gebhart/patrepeval huggingface dataset:
A Single‐lead ECG algorithm to differentiate right from left manifest accessory pathways: A reappraisal of the P‐Delta interval (2023)

A novel single-lead ECG algorithm incorporating the PDI interval with previous conventional criteria showed high accuracy in differentiating right from left manifest AP comprising pediatric and minimal pre-excitation subgroups in the current study.
Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads (2011)

Unchained base reads on self-assembling DNA nanoarrays have recently emerged as a promising approach to low-cost, high-quality resequencing of human genomes. Because of unique characteristics of these mated pair reads, existing computational methods for resequencing assembly, such as those based on map-consensus calling, are not adequate for accurate variant calling. We describe novel computational methods developed for accurate calling of SNPs and short substitutions and indels (<100 bp); the same methods apply to evaluation of hypothesized larger, structural variations. We use an optimization process that iteratively adjusts the genome sequence to maximize its a posteriori probability given the observed reads. For each candidate sequence, this probability is computed using Bayesian statistics with a simple read generation model and simplifying assumptions that make the problem computationally tractable. The optimization process iteratively applies one-base substitutions, insertions, and deletions until convergence is achieved to an optimum diploid sequence. A local de novo assembly procedure that generalizes approaches based on De Bruijn graphs is used to seed the optimization process in order to reduce the chance of converging to local optima. Finally, a correlation-based filter is applied to reduce the false positive rate caused by the presence of repetitive regions in the reference genome.
Crocin promotes non‐rapid eye movement sleep in mice (2011)

Crocus sativus L. (saffron) has been traditionally used for the treatment of insomnia and other diseases of the nervous systems. Two carotenoid pigments, crocin and crocetin, are the major components responsible for the various pharmacological activities of C. sativus L. In this study, we examined the sleep‐promoting activity of crocin and crocetin by monitoring the locomotor activity and electroencephalogram after administration of these components to mice. Crocin (30 and 100 mg/kg) increased the total time of non‐rapid eye movement (non‐REM) sleep by 60 and 170%, respectively, during a 4‐h period from 20:00 to 24:00 after its intraperitoneal administration at a lights‐off time of 20:00. Crocetin (100 mg/kg) also increased the total time of non‐REM sleep by 50% after the administration. These compounds did not change the amount of REM sleep or show any adverse effects, such as rebound insomnia, after the induction of sleep.
Low birth weight, family history of diabetes, and glucose intolerance in Swedish middle-aged men. (1999)

This study indicated that low birth weight is associated with type 2 diabetes, impaired glucose tolerance, and impaired fasting glucose in men. This finding was most pronounced in subjects with diabetes in the family, but it was also indicated in those without a family history of diabetes. Men with the combination of low birth weight and family history of diabetes seem to be at particularly high risk of developing type 2 diabetes.
Caching single-assignment structures to build a robust fine-grain multi-threading system (2002)

We present the design, implementation, and evaluation of single assignment data structures and of a software controlled cache in an existing multi-threaded architecture platform-the Efficient Architecture for Running Threads (EARTH). The software-controlled cache (ISSC) exploits temporal and spatial locality of EARTH split-phased memory transactions for single-assignment memory references. Our experimental evaluation indicates that the caching mechanism for single-assignment storage makes the EARTH memory system more robust to variations in the latency of memory operations. As a consequence the system can be ported to a wider range of machine platforms and deliver speedup for both regular and irregular application.
Germ cells and fatty acids induce translocation of CD36 scavenger receptor to the plasma membrane of Sertoli cells (2005)

The CD36 scavenger receptor is involved in the uptake and transport of fatty acids, as well as the phagocytosis process in macrophages. We show here that the CD36 protein is expressed by Sertoli cells in the seminiferous epithelium, mainly during the stages where phagocytosis takes place. Using a Sertoli-derived cell line, we show that addition of germ cells and residual bodies triggers a re-localization of CD36 from the cytoplasm to the plasma membrane of the cells, while latex beads do not. Moreover, Sertoli cell phagocytosis of germ cells, but not of latex beads, is reduced by the presence of fatty acids in the culture medium. In the testis, CD36 plays a key role in both phagocytosis and lipid recycling, for constant production of mature spermatozoa.
Apoptotic cell death of human leukaemia U937 cells by ubiquinone-9 purified fromPleurotus eryngii (2009)

A chloroform extract of the edible mushroom Pleurotus eryngii showed an inhibitory effect on mammalian DNA topoisomerase I. The topoisomerase I inhibitory compound was purified and identified as ubiquinone-9. Ubiquinone-9 was shown to inhibit the activity of topoisomerase I with IC(50) of about 50 microM. Concentration of 110 microM ubiquinone-9 caused 50% growth inhibition of human leukaemia U937 cells, but not that of normal fibroblast NIH3T3 and 3Y1 cells. Ubiquinone-9-induced cell death was characterised with the cleavage of poly (ADP-ribose) polymerase and pro-caspase 3. Furthermore, ubiquinone-9 induced the fragmentation of DNA into an apoptotic DNA ladder, indicating that the inhibitor triggered apoptosis. The induction of apoptosis by ubiquinone-9 was also confirmed using flow cytometry analysis. Taken together, these results suggest that ubiquinone-9 may function by inhibiting oncogenic disease, at least in part, through the inhibition of topoisomerase I activity.
Tissue-based SARS-CoV-2 detection in fatal COVID-19 infections: Sustained direct viral-induced damage is not necessary to drive disease progression (2021)

Coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although viral infection is known to trigger inflammatory processes contributing to tissue injury and organ failure, it is unclear whether direct viral damage is needed to sustain cellular injury. An understanding of pathogenic mechanisms has been handicapped by the absence of optimized methods to visualize the presence and distribution of SARS-CoV-2 in damaged tissues. We first developed a positive control cell line (Vero E6) to validate SARS-CoV-2 detection assays. We then evaluated multiple organs (lungs, kidneys, heart, liver, brain, intestines, lymph nodes, and spleen) from fourteen COVID-19 autopsy cases using immunohistochemistry (IHC) for the spike and the nucleoprotein proteins, and RNA in situ hybridization (RNA ISH) for the spike protein mRNA. Tissue detection assays were compared with quantitative polymerase chain reaction (qPCR)-based detection. SARS-CoV-2 was histologically detected in the Vero E6 positive cell line control, 1 of 14 (7%) lungs, and none (0%) of the other 59 organs. There was perfect concordance between the IHC and RNA ISH results. qPCR confirmed high viral load in the SARS-CoV-2 ISH-positive lung tissue, and absent or low viral load in all ISH-negative tissues. In patients who die of COVID-19-related organ failure, SARS-CoV-2 is largely not detectable using tissue-based assays. Even in lungs showing widespread injury, SARS-CoV-2 viral RNA or proteins were detected in only a small minority of cases. This observation supports the concept that viral infection is primarily a trigger for multiple-organ pathogenic proinflammatory responses. Direct viral tissue damage is a transient phenomenon that is generally not sustained throughout disease progression.
Defect in cytosolic Neu2 sialidase abrogates lipid metabolism and impairs muscle function in vivo (2022)

Sialic acid (SA) is present in glycoconjugates and important in cell-cell recognition, cell adhesion, and cell growth and as a receptor. Among the four mammalian sialidases, cytosolic NEU2 has a pivotal role in muscle and neuronal differentiation in vitro. However, its biological functions in vivo remain unclear due to its very low expression in humans. However, the presence of cytoplasmic glycoproteins, gangliosides, and lectins involved in cellular metabolism and glycan recognition has suggested the functional importance of cytosolic Neu2 sialidases. We generated a Neu2 knockout mouse model via CRISPR/Cas9-mediated genome engineering and analyzed the offspring littermates at different ages to investigate the in vivo function of cytosolic Neu2 sialidase. Surprisingly, knocking out the Neu2 gene in vivo abrogated overall lipid metabolism, impairing motor function and leading to diabetes. Consistent with these results, Neu2 knockout led to alterations in sialylated glycoproteins involved in lipid metabolism and muscle function, as shown by glycoproteomics analysis.
MP36-06 VALIDATION OF AUA BEST PRACTICE GUIDELINES FOR PROSTATE BIOPSY INFECTIOUS COMPLICATIONS AND REDUCING VARIABILITY AND DURATION OF ANTIMICROBIAL UTILIZATION: QUALITY IMPROVEMENT INITIATIVE (2016)

CONCLUSIONS: Among men undergoing a 2-year repeat prostate biopsy, the use of dutasteride for 2 years was associated with a reduced the risk of overall and severe TBPA-UTI. Future studies evaluating whether on-demand shorter course of dutasteride can also reduce the risk of TBPA-UTI are warranted.
A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles (2017)

SUMMARY We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts. We further show that the expanded CMap can be used to discover mechanism of action of small molecules, functionally annotate genetic variants of disease genes, and inform clinical trials. The 1.3 million L1000 profiles described here, as well as tools for their analysis, are available at https://clue.io . HIGHLIGHTS A new gene expression profiling method, L1000, dramatically lowers cost The Connectivity Map database now includes 1.3 million publicly accessible L1000 perturbational profiles This expanded Connectivity Map facilitates discovery of small molecule mechanism of action and functional annotation of genetic variants The work establishes feasibility and utility of a truly comprehensive Connectivity Map
Incidence and outcome of lung cancer in patients with chronic respiratory failure (2019)

<b>Rationale:</b> There is few data available regarding the incidence of lung cancer (LC) and treatment efficacy in patients with chronic respiratory failure (CRF) under long-term oxygen therapy (LTOT). <b>Methods:</b> In this single center study, charts from 7631 patients under LTOT from 2009 to 2018 were retrospectively reviewed. Patients diagnosed with LC were included in the subsequent analysis, for tumor characteristics, underlying respiratory failure, cancer treatment and outcome . <b>Results:</b> A total of 29 patients developped LC during the study period (Incidence rate 0.38±0.18%). At LC diagnosis, patients were 70 [66 to 78] years old and on LTOT for 2.2 [1.2 to 3.9] years. Histology was adenocarcinoma (n=9), squamous cell (n=12), small-cell lung cancer (n=2) and unknown (n=6). 14/29 patients had stage IV at diagnosis. Ten patients did not received specific LC treatment, whereas 7 patients received chemotherapy, 4 concomitant radio-chemotherapy, 4 exclusive radiotherapy, 2 tyrosine kinase inhibitors, and one tumor was surgically removed. Underlying respiratory diseases were: COPD (n=25), interstitial pneumonia (n=3), pulmonary hypertension (n=1). Overall median survival from LC diagnosis was 285 [69 to 566] days, 727 days in patients treated by surgery or radiotherapy (±chemotherapy) and 241 days in those treated by chemotherapy alone (p= 0.054). <b>Conclusion:</b> LC incidence in patients under LTOT appears low. Specific non surgical LC treatment could be administered in 2/3 of the patients with results comparable to non surgical patients without CRF.
Equilibrium Phase Densities, Interfacial Tensions for the Ethane +n-Pentane System at 294.15 K (2011)

The equilibrium phase densities and interfacial tensions of the binary mixture (ethane + n-pentane) have been measured simultaneously using the pendant drop method at 294.15 K. The experimental pressure was in the range of (6 to 30) bar. The measured phase densities are compared with calculated equilibrium densities by applying the GERG2004 equation. The deviations of the measured interfacial tension at each experimental condition are calculated on the basis of ISO combined standard uncertainty calculation recommendations. No open interfacial tension data for the system have been reported at any isothermal conditions. The measurement results extend the range of previous interfacial tension data of the hydrocarbon mixtures in the open literature.
Digital holographic microscopy (DHM) for metrology and dynamic characterization of MEMS and MOEMS (2006)

Digital Holographic Microscopes (DHM) enables recording the whole information necessary to provide real time nanometric vertical displacement measurements with a single image acquisition. The use of fast acquisition camera or stroboscopic acquisition mode makes these new systems ideal tools for investigating the topography and dynamical behavior of MEMS and MOEMS. This is illustrated by the investigation of resonant frequencies of a dual axis micromirror. This enables the definition of the linear, non-linear, and modal resonance zones of its dynamical response.
Online Evaluation for Effective Web Service Development (2018)

Development of the majority of the leading web services and software products today is generally guided by data-driven decisions based on evaluation that ensures a steady stream of updates, both in terms of quality and quantity. Large internet companies use online evaluation on a day-to-day basis and at a large scale. The number of smaller companies using A/B testing in their development cycle is also growing. Web development across the board strongly depends on quality of experimentation platforms. In this tutorial, we overview state-of-the-art methods underlying everyday evaluation pipelines at some of the leading Internet companies. Software engineers, designers, analysts, service or product managers --- beginners, advanced specialists, and researchers --- can learn how to make web service development data-driven and do it effectively.
Fully integrated electrically driven optical frequency comb at communication wavelength (2022)

To meet the high demand of data transmission capacity, optical communications systems have been developed. In order to increase the channel numbers for larger communication bandwidth, multi-mode lasers and laser arrays can be used. As an alternative coherent light source, optical frequency comb (OFC) contains multi-wavelength signal, and hence enables communication with data stream of tens of terabit/s. Fully integrated electrically driven OFCs are expected as a compact, robust, and low-cost light source for data communication. In this review article, the recent development progress on fully integrated electrically driven OFC generators are reviewed, with focus on the demonstrations in the past five years. Based on comb generation approaches, the works are categorized into two main types: one is OFC generators based on four-wave mixing in high-<i>Q</i> resonator, and the other is OFC generators based on mode-locked laser. At the end, a summary and future outlook are provided.
Human Retinal Progenitor Cells Grown as Neurospheres Demonstrate Time‐Dependent Changes in Neuronal and Glial Cell Fate Potential (2005)

The spatiotemporal birth order of the seven major classes of retinal cells is highly conserved among vertebrates. During retinal development, long projection neurons (ganglion cells) are produced first from resident progenitors, followed by the appearance of retinal interneurons, photoreceptors, and Muller glia. This sequence is maintained through the complex orchestration of cell-intrinsic and cell-extrinsic events and factors, including local influences between neighboring cells. Here we asked whether cultures of human prenatal retinal cells might also yield different ratios of cell types based on gestational age and time spent in vitro, thus recapitulating in vivo development. An established chopping technique was used to passage human prenatal retinal cells as neurospheres, avoiding the use of proteases and preserving cell-cell contacts and native microenvironments present in vivo. Retinal neurospheres cultured in this manner demonstrated specific patterns of growth over a limited time period, possibly reflecting trends in normal retinal development. Upon differentiation, immunocytochemical analysis revealed that retinal neurospheres produce predominantly glial cells with increasing gestational age and time in culture. Conversely, the percentage of betaIII tubulin-positive neurons declined over time. This provides information for optimizing culture systems aimed at the study of human retinal development and the generation of specific retinal cell types for therapeutic use or drug testing.
Atrophy but not death of adult septal cholinergic neurons after ablation of target capacity to produce mRNAs for NGF, BDNF, and NT3 (1993)

The effect of unilateral excitotoxic ablation of hippocampal neurons was investigated on (1) the local production of mRNA for NGF and related neurotrophins, (2) the amount of NGF protein in the septal region, and (3) the viability and appearance of afferent septal cholinergic neurons in adult rats. After near complete ablation of hippocampal neurons, total levels of NGF, brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT3) mRNA measured by quantitative Northern blot analysis in the hippocampal remnant fell significantly, to less than 25% of control values by 28 d and to less than 9% by 300 d. In the septal region ipsilateral to such lesions, NGF protein levels measured by ELISA fell significantly, to about 35% of control values, but the number of immunohistochemically detected cholinergic neurons did not decline significantly for up to 500 d. Instead, the cholinergic neurons persisted in an atrophied state, exhibiting severe shrinkage and reduced staining for the transmitter-synthesizing enzyme ChAT. The parameters of cell size and ChAT staining intensity correlated significantly with the amount of hippocampal tissue present. These findings indicate that in adult rats, target-derived NGF, BDNF, and NT3 do not regulate the survival of septal cholinergic neurons in proportion to the number of target neurons present. Moreover, the findings suggest that one or more of these target-derived neurotrophins regulate the structural and chemical phenotype of these neurons in the adult.
Intracardiac Echocardiography-Guided Cardiac Tumor Biopsy (2009)

A 63-year-old woman was admitted to hospital with the chief complaint of new onset chest discomfort and pretibial pitting edema. Transthoracic echocardiography revealed a large invasive tumor on the heart protruding into the right atrium and right ventricle, which obstructed the outflow tract. She underwent transvenous 9Fr, 9-MHz ultra intracardiac echocardiography (ICE) (EP Technologies, Boston Scientific Corporation, San Jose, CA, USA) guided biopsy, and a diagnosis of malignant lymphoma was established from the specimen obtained. ICE-guided cardiac tumor biopsy may be one of the most useful strategies for diagnosis of cardiac tumors.
Polyphenol oxidase inactivation in viscous fluids by ohmic heating and conventional thermal processing (2019)

Abstract This study investigated polyphenol oxidase (PPO) inactivation in a viscous solution of carboxymethyl cellulose (CMC) by ohmic processing (OH) and conventional thermal processing (CTP) at several temperatures and to assess the impact of CMC consistency on PPO inactivation. OH affects the PPO activity in temperatures higher than 50°C (reduction to 20% at 50°C, 12 min and complete inactivation after 2 min at 80°C), whereas CTP caused a significant reduction in PPO activity only above 60°C (reduction to 90% at 60°C, 8 min and complete inactivation after 2 min at 80°C). The rate of PPO inactivation by ohmic heating was higher than by CTP under all conditions tested, represented by a reduction of D 70°C (OH: 3.61 min, CTP 7.32 min), except D 80°C was ∼0.5 for both techniques. The Z‐value was higher for OH (14.68°C) than for CTP (8.60°C). Consistency did not have a major impact on inactivation rate. Practical Applications Inactivating enzymes that alter quality aspects of food products, such as polyphenol oxidase (PPO), is an important objective of a food processing technology. PPO is an enzyme commonly found in fruits and vegetables that catalyzes browning reactions. Ohmic heating (OH) is a technology known for its potential for processing highly viscous products. This study corroborates the potential of OH for processing highly viscous fluids over conventional thermal processing (CTP), having a great potential to be an alternative technique to food processing. In addition, it gave more evidence of the nonthermal effects due to the electrical current during the ohmic processing.
Variable bandwidth computation for tap changer control in distribution grids (2016)

The growing share of distributed generation and electric vehicles has led to an increased deployment of on-load tap changers for voltage regulation in distribution grids. This trend entails changing requirements for tap changer control. This paper briefly discusses some recent developments in this field, while we focus on the variable bandwidth concept and its computational methods. Three different computation techniques are introduced. By means of a set of simplified equations, in-depth insight into the variable bandwidth concept is gained. For simple grid configurations this concept is suitable for bandwidth determination. For more complex networks we introduce a more accurate method using power system simulations. However, for realistic grids we propose an equally accurate, yet computational more efficient approach based on optimization.