gebhart/patrepeval huggingface dataset:
The Two-Dimensional Histogram as a Constraint for Protein Phase Improvement (1998)

The joint distribution of electron density and its gradient in a protein electron-density map was examined. This joint distribution was represented by a two-dimensional histogram (2D histogram) of electron-density values and the modulus of the gradient. 16 structures representing distinct protein-fold families were selected to study the dependence of the 2D histogram on resolution, overall temperature factor, structural conformation and phase error. The similarity between the histograms for a pair of structures was measured by correlation coefficient, and the residual provided a measure of the difference. The 2D histogram was found to vary with resolution and overall temperature factor, but was found to be insensitive to structure conformation. The average correlation coefficient between pairs of 2D histograms at three different resolutions examined was 0.90 with a standard deviation of 0.04. The average residual for the same condition was 0.13 with a standard deviation of 0.03. The 2D histogram was also found to be sensitive to phase error. The average correlation coefficient and residual between 2D histograms with 10 degrees phase difference are 0.71 and 0.18, respectively. The variation of the 2D histogram resulting from structure-conformation changes was estimated to be equivalent to that of a 4 degrees phase error. This establishes the minimal phase error that a 2D histogram-matching method could achieve. The conservation of the 2D histogram with respect to structure conformation enables the prediction of the ideal 2D histogram for unknown structures. The sensitivity of the 2D histogram to phase error suggests that it could be used as a target for the density-modification method and also could be used as a figure of merit for phase selection in ab initio phasing.
29 gauge needles improve patient satisfaction over 27 gauge needles for daily glatiramer acetate injections (2009)

Using three surveys, a comparative assessment of needle performance and patient preference for 27-gauge (G) and 29G needles for glatiramer acetate administration for multiple sclerosis therapy was performed. Eligible patients participated in a specialty pharmacy program and administered glatiramer acetate for ≥1 month. In Survey 1 on the 27G needle, 545 (82.70%) patients reported no needle problems, 106 (16.09%) cited one type (dull, bent, or broken), five (0.76%) cited two types, and three (0.46%) cited all three types. In Survey 2 on the 29G needle, 553 (98.05%) indicated no problems, two (0.35%) cited dull needles, and nine (1.60%) cited bent needles. On the 29G needles versus 27G needles pain comparison, 219 (38.83%) reported the 29G needle was a little better, and 155 (27.48%) reported it was a lot better than the 27G. For injection-site experiences, 515 patients (91.31%) reported no, very slight, or mild reactions with the 29G needle. In Survey 3, over 76% of patients preferred the 29G to the 27G needle and significantly fewer patients reported one or more problems with the 29G needle compared to patients reporting problems with the 27G needle (P < 0.00001). In conclusion, significantly fewer patients reported problems after 30 days of use of the 29G than the 27G needle. Fewer injection-site experiences occurred with the 29G needle and the 29G needle was preferred overall.
Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA (2000)

Traditional methods to assay enzymatic cleavage of DNA are discontinuous and time consuming. In contrast, recently developed fluorescence methods are continuous and convenient. However, no fluorescence method has been developed for single-stranded DNA digestion. Here we introduce a novel method, based on molecular beacons, to assay single-stranded DNA cleavage by single strand-specific nucleases. A molecular beacon, a hairpin-shaped DNA probe labeled with a fluorophore and a quencher, is used as the substrate and enzymatic cleavage leads to fluorescence enhancement in the molecular beacon. This method permits real time detection of DNA cleavage and makes it easy to characterize the activity of DNA nucleases and to study the steady-state cleavage reaction kinetics. The excellent sensitivity, reproducibility and convenience will enable molecular beacons to be widely useful for the study of single-stranded DNA cleaving reactions.
Multiple renal cysts, urinary concentration defects, and pulmonary emphysematous changes in mice lacking TAZ (2008)

TAZ (transcriptional coactivator with PDZ-binding motif), also called WWTR1 (WW domain containing transcription regulator 1), is a 14-3-3-binding molecule homologous to Yes-associated protein. TAZ acts as a coactivator for several transcription factors as well as a modulator of membrane-associated PDZ domain-containing proteins, but its (patho)physiological roles remain unknown. Here we show that gene inactivation of TAZ in mice resulted in pathological changes in the kidney and lung that resemble the common human diseases polycystic kidney disease and pulmonary emphysema. Taz-null/lacZ knockin mutant homozygotes demonstrated renal cyst formation as early as embryonic day 15.5 with dilatation of Bowman's capsules and proximal tubules, followed by pelvic dilatation and hydronephrosis. After birth, only one-fifth of TAZ-deficient homozygotes grew to adulthood and demonstrated multicystic kidneys with severe urinary concentrating defects and polyuria. Furthermore, adult TAZ-deficient homozygotes exhibited diffuse emphysematous changes in the lung. Thus TAZ is essential for developmental mechanisms involved in kidney and lung organogenesis, whose disturbance may lead to the pathogenesis of common human diseases.
Emendation of genus Collinsella and proposal of Collinsella stercoris sp. nov. and Collinsella intestinalis sp. nov. (2000)

Collinsella aerofaciens-like strains isolated from human faeces were characterized by biochemical tests, cell wall murein analysis and 16S rDNA analysis. The results indicated that these strains are phylogenetically a member of the family Coriobacteriaceae and close to the genus Collinsella. Their phenotypic characters resembled those of Collinsella aerofaciens. Determination of DNA-DNA relatedness showed that these strains could be divided into two groups (groups 1 and 2). Collinsella aerofaciens and both new groups have A4-type cell wall murein. Based on their phenotypic and phylogenetic characters, two new species of the genus Collinsella are proposed for the isolated strains: Collinsella stercoris for group 1 and Collinsella intestinalis for group 2. Species-specific PCR primer sets for these two species were also constructed. Using these primer sets, Collinsella stercoris and Collinsella intestinalis can be identified easily and rapidly.
RNAi: a novel antisense technology and its therapeutic potential. (2006)

Antisense oligonucleotide agents induce the inhibition of target gene expression in a sequence-specific manner by exploiting the ability of oligonucleotides to bind to target RNAs via Watson-Crick hybridization. Once bound, the antisense agent either disables or induces the degradation of the target RNA. This technology may be used for therapeutic purposes, functional genomics, and target validation. There are three major categories of gene-silencing molecules: (1) antisense oligonucleotide derivatives that, depending on their type, recruit RNase H to cleave the target mRNA or inhibit translation by steric hindrance; (2) ribozymes and deoxyribozymes--catalytically active oligonucleotides that cause RNA cleavage; (3) small interfering double-stranded RNA molecules that induce RNA degradation through a natural gene-silencing pathway called RNA interference (RNAi). RNAi is the latest addition to the family of antisense technologies and has rapidly become the most widely used approach for gene knockdown because of its potency. In this mini-review, we introduce the RNAi effect, briefly compare it with existing antisense technologies, and discuss its therapeutic potential, focusing on recent animal studies and ongoing clinical trials. RNAi may provide new therapeutics for treating viral infections, neurodegenerative diseases, septic shock, macular degeneration, cancer, and other illnesses, although in vivo delivery of small interfering RNAs remains a significant obstacle.
FGFR1 Amplification Drives Endocrine Therapy Resistance and Is a Therapeutic Target in Breast Cancer (2010)

Amplification of fibroblast growth factor receptor 1 (FGFR1) occurs in approximately 10% of breast cancers and is associated with poor prognosis. However, it is uncertain whether overexpression of FGFR1 is causally linked to the poor prognosis of amplified cancers. Here, we show that FGFR1 overexpression is robustly associated with FGFR1 amplification in two independent series of breast cancers. Breast cancer cell lines with FGFR1 overexpression and amplification show enhanced ligand-dependent signaling, with increased activation of the mitogen-activated protein kinase and phosphoinositide 3-kinase-AKT signaling pathways in response to FGF2, but also show basal ligand-independent signaling, and are dependent on FGFR signaling for anchorage-independent growth. FGFR1-amplified cell lines show resistance to 4-hydroxytamoxifen, which is reversed by small interfering RNA silencing of FGFR1, suggesting that FGFR1 overexpression also promotes endocrine therapy resistance. FGFR1 signaling suppresses progesterone receptor (PR) expression in vitro, and likewise, amplified cancers are frequently PR negative, identifying a potential biomarker for FGFR1 activity. Furthermore, we show that amplified cancers have a high proliferative rate assessed by Ki67 staining and that FGFR1 amplification is found in 16% to 27% of luminal B-type breast cancers. Our data suggest that amplification and overexpression of FGFR1 may be a major contributor to poor prognosis in luminal-type breast cancers, driving anchorage-independent proliferation and endocrine therapy resistance.
Glycosylation-dependent collagen-binding activities of two membrane glycoproteins in MDAY-D2 tumor cells. (1988)

Two highly glycosylated membrane sialoglycoproteins designated P2A and P2B were isolated from the lymphoreticular tumor cell line called MDAY-D2 and shown to be structurally similar to the lymphocyte glycoprotein called leukosialin and to lysosome-associated membrane glycoprotein termed LAMP-1, respectively. The loss of sialic acid and polylactosamine sequences in glycosylation mutants of MDAY-D2 has been correlated previously with enhanced cell adhesion on extracellular matrix proteins. Since these two glycoproteins bear the majority of the sialylated oligosaccharides found in membrane fractions of MDAY-D2, they were tested for binding activity on extracellular matrix proteins. Both isolated glycoproteins bound to immobilized collagen type I with affinities that were dependent on their glycosylation. Enzymatic removal of sialic acid, polylactosamine, or complete asparagine-linked chains from purified P2B enhanced its binding to collagen, laminin, and fibronectin. In contrast, P2A bound specifically to collagen type I and the interaction required the presence of sialic acid residues which were sensitive to neuraminidase digestion but not to endoglycosidase F. The results suggest that oncodevelopmental regulation of oligosaccharide expression on P2A and P2B glycoproteins may modulate their binding to extracellular matrix glycoproteins.
AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants (1996)

Multiple-antibiotic-resistance (Mar) mutants of Escherichia coli are resistant to a wide variety of antibiotics, and increased active efflux is known to be responsible for the resistance to some drugs. The identity of the efflux system, however, has remained unknown. By constructing an isogenic set of E. coli K-12 strains, we showed that the marR1 mutation was incapable of increasing the resistance level in the absence of the AcrAB efflux system. This experiment identified the AcrAB system as the major pump responsible for making the Mar mutants resistant to many agents, including tetracycline, chloramphenicol, ampicillin, nalidixic acid, and rifampin.
Extended Pilot-Based Coding for Lossless Bit Rate Reduction of MPEG Surround (2007)

Pilot-based coding (PBC), which is used for lossless bit rate reduction of audio coding, has been recently proposed for MPEG Surround. We propose extended PBC for further lossless bit rate reduction of MPEG Surround. Extended PBC selects the number of pilots depending on the parameter band number and the type of spatial parameter. It then encodes the pilots and the relevant difference data. Experiments show that extended PBC is more effective than the original PBC, especially for high bit rate modes, with a negligible complexity increase on the decoder side.
Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study (2017)

The gene expression approach has provided promising insights into the pathophysiology of posttraumatic stress disorder (PTSD). However, few studies used hypothesis-free transcriptome-wide approach to comprehensively understand gene expression underpinning PTSD. A transcriptome-wide expression study using RNA sequencing of whole blood was conducted in 324 World Trade Center responders (201 with never, 81 current, 42 past PTSD). Samples from current and never PTSD reponders were randomly split to form discovery (N = 195) and replication (N = 87) cohorts. Differentially expressed genes were used in pathway analysis and to create a polygenic expression score. There were 448 differentially expressed genes in the discovery cohort, of which 99 remained significant in the replication cohort, including FKBP5, which was found to be up-regulated in current PTSD regardless of the genotypes. Several enriched biological pathways were found, including glucocorticoid receptor signaling and immunity-related pathways, but these pathways did not survive FDR correction. The polygenic expression score computed by aggregating 30 differentially expressed genes using the elastic net algorithm achieved sensitivity/specificity of 0.917/0.508, respectively for identifying current PTSD in the replication cohort. Polygenic scores were similar in current and past PTSD, with both groups scoring higher than trauma-exposed controls without any history of PTSD. Together with the pathway analysis results, these findings point to HPA-axis and immune dysregulation as key biological processes underpinning PTSD. A novel polygenic expression aggregate that differentiates PTSD patients from trauma-exposed controls might be a useful screening tool for research and clinical practice, if replicated in other populations.
Speech overlap detection in a two-pass speaker diarization system (2009)

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The Complex of C5b and C6: Isolation, Characterization, and Identification of a Modified form of C5b Consisting of Three Polypeptide Chains (1978)

Abstract A new method for isolation of the complex of C5b and C6 (C5b-6) which yielded milligram quantities of C5b-6 of high purity was devised. C5 and C6 first were separated from C7 by column chromatography on DEAE-cellulose. C5b-6 then was generated from the C7-free reagent by incubation with serum-treated zymosan, and purified by DEAE-cellulose and Bio-Gel A 1.5 m column chromatography. Upon analysis by sucrose density gradient ultracentrifugation and gel filtration, two forms of the C5b-6 complex were recognized. The first maintained its complexed state (10.4S) during ultracentrifugation, and formed aggregates (&amp;gt;16S) upon reaction with C7. The second and predominant form dissociated into C5b (7.6S) and C6 (5.7S) during ultracentrifugation and did not form aggregates with C7. Both forms retained their elution characteristics on gel filtration over a 1-month period at 4°C. SDS-polyacrylamide gel electrophoretic analysis also revealed two different forms of the C5b-6 complex. C5b-6 capable of aggregating with C7 was a complex of unmodified C5b and C6. The predominant form was, however, a complex of modified C5b (designated C5b′) and C6. In the absence of a reducing agent, both forms of C5b had an apparent m.w. of 180,000 daltons. Upon reduction, C5b yielded two polypeptide chains designated α′ (103,000 daltons) and β (75,000 daltons), whereas C5b′ dissociated into three polypeptide chains, i.e., two fragments of the α′ chain designated α′1 (75,000 daltons) and α′2 (27,500 daltons), and the β chain (75,000 daltons). The possible significance of this proteolytic modification of C5b in relation to the hemolytic efficiency of lysis mediated by C5b-6 is discussed.
Improved electrospray ionization interface for capillary zone electrophoresis-mass spectrometry (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImproved electrospray ionization interface for capillary zone electrophoresis-mass spectrometryRichard D. Smith, Charles J. Barinaga, and Harold R. UdsethCite this: Anal. Chem. 1988, 60, 18, 1948–1952Publication Date (Print):September 15, 1988Publication History Published online1 May 2002Published inissue 15 September 1988https://pubs.acs.org/doi/10.1021/ac00169a022https://doi.org/10.1021/ac00169a022research-articleACS PublicationsRequest reuse permissionsArticle Views1527Altmetric-Citations452LEARN 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
Orthogonal full diversity space-time block coding based on transmit channel state information for 4 Tx antennas (2003)

In this paper we consider the design of space-time block codes to benefit from multiple antennas at the emitter and possibly at the receiver. Theory of orthogonal designs has shown that such codes can not simultaneously be orthogonal, of rate 1, with full diversity order, for more than 2 transmit antennas. We propose in this paper to exploit channel state information available at the emitter to overcome this limitation and we describe a new rate 1 coding scheme with full diversity for 3 or 4 transmit antennas. This scheme is an orthogonal one thanks to transmit weights, which allow to use a simple linear receiver having optimal performance. The performance of the code is assessed by simulations in the 5 GHz OFDM-based WLAN environment (HIPERLAN/2). The practical interest of such approach is finally discussed.
Human activity analysis (2011)

Human activity recognition is an important area of computer vision research. Its applications include surveillance systems, patient monitoring systems, and a variety of systems that involve interactions between persons and electronic devices such as human-computer interfaces. Most of these applications require an automated recognition of high-level activities, composed of multiple simple (or atomic) actions of persons. This article provides a detailed overview of various state-of-the-art research papers on human activity recognition. We discuss both the methodologies developed for simple human actions and those for high-level activities. An approach-based taxonomy is chosen that compares the advantages and limitations of each approach. Recognition methodologies for an analysis of the simple actions of a single person are first presented in the article. Space-time volume approaches and sequential approaches that represent and recognize activities directly from input images are discussed. Next, hierarchical recognition methodologies for high-level activities are presented and compared. Statistical approaches, syntactic approaches, and description-based approaches for hierarchical recognition are discussed in the article. In addition, we further discuss the papers on the recognition of human-object interactions and group activities. Public datasets designed for the evaluation of the recognition methodologies are illustrated in our article as well, comparing the methodologies' performances. This review will provide the impetus for future research in more productive areas.
High solubility and photoluminescence quantum yield water-soluble polyfluorenes with dendronized amino acid side chains: synthesis, photophysical, and metal ion sensing properties (2010)

A series of anionic water-soluble dendronized conjugated polymers PG0, PG1 and PG2 are synthesized by copolymerization of dendritic macromonomers and phenyldiboronic ester via direct Suzuki polycondensation reaction in THF–water solution. Water solubility and solution photoluminescence quantum yield increase with increasing the generation of the dendrons. PG2 exhibits an extremely high solubility which achieves 200 mg mL−1 in aqueous solution and the corresponding quantum yield was measured to be 95%. The absorption and fluorescence spectra of the dendronized polymers are pH-dependent due to the aggregation of the polymer chains. PL spectrum of PG2 also exhibits better stability among large window of pH and high salt concentration than the other two polymers. Three polymers demonstrate different sensory behavior to metal ions. Among them, most metal ions can moderately quench the fluorescence of PG0, on the other hand, PG1 and PG2 have good selectivity and sensitivity to Hg2+ and Cu2+, respectively. Thin-films based on PG0, PG1, and PG2 are fabricated by spin-coating, layer-by-layer (LbL) deposition, and self-assembly on amine-functionalized quartz followed by thermal-annealing. Among them, the annealed films have good spectral stability in aqueous solution, which makes them promising materials for the application in the field of chemo- and biosensors and light-emitting devices.
Fluorimetric determination of human serum albumin with Eriochrome Cyanine R (1988)

A sensitive spectofluorimetric method has been developed for the determination of human serum albumin (HSA). The complex of Eriochrome Cyanine R (ECR) with HSA fluoresces at 423 nm (with excitation at 308 nm). The limit of determination is 0.5 µg ml–1 and the relative standard deviation is less than 2%. The composition of the fluorescent complex is 1 : 4 (HSA : ECR).