gebhart/patrepeval huggingface dataset:
Chondrocyte Apoptosis in the Pathogenesis of Osteoarthritis (2015)

Apoptosis is a highly-regulated, active process of cell death involved in development, homeostasis and aging. Dysregulation of apoptosis leads to pathological states, such as cancer, developmental anomalies and degenerative diseases. Osteoarthritis (OA), the most common chronic joint disease in the elderly population, is characterized by progressive destruction of articular cartilage, resulting in significant disability. Because articular cartilage depends solely on its resident cells, the chondrocytes, for the maintenance of extracellular matrix, the compromising of chondrocyte function and survival would lead to the failure of the articular cartilage. The role of subchondral bone in the maintenance of proper cartilage matrix has been suggested as well, and it has been proposed that both articular cartilage and subchondral bone interact with each other in the maintenance of articular integrity and physiology. Some investigators include both articular cartilage and subchondral bone as targets for repairing joint degeneration. In late-stage OA, the cartilage becomes hypocellular, often accompanied by lacunar emptying, which has been considered as evidence that chondrocyte death is a central feature in OA progression. Apoptosis clearly occurs in osteoarthritic cartilage; however, the relative contribution of chondrocyte apoptosis in the pathogenesis of OA is difficult to evaluate, and contradictory reports exist on the rate of apoptotic chondrocytes in osteoarthritic cartilage. It is not clear whether chondrocyte apoptosis is the inducer of cartilage degeneration or a byproduct of cartilage destruction. Chondrocyte death and matrix loss may form a vicious cycle, with the progression of one aggravating the other, and the literature reveals that there is a definite correlation between the degree of cartilage damage and chondrocyte apoptosis. Because current treatments for OA act only on symptoms and do not prevent or cure OA, chondrocyte apoptosis would be a valid target to modulate cartilage degeneration.
National Institute of Mental Health Collaborative Multimodal Treatment Study of Children With ADHD (the MTA) (1997)

The Collaborative Multimodal Treatment Study of Children with Attention Deficit Hyperactivity Disorder (ADHD), the MTA, is the first child multisite cooperative agreement treatment study of children conducted by the National Institute of Mental Health, Rockville, Md. It examines the long-term effectiveness of medication vs behavioral treatment vs both for treatment of ADHD and compares state-of-the-art treatment with routine community care. In a parallel-groups design, 576 children (age, 7-9 years) with ADHD (96 at each site) are thoroughly assessed and randomized to 4 conditions: (1) medication alone, (2) psychosocial treatment alone, (3) the combination of both, (4) or community comparison. The first 3 groups are treated for 14 months and all are reassessed periodically for 24 months. Designers met the following challenges: framing clinically relevant primary questions; defining the target population; choice, intensity, and integration and combination of treatments for fair comparisons; combining scientific controls and standardization with clinical flexibility; and implementing a controlled clinical trial in a nonclinical setting (school) controlled by others. Innovative solutions included extensive decision algorithms and manualized adaptations of treatments to specific needs.
Simultaneous detection of antibodies to cytomegalovirus and herpes simplex virus by using flow cytometry and a microsphere-based fluorescence immunoassay (1988)

A sensitive assay for the simultaneous detection of anti-cytomegalovirus and anti-herpes simplex virus antibodies was developed. Two different sizes of polystyrene microspheres were coated with purified viral antigens. Human antiviral antibodies were detected with a biotin-streptavidin amplification procedure with phycoerythrin as the fluorescent label. Microsphere-associated fluorescence was quantitated with a flow cytometer. Sixteen percent of samples initially scored as seronegative for cytomegalovirus and 35% of samples initially scored as seronegative for herpes simplex virus by conventional assays were clearly found positive by the microsphere technique. This flow cytometric assay can simultaneously detect several specific antibodies at levels which are below the sensitivity of standard assays. The dynamic range of this assay is at least sixfold greater than that of enzyme immunoassays. This technique is amenable to numerous serologic assays and could greatly expand the clinical laboratory applications of flow cytometry.
Characterization of Kallikrein cDNAs from the African Rodent Mastomys (1994)

Kallikreins comprise a family of serine proteases that are required for the processing of hormone precursors, thereby controlling many physiological processes including blood flow, ion transport, and inflammation. In rodents such as mouse, rat, and Mastomys, many kallikreins are expressed in the submandibular gland (SMG), but only a limited number, notably true tissue (glandular) kallikrein, are expressed in the kidney. We report here the cloning and characterization of kallikrein cDNAs from the Mastomys SMG. Two of these are expressed in the kidney as well as in the SMG, and one may code for the true tissue kallikrein of Mastomys. A third kallikrein is expressed only in the SMG and bears some resemblance to a murine nerve growth factor-associated protein. The existence of a family of Mastomys SMG kallikreins suggests that these enzymes act as prohormone-processing enzymes in Mastomys. DNA sequence analysis and hybridization studies demonstrate that, although Mastomys kallikreins are very similar in structure to both mouse and rat kallikreins, their expression patterns differ. The expression of more than one Mastomys glandular kallikrein in the kidney is similar to that in the rat, but the sequence and nonsexually dimorphic expression of the putative tissue kallikrein most closely resembles mouse. Mastomys represents an interesting hybrid between mouse and rat, providing an important animal model for studies of kallikrein expression and regulation.
Cloning and Expression of the HumanN-Acetylneuraminic Acid Phosphate Synthase Gene with 2-Keto-3-deoxy-d-glycero- d-galacto-nononic Acid Biosynthetic Ability (2000)

Sialic acids participate in many important biological recognition events, yet eukaryotic sialic acid biosynthetic genes are not well characterized. In this study, we have identified a novel human gene based on homology to the Escherichia coli sialic acid synthase gene (neuB). The human gene is ubiquitously expressed and encodes a 40-kDa enzyme. The gene partially restores sialic acid synthase activity in a neuB-negative mutant of E. coli and results in N-acetylneuraminic acid (Neu5Ac) and 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN) production in insect cells upon recombinant baculovirus infection. In vitro the human enzyme uses N-acetylmannosamine 6-phosphate and mannose 6-phosphate as substrates to generate phosphorylated forms of Neu5Ac and KDN, respectively, but exhibits much higher activity toward the Neu5Ac phosphate product.
Adoptive transfer of allogeneic cytotoxic T lymphocytes equipped with a HLA-A2 restricted MART-1 T-cell receptor: a phase I trial in metastatic melanoma. (2006)

Intratumoral injections of C Cure 709 are feasible, safe, and capable of inducing tumor regression. Further investigation in a phase II setting is warranted.
Identification of the homophilic binding site of the receptor protein tyrosine phosphatase PTP mu. (1994)

The receptor-type protein tyrosine phosphatase PTP mu comprises an extracellular segment containing a MAM domain, an immunoglobulin domain and four fibronectin type III repeats, a transmembrane segment, and two intracellular PTP domains. We have previously shown that PTP mu binds homophilically, i.e. PTP mu on the surface of one cell binds to PTP mu on an apposing cell, and that the extracellular segment alone is sufficient for homophilic binding. In this study we report that in MvLu cells PTP mu is proteolytically processed into two noncovalently associated fragments, one comprising most of the extracellular segment (approximately 100 kDa) and the other containing predominantly the transmembrane and intracellular portions (approximately 100 kDa). We have also identified the homophilic binding site within the extracellular segment. We have generated, expressed, and purified various fragments of the extracellular segment of PTP mu and have used fluorescent beads (Covaspheres) coated with these fragments in three binding assays: (i) measurement of bead aggregation, (ii) binding of beads to surfaces of dishes coated with purified PTP mu, or (iii) binding to MvLu cells. Only beads coated with recombinant fragments that contained the immunoglobulin domain underwent aggregation or bound to surfaces displaying PTP mu, suggesting that neither the MAM domain nor the fibronectin type III repeats bound homophilically in these assays. The fragment containing the Ig domain alone bound as well as any other Ig domain-containing fragment, suggesting that the Ig domain is both necessary and sufficient for homophilic binding under these conditions.
Formation of hollow nanocrystals through the nanoscale kirkendall \neffect (2004)

Hollow nanocrystals can be synthesized through a mechanism analogous to the Kirkendall Effect, in which pores form because of the difference in diffusion rates between two components in a diffusion couple. Starting with cobalt nanocrystals, we show that their reaction in solution with oxygen and either sulfur or selenium leads to the formation of hollow nanocrystals of the resulting oxide and chalcogenides. This process provides a general route to the synthesis of hollow nanostructures of a large number of compounds. A simple extension of the process yielded platinum-cobalt oxide yolk-shell nanostructures, which may serve as nanoscale reactors in catalytic applications.
Angle dependence of transparent photovoltaics in conventional and optically inverted configurations (2013)

Integration of transparent photovoltaics into the building envelope creates unique opportunities to reduce the levelized electricity cost of solar power. However, this integration warrants consideration of the angular dependence of these devices as illumination around the building envelope is rarely at normal incidence. Here we correctly update transfer-matrix and equations to accurately model the quantum efficiency and optical properties under oblique illumination. We use this model to demonstrate the various angular performance characteristics possible for proof-of-concept optimizations of transparent planar-heterojunction solar cells and discuss considerations needed to fully account for optical, electrical, and positional configurations in this optimization.
Every smart phone is a backscatter reader: Modulated backscatter compatibility with Bluetooth 4.0 Low Energy (BLE) devices (2015)

In this work, we show how modulated backscatter signals can be crafted to yield channelized band-pass signals akin to those transmitted by many conventional wireless devices. As a result, conventional wireless devices can receive these backscattered signals without any modification (neither hardware nor software) to the conventional wireless device. We present a proof of concept using the Bluetooth 4.0 Low Energy, or BLE, standard widely available on smart phones and mobile devices. Our prototype backscatter tag produces three-channel bandpass frequency shift keying (FSK) packets at 1 Mbps that are indistinguishable from conventional BLE advertising packets. An unmodified Apple iPad is shown to correctly receive and display these packets at a range of over 9.4 m using its existing iOS Bluetooth stack with no changes whatsoever. We create all three BLE channels by backscattering a single incident CW carrier using a novel combination of fundamentalmode and harmonic-mode backscatter subcarrier modulation, with two of the band-pass channels generated by the fundamental mode and one of the band-pass channels generated by the second harmonic mode. The backscatter modulator consumes only 28.4 pJ/bit, compared with over 10 nJ/bit for conventional BLE transmitters. The backscatter approach yields over 100X lower energy per bit than a conventional BLE transmitter, while retaining compatibility with billions of existing Bluetooth enabled smartphones and mobile devices.
Regulation of phosphoinositide kinases in T cells. Evidence that phosphatidylinositol 3-kinase is not a substrate for T cell antigen receptor-regulated tyrosine kinases. (1992)

A phosphoinositide kinase that can phosphorylate phosphatidylinositol (PtdIns) is present in 4G10 monoclonal antibody (mAb) phosphotyrosine immunoprecipitates isolated from T cells activated via the T cell antigen receptor (TCR).CD3 complex. This PtdIns kinase is not the PtdIns 3-kinase that associates with activated protein tyrosine kinases in fibroblasts, since Western blotting and immunoprecipitation experiments with antibodies specific for the p85 alpha subunit of the PtdIns 3-kinase indicate that this polypeptide is not immunoprecipitated by the 4G10 mAb from TCR.CD3-activated Jurkat cells. Moreover, immunoprecipitated PtdIns 3-kinase isolated from T cells with p85 antibodies is inhibited when PtdIns is presented in Nonidet P-40, whereas the PtdIns kinase activity present in 4G10 mAb phosphotyrosine immunoprecipitates is enhanced in the presence of Nonidet P-40. In vitro kinase assays of PtdIns 3-kinase immunoprecipitated with p85 antibodies from T cells indicate that it associates with a serine kinase that can phosphorylate a p85 polypeptide. However, no protein tyrosine kinase activity capable of tyrosine phosphorylating p85 in vitro associates with p85 alpha immunoprecipitates in quiescent or TCR.CD3-activated T cells. These data suggest that the TCR.CD3 complex does not regulate PtdIns 3-kinase activity by a mechanism that involves protein tyrosine kinases.
Co-barcoded sequence reads from long DNA fragments: a cost-effective solution for â€œperfect genomeâ€ sequencing (2015)

Next generation sequencing (NGS) technologies, primarily based on massively parallel sequencing, have touched and radically changed almost all aspects of research worldwide. These technologies have allowed for the rapid analysis, to date, of the genomes of more than 2,000 different species. In humans, NGS has arguably had the largest impact. Over 100,000 genomes of individual humans (based on various estimates) have been sequenced allowing for deep insights into what makes individuals and families unique and what causes disease in each of us. Despite all of this progress, the current state of the art in sequence technology is far from generating a "perfect genome" sequence and much remains to be understood in the biology of human and other organisms' genomes. In the article that follows, we outline why the "perfect genome" in humans is important, what is lacking from current human whole genome sequences, and a potential strategy for achieving the "perfect genome" in a cost effective manner.
A High-Throughput Screening Method for the Determination of Aqueous Drug Solubility Using Laser Nephelometry in Microtiter Plates (2000)

The determination of aqueous solubility in a high-throughput screening environment is invaluable in the selection of the most promising potential drug candidates. We describe a fast method based on laser nephelometry that can determine the solubility of potential drug candidates (usually from combinatorial chemistry) supplied as dimethyl sulfoxide (DMSO) solutions in 96-well plates. In the sample, the percent DMSO is kept constant allowing direct comparison of results. The nephelometric method has been shown to produce results equivalent to those produced by an HPLC method and to be largely unaffected by colored solutions.
A Rational Strategy to Design Multiepitope Immunogens Based on Multiple Th Lymphocyte Epitopes (2002)

Four HLA-DR-restricted HIV-derived Th lymphocyte (HTL) epitopes cross-reactive with the murine I-A(b) class II molecule were used to evaluate different vaccine design strategies to simultaneously induce multiple HTL responses. All four epitopes were immunogenic in H-2(b) mice, demonstrating the feasibility of murine models to evaluate epitope-based vaccines destined for human use. Immunization with a pool of peptides induced responses against all four epitopes; illustrating immunodominance does not prevent the induction of balanced multispecific responses. When different delivery systems were evaluated, a multiple Ag peptide construct was found to be less efficient than a linear polypeptide encompassing all four epitopes. Further characterization of linear polypeptide revealed that the sequential arrangement of the epitopes created a junctional epitope with high affinity class II binding. Disruption of this junctional epitope through the introduction of a GPGPG spacer restored the immunogenicity against all four epitopes. Finally, we demonstrate that a GPGPG spacer construct can be used to induce HTL responses by either polypeptide or DNA immunization, highlighting the flexibility of the approach.
Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli. (1994)

The bidirectional self-assembly of tobacco mosaic virus (TMV, common or U1 strain) has been studied extensively in vitro. Foreign single-stranded RNA molecules containing the TMV origin-of-assembly sequence (OAS, 75-432 nt in length) are also packaged by TMV coat protein (CP) in vitro to form helical pseudovirus particles. To study virus assembly in vivo requires an easily manipulated model system, independent of replication in plants. The TMV assembly machinery also provides a convenient means to protect and recover chimeric gene transcripts of almost any length or sequence for a variety of applications. Native TMV CP expressed in and purified from Escherichia coli formed nonhelical, stacked aggregates after dialysis into pH 5 buffer and was inactive for in vitro assembly with TMV RNA. U1 CP derivatives in which the second amino acid was changed from Ser to Ala or Pro, nonacetylated N termini found in two natural strains of the virus, failed to remediate these anomalous properties. However, in vivo coexpression of CP and single-stranded RNAs (up to approximately 2 kb) containing the TMV OAS gave high yields of helical pseudovirus particles of the predicted length (up to 7.4 +/- 1.4 micrograms/mg of total bacterial protein). If the OAS-containing RNA was first recruited into bacterial polyribosomes, elongation of pseudovirus assembly was blocked. In vivo, E. coli expression of a full-length cDNA clone of the TMV genome (6.4 kb) resulted in high, immunodetectable levels of CP and assembly of sufficient intact genomic RNA to initiate systemic infection of susceptible tobacco plants.
Genome amplification of single sperm using multiple displacement amplification (2005)

Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.
Localization of tumor necrosis factor receptors in the synovial tissue and cartilage‐pannus junction in patients with rheumatoid arthritis. Implications for local actions of tumor necrosis factor α (1992)

These results provide histologic evidence that both p55 TNF-R and p75 TNF-R are expressed by a variety of cell types in RA synovial tissue, reflecting the fact that a wide range of cells are potential targets for TNF alpha in this tissue. This study further supports the hypothesis that TNF alpha plays a major role in the pathogenesis of RA.
Structure‐activity studies on bradykinin and related peptides: agonists (1990)

1. Bradykinin, kallidin, T-kinin, [Hyp3]-bradykinin and several analogues were prepared by solid-phase synthesis and purified by high performance liquid chromatography. 2. The various peptides were tested for their abilities to relax the dog carotid and renal arteries, or to contract the rabbit jugular vein and aorta, in order to measure their activities on BK2 (the first three preparations) or BK1 (the rabbit aorta) receptors. The dog renal artery without endothelium was also used as a BK1 receptor system. 3. T-kinin was found to be less active than bradykinin, while the replacement of Pro3 with Hyp favoured BK2 receptor occupation. [Hyp3,Tyr(Me)8]-BK was found to be a selective BK2 receptor agonist. 4. Amidation or methylation of the C-terminal carboxyl decreased activity, while extension of the N-terminal with Sar or D-Arg increased affinity and selectivity for BK1 (Sar) and affinity for BK2 (D-Arg) receptors. Acetylation of N-terminal amide brought affinity down to 10% or less. 5. Replacement of the peptide bonds Phe8-Arg9 to protect from kininase I and II, decreased affinities slightly, but was incompatible with additional changes at the N-terminal or in the peptide bond Gly4-Phe5. 6. Substitution of C-terminal Phe in desArg9-BK (the BK1 receptor stimulant) with D-Phe increased potency and selectivity for BK1 receptors while protecting from carboxypeptidases. Sar[D-Phe8]desArg9-BK was found to be a potent and selective BK1 receptor agonist.
STP Position Paper (2013)

The Society of Toxicologic Pathology charged a Nervous System Sampling Working Group with devising recommended practices to routinely screen the central nervous system (CNS) and peripheral nervous system (PNS) in Good Laboratory Practice-type nonclinical general toxicity studies. Brains should be weighed and trimmed similarly for all animals in a study. Certain structures should be sampled regularly: caudate/putamen, cerebellum, cerebral cortex, choroid plexus, eye (with optic nerve), hippocampus, hypothalamus, medulla oblongata, midbrain, nerve, olfactory bulb (rodents only), pons, spinal cord, and thalamus. Brain regions may be sampled bilaterally in rodents using 6 to 7 coronal sections, and unilaterally in nonrodents with 6 to 7 coronal hemisections. Spinal cord and nerves should be examined in transverse and longitudinal (or oblique) orientations. Most Working Group members considered immersion fixation in formalin (for CNS or PNS) or a solution containing acetic acid (for eye), paraffin embedding, and initial evaluation limited to hematoxylin and eosin (H&E)-stained sections to be acceptable for routine microscopic evaluation during general toxicity studies; other neurohistological methods may be undertaken if needed to better characterize H&E findings. Initial microscopic analyses should be qualitative and done with foreknowledge of treatments and doses (i.e., "unblinded"). The pathology report should clearly communicate structures that were assessed and methodological details. Since neuropathologic assessment is only one aspect of general toxicity studies, institutions should retain flexibility in customizing their sampling, processing, analytical, and reporting procedures as long as major neural targets are evaluated systematically.