Miracle-dz/UniFAR-FTUs huggingface dataset:
Socioeconomic Status and Health in Blacks and Whites: The Problem of Residual Confounding and the Resiliency of Race

A large number of epidemiologic studies have focused on racial/ethnic differences, particularly between blacks and whites. Because health endpoints and racial categorizations are associated with socioeconomic status, investigators generally adjust for socioeconomic indicators. The intention is usually to control for confounding, thereby making groups comparable and excluding socioeconomic status as an alternative explanation to hypotheses of innate physiologic differences. A threat to the validity of these analyses is therefore the presence of residual confounding. We identify four potential sources of residual confounding in this analytical design: categorization of socioeconomic status variables, measurement error in socioeconomic indicators, use of aggregated socioeconomic status measures, and incommensurate socioeconomic indicators. Using simulations and examples from the literature, we demonstrate that the effect of residual confounding is to bias interpretation of data toward the conclusion of independent racial/ethnic group effects. Investigators often refer to possible “genetic” differences on the basis of models that control for socioeconomic status. We propose that such conclusions on the basis of this analytical strategy are generally unwarranted. Racial/ethnic differences in disease are a pressing public health concern, but the current approach does not often provide a basis for inference about putative biological factors in the etiology of this disparity.
Tolerance and pharmacokinetics of ciprofloxacin in the chick. Preliminary experience in subjects of pediatric age with urinary tract infections (UTI).

We studied the tolerance and pharmacokinetic parameters of ciprofloxacin in (2 mg/kg, i.v.) in 45 chicks. Serum concentrations of ciprofloxacin at various times of drawing (15 min, 30 min, 1 hr, 3 hr, 6 hr, 8 hr and 12 hr) peaked in the first 15 min with a trough after 6 hr, and were completely absent after 8 hr. We found no neurotoxic effects or behavioral changes. Encouraged by a good tolerance for this quinolone, we conducted a preliminary study concerning the therapeutic efficacy of ciprofloxacin in 8 subjects of pediatric age (8-14 years) with urinary tract infections (UTI) that are resistant to classic antibiotics. The results and normality of hematologic parameters, checked before and after therapy, allow us to recommend the monitored use of ciprofloxacin in children with UTI resulting from bacteria resistant to other antibiotics.
Granularity Issues in the Alignment of Upper Ontologies

Summary Objectives: The application of upper ontologies has been repeatedly advocated for to support the interoperability between different domain ontologies for facilitating the shared use of data within and across disciplines. BioTop is an upper domain ontology that aims at aligning more specialized biomolecular and biomedical ontologies. The integration of BioTop and the upper ontology Basic Formal Ontology (BFO) is the objective of this study. Methods: BFO was manually integrated into BioTop, observing both its free text and formal definitions. BioTop classes were attached to BFO classes as children and BFO classes were reused in the formal definitions of BioTop classes. A description logics reasoner was used to check the logical consistency of this integration. The domain adequacy was checked manually by domain experts. Results: Logical inconsistencies were found by the reasoner when applying the BFO classes for fiat and aggregated objects in some of the BioTop class definitions. We discovered that the definition of those particular classes in BFO was dependent on the notion of physical connectedness. Hence we suggest ignoring a BFO subbranch in order not to hinder cross-granularity integration. Conclusion: Without introducing a more sophisticated theory of granularity, the described problems cannot be properly dealt with. Whereas we argue that an upper ontology should be granularity-independent, we illustrate how granularity-dependent domain ontologies can still be embedded into the framework of BioTop in combination with BFO.
Blood transfusion and autologous donation: a survey of post‐surgical patients, interest group members and the public

Summary. Before planned surgery, patients may choose autologous donation in order to avoid the small, but potential, risks of receiving an allogeneic blood transfusion. This study examined the perceived risks of allogeneic blood transfusions, preferences and willingness to pay for autologous donation and the desired role in the decision‐making process in three populations: post‐surgical patients, special interest group members and the general public. Quantitative and qualitative data were collected from 206 respondents with the help of computer‐assisted semi‐structured telephone interviews. Thirty‐three per cent of the sample voiced concerns about receiving allogeneic blood transfusions. The risks of hepatitis C virus, human immunodeficiency virus, variant Creutzfeldt–Jakob disease and a haemolytic reaction were perceived as being low, but were rated as numerically higher than those of other life events that have equal probability. Autologous donation was perceived as removing all the risks associated with transfusion, and respondents were willing to pay a median $976 AUD ($664 US) to use this technique. Over 80% of respondents preferred to be involved in making the decision about whether to use autologous donation. Even though autologous donation is not ‘risk‐free’ and the blood supply is very safe, people overestimate the associated risks and have a preference for their own blood. Decision aids presenting balanced information on the advantages and disadvantages of both allogeneic and autologous blood may be required.
Recovery of Contractile Function of Postischemic, Reperfused Myocardium: Influence of 2,3‐Butanedione-2‐Monoxime

Inhibition of mechanical activity during ischemia could improve recovery of stunned myocardium. In this study, the effect of 2,3-butanedione-2-monoxime (BDM), an agent that disrupts excitation-contraction coupling, on the time course of recovery of contractile function of postischemic reperfused myocardium was studied in open-chest anesthetized dogs. Ischemia was produced by occluding the left anterior descending coronary artery (LAD) for 15 mins. In separate experimental groups, during the occlusion period, 6 ml of either 100 mM BDM or drug vehicle (0.9% normal saline) was infused into the distal perfusion bed subjected to occlusion. Regional myocardial function (percentages of segment shortening % SS) was assessed by sonomicrometry. LAD occlusion resulted in similar degrees of dyskinesia in both experimental groups. Subsequent recovery of contractile function during reperfusion was evaluated for 3 h. In control experiments, segment shortening remained significantly (p < 0.05) decreased throughout the reperfusion period, returning to only 36.1 ± 9.2% of the preocclusion value at 3 h postreperfusion. In BDM experiments, regional contractile function returned to 72.4 ± 11.3% of the preocclusion value at 1 h of reperfusion. Rapid recovery was sustained throughout reperfusion. Regional stroke work area (RSWA) also demonstrated rapid sustained recovery of function after treatment with BDM. RSWA was significantly greater in BDM experiments as compared with control experiments at all times during the reperfusion period. These results demonstrate that selective intracoronary (i.e.) administration of BDM during ischemia markedly enhances postischemic recovery of contractile function. The underlying mechanism for this action may involve modulation of several aspects of impaired cellular function in postischemic tissues. Use of BDM to reduce postischemic myocardial dysfunction, particularly as a cardioplegic agent, warrants further study.
The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression

Ecosystem retrogression following long‐term pedogenesis is attributed to phosphorus (P) limitation of primary productivity. Arbuscular mycorrhizal fungi (AMF) enhance P acquisition for most terrestrial plants, but it has been suggested that this strategy becomes less effective in strongly weathered soils with extremely low P availability. Using next generation sequencing of the large subunit ribosomal RNA gene in roots and soil, we compared the composition and diversity of AMF communities in three contrasting stages of a retrogressive >2‐million‐year dune chronosequence in a global biodiversity hotspot. This chronosequence shows a ~60‐fold decline in total soil P concentration, with the oldest stage representing some of the most severely P‐impoverished soils found in any terrestrial ecosystem. The richness of AMF operational taxonomic units was low on young (1000's of years), moderately P‐rich soils, greatest on relatively old (~120 000 years) low‐P soils, and low again on the oldest (>2 000 000 years) soils that were lowest in P availability. A similar decline in AMF phylogenetic diversity on the oldest soils occurred, despite invariant host plant diversity and only small declines in host cover along the chronosequence. Differences in AMF community composition were greatest between the youngest and the two oldest soils, and this was best explained by differences in soil P concentrations. Our results point to a threshold in soil P availability during ecosystem regression below which AMF diversity declines, suggesting environmental filtering of AMF insufficiently adapted to extremely low P availability.
Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates

Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.
Treatment of early-onset schizophrenia spectrum disorders (TEOSS): demographic and clinical characteristics.

OBJECTIVE We examined baseline demographic and clinical profiles of youths enrolled from 2001 to 2006 in the publicly funded multicenter, randomized controlled trial Treatment of Early-Onset Schizophrenia Spectrum Disorders. METHOD Youths (8-19 years) with schizophrenia (SZ) and schizoaffective disorder were recruited at four academic sites. Diagnosis was made via structured and clinical interviews. Assessments of psychiatric symptoms and social and global functioning were included. RESULTS A total of 119 youths were enrolled. The mean age at illness onset was 11.1 +/- 3.5 years. Patients with SZ and schizoaffective disorder had similar ratings on the Positive and Negative Symptom Scale, Brief Psychiatric Rating Scale for Children, and Clinical Global Impression-Severity Scale. The overall level of functioning was similar in the two groups. A comparison to published reports of adults with SZ indicates that these youths may have more severe symptoms based on results of the Positive and Negative Symptom Scale. CONCLUSIONS This is one of the largest samples of youths with SZ spectrum disorders studied to date and the largest assessment of youths with schizoaffective disorder. High rates of symptoms and general psychopathology were noted. There was a substantial degree of social and functional impairment. The symptom profiles are consistent with, but more severe than, those reported in the adult literature.
Crystal structure of the complex formed between a group I Phospholipase A2 and a naturally occurring fatty acid at 2.7 Å resolution

This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A2 (PLA2) and also to a PLA2 with Asp 49. The fatty acid identified as n‐tridecanoic acid is observed at the substrate recognition site of PLA2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA2 was determined using the cDNA method. Three‐dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 Å. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n‐tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium‐binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n‐tridecanoic acid was clearly fitted. The MALDI–TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA2 by 212 Da over the native PLA2. A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA2 in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium‐binding loop.
Statistical spectral analysis of random Gramian matrices

In this paper we perform the statistical analysis on the spectrum of random N × N Gramian matrices of the form G<sup>*</sup><inf>T</inf> ≙ V<sup>T</sup> · GT · V, where G and G<inf>T</inf> are themselves Gramian matrices with subspace distance Δ(G,G<inf>T</inf>) and V is the diagonalizer of G. In particular, we employ an extreme-value and asymptotic take on the theory of Gershgorin spectrum bounds to characterize the statistical structure of G<sup>*</sup><inf>T</inf>. The results reveal that even for relatively large Δ(G,G<inf>T</inf>), the matrix G<sup>*</sup><inf>T</inf> is, with a high probability, brought to such a structure that can it be quickly diagonalized. This feature is exploited to design a statistically optimized and truncated variation of the Jacobi algorithm which is found to converge to the dominant eigenspace of G<sup>*</sup><inf>T</inf> as fast as the deterministic optimal sweeping strategy but without requiring its typical exhaustive search.
Electrical characteristics of silicon nanowire transistors fabricated by scanning probe and electron beam lithographies

Silicon nanowire (SiNW) field-effect transistors have been fabricated by oxidation scanning probes and electron beam lithographies. The analysis and comparison of the electron mobility and subthreshold swing shows that the device performance is not affected by the top-down fabrication method. The two methods produce silicon nanowire transistors with similar electrical features, although oxidation scanning probe lithography generates nanowires with smaller channel widths. The values of the electron mobility and the subthreshold swing, 200 cm2 V−1 s−1 and 500 mV dec−1, respectively, are similar to those obtained from bottom-up methods. The compatibility of top-down methods with CMOS (complementary metal–oxide–semiconductor) procedures, the good electrical properties of the nanowire devices and the potential for making sub-10 nanowires, in particular by using oxidation scanning probe lithography, make those methods attractive for device fabrication.
Characterization of a Large Panel of Patient-Derived Tumor Xenografts Representing the Clinical Heterogeneity of Human Colorectal Cancer

Purpose: Patient-derived xenograft models are considered to represent the heterogeneity of human cancers and advanced preclinical models. Our consortium joins efforts to extensively develop and characterize a new collection of patient-derived colorectal cancer (CRC) models. Experimental Design: From the 85 unsupervised surgical colorectal samples collection, 54 tumors were successfully xenografted in immunodeficient mice and rats, representing 35 primary tumors, 5 peritoneal carcinoses and 14 metastases. Histologic and molecular characterization of patient tumors, first and late passages on mice includes the sequence of key genes involved in CRC (i.e., APC, KRAS, TP53), aCGH, and transcriptomic analysis. Results: This comprehensive characterization shows that our collection recapitulates the clinical situation about the histopathology and molecular diversity of CRC. Moreover, patient tumors and corresponding models are clustering together allowing comparison studies between clinical and preclinical data. Hence, we conducted pharmacologic monotherapy studies with standard of care for CRC (5-fluorouracil, oxaliplatin, irinotecan, and cetuximab). Through this extensive in vivo analysis, we have shown the loss of human stroma cells after engraftment, observed a metastatic phenotype in some models, and finally compared the molecular profile with the drug sensitivity of each tumor model. Through an experimental cetuximab phase II trial, we confirmed the key role of KRAS mutation in cetuximab resistance. Conclusions: This new collection could bring benefit to evaluate novel targeted therapeutic strategies and to better understand the basis for sensitivity or resistance of tumors from individual patients. Clin Cancer Res; 18(19); 5314–28. ©2012 AACR.
Annotated type catalogue of the Megaspiridae, Orthalicidae, and Simpulopsidae (Mollusca, Gastropoda, Orthalicoidea) in the Natural History Museum, London

Abstract The type status is described for 65 taxa of the Orthalicoidea, classified within the families Megaspiridae (14), Orthalicidae (30), and Simpulopsidae (20); one taxon is considered a nomen inquirendum. Lectotypes are designated for the following taxa: Helix brephoides d’Orbigny, 1835; Simpulopsis cumingi Pfeiffer, 1861; Bulimulus (Protoglyptus) dejectus Fulton, 1907; Bulimus iris Pfeiffer, 1853. The type status of Bulimus salteri Sowerby III, 1890, and Strophocheilus (Eurytus) subirroratus da Costa, 1898 is now changed to lectotype according Art. 74.6 ICZN. The taxa Bulimus loxostomus Pfeiffer, 1853, Bulimus marmatensis Pfeiffer, 1855, Bulimus meobambensis Pfeiffer, 1855, and Orthalicus powissianus var. niveus Preston 1909 are now figured for the first time. The following taxa are now considered junior subjective synonyms: Bulimus marmatensis Pfeiffer, 1855 = Helix (Cochlogena) citrinovitrea Moricand, 1836; Vermiculatus Breure, 1978 = Bocourtia Rochebrune, 1882. New combinations are: Kuschelenia (Bocourtia) Rochebrune, 1882; Kuschelenia (Bocourtia) aequatoria (Pfeiffer, 1853); Kuschelenia (Bocourtia) anthisanensis (Pfeiffer, 1853); Kuschelenia (Bocourtia) aquila (Reeve, 1848); Kuschelenia (Bocourtia) badia (Sowerby I, 1835); Kuschelenia (Bocourtia) bicolor (Sowerby I, 1835); Kuschelenia (Bocourtia) caliginosa (Reeve, 1849); Kuschelenia (Bocourtia) coagulata (Reeve, 1849); Kuschelenia (Bocourtia) cotopaxiensis (Pfeiffer, 1853); Kuschelenia (Bocourtia) filaris (Pfeiffer, 1853); Kara indentata (da Costa, 1901); Clathrorthalicus magnificus (Pfeiffer, 1848); Simpulopsis (Eudioptus) marmartensis (Pfeiffer, 1855); Kuschelenia (Bocourtia) nucina (Reeve, 1850); Kuschelenia (Bocourtia) ochracea (Morelet, 1863); Kuschelenia (Bocourtia) peaki (Breure, 1978); Kuschelenia (Bocourtia) petiti (Pfeiffer, 1846); Clathrorthalicus phoebus (Pfeiffer, 1863); Kuschelenia (Bocourtia) polymorpha (d’Orbigny, 1835); Scholvienia porphyria (Pfeiffer, 1847); Kuschelenia (Bocourtia) purpurata (Reeve, 1849); Kuschelenia (Bocourtia) quechuarum Crawford, 1939; Quechua salteri (Sowerby III, 1890); Kuschelenia (Bocourtia) subfasciata Pfeiffer, 1853; Clathrorthalicus victor (Pfeiffer, 1854). In an addedum a lectotype is being designated for Bulimulus (Drymaeus) interruptus var. pallidus Preston, 1909. An index is included to all taxa mentioned in this paper and the preceding ones in this series (Breure and Ablett 2011, 2012, 2014).
Populations stellaires et systèmes planétaires observés par CoRoT

Dans le cadre de ma these, j'ai effectue l'analyse spectrale d'un echantillon massif de spectres stellaires dans le contexte du programme exoplanete de la mission CoRoT. J'ai tire avantage des instruments Flames/GIRAFFE pour observer pres de 2000 etoiles dans le but de comprendre les populations stellaires dans les champs CoRoT. Dans ce but, j'ai implemente, calibre, teste, et applique une chaine de traitement et de reduction fiable et efficace afin de reduire et d'analyser automatiquement (en utilisant l'algorithme de parametrisation MATISSE, Gazzano et al. 2010) un large echantillon de spectres stellaires. J'ai determine la vitesse barycentrique radiale, une estimation de la vitesse de rotation projetee sur la ligne de visee, la temperature effective, la gravite de surface, de la metallicite global et l'enrichissement des elements par rapport au fer pour 1 227 etoiles dans trois des champs CoRoT. Ainsi, j'ai construit un des premiers echantillons affranchis de biais de selection pour toute etude concernant la relation planete metallicite dans les champs CoRoT et demontre que le nombre des etoiles naines a ete generalement sous-estime par la classification photometrique (Exo-Dat, Deleuil et al. 2009). J'ai applique la relation reliant le nombre de planetes detectees a la metallicite de l'etoile hote (Udry & Santos 2007), parfaitement en accord avec le nombre actuel de detection planetaire dans les champs CoRoT correspondant (Gazzano et al. 2010). En utilisant les parametres atmospheriques MATISSE, nous avons determine les distances et nous les avons combinees avec des informations cinematiques (les mouvements propres du catalogue PPMXL - Roeser et al. (2010), et l'astrometrie). Nous avons derive les composantes de cinematique Galactique : position et vitesse. Cela m'a permis d'etudier les populations stellaires dans les champs CoRoT /exoplanete et de quantifier le gradient de metallicite dans la Galaxie (Gazzano et al. En preparation). J'ai par ailleurs montre que les etoiles a planetes detectees dans les champs consideres pour ma these sont exclusivement des etoiles de disque mince. J'ai egalement participe au suivi des candidats planete CoRoT a l'aide de spectroscopie a haute resolution. J'ai effectue l'analyse spectrale, avec le logiciel VWA (Bruntt et al. 2010b,a), des etoiles hotes pour la mission spatiale CoRoT. Ces etudes ont conduit a la determination des parametres fondamentaux de l'etoile, qui est une etape indispensable pour la caracterisation complete de la planete.