gebhart/patrepeval huggingface dataset:
Diagnosis of Helicobacter pylori Infection in Patients with Atrophic Gastritis: Comparison of Histology, 13C-Urea Breath Test, and Serology (2000)

H. pylori infection would have been missed in most patients with atrophic gastritis without the analysis of H. pylori antibodies. Therefore, in patients with atrophic gastritis, the use of serology is encouraged in diagnosing H. pylori infection.
Sympathetic nervous system involvement in the lateral hypothalamic lesion syndrome (1977)

The role of the sympathetic nervous system in the lateral hypothalamic syndrome of body-weight loss was investigated. Bilateral electrolytic lesions of the lateral hypothalamus (LH) were performed in 90-day-old male albino rats. In experiment 1, the splanchnic nerves were resected at 35 days (right) and 70 days (left) postlesion. In experiment 2, bilateral adrenal demedullations were performed in a second group of rats with LH lesions (LH rats) at 35 days postlesion. The results indicated that lesions of the lateral hypothalamic area lowered body-weight maintenance levels to approximately 87% of nonlesion control values. Bilateral splanchnicetomy produced a significantly greater body-weight loss in nonlesion animals than in LH rats. Following adrenal demedullation, nonlesion rats also reduced body-weight levels whereas LH rats significantly increased weight-maintenance levels. In addition, the adrenal glands of LH rats with sham demedullations weighed significantly more than the adrenals of nonlesion-sham demedullated animals. These data are discussed in relation to metabolic-autonomic mechanisms that may play a role in LH lesion-induced weight loss.
An integrated map of genetic variation from 1,092 human genomes (2012)

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations.
Towards efficient cancer immunotherapy: advances in developing artificial antigen-presenting cells (2014)

Active anti-cancer immune responses depend on efficient presentation of tumor antigens and co-stimulatory signals by antigen-presenting cells (APCs). Therapy with autologous natural APCs is costly and time-consuming and results in variable outcomes in clinical trials. Therefore, development of artificial APCs (aAPCs) has attracted significant interest as an alternative. We discuss the characteristics of various types of acellular aAPCs, and their clinical potential in cancer immunotherapy. The size, shape, and ligand mobility of aAPCs and their presentation of different immunological signals can all have significant effects on cytotoxic T cell activation. Novel optimized aAPCs, combining carefully tuned properties, may lead to efficient immunomodulation and improved clinical responses in cancer immunotherapy.
Temperature compensation of birefringent optical filters (1971)

Temperature characteristics of birefringent optical filters were improved by two orders of magnitude by combining calcite and LiTaO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> crystals in series. Theoretical treatment of the temperature compensation and experimental results are presented.
High stereo- and regioselectivities in the transition metal catalyzed epoxidations of olefinic alcohols by tert-butyl hydroperoxide (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh stereo- and regioselectivities in the transition metal catalyzed epoxidations of olefinic alcohols by tert-butyl hydroperoxideK. B. Sharpless and R. C. MichaelsonCite this: J. Am. Chem. Soc. 1973, 95, 18, 6136–6137Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/ja00799a061https://doi.org/10.1021/ja00799a061research-articleACS PublicationsRequest reuse permissionsArticle Views8492Altmetric-Citations678LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cation-Exchange Properties of (Al + Na)-Substituted Synthetic Tobermorites (1987)

Abstract Tobermorite, Ca 5 Si 6 O 16 (OH) 2 ·4H 2 O, is a hydrous calcium silicate that has a layer-type of structure similar to that of the 2:1 clay minerals. In its natural form, tobermorite exhibits little or no exchange for alkali cations; synthetic tobermorites, however, exhibit reversible alkali cation exchange and selective cesium uptake upon a coupled substitution of (Al 3+ + Na + ) for Si 4+ . Substituted tobermorites were synthesized using aluminosilicate gels, NaOH, and CaO, in Parr bombs at 175°C for 4 days. Unsubstituted tobermorite was synthesized using quartz and CaO in a Parr bomb at 175°C for 20 hr. Two (Al + Na)-substituted tobermorites showed cation-exchange capacities (CEC) of 77 and 71 meq/100 g, whereas an unsubstituted tobermorite showed a CEC of 12 meq/100 g. The substituted tobermorites exhibited selective Cs exchange from either NaCl or CaCl 2 solutions. For example, one substituted tobermorite showed a Cs-exchange coefficient (K d ) of 15,100, whereas unsubstituted tobermorite showed a K d of only 90 from a 0.02 N CaCl 2 solution containing 0.0002 moles/liter CsCl. Exchange isotherms for Na + ⇋ Cs + showed that Cs + is preferred over Na + throughout the exchange in the (Al + Na)-substituted tobermorites. This group of cation exchangers is expected to find applications in radioactive waste disposal.
Localization of the Lys, Asp, Glu, Leu tetrapeptide receptor to the Golgi complex and the intermediate compartment in mammalian cells. (1994)

The carboxyl-terminal Lys-Asp-Glu-Leu (KDEL), or a closely-related sequence, is important for ER localization of both lumenal as well as type II membrane proteins. This sequence functions as a retrieval signal at post-ER compartment(s), but the exact compartment(s) where the retrieval occurs remains unresolved. With an affinity-purified antibody against the carboxyl-terminal sequence of the mammalian KDEL receptor, we have investigated its subcellular localization using immunogold labeling on thawed cryosections of different tissues, such as mouse spermatids and rat pancreas, as well as HeLa, Vero, NRK, and mouse L cells. We show that rab1 is an excellent marker of the intermediate compartment, and we use this marker, as well as budding profiles of the mouse hepatitis virus (MHV) in cells infected with this virus, to identify this compartment. Our results demonstrate that the KDEL receptor is concentrated in the intermediate compartment, as well as in the Golgi stack. Lower but significant labeling was detected in the rough ER. In general, only small amounts of the receptor were detected on the trans side of the Golgi stack, including the trans-Golgi network (TGN) of normal cells and tissues. However, some stress conditions, such as infection with vaccinia virus or vesicular stomatitis virus, as well as 20 degrees C or 43 degrees C treatment, resulted in a significant shift of the distribution towards the trans-TGN side of the Golgi stack. This shift could be quantified in HeLa cells stably expressing a TGN marker. No significant labeling was detected in structures distal to the TGN under all conditions tested. After GTP gamma S treatment of permeabilized cells, the receptor was detected in the beta-COP-containing buds/vesicles that accumulate after this treatment, suggesting that these vesicles may transport the receptor between compartments. We propose that retrieval of KDEL-containing proteins occurs at multiple post-ER compartments up to the TGN along the exocytotic pathway, and that within this pathway, the amounts of the receptor in different compartments varies according to physiological conditions.
CD40L-deficient mice show deficits in antiviral immunity and have an impaired memory CD8+ CTL response. (1996)

The ligand for CD40 (CD40L) is expressed on the surface of activated CD4+ T cells and its role in T-B cell collaborations and thymus-dependent humoral immunity is well established. Recently, by generating CD40L-knockout mice, we have confirmed its previously described role in humoral immunity and defined another important function of this molecule in the in vivo clonal expansion of antigen-specific CD4+ T cells. Here, we investigated the potential in vivo role of CD40L in antiviral immunity by examining the immune response mounted by CD40L-deficient mice following infection with lymphocytic choriomeningitis virus (LCMV), Pichinde virus, or vesicular stomatitis virus. Humoral immune responses of CD40L-deficient mice to these viruses were severely compromised, although moderate titres of antiviral IgM and some IgG2a were produced by virus-infected CD40L-deficient mice by a CD4+ T cell-independent mechanism. By contrast, CD40L-deficient mice made strong primary CTL responses to all three viruses. Interestingly however, although memory CTL activity was detectable in CD40L-deficient mice two months after infection with LCMV, the memory CTL response was much less efficient than in wild-type mice. Together, the results show that CD40-CD40L interactions are required for strong antiviral humoral immune responses, and reveal a novel role for CD40L in the establishment and/or maintenance of CD8+ CTL memory.
Switch in the protein tyrosine phosphatase associated with human CD100 semaphorin at terminal B-cell differentiation stage (2000)

Human CD100, the first semaphorin identified in the immune system, is a transmembrane protein involved in T-cell activation. In the present study, we showed that activation of peripheral blood or tonsillar B lymphocytes induced the expression of CD100 in CD38(+)CD138(-) cell populations, including in CD148(+) subpopulations, thus expressing a memory B-cell-like phenotype. Using an in vitro enzymatic assay, we found that protein tyrosine phosphatase (PTP) activities were immunoprecipitated with CD100 in these cell populations, which were isolated by cell sorting, as well as in most B-cell lines representing various stages of B-cell differentiation. Immunodepletion and Western blotting experiments demonstrated that CD45 was the PTP associated with CD100 in cell lines displaying pre-B, activated B, and pre-plasma cell phenotypes. CD45 also accounted for PTP activity immunoprecipitated with CD100 in CD38(+)CD138(-) cells sorted after activation of peripheral blood or tonsillar B lymphocytes. In contrast, no CD100-CD45 association was observed in plasma cell lines corresponding to the terminal B-cell differentiation stage. CD148, the other transmembrane PTP known to be implicated in lymphocyte signaling pathways, was either only partly involved in the CD100-associated PTP activity or not expressed in plasma cell lines, indicating the association of CD100 with another main PTP. Our data show that CD100 is differentially expressed and can functionally associate with distinct PTPs in B cells depending on their activation and maturation state. They also provide evidence for a switch in the CD100-associated PTP at terminal stage of B-cell differentiation.
Identification of a nonkinase target mediating cytotoxicity of novel kinase inhibitors (2008)

Abstract In developing inhibitors of the LIM kinases, the initial lead molecules combined potent target inhibition with potent cytotoxic activity. However, as subsequent compounds were evaluated, the cytotoxic activity separated from inhibition of LIM kinases. A rapid determination of the cytotoxic mechanism and its molecular target was enabled by integrating data from two robust core technologies. High-content assays and gene expression profiling both indicated an effect on microtubule stability. Although the cytotoxic compounds are still kinase inhibitors, and their structures did not predict tubulin as an obvious target, these results provided the impetus to test their effects on microtubule polymerization directly. Unexpectedly, we confirmed tubulin itself as a molecular target of the cytotoxic kinase inhibitor compounds. This general approach to mechanism of action questions could be extended to larger data sets of quantified phenotypic and gene expression data. [Mol Cancer Ther 2008;7(11):3490–8]
Prognostic value of a cell cycle progression signature for prostate cancer death in a conservatively managed needle biopsy cohort (2012)

For conservatively managed patients, the CCP score is the strongest independent predictor of cancer death outcome yet described and may prove valuable in managing clinically localised prostate cancer.
Thermally assisted electrospray interface for liquid chromatography/mass spectrometry (1992)

Abstract An electrospray interface for liquid chromatography/mass spectrometry (LC/MS) is described that combines the direct heating of High‐performance liquid chromatography (HPLC) effluent that is characteristic of thermoooospray‐type interfaces. This interface is called the thermally assisted electrospray interface for LC/MS. The device can accept the total effluent from a liquid chromatograph at flow rates ranging up to 500 μL/min. The HPLC effluent is nebulized into charged droplets by a combination of heat and an applied electric field. Ions emitted from charged droplets are mass‐analyzed by a triple quadraupole mass spectrometer equipped with an atmospheric pressure ion sampling orifice. Singly or multiply charged ions, indicating the molecular weight of a sample, are observed with minimal fragmentation. The extent of multiple charging observed in electrospray and ion spray mass spectrometry is decreased somewhat in thermally assisted electrospray. Labile compounds which undergo thermal decomposition by conventional thermospray show no decomposition with thermally assisted electrospray.
Macrophage colony‐stimulating factor and interleukin‐6 release by periprosthetic cells stimulates osteoclast formation and bone resorption (1999)

Periprosthetic bone loss is an important contributory factor for aseptic loosening of total joint replacements. It has recently been shown that osteoclast precursor cells are present in the wear particle-associated macrophage infiltrate found in the membrane surrounding loose implants and that these cells are capable of differentiating into osteoclastic bone-resorbing cells. Long-term co-culture of arthroplasty-derived macrophages and the rat osteoblast-like cell line, UMR-106, in the presence of 1,25(OH)2D3 results in the formation of numerous multinucleated cells that are positive for tartrate-resistant acid phosphatase and vitronectin receptor and capable of extensive lacunar bone resorption. The aim of this study was to determine the effect of cytokines/growth factors, known to be present in the arthroplasty membrane, on this process of osteoclast differentiation. During osteoclast formation, increased levels of macrophage colony-stimulating factor, interleukin-6, and to a lesser extent, interleukin-1beta, but not tumour necrosis factor alpha, were detected in the co-culture supernatants. Addition of neutralising antibodies to human interleukin-1beta or tumour necrosis factor alpha to the co-culture system did not inhibit osteoclast formation. In contrast, co-cultures to which neutralising antibodies to human macrophage colony-stimulating factor or interleukin-6 were added contained fewer cells positive for tartrate-resistant acid phosphatase and vitronectin receptor and formed significantly fewer resorption pits. Time-course studies showed that macrophage colony-stimulating factor and interleukin-6 increase osteoclast formation mainly in the early stages of osteoclast differentiation. These results indicate that the release of macrophage colony-stimulating factor and interleukin-6 by activated cells in the arthroplasty membrane is likely to contribute to pathological bone resorption associated with aseptic loosening by stimulating differentiation of mononuclear phagocyte osteoclast precursors into mature bone-resorbing cells.
VMR: VLSI-compatible metallic carbon nanotube removal for imperfection-immune cascaded multi-stage digital logic circuits using Carbon Nanotube FETs (2009)

Metallic carbon nanotubes (CNTs) create source-drain shorts in Carbon Nanotube Field Effect Transistors (CNFETs) resulting in excessive leakage (I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</inf> /I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</inf> ≪ 5) and highly degraded noise margins. A new technique, VLSI-compatible Metallic-CNT Removal (VMR), overcomes metallic CNT challenges by combining layout design with CNFET processing. VMR produces CNFET circuits with I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</inf> /I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</inf> in the range of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> -10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> , and overcomes the limitations of existing metallic-CNT removal techniques. VMR enables first experimental demonstration of complex cascaded CNFET logic circuits. Such logic circuits are immune to both mis-positioned and metallic CNTs.
Human Enhancers Are Fragile and Prone to Deactivating Mutations (2015)

To explore the underlying mechanisms whereby noncoding variants affect transcriptional regulation, we identified nucleotides capable of disrupting binding of transcription factors and deactivating enhancers if mutated (dubbed candidate killer mutations or KMs) in HepG2 enhancers. On average, approximately 11% of enhancer positions are prone to KMs. A comparable number of enhancer positions are capable of creating de novo binding sites via a single-nucleotide mutation (dubbed candidate restoration mutations or RSs). Both KM and RS positions are evolutionarily conserved and tend to form clusters within an enhancer. We observed that KMs have the most deleterious effect on enhancer activity. In contrast, RSs have a smaller effect in increasing enhancer activity. Additionally, the KMs are strongly associated with liver-related Genome Wide Association Study traits compared with other HepG2 enhancer regions. By applying our framework to lymphoblastoid cell lines, we found that KMs underlie differential binding of transcription factors and differential local chromatin accessibility. The gene expression quantitative trait loci associated with the tissue-specific genes are strongly enriched in KM positions. In summary, we conclude that the KMs have the greatest impact on the level of gene expression and are likely to be the causal variants of tissue-specific gene expression and disease predisposition.
Chemistry and Function of the Complement System (1977)

Awareness of the cytolytic complement system and its major role in defense against infection began a century ago. But it has only been in the last half dozen years or so that protein chemistry has advanced to the point at which the specific complement sequences—both the classic and alternate pathways—have been elucidated, and their control mechanisms, their versatility, and their biologic elegance understood.
Prevalence of Sleep Disordered Breathing in a Heart Failure Program (2004)

Recent data show that a high percentage of patients with systolic left ventricular dysfunction have sleep-disordered breathing (SDB), contributing to the incidence of morbidity and mortality in heart failure. This study examines the prevalence of sleep disorders in stable heart failure patients regardless of ejection fraction. On three consecutive days in a heart failure clinic, all patients were asked to participate in a screening for SDB. This screening involved the placement of an outpatient device (ClearPath, Nexan, Inc., Alpharetta, GA), which collects thoracic impedance, oxyhemoglobin saturation, and 2-lead electrocardiogram data. Sixteen patients (42%) had moderate or severe SDB, and 22 patients (55%) had mild or no significant SDB. Fourteen of the 16 patients with moderate or severe SDB subsequently received treatment by confirming SDB and the continuous positive airway pressure in a sleep lab. Forty-two percent of patients with stable heart failure presenting to a heart failure clinic screened positive for SDB, despite receiving optimal standard of care.