gebhart/patrepeval huggingface dataset:
Differentiation of Highly Virulent Strains of Streptococcus suis Serotype 2 According to Glutamate Dehydrogenase Electrophoretic and Sequence Type (2008)

The glutamate dehydrogenase (GDH) enzymes of 19 Streptococcus suis serotype 2 strains, consisting of 18 swine isolates and 1 human clinical isolate from a geographically varied collection, were analyzed by activity staining on a nondenaturing gel. All seven (100%) of the highly virulent strains tested produced an electrophoretic type (ET) distinct from those of moderately virulent and nonvirulent strains. By PCR and nucleotide sequence determination, the gdh genes of the 19 strains and of 2 highly virulent strains involved in recent Chinese outbreaks yielded a 1,820-bp fragment containing an open reading frame of 1,344 nucleotides, which encodes a protein of 448 amino acid residues with a calculated molecular mass of approximately 49 kDa. The nucleotide sequences contained base pair differences, but most were silent. Cluster analysis of the deduced amino acid sequences separated the isolates into three groups. Group I (ETI) consisted of the seven highly virulent isolates and the two Chinese outbreak strains, containing Ala(299)-to-Ser, Glu(305)-to-Lys, and Glu(330)-to-Lys amino acid substitutions compared with groups II and III (ETII). Groups II and III consisted of moderately virulent and nonvirulent strains, which are separated from each other by Tyr(72)-to-Asp and Thr(296)-to-Ala substitutions. Gene exchange studies resulted in the change of ETI to ETII and vice versa. A spectrophotometric activity assay for GDH did not show significant differences between the groups. These results suggest that the GDH ETs and sequence types may serve as useful markers in predicting the pathogenic behavior of strains of this serotype and that the molecular basis for the observed differences in the ETs was amino acid substitutions and not deletion, insertion, or processing uniqueness.
ZnO Hard Templating for Synthesis of Hierarchical Porous Carbons with Tailored Porosity and High Performance in Lithium‐Sulfur Battery (2014)

Hierarchical porous carbon (HPC, DUT‐106) with tailored pore structure is synthesized using a versatile approach based on ZnO nanoparticles avoiding limitations present in conventional silica hard templating approaches. The benefit of the process presented here is the removal of all pore building components by pyrolysis of the ZnO/carbon composite without any need for either toxic/reactive gases or purification of the as‐prepared hierarchical porous carbon. The carbothermal reduction process is accompanied by an advantageous growing of distinctive micropores within the thin carbon walls. The resulting materials show not only high internal porosity (total pore volume up to 3.9 cm 3 g −1 ) but also a large number of electrochemical reaction sites due to their remarkably high specific surface area (up to 3060 m 2 g −1 ), which renders them particularly suitable for the application as sulfur host material. Applied in the lithium‐sulfur battery, the HPC/sulfur composite exhibits a capacity of &gt;1200 mAh g −1 ‐sulfur (&gt;750 mAh g −1 electrode) at a high sulfur loading of ≥ 3 mg cm −2 as well as outstanding rate capability. In fact, this impressive performance is achieved even using a low amount of electrolyte (6.8 μl mg −1 sulfur ) allowing for further weight reduction and maintenance of high energy density on cell level.
Homing of naive and memory T lymphocyte subsets to Peyer’s patches, lymph nodes, and spleen (1997)

The specificity and efficiency of extravasation of subsets of memory and naive lymphocytes into organized lymphoid tissues has been the subject of recent controversy, but has not been directly assessed in physiologic systems. Here, we compare the lymphoid organ homing of naive and phenotypically defined memory T cells, focusing on memory subsets differentially expressing the integrin receptor alpha4beta7, which is implicated in homing to mucosal sites. Naive T cells (CD44(low), Thy1+) home to all secondary lymphoid organs. Alpha4beta7(high) memory-phenotype (CD44(high)) T cells home to Peyer's patches as efficiently as naive lymphocytes, whereas alpha4beta7- memory-phenotype T cells are essentially excluded from entry into these mucosal lymphoid organs. In contrast, alpha4beta7- memory-phenotype cells home approximately twice as efficiently as alpha4beta7(high) T cells to peripheral lymph nodes, but only approximately 20% as well as naive T cells. Interestingly, the spleen recruits all three identified subsets with nearly equal efficiency. The relative subset localization is similar 2.5 h after injection and after overnight trafficking, suggesting that memory cells can directly extravasate from blood into Peyer's Patches and lymph nodes. We conclude that subsets of memory T cells defined by patterns of homing receptor expression display differential homing to organized lymphoid tissues, an ability that may facilitate homeostatic interactions and target contributions to specialized regional immune responses.
Associations between IgG reactivity to Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) antigens and Burkitt lymphoma in Ghana and Uganda case-control studies (2018)

Intramural Research Program, National Cancer Institute and National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services.
GRID codes (2009)

As storage systems grow in size and complexity, they are increasingly confronted with concurrent disk failures together with multiple unrecoverable sector errors. To ensure high data reliability and availability, erasure codes with high fault tolerance are required. In this article, we present a new family of erasure codes with high fault tolerance, named GRID codes. They are called such because they are a family of strip-based codes whose strips are arranged into multi-dimensional grids. In the construction of GRID codes, we first introduce a concept of matched codes and then discuss how to use matched codes to construct GRID codes. In addition, we propose an iterative reconstruction algorithm for GRID codes. We also discuss some important features of GRID codes. Finally, we compare GRID codes with several categories of existing codes. Our comparisons show that for large-scale storage systems, our GRID codes have attractive advantages over many existing erasure codes: (a) They are completely XOR-based and have very regular structures, ensuring easy implementation; (b) they can provide up to 15 and even higher fault tolerance; and (c) their storage efficiency can reach up to 80% and even higher. All the advantages make GRID codes more suitable for large-scale storage systems.
Heterogeneous susceptibility of circulating SIV isolate capsids to HIV-interacting factors (2013)

Circulating SIV present a variety of phenotypes with regard to CA-interacting restricting or facilitating factors. Altogether, we unveiled unidentified pathways for SIV CA, which could also be exploited by HIV in different cellular contexts, to drive entry into the nucleus. Our findings warrant a closer evaluation of other potential defenses against circulating SIV.
Hydrocarbon continuous-monitoring systems for hazardous-waste-incinerator emissions measurement (1991)

The U.S. Environmental Protection Agency has sponsored an extended laboratory and field evaluation of continuous emission monitoring systems available to measure hydrocarbon emissions from hazardous waste incinerators. Performance tests of calibration drift, calibration error, response time, and instrument sensitivity to various hydrocarbons were conducted during the laboratory evaluation and two six-week field tests. Comparisons were also made between hydrocarbon emissions as measured by heated and unheated sample delivery systems. Long-term measurement of hydrocarbon emissions using a heated sampling system and flame ionization detector has been difficult to achieve at hazardous waste incinerators. During this test program, it was demonstrated that it is possible to operate a heated hydrocarbon monitoring system continuously for extended time periods with no system repair or maintenance. A gas sampling system providing simultaneous carbon monoxide and oxygen emissions data was also operated during the field tests.
Enhanced Epithelial-Mesenchymal Transition-like Phenotype in N-Acetylglucosaminyltransferase V Transgenic Mouse Skin Promotes Wound Healing (2011)

N-Acetylglucosaminyltransferase V (GnT-V) catalyzes the β1,6 branching of N-acetylglucosamine on N-glycans. GnT-V expression is elevated during malignant transformation in various types of cancer. However, the mechanism by which GnT-V promotes cancer progression is unclear. To characterize the biological significance of GnT-V, we established GnT-V transgenic (Tg) mice, in which GnT-V is regulated by a β-actin promoter. No spontaneous cancer was detected in any organs of the GnT-V Tg mice. However, GnT-V expression was up-regulated in GnT-V Tg mouse skin, and cultured keratinocytes derived from these mice showed enhanced migration, which was associated with changes in E-cadherin localization and epithelial-mesenchymal transition (EMT). Further, EMT-associated factors snail, twist, and N-cadherin were up-regulated, and cutaneous wound healing was accelerated in vivo. We further investigated the detailed mechanisms of EMT by assessing EGF signaling and found up-regulated EGF receptor signaling in GnT-V Tg mouse keratinocytes. These findings indicate that GnT-V overexpression promotes EMT and keratinocyte migration in part through enhanced EGF receptor signaling.
Pressure fields from high-resolution time-resolved particle tracking velocimetry in 3D turbulent flows (2015)

We present the measurement of unsteady 3D pressure fields in turbulent flows. The pressure gradient field is obtained based on the material acceleration of single particle trajectories from high-density particle tracking velocimetry (PTV), assuming the governing momentum equation. For the integration of the pressure gradient, we propose a new method that is based on Helmholtz decomposition and integration in Fourier space. We show pressure fields for two experiments, a large-scale convective flow in air and a jet flow in water.
Smooth muscle cell immediate-early gene and growth factor activation follows vascular injury. A putative in vivo mechanism for autocrine growth. (1993)

To understand the molecular events governing smooth muscle cell (SMC) proliferation in vivo, immediate-early gene (IEG) expression was assessed and related to growth factor ligand and receptor mRNA and SMC DNA synthesis after aortic injury. Balloon catheter injury evoked increases in SMC c-myc and thrombospondin (tsp) within 2 hours. The induction of these IEGs was followed by elevated transcripts to platelet-derived growth factor-A (PDGF-A), transforming growth factor-beta 1 (TGF-beta 1) and a basic fibroblast growth factor (bFGF) receptor. Whereas PDGF type-beta receptor mRNA was demonstrated in SMCs from control and balloon-injured aortas, no detectable signal was observed for the PDGF type-alpha receptor. To explore the potential linkage between IEG products and growth factor mRNA expression, cycloheximide was employed to block early protein synthesis after balloon injury. Induction of PDGF-A and TGF-beta 1 was attenuated by cycloheximide, but bFGF induction was unaffected. Moreover, cycloheximide superinduced IEGs and revealed PDGF-B transcripts, which were otherwise undetected. Seven days after aortic injury, a spontaneous increase in c-myc and tsp mRNA was noted. This IEG reactivation was followed 12 hours later by a twofold increase in SMC DNA synthesis. These findings corroborate an autocrine mode of SMC proliferation in vivo and suggest the IEG products may control such growth by stimulating growth factor genes.
Metal-catalyzed organic reactions by Resonant Acoustic Mixing (2021)

We introduce catalytic organic synthesis by Resonant Acoustic Mixing (RAM): a mechanochemical methodology that does not require bulk solvent or milling media. Using as model reactions ruthenium-catalyzed ring-closing metathesis, ene-yne metathesis and copper-catalyzed sulfonamide-isocyanate coupling, we demonstrate RAM-based mechanochemical synthesis that is faster and operationally simpler than conventional ball milling. Moreover, the method can be readily scaled-up, as demonstrated by straightforward catalytic synthesis of the antidiabetic drug Tolbutamide from hundreds of milligrams to at least 10 grams, without any significant changes in reaction conditions.
A microbial expression system for high-level production of scFv HIV-neutralizing antibody fragments in Escherichia coli (2019)

Monoclonal antibodies (mABs) are of great biopharmaceutical importance for the diagnosis and treatment of diseases. However, their production in mammalian expression hosts usually requires extensive production times and is expensive. Escherichia coli has become a new platform for production of functional small antibody fragment variants. In this study, we have used a rhamnose-inducible expression system that allows precise control of protein expression levels. The system was first evaluated for the cytoplasmic production of super folder green fluorescence protein (sfGFP) in various production platforms and then for the periplasmic production of the anti-HIV single-chain variable antibody fragment (scFv) of PGT135. Anti-HIV broadly neutralizing antibodies, like PGT135, have potential for clinical use to prevent HIV transmission, to promote immune responses and to eradicate infected cells. Different concentrations of L-rhamnose resulted in the controlled production of both sfGFP and scFv PGT135 antibody. In addition, by optimizing the culture conditions, the amount of scFv PGT135 antibody that was expressed soluble or as inclusions bodies could be modulated. The proteins were produced in batch bioreactors, with yields of 4.9 g/L for sfGFP and 0.8 g/L for scFv. The functionality of the purified antibodies was demonstrated by their ability to neutralize a panel of different HIV variants in vitro. We expect that this expression system will prove very useful for the development of a more cost-effective production process for proteins and antibody fragments in microbial cells.
Using chronobiology-based second-generation artificial intelligence digital system for overcoming antimicrobial drug resistance in chronic infections (2023)

Antimicrobial resistance results from the widespread use of antimicrobial agents and is a significant obstacle to the effectiveness of these agents. Numerous methods are used to overcome this problem with moderate success. Besides efforts of antimicrobial stewards, several artificial intelligence (AI)-based technologies are being explored for preventing resistance development. These first-generation systems mainly focus on improving patients' adherence. Chronobiology is inherent in all biological systems. Host response to infections and pathogens activity are assumed to be affected by the circadian clock. This paper describes the problem of antimicrobial resistance and reviews some of the current AI technologies. We present the establishment of a second-generation AI chronobiology-based approach to help in preventing further resistance and possibly overcome existing resistance. An algorithm-controlled regimen that improves the long-term effectiveness of antimicrobial agents is being developed based on the implementation of variability in dosing and drug administration times. The method provides a means for ensuring a sustainable response and improved outcomes. Ongoing clinical trials determine the effectiveness of this second-generation system in chronic infections. Data from these studies are expected to shed light on a new aspect of resistance mechanisms and suggest methods for overcoming them.IMPORTANCE SECTIONThe paper presents the establishment of a second-generation AI chronobiology-based approach to help in preventing further resistance and possibly overcome existing resistance.Key messagesAntimicrobial resistance results from the widespread use of antimicrobial agents and is a significant obstacle to the effectiveness of these agents.We present the establishment of a second-generation AI chronobiology-based approach to help in preventing further resistance and possibly overcome existing resistance.
MSMO: Multimodal Summarization with Multimodal Output (2018)

Multimodal summarization has drawn much attention due to the rapid growth of multimedia data. The output of the current multimodal summarization systems is usually represented in texts. However, we have found through experiments that multimodal output can significantly improve user satisfaction for informativeness of summaries. In this paper, we propose a novel task, multimodal summarization with multimodal output (MSMO). To handle this task, we first collect a large-scale dataset for MSMO research. We then propose a multimodal attention model to jointly generate text and select the most relevant image from the multimodal input. Finally, to evaluate multimodal outputs, we construct a novel multimodal automatic evaluation (MMAE) method which considers both intramodality salience and intermodality relevance. The experimental results show the effectiveness of MMAE.
Prevalence and predictors of probable depression in prostate cancer survivors (2023)

Background: The early diagnosis and treatment of depression are cancer care priorities. These priorities are critical for prostate cancer survivors because men rarely seek mental health care. However, little is known about the epidemiology of depression in this patient population. The goal of this study was to describe the prevalence and predictors of probable depression in prostate cancer survivors. Methods: The data were from a population-based cohort of North Carolinian prostate cancer survivors who were enrolled from 2004 to 2007 in the North Carolina–Louisiana Prostate Cancer Project (n = 1031) and were prospectively followed annually from 2008 to 2011 in the Health Care Access and Prostate Cancer Treatment in North Carolina study (n = 805). Generalized estimating equations were used to evaluate an indicator of probable depression (Short Form 12 mental composite score ≤48.9; measured at enrollment and during the annual follow-up) as a function of individual-level characteristics within the longitudinal data set. Results: The prevalence of probable depression fell from 38% in the year of the cancer diagnosis to 20% 6 to 7 years later. Risk factors for probable depression throughout the study were African American race, unemployment, low annual income, younger age, recency of cancer diagnosis, past depression, comorbidities, treatment decisional regret, and nonadherence to exercise recommendations. Conclusions: Depression is a major challenge for prostate cancer survivors, particularly in the first 5 years after the cancer diagnosis. To the authors' knowledge, this is the first study to demonstrate an association between treatment decisional regret and probable depression.
Peripheral Type Benzodiazepine Receptors (1989)

Over the past two decades, deadly coronaviruses, with the most recent being the severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) 2019 pandemic, have majorly challenged public health. The path for virus invasion into humans and other ...Read More
Indications and range of surgery in the treatment of spine metastatic tumours. (2003)

Background. Spine is the most common place of metastatic tumors in the skeletal system. Due to diagnostic problems and the risk of quickly increasing neurological defects, the treatment of metastatic spine tumors is a significant clinical problem. The goal of surgical treatment is decreasing pain, neurological improvement and achieving full spinal stability. <br /> Material and methods. Material consists of 31 patients with metastases in spine, who underwent spine surgery. Tumors were placed in thoracic spine at 48% patients, at lumbar spine - 42% patients, and at cervical spine in 10% patients; one level was involved in 56% cases, two or more levels - in 44 % cases. Qualification for surgery contained: the type of primary tumor, the amount of metastases to the spine impairment of spinal biomechanics and overall patient's condition of the. Corporectomy with anterior stabilization (intervertebral cage) was performed at 13 patients, and with additional anterior implants at 2 cases. At 8 patients, with destabilization of posterior spinal column, in spite of corporectomy, posterior stabilization was done. Surgery from posterior approach was performed in 3 cases. <br /> Results. After operation, we noted pain relief at 34% of patients, while in 14% of them transient increase of pain occurred. Neurological status worsened after surgery at 1 patient. We achieved proper spine stabilization, without the need of use of external orthoses at 30 patients. At one patients, reoperation with change of implants and the range of stabilization was necessary. The amount of complications correlated with patient's general condition at the time of surgery.<br /> Conclusions. 1. The main condition of success in operative treatment of spinal metastatic tumors is individual patient's qualification for surgery, including the extent of disease and general patient's condition. 2. Good stabilization with use of implants is a necessary element of surgery of spinal metastases from both anterior and posterior approach.
A probabilistic framework for graph clustering (2005)

The paper describes a probabilistic framework for graph clustering. We commence from a set of pairwise distances between graph structures. From this set of distances, we use a mixture model to characterize the pairwise affinity of the different graphs. We present an EM-like algorithm for clustering the graphs by iteratively updating the elements of the affinity matrix. In the M-step we apply eigendcomposition to the affinity matrix to locate the principal clusters. In the M-step we update the affinity probabilities. We apply the resulting unsupervised clustering algorithm to two practical problems. The first of these involves locating shape-categories using shock trees extracted from 2D silhouettes. The second problem involves finding the view structure of a polyhedral object using the Delaunay triangulation of corner features.
Phase behavior and characterization of heptamethyltrisiloxane-based de Vries smectic liquid crystal by electro-optics, x rays, and dielectric spectroscopy (2017)

A heptamethyltrisiloxane liquid crystal (LC) exhibiting I-SmA^{*}-SmC^{*} phases has been characterized by calorimetry, polarizing microscopy, x-ray diffraction, electro-optics, and dielectric spectroscopy. Observations of a large electroclinic effect, a large increase in the birefringence (Δn) with electric field, a low shrinkage in the layer thickness (∼1.75%) at 20 °C below the SmA^{*}-SmC^{*} transition, and low values of the reduction factor (∼0.40) suggest that the SmA^{*} phase in this material is of the de Vries type. The reduction factor is a measure of the layer shrinkage in the SmC^{*} phase and it should be zero for an ideal de Vries. Moreover, a decrease in the magnitude of Δn with decreasing temperature indicates the presence of the temperature-dependent tilt angle in the SmA^{*} phase. The electro-optic behavior is explained by the generalized Langevin-Debye model as given by Shen et al. [Y. Shen et al., Phys. Rev. E 88, 062504 (2013)10.1103/PhysRevE.88.062504]. The soft-mode dielectric relaxation strength shows a critical behavior when the system goes from the SmA^{*} to the SmC^{*} phase.
Special issue on telematics communications and vehicular networking (2013)

This special issue on Telematics Communication and Vehicular Networks examines the critical issues involved with telematics such as vehicular network infrastructure, vehicular network communication protocols, and vehicular services and applications.