gebhart/patrepeval huggingface dataset:
Germline determinants of humoral immune response to HPV-16 protect against oropharyngeal cancer (2021)

Although several oropharyngeal cancer (OPC) susceptibility loci have been identified, most previous studies lacked detailed information on human papillomavirus (HPV) status. We conduct a genome-wide analysis by HPV16 serology status in 4,002 oral cancer cases (OPC and oral cavity cancer (OCC)) and 5,256 controls. We detect four susceptibility loci pointing to a distinct genetic predisposition by HPV status. Our most notable finding in the HLA region, that is now confirmed to be specific of HPV(+)OPC risk, reveal two independent loci with strong protective effects, one refining the previously reported HLA class II haplotype association. Antibody levels against HPV16 viral proteins strongly implicate the protective HLA variants as major determinants of humoral response against L1 capsid protein or E6 oncoprotein suggesting a natural immune response against HPV(+)OPC promoted by HLA variants. This indicates that therapeutic vaccines that target E6 and attenuate viral response after established HPV infections might protect against HPV(+)OPC.
Epitopes of group A streptococcal M protein shared with antigens of articular cartilage and synovium (1991)

Rabbit antisera evoked by purified pepsin-extracted group A streptococcal M proteins were screened for the presence of joint cross-reactive antibodies by indirect immunofluorescence using thin sections of mouse knee joints. Pep M1, M5, and M18 antisera contained antibodies that cross-reacted with chondrocytes, cartilage, and synovium. Immunofluorescence inhibition assays showed that some of the joint cross-reactive epitopes were shared among the three heterologous serotypes of M protein. The pep M5 joint cross-reactive epitopes were localized to three different synthetic peptides of the C-terminal region of pep M5. Immunoblot analyses showed that the M5 joint cross-reactive antibodies recognized two proteins of human synovium and cartilage of molecular mass 56 and 58 kDa. The cross-reactive antibodies binding to the 56-kDa protein were inhibited by purified vimentin in immunoblot inhibition experiments. M protein-specific antibodies from patients with acute rheumatic fever were also shown to cross-react with joint tissue in a pattern similar to the rabbit antisera. Rabbit and human M protein-specific antibodies that were bound to articular cartilage activated significant levels of complement when compared to control serum, suggesting that M protein joint cross-reactive antibodies could potentially be involved in the pathogenesis of ARF and arthritis.
Supplementary Figure 2 from BRAF Inhibitor Vemurafenib Improves the Antitumor Activity of Adoptive Cell Immunotherapy (2023)

&lt;p&gt;PDF file - 190K, Flow cytometric analysis of H2-Db expression by SM1 with or without exposure to vemurafenib for different periods&lt;/p&gt;
Ranking with Uncertain Scores (2009)

Large databases with uncertain information are becoming more common in many applications including data integration, location tracking, and Web search. In these applications, ranking records with uncertain attributes needs to handle new problems that are fundamentally different from conventional ranking. Specifically, uncertainty in records' scores induces a partial order over records, as opposed to the total order that is assumed in the conventional ranking settings. In this paper, we present a new probabilistic model, based on partial orders, to encapsulate the space of possible rankings originating from score uncertainty. Under this model, we formulate several ranking query types with different semantics. We describe and analyze a set of efficient query evaluation algorithms. We show that our techniques can be used to solve the problem of rank aggregation in partial orders. In addition, we design novel sampling techniques to compute approximate query answers. Our experimental evaluation uses both real and synthetic data. The experimental study demonstrates the efficiency and effectiveness of our techniques in different settings.
Metabolism and elimination of <sup>14</sup>C‐donepezil in healthy volunteers: a single‐dose study (1998)

Donepezil is hepatically metabolized and the predominant route for the elimination of both parent drug and its metabolites is renal, as 79% of the recovered dose was found in the urine with the remaining 21% found in the faeces. Moreover, the parent compound, donepezil, is the predominant elimination product in urine. The major metabolites of donepezil include M1 and M2 (via O-dealkylation and hydroxylation), M11 and M12 (via glucuronidation of M1 and M2, respectively), M4 (via hydrolysis) and M6 (via N-oxidation).
Minimizing Shortfall (revised) - eScholarship (2012)

(from the introduction...) In this paper, we combine the innovations described above in an empirical study of expected shortfall optimization with Factor-Based Extreme Risk. We avoid the issue of forecasting mean return by comparing minimum expected shortfall to minimum variance portfolios. Our study is carried out for the US, UK, and Japanese equity markets and it uses Barra Style Factors (Value, Growth, Momentum, etc.). We show that minimizing expected shortfall generally improves performance over minimizing variance, especially during down-markets, over the period 1985-2010. The outperformance of expected shortfall is due to intuitive tilts towards protective factors like Value, and away from aggressive factorslike Growth and Momentum. The outperformance is largest for the expected shortfall at relatively low confidence levels, which measures distributional asymmetry rather than the extreme losses.
Designing the EIC electron storage ring lattice for a wide energy range (2023)

Abstract The Electron-Ion Collider (EIC) will collide electrons with hadrons at center-of-mass energies up to 140 GeV (in the case of electron-proton collisions). A 3.8-kilometer electron storage ring is being designed, which will store electrons with a range of energies up to 18 GeV for collisions at one or two interaction points. At energies up to 10 GeV the arcs will be tuned to provide 60 degree phase advance per cell in both planes, whereas at top energy of 18 GeV a 90 degree phase advance per cell will be used, which largely compensates for the horizontal emittance increase with energy. The optics must be matched at three separate energies, and the different phase-advance requirements in both the arc cells and the straight sections make this challenging. Moreover, the spin rotators must fulfill requirements for polarization and spin matching at widely different energies while satisfying technical constraints. In this paper these challenges and proposed solutions are presented and discussed.
Supplementary Methods from Opposing Effects of Pigment Epithelium–Derived Factor on Breast Cancer Cell versus Neuronal Survival: Implication for Brain Metastasis and Metastasis-Induced Brain Damage (2023)

&lt;p&gt;PDF file - 75K&lt;/p&gt;
Comprehensive Survey of Combinatorial Library Synthesis:  2004 (2005)

ADVERTISEMENT RETURN TO ISSUEReviewNEXTComprehensive Survey of Combinatorial Library Synthesis: 2004Roland E. DolleView Author Information Department of Chemistry, Adolor Corporation, 700 Pennsylvania Drive, Exton, Pennsylvania 19341 Cite this: J. Comb. Chem. 2005, 7, 6, 739–798Publication Date (Web):September 17, 2005Publication History Received29 June 2005Published online17 September 2005Published inissue 1 November 2005https://pubs.acs.org/doi/10.1021/cc050082thttps://doi.org/10.1021/cc050082treview-articleACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views1646Altmetric-Citations97LEARN 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 options SUBJECTS:Amines,Ligands,Organic polymers,Peptides and proteins,Receptors Get e-Alerts
Passing the initiative for visualizing data to readers (2016)

Data visualizations are often generated to reflect the intentions of their creators. Readers of such visualizations cannot always obtain the information they want, because there is often a gap between the creators' intentions and readers' interests. To bridge such gaps, we propose passing the initiative of visualizing data to the readers. For most readers, who are not experts in visual representations, it can be difficult to design or to choose the appropriate options for visualizations that meet their needs; therefore, we consider a system that utilizes readers' interest. We organized problems to develop a framework for passing the initiative for visualizing data to readers. Moreover, we devised a method for express visual representations from the viewpoint of readers' interests. Through a thought experiment, we investigated the aspects of data that readers are interested in, and propose a formal expression for that interest.
Direct Evidence for Catalase as the Predominant H2O2 -Removing Enzyme in Human Erythrocytes (1997)

Decomposition of hydrogen peroxide (H2O2 ) at physiological levels was studied in human erythrocytes by means of a recently developed sensitive H2O2 assay. The exponential decay of H2O2 in the presence of purified erythrocyte catalase was followed down to 10(-9) mol/L H2O2 at pH 7.4. H2O2 decomposition by purified erythrocyte glutathione peroxidase (GPO) could be directly observed down to 10(-7) mol/L H2O2 . No enzyme inhibition was observed at these low H2O2 concentrations. Catalase and GPO activities can be determined separately in a titrated mixture of purified enzymes, which simulates the conditions of H2O2 removal by the erythrocyte. Experiments with fresh human hemolysate allowed us to determine H2O2 decomposition by catalase and GPO using these enzymes in their original quantitative ratio. The different kinetics of these enzymes are shown: H2O2 decomposition by catalase depends linearly on H2O2 concentration, whereas that by GPO becomes saturated at concentrations above 10(-6) mol/L H2O2. Even at very low H2O2 concentrations GPO reaches only approximately 8% of the rate at which catalase simultaneously degrades H2O2. These data indicate an almost exclusive role for catalase in the removal of H2O2 in normal human erythrocytes.
Possible Role of Interferon-.TAU. on In Vitro Development of Bovine Embryos (2003)

The effect of interferon-tau on in vitro development of bovine embryos was investigated. After in vitro fertilization, embryos developed to the morula stage were cultured for 3 days in TCM-199 or CR1 medium containing BSA or FCS supplemented with or without recombinant IFN-tau produced by a baculovirus expression system. Addition of baculovirus-expressed IFN-tau (100 ng/ml) significantly promoted development to the blastocyst stage in both culture media. Addition of E. coli expressed IFN-tau (2 microg/ml) also significantly promoted the embryonic development. Supplementation of BSA or FCS did not affect the growth-promoting effect of IFN-tau. To determine whether the growth-promoting effect of IFN-tau is related to the interferon type I receptors that bind to type I interferon such as IFN-alpha, embryos were cultured with IFN-alpha. Although IFN-alpha significantly promoted the development, a much higher concentration (25 microg/ml) was required than IFN-tau. A reverse transcription polymerase chain reaction analysis revealed the expression of mRNA encoded type-I IFN receptor subunit from morula to blastocyst stage embryos. The overall results suggest a novel function for IFNs in promoting embryonic development and the effect may be related to type-I IFN receptor expressed in the early stages of preimplantation embryos.
Optimal Control of SonoVue Microbubbles to Estimate Hydrostatic Pressure (2019)

The measurement of cardiac and aortic pressures enables diagnostic insight into cardiac contractility and stiffness. However, these pressures are currently assessed invasively using pressure catheters. It may be possible to estimate these pressures less invasively by applying microbubble ultrasound contrast agents as pressure sensors. The aim of this study was to investigate the subharmonic response of the microbubble ultrasound contrast agent SonoVue (Bracco Spa, Milan, Italy) at physiological pressures using a static pressure phantom. A commercially available cell culture cassette with Luer connections was used as a static pressure chamber. SonoVue was added to the phantom, and radio frequency data were recorded on the ULtrasound Advanced Open Platform (ULA-OP). The mean subharmonic amplitude over a 40% bandwidth was extracted at 0-200-mmHg hydrostatic pressures, across 1.7-7.0-MHz transmit frequencies and 3.5%-100% maximum scanner acoustic output. The Rayleigh-Plesset equation for single-bubble oscillations and additional hysteresis experiments were used to provide insight into the mechanisms underlying the subharmonic pressure response of SonoVue. The subharmonic amplitude of SonoVue increased with hydrostatic pressure up to 50 mmHg across all transmit frequencies and decreased thereafter. A decreasing microbubble surface tension may drive the initial increase in the subharmonic amplitude of SonoVue with hydrostatic pressure, while shell buckling and microbubble destruction may contribute to the subsequent decrease above 125-mmHg pressure. In conclusion, a practical operating regime that may be applied to estimate cardiac and aortic blood pressures from the subharmonic signal of SonoVue has been identified.
A Crowdsourced Consensus on Supratotal Resection Versus Gross Total Resection for Anatomically Distinct Primary Glioblastoma (2021)

We established a consensus definition for SpTR of glioblastoma and identified anatomically distinct locations deemed most amenable to SpTR. These results may be used to plan prospective trials investigating the potential clinical utility of SpTR for glioblastoma.
Virtual Design and Dynamical Simulation of Flexible Cables, Hoses, and Wires (2014)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Computer simulation can provide significant help to solve practical problems concerning the optimal design and the dynamical behavior of flexible cables, hoses, and wires in vehicles and on production equipment like robots.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Typical questions are the ideal cable's length, its minimal bending radius, possible collision to surrounding parts, and designed space. To solve these problems, we developed a non-linear beam model, which accounts for large global deformations of the cable. It is based on Cosserat's geometrically exact theory of rods and is able to represent extension, shearing, bending and torsion of the cable. With our innovative approach, one can optimize the cables design and their assembly positions in real time and with high accuracy. One can also consider a variety of material types and cross-sections profiles. Our implementation allows one to import CAD files and rigid body motions as well as the analysis of the local stress distribution within the cable volume.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Important questions like finding the optimal length or the ideal assembly positions can be efficiently answered. Material and the necessary physical space can be already reduced during the design process, without the need of costly tests with hardware prototypes.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;We present relevant industrial examples of applicability our approach. Finally, we introduce a dynamical viscoelastic version our model, which is suitable for fast and accurate dynamical simulation of multi-body systems (MBS).&lt;/div&gt;&lt;/div&gt;
Neurotoxicity following acute inhalation of aerosols generated during resistance spot weld-bonding of carbon steel (2014)

Welding generates complex metal aerosols, inhalation of which is linked to adverse health effects among welders. An important health concern of welding fume (WF) exposure is neurological dysfunction akin to Parkinson's disease (PD). Some applications in manufacturing industry employ a variant welding technology known as "weld-bonding" that utilizes resistance spot welding, in combination with adhesives, for metal-to-metal welding. The presence of adhesives raises additional concerns about worker exposure to potentially toxic components like Methyl Methacrylate, Bisphenol A and volatile organic compounds (VOCs). Here, we investigated the potential neurotoxicological effects of exposure to welding aerosols generated during weld-bonding. Male Sprague-Dawley rats were exposed (25 mg/m³ targeted concentration; 4 h/day × 13 days) by whole-body inhalation to filtered air or aerosols generated by either weld-bonding with sparking (high metal, low VOCs; HM) or without sparking (low metal; high VOCs; LM). Fumes generated under these conditions exhibited complex aerosols that contained both metal oxide particulates and VOCs. LM aerosols contained a greater fraction of VOCs than HM, which comprised largely metal particulates of ultrafine morphology. Short-term exposure to LM aerosols caused distinct changes in the levels of the neurotransmitters, dopamine (DA) and serotonin (5-HT), in various brain areas examined. LM aerosols also specifically decreased the mRNA expression of the olfactory marker protein (Omp) and tyrosine hydroxylase (Th) in the olfactory bulb. Consistent with the decrease in Th, LM also reduced the expression of dopamine transporter (Slc6a3; Dat), as well as, dopamine D2 receptor (Drd2) in the olfactory bulb. In contrast, HM aerosols induced the expression of Th and dopamine D5 receptor (Drd5) mRNAs, elicited neuroinflammation and blood-brain barrier-related changes in the olfactory bulb, but did not alter the expression of Omp. Our findings divulge the differential effects of LM and HM aerosols in the brain and suggest that exposure to weld-bonding aerosols can potentially elicit neurotoxicity following a short-term exposure. However, further investigations are warranted to determine if the aerosols generated by weld-bonding can contribute to persistent long-term neurological deficits and/or neurodegeneration.
Photoassociation of Sodium in a Bose-Einstein Condensate (2002)

We form ultracold Na2 molecules by single-photon photoassociation of a Bose-Einstein condensate, measuring the photoassociation rate, linewidth, and light shift of the J = 1, v = 135 vibrational level of the A1 Sigma (+)(u) molecular state. The photoassociation rate constant increases linearly with intensity, even where it is predicted that many-body effects might limit the rate. Our observations are in good agreement with a two-body theory having no free parameters.
Lead(IV) ester and electrochemical oxidations of phenolic compounds: a comparative study (1988)

Oxidation of 3-acetyl-1 -propyl-5,6,7,8-tetrahydro-2-naphthol (6) with lead(IV) acetate or lead(IV) benzoate is shown to produce almost entirely the o-quinol esters, (8) and (20), respectively. By contrast, electrochemical oxidation of (6) in acetic acid at a platinum anode leads largely to the corresponding p-quinol acetate (7) in addition to (8), and also to other products [(10) and (11)]. Structure (8) was assigned unambiguously from a two-dimensional homonuclear shift-correlated 13C spectrum obtained by using a symmetrised INADEQUATE program, and an X-ray crystal structure determination was carried out on the benzoate (20). Treatment of the o-quinol acetate (8) with acetic anhydride containing sulphuric acid leads to the diacetate (9a), whereas dissolution of the p-quinol acetate (7) in dichloromethane containing ethanolic sulphuric acid produces the phenol (12). Saponification of either (12) or (9a) gives the 2′,6′-dihydroxyacetophenone (9b), a useful precursor to proxicromil (2).
Sustainable remediation panel—Measuring the social and economic benefits of a sustainable remediation project (2010)

Abstract Remediation developed a Sustainable Remediation Panel in the Summer 2009 issue, which featured the Sustainable Remediation Forum White Paper. The panel is composed of leaders in the field of sustainable remediation who have volunteered to provide their opinions on difficult subjects related to the topic of how to integrate sustainability principles into the remediation practice. The panel's opinions are provided in a question‐and‐answer format, whereby selected experts provide an answer to a question. This issue's question is provided below, followed by opinions from five experts in the remediation field. What are the best methods of measuring the social and economic benefits of a sustainable remediation project? Are there ways to develop quantitative metrics or are qualitative metrics the best alternative for measuring the social and economic benefits of sustainable remediation? © 2010 Wiley Periodicals, Inc.
Prevalence of Hip Dysplasia and Associated Conditions in Children Treated for Infantile Scoliosis - Don’t Just Look at the Spine (2019)

Purpose: Hip dysplasia, congenital muscular torticollis, plagiocephaly and metatarsus adductus are known to be associated with one another. The etiology of infantile idiopathic scoliosis is unknown and its association with the aforementioned conditions has not been examined. This study reviews a large series of infantile scoliosis patients to address this gap. Methods: Following IRB approval, the medical records of all patients at a tertiary care hospital, which is a referral center for cast treatment of infantile scoliosis, treated with casting between 2001 and 2016 …
A Study of Native Defects in Ag-doped HgCdTe by Positron Annihilation (1997)

Native defects in undoped and Ag-doped Hg 0.78 Cd 0.22 Te were studied using positron annihilation technique. For undoped specimens, the concentration of vacancy-type defects in subsurface regions (≤500 nm) was higher than that in the bulk. This was attributed to the introduction of Hg vacancies, V Hg , resulting from the diffusion of Hg atoms out of the specimen. Before Ag doping, the major species of vacancy-type defects in the specimens ( p -type) was identified as V Hg , and the concentration of V Hg was estimated to be 6×10 15 cm -3 . After Ag doping, the concentration of vacancy-type defects was under the detection limit of positron annihilation (≤10 14 cm -3 ). This was attributed to an occupation of Ag atoms at Hg sites, and the resultant decrease in the concentration of V Hg . For the Ag-doped specimens before and after thermal treatment, no large change in the concentration of vacancy-type defects was observed. Thus, the diffusion processes of Ag atoms are unlikely to involve the interaction between Ag atoms and V Hg .