Miracle-dz/UniFAR-FTUs huggingface dataset:
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

MOTIVATION Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse species. Chromatin modification profiles are frequently noisy and diffuse, spanning regions ranging from several nucleosomes to large domains of multiple genes. Much of the early work on the identification of ChIP-enriched regions for ChIP-Seq data has focused on identifying localized regions, such as transcription factor binding sites. Bioinformatic tools to identify diffuse domains of ChIP-enriched regions have been lacking. RESULTS Based on the biological observation that histone modifications tend to cluster to form domains, we present a method that identifies spatial clusters of signals unlikely to appear by chance. This method pools together enrichment information from neighboring nucleosomes to increase sensitivity and specificity. By using genomic-scale analysis, as well as the examination of loci with validated epigenetic states, we demonstrate that this method outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles. We demonstrate the application of this unbiased method in important issues in ChIP-Seq data analysis, such as data normalization for quantitative comparison of levels of epigenetic modifications across cell types and growth conditions. AVAILABILITY http://home.gwu. edu/ approximately wpeng/Software.htm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Complications of indwelling pleural catheter use and their management

The growing utilisation of indwelling pleural catheters (IPCs) has put forward a new era in the management of recurrent symptomatic pleural effusions. IPC use is safe compared to talc pleurodesis, though complications can occur. Pleural infection affects <5% of patients, and is usually responsive to antibiotic treatment without requiring catheter removal or surgery. Pleural loculations develop over time, limiting drainage in 10% of patients, which can be improved with intrapleural fibrinolytic therapy. Catheter tract metastasis can occur with most tumours but is more common in mesothelioma. The metastases usually respond to analgaesics and/or external radiotherapy. Long-term intermittent drainage of exudative effusions or chylothorax can potentially lead to loss of nutrients, though no data exist on any clinical impact. Fibrin clots within the catheter lumen can result in blockage. Chest pain following IPC insertion is often mild, and adjustments in analgaesics and drainage practice are usually all that are required. As clinical experience with the use of IPC accumulates, the profile and natural course of complications are increasingly described. We aim to summarise the available literature on IPC-related complications and the evidence to support specific strategies.
Synaptic Enhancement and Enhanced Excitability in Presynaptic and Postsynaptic Neurons in the Conditioned Stimulus Pathway ofHermissenda

Identified type A photoreceptors of Hermissendaexpress differential effects of classical conditioning. Lateral type A photoreceptors exhibit an increase in excitability to both the conditioned stimulus (CS; light) and extrinsic current. In contrast, medial type A photoreceptors do not express enhanced excitability, but do show enhancement of the medial B to medial A synaptic connection. Therefore, both enhanced excitability and changes in synaptic strength may contribute to long-term plasticity underlying classical conditioning. The activation of protein kinase C (PKC) is involved in the induction of enhanced excitability of identified type B photoreceptors produced by one-trial conditioning and the expression of enhanced excitability in B photoreceptors after multitrial classical conditioning. We have examined a possible role for persistent kinase activity in the expression of enhanced excitability in lateral type A photoreceptors and enhancement of the medial B to medial type A synaptic connection after classical conditioning. Injection of the PKC inhibitor peptide PKC(19–36) into medial type B photoreceptors of conditioned animals did not significantly change the amplitude of medial A IPSPs elicited by single spikes in the medial B photoreceptor. Injections of PKC(19–36) into medial B photoreceptors of pseudorandom controls also did not significantly change the amplitude of IPSPs recorded from the medial A photoreceptor. In contrast, spikes elicited by extrinsic current in lateral type A photoreceptors of conditioned animals were significantly reduced in frequency after intracellular injection of PKC(19–36) as compared with pseudorandom controls. Injection of the noninhibitory analog peptide [glu27]PKC(19–36) did not affect excitability. Thus, enhanced excitability in the lateral A photoreceptor of conditioned animals seems to be influenced, in part, by a constitutively active kinase or a persistent kinase activator, whereas synaptic enhancement of the connection between the medial B and medial A photoreceptors of conditioned animals may involve a different mechanism.
Higher Total Serum Cholesterol Levels Are Associated With Less Severe Strokes and Lower All-Cause Mortality: Ten-Year Follow-Up of Ischemic Strokes in the Copenhagen Stroke Study

Background and Purpose— Evidence of a causal relation between serum cholesterol and stroke is inconsistent. We investigated the relation between total serum cholesterol and both stroke severity and poststroke mortality to test the hypothesis that hypercholesterolemia is primarily associated with minor stroke. Methods— In the study, 652 unselected patients with ischemic stroke arrived at the hospital within 24 hours of stroke onset. A measure of total serum cholesterol was obtained in 513 (79%) within the 24-hour time window. Stroke severity was measured with the Scandinavian Stroke Scale (0=worst, 58=best); a full cardiovascular risk profile was established for all. Death within 10 years after stroke onset was obtained from the Danish Registry of Persons. Results— Mean±SD age of the 513 patients was 75±10 years, 54% were women, and the mean±SD Scandinavian Stroke Scale score was 39±17. Serum cholesterol was inversely and almost linearly related to stroke severity: an increase of 1 mmol/L in total serum cholesterol resulted in an increase in the Scandinavian Stroke Scale score of 1.32 (95% CI, 0.28 to 2.36, P=0.013), meaning that higher cholesterol levels are associated with less severe strokes. A survival analysis revealed an inverse linear relation between serum cholesterol and mortality, meaning that an increase of 1 mmol/L in cholesterol results in a hazard ratio of 0.89 (95% CI, 0.82 to 0.97, P=0.01). Conclusions— The results of our study support the hypothesis that a higher cholesterol level favors development of minor strokes. Because of selection, therefore, major strokes are more often seen in patients with lower cholesterol levels. Poststroke mortality, therefore, is inversely related to cholesterol.
The Impact of a Student-Led Pedometer Intervention Incorporating Cognitive-Behavioral Strategies on Step Count and Self-Efficacy

Abstract This study evaluated the effectiveness of a student-led physical activity intervention that incorporated pedometers and cognitive-behavioral strategies. Undergraduate students (N = 117) enrolled in upper division exercise and sport science courses recruited participants. Participants in the cognitive-behavioral intervention condition received weekly mentoring from students on strategies to foster self-regulation, whereas those in a minimal intervention control condition (i.e., pedometer and self-monitoring) did not. All volunteers wore a pedometer for 6 weeks, maintained a step-count log, and completed physical activity and barrier self-efficacy measures pre- and postintervention. Repeated measures analysis of variance revealed that intervention condition participants increased their steps more so than those in the control condition, F(5, 570) = 10.1, p < . 0001, starting at Week 3, with effect sizes in the moderate range. Intervention condition participants also reported increased physical activity self-efficacy, whereas those in the control condition did not, F(1, 77) = 5.6, p < . 03, Cohen d = . 47. There were no significant changes in barrier self-efficacy for either group. Overall, these findings suggest a student-led cognitive-behavioral pedometer intervention results in more favorable changes in step counts and physical activity self-efficacy than simply wearing a pedometer and self-monitoring step counts.
Enhancing bioplastic–substrate interaction via pore induction and directed migration of enzyme location

We demonstrate two novel approaches to enhance interactions of polymer‐immobilized biomolecules with their substrates. In the first approach, diisopropylfluorophosphatase (DFPase) containing poly(urethane) (PU) coatings were made microporous by incorporating, then extracting, poly(ethylene glycol)‐based diesters as porogens. Incorporation of 2% w/w porogen increased the effective diffusion coefficient of diisopropylfluorophosphate (DFP) through the coatings by 30% and increased the apparent turnover number of immobilized DFPase 3‐fold. In the second approach, prior to immobilization, hydrophobic modification of DFPase was achieved through its conjugation with a dimer/trimer mixture of a uretdione based on 1,6‐diisocyanatohexane. When the hydrophobically modified DFPase was immobilized in coatings, catalytic activity was 4‐fold higher than that of the equivalent, immobilized, native DFPase. This activity enhancement was independent of the presence or absence of pores. Confocal microscopy images of coatings containing fluorescently labeled lysozyme show that the native enzyme is distributed uniformly over the entire thickness of the coatings. Hydrophobically modified and fluorescently labeled lysozyme is accumulated only in the upper 10 μm cross‐sectional layer of a 100 μm‐thick coating. Interactions of bioplastics with their substrates are tunable either by pore induction in a polymer or by directed migration of the hydrophobically modified biomolecule to the desired location. The latter approach has broad implications, including overcoming mass transfer limitations experienced by immobilized biocatalysts. © 2004 Wiley Periodicals, Inc.
Experimental RSSI-based localization system using wireless sensor networks

Many ICT-based future industrial applications will require the localization of machines, devices or even workers. This work presents the experimental implementation, evaluation and optimization of an RSSI-based localization solution using IEEE 802.15. 4 wireless sensor networks. The localization accuracy is analysed under different densities of deployed reference nodes. The paper also proposes a simple optimization process that helps improving the localization accuracy.
Exact reconstruction of a class of nonnegative measures using model sets

In this paper we are concerned with the reconstruction of a class of measures on the square from the sampling of its Fourier coefficients on some sparse set of points. We show that the exact reconstruction of a weighted Dirac sum measure is still possible when one knows a finite number of non-adaptive linear measurements of the spectrum. Surprisingly, these measurements are defined on a model set, i.e quasicrystal.
SIMD-based decoding of posting lists

Powerful SIMD instructions in modern processors offer an opportunity for greater search performance. In this paper, we apply these instructions to decoding search engine posting lists. We start by exploring variable-length integer encoding formats used to represent postings. We define two properties, byte-oriented and byte-preserving, that characterize many formats of interest. Based on their common structure, we define a taxonomy that classifies encodings along three dimensions, representing the way in which data bits are stored and additional bits are used to describe the data. Using this taxonomy, we discover new encoding formats, some of which are particularly amenable to SIMD-based decoding. We present generic SIMD algorithms for decoding these formats. We also extend these algorithms to the most common traditional encoding format. Our experiments demonstrate that SIMD-based decoding algorithms are up to 3 times faster than non-SIMD algorithms.
EXPLORING THE CONSUMERS' ACCEPTANCE OF ELECTRONIC RETAILING USING TECHNOLOGY ACCEPTANCE MODEL

Following the approach of Pavlou (2003), we investigate key drivers for consumers` electronic retailing (e-tailing) acceptance that are integrated into TAM (technology acceptance model). TAM is one of the better known models for explaining the intention to use technology and it integrates two perceptions: usefulness and ease of use. The main purpose of this paper is to explore the relationship between perceived ease of use and perceived usefulness in accepting e-tailing among Croatian consumers. In particular, the focus of the paper is on the areas which influenced customer commitment and loyalty in e-tailing. The results of the quantitative study among Croatian consumers show that electronic retailing, e.g. purchasing via the Internet, would enhance consumers` effectiveness in getting product information and their effectiveness in purchasing products.
SCTP subflows for survivable FCS applications

The Stream Control Transmission Protocol (SCTP), a general-purpose transport layer protocol standardized by the IETF, has been a promising candidate to join UDP and TCP as a core protocol. The new SCTP features such as multi-homing, multi-streaming, and enhanced security can significantly improve the performance of FCS applications. Multi-streaming provides an aggregation mechanism in an SCTP association to accommodate heterogeneous objects, which belong to the same application but may require different type of QoS from the network. However, the current SCTP specification lacks an internal mechanism to support the preferential treatment among its streams. We introduce the concept of subflow and propose to modify the current SCTP such that the streams are grouped into several subflows according to their required QoS. It is also proposed that each subflow should implement its own congestion control to prevent the so-called false sharing. To compare the throughput differences, analytic models have been derived for the current SCTP and for the subflow-capable SCTP with different congestion control mechanisms. Simulations with ns-2 have been used to qualitatively demonstrate the throughput differences of these designs in a simplified diff-serv network. The analytical models are confirmed to accurately reflect the SCTP behavior. The simulation also shows that our proposed solution is able to efficiently support QoS among the SCTP streams.
Effects of Load-Distributed Width on Split Tension of Unnotched and Notched Cylindrical Specimens

Unnotched and notched cylinders in split tension are analyzed. The load-distributed width has been shown to affect the stress and displacement distributions. Based on finite element analysis, linear elastic fracture mechanics (LEFM) formulas for the stress intensity factor KI, crack mouth opening displacement (CMOD), and the crack opening displacement (COD) profile for the split tension of notched cylinders are first provided in terms of load-distributed width as well as load magnitude, specimen size, and notch length. A formula expressing the effect of load-distributed width on maximum tensile stress in an unnotched cylinder is also provided.
Effect of nursing interventions on stressors of parents of premature infants in neonatal intensive care unit.

AIM This study was planned for the purpose of determining the effect of stress-reducing nursing interventions on the stress levels of mothers and fathers of premature infants in a Neonatal Intensive Care Unit (NICU). DESIGN Randomised intervention. BACKGROUND The physical and psychosocial environment of the NICU is a major factor in the stress experienced by the family. METHOD Interviews were conducted with the parents of premature infants who agreed to participate in the research. An approximately 30-minute educational programme about their infant and the intensive care unit was held for the mothers and fathers in the intervention group within the first week after their infant was admitted to the intensive care unit. Then they were introduced to the unit and personnel. They were given the information they requested and their questions were responded to. The parents in the control group received nothing in addition to the routine unit procedures. The mothers and fathers' stress scores were measured for both groups after their infants' 10th day in the NICU with the Parental Stress Scale: NICU (PSS:NICU). RESULTS The difference between the intervention group and the control group mothers' mean stress score was found to be statistically significant (t = 4.05, p < 0.05). It was determined that the stress scores for the fathers in the treatment group in this research were lower, but the difference between the two groups was not found to be statistically significant (p > 0.05). CONCLUSION It has been determined that parents experience very high stress levels when their infants are admitted to an NICU and that there are nursing interventions which can be implemented to decrease their levels of stress. RELEVANCE TO CLINICAL PRACTICE Determining the sources of stress experienced by parents can help NICU nurses use appropriate interventions in cooperation with other members of the team to decrease the stress that parents experience.
The inheritance of mitochondrial DNA in interspecific Saccharomyces hybrids and their properties in winemaking

The inheritance of mitochondrial DNA (mtDNA) in yeast hybrids is heteroplasmic, turning into homoplasmic after few cell cycles. Mitotype restoration is reported to be biparental and random. This study shows that mitotype restoration follows fixed schemata. We created isogenic, interspecific Saccharomyces cerevisiae × Saccharomyces uvarum hybrids through direct mating and analysed their mating frequency and mitotype. The mating frequency increased for most crosses in staggered mating. Mitotyping revealed that breeding lines with the same parental strain of S. cerevisiae and different parental strains of S. uvarum give rise to the same mitotype. According to our results, we postulate that the inheritance of mtDNA is dominated by one parental strain and that the superior mitotype is specific to each breeding line. Technological tests showed typical hybrid heterosis. Copyright © 2017 John Wiley & Sons, Ltd.
Geometry of Higher Helicities

We revisit an interpretation of higher-dimensional helicities and Hopf–Novikov invariants from the point of view of the Brownian ergodic theorem. We also survey various results related to Arnold’s theorem on the asymptotic Hopf invariant on three-dimensional manifolds and recent work on linking of a vector field with a foliation, the asymptotic crossing number, short path systems, and relations with the Calabi invariant. 2000 Math. Subj. Class. 37A15, 55Q25, 76W05.
Advanced coordinated beamforming for the downlink of future LTE cellular networks

Modern cellular networks in traditional frequency bands are notoriously interference-limited, especially in urban areas, where base stations are deployed in close proximity to one another. The latest releases of LTE incorporate features for coordinating downlink transmissions as an efficient means of managing interference. Recent field trial results and theoretical studies of the performance of JT CoMP schemes revealed, however, that their gains are not as high as initially expected, despite the large coordination overhead. These schemes are known to be very sensitive to defects in synchronization or information exchange between coordinating base stations as well as uncoordinated interference. In this article, we review recent advanced CB schemes as alternatives, requiring less overhead than JT CoMP while achieving good performance in realistic conditions. By stipulating that in certain LTE scenarios of increasing interest, uncoordinated interference constitutes a major factor in the performance of CoMP techniques at large, we hereby assess the resilience of the state-of- the-art CB to uncoordinated interference. We also describe how these techniques can leverage the latest specifications of current cellular networks, and how they may perform when we consider standardized feedback and coordination. This allows us to identify some key road blocks and research directions to address as LTE evolves toward the future of mobile communications.
Duality Theory and Approximate Dynamic Programming for Pricing American Options and Portfolio Optimization 1

This chapter describes how duality and approximate dynamic programming (ADP) methods can be used in financial engineering. It focuses on American option pricing and portfolio optimization problems when the underlying state space is highdimensional. In general, it is not possible to solve these problems exactly due to the so-called “curse of dimensionality” and as a result, approximate solution techniques are required. ADP and dual-based methods have been proposed for constructing and evaluating good approximate solutions to these problems. In this chapter we describe these methods. Some directions for future research are also outlined.
Instability of the Parent Phase in Nearly Ordered Fe3Pt Invar Alloys

The martensitic transformation in a nearly ordered Fe3Pt is weak first order, and the martensite phase shows a large magnetic field-induced strain of several percent. We have investigated the origin of this transformation from its electronic structure. A characteristic feature in the electronic structure is the existence of a relatively high peak in the density of states of the minority spin band just below the Fermi energy. This peak splits into two peaks by tetragonal distortion, and one of them shifts to lower energy by the distortion, suggesting that the band Jahn-Teller effect is the main cause for the transformation.
Kv7-type Channel Currents in Spiral Ganglion Neurons

Alterations in Kv7-mediated currents in excitable cells result in several diseased conditions. A case in DFNA2, an autosomal dominant version of progressive hearing loss, involves degeneration of hair cells and spiral ganglion neurons (SGNs) from basal to apical cochlea, manifesting as high-to-low frequency hearing loss, and has been ascribed to mutations in Kv7.4 channels. Analyses of the cellular mechanisms of Kv7.4 mutations and progressive degeneration of SGNs have been hampered by the paucity of functional data on the role Kv7 channels play in young and adult neurons. To understand the cellular mechanisms of the disease in SGNs, we examined temporal (young, 0.5 months old, and senescent, 17 months old) and spatial (apical and basal) roles of Kv7-mediated currents. We report that differential contribution of Kv7 currents in mice SGNs results in distinct and profound variations of the membrane properties of basal versus apical neurons. The current produces a major impact on the resting membrane potential of basal neurons. Inhibition of the current promotes membrane depolarization, resulting in activation of Ca2+ currents and a sustained rise in intracellular Ca2+. Using TUNEL assay, we demonstrate that a sustained increase in intracellular Ca2+ mediated by inhibition of Kv7 current results in significant SGN apoptotic death. Thus, this study provides evidence of the cellular etiology and mechanisms of SGN degeneration in DFNA2.
Open‐labeled pilot study of cysteine‐rich whey protein isolate supplementation for nonalcoholic steatohepatitis patients

Background and Aims: Glutathione (GSH) depletion contributes to liver injury and development of steatohepatitis. Undenatured cysteine‐rich whey protein isolate has been clinically proven to raise GSH in several patient groups. The aim of this study was to evaluate the effect of oral supplementation with whey protein on patients with nonalcoholic steatohepatitis (NASH).