Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuroendocrine Control of Drosophila Larval Light Preference

Looking for the Dark Mature Drosophila larvae wander away from food and seek a dark site for pupation. While investigating this phenomenon Yamanaka et al. (p. 1113) found that four prothoracicotropic hormone (PTTH)–producing neurons mediate light preference in the central brain. PTTH circulates in the hemolymph and signals via its receptor, Torso, to two light sensors, sensitizing them for light detection. The larvae can then transform from wandering larvae into immobile pupae hidden from light and predatory eyes. The hormone that triggers the transition from larva to adult also induces the larvae to find a dark spot to do this safely. Animal development is coupled with innate behaviors that maximize chances of survival. Here, we show that the prothoracicotropic hormone (PTTH), a neuropeptide that controls the developmental transition from juvenile stage to sexual maturation, also regulates light avoidance in Drosophila melanogaster larvae. PTTH, through its receptor Torso, acts on two light sensors—the Bolwig’s organ and the peripheral class IV dendritic arborization neurons—to regulate light avoidance. We found that PTTH concomitantly promotes steroidogenesis and light avoidance at the end of larval stage, driving animals toward a darker environment to initiate the immobile maturation phase. Thus, PTTH controls the decisions of when and where animals undergo metamorphosis, optimizing conditions for adult development.
Supplements of interest for sport-related injury and sources of supplement information among college athletes.

PURPOSE This study examined incidence of sport-related injury, interest in supplements to treat injury, and sources of supplement information among 145 college athletes (89 males, 56 females). MATERIALS AND METHODS A survey was used to assess sport-related injuries, interest in three categories of supplements to treat injury, and sources of supplement information among college athletes who used athletic training room and weight training facilities. Pearson chi2 was used to evaluate differences in frequency distribution of responses by sex. RESULTS Sport-related injuries were experienced by 91% of athletes (93% males, 88% females). Overall, 17% of participants were interested in supplements to improve circulation, 34% for joint and soft tissue repair, and 22% to reduce inflammation. Significant sex differences were not found for any supplements in any categories evaluated. Males were more likely than females to rely on strength coaches (37%, 20%) for supplement information. Athletic trainers (71% of athletes), coaches (60%), and physicians (41%) were the primary professionals, and the internet (79%), magazines (68%), and television (52%) the most popular sources of media for supplement information. CONCLUSIONS The majority of athletes experience injury during their college athletic career and 17% to 34% express an interest in supplements for injury treatment. Athletes would benefit from scientifically sound guidance to identify appropriate supplements for injury treatment and internet sites for supplement information. Future research should identify if athletes are more likely to increase supplement use when they are injured or if supplement use is more prevalent among athletes who are prone to injury.
TLR ligands and butyrate increase Pyy expression through two distinct but inter‐regulated pathways

The intestinal epithelium is an active barrier separating the host from its microbiota. It senses microbial compounds through expression of a wide range of receptors including the Toll‐like receptors (TLRs). TLRs have been shown to regulate epithelium permeability or secretion of defensin by Paneth cells. However, the expression and function of TLRs in enteroendocrine L‐cells, a specific subtype of intestinal cells secreting PYY and GLP‐1, have not yet been assessed. PYY and GLP‐1 are implicated in regulation of gut motility, food intake and insulin secretion, and are of great interest regarding obesity and type 2 diabetes. Using a cellular model of human L‐cells and a reporter system for NF‐κB activation pathway, we reported functional expression of TLRs in these cells. Stimulation with specific TLR‐agonists increased expression of Pyy but not Proglucagon in an NF‐κB‐dependent manner. Moreover, the effect of TLR stimulation was additive to butyrate, a product of bacterial fermentation, on Pyy expression. Additionally, butyrate also increased Tlr expression, including Tlr4, and the NF‐κB response to TLR stimulation. Altogether, our results demonstrated a role of TLRs in the modulation of Pyy expression and the importance of butyrate, a product of bacterial fermentation in regulation of microbial TLR‐dependent sensing.
Continuum sea ice rheology determined from subcontinuum mechanics

[1] A method is presented to calculate the continuum-scale sea ice stress as an imposed, continuum-scale strain-rate is varied. The continuum-scale stress is calculated as the area-average of the stresses within the floes and leads in a region (the continuum element). The continuum-scale stress depends upon: the imposed strain rate; the subcontinuum scale, material rheology of sea ice; the chosen configuration of sea ice floes and leads; and a prescribed rule for determining the motion of the floes in response to the continuum-scale strain-rate. We calculated plastic yield curves and flow rules associated with subcontinuum scale, material sea ice rheologies with elliptic, linear and modified Coulombic elliptic plastic yield curves, and with square, diamond and irregular, convex polygon-shaped floes. For the case of a tiling of square floes, only for particular orientations of the leads have the principal axes of strain rate and calculated continuum-scale sea ice stress aligned, and these have been investigated analytically. The ensemble average of calculated sea ice stress for square floes with uniform orientation with respect to the principal axes of strain rate yielded alignment of average stress and strain-rate principal axes and an isotropic, continuum-scale sea ice rheology. We present a lemon-shaped yield curve with normal flow rule, derived from ensemble averages of sea ice stress, suitable for direct inclusion into the current generation of sea ice models. This continuum-scale sea ice rheology directly relates the size (strength) of the continuum-scale yield curve to the material compressive strength.
An empirical comparison of C, C++, Java, Perl, Python, Rexx, and Tcl for a search/string-processing program

implementations of the same set of requirements, created by 74 different programmers in vari- ous languages, are compared for several properties, such as run time, memory consumption, source text length, comment density, program structure, reliability, and the amount of effort required for writing them. The results indicate that, for the given programming problem, "scripting languages" (Perl, Python, Rexx, Tcl) are more productive than conventional languages. In terms of run time and memory consumption, they often turn out better than Java and not much worse than C or C++. In general, the differences between languages tend to be smaller than the typical differences due to different programmers within the same language.
State-Dependent Decisions Cause Apparent Violations of Rationality in Animal Choice

Normative models of choice in economics and biology usually expect preferences to be consistent across contexts, or “rational” in economic language. Following a large body of literature reporting economically irrational behaviour in humans, breaches of rationality by animals have also been recently described. If proven systematic, these findings would challenge long-standing biological approaches to behavioural theorising, and suggest that cognitive processes similar to those claimed to cause irrationality in humans can also hinder optimality approaches to modelling animal preferences. Critical differences between human and animal experiments have not, however, been sufficiently acknowledged. While humans can be instructed conceptually about the choice problem, animals need to be trained by repeated exposure to all contingencies. This exposure often leads to differences in state between treatments, hence changing choices while preserving rationality. We report experiments with European starlings demonstrating that apparent breaches of rationality can result from state-dependence. We show that adding an inferior alternative to a choice set (a “decoy”) affects choices, an effect previously interpreted as indicating irrationality. However, these effects appear and disappear depending on whether state differences between choice contexts are present or not. These results open the possibility that some expressions of maladaptive behaviour are due to oversights in the migration of ideas between economics and biology, and suggest that key differences between human and nonhuman research must be recognised if ideas are to safely travel between these fields.
Rhythm in read british English: interdialect variability

Duration features have been thought to be the most obvious correlates of speech rhythm. Previous studies have shown that they can be used to distinguish among some world's languages. This paper investigates to what extent the methods employed in these studies can be applied to the dialects of British English. We have tested whether a set of variables derived from automatically extracted duration measurements constitute reliable predictors that could be used for automatic dialect identification. Preliminary results show that the automatic procedure, combined with the high interspeaker variability, yield overlapping rather than crisp dialectal categories.
Investigation of Anti-Toxocara Antibodies in Epileptic Patients and Comparison of Two Methods: ELISA and Western Blotting

The relationship between Toxocara infection and epilepsy was previously demonstrated by several case-control studies and case reports. These previous studies were often based on the enzyme-linked immunosorbent assay (ELISA) using Toxocara excretory-secretory antigens, which are not specific due to cross-reactivity with other parasitic infections such as ascariasis, trichuriasis, and anisakiasis. An immunoblot analysis is highly specific and can detect low levels of Toxocara antibodies. Therefore, this assay may be useful in the identification of toxocariasis in epileptic patients. We examined patients who had epilepsy and healthy subjects for seropositivity for Toxocara infection by ELISA and Western blotting. Out of 85 epileptic patients, 10 (11.8%) and 3 (3.5%) persons exhibited Toxocara immunoglobulin G (IgG) antibodies responses by ELISA and by both techniques, respectively. Moreover, in the healthy group (n = 85), 3 (3.5%) persons were positive by ELISA, but none was detected by Western blotting. This study indicates that Toxocara infection is a risk factor for epilepsy in Iran. These findings strongly suggest the need to perform Western blotting immunodiagnosis, as well as the ELISA using Toxocara excretory-secretory antigens, to improve diagnosis of human toxocariasis in patients with epilepsy.
Assessing Reliable Change Using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) for Patients with Parkinson's Disease Undergoing Deep Brain Stimulation (DBS) Surgery

Parkinson's disease (PD) is progressive neurological disease characterized by resting tremor, rigidity, akinesia, postural instability and cognitive changes. The symptoms of PD are debilitating and often become unsatisfactorily treated by medication. Deep brain stimulation (DBS) is an effective treatment to significantly reduce the cardinal motor symptoms of PD. However, the neuropsychological effects of this treatment are less clear. This study examined pre- to post-DBS scores on the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) using Reliable Change Indices (RCIs) derived from 20 patients with PD who were medically managed, and then compared to 20 patients with PD treated with DBS and medication. When using group statistical analyses and false discovery rate correction, no significant differences between or within groups were evident at baseline or at follow-up. However, when using the RCIs more patients in the DBS group exhibited reliable change in RBANS scores than did the Med Tx group. Although preliminary, these RCIs provide clinicians and researchers a foundational tool for assessing the effects of interventions (e.g., DBS) independent of the effects of PD and measurement error when using the RBANS.
Allele-specific tumor spectrum in Pten knockin mice

Germline mutations in the tumor suppressor gene PTEN (phosphatase and tensin homology deleted on chromosome 10) cause Cowden and Bannayan–Riley–Ruvalcaba (BRR) syndromes, two dominantly inherited disorders characterized by mental retardation, multiple hamartomas, and variable cancer risk. Here, we modeled three sentinel mutant alleles of PTEN identified in patients with Cowden syndrome and show that the nonsense Pten∆4–5 and missense PtenC124R and PtenG129E alleles lacking lipid phosphatase activity cause similar developmental abnormalities but distinct tumor spectra with varying severity and age of onset. Allele-specific differences may be accounted for by loss of function for Pten∆4–5, hypomorphic function for PtenC124R, and gain of function for PtenG129E. These data demonstrate that the variable tumor phenotypes observed in patients with Cowden and BRR syndromes can be attributed to specific mutations in PTEN that alter protein function through distinct mechanisms.
Ad Hoc Synchronization Considered Harmful

Many synchronizations in existing multi-threaded programs are implemented in an ad hoc way. The first part of this paper does a comprehensive characteristic study of ad hoc synchronizations in concurrent programs. By studying 229 ad hoc synchronizations in 12 programs of various types (server, desktop and scientific), including Apache, MySQL, Mozilla, etc., we find several interesting and perhaps alarming characteristics: (1) Every studied application uses ad hoc synchronizations. Specifically, there are 6-83 ad hoc synchronizations in each program. (2) Ad hoc synchronizations are error-prone. Significant percentages (22-67%) of these ad hoc synchronizations introduced bugs or severe performance issues. (3) Ad hoc synchronization implementations are diverse and many of them cannot be easily recognized as synchronizations, i.e. have poor readability and maintainability. The second part of our work builds a tool called SyncFinder to automatically identify and annotate ad hoc synchronizations in concurrent programswritten in C/C++ to assist programmers in porting their code to better structured implementations, while also enabling other tools to recognize them as synchronizations. Our evaluation using 25 concurrent programs shows that, on average, SyncFinder can automatically identify 96% of ad hoc synchronizations with 6% false positives. We also build two use cases to leverage SyncFinder's auto-annotation. The first one uses annotation to detect 5 deadlocks (including 2 new ones) and 16 potential issues missed by previous analysis tools in Apache, MySQL and Mozilla. The second use case reduces Valgrind data race checker's false positive rates by 43-86%.
Root canal morphology of mandibular incisors in a Jordanian population.

AIM To investigate the root canal morphology of mandibular incisors in a Jordanian population using a canal staining and tooth-clearing technique. METHODOLOGY Four hundred and fifty extracted mandibular incisors were collected from dental clinics within north Jordan. Following pulp tissue removal and staining of the canal systems, the teeth were decalcified with 5% nitric acid, dehydrated with ascending concentrations of alcohol and rendered clear by immersion in methyl salicylate. Cleared teeth were examined by eye and the following features were evaluated: (i) number and type of root canals; (ii) presence and location of lateral canals and intercanal communications; (iii) location of apical foramina; and (iv) frequency of apical deltas. RESULTS The majority of mandibular incisors had a single canal (73.8% of teeth possessed a Type I canal system). Although 26.2% of the roots possessed two canals, only 8.7% had two separate apical foramina. CONCLUSIONS The prevalence of two canals in this group of mandibular incisors was 26.2% and is within the range of previous studies performed on populations of different racial origin.
Role of Bio-Based Polymers on Improving Turbulent Flow Characteristics: Materials and Application

The remarkable ability of polymeric additives to reduce the level of frictional drag significantly in turbulent flow, even under extremely low dilutions, is known as turbulent drag-reduction behavior. Several bio-polymers have been assessed as promising drag-reducing agents for the potential replacement of high molecular weight synthetic polymers to improve safety and ameliorate environmental concerns. This article reviews the recent advances regarding the impact of several bio-polymer additives on turbulent drag reduction in either pipe or rotating disk flow systems, and their potential applications in the petroleum, biomedical, and agricultural industries.
The perception of changing emotion expressions

The utility of recognising emotion expressions for coordinating social interactions is well documented, but less is known about how continuously changing emotion displays are perceived. The nonlinear dynamic systems view of emotions suggests that mixed emotion expressions in the middle of displays of changing expressions may be decoded differently depending on the expression origin. Hysteresis is when an impression (e.g., disgust) persists well after changes in facial expressions that favour an alternative impression (e.g., anger). In expression changes based on photographs (Study 1) and avatar images (Studies 2a–c, 3), we found hystereses particularly in changes between emotions that are perceptually similar (e.g., anger–disgust). We also consistently found uncertainty (neither emotion contributing to the mixed expression was perceived), which was more prevalent in expression sequences than in static images. Uncertainty occurred particularly in changes between emotions that are perceptually dissimilar, such as changes between happiness and negative emotions. This suggests that the perceptual similarity of emotion expressions may determine the extent to which hysteresis and uncertainty occur. Both hysteresis and uncertainty effects support our premise that emotion decoding is state dependent, a characteristic of dynamic systems. We propose avenues to test possible underlying mechanisms.
Stock Options and Credit Default Swaps: A Joint Framework for Valuation and Estimation

We propose a dynamically consistent framework that allows joint valuation and estimation of stock options and credit default swaps written on the same reference company. We model default as controlled by a Cox process with a stochastic arrival rate. When default occurs, the stock price drops to zero. Prior to default, the stock price follows a jump-diffusion process with stochastic volatility. The instantaneous default rate and variance rate follow a bivariate continuous process, with its joint dynamics specified to capture the observed behavior of stock option prices and credit default swap spreads. Under this joint specification, we propose a tractable valuation methodology for stock options and credit default swaps. We estimate the joint risk dynamics using data from both markets for eight companies that span five sectors and six major credit rating classes from B to AAA. The estimation highlights the interaction between market risk (return variance) and credit risk (default arrival) in pricing stock options and credit default swaps. Copyright The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org, Oxford University Press.
Adjuvant Effect of Bacille Calmette–Guérin on Hepatitis B Vaccine Immunogenicity in the Preterm and Term Newborn

Immunization is key to protecting term and preterm infants from a heightened risk of infection. However, preterm immunity is distinct from that of the term, limiting its ability to effectively respond to vaccines routinely given at birth, such as hepatitis B vaccine (HBV). As part of the Expanded Program on Immunization, HBV is often given together with the live-attenuated vaccine Bacille Calmette–Guérin (BCG), known to activate multiple pattern-recognition receptors. Of note, some clinical studies suggest BCG can enhance efficacy of other vaccines in term newborns. However, little is known about whether BCG can shape Th-polarizing cytokine responses to HBV nor the age-dependency of such effects, including whether they may extend to the preterm. To characterize the effects of BCG on HBV immunogenicity, we studied individual and combined administration of these vaccines to cord newborn and adult human whole blood and mononuclear cells in vitro and to neonatal and adult mice in vivo. Compared to either BCG or HBV alone, (BCG + HBV) synergistically enhanced in vitro whole blood production of IL-1β, while (BCG + HBV) also promoted production of several cytokines/chemokines in all age groups, age-specific enhancement included IL-12p70 in the preterm and GM-CSF in the preterm and term. In human mononuclear cells, (BCG + HBV) enhanced mRNA expression of several genes including CSF2, which contributed to clustering of genes by vaccine treatment via principle component analysis. To assess the impact of BCG on HBV immunization, mice of three different age groups were immunized subcutaneously with, BCG, HBV, (BCG + HBV) into the same site; or BCG and HBV injected into separate sites. Whether injected into a separate site or at the same site, co-administration of BCG with HBV significantly enhanced anti-HBV IgG titers in mice immunized on day of life-0 or -7, respectively, but not in adult mice. In summary, our data demonstrate that innate and adaptive vaccine responses of preterm and term newborns are immunologically distinct. Furthermore, BCG or “BCG-like” adjuvants should be further studied as a promising adjuvantation approach to enhance immunogenicity of vaccines to protect these vulnerable populations.