gebhart/patrepeval huggingface dataset:
<i>HLA-Cw*04</i> and Hepatitis C Virus Persistence (2002)

In studies of acute hepatitis C virus (HCV) infection, the early host immune response is one of the determinants of viral persistence. The class I human leukocyte antigens (HLA), which present foreign antigen to cytolytic T cells, are integral components of this response. We hypothesized that the highly polymorphic HLA genes affect the outcome of an HCV infection. To test this hypothesis, we molecularly typed 231 persons with well-documented clearance of an HCV infection and 444 matched persistently infected persons. HLA-A*1101 (odds ratio [OR], 0.49; 95% confidence interval [95% CI], 0.27 to 0.89), HLA-B*57 (OR, 0.62; 95% CI, 0.39 to 1.00), and HLA-Cw*0102 (OR, 0.43; 95% CI, 0.21 to 0.89) were associated with viral clearance, whereas HLA-A*2301 (OR, 1.78; 95% CI, 1.01 to 3.11) and HLA-Cw*04 (OR, 1.78; 95% CI, 1.21 to 2.59) were associated with viral persistence. HLA-Cw*04 is in strong linkage disequilibrium with HLA-B*53 and HLA-B*35, but only HLA-B*53 (OR, 1.70; 95% CI, 0.95 to 3.06) and the Cw*04-B*53 haplotype (OR, 1.76; 95% CI, 0.94 to 3.26) were weakly associated with viral persistence. HLA-B*53 has similar, but not necessarily identical, binding specificity to some HLA-B*35 subtypes (B*35-Px group). The association with the B*35-Px group was less strong than with HLA-B*53 alone. The association of HLA-Cw*04 with HCV persistence was codominant (two copies of the gene were more strongly associated with persistence than one copy). However, HLA-Cw*04 was not associated with HCV RNA levels among the persistently infected individuals. Since Cw*04 is a ligand for the killer immunoglobulin-like receptors on natural killer cells, these cells may be involved in recovery from HCV infection. Further investigation is needed to understand the relationship between class I alleles and HCV clearance.
Novel Instrument for Parallel Superposition Measurements (2008)

A set up consisting of a rotational rheometer and a mechanical oscillator is presented which is able to perform rheological measurements by parallel superposition measurements of a macroscopic shear rate and a very small oscillation. The basic model equations are shown and first measurements with Newtonian fluids are presented. The oscillation makes use of small amplitudes (<100 nm) which allows a practically interference‐free measurement. This set up makes it possible to measure the viscosity from zero constant shear rate to the usually used constant shear rates.
A new polyoxo–alkoxo titanium cluster of the Keggin family: synthesis and characterization by X-ray diffraction and NMR spectroscopy (1999)

Rotatable 3-D crystal structure diagram of compound 1 XYZ (7K) Crystal structure data TXT (51K) 13C NMR spectrum of compound 1 DOC (43K) 17O NMR spectrum of compound 1 DOC (49K) 1H NMR spectrum of compound 1 DOC (37K)
Resonance Raman deenhancement caused by excited-state potential surface crossing (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTResonance Raman deenhancement caused by excited-state potential surface crossingChristian Reber and Jeffrey I. ZinkCite this: J. Phys. Chem. 1992, 96, 2, 571–576Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/j100181a015https://doi.org/10.1021/j100181a015research-articleACS PublicationsRequest reuse permissionsArticle Views108Altmetric-Citations36LEARN 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 Get e-Alerts
Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structureThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process. (2011)

Genetic information in eukaryotes is managed by strategic hierarchical organization of chromatin structure. Primary chromatin structure describes an unfolded nucleosomal array, often referred to as "beads on a string". Chromatin is compacted by the nonlinear rearrangement of nucleosomes to form stable secondary chromatin structures. Chromatin conformational transitions between primary and secondary structures are mediated by both nucleosome-stacking interactions and the intervening linker DNA. Chromatin model system studies find that the topography of secondary structures is sensitive to the spacing of nucleosomes within an array. Understanding the relationship between nucleosome spacing and higher order chromatin structure will likely yield important insights into the dynamic nature of secondary chromatin structure as it occurs in vivo. Genome-wide nucleosome mapping studies find the distance between nucleosomes varies, and regions of uniformly spaced nucleosomes are often interrupted by regions of nonuniform spacing. This type of organization is found at a subset of actively transcribed genes in which a nucleosome-depleted region near the transcription start site is directly adjacent to uniformly spaced nucleosomes in the coding region. Here, we evaluate secondary chromatin structure and discuss the structural and functional implications of variable nucleosome distributions in different organisms and at gene regulatory junctions.
RETRACTED: Identification and characterization of GRIM-1, a cell-death-associated gene product (2010)

Using a genome-wide technical knockout, we isolated a newly identified set of GRIM (genes associated with retinoid-interferon-induced mortality) genes; GRIM genes mediate IFN- and retinoic-acid (RA)-induced cell death. Here, we describe the isolation and characterization of one such gene, GRIM-1. Three proteins, with identical C-termini, were produced from the GRIM-1 open reading frame when this gene was transcribed and translated in vitro. These protein isoforms, designated GRIM-1alpha, GRIM-1beta and GRIM-1gamma, differentially suppressed growth via apoptosis in various cell lines. We also show that a caspase-dependent mechanism generates the proapoptotic GRIM-1 isoforms. Lastly, GRIM-1 isoforms differentially blocked maturation of 18S ribosomal RNA, consistent with their respective growth-suppressive ability. Together, these studies identified a novel protein involved in growth suppression and cell death.
Does the microenvironment influence the cell types of origin for prostate cancer? (2013)

Despite several recent studies addressing the cells of origin for prostate cancer, there is still considerable discussion in the field regarding the most relevant target populations for transformation. Tissue regeneration studies have pointed to a basal cell origin for mouse and human prostate cancer. In contrast, genetically engineered mouse models demonstrate that cells within both the basal and luminal layers can initiate murine prostate cancer. Based on differences between these two approaches, we propose that further work should address the requirement for microenvironmental components such as immune or mesenchymal cells on epithelial cell types of origin for prostate cancer.
Growth Hormone Deficiency in Autoimmune Polyglandular Syndrome (1997)

We describe a boy with autoimmune adrenal failure and compensated hypothyroidism, associated with isolated growth hormone deficiency (GHD). We suggest an autoimmune mechanism as the underlying etiology for the GHD in this case.
Self-localizing smart camera networks (2012)

This article describes a novel approach to localizing networks of embedded cameras and sensors. In this scheme, the cameras and the sensors are equipped with controllable light sources (either visible or infrared), which are used for signaling. Each camera node can then determine automatically the bearing to all of the nodes that are visible from its vantage point. By fusing these measurements with the measurements obtained from onboard accelerometers, the camera nodes are able to determine the relative positions and orientations of other nodes in the network. The method uses angular measurements derived from images, rather than range measurements derived from time-of-flight or signal attenuation. The scheme can be implemented relatively easily with commonly available components, and it scales well since the localization calculations exploit the sparse structure of the system of measurements. Additionally, the method provides estimates of camera orientation which cannot be determined solely from range measurements. The localization technology could serve as a basic capability on which higher-level applications could be built. The method could also be used to automatically survey the locations of sensors of interest, to implement distributed surveillance systems, or to analyze the structure of a scene, based on images obtained from multiple registered vantage points. It also provides a mechanism for integrating the imagery obtained from the cameras with the measurements obtained from distributed sensors.
Electrochemical Double-Layer Capacitors Using Carbon Nanotube Electrode Structures These capacitors can store large amounts of energy and deliver very high peak power; they are used in electric vehicles and may have applications in linear motor drives. (2009)

The structure and behavior of the electrical double-layer capacitor (EDLC) are described. The use of activated carbon electrodes is discussed and the limitations on voltage and accessible surface area are presented. Metrics for evaluating EDLC performance are defined and previously reported results of experimental carbon nanotube (CNT) electrodes are tabulated. New experimental results of electro- des constructed of vertically aligned CNTs grown on a conduct- ing substrate are presented. By extrapolating prior and new experimental data the energy density of CNT-based EDLCs is shown to be potentially up to seven times that of commercial activated carbon-based EDLCs.
Colloid-roughened surfaces as templates for the heterogeneous nucleation of lepidocrocite γ-FeO(OH) nanoparticles (1998)

Lepidocrocite γ-FeO(OH) crystals can be specifically nucleated by sulfonate-terminated SAM/gold surfaces from solutions at room temperature; previously ‘roughening’ the gold surface through the tethering of gold colloids increases yields.
The Wyss institute: A new model for medical technology innovation and translation across the academic‐industrial interface (2017)

The Wyss Institute for Biologically Inspired Engineering at Harvard University was formed based on the recognition that breakthrough discoveries cannot change the world if they never leave the laboratory. The Institute's mission is to discover the biological principles that Nature uses to build living things, and to harness these insights to create biologically inspired engineering innovations to advance human health and create a more sustainable world. Since its launch in 2009, the Institute has developed a new model for innovation, collaboration, and technology translation within academia, breaking "silos" to enable collaborations that cross institutional and disciplinary barriers. Institute faculty and staff engage in high-risk research that leads to transformative breakthroughs. The biological principles uncovered are harnessed to develop new engineering solutions for medicine and healthcare, as well as nonmedical areas, such as energy, architecture, robotics, and manufacturing. These technologies are translated into commercial products and therapies through collaborations with clinical investigators, corporate alliances, and the formation of new start-ups that are driven by a unique internal business development team including entrepreneurs-in-residence with domain-specific expertise. Here, we describe this novel organizational model that the Institute has developed to change the paradigm of how fundamental discovery, medical technology innovation, and commercial translation are carried out at the academic-industrial interface.
Fiber interferometer for hybrid optical and optoacoustic intravital microscopy (2017)

The addition of optoacoustic sensing to optical microscopy may supplement fluorescence contrast with label-free measurements of optical absorption, enhancing biological observation. However, the physical dimensions of many optoacoustic systems have restricted the implementation of hybrid optical and optoacoustic (O2A) microscopy to imaging thin samples in transmission mode or to ex-vivo investigations. Here we describe a miniaturized optoacoustic sensor, based on a
Lumbar spine posterior corner detection in X-rays using Haar-based features (2016)

3D reconstruction of the spine using biplanar X-rays remains approximate and sometimes requires human-machine interactions to adjust the position of important features such as vertebral corners and endplates. The purpose of this study is to develop a method to extract automatically the accurate position of lumbar vertebrae posterior corners. In the proposed method we select corner point candidates from an initial edge map. A dedicated pipeline is designed to discard unwanted candidates, involving polyline simplification, curvature thresholding and multiscale Haar filtering. Ultimately, we use a priori knowledge derived from an initial 3D spine model to define search areas and select the final corner points. The framework was tested on 21 biplanar X-rays from scoliotic children. Corner positions are compared with manual selections by two experts. The results report a localization accuracy between 0.6 mm and 1.4 mm, comparable to manual expert variability.
Just-in-time data integration in action (2010)

Today's data integration systems must be flexible enough to support the typical iterative and incremental process of integration, and may need to scale to hundreds of data sources. In this work we present a novel data integration system that offers great flexibility and scalability. Our approach to data integration is unique in that it executes mapping rules at query runtime using annotations. On top, we have built the People People People application. It allows users to search for people, display information about people, and browse through a network of related people, where the data is integrated from local and remote data sources. The demo presents all features of our underlying data integration engine through a set of motivating scenarios.
Rapid assessment of induced cytochrome P4501 a protein and catalytic activity in fish hepatoma cells grown in multiwell plates: Response to TCDD, TCDF, and two planar PCBS (1996)

Abstract Induction of cytochrome P4501A1 (CYP1A1) in cultured cells can be used to determine taxon-specific relative potencies of Ah receptor agonists. This report describes optimized methods for growth and treatment of PLHC-1 fish hepatoma cells in multiwell plates, in situ analysis of ethoxyresorufin O -deethylase (EROD) activity, and measurement of CYP1A protein by immunoblotting of cell lysates. EROD activity was undetectable (&amp;lt;1 pmol min−1 mg−1) in untreated or dimethyl sulfoxide-treated cells, but was highly induced (up to 150 pmol min−1 mg−1) in cells exposed to Ah receptor agonists such as 2,3,7,8–tetrachlorodibenzo-p-dioxin (TCDD), 2,3,7,8–tetrachlorodibenzofuran (TCDF), or planar chlorobiphenyls (CB). Addition of exogenous NADPH was not required for measurement of EROD activity in PLHC-1 cells. As inducers of EROD activity, TCDD, TCDF, 3,3′,4,4′,5– pentachlorobiphenyl (CB-126), and 3,3′,4,4′-tetrachlorobiphenyl (CB-77) differed both in potency and in apparent efficacy (maximal level of induced activity). In each case, EROD induction was biphasic, with stronger induction at lower concentrations and an attenuated response at higher concentrations. In contrast, the content of immunodetectable CYP1A protein increased monotonically with dose of CB, and the maximum level achieved was similar for all inducers. The discrepancy in results obtained for EROD activity versus CYP1A protein may result from inhibition or inactivation of catalytic function at high concentrations of inducer. By reducing peak EROD values, this inhibition leads to lower apparent EC50 values and thus the overestimation of relative potencies or toxic equivalency factors (TEFs) for many inducers. These studies demonstrate the necessity of measuring both EROD activity and immunodetectable CYP1A protein for the accurate assessment of CYP1A induction and relative potencies in cultured cells.
&lt;title&gt;Precision of the petrochemical process analysis using NIR spectroscopy&lt;/title&gt; (1992)

Quantitation of benzene in gasoline is becoming important due to new federal and state regulations. To meet these regulations an on-line analysis method for benzene in gasoline is needed. It has been shown that NIR is an ideal instrument for on-line analytical measurements. We report in this paper an analysis of benzene in synthetic gasoline with a standard error of prediction of 0.22 wt%. Both principal component analysis and partial least squares chemometric calibration methods were used. Both methods gave the same results for the prediction of the validation sample set.
Cathode Electrolyte Interphase Formation and Electrolyte Oxidation Mechanism for Ni-Rich Cathode Materials (2020)

Herein, we investigate the formation of a cathode electrolyte interphase (CEI) by electrolyte oxidation on a LiNixM1–xO2 (x > 0.5; M, transition metal) layered oxide (Ni-rich) cathode and compare this phenomenon with a Li-rich layered oxide (Li-rich) cathode. Our investigations focused on two electrochemical properties, the potential and kinetics of electrolyte oxidation, studied using hard X-ray photoelectron spectroscopy (HAXPES), soft X-ray absorption spectroscopy, and density functional theory calculations. HAXPES revealed that a thicker CEI formed on the Ni-rich cathode compared to that on the Li-rich cathode, despite the operation potential of the Ni-rich cathode being lower than that of the Li-rich cathode. Thus, the Ni-rich cathode induces the CEI formation through active oxidation of the electrolyte during charge–discharge cycles. The electronic state of the Ni-rich cathode indicates that the antibonding hybrid orbital of the transition metal 3d–O 2p corresponds to the lowest unoccupied molecular orbital energy level, that is, the hole, and lies near the highest occupied molecular orbital energy level of the electrolyte. In addition, the hole concentration in the charged state was found to be significantly increased, in comparison to other active materials, which promotes oxidization of the electrolyte.
The <b>β</b>‐<i>N</i>‐acetylglucosaminidases NAG1 and NAG2 are essential for growth of <i>Trichoderma atroviride</i> on chitin (2009)

The chitinolytic enzyme machinery of fungi consists of chitinases and beta-N-acetylglucosaminidases. These enzymes are important during the fungal life cycle for degradation of exogenous chitin, which is the second most abundant biopolymer, as well as fungal cell-wall remodelling. In addition, involvement of chitinolytic enzymes in the lysis of the host cell wall in mycoparasitic Trichoderma spp. has been reported. In view of the fact that fungi have on average 15-20 chitinases, but only two beta-N-acetylglucosaminidases, the question arises how important the latter enzymes actually are for various aspects of chitin degradation. In this study, the role of two beta-N-acetylglucosaminidases, NAG1 and NAG2, was analysed in the mycoparasitic fungus Trichoderma atroviride. No beta-N-acetylglucosaminidase activity was detected in T. atrovirideDeltanag1Deltanag2 strains, suggesting that NAG1 and NAG2 are the only enzymes in T. atroviride that possess this activity. Deltanag1Deltanag2 strains were not able to grow on chitin and chitobiose, but the presence of either NAG1 or NAG2 was sufficient to restore growth on chitinous carbon sources in solid media. Our results demonstrated that T. atroviride cannot metabolize chitobiose but only the monomer N-acetylglucosamine, and that N-acetylglucosaminidases are therefore essential for the use of chitin as a nutrient source. NAG1 is predominantly secreted into the medium, whereas NAG2 mainly remains attached to the cell wall. No physiological changes or reduction of the mycoparasitic potential of T. atroviride was detected in the double knockout strains, suggesting that the use of chitin as carbon source is only of minor importance for these processes.
Impact of Antimicrobial Dosing Regimen on Evolution of Drug Resistance In Vivo: Fluconazole and<i>Candida albicans</i> (2006)

Numerous factors have been theorized to affect the development of antimicrobial resistance, including those specific to the host, the organism, the environment, the drug, and the drug prescriber. One variable under the control of the prescriber is the drug dosing regimen. Dosing regimens can vary in dose level, dosing interval, and treatment duration. The current studies examined the relationships between antimicrobial dosing regimens and resistance development by use of an in vivo model. A murine model of systemic Candida albicans infection was used to examine resistance emergence during exposure to the triazole antifungal fluconazole. Data from this experimental model demonstrated that the more frequently administered dosing prevented selection of the isogenic resistant cell populations. Conversely, dosing regimens producing prolonged sub-MIC effects appeared to contribute to the outgrowth of isogenic resistant strains. The association between dosing and resistance emergence observed in the current investigation is disparate from that described for antimicrobial compounds with cidal killing characteristics. The inhibitory or static antimicrobial activity of the triazole compounds may explain these differences.
Nymble: Blocking Misbehaving Users in Anonymizing Networks (2009)

Anonymizing networks such as Tor allow users to access Internet services privately by using a series of routers to hide the client's IP address from the server. The success of such networks, however, has been limited by users employing this anonymity for abusive purposes such as defacing popular Web sites. Web site administrators routinely rely on IP-address blocking for disabling access to misbehaving users, but blocking IP addresses is not practical if the abuser routes through an anonymizing network. As a result, administrators block all known exit nodes of anonymizing networks, denying anonymous access to misbehaving and behaving users alike. To address this problem, we present Nymble, a system in which servers can “blacklist” misbehaving users, thereby blocking users without compromising their anonymity. Our system is thus agnostic to different servers' definitions of misbehavior-servers can blacklist users for whatever reason, and the privacy of blacklisted users is maintained.