Miracle-dz/UniFAR-FTUs huggingface dataset:
What drives parallel evolution?

Parallel evolution is the repeated evolution of the same phenotype or genotype in evolutionarily independent populations. Here, we use evolve‐and‐resequence experiments with bacteria and yeast to dissect the drivers of parallel evolution at the gene level. A meta‐analysis shows that parallel evolution is often rare, but there is a positive relationship between population size and the probability of parallelism. We present a modeling approach to estimate the contributions of mutational and selective heterogeneity across a genome to parallel evolution. We show that, for two experiments, mutation contributes between ∼10 and 45%, respectively, of the variation associated with selection. Parallel evolution cannot, therefore, be interpreted as a phenomenon driven by selection alone; it must also incorporate information on heterogeneity in mutation rates along the genome. More broadly, the work discussed here helps lay the groundwork for a more sophisticated, empirically grounded theory of parallel evolution.
Antecedents of Electricity-Saving Behavior in Mountain Road Tunnel-Construction Sites: A Multi-Level Modeling Analysis

The electricity-saving behavior of construction workers is helpful in reducing construction costs, protecting the ecological environment, and preventing global climate change. However, there is insufficient research on the electricity-saving behavioral mechanisms of tunnel-construction workers, and their behavior is influenced by their surrounding people including supervisors and co-workers because they are nested in various construction sites and isolated from other acquaintances. This study aims to develop a hierarchical linear model that explores the interrelationships between tunnel-construction workers’ electricity-saving behavior and four influencing factors theoretically and empirically. An organizational-level factor, electricity-saving climate, and three individual-level factors, including attitude, perceived behavioral control, and moral norms, are considered, and 1567 tunnel-construction workers from 41 construction sites mainly located in the southwest of China participated in this study. A six-step procedure for statistical analyses is adopted to test eight hypotheses using questionnaire survey data. The results supported all the hypotheses within the multi-level model and showed that the organizational-level factor played a leading role in predicting workers’ electricity-saving intentions with three individual-level factors positively associated with workers’ electricity-saving intentions. Further, the organizational electricity-saving climate also indirectly affects workers’ electricity-saving intentions through three mediators (individual-level factors), and electricity-saving intention is positively associated with electricity-saving behavior. Consequently, cultivating an electricity-saving climate within an organization is of great benefit to electricity conservation and environmental protection, and several recommendations are provided to improve the practical operability of results. The findings enable a better understanding of electricity-saving behavioral mechanisms and promote a low-carbon lifestyle among tunnel-construction workers.
The effectiveness of low-vision rehabilitation in 2 cohorts derived from the veterans affairs Low-Vision Intervention Trial.

OBJECTIVE To evaluate the effectiveness of low-vision rehabilitation in 2 cohorts derived from the Veterans Affairs Low-Vision Intervention Trial. METHODS In a prospective study, we observed 44 participants randomly assigned to outpatient low-vision rehabilitation who did not receive additional treatment after the trial ended at 4-month follow-up and 56 participants randomly assigned to the waiting-list control group and thereafter to standard therapy. The outcome measures included visual ability domains (reading, mobility, visual information processing, and visual motor skills) and overall visual ability estimated from difficulty ratings using the 48-item Veterans Affairs Low-Vision Visual Functioning Questionnaire. Mean visual ability scores for the treatment and control groups were compared at baseline, 4 months, and 1 year. A mixed-effects model was used to test treatment effects between groups over time. Differences in visual ability mean scores from baseline to 1 year were compared between the 2 groups. Within-group changes in visual ability were compared from baseline to 1 year, from baseline to 4 months, and from 4 months to 1 year. RESULTS At baseline, there were no significant differences in mean visual ability scores between groups. From baseline to 4 months, the treatment effects for all visual ability domains and overall visual ability increased to a maximum in the treatment group (P< .001), whereas the mean scores (except visual motor skills) decreased in the control group (P< .01). From 4 months to 1 year, the differences became smaller. There was a loss of visual ability in reading and visual information processing (but not in visual motor skills, mobility, or overall visual ability) in the treatment group and a gain in all visual ability measures in the control group. Interactions of treatment and follow-up time in the mixed models showed the trend of treatment effects significantly changed over time from baseline to 1 year (P< .001) for all visual ability domains and overall visual ability. Both groups demonstrated improvement in visual ability from baseline to 1 year (P< .001) (except for mobility in the control group). Overall visual ability (but not other visual ability domains) improved more in the treatment group than in the control group (P= .01). CONCLUSIONS Visual ability improved significantly in both groups from baseline to 1 year. The Low-Vision Intervention Trial treatment effect is robust and well maintained for patients with macular diseases.
Turn Around Freezing: Community-Living Turning Behavior in People with Parkinson’s Disease

Difficulty in turning while walking is common among patients with Parkinson’s disease (PD). This difficulty often leads to significant disability, falls, and loss of function; moreover, turning is a common trigger for freezing of gait (FoG). We hypothesized that the quantity and quality of turning mobility while walking during daily life would be different among subjects with PD with and without FoG. Here, we investigated, for the first time, the turning quality during daily life as it relates to FoG in people with PD using a single inertial sensor. Ninety-four subjects with PD (among whom 25 had FoG) wore an inertial sensor attached by a belt on the lower back during normal daily activity consecutively for 3 days. An algorithm identified periods of walking and calculated the number and quality metrics of turning. Quality, but not the quantity, of turning at home was different in freezers compared to the non-freezers. The number of turns (19.3 ± 9.2/30 min in freezers, 22.4 ± 12.9/30 min non-freezers; p = 0.194) was similar in the two groups. Some aspects of quality of turns, specifically mean jerkiness, mean and variability of medio-lateral jerkiness were significantly higher (p < 0.05) in the freezers, compared to non-freezers. Interestingly, subjects with FoG showed specific turning differences in the turns with larger angles compared to those without FoG. These findings suggest that turning during daily activities among patients with PD is impaired in subjects with FoG, compared to subject without freezing. As such, clinical decision-making and rehabilitation assessment may benefit from measuring the quality of turning mobility during daily activities in PD.
Total Colourings of Planar Graphs with Large Girth

It is proved that ifGis a planar graph with total (vertex? edge) chromatic number ? , maximum degree ? and girthg, then ? =? +1 if ? 5 andg? 5, or ? 4 andg? 6, or ? 3 andg? 10. These results hold also for graphs in the projective plane, torus and Klein bottle.
Advance Information and Distorted Beliefs in Macroeconomic and Financial Fluctuations

Fluctuations in the beliefs of economic agents can be driven by current fundamentals, advance information about future fundamentals, or distortions resulting from informational or psychological limitations. This paper presents a dynamic stochastic general equilibrium (DSGE) model that jointly considers all three possibilities and estimates their relative importance for explaining macroeconomic and financial data. To discipline the estimation, direct data on subjective forecasts is included in the set of observable variables. Results indicate that both advance information and distorted beliefs are important. On average about two-thirds of the fluctuations in endogenous variables can be attributed to these two sources. While they are equally important for output and employment, advance information is most important for explaining inflation and investment, and distorted beliefs are most important for explaining stock returns and consumption.
Reduction of Gradient Acoustic Noise in MRI Using SENSE-EPI

A new approach to reduce gradient acoustic noise levels in EPI experiments is presented. Using multichannel RF receive coils, combined with SENSE data acquisition and reconstruction, gradient slew-rates in single-shot EPI were reduced fourfold for rate-2 and ninefold for rate-3 SENSE. Multislice EPI experiments were performed on three different scanner platforms. With 3.4 mm in-plane resolution, measuring 6 slices per second (12 slices with 2000 ms TR), this resulted in average sound pressure level reductions of 11.3 dB(A) and 16.5 dB(A) for rate-2 and rate-3 SENSE, respectively. BOLD fMRI experiments, using visually paced finger-tapping paradigms, showed no detrimental effect of the acoustic noise reduction strategy on temporal noise levels and t scores.
The Effects of School Garden Experiences on Middle School-Aged Students’ Knowledge, Attitudes, and Behaviors Associated With Vegetable Consumption

This study describes the effects of garden-based education on children’s vegetable consumption. As part of a pre—post panel study, 236 students complete the Garden Vegetable Frequency Questionnaire and 161 complete a taste test. Results indicate that school gardening may affect children’s vegetable consumption, including improved recognition of, attitudes toward, preferences for, and willingness to taste vegetables. Gardening also increases the variety of vegetables eaten. Future research should explore whether effects persist over time and if and how changes in children’s behavior affect the behavior of their caregivers. Implications of study findings for policy and practice are discussed. Suggestions for applying results to future health promotions are provided.
Postponement of the Newborn Hearing Screening during the COVID-19 Pandemic; Parental Experiences and Worries

Early identification of hearing loss through newborn hearing screening followed by an early start of intervention has proven to be effective in promoting speech and language development in children with hearing loss. During the COVID-19 pandemic, newborn hearing screening was postponed for a group of newborns in the Netherlands. Therefore, meeting the guidelines for early identification was at risk. In this study, we examine parental attitudes, beliefs, and experiences concerning the hearing screening during the COVID-19 pandemic. Our results indicated that parents (n = 1053) were very positive about newborn hearing screening and their experiences with the screening, even during the COVID-19 pandemic. Parents’ beliefs on the information provision around newborn hearing screening were more inconsistent. The results showed that parents with a postponed hearing screening felt less informed about the hearing screening than parents without a postponed screening. Furthermore, child and family characteristics affected how parents experienced newborn hearing screening. Parents with a premature child were more worried about the hearing abilities of their child before the screening took place. The results also indicate that deafness in the family might lead to parental worries around newborn hearing screening.
Role of E-selectin in Cell Apoptosis Induced by Allogeneic Blood Perfusion in Isolated Mouse Lung

Background. In a model of mouse isolated lung, we have recently demonstrated that E-selectin is involved in the activation of endothelial cells induced by allogeneic blood perfusion. In the present study, we explored the signaling pathway of apoptosis induced by E-selectin triggering. Methods. Lungs were perfused for 3 hours with fresh blood in the absence or presence of an anti-E-selectin monoclonal antibody, or a protein kinase C (PKC), protein tyrosine phosphatase (PTP), or protein tyrosine kinase (PTK) inhibitor. The number of apoptotic cells in lung sections was determined by a TUNEL method. mRNAs for Fas, FasL and caspase-8, and for Bad, Bax, Bcl-w, Bcl-xL and caspase-9, for the FasL and the mitochondrial cytochrome-c pathways of apoptosis, respectively, and mRNA for the effector caspase-3 were quantified in lung tissues by RT-PCR. PTP and Src-PTK activities were also measured. Results. After 3 hours of allogeneic perfusion, we observed a significant increase in: 1) the number of apoptotic cells in lung sections, 2) mRNA levels of FasL, Bcl-xL, caspase-8 and caspase-3, and 3) PTP activity (P < 0.05 compared with isogeneic perfusion). Surprisingly, mRNA levels of the proapoptotic genes Bad and Bax were significantly decreased (P < 0.05). PTK activity and caspase-9 mRNA level were not affected. Blocking anti-E-selectin mAbs and inhibitors for PKC, PTP, and PTK resulted in a significant reduction of apoptosis. Conclusions. In our model, the engagement of E-selectin induced by endothelial cell allogeneic activation appeared to be a prerequisite for lung apoptosis, which involved FasL and increase of PTP activity. Blockade of apoptosis with selective inhibitors may be a promising approach to the treatment/prevention of lung graft injury.
Taming Subgraph Isomorphism for RDF Query Processing

RDF data are used to model knowledge in various areas such as life sciences, Semantic Web, bioinformatics, and social graphs. The size of real RDF data reaches billions of triples. This calls for a framework for efficiently processing RDF data. The core function of processing RDF data is subgraph pattern matching. There have been two completely different directions for supporting efficient subgraph pattern matching. One direction is to develop specialized RDF query processing engines exploiting the properties of RDF data for the last decade, while the other direction is to develop efficient subgraph isomorphism algorithms for general, labeled graphs for over 30 years. Although both directions have a similar goal (i.e., finding subgraphs in data graphs for a given query graph), they have been independently researched without clear reason. We argue that a subgraph isomorphism algorithm can be easily modified to handle the graph homomorphism, which is the RDF pattern matching semantics, by just removing the injectivity constraint. In this paper, based on the state-of-the-art subgraph isomorphism algorithm, we propose an in-memory solution, TurboHOM++, which is tamed for the RDF processing, and we compare it with the representative RDF processing engines for several RDF benchmarks in a server machine where billions of triples can be loaded in memory. In order to speed up TurboHOM++, we also provide a simple yet effective transformation and a series of optimization techniques. Extensive experiments using several RDF benchmarks show that TurboHOM++ consistently and significantly outperforms the representative RDF engines. Specifically, TurboHOM++ outperforms its competitors by up to five orders of magnitude.
Detection of nasopharyngeal cancer using confocal Raman spectroscopy and genetic algorithm technique

Abstract. Raman spectroscopy (RS) and a genetic algorithm (GA) were applied to distinguish nasopharyngeal cancer (NPC) from normal nasopharyngeal tissue. A total of 225 Raman spectra are acquired from 120 tissue sites of 63 nasopharyngeal patients, 56 Raman spectra from normal tissue and 169 Raman spectra from NPC tissue. The GA integrated with linear discriminant analysis (LDA) is developed to differentiate NPC and normal tissue according to spectral variables in the selected regions of 792–805, 867–880, 996–1009, 1086–1099, 1288–1304, 1663–1670, and 1742–1752 cm−1 related to proteins, nucleic acids and lipids of tissue. The GA-LDA algorithms with the leave-one-out cross-validation method provide a sensitivity of 69.2% and specificity of 100%. The results are better than that of principal component analysis which is applied to the same Raman dataset of nasopharyngeal tissue with a sensitivity of 63.3% and specificity of 94.6%. This demonstrates that Raman spectroscopy associated with GA-LDA diagnostic algorithm has enormous potential to detect and diagnose nasopharyngeal cancer.
Activator‐independent transcription of Snf1‐dependent genes in mutants lacking histone tails

Transcriptional regulation of Snf1‐dependent genes occurs in part by histone‐acetylation‐dependent binding of the transcription factor Adr1. Analysis of previously published microarray data indicated unscheduled transcription of a large number of Snf1‐ and Adr1‐dependent genes when either the histone H3 or H4 tail was deleted. Quantitative real‐time PCR confirmed that the tails were important to preserve stringent transcriptional repression of Snf1‐dependent genes when glucose was present. The absence of the tails allowed Adr1 and RNA Polymerase II to bind promoters in normally inhibitory conditions. The promoters escaped glucose repression to a limited extent and the weak constitutive ADH2 transcription induced by deletion of the histone tails was transcription factor‐ and Snf1‐independent. These effects were apparently due to a permissive chromatin structure that allowed transcription in the absence of repression mediated by the histone tails. Deleting REG1, and thus activating Snf1 in the H3 tail mutant enhanced transcription in repressing conditions, indicating that Snf1 and the H3 tail influence transcription independently. Deleting REG1 in the histone H4 tail mutant appeared to be lethal, even in the absence of Snf1, suggesting that Reg1 and the H4 tail have redundant functions that are important for cell viability.
Informally Governing Information: How Criminal Rivalry Leads to Violence against the Press in Mexico

A well-functioning press is crucial for sustaining a healthy democracy. While attacks on journalists occur regularly in many developing countries, previous work has largely ignored where and why journalists are attacked. Focusing on violence by criminal organizations (COs) in Mexico, we offer the first systematic, micro-level analysis of the conditions under which journalists are more likely to be violently targeted. Contrary to popular belief, our evidence reveals that the presence of large, profitable COs does not necessarily lead to fatal attacks against the press. Rather, the likelihood of journalists being killed only increases when rival criminal groups inhabit territories. Rivalry inhibits COs’ ability to control information leaks to the press, instead creating incentives for such leaks to be used as weapons to intensify official enforcement operations against rivals. Without the capacity to informally govern press content, rival criminals affected by such press coverage are more likely to target journalists.
ACL Reconstruction Decision Support

Summary Introduction: This article is part of the Focus Theme of Methods of Information in Medicine on “Methodologies, Models and Algorithms for Patients Rehabilitation”. Objectives: The objective of the proposed approach is to develop a clinical decision support system (DSS) that will help clinicians optimally plan the ACL reconstruction procedure in a patient specific manner. Methods: A full body model is developed in this study with 23 degrees of freedom and 93 muscles. The knee ligaments are modeled as non-linear spring-damper systems and a tibiofemoral contact model was utilized. The parameters of the ligaments were calibrated based on an optimization criterion. Forward dynamics were utilized during simulation for predicting the model’s response to a given set of external forces, posture configuration and physiological parameters. Results: The proposed model is quantified using MRI scans and measurements of the well-known Lachman test, on several patients with a torn ACL. The clinical potential of the proposed framework is demonstrated in the context of flexion-extension, gait and jump actions. The clinician is able to modify and fine tune several parameters such as the number of bundles, insertion position on the tibia or femur and the resting length that correspond to the choices of the surgical procedure and study their effect on the bio-mechanical behavior of the knee. Conclusion: Computational knee models can be used to predict the effect of surgical decisions and to give insight on how different parameters can affect the stability of the knee. Special focus has to be given in proper calibration and experimental validation.
Enhancing soil physical quality and cotton yields through diversification of agricultural practices in central Brazil

Brazil plays an important role in the global agricultural production, making Brazilian productive land use and management a critical issue. This study tested the hypothesis that soil physical quality (SPQ) of the Cerrado biome in central Brazil depends on appropriate crop rotation and tillage practices in cotton (Gossypium hyrsutum [L.])‐based cropping systems and is critical to achieve optimal cotton yields (COT). SPQ of an Oxisol was accessed for layers of 0.0–0.1, 0.1–0.2, and 0.2–0.4 m under conventional tillage (CT) and no‐tillage (NT) systems, in different farming systems, such as cotton monoculture, crop succession, and crop rotation in central Brazil. Variables studied were soil bulk density, total porosity, air permeability, pore continuity index, water content at field capacity, relative saturation at field capacity, the least limiting water range (LLWR), and COT. Soil sampling was performed in 2014, and COT was obtained in the 2013 and 2014 cropping seasons. Conservationist practices, such as crop diversity and absence of soil tillage, improved water availability, enlarged the LLWR, and indicated that brachiaria cultivation positively influences the SPQ, whereas continuous soil tillage and less crop diversity adversely affected SPQ. COT was positively influenced by SPQ aspects regarding the increased water access in the 0.2–0.4 m layer of NT and in the 0.0–0.1 m of CT management. Differences in SPQ, as indicated by the LLWR, were reflected in differences in COT, as well as in soil air permeability in the CT treatments for the 2014 cropping season. Other SPQ variables had no relation to COT.