gebhart/patrepeval huggingface dataset:
Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype (1997)

The biological phenotype of primary human immunodeficiency virus type 1 (HIV-1) isolates varies according to the severity of the HIV infection. Here we show that the two previously described groups of rapid/high, syncytium-inducing (SI) and slow/low, non-syncytium-inducing (NSI) isolates are distinguished by their ability to utilize different chemokine receptors for entry into target cells. Recent studies have identified the C-X-C chemokine receptor CXCR4 (also named fusin or Lestr) and the C-C chemokine receptor CCR5 as the principal entry cofactors for T-cell-line-tropic and non-T-cell-line-tropic HIV-1, respectively. Using U87.CD4 glioma cell lines, stably expressing the chemokine receptor CCR1, CCR2b, CCR3, CCR5, or CXCR4, we have tested chemokine receptor specificity for a panel of genetically diverse envelope glycoprotein genes cloned from primary HIV-1 isolates and have found that receptor usage was closely associated with the biological phenotype of the virus isolate but not the genetic subtype. We have also analyzed a panel of 36 well-characterized primary HIV-1 isolates for syncytium induction and replication in the same series of cell lines. Infection by slow/low viruses was restricted to cells expressing CCR5, whereas rapid/high viruses could use a variety of chemokine receptors. In addition to the regular use of CXCR4, many rapid/high viruses used CCR5 and some also used CCR3 and CCR2b. Progressive HIV-1 infection is characterized by the emergence of viruses resistant to inhibition by beta-chemokines, which corresponded to changes in coreceptor usage. The broadening of the host range may even enable the use of uncharacterized coreceptors, in that two isolates from immunodeficient patients infected the parental U87.CD4 cell line lacking any engineered coreceptor. Two primary isolates with multiple coreceptor usage were shown to consist of mixed populations, one with a narrow host range using CCR5 only and the other with a broad host range using CCR3, CCR5, or CXCR4, similar to the original population. The results show that all 36 primary HIV-1 isolates induce syncytia, provided that target cells carry the particular coreceptor required by the virus.
Anti-SIRPα antibody immunotherapy enhances neutrophil and macrophage antitumor activity (2017)

Cancer immunotherapy has emerged as a promising therapeutic intervention. However, complete and durable responses are only seen in a fraction of patients who have cancer. A key factor that limits therapeutic success is the infiltration of tumors by cells of the myeloid lineage. The inhibitory receptor signal regulatory protein-α (SIRPα) is a myeloid-specific immune checkpoint that engages the "don't eat me" signal CD47 expressed on tumors and normal tissues. We therefore developed the monoclonal antibody KWAR23, which binds human SIRPα with high affinity and disrupts its binding to CD47. Administered by itself, KWAR23 is inert, but given in combination with tumor-opsonizing monoclonal antibodies, KWAR23 greatly augments myeloid cell-dependent killing of a collection of hematopoietic and nonhematopoietic human tumor-derived cell lines. Following KWAR23 antibody treatment in a human <i>SIRPA</i> knockin mouse model, both neutrophils and macrophages infiltrate a human Burkitt's lymphoma xenograft and inhibit tumor growth, generating complete responses in the majority of treated animals. We further demonstrate that a bispecific anti-CD70/SIRPα antibody outperforms individually delivered antibodies in specific types of cancers. These studies demonstrate that SIRPα blockade induces potent antitumor activity by targeting multiple myeloid cell subsets that frequently infiltrate tumors. Thus, KWAR23 represents a promising candidate for combination therapy.
Divergent Regulation of Ryanodine Receptor 2 Calcium Release Channels by Arrhythmogenic Human Calmodulin Missense Mutants (2014)

A small proportion of CPVT-CaM is sufficient to evoke arrhythmogenic Ca disturbances, whereas LQTS-CaMs do not. Our findings explain the clinical presentation and autosomal dominant inheritance of CPVT-CaM mutations and suggest that RyR2 interactions are unlikely to explain arrhythmogenicity of LQTS-CaM mutations.
Synthesis and Characterization of Supported Phospholipid Monolayers:  A Correlative Investigation by Radiochemical Titration and Atomic Force Microscopy (1998)

Membrane-mimetic lipid films with or without cholesterol were formed on alkylsilane self-assembled monolayers on glass by a process of lipid vesicle fusion. Using a combination of radiochemical titration with 14C-labeled dipalmitoylphosphatidylcholine (DPPC) and AFM imaging in an aqueous environment, we have characterized both molecular packing density and, in an homologous series of lipid monolayers, film thickness. These data confirm that a monolayer phospholipid membrane can be produced by vesicle fusion to an alkylated glass substrate.
Large-Scale Depletion of CD25+ Regulatory T Cells from Patient Leukapheresis Samples (2005)

The ability to selectively enrich or deplete T lymphocytes of specific phenotype and function holds significant promise for application in adoptive immunotherapy protocols. Although CD4+ T cells can have an impact on CD8+ T-cell effector function, memory, and maintenance, a subset of CD4+ T cells, CD25+ regulatory T cells (Treg), can regulate peripheral self tolerance and possess the ability to suppress antitumor responses. The authors report the ability to selectively deplete CD25+ Treg cells from patient leukapheresis samples using a clinical-grade, large-scale immunomagnetic system. Using leukapheresis samples containing up to 1.3 x 10(10) white blood cells, efficient depletion of Treg cells was measured by flow cytometric analysis of CD25 expression and FOXP3 expression on post-depletion products. Remnant CD25+ cells could not be detected in CD25-depleted products after short-term culture in IL-2 or enriched following secondary immunomagnetic selection for CD25+ cells, confirming that efficient depletion had occurred. In parallel to efficient enrichment of CD25- cells, immunomagnetic selection resulted in the recovery of Treg cells, since CD25+ lymphocytes removed during depletion were primarily composed of CD4+ T cells that expressed high levels of FOXP3 and possessed suppressive activity against autologous TCR-stimulated CD4+ CD25- T cells in vitro. These results show that selective separation of functional CD25+ Treg cells from large-scale samples can be performed in large scale under clinical-grade conditions with sufficient selection, recovery, viability, ability to expand, and function for potential use in adoptive immunotherapy.
Using microcontact printing to fabricate microcoils on capillaries for high resolution proton nuclear magnetic resonance on nanoliter volumes (1997)

This letter describes a method for producing conducting microcoils for high resolution proton nuclear magnetic resonance (1H-NMR) spectroscopy on nanoliter volumes. This technique uses microcontact printing and electroplating to form coils on microcapillaries. Nuclear magnetic resonance spectra collected using these microcoils, have linewidths less than 1 Hz for model compounds and a limit of detection (signal-to-noise ratio=3) for ethylbenzene of 2.6 nmol in 13 min.
Human homologue of murine T200 glycoprotein. (1980)

We report the identification of the human homologue of murine T200 glycoprotein. Peptide-mapping experiments suggest that the structure of the glycoprotein is highly conserved between the two species. Many of the properties of human T200 homologue are similar to those of murine T200 glycoprotein: it is broadly distributed within the hematopoietic system but is not detectable on nonhematopoietic cells; there are also structural differences between the forms of the glycoprotein found on T and B lymphoblastoid cell lines. These results suggest the homologous glycoproteins may play similar functional roles in both species.
XenMon: QoS Monitoring and Performance Profiling Tool (2005)

Abstract. The goal of this short paper is twofold: 1) it briefly describes a new performance monitoring tool, XenMon, that we built for the Xen-based virtual environment, and 2) it presents a performance case study that demonstrates and explains how different metrics reported by XenMon can be used in gaining insight into an application’s performance and its resource usage/requirements, especially in the case of I/O intensive applications. 1
Synthesis and processing of bovine herpesvirus 1 glycoproteins (1986)

Four unique glycoproteins or glycoprotein complexes were recognized by a panel of monoclonal antibodies to bovine herpesvirus 1 (BHV-1), i.e., GVP 6/11a/16 (130,000-molecular-weight glycoprotein [130K glycoprotein]/74K/55K), GVP 7 (108K), GVP 3/9 (180K/91K), and GVP 11b (71K). The absence of any antigenic or structural relationship between GVP 11a and GVP 11b, which were previously identified as one glycoprotein, GVP 11, demonstrated that these two GVP 11 species are unique glycoproteins. GVP 3 and GVP 9 showed complete sequence homology, as shown by the identity of their antigenic determinants and by partial peptide mapping. This observation, as well as the ratio of their apparent molecular weights, indicated that GVP 3 (180K) is a dimeric form of GVP 9 (91K). GVP 6 and GVP 11a, as well as GVP 6 and GVP 16, showed at least partial sequence homology, since they shared several antigenic determinants and peptides. In addition, GVP 6, GVP 11a, and GVP 16 were derived from one primary precursor. These results, as well as the ratio of their apparent molecular weights, indicated that the GVP 6/11a/16 complex consists of two forms: one in which GVP 6 (130K) is uncleaved and the other one in which GVP 6 is cleaved and composed of GVP 11a (74K) and GVP 16 (55K), linked by disulfide bridges. An antigenically distinct precursor to each of the four BHV-1 glycoproteins or glycoprotein complexes was identified by monoclonal antibodies. These precursors, pGVP 6 (117K), pGVP 11a (62K), pGVP 7 (100K), pGVP 9 (69K), and pGVP 11b (63K) were sensitive to endo-beta-N-acetylglucosaminidase H treatment, indicating that they represent the partially glycosylated high-mannose-type intermediate forms generated by cotranslational glycosylation of the primary, unglycosylated precursors to GVP 6/11a/16, GVP 7, GVP 3/9, and GVP 11b, which were identified as having apparent molecular weights of 105,000, 90,000, 61,000, and 58,000, respectively. A new nomenclature for the BHV-1 glycoproteins, based on roman numerals, is proposed.
Mesenchymal cells isolated after acute lung injury manifest an enhanced proliferative phenotype. (1992)

After acute lung injury, mesenchymal cells migrate into the alveolar airspace where they proliferate and deposit connective tissue macromolecules. Early in the disease process, inflammatory cell-derived trophic factors modulate these mesenchymal cell functions. However, in those patients who die, even as the inflammatory response abates, the fibroproliferative response continues, resulting in extensive intraalveolar fibrosis. We therefore hypothesized that lung mesenchymal cells obtained from individuals dying with acute alveolar fibrosis would manifest an enhanced proliferative capacity that was independent of persistent exogenous signals. To examine this hypothesis, the in vitro growth properties of mesenchymal cells prepared from patients dying with acute lung injury (n = 3) were analyzed in defined medium and compared with those of mesenchymal cells similarly prepared from patients dying with histologically normal lungs (n = 3). Isolates were characterized as mesenchymal cells by using morphological and immunohistochemical criteria. In accord with the hypothesis, mesenchymal cells isolated from lung-injured patients doubled within 3 d in the complete absence of exogenous peptide growth factors, reaching a saturation density of approximately 15 x 10(3) cells/cm2. As expected, lung mesenchymal cells from normal individuals failed to significantly increase in number. Consistent with this proliferative phenotype, the immediate early cell division cycle genes c-fos and c-jun were constitutively expressed in each cell strain prepared from injured lungs, but not in those from control lungs. The observed proliferative phenotype was stable through the fifth subcultivation of the cells. Despite these proliferative properties, three separate criteria indicated the mesenchymal cells from injured lungs were not transformed: normal karyotype; finite lifespan in vitro (9-10 subcultivations); and inability to disseminate in mice with severe combined immunodeficiency. These data support the hypothesis that mesenchymal cells manifest an enhanced proliferative state after acute lung injury.
Encapsulation of platinum anticancer drugs by apoferritin (2007)

Apoferritin derived from the native protein ferritin was employed to encapsulate anticancer drugs cisplatin and carboplatin.
Lung adenocarcinomas induced in mice by mutant EGF receptors foundin human lung cancers respondto a tyrosine kinase inhibitor orto down-regulation of the receptors (2006)

Somatic mutations in exons encoding the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are found in human lung adenocarcinomas and are associated with sensitivity to the tyrosine kinase inhibitors gefitinib and erlotinib. Nearly 90% of the EGFR mutations are either short, in-frame deletions in exon 19 or point mutations that result in substitution of arginine for leucine at amino acid 858 (L858R). To study further the role of these mutations in the initiation and maintenance of lung cancer, we have developed transgenic mice that express an exon 19 deletion mutant (EGFR(DeltaL747-S752)) or the L858R mutant (EGFR(L858R)) in type II pneumocytes under the control of doxycycline. Expression of either EGFR mutant leads to the development of lung adenocarcinomas. Two weeks after induction with doxycycline, mice that express the EGFR(L858R) allele show diffuse lung cancer highly reminiscent of human bronchioloalveolar carcinoma and later develop interspersed multifocal adenocarcinomas. In contrast, mice expressing EGFR(DeltaL747-S752) develop multifocal tumors embedded in normal lung parenchyma with a longer latency. With mice carrying either EGFR allele, withdrawal of doxycycline (to reduce expression of the transgene) or treatment with erlotinib (to inhibit kinase activity) causes rapid tumor regression, as assessed by magnetic resonance imaging and histopathology, demonstrating that mutant EGFR is required for tumor maintenance. These models may be useful for developing improved therapies for patients with lung cancers bearing EGFR mutations.
Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain (2010)

A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four human brain regions each from 150 individuals (600 samples total). We find an abundance of genetic cis regulation of mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation across the genome. We show peak enrichment for cis expression QTLs to be approximately 68,000 bp away from individual transcription start sites; however, the peak enrichment for cis CpG methylation QTLs is located much closer, only 45 bp from the CpG site in question. We observe that the largest magnitude quantitative trait loci occur across distinct brain tissues. Our analyses reveal that CpG methylation quantitative trait loci are more likely to occur for CpG sites outside of islands. Lastly, we show that while we can observe individual QTLs that appear to affect both the level of a transcript and a physically close CpG methylation site, these are quite rare. We believe these data, which we have made publicly available, will provide a critical step toward understanding the biological effects of genetic variation.
In Vitro Selection of Integration Host Factor Binding Sites (1999)

Integration host factor (IHF) is a bacterial protein that binds and severely bends a specific DNA target. IHF binding sites are approximately 30 to 35 bp long and are apparently divided into two domains. While the 3' domain is conserved, the 5' domain is degenerate but is typically AT rich. As a result of physical constraints that IHF must impose on DNA in order to bind, it is believed that this 5' domain must possess structural characteristics conducive for both binding and bending with little regard for specific contacts between the protein and the DNA. We have examined the sequence requirements of the 5' binding domain of the IHF binding target. Using a SELEX procedure, we randomized and selected variants of a natural IHF site. We then analyzed these variants to determine how the 5' binding domain affects the structure, affinity, and function of an IHF-DNA complex in a native system. Despite finding individual sequences that varied over 100-fold in affinity for IHF, we found no apparent correlation between affinity and function.
A newly described cellulosomal cellobiohydrolase, CelO, from Clostridium thermocellum: investigation of the exo-mode of hydrolysis, and binding capacity to crystalline cellulose The GenBank accession number for the sequence determined in this work is AJ275975. (2002)

The sequence of the celO gene from Clostridium thermocellum F7 was determined. The gene product, cellulase CelO (Ct-Cel5F), had a modular structure consisting of a carbohydrate-binding module of the CBM3 family and a catalytic domain of the glycosyl hydrolase family 5. The presence of the dockerin module indicated that the enzyme was a component of the cellulosome complex. The thermostable recombinant gene product was active on cellodextrins, barley beta-glucan, carboxymethylcellulose and insoluble cellulose. Cellobiose was the only product released from amorphic and crystalline cellulose, cellotetraose and higher cello-oligosaccharides, identifying CelO as a cellobiohydrolase. The cleavage pattern of p-nitrophenyl beta-D-cellotetraoside, blockage of the hydrolysis of NaBH(4)-reduced cellopentaose and the reduction in substrate viscosity suggested activity from the reducing end in a processive mode after making random cuts. Binding to insoluble, i.e. amorphous, and crystalline cellulose was mediated by the carbohydrate-binding module CBM3b, with a preference for the crystalline substrate.
Ultralow drive voltage silicon traveling-wave modulator (2012)

There has been great interest in the silicon platform as a material system for integrated photonics. A key challenge is the development of a low-power, low drive voltage, broadband modulator. Drive voltages at or below 1 Vpp are desirable for compatibility with CMOS processes. Here we demonstrate a CMOS-compatible broadband traveling-wave modulator based on a reverse-biased pn junction. We demonstrate operation with a drive voltage of 0.63 Vpp at 20 Gb/s, a significant improvement in the state of the art, with an RF energy consumption of only 200 fJ/bit.
Trimethylamine: Metabolic, Pharmacokinetic and Safety Aspects (2005)

Trimethylamine (TMA) is a volatile tertiary aliphatic amine that is derived from the diet either directly from the consumption of foods containing TMA, or by the intake of food containing precursors to TMA such as trimethylamine-N-oxide (TMNO), choline and L-carnitine. Following oral absorption in humans, TMA undergoes efficient N-oxidation to TMNO, a reaction catalyzed by the flavin-containing monooxygenase (FMO) isoform 3 enzyme. TMNO subsequently undergoes excretion in the urine, although, evidence also suggests that metabolic retro-reduction of TMNO can occur. Whilst the pharmacokinetics of TMA and TMNO has not been fully elucidated in humans, a number of studies provide information on the likely fate of dietary derived TMA. Trimethylaminuria is a condition that is characterized by a deficiency in FMO3 enzyme activity, resulting in the excretion of increased amounts of TMA in bodily fluids such as urine and sweat, and breath. A human FMO3 database has been established and currently twenty-eight variants of the FMO3 gene have been reported including twenty-four missense, three nonsense, and one gross deletion mutation. Whilst TMA and TMNO are generally regarded as non-toxic substances, they are of clinical interest because of their potential to form the carcinogen N-nitrosodimethylamine.
Hydrodynamic Dimensions, Electrophoretic Mobility, and Stability of Hydrophilic Quantum Dots (2006)

Luminescent semiconductor quantum dots (QDs) have great potential for use in biological assays and imaging. These nanocrystals are capped with surface ligands (bifunctional molecules, amphiphilic polymers, phospholipids, etc.) that render them hydrophilic and provide them with functional properties. These coatings alters their hydrodynamic radii and surface charge, which can drastically affect properties such as diffusion within the cell cytoplasm. Heavy atom techniques such as transmission electron microscopy and X-ray scattering probe the inorganic core and do not take into account the ligand coating. Herein we use dynamic light scattering to characterize the hydrodynamic radius (R(H)) of CdSe-ZnS QDs capped with various hydrophilic surface coatings (including dihydrolipoic acid and amphiphilic polymers) and self-assembled QD-protein bioconjugates. Experiments were complemented with measurements of the geometric size and zeta potential using agarose gel electrophoresis and laser Doppler velocimetry. We find that the effects of surface ligands on the hydrodynamic radius and on the nanoparticle mobility are complex and strongly depend on a combination of the inorganic core size and nature and lateral extension of the hydrophilic surface coating. These properties are critical for the design of QD-based biosensing assays as well as QD bioconjugate diffusion in live cells.
Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus (2012)

The influenza A virus genome consists of eight single-stranded negative-sense RNA (vRNA) segments. Although genome segmentation provides advantages such as genetic reassortment, which contributes to the emergence of novel strains with pandemic potential, it complicates the genome packaging of progeny virions. Here we elucidate, using electron tomography, the three-dimensional structure of ribonucleoprotein complexes (RNPs) within progeny virions. Each virion is packed with eight well-organized RNPs that possess rod-like structures of different lengths. Multiple interactions are found among the RNPs. The position of the eight RNPs is not consistent among virions, but a pattern suggests the existence of a specific mechanism for assembly of these RNPs. Analyses of budding progeny virions suggest two independent roles for the viral spike proteins: RNP association on the plasma membrane and the subsequent formation of the virion shell. Our data provide further insights into the mechanisms responsible for segmented-genome packaging into virions.
A rapid method to identify cosmids containing rare restriction site (1987)

A procedure for identifying specific cosmid clones containing recognition sites for "rare cutting" restriction enzymes has been developed. Cosmid clones containing human inserts were selected by hybridisation to human repetitive DNA. An oligonucleotide corresponding to the NotI recognition site, eight bases long, was labelled and used to probe DNA samples from one hundred cosmids. By optimising the difference in melting characteristics between eight-base perfect match and six-base match/two base mismatch hybrids, we were able to detect the cosmids containing either NotI (8 bp match) or XmaIII/EagI (6 bp match) sites. The generation of a map for rare cutter sites along a human chromosome, or a chromosome region, should be simplified using this approach, which will enable the identification of a set of "milestones" at intervals of several hundred kilobases (kb) along the DNA sequence.