gebhart/patrepeval huggingface dataset:
De novo detection and HLA-association of public T cell responses to Cytomegalovirus using high-throughput immune repertoire sequencing (VIR1P.1134) (2015)

Abstract We investigated the public T cell response to cytomegalovirus by sequencing rearranged T cell receptors (TCRs) in 640 subjects (287 with &amp; 353 without CMV). We performed an experiment similar to a GWAS study, assessing the concordance of millions of unique TCRs with CMV serostatus, looking for significant associations. With CMV serostatus and TCR sequencing data, we identify 142 public T cell responses to CMV (each with p ≤ 1.0 x 10-4; FDR ≈ 0.20). Using this method to identify public clones, we predict CMV serostatus in a leave-one-out cross-validation experiment with a diagnostic odds ratio of 66. Using HLA typing, we then estimate the HLA-association of each public CMV clone by assessing the over-representation of particular HLA types in associated subjects. Of 142 CMV public clones, 26 were HLA-associated at p &amp;lt; 10-6; no clones were significantly associated with multiple HLA alleles. When comparing our results to the literature, we find substantial concordance; most previously-reported public CMV clones are seen in our data, though only 2 are significantly associated with CMV serostatus in this cohort; both were significantly HLA-associated and in both cases the associated allele confirms previous findings. We demonstrate the validity of association studies using immunosequencing for detection and HLA-association of public T cell responses to infection, and report that assessing the presence of public T cell responses can serve as a powerful diagnostic classifier.
An integrated microfluidic device for influenza and other genetic analyses (2005)

An integrated microfluidic device capable of performing a variety of genetic assays has been developed as a step towards building systems for widespread dissemination. The device integrates fluidic and thermal components such as heaters, temperature sensors, and addressable valves to control two nanoliter reactors in series followed by an electrophoretic separation. This combination of components is suitable for a variety of genetic analyses. As an example, we have successfully identified sequence-specific hemagglutinin A subtype for the A/LA/1/87 strain of influenza virus. The device uses a compact design and mass production technologies, making it an attractive platform for a variety of widely disseminated applications.
Neural invasion and lymph node metastasis in the head of the pancreas carcinoma. (1991)

膵頭部癌切除例44例を対象に神経浸潤を膵内神経浸潤と神経叢内神経浸潤にわけ, リンパ管浸潤, リンパ節転移との関係を臨床病理学的に比較検討した. 44例中39例がrpeであり, 膵内神経浸潤を40例 (91%) にみた.神経叢浸潤はrpe39例中27例 (69%) に認められ, 膵内神経浸潤とリンパ管浸潤, リンパ節転移とは相関がなかった.神経叢浸潤と膵内神経浸潤は有意な正の相関がみられたが, リンパ管浸潤やリンパ節転移とは明らかな相関はみられなかった.リンパ管浸潤とリンパ節転移は正の相関をみた.神経叢浸潤陽性例が陰性例に比べ, リンパ節転移率が高く, とくに (14) 転移率は神経叢浸潤陽性例が有意に高率であった. しかし,(14) 転移陰性例でも10例に膵頭神経叢第2部に浸潤がみられ, 神経叢の完全切除が重要と考えられた.
Understanding Cost and Production Using a Cooperative Learning Technique in a Microeconomics Class (2013)

This article examines the cooperative learning technique of Structured Problem-Solving that induces students to work together to understand cost-calculations in microeconomics. Cooperative learning methods can help students better extract and interpret knowledge about economic issues and then display their command of that knowledge, thereby accomplishing some of Hansen’s proficiencies. The article investigates the effectiveness of this technique by comparing exam results between students who engaged in cooperative learning and those who did not. I find that cooperative learning enhances academic outcomes and helps students retain their knowledge of the material.
Recent advances in protein tyrosine phosphatase 1B inhibitors (2004)

Type 2 diabetes and obesity are characterised by insulin and leptin resistance. Studies suggest that these may be due to defects in the insulin and leptin signalling pathways. Over the last decade, a considerable body of evidence has been amassed indicating that protein tyrosine phosphatase 1B (PTP1B) is involved in the downregulation of insulin and leptin signalling. Consequently, compounds that inhibit PTP1B have potential as therapeutics for treating Type 2 diabetes and obesity. This review covers recent advances in PTP1B inhibitors with an emphasis on recent attempts to create potent, selective and cell-permeable small-molecule inhibitors.
Tumor necrosis factor impairs insulin action on peripheral glucose disposal and hepatic glucose output. (1992)

The present study examined whether a prolonged infusion of tumor necrosis factor (TNF) into rats could sustain the increased rate of whole body glucose metabolism observed with short term exposure, and whether TNF produced hepatic or peripheral insulin resistance. Basal glucose metabolism was determined with the use of [3-3H]glucose 18 h after initiating a constant infusion of recombinant human TNF (1 microgram/kg.h). Thereafter, a two-step euglycemic hyperinsulinemic clamp was performed to determine whether TNF impaired insulin action. The overnight infusion of TNF minimally elevated plasma glucose concentrations (17%), but produced large increases in the whole body rate of glucose production and utilization (133%). Under hyperinsulinemic conditions, the glucose infusion rate necessary to maintain euglycemia was 30% lower in TNF-treated rats, indicating an insulin-resistant condition. This resulted from an impaired ability of insulin to both suppress hepatic glucose production and stimulate peripheral glucose utilization in TNF-infused animals. A second series of experiments was performed, using the in vivo tracer [U-14C]2-deoxyglucose technique, to elucidate which tissues were responsible for the TNF-induced increase in basal (no exogenous insulin) glucose disposal and peripheral insulin resistance. Under basal conditions, TNF increased glucose uptake by various muscles (gastrocnemius, heart, and diaphragm) as well as nonmuscle tissues (liver, lung, spleen, gut, skin and fat). Because of their relatively large mass and/or high rate of glucose uptake, the increased uptake by skin (25%), intestine (24%), muscle (23%), and liver (15%) accounted for the majority of the TNF-induced increment in whole body glucose disposal. Under euglycemic hyperinsulinemic conditions, the increment in glucose uptake by muscle and skin (85%) accounted for the majority of the glucose disposal in control rats. However, in TNF-infused animals, hyperinsulinemia failed to increase glucose uptake by skin and blunted the insulin-mediated increase in muscle by 73%. These results suggest that sustained elevations of TNF during chronic therapy and prolonged production of TNF by patients and experimental animals with malignancies or infectious diseases may be an important mechanism for the enhanced glucose flux as well as the insulin resistance seen in these conditions.
Comparison of Linear Single-Sideband Transmitters with Envelope Elimination and Restoration Single-Sideband Transmitters (1956)

The Elimination and Restoration System was originally described in 1952 [1]. The purpose of the following is to evaluate certain basic characteristics of the Envelope Elimination and Restoration System and to compare it with the Linear Amplifier System [2,3].
Modification of an Automated Liquid-Handling System for Reagent-Jet, Nanoliter-Level Dispensing (2001)

Reducing the scale of biochemical reactions is becoming commonplace. Examples include the screening of large libraries of chemical compounds or gene sequences. These applications demand the ability to transfer sub-microliter volumes of fluid. To this end, we have modified a Hamilton MICROLAB 2200 with high-speed solenoids and a liquid pressurization system to modulate volume delivery down to the nanoliter level. Additional modifications include the use of sapphire-tipped dispensing nozzles and a high-resolution substage to assist in the construction of DNA microarrays. Techniques for characterizing the dispensed volume are presented.
Dizygotic twin sisters with myelokathexis: Mechanism of its neutropenia (1999)

Dizygotic twin sisters were first found to have neutropenia at 1 year of age when evaluated for recurrent pulmonary infections. Since then they have remained neutropenic (0.05∼0.5 × 109/l). Despite of their neutropenia, myeloid hyperplasia was evident on a marrow smear examination, and a number of cells were hypersegmented with fine interlobular bridging with chromatin strands and cytoplasmic vacuolation. Electron microscopy showed apoptotic cells with condensed nuclei and apoptotic bodies in the cytoplasm. Although life span, hydrogen peroxide production, phagocytosis, spreading, and chemotaxis of peripheral neutrophils were normal, the survival of bone marrow neutrophils in both infants was markedly decreased when compared with that of normal bone marrow neutrophils. During the bone marrow culture apoptotic neutrophils were observed at an earlier stage in both patients than in normal controls, biochemically and morphologically. Morphology of bone marrow neutrophils in both patients resembled that of cultured control bone marrow neutrophils. Peripheral neutropenia and appearance of characteristic neutrophils in the bone marrow in myelokathexis are considered to be an expression of apoptosis of bone marrow neutrophils. Am. J. Hematol. 62:106–111, 1999. © 1999 Wiley-Liss, Inc.
A Stereospecific Synthesis of L-Desosamine (1974)

L-Desosamine (3,4,6-trideoxy-3-dimethylamino-L-xylo-hexose), the enantiomer of a widely distributed antibiotics component, was synthesized by borohydride reduction of methyl 3,4,6-trideoxy-3-nitro-α-L-erythro-hex-3-enopyranoside followed by catalytic hydrogenation of the nitro group, N,N-dimethylation of the resulting saturated amino glycoside, and acid hydrolysis of the glycosidic bond.
First total synthesis of (+)-chenodeoxycholic acid (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFirst total synthesis of (+)-chenodeoxycholic acidTetsuji Kametani, Koji Suzuki, and Hideo NemotoCite this: J. Am. Chem. Soc. 1981, 103, 10, 2890–2891Publication Date (Print):May 1, 1981Publication History Published online1 May 2002Published inissue 1 May 1981https://doi.org/10.1021/ja00400a078RIGHTS & PERMISSIONSArticle Views520Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (258 KB) Get e-Alertsclose Get e-Alerts
Techniques for increasing effective data bandwidth (2008)

In this paper we examine techniques for increasing the effective bandwidth of the microprocessor off-chip interconnect. We focus on mechanisms that are orthogonal to other techniques currently being studied (3-D fabrication, optical interconnect, etc.) Using a range of full-system simulations we study the distribution of values being transferred to and from memory, and find that (as expected) high entropy data such as floating point numbers have limited compressibility, but that other data types offer more potential for compression. By using a simple heuristic to classify the contents of a cache line and providing different compression schemes for each classification, we show it is possible to provide overall compression at a cache line granularity comparable to that obtained by using a much more complex Lempel-Ziv-Welch algorithm.
Left ventricular rupture threshold during the healing phase after myocardial infarction in the dog (1987)

The mechanical resistance of the infarcted left ventricle to rupture, or rupture threshold, was measured by the balloon technique 1-42 days after left anterior descending coronary artery ligation in 70 dogs: 26 without infarction (18 sham, 8 with ligation) and 44 with infarction. Rupture threshold in noninfarcted hearts was higher than in infarcted hearts (1168 +/- 165 (SD) vs. 754 +/- 223 mmHg (1 mmHg = 133.32 Pa), p less than 0.001) and did not change over 6 weeks. In contrast, rupture threshold in infarcted hearts decreased (p less than or equal to 0.05) after 14 days, the average value for 21-42 days being less than that for 1-14 days: 577 +/- 140 vs. 867 +/- 191 mmHg, p less than 0.001. Passive left ventricular stiffness in infarcted hearts was higher than for noninfarcted hearts throughout the 6 weeks during early filling (11.1 +/- 3.9 vs. 7.1 +/- 1.4 mmHg/mL, p less than 0.001) but decreased (p less than or equal to 0.05) after 14 days during the prerupture phase (11.3 +/- 5.3 vs. 6.2 +/- 3.0 mmHg/mL, p less than 0.005). Between 7 and 42 days, the infarct zone showed marked increase in hydroxyproline (10.0 +/- 2.0 vs. 48.8 +/- 19.7 mg/g dry weight, p less than 0.001), shrinkage (infarct size, 25 +/- 9 vs. 9 +/- 5% of the left ventricle, p less than 0.005), and thinning (infarct to normal wall thickness ratio, 0.83 +/- 0.11 vs. 0.51 +/- 0.09, p less than 0.001) but little further stretching (expansion index or the ratio of lengths of infarcted and noninfarcted segments, 1.14 +/- 0.10 vs. 1.28 +/- 0.17, p less than 0.2). A mild decrease (p less than 0.05) in left atrial pressure and increase (p less than 0.05) in diastolic area and fractional change in area (two-dimensional echocardiography) were detected at 6 weeks. The late decrease in rupture threshold and prerupture stiffness of the infarcted left ventricle and thinning of the scar suggest a late decrease in mechanical strength and resistance of the infarcted left ventricle to distension.
Glutamine Synthetase in Cerebrospinal Fluid, Serum, and Brain (1999)

Level of GS in lumbar CSF of patients with AD is increased significantly but nonspecifically, probably related to the strong astrogliosis in brain. Glutamine synthetase in lumbar CSF is mainly brain derived.
Engineering of an Artificial Light-Modulated Potassium Channel (2012)

Ion Channel-Coupled Receptors (ICCRs) are artificial receptor-channel fusion proteins designed to couple ligand binding to channel gating. We previously validated the ICCR concept with various G protein-coupled receptors (GPCRs) fused with the inward rectifying potassium channel Kir6.2. Here we characterize a novel ICCR, consisting of the light activated GPCR, opsin/rhodopsin, fused with Kir6.2. To validate our two-electrode voltage clamp (TEVC) assay for activation of the GPCR, we first co-expressed the apoprotein opsin and the G protein-activated potassium channel Kir3.1(F137S) (Kir3.1*) in Xenopus oocytes. Opsin can be converted to rhodopsin by incubation with 11-cis retinal and activated by light-induced retinal cis→trans isomerization. Alternatively opsin can be activated by incubation of oocytes with all-trans-retinal. We found that illumination of 11-cis-retinal-incubated oocytes co-expressing opsin and Kir3.1* caused an immediate and long-lasting channel opening. In the absence of 11-cis retinal, all-trans-retinal also opened the channel persistently, although with slower kinetics. We then used the oocyte/TEVC system to test fusion proteins between opsin/rhodopsin and Kir6.2. We demonstrate that a construct with a C-terminally truncated rhodopsin responds to light stimulus independent of G protein. By extending the concept of ICCRs to the light-activatable GPCR rhodopsin we broaden the potential applications of this set of tools.
Two-stage adaptive noise cancellation for intermittent-signal applications (Corresp.) (1980)

A novel two-stage adaptive signal extractor for intermittent signal applications is presented. If the presence and absence of the signal can be detected, the first stage will adapt only while the signal is absent and thereby effect a reduction in noise, whereas the second stage will adapt only when the signal is present and thereby effect a reduction in the distortion caused by the gust stage. Bounds on performance are derived, and performance improvement relative to a conventional one-stage adaptive noise canceller is assessed.
Retorting kinetics for oil shale from fluidized-bed pyrolysis (1981)

A quartz isothermal fluidized-bed reactor has been constructed in order to measure kinetics and oil properties relevant to surface processing of oil shale. The rate of volatile hydrocarbon evolution is measured with a flame-ionization detector. Oil yield and composition is determined via subsequent analysis. This work is an extension and expansion of that originally reported by P. H. Wallman and co-workers at Chevron. We are determining gas evolution kinetics, oil yield, and oil composition as a function of both oil shale parameters (e.g., particle size, grade) and fluidized-bed parameters (temperature, sweep gas composition and velocity, bed particle size). Various techniques are evaluated for ;measuring species-selective (as opposed to total hydrocarbon) kinetics; an ultimate goal is the development of diagnostic methods relating oil yield and composition to processing parameters.
Apoptosis of immature thymocytes mediated by E2/CD99 (1997)

E2/CD99 is a 32-kDa transmembrane molecule that does not belong to any known family of proteins. It appears to regulate adhesion properties of T cells as previously reported, in particular, the induction of homotypic adhesion in CD4+ CD8+ thymocytes. Apoptosis induced via E2/CD99 displays characteristic morphologic features, but includes early mitochondrial alterations and phosphatidylserine exposure at the outer leaflet of the plasma membrane. It is not followed by detectable DNA fragmentation, and its time course is much longer than apoptosis induced via the Fas/CD95 pathway. It requires 18 h for completion. E2/CD99-induced apoptosis does not require any RNA or protein synthesis and still occurs following blockage of the Fas pathway. It is, however, dependent on CPP32 and IL-1beta-converting enzyme-type cysteine proteases, as shown by blockade with their respective specific inhibitors. This effect is restricted to double-positive thymocytes carrying an intermediate density of CD3 and including all CD69+ cells. Thus, E2/CD99 apears to mediate a distinctive apoptotic signal at a critical stage of thymocyte differentiation, i.e., when positive selection is known to occur.
Nanocrystalline p-type transparent Cu–Al–O semiconductor prepared by chemical-vapor deposition with Cu(acac)2 and Al(acac)3 precursors (2000)

P-type transparent copper–aluminum–oxide semiconductor films are prepared by the use of the chemical-vapor deposition (CVD) technique with Cu(acac)2 and Al(acac)3 precursors. Transmission electron microscopy and electron diffraction suggest that the films contain nanocrystalline phases of CuAlO2 and Cu2O, in which CuAlO2 is dominant. Both Hall technique and Seebeck measurement reveal that the film is p type, and a very high room-temperature conductivity of 2 S cm−1 is achieved. This success of high-conductive p-type transparent semiconductor using CVD further paves the way for transparent semiconductor p–n junctions as well as industrial mass production of the relevant devices. The Hall measurement of the film shows a sheet mobility of 0.16 cm2 V−1 S−1 and a carrier concentration of 1.8×1019 cm−3. A wide optical gap of 3.75 eV due to quantum confinement is found, and the activation energy for the positive holes is 0.12 eV.
Glutathione S-transferase P1 (GSTP1) directly influences platinum drug chemosensitivity in ovarian tumour cell lines (2014)

Glutathione S-transferase P1 has an important role in cisplatin and carboplatin metabolism in ovarian cancer cells. Inter-tumour differences in GSTP1 expression may therefore influence response to platinum-based chemotherapy in ovarian cancer patients.
Increased levels of MIP-1αin CSF and serum of ALS (2015)

MIP-1α levels increased in both CSF and serum of patients with ALS, and it may be a potential neuroprotective biomarker in ALS.
Glycyl-tRNA synthetase specifically binds to the poliovirus IRES to activate translation initiation (2012)

Adaptation to the host cell environment to efficiently take-over the host cell's machinery is crucial in particular for small RNA viruses like picornaviruses that come with only small RNA genomes and replicate exclusively in the cytosol. Their Internal Ribosome Entry Site (IRES) elements are specific RNA structures that facilitate the 5' end-independent internal initiation of translation both under normal conditions and when the cap-dependent host protein synthesis is shut-down in infected cells. A longstanding issue is which host factors play a major role in this internal initiation. Here, we show that the functionally most important domain V of the poliovirus IRES uses tRNA(Gly) anticodon stem-loop mimicry to recruit glycyl-tRNA synthetase (GARS) to the apical part of domain V, adjacent to the binding site of the key initiation factor eIF4G. The binding of GARS promotes the accommodation of the initiation region of the IRES in the mRNA binding site of the ribosome, thereby greatly enhancing the activity of the IRES at the step of the 48S initiation complex formation. Moonlighting functions of GARS that may be additionally needed for other events of the virus-host cell interaction are discussed.
Inhibition of the epidermal growth factor receptor tyrosine kinase activity by leflunomide (1993)

The active metabolite of leflunomide, A77 1726 inhibits the proliferation of a variety of mammalian cell lines in culture. Epidermal growth factor (EGF)-dependent proliferation is inhibited by A77 1726 at an effective dose of 30-40 microM. A77 1726 appears to directly inhibit the EGF receptor tyrosine-specific kinase activity both in intact cells and purified EGF receptors at the same effective dose. These data suggest that leflunomide inhibits cellular proliferation by the inhibition of tyrosine-specific kinase activities.
The association of human fibulin-1 with elastic fibers: an immunohistological, ultrastructural, and RNA study. (1995)

We examined the pattern of fibulin-1 mRNA and protein expression in human tissues and cell lines. Fibulin-1 transcripts were found in RNA isolated from most tissues and a variety of cultured cells, including fibroblasts, smooth muscle cells, and several epithelial cell lines, but not endothelial cells, lymphomyloid cells, or a number of carcinoma and melanoma lines. Immunohistochemical analysis showed that fibulin-1 is an intercellular component of connective tissues, predominantly associated with matrix fibers in tissues such as the cervix, dermis, intimal and medial layers of blood vessels, heart valves, meningeal tissue of the brain, Wharton's jelly of the umbilical cord, testis, and lung. Most of the fibers that were immunoreactive with fibulin-1 antibodies also stained with antibodies to the elastic fiber proteins elastin and fibrillin, as well as with Verhoeff's elastin stain. Immunoelectron microscopic analysis of elastin fibers of skin and saphenous vein revealed that fibulin-1 was located within the amorphous core of the fibers, similar to elastin, but it was not in the fibrillin-containing, elastin-associated microfibrils. Our finding that fibulin-1 is an elastic fiber component suggests several possible new functions for fibulin-1, e.g., that it is a structural protein that contributes to the elastic properties of connective tissue fibers or that is involved with the process of fibrogenesis.