Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic utility of telomere length measurement in a hospital setting

Very short telomere length (TL) provokes cellular senescence in vitro, but the clinical utility of TL measurement in a hospital-based setting has not been determined. We tested the diagnostic and prognostic value of TL measurement by flow cytometry and fluorescence in situ hybridization (flowFISH) in individuals with mutations in telomerase and telomere maintenance genes, and examined prospectively whether TL altered treatment decisions for patients with bone marrow failure. TL had a definable normal range across populations with discrete lower and upper boundaries. TL above the 50th age-adjusted percentile had a 100% negative predictive value for clinically relevant mutations in telomere maintenance genes, but the lower threshold for diagnosis was age-dependent. The extent of deviation from the age-adjusted median correlated with the age at diagnosis of a telomere syndrome as well as the predominant complication. Mild short telomere defects manifested in adults as pulmonary fibrosis-emphysema, while severely short TL manifested in children as bone marrow failure and immunodeficiency. Among 38 newly diagnosed patients with bone marrow failure, TL shorter than the 1st age-adjusted percentile enriched for patients with germline mutations in inherited bone marrow failure genes, such as RUNX1, in addition to telomere maintenance genes. The TL result modified the hematopoietic stem cell donor choice and/or treatment regimen in one-fourth of the cases (9 of 38,24%). TL testing by flowFISH has diagnostic and predictive value in definable clinical settings. In patients with bone marrow failure, it altered treatment decisions for a significant subset.
Biomass yield, nutritional status and industrial quality of sugarcane as a function of nitrogen and potassium fertilization

Sugarcane plant uptakes a large amount of nutrients from the soil. Thus, crop yield may decrease due to the reduced availability of nutrients in the soil. The aim of this study was to evaluate plant nutritional status, yield and juice quality of variety RB867515 in the first regrowth cycle, fertilized with doses of nitrogen and potassium. Therefore, a study was set up in a randomized complete block design (RCBD) with four replicates. The following treatments were applied to the first regrowth sugarcane: (T1) control: no nitrogen (N) and potassium (K) fertilization; (T2) N and K fertilization, replenishing 75% of the N and K removed by cane-plant harvest; (T3) N and K fertilization, replenishing 100% of the N and K removed by the cane-plant harvest; (T4) N and K fertilization, replenishing 125% of the N and K removed by the cane-plant harvest. The increase in the fertilizer dose promoted a linear effect in leaf N content and biomass of N and K concentration, but did not influence the quality of the juice, which had average concentrations of 22.23; 19.63; 88.30 and 16.50 (Brix, Pol, Purity and PC, respectively). TRS was also not influenced by fertilization, with an average value of 162.82 kg t-1. Biomass yield increased linearly with fertilization, yielding the regression equation of Y = 82.74 + 0.3394 x, with R2 of 0.9824. The values obtained indicated excellent quality sugarcane.
Predation threat modifies relationships between metabolism and behavioural traits but not their ecological relevance in Chinese bream

Abstract The aims of this study were to test whether the metabolism, behavioural traits, growth and survival under predation of a fish species phenotypically changed under predation threat with the particular emphasis on whether short-time predator exposure would amplify the relationships between metabolic rate and behavioural traits and their fitness consequences (growth and survival). We found that Chinese bream under predation threat for 20 days exhibited a lower specific growth rate (SGR), feeding rate (FR) and feeding efficiency (FE) but a higher standard metabolic rate (SMR) and survival when encountering predators compared to the bream in the no-predator group. Both activity and boldness showed no correlation to SMR in the no-predator group, while it was vice versa in the predator group according to Pearson correlation. It thus demonstrated that short-time predator exposure can mediate the relationships between metabolism and behavioural traits, suggesting that predation may play an important evolutionary role in modifying intraspecific behavioural differences via metabolism. However, no significant effect of predator treatment acted on relationships between behaviour traits and SMR according to ANCOVA, which possibly due to the small sample size of this study. Additionally, the SMR of both groups was positively correlated with survival under predation, whereas the relationships between SMR and fitness cost such as growth and survival are rather complicated and need further investigation.
From traits to life‐history strategies: Deconstructing fish community composition across European seas

The life history of a species is determined by trade-offs between growth, survival and reproduction to 33 maximize fitness in a given environment. Following a theoretical model, we investigate whether the 34 composition of marine fish communities can be understood in terms of a set of life history strategies and 35 whether the prevalence of the strategies follows specific spatial patterns that can be related to the 36 environment. An extensive set of scientific bottom trawl surveys were collected to obtain the species composition of fish 41 communities across European Seas. We complemented this data with species-specific information 42 regarding six life history traits, reflecting reproductive, growth and feeding modes. We then calculated the 43 optimal number of strategies needed to summarize the information contained in the traits by using an 44 archetypal analysis. The proportion of each obtained strategy in the communities and their spatial patterns 45 were explained as a function of the environment and their temporal changes were investigated.
A Review on the Medicinal Significance of Common Fruits

Since antiquity, fruits have been served as an important source for human nutrition. Recent development of biological sciences helped to understand the nutritional and medicinal roles of fruits on human life. All the studies are pointing that fruits possess some natural chemicals called secondary metabolites that are biologically active and help to prevent various diseases. In this review paper, medicinal significance of some common fruits such as apple, banana, berries, cherry, citrus, custard apple, gooseberry, grape, mangosteen and pomegranate were discussed. This review suggests that these fruits are excellent source for maintaining human health by providing essential nutrients and preventing diseases.
An application in bioinformatics : a comparison of affymetrix and compugen human genome microarrays

AN APPLICATION IN BIOINFORMATICS: A COMPARISON OF AFFYMETRIX AND COMPUGEN HUMAN GENOME MICROARRAYS The human genome microarrays from Compugen® and Affymetrix® were compared in the context of the emerging field of computational biology. The two premier database servers for genomic sequence data, the National Center for Biotechnology Information and the European Bioinformatics Institute, were described in detail. The various databases and data mining tools available through these data servers were also discussed. Microarrays were examined from a historical perspective and their main current applications—expression analysis, mutation analysis, and comparative genomic hybridization—were discussed. The two main types of microarrays, cDNA spotted microarrays and high-density spotted microarrays were analyzed by exploring the human genome microarray from Compugen ® and the HG-U133 Set from Affymetrix® respectively. Array design issues, sequence collection and analysis, and probe selection processes for the two representative types of arrays were described. The respective chip design of the two types of microarrays was also analyzed. It was found that the human genome microarray from Compugen ® contains probes that interrogate 1,119,840 bases corresponding to 18,664 genes, while the HG-U133 Set from Affymetrix ® contains probes that interrogate only 825,000 bases corresponding to 33,000 genes. Based on this, the efficiency of the 25-mer probes of the HG-U133 Set from Affymetrix ® compared to the 60-mer probes of the microarray from Compugen ® was questioned. AN APPLICATION IN BIOINFORMATICS: A COMPARISON OF AFFYMETRIX AND COMPUGEN HUMAN GENOME MICROARRAYS
Deciphering the Role of Alternative nonhomologous End Joining (Alt NHEJ) DNA Repair in Breast Cancer

Mammalian polymerase theta (Polθ; encoded by POLQ) is a unique multifunctional enzyme that promotes error-prone DNA repair by alternative-NHEJ (alt-NHEJ). Here we perform structurefunction analyses and report that, in addition to the polymerase domain, the helicase activity plays a central role during Polθ-mediated double-stranded break (DSB) repair. Our results show that Polθ-helicase promotes chromosomal translocations by alt-NHEJ in mouse embryonic stem cells. In addition, the helicase activity suppresses CRISPR/Cas9 mediated gene targeting by homologous recombination (HR). In vitro experiments reveal that Polθ–helicase displaces RPA to facilitate the annealing of complementary DNA during alt-NHEJ. Consistent with an antagonistic role for RPA during alt-NHEJ, we show that the inhibition of RPA1 subunit enhances end-joining and suppresses recombination at telomeres. Taken together, our results reveal that the balance between HR and alt-NHEJ is regulated by opposing activities of Polθ and RPA, providing critical insight into the mechanism that control DSB repair pathway choice in mammalian cells. Mateos-Gomez et al., 3
Phosphate Role in the Rhizobium-Legume Symbiosis- A Review

The international emphasis on maintaining farming systems productivity and sustainability is focusing on the use of renewable plant nutrients resources. In case of nitrogen (N), biological N 2 fixation via symbiosis is the most important input for agricultural systems sustainability. Research studying the association between rhizobia and the host legume plants has enhanced our knowledge and understanding of this symbiosis process. Our current knowledge establishes that any interruption in the flow of nutrients between symbionts affects this association. Since phosphorus (P) is one of the essential nutrients in Rhizobium -legume symbiosis, and its limitation affects every aspect of the symbiosis, it is important to understand its function in the symbiosis process. This review will emphasis on the role of P in nodulation and in the functional symbiosis between rhizobia and legumes.
Heat stress impact and genetic diversity among some bread wheat genotypes

Wheat is the most widely grown crop in the world especially in the developing countries. Recently, the climatological extremes including high temperatures is predicted to have a general negative effect on wheat production due to the damaging effect on plant development especially during anthesis stage. Heat tolerance is a complex trait and influenced by different components. A panel of 40 wheat genotypes were evaluated for 8 yield and yield-contributing traits under recommended sowing date of the Egyptian ministry of agriculture as a control and two other different sowing dates as plants will face heat-stressed conditions at anthesis and grain-filling phases. All measured phenotypic traits exhibited highly significant differences both among evaluated accessions and sowing dates in both growing seasons. A continuous phenotypic variation in all measured traits were found, indicating a polygenic inheritance of measured traits. The ANOVA revealed highly significant genotype × environment interaction which is expected for quantitative traits. Cluster analysis revealed two distinct groups with respect to stress tolerance index with substantial diversity among genotypes either susceptible or tolerant to heat stress. Cophenetic correlation between ultrametric similarities of tree and similarity matrix was found to be relatively high (r = 0.76, P < 0.01), suggesting that the cluster analysis strongly represents the similarity matrix.
Investigating the pharmacology, dimerisation and receptor-dependent toxicology of metabotropic glutamate receptor 5

G protein-coupled receptors represent the largest family of druggable targets in the human genome, with over half of drugs currently on the market acting at these receptors. Metabotropic glutamate receptor 5 is one such receptor, thought to be involved in several neurological diseases such as schizophrenia, anxiety, and depression as well as many neurodegenerative disorders. Allosteric modulators, ligands which act at a site topographically different from that of the endogenous ligand, have shown promise in overcoming many of the problems associated with previous drug development efforts targeting this receptor. Understanding the mechanistic action of these compounds is fundamental to driving further drug discovery, and as such the way in which compounds interact with metabotropic receptor 5 both in vitro and ex vivo is a key focus of this thesis. In this thesis, previous studies of the allosteric mechanism of action of two allosteric modulators, CDPPB and ADX-47273, are extended to the human metabotropic glutamate receptor 5 using recombinant cell lines and show that the action of these compounds is preserved across species. Furthermore, the allosteric mode of action of LSN-2814617 and VU0430644 is demonstrated and shown to be efficacy driven at both the human and rat receptor homologues. The pharmacological consequences of heterodimerisation between group I metabotropic glutamate receptors is explored using mutant receptors which constitutively dimerise. Data herein demonstrates that metabotropic glutamate receptor 1 inhibits the action of compounds acting at metabotropic glutamate receptor 5 in a non-reciprocal manner. Finally, the receptor-dependent neurotoxicity of LSN2814617 is demonstrated in ex vivo tissue samples with chronic, high-dose administration of LSN-2814617 inducing neuronal cell death in the anterior cortex of the rodent brain. Understanding the interactions between metabotropic glutamate receptor 5, compounds acting at this receptor, and other receptors will be key in the development of compounds for progression to the clinic.
Freezing the biological clock : the experience of undergoing social egg freezing for delayed childbearing

In 2012, egg freezing was made available as an elective procedure for healthy reproductive-age women to attempt to preserve their fertility. To date, limited research has examined the experiences of women who have undergone this procedure or the meanings they attribute to this phenomenon. This study was designed to address this gap in the literature, using a hermeneutic phenomenological methodology. The research question that guided this inquiry was: “What is the meaning and experience of undergoing social egg freezing for the purpose of delaying child-bearing? ” In-depth qualitative research interviews were conducted with six women between the ages of 28 and 41. Interviews were transcribed verbatim and a thematic analysis was performed. Six common themes emerged from the women’s stories: (a) the sense of reducing the pressure to have a child, (b) the sense of taking control and of reproductive agency, (c) the sense of personal empowerment and acceptance, (d) the sense of feeling fortunate, (e) the sense of keeping reproductive and parenting options open, and (f) openness and support. The findings highlight the challenges and the perceived benefits of egg freezing to delay child-bearing and present important implications for counselling practice.
The Role of the DELSEED Motif of the b Subunit in Rotation

F1-ATPase is a rotary motor protein, and ATP hydrolysis generates torque at the interface between the g subunit, a rotor shaft, and the a3b3 substructure, a stator ring. The region of conserved acidic “DELSEED” motif of the b subunit has a contact with g subunit and has been assumed to be involved in torque generation. Using the thermophilic a3b3g complex in which the corresponding sequence is DELSDED, we replaced each residue and all five acidic residues in this sequence with alanine. In addition, each of two conserved residues at the counterpart contact position of g subunit was also replaced. Surprisingly, all of these mutants rotated with as much torque as the wild-type. We conclude that side chains of the DELSEED motif of the b subunit do not have a direct role in torque generation.
Lemurs of Madagascar : a strategy for their conservation 2013-2016

Many lemur species are on the very brink of extinction. Ninety-one per cent of all lemur taxa (species and subspecies) are now classified as Critically Endangered, Endangered, or Vulnerable on the IUCN Red List of Threatened Species. This publication outlines a three-year strategy for the conservation of the lemurs of Madagascar. The strategy contains 30 action plans for 30 different priority sites for lemur conservation.
Évolution et mécanismes d’évitement de la consanguinité chez un hyménoptère parasitoïde Venturia canescens

La consanguinite est connue par les biologistes pour diminuer la valeur selective des individus en diminuant par exemple leur survie ou leur fertilite. De ce fait, la selection naturelle devrait favoriser l'apparition de comportements permettant l'evitement des accouplements entre apparentes pour limiter les consequences nefastes dues a la depression de consanguinite. Cette depression de consanguinite est particulierement visible chez les Hymenopteres avec un systeme de determination du sexe appele single-locus Complementary Sex Determination (sl-CSD), ou elle amene a la production de males diploides non viables ou steriles. Mon travail de these a ainsi consiste a etudier le phenomene d'evitement d'accouplements entre apparentes dans des populations naturelles d'un hymenoptere parasitoide avec sl-CSD, Venturia canescens, ainsi que des signaux utilises par les femelles pour determiner l'apparentement qu'elles ont avec les individus qu'elles rencontrent. Nous avons d'abord etudie le lien unissant type d'habitat (continental, iles ou laboratoire), diversite genetique et production de males diploides dans 11 populations de V. canescens. En effet, un cadre theorique nomme "Vortex d'extinction du aux males diploides" predit une correlation negative entre isolations des populations, diversite genetique et production de males diploides pouvant amener a l'extinction de populations d'Hymenopteres. Nous avons ainsi demontre une correlation negative entre diversite genetique et production de males diploides dans les populations isolees de V. canescens. Ensuite, il a ete montre precedemment que les femelles de cette espece etaient capables de discriminer les males qui leur etaient apparentes et d'eviter les accouplements entre apparentes en laboratoire. Nous nous sommes ainsi interesses a ce phenomene d'evitement d'accouplement entre apparentes dans des populations naturelles grâce au genotypage de 450 individus du terrain et leur descendants. Nous avons montre que les femelles toleraient les accouplements entre apparentes sur le terrain ainsi qu'en laboratoire en presence de plusieurs males, nous permettant de mettre en lumiere l'importance des conditions environnementales sur le choix du partenaire sexuel. Nous nous sommes enfin concentres sur le systeme de reconnaissance des apparentes au niveau mecanistique en etudiant les signaux chimiques utilises par les femelles pour reconnaitre leurs apparentes dans deux contextes ecologiques differents, le choix du partenaire sexuel et l'evitement du superparasitisme lors de la ponte. Nous avons ainsi montre des similitudes entre les compositions chimiques de ces deux signaux mais aussi qu'ils n'etaient pas interchangeables entre les deux contextes ecologiques etudies. Au final, les resultats obtenus apportent un nouvel eclairage sur les conditions necessaires a l'apparition d'un evitement d'accouplements entre apparentes dans des populations naturelles ainsi que sur les signaux utilises lors de la reconnaissance de parentele chez un hymenoptere parasitoide
HCAtk and pyHCA: A Toolkit and Python API for the Hydrophobic Cluster Analysis of Protein Sequences

Motivation: Detecting protein domains sharing no similarity to known domains, as stored in domain databases, is a challenging problem, particularly for unannotated proteomes, domains emerged recently, fast diverging proteins or domains with intrinsically disordered regions. Results: We developed pyHCA and HCAtk, a python API and standalone tool gathering together improved versions of previously developed methodologies, with new functionalities. The developed tools can be either used from command line or from a python API. Availability: HCAtk and pyHCA are available at https://github.com/T-B-F/pyHCA under the CeCILL-C license.
PATTERNS OF MOLECULAR POPULATION GENETIC AND PHENOTYPIC VARIATION ASSOCIATED WITH URBANIZATION IN THE WESTERN BLACK WIDOW SPIDER

PATTERNS OF MOLECULAR POPULATION GENETIC AND PHENOTYPIC VARIATION ASSOCIATED WITH URBANIZATION IN THE WESTERN BLACK WIDOW SPIDER By Lindsay S. Miles, Ph.D. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2018. Major Director: Dr. Brian Verrelli, Graduate program director, Integrative Life Sciences Doctoral Program In urban population genetic studies, the "urban fragmentation model" predicts that urbanization acts as a barrier that isolates native populations, and can lead to reduced gene flow and increased genetic drift between populations. The “urban facilitation model” predicts urban areas act as corridors to increase dispersal among urban areas, and can lead to higher genetic diversity within and lower differentiation between urban areas. In a review of the current literature, we found that there is no consistent signature of reduced within-population genetic diversity or increased between-population genetic differentiation. Analyses that investigate the urban barriers to gene flow also found no consistent results. Thus, the response to urbanization may be species and city specific. We used social network genetic analyses, which can identify connections that both fragment and facilitate gene flow, to investigate the impact of anthropogenic disturbance on connectivity in a model urban pest of significant medical-relevance, the Western black widow spider, Latrodectus hesperus. In comparison to non-urban locales, urban locales have higher within-population genetic diversity, lower between-population genetic differentiation, and higher overall estimates of genetic connectivity. We found that not all cities are highly connected, with specific urban hubs driving gene flow among historically isolated non-urban locales. We compared and contrasted our previous broad-scale patterns of urban gene flow with a new fine-scale locale sampling from within three Southwestern U.S. cities. Urban areas have significantly different patterns of connectivity to the overall network that generate contrasting patterns of withinand between-city genetic diversity. There is significant heterogeneity among the fine-scale city samples, such that certain urban hubs are impacting the network of urban and non-urban locales on the whole. We examined differences in gene expression between three paired urban and non-urban populations from the cephalothorax (metabolism), ovary (fertility), and silk glands (web architecture). There is significant differential expression in each tissue type observed between urban and non-urban locales, among both urban and among non-urban locales, and specific to geographic locations independent of urban or non-urban habitat. These results imply that not all cities are created equal with respect to demographic and gene flow patterns, but also with phenotypic patterns.