gebhart/patrepeval huggingface dataset:
Enhanced Peptide Mass Fingerprinting through High Mass Accuracy:  Exclusion of Non-Peptide Signals Based on Residual Mass (2006)

Peptide mass fingerprinting (PMF) is among the principle methods of contemporary proteomic analysis. While PMF is routinely practiced in many laboratories, the complexity of protein tryptic digests is such that PMF based on unrefined mass spectrometric peak lists is often inconclusive. A number of data processing strategies have thus been designed to improve the quality of PMF peak lists, and the development of increasingly elaborate tools for PMF data reduction remains an active area of research. In this report, a novel and direct means of PMF peak list enhancement is suggested. Since the monoisotopic mass of a peptide must fall within a predictable range of residual values, PMF peak lists can in principle be relieved of many non-peptide signals solely on the basis of accurately determined monoisotopic mass. The calculations involved are relatively simple, making implementation of this scheme computationally facile. When this procedure for peak list processing was used, the large number of unassigned masses typical of PMF peak lists was considerably attenuated. As a result, protein identifications could be made with greater confidence and improved discrimination as compared to PMF queries submitted with raw peak lists. Importantly, this scheme for removal of non-peptide masses was found to conserve peptides bearing various post-translational and artificial modifications. All PMF experiments discussed here were performed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), which provided the high mass resolution and high mass accuracy essential for this application. Previously reported equations relating the nominal peptide mass to the permissible range of fractional peptide masses were slightly modified for this application, and these adjustments have been illustrated in detail. The role of mass accuracy in application of this scheme has also been explored. Keywords: Peptide mass fingerprinting • peptide residual mass • matrix-assisted laser desorption/ionization • Fourier transform ion cyclotron resonance mass spectrometry
Losartan Attenuates Bleomycin-Induced Pulmonary Fibrosis in Rats (2005)

Losartan had an inhibitory effect on bleomycin-induced pulmonary fibrosis, and its effect may be associated with its anti-free radicals and the reduction in TGF-beta1.
Secure Processors Part II: Intel SGX Security Analysis and MIT Sanctum Architecture (2017)

This manuscript is the second in a two part survey and analysis of the state of the art in secure processor systems, with a specific focus on remote software attestation and software isolation. The first part established the taxonomy and prerequisite concepts relevant to an examination of the state of the art in trusted remote computation: attested software isolation containers (enclaves). This second part extends Part I’s description of Intel’s Software Guard Extensions (SGX), an available and documented enclave-capable system, with a rigorous security analysis of SGX as a system for trusted remote computation. This part documents the authors’ concerns over the shortcomings of SGX as a secure system and introduces the MIT Sanctum processor developed by the authors: a system designed to offer stronger security guarantees, lend itself better to analysis and formal verification, and offer a more straightforward and complete threat model than the Intel system, all with an equivalent programming model. This two part work advocates a principled, transparent, and well-scrutinized approach to system design, and argues that practical guarantees of privacy and integrity for remote computation are achievable at a reasonable design cost and performance overhead.
A pilot study: 131I-Antitenascin monoclonal antibody 81c6 to deliver a 44-Gy resection cavity boost (2008)

The purpose of this study was to determine the feasibility and assess the efficacy and toxicity, among newly diagnosed malignant glioma patients, of administering (131)I-labeled murine antitenascin monoclonal antibody 81C6 ((131)I-81C6) into a surgically created resection cavity (SCRC) to achieve a patient-specific, 44-Gy boost to the 2-cm SCRC margin. A radioactivity dose of (131)I-81C6 calculated to achieve a 44-Gy boost to the SCRC was administered, followed by conventional external beam radiotherapy (XRT) and chemotherapy. Twenty-one patients were enrolled in the study: 16 with glioblastoma multiforme (GBM) and 5 with anaplastic astrocytoma. Twenty patients received the targeted 44-Gy boost (+/-10%) to the SCRC. Attributable toxicity was mild and limited to reversible grade 3 neutropenia or thrombocytopenia (n = 3; 14%), CNS wound infections (n = 3; 14%), and headache (n = 2; 10%). With a median follow-up of 151 weeks, median overall survival times for all patients and those with GBM are 96.6 and 90.6 weeks, respectively; 87% of GBM patients are alive at 1 year. It is feasible to consistently achieve a 44-Gy boost dose to the SCRC margin with patient-specific dosing of (131)I-81C6. Our study regimen ((131)I-81C6 + XRT + temozolomide) was well tolerated and had encouraging survival. To determine if selection of good-prognosis patients affects outcome associated with this approach, the U.S. Food and Drug Administration has approved a trial randomizing newly diagnosed GBM patients to either our study regimen or standard XRT plus temozolomide.
Stressed to Death: Regulation of Apoptotic Signaling Pathways by the Heat Shock Proteins (2001)

Cellular damage can engage two fundamental cellular responses: apoptosis, a precisely regulated form of cell death; and the heat shock protein (Hsp), or stress response, which functions to protect cells and to mediate an accelerated recovery following damage. The coordinated balance between these two opposing pathways governs the ultimate fate of the cell--whether it lives or dies. The self-destruction of a cell is mediated by one of many signaling pathways culminating in the activation of the caspase proteases. The Hsps regulate the activity of multiple intracellular signaling intermediates, many of which are intimately involved in the execution of the apoptotic signaling pathways. This review addresses whether the antiapoptotic activities of several Hsps, including Hsp70, Hsp90, and Hsp27, can be attributed to their collective ability to regulate the activities, expression, or both of apoptotic signaling molecules. In summary, the functional interface between the ancient heat shock or stress protein response and the highly conserved biochemical pathways leading to the activation of apoptosis governs the susceptibility of a cell to damaging stimuli.
A novel assay for DNA ligase (1991)

Journal Article A novel assay for DNA ligase Get access John Goodchild, John Goodchild * Worcester Foundation for Experimental Biology222 Maple Avenue, Shrewsbury, MA 01545, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Jamboor K. Vishwanatha Jamboor K. Vishwanatha Worcester Foundation for Experimental Biology222 Maple Avenue, Shrewsbury, MA 01545, USA + Present address: Department of Biochemistry, University of Nebraska Medical Center, 600 South 42nd St., Omaha, NE 68198, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 13, 11 July 1991, Page 3745, https://doi.org/10.1093/nar/19.13.3745 Published: 11 July 1991 Article history Accepted: 21 May 1991 Published: 11 July 1991
The 2B domain of the <i>Escherichia coli</i> Rep protein is not required for DNA helicase activity (2002)

The Escherichia coli Rep protein is a 3' to 5' SF1 DNA helicase required for replication of bacteriophage phiX174 in E. coli, and is structurally homologous to the E. coli UvrD helicase and the Bacillus stearothermophilus PcrA helicase. Previous crystallographic studies of Rep protein bound to single-stranded DNA revealed that it can undergo a large conformational change consisting of an approximately 130 degrees rotation of its 2B subdomain about a hinge region connected to the 2A subdomain. Based on crystallographic studies of PcrA, its 2B subdomain has been proposed to form part of its duplex DNA binding site and to play a role in duplex destabilization. To test the role of the 2B subdomain in Rep-catalyzed duplex DNA unwinding, we have deleted its 2B subdomain, replacing it with three glycines, to form the RepDelta2B protein. This RepDelta2B protein can support phiX174 replication in a rep(-) E. coli strain, although the growth rate of E. coli containing the repDelta2B gene is approximately 1.5-fold slower than with the wild-type rep gene. Pre-steady-state, single-turnover DNA unwinding kinetics experiments show that purified RepDelta2B protein has DNA helicase activity in vitro and unwinds an 18-bp DNA duplex with rates at least as fast as wild-type Rep, and with higher extents of unwinding and higher affinity for the DNA substrate. These studies show that the 2B domain of Rep is not required for DNA helicase activity in vivo or in vitro, and that it does not facilitate DNA unwinding in vitro.
Probiotic strains detect and suppress cholera in mice (2018)

Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy to promote colonization resistance and point-of-need diagnosis of cholera, an acute diarrheal disease caused by the pathogen <i>Vibrio cholerae</i> Oral administration of <i>Lactococcus lactis</i>, a common dietary fermentative bacterium, reduced intestinal <i>V. cholerae</i> burden and improved survival in infected infant mice through the production of lactic acid. Furthermore, we engineered an <i>L. lactis</i> strain that specifically detects quorum-sensing signals of <i>V. cholerae</i> in the gut and triggers expression of an enzymatic reporter that is readily detected in fecal samples. We postulate that preventive dietary interventions with fermented foods containing natural and engineered <i>L. lactis</i> strains may hinder cholera progression and improve disease surveillance in populations at risk of cholera outbreaks.
From location to position management: User tracking for location-based services (2005)

A "new" scenario is proposed for baryogenesis. We show that the delayed decay of colored Higgs particles in grand unified theories may generate an excess baryon number of the empirically desired amount, if the mass of the heaviest neutrino is in the range 0.02 eV<m(nu(3))<0.8 eV, provided that neutrinos are of the Majorana type. The scenario accommodates the case of degenerate neutrino masses, in contrast to the usual leptogenesis scenario, which does not work when three neutrino masses are degenerate.
A STUDY ON ETHNOMEDICINAL USES OF YARTSHAGUMBA, CORDYCEPS SINENSIS (BERK.) SACC. (CORDYCIPITACEAE), BY THE TRIBAL COMMUNITIES OF NORTH SIKKIM AND ITS CONSERVATION (2013)

Cordyceps sinensis (Berk.) Sacc. is commonly known as ‘Caterpillar Fungus’ as it is parasitic on the larvae of different insects of Dipters and Lepidoptera groups. This fungus is of great medicinal value. The whole range of Himalayas, particularly the eastern region is the native place of this taxon. Sikkim, a tiny beautiful state of India also harbours this fungus in some specific high altitude areas (4000-5500 m). The stromatic part develops from the head of the caterpillar having pungent odour even when dried. The ethnic communities of Sikkim, viz. Lapchas, Nepalese, Bhutias, Sherpas etc. use this organism for the remedy of different physical disorders including sexual impotency. It has also some effect on wild animals like Yak. The traditional uses, of this fungus by different tribal communities of North Sikkim including its other medicinal uses and conservation aspects are described.
Evaluation of Factors Affecting CGMS Calibration (2006)

Although accuracy is slightly improved with more calibrations, the timing of the calibrations appears more important. Modifying the algorithm to put less weight on daytime calibrations for nighttime values and calibrating during times of relative glucose stability may have greater impact on accuracy.
An agent control mechanism in virtual worlds for mobile users (2005)

We are developing a system that defines virtual worlds and present them as overlaying them onto the real world. People can visit them when they are walking about in a real city, with mobile terminals. We can define virtual buildings and virtual creatures as elements of a virtual world. For example, a virtual world may be an imaginary space of a role playing game scenario, and virtual creatures take their roles in the game. In this paper, we describe the agent control mechanism in virtual worlds and its implementation.
Views of Helical Peptides: A Proposal for the Position of 310-Helix along the Thermodynamic Folding Pathway (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTViews of Helical Peptides: A Proposal for the Position of 310-Helix along the Thermodynamic Folding PathwayGlenn L. MillhauserCite this: Biochemistry 1995, 34, 12, 3873–3877Publication Date (Print):March 28, 1995Publication History Published online1 May 2002Published inissue 28 March 1995https://pubs.acs.org/doi/10.1021/bi00012a001https://doi.org/10.1021/bi00012a001research-articleACS PublicationsRequest reuse permissionsArticle Views435Altmetric-Citations157LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Wound healing for the clinician. (1987)

Wound healing is a complex sequence of events, beginning with tissue injury, mediated by inflammation, and ending long after reepithelialization is complete. Research and controlled clinical experience have provided a better understanding so that clinicians can influence the events of healing to decrease pain, control bleeding, infection, and cosmetic result as well as speed the time for complete healing. The following is a summary of guidelines for the management of wound healing: (1) wound creation; wounds should be created with minimal necrosis of tissue in order to prevent delays in healing. Electrosurgical, cryosurgical, and laser surgical wounds heal more slowly than wounds created by scalpel excision or curettage. Electro-coagulation should be used sparingly in sutured wounds. Large lesions are best treated in a single stage rather than in divided treatments since the rate of wound healing is not proportional to the area but instead to the logarithm of the area. Thus, the total healing time is much shorter if done in a single treatment session. (2) use of drugs; corticosteroids given before or within three days of wounding in dose of prednisone 40 mg or greater will inhibit wound healing. Vitamin A topically or systemically may reverse this inhibition. Aspirin and other nonsteroidal anti-inflammatory agents are more important for their effects on platelet function and bleeding than on wound healing. (3) wound dressings; the use of occlusive dressings to promote moist wound healing is the most significant advance in wound management. Occlusive dressings shorten the time for healing, decrease pain, reduce wound contamination, and improve the cosmetic result. (4) control of wound contraction and scar formation; at the time of wound formation, guiding sutures may be helpful in wound healing by secondary intention in order to control the direction of wound contraction and prevent distortion. Intralesional steroids may be useful for hypertrophic scars and keloids. (5) identification of complications; early identification of certain complications can prevent the delays in healing. These include infection, remembering infrequently cultured organisms such as yeast, malnourishment with protein and mineral deficiency, and the knowledge that adhesive-backed wound dressings can cause rewounding of otherwise normally healing wounds. (6) predicting the cosmetic result; wounds healed by secondary intention may provide a cosmetic result superior to surgical repair. Wounds in concave areas usually heal with a better result than wounds managed by flaps or grafts although wounds on convex surfaces usually look best if a skillful primary closure can be performed without distortion.(ABSTRACT TRUNCATED AT 400 WORDS)
Venous leg ulcer patient priorities and quality of care: results of a survey. (2004)

A comprehensive patient evaluation of quality of care encompasses assessment and patient-rated prioritization of the various provisions of care. One hundred consecutive venous leg ulcer patients treated in a multidisciplinary wound healing center were invited to participate in a cross-sectional study to assess the quality of and assign priority to 28 aspects of medical technical, interpersonal, and organizational care. The response rate to the mailed questionnaire and follow-up telephone survey was 80%. Almost half (46%) of patients (median age 76 years, range 30 to 92) had an ulcer history of >5 years. Seventy-three patients (91%) were satisfied with the overall quality of care. A linear relationship was observed between average assessment score and the relative importance of the quality aspects studied. The quality of medical technical care and empathy aspects of interpersonal care received the most positive assessments and were given highest priority. Next in importance were the quality and coherence of information provided and cooperation between different healthcare sectors. Organizational aspects of care were less positively assessed and received lower priority ratings. Venous leg ulcer care, as provided in a multidisciplinary wound healing center, was assessed as satisfactory by patients, but areas for improvement - notably, cooperation between healthcare sectors and continuity of care - were observed.
A compact dual-band common-mode filtering component for EMC in wireless communication (2015)

A dual-band common-mode filter is proposed to improve the electromagnetic compatibility (EMC) of wireless communication. Implemented in low-temperature co-fired ceramic (LTCC) fabrication as a component, the filter is with a compact size of 3 × 3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The common mode noise can be reduced over 10 dB form 1.3 GHz to 3.2 GHz and from 5.0 GHz to 6.0 GHz, where the most-used wireless communication bands are involved. Besides, insertion loss of differential mode signal is less than 3 dB from DC to 8 GHz, which implies high data transmission quality.
Growth characteristics of marrow hematopoietic progenitor/precursor cells from patients on a phase I clinical trial with purified recombinant human granulocyte-macrophage colony-stimulating factor. (1988)

Bone marrow cells from patients with leukemia, myelodysplastic syndromes, cancer, and other disorders on a phase I clinical trial with recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) were assessed in vitro for numbers of granulocyte-macrophage (CFU-GM), erythroid (BFU-E), and multipotential (CFU-GEMM) progenitor cells, and for growth patterns (colony-to-cluster ratio) of CFU-GM, cycling rates of CFU-GM, and responsiveness in vitro to colony-stimulating and colony-inhibiting factors. The colony-to-cluster ratio of CFU-GM and the dose-response curves of CFU-GM to stimulation by rhGM-CSF in vitro did not change during the clinical trial. However, the percentage of CFU-GM in DNA synthesis, which is a measure of the proliferative rates of these cells, determined by the high specific activity tritiated thymidine kill technique in vitro, was markedly enhanced in a reversible fashion after administration in vivo of rhGM-CSF. The increased cycling rates of CFU-GM were consistent with the induced increase in neutrophil counts in these patients that has been reported elsewhere. Additionally, marrow CFU-GM from patients given rhGM-CSF in vivo were increased in sensitivity to inhibition in vitro by recombinant human H-subunit (acidic) ferritin in two of eight cases, and were increased in sensitivity to inhibition by lower dosages of recombinant human tumor necrosis factor alpha in all patients evaluated. The sensitivity of CFU-GM to inhibition in vitro by recombinant human interferon gamma and prostaglandin E1 did not change during the clinical trial. These studies demonstrate that the rhGM-CSF is having an effect on CFU-GM in the patients on the phase I clinical trial. This information may be of significance in planning future clinical studies combining rhGM-CSF with chemotherapy and/or other biotherapy.
Heavy‐Metal Oxide Glasses (1992)

Heavy‐metal oxide glasses might arbitrarily be defined as those containing over 50 cation percent of bismuth and lead which participate in the glass structure as network formers. Glass systems based on these heavy‐metal oxides in silicates, borates, phosphates, germanates, and ferrites are surveyed. Gallate systems are emphasized since they have a unique ability to form stable glasses while maintaining key properties, such as the best infrared transmission and the highest nonlinear optical susceptibilities and diamagnetic Verdet constants for oxide glasses.
Real-Time Analysis of G Protein-Coupled Receptor Signaling in Live Cells (2006)

Seven transmembrane-spanning receptors, widely referred to as G protein-coupled receptors (GPCRs), mediate a broad spectrum of extracellular signals at the plasma membrane through G proteins, thereby modulating a variety of biological processes. In addition to G proteins, they also interact with a number of other cytoplasmic proteins. Thus, methods to understand GPCR signaling and their interactions with intracellular proteins in real time in live cells are of importance. Recent developments in microscopy methods and the availability of fluorescent proteins facilitated the development of techniques to unravel these interactions more precisely. This chapter describes the methodology for sequential capturing of images of membrane and cytoplasmic proteins fused to different fluorescence probes to understand GPCR interaction with cytosolic proteins and their colocalization.