Miracle-dz/UniFAR-FTUs huggingface dataset:
Protective effects elicited by levosimendan against liver ischemia/reperfusion injury in anesthetized rats

As in other organs, oxidative stress–induced injury and cell death may result from free oxygen radical–dependent mechanisms and alterations in signal transduction pathways leading to apoptosis. Among the new suggested therapies for injuries caused by oxidative stress, the use of levosimendan has been reported to be quite promising. In the present study, we aimed to examine the protective effects of levosimendan against liver oxidative stress in anesthetized rats and to analyze the involvement of mitochondrial adenosine triphosphate–dependent potassium (mitoKATP) channels and nitric oxide (NO). In 50 anesthetized rats, liver ischemia/reperfusion (I/R) was performed via nontraumatic portal occlusion. In some animals, levosimendan was infused into the portal vein at the onset of reperfusion, whereas other rats received the vehicle only. Moreover, in some rats, levosimendan was given after the intraportal administration of l‐Nω‐nitro‐arginine methyl ester (l‐NAME) or 5‐hydroxydecanoate (5HD). The portal vein blood flow was measured, and blood samples were taken for the determination of transaminases, thiobarbituric acid reactive substances (TBARS), and reduced glutathione (GSH); liver biopsy samples were used for B cell lymphoma 2–associated X protein, caspase‐9, Akt, and endothelial nitric oxide synthase (eNOS) activation through western blotting. Also, caspase‐3 activity was measured. In rats, I/R caused an increase in apoptotic markers, transaminases, and TBARS and a decrease in GSH and Akt activation. Levosimendan administration was able to counteract oxidative damage and apoptosis in a dose‐dependent way and to increase GSH, Akt, and eNOS activation. All effects of levosimendan were abolished by pretreatment with l‐NAME and 5HD. In conclusion, the results of the present study show that levosimendan can exert protection against ischemic liver damage through mechanisms related to NO production and mitoKATP channel function. These data provide interesting perspectives into the use of levosimendan in hepatic surgery and transplantation. Liver Transpl 20:361‐375, 2014. © 2013 AASLD.
A Survey on Position‐Based Simulation Methods in Computer Graphics

The dynamic simulation of mechanical effects has a long history in computer graphics. The classical methods in this field discretize Newton's second law in a variety of Lagrangian or Eulerian ways, and formulate forces appropriate for each mechanical effect: joints for rigid bodies; stretching, shearing or bending for deformable bodies and pressure, or viscosity for fluids, to mention just a few. In the last years, the class of position‐based methods has become popular in the graphics community. These kinds of methods are fast, stable and controllable which make them well‐suited for use in interactive environments. Position‐based methods are not as accurate as force‐based methods in general but they provide visual plausibility. Therefore, the main application areas of these approaches are virtual reality, computer games and special effects in movies. This state‐of‐the‐art report covers the large variety of position‐based methods that were developed in the field of physically based simulation. We will introduce the concept of position‐based dynamics, present dynamic simulation based on shape matching and discuss data‐driven upsampling approaches. Furthermore, we will present several applications for these methods.
UCD SIFT in the TREC 2009 Web Track

The SIFT (SIFT Information Fusion Techniques) group in UCD is dedicated to researching Data Fusion in Information Retrieval. This area of research involves the merging of multiple sets of results into a single result set that is presented to the user. As a means of evaluating the eectiveness of this work, the group entered Category B of the TREC 2009 Web Track. This paper discusses the strategies and experiments employed by the UCD SIFT group in entering the TREC Web Track 2009. This involved the use of freely-available Information Retrieval tools to provide inputs to the data fusion process, with the aim of contrasting with more sophis- ticated systems.
Daily negative mood affects fasting glucose in type 2 diabetes.

OBJECTIVE To examine the relationship between mood and blood glucose in a 21-day daily diary study. DESIGN During a home visit, information was gathered from 206 persons with Type 2 diabetes regarding demographics, disease characteristics and treatment, and depressive symptoms. They had blood drawn at a laboratory, yielding HbA1C. The participants were then telephoned each evening for 21 days and were asked about their positive and negative mood during the past 24 hours. They also tested their blood glucose upon rising in the morning. MAIN OUTCOME MEASURES The main outcomes measures were positive and negative affect and fasting glucose. RESULTS Multilevel analyses revealed a relationship between negative affect on one day and morning glucose on the next day. There was no such relationship between positive affect and glucose, nor was there a comparable effect of glucose on one day and either positive or negative affect on the next day. CONCLUSION The observed relationship between mood and blood glucose appears to be because of negative affect, not positive, with no evidence of a lagged effect of glucose on mood.
Co‐administration of ibuprofen and nitric oxide is an effective experimental therapy for muscular dystrophy, with immediate applicability to humans

Background and purpose: Current therapies for muscular dystrophy are based on corticosteroids. Significant side effects associated with these therapies have prompted several studies aimed at identifying possible alternative strategies. As inflammation and defects of nitric oxide (NO) generation are key pathogenic events in muscular dystrophies, we have studied the effects of combining the NO donor isosorbide dinitrate (ISDN) and the non‐steroidal anti‐inflammatory drug ibuprofen.
Killing of Escherichia coli by Crohn's Disease Monocyte-derived Macrophages and Its Enhancement by Hydroxychloroquine and Vitamin D

Background:Crohn's disease (CD) is associated with defective innate immunity, including impaired neutrophil chemotaxis, and mucosal invasion by bacteria, particularly adherent and invasive Escherichia coli that replicate inside macrophage phagolysosomes. We compared CD and healthy control (HC) macrophages for their abilities to kill E. coli and generate neutrophil chemoattractants and also assessed the effects of hydroxychloroquine (HCQ) and vitamin D on killing of phagocytosed E. coli. Methods:Peripheral blood monocyte-derived macrophages from CD and HC were compared for bacterial killing and generation of neutrophil chemoattractants in response to CD-derived E. coli. Escherichia coli replication was also assessed in the presence and absence of HCQ, alone and with antibiotics, and vitamin D. Results:Monocyte-derived macrophages from patients with CD were similar to HC in allowing replication of phagocytosed CD-derived E. coli: HM605 {CD: N = 10, mean fold replication in 3 hr = 1.08 (95% confidence interval [CI], 0.39–1.78); HC: N = 9, 1.50 (95% CI, 1.02–1.97); P = 0.15} and also in generation of neutrophil chemoattractants in response to E. coli (mean fold chemotaxis relative to control: CD = 2.55 [95% CI, 2.31–2.80]; HC = 2.65 [95% CI, 2.46–2.85], P = 0.42). HCQ and 1,25 OH2-vitamin D3 both caused dose-dependent inhibition of intramacrophage E. coli replication 3-hour postinfection; HCQ: 73.9% inhibition (P < 0.001) at 1 &mgr;g/mL, accompanied by raised intraphagosomal pH, and 1,25 OH2-vitamin D3: 80.7% inhibition (P < 0.05) at 80 nM. HCQ had synergistic effects with doxycycline and ciprofloxacin. Conclusions:CD and HC macrophages perform similarly in allowing replication of phagocytosed E. coli and generating neutrophil chemoattractants. Replication of phagocytosed E. coli was substantially decreased by HCQ and vitamin D. These warrant further therapeutic trials in CD in combination with relevant antibiotics.
Choosing a Data Model and Query Language for Provenance

The ancestry relationships found in provenance form a directed graph. Many provenance queries require traversal of this graph. The data and query models for provenance should directly and naturally address this graph-centric nature of provenance. To that end, we set out the requirements for a provenance data and query model and discuss why the common solutions (relational, XML, RDF) fall short. A semistructured data model is more suited for handling provenance. We propose a query model based on the Lorel query language, and briefly describe how our query language PQL extends Lorel.
Stacking the Deck for Efficiency: RF- to Millimeter-Wave Stacked CMOS SOI Power Amplifiers

The emerging demand for high-capacity wireless mobile communication and the advent of the Internet of Things and fifthgeneration communication standards have motivated the development of high-performance transceivers. The power amplifier (PA) is the most critical part in the transmit path and dominates the transceiver's performance, including coverage range, data rate, spectrum compliance, and dc power dissipation. Integration capability and the relatively low cost of complementary-metal-oxide-semiconductor (CMOS) technology, on the other hand, have propelled it into the wireless market. CMOS technology enables complete system-on-chip solutions, resulting in a simple front-end assembly process, straightforward testing, and improved reliability. Today, in addition to the baseband, including the modulator/demodulator circuit, a big portion of the RF front end of the transceiver circuit is implemented in CMOS technology.
Multi-Sided Compression Performance Assessment of ABI SOLiD WES Data

Data storage is a major and growing part of IT budgets for research since manyyears. Especially in biology, the amount of raw data products is growing continuously,and the advent of the so-called "next-generation" sequencers has made things worse.Affordable prices have pushed scientists to massively sequence whole genomes and to screenlarge cohort of patients, thereby producing tons of data as a side effect. The need formaximally fitting data into the available storage volumes has encouraged and welcomednew compression algorithms and tools. We focus here on state-of-the-art compression toolsand measure their compression performance on ABI SOLiD data.
Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology

The utility of parallel hybridization of environmental nucleic acids to many oligonucleotides immobilized in a matrix of polyacrylamide gel pads on a glass slide (oligonucleotide microchip) was evaluated. Oligonucleotides complementary to small-subunit rRNA sequences of selected microbial groups, encompassing key genera of nitrifying bacteria, were shown to selectively retain labeled target nucleic acid derived from either DNA or RNA forms of the target sequences. The utility of varying the probe concentration to normalize hybridization signals and the use of multicolor detection for simultaneous quantitation of multiple probe-target populations were demonstrated.
Substantial creep in healing human Achilles tendons. A pilot study.

BACKGROUND healing after rupture of the Achilles tendon can be described in terms of mechanical properties of the new-formed tissue, constituting the tendon callus. In previous human studies, the elastic modulus and the density remained almost constant during 3 months after mobilization started, and then improved up to one year. So far, time-dependent deformation of the healing human tendon has not been reported. METHODS in a series of 16 patients, operated with Achilles tendon suture, we implanted tantalum beads into the tendon and measured the distance between them repeatedly during 3 min of constant loading, using an ordinary image intensifier. The patients unloaded their leg for 30 min before the test. To avoid bias, all images were investigated in a randomized and blinded order. RESULTS total strain during 3 min of constant loading at 7 weeks post injury amounted to 5%, and at 19 weeks to 3%. About half of the strain, after the loading was applied, occurred during the second and third min. Considerable strain also occurred just before loading, when the patient was told that a load would be applied, but before this was actually done. CONCLUSION the measurements were crude, and this study should be seen as a pilot. Still, visco-elastic properties seem to dominate the mechanical behavior the healing Achilles tendon from start of mobilization to 19 weeks, at least when tested after 30 min rest. This deserves further studies with more precise methods.
Internal displacement and strain imaging using ultrasonic speckle tracking

Previous ultrasound speckle tracking methods have been extended, permitting measurement of internal displacement and strain fields over a wide dynamic range of tissue motion. The markedly increased dynamic range of this approach should lead to enhanced contrast resolution in strain and elasticity images. Results of experiments on gelatin-based, tissue equivalent phantoms show the capabilities of the method. <<ETX>>
Quantitative analysis of total macrophage content in adult mouse tissues. Immunochemical studies with monoclonal antibody F4/80

We have estimated the macrophage content of different tissues of the normal adult mouse using F4/80, a highly specific antigen marker for mature mouse macrophages. An absorption indirect binding assay was used to quantitate F4/80 antigen against a calibration standard made from the J774.2 macrophage-like cell line. The richest sources of tissue F4/80 antigen were found to be bone marrow, spleen, cervical and mesenteric lymph nodes, large bowel, liver, kidneys, and small bowel. The organs that have the highest total F4/80 antigen content are the liver, large bowel, small bowel, bone marrow, spleen, cervical and mesenteric lymph nodes, and kidney. We conclude that the mononuclear phagocyte system is mainly distributed in the gastrointestinal tract and liver, followed by hemopoietic and lymphoid tissues.
Geometric Manifold Learning

We present algorithms for analyzing massive and high dimensional data sets motivated by theorems from geometry and topology. Optimization criteria for computing data projections are discussed and skew radial basis functions (sRBFs) for constructing nonlinear mappings with sharp transitions are demonstrated. Examples related to modeling dynamical systems, including hurricane intensity and financial time series prediction, are presented. The article represents an overview of the authors' and collaborators' work in manifold learning.
The Influence of Successful Ageing Indicators on Life Satisfaction among Elders in Korea

This study investigated differences in related factors affecting life satisfaction with the elderly in or above middle class experiencing successful ageing. In the study, the respondents were 206 elderly people whose occupation (professional career) placed them in the middle and upper class range residing in metropolitan Seoul. Major results are summarized as follows: (1) In order to test gender differences, results of t-test show that there are 13 variables with seven of those being statistically significant and the rest being insignificant. (2) Needs fulfillment and physical functioning are significant factors for Korean male elders to be satisfied with their later lives. Needs fulfillment, physical functioning, group activity, and learning activity are significant factors for Korean female elders to be satisfied with their later lives.
Estrogen-related receptor-α is a metabolic regulator of effector T-cell activation and differentiation

Stimulation of resting CD4+ T lymphocytes leads to rapid proliferation and differentiation into effector (Teff) or inducible regulatory (Treg) subsets with specific functions to promote or suppress immunity. Importantly, Teff and Treg use distinct metabolic programs to support subset specification, survival, and function. Here, we describe that the orphan nuclear receptor estrogen-related receptor-α (ERRα) regulates metabolic pathways critical for Teff. Resting CD4+ T cells expressed low levels of ERRα protein that increased on activation. ERRα deficiency reduced activated T-cell numbers in vivo and cytokine production in vitro but did not seem to modulate immunity through inhibition of activating signals or viability. Rather, ERRα broadly affected metabolic gene expression and glucose metabolism essential for Teff. In particular, up-regulation of Glut1 protein, glucose uptake, and mitochondrial processes were suppressed in activated ERRα−/− T cells and T cells treated with two chemically independent ERRα inhibitors or by shRNAi. Acute ERRα inhibition also blocked T-cell growth and proliferation. This defect appeared as a result of inadequate glucose metabolism, because provision of lipids, but not increased glucose uptake or pyruvate, rescued ATP levels and cell division. Additionally, we have shown that Treg requires lipid oxidation, whereas Teff uses glucose metabolism, and lipid addition selectively restored Treg—but not Teff—generation after acute ERRα inhibition. Furthermore, in vivo inhibition of ERRα reduced T-cell proliferation and Teff generation in both immunization and experimental autoimmune encephalomyelitis models. Thus, ERRα is a selective transcriptional regulator of Teff metabolism that may provide a metabolic means to modulate immunity.
Displacement interpolation using Lagrangian mass transport

Interpolation between pairs of values, typically vectors, is a fundamental operation in many computer graphics applications. In some cases simple linear interpolation yields meaningful results without requiring domain knowledge. However, interpolation between pairs of distributions or pairs of functions often demands more care because features may exhibit translational motion between exemplars. This property is not captured by linear interpolation. This paper develops the use of displacement interpolation for this class of problem, which provides a generic method for interpolating between distributions or functions based on advection instead of blending. The functions can be non-uniformly sampled, high-dimensional, and defined on non-Euclidean manifolds, e.g., spheres and tori. Our method decomposes distributions or functions into sums of radial basis functions (RBFs). We solve a mass transport problem to pair the RBFs and apply partial transport to obtain the interpolated function. We describe practical methods for computing the RBF decomposition and solving the transport problem. We demonstrate the interpolation approach on synthetic examples, BRDFs, color distributions, environment maps, stipple patterns, and value functions.
A Quantitative Risk Assessment for Stachybotrys chartarum- Toxic Mold

The inhalation exposure to Stachybotrys chartarum (SC) has been playing a critical role in public health domain due to its ability to produce toxins (trichothecene and other mycotoxins), that are implicated in the cases of acute idiopathic pulmonary hemorrhages (AIPH) in infants. Despite multiple studies reporting an association of exposure to airborne mold with negative human health effects such as respiratory, immunological, and hematological diseases, there currently are no regulatory guidelines for quantifying the airborne exposure threat associated with SC spores/toxins in indoor environments. The primary goal for this study was to use risk assessment framework as a mechanism to quantify the potential risk of death associated with known concentrations of S. chartarum spores and toxins. Additionally, an attempt was made to provide a benchmark dose level above which an adverse effect may occur in human infants. To this end, best-fit dose-response models were generated by using published animal studies, followed by stochastic risk assessment to predict the likelihood of death in infants from AIPH. By using 10% as the benchmark response level, permissible exposure limits were obtained as 413 SC-spores/m3 or 2.66 x 10 -04 mg-toxin/m3. The predicted risk of death in infants for acute 24-hour exposure to toxins ranged from 1.0 x 10-11 to 3.0 x 10-06. Sensitivity analysis was conducted using Monte Carlo simulations to identify factors that are highly correlated with risk estimates. This study suggests that S. chartarum exposure via inhalation in residential conditions may pose a risk for AIPH resulting in mortality in human infants, but a conclusive epidemiological study is needed to validate risk estimates.
Development and function of human cerebral cortex neural networks from pluripotent stem cells in vitro

A key aspect of nervous system development, including that of the cerebral cortex, is the formation of higher-order neural networks. Developing neural networks undergo several phases with distinct activity patterns in vivo, which are thought to prune and fine-tune network connectivity. We report here that human pluripotent stem cell (hPSC)-derived cerebral cortex neurons form large-scale networks that reflect those found in the developing cerebral cortex in vivo. Synchronised oscillatory networks develop in a highly stereotyped pattern over several weeks in culture. An initial phase of increasing frequency of oscillations is followed by a phase of decreasing frequency, before giving rise to non-synchronous, ordered activity patterns. hPSC-derived cortical neural networks are excitatory, driven by activation of AMPA- and NMDA-type glutamate receptors, and can undergo NMDA-receptor-mediated plasticity. Investigating single neuron connectivity within PSC-derived cultures, using rabies-based trans-synaptic tracing, we found two broad classes of neuronal connectivity: most neurons have small numbers (<10) of presynaptic inputs, whereas a small set of hub-like neurons have large numbers of synaptic connections (>40). These data demonstrate that the formation of hPSC-derived cortical networks mimics in vivo cortical network development and function, demonstrating the utility of in vitro systems for mechanistic studies of human forebrain neural network biology. Summary: Human PSC-derived cerebral cortex neurons form large-scale functional networks that change over time and mimic those found in the developing cerebral cortex in vivo.
Twitter in the classroom

High schoolers at Roosevelt High School in Minneapolis, Minn. are being engaged in the classroom in a whole new way. By using social media tools and giving them access to the Internet, students are able to learn in different ways. Having discussions about their English class online has increased their level of attention and engagement in their studies.
An architecture for wavelet-packet based speech enhancement for hearing aids

Wavelet packets have been applied in order to compensate the speech signal to improve the intelligibility for a common hearing impairment known as recruitment of loudness, a sensorineural hearing loss of cochlear origin. We present an architecture that allows selection of the best decomposition tree for each patient, in order to apply this wavelet-packet based parametric compression algorithm.