gebhart/patrepeval huggingface dataset:
Structure of Ddn, the Deazaflavin-Dependent Nitroreductase from Mycobacterium tuberculosis Involved in Bioreductive Activation of PA-824 (2012)

Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F(420) deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F(420) and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.
Filterless Reception of 80×112 Gb/s WDM Channels Using Single Ended Photodiodes and Digital Interference Reduction (2012)

A cost-effective filterless coherent receiving architecture is proposed using single-ended photodiodes. By dedicating two additional direct detection signal lanes to reject signal-signal interference in the digital domain, we successfully achieved the reception of 80×112-Gb/s WDM channels after 2000-km transmission with only 1.7-dB Q penalty.
In vitro PUVA treatment triggers calreticulin exposition and HMGB1 release by dying T lymphocytes in GVHD: New insights in extracorporeal photopheresis (2019)

Altogether, in our experimental settings, in vitro PUVA-treatment induces a partially immunogenic phenotype allowing phagocytosis of apoptotic cells by macrophages and DC, however not sufficient to induce dendritic cell maturation and T cell activation. These data refine current models of ECP-mediated immune modulation and emphasize the need to further analyze PUVA-treated cell interactions with immune cells.
Neutrophil-Specific Antigens: Immunobiology, Genetics and Roles in Clinical Disorders (2022)

Neutrophils are the most abundant nucleated cells in blood circulation and play important roles in the innate and adaptive immune responses. Neutrophil-specific antigens, only expressed on neutrophils, are glycoproteins originally identified in studies on neonatal neutropenia due to fetal-maternal incompatibility and autoimmune neutropenia of infancy. The most investigated neutrophil–specific antigens are the NA and NB antigens that their incompatibilities also cause transfusion-induced febrile reactions and acute lung injury, a potentially fatal reaction, and in bone marrow transplantation, causing graft rejection. NA antigens are members of the immunoglobulin superfamily and are low-affinity Fc-receptors FcγRIIIb (CD16b). Fc receptors connect the F(ab), the antigen-binding fragment of the antibody molecules, to neutrophils and lead them to recognize and phagocytize the targeted antigens. The NB (CD177) antigen belongs to the urokinase-type Plasminogen Activator Receptor Superfamily (uPAR, CD59, Ly6), but its specific functions have not been fully determined. It is known, however, that NB antigen binds proteinase-3 (PR3 to the neutrophil membrane), a serine protease. In clinical studies, it was also demonstrated that NB expression is highly elevated in Polycythemia Vera and is unexpectedly expressed in some cancer tissues. Neutrophil-specific antigens are examples of antigens that have important biological and clinical activities beyond antigenicity.
Music models for music-speech separation (2012)

We consider the task of speech recognition with loud music background interference. We use model-based music-speech separation and train GMM models for music on the audio prior to speech. We show over 8% relative improvement in WER at 10 dB SNR for a real world Voice Search ASR system. We investigate the relationship between ASR accuracy and the amount of music background used as prologue and the the size of music models. Our study shows that performance peaks when using a music prologue of around 6 seconds to train the music model. We hypothesize that this is due to the dynamic nature of music and the structure of popular music. Adding more history beyond a certain point does not improve results. Additionally, we show moderately sized 8-component music GMM models suffice to model this amount of music prologue.
Binding of laminin and fibronectin by the trypsin-resistant major structural domain of the crystalline virulence surface array protein of Aeromonas salmonicida. (1992)

The surface of Aeromonas salmonicida is covered by a tetragonal paracrystalline array (A-layer) composed of a single protein (A-protein, Mr = 50,778). This array is a virulence factor. Cells containing A-layer and isolated A-layer sheets specifically bound laminin and fibronectin with high affinity. Binding by cells was inactivated by selective removal of A-layer at pH 2.2, and neither isogenic A-layer-deficient A. salmonicida mutants nor tetragonal paracrystalline array producing Aeromonas hydrophila and Aeromonas sobria strains bound either matrix protein. Laminin binding was by a single class of high affinity interactions (cell Kd = 1.52 nM), whereas fibronectin bound via two classes of interactions, one being similar to that of laminin (cell Class 2 interaction Kd = 6.6 nM). This interaction with both proteins was partly hydrophobic. The Class 1 fibronectin interaction was of lower affinity (cell Kd = 218 nM) and distinct. Purified A-protein inhibited binding of both matrix proteins to A-layer, and trypsin cleavage localized the matrix-protein binding region to the N-terminal major trypsin-resistant structural domain of A-protein. Monoclonal antibody inhibition studies showed that A-protein was folded such that Fabs of only one of two antibodies with epitopes mapping C-terminal to this trypsin-resistant peptide was capable of blocking binding.
A condition-based monitoring system for mechanical seals (1998)

The importance of condition-based maintenance strategies is constantly growing, driven by both economic and safety factors. Mechanical seals are still one of the main components in refineries and chemical plants for which no condition-based maintenance commonly exists. Based on its mechanical seal experience, Flexibox decided to develop and offer this tool to its customers.
The Large Pharmaceutical Company Perspective (2017)

arge pharmaceutical companies conduct clinical trials to evaluate efficacy and identify safety issues for candidate drugs as effectively, efficiently, and expeditiously as possible, while addressing simultaneously the requirements of regulatory authorities across the globe. To put the fewest people at risk and to learn the most, these trials often are configured to provide evidence for health care providers, regulatory approval, and reimbursement from health agencies. Because there are so many unknowns, pharmaceutical research and development is a high-risk business with the highest failure rate for new product candidates of any industry.
Calmodulin binding properties of peptide analogues and fragments of the calmodulin-binding domain of simian immunodeficiency virus transmembrane glycoprotein 41 (2000)

The calcium-regulatory protein calmodulin (CaM) can bind with high affinity to a region in the cytoplasmic C-terminal tail of glycoprotein 41 of simian immunodeficiency virus (SIV). The amino acid sequence of this region is (1)DLWETLRRGGRW(13)ILAIPRRIRQGLELT(28)L. In this work, we have used near- and far-uv CD, and fluorescence spectroscopy, to study the orientation of this peptide with respect to CaM. We have also studied biosynthetically carbon-13 methyl-Met calmodulin by (1)H, (13)C heteronuclear multiple quantum coherence NMR spectroscopy. Two Trp-substituted peptides, SIV-W3F and SIV-W12F, were utilized in addition to the intact SIV peptide. Two half-peptides, SIV-N (residues 1-13) and SIV-C (residues 13-28) were also synthesized and studied. The spectroscopic results obtained with the SIV-W3F and SIV-W12F peptides were generally consistent with those obtained for the native SIV peptide. Like the native peptide, these two analogues bind with an alpha-helical structure as shown by CD spectroscopy. Fluorescence intermolecular quenching studies suggested binding of Trp3 to the C-lobe of CaM. Our NMR results show that SIV-N can bind to both lobes of calcium-CaM, and that it strongly favors binding to the C-terminal hydrophobic region of CaM. The SIV-C peptide binds with relatively low affinity to both halves of the protein. These data reveal that the intact SIV peptide binds with its N-terminal region to the carboxy-terminal region of CaM, and this interaction initiates the binding of the peptide. This orientation is similar to that of most other CaM-binding domains.
SUPERFICIAL FEMORAL ARTERY ANEURYSMAL DEGENERATION — SIXTEEN YEARS AFTER SUPERFICIAL FEMORAL ARTERY ENDARTERECTOMY AND VEIN PATCH ANGIOPLASTY (2019)

Superficial femoral artery (SFA) aneurysms are rare clinical disorders, with few case reports and small series published concerning atherosclerotic aneurysms. We report a clinical case a giant aneurysm of the SFA, in a patient previously submitted to extensive SFA endarterectomy and vein angioplasty. A 73-year-old man presented at a routine vascular surgery consultation. The patient had been submitted to a right SFA endartectomy and vein patch angioplasty, sixteen years ago, for intermittent claudication. Physical examination demon- strated a large pulsatile mass of the right thigh. His right pedal pulse was palpable. Ultrasound and computed tomography scan confirmed a 78x71x240mm aneurysm of the right superficial femoral artery. He was proposed to aneurysmectomy and femoro-popliteal bypass. During operative intervention, proximal and distal control was obtained and the aneurysm opened. A large amount of thrombus was removed and a femoro-popliteal bypass was performed using the ipsilateral great saphenous vein. The postoperative period was uneventful, as was the patient recovery. In our report, the aneurysmal area matched precisely to the endarterectomised area and no other aneurysms were found. So we are facing an uncommon case of a SFA degeneration into a giant aneurysm after extensive endarterectomy and vein angioplasty.
Projectively invariant intersection detections for solid modeling (1994)

An intersection detection method for solid modeling which is invariant under projective transformations is presented. We redefine the fundamental geometric figures necessary to describe solid models and their dual figures in a homogeneous coordinate representation. Then we derive conditions, which are projectively invariant, for intersections between these primitives. We will show that a geometric processor based on the 4 x 4 determinant method is applicable to a wide range of problems with little modification. This method has applications in intersection detections of rational parametric curves and surfaces and hidden-line/surface removal algorithms.
3D Audio and Acoustic Environment Modeling (1999)

Recently, there has been a proliferation of... This paper describes the 3D audio and acoustic environment modeling technology developed by Wave Arts, Inc. Wave Arts technology is the result of extensive research and development by Bill Gardner, a graduate of the MIT Media Lab. Dr. Gardner&amp;apos;s research at the Media Lab focussed on the key technologies of 3D audio: binaural synthesis [8,11,13], crosstalk cancellation [9,11-13], and reverberation algorithms [4,5,7,10]. The Wave Arts 3D technology has recently been incorporated into the InMotion 3D Audio Producer software, developed jointly with Human Machine Interfaces, Inc. This paper both gives a...
Isolation of the Spermatogonial Stem Cell-Containing Fraction from Testes (2017)

A testis cell fraction enriched for spermatogonial stem cells (SSCs) compared with the unfractionated total testis cell population can be isolated from testes after birth and adult stages. This protocol involves dissociating the seminiferous tubules into a single-cell suspension, using enzymes and mechanical disruption. This is followed by the selection of the Thy1<sup>+</sup> cell fraction that contains nearly the entire SSC population and is enriched for these cells compared with the total testis cell population. This isolated fraction can be used for molecular studies, transfer into culture to establish primary cultures, or transplantation into the testes of recipients for spermatogenesis. Typically, if the SSCs are destined for transplantation, a marker is included to visualize the clones of spermatogenesis (e.g., <i>lacZ</i> or green fluorescent protein [GFP] transgenes). It is important to note that the isolated Thy1<sup>+</sup> cell fraction does not consist of pure SSCs and that most germ cells are non-stem-cell progenitors, and a smaller portion of the population is somatic cells.
Big data challenges in simulation-based science (2014)

Data-related challenges are quickly dominating computational and data-enabled sciences, and are limiting the potential impact of scientific applications enabled by current and emerging high-performance distributed computing environments. These data-intensive application workflows involve dynamic coordination, interactions and data coupling between multiple application process that run at scale on different resources, and with services for monitoring, analysis and visualization and archiving. In this talk I will explore data grand challenges in simulation-based science and investigate how solutions based on data sharing abstractions, managed data pipelines, in-memory data-staging, in-situ placement and execution, and in-transit data processing can be used to address these data challenges at extreme scales.
The Fabrication of Gold Nanoparticle Assemblies on the Functionalized Surface Patterned by AFM Lithography (2001)

Abstract Selective deposition of gold particles on a patterned substrate was studied for fabrication of a single electrons transistor. In the present study, a selective positioning technique was achieved using atomic force microscope (AFM). Various self-assembled monolayers (SAMs) on silicon surface such as hexamethyldisilazane (HMDS) and octadecyl dimethylmethoxy silane (ODMS) SAMs were prepared as a system for AFM lithography. A uniform pattern was engraved on the SAMs. The selective deposition of gold was efficiently accomplished. This gold particle assembly was characterized by AFM. Key Words: self-assembled monolayers (SAMs)atomic force microscope (AFMnanolithographygold nanoparticle
The Influence of Low-Temperature Disintegration on the Co-Fermentation Process of Distillation Residue and Waste-Activated Sludge (2022)

Innovative low-temperature disintegration (process temperature 55 °C and oxygen concentration 0.2 mg/dm3) can be an economically rational technology to intensifying energy production from renewable sources. The proposed process can achieve a degree of disintegration—under optimal conditions—of about 50%, which is excellent when compared with other methods of feed pre-treatment. The low-temperature disintegration of distillation residue and waste-activated sludge before the co-fermentation process increased biogas production by 30% and methane production by 65% (over a 26 d duration). The obtained results confirm that the low-temperature disintegration method can be effectively used to pre-prepare this type of feed. At the same time, it was discovered that the Gompertz model can be used to mathematically describe the biogas accumulation curves in the methane co-fermentation processes of the tested feeds (the correlation coefficients were higher than 0.98).
A Fast Response Current-Compensation Circuit for POL (2006)

A current-compensation circuit system for POLs is introduced. The proposed circuit employs MOSFETs, resistors and capacitors without any discrete magnetic devices. The system is activated only during transient responses and its total power loss is very small. Simulation results revealed that the output POL voltage is maintained within 5 % of 1.5 V during a load change between 1 A and 10 A
62541 Continuity of Care for Patients with Chronic Gastrointestinal Disease: A Latent Class Analysis of Patients With High-Intensity Specialty Care Needs (2021)

ABSTRACT IMPACT: Grouping patients with potentially high intensity specialty care needs based on their propensity for healthcare continuity patterns can inform the development of personalized care coordination and care navigation interventions OBJECTIVES/GOALS: To examine variation in healthcare continuity patterns across primary care, mental health care, and specialty care for a patient population with chronic gastrointestinal conditions and a high risk for healthcare utilization. METHODS/STUDY POPULATION: We analyzed data for Veterans Affairs patients with chronic gastrointestinal disease (cirrhosis, inflammatory bowel disease, chronic pancreatitis) whose 1-year hospitalization risk was ≥90th percentile in 2014, and who had a minimum of 4 office visits. To assess continuity, we examined frequency of office visits, number of outpatient providers, and two established continuity of care measures (the usual provider of care index and the Bice-Boxerman continuity of care index) over 12 months. We used latent class analysis to categorize patients into classes based on overall, primary care (PCP)-specific, gastroenterology (GI)-specific, and mental health specific-healthcare continuity patterns. RESULTS/ANTICIPATED RESULTS: The 26,751 Veterans in the analytic cohort had a mean of 13.3 (sd 8.63) office visits and 7.2 (sd 3.83) providers per patient. Patients were classified into five phenotypes: (1) moderate overall use and continuity; (2) low overall continuity of care; (3) high GI- and PCP-specific continuity of care; (4) low overall continuity of care with some mental health use; and (5) high utilization with substantial mental health use. In the subsequent year, 11,259 (42.1%) patients had a hospitalization and 16,167 (60.4%) had an emergency department visit. These groups varied in their sociodemographic and clinical characteristics, and in their risk for hospitalization and emergency department use. DISCUSSION/SIGNIFICANCE OF FINDINGS: Latent class analysis revealed five distinct primary and specialty care utilization patterns. Grouping patients with high intensity specialty care needs based on their propensity for healthcare continuity patterns can inform the development of personalized care navigation interventions.
Influence of Extracted Solute on the Organization of a Monoamide Organic Solution (2012)

The amounts of extracted water, nitric acid and uranyl nitrate by organic phases of 0.5 mol.L-1 N,N-di–(ethylhexyl)isobutyramide (DEHiBA) in heptane have been measured experimentally. With the aim of investigating the influence of the solutes on the aggregation in these organic phases, Vapor Pressure Osmometry (VPO) and Small Angle X–rays Scattering (SAXS) measurements were carried out. The extraction of the different solutes promotes the aggregation in the order water < nitric acid < uranyl nitrate. Water extraction according to water activity seems to indicate the absence of chemical association between water and DEHiBA. The presence of nitric acid leads to the formation of small aggregates while uranyl extraction increases the organization of the organic solutions. This study is the first step to understand and quantify aggregation phenomenon in monoamide organic phases after solute extraction, which could explain the particular physical chemical behavior of such systems.
Progress in research on ice accretions on overhead transmission lines and its influence on mechanical and insulating performance (2012)

传播线上的大气的冰生长具有到电力系统的服务的安全的大危险。这篇论文在在传播线的机械、电的表演上在传播线和冰的效果上处理冰生长的形成的研究考察进步。结果证明传播线上的冰生长能被分成五种类型：呆滞，难白霜，软白霜，灰白的霜，和雪和冻雨。在冰生长的所有类型，呆滞在湿政体成年具有到传播线的最大的危险。气象学的条件，地面和地理条件，和一些另外的因素显著地影响冰累积速度和冰数量。由于严重糖衣的机械性质和电的性质的激烈的减少是为冰事故的主要原因。冰，不均匀的冰生长，和流的异步的冰的数量能更加改变售票员紧张，售票员下垂，跨度，绝缘体绳的排水量，和紧张差别的变化数量。冰，冰累积的一致性，和冻结水的传导性的数量和类型在盖住冰的绝缘体的飞弧电压上有重要影响。
Exercise capacity at 18 years of age in two extremely preterm born cohorts from the 1980's and 1990's (2014)

Introduction Physical activity (PA) contributes to a healthy lifestyle; however, in subjects born extremely preterm (EP) both reduced PA and exercise capacity has been reported. Aim To examine relationships between PA and exercise capacity in adolescents born EP and at term in two different decades. Methods Two area-based cohorts born at gestational age ≤28 weeks or with birth weight ≤1000 grams in 1982-85 and 1991-92 and matched term-born controls were examined with standardized maximal cardiopulmonary treadmill exercise tests at 18 years of age in 2001 and 2008, respectively. Background data were obtained from questionnaires, and statistical analyses were adjusted for gender. Results In the 1980-cohort (40/46 born EP vs. 46/46 controls) mean peakVO 2 (ml/kg/min) was 47.1 vs. 49.3 (p=0.226), peakVO 2 (L/min) 3.0 vs. 3.3 (p=0.012) and the treadmill distance (meters) 997 vs. 1079 (p=0.062). In the 1990-cohort (26/31 born EP vs. 22/28 controls) the respective results were 42.3 vs. 45.3 (p=0.040), 2.7 vs. 3.0 (p&amp;lt;0.001) and 915 vs. 1017 (p=0.022). Exercise capacity was similar in term controls born in the two decades, whereas mean peakVO 2 (ml/kg/min) was lower in the group born EP in the 1990's (p=0.032); however, interaction terms were not significant. PA was higher in the 1990-cohort (p=0.002), but similarly and positively associated with exercise capacity in both cohorts. Conclusion Compared to controls born at term, exercise capacity was modestly reduced in 18 year old subjects born EP, more so for those born in the 1990's than in the 1980's. PA and peakVO 2 were similarly associated in adolescents born EP and at term in both decades indicating similar benefits from PA.
SIGNIFICANCE OF REQUIREMENTS FOR THE IMPLEMENTATION OF NEW TECHNOLOGIES USING SHAPE MEMORY TECHNOLOGY (2011)

In this paper the assumption of a conflict between existing requirements and the application of new technologies will be illustrated by using examples based on shape memory technology. For this purpose, two product concepts are analyzed. Starting with the planning phase and the definition of system requirements, the described design processes also include conceptual, embodiment and detail design phases. Special attention is paid to the specification of requirements and their effect on the respective product concept. The aim of this paper is to identify influences on the product concept caused by the conflict between existing requirements and the application of new technologies. Certain requirements, e.g. historically based requirements, prevent the application of those new technologies in many cases. Therefore, the application of new technologies in combination with established requirements is investigated and then re-evaluated after the adaption of critical requirements.
Access to 3‐Methyl‐4‐methylene‐N‐tosylpyrrolidine and 3,4‐Dimethyl‐N‐tosylpyrroline by Ruthenium‐Catalyzed Cascade Cycloisomerization/Isomerization Reactions. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Mesenchymal stem cells protect against acetaminophen hepatotoxicity by secreting regenerative cytokine hepatocyte growth factor (2022)

MSCs are comparable to NAC against APAP-induced liver failure by secreting HGF with less regenerative retardation concerns, thus facilitating the application of MSCs in clinical therapy for APAP liver failure.