gebhart/patrepeval huggingface dataset:
Respiratory Disease Trends in the Pulmonary Complications of HIV Infection Study Cohort. Pulmonary Complications of HIV Infection Study Group (1997)

We examined trends in the incidence of specific respiratory disorders in a multicenter cohort with progressive human immunodeficiency virus (HIV) disease during a 5-yr period. Individuals with a wide range of HIV disease severity belonging to three transmission categories were evaluated at regular intervals and for episodic respiratory symptoms using standard diagnostic algorithms. Yearly incidence rates of respiratory diagnoses were assessed in the cohort as a whole and according to CD4 count or HIV transmission category. The most frequent respiratory disorders were upper respiratory tract infections, but the incidence of lower respiratory tract infections increased as CD4 counts declined. Specific lower respiratory infections followed distinctive patterns according to study-entry CD4 count and transmission category. Acute bronchitis was the predominant lower respiratory infection of cohort members with entry CD4 counts > or = 200 cells/mm3. In cohort members with entry CD4 counts of 200 to 499 cells/mm3, the incidence of bacterial and Pneumocystis carinii pneumonia each increased an average of 40% per year. In members with entry CD4 counts < 200 cells/mm3, acute bronchitis, bacterial pneumonia, and P. carinii pneumonia occurred at high rates without discernible time trends, despite chemoprophylaxis in more than 80% after Year 1, and the rate of other pulmonary opportunistic infections increased over time. Each year, injecting drug users had a higher incidence of bacterial pneumonia than did homosexual men. The yearly rate of tuberculosis was < 3 episodes/100 person-yr in each entry CD4 and HIV-transmission group. We conclude that the time trends of HIV-associated respiratory disorders are determined by HIV disease stage and influenced by transmission category. Whereas acute bronchitis is prevalent during all stages of HIV infection, incidence rates of bacterial pneumonia and P. carinii pneumonia rise continuously during progression to advanced disease. In advanced disease, the incidence of acute bronchitis, bacterial pneumonia and P. carinii pneumonia is high despite widespread chemoprophylaxis.
Intrinsically Disordered Proteins in Human Diseases: Introducing the D2Concept (2008)

Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structures under physiological conditions in vitro. They are highly abundant in nature and their functional repertoire complements the functions of ordered proteins. IDPs are involved in regulation, signaling, and control, where binding to multiple partners and high-specificity/low-affinity interactions play a crucial role. Functions of IDPs are tuned via alternative splicing and posttranslational modifications. Intrinsic disorder is a unique structural feature that enables IDPs to participate in both one-to-many and many-to-one signaling. Numerous IDPs are associated with human diseases, including cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, and diabetes. Overall, intriguing interconnections among intrinsic disorder, cell signaling, and human diseases suggest that protein conformational diseases may result not only from protein misfolding, but also from misidentification, missignaling, and unnatural or nonnative folding. IDPs, such as alpha-synuclein, tau protein, p53, and BRCA1, are attractive targets for drugs modulating protein-protein interactions. From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept.
Isolation of cairomycins A and C (1981)

Cairomycin B in the fermentation broths of Streptomyces sp. strain AS-C-19 accompanied cairomycin A and cairomycin C. The cairomycins are peptides with potent activity against gram-positive bacteria. On acid hydrolysis, cairomycin A yielded valine and aspartic acid, whereas cairomycin C yielded lysine, glycine, valine, leucine, and aspartic acid, as identified by paper and gas chromatography. These amino acids were found to exist in their alpha-L form. Cairomycin A was tentatively assigned a 6-isopropyl-2,5-diketopiperazine-3-acetic acid structure. The three cairomycins were distinct from each other in their ultraviolet, infrared, and mass spectra; elemental analyses; and their chromatographic behavior in different developing solvents.
Studies on Reactive Surfactants. I. (1966)

Some higher hydroxamic acids and their acetyl derivatives were prepared from methyl esters of various fatty acids, and cotton clothes were treated with aqueous dispersion or solution of these reactive surfactants.Authors found that acetylated hydroxamic acids except that from perfluoro fatty acid easily reacted with cotton in the presence of alkali such as Na2CO3 and that the cotton treated with homologues higher than C16 showed durable water-repellency and excellent softness.It seemed that the inactivity of perfluoro dihydroxamate was due to the difficulty of its Lossen rearrangement.
Poly(ADP-ribose) polymerase is a catalytic dimer and the automodification reaction is intermolecular. (1993)

We have determined the molecular mechanism of the automodification reaction of poly(ADP-ribose) polymerase (PARP) (EC 2.4.2.30). While PARP-mono(ADP-ribose) conjugates were the predominant products of automodification at 200 nM NAD, enzyme-bound branched polymers were preferentially synthesized at 200 microM NAD. Thus, the initiation, elongation, and branching reactions catalyzed by PARP appear to be [NAD]-dependent. Initial rates of automodification increased with second order kinetics as a function of [PARP] at both 200 nM and 200 microM NAD. Therefore, 2 molecules of PARP, i.e. a catalytic dimer, are required for the auto-mono(ADP-ribosyl)ation and the auto-poly(ADP-ribosyl)ation reactions. Initial rates of automodification also increased with second order kinetics at low NAD concentrations. Therefore, the catalytic dimer also requires 2 molecules of NAD. These results are consistent with the conclusion that the automodification reaction of PARP is intermolecular and that the 2 monomeric units of PARP may simultaneously function as catalyst and acceptor molecules in the automodification reaction. Confirmatory evidence for the catalytic role of protein-protein interactions in the automodification reaction was manifested by a marked inhibition of auto-poly(ADP-ribosyl)ation at 40 nM or higher [PARP].
Specific Cues Associated With Honey Bee Social Defence against Varroa destructor Infested Brood (2016)

Social immunity forms an essential part of the defence repertoire of social insects. In response to infestation by the parasitic mite Varroa destructor and its associated viruses, honey bees (Apis mellifera L.) have developed a specific behaviour (varroa-sensitive hygiene, or VSH) that helps protect the colony from this parasite. Brood cells heavily infested with mites are uncapped, the brood killed, and the cell contents removed. For this extreme sacrifice to be beneficial to the colony, the targeting of parasitized brood for removal must be accurate and selective. Here we show that varroa-infested brood produce uniquely identifiable cues that could be used by VSH-performing bees to identify with high specificity which brood cells to sacrifice. This selective elimination of mite-infested brood is a disease resistance strategy analogous to programmed cell death, where young bees likely to be highly dysfunctional as adults are sacrificed for the greater good of the colony.
Targeted delivery of antigens to the gut-associated lymphoid tissues: 2.Ex vivoevaluation of lectin-labelled albumin microspheres for targeted delivery of antigens to the M-cells of the Peyer's patches (2010)

The purpose of this study was to evaluate the possibility of lectin-coupled microspheres to improve the targeted delivery of protein antigens to the lymphoid tissues of mucosal surfaces. Bovine serum albumin containing acid phosphatase model protein and polystyrene microspheres were coupled with mouse M-cell-specific Ulex europaeus lectin. The coupling efficiency, physical characteristics and the binding capabilities of the microspheres to the follicle associated epithelium of the Peyer's patches were evaluated in vitro and ex vivo in mice intestine. The results showed that coupling of lectin to albumin microspheres did not significantly affect the bioactivity of the encapsulated acid phosphatase model protein. It was also shown that there was preferential binding of the lectin-coupled microspheres to the follicle-associated epithelium. It was concluded from the results of the study that coupling of ligands such as lectin specific to cells of the follicle associated epithelium can increase the targeting of encapsulated candidate antigens for delivery to the Peyer's patches of the intestine for improved oral delivery.
Transferring Age and Gender Attributes for Dimensional Emotion Prediction from Big Speech Data Using Hierarchical Deep Learning (2018)

The continuous speech emotion prediction is a challenging task. This research has many important applications in real-life, especially on human-computer interaction and its applications are expected to become increasingly wider and deeper. Previous studies have show that three dimensional attributes of emotion such as arousal, valence and dominance are related each other. Moreover, age and gender of speaker affect the recognition of speech emotion. Based on these observation, we propose a new dimensional attributes prediction model using multi-task learning, aiming to improve the emotion recognition performance and generalization capabilities. The present methods utilize the big speech data to train the age and gender submodel, which will be transferred to the main modelłła hierarchical deep learning model, using age and gender as the high level attributes of the emotion. The publicly available databases IEMOCAP and aGender have been conducted to evaluate the performance and the accuracy of the proposed work. Experiment results of within-corpus evaluation show that the proposed approach has superior performance compared to state of the art result.
Segmentation of tuberculosis bacilli in ziehl-neelsen-stained tissue images based on k-mean clustering procedure (2010)

In this paper, an automatic k-mean clustering based on C-Y colour model was proposed. First, initial filter is used to remove the tissues images which remain blue after counterstaining process. Secondly, k-mean clustering using saturation component of C-Y colour model is used to segment the TB bacilli from its undesirable background which also remains red even after decolourization process. Thirdly, a 5 × 5 median filter and region growing was used to eliminate small regions and noises. The proposed methods have been analysed for several TB slide images under various conditions. The results show that the proposed techniques were successfully segment TB bacilli from its background. Hence, the resultant images would furnish more useful information for further analysis by pathologists.
Analysis of a Protein-Binding Domain of p53 (1993)

The tumor suppressor protein p53 was first isolated as a simian virus 40 large T antigen-associated protein and subsequently was found to function in cell proliferation control. Tumor-derived mutations in p53 occur predominantly in four evolutionarily conserved regions spanning approximately 50% of the polypeptide. Previously, three of these regions were identified as essential for T-antigen binding. We have examined the interaction between p53 and T antigen by using Escherichia coli-expressed human p53. By a combination of deletion analysis and antibody inhibition studies, a region of p53 that is both necessary and sufficient for binding to T antigen has been localized. This function is contained within residues 94 to 293, which include the four conserved regions affected by mutation in tumors. Residues 94 to 293 of p53 were expressed in both wild-type and mutant forms. T-antigen binding was unaffected by tumor-derived mutations which have been associated with the wild-type conformation of p53 but was greatly reduced by mutations which were previously shown to alter p53 conformation. Our results show that, like T-antigen binding to the Rb tumor suppressor protein, T antigen appears to interact with the domain of p53 that is commonly mutated in human tumors.
Morphoregulatory molecules (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMorphoregulatory moleculesGerald M. EdelmanCite this: Biochemistry 1988, 27, 10, 3533–3543Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://doi.org/10.1021/bi00410a001RIGHTS & PERMISSIONSArticle Views90Altmetric-Citations233LEARN 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 InReddit PDF (6 MB) Get e-Alerts Get e-Alerts
Alkaline quinone flow battery (2015)

Storage of photovoltaic and wind electricity in batteries could solve the mismatch problem between the intermittent supply of these renewable resources and variable demand. Flow batteries permit more economical long-duration discharge than solid-electrode batteries by using liquid electrolytes stored outside of the battery. We report an alkaline flow battery based on redox-active organic molecules that are composed entirely of Earth-abundant elements and are nontoxic, nonflammable, and safe for use in residential and commercial environments. The battery operates efficiently with high power density near room temperature. These results demonstrate the stability and performance of redox-active organic molecules in alkaline flow batteries, potentially enabling cost-effective stationary storage of renewable energy.
Covalently-Immobilized Vascular Endothelial Growth Factor Promotes Endothelial Cell Tubulogenesis in Poly(ethylene glycol) Diacrylate Hydrogels (2009)

The development and use of functional tissue-engineered products is currently limited by the challenge of incorporating microvasculature. To this end, we have investigated strategies to facilitate vascularization in scaffold materials, in this case poly(ethylene glycol) (PEG) hydrogels. These hydrogels are hydrophilic and resist protein adsorption and subsequent non-specific cell adhesion, but can be modified to contain cell-adhesive ligands and growth factors to support cell and tissue function. Additionally, the hydrogel matrix can include proteolytically degradable peptide sequences in the backbone of the structure to allow cells to control scaffold biodegradation, allowing three-dimensional migration. Vascular endothelial growth factor (VEGF), a potent angiogenic signal, and the cell-adhesive peptide RGDS were each covalently attached to PEG monoacrylate linkers. PEGylated RGDS and VEGF were then covalently immobilized in PEG-diacrylate (PEGDA) hydrogels in 2D and 3D. Immobilized VEGF increased endothelial cell tubulogenesis on the surface of non-degradable PEGDA hydrogels 4-fold compared to controls without the growth factor. Endothelial cell behavior in 3D collagenase-degradable hydrogels modified with RGDS and VEGF was observed using time-lapse confocal microscopy. Bulk immobilization of VEGF in 3D collagenase-degradable RGDS-modified hydrogels increased endothelial cell motility 14-fold and cell-cell connections 3-fold. Covalent incorporation of PEGylated VEGF in PEG hydrogels can be a useful tool to promote endothelial cell migration, cell-cell contact formation and tubulogenesis in an effort to produce vascularized tissue-engineered constructs.
Electroanalysis of nicotine at an electroreduced carboxylated graphene modified glassy carbon electrode (2014)

Nicotine is determined at a glassy carbon electrode modified with partially electroreduced carboxylated graphene by cyclic voltammetry and semi-derivative treatment after enrichment at −1.1 V in 0.1 M pH 7.0 phosphate buffer solution.
Urinary Proteome Analysis using Capillary Electrophoresis Coupled to Mass Spectrometry: A Powerful Tool in Clinical Diagnosis, Prognosis and Therapy Evaluation (2009)

Urinary Proteome Analysis using Capillary Electrophoresis Coupled to Mass Spectrometry: A Powerful Tool in Clinical Diagnosis, Prognosis and Therapy Evaluation Proteome analysis has emerged as a powerful tool to decipher (patho) physiological processes, resulting in the establishment of the field of clinical proteomics. One of the main goals is to discover biomarkers for diseases from tissues and body fluids. Due to the enormous complexity of the proteome, a separation step is required for mass spectrometry (MS)-based proteome analysis. In this review, the advantages and limitations of protein separation by two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization and capillary electrophoresis (CE) for proteomic analysis are described, focusing on CE-MS. CE-MS enables separation and detection of the small molecular weight proteome in biological fluids with high reproducibility and accuracy in one single processing step and in a short time. As sensitive and specific single biomarkers generally may not exist, a strategy to overcome this diagnostic void is shifting from single analyte detection to simultaneous analysis of multiple analytes that together form a disease-specific pattern. Such approaches, however, are accompanied with additional challenges, which we will outline in this review. Besides the choice of adequate technological platforms, a high level of standardization of proteomic measurements and data processing is also necessary to establish proteomic profiling. In this regard, demands concerning study design, choice of specimens, sample preparation, proteomic data mining, and clinical evaluation should be considered before performing a proteomic study.
Spatio-temporal modeling of video data for on-line object-oriented query processing (2002)

The paper presents a framework for data modeling and semantic abstraction of image/video data. The framework is based on spatio-temporal information associated with salient objects in an image or in a sequence of video frames and on a set of generalized n-ary operators defined to specify spatial and temporal relationships of objects present in the data. The methodology presented in this paper can manifest itself effectively in conceptualizing events and heterogeneous views in multimedia data as perceived by individual users. The proposed paradigm induces a multilevel indexing and searching mechanism that models information at various levels of granularity and hence allows processing of content-based queries in real time. We also devise a unified object-oriented interface for users with heterogeneous views to specify queries on the unbiased encoded data. This framework is being developed to realize a highly integrated multimedia database architecture.
Removal of Arsenic(III) from Groundwater by Nanoscale Zero-Valent Iron (2005)

Nanoscale zero-valent iron (NZVI) was synthesized and tested for the removal of As(III), which is a highly toxic, mobile, and predominant arsenic species in anoxic groundwater. We used SEM-EDX, AFM, and XRD to characterize particle size, surface morphology, and corrosion layers formed on pristine NZVI and As(III)-treated NZVI. AFM results showed that particle size ranged from 1 to 120 nm. XRD and SEM results revealed that NZVI gradually converted to magnetite/maghemite corrosion products mixed with lepidocrocite over 60 d. Arsenic(III) adsorption kinetics were rapid and occurred on a scale of minutes following a pseudo-first-order rate expression with observed reaction rate constants (K(obs)) of 0.07-1.3 min(-1) (at varied NZVI concentration). These values are about 1000x higher than K(obs) literature values for As(III) adsorption on micron size ZVI. Batch experiments were performed to determine the feasibility of NZVI as an adsorbent for As(III) treatment in groundwater as affected by initial As(III) concentration and pH (pH 3-12). The maximum As(III) adsorption capacity in batch experiments calculated by Freundlich adsorption isotherm was 3.5 mg of As(III)/g of NZVI. Laser light scattering (electrophoretic mobility measurement) confirmed NZVI-As(III) inner-sphere surface complexation. The effects of competing anions showed HCO3-, H4SiO4(0), and H2P04(2-) are potential interferences in the As(III) adsorption reaction. Our results suggest that NZVI is a suitable candidate for both in-situ and ex-situ groundwater treatment due to its high reactivity.
siRNA Versus miRNA as Therapeutics for Gene Silencing (2015)

Discovered a little over two decades ago, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are noncoding RNAs with important roles in gene regulation. They have recently been investigated as novel classes of therapeutic agents for the treatment of a wide range of disorders including cancers and infections. Clinical trials of siRNA- and miRNA-based drugs have already been initiated. siRNAs and miRNAs share many similarities, both are short duplex RNA molecules that exert gene silencing effects at the post-transcriptional level by targeting messenger RNA (mRNA), yet their mechanisms of action and clinical applications are distinct. The major difference between siRNAs and miRNAs is that the former are highly specific with only one mRNA target, whereas the latter have multiple targets. The therapeutic approaches of siRNAs and miRNAs are therefore very different. Hence, this review provides a comparison between therapeutic siRNAs and miRNAs in terms of their mechanisms of action, physicochemical properties, delivery, and clinical applications. Moreover, the challenges in developing both classes of RNA as therapeutics are also discussed.
Mechanical properties of human middle ear tissues. (2007)

Mechanical properties of four middle ear tissues were then employed in a published 3-dimensional finite element model of human ear with an accurate geometric configuration to investigate the transfer function of human middle ear in ligament related pathological conditions. The model predicted results were compared with temporal bone experimental data, and a good agreement between modeling results and experimental data were observed.
Corticosteroid Treatment and Functional Improvement in Duchenne Muscular Dystrophy (2005)

Prednisone and deflazacort have a significant beneficial effect on slowing the disease progress. Their usage in Duchenne muscular dystrophy may prolong ambulation and upper limb function with similar potency. Both steroids also improve pulmonary function, in addition to delaying the need for spinal interventions, with similar therapeutic profiles.