gebhart/patrepeval huggingface dataset:
Detection of Mycobacterium tuberculosis bacilli in bio-aerosols from untreated TB patients (2017)

<ns4:p> <ns4:bold>Background</ns4:bold> : Tuberculosis (TB) is predominantly an airborne disease. However, quantitative and qualitative analysis of bio-aerosols containing the aetiological agent, <ns4:italic>Mycobacterium tuberculosis (Mtb)</ns4:italic> , has proven very challenging. Our objective is to sample bio-aerosols from newly diagnosed TB patients for detection and enumeration of <ns4:italic>Mtb</ns4:italic> bacilli. </ns4:p> <ns4:p> <ns4:bold>Methods</ns4:bold> : We monitored each of 35 newly diagnosed, GeneXpert sputum-positive, TB patients during 1 hour confinement in a custom-built Respiratory Aerosol Sampling Chamber (RASC). The RASC (a small clean-room of 1.4m <ns4:sup>3</ns4:sup> ) incorporates aerodynamic particle size detection, viable and non-viable sampling devices, real-time CO <ns4:sub>2</ns4:sub> monitoring, and cough sound-recording. Microbiological culture and droplet digital polymerase chain reaction (ddPCR) were used to detect <ns4:italic>Mtb</ns4:italic> in each of the bio-aerosol collection devices. </ns4:p> <ns4:p> <ns4:bold>Results</ns4:bold> : <ns4:italic>Mtb</ns4:italic> was detected in 27/35 (77.1%) of aerosol samples; 15/35 (42.8%) samples were positive by mycobacterial culture and 25/27 (92.96%) were positive by ddPCR. Culturability of collected bacilli was not predicted by radiographic evidence of pulmonary cavitation, sputum smear positivity, or cough rate. <ns4:italic>Mtb</ns4:italic> was detected on all viable cascade impactor stages with a peak at aerosol sizes 2.0-3.5μm. This suggests a median of 0.09 CFU/litre of exhaled air (IQR: 0.07 to 0.3 CFU/l) for the aerosol culture positives and an estimated median concentration of 4.5x10 <ns4:sup>7</ns4:sup> CFU/ml (IQR: 2.9x10 <ns4:sup>7</ns4:sup> -5.6x10 <ns4:sup>7</ns4:sup> ) of exhaled particulate bio-aerosol. </ns4:p> <ns4:p> <ns4:bold>Conclusions</ns4:bold> : <ns4:italic>Mtb</ns4:italic> was identified in bio-aerosols exhaled by the majority of untreated TB patients using the RASC. Molecular detection was more sensitive than mycobacterial culture on solid media, suggesting that further studies are required to determine whether this reflects a significant proportion of differentially detectable bacilli in these samples. </ns4:p>
Design of enhanced agonists through the use of a new virtual screening method: Application to peptides that bind class I major histocompatibility complex (MHC) molecules (2005)

Abstract A new screening procedure is described that uses docking calculations to design enhanced agonist peptides that bind to major histocompatibility complex (MHC) class I receptors. The screening process proceeds via single mutations of one amino acid at the positions that directly interact with the MHC receptor. The energetic and structural effects of these mutations have been studied using fragments of the original ligand that vary in length. The results of these docking studies indicate that the mutant affinity ranking of long peptides can be practically reproduced with a screening approach performed using fragments of six residues. Fragments of four and five residues could mimic, in some cases, the structural arrangement of the side chains of the full‐length peptide. We have compared the structural and energetic results of the docking calculations with experimental data using three unrelated ligand peptides that differ greatly in their affinity for the MHC complex. Analysis of the affinity of the fragments led to the identification of three important parameters in the construction of fragments that mimic the structural and energetic properties of the full‐length ligand: the length of the fragment; its intermolecular energy; and the number and localization, internal or terminal, of the anchor residues. The results of this new peptide‐design methodology have been applied to suggest new peptides derived from the MUC1–8 peptide that could be used as murine vaccines that trigger the immune response through the MHC class I protein H‐2K b .
Identification of an HLA-A2-Restricted Epitope Peptide Derived from Hypoxia-Inducible Protein 2 (HIG2) (2014)

We herein report the identification of an HLA-A2 supertype-restricted epitope peptide derived from hypoxia-inducible protein 2 (HIG2), which is known to be a diagnostic marker and a potential therapeutic target for renal cell carcinoma. Among several candidate peptides predicted by the HLA-binding prediction algorithm, HIG2-9-4 peptide (VLNLYLLGV) was able to effectively induce peptide-specific cytotoxic T lymphocytes (CTLs). The established HIG2-9-4 peptide-specific CTL clone produced interferon-γ (IFN-γ) in response to HIG2-9-4 peptide-pulsed HLA-A*02:01-positive cells, as well as to cells in which HLA-A*02:01 and HIG2 were exogenously introduced. Moreover, the HIG2-9-4 peptide-specific CTL clone exerted cytotoxic activity against HIG2-expressing HLA-A*02:01-positive renal cancer cells, thus suggesting that the HIG2-9-4 peptide is naturally presented on HLA-A*02:01 of HIG-2-expressing cancer cells and is recognized by CTLs. Furthermore, we found that the HIG2-9-4 peptide could also induce CTLs under HLA-A*02:06 restriction. Taken together, these findings indicate that the HIG2-9-4 peptide is a novel HLA-A2 supertype-restricted epitope peptide that could be useful for peptide-based immunotherapy against cancer cells with HIG2 expression.
[Valine and branched-chain amino acids in the treatment of hepatic encephalopathy]. (1993)

We studied the effects of infusion of a liver adapted amino acid solution (Amino-Mel hepa: Group A) versus a liver adapted amino acid solution plus L-valine (Amino-Mel hepa + L-valine: Group B) in 30 patients with decompensated liver cirrhosis with coma. Each 15 patients were randomly allocated to the group A and B, respectively. Both regimens included the infusion of glucose and fat, further supplementation of vitamins and trace elements in addition to the amino acid solution. The results of this study show that in patients with advanced stage of hepatic coma a valine increased supply of branched chain amino acids neither influences the course of the disease nor the death rate. The prognosis of patients with this disease is mainly determined by liver function and accompanying complications.
Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode (2016)

Electroanalysis was performed using a boron-doped diamond (BDD) electrode for the simultaneous detection of 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline (HHQ) and pyocyanin (PYO). PQS and its precursor HHQ are two important signal molecules produced by Pseudomonas aeruginosa, while PYO is a redox active toxin involved in virulence and pathogenesis. This Gram-negative and opportunistic human pathogen is associated with a hospital-acquired infection particularly in patients with compromised immunity and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. Early detection is crucial in the clinical management of this pathogen, with established infections entering a biofilm lifestyle that is refractory to conventional antibiotic therapies. Herein, a detection procedure was optimized and proven for the simultaneous detection of PYO, HHQ and PQS in standard mixtures, biological samples, and P. aeruginosa spiked CF sputum samples with remarkable sensitivity, down to nanomolar levels. Differential pulse voltammetry (DPV) scans were also applicable for monitoring the production of PYO, HHQ and PQS in P. aeruginosa PA14 over 8 h of cultivation. The simultaneous detection of these three compounds represents a molecular signature specific to this pathogen.
Haemozoin detection in infected erythrocytes for Plasmodium falciparum malaria diagnosis—Prospects and limitations (2012)

Several methods based on the detection of the parasite-specific pigment haemozoin (Hz) in blood are currently being investigated as alternative diagnostic methods for malaria. Although this approach may appear attractive, the fact that in Plasmodium falciparum (P. f.) malaria, the severity of which should give it the highest diagnostic priority, the fact that most circulating intra-erythrocytic P. f. parasites contain little or no Hz raises some concern. We used flow cytometry to investigate the possibilities and limitations of the detection of intra-erythrocytic Hz in malaria infected patient blood samples and in vitro cultures. However, reliable detection of ring-forms or young trophozoites of P. f. parasites could not be achieved, although one-quarter of mature parasites could be detected after 24-48 h in culture. Our results strongly suggest that, although it may be useful for monitoring maturation, detection of intra-erythrocytic Hz by flow cytometry will not provide an optimal method for diagnosis of P. falciparum malaria.
LIQUID SLOSHING LOADS UNDER RANDOM EXCITATIONS (1988)

A series of experimental investigations was conducted to examine the liquid sloshing loads under random excitations, using realistic sea states and ship motion characteristics. Short- and long-term probability distributions were then derived form the experimental data. It was found that (1) the randomly excitated sloshing loads are much smaller than those resulting from harmonic excitations with the same RMS excitation amplitude, (2) the observed probabilities are reasonably well represented by the fitted straight lines on a Weibull probability paper, and (3) for non-impulsive forces, the distribution follows closely to the Rayleigh distribution function while some deviation exists for the impulsive forces.
Surface micropattern limits bacterial contamination (2014)

The assays developed in this study mimic hospital environmental contamination events to demonstrate the performance of a MP to limit contamination under multiple conditions. Antimicrobial copper has been implemented in hospital room studies to evaluate its impact on nosocomial infections and a decrease in HAI rate was shown. Similar implementation of the MP has potential to reduce the incidence of HAIs although future clinical studies will be necessary to validate the MP's true impact.
MOS GP computer (1968)

When the 2-phase, 20-bit shift registers using P-channel enhancement mode MOS-FET's were first introduced on the market many of us did not have the foggiest idea of what a MOS-FET was. Logical designers were intrigued by the functional complexity which the technology appeared to offer. System designers were pleased with the prospect of lower power and fewer package requirements. Semiconductor manufacturers predicted that MOS would be forgotten sooner than the tunnel diode.
Fluorescence energy transfer between two triple helix-forming oligonucleotides bound to duplex DNA (1994)

An 11-mer oligopyrimidine was covalently linked via its 5'-phosphate to an acridine derivative (acridine-11-mer), and a 13-mer was covalently linked via its 3'-phosphate to an ethidium derivative (13-mer-ethidium). Each of them formed a triple helix with a 31-bp DNA fragment containing two oligopurine-oligopyrimidine sequences, 11 and 13 bp in length, separated by a variable number of base pairs. When both oligonucleotides were bound to the 31-bp DNA fragment, fluorescence energy transfer (FET) from acridine to ethidium was observed, as revealed by a quenching of acridine fluorescence and a sensitized ethidium emission. FET was temperature-dependent and occurred only when both oligonucleotides were simultaneously bound to the DNA matrix. A single base-pair change in one of the target sequences strongly reduced the energy-transfer efficiency. This method was used to discriminate between a fully complementary and a mismatched target sequence.
Variation for homoeologous gene silencing in hexaploid wheat (2008)

The absence of expression of individual members of a homoeologous set of genes in a polyploid is a well-established phenomenon. However, the extent to which such 'homoeologous silencing' can vary between individual genotypes within a species is unexplored. We have used the single-strand conformation polymorphism assay to identify homoeologue non-expression at 15 single-copy genes across a panel of 16 wheat varieties, representative of the genetic diversity present in modern northern European winter wheat (Triticum aestivum). There was no evidence for any homoeologous silencing at seven of the fifteen genes, but in the remaining eight, at least one of the three homoeologues varied qualitatively for expression in either the root or the seedling leaf. The identity of the non-expressed homoeologue was generally consistent, but when the expression profiles of eight informative genes were compared, only two varieties shared the same pattern of silencing. A small-scale study suggested that silencing patterns were largely inherited across self-pollinated generations, and some evidence is presented for the epigenetic segregation of these patterns in a population bred from parents having contrasting silencing profiles. Epigenetic variation exerts a significant effect on phenotype, so given the ubiquity and variability in homoeologous silencing observed in wheat, we suggest that it is likely to play a considerable role in generating phenotypic variation. Thus epigenetic profiling may need to be incorporated as part of the analytical tool kit for predictive wheat breeding.
A Siglec-like sialic-acid-binding motif revealed in an adenovirus capsid protein (2012)

Sialic-acid-binding immunoglobulin-like lectins (Siglecs) are a family of transmembrane receptors that are well documented to play roles in regulation of innate and adaptive immune responses. To see whether the features that define the molecular recognition of sialic acid were found in other sialic-acid-binding proteins, we analyzed 127 structures with bound sialic acids found in the Protein Data Bank database. Of these, the canine adenovirus 2-fiber knob protein showed close local structural relationship to Siglecs despite low sequence similarity. The fiber knob harbors a noncanonical sialic-acid recognition site, which was then explored for detailed specificity using a custom glycan microarray comprising 58 diverse sialosides. It was found that the adenoviral protein preferentially recognizes the epitope Neu5Acα2-3[6S]Galβ1-4GlcNAc, a structure previously identified as the preferred ligand for Siglec-8 in humans and Siglec-F in mice. Comparison of the Siglec and fiber knob sialic-acid-binding sites reveal conserved structural elements that are not clearly identifiable from the primary amino acid sequence, suggesting a Siglec-like sialic-acid-binding motif that comprises the consensus features of these proteins in complex with sialic acid.
Self‐diffusion of poly (ethylene oxide) fractions and its influence on the crystalline texture (1991)

Abstract Two somewhat separate issues have been delat with: the diffusion coefficients of various poly(ethylene oxide) (PEO) fractions at different temperatures; and morphological observations of spherulitic textures of a PEO mixture containing low‐ and high‐molecular mass components at different supercooling and cooling rates. We found that simultaneous knowledge of diffusion coefficient of PEO fractions and crystal growth rate of the mixture leads to a better description of the crystal growth. As observed, the spherulitic texture of the PEO mixture comprises three texture levels: the spherulite as a whole; the crystalgrowth unit comprised of different number of lamellae in a stack; and the individual lamellar crystal. Under certain crystallization conditions, the thickness of the lamellar stack is on the same order of magnitude as the parameter δ proposed by Keith and Padden.
`Bettergreen' Southernpea (1993)

Additional index words. cowpea, Vigna unguiculata, green cotyledon 'Bettergreen' is a new southernpea [Vigna unguiculata (L.) Walp.] that was
Error concealment using layer structure for JPEG2000 images (2003)

A method of error concealment for JPEG2000 images is proposed in this paper. The proposed method uses the layer structure that is a feature of JPEG2000. The most significant layer is hidden in the lowest layer of the JPEG2000 bit stream, and this embedded layer is used for error concealment. The most significant layer is duplicated because JPEG2000 uses bit-plane coding. In this coding, when the upper layers are affected by errors, the coefficients of the lower layers become meaningless. A bit stream encoded using the proposed method has the same data structure as a standard JPEG2000. Therefore, it can be decoded by a standard decoder. Our simulation results demonstrated the effectiveness of the proposed method.
Structure of chelocardin, a novel tetracycline antibiotic (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of chelocardin, a novel tetracycline antibioticLester A. Mitscher, Janardan V. Juvarkar, William Rosenbrook Jr., William W. Andres, Jay R. Schenck, and Richard S. EganCite this: J. Am. Chem. Soc. 1970, 92, 20, 6070–6071Publication Date (Print):October 1, 1970Publication History Published online1 May 2002Published inissue 1 October 1970https://pubs.acs.org/doi/10.1021/ja00723a049https://doi.org/10.1021/ja00723a049research-articleACS PublicationsRequest reuse permissionsArticle Views253Altmetric-Citations35LEARN 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
Detection of the Free Neutrino: a Confirmation (1956)

8997MetricsTotal Downloads899Last 6 Months141Last 12 Months344Total Citations7Last 6 Months0Last 12 Months0View all metrics
Examination of mitochondrial protein targeting of haem synthetic enzymes: <i>in vivo</i> identification of three functional haem-responsive motifs in 5-aminolaevulinate synthase (2005)

The initial and the terminal three enzymes of the mammalian haem biosynthetic pathway are nuclear encoded, cytoplasmically synthesized and post-translationally translocated into the mitochondrion. The first enzyme, ALAS (5-aminolaevulinate synthase), occurs as an isoenzyme encoded on different chromosomes and is synthesized either as a housekeeping protein (ALAS-1) in all non-erythroid cell types, or only in differentiating erythroid precursor cells (ALAS-2). Both ALAS proteins possess mitochondrial targeting sequences that have putative haem-binding motifs. In the present study, evidence is presented demonstrating that two haem-binding motifs in the leader sequence, as well as one present in the N-terminus of the mature ALAS-1 function in vivo in the haem-regulated translocation of ALAS-1. Coproporphyrinogen oxidase, the antepenultimate pathway enzyme, possesses a leader sequence that is approx. 120 residues long. In contrast with an earlier report suggesting that only 30 residues were required for translocation of the coproporphyrinogen oxidase, we report that the complete leader is necessary for translocation and that this process is not haem-sensitive in vivo. PPO (protoporphyrinogen oxidase) lacks a typical mitochondrial targeting leader sequence and was found to be effectively targeted by just 17 N-terminal residues. Bacillus subtilis PPO, which is very similar to human PPO at its N-terminal end, is not targeted to the mitochondrion when expressed in mammalian cells, demonstrating that the translocation is highly specific with regard to both the length and spacing of charged residues in this targeting region. Ferrochelatase, the terminal enzyme, possesses a typical N-terminal leader sequence and no evidence of a role for the C-terminus was found in mitochondrial targeting.
Absence of lupus anticoagulants in Behcet's disease (1991)

The presence of a lupus anticoagulant was evaluated in patients with Bechet's disease by the kaolin clotting time method. Four percents (three patients) of 69 patients analyzed were found positive for the lupus anticoagulant. However, no statistically significant association existed between the presence of this antibody and the presence of thrombosis, clinical activity, clinical type, antinuclear antibodies and the positive VDRL test.
An Experimental Study on Fire Resistance Performance and Evaluation of Asymmetric Slim Floor Beam (2012)

Composite beam using asymmetric H-shaped steel is one of the constructional structures developed in the advanced countries in Europe since early 1990s. The purpose of this study on composite beams where H-shaped steel is partially laid in concrete slabs was to find how to design fire protection and improve fire-resistance to make deep deck plates provide the beams with advantages upon a fire and to improve stiffness in structural aspect. Only lower flange which is directly exposed to a fire was included in fire-resistance design in order to decide optimal fire- protection design condition and test was conducted for spray-coating and paint-coating. In the fire resistance test, web thickness and lower flange thickness were varied to derive the optimum condition for improving fire-resistance performance. It was observed from the test that 90-minute-protection employed to lower flange provided fire resistance for 3 hours. It was also observed that the basic shape resisted fire for 89 minutes, while web reinforcement and lower flange reinforcement provided fire-resistance for 112 and 157 minutes, respectively. The result showed that lower flange reinforcement is the most effective way to improve fire-resistance.