gebhart/patrepeval huggingface dataset:
Reduction of Clofazimine by Mycobacterial Type 2 NADH:Quinone Oxidoreductase (2010)

The mechanism of action of clofazimine (CFZ), an antimycobacterial drug with a long history, is not well understood. The present study describes a redox cycling pathway that involves the enzymatic reduction of CFZ by NDH-2, the primary respiratory chain NADH:quinone oxidoreductase of mycobacteria and nonenzymatic oxidation of reduced CFZ by O(2) yielding CFZ and reactive oxygen species (ROS). This pathway was demonstrated using isolated membranes and purified recombinant NDH-2. The reduction and oxidation of CFZ was measured spectrally, and the production of ROS was measured using a coupled assay system with Amplex Red. Supporting the ROS-based killing mechanism, bacteria grown in the presence of antioxidants are more resistant to CFZ. CFZ-mediated increase in NADH oxidation and ROS production were not observed in membranes from three different Gram-negative bacteria but was observed in Staphylococcus aureus and Saccharomyces cerevisiae, which is consistent with the known antimicrobial specificity of CFZ. A more soluble analog of CFZ, KS6, was synthesized and was shown to have the same activities as CFZ. These studies describe a pathway for a continuous and high rate of reactive oxygen species production in Mycobacterium smegmatis treated with CFZ and a CFZ analog as well as evidence that cell death produced by these agents are related to the production of these radical species.
Integrated-optic spectrum analyzer: a first demonstration (1981)

This paper reports the first demonstration of a fully integrated optical spectrum analyzer (IOSA) using a GaAIAs semiconductor laser, a LiNbO3 integrated optic Chip, and a silicon detector/CCD array chip. The complete device was delivered to the Air Force Avionics Laboratory. This device exhibited a 3-dB bandwidth of 280 MHz with a diffraction efficiency of 5% (at 500-MW rf power and λ0 = 0.82 μm).
Osteoid osteoma: percutaneous radio-frequency ablation. (1995)

Radio-frequency ablation of osteoid osteoma is a promising alternative to surgery in selected patients.
Investigating deep neural network based transforms of robust audio features for LVCSR (2013)

Micro-modulation components such as the formant frequencies are very important characteristics of spoken speech that have allowed great performance improvements in small-vocabulary ASR tasks. Yet they have limited use in large vocabulary ASR applications. To enable the successful application, in real-life tasks, of these frequency measures, we investigate their combination with traditional features (MFCC's and PLP's) by linear (e.g. HDA), and non-linear (bottleneck MLP) feature transforms. Our experiments show that such integration, using non-linear MLP-based transforms, of micro-modulation and cepstral features greatly improves the ASR with respect to the cepstral features alone. We have applied this novel feature extraction scheme onto two very different tasks, i.e. a clean speech task (DARPA-WSJ) and a real-life, open-vocabulary, mobile search task (Speak4it <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SM</sup> ), always reporting improved performance. We report relative error rate reduction of 15% for the Speak4it <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SM</sup> task, and similar improvements, up to 21%, for the WSJ task.
Molecular Cloning, Nucleotide Sequence, and Expression in <i>Escherichia coli</i> of a Hemolytic Toxin (Aerolysin) Gene from <i>Aeromonas trota</i> (1998)

Aeromonas trota AK2, which was derived from ATCC 49659 and produces the extracellular pore-forming hemolytic toxin aerolysin, was mutagenized with the transposon mini-Tn5Km1 to generate a hemolysin-deficient mutant, designated strain AK253. Southern blotting data indicated that an 8.7-kb NotI fragment of the genomic DNA of strain AK253 contained the kanamycin resistance gene of mini-Tn5Km1. The 8.7-kb NotI DNA fragment was cloned into the vector pGEM5Zf(-) by selecting for kanamycin resistance, and the resultant clone, pAK71, showed aerolysin activity in Escherichia coli JM109. The nucleotide sequence of the aerA gene, located on the 1.8-kb ApaI-EcoRI fragment, was determined to consist of 1,479 bp and to have an ATG initiation codon and a TAA termination codon. An in vitro coupled transcription-translation analysis of the 1.8-kb region suggested that the aerA gene codes for a 54-kDa protein, in agreement with nucleotide sequence data. The deduced amino acid sequence of the aerA gene product of A. trota exhibited 99% homology with the amino acid sequence of the aerA product of Aeromonas sobria AB3 and 57% homology with the amino acid sequences of the products of the aerA genes of Aeromonas salmonicida 17-2 and A. sobria 33.
Sequentially acting Sox transcription factors in neural lineage development (2011)

Pluripotent embryonic stem (ES) cells can generate all cell types, but how cell lineages are initially specified and maintained during development remains largely unknown. Different classes of Sox transcription factors are expressed during neurogenesis and have been assigned important roles from early lineage specification to neuronal differentiation. Here we characterize the genome-wide binding for Sox2, Sox3, and Sox11, which have vital functions in ES cells, neural precursor cells (NPCs), and maturing neurons, respectively. The data demonstrate that Sox factor binding depends on developmental stage-specific constraints and reveal a remarkable sequential binding of Sox proteins to a common set of neural genes. Interestingly, in ES cells, Sox2 preselects for neural lineage-specific genes destined to be bound and activated by Sox3 in NPCs. In NPCs, Sox3 binds genes that are later bound and activated by Sox11 in differentiating neurons. Genes prebound by Sox proteins are associated with a bivalent chromatin signature, which is resolved into a permissive monovalent state upon binding of activating Sox factors. These data indicate that a single key transcription factor family acts sequentially to coordinate neural gene expression from the early lineage specification in pluripotent cells to later stages of neuronal development.
GeNVoM: Read Mapping Near Non-Volatile Memory (2021)

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology (termed Next Generation Sequencing, NGS) revolutionized genomic research. As a result, modern NGS platforms can sequence hundreds of millions of short DNA fragments in parallel. The sequenced DNA fragments, representing the output of NGS platforms, are termed reads. Besides genomic variations, NGS imperfections induce noise in reads. Mapping each read to (the most similar portion of) a reference genome of the same species, i.e., read mapping, is a common critical first step in a diverse set of emerging bioinformatics applications. Mapping represents a search-heavy memory-intensive similarity matching problem, therefore, can greatly benefit from near-memory processing. Intuition suggests using fast associative search enabled by Ternary Content Addressable Memory (TCAM) by construction. However, the excessive energy consumption and lack of support for similarity matching (under NGS and genomic variation induced noise) renders direct application of TCAM infeasible, irrespective of volatility, where only non-volatile TCAM can accommodate the large memory footprint in an area-efficient way. This paper introduces GeNVoM, a scalable, energy-efficient and high-throughput solution. Instead of optimizing an algorithm developed for general-purpose computers or GPUs, GeNVoM rethinks the algorithm and non-volatile TCAM-based accelerator design together from the ground up. Thereby GeNVoM can improve the throughput by up to 3.67×; the energy consumption, by up to 1.36×, when compared to an ASIC baseline, which represents one of the highest-throughput implementations known.
VEGFR1/CXCR4-positive progenitor cells modulate local inflammation and augment tissue perfusion by a SDF-1-dependent mechanism (2008)

Recruitment and retention of circulating progenitor cells at the site of injured or ischemic tissues facilitates adult neo-vascularization. We hypothesized that cell therapy could modulate local neo-vascularization through the vascular endothelial growth factor (VEGF)/stromal cell-derived factor-1 (SDF-1) axis and by paracrine effects on local endothelial cells. We isolated from rat bone marrow a subset of multipotent adult progenitor cell-derived progenitor cells (MDPC). In vitro, MDPCs secreted multiple cytokines related to inflammation and angiogenesis, including monocyte chemotactic protein-1, SDF-1, basic fibroblast growth factor, and VEGF, and expressed the chemokine receptors CXCR4 and VEGFR1. To investigate in vivo properties, we transplanted MDPCs into the ischemic hind limbs of rats. Elevated levels of the chemokine SDF-1 and colocalization of CD11b(+) cells marked the initial phase of tissue remodeling after cell transplantation. Prolonged engraftment was observed in the adventitial-medial border region of arterioles of ischemic muscles. However, engrafted cells did not differentiate into endothelial or smooth muscle cells. Limb perfusion normalized 4 weeks after cell injection. Inhibition of SDF-1 reduced the engraftment of transplanted cells and decreased endothelial cell proliferation. These findings suggest a two-stage model whereby transplanted MDPCs modulate wound repair through recruitment of inflammatory cells to ischemic tissue. This is an important potential mechanism for cell transplantation, in addition to the direct modulation of local vascular cells through paracrine mechanisms.
Mechanism of Sodium Ion Storage in Na<sub>7</sub>[H<sub>2</sub>PV<sub>14</sub>O<sub>42</sub>] Anode for Sodium‐Ion Batteries (2018)

Abstract In this work, the authors explore the sodium salt of the 14‐vanado(V)phosphate, Na 7 [H 2 PV 14 O 42 ], as a potential anode material for sodium‐ion batteries (NIBs). The multi‐electron redox activity of the polyoxovanadate [H 2 PV 14 O 42 ] 7‐ leads to high capacity. This polyanion is synthesized by a simple aqueous solution procedure and isolate as a sodium salt with different numbers of crystal waters, Na 7 [H 2 PV 14 O 42 ]·nH 2 O (n = 15–24). Na 7 [H 2 PV 14 O 42 ] as anode in NIBs exhibits a high and reversible capacity of 322 mA h g −1 at 25 mA g −1 with a high cycling stability (with capacity retention of 87% after 120 cycles). Some of the V 5+ ions in [H 2 PV 14 O 42 ] 7‐ can be reduced to V 3+ after being discharged to 0.01 V versus Na/Na + , resulting in an average oxidation state of V 3.7+ , as based on ex situ X‐ray photoelectron spectroscopy and in situ synchrotron X‐ray absorption near edge structure studies. The crystalline material becomes amorphous during the charge/discharge processes, which can be observed by in situ synchrotron X‐ray diffraction, indicating that functionality does not require crystallinity. The authors propose that the charge storage mechanism of Na 7 [H 2 PV 14 O 42 ] anodes mainly involves redox reactions of V accompanied by insertion/extraction of Na ions in‐between polyoxo‐14‐vanadate ions and adsorption/desorption of Na ions on the surface of the vanadate material.
TiO2-Mediated Photoelectrocatalytic Purification of Water (1998)

Abstract Sol-gel processing methods were employed to coat thin, porous films of titania on metal plates, specifically on aluminum, 304 stainless steel, and titanium. After coating and firing, all of these materials displayed photocatalytic activity when tested with a solution of formic acid that contained dissolved sodium chloride. However, only the titanium-supported photoelectrodes were stable with repeated use. Activities of these titaniumsupported photoelectrodes increased, often by factors of two to three, when positive potentials were applied across the titania coatings. Electrode activities increased when multiple coatings of titania were applied to the electrodes, although electrode stability was problematic when multiple coatings were deposited. Photoelectrocatalytic activities were not inhibited significantly by the presence of sodium chloride in the test solutions, while copper could be deposited on platinum cathodes when the test solutions contained dissolved copper in addition to sodium chloride and formic acid.
<i>In vitro</i> immune responses to a T cell-dependent antigen by cultures of disassociated murine Peyer's patch (1982)

The first line of defense against pathogens that enter the host by the oral route appears to involve the gut-associated lymphoreticular tissue-e.g., Peyer's patches (PP). Although animals can readily be immunized by orally administered antigen that mobilizes the secretory immune system, there is a total lack of local antibody synthesis in the PP and the cellular basis for this deficiency remains a mystery. A lymphoreticular cell population, obtained when murine PP were treated with a neutral protease (Dispase), consisted of accessory cells [macrophages (MPhi)] and T and B lymphocytes. In vitro cultures of these PP cell preparations with the thymic-dependent antigen sheep erythrocytes (SRBC) resulted in good anti-SRBC plaque-forming cell (PFC) responses. The time courses of these responses were identical to those seen with spleen cell cultures. Submitogenic concentrations of concanavalin A (Con A) and optimal doses of N-acetylmuramyl-L-alanyl-D-isoglutamine (MDP) and lipopolysaccharide (LPS) enhanced in vitro responses of PP cell cultures to SRBC. PP possess fully functional antigen-presenting MPhi because incubation of optimal proportions of splenic T and B cells with purified populations of PP MPhi supported good in vitro immune responses. Murine PP possess all of the necessary elements for an IgA immune response because PP cell cultures derived from mice orally primed with SRBC and immunized with SRBC in vitro gave high IgA anti-SRBC PFC responses. All of the adjuvants tested (LPS, MDP, and Con A) enhanced IgA responses in PP cell cultures from orally primed mice; however, Con A induced the greatest enhancement. These results demonstrate that murine PP possess MPhi capable of accessory cell functions for in vitro immune responses and that oral priming with antigen induces the precursor T- and B-cell populations necessary for IgA responses, that are potentiated by adjuvants, in PP cell cultures. Thus, murine PP possess the lymphoreticular cells required for antibody responses; however, the tissue architecture likely prevents local responses in vivo. The finding that enzymatically dissociated PP contain all of the necessary cellular components for antibody synthesis, whereas the in vivo tissue architecture prevents the complex interactions necessary for this response, suggests that the initial inductive events take place in situ, and additional cell interactions are required for final differentiation of IgA-synthesizing plasma cells to occur at distant mucosal sites.
<i>Salmonella</i>vaccines for use in humans: present and future perspectives (2002)

In recent years there has been significant progress in the development of attenuated Salmonella enterica serovar Typhi strains as candidate typhoid fever vaccines. In clinical trials these vaccines have been shown to be well tolerated and immunogenic. For example, the attenuated S. enterica var. Typhi strains CVD 908-htrA (aroC aroD htrA), Ty800 (phoP phoQ) and chi4073 (cya crp cdt) are all promising candidate typhoid vaccines. In addition, clinical trials have demonstrated that S. enterica var. Typhi vaccines expressing heterologous antigens, such as the tetanus toxin fragment C, can induce immunity to the expressed antigens in human volunteers. In many cases, the problems associated with expression of antigens in Salmonella have been successfully addressed and the future of Salmonella vaccine development is very promising.
Watching the assembly of an organ a single cell at a time using confocal multi-position photoactivation and multi-time acquisition (2009)

Tracing cell movements in vivo yields important clues to organogenesis, yet it has been challenging to accurately and reproducibly fluorescently mark single and small groups of cells to build a picture of tissue assembly. In the early embryo, the small size (hundreds of cells) of progenitor cell regions has made it easier to identify and selectively mark superficially located cells by glass needle injection. However, during early organogenesis, subregions of interest may be several millions of cells in volume located deeper within the embryo requiring an alternative approach. Here, we combined (confocal and 2-photon) photoactivation cell labeling and multi-position, multi-time imaging to trace single cell and small subgroups of cells in the developing brain and spinal cord. We compared the photostability and photoefficiency of a photoswitchable fluorescent protein, PSCFP2, with a novel nuclear localized H2B-PSCFP2 protein. We showed that both fluorescent proteins have similar photophysical properties and H2B-PSCFP2 is more effective in single cell identification in dense tissue. To accurately and reproducibly fluorescently trace subregions of cells in a 3D tissue volume, we developed a protocol for multi-position photoactivation and multi-time acquisition in the chick spinal cord in up to 8 tissue sections. We applied our techniques to address the formation of the sympathetic ganglia, a major component of the autonomic nervous system, and showed there are phenotypic differences between early and later emerging neural crest cells and their positions in the developing ganglia. Thus, targeted fluorescent cell marking by confocal or 2-photon multi-position photoactivation and multi-time acquisition offer a more efficient, less invasive technique to trace cell movements in large regions of interest and move us closer towards mapping the cellular events of organogenesis.
EEG in the differential diagnosis between Alzheimer's disease and vascular dementia (1988)

A prospective series of consecutively admitted patients with Alzheimer's disease (AD) (n = 68), multi-infarct dementia (MID) (n = 79) and probable vascular dementia (PVD) (n = 46) were studied by CT of the head. In MID 88.6% and in PVD 41.3% of the patients had at least one brain infarct on CT, but only one patient (1.5%) with AD. White matter low attenuation (WMLA) also differentiated MID and PVD from AD, especially among patients aged 75 years or less, and with mild or moderate dementia. In all types, brain atrophy on CT had a positive correlation with the degree of dementia. Infarcts and WMLA on CT, but not brain atrophy seem to be of differential diagnostic value between vascular and degenerative dementia.
Thermal Conductivity, Electrical Resistivity, and Seebeck Coefficient of Silicon from 100 to 1300°K (1968)

Results are presented of measurements of the thermal conductivity (90-1328\ifmmode^\circ\else\textdegree\fi{}K), the electrical resistivity (300-1273\ifmmode^\circ\else\textdegree\fi{}K), and the Seebeck coefficient (350-1273\ifmmode^\circ\else\textdegree\fi{}K) for single-crystal and large-grained polycrystalline specimens of 99.99+% pure silicon. The thermal conductivity above 387\ifmmode^\circ\else\textdegree\fi{}K was measured by an absolute radial-heat-flow technique; below 350\ifmmode^\circ\else\textdegree\fi{}K, by an absolute longitudinal technique. Some intermediate thermal-conductivity measurements from 300-400\ifmmode^\circ\else\textdegree\fi{}K were made on the polycrystalline material using a comparative longitudinal-heat-flow apparatus. The estimated errors of these three thermal-conductivity methods were \ifmmode\pm\else\textpm\fi{}2%\ifmmode\pm\else\textpm\fi{}2\ifmmode^\circ\else\textdegree\fi{}K, \ifmmode\pm\else\textpm\fi{}1.2%\ifmmode\pm\else\textpm\fi{}0.1\ifmmode^\circ\else\textdegree\fi{}K, and \ifmmode\pm\else\textpm\fi{}4.0%\ifmmode\pm\else\textpm\fi{}1\ifmmode^\circ\else\textdegree\fi{}K, respectively. The estimated error for the electrical-resistivity measurements was \ifmmode\pm\else\textpm\fi{}1.4%\ifmmode\pm\else\textpm\fi{}2\ifmmode^\circ\else\textdegree\fi{}K, and for the Seebeck measurements \ifmmode\pm\else\textpm\fi{}1.6%\ifmmode\pm\else\textpm\fi{}2\ifmmode^\circ\else\textdegree\fi{}K. The thermal-conductivity values were compared with conflicting data from the literature, and they corroborate the higher-temperature results obtained by Glassbrenner and Slack. Therefore, we agree with their conclusion that the electronic contribution is reasonably close to theoretical estimates which include a large ambipolar-diffusion term. The temperature dependence of the lattice thermal resistance has been compared to various theoretical models but no approach seems to explain the data in detail. An abrupt slope change in the thermal resistivity at about 670\ifmmode^\circ\else\textdegree\fi{}K is a major cause of the difficulty.
Scripting the cloud with skywriting (2010)

Recent distributed computing frameworks—such as MapReduce, Hadoop and Dryad—have made it simple to exploit multiple machines in a compute cloud. However, these frameworks use coordination languages that are insufficiently expressive for many classes of computation, including iterative and recursive algorithms. To address this problem, and generalise previous approaches, we introduce Skywriting: a Turing-powerful, purely-functional script language for describing distributed computations. In this paper, we introduce the main features of Skywriting, and outline our novel cooperative task farming execution engine.
Object Tracking Based on RFID Coverage Visual Compensation in Wireless Sensor Network (2007)

This paper proposes objects tracking method by association with RFID and visual sensors. The detection from RFID readers with proximity to each object results in coarse localization. The estimation is determined by a virtual sensor which is comprised of RFID readers detection combination. Each virtual sensor has a reference point which represents the center of possible positions. After the coarse estimation, image frames from two cameras improve the estimation close to a real position based on parallel projection model. The visual compensation sufficiently accomplishes the refined tracking. The experimental results show our proposed algorithm remarkably accomplishes the localization performance.
[Genetic counseling and clinical outcome of fetus with de novo chromosomal aberrations]. (2011)

Detailed cytogenetic and molecular study will be adjunctive tools for predicting the phenotype of fetus with de novo chromosomal aberrations. Fetal ultrasound examination will provide convincible demonstration to determine the outcome of pregnancy.
Creatine Phosphokinase: A Spectrophotometric Method with Improved Sensitivity (1968)

Journal Article Creatine Phosphokinase: A Spectrophotometric Method with Improved Sensitivity Get access Joseph W. Hess, M.D., Joseph W. Hess, M.D. Department of Medicine, Wayne Stale University School of Medicine, Detroit, Michigan 48207 Search for other works by this author on: Oxford Academic Google Scholar Kenneth J. Mtjrdock, B.S., Kenneth J. Mtjrdock, B.S. Department of Medicine, Wayne Stale University School of Medicine, Detroit, Michigan 48207 Search for other works by this author on: Oxford Academic Google Scholar George J. W. Natho, B.S. George J. W. Natho, B.S. Department of Medicine, Wayne Stale University School of Medicine, Detroit, Michigan 48207 Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 50, Issue 1, 1 July 1968, Pages 89–97, https://doi.org/10.1093/ajcp/50.1.89 Published: 01 July 1968 Article history Received: 24 August 1967 Published: 01 July 1968