gebhart/patrepeval huggingface dataset:
Fairness in Matching under Uncertainty (2023)

The prevalence and importance of algorithmic two-sided marketplaces has drawn attention to the issue of fairness in such settings. Algorithmic decisions are used in assigning students to schools, users to advertisers, and applicants to job interviews. These decisions should heed the preferences of individuals, and simultaneously be fair with respect to their merits (synonymous with fit, future performance, or need). Merits conditioned on observable features are always \emph{uncertain}, a fact that is exacerbated by the widespread use of machine learning algorithms to infer merit from the observables. As our key contribution, we carefully axiomatize a notion of individual fairness in the two-sided marketplace setting which respects the uncertainty in the merits; indeed, it simultaneously recognizes uncertainty as the primary potential cause of unfairness and an approach to address it. We design a linear programming framework to find fair utility-maximizing distributions over allocations, and we show that the linear program is robust to perturbations in the estimated parameters of the uncertain merit distributions, a key property in combining the approach with machine learning techniques.
Annotating the biomedical literature for the human variome (2013)

This article introduces the Variome Annotation Schema, a schema that aims to capture the core concepts and relations relevant to cataloguing and interpreting human genetic variation and its relationship to disease, as described in the published literature. The schema was inspired by the needs of the database curators of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database, but is intended to have application to genetic variation information in a range of diseases. The schema has been applied to a small corpus of full text journal publications on the subject of inherited colorectal cancer. We show that the inter-annotator agreement on annotation of this corpus ranges from 0.78 to 0.95 F-score across different entity types when exact matching is measured, and improves to a minimum F-score of 0.87 when boundary matching is relaxed. Relations show more variability in agreement, but several are reliable, with the highest, cohort-has-size, reaching 0.90 F-score. We also explore the relevance of the schema to the InSiGHT database curation process. The schema and the corpus represent an important new resource for the development of text mining solutions that address relationships among patient cohorts, disease and genetic variation, and therefore, we also discuss the role text mining might play in the curation of information related to the human variome. The corpus is available at http://opennicta.com/home/health/variome.
Apoptosis-Associated Speck-Like Protein Containing a Caspase Recruitment Domain Is a Regulator of Procaspase-1 Activation (2003)

Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC)/target of methylation-induced silencing/PYCARD represents one of only two proteins encoded in the human genome that contains a caspase recruitment domain (CARD) together with a pyrin, AIM, ASC, and death domain-like (PAAD)/PYRIN/DAPIN domain. CARDs regulate caspase family proteases. We show here that ASC binds by its CARD to procaspase-1 and to adapter proteins involved in caspase-1 activation, thereby regulating cytokine pro-IL-1beta activation by this protease in THP-1 monocytes. ASC enhances IL-1beta secretion into the cell culture supernatants, at low concentrations, while suppressing at high concentrations. When expressed in HEK293 cells, ASC interferes with Cardiak/Rip2/Rick-mediated oligomerization of procaspase-1 and suppresses activation this protease, as measured by protease activity assays. Moreover, ASC also recruits procaspase-1 into ASC-formed cytosolic specks, separating it from Cardiak. We also show that expression of the PAAD/PYRIN family proteins pyrin or cryopyrin/PYPAF1/NALP3 individually inhibits IL-1beta secretion but that coexpression of ASC with these proteins results in enhanced IL-1beta secretion. However, expression of ASC uniformly interferes with caspase-1 activation and IL-1beta secretion induced by proinflammatory stimuli such as LPS and TNF, suggesting pathway competition. Moreover, LPS and TNF induce increases in ASC mRNA and protein expression in cells of myeloid/monocytic origin, revealing another level of cross-talk of cytokine-signaling pathways with the ASC-controlled pathway. Thus, our results suggest a complex interplay of the bipartite adapter protein ASC with PAAD/PYRIN family proteins, LPS (Toll family receptors), and TNF in the regulation of procaspase-1 activation, cytokine production, and control of inflammatory responses.
Body Surface Area of Female Swine (1973)

Knowledge of the surface area over which heat exchange occurs is crucial to understanding thermal relations between swine and their environments. Brody's equation is generally used for predicting swine surface area from body weight. However, our 36 direct measurements of surface area on five Hampshire-Yorkshire and four Duroc gilts, ranging in weight from 30 to 123 kg, yielded estimates which all fell below the surface area as predicted by Brody's equation. This finding was confirmed photogrammetrically. The results indicate that our formula—(surface area in cm2)=734 (body weight in kg).656—predicts surface area of female swine of the current “meat type” more accurately than does Brody's formula.
Oxygen profile engineering in silicon by germanium addition and high-temperature annealing (2003)

The formation of multilayer structures in oxygen-implanted silicon by the introduction of germanium is reported. Our results show that the oxygen distribution can be split under carefully controlled annealing conditions. The typical annealing process consists of first raising the furnace temperature from 600 to 1200 °C within 30 min and then holding the temperature at 1200 °C for 2 h. The faster crystallization rate of amorphous silicon germanium (SiGe) and germanium rejection from the oxide contribute to the final multilayer structure. Our findings suggest that oxygen profile engineering is possible and single-energy ion implantation can be utilized to fabricate multilayer structures containing multiple buried oxide layers. In addition, our results suggest that, in SiGe-on-insulator fabrication, the annealing step at a moderate temperature or a slow temperature ramp-up rate during the high-temperature annealing step is much more critical than in conventional silicon-on-insulator fabrication.
Expression of fatty acyl-CoA ligase drives one-pot de novo synthesis of membrane-bound vesicles in a cell free transcription-translation system (2021)

Abstract Despite the central importance of lipid membranes in cellular organization, it is challenging to reconstitute their de novo formation from minimal chemical and biological elements. Here we describe a chemoenzymatic route to membrane-forming non-canonical phospholipids in which cysteine-modified lysolipids undergo spontaneous coupling with fatty acyl-CoA thioesters generated enzymatically by a fatty acyl-CoA ligase. Due to the high efficiency of the reaction, we were able to optimize phospholipid membrane formation in a cell-free transcription-translation (TX-TL) system. Combining DNA encoding for the fatty acyl-CoA ligase with suitable lipid precursors, enabled spontaneous one-pot de novo synthesis of membrane-bound vesicles. Non-canonical sphingolipid synthesis was also possible by using a cysteine-modified lysosphingomyelin as a precursor. When the sphingomyelin-interacting protein lysenin is co-expressed alongside the acyl CoA ligase, the in situ assembled membranes were spontaneously modified with protein. Our strategy of coupling gene expression with membrane lipid synthesis in a one-pot fashion could facilitate the generation of proteoliposomes and brings us closer to the bottom-up generation of synthetic cells using recombinant synthetic biology platforms.
Environmental Studies on Titanium Aluminide Alloys (2005)

Titanium aluminides are attractive alternatives to superalloys in moderate temperature applications (600 to 850 C) by virtue of their high strength-to-density ratio (high specific strength). These alloys are also more ductile than competing intermetallic systems. However, most Ti-based alloys tend to degrade through interstitial embrittlement and rapid oxidation during exposure to elevated temperatures. Therefore, their environmental behavior must be thoroughly investigated before they can be developed further. The goals of titanium aluminide environmental studies at the NASA Lewis Research Center are twofold: characterize the degradation mechanisms for advanced structural alloys and determine what means are available to minimize degradation. The studies to date have covered the alpha 2 (Ti3Al), orthorhombic (Ti2AlNb), and gamma (TiAl) classes of alloys.
Crystallinity and Microstructural Versatility in the Spin‐Crossover Polymeric Material [Fe(Htrz)2(trz)](BF4) (2017)

The room‐temperature microstructure of the spin‐crossover (SCO) 1D polymeric iron(II) compound [Fe(Htrz) 2 (trz)](BF 4 ) has been investigated by means of powder X‐ray diffraction and compared with the SCO features determined by magnetic measurements. The microstructural parameters, such as the sizes of the coherent domains, of a number of samples and their morphologies have revealed new features of this material. Heating can significantly improve the crystallinity of the material by doubling the coherent domain size, which may open a route to regenerating this system after the reported mechanical fatigue it undergoes after suffering numerous SCO cycles. In addition, the correlation between the length of the coherent domain and the SCO temperature shows that the longer the domains, that is, the longer the iron chains, the higher the SCO temperatures.
Caveolae and Vesiculo-Vacuolar Organelles in Bovine Capillary Endothelial Cells Cultured with VPF/VEGF on Floating Matrigel-collagen Gels (1999)

In situ vascular endothelium is characterized by many cytoplasmic vesicles (caveolae) and vacuoles. In venules these are organized into prominent clusters called vesiculo-vacuolar organelles or VVOs. VVOs provide an important pathway for plasma protein extravasation in response to vasoactive mediators. In contrast, cultured endothelial cells isolated from many sources lack VVOs and generally have few caveolae. Our goal was to preserve VVOs in cultured endothelium. Bovine adrenal microvascular endothelial cells (BCEs) cultured on floating Matrigel-collagen Type I gels with vascular permeability factor/vascular endothelial growth factor (VPF/VEGF) exhibited typical VVOs by electron microscopy. Both in vivo and in culture VVOs were caveolin-positive by immunoelectron microscopy. On the basis of caveolin immunostaining, VVOs could also be detected by light (confocal) microscopy. When BCEs were cultured without VPF/VEGF, caveolin staining was finely punctate and electron microscopy confirmed the near absence of VVOs. BCE VVOs were sensitive to N-ethylmaleimide. Other types of endothelium cultured on Matrigel-collagen gels with or without VPF/VEGF exhibited few caveolae and no VVOs. Therefore, preservation of VVOs in cultured endothelium required a specific combination of endothelial cells (BCEs), surface matrix (Matrigel-collagen), and growth factor (VPF/VEGF). These endothelial cells should be useful for in vitro studies of trans-endothelial transport.
An antiserum raised against the recombinant cytoplasmic tail of the human CD43 glycoprotein identifies CD43 in many mammalian species (1999)

Leukosialin or CD43 is a heavily O-glycosylated transmembrane protein expressed on all cells of the haematopoietic cell lineage with the exception of red blood cells and mature B cells. This antigen has been identified in human, mouse and rat with monoclonal antibodies. Although orthologues of many human and rodent leucocyte cell surface antigens have been described in recent years, CD43, despite its abundance on human and rodent cells, remained uncharacterized in other vertebrate species. The comparison of CD43 amino acid sequences from human, mouse and rat indicated a high level of homology in the cytoplasmic domain. A serum, (p.aCD43cp) raised against the recombinant cytoplasmic tail of the human CD43, was shown not only to recognize human CD43, but it bound to putative CD43 orthologues in many mammalian species. CD43 was found to be expressed in the same leucocyte subpopulations and circumstantial evidence suggested that CD43 is also regulated similarly during leucocyte ontogeny in all species investigated. As CD43+ cells were readily observed in fixed tissues, the p.aCD43cp serum may be used as a reliable reagent for the verification of the haematopoietic origin of infiltrations and, used together with other reagents, for the serological characterization of normal and pathological lymphoid tissues and lymphoid infiltrations in experimental work and in animal disease.
New material platform for superconducting transmon qubits with coherence times exceeding 0.3 milliseconds (2020)

The superconducting transmon qubit is a leading platform for quantum computing and quantum science. Building large, useful quantum systems based on transmon qubits will require significant improvements in qubit relaxation and coherence times, which are orders of magnitude shorter than limits imposed by bulk properties of the constituent materials. This indicates that relaxation likely originates from uncontrolled surfaces, interfaces, and contaminants. Previous efforts to improve qubit lifetimes have focused primarily on designs that minimize contributions from surfaces. However, significant improvements in the lifetime of two-dimensional transmon qubits have remained elusive for several years. Here, we fabricate two-dimensional transmon qubits that have both lifetimes and coherence times with dynamical decoupling exceeding 0.3 milliseconds by replacing niobium with tantalum in the device. We have observed increased lifetimes for seventeen devices, indicating that these material improvements are robust, paving the way for higher gate fidelities in multi-qubit processors.
Direct Redox Deposition of Manganese Oxide on Multiscaled Carbon Nanotube/Microfiber Carbon Electrode for Electrochemical Capacitor (2009)

Manganese oxide was synthesized by direct reduction of ions on microfibrous carbon paper (CP) and a multiscaled substrate, which consists of microfibrous CP coated with carbon nanotubes. This process is much simpler than that used for the formation of composite electrode. Scanning electron microscopy and energy dispersive X-ray analysis revealed that the multiscaled carbon nanotube/microfibrous CP is efficient for the reduction of ions that leads to the direct formation of . The capacitive behavior of the composite manganese oxide/CP composite and the multiscaled carbon nanotube/microfibrous CP nanocomposite electrode was characterized by cyclic voltammetry in neutral aqueous electrolyte (e.g., ) aqueous solution. The specific capacitance of the nanocomposite is as high as in comparison to that one of , which is . The electrochemical impedance spectroscopy technique showed that the multiscaled nanocomposite electrode is characterized by a good electrical conductivity and an excellent electrical contact between the active material and the current collector.
Carbon‐Nanotube/Silver Networks in Nitrile Butadiene Rubber for Highly Conductive Flexible Adhesives (2012)

An adhesive with high conductivity, flexibility, cyclability, oxidation resistance, and good adhesion is developed using microscale silver flakes, multiwalled carbon nanotubes decorated with nanoscale silver particles, and nitrile butadiene rubber. Light-emitting-diode chips are attached to the conductive, flexible adhesive pattern on a poly(ethylene terephthalate) substrate as a visual demonstration. The brightness is invariant during bending tests.
Database System Support for Personalized Recommendation Applications (2017)

Personalized recommendation has become popular in modern web services. For instance, Amazon recommends new items to shoppers. Also, Netflix recommends shows to viewers, and Facebook recommends friends to its users. Despite the ubiquity of recommendation applications, classic database management systems still do not provide in-house support for recommending data stored in the database. In this paper, we present the anatomy of RecDB an open source PostgreSQLbased system that provides a unified approach for declarative data recommendation inside the database engine. RecDB realizes the personalized recommendation functionality as query operators inside the database kernel. That facilitates applying the recommendation functionality and typical database operations (e.g., Selection, Join, Top-k) side-by-side. To further reduce the application latency, RecDB pre-computes and caches the generated recommendation in the database. In the paper, we present extensive experiments that study the performance of personalized recommendation applications based on an actual implementation inside PostgreSQL 9.2 using real Movie recommendation and location-aware recommendation scenarios. The results show that a recommendation-aware database engine, i.e., RecDB, outperforms the classic approach that implements the recommendation logic on-top of the database engine in various recommendation applications.
Marek's Disease Virus Influences the Expression of Genes Associated with IFN-γ-Inducible MHC Class II Expression (2010)

Chickens infected with Marek's disease virus (MDV) become lifelong carriers regardless of their susceptibility to clinical disease. Therefore various viral immune-evasive mechanisms must play a role in MDV-host interactions. MDV has previously been shown to influence the expression of major histocompatibility complex (MHC) class II molecules. However, little is known about the underlying mechanisms of this phenomenon. In the present study, we studied the effect of MDV infection on the expression of several genes associated with IFN-gamma-inducible MHC class II expression at 4, 7, 14, and 21 days post-infection (dpi). There was a significant (p <or= 0.05) downregulation of MHC class II beta chain expression throughout the experiment, while other components of the MHC class II heterotrimer (i.e., alpha chain and the invariant chain) were significantly downregulated only at 4 and 21 dpi. Furthermore, the expression of components of the IFN-gamma-receptor complex was significantly downregulated at 4 dpi. In contrast, a number of other IFN-gamma-signaling molecules, including signal transducer and activator of transcription 1 (STAT1), interferon-responsive factor 1 (IRF-1), and class II transactivator (CIITA) were significantly upregulated at most time points. The results of this study shed light on the possible mechanisms by which MDV may evade host immunosurveillance.
Schoenocaulon Alkaloids. III. The Bismuth Oxide Oxidation of Veracevine, Cevagenine and Cevine1a (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSchoenocaulon Alkaloids. III. The Bismuth Oxide Oxidation of Veracevine, Cevagenine and Cevine1aS. Morris Kupchan and David LavieCite this: J. Am. Chem. Soc. 1955, 77, 3, 683–686Publication Date (Print):February 1, 1955Publication History Published online1 May 2002Published inissue 1 February 1955https://pubs.acs.org/doi/10.1021/ja01608a041https://doi.org/10.1021/ja01608a041research-articleACS PublicationsRequest reuse permissionsArticle Views58Altmetric-Citations12LEARN 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
Proteolytic cleavage of cellubrevin and vesicle-associated membrane protein (VAMP) by tetanus toxin does not impair insulin-stimulated glucose transport or GLUT4 translocation in rat adipocytes (1997)

Acute insulin stimulation of glucose transport in fat and skeletal muscle occurs principally as a result of the hormonal induced translocation of the GLUT4 glucose transporter from intracellular vesicular stores to the plasma membrane. The precise mechanisms governing the fusion of GLUT4 vesicles with the plasma membrane are very poorly understood at present but may share some similarities with synaptic vesicle fusion, as vesicle-associated membrane protein (VAMP) and cellubrevin, two proteins implicated in the process of membrane fusion, are resident in GLUT4-containing vesicles isolated from rat and murine 3T3-L1 adipocytes respectively. In this study we show that proteolysis of both cellubrevin and VAMP, induced by electroporation of isolated rat adipocytes with tetanus toxin, does not impair insulin-stimulated glucose transport or GLUT4 translocation. The hormone was found to stimulate glucose uptake by approx. 16-fold in freshly isolated rat adipocytes. After a single electroporating pulse, the ability of insulin to activate glucose uptake was lowered, but the observed stimulation was nevertheless nearly 5-fold higher than the basal rate of glucose uptake. Electroporation of adipocytes with 600 nM tetanus toxin resulted in a complete loss of both cellubrevin and VAMP expression within 60 min. However, toxin-mediated proteolysis of both these proteins had no effect on the ability of insulin to stimulate glucose transport which was elevated approx. 5-fold, an activation of comparable magnitude to that observed in cells electroporated without tetanus toxin. The lack of any significant change in insulin-stimulated glucose transport was consistent with the finding that toxin-mediated proteolysis of both cellubrevin and VAMP had no detectable effect on insulin-induced translocation of GLUT4 in adipocytes. Our findings indicate that, although cellubrevin and VAMP are resident proteins in adipocyte GLUT4-containing vesicles, they are not required for the acute insulin-induced delivery of GLUT4 to the plasma membrane.
Strain variation limits protective activity of vaccines based on soluble Babesia canis antigens (1995)

Groups of five dogs were immunized with vaccines containing soluble parasite antigens (SPA) derived from in vitro culture of Babesis canis parasites, either obtained commercially (Pirodog) or produced at laboratory scale. Both vaccines generated antibodies that reacted with parasitised erythrocytes (PE). Upon challenge infection with homologous parasites, protection was evident from less severe decreases of haematocrit values, and reduced morbidity. Vaccinated animals, however, were not protected against challenge infection with heterologous B. canis parasites. Recovery from challenge infection coincided with the production of antibodies against parasitized erythrocytes. The results suggest that SPA from B. canis carry strain-specific determinants that are crucial for inducing protection in dogs against challenge infection, and explain vaccination failures in the field.