Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary potential and constraints in wild populations

The question of how the evolutionary forces of natural selection, genetic drift and mutation shape the evolutionary potential of traits (i.e. properties of the genetic variance–covariance matrix, G), and translate to microevolutionary changes and population differentiation, forms one of the core areas of research in contemporary evolutionary biology. Understanding these issues is key to reconciling the causes of underlying evolutionary stasis (Hansen & Houle 2004) as well as to our understanding of whether and which populations will adapt or become extinct in the face of environmental changes (Futuyma 2010). For instance, concerns about the ability of populations to adapt to ongoing global changes are as pressing as ever, not only in case of currently endangered populations, but for organisms in general (e.g. Hoffmann & Sgro 2011; Merila 2012), and understanding the evolutionary potential of populations at the edge of their range distribution can give insights into the factors shaping species range limits (Sexton et al. 2009). In addition to its theoretical interest, such knowledge could also allow us to predict the rate of adaptation to ongoing climate change and to estimate sustainable rates of environmental change (Chevin et al. 2010), information needed to evaluate and implement appropriate management and conservation actions. In the case of invasive species, an accurate evaluation of their evolutionary potential could improve our understanding of their success and potential to spread to new areas (Lee & Gelembiuk 2008; Bacigalupe 2009). A crucial step towards resolving these issues depends on understanding the genetic architecture, expression and dynamics of standing genetic variation in ecologically important traits, and thus, the evolutionary potential of wild populations. The amount of additive genetic variance in a single trait is often used as a first approximation of a trait’s and population’s evolutionary potential (Falconer & Mackay 1996). However, this may be an oversimplification in the sense that evolutionary potential can be impacted by various environmental factors (e.g. genotype–environment interactions, G × E) and by genetic correlations among traits. Hence, an “inclusive” measure of evolutionary potential would require the integration of several other aspects—such as developmental effects (ontogeny and individual history; see Chapter 5, Charmantier et al.), the influence of the biotic environment (G × E and indirect genetic effects (IGEs); see Chapter 6, McAdam et al.) and the genetic associations, or integration, among traits—into our models. As vividly pointed out by Gould and Lewontin (1979), traits within an organism are not free to evolve independently, but form integrated units. From an adaptive point of view, this ensures that traits can function together. In this perspective,
A taxonomic overview of methanogens

Methanogenic bacteria are a morphologically diverse group of bacteria unified by their ability to produce methane. This property has been used to distinguish these bacteria from the other groups of bacteria. In the process scientists have isolated many new genera and species of methanogens. Taxonomy of methanogens has been discussed in some of the recent articles (11, 12, 37-39); however, the increase in isolation of new methanogenic species in the past few years has necessitated a review of the updated published information. Three-letter abbreviations for some generic names have been used to avoid confusion while retaining the two-letter abbreviations for others
Cancer Detection in Mass Spectrometry Imaging Data by Recurrent Neural Networks

Mass spectrometry imaging (MSI) reveals the localization of a broad scale of compounds ranging from metabolites to proteins in biological tissues. This makes MSI an attractive tool in biomedical research for studying diseases. Computer-aided diagnosis (CAD) systems facilitate the analysis of the molecular profile in tumor tissues to provide a distinctive fingerprint for finding biomarkers. In this paper, the performance of recurrent neural networks (RNNs) is studied on MSI data to exploit their learning capabilities for finding irregular patterns and dependencies in sequential data. In order to design a better CAD model for tumor detection/classification, several configurations of Long Short-Time Memory (LSTM) are examined. The proposed model consists of a 2-layer bidirectional LSTM, each containing 100 LSTM units. The proposed RNN model outperforms the state-of-the-art CNN model by 1.87% and 1.45% higher accuracy in mass spectra classification on lung and bladder cancer datasets with a sixfold faster training time.
Identification des critères du grain de blé (Triticum aestivum L.) favorables à la production de bioéthanol par l'étude d'un ensemble de cultivars et par l'analyse protéomique de lignées isogéniques waxy

Dans le but d’identifier des criteres de selection du ble (T. aestivum L.) destine a la production de bioethanol, les objectifs de cette these etaient (1) de mettre en evidence les caracteristiques physico-chimiques du grain associees aux rendements en glucose et ethanol, et (2), d’etudier par approche proteomique l’effet de variants genetiques affectant la quantite d’amylose sur le metabolisme des sucres et de l’amidon. L’analyse de trente varietes implantees dans un essai multilocal pluriannuel a mis en evidence l’importance du taux de proteines, de la durete et de la distribution des granules d’amidon sur les rendements en glucose et ethanol. Dans une moindre mesure, la composition allelique des proteines de reserves et la viscosite des arabinoxylanes ont egalement un effet lors de l’etape de transformation de l’amidon en sucres fermentescibles. Huit lignees isogeniques waxy de trois varietes francaises ont ete implantees dans un essai multilocal. Les lignees depourvues d’amylose ont produit moins de glucose et d’ethanol que les varietes normales. Les analyses proteomiques des proteines de l’albumen (albumines, globulines et amphiphiles) ainsi que des proteines associees aux granules d’amidon des grains matures des lignees isogeniques de la variete Tremie ont mis en evidence : (1) une relation entre le volume specifique des GBSS et la quantite d’amylose et (2) une modification de l’expression d’enzymes impliquees dans le metabolisme des sucres et de l’amidon (Susy, AGPase, fructose biphosphate aldolase) mais aussi de proteines de stress et de defense (serpines et HSP). Ces observations suggerent un developpement du grain incomplet pour la lignee depourvue d’amylose.
Studies on Water Extractable Feruloyl Polysaccharides from Native and Germinated Rice (Oryza Sativa) and Ragi (Eleusine Coracana)

Carbohydrates are the principal components/macronutrients of food,and apart from providing bulk of the caloric intake they play a variety of functions in human food and nutrition. In particular, arabinoxylans have attracted the attention of many researchers because of the complexity of their structure-function relationships. They are the major non-starch polysaccharides in cereals and represent bulk of the soluble and insoluble dietary fiber (unavailable/un-digestible carbohydrates) intake in human food. Nutritionally, dietary fibers/non-starch polysaccharides are known to exert many physiological/metabolic effects in reducing the risks of diseases (known as diseases of lifestyle/civilization) such as diabetes, obesity, atherosclerosis, hypertension, constipation, diverticulosis, colorectal cancer and so on. Due to their various physicochemical properties, water soluble non-starch polysaccharides (NSP), mainly arabinoxylans, are also known to have many functional roles in human food. Although general structure of arabinoxylans is known from many cereals, detailed investigations pertaining to the water soluble arabinoxylans/feruloyl arabinoxylans (feraxans) are sparse. Moreover, large variations in the fine structure of arabinoxylans isolated from various cereals are observed and they in turn may have influence on their physicochemical/functional roles. Thus for better understanding of fine structure of arabinoxylans and for their utilization in human food and nutrition with precise functional effects, arabinoxylans are characterized from diverse sources and conditions.The present study is taken up as there was no detailed investigation on the water soluble feraxans from rice and ragi, the major cereal and millet respectively. Structural and functional characterizations of water soluble feraxans from these two cereal grains were investigated with the following objectives: (a) Isolation and preliminary characterization of water extractable feruloyl polysaccharides from native and germinated rice and ragi, (b) Fractionation and purification of water extractable feruloyl polysaccharides, (c) Structural characterization of purified polysaccharides using methylation, GLC-MS analysis, Smith degradation and 13C-NMR and (d) Functional properties of water soluble feruloyl polysaccharides i.e., viscosity, gelling and foam stabilization and effect on dough characteristics, determination of their antioxidant and prebiotic activity in vitro.
Occurence of pathogenic and indicator microorganisms on produce irrigated with dairy wastewater

This project was designed to assess the potential for contamination of produce during irrigation with wastewater from animal operations. Dairy wastewater from the University of Arizona Campus Dairy Research Center was used to irrigate three different types of vegetable crops: lettuce, carrot, and bell pepper. This study was conducted over twoconsecutive years. The crops were planted in February and vegetables were harvested from May through July. Irrigation water and vegetable samples were examined for Escherichia coli, Clostridium perfringens. Listeria monocytogenes, and coliphage. In the dairy wastewater, E. coli concentrations averaged 5.7 x 10^ MPN/100 mL in the first year (2000), and 9.9 x 10^ MPN/100 mL in the second year (2001). C. perfringens concentrations were nearly the same in both years (1.7 x 10'' and 3.4 x 10"* CPU per 100 mL). Coliphage averaged 2.0 PPU/mL in 2000 and 1.3 x lO'' PFU/mL in 2001 in wastewater. E. coli was detected with greater frequency on carrots (100 and 96%) succeeded by lettuce (67 and 96%) and bell peppers (63 and 58%). The same was true for C. perfringens: carrots (100%), lettuce (86 and 88%), and bell peppers (100 and 50%). Coliphages were not detected on any of the vegetable crops except for average concentrations of 2 PFU/g on lettuce in the first year. L. monocytogenes was not detected on any of the vegetable samples. ANOVA test results indicates that E. coli and C. perfringens concentrations on three crops were statistically different (p <0.0001) which suggest that the degree of contamination on the surface of the vegetables depends on where the edible portion of the crop is situated (above the soil or under the soil). The greatest contamination occurred on the carrots followed by lettuce and bell peppers. E.
The Expression of P-Responsive Genes is Related to Root Hair Growth

Phosphorus deficiency results in the formation of longer root hairs in Brassica carinata cv. Bale to exhaust a greater soil volume. Recently, suppression subtractive hybridization revealed genes that were regulated in P-starved roots in Brassica carinata. Sequencing identified genes sharing homologies to a leucine-rich repeat protein kinase (LRR), a transcription factor of the 14-3-3 family, and a proline rich family protein (PRP) in Arabidopsis thaliana. This study aims at characterizing the expression pattern of these putative P-responsive genes by specifying the response to several nutritional stress factors and by inducing or discontinuing phosphorus deprivation. Root hair length was enhanced with phosphorus and nitrogen deprivation but not with potassium depletion. Likewise, the transcription level of LRR and PRP was increased in -P and -N conditions whereas there was no clear response for 14-3-3. One day after varying P supply, phenotypically the root hair length was changed. Correspondingly, the expression of the root-specific LRR and PRP was induced by P-deficiency and inhibited by the addition of P. The response to P starvation of 14-3-3 followed no clear trend. P-resupply increased the gene expression as well as P removal with a short term repression after 3 hours. In summary, the expression of a LRR receptor-like protein kinase and a proline rich protein suggests a function of these genes in inducing root hair growth. The putative transcription factor 14-3-3 may be of importance in rapid but unspecific stress response.
The role of a glycosyltransferase, ST6Gal I in regulating viral specific T and B cell responses

Post-translational modification of proteins, such as glycosylation, can impact cell signaling and function. ST6Gal I, a glycosyltransferase expressed by B cells, catalyzes the addition of α-2, 6 sialic acid to galactose (Siaα2-6Gal), a modification found on N-linked glycoproteins such as CD22, a negative regulator of B cell activation. We show that SNA lectin, which binds Siaα2-6Gal, shows high binding on plasma blasts and germinal center B cells following viral infection, suggesting ST6Gal I expression remains high on activated B cells in vivo. To understand the relevance of this modification on the antiviral B cell immune response, we infected ST6Gal I mice with influenza A/HKx31. We demonstrate that the loss of ST6Gal I expression results in similar influenza infectivity in the lung, but significantly reduced early influenza-specific IgM and IgG levels in the serum, as well as significantly reduced numbers of early viral specific antibody-secreting cells (ASCs). At later memory time points, ST6Gal I
Identification of Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) with species-specific COI (SS-COI) primers.

Phenacoccus solenopsis Tinsley,a new invasive species in China,is a worldwide pest causing serious threat to the production of agriculture and forestry. Morphological identification of this mealybug species is limited by high degree of similarity and polymorphism. In the present study,a method was described for the development of DNA markers for rapidly identifying P. solenopsis. A pair of universal primers was designed based on published mitochondrial DNA cytochrome c oxidase subunit Ⅰ (mtDNA COI) gene sequences of mealybugs in GenBank. The mtDNA COI genes from P. solenopsis and seven other mealybug species common in China including Pseudococcus comstocki Kuwana,Planococcus lilacius Cockerell, Maconellicoccus hirsutus ( Green ), Saccharicoccus sacchari ( Cockerell ), Dysmicoccus neobrevipes Beardsley ,Planococcus minor Maskel and Phenacoccus solani Ferris were amplified and sequenced. And then one pair of species-specific COI ( SS-COI) primers was designed. The SS-COI primers amplified a single band of 546 bp from P. solenopsis. The specificity of the primer pair was validated using the seven other mealybug species mentioned above. The results showed that all and only P. solenopsis specimens were detected,and no cross reactions with other mealybugs were observed. The method was tested with individuals of the egg , 1st,2nd and 3rd instar nymph and female adult,and demonstrated to be applicable for all life stages. Furthermore,the primer set was tested with one P.solenopsis population from Pakistan and fourteen P. solenopsis populations from invaded areas in China and proved to be applicable for all geographic populations. The diagnostic PCR assay developed here provides a quick,simple and reliable molecular technique for the identification and monitoring of P. solenopsis , which will be useful in intercepting and blocking the further spreading of P. solenopsis.
Analyse génétique et écophysiologique de l'écart à la relation teneur en protéines - rendement en grains chez le blé tendre (Triticum aestivum L.)

Le rendement en grains (Rdt) et la teneur en proteines (%Prot) sont deux cibles majeures dans les programmes de selection varietale chez le ble car ces caracteres contribuent a la valeur economique de cette culture. Malheureusement, leur amelioration simultanee est empechee par la relation negative %Prot-Rdt. Il a ete montre que l’ecart a cette relation (“Grain Protein Deviation”, GPD) est determine en partie genetiquement et serait utile pour modifier cette relation negative mais ses bases biologiques restent mal comprises a ce jour. Nous avons montre que le GPD est principalement relie a la variabilite genetique pour l’absorption d’azote post-floraison (ABSN) dans les conditions agro-climatiques du Nord-Ouest de l’Europe. Nous proposons que la variabilite genetique pour l’acces a l’azote du sol (architecture et fonctionnement racinaire) ou pour la regulation de ABSN par le statut azote (transport et assimilation de l’azote) pourrait expliquer le GPD. Etant donne que le retardement de la senescence durant la periode post-floraison peut resulter en une augmentation de ABSN, nous avons analyse les determinants genetique des relations entre duree de senescence des feuilles apres floraison et Rdt ou %Prot, observees au niveau phenotypique, en utilisant des donnees acquises sur une population de cartographie de ble cultivee au sein d’un large reseau experimental. Une association positive entre duree de senescence des feuilles apres floraison et %Prot ou Rdt a ete observee selon les environnements etudies. Nous faisons l’hypothese que l’impact d’un retardement de la senescence des feuilles apres floraison pourrait etre module selon la disponibilite en azote durant cette periode, ce qui conduirait a modifier la relation %Prot-Rdt selon les environnements etudies. Enfin, des donnees obtenues sur trois populations de cartographie cultivees dans un large reseau experimental ont permis de suggerer, apres meta-analyse de QTL, des regions genomiques potentiellement utiles en selection pour ameliorer la %Prot sans diminuer le Rdt. Ceci a permis de mettre en avant des regions situees sur les chromosomes 2A et 3B. En particulier, la region situee sur le 2A pourrait etre reliee a la presence d’un gene codant pour une glutamine synthetase chloroplastique qui a ete associee a la variabilite genetique pour %Prot chez le ble tendre dans une etude anterieure.
Examining the biological consequences of DNA damage caused by irradiated J2-3T3 fibroblast feeder cells and HPV16 : characterisation of the biological functions of Mll

The study of human papillomavirus (HPV) utilises human keratinocytes as host cells that are co-cultured with lethally irradiated mouse fibroblasts. Although this co-culture system has been effective in recapitulating HPV’s life cycle, it resembles studies whereby radiation-induced bystander effect (RIBE) has been identified. We considered the possibility that Normal Immortalised Keratinocytes (NIKs) that we used as host cell for HPV16 may be in receipt of DNA damaging agents from heavily irradiated J2-3T3 fibroblasts. We report that NIKs (+/ - HPV16) cells respond to the presence of feeders by increasing DNA damage response leading to H2AX phosphorylation. NIKs receive DNA damaging agents from irradiated feeder cells primarily through direct cell-to-cell contact and secondarily through the culture media. Although ATM, ATR, and DNA-PK were activated by RIBE in NIKs, we found that feeders inhibited ATM activation in NIKs (+HPV16). Moreover, we found that expression of HPV16 E6 and E7 oncoproteins activated ATM, ATR, and DNA-PK. HPV16 also activated H2AX, 53BP1, RPA32, and NBS-1. We considered that both feeder cells and HPV16 could induce DNA damage response in NIKs. This would change the interpretations of HPV16’s interactions with host cell’s DNA damage surveillance system in NIKs (+ HPV16) cells co-cultured with feeders. We proceeded to enhance our understanding of how feeder cells and/ or HPV16 changed the way NIKs cells respond to direct DNA damage. We found that NIKs cells (+feeders or +HPV16) respond to direct gamma radiation in a broadly similar way, whereby activation of ATM was inhibited, increase in ATR was extremely small and delayed, while activation of DNA-PK was still generally responsive. We report that presence of HPV16 sensitised NIKs cells to direct gamma radiation and as such, the implications of these observations could be considered for radiotherapy of cancers with HPV. Our initial belief that feeder cells were essential in ensuring stable autonomous replication of HPV16 in NIKs cells was proven otherwise, as NIKs maintained HPV16 DNA episomal copies in the absence of feeders. Contrary to current accepted publication, ATM was found be unnecessary for maintenance of HPV16 DNA episomes and viral genome amplification.
A Systematic Review and Meta-analysis on the Average Age of Menopause among Iranian Women

Background: Menopause age is a determinant of health status and the risks for future diseases. Aim: The current study aimed to determine the average age of menopause among Iranian women in a meta-analysis. Method: This systematic review and meta-analysis was performed in August 2017. The articles were searched in Persian databases, including Iran Medex, SID, and Magiran, as well as international databases, including Scopus, PubMed, and Web of Knowledge, without any time limitation. The search process was accomplished using the following keywords: “Menopause” OR “Menopause age” OR “Age of menopause” OR “Menopause age and Iran”. Begg’s and Egger tests were used to identify publication bias. Data analysis was performed in Stata statistical software (version 14) using random effect model. Results: The search process resulted in the inclusion of 28 articles with a total of 40,042 subjects published during 1998-2017. The mean age of menopause was evaluated as 48.57 years (CI: 47.96- 49.18). Analysis of subgroups indicated that the mean ages of menopause were evaluated as 47.21 (CI: 46.94-47.48), 48.43 (CI: 47.76-49.10), 47.53 (CI: 47.17-47.88), 47.80 (CI: 47.49-48.11), and 47.83 (CI: 47.34-48.32) in smoking women (based on nine studies), non-smoking women, women with normal body mass index (based on eight studies), overweight women (based on seven studies), and obese women (based on six studies), respectively. The minimum mean age was 47.97 years, which belonged to the north region. Implications for Practice: The results suggested that the average age of menopause is still within a normal range despite its rise with a normal slope. It seems that the changes in the women’s lifestyle have affected the menopause age. Consequently, special attention should be paid to some factors confounding menopause age among Iranian women to promote their health and reduce the health problems related to menopause.
Expansion of forest stands into tundra in the Noatak National Preserve, northwest Alaska

AbstractTemperatures across the northern regions of North America have been increasing for 150 years, and forests have responded to this increase. In the Noatak National Preserve in Alaska, white spruce (Picea glauca [Moench] Voss) forests reach their northern limit, occurring primarily on well-drained sites and as gallery forests along streams. Rolling plateaus of tundra separate the white spruce forests into disjunct stands. We examined patterns of tree age, tree growth, and tree encroachment into tundra ecosystems in six stands along the Agashashok River. Warming over the past 150 years appears to have increased tree growth and resulted in forest expansion into adjacent tundra ecosystems. The forest/tundra ecotone shifted by about 80 to 100 m into the tundra in the past 200 years, as evidenced by declining maximum tree age with distance towards the tundra. The decadal-scale pattern of tree establishment at the farthest extent of trees into the tundra (the tundra-forest ecotone) correlated with the detr.