gebhart/patrepeval huggingface dataset:
A naval infrared search and track demonstrator and its fusion with other ship sensors (2006)

A Naval Infrared Search and Track (IRST) demonstrator has been developed for the UK Ministry of Defence. The system uses two staring infrared cameras and split field of view optics to provide panoramic surveillance of the horizon and has real time processing for detection and tracking. The fusion of IRST and radar sensors offers an improvement in tracking due to their complementary nature. The benefit of integrating an IRST with other sensors has been assessed with simulated and real trials data. The high fidelity simulation begins with infrared scene rendering, followed by addition of targets, atmospheric effects, sensor characteristics and ends with plot extraction. This paper describes the simulation and compares the results with real data gathered with the IRST demonstrator.
A Novel Topology for Photovoltaic Series Connected DC/DC Converter with High Efficiency Under Wide Load Range (2007)

The paper proposes a new topology for photovoltaic DC/DC converter with high efficiency under wide input voltage range is proposed. Photovoltaic DC/DC is a very crucial part of power conditioning system(PCS). Considering that output characteristic of photovoltaic cell has wide voltage range, depending on the operating conditions of photovoltaic cell, the DC/DC converter also needs to have wide input voltage range to regulate the constant output voltage. In addition, a high rated voltage of power switch (MOSFET) for DC/DC converter is necessary in order to be compatible with the high maximum output voltage of photovoltaic cell's maximum output voltage. Also photovoltaic power conditioning system should have a high efficiency under operation condition. To satisfy PV PCS condition series connected non-isolated DC/DC converter topology is proposed. This paper examines the proposed topology employing four modules and shows that it dramatically enhances the energy efficiency from low load to high load condition by reducing the required power level for DC/DC converter by one-third of conventional DC/DC converter. A case of 20 kW prototype as the PV DC/DC converter is introduced to experimentally verify the proposed topology.
Acetyl:Succinate CoA-transferase in Procyclic Trypanosoma brucei (2004)

Acetyl:succinate CoA-transferase (ASCT) is an acetate-producing enzyme shared by hydrogenosomes, mitochondria of trypanosomatids, and anaerobically functioning mitochondria. The gene encoding ASCT in the protozoan parasite Trypanosoma brucei was identified as a new member of the CoA transferase family. Its assignment to ASCT activity was confirmed by 1) a quantitative correlation of protein expression and activity upon RNA interference-mediated repression, 2) the absence of activity in homozygous Deltaasct/Deltaasct knock out cells, 3) mitochondrial colocalization of protein and activity, 4) increased activity and acetate excretion upon transgenic overexpression, and 5) depletion of ASCT activity from lysates upon immunoprecipitation. Genetic ablation of ASCT produced a severe growth phenotype, increased glucose consumption, and excretion of beta-hydroxybutyrate and pyruvate, indicating accumulation of acetyl-CoA. Analysis of the excreted end products of (13)C-enriched and (14)C-labeled glucose metabolism showed that acetate excretion was only slightly reduced. Adaptation to ASCT deficiency, however, was an infrequent event at the population level, indicating the importance of this enzyme. These studies show that ASCT is indeed involved in acetate production, but is not essential, as apparently it is not the only enzyme that produces acetate in T. brucei.
Infrared Properties Of Nematic Liquid Crystals: An Overview (1987)

Infrared properties and electro-optic effects of nematic liquid crystals are reviewed. Physical origins and characterization techniques of infrared birefringence and rotatory power are described. Advantages and disadvantages of three device configurations--parallel, twisted, and perpendicular alignments--are analyzed. Among them, parallel alignment shows the best potential for long-wavelength applications. Several methods for improving the response times of nematic liquid crystals with emphasis in the infrared region are briefly discussed.
Folding of human superoxide dismutase: Disulfide reduction prevents dimerization and produces marginally stable monomers (2004)

The molecular mechanism by which the homodimeric enzyme Cu/Zn superoxide dismutase (SOD) causes neural damage in amytrophic lateral sclerosis is yet poorly understood. A striking, as well as an unusual, feature of SOD is that it maintains intrasubunit disulfide bonds in the reducing environment of the cytosol. Here, we investigate the role of these disulfide bonds in folding and assembly of the SOD apo protein (apoSOD) homodimer through extensive protein engineering. The results show that apoSOD folds in a simple three-state process by means of two kinetic barriers: 2D<==>2M<==>M(2). The early predominant barrier represents folding of the monomers (M), and the late barrier the assembly of the dimer (M(2)). Unique for this mechanism is a dependence of protein concentration on the unfolding rate constant under physiological conditions, which disappears above 6 M Urea where the transition state for unfolding shifts to first-order dissociation of the dimer in accordance with Hammond-postulate behavior. Although reduction of the intrasubunit disulfide bond C57-C146 is not critical for folding of the apoSOD monomer, it has a pronounced effect on its stability and abolishes subsequent dimerization. Thus, impaired ability to form, or retain, the C57-C146 bond in vivo is predicted to increase the cellular load of marginally stable apoSOD monomers, which may have implications for the amytrophic lateral sclerosis neuropathology.
Gentamicin-induced mobilization of iron from renal cortical mitochondria (1993)

Iron, presumably by participating in generation of hydroxyl radical or other oxidant species or initiation of lipid peroxidation, has been shown to play an important role in several models of tissue injury, including acute renal failure induced by the antibiotic gentamicin. However, the sources of iron remain unknown. Rat renal mitochondria incubated at 37 degrees C with gentamicin resulted in a time- (15-60 min) and a dose-dependent (0.01-5 mM) iron release as measured by formation of iron-bathophenanthroline sulfonate complex FeII-(BPS)3 [at 60 min, control: 1.2 +/- 0.1 nmol/mg protein, n = 7; gentamicin (5 mM): 5.1 +/- 0.4 nmol/mg protein, n = 7]. No formation of FeII(BPS)3 complex was detected in the absence of mitochondria or when incubations were carried out at 0 degrees C. Similar results were obtained when 2,2'-dipyridyl, another iron chelator, was used for measurement of iron release. On the basis on our previous study that gentamicin enhances generation of hydrogen peroxide by renal cortical mitochondria, we examined whether effect of gentamicin on iron release is mediated by hydrogen peroxide. Catalase (which decomposes hydrogen peroxide), but not heat-inactivated catalase, as well as pyruvate, a potent scavenger of hydrogen peroxide, prevented gentamicin-induced iron mobilization. Superoxide dismutase, a scavenger of superoxide anion, or hydroxyl radical scavengers (dimethylthiourea or sodium benzoate) had no effect. Taken together, the data with scavengers indicate that gentamicin-induced iron mobilization from mitochondria is mediated by hydrogen peroxide.
Molecular cloning of mesothelin, a differentiation antigen present on mesothelium, mesotheliomas, and ovarian cancers. (1996)

Monoclonal antibody MAb K1 recognizes a 40-kDa glycoprotein present on the surface of mesothelial cells, mesotheliomas, and ovarian cancers. We have used MAb K1 to isolate a 2138-bp cDNA that encodes this antigen. The cDNA has an 1884-bp open reading frame encoding a 69-kDa protein. When the cDNA was transfected into COS and NIH 3T3 cells, the antigen was found on the cell surface and could be released by treatment with phosphatidylinositol-specific phospholipase C. The 69-kDa precursor is processed to the 40-kDa form. The protein has been named mesothelin because it is made by mesothelial cells. Mesothelin may play a role in cellular adhesion.
Tissue-engineered vascular grafts transform into mature blood vessels via an inflammation-mediated process of vascular remodeling (2010)

Biodegradable scaffolds seeded with bone marrow mononuclear cells (BMCs) are the earliest tissue-engineered vascular grafts (TEVGs) to be used clinically. These TEVGs transform into living blood vessels in vivo, with an endothelial cell (EC) lining invested by smooth muscle cells (SMCs); however, the process by which this occurs is unclear. To test if the seeded BMCs differentiate into the mature vascular cells of the neovessel, we implanted an immunodeficient mouse recipient with human BMC (hBMC)-seeded scaffolds. As in humans, TEVGs implanted in a mouse host as venous interposition grafts gradually transformed into living blood vessels over a 6-month time course. Seeded hBMCs, however, were no longer detectable within a few days of implantation. Instead, scaffolds were initially repopulated by mouse monocytes and subsequently repopulated by mouse SMCs and ECs. Seeded BMCs secreted significant amounts of monocyte chemoattractant protein-1 and increased early monocyte recruitment. These findings suggest TEVGs transform into functional neovessels via an inflammatory process of vascular remodeling.
Ultrasonic vs. hand instrumentation in periodontal therapy: clinical outcomes (2016)

Periodontal disease is the most common oral disease in adults. Traditional nonsurgical periodontal therapy involves subgingival removal of hard and soft deposits on the root surface, along with maintenance of good oral hygiene. Nonsurgical periodontal therapy can either be definitive or part of the initial phase before surgical therapy. Mechanical therapy, either with hand or ultrasonic instrumentation, is the keystone of nonsurgical periodontal therapy. This requires considerable amounts of time and a high level of operator skill. The use of appropriate instruments greatly increases clinical efficiency. This article discusses the use of ultrasonic and hand instrumentation, along with recent advances, and the benefits of adjunctive therapy during nonsurgical periodontal therapy.
Review of Rapid Diagnostic Tests Used by Antimicrobial Stewardship Programs (2014)

Rapid microbiologic tests provide opportunities for antimicrobial stewardship programs to improve antimicrobial use and clinical and economic outcomes. Standard techniques for identification of organisms require at least 48-72 hours for final results, compared with rapid diagnostic tests that provide final organism identification within hours of growth. Importantly, rapid microbiologic tests are considered "game changers" and represent a significant advancement in the management of infectious diseases. This review focuses on currently available rapid diagnostic tests and, importantly, the impact of rapid testing in combination with antimicrobial stewardship on patient outcomes.
A single‐chain murine class I major transplantation antigen (1991)

Single-chain mouse Kd molecules (SC-Kd) were engineered by connecting residue 276 of Kd heavy chain to the first residue of beta 2-microglobulin through spacers of various lengths, and expressed intracellularly in monkey COS-1 cells. Labeled SC-Kd molecules were found to react with several monoclonal antibodies which recognize native Kd molecules. SC-Kd-15 (with a spacer of 15 residues) was studied in more details. It could be purified and shown to regain a native-like structure after treatment with denaturing agents. Purified SC-Kd-15 could bind certain peptides in a manner qualitatively similar to the Kd.
Ferumoxytol for the treatment of iron deficiency anemia (2018)

Ferumoxytol is a superparamagnetic molecule originally developed as a contrast agent for magnetic resonance imaging. Elemental iron is contained within the carbohydrate core and is released slowly after infusion allowing a large dose of iron to be administered in a short period of time. Ferumoxytol, originally approved for iron deficiency in chronic kidney disease, received a broad label for any cause of iron deficiency after oral iron intolerance or in those circumstances when oral iron is ineffective or harmful. Areas covered: The chemistry, pharmacology and pharmacokinetics of ferumoxytol were reviewed. Retrospective, observational, and prospective phase II and III trials were reviewed. When appropriate, comparative safety and efficacy parameters were reported. Differentiation between minor infusion reactions and more severe hypersensitivity reactions that may lead to anaphylaxis is described. Expert commentary: Ferumoxytol is a safe and effective iron formulation providing a means of iron repletion in persons with iron deficiency with or without anemia. Relative to iron sucrose, ferric gluconate, and iron dextran and similar to ferric carboxymaltose and iron isomaltoside, ferumoxytol yields relatively low quantities of labile free iron. Hypersensitivity and anaphylaxis is extremely rare. Hypophosphatemia with ferumoxytol's administration is extremely rare. Optimal strategies for application of ferumoxytol-enhanced imaging and full replacement dosing in a single setting remain to be determined.
Plasma Membrane Is the Site of Productive HIV-1 Particle Assembly (2006)

Recently proposed models that have gained wide acceptance posit that HIV-1 virion morphogenesis is initiated by targeting the major structural protein (Gag) to late endosomal membranes. Thereafter, late endosome-based secretory pathways are thought to deliver Gag or assembled virions to the plasma membrane (PM) and extracellular milieu. We present several findings that are inconsistent with this model. Specifically, we demonstrate that HIV-1 Gag is delivered to the PM, and virions are efficiently released into the extracellular medium, when late endosome motility is abolished. Furthermore, we show that HIV-1 virions are efficiently released when assembly is rationally targeted to the PM, but not when targeted to late endosomes. Recently synthesized Gag first accumulates and assembles at the PM, but a proportion is subsequently internalized via endocytosis or phagocytosis, thus accounting for observations of endosomal localization. We conclude that HIV-1 assembly is initiated and completed at the PM, and not at endosomal membranes.
Poly(carbonate urethane) and poly(ether urethane) biodegradation: In vivo studies (2004)

Several strategies have been used to increase the biostability of medical-grade polyurethanes while maintaining biocompatibility and mechanical properties. One approach is to chemically modify or replace the susceptible soft segment. Currently, poly(carbonate urethanes) (PCUs) are being evaluated as a replacement of poly(ether urethanes) (PEUs) in medical devices because of the increased oxidative stability of the polycarbonate soft segment. Preliminary in vivo and in vitro studies have reported improved biostability of PCUs over PEUs. Although several studies have reported evidence of in vitro degradation of these new polyurethanes, there has been no evidence of significant in vivo degradation that validates a degradation mechanism. In this study, the effect of soft segment chemistry on the phase morphology, mechanical properties, and in vivo response of commercial-grade PEU and PCU elastomers was examined. Results from dynamic mechanical testing and infrared spectroscopy suggested that the phase separation was better in PCU as compared with PEU. In addition, the higher modulus and reduced ultimate elongation of PCU was attributed to the reduced flexibility of the polycarbonate soft segment. Following material characterization, the in vivo biostability and biocompatibility of PEU and PCU were studied using a subcutaneous cage implant protocol. The results from the cage implant study and cell culture experiments indicated that monocytes adhere, differentiate, and fuse to form foreign body giant cells on both polyurethanes. It is now generally accepted that the reactive oxygen species released by these adherent macrophages and foreign body giant cells initiate PEU biodegradation. Attenuated total reflectance-Fourier transform infrared analysis of explanted samples provided evidence of chain scission and crosslinking in both polyurethanes. This indicated that the PCU was also susceptible to biodegradation by agents released from adherent cells. These results reinforce the need to evaluate and understand the biodegradation mechanisms of PCUs.
Polymer-Bound Triarylphosphine-Iodine Complexes, Convenient Coupling Reagent Systems in Peptide Synthesis (1995)

N-protected α-amino acids are readily coupled with α-aminoacyl esters by polystyryl diphenylphosphine-iodine complex in very high yields and without detectable racemization. Protecting groups of general use for both amine and carboxyl functions, as well as the common side-chain-function protecting groups, are well tolerated under our experimental conditions. The workup is very easy since the only byproduct formed is a polymer-linked phosphine oxide that is simply filtered off to achieve the coupling product.
Role of Platelets and Fibrin in the Healing Sequence (1982)

Thrombin-released platelets produced angiogenesis and opacification. Histology showed fibroplasia, corneal thickening, and neovascularization. Collagen synthesis was elevated to twice control levels in thrombin-activated platelet preparations. Various control platelet preparations produced no angiogenesis, no opacification, and no histologic change. All fibrin injections elicited a cellular exudate from the limbal vessels, followed by angiogenesis and corneal opacification. Histology showed a mononuclear infiltrate with neovascularization and fibroplasia. Control injections of rabbit skin collagen and fibroblasts produced no response.
Prostaglandins E1and E2, but not F2αor Latanoprost, Inhibit Monkey Ciliary Muscle Contraction (2005)

Our results indicate that PGF2alpha and latanoprost acid do not interact with the prostanoid receptor involved at the pre- and/or postsynaptic site. Therefore, it is unlikely that the hypotensive action by these agents is due to relaxation of the ciliary muscle.
Alterations in the Chlamydomonas Plastocyanin Transit Peptide Have Distinct Effects on in VitroImport and in Vivo Protein Accumulation (1997)

Nucleus-encoded chloroplast proteins that reside in the thylakoid lumen are synthesized as precursors with bipartite transit peptides that contain information for uptake and intra-chloroplast localization. We have begun to apply the superb molecular and genetic attributes of Chlamydomonas to study chloroplast protein import by creating a series of deletions in the transit peptide of plastocyanin and determining their effects on translocation into isolated Chlamydomonas chloroplasts. Most N-terminal mutations dramatically inhibited in vitro import, whereas replacement with a transit peptide from the gamma-subunit of chloroplast ATPase restored uptake. Thus, the N-terminal region has stroma-targeting function. Deletions within the C-terminal portion of the transit peptide resulted in the appearance of import intermediates, suggesting that this region is required for lumen translocation and processing. Thus, despite its short length and predicted structural differences, the Chlamydomonas plastocyanin transit peptide has functional domains similar to those of vascular plants. Similar mutations have been analyzed in vivo by transforming altered genes into a mutant defective at the plastocyanin locus (K. L. Kindle, manuscript in preparation). Most mutations affected in vitro import more severely than plastocyanin accumulation in vivo. One exception was a deletion that removed residues 2-8, which nearly eliminated in vivo accumulation but had a modest effect in vitro. We suggest that this mutant precursor may not compete successfully with other proteins for the translocation pathway in vivo. Apparently, in vivo and in vitro analyses reveal different aspects of chloroplast protein biogenesis.
Oligonucleotides with cyclohexene-nucleoside building blocks: crystallization and preliminary X-ray studies of a left-handed sequence GTGTACAC (2005)

Cyclohexene nucleic acids contain a cyclohexene ring instead of the normal beta-D-2'-deoxyribose. The cyclohexene oligonucleotide GTGTACAC was synthesized using phosphoramidite chemistry and standard protecting groups. Crystals of GTGTACAC were obtained at 289 K by the hanging-drop vapour-diffusion technique. The crystals diffract to 1.7 A resolution and belong to the trigonal space group R3, with unit-cell parameters a = 41.434, c = 66.735 A.
SAMBLASTER: fast duplicate marking and structural variant read extraction (2014)

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times. Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results. Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster. Contact: imh4y@virginia.edu
Mechanisms of action, physiological effects, and complications of hypothermia (2009)

Therapeutic hypothermia is a highly promising treatment, but the potential side effects need to be properly managed particularly if prolonged treatment periods are required. Understanding the underlying mechanisms, awareness of physiological changes associated with cooling, and prevention of potential side effects are all key factors for its effective clinical usage.
Light-influenced extracellular accumulation of b (pathogenesis-related) proteins in Nicotiana green tissue induced by various chemicals or prolonged floating on water (1985)

The extracellular accumulation of b (pathogenesis-related) proteins in Nicotiana tabacum cv. Xanthi-nc and cv. Samsun and in Nicotiana sylvestris was studied by floating leaf disks on solutions (50 μM – 5 mM) of putative inducers at pH 4 to 8 for 72 h. Intercellular fluid b proteins were detected only in green tissue, and optimal conditions required specific light regimes. Amino acids, organic acids, sugars, nucleotides, amines, vitamins, hormones, metals, and several other chemicals were compared with acetylsalicylate at 0.3 mM for the presence of b proteins in intercellular fluid extracts analyzed by native polyacrylamide gel electrophoresis. Several protein and non-protein amino acids and some of their derivatives were inducers in addition to thiamine, thiamine derivatives, and a few other chemicals at concentrations ranging from 200 μM to 5 mM. Various ways of introducing inducers into tissue (floating, injection, infiltration, root uptake) allowed b protein accumulation. Stimulation of b protein accumulation was observed when osmotica (sucrose at 200 mM) were added to inducers. Chelating agents, spermidine, lysine, and hydroquinone could inhibit b protein accumulation induced by L-serine, thiamine, L-α-aminoisobutyrate, and silver nitrate. Results with inducing chemicals and with prolonged floating of tissue on water, which was also conducive to b protein accumulation, support the hypothesis that b protein accumulation is a green tissue generalized response to various forms of prolonged stress.