Miracle-dz/UniFAR-FTUs huggingface dataset:
Resveratrol- and melatonin-abated ovariectomy and fructose diet–induced obesity and metabolic alterations in female rats

ObjectiveThis study was designed to investigate the effects of bilateral ovariectomy and fructose diet on obesity-related metabolic parameters in female rats. The potential of resveratrol, alone and in combination with melatonin, to counter ensuing obesity and precipitated metabolic disturbances was explored. MethodsEight-week-old female Sprague-Dawley rats were subjected to bilateral ovariectomy (OVX) or sham operation and randomly assigned to standard diet (SD) or fructose diet (FD) groups (n = 6 rats per group) as follows: Sham; OVX + FD; OVX + SD; OVX + FD + resveratrol 50 mg/kg/day PO (RESV); OVX + SD + RESV; OVX + FD + melatonin 3 mg/kg/day PO in drinking water (M); OVX + SD + M; OVX + FD + RESV + M; OVX + SD + RESV + M. All treatments were given for 7 weeks. Biochemical, dietary, and anthropometrical parameters were estimated, and abdominal fat pads and the liver were examined for histopathological alterations. ResultsOvariectomy caused an increase in body weight, body mass index, feed efficiency, serum glucose, cholesterol, triglycerides, and free fatty acids, which was further exacerbated by fructose diet. These parameters were significantly decreased by resveratrol, alone and in combination with melatonin. Histopathological examination revealed reduced hypertrophy of adipocytes in adipose tissue and reduced macrophage infiltration in the liver. ConclusionsResveratrol/melatonin combination effectively normalizes anthropometrical, biochemical, and histopathological parameters in ovariectomized rats with fructose diet–induced obesity and associated metabolic alterations. The combination should be explored for potential benefits in postmenopausal women.
Proximity Queries and Penetration Depth Computation on 3d Game Objects

This paper discusses methods for performing proximity queries (collision detection, distance computation) and penetration depth computation on a large class of convex objects. The penetration depth of a pair of intersecting objects is the shortest vector over which one object needs to be translated in order to bring the pair in touching contact. The class of objects includes convex primitives such as polytopes (line segments, triangles, convex polyhedra) and quadrics (spheres, cones, cylinders), as well as shapes derived from these primitives by affine transformation and spherical expansion (inflating an object by a given offset).
ARC: a bottom-up approach to negotiated QoS

Mobile systems operate in a resource-scarce environment and thus must adapt to external conditions; all layers must make cost-based decisions about what mode of operation to use in response to performance feedback. This paper focuses on the generic interface between adjacent layers (client and server) in a multi-level hierarchy. The Adaptive Research Contracts (ARC) framework uses a bottom-up approach in which the server exposes a range of quality/cost modes to the client above. This allows the client to trade off various algorithms generating different workloads for multiple resources. A case study shows that control can be distributed effectively over multiple layers with ARC; global cost-effective solutions can be obtained by exchanging a small fraction of all possible control settings.
You've Gotta Be Lucky: Coverage and the Elusive Gene–Gene Interaction

Genome‐wide association studies (GWAS) have led to a large number of single‐SNP association findings, but there has been, so far, no investigation resulting in the discovery of a replicable gene–gene interaction. In this paper, we examine some of the possible explanations for the lack of findings, and argue that coverage of causal variation not only has a large effect on the loss in power, but that the effect is larger than in the single‐SNP analyses. We show that the product of linkage disequilibrium measures, r2, between causal and tested SNPs offers a good approximation to the loss in efficiency as defined by the ratio of sample sizes that lead to similar power. We also demonstrate that, in addition to the huge search space, the loss in power due to coverage when using commercially available platforms makes the search for gene–gene interactions daunting.
Common Variants in Epithelial Sodium Channel Genes Contribute to Salt Sensitivity of Blood Pressure: The GenSalt Study

Background— Rare mutations of the epithelial sodium channel (ENaC) lead to mendelian forms of salt-sensitive hypertension or salt-wasting hypotension. We aimed to examine the association between common variants in the ENaC genes and salt sensitivity of blood pressure (BP). Methods and Results— A total of 1906 Han Chinese participated in the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) study, which includes a 7-day low-sodium intake (51.3 mmol sodium/d) followed by a 7-day high-sodium intake (307.8 mmol sodium/d). Nine BP measurements were obtained at baseline and each intervention period using a random-zero sphygmomanometer. Single-nucleotide polymorphisms, both tagging and functional, from the 3 ENaC subunits, &agr;, &bgr;, and &ggr; (SCNN1A, SCNN1B, and SCNN1G), were genotyped. Multiple common single-nucleotide polymorphisms in SCNN1G were significantly associated with BP response to low-sodium intervention (rs4073930, P=1.7×10−5; rs4073291, P=1.1×10−5; rs7404408, P=1.9×10−5; rs5735, P=3.0×10−4; rs4299163, P=0.004; and rs4499238, P=0.002) even after correcting for multiple testing. For example, under an additive model, the minor allele G of SNP rs4073291 was associated with 1.33 mm Hg lower systolic BP reduction during low-sodium intervention. Conclusions— This large dietary sodium intervention study indicates that common variants of ENaC subunits may contribute to the variation of BP response to dietary sodium intake. Future studies are warranted to confirm these findings in an independent population and to identify functional variants for salt sensitivity. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00721721.
Cytoplasmic dynein binds dynactin through a direct interaction between the intermediate chains and p150Glued

Cytoplasmic dynein is a retrograde microtubule motor thought to participate in organelle transport and some aspects of minus end- directed chromosome movement. The mechanism of binding to organelles and kinetochores is unknown. Based on homology with the Chlamydomonas flagellar outer arm dynein intermediate chains (ICs), we proposed a role for the cytoplasmic dynein ICs in linking the motor protein to organelles and kinetochores. In this study two different IC isoforms were used in blot overlay and immunoprecipitation assays to identify IC- binding partners. In overlays of complex protein samples, the ICs bound specifically to polypeptides of 150 and 135 kD, identified as the p150Glued doublet of the dynactin complex. In reciprocal overlay assays, p150Glued specifically recognized the ICs. Immunoprecipitations from total Rat2 cell extracts, rat brain cytosol, and rat brain membranes further identified the dynactin complex as a specific target for IC binding. using truncation mutants, the sites of interaction were mapped to amino acids 1-123 of IC-1A and amino acids 200-811 of p150Glued. While cytoplasmic dynein and dynactin have been implicated in a common pathway by genetic analysis, our findings identify a direct interaction between two specific component polypeptides and support a role for dynactin as a dynein "receptor". Our data also suggest, however, that this interaction must be highly regulated.
Characterization of CIPK Family in Asian Pear (Pyrus bretschneideri Rehd) and Co-expression Analysis Related to Salt and Osmotic Stress Responses

Asian pear (Pyrus bretschneideri) is one of the most important fruit crops in the world, and its growth and productivity are frequently affected by abiotic stresses. Calcineurin B-like interacting protein kinases (CIPKs) as caladium-sensor protein kinases interact with Ca2+-binding CBLs to extensively mediate abiotic stress responses in plants. Although the pear genome sequence has been released, little information is available about the CIPK genes in pear, especially in response to salt and osmotic stresses. In this study, we systematically identified 28 CIPK family members from the sequenced pear genome and analyzed their organization, phylogeny, gene structure, protein motif, and synteny duplication divergences. Most duplicated PbCIPKs underwent purifying selection, and their evolutionary divergences accompanied with the pear whole genome duplication. We also investigated stress -responsive expression patterns and co-expression networks of CIPK family under salt and osmotic stresses, and the distribution of stress-related cis-regulatory elements in promoter regions. Our results suggest that most PbCIPKs could play important roles in the abiotic stress responses. Some PbCIPKs, such as PbCIPK22, -19, -18, -15, -8, and -6 can serve as core regulators in response to salt and osmotic stresses based on co-expression networks of PbCIPKs. Some sets of genes that were involved in response to salt did not overlap with those in response to osmotic responses, suggesting the sub-functionalization of CIPK genes in stress responses. This study revealed some candidate genes that play roles in early responses to salt and osmotic stress for further characterization of abiotic stress responses medicated by CIPKs in pear.
Analysis of axonal and dendritic signal propagation-finite difference and finite element techniques

The prevalent model to describe propagation of neural membrane voltage responses to ion currents is the cable equation. The cable equation is a parabolic-type partial differential equation, which is frequently studied with the use of compartmental models. This paper explores other solution techniques for this type of partial differential equation, specifically the finite difference and finite element methods, and compares these methods to the traditional compartmental model solutions.
A Compositional and Interpretable Semantic Space

Vector Space Models (VSMs) of Semantics are useful tools for exploring the semantics of single words, and the composition of words to make phrasal meaning. While many methods can estimate the meaning (i.e. vector) of a phrase, few do so in an interpretable way. We introduce a new method (CNNSE) that allows word and phrase vectors to adapt to the notion of composition. Our method learns a VSM that is both tailored to support a chosen semantic composition operation, and whose resulting features have an intuitive interpretation. Interpretability allows for the exploration of phrasal semantics, which we leverage to analyze performance on a behavioral task.
Therapeutic Drug Monitoring of Posaconazole in Allogeneic Hematopoietic Stem Cell Transplantation Patients Who Develop Gastrointestinal Graft-versus-Host Disease

ABSTRACT Posaconazole (PCZ) is the latest triazole antifungal agent that has been approved for prophylaxis of invasive aspergillosis in high-risk immunocompromised patients, such as allogeneic hematopoietic stem cell transplantation patients, who develop graft-versus-host disease (GVHD). PCZ has high interindividual variability with regard to its plasma drug trough concentrations (Cmin). Moreover, the concentration-efficiency relationship remains to be better characterized in prophylaxis. To determine the variability factors in plasma drug concentrations, the PCZ Cmin and clinical parameters (localization of GVHD, presence of diarrhea, and diagnosis of invasive aspergillosis) were collected retrospectively in 29 consecutive allogeneic hematopoietic stem cell transplantation patients who developed GVHD and were receiving prophylactic PCZ (200 mg, 3 times/day, for ≥7 days). Blood samples were analyzed at steady state to determine the PCZ Cmin by liquid chromatography-tandem mass spectrometry. The average PCZ Cmin was 1.28 ± 0.82 mg/liter (mean ± standard deviation; n = 292 dosages), with an intraindividual variability of 49% and an interindividual variability of 64%. Twenty percent of Cmins were below 0.7 mg/liter, which is considered the threshold of efficacy by the Food and Drug Administration. The patients who had gastrointestinal (GI) GVHD experienced a 24% reduction in the posaconazole Cmin, compared with those with other localizations of GVHD. This decrease reached 33% when patients presented with diarrhea due to GI GVHD or an infectious etiology. PCZ Cmins were 26% lower when invasive aspergillosis was declared. These data demonstrate that GI disturbances affect drug concentrations. Thus, therapeutic monitoring of PCZ can be used to detect low drug concentrations, possibly resulting in a lack of efficacy of invasive aspergillosis prophylaxis.
Predicting local colonization and extinction dynamics from coarser‐scale surveys

The demand for methods to translate information between spatial scales (i.e. size of observational units and the total area of study) has intensified given increased recognition that empirical data collection and practical applications occur at scales ranging from individual organisms to landscapes. For example, there has been considerable interest in "scaling-down" methods that have been successful at predicting fine-scale species' distributions from coarse-scale distributional maps. Here, we describe the application of scaling-down methods to the estimation of colonization and extinction rates in metapopulations using long-term, large-scale data sets of two roadside plant species, Helianthus annuus and Silene latifolia. Fine-scale data collected from roadside populations were aggregated to generate data at several increasingly coarse scales. The relationships between occupancy, colonization, or extinction and the scale of measurement (scale-curves) were determined using the standard "fully-nested" method and the "stratified random sampling" method. Both methods were successful at predicting not only occupancy, but also the dynamic metapopulation processes of extinction and colonization (R 2 values, averaged across species and methods, were 88.5, 69.3, and 88.8%, respectively, for occupancy, extinction, and colonization). Scaling-down generated more accurate predictions in Helianthus (average R 2 = 88.4) compared to Silene (average R 2 = 63.4), and in both species, scaling-down generated more accurate predictions for occupancy and colonizations compared to extinctions. This is one of the first demonstrations that dynamic processes are scalable, and provides a useful methodology for dealing with the logistical challenges of collecting fine-scale data over large geographic areas when studying metapopulation processes or range limits.
Expanding the Neuroanalytical Toolkit: Electrochemical Measurements of Neurotransmitters Using Poly(3,4-Ethylenedioxythiophene) Conducting Polymer Materials

The human brain is an extraordinarily complex organ. The process of neurotransmission gives rise to sensory experience, cognition, and decision-making. Many common diseases of the brain are incurable and their symptoms are poorly treated. To better understand the underlying molecular problems in disease states, sensitive, selective, and rapid measurements of biomolecules are needed. Given the complexity of making biological measurements in vitro or in vivo, inquiring scientists must choose measurement tools wisely. While traditional electrode materials have been used to great success, conducting polymers such as PEDOT are an excellent way to modify or improve existing measurement tools. The chemical, spatial, and temporal resolution of in vivo and in vitro measurements can be improved, all while increasing the longevity of the sensor. Compared to existing electrode materials, PEDOT is amenable to a larger variety of substrates, easier to process, inexpensive, and has excellent electrochemical behavior for the detection of neurotransmitters. We have demonstrated the utility of PEDOT by fabricating and characterizing the first device for the separation of biogenic amines, and the first device for high-throughput measurements of exocytosis from single PC12 cells. These devices will allow scientists to inexpensively and rapidly study the effects of pharmacological challenges to model systems in disease states. A PEDOT and Nafion composite polymer coating has been developed for microelectrodes, granting increased sensitivity and selectivity towards dopamine. These improvements resulted in the first in vivo electrochemical measurements of dopamine transients without administration of a reuptake inhibitor. Lastly, we have expanded the chemistry of polythiophenes by developing the synthesis of oligo-EDOT:Nafion nanoparticles. These nanoparticles are easily prepared, inexpensive, and enable quantiative spectroscopic interrogations of water content in organic solvents.
Use of coconut fibre as an enhancement of concrete

This research describes experimental studies on the use of coconut fibre as enhancement of concrete. The addition of coconut-fibres significantly improved many of the engineering properties of the concrete, notably torsion, toughness and tensile strength. The ability to resist cracking and spalling were also enhanced. However, the addition of fibres adversely affected the compressive strength. When coconut fibre was added to plain concrete, the torsional strength increased (by up to about 25%) as well as the energy-absorbing capacity, but there is an optimum weight fraction (0.5% by weight of cement) beyond which the torsional strength started to decrease again. Similar results were also obtained for different fibre aspect ratios, where again results showed there was an optimum aspect ratio (125). An increase in fibre weight fraction provided a consistent increase in ductility up to the optimum content (0.5%) with corresponding fibre aspect ratio of 125. Overall the study has demonstrated that addition of coconut fibre to concrete leads to improvement of concrete the toughness torsion and the tensile stress, Further work is however ,required to assess the long term durability of concrete enhanced with coconut fibres.
Distributed dialogue policies for multi-domain statistical dialogue management

Statistical dialogue systems offer the potential to reduce costs by learning policies automatically on-line, but are not designed to scale to large open-domains. This paper proposes a hierarchical distributed dialogue architecture in which policies are organised in a class hierarchy aligned to an underlying knowledge graph. This allows a system to be deployed using a modest amount of data to train a small set of generic policies. As further data is collected, generic policies can be adapted to give in-domain performance. Using Gaussian process-based reinforcement learning, it is shown that within this framework generic policies can be constructed which provide acceptable user performance, and better performance than can be obtained using under-trained domain specific policies. It is also shown that as sufficient in-domain data becomes available, it is possible to seamlessly improve performance, without subjecting users to unacceptable behaviour during the adaptation period and without limiting the final performance compared to policies trained from scratch.
Data-Driven Haptic Modeling and Rendering of Viscoelastic and Frictional Responses of Deformable Objects

In this paper, we present an extended data-driven haptic rendering method capable of reproducing force responses during pushing and sliding interaction on a large surface area. The main part of the approach is a novel input variable set for the training of an interpolation model, which incorporates the position of a proxy - an imaginary contact point on the undeformed surface. This allows us to estimate friction in both sliding and sticking states in a unified framework. Estimating the proxy position is done in real-time based on simulation using a sliding yield surface - a surface defining a border between the sliding and sticking regions in the external force space. During modeling, the sliding yield surface is first identified via an automated palpation procedure. Then, through manual palpation on a target surface, input data and resultant force data are acquired. The data are used to build a radial basis interpolation model. During rendering, this input-output mapping interpolation model is used to estimate force responses in real-time in accordance with the interaction input. Physical performance evaluation demonstrates that our approach achieves reasonably high estimation accuracy. A user study also shows plausible perceptual realism under diverse and extensive exploration.
Improving language model perplexity and recognition accuracy for medical dictations via within-domain interpolation with literal and semi-literal corpora

We propose a technique for improving language modeling for automated speech recognition of medical dictations by interpolating finished text (25M words) with small humangenerated literal or/and machine-generated semiliteral corpora. By building and testing interpolated (ILM) with literal (LILM), semiliteral (SILM) and partial (PILM) corpora, we show that both perplexity and recognition results improve significantly with LILM and SILM; the two yielding very close results.
Constraint removal in linear MPC: An improved criterion and complexity analysis

Constraint removal accelerates model predictive control by detecting inactive constraints at the yet unknown optimal solution and removing them from the online optimization problem. We show in this paper that the number of removed constraints can be increased further by generalizing previously used inactivity criteria. The proposed generalization does not depend on information available at previous time steps, and consequently can also be applied at the initial state. In addition, we provide a detailed analysis of the computational complexity of the proposed variant and of existing constraint removal methods, applied to both active-set (AS) and interior-point (IP) solvers. Finally, we compare the different constraint removal variants in numerical experiments to corroborate the complexity analysis carried out, showing the greatest benefits of the proposed variant, especially with IP solvers.
Weakly Coupled Systems in Quantum Control

Weakly coupled systems are a class of infinite dimensional conservative bilinear control systems with discrete spectrum. An important feature of these systems is that they can be precisely approached by finite dimensional Galerkin approximations. This property is of particular interest for the approximation of quantum system dynamics and the control of the bilinear Schrödinger equation. The present study provides rigorous definitions and analysis of the dynamics of weakly coupled systems and gives sufficient conditions for an infinite dimensional quantum control system to be weakly coupled. As an illustration we provide examples chosen among common physical systems.