Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA methylation and histone acetylation: genotypic variations in hybrid poplars, impact of water deficit and relationships with productivity

Abstract• Several reports on annual plants have already shown the involvement of epigenetic modifiers such as DNA methylation in their adaptation to abiotic stresses. • Nevertheless, the genotypic variations of epigenetic modifiers, their possible correlations with morphological traits and the impact of water deficit have not been described for perennial plants. • Six genotypes of Populus deltoides × P. nigra were subjected or not to a moderate water deficit treatment. Various morphological traits such as the height of the plants, their biomass and the total leaf area were measured to characterize the productivity in both conditions. Levels of DNA methylation, histone acetylation and the activities and isoform accumulation of the corresponding enzymes were measured at the shoot apex, the site of morphogenesis. Genotypic variation was observed for the morphological traits and the epigenetic variables and correlations were established among them. Genotypic variation for DNA methylation was detected in hybrid poplars. A positive correlation was demonstrated between DNA methylation percentage and productivity under well watered conditions. • While there was a general decrease of growth for all genotypes in response to a moderate water deficit, genotypic dependant variations of DNA methylation were found suggesting different strategies among hybrids. Résumé• Plusieurs études sur des plantes annuelles ont déjà montré l’implication des modifications épigénétiques telles que la méthylation de l’ADN dans la plasticité de leurs réponses aux contraintes abiotiques. • Néanmoins, les variations génotypiques de ces modifications épigénétiques, leur possible corrélation avec des variables de croissance et l’impact d’un déficit hydrique n’ont pas été décrits sur une plante pérenne. • Six génotypes de Populus deltoïdes × P. nigra ont été soumis ou non à un déficit hydrique modéré et plusieurs variables de croissance ont été mesurées afin de caractériser leur productivité. Les niveaux de méthylation de l’ADN, d’acétylation des histones, les activités enzymatiques et l’accumulation des isoformes correspondantes ont été mesurés sur des apex caulinaires, site de la morphogenèse. Des variations génotypiques ont été observées pour les variables de croissance et épigénétiques. Une corrélation positive a été mise en évidence entre la méthylation de l’ADN et la productivité en condition hydrique favorable. • Bien qu’il y ait une diminution générale de la croissance de tous les génotypes en réponse à un déficit hydrique modéré, des variations génotype-dépendant de la méthylation de l’ADN ont été trouvées suggérant différentes stratégies entre hybrides.
Evaluation of splicing efficiency in lymphoblastoid cell lines from patients with splicing-factor retinitis pigmentosa

Purpose Retinitis pigmentosa (RP) is caused by mutations in a variety of genes, most of which have known functions in the retina. However, one of the most perplexing findings of recent retinal genetics research was the discovery of mutations causing dominant RP in four ubiquitously expressed splicing factors. The aim of this study was to use lymphoblast cell lines derived from RP patients to determine whether mutations in two of these splicing factors, PRPF8 and PRPF31, cause measurable deficiencies in pre-mRNA splicing. Methods cDNA was prepared from lymphoblastoid cell lines derived from RP patients bearing mutations in the splicing factor genes and controls, grown under a variety of conditions. Introns representing the U2 and U12 intron classes, with both canonical and noncanonical donor and acceptor sequences, were analyzed by real-time PCR to measure the ratio of spliced versus unspliced transcripts for these introns. In addition, plasmids encoding the retinal outer segment membrane protein-1 (ROM-1; exon 1 to exon 2) gene, both in the wild-type form and with mutations introduced into the splice donor sites, were transfected into cell lines. The spliced versus unspliced cDNA ratios were measured by real-time RT–PCR. Results Splicing of four canonical U2 introns in the actin beta (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), PRPF8, and retinitis pigmentosa GTPase regulator (RPGR) genes was unaffected in PRPF8 mutant cells. However, the splicing efficiency of RPGR intron 9 was significantly decreased in PRPF31 mutant cell lines. In contrast, a consistent decrease in the splicing efficiency of all U12 and noncanonical U2 introns was seen in PRPF8, but not in PRPF31, mutant cells, with statistical significance for STK11 intron 3. Conclusions In spite of the ubiquitous expression patterns of the genes implicated in splicing factor RP, no pathology has yet been documented outside the retina. The observed differences in splicing efficiency described herein favor the hypothesis that these mutations may have a subpathological effect outside the retina. These observations argue against a defect in some yet to be discovered additional function of these proteins and support the alternative hypothesis that this form of RP does indeed result from aberrant splicing of retinal transcripts.
Recent studies of genetic dysfunction in pelvic organ prolapse: The role of collagen defects

Gynaecologists are becoming increasingly aware that women with a family history of prolapse are at an increased risk of prolapse refractory to treatment. In the past five years, several genetic mutations have been shown to correlate with increased prolapse susceptibility. These mutations can result in disordered collagen metabolism, which weaken the fascial support of the pelvic organs. This review examines the contemporary evidence regarding the role of collagen in prolapse.
A Social Relations Analysis of Children's Trust in Their Peers across the Early Years of School

Two hundred and five (103 female and 102 male) children enrolled in school years 1 and 2 in the UK (mean age 6 years 1 month at Time 1) were tested twice over a 1-year period. The children reported the promise keeping and secret keeping behaviours of classmates (all peers and same-gender peers) and provided friendship nominations (Time 2 only). Round robin social relations analyses for all peers and same-gender peers revealed: (1) perceiver variance, demonstrating consistent individual differences in trust beliefs in peers; (2) target variance, demonstrating consistent individual differences in eliciting trust from peers; and, (3) dyadic reciprocity, demonstrating reciprocal trust between individuals. Replicability across measures, stability, and cross-measure stability of these effects were found for all peers only. As hypothesized, the perceiver and target effects of trust were associated with the number of friendships. The findings support the conclusion that young children demonstrate multiple components of trust in dyadic relationships, which are associated with their social relationships.
From Local Adaptation to Ecological Speciation in Copepod Populations from Neighboring Lakes

Continental copepods have been derived from several independent invasive events from the sea, but the subsequent evolutionary processes that account for the current diversity in lacustrine environments are virtually unknown. Salinity is highly variable among lakes and constitutes a source of divergent selection driving potential reproductive isolation. We studied four populations of the calanoid copepod Leptodiaptomus cf. sicilis inhabiting four neighboring lakes with a common history (since the Late Pleistocene) located in the Oriental Basin, Mexico; one lake is shallow and varies in salinity periodically (1.4–10 g L-1), while three are deep and permanent, with constant salinity (0.5, 1.1 and 6.5 g L-1, respectively). We hypothesized that (1) these populations belong to a different species than L. sicilis sensu stricto and (2) are experiencing ecologically based divergence due to salinity differences. We assessed morphological and molecular (mtDNA) COI variation, as well as fitness differences and tests of reproductive isolation. Although relationships of the Mexican populations with L. sicilis s.s. could not be elucidated, we identified a clear pattern of divergent selection driven by salinity conditions. The four populations can still be considered a single biological species (sexual recognition and hybridization are still possible in laboratory conditions), but they have diverged into at least three different phenotypes: two locally adapted, specialized in the lakes of constant salinity (saline vs. freshwater), and an intermediate generalist phenotype inhabiting the temporary lake with fluctuating salinity. The specialized phenotypes are poorly suited as migrants, so prezygotic isolation due to immigrant inviability is highly probable. This implication was supported by molecular evidence that showed restricted gene flow, persistence of founder events, and a pattern of allopatric fragmentation. This study showed how ecologically based divergent selection may explain diversification patterns in lacustrine copepods.
Multiple biochemical effects in the pathogenesis of alcoholic fatty liver

The pathogenesis of alcoholic fatty liver is unknown, but several causes have been proposed based on biochemical findings. These include the metabolism of alcohol leading to a shift in the cytosolic [NAD+]/[NADH] ratio to reduction, which in turn causes a direct inhibition of β‐oxidation and enhanced triacylglycerol formation via the [glycerol‐3‐phosphate]/[dihydroxyacetone phosphate] ratio. There are also chronic effects of ethanol on hepatic enzyme activities. Thus, increased activity of phosphatidate phosphohydrolase, an increased amount of fatty acid binding protein, decreased secretion of very low‐density lipoprotein and impairment of the respiratory chain as a result of decreased protein synthesis or decreased amounts of ubiquinone could all lead to fat accumulation and steatosis. The interplay of each of these with nutritional and genetic factors would then lead to the heterogeneity of the severity and characteristics of the steatosis observed in human alcoholics.
Interfaces endowed with non-constant surface energies revisited with the d'Alembert-Lagrange principle

The equation of motions and the conditions on surfaces and edges between fluids and solids in presence of non-constant surface energies, as in the case of surfactants attached to the fluid particles at the interfaces, are revisited under the principle of virtual work. We point out that adequate behaviors of surface concentrations may drastically modify the surface tension which naturally appears in the Laplace and the Young-Dupr\'e equations. Thus, the principle of virtual work points out a strong difference between the two revisited concepts of surface energy and surface tension.
Assessing risk and mortality of venous thromboembolism in pancreatic cancer patients.

BACKGROUND Venous thromboembolism (VTE) is associated with cancer. Cancer patient with thromboembolism have poorer prognosis. This study assessed the risk and mortality in pancreatic cancer patients who develop VTE. PATIENTS AND METHODS A retrospective chart review was performed of 201 patients with pancreatic cancer. RESULTS VTE was observed in 58 (28.9%) patients, 37/58 had deep vein thrombosis (DVT), 11/58 pulmonary embolism (PE) and 10/58 had both. Twenty-six out of 107 patients with tumor of head of the pancreas developed VTE (24%), compared to half of the patients with body of the pancreas involvement (11-22). Stage IV was defined in 99 patients, 39/99 had VTE (39%). Median survival time was 14.95 months for patients without VTE compared to 13.04 months with VTE. CONCLUSION Patients with body of the pancreas and stage IV tumors had increased risk of developing VTE. There was no survival difference between patients with VTE compared to those without.
Cognitive Performance and the Role of Control Beliefs in Midlife

Midlife has been touted as being a time of peak performance in many different areas of functioning. In the present study, we investigated whether this was true for cognitive functioning on tasks assessing speed, reasoning, short-term memory, and vocabulary. We also explored the extent to which levels of cognitive functioning could be attributed to individual differences in general control beliefs. Middle-aged adults showed little or no cognitive declines on speed, reasoning, and short-term memory measures relative to the young and outperformed the young on vocabulary. Relative to the elderly, middle-aged adults scored higher on all tasks except vocabulary, for which there were no differences. Adults in midlife, on the other hand, had lower scores on measures of general control beliefs compared to younger adults. Thus, although midlife is a time of high cognitive functioning, it is also a time of lower beliefs about control. To investigate the relationship between control beliefs and cognitive performance, we used structural equation modeling. The models showed that for adults in midlife, control beliefs were predictive of performance but only for the reasoning task after background variables were considered. Specifically, high levels of control beliefs were associated with better cognitive performance. More work is needed to identify mediational processes linking control beliefs and cognitive performance for various age groups and to determine whether some cognitive processes are more controllable than others.
Let’s Talk Music: A Corpus-Based Account of Musical Motion

This article aims to provide a corpus-based evidence of (a) the ubiquitous presence of metaphors in verbal discourse about classical music and (b) the embodied basis of metaphors for musical motion. We analyzed authentic examples extracted from a 5,000-word corpus of texts taken from peer-reviewed music academic journals. We applied a systematic method to identify metaphor-related words (Metaphor Identification Procedure Vrije Universiteit Amsterdam [MIPVU]; Steen, Dorst, Herrmann, Kaal, Krennmayer, & Pasma, 2010) and to label conceptual metaphors (Babarczy, Bencze, Fekele, & Simon, 2010) that reduces the analyst’s bias in the identification of metaphors. Our main findings are: (a) the presence of metaphors in academic discourse on music (29%) is significantly higher than in academic discourse in general (19%; Steen, Dorst, Herrmann, Kaal, Krennmayer, & Pasma, 2010); (b) most of the identified metaphors to describe musical motion are correlational metaphors (Grady, 1999); and (c) metaphors for musical motion are structured in the same way as the metaphors that make up Lakoff’s (1993) Event Structure Metaphor, thus giving rise to the Musical Event Structure Metaphor.
Refining clinical risk stratification for predicting stroke and thromboembolism in atrial fibrillation using a novel risk factor-based approach: the euro heart survey on atrial fibrillation.

BACKGROUND Contemporary clinical risk stratification schemata for predicting stroke and thromboembolism (TE) in patients with atrial fibrillation (AF) are largely derived from risk factors identified from trial cohorts. Thus, many potential risk factors have not been included. METHODS We refined the 2006 Birmingham/National Institute for Health and Clinical Excellence (NICE) stroke risk stratification schema into a risk factor-based approach by reclassifying and/or incorporating additional new risk factors where relevant. This schema was then compared with existing stroke risk stratification schema in a real-world cohort of patients with AF (n = 1,084) from the Euro Heart Survey for AF. RESULTS Risk categorization differed widely between the different schemes compared. Patients classified as high risk ranged from 10.2% with the Framingham schema to 75.7% with the Birmingham 2009 schema. The classic CHADS(2) (Congestive heart failure, Hypertension, Age > 75, Diabetes, prior Stroke/transient ischemic attack) schema categorized the largest proportion (61.9%) into the intermediate-risk strata, whereas the Birmingham 2009 schema classified 15.1% into this category. The Birmingham 2009 schema classified only 9.2% as low risk, whereas the Framingham scheme categorized 48.3% as low risk. Calculated C-statistics suggested modest predictive value of all schema for TE. The Birmingham 2009 schema fared marginally better (C-statistic, 0.606) than CHADS(2). However, those classified as low risk by the Birmingham 2009 and NICE schema were truly low risk with no TE events recorded, whereas TE events occurred in 1.4% of low-risk CHADS(2) subjects. When expressed as a scoring system, the Birmingham 2009 schema (CHA(2)DS(2)-VASc acronym) showed an increase in TE rate with increasing scores (P value for trend = .003). CONCLUSIONS Our novel, simple stroke risk stratification schema, based on a risk factor approach, provides some improvement in predictive value for TE over the CHADS(2) schema, with low event rates in low-risk subjects and the classification of only a small proportion of subjects into the intermediate-risk category. This schema could improve our approach to stroke risk stratification in patients with AF.
Analytical modeling of fast retransmission and recovery in TCP-RENO

This paper presents an analytical model to analyze the characteristics of fast retransmission and recovery when packets are lost in a TCP/IP network. In the model, we consider multiple packets that may be lost in a TCP congestion window, which makes this analysis technically different from the previous models as described in N. Caldwell et al. (2000), J. Padhye et al. (2000), B. Sikdar et al. (2003) and B. Sikdar et al. (2001). One of the significant observation revealed by this paper is that whether or not the lost packets can be fast retransmitted at the (y+1)-th RTT (round-trip time) round simply depends on N,[y], representing the number of packets followed by the first lost packet and were successfully received at receiver at th y-th RTT round. For clarification, the analytical model consists of two cases. The first case assumes that N,[y] is greater than or equal to a threshold k (the number of duplicate acknowledgments), while the second case assumes that N,[y] is less than the threshold k. From the analyses, we have found out that there are certain necessary conditions for the occurrence of fast retransmission, and we have derived an upper bound of the number of lost packets to be successfully recovered using the fast retransmission algorithm.
Where Have All the Majors Gone? Comment.

In the good old days of the 1980s, my colleagues at Barnard attributed the popularity of our economics major to the absence of a business major. Lured by the high salaries and high profiles of traders and investment bankers, an unprecedented proportion of our entering students planned careers on Wall Street. As a result, the economics major attracted the best and the brightest of students, if not the most interested. Those good old days came to end with the crash of October 1987. The popularity of the economics major plummeted overnight. In the class of the 1987, there were 50 majors; in the class of 1989, only 39. ' Salemi and Eubanks (1996) present a different version of this same hypothesis. The University of North Carolina (UNC) has an undergraduate business major. During the 1980s, the popularity of this major soared. The business school responded to this excess demand by increasing the entry requirements. At the end of their sophomore year, those students who did not meet the requirements were forced to find an alternative major. For most, that alternative was economics. Whereas at a liberal arts college like Barnard, the lure of Wall Street attracted the best and the brightest, the discouraged business majors at UNC had weaker credentials than other economics majors. Salemi and Eubanks investigate how much of the growth in economics majors over the 1980s and the subsequent decline in the 1990s was caused by fluctuations in the number of discouraged business majors. Their data are quite persuasive. The discouraged-business-major hypothesis does appear to explain why UNC experienced a bigger drop in the popularity of economics than the national average. The central task in the Salemi-Eubanks article is to distinguish discouraged business majors (DBMs) from other economics majors and to count changes in their numbers. Salemi and Eubanks identify discouraged business majors through an analysis of transcripts. This process is unavoidably imprecise. Another researcher might look at the same transcript and make a different judgment. This is particularly true when the key indicator of status is itself endogenous. Salemi and Eubanks sort students primarily on the basis of their grade point average in prebusiness courses. A student who has decided not to major in business will not work as hard in those courses and thus, earn a lower grade. Yet, he may
Relationship Between Sprint Times and the Strength/Power Outputs of a Machine Squat Jump

Strength testing is often used with team-sport athletes, but some measures of strength may have limited prognostic/diagnostic value in terms of the physical demands of the sport. The purpose of this study was to investigate relationships between sprint ability and the kinetic and kinematic outputs of a machine squat jump. Thirty elite level rugby union and league athletes with an extensive resistance-training background performed bilateral concentric-only machine squat jumps across loads of 20% to 90% 1 repetition maximum (1RM), and sprints over 10 meters and 30 or 40 meters. The magnitudes of the relationships were interpreted using Pearson correlation coefficients, which had uncertainty (90% confidence limits) of ∼±0.3. Correlations of 10-meter sprint time with kinetic and kinematic variables (force, velocity, power, and impulse) were generally positive and of moderate to strong magnitude (r = 0.32-0.53). The only negative correlations observed were for work, although the magnitude was small (r = −0.18 to −0.26). The correlations for 30- or 40-meter sprint times were similar to those for 10-meter times, although the correlation with work was positive and moderate (r = 0.35-0.40). Correlations of 10-meter time with kinetic variables expressed relative to body mass were generally positive and of trivial to small magnitude (r = 0.01-0.29), with the exceptions of work (r = −0.31 to −0.34), and impulse (r = −0.34 to −0.39). Similar correlations were observed for 30- and 40-meter times with kinetic measures expressed relative to body mass. Although correlations do not imply cause and effect, the preoccupation with maximizing power output in this particular resistance exercise to improve sprint ability appears problematic. Work and impulse are potentially important strength qualities to develop in the pursuit of improved sprinting performance.