Miracle-dz/UniFAR-FTUs huggingface dataset:
Transposable Elements Contribute to the Adaptation of Arabidopsis thaliana

Abstract Transposable elements (TEs) are mobile genetic elements with very high mutation rates that play important roles in shaping genome architecture and regulating phenotypic variation. However, the extent to which TEs influence the adaptation of organisms in their natural habitats is largely unknown. Here, we scanned 201 representative resequenced genomes from the model plant Arabidopsis thaliana and identified 2,311 polymorphic TEs from noncentromeric regions. We found expansion and contraction of different types of TEs in different A. thaliana populations. More importantly, we identified two TE insertions that are likely candidates to play a role in adaptive evolution. Our results highlight the importance of variations in TEs for the adaptation of plants in general in the context of rapid global climate change.
A randomized controlled-feeding trial based on the Dietary Guidelines for Americans on cardiometabolic health indexes.

Background The 2010 Dietary Guidelines for Americans (DGA) recommend nutrient needs be met by increasing fruit, vegetable, and whole-grain intake with the use of low-fat or fat-free dairy products and by reducing sodium, solid fats, and added sugars. However, the DGA, as a dietary pattern, have not been tested in an intervention trial. Objective The aim of this study was to evaluate the impact of a DGA-based diet compared with a representative typical American diet (TAD) on glucose homeostasis and fasting lipids in individuals at risk of cardiometabolic disease. Design A randomized, double-blind, controlled 8-wk intervention was conducted in overweight and obese women selected according to indexes of insulin resistance or dyslipidemia. Women were randomly assigned to the DGA or TAD group (n = 28 DGA and 24 TAD). The TAD diet was based on average adult intake from the NHANES 2009-2010. The DGA and TAD diets had respective Healthy Eating Index scores of 98 and 62. All foods and beverages were provided during the intervention. Oral-glucose tolerance and fasting lipids were evaluated at 0, 2, and 8 wk of the intervention. Insulin resistance and sensitivity were estimated with the use of surrogates (e.g., homeostasis model assessment of insulin resistance). Results By design, volunteers maintained their weight during the intervention. Fasting insulin, glucose, triglycerides, oral-glucose tolerance, and indexes of insulin resistance were not affected by either of the diets. Systolic blood pressure decreased in the DGA group (∼-9 mm Hg; P < 0.05). Total and HDL cholesterol also decreased in both groups (P < 0.05). Exploratory analysis comparing volunteers entering the study with insulin resistance and dyslipidemia with those with only dyslipidemia did not show an effect of pre-existing conditions on glucose tolerance or fasting lipid outcomes. Conclusions The consumption of a DGA dietary pattern for 8 wk without weight loss reduced systolic blood pressure. There were no differences between the DGA and TAD diets in fasting insulin, glucose, indexes of insulin resistance, or fasting lipids. This trial was registered at www.clinicaltrials. gov as NCT02298725.
Power Minimization-Based Joint Task Scheduling and Resource Allocation in Downlink C-RAN

In this paper, we consider the network power minimization problem in a downlink cloud radio access network (C-RAN), taking into account the power consumed at the baseband unit (BBU) for computation and the power consumed at the remote radio heads and fronthaul links for transmission. The power minimization problem for transmission is a fast time-scale issue, whereas the power minimization problem for computation is a slow time-scale issue. Therefore, the joint network power minimization problem is a mixed time-scale problem. To tackle the time-scale challenge, we introduce large system analysis to turn the original fast time-scale problem into a slow time-scale one that only depends on the statistical channel information. In addition, we propose a bound improving branch-and-bound algorithm and a combinational algorithm to find the optimal and suboptimal solutions to the power minimization problem for computation, respectively, and propose an iterative coordinate descent algorithm to find the solutions to the power minimization problem for transmission. Finally, a distributed algorithm based on hierarchical decomposition is proposed to solve the joint network power minimization problem. In summary, this paper provides a framework to investigate how execution efficiency and computing capability at BBU as well as delay constraint of tasks can affect the network power minimization problem in C-RANs.
Code-Mixed Sentiment Analysis Using Machine Learning and Neural Network Approaches

Sentiment Analysis for Indian Languages (SAIL)-Code Mixed tools contest aimed at identifying the sentence level sentiment polarity of the code-mixed dataset of Indian languages pairs (Hi-En, Ben-Hi-En). Hi-En dataset is henceforth referred to as HI-EN and Ben-Hi-En dataset as BN-EN respectively. For this, we submitted four models for sentiment analysis of code-mixed HI-EN and BN-EN datasets. The first model was an ensemble voting classifier consisting of three classifiers - linear SVM, logistic regression and random forests while the second one was a linear SVM. Both the models used TF-IDF feature vectors of character n-grams where n ranged from 2 to 6. We used scikit-learn (sklearn) machine learning library for implementing both the approaches. Run1 was obtained from the voting classifier and Run2 used the linear SVM model for producing the results. Out of the four submitted outputs Run2 outperformed Run1 in both the datasets. We finished first in the contest for both HI-EN with an F-score of 0.569 and BN-EN with an F-score of 0.526.
On the Dependability and Feasibility of Layperson Ratings of Divergent Thinking

A new system for subjective rating of responses to divergent thinking tasks was tested using raters recruited from Amazon Mechanical Turk. The rationale for the study was to determine if such raters could provide reliable (aka generalizable) ratings from the perspective of generalizability theory. To promote reliability across the Alternative Uses and Consequence task prompts often used by researchers as measures of Divergent Thinking, two parallel scales were developed to facilitate feasibility and validity of ratings performed by laypeople. Generalizability and dependability studies were conducted separately for two scoring systems: the average-rating system and the snapshot system. Results showed that it is difficult to achieve adequate reliability using the snapshot system, while good reliability can be achieved on both task families using the average-rating system and a specific number of items and raters. Additionally, the construct validity of the average-rating system is generally good, with less validity for certain Consequences items. Recommendations for researchers wishing to adopt the new scales are discussed, along with broader issues of generalizability of subjective creativity ratings.
The Racer's Mind—How Core Perceptual-Cognitive Expertise Is Reflected in Deliberate Practice Procedures in Professional Motorsport

The exceptional performance of elite practitioners in domains like sports or chess is not a reflection of just exceptional general cognitive ability or innate sensorimotor superiority. Decades of research on expert performance has consistently shown that experts in all fields go to extraordinary lengths to acquire their perceptual-cognitive and motor abilities. Deliberate Practice (DP) refers to special (sub)tasks that are designed to give immediate and accurate feedback and performed repetitively with the explicit goal of improving performance. DP is generally agreed to be one of the key ingredients in acquisition of expertise (not necessarily the only one). Analyzing in detail the specific aspects of performance targeted by DP procedures may shed light on the underlying cognitive processes that support expert performance. Document analysis of professional coaching literature is one knowledge elicitation method that can be used in the early phases of inquiry to glean domain information about the skills experts in a field are required to develop. In this study this approach is applied to the domain of motor racing - specifically the perceptual-cognitive expertise enabling high-speed curve negotiation. A systematic review procedure is used to establish a corpus of texts covering the entire 60 years of professional motorsport textbooks. Descriptions of specific training procedures (that can be unambiguously interpreted as DP procedures) are extracted, and then analyzed within the hierarchical task analysis framework driver modeling. Hypotheses about the underlying cognitive processes are developed on the basis of this material. In the traditional psychological literature, steering and longitudinal control are typically considered “simple” reactive tracking tasks (model-free feedback control). The present findings suggest that—as in other forms expertise—expert level driving skill is in fact dependent on vast body of knowledge, and driven by top-down information. The knowledge elicitation in this study represents a first step toward a deeper psychological understanding of the complex cognitive underpinnings of expert performance in this domain.
Glucocorticoid administration restores salience network activity in patients with spider phobia

Glucocorticoids reduce phobic fear in patients with anxiety disorders. Although the neurobiology of anxiety disorders is not fully understood, convergent structural and functional neuroimaging studies have identified abnormalities in various brain regions, including those in the salience network (SN) and default mode network (DMN). Here, we examine the effects of glucocorticoid administration on SN and DMN activity during the processing of phobic stimuli.
Effect of omega-3 supplements on plasma apolipoprotein C-III concentrations: a systematic review and meta-analysis of randomized controlled trials

Abstract Background: Apolipoprotein C-III (apo C-III) is a key regulator of triglycerides metabolism. The aim of this meta-analysis was to assess the effect of fish omega-3 polyunsaturated fatty acids (PUFAs) on apo C-III levels. Methods: Randomized placebo-controlled trials investigating the impact of omega-3 on apo C-III levels were searched in PubMed-Medline, SCOPUS, Web of Science and Google Scholar. A random-effects model and generic inverse variance method were used for quantitative data synthesis. Sensitivity analysis was conducted using the leave-one-out method. A weighted random-effects meta-regression was performed to evaluate the impact of potential confounders on glycemic parameters. Results: This meta-analysis comprising 2062 subjects showed a significant reduction of apo C-III concentrations following treatment with omega-3 (WMD: −22.18 mg/L, 95% confidence interval: −31.61, −12.75, p < .001; I2: 88.24%). Subgroup analysis showed a significant reduction of plasma apo C-III concentrations by eicosapentaenoic acid (EPA) ethyl esters but not omega-3 carboxylic acids or omega-3 ethyl esters. There was a greater apo C-III reduction with only EPA as compared with supplements containing EPA and docosahexaenoic acid (DHA) or only DHA. A positive association between the apo C-III-lowering effect of omega-3 with baseline apo C-III concentrations and treatment duration was found. Conclusions: This meta-analysis has shown that omega-3 PUFAs might significantly decrease apo C-III. Key messages Omega-3 PUFA supplements significantly reduce apo C-III plasma levels, particularly in hypertriglyceridemic patients when applied in appropriate dose (more than 2 g/day) Triglyceride (TG)-lowering effect is achieved via peroxisome proliferator-activated receptors α Further studies should address the effect of omega-3 PUFAs alone or with other lipid-lowering drugs in order to provide a final answer whether apo C-III could be an important target for prevention of cardiovascular disease New apo C-III antisense oligonucleotide drug (Volanesorsen) showed to be promising in decreasing elevated TGs by reducing levels of apo C-III mRNA
A Freeloader? The Highly Eroded Yet Large Genome of the Serratia symbiotica Symbiont of Cinara strobi

Abstract Genome reduction is pervasive among maternally inherited bacterial endosymbionts. This genome reduction can eventually lead to serious deterioration of essential metabolic pathways, thus rendering an obligate endosymbiont unable to provide essential nutrients to its host. This loss of essential pathways can lead to either symbiont complementation (sharing of the nutrient production with a novel co-obligate symbiont) or symbiont replacement (complete takeover of nutrient production by the novel symbiont). However, the process by which these two evolutionary events happen remains somewhat enigmatic by the lack of examples of intermediate stages of this process. Cinara aphids (Hemiptera: Aphididae) typically harbor two obligate bacterial symbionts: Buchnera and Serratia symbiotica. However, the latter has been replaced by different bacterial taxa in specific lineages, and thus species within this aphid lineage could provide important clues into the process of symbiont replacement. In the present study, using 16S rRNA high-throughput amplicon sequencing, we determined that the aphid Cinara strobi harbors not two, but three fixed bacterial symbionts: Buchnera aphidicola, a Sodalis sp. , and S. symbiotica. Through genome assembly and genome-based metabolic inference, we have found that only the first two symbionts (Buchnera and Sodalis) actually contribute to the hosts’ supply of essential nutrients while S. symbiotica has become unable to contribute towards this task. We found that S. symbiotica has a rather large and highly eroded genome which codes only for a few proteins and displays extensive pseudogenization. Thus, we propose an ongoing symbiont replacement within C. strobi, in which a once “competent” S. symbiotica does no longer contribute towards the beneficial association. These results suggest that in dual symbiotic systems, when a substitute cosymbiont is available, genome deterioration can precede genome reduction and a symbiont can be maintained despite the apparent lack of benefit to its host.
Development and Evolution of Cerebral and Cerebellar Cortex

Cerebral cortex and cerebellar cortex both vary enormously across species in their size and complexity of convolutions. We discuss the development and evolution of cortical structures in terms of anatomy and functional organization. We propose that the distinctive shapes of cerebral and cerebellar cortex can be explained by relatively few developmental processes, notably including mechanical tension along axons and dendrites. Regarding functional organization, we show how maps of myelin content in cerebral cortex are evolutionarily conserved across primates but differ in the proportion of cortex devoted to sensory, cognitive, and other functions. We summarize recent progress and challenges in (i) parcellating cerebral cortex into a mosaic of distinct areas, (ii) distinguishing cortical areas that correspond across species from those that are present in one species but not another, and (iii) using this information along with surface-based interspecies registration to gain deeper insights into cortical evolution. We also comment on the methodological challenges imposed by the differences in anatomical and functional organization of cerebellar cortex relative to cerebral cortex.
The “Golden Angels”: effects of trained volunteers on specialling and readmission rates for people with dementia and delirium in rural hospitals

ABSTRACT Objectives: Evaluate the clinical outcomes for patients with dementia, delirium, or at risk for delirium supported by the person-centered volunteer program in rural acute hospitals. Design: A non-randomized, controlled trial. Participants: Older adults admitted to seven acute hospitals in rural Australia. Intervention (n = 270) patients were >65 years with a diagnosis of dementia or delirium or had risk factors for delirium and received volunteer services. Control (n = 188) patients were admitted to the same hospital 12 months prior to the volunteer program and would have met eligibility criteria for the volunteer program, had it existed. Intervention: Trained volunteers provided 1:1 person-centered care with a focus on nutrition and hydration support, hearing and visual aids, activities, and orientation. Measures: Medical record audits provided data on volunteer visits, diagnoses, length of stay (LOS), behavioral incidents, readmission, specialling, mortality, admission to residential care, falls, pressure ulcers, and medication use. Results: Across all sites, there was a significant reduction in rates of 1:1 specialling and 28 day readmission for patients receiving the volunteer intervention. LOS was significantly shorter for the control group. There were no differences in other patient outcomes for the intervention and control groups. Conclusion: The volunteer intervention is a safe, effective, and replicable way to support older acute patients with dementia, delirium, or risk factors for delirium in rural hospitals. Further papers will report on cost effectiveness, family carer, volunteer, and staff experiences of the program.
p15PAF binding to PCNA modulates the DNA sliding surface

Abstract p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF–PCNA–DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η–PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.
Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid

ABSTRACT Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a growing health threat worldwide. Efforts to identify novel antibodies that target S. aureus cell surface antigens are a promising direction in the development of antibiotics that can halt MRSA infection. We biochemically and structurally characterized three patient-derived MRSA-targeting antibodies that bind to wall teichoic acid (WTA), which is a polyanionic surface glycopolymer. In S. aureus, WTA exists in both α- and β-forms, based on the stereochemistry of attachment of a N-acetylglucosamine residue to the repeating phosphoribitol sugar unit. We identified a panel of antibodies cloned from human patients that specifically recognize the α or β form of WTA, and can bind with high affinity to pathogenic wild-type strains of S. aureus bacteria. To investigate how the β-WTA specific antibodies interact with their target epitope, we determined the X-ray crystal structures of the three β-WTA specific antibodies, 4462, 4497, and 6078 (Protein Data Bank IDs 6DWI, 6DWA, and 6DW2, respectively), bound to a synthetic WTA epitope. These structures reveal that all three of these antibodies, while utilizing distinct antibody complementarity-determining region sequences and conformations to interact with β-WTA, fulfill two recognition principles: binding to the β-GlcNAc pyranose core and triangulation of WTA phosphate residues with polar contacts. These studies reveal the molecular basis for targeting a unique S. aureus cell surface epitope and highlight the power of human patient-based antibody discovery techniques for finding novel pathogen-targeting therapeutics.
Laparoscopic or open distal gastrectomy after neoadjuvant chemotherapy for advanced gastric cancer: study protocol for a randomised phase II trial

Introduction Current guidelines recommend open gastrectomy with D2 lymph node dissection and adjuvant chemotherapy as the standard treatment for advanced gastric cancer. However, the prognosis is not satisfactory. Perioperative chemotherapy has been proposed to improve survival. Although still in debate, the efficacy of laparoscopic distal gastrectomy (LDG) in patients with advanced gastric cancer has been demonstrated in a few trials. Therefore, LDG after neoadjuvant chemotherapy can be a candidate for future standard treatment on advanced distal gastric cancer. We propose a randomised phase II trial to compare LDG and open distal gastrectomy (ODG) after neoadjuvant chemotherapy for advanced gastric cancer. Methods and analysis To test the efficacy and safety, a randomised, open-label, single-centre, phase II trial was designed to evaluate the non-inferiority of LDG compared with ODG after neoadjuvant chemotherapy, with 3-year recurrence-free survival as the primary endpoint. The chosen critical value of a non-inferiority margin was an increase of <8%. The study started in 2015 and enrolled 96 patients according to a prior sample size calculation. Intention-to-treat and per-protocol approach will be used for efficacy analysis, and as-treated analysis will be applied for safety analysis. The survival curves will be constructed as time-to-event plots using the Kaplan-Meier method and compared using log-rank tests and Cox proportional hazards model. All statistical analyses will be conducted in standard statistical software with a significance level of 0.05. Ethics and dissemination This study was approved by the Peking University Cancer Hospital Ethics Committee. The results will be submitted for publication in peer-reviewed journals. Trial registration number NCT02404753; Pre-results.