gebhart/patrepeval huggingface dataset:
Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E (2000)

The human immunodeficiency virus type 1 (HIV-1) epidemic in Southeast Asia has been largely due to the emergence of clade E (HIV-1E). It has been suggested that HIV-1E is derived from a recombinant lineage of subtype A (HIV-1A) and subtype E, with multiple breakpoints along the E genome. We obtained complete genome sequences of clade E viruses from Thailand (93TH057 and 93TH065) and from the Central African Republic (90CF11697 and 90CF4071), increasing the total number of HIV-1E complete genome sequences available to seven. Phylogenetic analysis of complete genomes showed that subtypes A and E are themselves monophyletic, although together they also form a larger monophyletic group. The apparent phylogenetic incongruence at different regions of the genome that was previously taken as evidence of recombination is shown to be not statistically significant. Furthermore, simulations indicate that bootscanning and pairwise distance results, previously used as evidence for recombination, can be misleading, particularly when there are differences in substitution or evolutionary rates across the genomes of different subtypes. Taken jointly, our analyses suggest that there is inadequate support for the hypothesis that subtype E variants are derived from a recombinant lineage. In contrast, many other HIV strains claimed to have a recombinant origin, including viruses for which only a single parental strain was employed for analysis, do indeed satisfy the statistical criteria we propose. Thus, while intersubtype recombinant HIV strains are indeed circulating, the criteria for assigning a recombinant origin to viral structures should include statistical testing of alternative hypotheses to avoid inappropriate assignments that would obscure the true evolutionary properties of these viruses.
Enhancing STEM classes using weave: A collaborative web-based visualization environment (2011)

Learning within a STEM classroom environment can be greatly enhanced by engaging the students in real-world datasets. This provides the opportunity to go beyond textbook examples that are often only marginally close to those students will see in their future careers. The Weave (WEb-based Analysis and Visualization Environment) developed at the University of Massachusetts at Lowell allows collaborative data visualization in a web browser that is highly applicable to STEM classrooms. Larger and more field appropriate datasets can be loaded into the system, hypotheses can be made and confirmed, and students can collaboratively work together. This paper discusses the ways in which Weave could be used in the STEM classroom to foster learning.
Orthogonal Transformations on Solid Substrates: Efficient Avenues to Surface Modification (2009)

Abstract The performance of solid substrates is not only governed by their molecular constitution, but is also critically influenced by their surface constitution at the solid/gas or solid/liquid interface. In here, we critically review the use of orthogonal chemical transformations (so‐called click chemistry) to achieve efficient surface modifications of materials ranging from gold and silica nanoparticles, polymeric films, and microspheres to fullerenes as well as carbon nanotubes. In addition, the functionalization of surfaces via click chemistry with biomolecules is explored. Although a large host of reactions fulfilling the click ‐criteria exist, pericyclic reactions are most frequently employed for efficient surface modifications. The advent of the click chemistry concept has led—as evident from the current literature—to a paradigm shift in current approaches for materials modification: Away from unspecific and nonselective reactions to highly specific true surface engineering.
Intein-mediated protein ligation: Harnessing nature's escape artists (1999)

Inteins are naturally occurring proteins that are involved in the precise cleavage and formation of peptide bonds in a process known as protein splicing. Genetic engineering has allowed the controllable cleavage of peptide bonds at either the N- or C-terminus of the intein. Inteins displaying controllable cleavage have been used in the isolation of bacterially expressed proteins possessing either a C-terminal thioester or an N-terminal cysteine. The specific placement of these reactive groups has allowed either protein–protein or protein–peptide condensation through a native peptide bond. This review describes the methods used to specifically generate these reactive groups on bacterially expressed proteins and some applications of this technique, known as intein-mediated protein ligation. Furthermore, a versatile two intein (TWIN) system will be described which enables the circularization and polymerization of bacterially expressed proteins or peptides. © 2000 John Wiley & Sons, Inc. Biopoly 51: 333–342, 1999
Perspectives on Molecular Diagnostics Automation (2005)

After a lively discussion at LabAutomation2005 in San Jose, we asked three major diagnostic companies to share their vision for the molecular diagnostics “rapid-growing-and-more-than-ever” market. Happily, all of them complied and we are pleased to present insight from Bayer Healthcare, Beckman Coulter, and Roche Molecular Systems. To complement these perspectives, we invited a heavy user of molecular diagnostic assays to comment on today's situation and share his hopes for the future of molecular medicine. It is with pleasure that we feature insight from Philippe Halfon of Alphabio Laboratoire.
Structure and mapping of antigenic domains of protein antigen b, a 38,000-molecular-weight protein of Mycobacterium tuberculosis (1989)

Only a limited number of proteins from Mycobacterium tuberculosis have so far been shown to possess species-specific epitopes as defined by monoclonal antibodies. One such protein is protein antigen b (Pab) of molecular weight 38,000, which binds the monoclonal antibodies HYT 28, HAT 2, HBT 12, HGT 3, TB 71, and TB 72. The gene encoding this protein was isolated from a lambda gt11 M. tuberculosis DNA library. The nucleotide sequence of the recombinant mycobacterial insert was determined, and an open reading frame of 374 amino acids was identified. The amino acid sequence exhibited 30% homology to a phosphate-binding protein, PstS, from Escherichia coli. The pab gene was subcloned into pBR322 in conjunction with the lacZ gene, and deletions were obtained from the 3' end. The anti-Pab monoclonal antibodies were used to probe crude protein lysates of E. coli transformed with the deletion plasmids. The monoclonal antibodies showed two reactivity patterns; one group of antibodies were dependent on the presence of the ultimate 91 amino acids of the protein, whereas another group of antibodies recognized an antigenic domain located on the middle portion of the molecule. None of the antibodies bound to the N-terminal 117-amino-acid peptide.
Anchor-ligated cDNA libraries: a technique for generating a cDNA library for the immediate cloning of the 5' ends of mRNAs. (1993)

A new, efficient and simple method based on single-stranded anchor ligation has been developed that allows for the generation of an anchor-ligated library from which the 5' ends in many mRNAs can be cloned. Random hexamers are used to prime poly A+ RNA for the first strand synthesis of a cDNA library, and a modified single-stranded anchor is then ligated to the 3' end of the cDNA using T4 RNA ligase. The library can then be used to amplify the 5' end of any mRNA expressed in the tissue. The efficiency and utility of this method has been demonstrated by amplification of three human genes: transferrin receptor, tissue-type plasminogen activator and beta actin.
Creation of Rift Valley Fever Viruses with Four-Segmented Genomes Reveals Flexibility in Bunyavirus Genome Packaging (2014)

Rift Valley fever virus (RVFV) causes devastating disease in ruminants and occasionally humans. Virions capable of productive infection comprise at least one copy of the small (S), medium (M), and large (L) RNA genome segments. The M segment encodes a glycoprotein precursor (GPC) protein that is cotranslationally cleaved into Gn and Gc, which are required for virus entry and fusion. We studied the flexibility of RVFV genome packaging and developed experimental live-attenuated vaccines by applying a unique strategy based on the splitting of the GnGc open reading frame. Several RVFV variants, varying from viruses comprising two S-type segments to viruses consisting of four segments (RVFV-4s), of which three are M-type, could be rescued and were shown to induce a rapid protective immune response. Altogether, the segmentation of bunyavirus GPCs provides a new method for studying bunyavirus genome packaging and facilitates the development of novel live-attenuated bunyavirus vaccines.
DNA Fingerprinting Report (1993)

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[Ionic homeostasis and erythrocyte deformability in patients with primary arterial hypertension]. (1990)

Erythrocyte Na, K-ATPase was examined for its activity and relation to the concentration of the complexon EDTA in 39 patients with arterial hypertension (AH), 12 subjects with borderline hypertension, and 18 normotensives. The ionic composition and deformability of erythrocytes were also studied. As compared to normotensives, the patients with Stage I AH displayed a significantly lower activity of erythrocyte Na, K-ATPase, which may suggest that there is an enzyme inhibitor in the blood of the patients. According to the enzyme activity, the patients with Stage II AH were divided into two subgroups: 1) those with a lower activity and 2) those with a higher activity than healthy subjects. The patients with a Stage II AH who showed a lower activity of Na, K-ATPase exhibited a more elevated erythrocyte sodium level, whereas those who had a high activity of the enzyme displayed a decreased erythrocyte deformability. In addition, a positive correlation between erythrocyte sodium concentrations and Na, K-ATPase activity, as well as erythrocyte deformability was found in normotensives, whereas a negative correlation was established in AH patients.
Stat-3 is required for pulmonary homeostasis during hyperoxia (2004)

Acute lung injury syndromes remain common causes of morbidity and mortality in adults and children. Cellular and physiologic mechanisms maintaining pulmonary homeostasis during lung injury remain poorly understood. In the present study, the Stat-3 gene was selectively deleted in respiratory epithelial cells by conditional expression of Cre-recombinase under control of the surfactant protein C gene promoter. Cell-selective deletion of Stat-3 in respiratory epithelial cells did not alter prenatal lung morphogenesis or postnatal lung function. However, exposure of adult Stat-3-deleted mice to 95% oxygen caused a more rapidly progressive lung injury associated with alveolar capillary leak and acute respiratory distress. Epithelial cell injury and inflammatory responses were increased in the Stat-3-deleted mice. Surfactant proteins and lipids were decreased or absent in alveolar lavage material. Intratracheal treatment with exogenous surfactant protein B improved survival and lung histology in Stat-3-deleted mice during hyperoxia. Expression of Stat-3 in respiratory epithelial cells is not required for lung formation, but plays a critical role in maintenance of surfactant homeostasis and lung function during oxygen injury.
Direct design of a potent non-peptide fibrinogen receptor antagonist based on the structure and conformation of a highly constrained cyclic RGD peptide (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirect design of a potent non-peptide fibrinogen receptor antagonist based on the structure and conformation of a highly constrained cyclic RGD peptideThomas W. Ku, Fadia E. Ali, Linda S. Barton, John W. Bean, William E. Bondinell, Joelle L. Burgess, James F. Callahan, Raul R. Calvo, Lichong Chen, and Cite this: J. Am. Chem. Soc. 1993, 115, 19, 8861–8862Publication Date (Print):September 1, 1993Publication History Published online1 May 2002Published inissue 1 September 1993https://doi.org/10.1021/ja00072a058RIGHTS & PERMISSIONSArticle Views311Altmetric-Citations75LEARN 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 (311 KB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
ENZYME-LINKED IMMUNOSORBENT ASSAY SPOT DETECTION OF INTERFERON-?? AND INTERLEUKIN 5-PRODUCING CELLS AS AS PREDICTIVE MARKER FOR RENAL ALLOGRAFT FAILURE1 (1998)

In renal transplant recipients with acute allograft dysfunction, mitogen-induced peripheral blood lymphocyte IFN-gamma:IL-5 ratios > or = 15 were highly predictive of allograft failure within 6 months of the assay. This test may be a useful prognostic marker for identification of transplant recipients with acute graft dysfunction who are at high risk for future graft loss and thus allow targeted therapeutic interventions to prolong graft survival.
Abnormalities of lipid metabolism in hepatitis C virus infection (2010)

Hepatitis C virus (HCV) is a human pathogen responsible for acute and chronic liver disease, infecting an estimated 130-170 million persons worldwide. An intriguing feature of HCV infection is its peculiar relationship with lipids: (1) HCV virions circulate in serum bound to lipoproteins; (2) lipids have been shown to modulate (and, indeed, are essential to) the HCV life cycle; and (3) an occasionally severe accumulation of triglycerides is found in a distinct subgroup of patients in the form of hepatic steatosis. As a result, lipid metabolism is overall altered, conferring an idiosyncratic profile to HCV infection. The scope of this review is to discuss these aspects, focusing on both their molecular mechanisms and their clinical consequences.
Laboratory Workhorse Decoded (1997)

On page
 1453
 of this issue, researchers report the complete sequence of all 4.6 million base pairs in the genome of the bacterium
 Escherichia coli. The achievement not only marks the end of a 15-year race to determine the sequence, but because
 E. coli
 has been so well studied over the years, researchers can now use the sequence to provide a coherent picture of the organism9s complete biology. It will also help in identifying the genes of higher organisms, and together with the sequences of several other bacteria, it will increase our understanding of bacterial evolution.
Medaka as a model of transgenic fish. (1993)

The medaka (Oryzias latipes) is an egg-laying fresh-water fish. We describe the medaka as a model system of transgenic fish in germs of biological characteristics, manipulation of embryos, gene expression in development, and basic research in aquaculture. The fish are small (approximately 3 cm in length) and have a short generation time (approximately 3 months). The eggs are easy to manipulate. A foreign gene (e.g., the chicken delta crystallin gene) is transferred and expressed stage-dependently in development of medaka embryos. Growth hormone genes of vertebrates are transferred and expressed and, in some cases, accelerate growth of the fish. Thus, the medaka is one of the most promising models of transgenic fish for basic research of gene expression and aquaculture.
Ribozymes as antiviral agents. (2004)

Ribozymes are RNA molecules with cleavage activity that can be engineered to specifically target a given RNA molecule. The hammerhead, hairpin and hepatitis delta virus ribozymes have been widely studied for their use as therapeutical agents. This review discusses the structure and properties of these ribozymes, along with the advances made in the development of these molecules for their application in the treatment of hepatitis B, hepatitis C and human immunodeficiency virus infections.
Biochemical and structural analysis of missense mutations in N-acetylgalactosamine-6-sulfate sulfatase causing mucopolysaccharidosis IVA phenotypes (2000)

Mucopolysaccharidosis IVA (MPS IVA; OMIM#253000), a lysosomal storage disorder caused by a deficiency of N -acetylgalactosamine-6-sulfate sulfatase (GALNS), has variable clinical phenotypes. To date we have identified 65 missense mutations in the GALNS gene from MPS IVA patients, but the correlation between genotype and phenotype has remained unclear. We studied 17 missense mutations using biochemical approaches and 32 missense mutations, using structural analyses. Fifteen missense mutations and two newly engineered active site mutations (C79S, C79T) were characterized by transient expression analysis. Mutant proteins, except for C79S and C79T, were destabilized and detected as insoluble precursor forms while the C79S and C79T mutants were of a soluble mature size. Mutants found in the severe phenotype had no activity. Mutants found in the mild phenotype had a considerable residual activity (1.3-13.3% of wild-type GALNS activity). Sulfatases, including GALNS, are members of a highly conserved gene family sharing an extensive sequence homology. Thus, a tertiary structural model of human GALNS was constructed from the X-ray crystal structure of N -acetylgalacto-samine-4-sulfatase and arylsulfatase A, using homology modeling, and 32 missense mutations were investigated. Consequently, we propose that there are at least three different reasons for the severe phenotype: (i) destruction of the hydrophobic core or modification of the packing; (ii) removal of a salt bridge to destabilize the entire conformation; (iii) modification of the active site. In contrast, mild mutations were mostly located on the surface of the GALNS protein. These studies shed further light on the genotype-phenotype correlation of MPS IVA and structure-function relationship in the sulfatase family.
‘Click’ Chemistry in Polymer and Material Science: An Update (2008)

Abstract The metal catalyzed azide/alkyne ‘click’ reaction (a variation of the Huisgen 1,3‐dipolar cycloaddition reaction between terminal acetylenes and azides) has vastly increased in broadness and application in the field of polymer science. Thus, this reaction represents one of the few universal, highly efficient functionalization reactions, which combines both high efficiency with an enormously high tolerance of functional groups and solvents under highly moderate reaction temperatures (25–70 °C). The present review assembles an update of this reaction in the field of polymer science (linear polymers, surfaces) with a focus on the synthesis of functionalized polymeric architectures and surfaces. magnified image
Pathogenesis and management issues for non-alcoholic fatty liver disease (2007)

Nonalcoholic fatty liver disease (NAFLD) has, although it is a very common disorder, only relatively recently gained broader interest among physicians and scientists. Fatty liver has been documented in up to 10 to 15 percent of normal individuals and 70 to 80 percent of obese individuals. Although the pathophysiology of NAFLD is still subject to intensive research, several players and mechanisms have been suggested based on the substantial evidence. Excessive hepatocyte triglyceride accumulation resulting from insulin resistance is the first step in the proposed 'two hit' model of the pathogenesis of NAFLD. Oxidative stress resulting from mitochondrial fatty acids oxidation, NF-kappaB-dependent inflammatory cytokine expression and adipocytokines are all considered to be the potential factors causing second hits which lead to hepatocyte injury, inflammation and fibrosis. Although it was initially believed that NAFLD is a completely benign disorder, histologic follow-up studies have showed that fibrosis progression occurs in about a third of patients. A small number of patients with NAFLD eventually ends up with end-stage liver disease and even hepatocellular carcinoma. Although liver biopsy is currently the only way to confirm the NAFLD diagnosis and distinguish between fatty liver alone and NASH, no guidelines or firm recommendations can still be made as for when and in whom it is necessary. Increased physical activity, gradual weight reduction and in selected cases bariatric surgery remain the mainstay of NAFLD therapy. Studies with pharmacologic agents are showing promising results, but available data are still insufficient to make specific recommendations; their use therefore remains highly individual.
Formation of a stratified lanthanum silicate dielectric by reaction with Si(001) (2001)

We have characterized the structure and electrical properties of lanthanum silicate layers formed on Si(001) by reaction of lanthanum oxide with the substrate. Postoxidation of the deposited films results in the formation of a stacked dielectric with a lanthanum silicate layer atop an interfacial layer of SiO2. This structure combines the interfacial properties of SiO2 with the large permittivity of lanthanum silicate. Although the resulting film has leakage properties far superior to an equivalent thickness of SiO2, there is evidence of significant quantities of ionic charge that must be eliminated before use in electronic applications.
ESPRIT--A subspace rotation approach to estimation of parameters of cisoids in noise (1986)

The application of a subspace invariance approach (ESPRIT) to the estimation of parameters (frequencies and powers) of cisoids in noise is described. ESPRIT exploits an underlying rotational invariance of signal subspaces spanned by two temporally displaced data sets. The new approach has several advantages including improved resolution over Pisarenko's technique for harmonic retrieval.
Human visual processing: beyond 3 sensors (2005)

Much of image processing and vision uses 3 sensors because we ourselves have trichromatic vision. However, some solutions to vision problems use additional hardware not available to ourselves in order to get the best performance. For example, the idea of placing a coloured filter in front of a vision system, and capturing two images: one with-and another one without the filter has recently been revisited in the context of the illumination estimation problem. It was shown that the plus-filter illuminant estimation is easier to solve and so it is easier to estimate and discount illumination compared with traditional methods. In this paper we propose that this two image approach is in fact plausible for human visual processing. Indeed, a little known and little explained optical fact is that the light striking the central part of the retina is pre-filtered with a yellow filter (the macular pigment) but no pre-filtering occurs to light striking other parts of the retina. Since the world we see is a composite of several images taken at different fixation points we argue that the visual system in principle has access to two images: normal RGBs + RGBs measured through a yellow filter. Experiments demonstrate that the illumination estimation performance that is possible starting with the human vision system sensitivities is excellent and as for machine vision is much better than the non plus-filter algorithms. We discuss the wider relevance of this result to the vision and imaging community.