants had been vaccinated (95.1% (176/185)), with a majority reporting primary vaccination with Pfizer (57.8% (107/185)), followed by Moderna (33% (61/185)), and Johnson & Johnson (4.3% (8/185)). 8 participants (4.3%) were unvaccinated. Conclusions: In an inpatient setting, blood type O sustained less risk of COVID-19 mortality and O- demonstrated less risk of developing COVID-19 pneumonia. In a longitudinal setting, there was no association found between blood type and COVID-19 severity. As the novelty of COVID-19 infection declines with time, further studies on risk-stratification by blood type are encouraged.
ARTICLE | doi:10.20944/preprints202306.0651.v1
Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: Exome-wide association stud; Vitamin D deficiency; genetic determinants; polygenic risk score; Middle Eastern population.
Online: 8 June 2023 (14:18:18 CEST)
Middle East region experiences a high prevalence of hypovitaminosis D, yet most genetic studies on Vitamin D have focused on European populations. Furthermore, there is a lack of research on the genomic risk factors affecting the elderly population, who are more susceptible to health burden. We investigated the genetic determinants of 25-hydroxyvitamin D levels in elderly Lebanese individuals (n=199) through a whole exome-based genome-wide association study. We identified new loci with suggestive evidence of an association with Vitamin D levels, including rs141064014 in the MGAM gene (P-value of 4.40 × 10−06) and rs7036592 in PHF2 (P-value of 8.43 × 10−06). A meta-analysis of the Lebanese data and the largest European genome-wide association study confirmed consistence replication of numerous variants, including rs2725405 in SLC38A10 (P-value of 3.73 x 10-08). Despite the lower performance of European-derived polygenic risk scores compared to the European estimations, it still effectively predicted Vitamin D deficiency among elderly Lebanese individuals. Our findings provide novel insights into the genetic mechanisms of Vitamin D deficiency in Middle Eastern elderly populations, facilitating the development of personalized approaches for more effective management of hypovitaminosis D. Additionally, we demonstrated that whole exome-based genome-wide association study is an effective method for identifying genetic components associated with phenotypes.
CASE REPORT | doi:10.20944/preprints202206.0400.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Ganga; environmental flows; river conservation; Ramganga; Karula; irrigation water use efficiency; Water Users Association; minor canal
Online: 29 June 2022 (08:52:50 CEST)
The pressure on freshwater resources is leading to diminishing flows in some of the critical river systems across the globe and India is no exception and this is mainly because of water withdrawal for irrigation, which is often to the tune of 70% to 80% with some proportion for domestic and industrial use. While graduating from the concept of environmental flows and its assessment methodologies in India, the water-managers, the researchers and the conservationists are now moving towards answering the next question if the rivers are to be revived, then where will the water come from, especially in the case of over-allocated rivers, including the river Ganga. While the logical way is to look at the biggest user of water, i.e. irrigation, it remains to be seen whether the irrigation water savings will actually lead to enhancing flows in a river, complementing the efforts towards maintaining e-flows in rivers, or whether it will lead to more area under agriculture, bring changes in cropping patterns towards more water-intensive crops or result in something else. This is a growing debate across the globe, where India is no exception, and there has been a wide range of opinions in this regard. This paper discusses the process, findings and lessons from a joint initiative involving farmers, the Uttar Pradesh state Irrigation and Water Resources Department, Bijnor District Administration and a conservation organisation to enhance flows in a rivulet, called karula River, which is part of the Ganga river system.
REVIEW | doi:10.20944/preprints202307.0845.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: funding; ex situ; education; EAZA; European Association of Zoos and Aquaria; EUAC; European Union of Aquarium Curators
Online: 13 July 2023 (05:10:30 CEST)
The European Union of Aquarium Curators (EUAC) includes 150 members and is an important association for the European public aquarium community. Since 2004, over one quarter of a million euros were awarded by the EUAC Conservation Fund to approximately 50 projects, which spanned across the globe. While projects varied greatly in content and scope, several achieved a significant impact in local populations and/or their focus species. This paper reports on results achieved by these conservation efforts and what improvements can be made, to ensure that the funding is indeed invested in conservation efforts per se. Perhaps the most valid conclusion to be drawn from the list of projects covered in this work is the fact that, regardless of the outcome, as far as preservation of the species are concerned, local communities were actively engaged in a subject that would, otherwise, remain unknown to them. Additionally, these EUAC funded projects highlight how public aquarium activities reach far beyond the acrylic panels surrounding the tanks and indeed the walls of the institution, as they spread around the world and raise awareness within local communities to preserve biodiversity. These results further suggest that a future direction for EUAC, as well as the public aquaria it consists of, could – indeed should - include more strenuous lobbying with legislating bodies, to ensure more adequate – and stronger – in situ conservation measures. In conclusion, with so many doubts being raised by different movements about the existence of aquaria and zoos, it is important that the public is aware that it is their visit to see the ambassadors of different species of animals that supports the funding of many of these pilot projects that aim to preserve species in their natural environment.
ARTICLE | doi:10.20944/preprints202306.1361.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: n/a; epimutation score; breast cancer; EWAS; stochastic epimutation; methylation; epigenetic association study; epimutation; NOTCH; SUMO; ESR
Online: 19 June 2023 (13:09:54 CEST)
Oestrogen receptor expression in breast cancer (BC) cells is a marker of high cellular differentiation and allows the identification of two BC groups (ER-positive and ER-negative) that, although not completely homogeneous, differ in biological characteristics, clinical behaviour and therapeutic options. The study, based on three publicly available EWAS datasets, focuses on the comparison between these two groups of breast cancer using an epimutation score. The score is calculated not only based on the presence of the epimutation but also on the deviation amplitude of the methylation outlier value. For each dataset, we performed a functional analysis based first on the functional gene region of each annotated gene (we aggregated the data per gene region TSS1500, TSS200, first-exon, body-gene identified by the information from the Illumina Data Sheet) and then we performed a pathway enrichment analysis through the REACTOME database based on the genes with the highest epimutation score. Thus, we blended our results and found common pathways for all three data sets. We found that a higher and significant epimutation score due to hypermethylation in ER-positive BC is present in the promoter region of the genes belonging to the SUMOylation pathway, the NOTCH pathway, the IFN-$\gamma$ signalling pathway and the deubiquitination protease pathway; while a higher and significant level of epimutation due to hypomethylation in ER-positive BC is present in the promoter region of the genes belonging to the ESR-mediated pathway. The presence of this state of promoter hypomethylation in the ESR-mediated signalling genes is consistent and coherent with an active signalling pathway mediated by oestrogen function in the group of ER-positive BC. SUMOylation and NOTCH pathways are associated with BC pathogenesis and have been found to play distinct roles in the two BC subgroups. We speculated that the altered methylation profile may play a role in regulating signalling pathways with specific functions in the two subgroups of ER-BC.
ARTICLE | doi:10.20944/preprints202112.0305.v1
Subject: Biology And Life Sciences, Horticulture Keywords: replant disease; Malus; free-living nematodes; bacteria; fungi; rhizosphere; nematode-microbe association; disease complex; metabarcoding; nematode community
Online: 20 December 2021 (10:34:03 CET)
Apple replant disease is a severe problem in orchards and tree nurseries. Evidence for the involvement of a nematode-microbe disease complex was reported. To search for this complex, plots with a history of apple replanting, and control plots cultivated for the first time with apple were sampled in two fields in two years. Shoot weight drastically decreased with each replanting. Nematodes were extracted from soil samples by floatation-centrifugation, washed on a 20 µm-sieve, and used for DNA extraction. Nematode communities and co-extracted fungi and bacteria were analyzed by high-throughput sequencing of amplified ribosomal fragments. The nematode community and co-extracted fungal and bacterial communities significantly differed between replanted and control plots. Free-living nematodes of the genera Aphelenchus, Cephalenchus, and an unidentified Dorylaimida were associated with replanted plots, as indicated by linear discriminant analysis effect size. Among the co-extracted fungi and bacteria, Mortierella was most indicative of replanting. Some genera, mostly Rhabditis, indicated healthy control plots. Isolating and investigating the putative disease complexes will help to understand and alleviate stress-induced root damage of apple in replanted soil.
ARTICLE | doi:10.20944/preprints202212.0065.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: pulmonary tuberculosis; lymph node tuberculosis; extra-pulmonary tuberculosis; single nucleotide polymorphisms; cytokine; innate immunity; genetic association; genotype; serum
Online: 5 December 2022 (08:00:15 CET)
Background: Tuberculosis (TB) manifests itself primarily in the lungs as pulmonary disease (PTB) and sometimes disseminates to other organs to cause extra-pulmonary TB, such as lymph node TB (LNTB). This study aimed to investigate the role of host genetic polymorphism in immunity related genes to find a genetic basis for such differences. Methods: Sixty-three, Single nucleotide polymorphisms (SNPs) in twenty-three, TB-immunity related genes including eleven innate immunity (SLCA11, VDR, TLR2, TLR4, TLR8, IRGM, P2RX7, LTA4H, SP110, DCSIGN and NOS2A) and twelve cytokine (TNFA, IFNG, IL2, Il12, IL18, IL1B, IL10, IL6, IL4, IL1RA, IL8 and TNFB) genes were investigated to find genetic associations in both PTB and LNTB as compared to healthy community controls. The serum cytokine levels were correlated for association with the genotypes. Results: PTB and LNTB showed differential genetic associations. The genetic variants in the cytokine genes (IFNG, IL12, IL4, TNFB and IL1RA and TLR2,4 associated with PTB susceptibility and cytokine levels but not LNTB (p < 0.05). Similarly, genetic variants in LTA4H, P2RX7, DCSIGN and SP110 showed susceptibility to LNTB and not PTB. Pathway analysis showed abundance of cytokine related variants for PTB and apoptosis related variants for LNTB. Conclusions: PTB and LNTB outcomes of TB infection have a genetic component and should be considered for any future susceptibility and functional studies.
ARTICLE | doi:10.20944/preprints202205.0277.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: immunoglobulin A nephropathy; expression quantitative trait loci; summary data-based Mendelian randomization; genome-wide association study; functional mapping
Online: 20 May 2022 (12:13:06 CEST)
Background: Immunoglobulin A nephropathy (IgAN) is a complex autoimmune disease, and the exact pathogenesis remains to be elucidated. Methods: We conducted summary data-based Mendelian randomization (SMR) analysis and performed functional mapping and annotation using FUMA to explore genetic loci that are po-tentially involved in the pathogenies of IgAN. Both analyses used summarized data of a recent genome-wide association study (GWAS) on IgANs, which included 477,784 Europeans (15,587 cases and 462,197 controls) and 175,359 East Asians (71 cases and 175,288 controls). We performed separate SMR analysis using CAGE and GTEx eQTL data. Results: Using the CAGE eQTL data, our SMR analysis identified 32 probes tagging 25 unique genes that were pleiotropically/potentially causally associated with IgAN, with the top three probes being ILMN_2150787 (tagging HLA-C, PSMR=2.10×10-18), ILMN_1682717 (tagging IER3, PSMR=1.07×10-16) and ILMN_1661439 (tagging FLOT1, PSMR=1.16×10-14). Using GTEx eQTL data, our SMR analysis identified 24 probes tagging 24 unique genes, with the top three probes being ENSG00000271581.1 (tagging XXbac-BPG248L24.12, PSMR=1.44×10-10), ENSG00000186470.9 (tagging BTN3A2, PSMR=2.28×10-10), and ENSG00000224389.4 (tagging C4B, PSMR=1.23×10-9). FUMA analysis identified 3 independent, significant and lead SNPs, 2 genomic risk loci and 39 genes. Conclusion: We identified many genetic variants/loci that are potentially involved in the patho-genesis of IgAN.
ARTICLE | doi:10.20944/preprints202306.0510.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: Metaverse; Key Characteristics; Theoretical Framework; Digitalization of Assets; Governance by Law; Combination of Virtual and Real; Rule of Technological Association
Online: 7 June 2023 (08:17:38 CEST)
This study delves into the essential characteristics of the Metaverse and its impact on the real world. The Metaverse, a parallel universe composed of countless 3D virtual worlds, has become a hot topic in technology. With the development of advanced technologies such as Virtual Reality (VR), Augmented Reality (AR), blockchain, and Artificial Intelligence, the Metaverse is gradually changing people's lifestyles and work methods, expanding the boundaries of the digital economy. This study profoundly investigates the attributes of the Metaverse, such as asset digitization, application scenario-based, scope economy, industry universality, integrated innovation, and the platform ecosystem. Additionally, we propose a theoretical framework to aid in understanding and shaping this emerging field. We conducted a thorough study and analysis of a specific case, explored the key features of the Metaverse, unveiled the profound impact of Metaverse characteristics on social and economic development, and verified our theoretical framework with this case. This research provides new perspectives and methods for academic studies and offers robust support and guidance for practical applications and decision-making.
ARTICLE | doi:10.20944/preprints202003.0127.v1
Subject: Biology And Life Sciences, Insect Science Keywords: plant-insect interaction; host shift; parallel evolution; detoxification; experimental evolution; population genomics; genome-wide association mapping; gene expression; Callosobruchus maculatus
Online: 8 March 2020 (01:52:10 CET)
Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve and resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap, and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic data sets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution, and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.
REVIEW | doi:10.20944/preprints201812.0267.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Alzheimer’s disease; CTH gene; DNA methylation; epigenetics; epigenome-wide association study; methylome; MTHFR gene; nutrition; S-adenosylmethionine; vitamin B complex
Online: 24 December 2018 (04:48:53 CET)
DNA methylation and other epigenetic factors are important in the pathogenesis of late-onset Alzheimer’s disease (LOAD). Methylenetetrahydrofolate reductase (MTHFR) gene mutations occur in most elderly patients with memory loss. MTHFR is critical for production of S-adenosyl-L-methionine (SAM), the principal methyl donor. A common mutation (1364T/T) of the cystathionine-γ-lyase (CTH) gene affects the enzyme that converts cystathionine to cysteine in the trans-sulfuration pathway causing plasma elevation of total homocysteine (tHcy) or hyperhomocysteinemia – a strong and independent risk factor for cognitive loss and AD. Other causes of hyperhomocysteinemia include aging, nutritional factors, and deficiencies of B vitamins. We emphasize the importance of supplementing vitamin B12 (methylcobalamin), vitamin B9 (folic acid), vitamin B6 (pyridoxine), and SAM to patients in early stages of LOAD.
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Analysis of variance; Variance-decomposition; The Bayesian brain; High-dimensional data; Association; Explanation; Prediction; Causation; The neural law of large numbers
Online: 23 September 2021 (11:13:08 CEST)
We discuss what we believe could be an improvement in future discussions of the ever-changing brain. We do so by distinguishing different types of brain variability and outlining methods suitable to analyse them. We argue that, when studying brain and behaviour data, classical methods such as regression analysis and more advanced approaches both aim to decompose the total variance into sensible variance components. In parallel, we argue that a distinction needs to be made between innate and acquired brain variability. For varying high-dimensional brain data, we present methods useful to extract their low-dimensional representations. Finally, to trace potential causes and predict plausible consequences of brain variability, we discuss how to combine statistical principles and neurobiological insights to make associative, explanatory, predictive, and causal enquires; but cautions are needed to raise association- or prediction-based neurobiological findings to causal claims.
REVIEW | doi:10.20944/preprints202309.2070.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: Vaping; E cigarette; lung injury; lung disorder; association; relationship; adults; long term impact; vaping risk -benefit analysis; attitudes; mental health; side effect; EVALI
Online: 30 September 2023 (10:23:06 CEST)
The electronic cigarette or e-cigarette is the new alternative method to deliver nicotine. In 2007, the United States introduced vaping devices on the market. Due to their attractive taste and lack of adverse effects, these vaping devices have gained popularity among youth and adults. However, there has been increasing evidence that vaping can cause severe lung injury, and these devices release toxic chemicals into the body. E-cigarettes are recognized as a global threat to public health. Nicotine, the most prevalent chemical in vaping devices, is associated with neurological problems and cognitive decline. Long-term use of e-cigarettes can cause adverse health problems, including respiratory illnesses, asthma, bronchitis, and lung inflammation. In 2019, the Centers for Disease Control and Prevention (CDC) officially declared vaping-associated illness EVALI (e-cigarette or Vaping Product Associated Lung Injury). The US Surgeon General published an alarm in December 2016 that e-cigarette consumption among adolescents and teens in the US is a "major public health concern" and that more young people are now vaping than smoking traditional cigarettes and cigars. Since its commercial introduction in 2003, modern electronic cigarettes (or E-cigarette s) have become increasingly popular with smokers, non-smokers, and those who used to smoke who have switched to them. With such a rise in consumption, people are becoming more aware of the irritating, harmful, and perhaps cancer-causing effects on the lungs. (Chadi et al., 2019; Dinardo & Rome, 2019; Lyzwinski et al., 2022; Marrocco et al., 2022; O’Callaghan et al., 2022)
ARTICLE | doi:10.20944/preprints202104.0791.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: COVID-19 Vaccines; Cross-Sectional Studies; Decision Making; Dental Education; Dental Students; International Association of Dental Students; Mass Vaccination; Multicenter Study; Social Determinants of Health
Online: 30 April 2021 (15:26:07 CEST)
Background: Acceleration of mass vaccination strategies is the only pathway to overcome the COVID-19 pandemic. Healthcare professionals and students have a key role in shaping public opinion about vaccines. This study aimed to evaluate the attitudes of dental students globally towards COVID-19 vaccines and explore the potential drivers for students' acceptance levels; Methods: A global cross-sectional study was carried out in February 2021 using an online ques-tionnaire. The study was liaised by the scientific committee of the International Association of Dental Students (IADS), and data was collected through the national and local coordinators of IADS member organizations. The dependent variable was the willingness to take the COVID-19 vaccine, and the independent variables included demographic characteristics, COVID-19-related experi-ence, and the drivers of COVID-19 vaccine-related attitude suggested by the WHO-SAGE; Results: A total of 6639 students from 22 countries representing all world regions responded to the ques-tionnaire properly. Their mean age was 22.06 ± 2.79 (17-40) years, and the majority were females (70.5%), in clinical years (66.8%), and from upper-middle-income economies (45.7%). In general, 22.5% of dental students worldwide were hesitant, and 13.9% rejected COVID-19 vaccines. The students in low- and lower-middle-income (LLMI) economies had significantly higher levels of vaccine hesitancy compared to their peers in upper-middle- and high-income (UMHI) economies (30.4% vs 19.8%; p < 0.001); Conclusions: The global acceptance level of dental students for COVID-19 vaccines was suboptimal, and their worrisome level of vaccine hesitancy was influenced by the socioeconomic context where the dental students live and study. The media and social media, public figures, insufficient knowledge about vaccines, and mistrust of governments and the pharmaceutical industry were barriers to vaccination. The findings of this study call for further implementation of epidemiology (infectious diseases) education within undergraduate dental curricula.
ARTICLE | doi:10.20944/preprints202109.0021.v1
Subject: Computer Science And Mathematics, Probability And Statistics Keywords: Effect size; correlation coefficient; association measure; covariance; mean square contingency coefficient; mean square effect half-size; Pearson’s Phi; 2 × 2 table; binary crosstab; gross crosstab; contingency table
Online: 1 September 2021 (14:28:47 CEST)
Evidence-based medicine (EBM) is in crisis, in part due to bad methods, which are understood as misuse of statistics that is considered correct in itself. This article exposes two related common misconceptions in statistics, the effect size (ES) based on correlation (CBES) and a misconception of contingency tables (MCT). CBES is a fallacy based on misunderstanding of correlation and ES and confusion with 2 × 2 tables, which makes no distinction between gross crosstabs (GCTs) and contingency tables (CTs). This leads to misapplication of Pearson’s Phi, designed for CTs, to GCTs and confusion of the resulting gross Pearson Phi, or mean-square effect half-size, with the implied Pearson mean square contingency coefficient. Generalizing this binary fallacy to continuous data and the correlation in general (Pearson’s r) resulted in flawed equations directly expressing ES in terms of the correlation coefficient, which is impossible without including covariance, so these equations and the whole CBES concept are fundamentally wrong. MCT is a series of related misconceptions due to confusion with 2 × 2 tables and misapplication of related statistics. The misconceptions are threatening because most of the findings from contingency tables, including CBES-based meta-analyses, can be misleading. Problems arising from these fallacies are discussed and the necessary changes to the corpus of statistics are proposed resolving the problem of correlation and ES in paired binary data. Since exposing these fallacies casts doubt on the reliability of the statistical foundations of EBM in general, we urgently need to revise them.
ARTICLE | doi:10.20944/preprints201807.0397.v2
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: flax; genome-wide association study (GWAS); selective sweep; genotyping by sequencing (GBS); bi-parental population; single nucleotide polymorphism (SNP); seed yield; plant height; maturity; fatty acid composition
Online: 3 August 2018 (15:34:24 CEST)
A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 QTL for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48-73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8-14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.