Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinguishing Properties of Cells From the Myocardial Sleeves of the Pulmonary Veins: A Comparison of Normal and Abnormal Pacemakers

Background—A common source of arrhythmogenic spontaneous activity instigating atrial fibrillation is the myocardial tissue, or sleeves, at the base of the pulmonary veins. This study compared the properties of cells from the myocardial sleeves of the pulmonary veins (PVm) with cells from the normal cardiac pacemaker (the sinoatrial node) and regions of the atria. Our objective was to identify key features of these cells that predispose them to becoming the focus of cardiac arrhythmias. Methods and Results—Single cells were isolated from samples of rabbit PVm, central and peripheral sinoatrial node, crista terminalis, and left and right atria. Detailed morphology of cells was assessed and intracellular calcium concentrations measured with the use of Fluo-3. Cells from the PVm were smaller than atrial cells and showed large elevations in diastolic calcium during activation at physiological rates, a feature the PVm cells shared with cells from the sinoatrial node. Unstimulated spontaneous activity was observed in a minority of cells from the PVm, but numerous cells from this region showed spontaneous activity for a brief period immediately subsequent to stimulation at physiological rates. This was not observed in atrial cells. Assessment of calcium removal pathways showed sarcolemmal calcium extrusion in cells from the PVm to have a high reliance on “slow” extrusion pathways to maintain intracellular calcium homeostasis because of a low expression of sodium-calcium exchanger. Conclusions—We conclude that cells from the PVm share some features with cells from the sinoatrial node but also have distinctly unique features that predispose them to the development of spontaneous activity.
A generalized architecture for efficient multi-segment logarithm approximation

This paper presents a novel hardware architecture for the approximation of the base-2 logarithm of integers at a high accuracy and with low resource requirements. The generalized piecewise linear approximation approach allows the utilization of a very large number of linear segments for the approximation of the logarithm function, whereas state of the art architectures are limited to a maximum of six segments. In the proposed implementation, up to 1024 linear segments are employed. The exploitation of the capabilities of modern FPGAs, such as large BlockRAMs and fast multipliers allow a high frequency potential combined with low resource requirements, resulting in a pipelined implementation that only requires up to 329 slices, one BlockRAM and one multiplier. The selected number of segments affects the approximation error, which is lower than the comparable architectures by up to five orders of magnitude. The properties of the proposed architecture render it suitable for use as a generic component in systems that require fast, accurate and resource-efficient logarithm calculation.
PubAnnotation - a persistent and sharable corpus and annotation repository

There has been an active development of corpora and annotations in the BioNLP community. As those resources accumulate, a new issue arises about the reusability. As a solution to improve the reusability of corpora and annotations, we present PubAnnotation, a persistent and sharable repository, where various corpora and annotations can be stored together in a stable and comparable way. As a position paper, it explains the motivation and the core concepts of the repository and presents a prototype repository as a proof-of-concept.
Complexities of Genetic Testing in Familial Dilated Cardiomyopathy

A 59-year-old female with a personal and family history of dilated cardiomyopathy (DCM) was referred by her cardiologist for genetic testing and counseling. The patient was initially diagnosed with DCM after presenting with dyspnea and fatigue. Her symptoms also included mild bilateral pedal edema, but she denied orthopnea, paroxysmal nocturnal dyspnea, palpitations, presyncope, or syncope. An electrocardiogram showed sinus rhythm and a left bundle branch block morphology (Figure 1). She underwent a gadolinium-enhanced cardiac magnetic resonance imaging that showed an enlarged left ventricle (LV; internal diameter at end diastole and systole were 6.5 cm and 5.4 cm, respectively), and the LV ejection fraction was ≈25%. Abnormal septal wall motion consistent with a bundle branch block was noted. All other walls of the LV were diffusely hypokinetic. Mild midmyocardial hyperenhancement suggestive of idiopathic DCM was present. The right ventricle was normal in size and function. There were no valvular abnormalities. Left heart catheterization showed no significant epicardial coronary artery disease. She was treated with a β-adrenergic antagonist, an angiotensinogen inhibitor, a mineralocorticoid antagonist, and a loop diuretic. Her symptoms improved; however, the LV remained enlarged and had poor systolic function with an ejection fraction of ≈30%. She subsequently underwent biventricular implantable cardioverter-defibrillator implantation. Figure 1. ECG of proband. Heart rate (HR) in bpm, P–R interval (PR) in milliseconds (ms), QRS duration (QRS) in ms, Q–T interval (QT) in ms, and corrected Q–T interval using Bazett formula (QTc) in ms are shown. aVF indicates augmented vector foot; aVL, augmented vector left; and aVR, augmented vector right. At the time of her initial diagnosis, the patient’s family history was notable for a 86-year-old mother who had atrial fibrillation and valvular heart disease; a father who died at the age of 89 years with coronary artery disease; a 59-year-old sister who had hypertension; a 50-year-old brother …
Antimicrobial and cytotoxic activity of Ferula gummosa plant essential oil compared to NaOCl and CHX: a preliminary in vitro study

Objectives The usage of medicinal plants as natural antimicrobial agents has grown in many fields including dental medicine. The aim of this in vitro study was three-fold: (i) to determine the chemical compositions of the Ferula gummosa essential oil (FGEO), (ii) to compare the antimicrobial efficacy of the oil with sodium hypochlorite (NaOCl) and chlorhexidine (CHX), (iii) to assess the toxic behavior of FGEO in different concentrations compared to 5% NaOCl and 0.2% CHX. Materials and Methods Gas chromatography/mass spectrometry (GC/MS) was used to determine the chemical compositions of the oil. The disk diffusion method and a broth micro-dilution susceptibility assay were exploited to assess the antimicrobial efficacy against Enterococcus faecalis, Staphylococcus aureus, Streptococcus mitis, and Candida albicans. The cytocompatibility of the FGEO was assessed on L929 fibroblasts, and compared to that of NaOCl and CHX. Results Twenty-seven constituents were recognized in FGEO. The major component of the oil was β-pinene (51.83%). All three irrigants significantly inhibited the growth of all examined microorganisms compared to the negative control group. FGEO at 50 µg/mL was effective in lower concentration against Enterococcus faecalis than 5% NaOCl and 0.2% CHX, and was also more potent than 0.2% CHX against Candida albicans and Staphylococcus aureus. FGEO was a cytocompatible solution, and had significantly lower toxicity compared to 5% NaOCl and 0.2% CHX. Conclusions FGEO showed a promising biological potency as a root canal disinfectant. More investigations are required on the effectiveness of this oil on intracanal bacterial biofilms.
Measurement and Modeling of Rotational Core Losses of Soft Magnetic Materials Used in Electrical Machines: A Review

In many situations, for example, in the cores of a rotating electrical machine and the T-joints of multiphase transformers, the magnetic flux varies with time in terms of both magnitude and direction, i.e., the local flux density vector rotates with varying magnitude and varying speed. Therefore, it is important that the magnetic properties of the core materials under various rotational magnetizations be properly investigated, modeled, and applied in the design and analysis of electromagnetic devices with rotational flux. Drawing from the huge amount of papers published by various researchers in the past century, this paper presents an extensive survey on the measurement and modeling of rotational core losses of soft magnetic materials used in electrical machines, particularly from the view of practical engineering application. The paper aims to provide a broad picture of the historical development of measuring techniques, measuring apparatus, and practical models of rotational core losses.
The ecology of emerging neurotropic viruses

The authors review common themes in the ecology of emerging viruses that cause neurological disease. Three issues emerge. First, 49% of emerging viruses are characterized by encephalitis or serious neurological clinical symptoms. Second, all of these viruses are driven to emerge by ecological, environmental, or human demographic changes, some of which are poorly understood. Finally, the control of these viruses would be enhanced by collaborative multidisciplinary research into these drivers of emergence. The authors highlight this review with a case study of Nipah virus, which emerged in Malaysia due largely to shifts in livestock production and alterations to reservoir host habitat. Collaboration between virologists, ecologists, disease modelers and wildlife biologists has been instrumental in retracing the factors involved in this virus’s emergence.
Time course and predictors for cancer-related fatigue in a series of oropharyngeal cancer patients treated with chemoradiation therapy.

BACKGROUND Cancer-related fatigue (CRF) is a highly prevalent and underestimated symptom in cancer patients. This study aims to analyze CRF solely in a cohort of oropharyngeal cancer patients who underwent treatment with radiotherapy (RT). METHODS In January 2008 to June 2010, 87 consecutive oropharyngeal carcinoma patients underwent definitive RT. Concurrent chemotherapy was used for 94% of patients. The median prescription dose to the planning target volume of the gross or clinical tumor volume was 70 Gy for definitive cases (n = 84) and 66 Gy for postoperative cases (n = 3), both delivered over 6.5 weeks. A normalized 12-point numeric rating scale assessed CRF from patient visits before, during, and after RT. RESULTS The median follow-up of living patients was 14 months. Fatigue peaked 1-2 weeks post-RT and remained higher than baseline for up to 2 years post-RT in 50% of patients. The average fatigue score at the time of completion of therapy or maximum thereafter up to 1 year post-RT was significantly worse than baseline. Patients who experienced pain had a trend toward significance with association for a higher maximum difference in fatigue from baseline. Karnofsky performance status score, weight change, and mood disorders did not correlate with CRF. CONCLUSIONS Fatigue was a common treatment-related symptom in this uniform cohort of patients with oropharyngeal cancer. RT was highly correlated with worsening of CRF. Pain control has the potential to help mitigate CRF in patients experiencing pain, and will need to be confirmed using larger datasets.
123I-Iomazenil Single Photon Emission Computed Tomography Visualizes Recovery of Neuronal Integrity by Bone Marrow Stromal Cell Therapy in Rat Infarct Brain

Background and Purpose— This study was aimed to assess whether 123I-iomazenil (IMZ) single photon emission computed tomography can serially monitor the effects of bone marrow stromal cell (BMSC) transplantation on neuronal integrity in infarct brain of rats. Methods— The BMSCs were harvested from green fluorescent protein–transgenic rats and were cultured. The rats were subjected to permanent middle cerebral artery occlusion. Their motor function was serially quantified throughout the experiments. The BMSCs or vehicle was stereotactically transplanted into the ipsilateral striatum at 7 days after the insult. Using small-animal single photon emission computed tomography/computed tomography apparatus, the 123I-IMZ uptake was serially measured at 6 and 35 days after the insult. Finally, fluorescence immunohistochemistry was performed to evaluate the distribution of engrafted cells and their phenotypes. Results— The distribution of 123I-IMZ was markedly decreased in the ipsilateral neocortex at 6 days postischemia. The vehicle-transplanted animals did not show a significant change at 35 days postischemia. However, BMSC transplantation significantly improved the distribution of 123I-IMZ in the peri-infarct neocortex as well as motor function. The engrafted BMSCs were densely distributed around cerebral infarct, and some of them expressed neuronal nuclear antigen and &ggr;-aminobutyric acid type-A receptor. Conclusions— The present findings strongly suggest that the BMSCs may enhance functional recovery by improving the neuronal integrity in the peri-infarct area, when directly transplanted into the infarct brain at clinically relevant timing. 123I-IMZ single photon emission computed tomography may be a promising modality to scientifically prove the beneficial effects of BMSC transplantation on the host brain in clinical situation.
The Impact of Order Smoothing on the Performance of Supply Chain

This paper considers a single-echelon supply chain where a retailer holds an inventory to satisfy a customer demand and faces an external supplier who has a fixed supply capacity. It proposes an inventory replenishment policy that uses "order smoothing" to reduce order-size variability and reduce the total costs, including order cost and inventory cost. It studies two smoothing replenishment policies, generalized order-up-to policy and two-period moving average policy. It analyzes the impact of smoothing parameters, fixed supply capacity, and initial inventory on the performance of supply chain. Our analysis shows that order smoothing policies can reduce the total costs.
Phenotypic and Genotypic Characterization of Enterotoxigenic Escherichia coli Clinical Isolates from Northern Colombia, South America

Enterotoxigenic Escherichia coli (ETEC) are major causes of childhood diarrhea in low and middle income countries including Colombia, South America. To understand the diversity of ETEC strains in the region, clinical isolates obtained from northern Colombia children were evaluated for multiple locus sequencing typing, serotyping, classical and nonclassical virulence genes, and antibiotic susceptibility. Among 40 ETEC clinical isolates evaluated, 21 (52.5%) were positive for LT gene, 13 (32.5%) for ST gene, and 6 (15%) for both ST and LT. The most prevalent colonization surface antigens (CS) were CS21 and CFA/I identified in 21 (50%) and 13 (32.5%) isolates, respectively. The eatA, irp2, and fyuA were the most common nonclassical virulence genes present in more than 60% of the isolates. Ampicillin resistance (80% of the strains) was the most frequent phenotype among ETEC strains followed by trimethoprim-sulfamethoxazole resistance (52.5%). Based on multiple locus sequencing typing (MLST), we recognize that 6 clonal groups of ETEC clinical isolates circulate in Colombia. ETEC clinical isolates from children in northern Colombia are highly diverse, yet some isolates circulating in the community belong to well-defined clonal groups that share a unique set of virulence factors, serotypes, and MLST sequence types.
Differential Effects of the Type I Interferons α4, β, and ε on Antiviral Activity and Vaccine Efficacy1

The type I IFNs exert a range of activities that include antiviral, antiproliferative, and immunomodulatory effects. To study this further, we have constructed recombinant vaccinia viruses expressing HIV or hemagglutinin (HA) Ags along with murine type I IFNs, IFN-α4 (HA-VV-IFN-α4), IFN-β (HA-VV-IFN-β), or IFN-ε (HIV-VV-IFN-ε), a recently discovered member of this family. Our aims were to characterize IFN-ε functionality as a type I IFN and also to study the biological properties of these factors toward the development of safer and more effective vector-based vaccines. HIV-VV-IFN-ε and HA-VV-IFN-β grew to lower titers than did their parental controls in murine cell lines. In vivo, however, HIV-VV-IFN-ε growth was not attenuated, while IFN-β demonstrated potent local antiviral activity with no replication of HA-VV-IFN-β detected. Flow cytofluorometric analysis of B lymphocytes incubated with virally encoded IFN-ε showed up-regulation of activation markers CD69 and CD86, while RT-PCR of IFN-ε-treated cells revealed that gene expression levels of antiviral proteins were elevated, indicating the induction of an antiviral state. The use of these constructs in a poxvirus prime-boost immunization regime led to robust humoral and cellular immune responses against the encoded Ags, despite the lack of replication in the case of HA-VV-IFN-β. Thus, coexpression of these factors may be beneficial in the design of safer vector-based vaccines. Our data also indicate that while IFN-ε exhibits certain biological traits similar to other type I IFNs, it may also have a specific role in mucosal immune regulation that is quite distinct.
Analysis and parameter prediction of compiler transformation for graphics processors

In the last decade graphics processors (GPUs) have been extensively used to solve computationally intensive problems. A variety of GPU architectures by different hardware manufacturers have been shipped in a few years. OpenCL has been introduced as the standard cross-vendor programming framework for GPU computing. Writing and optimising OpenCL applications is a challenging task, the programmer has to take care of several low level details. This is even harder when the goal is to improve performance on a wide range of devices: OpenCL does not guarantee performance portability. In this thesis we focus on the analysis and the portability of compiler optimisations. We describe the implementation of a portable compiler transformation: thread-coarsening. The transformation increases the amount of work carried out by a single thread running on the GPU. The goal is to reduce the amount of redundant instructions executed by the parallel application. The first contribution is a technique to analyse performance improvements and degradations given by the compiler transformation, we study the changes of hardware performance counters when applying coarsening. In this way we identify the root causes of execution time variations due to coarsening. As second contribution, we study the relative performance of coarsening over multiple input sizes. We show that the speedups given by coarsening are stable for problem sizes larger than a threshold that we call saturation point. We exploit the existence of the saturation point to speedup iterative compilation. The last contribution of the work is the development of a machine learning technique that automatically selects a coarsening configuration that improves performance. The technique is based on an iterative model built using a neural network. The network is trained once for a GPU model and used for several programs. To prove the flexibility of our techniques, all our experiments have been deployed on multiple GPU models by different vendors.
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations

The Precision Medicine Track in BioCre-ative VI aims to bring together the Bi-oNLP community for a novel challenge focused on mining the biomedical litera-ture in search of mutations and protein-protein interactions (PPI). In order to support this track with an effective train-ing dataset with limited curator time, the track organizers carefully reviewed Pub-Med articles from two different sources: curated public PPI databases, and the re-sults of state-of-the-art public text mining tools. We detail here the data collection, manual review and annotation process and describe this training corpus charac-teristics. We also describe a corpus per-formance baseline. This analysis will provide useful information to developers and researchers for comparing and devel-oping innovative text mining approaches for the BioCreative VI challenge and other Precision Medicine related applica-tions.
Thermally Stable, Efficient Polymer Solar Cells with Nanoscale Control of the Interpenetrating Network Morphology

By applying the specific fabrication conditions summarized in the Experimental section and post‐production annealing at 150 °C, polymer solar cells with power‐conversion efficiency approaching 5 % are demonstrated. These devices exhibit remarkable thermal stability. We attribute the improved performance to changes in the bulk heterojunction material induced by thermal annealing. The improved nanoscale morphology, the increased crystallinity of the semiconducting polymer, and the improved contact to the electron‐collecting electrode facilitate charge generation, charge transport to, and charge collection at the electrodes, thereby enhancing the device efficiency by lowering the series resistance of the polymer solar cells.
GPR48 regulates epithelial cell proliferation and migration by activating EGFR during eyelid development.

PURPOSE Eyelid development is a dynamic process involving cell proliferation, differentiation, and migration regulated by a number of growth factors and cytokines. Mice deficient in the orphan G protein-coupled receptor 48 (GPR48) showed an eye open at birth (EOB) phenotype. In this study, the authors attempted to clarify the role of GPR48 in eyelid development and the molecular mechanisms leading to the EOB phenotype. METHODS Phenotypic analysis of the eyelids of Gpr48(-/-) mice was carried out using histology and scanning electron microscopy. GPR48 expression pattern was determined using X-gal staining. In vitro scratch assay was used to determine cell motility defects in Gpr48(-)(/)(-) keratinocytes. The molecular mechanism underlying GPR48-mediated eyelid closure was explored using Western blot and immunostaining analyses. Expression levels of EGFR and its phosphorylated counterpart were examined in Gpr48(-/-) and wild-type keratinocytes and in eyelids. RESULTS GPR48 is highly expressed in the epithelium and apical mesenchymal cells of eyelids during embryonic development. Detailed analysis revealed that Gpr48(-/-) mice exhibited delayed leading-edge extension, reduced filopodia formation, and decreased rounded periderm cell formation around eyelid margins. Keratinocytes lacking GPR48 are defective in cell proliferation and migration with reduced F-actin staining. In addition, the phosphorylation of EGFR was dramatically decreased in cultured keratinocytes and developing eyelids in the absence of GPR48. CONCLUSIONS Inactivation of GPR48 induces the EOB phenotype by reducing epithelial cell proliferation and migration, indicating that GPR48 plays an essential role in eyelid development. Furthermore, GPR48 contributes to eyelid development through the regulation of the EGFR signaling pathway.
Physical scaling of integrated inductor layout and model and its application to WLAN VCO design at 11GHz and 17GHz

A physical scaling procedure of integrated inductors is presented. The process consists of a linear layout geometry scaling and a linear or quadratic scaling of the double /spl pi/-model parameters according to their physical meaning. The proposed coil scaling is verified in 0.25/spl mu/m standard CMOS with measurements on fully integrated optimized inductors. The scaling allows a reuse of measured coils and can be used to reduce the size of coil libraries. The inductor scaling is shown as very useful for VCO-design reuse. This is illustrated in 0.12/spl mu/m standard CMOS by the design of fully integrated low power low phase noise VCOs at 11GHz and 17GHz out of a 51GHz VCO.