gebhart/patrepeval huggingface dataset:
Effect of pH on silk fibroin gelation. (1992)

Aqueous silk fibroin gelled when it was kept for a required time under suitable conditions.
Characterization of SH2D1A Missense Mutations Identified in X-linked Lymphoproliferative Disease Patients (2001)

X-linked lymphoproliferative disease (XLP) is a primary immunodeficiency characterized by extreme susceptibility to Epstein-Barr virus. The XLP disease gene product SH2D1A (SAP) interacts via its SH2 domain with a motif (TIYXXV) present in the cytoplasmic tail of the cell-surface receptors CD150/SLAM, CD84, CD229/Ly-9, and CD244/2B4. Characteristically, the SH2D1A three-pronged interaction with Tyr(281) of CD150 can occur in absence of phosphorylation. Here we analyze the effect of SH2D1A protein missense mutations identified in 10 XLP families. Two sets of mutants were found: (i) mutants with a marked decreased protein half-life (e.g. Y7C, S28R, Q99P, P101L, V102G, and X129R) and (ii) mutants with structural changes that differently affect the interaction with the four receptors. In the second group, mutations that disrupt the interaction between the SH2D1A hydrophobic cleft and Val +3 of its binding motif (e.g. T68I) and mutations that interfere with the SH2D1A phosphotyrosine-binding pocket (e.g. C42W) abrogated SH2D1A binding to all four receptors. Surprisingly, a mutation in SH2D1A able to interfere with Thr -2 of the CD150 binding motif (mutant T53I) severely impaired non-phosphotyrosine interactions while preserving unaffected the binding of SH2D1A to phosphorylated CD150. Mutant T53I, however, did not bind to CD229 and CD224, suggesting that SH2D1A controls several critical signaling pathways in T and natural killer cells. Because no correlation is present between identified types of mutations and XLP patient clinical presentation, additional unidentified genetic or environmental factors must play a strong role in XLP disease manifestations.
Unlocking the potential of CD70 as a novel immunotherapeutic target for non-small cell lung cancer (2015)

Although normally restricted to activated T and B cells and mature dendritic cells, constitutive expression of CD70, a member of the tumor necrosis family, has been described in both hematological and solid tumors, where it increases tumor cell and regulatory T cell survival by signaling through its receptor, CD27.We have assessed the co-expression of CD70 and CD27 in non-small cell lung cancer (NSCLC) by immunohistochemistry to explore a correlation between expression of the protein and tumor histologic subtype, genetic aberrations and prognosis. Furthermore, we tested the ability of ARGX-110, a CD70-blocking antibody, to induce NK cell-mediated cytotoxicity.Our results revealed CD70 expression on the surface of both primary and metastatic NSCLC tumor cells and in the tumor microenvironment. Moreover, CD27-expressing tumor infiltrating lymphocytes were found adjacent to the tumor cells, suggesting active CD70-mediated signaling. Finally, we have shown that ARGX-110, has potent cytotoxic effects on CD70+ NSCLC cell lines.
Process Development and Large-Scale Synthesis of a c-Met Kinase Inhibitor (2010)

A highly convergent synthesis of c-Met kinase inhibitor 1 has been demonstrated on a multikilogram scale using three key fragments: dihalotricyclic core 2, chiral sulfamide side chain 3, and pyrazole boronic ester 4. The chirality in sulfamide side chain 3 was installed using the cheap and readily available starting material (S)-epichlorohydrin. A total of 2.71 kg of 1 were isolated in seven steps (the longest linear sequence).
Surplus fair scheduling: a proportional-share CPU scheduling algorithm for symmetric multiprocessors (2000)

In this paper, we present surplus fair scheduling (SFS), a proportional-share CPU scheduler designed for symmetric multiprocessors. We first show that the infeasibility of certain weight assignments in multiprocessor environments results in unfairness or starvation in many existing proportional-share schedulers. We present a novel weight readjustment algorithm to translate infeasible weight assignments to a set of feasible weights. We show that weight readjustment enables existing proportional-share schedulers to significantly reduce, but not eliminate, the unfairness in their allocations. We then present surplus fair scheduling, a proportional-share scheduler that is designed explicitly for multiprocessor environments. We implement our scheduler in the Linux kernel and demonstrate its efficacy through an experimental evaluation. Our results show that SFS can achieve proportionate allocation, application isolation and good interactive performance, albeit at a slight increase in scheduling overhead. We conclude from our results that a proportional-share scheduler such as SFS is not only practical but also desirable for server operating systems.
Activity of a recombinant fusion protein between transforming growth factor type alpha and Pseudomonas toxin. (1987)

The transforming growth factor type alpha gene has been fused to a modified Pseudomonas toxin gene from which the cell-recognition domain has been deleted. The chimeric gene has been expressed in Escherichia coli, and the chimeric protein, PE40-TGF-alpha, has been highly purified. PE40-TGF-alpha kills cells expressing epidermal growth factor receptors and has little activity against cells with few receptors. This chimeric protein might be useful in treating cancers that contain high numbers of epidermal growth factor receptors.
Use of Up-Converting Phosphor Reporters in Lateral-Flow Assays to Detect Specific Nucleic Acid Sequences: A Rapid, Sensitive DNA Test to Identify Human Papillomavirus Type 16 Infection (2001)

The use of UPT in LF assays to detect specific nucleic acids provides low attamole-range sensitivity. Hybridization and consecutive detection of PCR-amplified HPV16 sequences were successful in a background of 10 microg of fish-sperm DNA. The sensitivity of UPT detection in these complex mixtures indicates that detection of viral infections without PCR or other amplification technique is achievable.
Riboflavin-UVA-Induced Corneal Collagen Cross-linking in Pediatric Patients (2011)

The study demonstrated significant and rapid functional improvement in pediatric patients younger than 18 years with progressive keratoconus, undergoing riboflavin-UVA–induced cross-linking. In pediatric age, a good functional response and keratoconus stability was obtained after corneal cross-linking in a 36-month follow-up.
Optimization of Allylic Oxidation of (1S,3R,8R)‐2,2‐Dichloro‐3,7,7,10‐tetramethyltricyclo[6,4,0,01,3]dodec‐9‐ene (2004)

Abstract The allylic oxidation of (1S,3R,8R)‐2,2‐dichloro‐3,7,7,10‐tetramethyltricyclo[6,4,0,01,3]dodec‐9‐ene into the corresponding enone with N‐bromosuccinimide (NBS), CrO3 and t‐BuOOH has been studied. A good yield and high selectivity were obtained in the presence of t‐BuOOH and a copper catalyst.
Surgery for glioma relapse factors that influence a favorable outcome (1988)

The role of cytoreductive surgery alone as effective salvage therapy for immediate palliation and durable symptom-free remission was examined in 17 patients (six with astrocytoma, seven with anaplastic astrocytoma, and four with glioblastoma) who developed symptomatic tumor relapse after initial surgery and irradiation. Individuals with widely disseminated subependymal, bihemispheral, or brainstem involvement were excluded. After reoperation, patients with astrocytoma and anaplastic tumors have been observed for an average of 31 and 29 months, respectively. As of this writing, all 13 patients are alive without evidence of tumor progression. Three of the four patients with glioblastomas have died 5, 12, and 17 months after reoperation, respectively. The 14 surviving patients overall have a current average Karnofsky performance level of 95. The durability of surgically induced palliation alone, the safe limits of resectability, and the clinical features associated with a favorable surgical response have been examined. The results indicate that, in selected individuals, durable remissions can be achieved by adequate resection of symptomatic tumor mass.
Reactive Polymer Coatings:  A First Step toward Surface Engineering of Microfluidic Devices (2003)

We report fabrication, characterization, and use of microfluidic analysis devices containing surface-immobilized cell-capturing molecules. Amino-terminated biotin ligands are immobilized onto the luminal surface of a microdevice and effectively support self-assembly of proteins, antibodies, and mammalian cells. For this purpose, chemical vapor deposition (CVD) polymerization is used to functionalize PDMS-made microfluidic devices with poly[para-xylylene carboxylic acid pentafluorophenolester-co-para-xylylene]. The resulting reactive coating shows excellent adhesion when deposited in thin films (approximately 100 nm, and the distribution of the pentafluorophenol ester groups is reasonably uniform within the microchannel inner surface, as examined by fluorescence microscopy. The utility of these devices for cell-based bioassays is demonstrated by monitoring the concentration-dependent effect of the disintegrin echistatin on cell adhesion. The described assay format could be relevant to clinical research in various fields, including angiogenesis research.
Spinal Cord Stimulation Frequency Influences the Hemodynamic Response in Patients with Disorders of Consciousness (2018)

Spinal cord stimulation (SCS) is a promising technique for treating disorders of consciousness (DOCs). However, differences in the spatio-temporal responsiveness of the brain under varied SCS parameters remain unclear. In this pilot study, functional near-infrared spectroscopy was used to measure the hemodynamic responses of 10 DOC patients to different SCS frequencies (5 Hz, 10 Hz, 50 Hz, 70 Hz, and 100 Hz). In the prefrontal cortex, a key area in consciousness circuits, we found significantly increased hemodynamic responses at 70 Hz and 100 Hz, and significantly different hemodynamic responses between 50 Hz and 70 Hz/100 Hz. In addition, the functional connectivity between prefrontal and occipital areas was significantly improved with SCS at 70 Hz. These results demonstrated that SCS modulates the hemodynamic responses and long-range connectivity in a frequency-specific manner (with 70 Hz apparently better), perhaps by improving the cerebral blood volume and information transmission through the reticular formation-thalamus-cortex pathway.
Painting and rendering textures on unparameterized models (2002)

This paper presents a solution for texture mapping unparameterized models. The quality of a texture on a model is often limited by the model's parameterization into a 2D texture space. For models with complex topologies or complex distributions of structural detail, finding this parameterization can be very difficult and usually must be performed manually through a slow iterative process between the modeler and texture painter. This is especially true of models which carry no natural parameterizations, such as subdivision surfaces or models acquired from 3D scanners. Instead, we remove the 2D parameterization and store the texture in 3D space as a sparse, adaptive octree. Because no parameterization is necessary, textures can be painted on any surface that can be rendered. No mappings between disparate topologies are used, so texture artifacts such as seams and stretching do not exist. Because this method is adaptive, detail is created in the map only where required by the texture painter, conserving memory usage.
Cellular Concentrations and Uniformity of Cell-Type Accumulation of Two Lea Proteins in Cotton Embryos. (1993)

The levels and cell-type distribution of late embryogenesis abundant (Lea) proteins D-7 and D-113 have been determined in mature cotton embryos by immunochemical methods. The two proteins were expressed in and purified from Escherichia coli and utilized for antibody production in rabbits. The antiserum to each protein was found to interact with all members of each protein family in cotton extracts by protein gel blotting. Using these antibodies in quantitative "rocket" immunoelectrophoreses, D-7 proteins were found to accumulate to ~8 x 1015 molecules per embryo, which is equivalent to ~109 molecules per "average cell." D-113 proteins accumulate to ~1016 molecules per embryo, which equates to ~1.3 x 109 molecules per average cell. These values calculate to concentrations of about 226 and 283 [mu]M, respectively, in the cell aqueous phase immediately prior to seed desiccation. In immunocytochemical studies using the fluorophor rhodamine linked to the secondary antibody, both proteins appeared to be evenly present in the cytosol of all cell types present in the embryo, including both cotyledon and axis epidermal cells. Thus, their function does not appear related to unique functions of specific cell or tissue types. The very high molar concentrations of the two proteins, coupled with their unusual predicted structure and their cytosol location, would seem to reduce the number of their conceivable functions.
BHT Blocks NF‐κB activation and Ethanol‐Induced Brain Damage (2006)

Binge-induced brain damage and activation of NF-kappaB-DNA binding are blocked by BHT. These studies support a neuroinflammatory mechanism of binge ethanol-induced brain damage.
The Selective Monobenzylidenation of Some Monosaccharides and Their Derivatives With α,α-Dimethoxytoluene (1988)

The treatment of some monosaccharides and their derivatives with a,a-dimethoxytoluene and an acid catalyst in dimethylformamide at about 80° can lead to selective benzylidenation , e.g. methyl a-D- mannopyranoside gives mainly methyl 4,6-Obenzylidene-a-D-mannoside, together with two other minor monobenzylidene derivatives (2,3-) and two minor dibenzylidene derivatives (2,3:4,6-). The treatment of various other pyranoses and pyranosides is also described. As well, a 1H n.m.r . study of the acid transformation of some of the above a-D- mannosides is reported, together with a single-crystal X-ray diffraction structure determination of a novel monobenzylidene derivative, namely methyl (S)- 2,3-O-benzylidene-a-D-mannopyranoside.
Chlorine Dioxide Water Disinfection: A Praspective Epidemiology Study (1981)

An epidemiologic study of 198 persons exposed for 3 months to drinking water disinfected with chlorine dioxide was conducted in a rural village. A control population of 118 nonexposed persons was also studied. Pre-exposure hematologic and serum chemical parameters were compared with test results after 115 days of exposure. Statistical analysis (ANOVA) of the data failed to identify any significant exposure-related effects. This study suggests that future evaluations of chlorine dioxide disinfection should be directed toward populations with potentially increased sensitivity to hemolytic agents.
Induction of monocytic differentiation and NF-kappa B-like activities by human immunodeficiency virus 1 infection of myelomonoblastic cells. (1992)

The effects of human immunodeficiency virus 1 (HIV-1) infection on cellular differentiation and NF-kappa B DNA binding activity have been investigated in a new model of myeloid differentiation. PLB-985 cells represent a bipotential myelomonoblastic cell population capable of either granulocytic or monocytic differentiation after induction with appropriate inducers. By virtue of the presence of CD4 on the cell surface, PLB-985 cells were chronically infected with HIV-1 strain IIIB. PLB-IIIB cells clearly possessed a more monocytic phenotype than the parental myeloblasts, as determined by differential staining, increased expression of the myeloid-specific surface markers, and transcription of the c-fms proto-oncogene. NF-kappa B binding activity was inducible by tumor necrosis factor and phorbol myristate acetate in PLB-985. However, in PLB-IIIB cells, constitutive expression of a novel NF-kappa B complex was detected, composed of proteins ranging between 70 and 110 kD. These proteins interacted specifically with the symmetric NF-kappa B site from the interferon beta (IFN-beta) promoter. Mutations affecting the 5' guanine residues of the kappa B site were unable to compete for these NF-kappa B-related proteins. Inducibility of endogenous IFN-beta and IFN-alpha RNA was also increased in PLB-IIIB cells. These studies indicate that HIV-1 infection of myelomonoblastic cells may select for a more mature monocytic phenotype and that unique subunit associations of NF-kappa B DNA binding proteins may contribute to differential NF-kappa B-mediated gene expression.
Comparison of Comet Assay, Electron Microscopy, and Flow Cytometry for Detection of Apoptosis (2003)

Differentiating apoptosis from necrosis is a challenge in single cells and in parenchymal tissues. The techniques available, including in situ TUNEL (Terminal deoxyribonucleotide transferase-mediated dUTP-X Nick End-Labeling) staining, DNA ladder assay, and flow cytometry, suffer from low sensitivity or from a high false-positive rate. This study, using a Jurkat cell model, initially evaluated the specificity of the neutral comet assay and flow cytometry compared to the gold standard, electron microscopy, for detection of apoptosis and necrosis. Neutral comet assay distinguished apoptosis from necrosis in Jurkat cells, as evidenced by the increased comet score in apoptotic cells and the almost zero comet score in necrotic cells. These findings were consistent with those of electron microscopy and flow cytometry. Furthermore, using rats with burn or ischemia/reperfusion injury, well-established models of skeletal and cardiac muscle tissue apoptosis, respectively, we applied the comet assay to detect apoptosis in these muscles. Neutral comet assay was able to detect apoptotic changes in both models. In the muscle samples from rats with burn or ischemia-reperfusion injury, the comet score was higher than that of muscle samples from their respective controls. These studies confirm the consistency of the comet assay for detection of apoptosis in single cells and provide evidence for its applicability as an additional method to detect apoptosis in parenchymal cells.
IL-1 enhances expansion, effector function, tissue localization, and memory response of antigen-specific CD8 T cells (2013)

Here, we show that interleukin-1 (IL-1) enhances antigen-driven CD8 T cell responses. When administered to recipients of OT-I T cell receptor transgenic CD8 T cells specific for an ovalbumin (OVA) peptide, IL-1 results in an increase in the numbers of wild-type but not IL1R1(-/-) OT-I cells, particularly in spleen, liver, and lung, upon immunization with OVA and lipopolysaccharide. IL-1 administration also results in an enhancement in the frequency of antigen-specific cells that are granzyme B(+), have cytotoxic activity, and/ or produce interferon γ (IFN-γ). Cells primed in the presence of IL-1 display enhanced expression of granzyme B and increased capacity to produce IFN-γ when rechallenged 2 mo after priming. In three in vivo models, IL-1 enhances the protective value of weak immunogens. Thus, IL-1 has a marked enhancing effect on antigen-specific CD8 T cell expansion, differentiation, migration to the periphery, and memory.
The Salmonella typhimurium virulence plasmid complement resistance gene rck is homologous to a family of virulence-related outer membrane protein genes, including pagC and ail (1992)

A fragment of the Salmonella typhimurium virulence plasmid containing the rck locus, when cloned in the recombinant cosmid pADE016, was shown previously to confer high-level complement resistance on both rough and smooth Escherichia coli, Salmonella minnesota, and S. typhimurium and was associated with the production of an outer membrane protein. We determined the nucleotide sequence of the fragment containing the rck locus. Mutations in the two major open reading frames confirmed that the complement resistance mediated by pADE016 was due to a single 555-bp rck gene encoding a 17-kDa outer membrane protein. Analysis of the rck gene revealed that the Rck outer membrane protein consisted of 185 amino acid residues, with a calculated postcleavage molecular mass of 17.4 kDa. Rck is homologous to a family of outer membrane proteins expressed in gram-negative bacteria, two of which have been associated with virulence-related phenotypes: PagC, required by S. typhimurium for survival in macrophages and for virulence in mice; and Ail, a product of the Yersinia enterocolitica chromosome capable of mediating bacterial adherence to and invasion of epithelial cell lines. Rck, most closely related to PagC, represents the third outer membrane protein in this five-member family with a distinct virulence-associated phenotype.
Measurement of acoustic properties of liquids using SH-type surface acoustic waves (2002)

A surface acoustic wave (SAW) viscosity sensor for liquid phase sensing utilizing a shear horizontal displacement of a leaky SAW is presented. The sensor is based on a dual SAW delay line oscillator. Leaky SAWs with shear horizontal displacement were excited on a 41 degrees -rotated Y-cut X-propagation LiNbO/sub 3/ substrate by using interdigital transducers (IDTs). It is shown that the viscosity sensor has a sensitivity of about 80 Hz/cP at an operating frequency of 30 MHz, with a threshold sensitivity of about 1 cP.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
V-nested parallelism in C (2002)

This paper describes the integration of nested data parallelism into imperative languages using the example of C. Unlike flat data parallelism, nested data parallelism directly provides means for handling irregular data structures and certain forms of control parallelism, such as divide-and-conquer algorithms, thus enabling the programmer to express such algorithms far more naturally. Existing work deals with nested data parallelism in a functional environment, which does help avoid a set of problems, but makes efficient implementations more complicated. Moreover functional languages are not readily accepted by programmers used to languages, such as Fortran and C, which are currently predominant in programming parallel machines. In this paper, we introduce the imperative data-parallel language V and give an overview of its implementation.