Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of Multiple Genomic Data Sources in a Bayesian Cox Model for Variable Selection and Prediction

Bayesian variable selection becomes more and more important in statistical analyses, in particular when performing variable selection in high dimensions. For survival time models and in the presence of genomic data, the state of the art is still quite unexploited. One of the more recent approaches suggests a Bayesian semiparametric proportional hazards model for right censored time-to-event data. We extend this model to directly include variable selection, based on a stochastic search procedure within a Markov chain Monte Carlo sampler for inference. This equips us with an intuitive and flexible approach and provides a way for integrating additional data sources and further extensions. We make use of the possibility of implementing parallel tempering to help improve the mixing of the Markov chains. In our examples, we use this Bayesian approach to integrate copy number variation data into a gene-expression-based survival prediction model. This is achieved by formulating an informed prior based on copy number variation. We perform a simulation study to investigate the model's behavior and prediction performance in different situations before applying it to a dataset of glioblastoma patients and evaluating the biological relevance of the findings.
Dopamine-Regulated MicroRNA MiR-181a Controls GluA2 Surface Expression in Hippocampal Neurons

ABSTRACT The dynamic expression of AMPA-type glutamate receptors (AMPA-R) at synapses is a key determinant of synaptic plasticity, including neuroadaptations to drugs of abuse. Recently, microRNAs (miRNAs) have emerged as important posttranscriptional regulators of synaptic plasticity, but whether they target glutamate receptors to mediate this effect is not known. Here we used microarray screening to identify miRNAs that regulate synaptic plasticity within the nucleus accumbens, a brain region critical to forming drug-seeking habits. One of the miRNAs that showed a robust enrichment at medium spiny neuron synapses was miR-181a. Using bioinformatics tools, we detected a highly conserved miR-181a binding site within the mRNA encoding the GluA2 subunit of AMPA-Rs. Overexpression and knockdown of miR-181a in primary neurons demonstrated that this miRNA is a negative posttranscriptional regulator of GluA2 expression. Additionally, miR-181a overexpression reduced GluA2 surface expression, spine formation, and miniature excitatory postsynaptic current (mEPSC) frequency in hippocampal neurons, suggesting that miR-181a could regulate synaptic function. Moreover, miR-181a expression was induced by dopamine signaling in primary neurons, as well as by cocaine and amphetamines, in a mouse model of chronic drug treatment. Taken together, our results identify miR-181a as a key regulator of mammalian AMPA-type glutamate receptors, with potential implications for the regulation of drug-induced synaptic plasticity.
Neuronal epigenetics and the aging synapse

Two of the most salient phenotypes of aging are cognitive decline and loss of motor function, both of which are controlled by the nervous system. Cognition and muscle contraction require that neuronal synapses develop and maintain proper structure and function. We review the literature on how normal physiological aging disrupts central and peripheral synapse function including the degradation of structure and/or control of neurotransmission. Here we also attempt to connect the work done on the epigenetics of aging to the growing literature of how epigenetic mechanisms control synapse structure and function. Lastly, we address possible roles of epigenetic mechanisms to explain why the basal rates of age-related dysfunction vary so widely across individuals.
Implicit Sensorimotor Mapping of the Peripersonal Space by Gazing and Reaching

Primates often perform coordinated eye and arm movements, contextually fixating and reaching towards nearby objects. This combination of looking and reaching to the same target is used by infants to establish an implicit visuomotor representation of the peripersonal space, useful for both oculomotor and arm motor control. In this work, taking inspiration from such behavior and from primate visuomotor mechanisms, a shared sensorimotor map of the environment, built on a radial basis function framework, is configured and trained by the coordinated control of eye and arm movements. Computational results confirm that the approach seems especially suitable for the problem at hand, and for its implementation on a real humanoid robot. By exploratory gazing and reaching actions, either free or goal-based, the artificial agent learns to perform direct and inverse transformations between stereo vision, oculomotor, and joint-space representations. The integrated sensorimotor map that allows to contextually represent the peripersonal space through different vision and motor parameters is never made explicit, but rather emerges thanks to the interaction of the agent with the environment.
Shelf‐lives and factors affecting the stability of morphine sulphate and meperidine (pethidine) hydrochloride in plastic syringes for use in patient‐controlled analgesic devices

Published reports regarding the stability of morphine are at variance, especially in syringes used in patient‐controlled analgesia (PCA) devices. In addition to the effects of container type and vehicle, reasons for this variation include the effect of excipients temperature and light during storage. Furthermore, the literature varies regarding the mechanisms of decomposition for morphine. To our knowledge, the stability of meperidine (pethidine) stored in plastic syringes has not been reported. The purposes of this study were to investigate the stability of morphine sulphate (1 and 5 mg/ml) and meperidine hydrochloride (5 and 10 mg/ml) in plastic syringes for use in PCA devices for a duration of 12 weeks, and evaluate the influence of light (240 foot‐candies), temperature (‐20, 4 and 23d̀C), diluent (5% dextrose or normal saline), and drug concentration on the stability of these narcotic analgesics.
Systematic Risk in Supply Chain Networks

Industrial production output is generally correlated with the state of the economy. Nonetheless, during times of economic downturn, some industries take the biggest hit, whereas at times of economic boom they reap most benefits. To provide insight into this phenomenon, we map supply networks of industries and firms and investigate how the supply network structure mediates the effect of economy on industry or firm sales. Previous research has shown that retail sales are correlated with the state of the economy. Since retailers source their products from other industries, the sales of their suppliers can also be correlated with the state of the economy. This correlation represents the source of systematic risk for an industry that propagates through a supply chain network. Specifically, we identify the following mechanisms that can affect the correlation between sales and the state of the economy in a supply chain network: propagation of systematic risk into production decisions, aggregation of orders from .
Update on the Antimicrobial Management of Foot Infections in Patients With Diabetes

IN BRIEF Foot infections are common problems in patients with diabetes and can lead to devastating complications and long-term morbidity. Although these infections invariably start in superficial soft tissues, they can involve deeper structures, including bone. Complications may include necrotizing fasciitis, soft tissue gangrene, septic arthritis, and osteomyelitis. This article reviews the factors involved in appropriate antibiotic selection and describes antimicrobial agents included in recently updated treatment guidelines from the Infectious Diseases Society of America.
How Task Types and User Experiences Affect Information-Seeking Behavior on the Web: Using Eye-tracking and Client-side Search Logs

We investigated what influence task type and user experience had on information-seeking behaviors on the Web by using screen-capture logs and eye-movement data. Five graduate students in library and information science and eleven undergraduate students with other majors performed two dierent Web searches, a report-writing and a tripplanning task, and their think-aloud protocols, behaviors, and eye movements were recorded. Analyses of the screencapture logs and eye-movement data revealed that the task type and user experience aected the participants’ informationseeking behaviors.
In vitro seed germination and node culture of the nutraceutical plant Grewia tenax

Grewia tenax is an important nutraceutical plant threatened due to excessive fruit collection and physiological dormancy of seeds. In vitro propagation is required for ex situ conservation of this neglected plant. Improving germination rate is vital for providing the uniform explant material required for propagation and in vitro studies. The aim of this study was to optimize cultivation conditions for in vitro seed germination and micropropagation of G. tenax. Full seed germination was achieved in all treatments. Tests in distilled water medium showed the least number of days for germination and highest seedling length. Full Murashige and Skoog medium produced the maximum number of nodes. Darkness promoted germination rate and seedling length, but decreased the number of nodes per seedling. Benzyladenine and kinetin slightly increased the number of nodes compared to the control. Each uninodal explant cultivated on Murashige and Skoog medium free of plant growth regulators developed into a plantlet within one week. Well-rooted plants were successfully established in a greenhouse with 95% survival rate. This plant growth regulator-free system can successfully overcome seed dormancy and provide a rapid-continuous supply of plant material of G. tenax.
Safety and Efficacy of Endovascular Sonolysis Using the EkoSonic Endovascular System in Patients with Acute Stroke

BACKGROUND AND PURPOSE: Sonolysis is a new therapeutic procedure for arterial recanalization. The aim of this study was to confirm the safety and efficacy of endovascular sonolysis by using the EkoSonic Endovascular System in subjects with acute ischemic stroke. MATERIALS AND METHODS: Patients with acute ischemic stroke with occlusion of the middle cerebral artery or basilar artery were enrolled consecutively in this prospective study. The control group (44 MCA and 12 BA occlusions) was selected from historical controls. EkoSonic Endovascular System was started within 8 hours after stroke onset. The NIHSS score at hospital admission, after 24 hours, and at 7 days; arterial recanalization; early neurologic improvement; symptomatic intracerebral hemorrhage; and favorable 3-month clinical outcome defined as a modified Rankin Scale score of 0–2 were evaluated by statistical means. RESULTS: Fourteen patients (10 men; mean age, 65.1 ± 11.2 years; median NIHSS score, 16.5) underwent EkoSonic endovascular sonolysis. Arterial recanalization after endovascular treatment was achieved in 6 of 7 (85.7%) patients with MCA occlusion (4 complete recanalizations) and in all 7 (100%) patients with BA occlusion (6 complete recanalizations). No (0%) symptomatic intracerebral hemorrhage or periprocedural complications occurred. Seven (50%) patients were independent at 3 months (median mRS score, 2). Early neurologic improvement and favorable clinical outcome were significantly more frequent in patients with MCA occlusion undergoing EkoSonic endovascular sonolysis than in controls (100% and 71.4% versus 4.6% and 13.6% of patients; P = .0001 and P = .003, respectively). Three-month mortality was significantly lower in patients with BA occlusion undergoing EkoSonic endovascular sonolysis than in controls (0% versus 66.7% patients, P = .013). CONCLUSIONS: In this small study, EkoSonic endovascular sonolysis allowed safe and potentially effective revascularization in patients experiencing acute ischemic stroke.
Frequency of Exercise for Body Fat Loss: A Controlled, Cohort Study

Willis, FB, Smith, FM, and Willis, AP. Frequency of exercise for body fat loss: a controlled, cohort study. J Strength Cond Res 23(8): 2377-2380, 2009-The purpose of this study is to examine the changes in body fat mass of previously sedentary, deconditioned subjects who began following the U.S. Surgeon General's recommendation in frequency of exercise. Ninety subjects of both sexes were recruited; ages ranged from 22 to 74 (mean 37.5 ± 13) years. Subjects were prescribed exercise of 4 times a week, 30 minutes of continuous exercise, for 8 weeks. Eighty subjects completed the 8-week study and were categorized based on voluntary compliance: control (no exercise); exercise less than 2 times/week; exercise 3 to 4 times/week; exercise 4 or more times/week. Body fat mass was the dependent variable in this study, as measured by air displacement plethysmography, and data analysis was accomplished with a repeated measures analysis of variance. There was a significant change in body fat mass in this study, but the only significant difference between groups was for the group that exercised 4 or more times/week, (p = 0.004). Adherence to the U.S. Surgeon General's Guidelines for frequency of exercising 4 times per week for 30 minutes was effective in reducing subjects' body fat mass in this study.
Lactate Dehydrogenase Activity in Gingival Crevicular Fluid as a Marker in Orthodontic Tooth Movement

Objectives: This study aims at analyzing the changes in gingival crevicular fluid (GCF) lactate dehydrogenase (LDH) activity during orthodontic movement. Methods: Twenty patients all requiring first premolar extractions were selected and treated with conventional straight wire mechanotherapy. Canine retraction was done using 125 g Nitinol closed coil springs. The maxillary canine on one side served as the experimental site while the contralateral canine served as the control. GCF was collected from the canines before initiation of retraction, then 1 hour after initiating canine retraction, followed by 1 day, 7 days, 14 days and 21 days. GCF LDH levels were estimated and compared with the control site. Results The results revealed significantly higher LDH levels on the 7th, 14th and 21st day at the sites where orthodontic force had been applied. The levels also showed a significant increase from 0 hour to the 21st day. Peak levels were seen on 14th and 21st day following initiation of retraction. Conclusions: The study showed that LDH could be successfully estimated in the GCF and its increased levels could indicate active tooth movement, which could aid the clinician in monitoring active orthodontic tooth movement.
Folate gene polymorphisms and the risk of Down syndrome pregnancies in young Italian women

Maternal impairments in folate metabolism and elevated homocysteinemia are known risk factors for having a child with Down syndrome (DS) at a young age. The 80G>A polymorphism of the reduced folate carrier gene (RFC‐1) has been recently demonstrated to affect plasma folate and homocysteine levels, alone or in combination with the 677C>T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene. We performed the present study on 80 Italian mothers of DS individuals, aged less than 35 at conception, and 111 Italian control mothers, to study the role of the RFC‐1 80G>A, MTHFR 677C>T, and MTHFR 1298A>C genotypes to the risk of a DS offspring at a young maternal age. When polymorphisms were considered alone, both allele and genotype frequencies did not significantly differ between DS mothers and control mothers. However, the combined MTHFR677TT/RFC‐1 80GG genotype was borderline associated with an increased risk (OR 6 (CI 95%: 1.0–35.9), P = 0.05), and to be MTHF1298AA/RFC‐1 80(GA or AA) was inversely associated with the risk (OR 0.36 (CI 95%: 0.14–0.96), P = 0.04). Present results seem to indicate that none of the RFC‐1 80G>A, MTHFR 677C>T, and MTHFR 1298A>C polymorphisms is an independent risk factor for a DS offspring at a young maternal age; however, a role for the combined MTHFR/RFC‐1 genotypes in the risk of DS pregnancies among young Italian women cannot be excluded. © 2006 Wiley‐Liss, Inc.
Contribution of the hyperpolarization-activated current (I(h)) to membrane potential and GABA release in hippocampal interneurons.

Intrinsic GABAergic interneurons provide inhibitory input to the principal neurons of the hippocampus. The majority of interneurons located in stratum oriens (s.o.) of the CA1 region express the hyperpolarization-activated cation current known as I(h). In an effort to elucidate the role of this current in regulating the baseline excitability of these neurons and its participation in the regulation of the release of GABA onto CA1 pyramidal neurons, we utilized whole cell electrophysiological recordings from both populations of cells. In voltage-clamp experiments, hyperpolarization of the interneuron membrane initiated a large inward current with an estimated activation threshold of 51.6 +/- 7.6 mV and a half-maximal voltage of -73.0 +/- 7.0 mV. This current was blocked by bath application of the I(h) inhibitors ZD 7288 (50 microM) or cesium (2 mM). Current-clamp experiments at the interneuron resting membrane potential (-61.3 +/- 1.2 mV) revealed a significant hyperpolarization, a decrease in the rate of spontaneous action potential discharge, an increase in the cellular input resistance, and the elimination of rebound afterdepolarizations during blockade of I(h) with ZD 7288 (50 microM). The hyperpolarizing effect of ZD 7288 was also substantially larger in interneurons clamped near -80 mV using current injection through the pipette. In addition to neurons exhibiting I(h), recordings were obtained from a small population of s.o. interneurons that did not exhibit this current. These cells demonstrated resting membrane potentials that were significantly more negative (-73.6 +/- 5.5 mV) than those observed in neurons expressing I(h), suggesting that this current contributes to more depolarized membrane potentials in these cells. Recordings from postsynaptic pyramidal neurons demonstrated that blockade of I(h) with ZD 7288 caused a substantial reduction (approximately 43%) in the frequency of spontaneous action potential-dependent inhibitory postsynaptic currents (IPSCs), without altering their average amplitude. However, miniature action-potential-independent IPSC frequency, amplitude, and decay kinetics were unaltered by ZD 7288. These data suggest that I(h) is active at the resting membrane potential in s.o. interneurons and as a result contributes to the spontaneous activity of these cells and to the tonic inhibition of CA1 pyramidal neurons in the hippocampus.
Information Asymmetry and Asset Prices: Evidence from the China Foreign Share Discount

We examine the effect of information asymmetry on equity prices in the local A- and foreign B-share market in China. We construct measures of information asymmetry based on market microstructure models, and find that they explain a significant portion of cross-sectional variation in B-share discounts, even after controlling for other factors. On a univariate basis, the price impact measure and the adverse selection component of the bid-ask spread in the A- and B-share markets explains 44% and 46% of the variation in B-share discounts. On a multivariate basis, both measures are far more statistically significant than any of the control variables.
Randomised cross-over trial evaluating the short-term effects of non-invasive ventilation as an adjunct to airway clearance techniques in adults with cystic fibrosis

Introduction Non-invasive ventilation (NIV) is used in cystic fibrosis (CF) to support airway clearance techniques (ACTs) by augmenting tidal volumes and reducing patient effort. However, the evidence base for this is limited. We hypothesised that NIV, in addition to usual ACT, would increase sputum clearance. In addition, we investigated ease of sputum clearance (EoC), work of breathing (WoB) and NIV tolerability. Methods Adults with CF (16+ years) at the end of hospitalisation for a pulmonary exacerbation were randomised to a cross-over trial of NIV-supported ACT or ACT alone in two consecutive days. No other changes to standard care were made. The primary outcome was the total 24-hour expectorated sputum wet weight after the intervention. Spirometry was completed pre-treatment and post-treatment. Oxygen saturations were measured pre-treatment, during treatment and post-treatment. EoC and WoB were assessed using Visual Analogue Scale. Results 14 subjects completed the study (7 male, mean age 35 [SD 17] years, mean forced expiratory volume in 1 s [FEV1] 49 [20] % predicted). The difference between treatment regimens was −0.98 g sputum (95% CI −11.5 to 9.6, p=0.84) over 24 hours. During treatment oxygen saturations were significantly higher with NIV-supported ACT (mean difference 2.0, 95% CI 0.9 to 2.6, p=0.0004). No other significant differences were found in post-treatment FEV1, EoC, WoB, oxygen saturations or subject preference. Conclusions There was no difference in treatment effect between NIV-supported ACT and ACT alone, although the study was underpowered. Oxygen saturations were significantly higher during NIV-supported ACT, but with no effect on post-treatment saturations. NIV was well tolerated. Trial registration number NCT01885650.
[Poster] AIBLE: An inquiry-based augmented reality environment for teaching astronomical phenomena

We present an inquiry-based augmented reality (AR) learning environment (AIBLE) designed for teaching basic astronomical phenomena in elementary classroom (children of 8-11 years old). The novelty of this environment lies in the combination of both Inquiry Based Sciences Education and didactics principles with AR features. This environment was user tested by 69 pupils in order to assess its impact on learning. The main results indicate that AIBLE provides new opportunities for the identification of learners' problem solving strategies.
Effects of different levels of glycine in the nutrient solution on the growth, nutrient composition, and antioxidant activity of coriander (Coriandrum sativum L.)

A nutrient solution experiment was performed using sand culture to evaluate the effects of different glycine levels on the growth and nutrient uptake of coriander (Coriandrum sativum L.). Different glycine concentrations of 0, 5, 10, 20, or 40 mg L−1 were applied to plants via Hoagland’s nutrient solution in a completely randomized design with four replications and under greenhouse conditions. The results showed that leaf SPAD (soil and plant analysis development; an indicator of leaf greenness) value, stem diameter, and fresh and dry weights of shoots and roots were significantly increased by 10 mg L−1 glycine in comparison to the control plants. Application of glycine at 40 mg L−1 reduced many plant growth parameters, whereas leaf proline concentration was increased. All glycine levels except for 40 mg L−1 increased root fresh weight. Leaf protein content was increased by glycine applied at 10 or 20 mg L−1, whereas leaf antioxidant activity was increased at all glycine levels. Application of glycine increased leaf concentrations of nitrogen and potassium (at 10 mg L−1), magnesium (at 5 mg L−1), and zinc (at all glycine levels) compared to the control plants. The results indicate that moderate level of glycine (10 mg L−1) in the nutrient solution can improve the growth and nutritional quality of coriander.