gebhart/patrepeval huggingface dataset:
Editorial: Current trends in peptide science (2002)

This “Current Trends in Peptide Science” issue features papers broadly based on the diversity of biologically-important interactions of peptides and proteins with cellular membranes. In the first paper, Unson focuses on the seven-helix transmembrane receptor for glucagon, a 29-residue peptide hormone that functions to counterbalance the effects of insulin in blood glucose levels. She describes progress toward the elucidation of molecular determinants of ligand specificity by the receptor, itself a member of the G-protein coupled receptor (GPCR) family, and discusses models which have been proposed for the specificity of binding of these so-called Family B receptors to a series of highly homologous peptide ligands. Noting the increasing resistance of bacteria to conventional antibiotics, Shai then presents an in-depth discussion of a new generation of antibiotic peptides. Because these peptides are active across a wide range of lengths and sequences, he presents evidence for the “carpet model” of peptide antibiotic action—a generalized mechanism for bacterial membrane binding and penetration which may be coupled in some instances with eventual targeting of the peptides to the cytoplasmic region of the organism. In a related theme, Tamm presents a review of membrane fusion peptides that are constituted of highly conserved hydrophobic segments of fusion proteins; these peptides which mediate processes requiring two cellular membranes to fuse into one. Focusing on influenza hemagglutinin fusion peptides, Tamm describes biophysical approaches—including NMR spectroscopy. ATR infrared techniques, and differential scanning calorimetry—to deduction of the structures and interactions of these peptides with phospholipid bilayers. McCafferty and his co-workers conclude this issue with a discussion of the wide-ranging properties of the peptide antibiotic ramaplanin family—compounds structurally related to cell wall-active lipodepsipeptides—which may find clinical use against vancomycin-resistant and methicillin-resistant pathogens. The collection of papers in this issue truly reflects the important advances in our understanding of peptide/protein interactions with membranes—whether involving receptor-mediated recognition, surface binding, membrane penetration/fusion, or mechanisms of antibiotic action—as well as highlighting the momentum for continuing research in these emerging fields.
Web surveys' hidden hazards. (2003)

The same question posed on the Web and in print can yield very different answers, dramatically distorting survey results and misleading management. But, as psychologist Palmer Morrel-Samuels demonstrates, the problems are readily fixed.
Comparaci??n Mec??nica del Clavo Intramedular y la Fijaci??n con Clavo Placa para la Artrodesis Tibiotalocalc??nea (2005)

Alfahd, Uosife MD; Roth, Sandra E MSc; Stephen, David MD FRCS(C); Whyne, Cari M PhD Author Information
Continuously operating laser jet for synthesis of double silicate systems (1994)

The method of laser aerosol distillation was used in a study of the synthesis of MxOy—SiO2 (M = Ti, Fe, Ni, Cu) double silicate systems in an erosion jet formed under the influence of cw CO2 laser radiation. The problem of the formation of a boiling melt on composite targets was studied and the conditions for the existence and energy efficiency of a continuously operating laser jet formed from such targets are discussed. The dependence of the concentration of the Ti ions in the grown samples on their concentration on the target surface was determined.
Denoising and segmentation of the second heart sound using matching pursuit (2012)

We propose a denoising and segmentation technique for the second heart sound (S2). To denoise, Matching Pursuit (MP) was applied using a set of non-linear chirp signals as atoms. We show that the proposed method can be used to segment the phonocardiogram of the second heart sound into its two clinically meaningful components: the aortic (A2) and pulmonary (P2) components.
Immune response of fishes to ciliates (1996)

Ciliates are highly evolved protists comprising a phylum of diverse species, many of which are opportunistic or obligate parasites. Ciliates parasitic to fish consist of salt and freshwater forms with endo- or ectoparasitic modes of infection. Some of the more commonly encountered genera include Chilodonella, Brooklynella, Ophryoglenina, Ichthyophthirius, Cryptocaryon, Uronema, Tetrahymena, Epistylus, and Trichodina. Species range from obligate parasites and commensals to opportunistic, facultative forms. Some parasitic ciliates are highly pathogenic and fishes in closed environments such as aquaria and farm ponds are particularly susceptible to high mortalities. Nevertheless, fish have evolved an immune system capable of mounting an effective protective response against parasite challenge. Much of the experimental research on immunity against ciliates has been carried out with Ichthyophthirius multifiliis, on obligate parasite that invades surface epithelia of virtually all freshwater fish species. Interest in the immune response against I. multifiliis stems from the fact that convalescent fish become resistant to subsequent challenge (suggesting the possibility of immunoprophylaxis), and the need to curtail severe losses caused by this parasite in intensively farmed fishes. Furthermore, I. multifiliis has proven to be a useful experimental model because it is amenable to study under laboratory conditions. In this review cellular and humoral factors involved in both innate and acquired immunity against ciliates are covered and include natural killer cells, phagocytic cells, and antibody responses. Current ideas on the mechanisms of antibody-mediated cutaneous immunity against I. multifiliis are discussed and approaches toward the development of vaccines against this and other ciliate parasites are presented.
Management of dry flue gas desulfurization by-products in underground mines. Quarterly report, October--December 1994 (1995)

On September 30, 1993, the US Department of Energy, Morgantown Energy Technology Center and Southern Illinois University at Carbondale (SIUC) entered into a cooperative agreement entitled ``Management of Dry Flue Gas Desulfurization By-Products in Underground Mines`` (DE-FC21-93MC30252). Under the agreement, Southern Illinois University at Carbondale will develop and demonstrate several technologies for the placement of coal combustion residues in abandoned coal mines, and will assess the environmental impact of such underground residues placement. The major event during the quarter was the demonstration of the SEEC, Inc. technology for loading and transporting coal combustion residues in the SEEC developed Collapsible Intermodal Containers (CIC). The demonstration was held on November 17, 1994, at the Illinois Power Company Baldwin power plant, and was attended by about eighty (80) invited guest. Also during the quarter meetings were held with Peabody Coal Company officials to finalize the area in the Peabody No. 10 mine to be used for the placement of coal combustion residues. Work under the Materials Handling and Systems Economics area continued, particularly in refining the costs and systems configuration and in economic evaluation of various systems using equipment leasing rather than equipment purchases. Likewise, work progressed on residues characterization, with some preparations being made for long-term testing.
Unusual Crystallographic Aspects of Microband Boundaries within {111}^|^lt;110^|^gt; Oriented Grains in a Cold Rolled Interstitial Free Steel (2014)

Microbands are well-known deformation features that generate in the rolling microstructures of many metals and alloys. The boundaries across two neighbouring microbands are comprised of dense dislocation walls and they accommodate a small average crystallographic rotation in the range of 1–4°. In this study, a combination of high resolution electron backscattered diffraction (EBSD) and transmission electron microscopy (TEM) was used to observe orientation differences of up to 20° across microband boundaries in the rolling substructures of {111}<110> oriented grains in steel. Despite their high angle nature, the microband interfaces maintain their well-known crystallographic characteristics, by being closely aligned with highly stressed slip planes. Rigid body rotations are argued to take place around the interface normal between adjacent microband lattices. This results in an unusual microstructure whereby alternating microband boundaries, oriented in equal and opposite relative angles, produce an array of orientation pairs in their spatial distributions.
Smart optical measurement probe for autonomously detecting nano-defects on bare semiconductor wafer surface: highly sensitive observation system using phase-contrast microscopy with a spatial light modulator (2022)

Nowadays, the yield rate of semiconductor process is strongly affected even by nanoscale defects on bare Si wafer surfaces. Therefore, a non-destructive and high-speed method for detection of nanoparticle contamination is highly demanded. In this research, a nanoparticle detection method is proposed based on the fact that the volatilization process of the volatile inert liquid behaves as an autonomous nanoparticle search probe. Dynamic phase contrast microscopy (Dynamic PCM) is proposed to detect small thickness changes of a thin liquid film with high sensitivity. The dynamic PCM is expected to have double sensitivity compared to normal PCM and it is experimentally verified. Based on previous results, 4% intensity change is expected for 10 nm particles and even over 1.5% intensity change is expected for 5 nm particles by using this proposed dynamic PCM.
Immunoglobulin-based strategies for half-life extension of recombinant proteins (2015)

With numerous small recombinant proteins being developed for treatment of various diseases, half-life extension strategies are becoming increasingly vital for the creation of long lasting and efficient biotherapeutics. Because of their small size, these proteins are rapidly cleared from plasma circulation and lose a lot of their potential as therapeutic. Using immunoglobulin-binding domains (IgBD), in particular domain C3 from Streptococcus protein G (SpGC3), can substantially increase the half-life by forming transient complexes with endogenous IgG molecules. This complex formation needs to occur at neutral pH to prevent rapid renal clearance, but also under acidic conditions, facilitating the salvage from lysosomal degradation via the neonatal Fc receptor (FcRn). In order to enable FcRn recycling, the major binding site of SpGC3 to the IgG-Fc part was eliminated, since it is overlapping with the FcRn binding site, generating the CH1 specific domain SpGC3Fab. Affinity maturation towards the Fab fragment resulted in domains SpGC3FabRR and SpGC3FabRR,E15V showing significantly increased terminal half-lives as scDb-IgBD fusion proteins. Since the IgBDs originate from bacterial proteins, they might provoke immunogenic reactions and the production of anti-drug antibodies. For deimmunization, possible T-cell epitopes were identified by sequence and structure-based analysis and eliminated by combination of single amino acid substitutions. This resulted in deimmunized IgBDs that were able to strongly increase the terminal half-life as scDb fusion proteins. The application of SpGC3FabRR to recombinant human erythropoietin (huEPO) resulted in a roughly 5-fold increased terminal half-life compared to the unmodified huEPO that also translated into increased hemoglobin concentration after one single intravenous injection. Furthermore, a comparative study of various Fc fusion proteins revealed that a multitude of factors is jointly responsible for the long half-life of full-length IgG molecules. Although possessing an identical huIgG1 Fc part and affinity to the moFcRn, neither an scFv-Fc nor an scDb-Fc or a single-chain version of the IgG molecule (scFv-scCLCH1-Fc) could reach the pharmacokinetic properties of the IgG molecule, not fully explainable by factors like size, isoelectric point and stability. All in all, the utilization of immunoglobulins and FcRn-mediated salvage via IgBDs and Fc fusion proteins is a powerful tool for the generation of recombinant fusion proteins with favorable pharmacokinetic properties.
Radiotherapy Matters for Locally Advanced Prostate Cancer (2011)

Despite the ability of prostate cancer screening to identify patients with clinically organ-confined (T1c) prostate cancer, a troubling number of men
Ionospheric modification: an initial report on artificially created equatorial spread F. Interim report (1978)

A numerical simulation code for investigating equatorial Spread F in the collisional Rayleigh-Taylor regime is utilized to follow the evolution of artificial plasma density depletions injected into the bottomside nighttime equatorial F region. The 70 km diameter hole rapidly rises and steepens, forming plasma density enhancements at altitudes below the rising hole. The distribution of enhancements and depletions is similar to natural equatorial Spread F phenomena, except it occurs on a much faster time scale.
Cross‐Linked Aggregates of the Hydroxynitrile Lyase from <i>Manihot esculenta</i>: Highly Active and Robust Biocatalysts (2006)

Abstract The precipitation and cross‐linking into CLEAs of the hydroxynitrile lyase (E.C. 4.1.2.10) from Manihot esculenta was investigated and an optimized procedure, which involved precipitation with (NH 4 ) 2 SO 4 , was developed. It was found that a fast (photometric) assay severely underestimated the activity recovery in the CLEA due to rate‐limiting diffusion, whereas in a synthetic assay the activity recovery was up to 93 % of the starting activity. The CLEA was applied in the hydrocyanation of various aldehydes and ketones in microaqueous medium, conditions that rendered the non‐enzymatic background reaction insignificant, even with unreactive substrates.
Fiber Type-Specific Nitric Oxide Protects Oxidative Myofibers against Cachectic Stimuli (2008)

Oxidative skeletal muscles are more resistant than glycolytic muscles to cachexia caused by chronic heart failure and other chronic diseases. The molecular mechanism for the protection associated with oxidative phenotype remains elusive. We hypothesized that differences in reactive oxygen species (ROS) and nitric oxide (NO) determine the fiber type susceptibility.
Culturable actinomycetes from desert ecosystem in northeast of Qinghai-Tibet Plateau (2012)

In this study, 53 actinomycetes strains were isolated from desert ecosystems located in northeast of Qinghai-Tibet Plateau and grouped into four RFLP patterns. Twenty-six actinomycetes with obvious morphology differences were chosen for phylogenetic diversity study and antimicrobial testing. As a result, the 16S rRNA gene sequencing showed that these strains belonged to Streptomyces, Micromonospora, Saccharothrix, Streptosporangium and Cellulomonas, and that most of the strains had antimicrobial bioactivity. The PKS and NRPS genes detection indicated diversified potential bioactive products of actinomycetes in this ecosystem. Among these strains, Sd-31 was chosen to study the bioactive products using HPLC-MS because of its optimum antimicrobial bioactivity. The result showed that it might produce Granatomycin A, Granatomycin C, and an unknown compound.
HpBase: A genome database of a sea urchin, <i>Hemicentrotus pulcherrimus</i> (2018)

To understand the mystery of life, it is important to accumulate genomic information for various organisms because the whole genome encodes the commands for all the genes. Since the genome of Strongylocentrotus purpratus was sequenced in 2006 as the first sequenced genome in echinoderms, the genomic resources of other North American sea urchins have gradually been accumulated, but no sea urchin genomes are available in other areas, where many scientists have used the local species and reported important results. In this manuscript, we report a draft genome of the sea urchin Hemincentrotus pulcherrimus because this species has a long history as the target of developmental and cell biology in East Asia. The genome of H. pulcherrimus was assembled into 16,251 scaffold sequences with an N50 length of 143 kbp, and approximately 25,000 genes were identified in the genome. The size of the genome and the sequencing coverage were estimated to be approximately 800 Mbp and 100×, respectively. To provide these data and information of annotation, we constructed a database, HpBase (http://cell-innovation.nig.ac.jp/Hpul/). In HpBase, gene searches, genome browsing, and blast searches are available. In addition, HpBase includes the "recipes" for experiments from each lab using H. pulcherrimus. These recipes will continue to be updated according to the circumstances of individual scientists and can be powerful tools for experimental biologists and for the community. HpBase is a suitable dataset for evolutionary, developmental, and cell biologists to compare H. pulcherrimus genomic information with that of other species and to isolate gene information.
GENT-53. SELF-ORGANIZATION OF GLIOMAS: GENETIC RODENT MODELS, GENOMIC NETWORKS, AND MATHEMATICAL MODELING (2016)

The existence of large scale organization in gliomas remains unknown. We here demonstrate that gliomas are indeed self-organized. We do so by uncovering the cellular, genomic, and mathematical networks that underlie glioma self-organization and aggressive behavior. Glioma self-organization was studied in genetically induced gliomas using the Sleeping Beauty Transposase system expressing/down-modulating N-Ras, large T ag from SV40, TP53, PDGF, ATRX, and IDH1-R132H. We discovered the existence of onco-streams within gliomas, the glioma equivalent of self-organizing flocks of birds. Onco-streams are 10-20 glioma cells wide, of variable length, formed by fusiform cells, and are distributed throughout tumors. Onco-streams participate in glioma growth, invasion, and lethality. Onco-streams play various roles: they enhance migration of slower moving glioma stem cells, and block immune cell invasion of gliomas. Both in human and in rodent gliomas the prevalence of onco-streams correlates positively with tumor aggressiveness. Secondly, we modeled gliomas’ onco-streams using agent based computational modeling. Cellular interactions in our model were exhaustively studied using numerical investigations of our agent- based model. Our model predicts that changes in cell shape affect the population behavior of glioma cells, induce the formation of onco-streams, and thereby increase tumor aggressiveness. These predictions are now being tested experimentally. Thirdly, we analyzed the genomic structure of gliomas’ self-organization. Utilizing RNA-seq and bioinformatic analyses we uncovered a gene expression network that underlies onco-stream formation, and aggressive glioma behavior. One of the most highly connected gene nodes was selected for inhibition. Specific pharmacological and genetic targeting of this network demonstrated strong inhibitory effects only of the most malignant glioma models, as predicted by our analysis. We conclude that gliomas are self-organizing structures. This is supported by experimental, mathematical, and genomic studies. Finally, this approach will lead to the discovery of hitherto unsuspected essential therapeutic targets as is illustrated herein.
Electrokinetic and Hemostatic Profiles of Nonwoven Cellulosic/Synthetic Fiber Blends with Unbleached Cotton (2014)

Greige cotton contains waxes and pectin on the outer surface of the fiber that are removed when bleached, but these components present potential wound dressing functionality. Cotton nonwovens blended with hydrophobic and hydrophilic fibers including viscose, polyester, and polypropylene were assessed for clotting activity with thromboelastography (TEG) and thrombin production. Clotting was evaluated based on TEG measurements: R (time to initiation of clot formation), K (time from end of R to a 20 mm clot), α (rate of clot formation according to the angle tangent to the curve as K is reached), and MA (clot strength). TEG values correlate to material surface polarity as measured with electrokinetic parameters (ζplateau, Δζ and swell ratio). The material surface polarity (ζplateau) varied from -22 to -61 mV. K values and thrombin concentrations were found to be inversely proportional to ζplateau with an increase in material hydrophobicity. An increase in the swell ratios of the materials correlated with decreased K values suggesting that clotting rates following fibrin formation increase with increasing material surface area due to swelling. Clot strength (MA) also increased with material hydrophobicity. Structure/function implications from the observed clotting physiology induced by the materials are discussed.
Polycrystalline Silicon Nanowires Synthesis Compatible With CMOS Technology for Integrated Gas Sensing Applications (2014)

Polysilicon nanowires are synthesized following a classical top-down approach using conventional UV lithography technique fully compatible with the existing silicon complementary metal-oxide-semiconductor technology. N- and P-type in situ doping of these nanowires is controlled over a large range of doping levels and the electrical properties of these nanowires are analyzed. The results show that resistivity dependence with the doping level is both related to the nanowire size-dependent structural quality and doping specie. Charged gas species (ammonia) sensitivity of these nanowires has also been studied. In addition, the feasibility of N- and P-channel polysilicon nanowire transistors is demonstrated.
Efavirenz-induced gynaecomastia in HIV-infected Nigerian men: A report of six cases (2011)

Highly active antiretroviral therapy (HAART) has revolutionized the treatment of HIV-infected patients. However, numerous adverse effects and limitations regarding tolerability remain a concern. We report six patients presenting in our treatment program with varying degrees of gynaecomastia following the use of efavirenz-based highly active antiretroviral therapy, despite adequate immunologic and virologic response. The time interval between commencement of treatment and appearance of gynaecomastia ranged from 8-16 months with a mean period of 10±3 months. Five of the patients experienced complete regression of gynaecomastia following efavirenz withdrawal within 6-10 weeks. One patient experienced partial regression and subsequently required bilateral mastectomy; he is without recurrence one year post surgery. Gynaecomastia is not uncommon in HIV-infected men receiving efavirenz-based highly active antiretroviral therapy. Careful attention need to be paid to the evaluation of these patients in order to institute appropriate therapy and effectively manage other comorbid conditions that could also cause gynaecomastia.
Application of the Injury Cost Scale (ICS) to Mercedes-Benz Accident Data (1990)

<div class="htmlview paragraph">As a supplement to officially published government accident statistics since 1969 Mercedes-Benz has been systematically investigating automobile accidents involving injured occupants in Mercedes-Benz cars.</div> <div class="htmlview paragraph">Typically our accident data has been analysed using the Abbreviated Injury Scale (AIS). This paper will describe the first application of the new Injury Cost Scale (ICS), published at the AAAM-conference 1989, to our real world accident data. A comparison for the handling of multiple injuries will be provided taking into account on the one hand only the most expensive injury and on the other hand each injury. The first experiences in the application of the ICS will be discussed. The ICS is intended as supplemental to the AIS.</div>