Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data1[OPEN]

Tools for mapping transcription factor binding sites are evaluated with a protocol to map gene regulatory from open chromatin data sets. Determining where transcription factors (TFs) bind in genomes provides insight into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these data sets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF-binding preferences, or motifs, to identify TF-binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here, we compare four motif-mapping tools widely used in the Arabidopsis (Arabidopsis thaliana) research community and evaluate their performance using chromatin immunoprecipitation data sets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of Find Individual Motif Occurrences, one of the most frequently used motif-mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a protocol is presented to effectively derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression data sets. This approach will pave the way to increase our understanding of GRNs in different cellular conditions.
Effects of Nonaction Videogames on Attention and Memory in Young Adults.

Objective: In this intervention study, we investigated the benefits of nonaction videogames on measures of selective attention and visuospatial working memory (WM) in young adults. Materials and Methods: Forty-eight young adults were randomly assigned to the experimental group or to the active control group. The experimental group played 10 nonaction adaptive videogames selected from Lumosity, whereas the active control group played two nonadaptive simulation-strategy games (SimCity and The Sims). Participants in both groups completed 15 training sessions of 30 minutes each. The training was conducted in small groups. All the participants were tested individually before and after training to assess possible transfer effects to selective attention, using a Cross-modal Oddball task, inhibition with the Stroop task, and visuospatial WM enhancements with the Corsi blocks task. Results: Participants improved videogame performance across the training sessions. The results of the transfer tasks show that the two groups benefited similarly from game training. They were less distracted and improved visuospatial WM. Conclusion: Overall, there was no significant interaction between group (group trained with adaptive nonaction videogames and the active control group that played simulation games) and session (pre- and post-assessment). As we did not have a passive nonintervention control group, we cannot conclude that adaptive nonaction videogames had a positive effect, because some external factors might account for the pre- and post-test improvements observed in both groups.
Habitat use by mice during winter on subantarctic Auckland Island

Introduced mice were trapped in the three main vegetation types on subantarctic Auckland Island, New Zealand, over three trapping sessions, in winter 2007. Fifty mice were trapped over 675 trap-nights. Mice were caught most often in upland tussock grassland and more often in rātā forest than in shrubland but there were no significant differences among the catch rates in these habitats. Upland tussock grassland appeared to have been a better vegetation type for mice, as adult females were trapped only there and mean weight of adult males was heavier there than of adult males from the other vegetation types.
Semantic halo of a meter: A keyword-based approach

The semantic halo of a meter (semantičeskij oreol metra) is a notion that was introduced by Mikhail Gasparov to describe semantic invariants of poetic texts composed using the same metrical scheme. Most studies addressing this phenomenon have been based on expert knowledge of the text corpus. In this study, I propose an automated approach to analyzing the semantic halo of various meters based on keyword extraction, using a simple measure of keyness as developed by Adam Kilgarriff. The method is applied to texts from the Poetic subcorpus of the Russian National Corpus. It allows us to discern basic motifs that are very close to those identified by literary scholars, which proves that it is a promising way to analyze the semantic halo of a meter. Some novel associations can also be inferred from the keyword lists. Clearly, keyword extraction cannot replace profound expert knowledge, but it can serve as a useful first step of the analysis.
Does motivation mediate the relationship between competence perceptions and patient outcomes among individuals with chronic low back pain? A multiple mediation analysis

Abstract Purpose The aim of this study was to examine: (1) motivations of patients with chronic low back pain to attend physical therapy; (2) relationships between competence perceptions, motivational regulations, and pain/disability; and (3) whether patient motivations to attend physical therapy mediate the relationship between competence perceptions and pain/disability. Methods A sample of 64 participants completed baseline assessment (1-week prior to initiation of physical therapy) and 6-week follow-up assessment. Differences between motivation variables at baseline were examined using one-way within-person ANOVA. Relationships between competence perceptions, motivation subscales, and pain/disability were calculated using bivariate correlations and multiple mediation analyses. Results Participants reported significantly higher levels of autonomous versus controlled motivation (mean difference = 3.5, p < 0.001, d = 2.3) and amotivation (mean difference = 3.6, p < 0.001, d = 2.4). Competence was positively associated with autonomous motivation (r = 0.45, p ≤ 0.05) and negatively associated with controlled motivation (r = −0.26, p ≤ 0.05), amotivation (r = −0.57, p ≤ 0.05), pain (r = −0.35, p ≤ 0.05), and disability (r = −0.34, p ≤ 0.05). Amotivation significantly mediated the competence–pain relationship (Amotivation IE = −0.19, 95% CI (−0.44, −0.06), p < 0.05) and the competence–disability relationship (Amotivation IE = −0.07, 95% CI (−0.17, −0.01), p < 0.05). Conclusion Findings highlight the role of competence perceptions in mitigating amotivation for physical therapy and the deleterious implications of amotivation for patient-centered outcomes. Implications for rehabilitation While it is normal for patients to experience periods where they lack motivation for rehabilitation exercises, practitioners can encourage patients to assume responsibility for their recovery by informing them that amotivated states may increase the likelihood of increased pain perceptions and disability. Health-care practitioners should seek to foster competence perceptions in patients about to undergo physical therapy. Competence building strategies such as patient education, goal setting, and role modeling may be valuable in facilitating autonomous motivation and reducing amotivation for physical therapy.
Diaphragm fatigue and inspiratory muscle metaboreflex in men and women matched for absolute diaphragmatic work during pressure‐threshold loading

The female diaphragm fatigues at a slower rate compared to that of males, with blunted cardiovascular consequences (i.e. inspiratory muscle metaboreflex). It is unclear if these findings are a function of relative or absolute diaphragmatic work. We asked if sex differences in diaphragm fatigue and the inspiratory muscle metaboreflex persisted during inspiratory loading performed at equal absolute intensities. We found that matching men and women for absolute diaphragmatic work resulted in an equal degree of diaphragm fatigue, despite women performing significantly greater work relative to body mass. Metabolite‐induced reflex influences in sympathetic outflow originating from the diaphragm are attenuated in women, with potential implications for blood flow distribution during exercise.
Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of Howea in the face of high gene flow

The idea that populations must be geographically isolated (allopatric) to evolve into separate species has persisted for a long time. It is now clear that new species can also diverge despite ongoing genetic exchange, but few accepted cases of speciation in sympatry have held up when scrutinized using modern approaches. Here, we examined evidence for speciation of the Howea palms of Lord Howe Island, Australia, in light of new genomic data. We used coalescence‐based demographic models combined with double digest restriction site associated DNA sequencing of multiple individuals and provide support for previous claims by Savolainen et al. that speciation in Howea did occur in the face of gene flow.
Open science: The open clinical trials data journey

Open data sharing and access has the potential to promote transparency and reproducibility in research, contribute to education and training, and prompt innovative secondary research. Yet, there are many reasons why researchers don’t share their data. These include, among others, time and resource constraints, patient data privacy issues, lack of access to appropriate funding, insufficient recognition of the data originators’ contribution, and the concern that commercial or academic competitors may benefit from analyses based on shared data. Nevertheless, there is a positive interest within and across the research and patient communities to create shared data resources. In this perspective, we will try to highlight the spectrum of “openness” and “data access” that exists at present and highlight the strengths and weakness of current data access platforms, present current examples of data sharing platforms, and propose guidelines to revise current data sharing practices going forward.
E-cadherin expression is associated with susceptibility and clinicopathological characteristics of thyroid cancer

Abstract Background: Recently, many studies have been carried out to investigate the clinicopathological significance of E-cadherin expression in thyroid cancer. However, the results remained inconsistent. In the present study, we performed a meta-analysis to evaluate the associations of E-cadherin expression with susceptibility and clinicopathological characteristics of thyroid cancer. Methods: Eligible studies were searched from Medicine, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), and Wanfang databases. The strength of associations between E-cadherin expression and susceptibility and clinicopathological features of thyroid cancer were assessed by pooled odds ratios (ORs) and 95% confidence intervals (CIs). Results: Forty-six studies with 1700 controls and 2298 thyroid cancer patients were included for this meta-analysis. Pooled results indicated that E-cadherin expression was significantly associated with susceptibility of papillary cancer and follicular cancer (papillary cancer, ORs = 14.31, 95% CIs = 3.42–59.90; follicular cancer, ORs = 10.14, 95% CI = 4.52–22.75). Significant association between E-cadherin expression and thyroid cancer risk was also observed in the subgroup analysis based on control group (normal thyroid tissue, ORs = 28.28, 95% CI = 8.36–95.63; adjacent thyroid tissue, ORs = 8.83, 95% CI = 3.27–23.85; benign thyroid tissue, ORs = 43.96, 95% CI = 9.91–194.95). In addition, E-cadherin expression was significantly correlated with lymph node metastasis, differentiation, and tumor-node-metastasis (TNM) stage of thyroid cancer (lymph node metastasis, ORs = 3.21, 95% CI = 1.98–5.20; differentiation, ORs = 0.25, 95% CI = 0.07–0.82; TNM stage, ORs = 4.85, 95% CI = 2.86–8.25). Conclusions: The present study showed that E-cadherin expression was significantly associated with susceptibility and clinicopathological characteristics of thyroid cancer, which suggested that E-cadherin expression might be a potential predictive factor for clinical progression of thyroid cancer.
Burnout and Satisfaction with Work-Life Integration Among Nurses.

OBJECTIVES To evaluate characteristics associated with burnout and satisfaction with work-life integration (WLI) among nurses and compare their experience to other American workers. METHODS We used data from 8638 nurses and 5198 workers to evaluate factors associated with burnout and satisfaction with WLI, and compare nurses to workers in other fields. RESULTS In the multivariable analysis, demographics, work hours, and highest academic degree obtained related to nursing were independent predictors of burnout. Factors independently associated with satisfaction with WLI included work hours. In pooled multivariable analyses including nurses and other workers, nurses were not more likely to have symptoms of burnout but were more likely to have lower satisfaction with WLI. CONCLUSIONS Work hours and professional development related to the risk of burnout among nurses. Nurses are at similar risk for burnout relative to other US workers but experience greater struggles with WLI.
Effects Of Folic Acid And Vitamin B 12 , Alone and in Combination on Cognitive Function and inflammatory Factors in the Elderly with Mild Cognitive Impairment: A Single-Blind Experimental Design.

BACKGROUND Folate and vitamin B 12 are well acknowledged as essential nutrients that play key roles in the normal functions of brain. Inflammatory processes play at least some role in the pathology of AD. Effective nutritional intervention approaches for improving cognitive deficits that reduce the peripheral inflammatory cytokine levels have garnered special attention. OBJECTIVE The present study aimed to determine whether supplementation with folic acid and vitamin B 12 , alone and in combination improves cognitive performance via reducing levels of peripheral inflammatory cytokines. METHODS 240 participants with MCI were randomly assigned in equal proportion to four treatment groups: Folic acid alone, vitamin B 12 alone, folic acid plus vitamin B 12 or control without treatment daily for 6 months. Cognition was measured with WAIS-RC. The levels of inflammatory cytokines were measured using ELISA. Changes in cognitive function or blood biomarkers were analyzed by repeated-measure analysis of variance or mixed-effects models. This trial has been registered with trial number ChiCTR-ROC-16008305. RESULTS Compared with control group, the folic acid plus vitamin B 12 group had significantly greater improvements in serum folate, homocysteine, vitamin B 12 and IL-6, TNF-α, MCP-1. The folic acid plus vitamin B 12 supplementation significantly changed the Full Scale IQ (effect size d = 0.169; P = 0.024), verbal IQ (effect size d = 0.146; P = 0.033), Information (d = 0.172; P = 0.019) and Digit Span (d = 0.187; P = 0.009) scores. Post hoc Tukey tests found that folic acid and vitamin B 12 supplementation was significantly more effective than folic acid alone for all endpoints. CONCLUSIONS The combination of oral folic acid plus vitamin B 12 in MCI elderly for six months can significantly improve cognitive performance and reduce the levels of inflammatory cytokines in human peripheral blood. The combination of folic acid and vitamin B 12 was significantly superior to either folic acid or vitamin B 12 alone.
Targeting AngII/AT1R signaling pathway by perindopril inhibits ongoing liver fibrosis in rat

The renin–angiotensin system (RAS) has a substantial role in liver fibrosis, cirrhosis, and portal hypertension. Hence, targeting RAS through angiotensin‐converting enzyme (ACE) inhibitors can mend hepatic fibrosis; the current study was designed to examine the potential fibrosis inhibition activity of perindopril using a rat model of liver fibrosis induced by thioacetamide (TAA). Four groups of rats were used throughout this study, Group I (control group); rats received the vehicle. TAA was used for inducing liver fibrosis in rats by intraperitoneal injection of 200‐mg/kg body weight twice a week for 6 weeks. Group II served as (TAA group). Rats of Groups III and IV were given perindopril at doses of 2 and 8 mg/kg 2 weeks after TAA administration and continued concomitantly with TAA till the end of the experiment. Injection of TAA resulted in a significant increase in aminotransferases' activities and bilirubin with a significant decrease in serum albumin and total protein and a significant decrease in hepatic content of GSH and SOD. Additionally, TAA injection raised the hepatic content of TGF‐β1, α‐SMA, TNF‐α, and level of MDA. Histological and immunohistochemical data presented marked fibrosis in liver sections of TAA‐administrated rats with increased collagen deposition, elevated METAVIR scoring, and increased expression of α‐SMA, caspase‐3, and AT1R. Oral dosing of perindopril for 4 weeks concomitant with TAA could mend the altered parameters near to normal values and abolished the ongoing fibrosis extension. In conclusion, these results demonstrated that perindopril, as ACE inhibitor, could grant a superior remedial nominee in preventing liver fibrosis progression through targeting angiotensin II formation.
Increased uptake of doxorubicin by cells undergoing heat stress does not explain its synergistic cytotoxicity with hyperthermia

Abstract Purpose: A proposed mechanism for the enhanced effectiveness of hyperthermia and doxorubicin (Dox) combinations is increased intracellular Dox concentrations resulting from heat-induced cell stress. The purpose of this study was to determine whether specific varied Dox and heat combinations produce measurable effects greater than the additive combination, and whether these effects can be attributed to heat-induced increases in intracellular Dox concentrations. Methods: HCT116, HT29 and CT26 cells were exposed to Dox and water bath heating independently. A clonogenic survival assay was used to determine cell killing and intracellular Dox concentrations were measured in HCT116 cells with mass spectrometry. Cells were exposed to heating at 42 °C (60 min) and 0.5 µg/ml of Dox at varying intervals. Synergy was determined by curve-fitting and isobologram analysis. Results: All cell lines displayed synergistic effects of combined heating and Dox. A maximum synergistic effect was achieved with simultaneous cell exposure to Dox and heat. For exposures at 42 °C, the synergistic effect was most pronounced at Dox concentrations <0.5 µg/ml. Increased intracellular concentrations of Dox in HCT116 cells caused by heat-stress did not generate a concomitant thermal enhancement. Conclusions: Simultaneous exposure of HCT116 cells to heating and Dox is more effective than sequential exposure. Heat-induced cell responses are accompanied by increased intracellular Dox concentrations; however, clonogenic survival data do not support this as the cause for synergistic cytotoxicity.
Effects of low-frequency noise on human cognitive performances in laboratory

Indoor working and living environments are increasingly exposed to low-frequency noise sources. The well-known relationship between noise conditions and effects on human health requires the development of a proper procedure to evaluate the stress due to acoustical factors. For this purpose, an experiment, based on Soft Metrology principles, was designed to measure the changes of cognitive and physiological parameters (response time and heart rate) on a sample of 25 male and female volunteers, aged 19–29 years, exposed to three types of noise in a hemi-anechoic room. Participants were involved in a cognitive task (Stroop effect) for 10 min in four different conditions: silence, stochastic broadband multi-tonal noise (BBN), stochastic low-frequency multi-tonal noise (LFN1), and low-frequency stationary noise with regular amplitude modulation (LFN2). All sounds were reproduced by two loudspeakers at equivalent sound pressure level of 93 dB. Results showed that in noise conditions, subjects reduced their response times. This is an evidence of growing stress, according to arousal theory. In particular, LFN1 and LFN2 produced cognitive stress comparable to stochastic broadband multi-tonal noise. Furthermore, subdividing the subjects in extroverts and introverts through the Eysenck Personality Questionnaire–Revised psychological test, it was shown that LFN1 and LFN2 produced higher stress effects than stochastic broadband multi-tonal noise on the cognitive performances and a physiological stress comparable to stochastic broadband multi-tonal noise in introverts, whereas no effects were observed in extroverts, as hypothesized by Eysenck. This result highlights the necessity in the future to consider the personality parameter as a key factor in the evaluation of the effects of noise on humans.
Cognitive Processes in Discourse Comprehension: Passive Processes, Reader-Initiated Processes, and Evolving Mental Representations

ABSTRACT As readers move through a text, they engage in various types of processes that, if all goes well, result in a mental representation that captures their interpretation of the text. With each new text segment the reader engages in passive and, at times, reader-initiated processes. These processes are strongly influenced by the readers’ representation of the preceding text and, in turn, update this very same representation. This updated representation forms the backdrop for the processing of the next text segment, and so on. Thus, passive and reader-initiated processes and the evolving representation engage in a continual, intricate interaction as the reader moves through the text. We provide a framework for conceptualizing the interplay between these three components of comprehension and propose that (1) passive and reader-initiated processes interact during reading; (2) a reader’s standards of coherence moderate what kind and to what extent reader-initiated processes take place; (3) reader-initiated processes lie along a continuum from close-to-the-text, coherence-building processes to far-from-the-text, interpretive processes; and (4) the moment-to-moment processes and the evolving mental representation interact in a reciprocal fashion. We present results from recent experiments on key aspects of the framework, and identify questions the framework raises. We conclude with implications from this conceptualization for theoretical models of reading comprehension.