gebhart/patrepeval huggingface dataset:
Consistent Cytotoxic-T-Lymphocyte Targeting of Immunodominant Regions in Human Immunodeficiency Virus across Multiple Ethnicities (2004)

Although there is increasing evidence that virus-specific cytotoxic-T-lymphocyte (CTL) responses play an important role in the control of human immunodeficiency virus (HIV) replication in vivo, only scarce CTL data are available for the ethnic populations currently most affected by the epidemic. In this study, we examined the CD8(+)-T-cell responses in African-American, Caucasian, Hispanic, and Caribbean populations in which clade B virus dominates and analyzed the potential factors influencing immune recognition. Total HIV-specific CD8(+)-T-cell responses were determined by enzyme-linked immunospot assays in 150 HIV-infected individuals by using a clade B consensus sequence peptide set spanning all HIV proteins. A total of 88% of the 410 tested peptides were recognized, and Nef- and Gag-specific responses dominated the total response for each ethnicity in terms of both breadth and magnitude. Three dominantly targeted regions within these proteins that were recognized by >90% of individuals in each ethnicity were identified. Overall, the total breadth and magnitude of CD8(+)-T-cell responses correlated with individuals' CD4 counts but not with viral loads. The frequency of recognition for each peptide was highly correlated with the relative conservation of the peptide sequence, the presence of predicted immunoproteasomal cleavage sites within the C-terminal half of the peptide, and a reduced frequency of amino acids that impair binding of optimal epitopes to the restricting class I molecules. The present study thus identifies factors that contribute to the immunogenicity of these highly targeted and relatively conserved sequences in HIV that may represent promising vaccine candidates for ethnically heterogeneous populations.
A decrease in S-adenosylmethionine synthetase activity increases the probability of spontaneous sporulation (1982)

Starting with a relaxed (relA) strain, mutants with reduced activity of adenosine triphosphate:L-methionine S-adenosyl transferase (EC 2.5.1.6; SAM synthetase) were isolated in Bacillus subtilis. One such mutant (gene symbol metE1) had only 3% of the normal SAM synthetase activity but grew almost as well as the parent strain. Another mutant was isolated (gene symbol spdC1) as being able to sporulate continually at a high frequency; it had one-half the normal SAM synthetase activity at 33 degrees C. Both mutants continually and spontaneously entered spore development at a higher frequency than the parent strain in a medium containing excess glucose, ammonium ions, and phosphate. Sporulation was prevented by a high concentration of SAM (1 mM or more) or by the combination of adenosine and methionine (0.5 mM or more each), both of which are precursors of SAM. In contrast to this continual increase in the spore titer, addition of decoyinine, an inhibitor of GMP synthetase, rapidly initiated massive sporulation. Various amino acid analogs also induced sporulation in the relA strain, the methionine analogs ethionine and selenomethionine being most effective.
Nuclear import and export of influenza virus nucleoprotein (1997)

Influenza virus nucleoprotein (NP) shuttles between the nucleus and the cytoplasm. A nuclear localization signal (NLS) has been identified in NP at amino acids 327 to 345 (J. Davey et al., Cell 40:667-675, 1985). However, some NP mutants that lack this region still localize to the nucleus, suggesting an additional NLS in NP. We therefore investigated the nucleocytoplasmic transport of NP from influenza virus A/WSN/33 (H1N1). NP deletion constructs lacking the 38 N-terminal amino acids, as well as those lacking the 38 N-terminal amino acids and the previously identified NLS, localized to both the cytoplasm and the nucleus. Nuclear localization of a protein containing amino acids 1 to 38 of NP fused to LacZ proved that these 38 amino acids function as an NLS. Within this region, we identified two basic amino acids, Lys7 and Arg8, that are crucial for NP nuclear import. After being imported into the nucleus, the wild-type NP and the NP-LacZ fusion construct containing amino acids 1 to 38 of NP were both transported back to the cytoplasm, where they accumulated. These data indicate that NP has intrinsic structural features that allow nuclear import, nuclear export, and cytoplasmic accumulation in the absence of any other viral proteins. Further, the information required for nuclear import and export is located in the 38 N-terminal amino acids of NP, although other NP nuclear export signals may exist. Treatment of cells with a protein kinase C inhibitor increased the amounts of nuclear NP, whereas treatment of cells with a phosphorylation stimulator increased the amounts of cytoplasmic NP. These findings suggest a role of phosphorylation in nucleocytoplasmic transport of NP.
Increased urinary 15-F2t-isoprostane concentrations in patients with non-ischaemic congestive heart failure: a marker of oxidative stress (2003)

Urinary 15-F2t-isoprostane concentrations increased in proportion to the severity of CHF in patients. This may be caused by increased 15-F2t-isoprostane production. These findings suggest that urinary 15-F2t-isoprostane may be a marker of morbidity as well as oxidative stress in patients with CHF.
8-Chloro-11-[4-(8-chloro-5H-dibenzo[b,e][1,4]diazepin-11-yl)piperazino]-5H-dibenzo[b,e][1,4]diazepine (1999)

A method to synthesize desmethylclozapine, 3, is reported. The procedure afforded the target compound in 69% yield. A by-product, isolated from the reaction mixture in 11% yield, proved to be the title compound, 4.
Primary Total Knee Arthroplasty in Patients With Fixed Valgus Deformity (1991)

Ninety-nine knees in 81 patients evaluated from two to ten years and having enough valgus deformity to require specific soft-tissue release were studied. They were also compared to a control group of 40 knees in 31 patients with no angular deformity greater than 5 degrees, who were matched for age and diagnosis. All procedures were performed using a minimally constrained, posterior-cruciate-ligament-sparing prosthesis. Pre- and postoperative axial alignment was measured on weight-bearing long-standing roentgenographs. Analysis included examination for lucent lines in postoperative fluoroscopically positioned roentgenographs and clinical data summarized using the 100-point scoring systems developed by The Knee Society. Knees were classified as having Type I, II, or III valgus deformities: Type I was defined as valgus deformity secondary to bone loss in the lateral compartment and soft-tissue contracture with medial soft tissues intact; Type II was defined as obvious attenuation of the medial capsular ligament complex; and Type III was defined as severe valgus deformity with valgus malpositioning of the proximal tibial joint line after overcorrected proximal tibial osteotomy. Only cases of Type I and Type II were represented in the 99 knees reported. Type I patients were treated with lateral soft-tissue release, and Type II patients were treated with medial capsular ligament tightening (i.e., ligament reconstruction procedures on the medial side). The Knee Society postoperative knee score was 87.6 (+/- 10.6) and mean postoperative functional score was 52.3. Alignment was well corrected and knee scores for the Type I and II groups were almost identical as were the functional scores. The results were grouped as 72% excellent, 18% good, 7% fair, and 2% poor. Notably, the control group was 39 of 40 patients excellent, and only one poor. Ligament stability was satisfactorily established by lateral release in Type I and with the combined medial plication in the Type II patients. The ligament-tightening procedures were on the average 40 minutes longer than those for the Type I or the control groups. The controversial nature of the simultaneous ligament reconstruction method is recognized, but good experience is reported.
Prediction of slug frequency in horizontal two‐phase slug flow (1990)

Abstract Available data on slug frequency in horizontal two‐phase intermittent flow are predicted with adequate accuracy by assuming that the slug frequency is one half of the frequency of the unstable waves precursors of slugs, as determined according to published analyses of finite amplitude waves in conduits. The experimental effects of gas and liquid flow rates, pipe diameter, gas density and liquid viscosity on slug frequency are explained by modifications of the wave properties due to changes in the liquid level of the stratified flow existing in the pipe inlet region prior to slug formation. Simple generalized equations are provided to estimate the slug frequency for engineering calculations.
Identification of dendritic cell colony-forming units among normal human CD34+ bone marrow progenitors that are expanded by c-kit-ligand and yield pure dendritic cell colonies in the presence of granulocyte/macrophage colony-stimulating factor and tumor necrosis factor alpha. (1995)

Several cytokines, especially granulocyte/macrophage colony-stimulating factor (GM-CSF) and tumor necrosis factor alpha (TNF-alpha), have been identified that foster the development of dendritic cells from blood and bone marrow precursors in suspension cultures. These precursors are reported to be infrequent or to yield small numbers of dendritic cells in colony-forming assays. Here we readily identify dendritic cell colony-forming units (CFU-DC) that give rise to pure dendritic cell colonies. Human CD34+ bone marrow progenitors were expanded in semi-solid cultures with serum-replete medium containing c-kit-ligand, GM-CSF, and TNF-alpha. The addition of TNF-alpha to GM-CSF did not alter the number of typical GM colonies but did generate pure dendritic cell colonies that accounted for approximately 40% of the total colony growth. When the two distinct types of colonies were plucked from methylcellulose and tested for T cell-stimulatory activity in the mixed leukocyte reaction, the potency of colony-derived dendritic cells exceeded that of CFU-GM progeny from the same cultures by at least 1.5-2 logs. Immunophenotyping and cytochemical staining of the CFU-DC-derived progeny was also characteristic of dendritic cells. Other myeloid cells were not identified in these colonies. The addition of c-kit-ligand to GM-CSF- and TNF-alpha-supplemented suspensions of CD34+ bone marrow cells expanded CFU-DCs almost 100-fold by 14 d. We conclude that normal human CD34+ bone marrow cells include substantial numbers of clonogenic progenitors, distinct from CFU-GMs, that can give rise to pure dendritic cell colonies. These CFU-DCs can be expanded for several weeks by in vitro culture with c-kit-ligand, and their differentiation requires exogenous TNF-alpha in addition to GM-CSF. We speculate that this dendritic cell-committed pathway may in the steady state contribute cells to the epidermis and afferent lymph, where dendritic cells are the principal myeloid cell type, and may increase the numbers of these specialized antigen-presenting cells during T cell-mediated immune responses.
Principles, mechanisms, and models (1986)

It gradually dawned on us that what we eventually came to identify as a “differentiated” cell of a given type, shape, structure, colour, and behavior, was really just the last scene of a long play of interactions, the earlier stages of which had been hidden from us. We came to realize that, in dynamic terms, the so-called “stages” of the development of a cell, an embryo, or a disease, represented simply cross-sections through a continuous stream of processes, recorded by whatever methods of assay and portrayal – whether in pictures or in graphs – we had at hand. The picture of an overt “character” thus emerged as merely the residual index of prior covert dynamics; “form,” as the registered outcome of formative processes.(Weiss, 1973)
CRISPR-directed mitotic recombination enables genetic mapping without crosses (2016)

Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation, but narrowing these regions to the underlying causal genes and variants has proven much more challenging. Resolution of genetic mapping is limited by the recombination rate. We developed a method that uses CRISPR (clustered, regularly interspaced, short palindromic repeats) to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a yeast chromosome arm, mapping trait variation, and then targeting a high density of recombination events to the region of interest. Using this approach, we fine-mapped manganese sensitivity to a single polymorphism in the transporter Pmr1. Targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences.
Effect on DNA transcription of nucleotide sequences upstream to T7 promoter (1996)

The T7 RNA polymerase-dependent transcription was studied as a function of nucleotide sequence structures positioned upstream of the T7 promoter. Model double-stranded DNA templates were constructed for this purpose. They contained a target sequence of 485 base pairs (cDNA fragment of Venesuelian encephalomyelitis equine virus genome), T7 promoter consensus and different extra base sequences upstream of the T7 promoter. The level of the target sequence transcription was clearly determined by the extra base sequence. The presence of one extra base pair G.C ensured the most pronounced effect, transcription was increased one order of magnitude in comparison with template which has only a canonical T7 promoter sequence at the 5'-end.
FORTH-83 controller for a pick-and-place robot (2003)

The design and implementation of the FORTH-83 Standard system for the MotionMate robotic controller are discussed. The system consists of a remote workstation communicating with an embedded robot controller. The remote workstation provides an F83 (personal computer version of FORTH-83 Standard) and communicates using serial protocol with the robot controller. A brief introduction to the FORTH language is given along with the design objectives and major design decisions of the project. The obstacles encountered throughout the design of the FORTH system are explained.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antimetastatic effects associated with platelet reduction. (1968)

We have previously reported that the number of metastases resulting from the inoculation of TA3 ascites tumor cells into mice could be reduced by 50 per cent if the mice were first injected with neuraminidase.'It was assumed that this effect probably reflected the action of neuraminidase on the sialic acid coat of tumor or host endothelial cells, since it was believed that mutual stickiness between these cell types was important in metastasis formation.'
CT-Guided Lead Placement for Selective Sacral Neuromodulation to Treat Lower Urinary Tract Dysfunctions (2015)

CT-guided tined lead placement was successful in eight patients after 12-month follow-up. Especially in patients with an altered anatomy in the sacral region, this new technique may prevent treatment failure.
Expression of 120 kilodalton protein and cytotoxicity in Helicobacter pylori. (1992)

Antral biopsy culture supernatants from 14 subjects with chronic gastritis, known to have IgA antibodies to the 120 kilodalton protein, showed positive recognition of this antigen in western blots against a cytotoxin positive strain of Helicobacter pylori but gave negative reactions with two cytotoxin negative strains. Control immunoblots with culture supernatants from 13 non-responders to the protein were all negative. This indicates a direct association between expression of the 120 kilodalton protein in H pylori strains and cytotoxicity.
Primary structure of human neutrophil elastase. (1987)

The complete amino acid sequence of human neutrophil elastase has been determined. The protein consists of 218 amino acid residues, contains two asparagine-linked carbohydrate side chains, and is joined together by four disulfide bonds. Comparison of the sequence to other serine proteinases indicates only moderate homology with porcine pancreatic elastase (43.0%) or neutrophil cathepsin G (37.2%). In particular, many of the residues suggested to play important roles in the mechanism by which the pancreatic elastase functions are significantly changed in the neutrophil enzyme, indicating alternative types of binding with the human proteinase.
SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories (2000)

Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. A detailed computer analysis of the structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA. The endonuclease fold, whose structural prototypes are the phage lambda exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs, repair nucleases such as RecB and Vsr, restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. Within the RNase H fold a new family of predicted HJRs, which is nearly ubiquitous in bacteria, was discovered, in addition to the previously characterized RuvC family. The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and AQUIFEX: Endonuclease VII of phage T4 is shown to serve as a structural template for many nucleases, including MCR:A and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. As a result of this analysis, the principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the lambda exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This analysis resulted in the prediction of numerous previously unnoticed nucleases, some of which are likely to be new restriction enzymes.
Large Area Light-Pulse Atom Interferometry (2000)

We report the experimental demonstration of a large area atom interferometer based on extended sequences of light pulses. We characterize the interferometer through measurement of the acceleration due to gravity and demonstrate a threefold enhancement in intrinsic acceleration sensitivity. The technique is applicable to many atom interferometer configurations, including those used for measurement of rotations, gravity gradients, and Planck's over 2pi/m.
Climate effects of the Three Gorges Reservoir as simulated by a high resolution double nested regional climate model (2012)

High resolution multi-annual regional climate model (RegCM3) experiments were performed to simulate the effects of the Three Gorges Reservoir (TGR) on the climate of the surrounding areas. The model was run in double nested mode. Firstly a 50 km resolution simulation was conducted over the China domain driven by the coarse resolution NCEP/NCAR re-analysis. Then the output of the simulation was used to drive the model over the Three Gorges Area (TGA) at a resolution of 10 km. SUB-BATS scheme was employed in the 10 km simulation to represent the land surface at 2 km. Two 10 km simulation, one with and the other without the inland water in TGR were conducted. Comparison of the simulations against observation were firstly carried out to validation the model performances over TGA. The 10 km sensitivity experiments with and without the TGR showed that little or negligible effects can be found except directly over the TGR. Most of the simulated effects are noisy and not statistically significant, except for cooling over the TGR water body in both June–July–August (JJA) and December–January–February (DJF). The cooling leads to an/a insignificant decrease/slight decrease of precipitation over the TGR and nearby grid points, respectively. The cooling is larger in JJA compared to DJF. As a typical river-like reservoir, the width and coverage of the TGR does not have significant influence on the local climate over the area.
Behavior of Lipid-Modified Peptides in Membrane-Mimetic Monolayers at the Air/Water Interface (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTBehavior of Lipid-Modified Peptides in Membrane-Mimetic Monolayers at the Air/Water InterfaceTheodore M. Winger and Elliot L. ChaikofView Author Information School of Chemical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, and Laboratory of Biomolecular Materials Research, Department of Surgery, Emory University School of Medicine, Atlanta, Georgia 30322 Cite this: Langmuir 1997, 13, 12, 3256–3259Publication Date (Web):June 11, 1997Publication History Received26 November 1996Revised1 April 1997Published online11 June 1997Published inissue 1 June 1997https://pubs.acs.org/doi/10.1021/la9620465https://doi.org/10.1021/la9620465brief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views87Altmetric-Citations9LEARN 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 SUBJECTS:Conjugate acid-base pairs,Lipids,Molecules,Monolayers,Peptides and proteins Get e-Alerts