gebhart/patrepeval huggingface dataset:
Isolation of a Human Anti-HIV gp41 Membrane Proximal Region Neutralizing Antibody by Antigen-Specific Single B Cell Sorting (2011)

Broadly neutralizing antibodies are not commonly produced in HIV-1 infected individuals nor by experimental HIV-1 vaccines. When these antibodies do occur, it is important to be able to isolate and characterize them to provide clues for vaccine design. CAP206 is a South African subtype C HIV-1-infected individual previously shown to have broadly neutralizing plasma antibodies targeting the envelope gp41 distal membrane proximal external region (MPER). We have now used a fluoresceinated peptide tetramer antigen with specific cell sorting to isolate a human neutralizing monoclonal antibody (mAb) against the HIV-1 envelope gp41 MPER. The isolated recombinant mAb, CAP206-CH12, utilized a portion of the distal MPER (HXB2 amino acid residues, 673-680) and neutralized a subset of HIV-1 pseudoviruses sensitive to CAP206 plasma antibodies. Interestingly, this mAb was polyreactive and used the same germ-line variable heavy (V(H)1-69) and variable kappa light chain (V(K)3-20) gene families as the prototype broadly neutralizing anti-MPER mAb, 4E10 (residues 672-680). These data indicate that there are multiple immunogenic targets in the C-terminus of the MPER of HIV-1 gp41 envelope and suggests that gp41 neutralizing epitopes may interact with a restricted set of naive B cells during HIV-1 infection.
Purification of a factor which provides a costimulatory signal for gamma interferon production (1993)

A protein factor which induces high levels of gamma interferon (IFN-gamma) in resting splenic nonadherent cells was isolated from the sera of mice with generalized inflammation caused by endotoxic shock. The factor was highly purified by ammonium sulfate precipitation followed by ion-exchange column chromatography on DEAE-Sepharose, molecular sieving on Ultrogel AcA 44, and hydrophobic column chromatography with phenyl-Sepharose. It was further purified to apparent homogeneity by polyacrylamide gel electrophoresis. It induced IFN-gamma production in a dose-dependent manner in the presence of interleukin-2, monoclonal anti-CD3 antibody (anti-CD3 MAb), or concanavalin A (ConA) in spleen cells deprived of plastic plate- and nylon wool-adherent cells. Anti-CD3 MAb induced the highest level of production of the three. The factor, interleukin-2, anti-CD3 MAb, or ConA alone induced a trace of or no detectable IFN-gamma in these cells. The factor also exhibited an accessory function during proliferation in these cells in the presence of a suboptimal dose of ConA. However, the factor failed to stimulate IFN-gamma production when staphylococcal enterotoxin A, a superantigenic T-cell mitogen, was employed. Treatment with pronase or heat abolished these activities. These studies confirm the existence of a soluble protein factor which is able to exhibit a novel accessory function in IFN-gamma production in resting T or natural killer cells. It will be of interest to compare this factor with the recently cloned human natural killer stimulatory factor (NKSF/IL-12).
Cloning of the low-affinity murine granulocyte-macrophage colony-stimulating factor receptor and reconstitution of a high-affinity receptor complex. (1992)

A cDNA clone (clone 71) that encodes a low-affinity receptor for murine granulocyte-macrophage colony-stimulating factor (GM-CSF) has been isolated by direct expression. This molecule is the homologue of the human GM-CSF receptor alpha subunit, although homology between these molecules is surprisingly low (less than 35% amino acid identity). The cDNA encodes a polypeptide of 387 amino acids, which contains the conserved features of the hematopoietin receptor superfamily. When expressed in COS-7 cells, this clone encodes a protein that binds radiolabeled murine GM-CSF with low affinity. Coexpression of clone 71 with a cDNA corresponding to a low-affinity interleukin 3 (IL-3) receptor (AIC2A) did not alter the affinity of binding of either GM-CSF or IL-3. However, coexpression of clone 71 with the IL-3 receptor-related cDNA AIC2B generated high-affinity binding sites for murine GM-CSF but not murine IL-3. These studies show that clone 71 and AIC2B are capable of forming an alpha beta complex capable of binding murine GM-CSF with high affinity, while AIC2A appears not to be a component of the murine GM-CSF receptor.
Prediction for Effectiveness of Steroid Pulse Therapy by MRI in Graves' Ophthalmopathy (1992)

Fifteen patients with Graves' ophthalmopathy (GO) were treated with intravenous methylprednisolone (steroid pulse therapy, 1g daily for 3 days a week, 2-4 times) and followed up by ophthalmological assessment and magnetic resonance imaging (MRI). The signal intensity of enlarged eye muscle and retrobulbar fat was examined with MRI at 0.5T with short inversion time inversion recovery (STIR) sequences. The signal intensity of eye muscle and retrobulbar fat tissue in STIR was evaluated as the ratio to cerebral substantia alba (signal intensity ratio). The thickness of enlarged eye muscle was measured by T1-weighted coronal images. The signal intensity ratios of enlarged eye muscle of GO patients were significantly higher than those of eight normal subjects. Although the signal intensity ratios of muscle and retrobulbar fat before therapy were not related to the severity of clinical findings of GO assessed by ophthalmopathy index, the initial signal intensity ratios of eye muscle and retrobulbar fat of ten patients with improved clinical findings of GO after steroid pulse therapy tended to be higher than those of five patients without improvement by the therapy. After the therapy the signal intensity ratios of muscle and retrobulbar fat were significantly decreased in ten patients with favorable response. Our data suggested that high signal intensity in STIR may reflect edema caused by acute inflammation associated with GO. In conclusion, MRI may be a useful tool for determining the indication and prognosis of steroid pulse therapy. We strongly recommend measuring the signal intensity of eye muscle as well as muscle thickness in MRI to evaluate the activity of GO.
A method for finding good Ashenhurst decompositions and its application to FPGA synthesis (1995)

In this paper, we present an algorithm for finding a good Ashenhurst decomposition of a switching function. Most current methods for performing this type of decomposition are based on the Roth-Karp algorithm. The algorithm presented here is based on finding an optimal cut in a BDD. This algorithm differs from previous decomposition algorithms in that the cut determines the size and composition of the bound set and the free set. Other methods examine all possible bound sets of an arbitrary size. We have applied this method to decomposing functions into sets of -variable functions. This is a required step when implementing a function using a lookup table (LUT) based FPGA. The results compare very favorably to existing implementations of Roth-Karp decomposition methods.
Exact Graph Structure Estimation with Degree Priors (2009)

We describe a generative model for graph edges under specific degree distributions which admits an exact and efficient inference method for recovering the most likely structure. This binary graph structure is obtained by reformulating the inference problem as a generalization of the polynomial time combinatorial optimization known as b-matching. Standard b-matching recovers a constant-degree constrained maximum weight subgraph from an original graph instead of a distribution over degrees. After this mapping, the most likely graph structure can be found in cubic time with respect to the number of nodes using max flow methods. Furthermore, in some instances, the combinatorial optimization problem can be solved exactly in near quadratic time by loopy belief propagation and max product updates even if the original input graph is dense. We show an example application to post-processing of recommender system predictions.
Production of Acetone Butanol Ethanol (ABE) by a Hyper-Producing Mutant Strain of Clostridium beijerinckii BA101 and Recovery by Pervaporation (1999)

A silicone membrane was used to study butanol separation from model butanol solutions and fermentation broth. Depending upon the butanol feed concentration in the model solution and pervaporation conditions, butanol selectivities of 20.88-68.32 and flux values of 158.7-215.4 g m(-)(2) h(-)(1) were achieved. Higher flux values (400 g m(-)(2) h(-)(1)) were obtained at higher butanol concentrations using air as sweep gas. In an integrated process of butanol fermentation-recovery, solvent productivities were improved to 200% of the control batch fermentation productivities. In a batch reactor the hyper-butanol-producing mutant strain C. beijerinckii BA101 utilized 57.3 g/L glucose and produced 24.2 g/L total solvents, while in the integrated process it produced 51.5 g/L (culture volume) total solvents. Concentrated glucose medium was also fermented. The C. beijerinckii BA101 mutant strain was not negatively affected by the pervaporative conditions. In the integrated experiment, acids were not produced. With the active fermentation broth, butanol selectivity was reduced by a factor of 2-3. However, the membrane flux was not affected by the active fermentation broth. The butanol permeate concentration ranged from 26.4 to 95.4 g/L, depending upon butanol concentration in the fermentation broth. Since the permeate of most membranes contains acetone, butanol, and ethanol (and small concentrations of acids), it is suggested that distillation be used for further purification.
Sulfur poisoning of catalysts. Quarterly progress report, 1 October--31 December 1976. [Fuels synthesis from H/sub 2/ and CO] (1977)

The emphasis in the work has been shifted from sulfur poisoning of catalysts for methanol synthesis to the role of carbon in catalysts for Fischer-Tropsch synthesis. In the latter, the preparation of catalysts by the reduction of iron oxides and then their carburization was studied by thermogravimetric and thermomagnetic techniques. This provided information on the processes involved in reduction and carburization, activation energies, kinetics, stoichiometry, phase transformations, crystallite size, Curie temperature, surface reactivity, etc. Further work on methanol synthesis catalysts pointed to copper as the primary gateway for the accumulation of sulfur. The surface of the catalyst was examined by scanning electron microscopy and energy dispersive x-ray analysis with the aim of determining the distribution of copper and zinc and evaluating the possibility of mobility on the catalyst surface of the adsorbed sulfur atoms to the zinc oxide phase. It was not possible to differentiate (or resolve) the copper and zinc phases on the catalyst surface so the possibility of sulfur mobility is being investigated by Auger electron spectroscopy. (LTN)
Protective responses in the ischemic myocardium (2000)

Acute coronary syndromes and heart failure arising as a consequence of ischemic injury to the myocardium account for a large proportion of all hospital admissions and of all causes of death in industrialized nations. Medical and surgical management of these conditions consumes enormous resources each year, but current therapeutic measures fall far short of reducing death and disability from ischemic heart disease to acceptable levels. Several recently successful advances in therapy of acute coronary syndromes are based on limiting the extent of myocardial damage that ensues following occlusion of a major coronary artery by rapid restoration of blood flow. However, many patients are not suitable candidates for thrombolytic drugs or revascularization procedures, and these approaches often are applied too late to prevent irreversible damage to the myocardium. A greater understanding of the mechanisms of ischemic injury, and of endogenous defense mechanisms, could foster additional improvements in clinical care.
Estrogen Receptor, Progesterone Receptor, Human Epidermal Growth Factor Receptor 2 (HER2), and Epidermal Growth Factor Receptor Expression and Benefit From Lapatinib in a Randomized Trial of Paclitaxel With Lapatinib or Placebo As First-Line Treatment in HER2-Negative or Unknown Metastatic Breast Cancer (2009)

Although subgroups are small, these analyses support the hypothesis that semiquantitative determination of hormone receptor status may be a surrogate for EGFR and/or HER2 dependency.
Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports (1994)

A simple and rapid method for the analysis of genetic polymorphisms has been developed using allele-specific oligonucleotide arrays bound to glass supports. Allele-specific oligonucleotides are covalently immobilized on glass slides in arrays of 3 mm spots. Genomic DNA is amplified by PCR using one fluorescently tagged primer oligonucleotide and one biotinylated primer oligonucleotide. The two complementary DNA strands are separated, the fluorescently tagged strand is hybridized to the support-bound oligonucleotide array, and the hybridization pattern is detected by fluorescence scanning. Multiple polymorphisms present in the PCR product may be detected in parallel. The effect of spacer length, surface density and hybridization conditions were evaluated, as was the relative efficacy of hybridization with single or double-stranded PCR products. The utility of the method was demonstrated in the parallel analysis of 5 point mutations from exon 4 of the human tyrosinase gene.
Review of Heather Wiebe. 2012. Britten’s Unquiet Pasts: Sound and Memory in Postwar Reconstruction. New York: Cambridge University Press (2020)

Britten as a public figure. Britten as a composer of music for children, amateurs, and the church. These are sides of Britten’s legacy that have attracted little scholarly attention prior to Heather Wiebe’s recent monograph Britten’s Unquiet Pasts: Sound and Memory in Postwar Reconstruction. More familiar is Britten as a composer of opera and art song, and as a man “at odds with . . . society” (Pears 1983: 152).1 Although anticipating the Britten centenary by one year, Britten’s Unquiet Pasts is much in keeping with the spirit of other Britten publications to be released this year, not least Paul Kildea’s (2013) biography. What emerges from these new perspectives is a more complex view of Britten, both as an artist whose breadth of work defies easy classification, and as a man with changing and often conflicting impulses towards his envisaged role in society.
Programming a crystalline shape memory polymer network with thermo- and photo-reversible bonds toward a single-component soft robot (2018)

The need to support the two most basic functions [three-dimensional (3D)-shaped support and actuation] independently for a typical robot demands that at least two components should be used in its construction. Therefore, component assembly is unavoidable despite the ultimate dream of creating assembly-free robots. We devise a strategy that uses a programmable crystalline shape memory polymer with thermo- and photo-reversible bonds to create a single-component robot. The global 3D-shaped structural support is fabricated via a plasticity-based origami technique enabled by the thermo-reversible bonds. More critically, precisely controlled localized actuation can be programmed into the 3D origami via spatially defined reversible shape memory using the photo-reversible bonds. The overall result is that a polymer thin film can be programmed into various soft robots including a 3D crane and an elephant. Besides reversible shape memory, other types of actuation mechanisms can be potentially introduced via a similar principle. Thus, our strategy represents a general method to create single-component soft robots.
c-Maf Induces Monocytic Differentiation and Apoptosis in Bipotent Myeloid Progenitors (1999)

The transcriptional mechanisms that drive colony-forming unit granulocyte-macrophage (CFU-GM) myeloid progenitors to differentiate into cells of either the granulocytic or monocytic lineage are not fully understood. We have shown that the c-Maf and c-Myb transcription factors physically interact in myeloid cells to form inhibitory complexes that hinder transactivation of c-Myb target genes through direct binding to Myb consensus sites. These complexes arise in a developmentally regulated pattern, peaking at the promyelocyte stage, or in cell model systems, appearing soon after the induction of monocytic differentiation. We wished to determine if this developmentally related interaction is a consequence of myeloid differentiation or an intrinsic differentiating stimulus. Because the elevated Myb:Maf status seen in differentiating cells can be recapitulated by overexpression of c-Maf in myeloid cell lines, we inducibly expressed the c-Maf cDNA in 2 bipotent human myeloid progenitor cells. Elevated levels of c-Maf protein led to marked increases in Myb:Maf complexes and the accumulation of monocyte/macrophage cells, followed by eventual programmed cell death. Analysis of targets that could mediate these phenotypic changes indicated that c-Maf likely plays a key role in myeloid cell development through dual mechanisms; inhibition of a select set of c-Myb regulated targets, such as Bcl-2 and CD13/APN, coupled with the activation of as yet undefined differentiation-promoting genes.
Footprinting with MPE{middle dot}Fe(II). Complementary-strand Analyses of Distamycin- and Actinomycin-binding Sites on Heterogeneous DNA (1983)

We recently reported a direct technique for determining the binding sites of small molecules on naturally occurring heterogeneous DNA (Van Dyke et al. 1982). Methidiumpropyl-EDTA·Fe(II) (MPE·Fe[II]) (Hertzberg and Dervan 1982) cleaves double-helical DNA with low sequence-specificity (Van Dyke et al. 1982). Using a combination of MPE·Fe(II) partial cleavage of drug-protected DNA fragments and Maxam-Gilbert sequencing methods, we determined the drug-protected sites on one strand of a double-helical fragment from pBR322 for the intercalator actinomycin D (Goldberg et al. 1962; Muller and Crothers 1968; Wells and Larson 1970; Sobell 1973; Krugh 1981; Patel et al. 1981; Takusagawa et al. 1982) and the minor-groove binders netropsin and distamycin A (Luck et al. 1974; Wartell et al. 1974; Zimmer 1975; Berman et al. 1979; Krylov et al. 1979). Netropsin and distamycin A gave identical DNA-cleavage inhibition patterns or footprints in regions rich in dA·dT base pairs. Actinomycin D afforded a completely different footprint...
Ex vivo differentiation of natural killer cells from human umbilical cord blood CD34+progenitor cells (2011)

Natural Killer (NK)-cells are peripheral blood lymphocytes that represent an important arm of the innate immune system. NK-cells play a critical role in the immune surveillance against tumors and virally infected cells in a major histocompatibiliy complex (MHC)-unrestricted fashion. We have explored such capacities of NK-cells after differentiation from hematopoietic stem and progenitor cells derived from human umbilical cord blood. Several culture conditions have been established supporting proliferation and subsequent differentiation of these cells in terms of receptor expression and specific lysis depending on the growth conditions in the presence and absence of supportive stromal feeders. We show that acquisition of Killer Immunoglobulin Receptor (KIR) as well as NK Cytotoxicity Receptor expressions is independent of culture condition whereas absence of stromal feeders did not support acquisition of CD94/NKG2A expression. Such KIR-positive/NKG2A-negative cells generated under different culture conditions showed strong and specific cytolytic activity which could have impact on further immunotherapeutic strategies.
Fine Mapping of the SCN Resistance Locus rhg1‐b from PI 88788 (2010)

Soybean cyst nematode (SCN) ( Heterodera glycines Ichinohe) is the most economically damaging soybean [ Glycine max (L.) Merr.] pest in the USA and genetic resistance is a key component for its control. Although SCN resistance is quantitative, the rhg1 locus on chromosome 18 (formerly known as Linkage Group G) confers a high level of resistance. The objective of this study was to fine‐map the rhg1‐b allele that is derived from plant introduction (PI) 88788. F 2 and F 3 plants and F 3:4 lines from crosses between SCN resistant and susceptible genotypes were tested with genetic markers to identify recombination events close to rhg1‐b . Lines developed from these recombinant plants were then tested for resistance to the SCN isolate PA3, which originally had an HG type 0 phenotype, and with genetic markers. Analysis of lines carrying key recombination events positioned rhg1‐b between the simple sequence repeat (SSR) markers BARCSOYSSR_18_0090 and BARCSOYSSR_18_0094. This places rhg1‐b to a 67‐kb region of the ‘Williams 82’ genome sequence. The receptor‐like kinase gene that has been previously identified as a candidate for the ‘Peking’‐derived SCN resistant rhg1 gene is adjacent to, but outside of, the rhg1‐b interval defined in the present study.
U.S. Department of Energy Commercial Reference Building Models of the National Building Stock (2011)

The U.S. Department of Energy (DOE) Building Technologies Program has set the aggressive goal of producing marketable net-zero energy buildings by 2025. This goal will require collaboration between the DOE laboratories and the building industry. We developed standard or reference energy models for the most common commercial buildings to serve as starting points for energy efficiency research. These models represent fairly realistic buildings and typical construction practices. Fifteen commercial building types and one multifamily residential building were determined by consensus between DOE, the National Renewable Energy Laboratory, Pacific Northwest National Laboratory, and Lawrence Berkeley National Laboratory, and represent approximately two-thirds of the commercial building stock.
The Transmembrane Domain and Cytoplasmic Tail of Herpes Simplex Virus Type 1 Glycoprotein H Play a Role in Membrane Fusion (2002)

Herpes simplex virus glycoprotein H (gH) is one of the four virion envelope proteins which are required for virus entry and for cell-cell fusion in a transient system. In this report, the role of the transmembrane and cytoplasmic tail domains of gH in membrane fusion was investigated by generating chimeric constructs in which these regions were replaced with analogous domains from other molecules and by introducing amino acid substitutions within the membrane-spanning sequence. gH molecules which lack the authentic transmembrane domain or cytoplasmic tail were unable to mediate cell-cell fusion when coexpressed with gB, gD, and gL and were unable to rescue the infectivity of a gH-null virus as efficiently as a wild-type gH molecule. Many amino acid substitutions of specific amino acid residues within the transmembrane domain also affected cell-cell fusion, in particular, those introduced at a conserved glycine residue. Some gH mutants that were impaired in cell-cell fusion were nevertheless able to rescue the infectivity of a gH-negative virus, but these pseudotyped virions entered cells more slowly than wild-type virions. These results indicate that the fusion event mediated by the coexpression of gHL, gB, and gD in cells shares common features with the fusion of the virus envelope with the plasma membrane, they point to a likely role for the membrane-spanning and cytoplasmic tail domains of gH in both processes, and they suggest that a conserved glycine residue in the membrane-spanning sequence is crucial for efficient fusion.