bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences
Authors: Che Xianli , Zhang Min , Zhao Yanyan , Zhang Qiang , Quan Qing , Møller Anders , Zou Fasheng 
Published: January 2018

AbstractEcological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.
Relationship between serum cortisol level and degree of false lumen thrombosis in patients with uncomplicated type B aortic dissection
Authors: Wu Yani , Sun Yudong , Wei Xiaolong , Zhang Lei , Han Tonglei , Zhao Zhiqing , Zhou Jian , Jing Zaiping 
Published: January 2018

AbstractPartial thrombosis of the false lumen in uncomplicated type B aortic dissection (uTBAD) is associated with an increased late mortality risk. Whether the serum cortisol level can affect false lumen thrombosis in patients with uTBAD has not been well characterized. This study was performed on 87 patients with uTBAD. A curve-fitting method was used to analyze the relationship between serum cortisol and partial thrombosis of false lumen. Univariate and multivariate logistic regression analyses were used to identify false lumen partial thrombosis–associated serum cortisol. Curve-fitting’s result revealed a characteristic U shape, and 14.0 µg/dL was considered as the cutoff point for serum cortisol. The results of univariate and multivariate logistic regression analyses suggested that when trisecting the serum cortisol level into three parts, the low and high levels of serum cortisol could significantly affect the occurrence of false lumen partial thrombosis compared with the middle level. The odds ratio value of the low and high levels of serum cortisol was 6.12 and 4.65, respectively, in the univariate analysis, and 24.32 and 3.93, respectively, in the multivariate analysis. Low or high levels of serum cortisol might influence the natural result of uTBAD through affecting the false lumen thrombosis.
Photonic spin Hall effect enabled refractive index sensor using weak measurements
Authors: Zhou Xinxing , Sheng Lijuan , Ling Xiaohui 
Published: January 2018

AbstractIn this work, we theoretically propose an optical biosensor (consists of a BK7 glass, a metal film, and a graphene sheet) based on photonic spin Hall effect (SHE). We establish a quantitative relationship between the spin-dependent shift in photonic SHE and the refractive index of sensing medium. It is found that, by considering the surface plasmon resonance effect, the refractive index variations owing to the adsorption of biomolecules in sensing medium can effectively change the spin-dependent displacements. Remarkably, using the weak measurement method, this tiny spin-dependent shifts can be detected with a desirable accuracy so that the corresponding biomolecules concentration can be determined.
Transcriptome Analysis in Spleen Reveals Differential Regulation of Response to Newcastle Disease Virus in Two Chicken Lines
Authors: Zhang Jibin , Kaiser Michael G. , Deist Melissa S. , Gallardo Rodrigo A. , Bunn David A. , Kelly Terra R. , Dekkers Jack C. M. , Zhou Huaijun , Lamont Susan J. 
Published: January 2018

AbstractEnhancing genetic resistance of chickens to Newcastle Disease Virus (NDV) provides a promising way to improve poultry health, and to alleviate poverty and food insecurity in developing countries. In this study, two inbred chicken lines with different responses to NDV, Fayoumi and Leghorn, were challenged with LaSota NDV strain at 21 days of age. Through transcriptome analysis, gene expression in spleen at 2 and 6 days post-inoculation was compared between NDV-infected and control groups, as well as between chicken lines. At a false discovery rate <0.05, Fayoumi chickens, which are relatively more resistant to NDV, showed fewer differentially expressed genes (DEGs) than Leghorn chickens. Several interferon-stimulated genes were identified as important DEGs regulating immune response to NDV in chicken. Pathways predicted by IPA analysis, such as "EIF-signaling", "actin cytoskeleton organization nitric oxide production" and "coagulation system" may contribute to resistance to NDV in Fayoumi chickens. The identified DEGs and predicted pathways may contribute to differential responses to NDV between the two chicken lines and provide potential targets for breeding chickens that are more resistant to NDV.
Plasma proteomic study of acute mountain sickness susceptible and resistant individuals
Authors: Lu Hui , Wang Rong , Li Wenbin , Xie Hua , Wang Chang , Hao Ying , Sun Yuhuan , Jia Zhengping 
Published: January 2018

AbstractAlthough extensive studies have focused on the development of acute mountain sickness (AMS), the exact mechanisms of AMS are still obscure. In this study, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis to identify novel AMS−associated biomarkers in human plasma. After 9 hours of hypobaric hypoxia the abundance of proteins related to tricarboxylic acid (TCA) cycle, glycolysis, ribosome, and proteasome were significantly reduced in AMS resistant (AMS−) group, but not in AMS susceptible (AMS+) group. This suggested that AMS− individuals could reduce oxygen consumption via repressing TCA cycle and glycolysis, and reduce energy consumption through decreasing protein degradation and synthesis compared to AMS+ individuals after acute hypoxic exposure. The inflammatory response might be decreased resulting from the repressed TCA cycle. We propose that the ability for oxygen consumption reduction may play an important role in the development of AMS. Our present plasma proteomic study in plateau of the Han Chinese volunteers gives new data to address the development of AMS and potential AMS correlative biomarkers.
Word Mode: a crowding-free reading protocol for individuals with macular disease
Authors: Wallis Stuart , Yang Yit , Anderson Stephen J. 
Published: January 2018

AbstractCentral retinal loss through macular disease markedly reduces the ability to read largely because identification of a word using peripheral vision is negatively influenced by nearby text, a phenomenon termed visual crowding. Here, we present a novel peripheral reading protocol, termed Word Mode, that eliminates crowding by presenting each word in isolation but in a position that mimics its natural position in the line of text being read, with each new word elicited using a self-paced button press. We used a gaze-contingent paradigm to simulate a central scotoma in four normally-sighted observers, and measured oral reading speed for text positioned 7.5° in the inferior field. Compared with reading whole sentences, our crowding-free protocol increased peripheral reading speeds by up to a factor of seven, resulted in significantly fewer reading errors and fixations per sentence, and reduced both the critical print size and the text size required for spot reading by 0.2–0.3 logMAR. We conclude that the level of reading efficiency afforded by the crowding-free reading protocol Word Mode may return reading as a viable activity to many individuals with macular disease.
Numerical inversion analysis on front‐face temperature rise of Al alloy suffered from long continuing current in lightning
Authors: Liu Yakun , Fu Zhengcai , Liu Quanzhen , Liu Baoquan , Xia Hailiang 
Published: January 2018

The front‐face temperature rise of Al alloy subjected to the high‐energy long continuing current (LCC) component in lightning is important but difficult to measure. Therefore, a numerical inversion model based on the control volume finite element method is proposed to analyse the front‐face temperature rise of Al alloy deduced from the rear‐face temperature rise measured in simulated LCC experiment. In this model, Al sample is divided into discrete control‐volume units with continuous medium by grids, forming internal nodes, surface nodes, edge nodes, and corner nodes. Temperature governing equations for different nodes are derived from Fourier's heat conduction law and solved with finite difference method in time and spatial domain. The secant method is used to make the optimal approximation to experimental data. The results show that subjected to LCC with amplitude 404 A and duration 520 ms, the highest front‐face temperature rise of Al alloy is 10,800 K. The damaged area calculated by the proposed model is 298.7 mm2. The relative error is 4.8% compared with the experimental result 314.0 mm2. The energy consumed in all processes is 6710.1 J calculated by this model, in contrast to the total energy 7140.9 J generated from the arc and Joule heat.
Single‐ended electrical impedance tomography
Authors: Salama Abdalla , Malekmohammadi Amin , Mohanna Shahram 
Published: January 2018

A novel prototype electrical impedance tomography (EIT) system, which uses single‐ended signalling, is presented. The single‐ended electrical impedance tomography system consists of a host computer, data acquisition system, switching box, MATLAB, and LabVIEW program. Ability of the system to detect and track hidden conductive and non‐conductive objects was examined using a beaker (cylindrical shape) of 180 mm diameter and 280 mm height, filled with 3000 mL tap water, and with 16 electrodes attached. Stainless steel and Teflon rods with different sizes were placed in different locations inside the beaker, and images were obtained. All the objects were tested under multiple signal injection frequencies in the range of 12–1000 kHz. The results showed that the system could detect and track conductive and non‐conductive objects during certain injection frequencies. The single‐ended EIT system requires one wire connection to make one signal injection or measurement, and this is controlled using a multiplexer or switching box. Alternatively, an ordinary EIT system requires additional wire connections for single data measurement or injection, and a more complex circuit to control the I/O signals. This greater number of wires and increased circuit complexity will increase the data error rate and the cost significantly.
Compact bandpass filter with reconfigurable X‐band using stepped impedance resonator and folded structure
Authors: Masood Molimoli Hajamohideen , Suseela Sreeja Balakrishnapillai 
Published: January 2018

A reconfigurable X‐band microstrip bandpass filter based on the stepped impedance resonator topology with two folded stubs is proposed. Reconfiguration is enabled in the microstrip filter using positive–intrinsic–negative (PIN) diode and the proposed filter performs frequency switching between uplink and downlink X‐band services. The prototype filter is realised ideally using open‐circuit and short‐circuit conditions that are designed in a way similar to the design using PIN diodes that provide the same results. From the simulation and measured results, it is inferred that by altering the ON/OFF states, the filter can work from downlink frequency range of 7.25–7.9 GHz to the uplink frequency range of 8.00–8.4 GHz. Comprehensive studies are conducted on a fabricated prototype to assess its performance from which encouraging results are obtained.
Tracking Advanced Planetary Systems (TAPAS) with HARPS-N
Authors: Adamów M. , Niedzielski A. , Kowalik K. , Villaver E. , Wolszczan A. , Maciejewski G. , Gromadzki M. 
Published: January 2018

Context.We present the latest results of our search for planets with HARPS-N at the 3.6 m Telescopio NazionaleGalileounder the Tracking Advanced Planetary Systems project: an in-depth study of the 15 most Li abundant giants from the PennState – Toruń Planet Search sample.Aims.Our goals are first, to obtain radial velocities of the most Li-rich giants we identified in our sample to search for possible low-mass substellar companions, and second, to perform an extended spectral analysis to define the evolutionary status of these stars.Methods.This work is based on high-resolution spectra obtained with theHobby-EberlyTelescope and its High Resolution Spectrograph, and with the HARPS-N spectrograph at the Telescopio NazionaleGalileo. Two stars, HD 181368 and HD 188214, were also observed with UVES at the VLT to determine beryllium abundances.Results.We report i) the discovery of two new planetary systems around the Li-rich giant stars: HD 238914 and TYC 3318-01333-1 (a binary system); ii) reveal a binary Li-rich giant, HD 181368; iii) although our current phase coverage is not complete, we suggest the presence of planetary mass companions around TYC 3663-01966-1 and TYC 3105-00152-1; iv) we confirm the previous result for BD+48 740 and present updated orbital parameters, and v) we find a lack of a relation between the Li enhancement and the Be abundance for the stars HD 181368 and HD 188214, for which we acquired blue spectra.Conclusions.We found seven stars with stellar or potential planetary companions among the 15 Li-rich giant stars. The binary star frequency of the Li-rich giants in our sample appears to be normal, but the planet frequency is twice that of the general sample, which suggests a possible connection between hosting a companion and enhanced Li abundance in giant stars. We also found most of the companions orbits to be highly eccentric.
Electrocatalytic Difunctionalization of Olefins as a General Approach to the Synthesis of Vicinal Diamines
Authors: Lin Song , Parry Joseph , Fu Niankai 
Published: January 2018

Vicinal diamines are highly prevalent structural motifs in therapeutic agents, bioactive natural products, and molecular catalysts. However, there are currently few unified methodological approaches for making these pertinent synthetic building blocks. This Synpacts article provides an overview of selected landmark developments in the area of olefin diamination. In particular, we highlight our recent contribution on the electrocatalytic diazidation of olefins as a general, selective, and sustainable method for the synthesis of vicinal diamines.1	Introduction2	Background: Intermolecular Diamination of Olefins3	Background: Intermolecular Diazidation of Olefins4	Electrocatalytic Diazidation of Olefins
Autoimmune Encephalitis in Children
Authors: Salfa Irene , Vigevano Federico , Valeriani Massimiliano , Papetti Laura 
Published: January 2018

AbstractAutoimmune encephalitis (AIE) can produce a very wide range of neuropsychiatric symptoms. A major challenge in diagnosis is that different symptoms may appear at different times and different levels of intensity, so the disease may mimic many other disorders. Pathogenesis is likely to be mediated by antibodies (Abs) to CNS proteins. This article focuses on recent clinical advances, newly characterized Abs, and treatment approaches to these disorders.
Anatomia quantitativa do atlas
Authors: de Carvalho Max Franco , Rocha Roberta Teixeira , Silva Monteiro João Tiago , Pereira Carlos Umberto , de Carvalho Alex Franco , Aparecido Defino Helton Luiz 
Published: January 2018

Resumo
Objetivo: Descrever as medidas anatômicas gerais do atlas por meio do estudo anatômico e por tomografia computadorizada helicoidal em 30 amostras do atlas isolado de cadáveres adultos brasileiros. Métodos: Todos os parâmetros observados foram analisados estatisticamente para a obtenção da média, desvio-padrão, o valor mínimo e o máximo das estruturas do atlas. Resultados: A reprodutibilidade foi considerada boa para coeficiente de correlação > 0,80 e ruim para coeficiente < 0,80. Em 12 parâmetros, a reprodutibilidade foi considerada boa. Apenas nos parâmetros da distância interligamento transverso e na dimensão do espaço odontóide, a reprodutibilidade foi considerada ruim, apresentando coeficientes de correlação interclasse < 0,06. Conclusão: Os dados obtidos fornecem um melhor entendimento de geometria, dimensões e detalhes quantitativos de morfometria atlantal. Este estudo fornece as dimensões gerais do atlas e demonstra uma proporção constante dos arcos anterior e posterior. Os autores acreditam que essas observações possam facilitar os estudos biomecânicos, radiológicos e cirúrgicos da transição craniocervical.
Pseudo-aneurisma traumático gigante da artéria temporal superficial: Relato de caso com 11 anos de evolução
Authors: Zanini Marco Antonio , Antunes Ferreira Ivan Tadeu , de Freitas Carlos Clayton Macedo , Souza Faleiros Antonio Tadeu de 
Published: January 2018

ResumoOs autores apresentam caso de paciente do sexo masculino, adulto, com pseudo-aneurisma traumático gigante da artéria temporal superficial, com história de 11 anos de evolução. O diagnóstico definitivo somente ocorreu durante investigação de hemorragia subaracnóidea espontânea, após passar por inúmeros especialistas investigando a tumoração pré-auricular. O tratamento, com ligadura proximal e distal e excisão completa da lesão, foi pela mesma via de abordagem pterional para clipagem de aneurisma intracraniano. Os autores fazem breve revisão da literatura, salientando os aspectos de fisiopatologia, diagnóstico e tratamento.
Different durations within the method of best practice affect the parameters of the speed–duration relationship
Authors: Triska Christoph , Karsten Bettina , Beedie Chris , Koller‐Zeisler Bernhard , Nimmerichter Alfred , Tschan Harald 
Published: January 2018

AbstractThe aim of the study was to determine whether estimates of the speed–duration relationship are affected using different time‐trial (TT) field‐based testing protocols, where exhaustive times were located within the generally recommended durations of 2–15 min. Ten triathletes (mean ± SD age: 31.0 ± 5.7 years; height: 1.81 ± 0.05 m; body mass: 76.5 ± 6.8 kg) performed two randomly assigned field tests to determine critical speed (CS) and the total distance covered above CS (D́). CS and D́ were obtained using two different protocols comprising three TT that were interspersed by 60 min passive rest. The TTs were 12, 7, and 3 min in Protocol I and 10, 5, and 2 min in Protocol II. A linear relationship of speed vs. the inverse of time (s = D́ × 1/t + CS) was used to determine parameter estimates. Significant differences were found for CS (p = 0.026), but not for D́ (p = 0.123). The effect size for CS (d = 0.305) was considered small, while that for D́ was considered moderate (d = 0.742). CS was significantly correlated between protocols (r = 0.934; p < 0.001), however, no correlation was found for D́ (r = 0.053; p = 0.884). The 95% limits of agreement were ±0.28m s−1 and ±73.9 m for CS and D́, respectively. These findings demonstrate that the choice of exhaustive times within commonly accepted durations results in different estimates of CS and D́, and thus protocols cannot be used interchangeably. The use of a consistent protocol is therefore recommended, when investigating or monitoring the speed–duration relationship estimates in well‐trained athletes.
Selective release of circRNAs in platelet‐derived extracellular vesicles
Authors: Preußer Christian , Hung Lee‐Hsueh , Schneider Tim , Schreiner Silke , Hardt Martin , Moebus Anna , Santoso Sentot , Bindereif Albrecht 
Published: January 2018

ABSTRACTCircular RNAs (circRNAs) are a novel class of noncoding RNAs present in all eukaryotic cells investigated so far and generated by a special mode of alternative splicing of pre‐mRNAs. Thereby, single exons, or multiple adjacent and spliced exons, are released in a circular form. CircRNAs are cell‐type specifically expressed, are unusually stable, and can be found in various body fluids such as blood and saliva. Here we analysed circRNAs and the corresponding linear splice isoforms from human platelets, where circRNAs are particularly abundant, compared with other hematopoietic cell types. In addition, we isolated extracellular vesicles from purified and in vitro activated human platelets, using density‐gradient centrifugation, followed by RNA‐seq analysis for circRNA detection. We could demonstrate that circRNAs are packaged and released within both types of vesicles (microvesicles and exosomes) derived from platelets. Interestingly, we observed a selective release of circRNAs into the vesicles, suggesting a specific sorting mechanism. In sum, circRNAs represent yet another class of extracellular RNAs that circulate in the body and may be involved in signalling pathways. Since platelets are essential for central physiological processes such as haemostasis, wound healing, inflammation and cancer metastasis, these findings should greatly extend the potential of circRNAs as prognostic and diagnostic biomarkers.
GTC: how to maintain huge genotype collections in a compressed form
Authors: Danek Agnieszka , Deorowicz Sebastian 
Published: January 2018

Abstract

Motivation
Nowadays, genome sequencing is frequently used in many research centers. In projects, such as the Haplotype Reference Consortium or the Exome Aggregation Consortium, huge databases of genotypes in large populations are determined. Together with the increasing size of these collections, the need for fast and memory frugal ways of representation and searching in them becomes crucial.

Results
We present GTC (GenoType Compressor), a novel compressed data structure for representation of huge collections of genetic variation data. It significantly outperforms existing solutions in terms of compression ratio and time of answering various types of queries. We show that the largest of publicly available database of about 60 000 haplotypes at about 40 million SNPs can be stored in &lt;4 GB, while the queries related to variants are answered in a fraction of a second.

Availability and implementation
GTC can be downloaded from https://github.com/refresh-bio/GTC or http://sun.aei.polsl.pl/REFRESH/gtc.

Supplementary information
Supplementary data are available at Bioinformatics online.