Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits

Abstract To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spring (W/1+, n = 47) samples of brown trout individuals belonging to the same cohort and stream were retrieved using electrofishing. A third group (H/1+, n = 48) comprised hatchery‐reared individuals, bred from a mixture of wild parents of the strain of the two former groups and from a neighboring stream. Pairwise analysis of FST outliers and analysis under a hierarchical model by means of ARLEQUIN software detected 421 (10.8%) candidates of selection, before multitest correction. BAYESCAN software detected 10 candidate loci, all of which were included among the ARLEQUIN candidate loci. Body length was significantly different across genotypes at 10 candidate loci in the W/0+, at 34 candidate loci in the W/1+ and at 21 candidate loci in the H/1+ group. The W/1+ sample was tested for genotype‐specific body length at all loci, and significant differences were found in 10.6% of all loci, and of these, 14.2% had higher frequency of the largest genotype in the W/1+ sample than in W/0+. The corresponding proportion among the candidate loci of W/1+ was 22.7% with genotype‐specific body length, and 88.2% of these had increased frequency of the largest genotype from W/0+ to W/1+, indicating a linkage between these loci and traits affecting growth and survival under this stream's environmental conditions. Bayesian structuring of all loci, and of the noncandidate loci suggested two (K = 2), alternatively four clusters (K = 4). This differed from the candidate SNPs, which suggested only two clusters. In both cases, the hatchery fish dominated one cluster, and body length of W/1+ fish was positively correlated with membership of one cluster both from the K = 2 and the K = 4 structure. Our analysis demonstrates profound genetic differentiation that can be linked to differential selection on a fitness‐related trait (individual growth) in brown trout living under natural vs. hatchery conditions. Candidate SNP loci linked to genes affecting individual growth were identified and provide important inputs into future mapping of the genetic basis of brown trout body size selection.
Spike–wave discharges are necessary for the expression of behavioral depression‐like symptoms

Purpose: The WAG/Rij strain of rats, a well‐established model for absence epilepsy, has comorbidity for depression. These rats exhibit depression‐like behavioral symptoms such as increased immobility in the forced swimming test and decreased sucrose intake and preference (anhedonia). These depression‐like behavioral symptoms are evident in WAG/Rij rats, both at 3–4 and 5–6 months of age, with a tendency to aggravate in parallel with an increase in seizure duration. Here we investigated whether the behavioral symptoms of depression could be prevented by the suppression of absence seizures.
Monopsony in Online Labor Markets

Despite the seemingly low switching and search costs of on-demand labor markets like Amazon Mechanical Turk, we find substantial monopsony power, as measured by the elasticity of labor supply facing the requester (employer). We isolate plausibly exogenous variation in rewards using a double machine learning estimator applied to a large dataset of scraped MTurk tasks. We also reanalyze data from five MTurk experiments that randomized payments to obtain corresponding experimental estimates. Both approaches yield uniformly low labor supply elasticities, around 0.1, with little heterogeneity. Our results suggest monopsony might also be present even in putatively “thick” labor markets. (JEL C44, J22, J23, J42)
Macrophage-Specific Expression of IL-37 in Hyperlipidemic Mice Attenuates Atherosclerosis

Atherosclerosis, the progressive buildup of plaque within arterial blood vessels, can lead to fatal downstream events, such as heart attack or stroke. A key event contributing to the development of atherosclerosis is the infiltration of monocytes and its associated inflammation, as well as the formation of lipid-laden macrophage foam cells within the vessel wall. IL-37 is recognized as an important anti-inflammatory cytokine expressed especially by immune cells. This study was undertaken to elucidate the role of macrophage-expressed IL-37 in reducing the production and effects of proinflammatory cytokines, preventing foam cell formation, and reducing the development of atherosclerosis. Expression of human IL-37 was achieved with a macrophage-specific overexpression system, using the CD68 promoter in mouse primary bone marrow–derived macrophages via retroviral transduction. Macrophage IL-37 expression in vitro resulted in decreased mRNA (e.g., IL-1B, IL-6, and IL-12) and secreted protein production (e.g., IL-6, M-CSF, and ICAM-1) of key inflammatory mediators. IL-37 expression also inhibited macrophage proliferation, apoptosis, and transmigration, as well as reduced lipid uptake, compared with controls in vitro. The in vivo effects of macrophage-expressed IL-37 were investigated through bone marrow transplantation of transduced hematopoietic stem cells into irradiated atherosclerosis-prone Ldlr−/− mice. After 10 wk on a high-fat/high-cholesterol diet, mice with IL-37–expressing macrophages showed reduced disease pathogenesis, which was demonstrated by significantly less arterial plaque development and systemic inflammation compared with control mice. The athero-protective effect of macrophage-expressed IL-37 has implications for development of future therapies to treat atherosclerosis, as well as other chronic inflammatory diseases.
Prevalence of obesity and owners' perceptions of body condition in pleasure horses and ponies in south-eastern Australia.

OBJECTIVE To determine the prevalence of obesity within a population of pleasure horses and ponies in Victoria, Australia, and to compare owners' perceptions of their animals' body condition with researchers' assessments. DESIGN An observational study plus owner questionnaire. METHODS Ten Pony Club rallies in different regions of Victoria were attended. Information regarding 229 horses and ponies were obtained from owner questionnaires, and owners' perceptions of the current body condition of their animals were assessed using a visual analogue scale. Body condition score (BCS) was assessed by the researchers using the modified Henneke method. RESULTS The prevalence of researcher-assessed obesity (BCS ≥7/9) in the total surveyed population was 23.1%. A higher prevalence of obesity was identified in Shetland ponies (71.5%) and other pony types (32.0%) compared with horse breeds (9.3%). Owners perceived their animals to be in significantly lower body condition compared with the researchers' assessments (P < 0.001). CONCLUSION Although the overall prevalence of obesity within Australian pleasure horses and ponies was 24.5%, a considerably higher proportion of pony breeds fell into this category. Owners frequently underestimated their own animal's body condition. Knowing the prevalence of obesity in this population and understanding how owners perceive the body condition of their animals may help with targeting education around preventative health care, with the aim of reducing the risk of conditions such as insulin dysregulation and laminitis.
Spectral Differentiation of Trace Concentrations of NO(2) from NO by Laser Photofragmentation with Fragment Ionization at 226 and 452 nm: Quantitative Analysis of NO-NO(2) Mixtures.

Laser-induced photofragmentation with fragment ionization is used to detect and spectrally differentiate trace concentrations of NO(2) from NO in NO-NO(2) mixtures. A laser operating near 226 or 452 nm ionizes the target molecules, and the resulting electrons are collected with miniature electrodes. NO is detected by (1 + 1) resonance-enhanced multiphoton ionization by means of its A (2)? (+) ? X (2)? (0, 0) transitions near 226 nm, whereas NO(2) is detected near 226 nm by laser photofragmentation with subsequent NO fragment ionization by means of both its A (2)? (+) ? X (2)? (0, 0) and (1, 1) transitions. The NO fragment generated from the photolysis of NO(2) is produced rovibrationally excited with a significant population in the first vibrational level of the ground electronic state (X (2)? , upsilon? = 1). In contrast, ambient NO has a room-temperature, Boltzmann population distribution favoring the lowest ground vibrational level (X (2)? , upsilon? = 0). Thus discrimination is possible when the internal energy distributions of both fragment NO and ambient NO are probed. We also demonstrate this approach using visible radiation, further simplifying the experimental apparatus because frequency doubling of the laser radiation is not required. We measured up to three decades of NO-NO(2) mixtures with limits of detection (signal-to-noise ratio of 3) in the low parts per billion for both NO and NO(2) for a 10-s integration time using both ultraviolet or visible radiation.
Empathy in Iranian medical students: Measurement model of the Jefferson Scale of Empathy

Background: Empathy is an important factor in patient–physician relationship that has beneficial effects in medical practice. Jefferson Scale of Empathy (JSE) has been specifically designed to assess empathy in health professionals (HP-version) and related students (S-version). Few validation studies have been performed on S-version of the scale. Aims: To examine empathy in a large sample of Iranian medical students, and also to study factor structure and psychometric properties of the Persian translation of the S-version of the JSE. Method: 1187 medical students (759 female) from 16 universities around the country participated in the study during 2009. Independent sample t-test, multivariate analysis of variance, and confirmatory factor analysis (CFA) were performed to analyze the data. Results: Female students outscored male students in empathy. The trend for empathy had a negative relationship with years of education. JSE showed an acceptable internal consistency and test re-test reliability. CFA upheld the original three-factor structure – Perspective Taking, Compassionate Care, and Standing in the Patient's Shoes – consisting 20 items. Conclusion: The decrease in empathy during medical education is consistent with previous studies. The Persian version of JSE is a valid and reliable measure to tap empathy in a Persian-speaking medical student.
Reproducibility of Subclassification of Squamous Intraepithelial Lesions: Conventional versus ThinPrep Paps

Objective. Liquid-based cytologic methods are increasingly used, and classification of squamous intraepithelial lesions (SIL) affects patient management. This study compared interobserver reproducibility in SIL subclassification on conventional (CV) and ThinPrep (TP) cytologic specimens. Materials and Methods. Four reviewers independently subclassified SIL on 69 CV and 60 TP Paps. Specimens were retrieved by computer search of biopsy-confirmed SIL cases. A consensus interpretation of low-grade SIL (LSIL) or high-grade SIL (HSIL) was assigned when three or four observers agreed. Results. All four observers agreed in 40 of 69 CV with consensus reached in 56 of 69 CV Paps (81%; 20 LSIL, 36 HSIL). For TP Paps, 38 of 60 had 100% agreement, with consensus reached in 56 of 60 TP Paps (93%; 28 LSIL, 26 HSIL, 2 SIL, difficult to grade). &kgr; values for all four observers were 0.48 for CV (fair agreement) and 0.63 for TP (substantial). Pairwise &kgr; values ranged from 0.44 to 0.60 for CV and 0.54 to 0.76 for TP. Most of the nonconsensus cases included SIL, difficult to grade interpretations; in several, the original cytologic or biopsy SIL classification, or both, was also indeterminate, or cytologic and biopsy results did not correlate exactly. High-grade biopsies followed 15% of LSIL CV and 36% of LSIL TP. Conclusions. Interobserver reproducibility in SIL subclassification may be better on TP Paps; however, both CV and TP have indeterminate lesions with low interobserver agreement. The TP specimens did not show improved correlation with histologic analysis, and specimens with consensus do not always have correlating biopsy findings.
Nerve growth factor promotes reorganization of the axonal microtubule array at sites of axon collateral branching

The localized debundling of the axonal microtubule array and the entry of microtubules into axonal filopodia are two defining features of collateral branching. We report that nerve growth factor (NGF), a branch‐inducing signal, increases the frequency of microtubule debundling along the axon shaft of chicken embryonic sensory neurons. Sites of debundling correlate strongly with the localized targeting of microtubules into filopodia. Platinum replica electron microscopy suggests physical interactions between debundled microtubules and axonal actin filaments. However, as evidenced by depolymerization of actin filaments and inhibition of myosin II, actomyosin force generation does not promote debundling. In contrast, loss of actin filaments or inhibition of myosin II activity promotes debundling, indicating that axonal actomyosin forces suppress debundling. MAP1B is a microtubule associated protein that represses axon branching. Following treatment with NGF, microtubules penetrating filopodia during the early stages of branching exhibited lower levels of associated MAP1B. NGF increased and decreased the levels of MAP1B phosphorylated at a GSK‐3β site (pMAP1B) along the axon shaft and within axonal filopodia, respectively. The levels of MAP1B and pMAP1B were not altered at sites of debundling, relative to the rest of the axon. Unlike the previously determined effects of NGF on the axonal actin cytoskeleton, the effects of NGF on microtubule debundling were not affected by inhibition of protein synthesis. Collectively, these data indicate that NGF promotes localized axonal microtubule debundling, that actomyosin forces antagonize microtubule debundling, and that NGF regulates pMAP1B in axonal filopodia during the early stages of collateral branch formation. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 75: 1441–1461, 2015
Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

ABSTRACT Plasmids are transmissible, extrachromosomal genetic elements that are often responsible for environmental or host-specific adaptations. In order to identify the forces driving the evolution of these important molecules, we determined the complete nucleotide sequence of the five-plasmid complement of the radish and Arabidopsis pathogen Pseudomonas syringae pv. maculicola ES4326 and conducted an intraspecific comparative genomic analysis. To date, this is the most complex fully sequenced plasmid complement of any gram-negative bacterium. The plasmid complement comprises two pPT23A-like replicons, pPMA4326A (46,697 bp) and pPMA4326B (40,110 bp); a pPS10-like replicon, pPMA4326C (8,244 bp); and two atypical, replicase-deficient replicons, pPMA4326D (4,833 bp) and pPMA4326E (4,217 bp). A complete type IV secretion system is found on pPMA4326A, while the type III secreted effector hopPmaA is present on pPMA4326B. The region around hopPmaA includes a shorter hopPmaA homolog, insertion sequence (IS) elements, and a three-element cassette composed of a resolvase, an integrase, and an exeA gene that is also present in several human pathogens. We have also identified a novel genetic element (E622) that is present on all but the smallest plasmid (pPMA4326E) that has features of an IS element but lacks an identifiable transposase. This element is associated with virulence-related genes found in a wide range of P. syringae strains. Comparative genomic analyses of these and other P. syringae plasmids suggest a role for recombination and integrative elements in driving plasmid evolution.
Do Cognitive Complaints in Euthymic Bipolar Patients Reflect Objective Cognitive Impairment?

Background: In clinical practice, bipolar patients complain of cognitive deficits such as attentional or memory disturbances. The main aim of this study was to determine whether subjective cognitive complaints were associated with objective neuropsychological impairments. Method: Sixty euthymic bipolar patients were assessed through a neuropsychological battery. A structured clinical interview was used to determine subjective cognitive complaints in patients. Thirty healthy controls were also included in the study in order to compare the neuropsychological performance among groups. Results: Bipolar patients with a higher number of episodes, especially the number of mixed episodes, longer duration of the illness and the onset of the illness at an earlier age showed more subjective complaints. Furthermore, bipolar patients with subjective complaints showed lower scores in several cognitive measures related to attention, memory and executive function compared with the control group. Nevertheless, patients without complaints also performed less well than controls in some neuropsychological measures. Conclusion: Bipolar patients who were aware of cognitive deficits were more chronic, had presented more previous episodes, especially mixed type, and their illness had started at an earlier age compared with patients who did not complain about cognitive problems. Moreover, patients with good cognitive insight also had a poorer social and occupational functioning as well as a poorer neuropsychological performance. However, the bipolar group without complaints also obtained lower scores in several tests compared with healthy controls. Cognitive status of bipolar patients should be routinely assessed, regardless of the patients awareness about their cognitive deficits.
Sodium butyrate enhances intestinal integrity, inhibits mast cell activation, inflammatory mediator production and JNK signaling pathway in weaned pigs

The present study aimed to investigate the effects of sodium butyrate on the intestinal barrier and mast cell activation, as well as inflammatory mediator production, and determine whether mitogen-activated protein kinase signaling pathways are involved in these processes. A total of 72 piglets, weaned at 28 ± 1 d age, were allotted to two dietary treatments (control vs. 450 mg/kg sodium butyrate) for 2 wk. The results showed that supplemental sodium butyrate increased daily gain, improved intestinal morphology, as indicated by greater villus height and villus height:crypt depth ratio, and intestinal barrier function reflected by increased transepithelial electrical resistance and decreased paracellular flux of dextran (4 kDa). Moreover, sodium butyrate reduced the percentage of degranulated mast cells and its inflammatory mediator content (histamine, tryptase, TNF-α and IL-6) in the jejunum mucosa. Sodium butyrate also decreased the expression of mast cell-specific tryptase, TNF-α and IL-6 mRNA. Sodium butyrate significantly decreased the phosphorylated ratio of JNK whereas not affecting the phosphorylated ratios of ERK and p38. The results indicated that the protective effects of sodium butyrate on intestinal integrity were closely related to inhibition of mast cell activation and inflammatory mediator production, and that the JNK signaling pathway was likely involved in this process.
Effects of low-dose milnacipran on event-related potentials and neuropsychological tests in persons with traumatic brain injury: A preliminary study

Abstract Introduction: Psychostimulants are among the most commonly used pharmacological agents for countering cognitive dysfunction and/or enhancing rehabilitation in persons with brain injury. It was postulated that milnacipran, a serotonin-norepinephrine reuptake inhibitor, would be effective against cognitive dysfunction in non-depressed persons with brain injury. Methods: Eighteen patients were recruited with at least moderate disability more than 4 months after a traumatic brain injury (TBI) and they were randomized to an 8-week, placebo-controlled, double-blind trial. Cognitive dysfunction was assessed at baseline with the Trail Making Test, the Wechsler Adult Intelligence Scale-Revised (WAIS-R), the Wechsler Memory Scale-Revised (WMS-R) and measurement of event-related potentials (ERPs) both before randomization and after an 8-week administration of milnacipran or placebo. Results: N2 and P3 latencies in the milnacipran group were significantly shortened by the intervention. Moreover, the Verbal Intelligence Quotient and Full Intelligence Quotient scores of the WAIS-R and the delayed recall score of the WMS-R were significantly higher than baseline after milnacipran intervention. Conclusion: Milnacipran administration improved ERP measures of attention and information processing in non-depressed persons with brain injury and also improved scores on three sub-scales of standard neuropsychological tests of cognitive dysfunction. Therefore, this intervention merits validation by additional, larger studies.
Molecular and Functional Characterization ofSalmonella enterica Serovar Typhimurium poxAGene: Effect on Attenuation of Virulence and Protection

ABSTRACT Salmonella enterica poxA mutants exhibit a pleiotropic phenotype, including reduced pyruvate oxidase activity; reduced growth rate; and hypersensitivity to the herbicide sulfometuron methyl, α-ketobutyrate, and amino acid analogs. These mutants also failed to grow in the presence of the host antimicrobial peptide, protamine. In this study, PoxA− mutants of S. entericaserovar Typhimurium (S. typhimurium) were found to be 10,000-fold attenuated in orally inoculated BALB/c mice and 1,000-fold attenuated in intraperitoneally inoculated BALB/c mice, compared to wild-type S. typhimurium UK-1. In addition,poxA mutants were found to be capable of colonizing the spleen, mesenteric lymph nodes, and Peyer’s patches; to induce strong humoral immune responses; and to protect mice against a lethal wild-type Salmonella challenge. A 2-kb DNA fragment was isolated from wild-type S. typhimurium UK-1 based on its ability to complement an isogenic poxA mutant. The nucleotide sequence of this DNA fragment revealed an open reading frame of 325 amino acids capable of encoding a polypeptide of 36.8 kDa that was confirmed in the bacteriophage T7 expression system. Comparison of the translated sequence to the available databases indicated high homology to a family of lysyl-tRNA synthetases. Our results indicate that a mutation of poxA has an attenuating effect onSalmonella virulence. Further, poxA mutants are immunogenic and could be useful in designing live vaccines with a variety of bacterial species. To our knowledge, this is the first report on the effect of poxA mutation on bacterial virulence.
Toll‐like receptor 3 deficiency decreases epileptogenesis in a pilocarpine model of SE‐induced epilepsy in mice

Epilepsy affects 60 million people worldwide. Despite the development of antiepileptic drugs, up to 35% of patients are drug refractory with uncontrollable seizures. Toll‐like receptors (TLRs) are central components of the nonspecific innate inflammatory response. Because TLR3 was recently implicated in neuronal plasticity, we hypothesized that it may contribute to the development of epilepsy after status epilepticus (SE).