gebhart/patrepeval huggingface dataset:
Presence of HLA-C-Restricted Cytotoxic T-Lymphocyte Responses in Long-Term Nonprogressors Infected with Human Immunodeficiency Virus (1998)

Approximately 5% of people with human immunodeficiency virus type 1 (HIV-1) infection remain free of disease for 10 or more years. These long-term nonprogressors (LTNPs) exhibit lower viral loads and stable CD4+ lymphocyte counts. The immunologic basis for this disease-free condition is not known. Because cytotoxic T lymphocytes (CTLs) constitute a major immune defense mechanism for sustained recovery from viral infections, we analyzed HIV-specific CTL responses in three asymptomatic LTNPs. We observed the presence of HIV-1 envelope-specific CTL responses mediated by HLA class I C-restricted CD8+ cells in these individuals. Using autologous target cells and a panel of HLA-matching and -mismatching B-cell lines as targets, we determined that HLA-Cw7 is the restricting element for the observed CTL activity. Additionally, we identified three peptides, one previously not reported, from conserved regions in the envelope protein as CTL epitopes. We previously reported these peptides to be efficient in inducing HIV-specific cellular immune responses in murine and nonhuman primate models. Our results support the role of the HLA-C locus in generating CTL responses and constitute the first report of an HLA-Cw7-restricted HIV-1 envelope-specific CTL response in HIV+ LTNPs, which may be important in the control of HIV replication in vivo.
Long‐lasting RNAi activity in mammalian neurons (2004)

The effect of RNA interference (RNAi) induced by synthetic small interfering RNAs (siRNAs) on proliferating mammalian cells appears to last for approximately 3-7 days after its induction. Here we show that the RNAi activity induced by a synthetic 21-nucleotide siRNA duplex in postmitotic neurons, mouse primary hippocampal neurons and neurons that differentiated from mouse embryonal carcinoma P19 cells persists for at least 3 weeks, suggesting long-lasting RNAi activity in mammalian neurons. In addition, we also show that an apoptotic (or antiviral) pathway triggered by long dsRNAs is generated during neuronal differentiation of P19 cells, by which the sequence-specific RNAi activity involving long dsRNA appears to be masked.
A Levansucrase from Streptococcus mutans (1970)

One of the predominant bacteria in early dental plaque, Streptococcus mutans, has been shown to synthesize levansucrase. This enzyme was obtained from the supernatant fluid of a glucose-broth culture. Purification of the enzyme was achieved in two steps by adsorption on hydroxylapatite followed by isoelectric focusing and fractionation. This resulted in a 10% yield and a 200-fold purification. Sucrose as well as raffinose could serve as substrate for the enzyme. In addition to levan (MW > 25 × 106), free fructose and oligosaccharides were formed from sucrose. The enzyme had a pH optimum at 6.0, optimal activity around 40° C and isoelectric point at pH 4.2. Iodoacetamide, cysteine, Tris and sodium fluoride in a concentration of 0.05 m had no effect on the enzyme activity. The enzyme was totally inhibited by 0.1 mM Hg++ and to about 40% by 1 mM Pb++, Ag+, Ni++ and Cu++. EDTA in a concentration of 1 mM reduced the over-all activity of the enzyme by 75% and specifically interfered with the synthesis of levan. Most divalent cations could restore the activity of the enzyme in the presence of EDTA. The properties of this streptococcal levansucrase were similar to those previously described for levansucrases from Aerobacter levanicum and Bacillus subtilis. The finding, that EDTA interfered with the synthesis of levan, may give new possibilities in elucidating the mechanism of this enzyme reaction.
Telomere conversion in trypanosomes (1983)

Activation of the gene coding for variant surface glycoprotein (VSG) 118 in Trypanosoma brucei proceeds via a duplicative transposition to a telomeric expression site. The resulting active expression-linked extra copy (ELC) is usually flanked by DNA that lacks sites for most restriction enzymes and that is thought to interfere with the cloning of the ELC as recombinant DNA in Escherichia coli. We have circumvented this problem by cloning an aberrant 118 ELC gene, flanked at the 3'-side by at least 1 kb DNA, that contains restriction enzyme sites. Our analysis shows that this DNA and the 3'-end of the 118 ELC gene are derived from another VSG gene (1.1006) that is permanently located at a telomeric position. We propose that the 3'-end of the 1.1006 gene and (all of) its 3' flanking sequence moved to the expression site by a telomere conversion. Such a telomere conversion can also account for the appearance of an extra copy of the 1.1006 gene detected in a sub-population of our trypanosome strain.
Assessment of the serological relatedness of genital human papillomaviruses by hemagglutination inhibition (1996)

To assess the potential for cross-protection among genital human papillomavirus (HPV) types in virus-like particle (VLP)-based vaccinations, inhibition of HPV VLP-mediated hemagglutination by rabbit antisera raised against HPV type 6b (HPV-6b), HPV-11, HPV-16, HPV-18, HPV-31, HPV-33, and HPV-45 was analyzed. Only highly homologous types (HPV-6b and HPV-11, and HPV-18 and HPV-45) exhibited detectable serological cross-reaction for the class of antibodies that inhibit virion-to-cell surface binding. However, analysis of neutralizing monoclonal antibodies to several animal and human papillomaviruses indicated that over half of these antibodies do not prevent cell surface binding, but these latter antibodies do not appear to be more cross-reactive in enzyme-linked immunosorbent assays than those that mediate inhibition of hemagglutination. The data strongly suggest that while there may be limited cross-protection between highly (>85% L1 amino acid identity) homologous types, protection by HPV VLP-based vaccines will be predominantly type specific.
Chlorination of Taurine by Human Neutrophils (1982)

The model hydrogen peroxide-myeloperoxidase-chloride system is capable of generating the powerful oxidant hypochlorous acid, which can be quantitated by trapping the generated species with the beta-amino acid, taurine. The resultant stable product, taurine chloramine, can be quantitated by its ability to oxidize the sulfhydryl compound, 5-thio-2-nitro-benzoic acid to the disulfide, 5,5'-dithiobis(2-nitroben-zoic acid) or to oxidize iodide to iodine. Using this system, purified myeloperoxidase in the presence of chloride and taurine converted stoichiometric quantities of hydrogen peroxide to taurine chloramine. Chloramine generation was absolutely dependent on hydrogen peroxide, myeloperoxidase, and chloride and could be inhibited by catalase, myeloperoxidase inhibitors, or chloride-free conditions. In the presence of taurine, intact human neutrophils stimulated with either phorbol myristate acetate or opsonized zymosan particles generated a stable species capable of oxidizing 5-thio-2-nitrobenzoic acid or iodide. Resting cells did not form this species. The oxidant formed by the stimulated neutrophils was identified as taurine chloramine by both ultraviolet spectrophotometry and electrophoresis. Taurine chloramine formation by the neutrophil was dependent on the taurine concentration, time, and cell number. Neutrophil-dependent chloramine generation was inhibited by catalase, the myeloperoxidase inhibitors, azide, cyanide, or aminotriazole and by chloride-free conditions, but not by superoxide dismutase or hydroxyl radical scavengers. Thus, it appears that stimulated human neutrophils can utilize the hydrogen peroxide-myeloperoxidase-chloride system to generate taurine chloramine. Based on the demonstrated ability of the myeloperoxidase system to generate free hypochlorous acid we conclude that neutrophils chlorinate taurine by producing this powerful oxidant. The biologic reactivity and cytotoxic potential of hypochlorous acid and its chloramine derivatives suggest that these oxidants play an important role in the inflammatory response and host defense.
Using an accelerometer sensor to measure human hand motion (2000)

Thesis (S.B. and M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.
Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides. (1986)

The enzyme exonuclease I from Escherichia coli hydrolyzes successive nucleotides from the 3'-termini of single-stranded deoxyribonucleotide homopolymers. When the reaction is stopped after partial hydrolysis, only intact starting material and small oligomers can be isolated. The distribution of oligomeric products varies with the base composition of the polymer but the largest oligomer that can be isolated from the reaction of exonuclease I with homopolymers of deoxyadenylate, deoxythymidylate, or deoxycytidylate is a decamer. These results suggest a model in which exonuclease I possesses at least two nucleotide binding sites. When both sites are filled, with 11-mers and longer polymers, the enzyme does not dissociate from the polymer during hydrolysis. When, with smaller oligomers, only a single site is filled, the reaction partitions at each oligomer between hydrolysis and dissociation. The kinetics of the reactions of exonuclease I with purified polydeoxyriboadenylates of defined size distributions have been investigated. The maximum rates of hydrolysis are nearly independent of polymer size while the apparent Michaelis constants are inversely proportional to the polymer size. A simple steady state model yields a kinetic equation that is consistent with our results. Competition experiments indicate that the rate at which exonuclease I associates with the 3'-terminus of a polydeoxyribonucleotide is independent of the polymer's chain length.
Distal myopathy with rimmed vacuoles is allelic to hereditary inclusion body myopathy (2003)

<h3>Background:</h3> Previous studies of differences in mental health care associated with children’s sociodemographic status have focused on access to community care. We examined differences associated with visits to the emergency department. <h3>Methods:</h3> We conducted a 6-year population-based cohort analysis using administrative databases of visits (<i>n</i> = 30 656) by children aged less than 18 years (<i>n</i> = 20 956) in Alberta. We measured differences in the number of visits by socioeconomic and First Nations status using directly standardized rates. We examined time to return to the emergency department using a Cox regression model, and we evaluated time to follow-up with a physician by physician type using a competing risks model. <h3>Results:</h3> First Nations children aged 15–17 years had the highest rate of visits for girls (7047 per 100 000 children) and boys (5787 per 100 000 children); children in the same age group from families not receiving government subsidy had the lowest rates (girls: 2155 per 100 000 children; boys: 1323 per 100 000 children). First Nations children (hazard ratio [HR] 1.64; 95% confidence interval [CI] 1.30–2.05), and children from families receiving government subsidies (HR 1.60, 95% CI 1.30–1.98) had a higher risk of return to an emergency department for mental health care than other children. The longest median time to follow-up with a physician was among First Nations children (79 d; 95% CI 60–91 d); this status predicted longer time to a psychiatrist (HR 0.47, 95% CI 0.32–0.70). Age, sex, diagnosis and clinical acuity also explained post-crisis use of health care. <h3>Interpretation:</h3> More visits to the emergency department for mental health crises were made by First Nations children and children from families receiving a subsidy. Sociodemographics predicted risk of return to the emergency department and follow-up care with a physician.
Atomic Layer Epitaxy in Deposition of Various Oxide and Nitride Thin Films (1995)

Atomic Layer Epitaxy (ALE) is a chemical vapor phase thin film deposition method which is based on saturative surface reactions. As the film is growing in a self-limiting manner ALE is a promising method to deposit thin, high-quality films for micro- and optoelectronics. In the present paper the deposition of different dielectric oxides, conducting oxides as well as nitrides is reviewed giving emphasis to precursors and their effect on growth mechanisms and film properties.
Structure of a Packaging-Defective Mutant of Minute Virus of Mice Indicates that the Genome Is Packaged via a Pore at a 5-Fold Axis (2011)

The parvovirus minute virus of mice (MVM) packages a single copy of its linear single-stranded DNA genome into preformed capsids, in a process that is probably driven by a virus-encoded helicase. Parvoviruses have a roughly cylindrically shaped pore that surrounds each of the 12 5-fold vertices. The pore, which penetrates the virion shell, is created by the juxtaposition of 10 antiparallel β-strands, two from each of the 5-fold-related capsid proteins. There is a bottleneck in the channel formed by the symmetry-related side chains of the leucines at position 172. We report here the X-ray crystal structure of the particles produced by a leucine-to-tryptophan mutation at position 172 and the analysis of its biochemical properties. The mutant capsid had its 5-fold channel blocked, and the particles were unable to package DNA, strongly suggesting that the 5-fold pore is the packaging portal for genome entry.
Foliar Absorption and Translocation of Dicamba from Aqueous Solution and Dicamba-Treated Soil Deposits (1992)

This study was conducted to compare foliar absorption and translocation of dicamba applied to plants as an aqueous solution or as dicamba-treated soil deposits. When applied as an aqueous solution, 65 to 95% of 14 C-dicamba was absorbed by pea, alfalfa, and grape; whereas, limited absorption (0.4 to 4.7%) occurred from dicamba-treated soil. Based on dose-response evaluation, the low levels absorbed from treated soil are unlikely to cause crop damage. 14 C-dicamba translocation was more than 80% of absorbed 14 C in pea, alfalfa, and grape. Acropetal translocation exceeded basipetal translocation.
Malignant melanoma (1991)

Malignant melanoma is not only one of the most aggressive and lethal types of neoplasm, but its incidence in the general population is currently increasing at an alarming pace. It is interesting that most melanomas retain many of their characteristics of differentiation, including a dendritic nature and the production of melanin. This review discusses the phenotypic properties of melanoma cells, including their state of differentiation, and their tumourigenic and metastatic potentials, and attempts to provide an overview of the state of current research on the interrelationships between those parameters in murine and human systems.
Oligonucleotide clamps arrest DNA synthesis on a single-stranded DNA target. (1993)

Triple helices can be formed on single-stranded oligopurine target sequences by composite oligonucleotides consisting of two oligonucleotides covalently linked by either a hexaethylene glycol linker or an oligonucleotide sequence. The first oligomer forms Watson-Crick base pairs with the target, while the second oligomer engages in Hoogsteen base pairing, thereby acting as a molecular clamp. The triple-helical complex formed by such an oligonucleotide clamp, or "oligonucleotide-loop-oligonucleotide" (OLO), is more stable than either the corresponding trimolecular triple helix or the double helix formed upon binding of the oligopyrimidine complement to the same oligopurine target. Attaching a psoralen derivative to the 5' end of the OLO allowed us to photoinduce a covalent linkage to the target sequence. The psoralen moiety became covalently linked to all three portions of the triplex, thereby making the oligonucleotide clamp irreversible. These crosslinking reactions introduced strong stop signals during DNA replication, as shown on a plasmid containing a portion of the HIV proviral sequence of human immunodeficiency virus. A 16-mer oligopurine sequence corresponding to the "polypurine tract" of human immunodeficiency virus was chosen as a target for a psoralen-OLO conjugate. Three different stop signals for DNA polymerase were observed, corresponding to different sites of polymerase arrest on its template. Even in the absence of photoinduced crosslinking, the psoralen-OLO conjugate was able to arrest DNA replication. The formation of triple-helical structures on single-stranded targets may provide an alternative to the antisense strategy for the control of gene expression.
Agrobacterium rhizogenes-Transformed Roots of Medicago truncatula for the Study of Nitrogen-Fixing and Endomycorrhizal Symbiotic Associations (2001)

Medicago truncatula, a diploid autogamous legume, is currently being developed as a model plant for the study of root endosymbiotic associations, including nodulation and mycorrhizal colonization. An important requirement for such a plant is the possibility of rapidly introducing and analyzing chimeric gene constructs in root tissues. For this reason, we developed and optimized a convenient protocol for Agrobacterium rhizogenes-mediated transformation of M. truncatula. This unusual protocol, which involves the inoculation of sectioned seedling radicles, results in rapid and efficient hairy root organogenesis and the subsequent development of vigorous "composite plants." In addition, we found that kanamycin can be used to select for the cotransformation of hairy roots directly with gene constructs of interest. M. truncatula composite plant hairy roots have a similar morphology to normal roots and can be nodulated successfully by their nitrogen-fixing symbiotic partner, Sinorhizobium meliloti. Furthermore, spatiotemporal expression of the Nod factor-responsive reporter pMtENOD11-gusA in hairy root epidermal tissues is indistinguishable from that observed in Agrobacterium tumefaciens-transformed lines. M. truncatula hairy root explants can be propagated in vitro, and we demonstrate that these clonal lines can be colonized by endomycorrhizal fungi such as Glomus intraradices with the formation of arbuscules within cortical cells. Our results suggest that M. truncatula hairy roots represent a particularly attractive system with which to study endosymbiotic associations in transgenically modified roots.
Coercing bisphosphonates to kill cancer cells with nanoscale coordination polymers (2012)

Nanoscale coordination polymers containing exceptionally high loadings of bisphosphonates were coated with single lipid bilayers to control the drug release kinetics and functionalized with a targeting ligand to endow cell-targeting capability, leading to much enhanced cytotoxicity against human lung and pancreatic cancer cells.
The Rice brassinosteroid-deficient dwarf2 Mutant, Defective in the Rice Homolog of Arabidopsis DIMINUTO/DWARF1, Is Rescued by the Endogenously Accumulated Alternative Bioactive Brassinosteroid, Dolichosterone (2005)

We have identified a rice (Oryza sativa) brassinosteroid (BR)-deficient mutant, BR-deficient dwarf2 (brd2). The brd2 locus contains a single base deletion in the coding region of Dim/dwf1, a homolog of Arabidopsis thaliana DIMINUTO/DWARF1 (DIM/DWF1). Introduction of the wild-type Dim/dwf1 gene into brd2 restored the normal phenotype. Overproduction and repression of Dim/dwf1 resulted in contrasting phenotypes, with repressors mimicking the brd2 phenotype and overproducers having large stature with increased numbers of flowers and seeds. Although brd2 contains low levels of common 6-oxo-type BRs, the severity of the brd2 phenotype is much milder than brd1 mutants and most similar to d2 and d11, which show a semidwarf phenotype at the young seedling stage. Quantitative analysis suggested that in brd2, the 24-methylene BR biosynthesis pathway is activated and the uncommon BR, dolichosterone (DS), is produced. DS enhances the rice lamina joint bending angle, rescues the brd1 dwarf phenotype, and inhibits root elongation, indicating that DS is a bioactive BR in rice. Based on these observations, we discuss an alternative BR biosynthetic pathway that produces DS when Dim/dwf1 is defective.
Evolving feature selection (2005)

Data preprocessing is an indispensable step in effective data analysis. It prepares data for data mining and machine learning, which aim to turn data into business intelligence or knowledge. Feature selection is a preprocessing technique commonly used on high-dimensional data. Feature selection studies how to select a subset or list of attributes or variables that are used to construct models describing data. Its purposes include reducing dimensionality, removing irrelevant and redundant features, reducing the amount of data needed for learning, improving algorithms' predictive accuracy, and increasing the constructed models' comprehensibility. This article considers feature-selection overfitting with small-sample classifier design; feature selection for unlabeled data; variable selection using ensemble methods; minimum redundancy-maximum relevance feature selection; and biological relevance in feature selection for microarray data.
Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior (2015)

Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics.
Genome-Wide Transcriptional Analysis of Aerobic and Anaerobic Chemostat Cultures of Saccharomyces cerevisiae (1999)

The yeast Saccharomyces cerevisiae is unique among eukaryotes in exhibiting fast growth in both the presence and the complete absence of oxygen. Genome-wide transcriptional adaptation to aerobiosis and anaerobiosis was studied in assays using DNA microarrays. This technique was combined with chemostat cultivation, which allows controlled variation of a single growth parameter under defined conditions and at a fixed specific growth rate. Of the 6,171 open reading frames investigated, 5,738 (93%) yielded detectable transcript levels under either aerobic or anaerobic conditions; 140 genes showed a >3-fold-higher transcription level under anaerobic conditions. Under aerobic conditions, transcript levels of 219 genes were >3-fold higher than under anaerobic conditions.