gebhart/patrepeval huggingface dataset:
Beyond the stomach: An updated view ofHelicobacter pyloripathogenesis, diagnosis, and treatment (2014)

Helicobacter pylori (H. pylori) is an extremely common, yet underappreciated, pathogen that is able to alter host physiology and subvert the host immune response, allowing it to persist for the life of the host. H. pylori is the primary cause of peptic ulcers and gastric cancer. In the United States, the annual cost associated with peptic ulcer disease is estimated to be $6 billion and gastric cancer kills over 700000 people per year globally. The prevalence of H. pylori infection remains high (> 50%) in much of the world, although the infection rates are dropping in some developed nations. The drop in H. pylori prevalence could be a double-edged sword, reducing the incidence of gastric diseases while increasing the risk of allergies and esophageal diseases. The list of diseases potentially caused by H. pylori continues to grow; however, mechanistic explanations of how H. pylori could contribute to extragastric diseases lag far behind clinical studies. A number of host factors and H. pylori virulence factors act in concert to determine which individuals are at the highest risk of disease. These include bacterial cytotoxins and polymorphisms in host genes responsible for directing the immune response. This review discusses the latest advances in H. pylori pathogenesis, diagnosis, and treatment. Up-to-date information on correlations between H. pylori and extragastric diseases is also provided.
Novel Synthesis of [33P]-(2-Chloroethyl)phosphonic Acid (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTNovel Synthesis of [33P]-(2-Chloroethyl)phosphonic AcidNanjing Zhang and John E. CasidaView Author Information Environmental Chemistry and Toxicology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720-3112 [email protected]Cite this: J. Org. Chem. 2001, 66, 1, 327–329Publication Date (Web):December 2, 2000Publication History Received14 September 2000Published online2 December 2000Published inissue 1 January 2001https://pubs.acs.org/doi/10.1021/jo0013608https://doi.org/10.1021/jo0013608brief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views676Altmetric-Citations7LEARN 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 SUBJECTS:Hydrolysis,Organophosphorus compounds,Phosphorus,Reaction products,Reagents Get e-Alerts
Dust storms come to central and southwestern China, too: implications from a major dust event in Chongqing (2009)

Abstract. Dust storms from major Asian sources are usually carried by northwesterly or westerly winds over northern and southeastern China to the Pacific Ocean. These pathways leave central and southwestern China nearly free of incursions. But a strong dust event on 5–6 May 2005 was captured in a 15-month series of weekly filter samples of PM2.5 at three sites in Chongqing. It illustrated that desert dust can be transported to this region, and sometimes strongly. Annual PM2.5 and dust were similar at the three sites, but higher than in simultaneous samples in Beijing. High correlations of dust concentration were found between the cites during spring, indicating that Asian dust affects a broader swath of China than is often realized. During the event, the concentrations of mineral dust were high at all sites (20–30 μg m−3; 15%–20% of PM2.5 in Chongqing, and 15 μg m−3; 20%–30% of PM2.5 in Beijing), and were part of a broader spring maximum. The proportions of crustal elements and pollution-derived components such as Pb, SO42−, and organic carbon indicated that the sources for this dust differed from Beijing. The dust was considerably enriched in Ca and Mg, characteristic of western deserts, whereas Beijing's dust had the lower Ca and Mg of eastern deserts. This observation agrees with synoptic patterns and back-trajectories. Driven by a cold air outbreak from the northwest, dust from the western Gobi Desert was transported at lower altitudes (&lt;2 km above ground level), while dust from the Takla Makan Desert was transported to Chongqing at higher altitudes. Desert dust can also be important to wide areas of China during the cold season, since almost all the weekly dust peaks in the two cities coincided with extensive dust emissions in source regions. These findings collectively suggest that the amount of Asian-dust in China has been underestimated both spatially and temporally, and that transported alkaline dust can even be mitigating the effects of acidic deposition in southern China.
Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein (2020)

Lasting protection has long been a goal for malaria vaccines. The major surface antigen on Plasmodium falciparum sporozoites, the circumsporozoite protein (PfCSP), has been an attractive target for vaccine development and most protective antibodies studied to date interact with the central NANP repeat region of PfCSP. However, it remains unclear what structural and functional characteristics correlate with better protection by one antibody over another. Binding to the junctional region between the N-terminal domain and central NANP repeats has been proposed to result in superior protection: this region initiates with the only NPDP sequence followed immediately by NANP. Here, we isolated antibodies in Kymab mice immunized with full-length recombinant PfCSP and two protective antibodies were selected for further study with reactivity against the junctional region. X-ray and EM structures of two monoclonal antibodies, mAb667 and mAb668, shed light on their differential affinity and specificity for the junctional region. Importantly, these antibodies also bind to the NANP repeat region with equal or better affinity. A comparison with an NANP-only binding antibody (mAb317) revealed roughly similar but statistically distinct levels of protection against sporozoite challenge in mouse liver burden models, suggesting that junctional antibody protection might relate to the ability to also cross-react with the NANP repeat region. Our findings indicate that additional efforts are necessary to isolate a true junctional antibody with no or much reduced affinity to the NANP region to elucidate the role of the junctional epitope in protection.
Characterization of Line Edge Roughness in Resist Patterns by Using Fourier Analysis and Auto-Correlation Function (2003)

We have evaluated periodicity of line edge roughness (LER) in electron beam (EB), KrF, and ArF resists. A set of 512 edge-point coordinates was obtained for a scanning electron microscope (SEM) image of one edge by using an in-house image-processing program. The edge-point fluctuations were given and analyzed by Fourier transform and auto-correlation function. Fourier analysis has shown that (1) the spatial frequency (f) distribution of LER can be described with the 1/f-rule and (2) an additional component appears at around 100 nm in the results from several kinds of ArF resists. The auto-correlation-function method gives histograms of the basic period of LER. The results from this method are consistent with those from Fourier analysis and show that several ArF resist samples have a specific period distribution at around 240 nm. Results from both of these methods show that not only the resist materials but also the lithographic tools and processes affect the period distribution.
Stimulation of Lung Innate Immunity Protects against Lethal Pneumococcal Pneumonia in Mice (2008)

We infer that protection derives from stimulation of local innate immune mechanisms, and that activated lung epithelium is the most likely cellular effector of this response. Augmentation of innate antimicrobial defenses of the lungs might have therapeutic value.
Synthesis, Biological Activity, Pharmacokinetic Properties and Molecular Modelling Studies of Novel 1H,3H-Oxazolo[3,4-a]Benzimidazoles: Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors (2001)

New 1H,3H-oxazolo[3,4-albenzimidazoles (OBZs) were synthesized as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTI) to extend the structure-activity relationships observed for an early series of related 1H,3H-thiazolo[3,4-a]benzimidazole derivatives (TBZs). The new compounds showed inhibitory activity against the replication of various HIV-1 strains, including NNRTI-resistant strains. Testing of a representative OBZ derivative in an HPLC assay on biological fluids, indicated that the sulphur substitution appreciably improved the metabolic stability of the TBZ compound. In addition, molecular modelling studies demonstrated that OBZs, TBZs and other NNRTIs have similar structural properties, that is a butterfly-like conformation, which is a key structural requirement for reverse transcriptase inhibition.
Applied nutritional investigation Breath acetone predicts plasma ketone bodies in children with epilepsy on a ketogenic diet (2006)

Objective: The high-fat ketogenic diet has long been used to treat refractory childhood seizures, but whether there is a relation between the degree of ketosis and effectiveness of seizure control remains unclear. Frequent measurements of plasma ketones are difficult in children so the goal was to determine the utility of breath acetone as a marker of systemic ketosis and seizure control in children given the ketogenic diet because of seizures refractory to medication. Methods: In experiment I, breath acetone and plasma ketones were assessed every 2 h during an 8-h test day in seven children. In experiment II, a preliminary assessment of the possible relation between breath acetone and seizure frequency was made over 14 d in five children and one adolescent on the ketogenic diet. Results: Breath acetone was positively and curvilinearly related to plasma acetone (r 2 0.99, P 0.0001), plasma acetoacetate (r 2 0.89, P 0.0001), and plasma -hydroxybutyrate (r 2 0.94,
Apoptotic cell clearance in chronic inflammation of lateral neck cysts (2011)

The mechanism driving accumulation of large numbers of apoptotic and necrotic neutrophils in inflamed lateral neck cysts (LNC), in the absence of infection, remains obscure. The cellular content of cysts obtained from 17 patients was co-cultured with human macrophages. Phagocytosis levels of cyst-derived neutrophils were determined and compared to the uptake of spontaneously apoptotic neutrophils. Simultaneously, the expression of cytokines in macrophages exposed to cyst contents was measured. In comparison to spontaneously apoptotic neutrophils, the phagocytosis of LNC-derived neutrophils by macrophages was inefficient. An inverse correlation between neutrophil content in LNC and their uptake was observed. Macrophages co-cultured with cyst contents responded with variable expression of IL-6, TNF-α and IL-10. The hindered clearance of apoptotic neutrophils in LNC may lead to secondary necrosis of these cells and stimulation of the inflammatory reaction. Together with local production of anti-inflammatory cytokines, this may fuel chronic inflammation in the cysts.
<title>Overwritable phase-change optical disk using an In<formula><inf><roman>3</roman></inf></formula>SbTe<formula><inf><roman>2</roman></inf></formula> ternary compound</title> (1990)

By employing transmission electron microscopy and thermal ana1yis, we examined overwrite repeatability of optical disks using In-Sb-Te alloys, which have high C/N ratio and excellent overwrite modulation characteristics. The overwrite repeatability of more than 10<sup>5</sup> was achieved by using an In<sub>3</sub>SbTe<sub>2</sub> single-phase ternary compound and heat-flow balanced disk structure.
2008 Summer Research Institute Interfacial and Condensed Phase Chemical Physics Annual Report (2008)

For the fifth year, the Pacific Northwest National Laboratory in Richland, Washington, invited graduate students, postdoctoral fellows, university faculty, and students entering graduate students from around the world to participate in the Summer Research Institute in Interfacial and Condensed Phase Chemical Physics. The institute offers participants the opportunity to gain hands-on experience in top-notch research laboratories while working along internationally respected mentors. Of the 38 applicants, 20 were accepted for the 8- to 10-week program. The participants came from universities as close as Seattle and Portland and as far away as Germany and Singapore. At Pacific Northwest National Laboratory, the 20 participants were mentored by 13 scientists. These mentors help tailor the participant’s experience to the needs of that person. Further, the mentors provide guidance on experimental and theoretical techniques, research design and completion, and other aspects of scientific careers in interfacial and condensed phase chemical physics. The research conducted at the institute can result in tangible benefits for the participants. For example, many have co-authored papers that have been published in peer-reviewed journals, including top-rated journals such as Science. Also, they have presented their research at conferences, such as the Gordon Research Conference on Dynamics at Surfaces and the AVS national meeting. Beyond that, many of the participants have started building professional connections with researchers at Pacific Northwest National Laboratory, connections that will serve them well during their careers.
In NIH-3T3 Fibroblasts, Insulin Receptor Interaction with Specific Protein Kinase C Isoforms Controls Receptor Intracellular Routing (1998)

Insulin increased protein kinase C (PKC) activity by 2-fold in both membrane preparations and insulin receptor (IR) antibody precipitates from NIH-3T3 cells expressing human IRs (3T3hIR). PKC-alpha, -delta, and -zeta were barely detectable in IR antibody precipitates of unstimulated cells, while increasing by 7-, 3.5-, and 3-fold, respectively, after insulin addition. Preexposure of 3T3hIR cells to staurosporine reduced insulin-induced receptor coprecipitation with PKC-alpha, -delta, and -zeta by 3-, 4-, and 10-fold, respectively, accompanied by a 1.5-fold decrease in insulin degradation and a similar increase in insulin retroendocytosis. Selective depletion of cellular PKC-alpha and -delta, by 24 h of 12-O-tetradecanoylphorbol-13-acetate (TPA) exposure, reduced insulin degradation by 3-fold and similarly increased insulin retroendocytosis, with no change in PKC-zeta. In lysates of NIH-3T3 cells expressing the R1152Q/K1153A IRs (3T3Mut), insulin-induced coprecipitation of PKC-alpha, -delta, and -zeta with the IR was reduced by 10-, 7-, and 3-fold, respectively. Similar to the 3T3hIR cells chronically exposed to TPA, untreated 3T3Mut featured a 3-fold decrease in insulin degradation, with a 3-fold increase in intact insulin retroendocytosis. Thus, in NIH-3T3 cells, insulin elicits receptor interaction with multiple PKC isoforms. Interaction of PKC-alpha and/or -delta with the IR appears to control its intracellular routing.
Mid-infrared extraordinary transmission through Ga-doped ZnO films with 2D hole arrays (2014)

Extraordinary optical transmission (EOT), through highly conductive ZnO films with sub-wavelength hole arrays is investigated in the long-wavelength infrared regime. EOT is facilitated by the excitation of surface plasmon polaritons (SPPs) on Ga-Doped ZnO films and can be tuned utilizing the physical parameters such as film thickness, period, hole size, and hole shape, as well as doping of the film. Analytical and finite-difference time-domain calculations are completed for 1 micron thick films with square, circular, and triangular hole arrays demonstrating SPP coupling and EOT. The fundamental plasmonic modes are observed in each of these hole shapes at wavelengths that correspond to strong EOT peaks. Doping tunability for these structures is also observed. Ga-doped ZnO films are grown via pulsed laser deposition (PLD) on silicon with plasma frequencies in the near-infrared. The sub-wavelength 2D hole arrays are fabricated in the Ga-doped ZnO films via standard lithography and etching processes. This highly conductive ZnO EOT structure may prove useful in novel integrated components such as tunable biosensors or surface plasmon coupling mechanisms.
Sinnvolle Therapieverfahren bei symptomatischem Zenker-Divertikel-Rezidiv (2006)

Einleitung: Neben der konventionell-chirurgischen Abtragung von Zenker-Divertikeln sind die Staplermyotomie, die Laser-Schwellenspaltung oder die Argon-Plasma-Koagulation (APC) als minimal-invasive, endoskopische Primärtherapieverfahren anerkannt.
The effect of IgG and IgG fragments on the absorption of inhaled antigens across the air-blood barrier of isolated perfused rabbit lungs. (1981)

The absorption of inhaled soluble protein antigens across the alveolocapillary membrane can be inhibited by passive immunization in isolated rabbit lungs. The present study was carried out to determine the immunoglobulin class and structural features (Fc-receptor binding, divalent antigen binding) required to effect the inhibition. Isolated rabbit lungs from unimmunized rabbits were perfused with autologous blood to which whole antiserum, IgG or IgG fragments specific for either ovalbumin (OA) or human serum albumin (HSA) was added. The lungs were insufflated with an aerosol containing 125I-OA and 131I-HSA and blood samples were analysed for 125I and 131I in trichloracetic acid (TCA)-precipitable and TCA-soluble forms for 4 hr after insufflation. Whole antiserum and the IgG immunoglobulin fraction of the whole antiserum were equally effective in inhibiting the antigen absorption, indicating that the IGG antibody is sufficient for the effect. The F(ab')2 and Fab' fragments of the IgG molecule were as effective as native IgG, indicating that the antigen-binding site is the only structural requirement and that Fc-receptor and divalent antigen binding are not required.
Adaptive Update of Reference Capacitances in Conductive Fabric Based Robotic Skin (2019)

This letter proposes a sensor using conductive fabric that can detect proximity and contact by measuring the capacitance between the sensor and the surrounding environment. Due to the flexibility of the sensor used, it can be easily integrated with industrial robot arms to monitor proximity and contact between the robot and the surrounding environment including humans for safety reasons. However, the surrounding environment is constantly changing and significantly affects the capacitance measurements. To apply such proximity sensors in this scenario, the environmental variations have to be considered and the influences on the capacitance measurements have to be eliminated to ensure stable and robust proximity measurements. Therefore, in this letter, we propose an approach to adaptively update the reference capacitance to eliminate the influence of the environment. To experimentally validate the proposed sensor and approach, we developed a two-link robot arm and embedded the proposed sensing technology with each link. Experimental results demonstrate that proximity and contact can be successfully detected by the proposed sensor, independently of whether the robot arm is at rest or moving in a potentially dynamic environment.
The coding microsatellite mutation profile of PMS2-deficient colorectal cancer (2021)

Lynch syndrome (LS) is caused by a pathogenic heterozygous germline variant in one of the DNA mismatch repair (MMR) genes: MLH1, MSH2, MSH6 or PMS2. LS-associated colorectal carcinomas (CRCs) are characterized by MMR deficiency and by accumulation of multiple insertions/deletions at coding microsatellites (cMS). MMR deficiency-induced variants at defined cMS loci have a driver function and promote tumorigenesis. Notably, PMS2 variant carriers face only a slightly increased risk of developing CRC. Here, we investigate whether this lower penetrance is also reflected by differences in molecular features and cMS variant patterns. Tumor DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue cores or sections (n = 90). Tumors originated from genetically proven germline pathogenic MMR variant carriers (including 14 PMS2-deficient tumors). The mutational spectrum was analyzed using fluorescently labeled primers specific for 18 cMS previously described as mutational targets in MMR-deficient tumors. Immune cell infiltration was analyzed by immunohistochemical detection of T-cells on FFPE tissue sections. The cMS spectrum of PMS2-deficient CRCs did not show any significant differences from MLH1/MSH2-deficient CRCs. PMS2-deficient tumors, however, displayed lower CD3-positive T-cell infiltration compared to other MMR-deficient cancers (28.00 vs. 55.00 per 0.1 mm2, p = 0.0025). Our study demonstrates that the spectrum of potentially immunogenic cMS variants in CRCs from PMS2 gene variant carriers is similar to that observed in CRCs from other MMR gene variant carriers. Lower immune cell infiltration observed in PMS2-deficient CRCs could be the result of alternative mechanisms of immune evasion or immune cell exclusion, similar to those seen in MMR-proficient tumors.
S-adenosylmethionine and Catechol-O-methyltransferase in Schizophrenia (1972)

The authors examined the hypothesis of disordered transmethylation in schizophrenia by comparing S-adenosylmethionine (SAMe) concentration and cathechol-O-methyltransferase (COMT) activities in venous blood of schizophrenic and nonschizophrenic patients. While they did not find a difference in blood SAMe concentration between the groups, they did find a significant correlation between blood COMT activity and SAMe concentration. This suggests that some schizophrenics may methylate biogenic amines more actively than others.
Expression of HSP105 and HSP60 during germ cell apoptosis in the heat-treated testes of adult cynomolgus monkeys (macaca fascicularis) (2005)

To confirm that transient increase in temperature of the testis (43C for 30 minutes once daily for 2 consecutive days) could induce apoptosis of germ cells in non-human primates and to investigate the possible roles of Hsp105 and Hsp60 in regulation of germ cell loss, we conducted the study on eight cynomolgus monkeys. The sperm concentration on day 28 after heat shock decreased to 8.4% of pretreatment levels and recovered to baseline on day 144. Using the TUNEL assay, increased numbers of apoptotic spermatocytes and round spermatids were detected on days 3, 8, and 30 post heat treatment. Hsp105 and Hsp60 mRNA and protein levels were analyzed using in situ hybridization, RT-PCR, immunohistochemical and Western blot methods. Hsp105 was confined to nuclei of spermatids before treatment, decreased dramatically with the loss of spermatids on days 3, 8, and 30, before returning to baseline levels on days 84 and 144. The expression of Hsp60 was high on days 3, 8, 30 and was only detected in Sertoli cells and spermatogonia. These results suggested that exposure of the testis to heat resulted in selective, but reversible damage to the seminiferous epithelium via increased germ cell apoptosis. Temporal changes in the expression pattern of Hsp105 and Hsp60 in relation to germ cell death suggests they may be involved in key processes in regulation of germ cell apoptosis.