gebhart/patrepeval huggingface dataset:
The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines (2022)

The emergence of several new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in recent months has raised concerns around the potential impact on ongoing vaccination programs. Data from clinical trials and real-world evidence suggest that current vaccines remain highly effective against the alpha variant (B.1.1.7), while some vaccines have reduced efficacy and effectiveness against symptomatic disease caused by the beta variant (B.1.351) and the delta variant (B.1.617.2); however, effectiveness against severe disease and hospitalization caused by delta remains high. Although data on the effectiveness of the primary regimen against omicron (B.1.1.529) are limited, booster programs using mRNA vaccines have been shown to restore protection against infection and symptomatic disease (regardless of the vaccine used for the primary regimen) and maintain high effectiveness against hospitalization. However, effectiveness against infection and symptomatic disease wanes with time after the booster dose. Studies have demonstrated reductions of varying magnitude in neutralizing activity of vaccine-elicited antibodies against a range of SARS-CoV-2 variants, with the omicron variant in particular exhibiting partial immune escape. However, evidence suggests that T-cell responses are preserved across vaccine platforms, regardless of variant of concern. Nevertheless, various mitigation strategies are under investigation to address the potential for reduced efficacy or effectiveness against current and future SARS-CoV-2 variants, including modification of vaccines for certain variants (including omicron), multivalent vaccine formulations, and different delivery mechanisms.
Effect of N-phenyl-N′-(4-pyridyl)urea on shoot formation in tobacco pith disk and callus cultured in vitro (1976)

N-Phenyl-N′-(4-pyridyl)urea (4PU), which was originally synthesized by Bruce et al. and also reported by Okamoto as a highly active cytokinin in the tobacco pith callus bioassay, showed a marked effect on shoot formation in tobacco pith disk and callus with a single application. Details of experiments and results are reported and the interrelation between auxin and 4PU for organ formation is discussed.
Automated image analysis for high‐throughput quantitative detection of ER and PR expression levels in large‐scale clinical studies: The TEAM Trial Experience (2009)

Semiautomated image analysis is appropriate for the analysis of tissue biomarkers within large clinical trials. These data provide support for the use of TMAs and image analysis in translational research.
Building Next-Generation AI systems: Co-Optimization of Algorithms, Architectures, and Nanoscale Memristive Devices (2019)

Computing systems inspired by the architecture of the human brain is poised to revolutionize the engines for information processing and data analytics. However, the efficiency and performance of these platforms pale in comparison with the human brain, especially when benchmarked in terms of metrics such as intelligence per Watt per square mm. In this paper, we review some recent progress and future prospects of building artificial intelligence systems that target the efficiency of the brain, leveraging the unique properties of nanoscale memristive device technologies.
The theory of diversity and redundancy in information system security : LDRD final report. (2010)

The goal of this research was to explore first principles associated with mixing of diverse implementations in a redundant fashion to increase the security and/or reliability of information systems. Inspired by basic results in computer science on the undecidable behavior of programs and by previous work on fault tolerance in hardware and software, we have investigated the problem and solution space for addressing potentially unknown and unknowable vulnerabilities via ensembles of implementations. We have obtained theoretical results on the degree of security and reliability benefits from particular diverse system designs, and mapped promising approaches for generating and measuring diversity. We have also empirically studied some vulnerabilities in common implementations of the Linux operating system and demonstrated the potential for diversity to mitigate these vulnerabilities. Our results provide foundational insights for further research on diversity and redundancy approaches for information systems.
A Survey of Control Mechanisms for Creative Pattern Generation (2021)

Abstract We review recent methods in 2D creative pattern generation and their control mechanisms, focusing on procedural methods. The review is motivated by an artist's perspective and investigates interactive pattern generation as a complex design problem. While the repetitive nature of patterns is well‐suited to algorithmic creation and automation, an artist needs more flexible control mechanisms for adaptable and inventive designs. We organize the state of the art around pattern design features, such as repetition, frames, curves, directionality, and single visual accents. Within those areas, we summarize and discuss the techniques' control mechanisms for enabling artist intent. The discussion includes questions of how input is given by the artist, what type of content the artist inputs, where the input affects the canvas spatially, and when input can be given in the timeline of the creation process. We categorize the available control mechanisms on an algorithmic level and categorize their input modes based on exemplars, parameterization, handling, filling, guiding, and placing interactions. To better understand the potential of the current techniques for creative design and to make such an investigation more manageable, we motivate our discussion with how navigation, transparency, variation, and stimulation enable creativity. We conclude our review by identifying possible new directions that can inspire innovation for artist‐centered creation processes and algorithms.
Adaptation to Spatial Offsets (1995)

After prolonged viewing of a three-element target in which the middle element is spatially offset, subsequent viewing of the same three elements in alignment results in the middle element appearing to be offset in the opposite direction. This adaptational aftereffect to a spatial offset was investigated with elements which were spatial-frequency narrowband and equidetectable to ascertain (a) the properties of the mechanisms involved and (b) the nature of the underlying computation. Evidence is presented in favour of an orientational-grouping, rather than a purely positional computation, underlying this aftereffect. A dual site of adaptation is proposed: one which receives input from the orientation extracted from the output of linear filters, and another which receives input from the orientation derived from grouping processes working on the contrast-energy representation. These may correspond to the mechanisms which are thought to underlie the processing of real and subjective contours.
Influence of Ligand Substitution on Excited State Structural Dynamics in Cu(I) Bisphenanthroline Complexes (2010)

This study explores the influences of steric hindrance and excited state solvent ligation on the excited state dynamics of Cu(I) diimine complexes. Ultrafast excited state dynamics of Cu(I)bis(3,8-di(ethynyltrityl)-1,10-phenanthroline) [Cu(I)(detp)(2)](+) are measured using femtosecond transient absorption spectroscopy. The steady state electronic absorption spectra and measured lifetimes are compared to those of Cu(I)bis(1,10-phenanthroline), [Cu(I)(phen)(2)](+), and Cu(I)bis(2-9-dimethyl-1,10-phenanthroline), [Cu(I)(dmp)(2)](+), model complexes to determine the influence of different substitution patterns of the phenanthroline ligand on the structural dynamics associated with the metal to ligand charge transfer excited states. Similarities between the [Cu(I)(detp)(2)](+) and [Cu(I)(phen)(2)](+) excited state lifetimes were observed in both coordinating and noncoordinating solvents and attributed to the lack of steric hindrance from substitution at the 2- and 9-positions. The solution-phase X-ray absorption spectra of [Cu(I)(detp)(2)](+), [Cu(I)(phen)(2)](+), and [Cu(I)(dmp)(2)](+) are reported along with finite difference method calculations that are used to determine the degree of ground state dihedral angle distortion in solution and to account for the pre-edge features observed in the XANES region.
Capacity limits of information transmission in optically-routed fiber networks (2010)

Optical networks are the backbone of our information society, and the single-mode optical fiber is its transmission medium. The “fiber channel” differs in many ways from other commonly encountered communication channels such as wireless and satellite channels. The most crucial difference is the presence of a nonlinear phenomenon in the fiber, the optical Kerr effect. Optimally managing the Kerr nonlinearity is currently viewed as central to determining the capacity limit of modern optically-routed networks. We present here a conservative estimate of the fiber channel capacity using reverse signal propagation in a band limited optical path of an optically-routed network. This study fully accounts for all instantaneous fiber Kerr nonlinearity's effects on both signal and noise. We predict capacity per unit of bandwidth (or spectral efficiency) well above current record experimental demonstrations. é 2010 Alcatel-Lucent.
Paradigms for Sale: Information systems in the process of radical change (1997)

The four paradigms by Burrell and Morgan (1976) and their interpretations within Information Systems Research are critically analysed. The dominant interpretation by Hirschheim and Klein (1992) is challenged by the construction of an alternative interpretation. The tension between the alternatives gives rise to a discussion of the paradigms and their relevance, need and usefulness.
Synthesis of microporous gallosilicates with the CGS topology (1999)

Zeolite TNU-1 (Taejon National University Number 1), a gallosilicate possesing the CGS topology with a three dimensional system of medium and small pores, crystallises in the presence of Ga in conditions in which the presence of Al yields merlinoite-type zeolites.
ChemInform Abstract: Preparation of Enantiomerically Pure 9‐Azabicyclo(3,3,1)nonene Derivatives. Stereochemical Requirements of Vinyl‐ and Allylsilanes in Iminium Ion Initiated Cyclization. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fabrication of TiO2Grating with Composites of Azobenzene Polymer and TiO2Nanoparticles (2007)

We have used the formation of surface relief gratings (SRG) on azobenzene polymers to manipulate TiO2 nanoparticles and to fabricate TiO2 nanoparticle gratings. Suspensions of an azobenzene polymer (PDO3) and TiO2 were used to spin coat thin films on glass slide substrates. By interfering coherent light from an Argon laser on the surface of the PDO3‐TiO2 composite films, SRGs were fabricated. Atomic force microscopic images of the SRGs show TiO2 nanoparticles dispersed throughout the sample, and in particular, at the peaks of the SRG after oxygen plasma treatment. The lateral forces acting on the azobenzene polymer during the SRG fabrication drag the TiO2 nanoparticles. These results indicated that it is feasible to create TiO2 nanoparticle gratings with the composites.
Sequential measurement of beta 2-microglobulin levels, p24 antigen levels, and antibody titers following transplantation of a human immunodeficiency virus-infected kidney allograft. (1991)

A renal allograft recipient developed symptoms suggestive of AIDS. Serological studies revealed that the donor was positive for human immunodeficiency virus (HIV). Retrospective testing of stored sequential serum samples showed that the recipient was negative for HIV pretransplant; anti-p24 and anti-p41 antibodies appeared 10 and 49 days posttransplant, respectively. The recipient's serum beta 2-microglobulin levels were elevated 14 days posttransplant, with normal renal function, 35 days before the detection of anti-p24 antibody. p24 Antigen was detected for the first time 21 days posttransplant. In addition to p24 antigen, elevated serum beta 2-microglobulins may be a useful marker for HIV infection prior to seroconversion.
Cost and Value in Contemporary Heart Failure Clinical Guidance Documents (2021)

Although most contemporary HF CGDs contain at least 1 cost/value statement, most CGDs focus on the high economic impact of HF and its related care; explicit inclusion of cost/value to support clinical guidance recommendations remains infrequent. These results highlight key opportunities for the integration of formalized cost/value considerations in future HF-focused CGDs.
Lachnellins A, B, C, D, and naphthalene-1,3,8-triol, biologically active compounds from a Lachnellula species (ascomycetes). (1997)

In the course of our search for new biologically active metabolites, lachnellin A (1), a metabolite with high cytotoxic and antimicrobial activities, the structurally related lachnellins B, C and D (3, 4, 7), and naphthalene-1,3,8-triol (8), an inhibitor of malate synthase (EC 4.1.3.2), were isolated from submerged cultures of the ascomycete Lachnellula sp. A 32-89. The antimicrobial, cytotoxic and phytotoxic activities of lachnellin A depended on its reactivity and could be abolished by the addition of cysteine. The enzyme inhibiting activity of (8) was due to reactive intermediates during melanization and was no longer observed in the presence of serum albumin. In addition, rac-scytalone (9), (+)-trans-3,4-dihydro-3,4,8-trihydroxy-1 (2H)-naphthalenone (10), 2,5-dihydroxytoluene (11), and (R)-(-)-5-methylmellein (12) were obtained from the same source and biologically characterized.
A Model-Based Standardization Approach that Separates True Bias/DIF from Group Ability Differences and Detects Test Bias/DTF as well as Item Bias/DIF (1993)

A model-based modification (SIBTEST) of the standardization index based upon a multidimensional IRT bias modeling approach is presented that detects and estimates DIF or item bias simultaneously for several items. A distinction between DIF and bias is proposed. SIBTEST detects bias/DIF without the usual Type 1 error inflation due to group target ability differences. In simulations, SIBTEST performs comparably to Mantel-Haenszel for the one item case. SIBTEST investigates bias/DIF for several items at the test score level (multiple item DIF called differential test functioning: DTF), thereby allowing the study of test bias/DIF, in particular bias/DIF amplification or cancellation and the cognitive bases for bias/DIF.
Pattern Dimensions and Feature Shapes of Ternary Blends of Block Copolymer and Low Molecular Weight Homopolymers Directed To Assemble on Chemically Nanopatterned Surfaces (2011)

Ternary blends of cylinder-forming polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) and low molecular weight PS and PMMA were directed to assemble on chemically patterned surfaces with hexagonal symmetry. The chemical patterns consisted of strongly PMMA preferential spots, patterned by electron-beam lithography, in a matrix of PS. The spot-to-spot spacing of the chemical patterns (L(s)) was varied between 0.9L(0) and 1.1L(0), where L(0) is the cylinder-to-cylinder spacing of the pure block copolymer in bulk. The homopolymer volume fraction of the blends (ϕ(H)) was varied between 0 and 0.3. In addition, chemical patterns were formed with selected spots missing from the perfect hexagonal array, such that the interpolation of domains between patterned spots could be examined on patterns where the polymer/pattern feature density ranged from 1:1 to 4:1. The assemblies were analyzed with top-down SEM, from which orientational order parameter (OP(o)) values were determined. The SEM analysis was complemented by Monte Carlo simulations, which offered insights into the shapes of the assembled cylindrical domains. It was found that, in comparison to pure block copolymer, adding homopolymer increased the range of L(s) values over which assemblies with high OP(o) values could be achieved for 1:1 assemblies. However, the corresponding simulations showed that in the 1:1 assemblies the shape of the cylinders was more uniform for pure block copolymer than for blends. In the case of the 4:1 assemblies, the range of L(s) values over which assemblies with high OP(o) values could be achieved was the same for all values of ϕ(H) tested, but the domains of the pure block copolymer had a more uniform shape. Overall, the results provided insights into the blend composition to be used to meet technological requirements for directed assembly with density multiplication.
Age-Dependent Association between Protein Expression of the Embryonic Stem Cell Marker Cripto-1 and Survival of Glioblastoma Patients (2013)

Exploring the re-emergence of embryonic signaling pathways may reveal important information for cancer biology. Nodal is a transforming growth factor-β (TGF-β)-related morphogen that plays a critical role during embryonic development. Nodal signaling is regulated by the Cripto-1 co-receptor and another TGF-β member, Lefty. Although these molecules are poorly detected in differentiated tissues, they have been found in different human cancers. Poor prognosis of glioblastomas justifies the search for novel signaling pathways that can be exploited as potential therapeutic targets. Because our intracranial glioblastoma rat xenograft model has revealed importance of gene ontology categories related to development and differentiation, we hypothesized that increased activity of Nodal signaling could be found in glioblastomas. We examined the gene expressions of Nodal, Cripto-1, and Lefty in microarrays of invasive and angiogenic xenograft samples developed from four patients with glioblastoma. Protein expression was evaluated by immunohistochemistry in 199 primary glioblastomas, and expression levels were analyzed for detection of correlations with available clinical information. Gene expression of Nodal, Lefty, and Cripto-1 was detected in the glioblastoma xenografts. Most patient samples showed significant levels of Cripto-1 detected by immunohistochemistry, whereas only weak to moderate levels were detected for Nodal and Lefty. Most importantly, the higher Cripto-1 scores were associated with shorter survival in a subset of younger patients. These findings suggest for the first time that Cripto-1, an important molecule in developmental biology, may represent a novel prognostic marker and therapeutic target in categories of younger patients with glioblastoma.
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core (2018)

VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4<sub>BS</sub>) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1-3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.
Coupling Explicit and Implicit Surface Representations for Generative 3D\n Modeling (2020)

We propose a novel neural architecture for representing 3D surfaces, which\nharnesses two complementary shape representations: (i) an explicit\nrepresentation via an atlas, i.e., embeddings of 2D domains into 3D; (ii) an\nimplicit-function representation, i.e., a scalar function over the 3D volume,\nwith its levels denoting surfaces. We make these two representations\nsynergistic by introducing novel consistency losses that ensure that the\nsurface created from the atlas aligns with the level-set of the implicit\nfunction. Our hybrid architecture outputs results which are superior to the\noutput of the two equivalent single-representation networks, yielding smoother\nexplicit surfaces with more accurate normals, and a more accurate implicit\noccupancy function. Additionally, our surface reconstruction step can directly\nleverage the explicit atlas-based representation. This process is\ncomputationally efficient, and can be directly used by differentiable\nrasterizers, enabling training our hybrid representation with image-based\nlosses.\n
Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption (2021)

(Cell 184, 1330–1347.e1–e13; March 4, 2021) As a result of an author oversight in the originally published version of this article, the name of an author, Alexander Corr, did not appear in the author list. This error has now been corrected in the article online, and the author contributions have been updated accordingly to reflect Alexander Corr's contributions to the scRNA-seq analysis.
Exploiting entities in social media (2013)

Over the past couple of years micro blogging platforms, such as Twitter, have become extremely popular for information generation and dissemination. Each day hundreds of millions of tweets are being published, containing fresh and trending information that is highly valuable for online users. However, discovering relevant information from such sources is becoming harder due to their rapid growth and the fact that social fragments are often short and noisy. Aggregation techniques such as clustering are often used for extracting this relevant information, since interesting signals begin to emerge when these fragments are grouped together. Clustering large amount of short tweets with limited features is however a challenging task in itself. In this paper, we propose to aggregate tweets by pivoting on entities and mapping them to topics that are already defined in websites such as Wikipedia and Freebase. This allows us to aggregate tweets in a more reliable and feasible way while providing interesting aggregated information about entities present in these fragments. Our analysis using large amounts of tweets shows that such an approach indeed works well. We present encouraging results and various interesting applications centered on entities.