gebhart/patrepeval huggingface dataset:
PalmPred: An SVM Based Palmitoylation Prediction Method Using Sequence Profile Information (2014)

Protein palmitoylation is the covalent attachment of the 16-carbon fatty acid palmitate to a cysteine residue. It is the most common acylation of protein and occurs only in eukaryotes. Palmitoylation plays an important role in the regulation of protein subcellular localization, stability, translocation to lipid rafts and many other protein functions. Hence, the accurate prediction of palmitoylation site(s) can help in understanding the molecular mechanism of palmitoylation and also in designing various related experiments. Here we present a novel in silico predictor called 'PalmPred' to identify palmitoylation sites from protein sequence information using a support vector machine model. The best performance of PalmPred was obtained by incorporating sequence conservation features of peptide of window size 11 using a leave-one-out approach. It helped in achieving an accuracy of 91.98%, sensitivity of 79.23%, specificity of 94.30%, and Matthews Correlation Coefficient of 0.71. PalmPred outperformed existing palmitoylation site prediction methods - IFS-Palm and WAP-Palm on an independent dataset. Based on these measures it can be anticipated that PalmPred will be helpful in identifying candidate palmitoylation sites. All the source datasets, standalone and web-server are available at http://14.139.227.92/mkumar/palmpred/.
Understanding Health Information Seeking from an Actor-Centric Perspective (2015)

This paper presents a conceptual approach for discussing health information seeking among poor households in Africa and Asia. This approach is part of a larger research endeavor aimed at understanding how health systems are adapting; with possibilities and constraints emerging. These health systems can be found in a context of the changing relationships between states, markets and civil society in low and middle income countries. The paper starts from an understanding of the health sector as a "health knowledge economy", organized to provide people with access to knowledge and advice. The use of the term "health knowledge economy" draws attention to the ways the health sector is part of a broader knowledge economy changing the way individuals and households obtain and use specialist information. The paper integrates an actor centric approach with the theory of planned behavior. It seeks to identify the actors engaged in the health knowledge economy as a precursor to longer term studies on the uptake of innovations integrating health services with mobile phones, commonly designated as mHealth, contributing to an understanding of the potential vulnerabilities of poor people, and highlighting possible dangers if providers of health information and advice are strongly influenced by interest groups.
STL-based Finish Machining of Rapid Manufacturing Parts and Tools (2001)

Accuracy and surface quality problems when utilizing layered manufacturing technologies have limited its use in tooling areas. Therefore, in some situations a CNC machine is still necessary for finish machining of rapid manufactured parts and tools. This paper presents a STL-based CNC machining technique for automating the finishing of RP tools and parts to obtain CNC accuracies and surface finishes. Preprocess operations, such as rotate and scale, are used to change the part orientation and compensate for shrinkage in the whole process. An offset algorithm is developed to add “skin” to the original STL file to make sure enough material is left for finish machining after the rapid manufacturing process. The machining strategy of adaptive raster milling of the surface, plus hole drilling and sharp edge contour machining, is proposed to finish the RP parts and tools. Corresponding algorithms of adaptive tool path generation for raster milling, automatic hole recognition and drilling tool path generation, and automatic sharp edge detection and tool path generation are developed. Finally, a designed benchmark is machined successfully by using the above mentioned machining strategies and tool paths generated by developed software.
Hello, It’s GPT-2 - How Can I Help You? Towards the Use of Pretrained Language Models for Task-Oriented Dialogue Systems (2019)

Data scarcity is a long-standing and crucial challenge that hinders quick development of task-oriented dialogue systems across multiple domains: task-oriented dialogue models are expected to learn grammar, syntax, dialogue reasoning, decision making, and language generation from absurdly small amounts of taskspecific data. In this paper, we demonstrate that recent progress in language modeling pretraining and transfer learning shows promise to overcome this problem. We propose a taskoriented dialogue model that operates solely on text input: it effectively bypasses explicit policy and language generation modules. Building on top of the TransferTransfo framework Our automatic and human evaluations show that the proposed model is on par with a strong task-specific neural baseline. In the long run, our approach holds promise to mitigate the data scarcity problem, and to support the construction of more engaging and more eloquent task-oriented conversational agents.
Integration of mass spectrometry in analytical biotechnology (1991)

Mass spectrometry (MS) has become an indispensable tool for peptide and protein structure analysis because of three unique capabilities that enable it to be used to solve structural problems not easily handled by conventional techniques. First, MS is able to provide accurate molecular weight information on low-picomole amounts of peptides and proteins independent of covalent modifications that may be present. Second, this information is obtainable for peptides present in complex mixtures such as those that result from a proteolytic digest of a protein. Third, by using tandem MS, partial to complete sequence information may be obtained for peptides containing up to 25 amino acid residues, even if the peptides are present in mixtures. Sensitivity and speed of the MS-based approaches now equal (and in some cases exceed) that of Edman-based sequence analysis. In this perspective we discuss how MS, tandem high-performance MS, and on-line liquid chromatography/MS using fast atom bombardment or electrospray ionization have been integrated with more conventional techniques in order to increase the accuracy and speed of peptide and protein structure characterization. The expanding role of matrix-assisted laser desorption MS in protein analysis is also described. The unique niche that MS occupies for locating and structurally characterizing posttranslational modifications of proteins is emphasized. Examples chosen from the authors' laboratory illustrate how MS is used to sequence blocked proteins, define N- and C-terminal sequence heterogeneity, locate and correct errors in DNA- and cDNA-deduced protein sequences, identify sites of deamidation, isoaspartyl formation, phosphorylation, oxidation, disulfide bond formation, and glycosylation, and define the structural class of carbohydrate at specific attachment sites in glycoproteins.
Cirrhotic Liver Expresses Low Levels of the Full-Length and Truncated Growth Hormone Receptors<sup>1</sup> (1998)

In cirrhosis, as in other conditions of protein catabolism, there is a state of acquired GH resistance, as defined by high circulating GH levels with low insulin-like growth factor I levels. However, patients with end-stage liver failure respond to supraphysiological doses of GH with an increase in circulating insulin-like growth factor I levels. The present study represents a detailed analysis of GH receptor (GHR) expression in cirrhotic liver from 17 patients with end-stage liver disease. Specific binding of labeled GH was identified in all cirrhotic livers studied. The binding affinity for the GHR was similar in cirrhotic and normal livers, but the number of binding sites per mg protein of liver membrane was variable in both normal and cirrhotic liver, although it were generally lower in cirrhotic liver. GHR expression was identified in cirrhotic liver by Northern blotting, RT-PCR, and ribonuclease protection assay. On Northern blotting, a single transcript of 4.8 kb was identified in normal and cirrhotic tissues. RT-PCR identified expression of both full-length GHR and a truncated form of the GHR; this was confirmed by ribonuclease protection assay. In situ hybridization and immunohistochemistry confirmed the expression of GHR in regenerating hepatocytes and isolated cells in fibrous tissue. In conclusion, 1) the low level of GHR in cirrhotic liver may contribute to the acquired GH resistance found in cirrhotic patients; 2) the reduced expression of both full-length and truncated GHR is compatible with the low level of GH-binding protein found in cirrhosis, as this truncated receptor has previously been reported to generate large amounts of GH-binding protein; and 3) the demonstration of GH binding to cirrhotic liver explains why these patients with GH resistance may still respond to supraphysiological doses of GH.
<i>Staphylococcus aureus</i> golden pigment impairs neutrophil killing and promotes virulence through its antioxidant activity (2005)

Golden color imparted by carotenoid pigments is the eponymous feature of the human pathogen Staphylococcus aureus. Here we demonstrate a role of this hallmark phenotype in virulence. Compared with the wild-type (WT) bacterium, a S. aureus mutant with disrupted carotenoid biosynthesis is more susceptible to oxidant killing, has impaired neutrophil survival, and is less pathogenic in a mouse subcutaneous abscess model. The survival advantage of WT S. aureus over the carotenoid-deficient mutant is lost upon inhibition of neutrophil oxidative burst or in human or murine nicotinamide adenine dinucleotide phosphate oxidase-deficient hosts. Conversely, heterologous expression of the S. aureus carotenoid in the nonpigmented Streptococcus pyogenes confers enhanced oxidant and neutrophil resistance and increased animal virulence. Blocking S. aureus carotenogenesis increases oxidant sensitivity and decreases whole-blood survival, suggesting a novel target for antibiotic therapy.
Distribution of VGF peptides in the human cortex and their selective changes in Parkinson’s and Alzheimer’s diseases (2010)

VGF mRNA and its precursor-derived products are selectively expressed in certain neurons and promptly respond to neurotrophins and to neural/electrical activity. Proteomic studies have previously revealed a reduction in some VGF peptides in the cerebrospinal fluid of patients affected by Alzheimer's disease and other conditions, suggesting their potential diagnostic and clinical significance. As the presence of VGF peptides within the human cortex has been somewhat elucidated, they were studied postmortem in the frontal, parietal, and temporal cortex areas of control subjects and patients affected by Parkinson's disease, and in parietal cortex samples from patients with Alzheimer's disease. We raised antibodies to the C-/N-terminal portions of the proVGF precursor protein, to the TPGH and TLQP sequences and to the neuroendocrine regulatory peptide (NERP)-1, all used for enzyme-linked immunosorbent assay coupled with gel chromatography and for immunohistochemistry. In the control brain samples, the levels of TPGH and C-terminus peptides were about 130-200 and 700-2000 pmol g⁻¹, respectively, the N-terminus and NERP-1 peptides were less represented (about 10-30 and 4-20 pmol g⁻¹, respectively), and the TLQP peptides were below detection limits. Upon gel chromatography, the VGF antisera mainly revealed small molecular weight forms (i.e. about 0.8-1.3 kDa), whereas VGF immunolocalisation was found within different types of neuron in rat and bovine brain cortices. In the Parkinson's disease samples, a clear-cut decrease was revealed in the parietal cortex only, exclusively for TPGH and NERP-1 peptides, whereas in the Alzheimer's disease samples, a reduction in all of the VGF peptides was shown. The results suggest the involvement of VGF in the physiological or pathophysiological mechanisms occurring in the parietal cortex of patients with Parkinson's and Alzheimer's diseases.
Distinct pathophysiologic mechanisms of septic acute kidney injury (2012)

Pathogenesis of septic acute kidney injury is thought to be different from that of ischemia/reperfusion-induced acute kidney injury. Our data showed a link between apoptosis, immune suppression, and the development of acute kidney injury during sepsis and suggest that strategies targeting apoptosis or enhancing immunity might be a potential therapeutic strategy for septic acute kidney injury.
Programming Tools for Rapid NFV-Based Media Application Development in 5G Networks (2018)

The emergence of virtualisation and Infrastructure-as-a-Service (IaaS) have dramatically transformed the telecom industry through network function virtualisation (NFV). A recently introduced cloud-native concept, Platform as a Service (PaaS), ensures to further boost the performance, portability and cost efficiency of the NFV. The 5G-MEDIA project proposes the application of a serverless paradigm known as Function-as-a- Service (FaaS) to NFV for the media applications exploiting the 5G technologies. In addition to integration of FaaS, the 5G-MEDIA application/service development kit (SDK) supports microservice-based application development for both hypervisor-based and containerized approaches, specifically supporting Docker, unikernel and LXC. In this paper, we provide an overview of the 5G-MEDIA SDK which is built to support NFV-based next generation media applications and to achieve a development time in the order of minutes. Furthermore, implementations of FaaS Emulation and FaaS command line interface (CLI) tools are also presented.
A Comparison of the Thermodynamic and Kinematic Features in Recent Blizzard and Near-Blizzard Events in Iowa (2022)

Abstract The purpose of this research is to determine the validity of the subjective, anecdotal rule that four isobars present across Iowa during a wintertime, snow-bearing, extratropical cyclone is sufficient to create the winds that attend a blizzard (the “Four Isobar Rule”). Using data from the National Centers for Environmental Information's online Storm Event Database, we identified 15 cases of blizzards in Iowa over the course of 10 years (1999-2009 plus one event in 2010). Subjective analyses of mean sea level pressure for those 15 events revealed an 87% success rate of having four isobars present corresponding with the Blizzard events. Conversely, we also analyzed 23 Near-Blizzard events and discovered that approximately 74% did not have four isobars present. Clearly, there is overlap between these types of events. Composite meteorological fields of both case sets were completed using the North America Regional Reanalysis datasets. The composite results are generally consistent with other recent findings on Iowa blizzards. The surface low is often fairly deep (&lt;1000 hPa), occluded or nearly so, featuring a convergent, descending lower troposphere, with 850-hPa winds of 45 kt or greater, and a near-surface layer whose lapse rate is nearly dry adiabatic. The composites of storms in the Blizzard category are slightly weaker than in prior literature, but the composites of storms in the Near-Blizzard category fail to meet any of the criteria for a blizzard in the state of Iowa.
Separation of Alcaligenes denitrificans sp. nov., nom. rev. from Alcaligenes faecalis on the Basis of DNA Base Composition, DNA Homology, and Nitrate Reduction (1983)

“Alcaligenes denitrificans” Leifson and Hugh 1954 was not included in the Approved Lists of Bacterial Names and hence has no standing in bacteriological nomenclature. However, Alcaligenes faecalis DSM 30026 (“A. denitrificans” Leifson and Hugh 1954, type strain) has a DNA base composition of 69.1 ± 0.3 mol% G+C, whereas A. faecalis DSM 30030 (type strain) and A. faecalis DSM 30033 (“A. odorans” type strain) have 57.6 ± 0.5 and 55.3 ± 0.8 mol% G+C, respectively. DNA hybridization revealed homologies of 27% between A. faecalis DSM 30026T and strain DSM 30030T, 26% between A. faecalis DSM 30026T and strain DSM 30033T, but 71% between strains DSM 30030T and DSM 30033T. A yellow fluorescent pigment in King medium B was produced by A. faecalis strains DSM 30030T and DSM 30033T but not by strain DSM 30026T. Only A. faecalis DSM 30026T was able to grow with nitrate or nitrite as sole source of nitrogen and to reduce nitrate to nitrite and gas. All three strains reduced nitrite to gas, but an additional nitrogen source, e.g., ammonium ion, was necessary for the growth of strains DSM 30030T and DSM 30033T. In mineral media, the nitrate reduction to nitrite and gas has been shown to be reproducible. Based on the differences among A. faecalis DSM 30026 and both A. faecalis DSM 30030T and DSM 30033T, the revival of the name Alcaligenes denitrificans is herein proposed.
Crystal structure and spectroscopic properties of violet glutathione-copper(II) complex with axial sulfur coordination and two copper sites via a disulfide bridge (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal structure and spectroscopic properties of violet glutathione-copper(II) complex with axial sulfur coordination and two copper sites via a disulfide bridgeKiyonori Miyoshi, Yukio Sugiura, Kazuhiko Ishizu, Yoichi Iitaka, and Hikaru NakamuraCite this: J. Am. Chem. Soc. 1980, 102, 19, 6130–6136Publication Date (Print):September 1, 1980Publication History Published online1 May 2002Published inissue 1 September 1980https://pubs.acs.org/doi/10.1021/ja00539a027https://doi.org/10.1021/ja00539a027research-articleACS PublicationsRequest reuse permissionsArticle Views687Altmetric-Citations68LEARN 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
Erste Demoprojekte zur solarunterstützten Nahwärmeversorgung (1995)

Die Ergebnisse einer standortspezifischen Machbarkeitsstudie (1992) für zentrale solarunterstützte Heizungsanlagen mit Langzeit-Wärmespeicher (engl. CSHPSS = Central Solar Heating Plant with Seasonal Storage) in Deutschland zeigen, daß solare Deckungsanteile von 50 – 70 % erreicht werden können zu solaren Wärmepreisen zwischen 20 und 30 Pf/kWh /1/.
Dual-band bandpass filter based on slow-wave resonant cell with dual-resonance (2016)

A novel dual-band bandpass filter (BPF) is proposed in this paper. The BPF consists of two slow-wave resonant cells, which is composed of a microstrip T-stub and nested interdigital defected ground structure with the broadside-coupled (BC) transition. Strong slow-wave effect is employed by this structure, which leads to ultra-wide stopband response. Meanwhile, the nested interdigital defected ground structure (DGS) utilized under the T-stub can allocate dual-resonance with a compact size. To verify the aforementioned mechanism, an ultra-wide stopband dual-band BPF with two passbands centered at 2.18 and 2.43 GHz with a 3-dB fractional bandwidth 9.1% and 7.5% is designed and fabricated. The results from the simulation and measurement show good agreement.
Naltrexone, an opioid receptor antagonist, attenuates liver fibrosis in bile duct ligated rats (2006)

This is the first study to demonstrate that administration of an opioid antagonist prevents the development of hepatic fibrosis in cirrhosis. Opioids can influence liver fibrogenesis directly via the effect on HSCs and regulation of the redox sensitive mechanisms in the liver.
Human Cytolytic Fusion Proteins: Modified Versions of Human Granzyme B and Angiogenin Have the Potential to Replace Bacterial Toxins in Targeted Therapies against CD64+ Diseases (2014)

Targeted therapies for the treatment of cancer, but also inflammation and autoimmune diseases will reduce major side effects accompanied with conventional treatment modalities. The immunotoxin concept uses bacterial or plant toxins, coupled to antibodies or natural ligands targeting cancer cells. Initially, immunotoxins suffered from drawbacks like nonspecific cytotoxicity. Even the third generation of immunotoxins comprised of truncated antibodies and modified effector molecules experienced clinical set-backs due to immune responses. Long-term treatment of cancer and non-life-threatening chronic inflammatory diseases requires their complete ‘humanization’. This lead to evaluating human cytolytic fusion proteins (hCFPs), based on human apoptosis-inducing proteins. Lacking an endogenous translocation domain dramatically reduces the cell-death inducing capacity of such proteins. Here, we report on optimizing hCFPs, based on the anti-CD64 single chain variable fragment H22(scFv), specifically eliminating CD64+ macrophages and malignant progenitor cells. We replaced the bacterial toxin in H22(scFv)-ETA' with the pro-apoptotic human granzyme B or angiogenin. Translocation was promoted by a sophisticated adapter containing a membrane transfer peptide (MTD) flanked by endosomal and cytosolic cleavable peptides, thus achieving in vitro cytotoxic activity comparable to bacterial immunotoxins. We demonstrate for the first time that optimized hCFPs, based on granzyme B or angiogenin, can compete with classical ETA-based immunotoxins.
Design, analysis and experiments of an omni-directional spherical robot (2011)

This paper presents a novel design of an omni-directional spherical robot that is mainly composed of a lucent ball-shaped shell and an internal driving unit. Two motors installed on the internal driving unit are used to realize the omni-directional motion of the robot, one motor is used to make the robot move straight and another is used to make it steer. Its motion analysis, kinematics modeling and controllability analysis are presented. Two typical motion simulations show that the unevenness of ground has big influence on the open-loop trajectory tracking of the robot. At last, motion performance of this spherical robot in several typical environments is presented with prototype experiments.
Cell based therapy for duchenne muscular dystrophy (2009)

Mutations in the dystrophin gene cause an X-linked genetic disorder: Duchenne muscular dystrophy (DMD). Stem cell therapy is an attractive method to treat DMD because a small number of cells are required to obtain a therapeutic effect. Here, we discussed about multiple types of myogenic stem cells and their possible use to treat DMD. The identification of a stem cell population providing efficient muscle regeneration is critical for the progression of cell therapy for DMD. We speculated that the most promising possibility for the treatment of DMD is a combination of different approaches, such as gene and stem cell therapy.