bluuebunny/crossref_metadata_2025_split huggingface dataset:
Botryosphaeria sinensia sp nov., a new species from China
Authors: Zhou Yupei , Dou Zhipeng , He Wei , Zhang Xiaodong , Zhang Ying 
Published: January 2016

A new Botryosphaeria species (B. sinensia) is described and illustrated from China. It is characterized by erumpent, botryose clustered ascostromata, ostiolate ascomata, bitunicate, 8-spored and clavate asci, filiform, rarely branched pseudoparaphyses, hyaline, 1-celled, fusiform ascospores, and a Fusicoccum asexual morph. The hyaline old and discharged conidia with 1–2 septa, broader spermatia formed in the culture and smaller ascostroma readily distinguished it from B. dothidea and other species in Botryosphaeria. The intergenic spacer (ITS) and translation elongation factor 1-alpha (EF1) DNA sequence analysis results also support its separation from other Botryosphaeria species. Its relationships with other species of Botryosphaeria are also discussed based on morphology and DNA sequence comparisons.
Epidemiology of Medial Ulnar Collateral Ligament Reconstruction
Authors: Hodgins Justin L. , Vitale Mark , Arons Raymond R. , Ahmad Christopher S. 
Published: January 2016

Background: Despite an increase in the prevalence of medial ulnar collateral ligament (UCL) reconstruction of the elbow in professional baseball and popularity within the media, there are no population-based studies examining the incidence of UCL reconstruction. Purpose: To examine the epidemiological trends of UCL reconstruction on a statewide level over a 10-year period. The primary endpoint was the yearly rate of UCL reconstruction over time; secondary endpoints included patient demographics, institution volumes, and concomitant procedures on the ulnar nerve. Study Design: Descriptive epidemiology study. Methods: The New York Statewide Planning and Research Cooperative System (SPARCS) database contains records for each ambulatory discharge in New York State. This database was used to identify all UCL reconstructions in New York State from 2002 to 2011 using the outpatient CPT-4 ( Current Procedural Terminology, 4th Revision) code. Assessed were patient age, sex, ethnicity, insurance status, and associated procedures, as well as hospital volume. Results: There was a significant yearly increase in the number of UCL reconstructions ( P < .001) performed in New York State from 2002 to 2011. The volume of UCL reconstructions increased by 193%, and the rate per 100,000 population tripled from 0.15 to 0.45. The mean ± SD age was 21.6 ± 8.89 years, and there was a significant trend for an increased frequency in UCL reconstruction in patients aged 17 to 18 and 19 to 20 years ( P < .001). Male patients were 11.8 times more likely to have a UCL reconstruction than female patients ( P < .001), and individuals with private insurance were 25 times more likely to have a UCL reconstruction than those with Medicaid ( P = .0014). There was a 400% increase in concomitant ulnar nerve release/transposition performed over time in the study period, representing a significant increase in the frequency of ulnar nerve procedures at the time of UCL reconstruction ( P < .001). Conclusion: The frequency of UCL reconstruction is steadily rising in New York State and becoming more common in adolescent athletes. Emphasis on public education on the risks of overuse throwing injuries and the importance of adhering to preventative guidelines is essential in youth baseball today.
Injection Technique and Pen Needle Design Affect Leakage From Skin After Subcutaneous Injections
Authors: Præstmark Kezia Ann , Stallknecht Bente , Jensen Morten Lind , Sparre Thomas , Madsen Nils Berg , Kildegaard Jonas 
Published: January 2016

Background: After a subcutaneous injection fluid might leak out of the skin, commonly referred to as leakage or backflow. The objective was to examine the influence of needle design and injection technique on leakage after injections in the subcutaneous tissue of humans and pigs. Method: Leakage data were obtained from a post hoc analysis of clinical trial data and from a pig study. Data from the clinical study were used to determine leakage as a function of injection volume, speed and region. Data from the pig study were used to determine leakage as a function of needle wall thickness, needle taper, injection angle, and wait time from end of injection to withdrawal of needle from skin. Results: Leakage volume was positively related to injection volume. Injections in the abdomen caused less leakage than thigh injections. A 32G needle caused less leakage than a 31G and a 32G tip (tapered) needle, and a “straight in” 90° needle insertion angle caused less leakage than an angled (~45°) insertion. Wait times of minimum 3 seconds caused less leakage than immediate withdrawal of the needle after injection. Needle wall thickness and injection speed did not influence leakage. Conclusions: Leakage will be minimized using a thin needle, using 90° needle insertion in the abdomen, injecting maximum 800 µL at a time, and waiting at least 3 seconds after the injection until the needle is withdrawn from the skin.
99mTc-anti-TNF-α antibody for the imaging of disease activity in pulmonary sarcoidosis
Authors: Vis Roeland , Malviya Gaurav , Signore Alberto , Grutters Jan C. , Meek Bob , van de Garde Ewoudt M.W. , Keijsers Ruth G.M. 
Published: January 2016

Infliximab, a monoclonal antibody directed against tumour necrosis factor (TNF)-α, is used in the treatment of refractory sarcoidosis. However, the clinical response is variable and a tool to select responders beforehand is highly desirable. In this study we evaluated scintigraphy with technetium-99m (99mTc)-labelled infliximab for the imaging of disease activity in patients with pulmonary sarcoidosis.10 patients were studied using single photon emission computed tomography/computed tomography (CT) 6 h and 20 h after intravenous administration of 370 MBq of99mTc-infliximab. Correlation analysis was performed between tissue accumulation of99mTc-infliximab and laboratory parameters (including soluble interleukin-2 receptor and angiotensin-converting enzyme), lung function parameters (including forced expiratory volume in 1 s and the diffusing capacity of the lung for carbon monoxide) and18F-fluorodeoxyglucose (FDG) positron emission tomography (PET)/CT.Analysis showed selective and variable accumulation of99mTc-infliximab in the target tissue. Accumulation correlated positively with all four laboratory parameters and negatively with all four lung function parameters, yielding better correlations than serum TNF-α levels or18F-FDG PET/CT.99mTc-infliximab accumulation reflects thein situTNF-α expression in an individual patient and therefore provides valuable information on the presence of the biological target for anti-TNF-α therapy.
The effect of sex and age on the comorbidity burden of OSA: an observational analysis from a large nationwide US health claims database
Authors: Mokhlesi Babak , Ham Sandra A. , Gozal David 
Published: January 2016

Obstructive sleep apnoea (OSA) is a highly prevalent condition but studies exploring the burden of OSA-associated comorbidities have been limited by small sample sizes with underrepresentation of women.We queried the Truven Health MarketScan Research Databases 2003–2012, which is a collection of health insurance claims for working adults and retirees with employer-sponsored health insurance. Adults with a diagnostic code for OSA with at least 12 months of follow-up from the index date of OSA diagnosis were compared to a matched random sample. Comorbidities were assessed using International Classification of Diseases, Ninth Edition, codes. A logistic regression model was constructed to test the independent association between OSA and comorbidities.Our cohort included 1 704 905 patients with OSA and 1 704 417 matched controls. All comorbidities were significantly more prevalent in OSA patients. Type 2 diabetes and ischaemic heart disease were more prevalent in men but hypertension and depression were more prevalent in women with OSA. In contrast, the sex differences in the prevalence of congestive heart failure, arrhythmias and stroke were less pronounced. The prevalence of comorbidities increased with age but the effect of age varied based on the specific comorbidity. The divergence between OSA and controls was more pronounced after the sixth decade of life for most cardiovascular diseases (i.e.heart failure, ischaemic heart disease, stroke and arrhythmias), while depression exhibited an opposite trend. In a fully adjusted model, the odds of all comorbidities were significantly increased in OSA patients.In a large, nationally representative sample of working and retired people, OSA is strongly associated with significant comorbidities in both men and women with unique sex differences emerging.
EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms
Authors: Janies Daniel A. , Witter Zach , Linchangco Gregorio V. , Foltz David W. , Miller Allison K. , Kerr Alexander M. , Jay Jeremy , Reid Robert W. , Wray Gregory A. 
Published: January 2016

Abstract
Background
One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echinoderm phylogeny and transcriptomics. We used RNA-Seq to profile adult tissues from 42 echinoderm specimens from 24 orders and 37 families. In order to achieve sampling members of clades that span key evolutionary divergence, many of our exemplars were collected from deep and polar seas.

Description
A small fraction of the transcriptome data we produced is being used for phylogenetic reconstruction. Thus to make a larger dataset available to researchers with a wide variety of interests, we made a web-based application, EchinoDB (http://echinodb.uncc.edu). EchinoDB is a repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity.

Conclusions
From transcripts we identified 749,397 clusters of orthologous loci. We have developed the information technology to manage and search the loci their annotations with respect to the Sea Urchin (Strongylocentrotus purpuratus) genome. Several users have already taken advantage of these data for spin-off projects in developmental biology, gene family studies, and neuroscience. We hope others will search EchinoDB to discover datasets relevant to a variety of additional questions in comparative biology.
Integrated analysis of microRNA regulatory network in nasopharyngeal carcinoma with deep sequencing
Authors: Wang Fan , Lu Juan , Peng Xiaohong , Wang Jie , Liu Xiong , Chen Xiaomei , Jiang Yiqi , Li Xiangping , Zhang Bao 
Published: January 2016

AbstractBackgroundMicroRNAs (miRNAs) have been shown to play a critical role in the development and progression of nasopharyngeal carcinoma (NPC). Although accumulating studies have been performed on the molecular mechanisms of NPC, the miRNA regulatory networks in cancer progression remain largely unknown. Laser capture microdissection (LCM) and deep sequencing are powerful tools that can help us to detect the integrated view of miRNA-target network.MethodsIllumina Hiseq2000 deep sequencing was used to screen differentially expressed miRNAs in laser-microdessected biopsies between 12 NPC and 8 chronic nasopharyngitis patients. The result was validated by real-time PCR on 201 NPC and 25 chronic nasopharyngitis patients. The potential candidate target genes of the miRNAs were predicted using published target prediction softwares (RNAhybrid, TargetScan, Miranda, PITA), and the overlay part was analyzed in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological process. The miRNA regulatory network analysis was performed using the Ingenuity Pathway Analysis (IPA) software.ResultsEight differentially expressed miRNAs were identified between NPC and chronic nasopharyngitis patients by deep sequencing. Further qRT-PCR assays confirmed 3 down-regulated miRNAs (miR-34c-5p, miR-375 and miR-449c-5p), 4 up-regulated miRNAs (miR-205-5p, miR-92a-3p, miR-193b-3p and miR-27a-5p). Additionally, the low level of miR-34c-5p (miR-34c) was significantly correlated with advanced TNM stage. GO and KEGG enrichment analyses showed that 914 target genes were involved in cell cycle, cytokine secretion and tumor immunology, and so on. IPA revealed that cancer was the top disease associated with those dysregulated miRNAs, and the genes regulated by miR-34c were in the center of miRNA-mRNA regulatory network, including TP53, CCND1, CDK6, MET and BCL2, and the PI3K/AKT/ mTOR signaling was regarded as a significant function pathway in this network.ConclusionOur study presents the current knowledge of miRNA regulatory network in NPC with combination of bioinformatics analysis and literature research. The hypothesis of miR-34c regulatory pathway may be beneficial in guiding further studies on the molecular mechanism of NPC tumorigenesis.
Protective role of microRNA-29a in denatured dermis and skin fibroblast cells after thermal injury
Authors: Zhou Jie , Zhang Xipeng , Liang Pengfei , Ren Licheng , Zeng Jizhang , Zhang Minghua , Zhang Pihong , Huang Xiaoyuan 
Published: January 2016

ABSTRACT
Our previous study has suggested that downregulated microRNA (miR)-29a in denatured dermis might be involved in burn wound healing. However, the exact role of miR-29a in healing of burn injury still remains unclear. Here, we found that expression of miR-29a was notably upregulated in denatured dermis tissues and skin fibroblast cells after thermal injury, and thereafter gradually downregulated compared with control group. By contrast, the expression of collagen, type I, alpha 2 (COL1A2) and vascular endothelial growth factor (VEGF-A) were first reduced and subsequently upregulated in denatured dermis tissues and skin fibroblast cells after thermal injury. We further identified COL1A2 as a novel target of miR-29a, which is involved in type I collagen synthesis, and showed that miR-29a negatively regulated the expression level of COL1A2 in skin fibroblast cells. In addition, VEGF-A, another target gene of miR-29a, was also negatively mediated by miR-29a in skin fibroblast cells. Inhibition of miR-29a expression significantly promoted the proliferation and migration of skin fibroblast cells after thermal injury, and knockdown of COL1A2 and VEGF-A reversed the effects of miR-29a on the proliferation and migration of skin fibroblast cells. Furthermore, we found that Notch2/Jagged2 signaling was involved in miR-29a response to burn wound healing. Our findings suggest that downregulated miR-29a in denatured dermis may help burn wound healing in the later phase, probably via upregulation of COL1A2 and VEGF-A expression, which can further enhance type I collagen synthesis and angiogenesis.
Nanog induces suppression of senescence through downregulation of p27KIP1 expression
Authors: Münst Bernhard , Thier Marc Christian , Winnemöller Dirk , Helfen Martina , Thummer Rajkumar P. , Edenhofer Frank 
Published: January 2016

ABSTRACT
A comprehensive analysis of the molecular network of cellular factors establishing and maintaining pluripotency as well as self renewal of pluripotent stem cells is key for further progress in understanding basic stem cell biology. Nanog is necessary for the natural induction of pluripotency in early mammalian development but dispensable for both its maintenance and its artificial induction. To gain further insight into the molecular activity of Nanog, we analyzed the outcomes of Nanog gain-of-function in various cell models employing a recently developed biologically active recombinant cell-permeant protein, Nanog-TAT. We found that Nanog enhances the proliferation of both NIH 3T3 and primary fibroblast cells. Nanog transduction into primary fibroblasts results in suppression of senescence-associated β-galactosidase activity. Investigation of cell cycle factors revealed that transient activation of Nanog correlates with consistent downregulation of the cell cycle inhibitor p27KIP1 (also known as CDKN1B). By performing chromatin immunoprecipitation analysis, we confirmed bona fide Nanog-binding sites upstream of the p27KIP1 gene, establishing a direct link between physical occupancy and functional regulation. Our data demonstrates that Nanog enhances proliferation of fibroblasts through transcriptional regulation of cell cycle inhibitor p27 gene.
«Using Computers in Physics Experiments» Elective Course Curriculum
Authors: Гуляев  , Gulyaev Igor 
Published: January 2016

Proposed is the curriculum for the elective course on using computers for physical experiments. This includes planning the students’ project activities on
studying physics phenomena based on using a computer as the main measuring instrument.
The students are expected to master technology of how to fabricate an electronic device, as well as computer oscillographic testing of physics processes;
to examine motions of physical bodies using the computer stroboscope, to learn to measure short time intervals and small temperature changes, to
study a pulse method for measuring the speed of sound. All projects are investigative by nature and intended to motivate students to study Physics
and contribute to their intellectual development. Consecutive implementation of the proposed investigative projects would help students to develop
experimental skills in the fi eld of natural computer-based experiments. Testing the elective course proposed at the school premises has confi rmed its
comprehensibility for students and suitability for the high school.
The Structure and Thermochemistry of Three Fe-Mg Chlorites
Authors: Aja Stephen , Omotoso Oladipo , Bertoldi Christian , Dachs Edgar , Benisek Artur 
Published: January 2016

AbstractChlorites are petrogenetically important minerals, exercise controls on petroleum reservoir qualities, are common in alteration zones during hydrothermal ore mineralization, and may form during carbon sequestration in sedimentary formations. Chlorite thermochemistry and structure have been investigated, in the present study, to facilitate an improved understanding of chlorite equilibria.Three natural IIb chlorites were studied by powder diffraction and calorimetric methods (low-temperature relaxation calorimetry using a Physical Properties Measurement System [PPMS] and differential scanning calorimetry [DSC]). The samples include a low-Fe clinochlore [Mg-Chl] and two Fe-rich chlorites from Windsor [Fe-Chl(W)] and Michigan [Fe-Chl(M)]. The structure of each chlorite was refined in the ideal C2/m symmetry using Rietveld techniques. Lattice parameters for the Windsor chlorite are a = 5.3786(6) Å, b = 9.3176(9) Å, c = 14.2187(6) Å, β = 96.98(10)°. The Michigan chlorite returned a = 5.3897(3) Å, b = 9.3300(3) Å, c = 14.2376(2) Å, β = 97.043(5)° whereas the low-Fe clinochlore yielded a = 5.3301(3) Å, b = 9.2231(8) Å, c = 14.2912(4) Å, β= 97.03(10)°.Heat capacities (Cp) for the three natural chlorites were measured using both PPMS (2–303 K) and DSC (282–564 K). Employing a combination of Debye-Einstein-Schottky functions, the lattice dynamics component of the Cp at lower temperature was evaluated allowing a separation of the magnetic spin ordering component of Cp from the lattice vibrational part. For Mg-Chl, Fe-Chl(W), and Fe-Chl(M), the polynomials defining the temperature dependencies of the heat capacities between 280 and 570 K are:Cp = 1185.44(±68.93) − 9753.21(±186.85)T−0.5 − 1.9094(±1.0288)·107T−2 + 3.3013(±1.5363)·109T−3Cp = 1006.06(±48.46) − 4134.83 (±1515.16)T−0.5 − 40.0949(±6.9413)·106T−2 + 5.9386(±1.0287)·109T−3andCp = 1268.60(±67.16) − 11983.09(±2107.07)T−0.5 − 7.6037(±9.6417)·106T−2 + 1.5398(±1.4187)·109T−3, respectively.Standard state molar thermodynamic functions, CP, ST, (HT−H0)/T, and φ were evaluated for the samples. S298.15 for Fe-Chl(W), Mg-Chl, and Fe-Chl(M) were found to be 499.14 ± 3.40, 437.81 ± 3.00 and 515.06 ± 3.60 J mol-1K-1, respectively, whereas S° for Fe-Chl(W) and Mg-Chl were determined to be 578.24 ± 3.76 and 503.21 ± 3.60 J mol−1K−1, −1
The Illite—Aluminoceladonite Series: Distinguishing Features and Identification Criteria from X-ray Diffraction and Infrared Spectroscopy Data
Authors: Zviagina Bella B. , Drits Victor A. , Środoń Jan , McCarty Douglas K. , Dorzhieva Olga V. 
Published: January 2016

AbstractAl-rich K-dioctahedral 1M and 1Md micas are abundant in sedimentary rocks and form a continuous compositional series from (Mg,Fe)-poor illite to aluminoceladonite through Mg-rich illite. The complexity and heterogeneity of chemical composition and structural features, as well as the lack of reliable diagnostic criteria, complicate the identification of these mica varieties. The objectives of the present study were to reveal the structural and crystal-chemical variability in the illite—aluminoceladonite series, and to define the composition ranges and identification criteria for the mica varieties in the series. A collection of illite and aluminoceladonite samples of various compositions was studied by X-ray diffraction (XRD) and Fourier-transform infrared (FTIR) spectroscopy. Analysis of the relationships between unit-cell parameters and cation composition showed that the series includes three groups, (Mg,Fe)-poor illites, Mg-rich illites, and aluminoceladonites, each characterized by a unique combination of unit-cell parameter variation ranges. The distinctive features of aluminoceladonite are reduced values of csinβ and |ccosβ/a| in combination with b parameters that are smaller than those for Mg-rich illites, and slightly greater than those of (Mg,Fe)-poor illites. The compositional boundary between illite and aluminoceladonite occurs at Si = ~3.7 and Mg + Fe2+ = ~ 0.6 atoms per O10(OH)2.A new approach to the interpretation of the FTIR spectroscopy data involving new relationships between band positons and cation composition of (Mg,Fe)-poor illites, Mg-rich illites, and aluminoceladonites provides additional diagnostic features that include the band positions and profile in the regions of Si—O bending, Si—O stretching, and OH-stretching vibrations. A sharp maximum from the AlOHMg stretching vibration at ~3600 cm−1, the presence of a MgOHMg stretching vibration at 3583–3585 cm−1, as well as characteristic band positions in the Si—O bending (435–, 468–472, and 509–520 cm−1) and stretching regions (985–1012 and 1090–1112 cm−1), are typical of aluminoceladonite.
Transport and Exchange Behavior of Ions in Bentonite During Electro-Osmotic Consolidation
Authors: Wu Hui , Hu Liming , Zhang Lin , Wen Qingbo 
Published: January 2016

AbstractElectro-osmotic consolidation is considered to be an efficient technique for dewatering and consolidation of soft soil. In the present study, four experiments were conducted on a Na-rich bentonite using two reactive electrodes (copper and iron) and two inert electrodes (graphite and stainless steel) to study the transport and exchange behavior of ions during electro-osmotic consolidation. The results showed that the changes in pH and ion contents were limited to the zone close to the electrode due to the buffering capacity of bentonite and the significant reduction in electric current density. The ion concentration profiles indicated that Na+ ions were largely responsible for carrying the pore water to the cathode. The reactive electrodes are better at transporting Na+ ions and therefore induce better drainage than inert electrodes. Ion-exchange reactions occurred between the Cu2+ and Fe2+/Fe3+ ions released and pre-existing Na+ ions in the electrical double layer, causing decreased water adsorption capacity and plasticity index. The swelling and shrinkage characteristics of the bentonite were thus reduced, and electroosmotic consolidation may therefore provide a new way to improve the stability of expansive soils and slopes.