gebhart/patrepeval huggingface dataset:
Evolution of B cell analysis and Env trimer redesign (2017)

HIV-1 and its surface envelope glycoproteins (Env), gp120 and gp41, have evolved immune evasion strategies that render the elicitation of effective antibody responses to the functional Env entry unit extremely difficult. HIV-1 establishes chronic infection and stimulates vigorous immune responses in the human host; forcing selection of viral variants that escape cellular and antibody (Ab)-mediated immune pressure, yet possess contemporary fitness. Successful survival of fit variants through the gauntlet of the human immune system make this virus and these glycoproteins a formidable challenge to target by vaccination, requiring a systematic approach to Env mimetic immunogen design and evaluation of elicited responses. Here, we review key aspects of HIV-1 Env immunogenicity and immunogen re-design, based on experimental data generated by us and others over the past decade or more. We further provide rationale and details regarding the use of newly evolving tools to analyze B cell responses, including approaches to use next generation sequencing for antibody lineage tracing and B cell fate mapping. Together, these developments offer opportunities to address long-standing questions about the establishment of effective B cell immunity elicited by vaccination, not just against HIV-1.
A Competition Dialysis Assay for the Study of Structure‐Selective Ligand Binding to Nucleic Acids (2002)

Unique DNA structures represent potential targets for small molecules, and provide a promising new avenue for drug development. However, attempts to rationally design small molecules that bind selectively to a particular DNA structure have been hampered by the lack of a rapid and convenient assay for structural selectivity. Determination of structure-selective ligand binding using competition dialysis is described in this unit. The competition dialysis assay is simple, straightforward, and rapid once stock solutions of the nucleic acid structures of interest have been prepared as described.
Projection-based performance modeling for inter/intra-die variations (2005)

Large-scale process fluctuations in nano-scale IC technologies suggest applying high-order (e.g., quadratic) response surface models to capture the circuit performance variations. Fitting such models requires significantly more simulation samples and solving much larger linear equations. In this paper, we propose a novel projection-based extraction approach, PROBE, to efficiently create quadratic response surface models and capture both inter-die and intra-die variations with affordable computation cost. PROBE applies a novel projection scheme to reduce the response surface modeling cost (i.e., both the required number of samples and the linear equation size) and make the modeling problem tractable even for large problem sizes. In addition, a new implicit power iteration algorithm is developed to find the optimal projection space and solve for the unknown model coefficients. Several circuit examples from both digital and analog circuit modeling applications demonstrate that PROBE can generate accurate response surface models while achieving up to 12/spl times/ speedup compared with the traditional methods.
Type I Interferon Signals in Macrophages and Dendritic Cells Control Dengue Virus Infection: Implications for a New Mouse Model To Test Dengue Vaccines (2014)

Dengue virus infects 400 million people every year worldwide, causing 100 million clinically apparent infections, which can be fatal if untreated. Despite many years of research, there are no effective vaccine and no antiviral treatment available for dengue. Development of vaccines has been hampered in particular by the lack of a suitable small animal model. Mouse models used to test dengue vaccine are deficient in interferon (IFN) type I signaling and severely immunocompromised and therefore likely not ideal for the testing of vaccines. In this study, we explored alternative models lacking the IFN receptor only on certain cell types. We show that mice lacking the IFN receptor on either CD11c- or LysM-expressing cells (conditional IFNAR mice) are susceptible to dengue virus infection. Importantly, we demonstrate that conditional IFN receptor knockout mice generate a better immune response to live virus and a candidate dengue vaccine compared to IFNAR mice and are resistant to subsequent challenge.
Free-standing polyaniline–porous carbon nanofiber electrodes for symmetric and asymmetric supercapacitors (2014)

Polyaniline–porous carbon nanofiber composites were introduced for use as flexible, binder-less electrodes for high-performance supercapacitors.
On the Mechanism of Toluene Disproportionation in a Zeolite Environment (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn the Mechanism of Toluene Disproportionation in a Zeolite EnvironmentYusheng Xiong, Paul G. Rodewald, and Clarence D. ChangCite this: J. Am. Chem. Soc. 1995, 117, 37, 9427–9431Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/ja00142a007https://doi.org/10.1021/ja00142a007research-articleACS PublicationsRequest reuse permissionsArticle Views967Altmetric-Citations55LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Coordination chemistry of microbial iron transport compounds. 16. Isolation, characterization, and formation constants of ferric aerobactin (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoordination chemistry of microbial iron transport compounds. 16. Isolation, characterization, and formation constants of ferric aerobactinWesley R. Harris, Carl J. Carrano, and Kenneth N. RaymondCite this: J. Am. Chem. Soc. 1979, 101, 10, 2722–2727Publication Date (Print):May 1, 1979Publication History Published online1 May 2002Published inissue 1 May 1979https://pubs.acs.org/doi/10.1021/ja00504a038https://doi.org/10.1021/ja00504a038research-articleACS PublicationsRequest reuse permissionsArticle Views856Altmetric-Citations135LEARN 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
Statistical modeling: The two cultures (2001)

Abstract. There are two cultures in the use of statistical modeling to reach conclusions from data. One assumes that the data are generated bya given stochastic data model. The other uses algorithmic models and treats the data mechanism as unknown. The statistical communityhas been committed to the almost exclusive use of data models. This commitment has led to irrelevant theory, questionable conclusions, and has kept statisticians from working on a large range of interesting current problems. Algorithmic modeling, both in theoryand practice, has developed rapidlyin fields outside statistics. It can be used both on large complex data sets and as a more accurate and informative alternative to data modeling on smaller data sets. If our goal as a field is to use data to solve problems, then we need to move awayfrom exclusive dependence on data models and adopt a more diverse set of tools. 1.
Security Policy Specification Using a Graphical Approach (1998)

A security policy states the acceptable actions of an information system, as the actions bear on security. There is a pressing need for organizations to declare their security policies, even informal statements would be better than the current practice. But, formal policy statements are preferable to support (1) reasoning about policies, e.g., for consistency and completeness, (2) automated enforcement of the policy, e.g., using wrappers around legacy systems or after the fact with an intrusion detection system, and (3) other formal manipulation of policies, e.g., the composition of policies. We present LaSCO, the Language for Security Constraints on Objects, in which a policy consists of two parts: the domain (assumptions about the system) and the requirement (what is allowed assuming the domain is satisfied). Thus policies defined in LaSCO have the appearance of conditional access control statements. LaSCO policies are specified as expressions in logic and as directed graphs, giving a visual view of policy. LaSCO has a simple semantics in first order logic (which we provide), thus permitting policies we write, even for complex policies, to be very perspicuous. LaSCO has syntax to express many of the situations we have found to be useful on policies or, more interesting, the composition of policies. LaSCO has an object-oriented structure, permitting it to be useful to describe policies on the objects and methods of an application written in an object-oriented language, in addition to the traditional policies on operating system objects. A LaSCO specification can be automatically translated into executable code that checks an invocation of a program with respect to a policy. The implementation of LaSCO is in Java, and generates wrappers to check Java programs with respect to a policy.
Structural analysis of the human papillomavirus type 16-E2 transactivator with antipeptide antibodies reveals a high mobility region linking the transactivation and the DNA-binding domains (1991)

In order to probe the structure of the transcription factor encoded by the E2 Open Reading Frame of papillomaviruses, we raised polyclonal antibodies against a series of synthetic peptides that cover the HPV16-E2 protein. In gel shift experiments with the native form of the protein, we detected supershifts (caused by the binding of antibodies to the E2-DNA complex) with antibodies synthesized against peptides covering a central region 50 residues long in the E2 protein. On the contrary, antibodies raised against peptides from the NH2- and COOH-termini did not give any supershifted band. Western blot experiments showed that several of these non reacting antibodies did however interact with the denatured protein. These results suggest that the central region that connects the NH2-terminal domain responsible for transcriptional activation and the COOH-domain involved in DNA-binding is exposed and maintained in a conformation resembling the peptide, indicating a high mobility region. In contrast, the DNA-binding and transactivation domains were not recognized by the antipeptide antibodies, in line with secondary structure predictions and sequence comparisons indicating that the E2 protein consists of structured and conserved NH2 and COOH-terminal regions separated by a non-conserved and unstructured region. This flexible 'hinge' region may facilitate contacts between E2 dimers at distance in mechanisms of transcriptional activation steps that involve homosynergy or DNA-looping.
Injury in vascular surgery--the intimal hyperplastic response. (2001)

Intimal hyperplasia is extensively studied in order to improve arterial reconstruction outcome. The mechanisms leading to stenosis or restenosis may vary according to the technique used for arterial reconstruction. Lesions are mostly made of an accumulation of smooth muscle cells and fibroblasts, with only sparse inflammatory cells. The accumulated material reduces the graft lumen and ultimately induces thrombosis. Intimal hyperplasia with smooth muscle cell and matrix accumulation is the prominent feature in all these situations with evidences of intense cell proliferation and cell death. The purpose of this review is to present the biology of intimal hyperplastic response based on the recently published data. Experiments in the rabbits have shown that the vein wall thickening is mainly regulated by the tangential wall stress which is applied transversely to the vein wall as a blood pressure. Experiments in the rat carotid artery balloon injury suggested that heparin could be used as a treatment to prevent intimal hyperplasia. Treatments for preventing restenosis after angioplasty or stenoses development in bypasses have been disappointing clinical evaluation suffers from insufficient prospective randomized studies. Intimal hyperplasia is the major cause of failure after arterial reconstruction. The biology of intimal hyperplasia is complex, and treatment disappointing. Some types of hyperplasia may need to be preserved in order to prevent functional atrophy and aneurysmal dilatation of vein grafts.
National Epidemiology of Mycoses Survey (NEMIS): Variations in Rates of Bloodstream Infections Due to Candida Species in Seven Surgical Intensive Care Units and Six Neonatal Intensive Care Units (1999)

Candida species are the fourth most frequent cause of nosocomial bloodstream infections, and 25%-50% occur in critical care units. During an 18-month prospective study period, all patients admitted for > or = 72 hours to the surgical (SICUs) or neonatal intensive care units (NICUs) at each of the participant institutions were followed daily. Among 4,276 patients admitted to the seven SICUs in six centers, there were 42 nosocomial bloodstream infections due to Candida species (9.8/1,000 admissions; 0.99/1,000 patient-days). Of 2,847 babies admitted to the six NICUs, 35 acquired a nosocomial bloodstream infection due to Candida species (12.3/1,000 admissions; 0.64/1,000 patient-days). The following were the most commonly isolated Candida species causing bloodstream infections in the SICU: Candida albicans, 48%; Candida glabrata, 24%; Candida tropicalis, 19%; Candida parapsilosis, 7%; Candida species not otherwise specified, 2%. In the NICU the distribution was as follows: C. albicans, 63%; C. glabrata, 6%; C. parapsilosis, 29%; other, 3%. Of the patients, 30%-50% developed incidental stool colonization, 23% of SICU patients developed incidental urine colonization, and one-third of SICU health care workers' hands were positive for Candida species.
Application of SketchUp in Coke Oven Three-Dimensional Digital Modeling (2013)

Coke oven, which is a large industrial furnace, is complex in structure. A two-dimensional structure diagram can hardly help one observe the inner structure of a coke oven or master its working principle comprehensively. In order to solve this problem, a complete 3D digital model of a coke oven is generated by assembling the three-dimensional models of coke oven components created with SketchUp. It enables users to section the various components of the cove oven. The outer appearance and inner structure of the oven components also can be displayed visually from several different orientations. Moreover, it is convenient to storage and carry, operation easily and fast. It can be displayed on an ordinary computer and occupies no space at the laboratory. Meanwhile, a large sum of money that used for purchasing a physical coke oven model can be saved.
Maximum Likelihood Estimation for Sample Surveys (2012)

Sample surveys provide data used by researchers in a large range of disciplines to analyze important relationships using well-established and widely used likelihood methods. The methods used to select samples often result in the sample differing in important ways from the target population and standard application of likelihood methods can lead to
Agronomic and silage quality traits of winter cereals (1996)

Agronomic and silage quality traits were examined for 12 winter cereals harvested at two stages of maturity. Forage dry matter (DM) yields were higher at the mid-dough than the early-heading stage. Post 90 barley had the highest whole-plant DM yield at the early-heading stage, and Presto triticale had the highest yield at the mid-dough stage. Newton wheat had the lowest whole-plant DM yield at both stages of maturity. The first cutting of all varieties originally was intended to be at the late-boot stage, but harvest was delayed by frequent rainfall and wet soils in May, and field-wilting conditions were less than ideal. The range in heads emerge d was 23 to 87%, and the range in the silage DM content at early-heading stage was 19.2 to 46.4%. Both crude protein (CP) and ash contents were higher for the early-heading cereals than the mid-dough. All 24 silages were of relatively low forage quality, as evidenced by high neutral detergent fiber (NDF) and acid detergent fiber (ADF) percentages. Only five silages, the early-heading stage Tomahawk wheat; mid-dough stage Presto triticale; and the mid-dough stage Kanby, Post, and Post 90 barleys, had less than 60% NDF and 40% ADF. Extensive lodging occurred in virtually all cereals before the mid-dough stage harvest.
(<i>R</i><sub>p</sub>)‐ and (<i>S</i><sub>p</sub>)‐8‐piperidino‐adenosine 3′,5′‐(cyclic)thiophosphates discriminate completely between site A and B of the regulatory subunits of cAMP‐dependent protein kinase type I and II (1994)

8-Piperidino-cAMP has been shown to bind with high affinity to site A of the regulatory subunit of cAMP-dependent protein kinase type I (AI) whereas it is partially excluded from the homologous site (AII) of isozyme II [Ogreid, D., Ekanger, R., Suva, R. H., Miller, J. P., and Døskeland, S. O. (1989), Eur. J. Biochem. 181, 19-31]. To further increase this selectivity, the (Rp)- and (Sp)-diastereoisomers of 8-piperidino-cAMP[S] were synthesized and analyzed for their potency to inhibit binding of [3H]cAMP to site A and site B from type I (rabbit skeletal muscle) and type II (bovine myocardium) cAMP-dependent protein kinases. (Sp)-8-Piperidino-cAMP[S] showed an enhanced relative affinity for site AI, thus being by far the best A-selective compound (more than 100-fold) tested for this isozyme. In contrast, the (Rp)-isomer was less selective for AI than 8-Piperidino-cAMP itself. The reduction in affinities for BII, compared to 8-piperidino-cAMP, were 10-fold and 50-fold for the (Sp)- and (Rp)-isomer, respectively. Both isomers were almost completely excluded from AII, with affinities about 1000-fold lower than 8-piperidino-cAMP itself. The (Rp)-isomer selected BII with an affinity about 10,000 times higher than for AII, whereas the (Sp)-isomer showed a preference of about 70,000-fold in favour of BII. 8-Piperidino-cAMP as well as its (Sp)-isomer activated both types of holoenzyme protein kinases whereas the (Rp)-isomer acted as an antagonist of cAMP-induced activation. The study concludes that the combination of piperidino- and exocyclic sulfur substitutions generate cAMP analogs that completely discriminate between site A and B of cAMP-dependent protein kinases.
Characterization of trapping states in polycrystalline-silicon thin film transistors by deep level transient spectroscopy (1993)

Polycrystalline-silicon (poly-Si) thin film transistors (TFTs) have been assessed using deep level transient spectroscopy (DLTS) based on the measurement of current transients due to the thermal emission of carriers trapped at deep levels in the poly-Si. Measurements were made on fully hydrogenated TFTs and the DLTS signal was found to vary continuously between 77 K and room temperature, without showing the characteristic peaks normally associated with point defects in single crystal Si. This demonstrates the existence of a continuous distribution of states through the band gap rather than discrete monoenergetic states. Analysis of the DLTS signal suggests the density of states increases rapidly toward the conduction band edge indicating the presence of a relatively high density of tail states. After annealing the TFTs at 450 °C the current DLTS signal was found to increase due to an increase in trap state density, which occurs because Si–H bonds are thermally unstable at this temperature. The increase in signal was over the whole temperature range of the measurement showing that hydrogen passivates states up to at least 0.1 eV below the conduction band as well as states nearer mid-gap. The effects of varying the fill voltage on the measurement and the time dependence of the current transient were also investigated and added weight to arguments that the current transient was due to the thermal emission of carriers trapped at deep levels.
Capacitance driven clock mesh synthesis to minimize skew and power dissipation (2013)

Tree driven mesh is gaining popularity as a viable method to distribute clock with minimum skew in Deep Sub Micron (DSM) technology. In the design of the leaf level mesh, the density of the mesh at various parts of the chip is a crucial factor which decides the clock skew and power dissipated in the mesh. We propose a capacitance driven mesh formation methodology which forms a minimum wire length, non-uniform mesh when compared to the traditional skew-driven mesh. After connecting the sinks to the mesh by a combination of Steiner tree and stubs, appropriately sized buffers are placed at optimal locations such that skew and power dissipation are minimized. When our algorithms were tested on ISPD2010 benchmarks, the power dissipated in the mesh was found to be 25% lesser and the skew was 32% to 45% lesser than the skew driven mesh.
Antimalarials. 3. 1,2,4-Triazines (1976)

The syntheses of a number of substituted 1,2,4-triazines as potential antimalarials are described. The structural requirements for antimalarial activity are discussed with reference to the substituents of a phenyl group in the 6 position and amino groups at the 3 and 5 positions. Of the compounds tested, 2,5, and 7 produced cures in mice infected with plasmodium berghei. Compounds 2(3,5-diamino-6-(4-trifluoromethylphenyl)-1,2,4-triazine),3,5,8,12,and 37 produced cures in chicks infected with Plasmodium gallinaceum.
Planar artificial magnetic conductors and patch antennas (2003)

Surfaces act as perfect magnetic conductors (PMC) if the phase shift of the reflection of an electromagnetic wave amounts to 180/spl deg/ compared to the reflection at a perfect electric conductor (PEC). One possibility to create PMC surfaces artificially is an array of closely spaced patches. In this paper, based on the relation between PMC surfaces and patch antennas, an explanation for the functioning of this artificial PMC is given. An equivalent network is derived that allows to understand the functioning and to provide a starting design for a numerical optimization by aid of fullwave methods. A planar PMC is used for the first time as a reflector for a large aperture coupled patch antenna array, especially in order to reduce the parallel-plate modes that are usually present in traditional aperture coupled patch arrays. An additional sidelobe suppression of over 6 dB has been achieved by the planar PMC reflector in comparison to a traditional reflector.