gebhart/patrepeval huggingface dataset:
Effects of space allocation and housing density on measures of wellbeing in laboratory mice: a review (2011)

In the majority of countries where there are legislative requirements pertaining to the use of animals in research, figures are quoted for minimum cage sizes or space allocation to be provided per animal. These figures are generally based on professional judgement and are in common usage. However, there is a growing trend and expectation that welfare science should inform regulatory decision-making. Given the importance of the potential welfare influences of cage size on the animals themselves, this paper presents the latest scientific knowledge on this topic in one of the most commonly used animals in research, the mouse. A comprehensive review of studies in laboratory mice was undertaken, examining the effects of space allocation per animal and animal density on established welfare indicators. To date, animal density studies have predominated, and the effects of space allocation per se are still relatively unclear. This information will guide those involved in facility management or legislative review, and provide a more solid foundation for further studies into the effects of routine husbandry practices on animal welfare.
Hsa, an adhesin of Streptococcus gordonii DL1, binds to α2‐3‐linked sialic acid on glycophorin A of the erythrocyte membrane (2008)

Bacterial recognition of host sialic acid-containing receptors plays an important role in microbial colonization of the human oral cavity. The aggregation of human platelets by Streptococcus gordonii DL1 is implicated in the pathogenesis of infective endocarditis. In addition, we consider that hemagglutination of this organism may act as an additive factor to increase the severity of this disease. We previously reported that this interaction requires the bacterial expression of a 203-kDa protein (Hsa), which has sialic acid-binding activity. In the present study, we confirmed that erythrocyte surface sialoglycoproteins are the receptors for Hsa. We examined the effects of proteinase K, chymotrypsin, phospholipase C, and alpha(2-3) or alpha(2-3, 6, 8) neuraminidase on hemagglutination activity and found that the interaction occurs between Hsa and alpha2-3-linked sialic acid-containing proteins of erythrocytes. We expressed recombinant NR2, which is the putative binding domain of Hsa, fused with GST in Escherichia coli BL21. Dot-blot analysis demonstrated that GST-HsaNR2 binds both glycophorin A (GPA) and band 3. Moreover, GPA and a small amount of band 3 were detected by GST pull-down assays. These findings indicate that S. gordonii Hsa specifically binds to GPA and band 3, alpha2-3-linked sialic acid membrane glycoproteins.
ChemInform Abstract: PHOTOLYSIS OF 2‐AZIDOPYRIDINE 1‐OXIDES. A CONVENIENT SYNTHESIS OF 1,2‐OXAZINES (1981)

Abstract Die Belichtung der Pyridin‐N‐Oxide (I) ergibt die Cyano‐1,2‐oxazine (II), die beim Erhitzen in die Cyano‐N‐hydroxy‐pyrrole (III) umgelagert werden.
An Investigation of the Solubility of Scandium in Iron-Bearing Constituent Particles in Aluminium Alloys (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Patients with Workersʼ Compensation Claims Have Worse Outcomes After Rotator Cuff Repair (2008)

Prognostic Level I. See Instructions to Authors for a complete description of levels of evidence.
Application-Layer Traffic Optimization (ALTO) Requirements (2012)

Many Internet applications are used to access resources, such as
pieces of information or server processes that are available in
several equivalent replicas on different hosts. This includes, but is
not limited to, peer-to-peer file sharing applications. The goal of
Application-Layer Traffic Optimization (ALTO) is to provide guidance
to applications that have to select one or several hosts from a set of
candidates capable of providing a desired resource. This guidance
shall be based on parameters that affect performance and efficiency of
the data transmission between the hosts, e.g., the topological
distance. The ultimate goal is to improve performance or Quality of
Experience in the application while reducing the utilization of the
underlying network infrastructure. This document enumerates
requirements for specifying, assessing, or comparing protocols and
implementations. This document is not an Internet Standards Track
specification; it is published for informational purposes.
A Nationwide Plasmidome Surveillance in Thailand Reveals a Limited Variety of New Delhi Metallo-β-Lactamase-Producing Carbapenem-Resistant Enterobacteriaceae Clones and Spreading Plasmids (2022)

Despite frequent identification of plasmids carrying carbapenemase genes, the transfer of plasmids carrying carbapenemase genes is not well recognized in clinical settings because of technical limitations. To investigate the detailed mechanisms of the spread of carbapenem-resistant <i>Enterobacteriaceae</i> (CRE), we performed multifaceted genomic surveillance of CRE isolates in Thailand and analyzed their plasmidome. We analyzed 371 <i>Enterobacteriaceae</i> isolates carrying <i>bla</i><sub>NDM-1</sub> and 114 <i>Enterobacteriaceae</i> isolates carrying <i>bla</i><sub>NDM-5</sub> obtained from clinical samples of 473 patients in 11 representative hospitals located in six provinces in Thailand between 2012 and 2017. The complete structures of plasmids carrying <i>bla</i><sub>NDM</sub> and chromosomal phylogeny were determined by combining Southern blotting hybridization analysis and our previously performed whole-genome short-read sequencing data. Dissemination of the <i>bla</i><sub>NDM-5</sub> gene among the <i>Enterobacteriaceae</i> isolates in Thailand was mainly owing to the nationwide clonal spread of Escherichia coli ST410 and regional clonal spreads of Escherichia coli ST361 and ST405. Analysis of <i>bla</i><sub>NDM-1</sub>-carrying isolates revealed nationwide dissemination of two specific plasmids and nationwide clonal dissemination of Klebsiella pneumoniae ST16 accompanied with regional disseminations of three distinctive K. pneumoniae clones (ST231, ST14, and ST147) with different plasmids. Dissemination of CRE carrying <i>bla</i><sub>NDM</sub> in Thailand is mainly based on nationwide clonal expansions of E. coli ST410 carrying <i>bla</i><sub>NDM-5</sub> and K. pneumoniae ST16 carrying <i>bla</i><sub>NDM-1</sub>, nationwide dissemination of two distinctive plasmids carrying <i>bla</i><sub>NDM-1</sub>, and accumulation of clonal expansions in regional areas. Although the overuse of antibiotics can promote CRE dissemination, the limited variety of transmitters highlights the importance of preventing horizontal dissemination among patients.
Inhibition of cyclic nucleotide phosphodiesterases from pig coronary artery by benzo-separated analogs of 3-isobutyl-1-methylxanthine (1986)

The linear and proximal benzo-separated analogues of 7-benzyl-3-isobutyl-1-methylxanthine, 3-isobutyl-1,8-dimethylxanthine, 3-isobutyl-8-tert-butyl-1-methylxanthine, 3-isobutyl-8-(methoxymethyl)-1-methylxanthine , and 1-isoamyl-3-isobutylxanthine have been prepared and assayed as inhibitors of the peak I and peak II forms of cyclic nucleotide phosphodiesterase from pig coronary artery. Most of the benzo analogues were less effective inhibitors of these phosphodiesterases when compared to 3-isobutyl-1-methylxanthine (IBMX) even though the active sites of both enzyme forms tolerated the stretched-out xanthines. Indeed, the linear benzo-separated analogue of 7-benzyl-IBMX was a more potent inhibitor of peak I activity than was IBMX.
New Chemistry and Stereochemistry of Organophosphorus Pseudohalogens (1991)

Abstract Synthesis, chemistry and stereochemistry of organo-phosphorus-sulfur(selenium)pseudohalogens are discussed and rationalized.
Evidence for the presence of cholesterol side chain cleavage cytochrome P-450 and adrenodoxin in fresh granulosa cells. Effects of follicle-stimulating hormone and cyclic AMP on cholesterol side chain cleavage cytochrome P-450 synthesis and activity. (1983)

The synthesis of cholesterol side chain cleavage cytochrome P-450 (cytochrome P-450scc) and adrenodoxin was studied both in freshly harvested bovine granulosa cells and in granulosa cells maintained in primary monolayer culture. In addition, the action of follicle-stimulating hormone (FSH) and cyclic AMP analogs to stimulate the synthesis of cytochrome P-450scc was investigated in cultured cells. Precursor forms of cytochrome P-450scc and adrenodoxin were immunoisolated from a cell-free translation system directed by RNA prepared from freshly obtained granulosa cells that were not luteinized. Furthermore, the presence of cytochrome P-450scc in lysates of granulosa cells freshly obtained from very small follicles (containing less than 0.1 ml of follicular fluid) and in mitochondria of freshly obtained granulosa cells was demonstrated by using an immunoblotting technique. Continuous treatment of cultured granulosa cells with FSH or with cyclic AMP analogs (dibutyryl cyclic AMP or 8-bromo cyclic AMP) for 72 h increased incorporation of [35S]methionine into immunoprecipitable cytochrome P-450scc. Moreover, FSH, dibutyryl cyclic AMP, and 8-bromo cyclic AMP stimulated pregnenolone production by cultured granulosa cells (2.3-, 4.0-, and 7.5-fold increase over control, respectively), indicative of an increase in cholesterol side chain cleavage activity. The results of this study demonstrate for the first time the presence of two components of the cholesterol side chain cleavage system in freshly obtained granulosa cells, and provide direct evidence for the trophic effect of FSH and its presumed mediator, cyclic AMP, on the synthesis of cytochrome P-450scc in granulosa cells.
Management and leadership in Australian nursing homes (1992)

This paper is based on the outcomes of a study undertaken by Deakin Institute of Nursing Research for the Department of Community Services and Health between 1988 and 1990 (1). The study, which looked at the relationship between skills mix and resident outcomes, involved gathering data from 200 nursing homes in four Australian states using questionnaires and a case study approach. One of the major findings related to the importance of the management and leadership style on the outcome of quality of care and life within the nursing home. The pivotal role of the senior nurse (ie the director of nursing or charge nurse) in affecting high quality is consistently reported in the literature and this was confirmed by the study. Factors drawn from the quantitative and qualitative parts of the study, which make an important contribution to the quality of care experienced by residents, included the director of nursing's attitude, commitment and interpersonal skills. Also important were the ideology of the staff, team cohesiveness and positive attitude and an overall staffing environment which adheres to an agreed philosophy and is stable, satisfied and friendly. All of these were found to be influenced by the senior nurse.
A synchrotron SAXS study of miscible blends of semicrystalline poly(vinylidenefluoride) and semicrystalline poly(1,4-butylene adipate). II. Crystallization, morphology, and PBA inclusion in PVF2 spherulites (2000)

The incorporation of poly(1,4-butylene adipate) (PBA) and its crystallization behavior within poly(vinylidenefluoride) (PVF2) spherulites in miscible PVF2/PBA blends have been further studied with small-angle X-ray synchrotron scattering (SAXS). The incorporation of PBA into the PVF2 interlamellar region was found to be dependent on the PVF2 crystallization conditions. In our previous work, where the blends were crystallized by a one-step quenching process directly from 190 (a single-phase region) to 20 °C (a three-phase region), the transition from PBA inclusion in the PVF2 interlamellar region to interlamellar exclusion occurred at a PBA weight fraction of ∼ 0.5. In this case, where the blends were first quenched from 190 (a single-phase region) to 130 °C (a two-phase region) and then further quenched to 20 °C (a three-phase region), the transition occurred at a PBA weight fraction of less than 0.3. That is, when a blend is crystallized under different conditions, different amounts of the PBA component are incorporated into the PVF2 interlamellar phase. The thickness of the PVF2 interlamellar phase, in turn, may affect the PBA crystalline structure in the interlamellar region. Time-resolved SAXS was used to probe the crystallization dynamics of both PVF2 and PBA components in a blend containing 60 wt % PBA. The blend was quenched from the single-phase region at 190 to 130 °C to crystallize the PVF2 component and was then further quenched to 20 °C to crystallize the PBA component. This study, together with our earlier results, shows that the time dependence of the PVF2 crystallization rate and crystalline lamellar thickness is a function of the PBA content in the blend. The glass-transition temperature of the blend and the PBA diffusion process are the two dominant factors that control the PVF2 crystallization dynamics. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2296–2308, 2000
Conclusion (1982)

When Conrad died in 1924, he left a large fragment entitled Suspense. Although had he lived he would undoubtedly have edited the manuscript, it runs to about 75,000 words. Since 1904, if not before, he had planned a large novel of the Napoleonic period and had been working on it intermittently. ‘Suspense’ refers to the period when Napoleon was exiled to Elba in 1814–15 and Europe was awaiting with great anticipation for the Congress of Vienna to reverse his actions. But in the incomplete novel we see Conrad probing in several directions for his subject. While he completed and revised The Rover in only seven months, he was having characteristic difficulty making progress on the far more ambitiously conceived Suspense, in part because of his age and ill health, but more because he had trouble deciding what kind of novel to write.
Vapor--liquid--solid phase equilibria of radioactive sodium salt wastes at Hanford (1976)

Phase equilibria of the seven-component system, NaOH-NaNO/sub 3/-NaNO/sub 2/-NaAlO/sub 2/-Na/sub 2/SO/sub 4/-Na/sub 2/CO/sub 3/-H/sub 2/O, were studied. This system simulates radioactive sodium salt wastes stored in underground tanks at Hanford. Equilibrium water vapor pressure of the aqueous phase and solubility of the salts were measured as a function of temperature and NaOH concentration. These data are used to predict deliquescence of stored salt wastes and also to predict the chemical identity of solid residues from evaporation of liquid wastes.
Solution-Processable Conductive Graphene-Based Materials for Flexible Electronics (2019)

This thesis work explores electrical conductors based on few-layer graphene flakes as an enabler for low-cost, mechanically flexible, and high-conductivity conductors in large area flexible and printed electronic devices. The flakes are deposited from aqueous solutions and processed at low temperature. Graphene is selected for its excellent properties in mechanical, optical, electronic, and electrical aspects. However, thin films of pristine few-layer graphene flakes deposited from dispersions normally exhibit inferior electrical conductivity. One cause responsible for this problem is the loose stacking and random orientation of graphene flakes in a graphene deposition. We have solved this problem by implementing a simple post-deposition treatment leading to dramatically densified and planarized thin films. Significantly increased electrical conductivity by ~20 times is obtained. The 1-pyrenebutyric acid tetrabutylammonium salt as an exfoliation enhancer and dispersant in water yields ~110 S/m in conductivity when the graphene based thin films are processed at 90 °C. In order to achieve higher conductivity, a room-temperature method for site-selective copper electroless deposition has been developed. This method is of particular interest for the self-aligned copper deposition to the predefined graphene films. The resultant two-layer graphene/copper structure is characterized by an overall conductivity of ~7.9 × 105 S/m, an increase by ~7000 times from the template graphene films. Several electronic circuits based on the graphene/copper bilayer interconnect have been subsequently fabricated on plastic foils as proof-of-concept demonstrators. Alternatively, highly conductive composites featuring graphene flakes coated with silver nanoparticles with electrical conductivity beyond 106 S/m can be readily obtained at 100 oC. Moreover, a highly conductive reduced-graphene-oxide/copper hybrid hydrogel has been achieved by mixing aqueous graphene oxide solution and copper-containing Fehling's solution. The corresponding aerogel of high porosity exhibits an apparent electrical conductivity of ~430 S/m and delivers a specific capacity of ~453 mAh g−1 at current density of 1 A/g. The experimental results presented in this thesis show that the solution-phase, low-temperature fabrication of highly conductive graphene-based materials holds promises for flexible electronics and energy storage applications.
Clinical Images: Hippokrates confirmed by positron emission tomography (2011)

2006;45:269–73. 27. Siebert S, Amos N, Fielding CA, Wang EC, Aksentijevich I, Williams BD, et al. Reduced tumor necrosis factor signaling in primary human fibroblasts containing a tumor necrosis factor receptor superfamily 1A mutant. Arthritis Rheum 2005;52: 1287–92. 28. Rebelo SL, Bainbridge SE, Amel-Kashipaz MR, Radford PM, Powell RJ, Todd I, et al. Modeling of tumor necrosis factor receptor superfamily 1A mutants associated with tumor necrosis factor receptor–associated periodic syndrome indicates misfolding consistent with abnormal function. Arthritis Rheum 2006;54: 2674–87. 29. Lobito AA, Kimberley FC, Muppidi JR, Komarow H, Jackson AJ, Hull KM, et al. Abnormal disulfide-linked oligomerization results in ER retention and altered signaling by TNFR1 mutants in TNFR1-associated periodic fever syndrome (TRAPS). Blood 2006;108:1320–7. 30. Simon A, Park H, Maddipati R, Lobito AA, Bulua AC, Jackson AJ, et al. Concerted action of wild-type and mutant TNF receptors enhances inflammation in TNF receptor 1-associated periodic fever syndrome. Proc Natl Acad Sci U S A 2010;107:9801–6.
sc-PDB:  an Annotated Database of Druggable Binding Sites from the Protein Data Bank (2006)

The sc-PDB is a collection of 6 415 three-dimensional structures of binding sites found in the Protein Data Bank (PDB). Binding sites were extracted from all high-resolution crystal structures in which a complex between a protein cavity and a small-molecular-weight ligand could be identified. Importantly, ligands are considered from a pharmacological and not a structural point of view. Therefore, solvents, detergents, and most metal ions are not stored in the sc-PDB. Ligands are classified into four main categories: nucleotides (< 4-mer), peptides (< 9-mer), cofactors, and organic compounds. The corresponding binding site is formed by all protein residues (including amino acids, cofactors, and important metal ions) with at least one atom within 6.5 angstroms of any ligand atom. The database was carefully annotated by browsing several protein databases (PDB, UniProt, and GO) and storing, for every sc-PDB entry, the following features: protein name, function, source, domain and mutations, ligand name, and structure. The repository of ligands has also been archived by diversity analysis of molecular scaffolds, and several chemoinformatics descriptors were computed to better understand the chemical space covered by stored ligands. The sc-PDB may be used for several purposes: (i) screening a collection of binding sites for predicting the most likely target(s) of any ligand, (ii) analyzing the molecular similarity between different cavities, and (iii) deriving rules that describe the relationship between ligand pharmacophoric points and active-site properties. The database is periodically updated and accessible on the web at http://bioinfo-pharma.u-strasbg.fr/scPDB/.
Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq (2017)

The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 <i>Oryza glaberrima</i> Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other <i>Oryza</i> species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the <i>O. glaberrima</i> collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole <i>O. glaberrima</i> collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.