gebhart/patrepeval huggingface dataset:
Herpes simplex virus type 1-encoded glycoprotein C enhances coagulation factor VIIa activity on the virus (2004)

Tissue factor (TF) is the blood coagulation initiator, whose cofactor function is required for physiological factor VIIa (FVIIa)-mediated activation of factor X (FX) to FXa. A previous study reported TF on herpes simplex virus type 1 (HSV1), but this explained only part of FVIIa-dependent FXa generation observed on the virus surface (Sutherland et al. (1997) Proc. Natl. Acad. Sci. USA. 94:13510-14). In the current study, we investigated the role of HSV1-encoded glycoprotein C (gC) in this process. Purified gC-deficient HSV1 facilitated several fold less FX activation by FVIIa than either wild type or gC-rescued strains. To confirm the implication of gC in FVIIa-dependent FX activation, purified soluble gC (sgC) enhanced FXa production in the absence of TF. sgC required FVIIa, calcium and anionic phospholipid to participate in FX activation, suggesting similarity to TF. When purified virus was combined with sgC, the sgC-dependent FXa generation was enhanced three orders of magnitude, suggesting synergy with an additional HSV1 component and explaining the relatively low activity of purified sgC compared to the viral counterpart. FX activation on gC-competent HSV1 was inhibited 20% by a gC-specific antibody, inhibited 40% by a TF-specific antibody, inhibited 65% by combining the gC- and TF-specific antibodies, and nearly completely inhibited by the TF antibody alone on gC-deficient HSV-1. Cumulatively, these observations show that two pathways initiating FX activation function in parallel on the virus surface. In addition to the previously described TF-dependent pathway, HSV-1-encoded gC also enhances FXa generation, and like TF, requires FVIIa.
Cooperative Interaction of Arginine-19 and the N-Terminal Signaling Domain in the Affinity and Potency of Parathyroid Hormone (2004)

Residue 19 of parathyroid hormone (PTH) plays a unique role in the interaction process with the PTH1 receptor. A Glu(19) --> Arg(19) substitution, based on the Arg(19) of the PTH-related protein (PTHrP), increases the binding affinity when incorporated into the N-terminus of PTH [i.e., PTH(1-20)] and has no effect when introduced into the C-terminus of PTH [i.e., PTH(15-31)]. To explore Arg(19) and the midregion (residues 10-15), we designed the novel PTH scaffold peptide, PG5, which has the PTH(1-9) domain linked to the PTH(15-31) segment via a pentaglycine spacer. Substitution of Glu(19) with Arg(19) in PG5 resulted in a 9-fold increase in binding affinity. Additionally, the substitution enhanced stimulated cAMP formation in cells expressing PTH1-delNt, a PTH1 receptor construct lacking most of the N-terminus, confirming that residue 19 is interacting with the juxtamembrane portion of PTH1. The binding and signaling capacities of the PG5 analogues were diminished relative to those of PTH(1-34), indicating that the residue 10-14 region of PTH provides more than just a simple linker function. To probe this further, the structural consequences of the glycine linker and its interaction with PTH1 were examined by circular dichroism, (1)H NMR, and extensive ligand/receptor molecular dynamics simulations. The structural data clearly illustrate the helix-stabilizing effect of Arg(19) substitution propagating N-terminally from position 19 to the pentaglycine linker. Overall, these studies suggest that an alpha-helix is the preferred conformation for the residue 15-20 region of PTH and that residues 10-14 are also required for full affinity and potency of the hormone.
A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesised on a glass support (1993)

An extensive analysis of oligonucleotide interactions was carried out by hybridising a synthetic pool of 256 10mers, A(C,T)8A, representing all oligopyrimidine octamer sequences to an array of four copies of all 256 different octapurine sequences. The resulting 256 duplexes were quantified by phosphorimaging and analysed to determine the dependence of duplex formation on base composition, sequence, and salt concentration. The results show that the base composition dependence of duplex formation can be reduced by high concentrations of tetramethylammonium chloride. This chaotropic solvent also increases duplex yield by up to fifty-fold.
The Calcium Messenger System (1986)

IN this brief review, only an overview of our rapidly expanding knowledge of the organization and function of the calcium messenger system will be possible. This messenger system has a central role in mediating the contraction of all forms of muscle, the secretion of exocrine, endocrine, and neurocrine products, the metabolic processes of glycogenolysis and gluconeogenesis, the transport and secretion of fluids and electrolytes, and the growth of cells. Hence, disorders of the function of the calcium messenger system underlie the development of a variety of disorders ranging from hypertension and vasospasm, bronchial asthma, clotting abnormalities related to platelet dysfunction, . . .
Biological Mediators of Acute Inflammation (2004)

Inflammation may be defined as the normal response of living tissue to injury or infection. It is important to emphasize two components of this definition. First, that inflammation is a normal response and, as such, is expected to occur when tissue is damaged. Indeed, if injured tissue did not exhibit signs of inflammation this would be considered abnormal. Secondly, inflammation occurs in living tissue, hence the need for an adequate blood supply to the tissues in order for an inflammatory response to be exhibited. The inflammatory response may be triggered by mechanical injury, chemical toxins, invasion by microorganisms, and hypersensitivity reactions. Three major events occur during the inflammatory response: the blood supply to the affected area is increased substantially, capillary permeability is increased, and leucocytes migrate from the capillary vessels into the surrounding interstitial spaces to the site of inflammation or injury. The inflammatory response represents a complex biological and biochemical process involving cells of the immune system and a plethora of biological mediators. Cell-to-cell communication molecules known collectively as cytokines play an extremely important role in mediating the process of inflammation. An extensive exposition of this complex phenomenon is beyond the scope of this article. Rather, the author provides a review of inflammation, an overview of the role of certain biological mediators in inflammation, and a discussion of the implications of certain biological response modifiers in clinical practice.
Expression, purification and characterization of glycosylated influenza H5N1 hemagglutinin produced in Pichia pastoris. (2014)

The A/swan/Poland/305-135V08/2006 (H5N1-subtype) hemagglutinin (HA) gene was cloned and expressed in yeast Pichia pastoris (P. pastoris). The HA cDNA lacking the C-terminal transmembrane anchor-coding sequence was fused to an α-factor leader peptide and placed under control of the methanol-inducible P. pastoris alcohol oxidase 1 (AOX1) promoter. Two P. pastoris strains: SMD 1168 and KM 71 were used for protein expression. Recombinant HA protein was secreted into the culture medium reaching an approximately 15 mg/L (KM 71 strain). Fusion protein with a His6 tag was purified to homogeneity in one step affinity chromatography. SDS-PAGE and MS/MS analysis indicated that the protein is cleaved into HA1 and HA2 domains linked by a disulfide bond. Analysis of the N-linked glycans revealed that the overexpressed HA is fully glycosylated at the same sites as the native HA in the vaccine strain. Immunological activity of the hemagglutinin protein was tested in mice, where rHA elicited a high immune response.
Isolation of a complementary DNA clone encoding a precursor to human eosinophil major basic protein. (1988)

A 14-kD protein was purified from human PMNs and its NH2-terminal sequence was determined. Comparison of a portion of the NH2-terminal sequence of this protein to the recently reported NH2-terminal sequence of eosinophil major basic protein (MBP) showed them to be identical. To aid further characterization of the structural and functional properties of this molecule, we isolated from an HL-60 cDNA library a single class of cDNA clones whose sequence matched exactly the NH2-terminal amino acid sequence of the 14-kD polypeptide. Northern analysis of HL-60 cells suggests that MBP is constitutively expressed in HL-60 cells and is highly transcribed from a single copy gene. The sequence of the full-length cDNA clones predicts that MBP is synthesized as a 23-kD precursor form (pro-MBP) which is subsequently cleaved to release the mature 14-kD MBP. The putative pro-MBP has a predicted pI of 6.0, but both the charged and the hydrophobic residues are asymmetrically distributed, creating a bipolar molecule. The NH2-terminal half has a predicted pI of 3.7 and is hydrophilic, while the COOH-terminal half (corresponding to mature MBP) has a predicted pI of 11.1 and is hydrophobic.
Nondestructive Measurement of Human Blood at Microwave Frequencies (2007)

This letter reports a novel in vitro test of blood analysis based on the measurement of the dielectric properties at microwave frequencies. The measurements were made using rectangular cavity perturbation technique at the S-band of microwave frequency with the different samples of blood obtained from healthy donors as well as from patients. It is observed that an appreciably change in the dielectric properties of patient samples with the normal healthy samples and this measurements were in good agreement with clinical analysis. This measurement technique is nondestructive in nature. These results indicate an alternative in-vitro method of diagnosing blood abnormalities using microwaves.
Smart building real time pricing for offering load-side Regulation Service reserves (2013)

Provision of Regulation Service (RS) reserves to Power Markets by smart building demand response has attracted attention in recent literature. This paper develops tractable dynamic optimal pricing algorithms for distributed RS reserve provision. It shows monotonicity and convexity properties of the optimal pricing policies and the associated differential cost function. Then, it uses them to propose and implement a modified Least Squares Temporal Differences (LSTD) Actor-Critic algorithm with a bounded and continuous action space. This algorithm solves for the best policy within a pre-specified broad family. In addition, the paper develops a novel Approximate Policy Iteration (API) algorithm and uses it successfully to optimize the parameters of an analytic policy function. Numerical results are obtained to demonstrate and compare the Actor-Critic and Approximate Policy Iteration algorithms, demonstrating that the novel API algorithm outperforms the Bounded LSTD Actor-Critic algorithm in both computational effort and policy minimum cost.
Quantitation of DNA Sequences in Environmental PCR Products by a Multiplexed, Bead-Based Method (2002)

A first application of a multiplexed, bead-based method is described for determining the abundances of target sequences in an environmental PCR product. Target sequences as little as 0.3% of the total amount of DNA can be quantified. Tests were conducted on 16S ribosomal DNA sequences from microorganisms collected from contaminated groundwater.
Solar cell efficiency tables (Version 38) (2011)

Abstract Consolidated tables showing an extensive listing of the highest independently confirmed efficiencies for solar cells and modules are presented. Guidelines for inclusion of results into these tables are outlined and new entries since January, 2011 are reviewed. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Injection locking characteristics of a 1 W broad stripe laser diode (1988)

Single narrow far-field lobe emission is observed in an injection-locked high-power broad stripe laser. Lobe widths below 1.3 times the diffraction limit for the 160-μm-wide stripe were observed for power levels up to 1.0 W. Decrease in the power contained within the narrow lobe for high laser bias currents is observed and is attributed to self-focusing effects in the active region. Small-signal external power gain of 21 dB was measured.
Splice Variant JAK2 Transcript Deleting Exon 14 in Patients with Chronic Myeloproliferative Neoplasms. (2009)

Abstract Abstract 2161 Poster Board II-138 The JAK2 V617F mutation in exon 14 is the most common mutation in chronic myeloproliferative neoplasms (MPNs). While other point mutations and small deletions and insertions in exons 12, 13, and 14 have been reported in the JAK2 JH2 domain, deletion of the entire exon 14 is rarely detected in patients with MPNs. In a series of &gt;10,000 samples from patients with suspected MPNs tested for JAK2 mutations by direct sequencing of mRNA, we detected a complete exon 14 (88 bp) deletion mutation in &lt;1% of those with JAK2 mutation. This appears to be an alternative splicing mutation, not detectable with DNA-based testing, leading to a frameshift deletion in the JAK2 JH2 domain and the expression of a truncated protein (S593I fsX8). Although this mutation was present at detectable levels (&gt;15% of total JAK2 transcript) in a small proportion of MPN cases, we decided to investigate the possibility it may be expressed at low levels (&lt;15% of JAK2 transcript) in patients with MPNs. Using a sensitive reverse transcription-PCR—based fluorescent fragment analysis method to quantify the percentage of truncated (minus exon 14) JAK2 mRNA as compared to wild-type, we tested 61 patients with confirmed MPN; 183 patients with suspected MPNs (93 V617F positive, 90 V617F negative); and 46 healthy normal control subjects. The wild-type PCR product was 273 bp, while the exon 14 splice mutant displayed a 185-bp peak. All samples with a splicing mutant expression to wild-type ratio &gt;15% were confirmed by direct sequencing. The JAK2 exon 14 splice mutation was detected at low levels in 9 of the 61 MPN patients (15%), accounting for 3.96% to 33.85% (mean=12.04%) of JAK2 transcript in these individuals. Among the 183 suspected MPN patients, the exon 14 splice variant was detected in 20 of the 93 (21.5%) with V617F (mean expression level relative to wild type=5.41%, range=2.13%-26.22%) and 31 of the 90 (34.4%) without V617F (mean expression=3.88%; range=2.08%-12.22%). All 46 normal individuals were considered negative for the alternatively spliced transcript. In conclusion, the expression of an alternatively spliced JAK2 mRNA with deletion of exon 14, leading to a truncated JAK2 protein, is a common abnormality in patients with MPNs. This alternatively spliced transcript is more common in MPN patients without V617F mutation and might contribute to the leukemogenesis in these patients. Low levels of JAK2 exon 14 splice mutation may also contribute to the effects of the V617F mutation in patients with MPNs. However, this mutation is missed if DNA and not the RNA is used for testing for JAK2 mutations. Disclosures: No relevant conflicts of interest to declare.
IFN-γ-Dependent Inhibition of Tumor Angiogenesis by Tumor-Infiltrating CD4+ T Cells Requires Tumor Responsiveness to IFN-γ (2001)

The importance of CD4(+) T cells in the induction of an optimal antitumor immune response has largely been attributed to their ability to provide costimulatory signals for the priming of MHC class I-restricted CD8(+) CTL. However, many reports have demonstrated a requirement for CD4(+) T cells in the effector phase of tumor rejection indicating a greater responsibility for CD4(+) T cells in controlling tumor outgrowth. We demonstrate here a critical role for CD4(+) T cells in restraining initial tumor development through the inhibition of tumor angiogenesis. Using a tumor variant that is unresponsive to IFN-gamma, we show that tumor responsiveness to IFN-gamma is necessary for IFN-gamma-dependent inhibition of tumor angiogenesis by CD4(+) T cells. These studies reveal a pivotal role for CD4(+) T cells in controlling early tumor development through inhibition of tumor angiogenesis.
Non-Overlapping Progesterone Receptor Cistromes Contribute to Cell-Specific Transcriptional Outcomes (2012)

The transcriptional effects of the ovarian hormone progesterone are pleiotropic, and binding to DNA of the nuclear progesterone receptor (PR), a ligand-activated transcription factor, results in diverse outcomes in a range of target tissues. To determine whether distinct patterns of genomic interaction of PR contribute to the cell specificity of the PR transcriptome, we have compared the genomic binding sites for PR in breast cancer cells and immortalized normal breast cells. PR binding was correlated with transcriptional outcome in both cell lines, with 60% of progestin-regulated genes associated with one or more PR binding regions. There was a remarkably low overlap between the PR cistromes of the two cell lines, and a similarly low overlap in transcriptional targets. A conserved PR binding element was identified in PR binding regions from both cell lines, but there were distinct patterns of enrichment of known cofactor binding motifs, with FOXA1 sites over-represented in breast cancer cell binding regions and NF1 and AP-1 motifs uniquely enriched in the immortalized normal line. Downstream analyses suggested that differential cofactor availability may generate these distinct PR cistromes, indicating that cofactor levels may modulate PR specificity. Taken together these data suggest that cell-specificity of PR binding is determined by the coordinated effects of key binding cofactors.
Amelioration of Hypertriglyceridemia with Hypo-Alpha-Cholesterolemia in LPL Deficient Mice by Hematopoietic Cell-Derived LPL (2011)

Hematopoietic cell-derived LPL could efficiently ameliorate severe hypertriglyceridemia and hypo-alpha-cholesterolemia at the compensation of increased triglyceride content of liver in LPL⁻/⁻ mice.
Soluble CD73 as biomarker in patients with metastatic melanoma patients treated with nivolumab (2017)

We observed a significant association between the activity of sCD73 in the blood and clinical outcomes in patients with metastatic melanoma stage IV, receiving nivolumab. Although our results need to be confirmed and validated, we suggest that sCD73 might be used as serologic prognostic biomarker. Potentially evaluating sCD73 enzyme activity in the peripheral blood before treatment could help to estimate the response to nivolumab.
Articular Geometry of the Glenohumeral Joint (1992)

Little quantitative data exists defining the true shape of the humeral head and glenoid articular surfaces. This study uses a precise stereophotogrammetry (SPG) technique and provides highly accurate quantitative results for determining the three-dimensional geometry of glenohumeral joint articular surfaces, including their “sphericity”, surface areas, cartilage thickness, and the difference in these quantities between the genders. Results indicate that glenohumeral joint surfaces may be approximated by a section of a sphere with small deviations from sphericity of less than 1% of the radius. Furthermore, results indicate that mating humeral head and glenoid articular surfaces are quite congruent and have radii within 2 mm in 88% of cases, and within 3 mm in all cases measured. The lack of anatomic stability of this joint is therefore not attributable to the relative shallow-ness or lack of congruence of the joint but rather to the small surface area of the glenoid which does not enclose the humeral head. Cartilage thickness results may partially explain perceptions of glenohumeral incongruity obtained from roentgenographic measurements where the glenoid appears flatter than the corresponding humeral head. Only when the actual articular cartilage surfaces are analyzed is it determined that the actual articulating surfaces do conform.
Molecular MRI of Cerebral Venous Sinus Thrombosis Using a New Fibrin-Specific MR Contrast Agent (2007)

The novel fibrin-targeted molecular MR contrast EP-2104R allows selective and high-contrast imaging of cerebral sinus vein thrombosis in an animal model.
Enterovirus variants in the serum of children at the onset of Type 1 diabetes mellitus (1999)

This study re-emphasizes that a link exists between enteroviral infection and the onset of Type 1 DM, particularly at a very early age, and suggests that these viruses are aetiologically important in diabetes in a significant proportion of children.
Ubiquitous mobile host internetworking (2002)

Argues that being a mobile host (or a mobile capable host) should be a standard property of all hosts in the Internet, and summarizes the design of a new protocol for transparently allowing these mobile hosts to interoperate in the Internet using IP. A mobile host may move from one network to another at any time, while always using only its "home" IP address. Any host may be configured to be a "mobile host" simply by running the appropriate software on it, and there is no penalty for this configuration, since the protocol automatically uses only the standard IP routing mechanisms, adding no overhead to IP, when a mobile host is currently connected to its home network. The protocol scales well to very large numbers of mobile hosts and adds little overhead for packets sent to a mobile host currently connected to a foreign network. The protocol is currently being implemented within the Berkeley networking code and is expected to be available shortly to interested groups outside Carnegie Mellon.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Simultaneous double immunoenzymatic labeling: a new procedure for the histopathologic routine. (1997)

We developed a new procedure for simultaneous immunohistoenzymatic double labeling that uses two mouse monoclonal antibodies of different isotypes or two antibodies from different species. The technique is a combination of the alkaline phosphatase-antialkaline phosphatase, avidin-biotin, and digoxigenin methods and uses horseradish peroxidase and alkaline-phosphatase detection systems. This standardized procedure can be carried out easily in the routine of a pathology laboratory and performed in parallel with single-antigen immunostaining, without the need for extra material or additional time for the laboratory technicians. This method can be applied to the detection of antigens localized in distinct cells or subcellular compartments and to the covisualization of different components from the same subcellular compartment.
Determination of Membrane Protein Structure by Rotational Resonance NMR: Bacteriorhodopsin (1991)

Rotationally resonant magnetization exchange, a new nuclear magnetic resonance (NMR) technique for measuring internuclear distances between like spins in solids, was used to determine the distance between the C-8 and C-18 carbons of retinal in two model compounds and in the membrane protein bacteriorhodopsin. Magnetization transfer between inequivalent spins with an isotropic shift separation, delta, is driven by magic angle spinning at a speed omega r that matches the rotational resonance condition delta = n omega r, where n is a small integer. The distances measured in this way for both the 6-s-cis- and 6-s-trans-retinoic acid model compounds agreed well with crystallographically known distances. In bacteriorhodopsin the exchange trajectory between C-8 and C-18 was in good agreement with the internuclear distance for a 6-s-trans configuration [4.2 angstroms (A)] and inconsistent with that for a 6-s-cis configuration (3.1 A). The results illustrate that rotational resonance can be used for structural studies in membrane proteins and in other situations where diffraction and solution NMR techniques yield limited information.