gebhart/patrepeval huggingface dataset:
Full Virulence of Pseudomonas aeruginosa Requires OprF (2010)

OprF is a general outer membrane porin of Pseudomonas aeruginosa, a well-known human opportunistic pathogen associated with severe hospital-acquired sepsis and chronic lung infections of cystic fibrosis patients. A multiphenotypic approach, based on the comparative study of a wild-type strain of P. aeruginosa, its isogenic oprF mutant, and an oprF-complemented strain, showed that OprF is required for P. aeruginosa virulence. The absence of OprF results in impaired adhesion to animal cells, secretion of ExoT and ExoS toxins through the type III secretion system (T3SS), and production of the quorum-sensing-dependent virulence factors pyocyanin, elastase, lectin PA-1L, and exotoxin A. Accordingly, in the oprF mutant, production of the signal molecules N-(3-oxododecanoyl)-l-homoserine lactone and N-butanoyl-l-homoserine lactone was found to be reduced and delayed, respectively. Pseudomonas quinolone signal (PQS) production was decreased, while its precursor, 4-hydroxy-2-heptylquinoline (HHQ), accumulated in the cells. Taken together, these results show the involvement of OprF in P. aeruginosa virulence, at least partly through modulation of the quorum-sensing network. This is the first study showing a link between OprF, PQS synthesis, T3SS, and virulence factor production, providing novel insights into virulence expression.
Tumor‐associated macrophages infiltrate plasmacytomas and can serve as cell carriers for oncolytic measles virotherapy of disseminated myeloma (2009)

In multiple myeloma, some of the neoplastic plasma cells are diffusely dispersed among the normal bone marrow cells (bone marrow resident), whereas others are located in discrete, well-vascularized solid tumors (plasmacytomas) that may originate in bone or soft tissue. Interactions between bone marrow-resident myeloma cells and bone marrow stromal cells (BMSCs) are important determinants of myeloma pathogenesis. However, little is known of the factors sustaining myeloma growth and cell viability at the centers of expanding plasmacytomas, where there are no BMSCs. Histologic sections of 22 plasmacytomas from myeloma patients were examined after immunostaining. Abundant CD68+, CD163+, S100-negative macrophage infiltrates were identified in all tumors, accompanied by scattered collections of CD3+ T lymphocytes. The CD68+ tumor-associated macrophages (TAM) accounted for 2-12% of nucleated cells and were evenly distributed through the parenchyma. The TAM generally had dendritic morphology, and each dendrite was in close contact with multiple plasma cells. In some cases, the TAM were strikingly clustered around CD34+ blood vessels. To determine whether cells of the monocytic lineage might be exploitable as carriers for delivery of therapeutic agents to plasmacytomas, primary human CD14+ cells were infected with oncolytic measles virus and administered intravenously to mice bearing KAS6/1 human myeloma xenografts. The cell carriers localized to KAS6/1 tumors, where they transferred MV infection to myeloma cells and prolonged the survival of mice bearing disseminated human myeloma disease. Thus, TAM are a universal stromal component of the plasmacytomas of myeloma patients and may offer a promising new target for therapeutic exploitation. Am. J. Hematol. 2009. (c) 2009 Wiley-Liss, Inc.
Analysis of Self-Attention Head Diversity for Conformer-based Automatic Speech Recognition (2022)

Attention layers are an integral part of modern end-to-end automatic speech recognition systems, for instance as part of the Transformer or Conformer architecture.Attention is typically multi-headed, where each head has an independent set of learned parameters and operates on the same input feature sequence.The output of multi-headed attention is a fusion of the outputs from the individual heads.We empirically analyze the diversity between representations produced by the different attention heads and demonstrate that the heads become highly correlated during the course of training.We investigate a few approaches to increasing attention head diversity, including using different attention mechanisms for each head and auxiliary training loss functions to promote head diversity.We show that introducing diversity-promoting auxiliary loss functions during training is a more effective approach, and obtain WER improvements of up to 6% relative on the Librispeech corpus.Finally, we draw a connection between the diversity of attention heads and the similarity of the gradients of head parameters.
Algorithms for tracking with an array of magnetic sensors (2008)

We consider the problem of tracking a magnetic target as it travels in a straight-line path in the vicinity of N magnetic sensors. The target is modeled as a magnetic dipole, and we study tracking algorithms when the sensors are total-field (scalar) magnetometers and vector magnetometers. A novel, computationally-efficient vector-field algorithm is presented that jointly processes the data from N sensors, yielding estimates of the track and the target dipole moment vector. Simulation examples are included to illustrate the performance of the total-field and vector algorithms.
Modified Magnesium Hydroxide Nanoparticles Inhibit the Inflammatory Response to Biodegradable Poly(lactide-co-glycolide) Implants (2018)

Biodegradable polymers have been extensively used in biomedical applications, ranging from regenerative medicine to medical devices. However, the acidic byproducts resulting from degradation can generate vigorous inflammatory reactions, often leading to clinical failure. We present an approach to prevent acid-induced inflammatory responses associated with biodegradable polymers, here poly(lactide- co-glycolide), by using oligo(lactide)-grafted magnesium hydroxide (Mg(OH)<sub>2</sub>) nanoparticles, which neutralize the acidic environment. In particular, we demonstrated that incorporating the modified Mg(OH)<sub>2</sub> nanoparticles within degradable coatings on drug-eluting arterial stents efficiently attenuates the inflammatory response and in-stent intimal thickening by more than 97 and 60%, respectively, in the porcine coronary artery, compared with that of drug-eluting stent control. We also observed that decreased inflammation allows better reconstruction of mouse renal glomeruli in a kidney tissue regeneration model. Such modified Mg(OH)<sub>2</sub> nanoparticles may be useful to extend the applicability and improve clinical success of biodegradable devices used in various biomedical fields.
Slow Onset Inhibitors of Bacterial Fatty Acid Biosynthesis: Residence Time, In Vivo Activity and In Vivo Imaging (2010)

The goal of our structure‐based drug discovery effort is to develop slow onset enzyme inhibitors, based on the premise that the long residence time of the compounds on the target is critical for in vivo activity. Targets for drug resistant bacterial infections include the enoyl‐ACP reductase and β‐ketoacyl‐ACP synthase enzymes in the bacterial fatty acid biosynthesis pathway. We have developed slow onset diaryl‐ether inhibitors of the enoyl‐ACP reductases from Francisella tularensis and Mycobacterium tuberculosis and have shown that the in vivo antibacterial activity of the compounds in animal models of infection correlates with their residence time on the enzyme targets. We are exploring the mechanistic basis for slow onset inhibition and are using this information to develop inhibitors with longer residence times. We have also developed methods to introduce short‐lived isotopes into these compounds and are using the labeled molecules to identify the target(s) for the inhibitors in live cells and to image drug distribution in vivo .
Enzymatically Synthesized Conducting Polyaniline Nanocomposites: A Solid‐State NMR Study (2003)

Abstract The chiral conducting polyaniline (PANI) nanocomposites [polyacrylic acid/polyaniline/(−) camphorsulphonic acid (CSA)] were synthesized using enzyme, horseradish peroxidase (HRP) in the aqueous buffer solution at pH 4.3. It appears that the enzyme HRP apart being a biocatalyst, plays an important role during the polymerization, which allows PANI to prefer a specific helical conformation whether the induced chirality in the monomer‐CSA complex is either by (+)CSA or (−)CSA. In this paper, we report, the structural characterization of these nanocomposites by solid‐state 13C cross‐polarization with magic angle spinning (CP/MAS) NMR techniques. The structural features of PANI in the conducting form of nanocomposite (as‐synthesized) are similar to that of enzymatically and chemically synthesized PANI. Preliminary data also suggest that some portion of nanocomposite samples are not completely doped. Dedoping of as‐synthesized PANI nanocomposite with aqueous NH4OH shows the spectral features that of the emeraldine base form. Solid‐state 13C NMR data suggest that it is possible to detach PAA and CSA from PANI in the nanocomposite material. Keywords: Solid‐state 13C NMR CP/MAS NMRConducting polyanilineNanocompositesEnzymatic polymerization Acknowledgments The authors thank the National Science Foundation for a research grant (Grant #DMR‐9986644). We thank Dr. Ramaswamy Nagarajan for conductivity measurement, Mr. Xiadong Wu and Mr. Jeff Njus for helpful discussions. This work is dedicated to memory of the late Professor S. K. Tripathy.
Investigating injury mechanism and occupant bmi for malleolar fractures in frontal motor vehicle collisions - biomed 2010. (2010)

Injury statistics show that lower extremity injuries follow second to head trauma in motor vehicle crashes. Fractures to the ankle/foot make up approximately 35% of all lower extremity injuries in motor vehicle crashes. Previous studies have shown that toe pan intrusion is one of the main causes of foot and ankle fractures in motor vehicle crashes (MVC). This study investigates injury mechanisms of malleolar fractures involving occupants enrolled in the Wake Forest University Crash Injury Research and Engineering Network (WFU CIREN) center. By narrowing cases to frontal impacts (+/- 20 degrees principal direction of force) with the case occupant as the driver with lower leg fractures, 16 cases are identified and investigated for trends in lower leg injury. Of these fractures, 81% of the occupants have a body mass index (BMI) greater than 25 kg/m2, with an average BMI of 32 kg/m2, which is obese. For occupants with malleolar fractures the average delta V is 44.1 kph (27.4 mph) and the average intrusion is 9.6 cm. Using radiology images of each ankle fracture in conjunction with interior vehicle evidence, injury mechanisms for malleolar fracture types are identified using the Lauge-Hansen and Weber classifications. The most common malleolar fracture type was supination-exorotation with a Weber B fibular fracture (4 cases). There were also four drivers that sustained trimalleolar fractures. Drivers sustaining lower leg fractures other than malleolar fractures had an average BMI of 30 kg/m2, an average delta V of 39.6 kph (24.6 mph), and average toe pan intrusion of 12.0 cm. Results show that the malleolar fracture and other lower leg fracture datasets have similar average delta Vs and toe pan intrusions, but the average BMI is slightly higher in the malleolar fracture group. These preliminary data suggest that occupants with increased BMI may be more susceptible to ankle fractures in frontal crashes, particularly malleolar fractures. The trends presented in this research will be used for the development of future studies for the enhancement of vehicle safety.
Efficient Multiple-Valued Signed-Digit Full Adder Based on NDR MOS Structures and its Application to an N-bit Current-Mode Constant-Time Adder (2007)

In this article, we present an efficient implementation for the current-mode radix-2 Signed-Digit Full Adder (SDFA). It is based on negative-differential-resistance (NDR) MOS structures. Simulations have been carried out using a 0.13-mu m SOI CMOS technology. Since it uses Dynamic Current-Mode Logic (DyCML) comparators and features a dual-rail structure, the NDR-MOS SDFA shows a higher speed and lower power consumption than previously reported implementations. It can be used to design an N-bit constant-time adder with a 227-ps delay and a power consumption of 33 mu W per digit at 2-GHz clock frequency. The 64-bit version exhibits higher performance than a state-of-the-art fully optimized 64-bit carry-select adder implemented on the same technology.
Spin-current emission governed by nonlinear spin dynamics (2015)

Coupling between conduction electrons and localized magnetization is responsible for a variety of phenomena in spintronic devices. This coupling enables to generate spin currents from dynamical magnetization. Due to the nonlinearity of magnetization dynamics, the spin-current emission through the dynamical spin-exchange coupling offers a route for nonlinear generation of spin currents. Here, we demonstrate spin-current emission governed by nonlinear magnetization dynamics in a metal/magnetic insulator bilayer. The spin-current emission from the magnetic insulator is probed by the inverse spin Hall effect, which demonstrates nontrivial temperature and excitation power dependences of the voltage generation. The experimental results reveal that nonlinear magnetization dynamics and enhanced spin-current emission due to magnon scatterings are triggered by decreasing temperature. This result illustrates the crucial role of the nonlinear magnon interactions in the spin-current emission driven by dynamical magnetization, or nonequilibrium magnons, from magnetic insulators.
Improved control strategies for the environment within cell culture bioreactors (2023)

This paper describes the development of improved control strategies for the standard environmental conditions in a fed-batch bioreactor used for monoclonal antibody cell culture. The consequences of relying on fixed parameter PID based controllers are considered and poor performance is demonstrated as a consequence of non-linearity and loop interactions. The benefits from adopting a more sophisticated control strategy are considered. Model Predictive Control (MPC) relies on a process model that can be identified from small system perturbations. It considers the predicted longer-term response and consequently can deliver improved control and satisfy user defined constraints. Results from experimental trials demonstrate the capability of MPC and the merits are discussed with regards to industrial application.
<title>Photodiode gain calibration of flat dynamic x-ray detectors using reset light</title> (2002)

Due to spatial gain differences of the photo diodes and inhomogeneities in the converter (CsI) a gain calibration is usually applied for flat dynamic X-ray detectors. This calibration is calculated from X-ray images. Using the reset light, integrated in the detector, a calibration of the photo diode gain is possible. Since neither the reset light intensity nor the X-ray field distribution in combination with the converter efficiency are spatially homogeneous the ratio of these two effects has to be measured and stored once in an X-ray reset-light map. In a reset light calibration the photo diode gain will be estimated and the final calibration is then calculated from this gain image and the stored X-ray reset-light map. The reset light gain image contains the same information as the X-ray image except the influence of the scintillator which should be very stable over time. Changes in the photo diode gain can easily and automatically be corrected using the reset light calibration. Defect pixels can be determined from the reset light gain images. This method would allow a continuous calibration during the lifetime of the detector without the need for any user interaction.
Clinical Predictors of Cardiovascular Implantable Electronic Device‐Related Infective Endocarditis (2011)

Certain comorbid conditions and systemic manifestations of infection were associated with CIED-IE. In contrast, pocket site infection was negatively associated with CIED-IE. These findings should assist clinicians in identifying patients who would more likely benefit from further investigation of CIED-IE with transesophageal echocardiography.
Was Coccidioides a Pre-Columbian Hitchhiker to Southcentral Washington? (2023)

<i>Coccidioides immitis</i>, a pathogenic environmental fungus that causes Valley fever (coccidioidomycosis) primarily in the American Southwest and parts of Central and South America, has emerged over the past 12 years in the Columbia River Basin region, near the confluence with the Yakima River, in southcentral Washington state, USA. An initial autochthonous Washington human case was found in 2010, stemming from a wound derived from soil contamination during an all-terrain vehicle crash. Subsequent analysis identified multiple positive soil samples from the park where the crash occurred (near the Columbia River in Kennewick, WA), and from another riverside location several kilometers upstream from the park location. Intensified disease surveillance identified several more cases of coccidioidomycosis in the region that lacked any relevant travel history to known endemic locales. Genomic analysis of both patient and soil isolates from the Washington cases determined that all samples from the region are phylogenetically closely related. Given the genomic and the epidemiological link between case and environment, <i>C. immitis</i> was declared to be a newly endemic fungus in the region, spawning many questions as to the scope of its presence, the causes of its recent emergence, and what it predicts about the changing landscape of this disease. Here, we review this discovery through a paleo-epidemiological lens in the context of what is known about <i>C. immitis</i> biology and pathogenesis and propose a novel hypothesis for the cause of the emergence in southcentral Washington. We also try to place it in the context of our evolving understanding of this regionally specific pathogenic fungus.
Reconstitution of t cell-depleted spleen cell populations by factors derived from t cells. I. Conditions for the production of active t cell supernatants. (1973)

At least part of the interaction between bone marrow-derived (B) and thymus-derived (T) lymphocytes during the initiation of an in vitro immune response to sheep erythrocytes (SRBC) is mediated by a nonspecific activity released from antigen-stimulated T cells. The release of the activity requires stimulation with specific antigen, but the activity produced by different antigens can reconstitute an in vitro response to SRBC. The assay used to investigate the activity has been the reconstitution of spleen cell populations treated with anti-θ antibody. Preparations active in this assay can also initiate immune responses in B cells obtained from thymectomized, irradiated, bone marrow-reconstituted mice and in B cells separated from normal bone marrow. Three pieces of evidence suggest that cells liberating the active factors are T cells. First, pretreatment of such a population of cells with anti-θ antibody abolishes its capacity to produce the activity. Second, the sedimentation profile of SRBC-stimulated factor-producing cells is identical to the sedimentation profile of T cells required to initiate anti-SRBC antibody production in vitro. Third, the sedimentation profile of factor-producing cells in a population of alloantigen-stimulated cells is identical to the sedimentation profile of cells involved in cell-mediated immunity in the same population.
Performance Evaluation of ATSC 3.0 Preamble for TxID Signal-Injected Use Cases (2022)

Advanced Systems Television Committee (ATSC) 3.0, the recently developed next-generation digital terrestrial television (DTT) standard, supports an enhanced single frequency network (SFN) for efficient spectrum usage. For constructing a nationwide SFN, transmitter identification (TxID) is a key technology that enables controlling transmitters and analyzing propagation channels between individual transmitters and a receiver. However, since the TxID signal is superimposed on the first preamble symbol of the host ATSC signal, the preamble may be contaminated depending on the injection level of the TxID signal. This paper describes the effects of the TxID signal on the preamble symbol according to the injection levels and protection modes from theoretical and practical perspectives.
Catechol-based layer-by-layer assembly of composite coatings: a versatile platform to hierarchical nano-materials (2015)

Inspired by the marine mussel's ability to adhere to surfaces underwater, an aqueous catechol-based dip coating platform was developed. Using a catechol-functionalized polyacrylamide binder in combination with inorganic nanoparticles enables the facile fabrication of robust composite coatings via a layer-by-layer process. This modular assembly of well-defined building blocks provides a versatile alternative to electrostatic driven approaches with layer thickness and refractive indices being readily tunable. The platform nature of this approach enables the fabrication of hierarchically ordered nano-materials such as Bragg stacks.
Asymmetric Synthesis of a Potent, Aminopiperidine-Fused Imidazopyridine Dipeptidyl Peptidase IV Inhibitor (2010)

A practical asymmetric synthesis of a novel aminopiperidine-fused imidazopyridine dipeptidyl peptidase IV (DPP-4) inhibitor 1 has been developed. Application of a unique three-component cascade coupling with chiral nitro diester 7, which is easily accessed via a highly enantioselective Michael addition of dimethyl malonate to a nitrostyrene, allows for the assembly of the functionalized piperidinone skeleton in one pot. Through a base-catalyzed, dynamic crystallization-driven process, the cis-piperidionone 16a is epimerized to the desired trans isomer 16b, which is directly crystallized from the crude reaction stream in high yield and purity. Isomerization of the allylamide 16b in the presence of RhCl(3) is achieved without any epimerization of the acid/base labile stereogenic center adjacent to the nitro group on the piperidinone ring, while the undesired enamine intermediate is consumed to <0.5% by utilizing a trace amount of HCl generated from RhCl(3). The amino lactam 4, obtained through hydrogenation and hydrolysis, is isolated as its crystalline pTSA salt from the reaction solution directly, as such intramolecular transamidation has been dramatically suppressed via kinetic control. Finally, a Cu(I) catalyzed coupling-cyclization allows for the formation of the tricyclic structure of the potent DPP-4 inhibitor 1. The synthesis, which is suitable for large scale preparation, is accomplished in 23% overall yield.
Do levels of airborne grass pollen influence asthma hospital admissions? (2007)

Our findings suggest that grass pollen levels influence asthma hospital admissions. High grass pollen days, currently defined as more than 50 grains/m3, are days when most sensitive individuals will experience allergic symptoms. However, some asthmatic patients may be at a significant risk even when airborne grass pollen levels are below this level. Patients with pollen allergies and asthma would be advised to take additional preventive medication at lower ambient concentrations.