bluuebunny/crossref_metadata_2025 huggingface dataset:
The Pogromnoe deposit as an unconventional commercial type of gold mineralization in Transbaikalia
Authors: Spiridonov A.M. , Zorina L.D. , Kulikova Z.I. , Budyak A.E. , Parshin A.V. , Granina E.M. , Pavlova L.A.
Published: September 2015

We studied the mineralogic and geochemical features of metasomatic rocks and ores from the Pogromnoe gold deposit, which is unconventional for Transbaikalia. The deposit, which formed in the Early Cretaceous, at the rifting stage of the regional evolution, is localized in the dynamoclastic strata of the Mongol–Okhotsk suture, along which the Siberian continent joined the Mongolia–China continent in the Early–Middle Jurassic. Gold mineralization occurs as two morphologic types of ores: stockwork quartz–carbonate–arsenopyrite–pyrite ores in altered volcanics (orebody no. 1) and veinlet–vein quartz ones (with disseminated sulfides) in altered carbonaceous shales (orebody no. 10). The host rocks of the deposit are the highly altered volcanosedimentary rocks of the Butorovskii Formation (Shadoron Group, J2-3), which transformed into metasomatic (by composition) and dynamoclastic (by texture and structure) rocks. It has been found that the formation of the metasomatic rocks and mineralization proceeded in several stages. Propylites formed at the preore stage (J3); tectonic schists and albitophyres, at the late preore stage; and sericitolites and albite–carbonate–sericite–quartz metasomatic rocks (quartzites), at the synore stage. The 40Ar/39Ar age of the stockwork system of ore-bearing fractures and metasomatic rocks which formed at the late preore stage is estimated as 139.5 ± 1.8 Ma. The gold-bearing rocks at the deposit are the late preore and synore metasomatic rocks formed after volcanics with sulfide mineralization (gold concentrators are pyrite II and III and arsenopyrite I and II) and after altered carbonaceous shales (gold concentrators are vein quartz and arsenopyrite II). Gold grade is completely consistent with silicification, saturation with quartz–sulfide and sulfide microveinlets, and fine sulfide dissemination. By genesis, the Pogromnoe deposit belongs to objects which formed in shear zones with the contribution of gold-bearing mantle fluids. The authors presume that the sources of mineralization are the ore-producing granitoids of the Amudzhikan–Sretensk intrusive assemblage within the Aprelkovo ore–magmatic system (OMS) (Os’kina and Urguchan plutons). This is confirmed by Pb isotope compositions (207Pb/204Pb and 206Pb/204Pb) for the pyrite and arsenopyrite of the Pogromnoe gold-bearing ores, which testify to the widespread occurrence of “mantle” Pb isotope signatures. The 40Ar/39Ar age of the ore-producing granitoids of the Aprelkovo OMS is 131.0 ± 1.2 Ma. Gold in the orebodies occurs in native form and is fine and very fine. By gold grade, the Pogromnoe deposit deserves very close attention as a new commercial type of gold mineralization in Transbaikalia.
Typomorphism of pyrite of the Sukhoi Log deposit (East Siberia)
Authors: Tauson V.L. , Akimov V.V. , Lipko S.V. , Spiridonov A.M. , Budyak A.E. , Belozerova O.Yu. , Smagunov N.V.
Published: September 2015

The typomorphic features of pyrite of the Sukhoi Log deposit were studied by a set of volumetric and surface methods: electron probe microanalysis, scanning electron and probe microscopy, powder X-ray diffraction, X-ray photoelectron and Auger electron spectroscopy, atomic-absorption spectrometry in the SSADSC (method of statistical sample of analytical data for single crystals) version, and atomic-emission spectrometry. Pyrite from the Sukhoi Log deposit has the following distinctive features: permanent presence of sulfite ion, which often dominates over other surface sulfur anions; weakly determined size dependence of the content of uniformly distributed Au owing to the presence of an internal concentrator of gold—dispersed carbonaceous material—in pyrite from ore zones; cell sculptures of the crystal faces, which appeared owing to the nanofragmentation of the growth surface; micro- and nanoinclusions of carbonaceous phases within crystals, associated with defects in their structure; and thin films enriched in O and C on the surface of and within the crystals. It has been shown that gold–sulfide mineralization at the Sukhoi Log deposit formed in a single ore-generating hydrothermal system, in which gold, sulfur, and carbon belonged to a microparagenesis. Some features (composition of surface, characteristics of submicroscopic structure, and elemental composition) evidence that the conditions of crystallization of pyrite in inter-ore space were different from the conditions of its genesis in the ore zones, which suggests the presence of at least two genetic types of pyrite. Carbonaceous micro- and nanoparticles and O- and C-containing films can favor an increase in the adsorption of gold from cyanide solutions on pyrite. To reduce this effect during gold recovery, a technique for surface modification should be elaborated. The ways for solving the most complicated problems dealt with the source of noble metals (NM) and the ore specialization of the deposit have been outlined. For this purpose, a detailed analysis of the main ore minerals for trace-element speciation is required. In the case of the magmatic source of NM, correlation between the contents of Au and PGE structural forms should exist. On the other hand, there is no correlation between the structural forms of Au or Pt and elements whose contents in fluid are determined by the host rock rather than the magmatic source.
Ta Nang gold deposit in the black shales of Central Vietnam
Authors: Anh Tran Tuan , Gaskov I.V. , Hoa Tran Trong , Borisenko A.S. , Izokh A.E. , Dung Pham Thi , Li Vu Hoang , Mai Nguyen Thi
Published: September 2015

The Ta Nang gold deposit is localized in Middle Jurassic black shales. The ore zone is a series of layer-by-layer crush zones and zones of hydrothermal rock alteration, ≤10 m in thickness and >2 km in length. It consists of quartz–sulfide veins, sulfidized black shales, and their hydrothermally altered varieties. Sulfide mineralization occurs as two assemblages: early pyrite–arsenopyrite and late chalcopyrite–sphalerite– galena. The pyrite–arsenopyrite assemblage is composed of different morphogenetic varieties. Coarse-crystalline arsenopyrite and pyrite aggregates and metacrystals of different orientations, 0.1 to 10 mm in size, are the most widespread. The chalcopyrite–sphalerite–galena assemblage is scarce. Along with the main ore minerals, it includes more rare minerals: pyrrhotite, lead sulfosalts (tsugaruite), and gold, which form a spatial assemblage with the main minerals or small inclusions in them. Gold occurs mainly as fine dissemination in cracks in pyrite, arsenopyrite, chalcopyrite, and quartz. Gold content in sulfidized carbonaceous shales is no more than tenths of ppm, averaging 0.38 ppm. This content in the quartz veins is considerably higher, averaging 3.92 ppm. Silver contents in the shales and quartz veins are similar and equal to 2.68 and 5.30 ppm, respectively. Also, the sulfidized rocks and veins have elevated contents of Fe, As, Pb, Zn, Cu, Cd, Ni, and Co; most of these elements (Fe, As, Pb, Zn, and Cu) make up their own sulfide minerals, and the others are trace elements. According to 39Ar/40Ar dating of sericite from the quartz–sulfide veins, their age is 129.3 ± 5.6 Ma, which is close to the age of the Cretaceous granite intrusions of the Deo Ca complex. These veins formed from moderately strong solutions (11.7–6.4 wt.% NaCl equiv) with the CH4 + N2 + CO2 gas phase at 340–130 °C. Judging from the S isotope composition (δ34S = 1.6–4.3‰), predominantly deep-seated endogenic sulfur participated in the formation of ore sulfide associations. Analysis of the distribution of gold shows that it was deposited together with sulfide minerals (galena, sphalerite, and chalcopyrite) at a later stage.
Electron probe microanalysis of rock-forming minerals with a JXA-8100 electron probe microanalyzer
Authors: Lavrent’ev Yu.G. , Korolyuk V.N. , Usova L.V. , Nigmatulina E.N.
Published: September 2015

The protocol for analysis of rock-forming mineral compositions by X-ray electron probe microanalysis used at the Institute of Geology and Mineralogy, Novosibirsk, Russia, is described. The analysis is conducted with a JXA-8100 electron probe microanalyzer capable to support a highly stable beam at relatively high probe currents for a long time. Elements that can be assayed range from sodium (atomic number Z = 11) to zinc (Z = 30). The operation conditions for routine analyses are substantiated: accelerating voltage 20 kV, probe current 50–100 nA, and signal accumulation time 10 s at both the peak and the background. The method of analytical problem formulation for measurements is presented. It is proven that the proprietary software is insufficient with the presence of the binary matrix effect and better correction methods are required. Metrological characteristics of the protocol have been studied. The variation coefficient, describing the reproducibility of results, averages 0.9% for major components (C > 10%), 2.5% for minor components (1 < C < 10%), and 6.8% for accessory components (0.3 < C < 1%). With still lower contents (0.05 < C < 0.3 %), the standard deviation of reproducibility is 0.02%. The values of the variation coefficient and standard deviation for measurement repeatability are approximately two times lower. The relative trueness of the method is within 1%. The detection limit (3σ criterion) is generally within 0.01–0.03%. It can be improved by an order of magnitude by increasing the accumulation time and probe current.
Geochemical factors for endogenic mineral formation in the bottom sediments of the Tazheran lakes (Baikal area)
Authors: Strakhovenko V.D. , Solotchina E.P. , Vosel’ Yu.S. , Solotchin P.A.
Published: September 2015

We studied recent sedimentation in small saline and brackish lakes located in the Ol’khon region (western Baikal area) with arid and semiarid climate. The lakes belong to the Tazheran system; it is a series of compactly located closed shallow lakes, with a limited catchment area and different mineralization, under the same landscape, climatic, geologic, and geochemical conditions. Two complementary approaches are applied in the research: (1) a detailed study of individual lake and (2) a comparison of the entire series of lakes, which can be considered a natural model for studying the relationship between endogenic mineral formation and the geochemistry of lake waters. The lake waters and bottom sediments were studied by a set of modern methods of geochemistry, mineralogy, and crystal chemistry. The mineral component of the bottom sediments was analyzed by powder X-ray diffraction (XRD), IR spectroscopy, and electron microscopy. The lakes are characterized by predominant carbonate sedimentation; authigenic pyrite, smectite, chlorite, and illite are detected in assemblage with carbonate minerals in the bottom sediments. Carbonate phases have been identified, and their proportions have been determined in the samples by decomposition of the complex XRD profiles of carbonate minerals into peaks using the Pearson VII function. Mathematical modeling of the XRD profiles of carbonates has revealed that predominantly Mg-calcites with variable Mg content and excess-Ca dolomite accumulate in lake bottom sediments influenced by biogenic processes. Aragonite, monohydrocalcite, and rhodochrosite form in some lakes along with carbonates of the calcite–dolomite series. We show a dependence of the composition of the assemblages of the newly formed endogenic carbonate minerals and their crystallochemical characteristics on the chemical composition of lake waters.
The biostratigraphy and sedimentary environments of the Lower Cretaceous section, Malaya Kheta structural-facies region, West Siberia
Authors: Marinov V.A. , Zlobina O.N. , Igol’nikov A.E. , Mogucheva N.K. , Urman O.S.
Published: September 2015

The biostratigraphic study of the Low Cretaceous sediments of the Middle Messoyakha swell (Malaya Kheta region) distinguished 12 biostratons based on biofossil data and thus confirmed Boreal Berriassian, Valanginian, and Lower Hauterivian strata. The genetic types of the sediments were determined by lithofacies and biofacies analyses. In the deposit, the Bazhenovo and Kulomzino horizons (Berriassian to basal Valanginian) consist of relatively deep-water marine, shallow-water marine, and coastal-continental facies that displace one another along the strike. The Tara and Ust’-Balyk horizons (middle Lower Valanginian to Lower Hauterivian) are composed of shallow-water marine facies. Paleontological data suggest a low-hilled island covered with conifer–gingko forests with fern understory in the place of the Middle Messoyakha swell in the Berriassian Age.
Unusual Devonian coal: A new type of jet
Authors: Shumilov I.Kh.
Published: September 2015

A new type of jet from continental Devonian sediments is described. The substrate for gagatization was fragments of Archaeopteris plants, whose burials in sandstone strata are characterized by a kind of spheroidal weathering of organic matter; the material is completely fusainized. This type of jet combines the properties of classical jet and inertinite. The new type of jet was named tsilmanite—after the place of its discovery.
Morphotectonics and paleoseismology of the eastern end of the Bolnay fault (Mongolia)
Authors: Arzhannikova A.V. , Vassallo R. , Arzhannikov S.G. , Jolivet M.
Published: September 2015

The Bolnay (Hangayn) fault is an active shear system which generated the M = 8.2–38.5 Bolnay earthquake of 23 July 1905, one of world’s largest recorded intracontinental event. The fault follows the Mesozoic suture formed during the closure of the Mongolia–Okhotsk ocean. The Late Cenozoic faulting in the region was induced by propagation of strain from the India–Eurasia collision that had reached Mongolia at about 5 ± 3 Ma. The left-lateral strike slip almost all over the fault length is compensated in its western end by Late Quaternary reverse motion. We estimated coseismic slip associated with the event of 1905 and the previous earthquakes in the eastern fault end and checked whether vertical offset compensates the strike slip in this part as well. The 1905 coseismic slip measured from a displaced dry stream bed and pebble bars in the Hasany-Gol river valley was 6.5–7.5 m. The 13 ± 1 m left-lateral displacement of pebble bars in the same valley represents a cumulative slip of two events. Paleoseismological studies across the strike of surface ruptures reveal at least two generations of rupture in two events that postdated the deposition of sediments with a 14C age of 4689 ± 94 yr. Hypsometry of the alluvial surface in the zone of deformation shows gradual elevation increase toward the mountains, but without abrupt change across the fault. This means the absence of vertical offset and reactivation of the fault as a left-lateral strike slip. The horizontal slip in the eastern extension of the Bolnay fault is compensated rather by parallel fault-bounded pull-apart basins trending northeastward oblique to the principal fault strike. The age of their sedimentary fill suggests no older than middle Pleistocene normal faulting that compensated the Bolnay strike slip.
Regional features of seismotectonic deformations in East Asia based on earthquake focal mechanisms and their use for geodynamic zoning
Authors: Kuchai O.A. , Kozina M.E.
Published: September 2015

Seismotectonic deformations of crustal volumes related to geographical coordinates were calculated from data on earthquake focal mechanisms. The crust of the western part of Asia, including the Tien Shan, Tarim massif, Tibet, Pamir-Karakorum, and Kun Lun, undergoes predominantly longitudinal shortening and latitudinal extension. In the eastern part, longitudinal extension and latitudinal shortening are observed. The notional boundary separating these parts is determined over a fairly wide range between longitudes 95° and 103° E and is apparently related to the northward compression from the Indian plate in the south and the westward compression from the Okhotsk and Philippine plates in the east. At the same time, this boundary may indicate the maximum zone of influence of the Indian plate. The boundaries of the Amurian plate are inferred from changes in seismotectonic deformations in the eastern part of Asia. Differences in the seismotectonic deformation of the Earth’s crust are found within the northern part of the Okhotsk plate and the surrounding area.
Determining the electrical conductivity tensor of the lithosphere of the Baltic Shield
Authors: Plotkin V.V.
Published: September 2015

Data of magnetovariational sounding (MVS) under the IMAGE (International Monitor for Auroral Geomagnetic Effects) project and data of magnetotelluric sounding (MTS) under the BEAR (Baltic Electromagnetic Array Research) project are processed with consideration of the lateral inhomogeneity of the electromagnetic field in order to fully determine the components of the electrical conductivity tensor of Baltic Shield rocks. In the reconstruction of the anisotropy characteristics from the MVS and MTS data, an approximate domain description of the bounded polygon area with an effective electrical conductivity tensor is used. Maps of the lateral distributions of its eigenvalues and the strike azimuth of maximum electrical conductivity are constructed. According to available experimental data, an azimuth angle of 40°–60° best describes the direction of the principal axis of the tensor with maximum electrical conductivity on the Baltic Shield. Comparison of the results obtained from seismic and electromagnetic data indicates a possible correlation between the strike azimuths of maximum electrical conductivity and low seismic velocities, as well as similarity of the boundaries of the corresponding domain structures of the Baltic Shield.
Autoevaluación de los profesores de clínica integral de medicina sobre su desempeño docente
Authors: Osornio-Castillo Leticia , Sánchez-Reyes Acela , Ríos-Saldaña M. Refugio , Méndez-Cruz Adolfo René , Moreno-Fernández América Anahí , Ángeles-Cruz Rocío Tomasa , Hurtado-Díaz José Luis
Published: September 2015

Introducción: Dadas las necesidades de la sociedad actual, es innegable que para lograr la mejora de la calidad educativa se hace indispensable la reflexión crítica del profesor sobre desempeño docente.
Objetivo: Describir la autoevaluación que hace el profesor de clínica integral de la carrera de médico cirujano sobre su desempeño docente.
Método: Estudio cuantitativo de tipo descriptivo, retrospectivo y transversal; participaron 381 profesores de los 4 niveles de ciclos clínicos de la carrera de médico cirujano a quienes se les aplicó de manera grupal una escala de autoevaluación docente previo consentimiento.
Resultados: Se presentaron diferencias estadísticamente significativas al comparar por ciclo, se autoevaluaron mejor los docentes del cuarto ciclo. En técnicas didácticas todos los ciclos se evaluaron más bajo; no se presentaron diferencias estadísticamente significativas por género, aunque se autoevaluaron mejor los profesores. Con respecto a la antigüedad también se encontraron diferencias estadísticamente significativas: los que tenían entre 20 y 30 años de antigüedad docente se evaluaron con menor puntaje.
Conclusiones: Los docentes de clínica integral, en lo referente a su desempeño docente, reconocen la necesidad de diversificar el uso de técnicas didácticas, consideran que fundamentan las actividades clínicas y que están comprometidos con la eseñanza.
La satisfacción escolar en los estudiantes del primer año de la carrera de Médico Cirujano
Authors: Osorio-Alvarez María Del Carmen , Parra Gámez Leticia
Published: September 2015

Introducción: Es un estudio que abordó la satisfacción escolar como un elemento importante en la evaluación cognitivo-afectiva de las experiencias escolares del estudiante de Medicina.  Se enfocó en las asignaturas del primer año de la carrera de Médico Cirujano de la UNAM en el plan de estudios de 2010.
Objetivo: Conocer la percepción de satisfacción escolar en cada una de las asignaturas correspondientes al primer año de la carrera de Médico Cirujano considerando aspectos del contexto escolar.
Método: Por medio de una encuesta tipo Likert se abordó la percepción del alumno en 8 categorías relacionadas con la organización escolar. Se contrastaron los resultados entre asignaturas de la misma área curricular y se utilizó la prueba Z, que compara proporciones.
Resultados: En la comparación de asignaturas del Área Biomédica se encontró que Embriología Humana resultó con mejor percepción en 6 de los 7 aspectos investigados. Para las asignaturas del Área Clínica, Integración Básico Clínica I obtuvo una mejor percepción en 3 de las 7 categorías en relación con Informática Biomédica I. En las asignaturas sociomédicas y Humanísticas se encontró que Introducción a la Salud Mental I aparece mejor posicionada en 4 de las 7 categorías en relación con Salud Pública y Comunidad.
Conclusiones: Al considerar las 3 áreas que establece el mapa curricular de la carrera de Médico Cirujano se observó en posición destacada a las Asignaturas Embriología Humana, Integración Básico Clínica I y Salud Mental I como aquellas asignaturas en las cuales los alumnos refieren una mejor satisfacción escolar. Los datos en algunas categorías abren la posibilidad de nuevos estudios, como, por ejemplo, «las horas de clase» y «la percepción de la utilidad de los contenidos»
Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom
Authors: Song Xiaoming , Duan Weike , Huang Zhinan , Liu Gaofeng , Wu Peng , Liu Tongkun , Li Ying , Hou Xilin
Published: September 2015

In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes inBrassica rapa(BraCOLgenes), the key flowering genes; (iii) exploration of the evolution ofCOLgenes in plant kingdom and construction of the evolutionary pattern ofCOLgenes; (iv) comparative analysis ofCOandFTgenes betweenBrassicaceaeandGrass, which identified several family-specific amino acids and revealed that CO and FT protein structures were similar inB. rapaandArabidopsisbut different in rice; and (v) expression analysis of photoperiod pathway-related genes inB. rapaunder different photoperiod treatments by RT-qPCR. This analysis will provide resources for understanding the flowering mechanisms and evolutionary pattern ofCOLgenes. In addition, this genome-wide comparative study ofCOLgenes may also provide clues for evolution of other flowering genes.
Atom-economical synthesis of a high silica CHA zeolite using a solvent-free route
Authors: Wang Xiong , Wu Qinming , Chen Chunyu , Pan Shuxiang , Zhang Weiping , Meng Xiangju , Maurer Stefan , Feyen Mathias , Müller Ulrich , Xiao Feng-Shou
Published: September 2015

A high silica CHA zeolite is successfully synthesized in the presence of a low-cost template of N,N,N-dimethylethylcyclohexylammonium bromide under solvent-free conditions.
A circular membrane for nano thin film micro solid oxide fuel cells with enhanced mechanical stability
Authors: Baek Jong Dae , Yoon Yong-Jin , Lee Wonyoung , Su Pei-Chen
Published: September 2015

We demonstrate a new architecture for a low temperature solid oxide fuel cell to enlarge the lateral dimension of the fragile nano thin film electrolyte from the micrometer to millimeter scale with greatly enhanced mechanical stability.
A master dynamic flow diagram for the shear thickening transition in micellar solutions
Authors: Bautista F. , Tepale N. , Fernández V. V. A. , Landázuri G. , Hernández E. , Macías E. R. , Soltero J. F. A. , Escalante J. I. , Manero O. , Puig J. E.
Published: September 2015

Shear thickening of micellar solutions of hexadecyltrimethylammonium-type surfactants and alkyltretradecylammonium bromide surfactants. A master flow diagram of the shear thickening transition. Intensity of shear thickening and a Hofmeister-like anion series.
Bidirectional three‐phase high‐frequency ac link dc–ac converter used for energy storage
Authors: Sha Deshang , Chen Jianliang
Published: September 2015

In this study, a bidirectional three‐phase high‐frequency ac link dc–ac converter is proposed for energy storage with low dc voltage. The operation of the converter changes with the direction of power flow. The proposed topology has the following advantages: high voltage conversion gain, high power factor, high conversion efficiency and high power density. The operation principle of the general control strategy, mode analysis and gate signals generation are discussed. The proposed architecture and the general control strategy have been validated by experimental results of a 300 W laboratory prototype using supercapacitors as the storage device.
Expression of maize heat shock transcription factor gene ZmHsf06 enhances the thermotolerance and drought-stress tolerance of transgenic Arabidopsis
Authors: Li Hui-cong , Zhang Hua-ning , Li Guo-liang , Liu Zi-hui , Zhang Yan-min , Zhang Hong-mei , Guo Xiu-lin
Published: September 2015

Based on the information of 25 heat shock transcription factor (Hsf) homologues in maize according to a genome-wide analysis, ZmHsf06 was cloned from maize leaves and transformed into Arabidopsis thaliana (L. Heynh.) (ecotype, Col-0). Three transgenic positive lines were selected to assess the basic and acquired thermotolerance and drought-stress tolerance under stresses and for some physiological assays. The sequence analysis indicates that ZmHsf06 contained the characteristic domains of class A type plant Hsfs. The results of qRT–PCR showed that the expression levels of ZmHsf06 were elevated by heat shock and drought stress to different extents in three transgenic lines. Phenotypic observation shows that compared with the Wt (wild-type) controls, the overexpressing ZmHsf06 of Arabidopsis plants have enhanced basal and acquired thermotolerance, stronger drought-stress tolerance and growth advantages under mild heat stress conditions. These results are further confirmed by physiological and biochemical evidence that transgenic Arabidopsis plants exhibit higher seed germination rate, longer axial-root length, higher activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT), higher leaf chlorophyll content, but lower relative electrical conductivity (REC), malondialdehyde (MDA) and osmotic potential (OP) than the Wt controls after heat shock and drought treatments. ZmHsf06 may be a central representative of maize Hsfs and could be useful in molecular breeding of maize or other crops for enhanced tolerances, particularly during terminal heat and drought stresses.
Exploring pharmacy and home-based sexually transmissible infection testing
Authors: Habel Melissa A. , Scheinmann Roberta , Verdesoto Elizabeth , Gaydos Charlotte , Bertisch Maggie , Chiasson Mary Ann
Published: September 2015

Background This study assessed the feasibility and acceptability of pharmacy and home-based sexually transmissible infection (STI) screening as alternate testing venues among emergency contraception (EC) users. Methods: The study included two phases in February 2011–July 2012. In Phase I, customers purchasing EC from eight pharmacies in Manhattan received vouchers for free STI testing at onsite medical clinics. In Phase II, three Facebook ads targeted EC users to connect them with free home-based STI test kits ordered online. Participants completed a self-administered survey. Results: Only 38 participants enrolled in Phase I: 90% female, ≤29 years (74%), 45% White non-Hispanic and 75% college graduates; 71% were not tested for STIs in the past year and 68% reported a new partner in the past 3 months. None tested positive for STIs. In Phase II, ads led to >45000 click-throughs, 382 completed the survey and 290 requested kits; 28% were returned. Phase II participants were younger and less educated than Phase I participants; six tested positive for STIs. Challenges included recruitment, pharmacy staff participation, advertising with discretion and cost. Conclusions: This study found low uptake of pharmacy and home-based testing among EC users; however, STI testing in these settings is feasible and the acceptability findings indicate an appeal among younger women for testing in non-traditional settings. Collaborating with and training pharmacy and medical staff are key elements of service provision. Future research should explore how different permutations of expanding screening in non-traditional settings could improve testing uptake and detect additional STI cases.
XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking
Authors: Schweppe Devin K. , Chavez Juan D. , Bruce James E.
Published: September 2015

Motivation: Chemical cross-linking with mass spectrometry (XL-MS) provides structural information for proteins and protein complexes in the form of crosslinked residue proximity and distance constraints between reactive residues. Utilizing spatial information derived from cross-linked residues can therefore assist with structural modeling of proteins. Selection of computationally derived model structures of proteins remains a major challenge in structural biology. The comparison of site interactions resulting from XL-MS with protein structure contact maps can assist the selection of structural models.

Availability and implementation: XLmap was implemented in R and is freely available at: http://brucelab.gs.washington.edu/software.php.

Contact:  jimbruce@uw.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data
Authors: Fidaner Işık Barış , Cankorur-Cetinkaya Ayca , Dikicioglu Duygu , Kirdar Betul , Cemgil Ali Taylan , Oliver Stephen G.
Published: September 2015

Motivation: Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets.

Results: We present a novel statistical application called CLUSTERnGO, which uses a model-based clustering algorithm that fulfils this need. This algorithm involves two components of operation. Component 1 constructs a Bayesian non-parametric model (Infinite Mixture of Piecewise Linear Sequences) and Component 2, which applies a novel clustering methodology (Two-Stage Clustering). The software can also assign biological meaning to the identified clusters using an appropriate ontology. It applies multiple hypothesis testing to report the significance of these enrichments. The algorithm has a four-phase pipeline. The application can be executed using either command-line tools or a user-friendly Graphical User Interface. The latter has been developed to address the needs of both specialist and non-specialist users. We use three diverse test cases to demonstrate the flexibility of the proposed strategy. In all cases, CLUSTERnGO not only outperformed existing algorithms in assigning unique GO term enrichments to the identified clusters, but also revealed novel insights regarding the biological systems examined, which were not uncovered in the original publications.

Availability and implementation: The C++ and QT source codes, the GUI applications for Windows, OS X and Linux operating systems and user manual are freely available for download under the GNU GPL v3 license at http://www.cmpe.boun.edu.tr/content/CnG.

Contact:  sgo24@cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling
Authors: Yu Jiyang , Silva Jose , Califano Andrea
Published: September 2015

Motivation: Functional genomics (FG) screens, using RNAi or CRISPR technology, have become a standard tool for systematic, genome-wide loss-of-function studies for therapeutic target discovery. As in many large-scale assays, however, off-target effects, variable reagents’ potency and experimental noise must be accounted for appropriately control for false positives. Indeed, rigorous statistical analysis of high-throughput FG screening data remains challenging, particularly when integrative analyses are used to combine multiple sh/sgRNAs targeting the same gene in the library.

Method: We use large RNAi and CRISPR repositories that are publicly available to evaluate a novel meta-analysis approach for FG screens via Bayesian hierarchical modeling, Screening Bayesian Evaluation and Analysis Method (ScreenBEAM).

Results: Results from our analysis show that the proposed strategy, which seamlessly combines all available data, robustly outperforms classical algorithms developed for microarray data sets as well as recent approaches designed for next generation sequencing technologies. Remarkably, the ScreenBEAM algorithm works well even when the quality of FG screens is relatively low, which accounts for about 80–95% of the public datasets.

Availability and implementation: R package and source code are available at: https://github.com/jyyu/ScreenBEAM.

Contact: ac2248@columbia.edu, jose.silva@mssm.edu, yujiyang@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
MDD–SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs
Authors: Bui Van-Minh , Lu Cheng-Tsung , Ho Thi-Trang , Lee Tzong-Yi
Published: September 2015

S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (–SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most of its physiological activities occur under control of S-hydroxylation. Therefore, discriminating the substrate site of S-sulfenylated proteins is an essential task in computational biology for the furtherance of protein structures and functions. Research into S-sulfenylated protein is currently very limited, and no dedicated tools are available for the computational identification of SOH sites. Given a total of 1096 experimentally verified S-sulfenylated proteins from humans, this study carries out a bioinformatics investigation on SOH sites based on amino acid composition and solvent-accessible surface area. A TwoSampleLogo indicates that the positively and negatively charged amino acids flanking the SOH sites may impact the formulation of S-sulfenylation in closed three-dimensional environments. In addition, the substrate motifs of SOH sites are studied using the maximal dependence decomposition (MDD). Based on the concept of binary classification between SOH and non-SOH sites, Support vector machine (SVM) is applied to learn the predictive model from MDD-identified substrate motifs. According to the evaluation results of 5-fold cross-validation, the integrated SVM model learned from substrate motifs yields an average accuracy of 0.87, significantly improving the prediction of SOH sites. Furthermore, the integrated SVM model also effectively improves the predictive performance in an independent testing set. Finally, the integrated SVM model is applied to implement an effective web resource, named MDD-SOH, to identify SOH sites with their corresponding substrate motifs.

Availability and implementation: The MDD-SOH is now freely available to all interested users at http://csb.cse.yzu.edu.tw/MDDSOH/. All of the data set used in this work is also available for download in the website.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  francis@saturn.yzu.edu.tw
Influence of call structure on the jamming avoidance response of echolocating bats
Authors: Gillam Erin H. , Montero B. Karina
Published: September 2015

Bats rely heavily on echolocation for orientation and prey detection, hence acoustic signals that interfere with echo reception are problematic. When flying in the presence of other bats, some species adjust their echolocation to avoid frequency overlap with the calls of nearby conspecifics, known as a jamming avoidance response (JAR). One aspect of JAR that has not been thoroughly examined is how the spectral structure of the jamming signal impacts the jamming response. Our objective was to examine how the structural characteristics of an echolocation broadcast impact JAR in free-flying Brazilian free-tailed bats, Tadarida brasiliensis . We created 4 echolocation playbacks that differed only in call shape and frequency modulation. We examined the response of bats when flying in the presence of an unchanging broadcast (static stimulus) and when the playback signal was abruptly switched as the bat approached the speaker (dynamic stimulus). Results revealed that the bandwidth of the interfering signal impacted the strength of the observed JAR, while the presence and/or length of a terminal quasi-constant frequency section in the interfering signal did not. Our results agree with laboratory studies documenting JAR in the presence of white noise, as well as field studies demonstrating extensive variability in the echolocation calls of Brazilian free-tailed bats. We relate these results to previous findings on JAR, including a recent study documenting no JAR in a bat species and suggest further experiments to tease apart the physiological limitations of JAR. Overall, this study provides additional insight into the signal processing capabilities of bats and improves our understanding of how bats are able to orient using sound in a noisy world.
First measurement of H i 21 cm emission from a GRB host galaxy indicates a post-merger system
Authors: Arabsalmani Maryam , Roychowdhury Sambit , Zwaan Martin A. , Kanekar Nissim , Michałowski Michał J.
Published: September 2015

We report the detection and mapping of atomic hydrogen in H i 21 cm emission from ESO 184-G82, the host galaxy of the gamma-ray burst 980425. This is the first instance where H i in emission has been detected from a galaxy hosting a gamma-ray burst (GRB). ESO 184-G82 is an isolated galaxy and contains a Wolf–Rayet region close to the location of the GRB and the associated supernova, SN 1998bw. This is one of the most luminous H ii regions identified in the local Universe, with a very high inferred density of star formation. The H i 21 cm observations reveal a high H i mass for the galaxy, twice as large as the stellar mass. The spatial and velocity distribution of the H i 21 cm emission reveals a disturbed rotating gas disc, which suggests that the galaxy has undergone a recent minor merger that disrupted its rotation. We find that the Wolf–Rayet region and the GRB are both located in the highest H i column density region of the galaxy. We speculate that the merger event has resulted in shock compression of the gas, triggering extreme star formation activity, and resulting in the formation of both the Wolf–Rayet region and the GRB. The high H i column density environment of the GRB is consistent with the high H i column densities seen in absorption in the host galaxies of high-redshift GRBs.
Discovery of two new bright magnetic B stars: i Car and Atlas
Authors: Neiner Coralie , Buysschaert Bram , Oksala Mary E. , Blazère Aurore
Published: September 2015

The BRITE (BRIght Target Explorer) constellation of nanosatellites performs seismology of bright stars via high-precision photometry. In this context, we initiated a high-resolution, high signal-to-noise, high-sensitivity, spectropolarimetric survey of all stars brighter than V = 4. The goal of this survey is to detect new bright magnetic stars and provide prime targets for both detailed magnetic studies and asteroseismology with BRITE. Circularly polarized spectra were acquired with Narval at TBL (Bernard Lyot Telescope, France) and HARPSpol at ESO (European Southern Observatory) in La Silla (Chile). We discovered two new magnetic B stars: the B3V star i Car and the B8V component of the binary star Atlas. Each star was observed twice to confirm the magnetic detections and check for variability. These bright magnetic B stars are prime targets for asteroseismology and for flux-demanding techniques, such as interferometry.
Epidemiology and Outcome of Trichosporon Fungemia: A Review of 185 Reported Cases From 1975 to 2014
Authors: Liao Yong , Lu Xuelian , Yang Suteng , Luo Yi , Chen Qi , Yang Rongya
Published: September 2015

Background.  Trichosporon species have emerged as an important non-Candida spp yeast pathogen in immunocompromised patients in recent decades; however, the systemic analysis of Trichosporon epidemiology has seldom been reported.

Methods.  We reviewed 185 reported cases of Trichosporon fungemia from 1975 to 2014 in the English-language literature, and the epidemiology and prognostic factors of the included cases are described.

Results.  The number of cases reported has increased with time, especially over the past decade. During the 3 decades from 1975 to 2004, the most commonly used antifungal compounds were amphotericin B/liposomal amphotericin B; however, in recent decades (2005–2014), triazoles (especially voriconazole) have become the most widely used agents, significantly improving outcome in the reported cases. Correlation analysis revealed that negative outcome is associated with several prognostic factors, including a history of antimicrobial use, bacterial bloodstream coinfection, prophylactic/empirical antifungal therapy, Trichosporon beigelii infection, and receiving the antifungal regimen of amphotericin B/liposomal amphotericin B. In addition, a significantly greater proportion of patients with a positive outcome had fungemia without invasive tissue infection and received a voriconazole regimen or an AmB-triazole combined regimen. Significant positive outcome was also associated with patients who had recovered from neutropenia or after central venous catheter removal.

Conclusions.  Voriconazole can be recommended as a first-line antifungal compound to treat Trichosporon fungemia; the immune status of the host plays a crucial role in the outcome of this infection, and the removal of vascular catheters should be considered if feasible.
Efficiency, Welfare, and Political Competition
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Authors: Bierbrauer Felix J. , Boyer Pierre C.
Published: September 2015

We study political competition in an environment in which voters have private information about their preferences. Our framework covers models of income taxation, public-goods provision, or publicly provided private goods. Politicians are vote-share maximizers. They can propose any policy that is resource-feasible and incentive-compatible. They can also offer special favors to subsets of the electorate. We prove two main results. First, the unique symmetric equilibrium is such that policies are surplus-maximizing and hence first-best Pareto-efficient. Second, there is a surplus-maximizing policy that wins a majority against any welfare-maximizing policy. Thus, in our model, policies that trade off equity and efficiency considerations are politically infeasible.
Prothrombin Complex Concentrate Is Effective in Treating the Anticoagulant Effects of Dabigatran in a Porcine Polytrauma Model
Authors: Honickel Markus , Braunschweig Till , van Ryn Joanne , ten Cate Hugo , Spronk Henri M. H. , Rossaint Rolf , Grottke Oliver
Published: September 2015

AbstractAbstract

In a porcine traumatic animal model of bleeding, 50 U/kg of a four-component prothrombin complex concentrates reversed dabigatran-associated bleeding. Higher doses of 100 U/kg were also effective but associated with a potential hypercoagulable effect.

Background

In the event of trauma, emergency reversal of anticoagulation therapy may be required. However, no specific reversal agents are routinely available for the direct oral anticoagulants such as dabigatran. The authors investigated four-factor prothrombin complex concentrate (PCC) for treating dabigatran-induced anticoagulation in a porcine polytrauma model.

Methods

Dabigatran etexilate was given orally for 3 days and intravenously on day 4 to 32 pigs. Animals were randomized 1:1:1:1 to PCC (25, 50, or 100 U/kg) or saline. Study medication was administered 12 min after bilateral femur fractures and blunt liver injury. The primary endpoint was blood loss at 300 min.

Results

The mean plasma concentration of dabigatran was 487 ± 161 ng/ml after intravenous administration. Blood loss was 3,855 ± 258 ml in controls and 3,588 ± 241 ml in the PCC25 group. In the PCC50 and PCC100 groups, blood loss was significantly lower: 1,749 ± 47 ml and 1,692 ± 97 ml, respectively. PCC50 and PCC100 effectively reduced dabigatran’s effects on coagulation parameters, whereas control and (to a lesser extent) PCC25 animals developed severe coagulopathy. Sustained increases in endogenous thrombin potential occurred with PCC50 and PCC100.

Conclusion

Four-factor PCC (50 or 100 U/kg) is effective in reducing blood loss in dabigatran-anticoagulated pigs, but higher doses may induce a procoagulant state.
Promoting Action on Research Implementation in Health Services framework applied to TeamSTEPPS implementation in small rural hospitals
Authors: Ward Marcia M. , Baloh Jure , Zhu Xi , Stewart Greg L.
Published: September 2015

Background:

A particularly useful model for examining implementation of quality improvement interventions in health care settings is the PARIHS (Promoting Action on Research Implementation in Health Services) framework developed by Kitson and colleagues. The PARIHS framework proposes three elements (evidence, context, and facilitation) that are related to successful implementation.

Purposes:

An evidence-based program focused on quality enhancement in health care, termed TeamSTEPPS (Team Strategies and Tools to Enhance Performance and Patient Safety), has been widely promoted by the Agency for Healthcare Research and Quality, but research is needed to better understand its implementation. We apply the PARIHS framework in studying TeamSTEPPS implementation to identify elements that are most closely related to successful implementation.

Methodology/Approach:

Quarterly interviews were conducted over a 9-month period in 13 small rural hospitals that implemented TeamSTEPPS. Interview quotes that were related to each of the PARIHS elements were identified using directed content analysis. Transcripts were also scored quantitatively, and bivariate regression analysis was employed to explore relationships between PARIHS elements and successful implementation related to planning activities.

Findings:

The current findings provide support for the PARIHS framework and identified two of the three PARIHS elements (context and facilitation) as important contributors to successful implementation.

Practice Implications:

This study applies the PARIHS framework to TeamSTEPPS, a widely used quality initiative focused on improving health care quality and patient safety. By focusing on small rural hospitals that undertook this quality improvement activity of their own accord, our findings represent effectiveness research in an understudied segment of the health care delivery system. By identifying context and facilitation as the most important contributors to successful implementation, these analyses provide a focus for efficient and effective sustainment of TeamSTEPPS efforts.