gebhart/patrepeval huggingface dataset:
Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events (2022)

The open reading frames (ORF)5 represents approximately 4% of the porcine reproductive and respiratory syndrome virus (PRRSV)-2 genome (whole-PRRSV) and is often determined by the Sanger technique, which rarely detects >1 PRRSV strain if present in the sample. Next-generation sequencing (NGS) may provide a more appropriate method of detecting multiple PRRSV strains in one sample. This work assessed the effect of PRRSV genetic variability and recombination events, using NGS, on the time-to-low prevalence (TTLP) and total losses in breeding herds (n 20) that detected a PRRSV outbreak and adopted measures to eliminate PRRSV. Serum, lung or live virus inoculation material collected within 3-weeks of outbreak, and subsequently, processing fluids (PFs) were tested for PRRSV by RT-qPCR and NGS. Recovered whole-PRRSV or partial sequences were used to characterize within and between herd PRRSV genetic variability. Whole-PRRSV was recovered in five out of six (83.3%) lung, 16 out of 22 (72.73%) serum and in five out of 95 (5.26%) PF. Whole-PRRSV recovered from serum or lung were used as farm referent strains in 16 out of 20 (80%) farms. In four farms, only partial genome sequences were recovered and used as farm referent strains. At least two wild-type PRRSV strains (wt-PRRSV) were circulating simultaneously in 18 out of 20 (90%) and at least one vaccine-like strain co-circulating in eight out of 20 (40%) farms. PRRSV recombination events were detected in 12 farms (59%), been 10 out of 12 between wt-PRRSV and two out of 12 between wt-PRRSV and vaccine-like strains. Farms having ≥3 strains had a 12-week increase TTLP versus herds ≤2 strains detected. Farms with ≤2 strains (n 10) had 1837 and farms with no recombination events detected (n 8) had 1827 fewer piglet losses per 1000 sows versus farms with ≥3 PRRSV strains (n 8) or detected recombination (n 10), respectively. NGS outcomes and novel visualization methods provided more thorough insight into PRRSV dynamics, genetic variability, detection of multiple strains co-circulating in breeding herds and helped establish practical guidelines for using PRRSV NGS outputs.
SH2-targeting Stat5 inhibitor IST5-002 has hightranscriptomic specificity and low toxicity in vivo (2020)

Stat5a/b (Stat5) is critical for growth and progression of solid tumors and hematological malignancies, specifically prostate cancer (PC) and Bcr-Ablâdriven leukemias. Also, Stat5 is known to induce cancer stem cell phenotype. For therapeutic suppression, transcription factors are typically considered suboptimal pharmacological targets because their function relies on proteinâprotein and proteinâDNA interactions that are not easily disrupted by small molecules. Targeting Stat5, however, offers a unique opportunity for development of pharmacological inhibitors because Stat5 serves both as a cytoplasmic signaling molecule and a nuclear transcription factor and can be suppressed when located in cytoplasm as a signaling protein. Using in silico screening, combined with medicinal chemistry, we developed a lead compound Stat5a/b inhibitor, IST5-002 (IST5). In order to evaluate the potential of IST5 for additional lead optimization for clinical development, we evaluated the transcriptomic specificity of IST5 vs. genetic knockdown of Stat5 in cells. In addition, we further evaluated the efficacy and the mechanism of action of IST5 in blocking the Jak2-Stat5 signaling cascade. Finally, we investigated the acute, sub-chronic and chronic toxicity profiles of IST5 in vivo in mice. Our results show that the SH2-domain targeting IST5 has high transcriptional specificity in PC cells. IST5 has minimal specific inhibitory activity against 54 typical kinases in cancer cells. Using two different assays of Stat5-dimerization, we demonstrate high efficacy of IST5 in suppressing dimerization step of Stat5 activation and that the phosphate group of IST5, which increases its transfer across the cell membrane, is not critical for its activity in cell-based assays. Finally, IST5 did not causeany significant acute, subchronic or chronic toxic effects or changes in the blood profiles in mice. In summary, the present work supports lead optimization of the Stat5 inhibitor IST5 towards clinical development for therapies for solid tumors, hematological malignancies and myeloproliferative disorders.
Central sleep apnoea. (2010)

Central sleep apnoea (CSA) is characterized by the cessation of breathing during sleep due to absent ventilatory drive and may be associated with symptoms of insomnia, excessive daytime sleepiness or frequent arousals. Central apnoeas occur through two pathophysiologic patterns, either post- hyperventilation or post-hypoventilation. The prevalence of CSA is dependent on the population being studied, the predominant risk factors being elderly age group and co-morbid conditions.Data regarding the racial distribution of this disorder are very limited. CSA may be a clinical marker of underlying medical disorders, including cardiac or neurological disease, with resultant significant morbidity and mortality. Given that the underlying pathogenesis remains poorly understood, therapeutic options are currently limited to empiric treatment with PAP devices and rudimentary attempts at pharmacologic therapy with respiratory stimulant drugs and/or oxygen/carbon dioxide gas supplementation as well as treating the underlying cause. The long-term impact of CSA on health and mortality needs further clarification. Future research should be aimed at elucidating the physiologic determinants and consequences of central breathing instability in populations of different age groups, gender and racial descent, as a prerequisite to the development of novel therapeutic interventions in the different populations.
Development of a Multilocus Sequence Typing Scheme for the Pig Pathogen <i>Streptococcus suis</i> : Identification of Virulent Clones and Potential Capsular Serotype Exchange (2002)

Streptococcus suis is an important pathogen of pigs and occasionally causes serious human disease. However, little is known about the S. suis population structure, the clonal relationships between strains, the potential of particular clones to cause disease, and the relevance of serotype as a marker for epidemiology. Here we describe a multilocus sequence typing (MLST) scheme for S. suis developed in order to begin to address these issues. Seven housekeeping gene fragments from each of 294 S. suis isolates obtained from various S. suis diseases and from asymptomatic carriage representing 28 serotypes and nine distinct countries of origin were sequenced. Between 32 and 46 alleles per locus were identified, giving the ability to distinguish >1.6 x 10(11) sequence types (STs). However only 92 STs were identified in this study. Of the 92 STs 18 contained multiple isolates, the most common of which, ST1, was identified on 141 occasions from six countries. Assignment of the STs to lineages resulted in 37 being identified as unique and unrelated STs while the remaining 55 were assigned to 10 complexes. ST complexes ST1, ST27, and ST87 dominate the population; while the ST1 complex was strongly associated with isolates from septicemia, meningitis, and arthritis, the ST87 and ST27 complexes were found to contain significantly higher numbers of lung isolates. In agreement with the observed distribution of disease-causing isolates of S. suis, most isolates previously characterized as of high virulence in porcine infection models belong to ST1, while isolates belonging to other STs appear to be less virulent in general. Finally nine STs were found to contain isolates of multiple serotypes, and many isolates belonging to the same serotypes were found to have very disparate genetic backgrounds. As well as highlighting that the serotype can often be a poor indicator of genetic relatedness between S. suis isolates, these findings suggest that capsular genes may be moving horizontally through the S. suis population.
Multistep Enzymatic Synthesis of Long‐Chain α,ω‐Dicarboxylic and ω‐Hydroxycarboxylic Acids from Renewable Fatty Acids and Plant Oils (2013)

A multistep enzyme catalysis was successfully implemented to produce long-chain α,ω-dicarboxylic and ω-hydroxycarboxylic acids from renewable fatty acids and plant oils. Sebacic acid as well as ω-hydroxynonanoic acid and ω-hydroxytridec-11-enoic acid were produced from oleic and ricinoleic acid.
Fundamentals Of Fixed Bed Adsorption Processes: Analysis Of Adsorption Breakthrough And Desorption Elution Curves (2020)

Abstract NOTE: The first page of text has been automatically extracted and included below in lieu of an abstract Main Menu Session 1613 Fundamentals of Fixed Bed Adsorption Processes: Analysis of Adsorption Breakthrough and Desorption Elution Curves. James M. Becnel, Charles E. Holland, James McIntyre, Michael A. Matthews, and James A. Ritter Department of Chemical Engineering University of South Carolina, Columbia, SC, 29205 Introduction Fixed bed adsorption processes are ubiquitous throughout the chemical process and other industries. This laboratory is an extension of a lab proposed by Cruz et. al. (2000), which is designed to allow students to explore essential operating features of a fixed bed adsorber through hands-on, data-gathering experiments. Students expand knowledge from the Unit Operations classroom, as well as develop their experimental, analytical, and communication skills. From the students' perspective, the laboratory will integrate experimental procedures and data with fundamental modeling, while providing insight into adsorption processes. An open-ended design challenge is also incorporated. Topics for student assessment are also presented. Learning Objectives This laboratory is designed to integrate analysis, evaluation, design, and communication skills. It is an extension of the adsorption/desorption experiment presented by Cruz, et. al. (2001). In their laboratory students: · Gather data in a hands-on experiment. o Experimental design. o Manual and automated controls. o Automated data acquisition. · Observe and model dynamic adsorption behavior: o Non-linear data fitting. o Solute Movement Theory / the Method of Characteristics. o Concentration shock waves. · Graphing data for clarity and to support explanations. Using a mostly identical apparatus, we have modified the lab to include: · Dynamic mass balances. · Numerical integration of data. · Numerical differentiation of data. · Equilibrium adsorption isotherms based on dynamic mass balances. · Equilibrium adsorption isotherms based on the Method of Characteristics. · An open-ended design challenge based directly from the student’s data. “Proceedings of the 2002 American Society for Engineering Education Annual Conference & Exposition Copyright © 2002, American Society for Engineering Education.” Main Menu
<i>C9orf72</i> -derived poly-GA DPRs undergo endocytic uptake in iNPC-derived astrocytes and spread to motor neurons (2021)

Abstract Dipeptide repeat proteins (DPRs) are aggregation-prone polypeptides encoded by the pathogenic G4C2 repeat expansion in the C9orf72 gene, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). In this study, we focus on the role of poly-GA DPRs in disease spread. We demonstrate that recombinant poly-GA oligomers can directly convert into solid-like aggregates and form characteristic &amp;[beta]-sheet fibrils in vitro. To dissect the process of cell-to-cell DPR transmission, we closely follow the fate of poly-GA DPRs in either their oligomeric or fibrillized form after administration in the cell culture medium. We observe that poly-GA DPRs are taken up via dynamin-dependent and - independent endocytosis, eventually converging at the lysosomal compartment and leading to axonal swellings in neurons. We then use a co-culture system to demonstrate astrocyte-to- motor neuron DPR propagation, showing that astrocytes may internalise and release aberrant peptides in disease pathogenesis. Overall, our results shed light on the mechanisms of poly- GA cellular uptake and cell-to-cell propagation, suggesting lysosomal impairment as a possible feature underlying the cellular pathogenicity of these DPR species.
A Clinical Study of 31 Cases with Submandibular Gland Carcinoma: A 22-year Review (2023)

唾液腺癌は頻度が低く, その中でも顎下腺癌の占める割合は低く希少癌である. 大阪医科薬科大学病院で加療を行った顎下腺癌31例の検討を行った. 男性23名, 女性8名であり, 年齢の中央値は65歳であった. 最も多い組織型は腺様嚢胞癌および唾液腺導管癌であり, 次いで粘表皮癌と多形腺腫由来癌であった. 病理組織学的悪性度は低／中悪性が12例, 高悪性が19例であった. 術前の穿刺吸引細胞診によって, 悪性と診断できた症例は21例, 悪性度が診断できた症例が11例であった. 5年疾患特異的生存率は59.2%であり, ステージ別では, ⅠからⅣでそれぞれ, 100%, 100%, 71.1%, 25.0%であった. 再発例と非再発例を比較したところ, 再発が有意に多い要因として, ステージⅣ, リンパ節転移陽性, 高齢が挙げられた. 顎下腺癌は耳下腺癌と比較して高悪性が多かった. 耳下腺癌の低／中悪性において頻度の高い基底細胞腺癌, 分泌癌, 上皮筋上皮癌が顎下腺癌では1例も認められなかったことが予後不良の要因であると考えられた.
Analysis and design of metasurfaces for wave manipulation using the multilevel green's function interpolation method (2016)

This paper presents the use of multilevel Green's function interpolation method (MLGFIM) for the analysis of design of metasurfaces for wave manipulation. MLGFIM allows fast matrix-vector multiplication in an iterative solution to large-scale problems. Due to the planar nature of typical metasurfaces, this multiplication can be further speed up by using fast Fourier transform technique (FFT). The convergence of the iterative solution is enhanced using the sparse approximate inverse (SAI) preconditioner tailored for MLGFIM.
ChemInform Abstract: Solvent Effects in Catalysis: Rational Improvements of Catalysts via Manipulation of Solvent Interactions (2016)

Abstract Review: 109 refs.
A Contemporary Look at Biomechanical Models of Myocardium (2019)

Understanding and predicting the mechanical behavior of myocardium under healthy and pathophysiological conditions are vital to developing novel cardiac therapies and promoting personalized interventions. Within the past 30 years, various constitutive models have been proposed for the passive mechanical behavior of myocardium. These models cover a broad range of mathematical forms, microstructural observations, and specific test conditions to which they are fitted. We present a critical review of these models, covering both phenomenological and structural approaches, and their relations to the underlying structure and function of myocardium. We further explore the experimental and numerical techniques used to identify the model parameters. Next, we provide a brief overview of continuum-level electromechanical models of myocardium, with a focus on the methods used to integrate the active and passive components of myocardial behavior. We conclude by pointing to future directions in the areas of optimal form as well as new approaches for constitutive modeling of myocardium.
Noisy-OR Component Analysis and its Application to Link Analysis (2006)

We develop a new component analysis framework, the Noisy-Or Component Analyzer (NOCA), that targets high-dimensional binary data. NOCA is a probabilistic latent variable model that assumes the expression of observed high-dimensional binary data is driven by a small number of hidden binary sources combined via noisy-or units. The component analysis procedure is equivalent to learning of NOCA parameters. Since the classical EM formulation of the NOCA learning problem is intractable, we develop its variational approximation. We test the NOCA framework on two problems: (1) a synthetic image-decomposition problem and (2) a co-citation data analysis problem for thousands of CiteSeer documents. We demonstrate good performance of the new model on both problems. In addition, we contrast the model to two mixture-based latent-factor models: the probabilistic latent semantic analysis (PLSA) and latent Dirichlet allocation (LDA).
Progression-Free Survival (2009)

In clinical trials of oncology drugs, overall survival (OS) is a direct measure of clinical efficacy and is considered the gold standard primary efficacy end point. The purpose of this study was to discuss the difficulties in using OS as a primary efficacy end point in the setting of evolving cancer therapies. We suggest that progression-free survival is an appropriate efficacy end point in many types of cancer, specifically those for which OS is expected to be prolonged and for which subsequent treatments are expected to affect OS.
Enhancements for Modeling Target Hydraulic Head by Automatic Calculation of Variable Pump Speed (2007)

To analyze a system of maintaining a fixed hydraulic head at a location for delivering adequate water supply with little or no storage, a conventional hydraulic model could be applied with constant speed pumps. However, modelers would need to iteratively adjust pump speed for each variable speed pump (VSP) to identify the appropriate speed factors at each time step. No doubt, this is a time consuming task, specially, when there are multiple VSPs installed in a system. This paper presents a technically enhanced approach that extends the hydraulic network model to automatically calculate the pump speed that is to deliver a prescribed hydraulic head. The improvement allows engineer to model not only a single VSP without rule-based control, but also multiple VSPs with simple and logic controls. The desired control head can be specified at any location in a system. This feature offers great flexibilities and modeling capabilities for engineers to efficiently analyze a variety of scenarios for the systems where VSPs are installed.
Graphene/alumina (G/Al2O3) composites by Spark Plasma Sintering; a simple, fast and upscalable method (2014)

Resumen del póster presentado a la 4th edition of Graphene Conference series, celebrada en Toulouse (Francia) del 6 al 9 de Mayo de 2014.
Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues (2019)

Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.
Algorithm to trade off between utility and privacy cost of online social search (2016)

Online social search such as Quora and Zhihu brings new ways to obtain answers to questions in social networks. However, personal and other sensitive information may be exposed to others when the question spreads via the social network. People obtain utility when they obtain answers to their questions but may suffer privacy cost when their personal information is known by others. Researchers are seeking methods and tools to help users get utility and protect their privacy at the same time. In this paper, we study this problem by proposing a framework to quantitatively evaluate the utility and privacy cost in online social search. Besides, we design an algorithm under our framework to help users trade off their utility and privacy cost. Simulations are performed to illustrate the concepts in our framework and demonstrate the advantages of our algorithm.
The Impact of Social Behavior on the Attenuation and Delay of Bacterial Nanonetworks (2016)

Molecular communication (MC) is a new paradigm for developing communication systems that exchanges information through the transmission and reception of molecules. One proposed model for MC is using bacteria to carry information encoded into DNA plasmids, and this is termed bacterial nanonetworks. However, a limiting factor in the models that have been studied so far is the environment considered only in ideal conditions with a single population. This is far from realistic in natural environments, where bacteria coexist in multiple populations of same and different species, resulting in a very complex social community. This complex community has social interactions that include cooperation, cheating, as well as competition. In this paper, the effects of these social interactions on the information delivery in bacterial nanonetworks are studied in terms of delay, attenuation and data rate. The numerical results show that the cooperative behavior of bacteria improves the performance of delay and attenuation leading to a higher data rate, and this performance can be degraded once their behavior switches towards cheating. The competitive social behavior shows that the performance can degrade delay as well as attenuation leading to slower data rates, as the population with the encoded DNA plasmids are prevented from reaching the receiver. The analysis of social interactions between the bacteria will pave the way for efficient design of bacterial nanonetworks enabling applications such as intrabody sensing, drug delivery, and environmental control against pollution and biological hazards.
Human galectin-1, -2, and -4 induce surface exposure of phosphatidylserine in activated human neutrophils but not in activated T cells (2006)

Cellular turnover is associated with exposure of surface phosphatidylserine (PS) in apoptotic cells, leading to their phagocytic recognition and removal. But recent studies indicate that surface PS exposure is not always associated with apoptosis. Here we show that several members of the human galectin family of glycan binding proteins (galectins-1, -2, and -4) induce PS exposure in a carbohydrate-dependent fashion in activated, but not resting, human neutrophils and in several leukocyte cell lines. PS exposure is not associated with apoptosis in activated neutrophils. The exposure of PS in cell lines treated with these galectins is sustained and does not affect cell viability. Unexpectedly, these galectins bind well to activated T lymphocytes, but do not induce either PS exposure or apoptosis, indicating that galectin's effects are cell specific. These results suggest novel immunoregulatory contribution of galectins in regulating leukocyte turnover independently of apoptosis.
Adaptive Mode Selection for Multiuser MIMO Downlink Systems (2006)

This paper proposes a block diagonalization (BD) method, which nullifies the multiuser interference and, hence, increases the sum capacity in a multiuser multiple-input multiple-output (MU-MIMO) downlink system. The proposed BD scheme employs all users' receive processing as well as channel information. In addition, this paper proposes three adaptive mode selection schemes for the proposed BD: namely, an exhaustive mode search (EMS); an up-tree-based mode search (UTMS); and a down-tree-based mode search (DTMS). The EMS is a greedy search, whereas UTMS and DTMS are simplified searches that reduce the EMS computations significantly but have almost the same performance as the EMS. Simulation results show that the proposed BD method with the proposed adaptive mode selection schemes can increase the sum capacity significantly.