Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone H3K9 modifications are a local chromatin event involved in ethanol-induced neuroadaptation of the NR2B gene

Expression of the NMDA receptor 2B (NR2B) gene is upregulated following chronic intermittent ethanol (CIE) treatment and withdrawal, which underlies behavioral alterations in addiction. The goal of this study was to characterize the changes of histone modifications induced by CIE treatment and its subsequent removal associated to the upregulation of NR2B gene transcription. To investigate the involvement of histone acetylation in the effect of ethanol on the NR2B gene, we examined the influence of CIE on histone acetylation in the 5' regulatory region of NR2B using a qChIP assay. CIE treatment and its subsequent removal produced a remarkable and selected increase in histone H3K9 acetylation. Interestingly, the majority of the increased H3K9 acetylation occurred after ethanol removal, which was coincident with a decrease in H3K9 methylation in the same time duration. Further examination of the mechanisms of ethanol-induced alterations on the histone modifications revealed that CIE-induced acetylation of H3K9 was not due to the changes in global enzyme activities or the expression of histone acetyltransferases (HATs) and deacetylase (HDACs). Instead, we found a significant downregulation in some histone methyltransferases (HMTs) at both the global level and the local chromatin of the NR2B gene following CIE treatment. Moreover, our experiments also indicated a decrease of G9a, Suv39 h1 and HDAC1-3 in the chromatin of the NR2B gene promoter, which may be responsible for the altered H3K9 modifications. Taken together, the findings suggest a mechanism where the changes in H3K9 modifications in the local chromatin of the NR2B gene underlie alcohol-induced neuroadaptation.
In Vitro Polymerization of Heparan Sulfate Backbone by the EXT Proteins*

Multiple exosotoses is a dominantly inherited bone disorder caused by defects in EXT1 and EXT2, genes encoding glycosyltransferases involved in heparan sulfate chain elongation. Heparan sulfate polymerization occurs by the alternating addition of glucuronic acid and N-acetylglucosamine units to the nonreducing end of the polysaccharide. EXT1 and EXT2 are suggested to be dual glucuronyl/N-acetylglucosaminyltransferases, and a heterooligomeric complex of EXT1 and EXT2 (EXT1/2) is considered to be the biological functional polymerization unit. Here, we have investigated the in vitro polymerization capacities of recombinant soluble EXT1, EXT2, and EXT1/2 complex on exogenous oligosaccharide acceptors derived from Escherichia coli K5 capsular polysaccharide. Incubations of recombinant EXT1 or EXT1/2 complex with 3H-labeled oligosaccharide acceptors and the appropriate nucleotide sugars resulted in conversion of the acceptors to higher molecular weight compounds but with different efficacies for EXT1 and EXT1/2. In contrast, incubations with recombinant EXT2 resulted in the addition of a single glucuronic acid but no further polymerization. These results indicate that EXT1 alone and the EXT1/2 heterocomplex can act as heparan sulfate polymerases in vitro without the addition of additional auxiliary proteins.
Dimensional contraction via Markov transportation distance

It is now well known that curvature conditions à la Bakry–Émery are equivalent to contraction properties of the heat semigroup with respect to the classical quadratic Wasserstein distance. However, this curvature condition may include a dimensional correction which up to now had not induced any strengthening of this contraction. We first consider the simplest example of the Euclidean heat semigroup, and prove that indeed it is so. To consider the case of a general Markov semigroup, we introduce a new distance between probability measures, based on the semigroup, and adapted to it. We prove, in the setting of a compact Riemannian manifold, that this Markov transportation distance satisfies the same properties as the Wasserstein distance does in the specific case of the Euclidean heat semigroup, namely dimensional contraction properties and evolution variational inequalities.
Exploring the relationship between fear of falling and neuroticism: a cross-sectional study in community-dwelling women over 70.

BACKGROUND Fear of falling in older adults has been associated with generalised anxiety and may lead to avoidance of activities, with a further negative impact on future falls. Individual differences in personality associated with anxiety have not been previously examined in relation to fear of falling. Current assessment measures and interventions designed to reduce fear of falling in older adults do not take into account perceptions of anxiety associated with individual differences in personality. AIM To determine whether the core personality trait dimension of neuroticism can predict fear of falling in a community-dwelling sample of women > or = 70 years of age. METHODS Cross-sectional data from 1,691 UK, community-dwelling female participants aged > or = 70 years were examined using multiple and logistic regression analysis. Fear of falling was measured on a 6-point Likert scale. Neuroticism was measured using the Eysenck personality inventory. RESULTS The significant independent odds ratios (OR) of predicting fear of falling were: neuroticism (OR 1.47 per SD increase, P<0.001), history of falling (OR 1.57, P<0.001), experience of fracture (OR 1.78, P = 0.014), need to use both arms to push up to rise from a chair (OR 1.56, P = 0.001), poor subjective general health, as measured by the SF12 (OR 1.63 per SD decrease, P<0.001) and living alone (OR 1.31, P = 0.031). CONCLUSIONS Neuroticism seems to be an important psychological factor in the experience of fear of falling in community-dwelling older women. It may be relevant for inclusion in current assessment measures and for consideration in the design of interventions to reduce fear of falling.
Multiantenna spectrum sensing for Cognitive Radio: overcoming noise uncertainty

Spectrum sensing is a key ingredient of the dynamic spectrum access paradigm, but it needs powerful detectors operating at SNRs well below the decodability levels of primary signals. Noise uncertainty poses a significant challenge to the development of such schemes, requiring some degree of diversity (spatial, temporal, or in distribution) for identifiability of the noise level. Multiantenna detectors exploit spatial independence of receiver thermal noise. We review this class of schemes and propose a novel detector trading off performance and complexity. However, most of these methods assume that the noise power, though unknown, is the same at all antennas. As it turns out, calibration errors have a substantial impact on these detectors. Another novel detector is proposed, based on an approximation to the Generalized Likelihood Ratio, outperforming previous schemes for uncalibrated multiantenna receivers.
Peering into the “Magnum Mysterium” of Culture

The purpose of this research is to test whether descriptive norms, or cognitions about typical beliefs, values, and behaviors of one's group, can explain cultural influence in the domains of blame attribution and harm perception. In Study 1, using participants from the United States and South Korea, the authors find that individuals with lower (vs. higher) collectivistic descriptive norms ascribed more blame after more intentional acts and less blame after less intentional acts. In the second study, using American and South Korean participants, the authors find that individuals with lower (vs. higher) collectivistic descriptive norms perceived more harm after right violations and less harm after duty violations. Collectivistic personal attitudes did not predict the expected differences in attribution of blame or perception of harm. The descriptive norm account of cultural influence provides an alternative to the currently dominant personal attitude paradigm.
Salvage of Severe Ankle Varus Deformity With Soft Tissue and Bone Rebalancing

The etiology of ankle varus is multifactorial. Treatment recommendations after failed conservative care include hindfoot and ankle fusions or total ankle arthroplasty (TAA) with ligament rebalancing. The purpose of this study was to evaluate chronic varus ankle deformities through corrective calcaneal osteotomies and lateral soft tissue reconstruction. All skeletally mature patients with at least 5 degrees of ankle varus were included in the study. Pre and postoperative radiographs were retrospectively reviewed measuring talar tilt. All patients had a lateral closing wedge (Dwyer) calcaneal osteotomy, joint debridement, and lateral ankle ligament reconstruction. Eight feet were included in the study. The average follow-up time was 20.6 months. Six patients (six feet) were asymptomatic and did not have any additional surgery at their most recent follow-up. Two patients failed treatment, requiring surgical intervention for persistent pain and/or deformity. The average postoperative ankle varus correction overall was 4.9 degrees. We found ankle varus on average of less than 10 degrees can be reliably corrected with a combination of lateral ligament reconstruction and calcaneal osteotomy. Approximately 50% of the deformity was corrected when comparing pre and postoperative talar tilt values. In patients with varus deformity greater than 10 degrees preoperatively, persistent varus may occur.
Climate Warming and Disease Risks for Terrestrial and Marine Biota

Infectious diseases can cause rapid population declines or species extinctions. Many pathogens of terrestrial and marine taxa are sensitive to temperature, rainfall, and humidity, creating synergisms that could affect biodiversity. Climate warming can increase pathogen development and survival rates, disease transmission, and host susceptibility. Although most host-parasite systems are predicted to experience more frequent or severe disease impacts with warming, a subset of pathogens might decline with warming, releasing hosts from disease. Recently, changes in El Niño–Southern Oscillation events have had a detectable influence on marine and terrestrial pathogens, including coral diseases, oyster pathogens, crop pathogens, Rift Valley fever, and human cholera. To improve our ability to predict epidemics in wild populations, it will be necessary to separate the independent and interactive effects of multiple climate drivers on disease impact.
Deep Models for Ensemble Touch-Screen Improvisation

For many, the pursuit and enjoyment of musical performance goes hand-in-hand with collaborative creativity, whether in a choir, jazz combo, orchestra, or rock band. However, few musical interfaces use the affordances of computers to create or enhance ensemble musical experiences. One possibility for such a system would be to use an artificial neural network (ANN) to model the way other musicians respond to a single performer. Some forms of music have well-understood rules for interaction; however, this is not the case for free improvisation with new touch-screen instruments where styles of interaction may be discovered in each new performance. This paper describes an ANN model of ensemble interactions trained on a corpus of such ensemble touch-screen improvisations. The results show realistic ensemble interactions and the model has been used to implement a live performance system where a performer is accompanied by the predicted and sonified touch gestures of three virtual players.
G2-Type SRMPC Scheme for Synchronous Manipulation of Two Redundant Robot Arms

In this paper, to remedy the joint-angle drift phenomenon for manipulation of two redundant robot arms, a novel scheme for simultaneous repetitive motion planning and control (SRMPC) at the joint-acceleration level is proposed, which consists of two subschemes. To do so, the performance index of each SRMPC subscheme is derived and designed by employing the gradient dynamics twice, of which a convergence theorem and its proof are presented. In addition, for improving the accuracy of the motion planning and control, position error, and velocity, error feedbacks are incorporated into the forward kinematics equation and analyzed via Zhang neural-dynamics method. Then the two subschemes are simultaneously reformulated as two quadratic programs (QPs), which are finally unified into one QP problem. Furthermore, a piecewise-linear projection equation-based neural network (PLPENN) is used to solve the unified QP problem, which can handle the strictly convex QP problem in an inverse-free manner. More importantly, via such a unified QP formulation and the corresponding PLPENN solver, the synchronism of two redundant robot arms is guaranteed. Finally, two given tasks are fulfilled by 2 three-link and 2 five-link planar robot arms, respectively. Computer-simulation results validate the efficacy and accuracy of the SRMPC scheme and the corresponding PLPENN solver for synchronous manipulation of two redundant robot arms.
New aspects on patients affected by dysferlin deficient muscular dystrophy

Mutations in the dysferlin gene lead to limb girdle muscular dystrophy 2B, Miyoshi myopathy and distal anterior compartment myopathy. A cohort of 36 patients affected by dysferlinopathy is described, in the first UK study of clinical, genetic, pathological and biochemical data. The diagnosis was established by reduction of dysferlin in the muscle biopsy and subsequent mutational analysis of the dysferlin gene. Seventeen mutations were novel; the majority of mutations were small deletions/insertions, and no mutational hotspots were identified. Sixty-one per cent of patients (22 patients) initially presented with limb girdle muscular dystrophy 2B, 31% (11 patients) with a Miyoshi phenotype, one patient with proximodistal mode of onset, one patient with muscle stiffness after exercise and one patient as a symptomatic carrier. A wider range of age of onset was noted than previously reported, with 25% of patients having first symptoms before the age of 13 years. Independent of the initial mode of presentation, in our cohort of patients the gastrocnemius muscle was the most severely affected muscle leading to an inability to stand on tiptoes, and lower limbs were affected more severely than upper limbs. As previous anecdotal evidence on patients affected by dysferlinopathy suggests good muscle prowess before onset of symptoms, we also investigated pre-symptomatic fitness levels of the patients. Fifty-three per cent of the patients were very active and sporty before the onset of symptoms which makes the clinical course of dysferlinopathy unusual within the different forms of muscular dystrophy and provides a challenge to understanding the underlying pathomechanisms in this disease.
Mixture of parts revisited: Expressive part interactions for Pose Estimation

Part-based models with restrictive tree-structured interactions for the Human Pose Estimation problem, leave many part interactions unhandled. Two of the most common and strong manifestations of such unhandled interactions are self-occlusion among the parts and the confusion in the localization of the non-adjacent symmetric parts. By handling the self-occlusion in a data efficient manner, we improve the performance of the basic Mixture of Parts model by a large margin, especially on difficult poses. We address the confusion in the symmetric limb localization using a combination of two complementing trees, showing an improvement in the performance on all the parts with a very small trade-off in the running time. Finally, we show that the combination of the two solutions improves the results. We compare our HOG-based method with other methods using similar features and report results equivalent to the best method on two standard datasets with a large reduction in the running time.
Resveratrol Inhibits Sodium/Iodide Symporter Gene Expression and Function in Rat Thyroid Cells

Resveratrol is a polyphenol found in grapes and berries that has antioxidant, antiproliferative and anti-inflammatory properties. For these reasons, it is available as a dietary supplement, and it is under investigation in several clinical trials. Few data are available regarding the effects of resveratrol on thyroid function. A previous study showed that resveratrol transiently increases iodide influx in FRTL-5 rat thyroid cells. Indeed, this increase arises after short treatment times (6–12 h), and no further effects are seen after 24 h. The aim of the present study was to investigate the effects of resveratrol on iodide uptake and sodium/iodide symporter expression in thyroid cells after longer times of treatment. For this purpose, the effects of resveratrol were evaluated both in vitro and in vivo using the rat thyroid FRTL-5 cell line and Sprague-Dawley rats, respectively. In FRTL-5 cells, resveratrol decreased the sodium/iodide symporter RNA and protein expression as a function of time. Furthermore, resveratrol decreased cellular iodide uptake after 48 h of treatment. The inhibitory effect of resveratrol on iodide uptake was confirmed in vivo in Sprague-Dawley rats. This study demonstrates that with longer-term treatment, resveratrol is an inhibitor of sodium/iodide symporter gene expression and function in the thyroid. These data suggest that resveratrol can act as a thyroid disruptor, which indicates the need for caution as a supplement and in therapeutic use.
Teaching lasers to control molecules.

We simulate a method to teach a laser pulse sequences to excite specified molecular states. We use a learning procedure to direct the production of pulses based on fitness'' information provided by a laboratory measurement device. Over a series of pulses the algorithm learns an optimal sequence. The experimental apparatus, which consists of a laser, a sample of molecules and a measurement device, acts as an analog computer that solves Schroedinger's equation n/Iexactly, in real time. We simulate an apparatus that learns to excite specified rotational states in a diatomic molecule.
Water and side‐chain embedded π‐turns

Elucidating protein function from its structure is central to the understanding of cellular mechanisms. This involves deciphering the dependence of local structural motifs on sequence. These structural motifs may be stabilized by direct or water‐mediated hydrogen bonding among the constituent residues. π‐Turns, defined by interactions between (i) and (i + 5) positions, are large enough to contain a central space that can embed a water molecule (or a protein moiety) to form a stable structure. This work is an analysis of such embedded π‐turns using a nonredundant dataset of protein structures. A total of 2965 embedded π‐turns have been identified, as also 281 embedded Schellman motif, a type of π‐turn which occurs at the C‐termini of α‐helices. Embedded π‐turns and Schellman motifs have been classified on the basis of the protein atoms of the terminal turn residues that are linked by the embedded moiety, conformation, residue composition, and compared with the turns that have terminal residues connected by direct hydrogen bonds. Geometrically, the turns have been fitted to a circle and the position of the linker relative to its center analyzed. The hydroxyl group of Ser and Thr, located at (i + 3) position, is the most prominent linker for the side‐chain mediated π‐turns. Consideration of residue conservation among homologous sequences indicates the terminal and the linker positions to be the most conserved. The embedded π‐turn as a binding site (for the linker) is discussed in the context of “nest,” a concave depression that is formed in protein structures with adjacent residues having enantiomeric main‐chain conformations. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 441–453, 2014.
AutomationML review support in multi-disciplinary engineering environments

[Context] In Multi-Disciplinary Engineering (MDE) environments, the engineering of industrial production systems requires the collaboration of engineers coming from different disciplines. Engineers typically apply discipline specific tools and data models with limited collaboration capabilities. These loosely coupled tools and heterogeneous data models hinder efficient change management and defect detection, which makes MDE projects unnecessarily risky and error prone. [Objective] This paper presents an adapted review approach, AML-Review, for multi-disciplinary engineering (MDE) projects based on best practices for reviews in software engineering. [Method] Software reviews have been successfully used for early defect detection in Software Engineering. However, adaptations are needed for defect detection in MDE environments. We focus on production systems models according to the emerging AutomationML standard. [Results] We evaluated the feasibility of the AML-Review process with requirements and an AutomationML model from a real-world application scenario. The AML-Review process provides the benefits of systematic and traceable review results for MDE projects based on AutomationML. [Conclusion] The prototype results imply that systematic and structured review processes help to improve traceability of requirements and defects and increase defect detection performance.
Analysis and Evolution of Journaling File Systems

We develop and apply two new methods for analyzing file system behavior and evaluating file system changes. First, semantic block-level analysis (SBA) combines knowledge of on-disk data structures with a trace of disk traffic to infer file system behavior; in contrast to standard benchmarking approaches, SBA enables users to understand why the file system behaves as it does. Second, semantic trace playback (STP) enables traces of disk traffic to be easily modified to represent changes in the file system implementation; in contrast to directly modifying the file system, STP enables users to rapidly gauge the benefits of new policies. We use SBA to analyze Linux ext3, ReiserFS, JFS, and Windows NTFS; in the process, we uncover many strengths and weaknesses of these journaling file systems. We also apply STP to evaluate several modifications to ext3, demonstrating the benefits of various optimizations without incurring the costs of a real implementation.
Environmental Tobacco Smoke Furthers Progression of Diabetic Nephropathy

Clinical studies suggest that smoking is a risk factor in the progression of chronic kidney disease, including diabetic nephropathy. The mechanisms involved are not completely understood. We have previously demonstrated that nicotine, one of the compounds present in large amounts in tobacco, promotes mesangial cell proliferation and fibronectin production. In this study, we hypothesized that exposure to environmental tobacco smoke (ETS) promotes the progression of diabetic nephropathy by increasing the expression of profibrotic cytokines such as transforming growth factor-beta (TGF-&bgr;) and the extracellular matrix proteins fibronectin and collagen IV. Six-week-old diabetic (db/db) mice were divided into 2 groups. The experimental group (n = 12) was exposed to ETS at a concentration of 30 mg/m3 for 6 hr/d, 5 d/wk for 8 weeks. The control group (n = 8) was exposed to room air. Urine was collected before euthanasia for albumin (enzyme-linked immunosorbent assay) and creatinine measurements (mass spectrometry). After euthanasia, the kidneys were harvested for morphometric analysis and Western blot analysis. Serum was saved for cotinine measurements by enzyme-linked immunosorbent assay. ETS exposure resulted in serum levels of cotinine similar to those found in human smokers. ETS exposure for 8 weeks induced significant mesangial expansion (approximately 50% increase) that was accompanied by concomitant increases in TGF-&bgr; and fibronectin expression (approximately 20%). However, ETS did not modify results in significant changes in urinary albumin excretion. These studies demonstrate that ETS exposure worsens the progression of diabetic nephropathy by increasing the amount of mesangial expansion and that these effects are likely mediated by increased expression of profibrotic cytokines such as TGF-&bgr;.