gebhart/patrepeval huggingface dataset:
Modulation of Phagocytosis of Apoptotic Neutrophils by Supernatant from Dexamethasone-Treated Macrophages and Annexin-Derived Peptide Ac2–26 (2005)

Phagocytic clearance of apoptotic leukocytes plays an important role in the resolution of inflammation. The glucocorticoid-inducible protein annexin 1 and annexin 1-derived peptides show potent anti-inflammatory responses in acute and chronic inflammation. In this study, we report that the annexin 1-derived peptide (Ac(2-26)) significantly stimulates nonphlogistic phagocytosis of apoptotic polymorphonuclear leukocytes (PMNs) by human monocyte-derived macrophages (Mphi). Peptide Ac(2-26)-stimulated phagocytosis is accompanied by rearrangement of the Mphi actin cytoskeleton. To investigate the potential role of endogenous annexin on clearance of apoptotic cells, Mphi were cultured for 5 days in the presence of dexamethasone. Supernatants collected from dexamethasone-treated Mphi significantly enhanced the ability of naive Mphi to engulf apoptotic PMNs. This effect was blocked by an annexin blocking Ab, by immunodepletion of the supernatants, and by the formyl peptide receptor/lipoxin receptor antagonist Boc1. In addition, we show that bone marrow-derived Mphi from annexin 1-null mice present a 40% decreased phagocytosis of apoptotic PMNs compared with cells taken from littermate controls. In conclusion, these results emphasize the pivotal role of annexin 1 as mediator for clearance of apoptotic cells and expand its potential therapeutic role in controlling inflammatory diseases.
GenDB--an open source genome annotation system for prokaryote genomes (2003)

The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To account for the individual needs of different projects, such a system should be modular and easily extensible. We present a genome annotation system for prokaryote genomes, which is well tested and readily adaptable to different tasks. The modular system was developed using an object-oriented approach, and it relies on a relational database backend. Using a well defined application programmers interface (API), the system can be linked easily to other systems. GenDB supports manual as well as automatic annotation strategies. The software currently is in use in more than a dozen microbial genome annotation projects. In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale evaluation of different annotation strategies. The system is open source.
Evaluation of Three Rapid Methods for Detection of Methicillin Resistance inStaphylococcus aureus (2000)

The probe-based Velogene Rapid MRSA Identification Assay (ID Biomedical Corp., Vancouver, British Columbia, Canada) and the latex agglutination MRSA-Screen (Denka Seiken Co., Tokyo, Japan) were evaluated for their ability to identify methicillin-resistant Staphylococcus aureus (MRSA) and to distinguish strains of MRSA from borderline oxacillin-resistant S. aureus (BORSA; mecA-negative, oxacillin MICs of 2 to 8 microgram/ml). The Velogene is a 90-min assay using a chimeric probe to detect the mecA gene. MRSA-Screen is a 15-min latex agglutination test with penicillin-binding protein 2a antibody-sensitized latex particles. We compared these assays with the BBL Crystal MRSA ID System (Becton Dickinson, Cockeysville, Md.) and with PCR for mecA gene detection. A total of 397 clinical isolates of S. aureus were tested, consisting of 164 methicillin-susceptible strains, 197 MRSA strains, and 37 BORSA strains. All assays performed well for the identification of MRSA with sensitivities and specificities for Velogene, MRSA-Screen, and BBL Crystal MRSA ID of 98.5 and 100%, 98.5 and 100%, and 98.5 and 98%, respectively. Three MRSA strains were not correctly identified by each of the Velogene and MRSA-Screen assays, but repeat testing with a larger inoculum resolved the discrepancies. The BBL Crystal MRSA ID test misclassified four BORSA strains as MRSA. Both the Velogene and the MRSA-Screen assays are easy to perform, can accurately differentiate BORSA isolates from MRSA isolates, and provide a rapid alternative for the detection of methicillin resistance in S. aureus in clinical laboratories, especially when mecA PCR gene detection is unavailable.
Mn2(2,5-disulfhydrylbenzene-1,4-dicarboxylate): A Microporous Metal–Organic Framework with Infinite (−Mn–S−)∞ Chains and High Intrinsic Charge Mobility (2013)

The reaction of MnCl2 with 2,5-disulfhydrylbenzene-1,4-dicarboxylic acid (H4DSBDC), in which the phenol groups in 2,5-dihydroxybenzene-1,4-dicarboxylic acid (H4DOBDC) have been replaced by thiophenol units, led to the isolation of Mn2(DSBDC), a thiolated analogue of the M2(DOBDC) series of metal-organic frameworks (MOFs). The sulfur atoms participate in infinite one-dimensional Mn-S chains, and Mn2(DSBDC) shows a high surface area and high charge mobility similar to that found in some of the most common organic semiconductors. The synthetic approach to Mn2(DSBDC) and its excellent electronic properties provide a blueprint for a potentially rich area of exploration in microporous conductive MOFs with low-dimensional charge transport pathways.
Heparinase I from Flavobacterium heparinum: The Role of the Cysteine Residue in Catalysis as Probed by Chemical Modification and Site-Directed Mutagenesis (1995)

Heparinase I (heparin lyase I, EC 4.2.2.7), a heparin-degrading enzyme produced by Flavobacterium heparinum, is used to deheparinize blood following extracorporeal procedures in surgery and in other applications. The present study of mapping and characterization of the cysteines of heparinase I represents the first structural characterization of a heparinase. [3H]Iodoacetic acid labeling demonstrated that heparinase I has two free cysteines. One of the two cysteines is surface accessible and lies in a hydrophilic environment while the other is in a hydrophobic environment. Chemical modification of the cysteines, both in the presence and in the absence of heparin, suggests that the surface-accessible cysteine lies in or near the active site of heparinase I. Preferential reactivity of this cysteine with negatively charged sulfhydryl-modifying reagents and the cysteines' high reactivity to iodoacetic acid at pH 6.5 indicate that the surface-accessible cysteine is in a positively charged region. The surface-accessible cysteine (cysteine-135) was mapped as the active-site cysteine by radiolabeling with [3H]iodoacetic acid and by tryptic digestion and peptide sequencing. Site-directed mutagenesis of cysteine-135 to a serine or an alanine in r-heparinase I demonstrates that this cysteine is essential for enzymatic activity. However, replacement of the surface-inaccessible cysteine by a serine or alanine has no effect.
Velvet-noise decorrelator (2017)

Decorrelation of audio signals is an important process in the spatial reproduction of sounds. For instance, a mono signal that is spread on multiple loudspeakers should be decorrelated for each channel to avoid undesirable comb-filtering artifacts. The process of decorrelating the signal itself is a compromise aiming to reduce the correlation as much as possible while minimizing both the sound coloration and the computing cost. A popular decorrelation method, convolving a sound signal with a short sequence of exponentially decaying white noise which, however, requires the use of the FFT for fast convolution and may cause some latency. Here we propose a decorrelator based on a sparse random sequence called velvet noise, which achieves comparable results without latency and at a smaller computing cost. A segmented temporal decay envelope can also be implemented for further optimizations. Using the proposed method, we found that a decorrelation filter, of similar perceptual attributes to white noise, could be implemented using 87% less operations. Informal listening tests suggest that the resulting decorrelation filter performs comparably to an equivalent white-noise filter.
TatC Is a Specificity Determinant for Protein Secretion via the Twin-arginine Translocation Pathway (2000)

The recent discovery of a ubiquitous translocation pathway, specifically required for proteins with a twin-arginine motif in their signal peptide, has focused interest on its membrane-bound components, one of which is known as TatC. Unlike most organisms of which the genome has been sequenced completely, the Gram-positive eubacterium Bacillus subtilis contains two tatC-like genes denoted tatCd and tatCy. The corresponding TatCd and TatCy proteins have the potential to be involved in the translocation of 27 proteins with putative twin-arginine signal peptides of which approximately 6-14 are likely to be secreted into the growth medium. Using a proteomic approach, we show that PhoD of B. subtilis, a phosphodiesterase belonging to a novel protein family of which all known members are synthesized with typical twin-arginine signal peptides, is secreted via the twin-arginine translocation pathway. Strikingly, TatCd is of major importance for the secretion of PhoD, whereas TatCy is not required for this process. Thus, TatC appears to be a specificity determinant for protein secretion via the Tat pathway. Based on our observations, we hypothesize that the TatC-determined pathway specificity is based on specific interactions between TatC-like proteins and other pathway components, such as TatA, of which three paralogues are present in B. subtilis.
Comparative ultrastructural study on the cell envelopes of Rickettsia prowazekii, Rickettsia rickettsii, and Rickettsia tsutsugamushi (1978)

Rickettsia tsutsugamushi differs from other rickettsiae in its cell envelope organization. The differences were made evident through a comparative study of the outer envelope of R. tsutsugamushi, R. prowazekii, and R. rickettsii by electron microscopy.
Graphene-based materials as supercapacitor electrodes (2010)

Graphene is an emerging carbon material that may soon find practical applications. With its unusual properties, graphene is a potential electrode material for electrochemical energy storage. This article highlights recent research progress in graphene-based materials as supercapacitor electrodes. With a brief description of the working principle of supercapacitors, research progress towards the synthesis and modification of graphene-based materials, including graphene oxide, fullerenes, and carbon nanotubes, is presented. Applications of such materials with desirable properties to meet the specific requirements for the design and configuration of advanced supercapacitor devices are summarized and discussed. Future research trends towards new approaches to the design and synthesis of graphene-based nanostructures and architectures for electrochemical energy storage are proposed.
Dependence of polymerase chain reaction product inactivation protocols on amplicon length and sequence composition (1993)

Specific diagnostic test results generated by polymerase chain reaction (PCR) depend upon control of amplicon contamination in the clinical laboratory. We compared photochemical (isopsoralen [IP]) and enzymatic (uracil N-glycosylase [UNG]) methods for their ability to prevent carryover of amplicons generated from genomic targets of five viruses. PCR products (amplicons) (herpes simplex virus, 342 bp; cytomegalovirus, 250 bp; Epstein-Barr virus, 240 bp) exposed to UV light in the presence of various concentrations of IP compound 10 (IP-10) resulted in apparent increased molecular sizes of the products, as indicated by migration patterns after gel electrophoresis, and were predictive of inactivation by the agent. For amplicons of < or = 100 bp, IP-10-induced electrophoretic shifts were related to the guanidine-cytidine (G + C) content of the PCR product; no apparent shift and no inactivation were observed for a 92-bp herpes simplex virus amplicon (G + C content, 65%), whereas the 100-bp human papillomavirus product (G + C content, 42%) showed a concentration-dependent shift (25 to 100 micrograms/ml) in electrophoretic migration and was partially inactivated. UNG effectively controlled amplicon carryover for target DNA of > or = 240 bp; however, this treatment did not inactivate the two amplicons of < or = 100 bp, regardless of the G + C content of the product. Larger products were inactivated efficiently by both methods, regardless of their G + C contents. We concluded that both IP and UNG effectively inactivated PCR amplicons but not short amplicons of < or = 100 bp. We recommend that with the adoption of PCR technology in clinical laboratories, primers should be designed to produce amplicons of at least 240 to 350 bp (depending on G + C content) and that at least one effective method of controlling carryover contamination should be incorporated into each PCR protocol.
Service-oriented device communications using the devices profile for web services (2005)

This paper outlines the benefits of adopting service-oriented architectures at the level of communications between resource-constrained embedded devices. It focuses on the usage of the Devices Profile for Web Services as the underpinning of such architectures for "smart" devices and discusses an early implementation thereof. It further illustrates how "dumb" or "legacy" devices can be integrated using a gatewaying approach.
Transcriptional regulation of immunoglobulin V genes (1981)

The relative transcriptional activity of rearranged and unrearranged (germline) VK genes in secreting plasmacytoma cells was assessed by two independent methods. Measurements of V sequence abundance by hybridization kinetic (Rot) analysis indicated that the steady state content of transcripts from a rearranged VK gene is at least 16,000-fold greater than that from an unrearranged VK gene. Direct measurements of transcriptional activity in isolated nuclei indicated that this difference is due, in large part to a difference in transcription rate. Since the primary sequences of V genes and their 5' flanking regions are not altered during rearrangement, these results suggest that VK gene transcription might be controlled by elements on the 3' side of the VK genes or at the CK locus, perhaps via an influence on chromatin structure.
Inhibition of Translation of mRNAs Containing γ-Monomethylphosphate Cap Structure in Frog Oocytes and in Mammalian Cells (2001)

The gamma-monomethylphosphate cap structure is found in several eukaryotic small RNAs including nuclear U6, U6atac, 7SK, plant nucleolar U3, and rodent cytoplasmic B2 RNAs. In the case of human U6 snRNA, the 5' end sequence corresponding to nucleotides 1-25 serves as the capping signal and directs the formation of methylphosphate cap structure. In this study, we show that the U6 RNA capping signal, when introduced at the 5' end of RNAs, can efficiently direct the methylphosphate cap formation in RNAs of up to 2.7 kb long, as well as in different mRNAs. These data show that the methylphosphate capping signal functions in mRNAs having different primary sequences and different lengths. Presence of the methylphosphate cap structure on the 5' end of a luciferase mRNA with EMCV 5' noncoding region, which is translated in an IRES-dependent pathway, resulted in a 6- to 100-fold inhibition of translation compared to the same mRNA with a 5' triphosphate when microinjected into frog oocytes or expressed in mouse cells in tissue culture. Thus, conversion of the pppG structure to a methyl-pppG structure on the 5' end of an mRNA, which is translated in an IRES-dependent pathway, results in severe inhibition of translation. These data show that the 5' end motif of mRNAs plays an important role even in the IRES-mediated mRNA translation.
Unfolding of apomyoglobin helices by synchrotron radiolysis and mass spectrometry (2001)

The synchrotron X-ray protein radiolysis technique is based on a quantitative determination of the extent and the site of millisecond radiolytic oxidation of amino-acid side chains by mass spectrometry. The amino acids most susceptible to radiolytic oxidation are cysteine, methionine, phenylalanine, tyrosine, tryptophan, proline, histidine, and leucine. These residues serve as reactive markers within a protein structure that can be used to monitor changes in solvent accessibility during folding or as part of macromolecular interactions. To monitor the unfolding, the extent of radiolytic products of side chains of reactive amino acids is quantitatively measured by mass spectrometry as a function of the denaturant concentration following proteolysis. This approach provides site-specific unfolding isotherms for various segments of a protein without the use of mutation or labeling techniques. Application of this technique to the equilibrium urea unfolding of apomyoglobin at pH 7.8 has demonstrated the cooperative unfolding of helices A to C consistent with midpoints, DeltaG, and m values derived from fluorescence data. The G helix, in contrast, showed a local unfolding behavior. The similarity of the thermodynamic data derived by this synchrotron-based method for helix A (containing two oxidizable tryptophan residues) to that of the fluorescence data indicates that the limited oxidation of proteins by exposure to X-rays on millisecond timescales does not alter the structure of apomyglobin. This supports the viability of the method for the study of protein folding and the mapping of protein interaction sites.
The Wilms tumor suppressor gene WT1 induces G1 arrest and apoptosis in myeloblastic leukemia M1 cells (1997)

WT1 was isolated as a tumor suppressor gene of Wilms tumor. However, high expression of WT1 correlates with poor prognosis in acute leukemia. In addition suppression of WT1 expression by WT1 anti-sense oligonucleotide inhibits proliferation of leukemia cells, suggesting that WT1 is important for their proliferation. To further elucidate the biological significance of WT1 in leukemic cell growth, we overexpressed exogenous WT1 in murine M1 myeloblastic leukemia cells using the isopropyl-beta-D-thiogalactoside (IPTG)-controlled expression system. We found that induction of one splicing variant of WT1 [WT1-17AA(+)-KTS(-)] in M1 cells induces cell cycle arrest and apoptotic cell death. These results suggest that the role of WT1 is different depending on the type of leukemia cell in which it is expressed.
Very Mild Senile Dementia of the Alzheimer Type (1989)

We report a longitudinal study of 16 subjects originally enrolled in the Washington University (St Louis, Mo) Memory and Aging Project with Clinical Dementia Rating (CDR) of "questionable" dementia (CDR 0.5). A 0.5 rating was intended to characterize subjects in whom mild cognitive impairment due to senile dementia of the Alzheimer type was suspected but was insufficient in degree to warrant a diagnosis of definite dementia. Over an 84-month follow-up period, 11 of the 16 subjects either had Alzheimer's disease verified post mortem or had clinically progressed to a more advanced CDR stage in which the dementia was clearly evident. These results suggest that the CDR 0.5 stage likely represents the incipient clinical manifestation of Alzheimer's disease and that the majority of subjects with CDR 0.5 have "very mild senile dementia of the Alzheimer type." Performance on several standard clinical scales was significantly different when comparing a larger sample of controls (n = 83), subjects with CDR 0.5 (n = 41), and subjects with mild senile dementia of the Alzheimer type (score of 1; n = 68).
An Active Immune Defense with a Minimal CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) RNA and without the Cas6 Protein (2014)

The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3' handle are still active in triggering an interference reaction. The complete 3' handle could be removed without loss of activity. However, manipulations of the 5' handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference.
An ontological approach to domain engineering (2002)

Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain engineering that aims to join ontologies and object-oriented technology.
Clinical effects of tumor-associated macrophages and dendritic cells on renal cell carcinoma. (2003)

Several reports have documented infiltration of many monocytes in renal cell carcinoma (RCC). Since few studies have examined the relationship between monocyte infiltration and clinical prognosis in RCC, we clinically investigated this relationship by semi-quantitative analysis of monocyte infiltration and tumor angiogenesis. The following six parameters were measured immunohistologically in 98 RCC patients who underwent nephrectomy between 1987 and 1997: tumor-associated macrophage (TAM), microvessel density (MVD), S-100 protein-positive cells (S-100(+) cells), HLA-DR-positive cells, apoptosis index and proliferative index (PI). We then assessed intercorrelations among parameters and correlations to prognosis. Significant positive correlations were identified for TAM, MVD and PI, with a tendency for higher parameter values to reflect poorer prognosis. The prognosis of patients without metastasis was poor for the high TAM group even when levels of MVD were low. These findings suggest that TAM facilitates the growth of RCC via angiogenesis and other mechanisms. Prognosis was significantly better in metastatic RCC patients who underwent interferon-alpha (IFN-alpha) therapy when the levels of S-100(+) cells were high. Nonetheless, the levels of S-100(+) cells among these IFN-treated patients did not correlate with other parameters, and none of the other parameters correlated with prognosis. One of the antitumor effects of IFN-alpha for RCC could therefore be mediated by dendritic cells.
Detecting Graves' Disease (1996)

Graves' disease has a multitude of presentations, and certain symptoms can mimic sports-related concerns such as overtraining. A review of three cases of Graves' disease in young athletes illustrates the spectrum of symptoms and the pathophysiology. Diagnosis involves a detailed patient history, physical exam, and appropriate lab studies, including a thyroid radioactive iodine uptake scan. Treatment consists of symptom management and antithyroid medication, radioactive iodine thyroid ablation, or, rarely, thyroidectomy.
Characterization of Mucosal Biofilms on Human Adenoid Tissues (2008)

This study demonstrates that adenoid tissue in children with chronic or/and recurrent otitis media contains mucosal biofilms in 54% of the cases. The existence of living bacteria has been demonstrated. Further studies are required to describe the panel of bacteria that can be harbored in the biofilms present in adenoids and the mechanisms involved in the physiopathology of otitis prone children.