Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Genetic Sex in Affect Regulation and Expression of GABA-Related Genes Across Species

Although circulating hormones and inhibitory gamma-aminobutyric acid (GABA)-related factors are known to affect mood, considerable knowledge gaps persist for biological mechanisms underlying the female bias in mood disorders. Here, we combine human and mouse studies to investigate sexual dimorphism in the GABA system in the context of major depressive disorder (MDD) and then use a genetic model to dissect the role of sex-related factors in GABA-related gene expression and anxiety-/depressive-like behaviors in mice. First, using meta-analysis of gene array data in human postmortem brain (N = 51 MDD subjects, 50 controls), we show that the previously reported down-regulation in MDD of somatostatin (SST), a marker of a GABA neuron subtype, is significantly greater in women with MDD. Second, using gene co-expression network analysis in control human subjects (N = 214; two frontal cortex regions) and expression quantitative trait loci mapping (N = 170 subjects), we show that expression of SST and the GABA-synthesizing enzymes glutamate decarboxylase 67 (GAD67) and GAD65 are tightly co-regulated and influenced by X-chromosome genetic polymorphisms. Third, using a rodent genetic model [Four Core Genotypes (FCG) mice], in which genetic and gonadal sex are artificially dissociated (N ≥ 12/group), we show that genetic sex (i.e., X/Y-chromosome) influences both gene expression (lower Sst, Gad67, Gad65 in XY mice) and anxiety-like behaviors (higher in XY mice). This suggests that in an intact male animal, the observed behavior represents the outcomes of male genetic sex increasing and male-like testosterone decreasing anxiety-like behaviors. Gonadal sex was the only factor influencing depressive-like behavior (gonadal males < gonadal females). Collectively, these combined human and mouse studies provide mechanistic insight into sexual dimorphism in mood disorders, and specifically demonstrate an unexpected role of male-like factors (XY genetic sex) on GABA-related genes and anxiety-like behaviors.
Static deflection and dynamic behavior of higher-order hyperbolic shear deformable compositionally graded beams

In this work we introduce a higher-order hyperbolic shear deformation model for bending and frees vibration analysis of functionally graded beams. In this theory and by making a further supposition, the axial displacement accounts for a refined hyperbolic distribution, and the transverse shear stress satisfies the traction-free boundary conditions on the beam boundary surfaces, so no need of any shear correction factors (SCFs). The material properties are continuously varied through the beam thickness by the power-law distribution of the volume fraction of the constituents. Based on the present refined hyperbolic shear deformation beam model, the governing equations of motion are obtained from the Hamilton’s principle. Analytical solutions for simply-supported beams are developed to solve the problem. To verify the precision and validity of the present theory some numerical results are compared with the existing ones in the literature and a good agreement is showed.
Factors affecting outcome after anterior cruciate ligament injury: a prospective study with a six‐year follow‐up

The aim of this study was to investigate whether gender, age, stable personality traits, associated meniscus and/or articular cartilage injuries, treatment (non‐operative or reconstructive surgery), additional subsequent trauma to the anterior cruciate ligament (ACL)‐injured knee and activity level before injury affect the intermediate outcome after ACL injury. The primary outcome was the Knee injury and Osteoarthritis Outcome Score (KOOS). Fifty‐seven patients, 18–50 years old with an acute, unilateral ACL tear were included in the study. At the time of inclusion, the patients completed the Tegner score, regarding activity level before injury, and Swedish universities Scales of Personality (SSP). At follow‐up, after 5.6 years they completed the KOOS, the Tegner score and a general questionnaire concerning ACL reconstruction and subsequent knee trauma. The subjects who had sustained additional trauma subsequent to their ACL injury had a significantly worse outcome according to the KOOS than those who had not. Furthermore, low ratings in the embitterment scale in the SSP were correlated to a better outcome in the KOOS. Treatment did not affect the KOOS total score. However, the non‐operatively treated subjects had a significantly better outcome according to the knee‐related quality‐of‐life domain in the KOOS.
Parental concerns and control in feeding of 9 to 12-year-old children in a primary school in Kuala Lumpur, Malaysia.

INTRODUCTION Body weight of children is affected by many factors including food habits which are influenced by their parents. Studies in the West have shown that parents tend to control child feeding in response to their child's weight status. The aim of this study was to assess Malaysian parental concerns about child weight and the control they exert on child feeding. METHODS This cross-sectional study was conducted on parents and their children aged 9 to 12 years from a primary school in Kuala Lumpur. The weight status of the children was classified according to the body mass index-for-age growth chart. Parental concerns about child weight and control in child feeding was assessed using the adapted Malay version of Child Feeding Questionnaire. RESULTS A total of 204 parents participated in this study. The study found that being a female served as a protective factor against becoming overweight (OR: 0.28, CI: 0.13-0.62). Parents with overweight children were significantly older (OR: 1.08, CI: 1.01-1.15), concerned about their child's weight (OR: 2.77, CI: 1.49-5.12) and controlled their child's feeding by restricting food intake (OR: 2.70, CI: 1.30-5.60). They were less likely to pressure their children to eat (OR: 0.32, CI: 0.19-0.56). Parents from the low income group were more likely to have underweight children (OR: 4.15, CI: 1.28-13.47). CONCLUSION There was significant difference in level of parental concern across differing child weight status. Parents with overweight children were likely to be more concerned about their child's weight, tending to control their feeding. In contrast, parents with underweight children did not exert control on their feeding.
Bifunctional Avidin with Covalently Modifiable Ligand Binding Site

The extensive use of avidin and streptavidin in life sciences originates from the extraordinary tight biotin-binding affinity of these tetrameric proteins. Numerous studies have been performed to modify the biotin-binding affinity of (strept)avidin to improve the existing applications. Even so, (strept)avidin greatly favours its natural ligand, biotin. Here we engineered the biotin-binding pocket of avidin with a single point mutation S16C and thus introduced a chemically active thiol group, which could be covalently coupled with thiol-reactive molecules. This approach was applied to the previously reported bivalent dual chain avidin by modifying one binding site while preserving the other one intact. Maleimide was then coupled to the modified binding site resulting in a decrease in biotin affinity. Furthermore, we showed that this thiol could be covalently coupled to other maleimide derivatives, for instance fluorescent labels, allowing intratetrameric FRET. The bifunctional avidins described here provide improved and novel tools for applications such as the biofunctionalization of surfaces.
Classifying ASR Transcriptions According to Arabic Dialect

We describe several systems for identifying short samples of Arabic dialects. The systems were prepared for the shared task of the 2016 DSL Workshop. Our best system, an SVM using character tri-gram features, achieved an accuracy on the test data for the task of 0.4279, compared to a baseline of 0.20 for chance guesses or 0.2279 if we had always chosen the same most frequent class in the test set. This compares with the results of the team with the best weighted F1 score, which was an accuracy of 0.5117. The team entries seem to fall into cohorts, with all the teams in a cohort within a standard-deviation of each other, and our three entries are in the third cohort, which is about seven standard deviations from the top.
A Comparison of Baseline Hearing Thresholds Between Pilots and Non-Pilots and the Effects of Engine Noise

Abstract : Observations in simulator studies suggested that the older segments of the general aviation pilot population were having difficulty hearing specific auditory warnings in the cockpit. These observations, in combination with data from Tobias (1968a; 1968b; 1972), prompted a reexamination of the hearing capabilities of pilots and non-pilots. In Phase 1, threshold data were collected for 150 non-pilots and 150 pilots using stratified age sampling. The usual higher-frequency decrements attributable to aging and general environmental exposure were found in both samples. Significant differences were found between the non-pilot and pilot samples, with greater threshold shifts between 2 and 6 kHz in evidence among the pilots. In Phase 2, participants' thresholds were measured during both a quiet condition and during exposure to simulated aircraft engine noise. Results of both phases are discussed in terms of implications for the design of auditory warnings for general aviation aircraft.
X-ray diffraction and equation of state of solid neon to 110 GPa.

Solid neon was compressed under static conditions at 300 K to pressures in the 100 GPa (megabar) range using diamond-anvil cell techniques. The crystal structure and /ital P/-/ital V/ equation of state were determined by energy-dispersive x-ray diffraction with microcollimated synchrotron radiation. Pressures were determined from ruby fluorescence spectra and from x-ray diffraction of tungsten powder contained within the sample. Solid neon remains an insulator with the fcc structure to the maximum pressure of 110 GPa at 300 K, where the compression /ital V///ital V//sub 0/ is 0.28. The 300-K /ital P/-/ital V/ isotherm measured at high pressure is in excellent agreement with the results of electronic structure calculations but is incorrectly described by pure pair potentials recently developed for neon. These results indicate that there is a significant softening of the material by many-body interactions at high pressures. Finally, the measurements of ruby fluorescence and tungsten x-ray diffraction in the neon medium obtained in this study provide an extension of the quasihydrostatic ruby pressure scale above 100 GPa.
Comparison of methods for the isolation of human breast epithelial and myoepithelial cells

Two lineages, epithelial, and myoepithelial cells are the main cell populations in the normal mammary gland and in breast cancer. Traditionally, cancer research has been performed using commercial cell lines, but primary cell cultures obtained from fresh breast tissue are a powerful tool to study more reliably new aspects of mammary gland biology, including normal and pathological conditions. Nevertheless, the methods described to date have some technical problems in terms of cell viability and yield, which hamper work with primary mammary cells. Therefore, there is a need to optimize technology for the proper isolation of epithelial and myoepithelial cells. For this reason, we compared four methods in an effort to improve the isolation and primary cell culture of different cell populations of human mammary epithelium. The samples were obtained from healthy tissue of patients who had undergone mammoplasty or mastectomy surgery. We based our approaches on previously described methods, and incorporated additional steps to ameliorate technical efficiency and increase cell survival. We determined cell growth and viability by phase-contrast images, growth curve analysis and cell yield, and identified cell-lineage specific markers by flow cytometry and immunofluorescence in 3D cell cultures. These techniques allowed us to better evaluate the functional capabilities of these two main mammary lineages, using CD227/K19 (epithelial cells) and CD10/K14 (myoepithelial cells) antigens. Our results show that slow digestion at low enzymatic concentration combined with the differential centrifugation technique is the method that best fits the main goal of the present study: protocol efficiency and cell survival yield. In summary, we propose some guidelines to establish primary mammary epithelial cell lines more efficiently and to provide us with a strong research instrument to better understand the role of different epithelial cell types in the origin of breast cancer.
Pharmacokinetics and bactericidal activity of cefuroxime axetil

The pharmacokinetics of cefuroxime axetil were studied in 10 adult volunteers aged 24 to 31 years (mean age, 27), 22 infants and children aged 11 to 68 months (mean age, 33 months), and 11 children aged 7 years, 7 months to 12 years, 3 months (mean age, 11 years, 1 month). Mean peak plasma concentrations of cefuroxime occurred between 90 and 120 min in all study patients and were independent of the fasting or feeding status. The areas under the concentration-time curves were significantly higher in adult volunteers who received cefuroxime axetil with milk than in those who received the drug while fasting or with applesauce. The bioavailability of cefuroxime axetil was significantly enhanced in children by the concomitant ingestion of cefuroxime axetil and infant formula or whole milk. The areas under the concentration-time curves were 25 to 88% higher when cefuroxime axetil and milk were administered simultaneously than when the same dose was given to all fasting patients. The plasma bactericidal activities of cefuroxime against beta-lactamase-positive and -negative strains of Haemophilus influenzae and Staphylococcus aureus at the time of peak plasma concentrations were independent of feeding status and were similar in adults and in children. Against these strains, 52% of the children and 38% of the adults had peak bactericidal levels of 1:8 or greater.
Long‐range PCR facilitates the identification of PMS2‐specific mutations

Mutations within the DNA mismatch repair gene, “postmeiotic segregation increased 2” (PMS2), have been associated with a predisposition to hereditary nonpolyposis colorectal cancer (HNPCC; Lynch syndrome). The presence of a large family of highly homologous PMS2 pseudogenes has made previous attempts to sequence PMS2 very difficult. Here, we describe a novel method that utilizes long‐range PCR as a way to preferentially amplify PMS2 and not the pseudogenes. A second, exon‐specific, amplification from diluted long‐range products enables us to obtain a clean sequence that shows no evidence of pseudogene contamination. This method has been used to screen a cohort of patients whose tumors were negative for the PMS2 protein by immunohistochemistry and had not shown any mutations within the MLH1 gene. Sequencing of the PMS2 gene from 30 colorectal and 11 endometrial cancer patients identified 10 novel sequence changes as well as 17 sequence changes that had previously been identified. In total, putative pathologic mutations were detected in 11 of the 41 families. Among these were five novel mutations, c.705+1G>T, c. 736_741del6ins11, c. 862_863del, c.1688G>T, and c.2007–1G>A. We conclude that PMS2 mutation detection in selected Lynch syndrome and Lynch syndrome‐like patients is both feasible and desirable. Hum Mutat 27(5), 490–495, 2006. Published 2006 Wiley‐Liss, Inc.
Antifibrotic effect of captopril and enalapril on paraquat‐induced lung fibrosis in rats

Although different treatment modalities have been implemented for pulmonary fibrosis, the results have not been promising and these conditions have been considered untreatable and irreversible. Thus, a plethora of new drugs has been tried for the control of this condition in recent years. This study examined the effects of two angiotensin‐converting enzyme inhibitors, captopril and enalapril, on paraquat‐induced pulmonary fibrosis in rats, through biochemical and histopathological parameters. Male albino Wistar rats were divided into eight groups (n = 4–5 each), including control, paraquat, captopril alone, captopril treatment and pre‐treatment, enalapril alone, enalapril treatment and pre‐treatment. After 21 days of treatment, the lungs were removed and the levels of hydroxyproline, glutathione and lipid peroxidation were determined. Angiotensin‐converting enzyme inhibitors showed no effect on glutathione and lipid peroxidation. The results also demonstrated that captopril and enalapril improved pulmonary fibrosis as shown by histopathology, as well as a decreased content of hydroxyproline (P < 0.001) in the lung tissue. In conclusion, the present findings suggest that the antifibrotic effect of these drugs may be related to the inhibition of angiotensin‐converting enzyme. Copyright © 2007 John Wiley & Sons, Ltd.
Developmental lineage priming in Dictyostelium by heterogeneous Ras activation

In cell culture, genetically identical cells often exhibit heterogeneous behavior, with only ‘lineage primed’ cells responding to differentiation inducing signals. It has recently been proposed that such heterogeneity exists during normal embryonic development to allow position independent patterning based on ‘salt and pepper’ differentiation and sorting out. However, the molecular basis of lineage priming and how it leads to reproducible cell type proportioning are poorly understood. To address this, we employed a novel forward genetic approach in the model organism Dictyostelium discoideum. These studies reveal that the Ras-GTPase regulator gefE is required for normal lineage priming and salt and pepper differentiation. This is because Ras-GTPase activity sets the intrinsic response threshold to lineage specific differentiation signals. Importantly, we show that although gefE expression is uniform, transcription of its target, rasD, is both heterogeneous and dynamic, thus providing a novel mechanism for heterogeneity generation and position-independent differentiation. DOI: http://dx.doi. org/10.7554/eLife.01067. 001
Looking To Understand: The Coupling Between Speakers' and Listeners' Eye Movements and Its Relationship to Discourse Comprehension

We investigated the coupling between a speaker's and a listener's eye movements. Some participants talked extemporaneously about a television show whose cast members they were viewing on a screen in front of them. Later, other participants listened to these monologues while viewing the same screen. Eye movements were recorded for all speakers and listeners. According to cross-recurrence analysis, a listener's eye movements most closely matched a speaker's eye movements at a delay of 2 sec. Indeed, the more closely a listener's eye movements were coupled with a speaker's, the better the listener did on a comprehension test. In a second experiment, low-level visual cues were used to manipulate the listeners' eye movements, and these, in turn, influenced their latencies to comprehension questions. Just as eye movements reflect the mental state of an individual, the coupling between a speaker's and a listener's eye movements reflects the success of their communication.
STOPPING CRITERIA FOR MIXED FINITE ELEMENT PROBLEMS

We study stopping criteria that are suitable in the solution by Krylov space based methods of linear and non linear systems of equations arising from the mixed and the mixed-hybrid finiteelement approximation of saddle point problems. Our approach is based on the equivalence between the Babuška and Brezzi conditions of stability which allows us to apply some of the results obtained in Arioli, Loghin and Wathen [1]. Our proposed criterion involves evaluating the residual in a norm defined on the discrete dual of the space where we seek a solution. We illustrate our approach using standard iterative methods such as MINRES and GMRES. We test our criteria on Stokes and Navier-Stokes problems both in a linear and nonlinear context.
Hematopoietic cell transplantation-associated thrombotic microangiopathy: a review of pathophysiology, diagnosis, and treatment

Transplant-associated thrombotic microangiopathy (TA-TMA) is a multifactorial disorder caused by systemic vascular endothelial injury that can be triggered by several mechanisms during the transplant process. Thrombotic microangiopathy may affect multiple systems and occurs in ~30% of patients undergoing hematopoietic stem cell transplantation. A subgroup of patients with thrombotic microangiopathy develop TA-TMA, and the other may develop other thrombotic microangiopathic disorders such as thrombotic thrombocytopenic purpura, a condition with similar finding but different pathophysiology involving ADAMTS-13. The mortality rates in patients who develop severe TA-TMA are in excess of 80%. Recent investigations show that complement system activation in patients with TA-TMA is a very poor prognostic sign and implicates complement dysregulation as a key pathway in the pathogenesis of TA-TMA and its disease phenotype. The original diagnostic criteria for TA-TMA included hematologic and renal injury markers, which are limited in their ability to detect only advanced disease, and therefore may result in delayed TA-TMA diagnosis in transplant patients. A recent set of diagnostic criteria added markers of complement activation, proteinuria, and hypertension, with predicted improved detection of early TA-TMA. Supportive care that includes elimination of potentially toxic agents such as calcineurin inhibitors and sirolimus, adequate antimicrobial treatment, and maintaining adequate renal functions using renal replacement therapy may be sufficient for treatment of mild-to-moderate TA-TMA. Plasma exchange, which is a potentially curative therapy in thrombotic thrombocytopenic purpura, has no proven efficacy in TA-TMA. Blocking the complement system with eculizumab is currently the most effective treatment to circumvent the poor outcome in patients with severe TA-TMA.
The Patient’s Perspective of in-Home Telerehabilitation Physiotherapy Services Following Total Knee Arthroplasty

This study aimed at exploring patients’ perceptions regarding telerehabilitation services received post total knee replacement. In this qualitative embedded single case study, semi-structured interviews were conducted with five patients who had previously received in-home telerehabilitation post total knee arthroplasty. Participants were asked to reflect on their 8-week rehabilitation process and on their experience with the home telerehabilitation program. Interviews were transcribed and a qualitative thematic analysis was conducted. Six overarching themes emerged from the patients’ perceptions: (1) improving access to services with reduced need for transportation; (2) developing a strong therapeutic relationship with therapist while maintaining a sense of personal space; (3) complementing telerehabilitation with in-person visits; (4) providing standardized yet tailored and challenging exercise programs using telerehabilitation; (5) perceived ease-of-use of telerehabilitation equipment; and (6) feeling an ongoing sense of support. Gaining a better understating of the patient’s experience in telerehabilitation will be essential as programs continue to be developed and implemented.