Miracle-dz/UniFAR-FTUs huggingface dataset:
REVIEW: PART OF A SPECIAL ISSUE ON DEVELOPMENTAL ROBUSTNESS AND SPECIES DIVERSITY Developmental mechanisms underlying variable, invariant and plastic phenotypes

Background Discussions of phenotypic robustness often consider scenarios where invariant phenotypes are optimal and assume that developmental mechanisms have evolved to buffer the phenotypes of speciﬁc traits against stochastic and environmental perturbations. However, plastic plant phenotypes that vary between environments or variable phenotypes that vary stochastically within an environment may also be advantageous in some scenarios. (cid:2) Scope Here the conditions under which invariant, plastic and variable phenotypes of speciﬁc traits may confer a selective advantage in plants are examined. Drawing on work from microbes and multicellular organisms, the mechanisms that may give rise to each type of phenotype are discussed. (cid:2) Conclusion In contrast to the view of robustness as being the ability of a genotype to produce a single, invariant phenotype, changes in a phenotype in response to the environment, or phenotypic variability within an environment, may also be delivered consistently (i.e. robustly). Thus, for some plant traits, mechanisms have probably evolved to produce plasticity or variability in a reliable manner.
From personal fear to mass panic: The neurological basis of crowd perception

Recent studies have investigated the neural correlates of how we perceive emotions of individuals or a group of individuals using images of individual bodily expressions. However, it is still largely unknown how we perceive the emotion of a dynamic crowd. This fMRI study used realistic videos of a large group of people expressing fearful, happy or neutral emotions. Furthermore, the emotions were expressed by either unrelated individuals in the group or by an interacting group. It was hypothesized that the dynamics between the people in a crowd is a more salient signal than merely the emotion of the crowd. Second, it was expected that the group interaction is of special importance in a fearful or “panic” situation, as opposed to a happy or neutral situation. Using a fast‐event related design, it was revealed that observing interactive individuals, more so than independently expressive individuals, activated networks related to the perception, execution and integration of action and emotion. Most importantly, the interactive or panicked crowds, as opposed to the individually fearful crowds, triggered more anticipatory and action preparation activity, whereas the brain was less sensitive to the dynamics of individuals in a happy or neutral crowd. This is the first study to assess the effect of the dynamics between people and the collectively displayed emotion as an important aspect of emotional crowd perception. Hum Brain Mapp 36:2338–2351, 2015. © 2015 Wiley Periodicals, Inc.
Perceived mother and father acceptance-rejection predict four unique aspects of child adjustment across nine countries.

BACKGROUND It is generally believed that parental rejection of children leads to child maladaptation. However, the specific effects of perceived parental acceptance-rejection on diverse domains of child adjustment and development have been incompletely documented, and whether these effects hold across diverse populations and for mothers and fathers are still open questions. METHODS This study assessed children's perceptions of mother and father acceptance-rejection in 1,247 families from China, Colombia, Italy, Jordan, Kenya, the Philippines, Sweden, Thailand, and the United States as antecedent predictors of later internalizing and externalizing behavior problems, school performance, prosocial behavior, and social competence. RESULTS Higher perceived parental rejection predicted increases in internalizing and externalizing behavior problems and decreases in school performance and prosocial behavior across 3 years controlling for within-wave relations, stability across waves, and parental age, education, and social desirability bias. Patterns of relations were similar across mothers and fathers and, with a few exceptions, all nine countries. CONCLUSIONS Children's perceptions of maternal and paternal acceptance-rejection have small but nearly universal effects on multiple aspects of their adjustment and development regardless of the family's country of origin.
OUTER NUCLEAR LAYER THINNING IN PACHYCHOROID PIGMENT EPITHELIOPATHY

Purpose: To compare the average thicknesses of central inner retinal layers in eyes with pachychoroid pigment epitheliopathy (PPE), with uncomplicated pachychoroid (UCP), and of healthy subjects. Methods: Medical records of patients with PPE and UCP were retrospectively reviewed. Twenty-nine eyes with foveal PPE, 30 eyes with UCP, and 29 eyes of healthy subjects were included. Spectral-domain optical coherence tomography with enhanced depth imaging was used for all optical coherence tomography scans. Mean central inner retinal layer thicknesses were measured in 1-mm-diameter circle with Spectralis automated segmentation software and compared between groups. Results: The outer nuclear layer (ONL) and the sum of the outer plexiform layer and ONL were significantly thinner in the PPE group than the UCP and control groups (ONL: P < 0.001, P < 0.001; outer plexiform layer + ONL: P = 0.002, P = 0.002, respectively). There was no significant difference between groups regarding thickness of the outer plexiform layer and other inner retinal layers. Eyes with UCP and normal eyes did not differ. Conclusion: The ONL is thinner in eyes with PPE. The degenerative process of pachychoroid spectrum diseases may begin with retinal pigment epithelium alterations before subretinal fluid accumulation. The PPE lesions, commonly seen above pachyvessels, may be an indicator of photoreceptor apoptosis.
The cellular composition of the marsupial neocortex

In the current investigation we examined the number and proportion of neuronal and non‐neuronal cells in the primary sensory areas of the neocortex of a South American marsupial, the short‐tailed opossum (Monodelphis domestica). The primary somatosensory (S1), auditory (A1), and visual (V1) areas were dissected from the cortical sheet and compared with each other and the remaining neocortex using the isotropic fractionator technique. We found that although the overall sizes of V1, S1, A1, and the remaining cortical regions differed from each other, these divisions of the neocortex contained the same number of neurons, but the remaining cortex contained significantly more non‐neurons than the primary sensory regions. In addition, the percent of neurons was higher in A1 than in the remaining cortex and the cortex as a whole. These results are similar to those seen in non‐human primates. Furthermore, these results indicate that in some respects, such as number of neurons, the neocortex is homogenous across its extent, whereas in other aspects of organization, such as non‐neuronal number and percentage of neurons, there is non‐uniformity. Whereas the overall pattern of neuronal distribution is similar between short‐tailed opossums and eutherian mammals, short‐tailed opossum have a much lower cellular and neuronal density than other eutherian mammals. This suggests that the high neuronal density cortices of mammals such as rodents and primates may be a more recently evolved characteristic that is restricted to eutherians, and likely contributes to the complex behaviors we see in modern mammals. J. Comp. Neurol. 522:2286–2298, 2014. © 2014 Wiley Periodicals, Inc.
Asynchronous Transmitter Release from Cholecystokinin-Containing Inhibitory Interneurons Is Widespread and Target-Cell Independent

Neurotransmitter release at most central synapses is synchronized to the timing of presynaptic action potentials. Here, we show that three classes of depolarization-induced suppression of inhibition-expressing, cholecystokinin (CCK)-containing, hippocampal interneurons show highly asynchronous release in response to trains of action potentials. This asynchrony is correlated to the class of presynaptic interneuron but is unrelated to their postsynaptic cell target. Asynchronous and synchronous release from CCK-containing interneurons show a slightly different calcium dependence, such that the proportion of asynchronous release increases with external calcium concentration, possibly suggesting that the modes of release are mediated by different calcium sensors. Asynchronous IPSCs include very large (up to 500 pA/7nS) amplitude events, which persist in low extracellular calcium and strontium, showing that they result from quantal transmitter release at single release sites. Finally, we show that asynchronous release is prominent in response to trains of presynaptic spikes that mimic natural activity of CCK-containing interneurons. That asynchronous release from CCK-containing interneurons is a widespread phenomenon indicates a fundamental role for these cells within the hippocampal network that is distinct from the phasic inhibition provided by parvalbumin-containing interneurons.
Do children and their parents eat a similar diet? Resemblance in child and parental dietary intake: systematic review and meta-analysis

Objectives Parents are believed to have a strong influence on children's eating behaviours. However, previous findings on child–parent resemblance in dietary intakes are mixed. We systematically reviewed and meta-analysed the association (correlations) based on published studies. Methods We searched related studies published since 1980 and found 24 studies meeting inclusion criteria for review and 15 for meta-regression analysis. We compared the associations between parent–child pairs, nutrients, over time and by dietary assessment method. Results Most studies were based on small samples. Overall, they suggest a moderate or weak association, but findings varied remarkably. Our meta-analysis showed that average Fisher's transformed correlations were 0.20 (95% CI 0.13 to 0.28) for fat (% energy); for energy, 0.21 (0.18 to 0.24). The correlations varied by parent–child pairs, dietary assessment and countries. Food frequency questionnaires or mixed approaches yielded lower correlation than 24-h recalls or food records. Child self-reported intakes showed weaker correlation and better methodology quality showed stronger correlation in fat intake (% energy), which also became weaker over time. Conclusions Overall, the resemblance is weak, and it varied considerably across studies, nutrients, foods and parent–child pairs.
Pathway analysis by adaptive combination of P‐values

It is increasingly recognized that pathway analyses—a joint test of association between the outcome and a group of single nucleotide polymorphisms (SNPs) within a biological pathway—could potentially complement single‐SNP analysis and provide additional insights for the genetic architecture of complex diseases. Building upon existing P‐value combining methods, we propose a class of highly flexible pathway analysis approaches based on an adaptive rank truncated product statistic that can effectively combine evidence of associations over different SNPs and genes within a pathway. The statistical significance of the pathway‐level test statistics is evaluated using a highly efficient permutation algorithm that remains computationally feasible irrespective of the size of the pathway and complexity of the underlying test statistics for summarizing SNP‐ and gene‐level associations. We demonstrate through simulation studies that a gene‐based analysis that treats the underlying genes, as opposed to the underlying SNPs, as the basic units for hypothesis testing, is a very robust and powerful approach to pathway‐based association testing. We also illustrate the advantage of the proposed methods using a study of the association between the nicotinic receptor pathway and cigarette smoking behaviors. Genet. Epidemiol. 33:700–709, 2009. Published 2009 Wiley‐Liss, Inc.
Auditory mechanics of the tectorial membrane and the cochlear spiral

Purpose of reviewThis review is timely and relevant because new experimental and theoretical findings suggest that cochlear mechanics from the nanoscale to the macroscale are affected by the mechanical properties of the tectorial membrane and the cochlea's spiral shape. Recent findingsMain tectorial membrane themes addressed in this review are composition and morphology, nanoscale mechanical interactions with the outer hair cell bundle, macroscale longitudinal coupling, fluid interaction with inner hair cell bundles, and macroscale dynamics and waves. Main cochlear spiral themes are macroscale, low-frequency energy focusing and microscale organ of Corti shear gain. SummaryRecent experimental and theoretical findings reveal exquisite sensitivity of cochlear mechanical performance to tectorial membrane structural organization, mechanics, and its positioning with respect to hair bundles. The cochlear spiral geometry is a major determinant of low-frequency hearing. These findings suggest a number of important research directions.
Can auditory and visual speech perception be trained within a group setting?

PURPOSE This study attempted to determine whether auditory-only and auditory-visual speech perception could be trained in a group format. METHOD A randomized controlled trial with at least 16 participants per group was completed. A training-only group completed at least 5 hr of group speech perception training; a training plus psychosocial group completed at least 5 hr of group speech perception training and psychosocial exercises; and a control group did not receive training. Evaluations were conducted before and after training and included analytic and synthetic measures of speech perception, hearing loss-related and generic quality of life scales, and a class evaluation form. RESULTS No significant group changes were measured on any of the analytic auditory-only or auditory-visual measures of speech perception, yet the majority of training participants (regardless of training group) reported improvement in auditory and auditory-visual speech perception. The training participants demonstrated a significant reduction on the emotional subscale of the hearing loss-related quality of life scale, while the control participants did not demonstrate a change on this subscale. CONCLUSIONS Benefits of group audiologic rehabilitation classes may not result from an actual improvement in auditory or visual speech perception abilities, but participants still perceive training in these areas as useful.
An in vitro human skeletal muscle model: coculture of myotubes, neuron-like cells, and the capillary network

This study reports the generation of a new human muscle tissue equivalent from skeletal muscle-derived stem cells and human umbilical vein endothelial cells (HUVECs). Skeletal muscle stem cells were isolated by the preplate technique and differentiated into neuron-like cells that were positive for neuronal beta-tubulin3 and nestin and negative for the astrocyte marker glial fibrillary acidic protein (GFAP). Coculture of skeletal muscle stem cells with the HUVECs under optimized fetal bovine serum and media conditions resulted in formation of a capillary network among the multinucleated myotubes. The neuron-like cells derived from the human skeletal muscle stem cells were seeded onto vascularized myotubes to obtain the neuromuscular junctions in the coculture. At the end of 24 h of coculture, the neuron-like cells were found to be in association with the myotubes. This model represents a novel complex in vitro human skeletal muscle model containing advanced capillary networks and interacting myotubes and neurons, and it can be used for in vitro drug testing or for skeletal muscle regeneration either through application of cellular therapy or cell-laden tissue-engineered muscle constructs.
Digital pancreatoscopy in the evaluation of main duct intraductal papillary mucinous neoplasm: a multicenter study

Abstract Background The aim of this study was to investigate the outcomes of digital pancreatoscopy in main duct intraductal papillary mucinous neoplasm (MD-IPMN). Methods This was a multicenter retrospective study. Outcomes analyzed were safety, incremental pathology yield compared with previous cross-sectional/endoscopic ultrasound (EUS) imaging, and whether the surgical procedure was dictated by the pancreatoscopy. Results A total of 31 patients were enrolled from six tertiary care centers. Overall, 42 % of cases had findings on pancreatoscopy that were not seen on cross-sectional imaging or EUS. Digital pancreatoscopy dictated the type of surgery performed in 13 patients (42 %) who underwent surgery. However, in patients with a diffusely dilated pancreatic duct (> 10 mm), the pancreatoscopy dictated the type of surgery in 77 % of cases vs. 17 % of cases in the focally dilated pancreatic duct group (10/13 vs. 3/18; P = 0.001). Conclusion Digital pancreatoscopy should be considered in the diagnostic algorithm of MD-IPMN in patients with a diffusely dilated pancreatic duct and without any focal lesions seen on cross-sectional imaging or EUS.
Strategies to Prevent Transmission of Methicillin-Resistant Staphylococcus aureus in Acute Care Hospitals

Previously published guidelines are available that provide comprehensive recommendations for detecting and preventing healthcare-associated infections (HAIs). Our intent in this document is to highlight practical recommendations in a concise format to assist acute care hospitals in their efforts to prevent transmission of methicillin-resistant Staphylococcus aureus (MRSA). Refer to the Society for Healthcare Epidemiology of America/Infectious Diseases Society of America “Compendium of Strategies to Prevent Healthcare-Associated Infections” Executive Summary, Introduction, and accompanying editorial for additional discussion. 1. Burden of HAIs caused by MRSA in acute care facilities a. In the United States, the proportion of hospital-associated S. aureus infections that are caused by strains resistant to methicillin has steadily increased. In 2004, MRSA accounted for 63% of S. aureus infections in hospitals. b. Although the proportion of S. aureus–associated HAIs among intensive care unit (ICU) patients that are due to methicillin-resistant strains has increased (a relative measure of the MRSA problem), recent data suggest that the incidence of central line–associated bloodstream infection caused by MRSA (an absolute measure of the problem) has decreased in several types of ICUs since 2001. Although these findings suggest that there has been some success in preventing nosocomial MRSA transmission and infection, many patient groups continue to be at risk for such transmission. c. MRSA has also been documented in other areas of the hospital and in other types of healthcare facilities, including those that provide long-term care.
Who Subscribe to Identity Theft Protection Service? An Exploration of Antecedent Factors

This study explores the antecedent factors that influence a person’s adoption of identity theft protection service. Fifteen factors related to the demographic, behavioral, and psychological attributes of individuals are examined. Data gathered from 600 consumers (including 145 subscribers and 455 non-subscribers) were tested using Logistic Regression, Decision Tree, Neural Network, and Support Vector Machines (SVM) methods. The accuracy and sensitivity measures suggest that SVM performs the best. Further analysis based on SVM suggests that past victimization related to personal information and credit cards, and also gender, are the three most important antecedents to subscription to identity theft protection service.
Rap‐GEF/Rap signaling restricts the formation of supernumerary spermathecae in Drosophila melanogaster

Sperm storage in the female is a key factor for reproductive success in a variety of organisms, including Drosophila melanogaster. The spermathecae (SP) are the Drosophila organs for long‐term storage. While wild‐type female flies have two SP, occasionally, three or four SP have been observed in mutant flies. However, the molecular mechanism of SP formation is unknown. Here we show that loss of function of a Drosophila Rap‐GEF (GEF26) result in an occurrence of the supernumerary SP; females have three SP (varies from 11 to 62% in different allele combinations) instead of the normal two SP. In addition, the Gef26 mutant flies also have ectopic wing veins and extra mechanosensory organs. The supernumerary SP phenotype of the Gef26 mutation can be enhanced by the Drosophila Rap mutations and rescued by overexpressing the cell adhesion molecule DE‐cadherin. These data suggest that the Rap‐GEF/Rap signaling controls the formation of supernumerary spermathecae through modulating cell adhesion in Drosophila.
Phase I Clinical Trial of Ipilimumab in Pediatric Patients with Advanced Solid Tumors

Purpose: Ipilimumab is a first-in-class immune checkpoint inhibitor approved for treatment of metastatic melanoma but not studied in children until this phase I protocol. Experimental Design: This study examined safety, pharmacokinetics, and immunogenicity, and immune correlates of ipilimumab administered to subjects ≤21 years old with recurrent or progressive solid tumors. Dose escalation cohorts received 1, 3, 5, or 10 mg/m2 intravenously every 3 weeks in a 3 + 3 design. Response was assessed after 6 weeks and 12 weeks, and then every 3 months. Treatment was continued until disease progression or unacceptable toxicity. Results: Thirty-three patients received 72 doses of ipilimumab. Patients enrolled had melanoma (n = 12), sarcoma (n = 17), or other refractory solid tumors (n = 4). Immune-related adverse events included pancreatitis, pneumonitis, colitis, endocrinopathies, and transaminitis with dose-limiting toxicities observed at 5 and 10 mg/kg dose levels. Pharmacokinetics revealed a half-life of 8 to 15 days. At day 21, subjects had increased levels of cycling T cells, but no change in regulatory T-cell populations. Six subjects had confirmed stable disease for 4 to 10 cycles (melanoma, osteosarcoma, clear cell sarcoma, and synovial sarcoma). Conclusions: Ipilimumab was safely administered to pediatric patients using management algorithms for immune-related toxicities. The spectrum of immune-related adverse events is similar to those described in adults; however, many of the pediatric toxicities were evident after a single dose. Although no objective tumor regressions were observed with ipilimumab as a single agent, subjects with immune-related toxicities had an increased overall survival compared with those who showed no evidence of breaking tolerance. Clin Cancer Res; 22(6); 1364–70. ©2015 AACR.
Case based Indonesian closed domain question answering system with real world questions

Number of people having expertise in a certain domain is less than people who need information in that domain. In this situation, an automatic question answering (QA) system is necessary. Observing available manual QA sites on internet, the real world question that people usually ask have different expected answer type (EAT) compared to a common automatic QA. Addressing a case study of a religion domain which makes it a closed domain QA, we proposed the EAT into 6 types: LAW, DEFINITION, COMPARISON, METHOD, TIME and PERSON. Different with common QA approach, we built the QA system using case based approach which consists of two main components: Question Analyzer and Case Retriever. Related with the case based reasoning (CBR) framework, these two main components act as the Retrieve and Reuse process while the Revise and Retain process is handle by Case Retainer component. The QA system was built using available Indonesian Natural Language Processing (NLP) tools and FreeCBR as the CBR library. The experiments were done to calculate the accuracy and testing the system with unknown case. By using 77 cases collected from internet with assumption that all answers are available, the experiments achieved 97% accuracy. And by using 10 test cases for the unknown case, the similarity score calculated by the system showed that the test questions have no answer in the available case base.