bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interannual and Interdecadal Variabilities of Spring Rainfall over Northeast China and Their Associated Sea Surface Temperature Anomaly Forcings
Authors: Lu Rui , Zhu Zhiwei , Li Tim , Zhang Haiyang 
Published: November 2019

AbstractAn empirical orthogonal function (EOF) analysis was conducted for spring precipitation gauge data over northeast China (NEC). The first EOF mode is characterized by a homogenous rainfall pattern throughout NEC. The corresponding principal component has both significant interannual and interdecadal variations. This leading mode explains a large portion of the total NEC spring rainfall (NECSR) variances and is statistically independent from other higher modes. The physical processes responsible for the interannual and interdecadal variabilities were investigated via observational diagnoses and numerical experiments. On the interannual time scale, NECSR is mainly affected by the SST anomalies (SSTAs) in the northern tropical Atlantic Ocean. When the SSTAs are positive, the subsequently induced positive precipitation and convection can stimulate two quasi-barotropic Rossby wave trains over the mid- to high latitudes. A cyclonic anomaly center of the Rossby wave train appears over northeastern Asia, leading to a positive rainfall anomaly in the region. On the interdecadal time scale, NECSR is mainly influenced by the SSTAs over the warm-pool region. Positive SSTAs in the warm-pool region result in enhanced convection (ascending motion) around the Maritime Continent and suppressed convection (descending motion) over the central equatorial Pacific Ocean. This zonal dipole convection pattern stimulates a quasi-barotropic circulation pattern with an anticyclonic anomaly over the Tibetan Plateau and a cyclonic anomaly over northeastern Asia. The cyclonic anomaly over northeastern Asia enhances the NECSR. Numerical experiments further suggested that the convective heating anomaly over the Maritime Continent, rather than cooling over the central equatorial Pacific, plays a more essential role in driving the interdecadal rainfall variability of NECSR.
On the Construction Principle of Conceptual Models for Severe Convective Weather Forecasting Operations in China
Authors: Liu Xinhua , Zhou Kanghui , Lan Yu , Mao Xu , Trapp Robert J. 
Published: November 2019

AbstractIt is argued here that even with the development of objective algorithms, convection-allowing numerical models, and artificial intelligence/machine learning, conceptual models will still be useful for forecasters until all these methods can fully satisfy the forecast requirements in the future. Conceptual models can help forecasters form forecast ideas quickly. They also can make up for the deficiencies of the numerical model and other objective methods. Furthermore, they can help forecasters understand the weather, and then help the forecasters lock in on the key features affecting the forecast as soon as possible. Ultimately, conceptual models can help the forecaster serve the end users faster, and better understand the forecast results during the service process. Based on the above considerations, construction of new conceptual models should have the following characteristics: 1) be guided by purpose, 2) focus on improving the ability of forecasters, 3) have multiangle consideration, 4) have multiscale fusion, and 5) need to be tested and corrected continuously. The traditional conceptual models used for forecasts of severe convective weather should be replaced gradually by new models that incorporate these principles.
metaSPARSim: a 16S rRNA gene sequencing count data simulator
Authors: Patuzzi Ilaria , Baruzzo Giacomo , Losasso Carmen , Ricci Antonia , Di Camillo Barbara 
Published: November 2019

AbstractBackgroundIn the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable popularity of this technique, an exiguous number of specific tools are currently available for proper 16S rDNA-seq count data preprocessing and simulation. Indeed, the great majority of tools have been developed adapting methodologies previously used for bulk RNA-seq data, with poor assessment of their applicability in the metagenomics field. For such tools and the few ones specifically developed for 16S rDNA-seq data, performance assessment is challenging, mainly due to the complex nature of the data and the lack of realistic simulation models. In fact, to the best of our knowledge, no software thought for data simulation are available to directly obtain synthetic 16S rDNA-seq count tables that properly model heavy sparsity and compositionality typical of these data.ResultsIn this paper we present metaSPARSim, a sparse count matrix simulator intended for usage in development of 16S rDNA-seq metagenomic data processing pipelines. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric distribution in order to realistically simulate 16S rDNA-seq count table, resembling real experimental data compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios and to estimate simulation parameters from real experimental data. The tool is made available athttp://sysbiobig.dei.unipd.it/?q=Software#metaSPARSimandhttps://gitlab.com/sysbiobig/metasparsim.ConclusionmetaSPARSim is able to generate count matrices resembling real 16S rDNA-seq data. The availability of count data simulators is extremely valuable both for methods developers, for which a ground truth for tools validation is needed, and for users who want to assess state of the art analysis tools for choosing the most accurate one. Thus, we believe that metaSPARSim is a valuable tool for researchers involved in developing, testing and using robust and reliable data analysis methods in the context of 16S rRNA gene sequencing.
MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
Authors: Qian Jia , Comin Matteo 
Published: November 2019

Abstract
Motivation
Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it is crucial to group them into putative species for further taxonomic profiling and down-streaming functional analysis. Taxonomic analysis of microbial communities requires contig clustering, a process referred to as binning, that is still one of the most challenging tasks when analyzing metagenomic data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species, sequencing errors, and the limitations due to binning contig of different lengths.

Results
In this context we present MetaCon a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage. MetaCon uses a signature based on k-mers statistics that accounts for the different probability of appearance of a k-mer in different species, also contigs of different length are clustered in two separate phases. The effectiveness of MetaCon is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, MaxBin and MetaBAT.
Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data
Authors: Spirito Giovanni , Mangoni Damiano , Sanges Remo , Gustincich Stefano 
Published: November 2019

Abstract
Background
Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human.

Results
In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits.

Conclusion
We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.
BITS2018: the fifteenth annual meeting of the Italian Society of Bioinformatics
Authors: Cordero Francesca , Calogero Raffaele A. , Caselle Michele 
Published: November 2019

AbstractThis preface introduces the content of the BioMed Central Bioinformatics journal Supplement related to the 15th annual meeting of the Bioinformatics Italian Society, BITS2018. The Conference was held in Torino, Italy, from June 27th to 29th, 2018.
Factors associated with permanent hypothyroidism in infants with congenital hypothyroidism
Authors: Park Eun Sil , Yoon Ju Young 
Published: November 2019

Abstract
Background
Congenital hypothyroidism (CH) is one of the most common endocrine diseases in childhood. A significant proportion of CH cases are transient, but the risk factors for permanent CH (PCH) are not yet well established. The current guidelines suggest using levothyroxine until the age of 3 years, but some studies suggest the possibility of earlier discontinuation. However, few, if any, studies have followed up on the results of early discontinuation. This study aimed to identify predictive factors of transient CH among infants with CH. We also investigated the results in patients who underwent a trial of early discontinuation.

Methods
We gathered data regarding infants diagnosed with CH between July 2005 and July 2015 by retrospective chart review. Those with aplastic, hypoplastic or ectopic glands on thyroid ultrasonography or scan were excluded. Among them, early discontinuation subgroup was defined as those who discontinued levothyroxine before 30 months of age.

Results
From the 80 infants (40 males, 40 females) enrolled in this study, 51 were preterm. Nine (11.3%) were diagnosed with PCH. Compared with transient cases, those with PCH were on higher levothyroxine dose at discontinuation (4.3 vs 2.9 μg/kg, P < 0.001). There was no difference in the proportion of permanent cases between preterm and full-term groups. In preterm group,infants with PCH required higher levothyroxine dose at discontinuation than those with transient CH (3.8 vs 2.5 μg/kg, P = 0.018). Levothyroxine discontinuation at a dose of 2.86 μg/kg could suggest PCH (sensitivity, 88.9%; specificity, 71.0%). Among the 9 patients who underwent a trial of early discontinuation, 8 successfully discontinued levothyroxine.

Conclusion
The majority of CH patients discontinued levothyroxine successfully, including those who underwent a trial of early discontinuation. Higher levothyroxine dose at the time of discontinuation was found to be a predictive factor for PCH.
Hydroxysteroid sulfotransferase 2B1 affects gastric epithelial function and carcinogenesis induced by a carcinogenic agent
Authors: Hong Wenting , Guo Fenghua , Yang Mingjie , Xu Dongke , Zhuang Ziyan , Niu Baolin , Bai Qianming , Li Xiaobo 
Published: November 2019

Abstract
Background
A healthy gastric mucosal epithelium exhibits tumor-suppressive properties. Gastric epithelial cell dysfunction contributes to gastric cancer development. Oxysterols provided from food or cholesterol oxidation in the gastric epithelium may be further sulfated by hydroxysteroid sulfotransferase 2B1 (SULT2B1), which is highly abundant in the gastric epithelium. However, the effects of SULT2B1 on gastric epithelial function and gastric carcinogenesis are unclear.

Methods
A mouse gastric tumor model was established using carcinogenic agent 3-methylcholanthrene (3-MCA). A SULT2B1 deletion (SULT2B1−/−) human gastric epithelial line GES-1 was constructed by CRISPR/CAS9 genome editing system.

Results
The gastric tumor incidence was higher in the SULT2B1−/− mice than in the wild-type (WT) mice. In gastric epithelial cells, adenovirus-mediated SULT2B1b overexpression reduced the levels of oxysterols, such as 24(R/S),25-epoxycholesterol (24(R/S),25-EC) and 27-hydroxycholesterol (27HC). This condition also increased PI3K/AKT signaling to promote gastric epithelial cell proliferation, epithelization, and epithelial development. However, SULT2B1 deletion or SULT2B1 knockdown suppressed PI3K/AKT signaling, epithelial cell epithelization, and wound healing and induced gastric epithelial cell malignant transition upon 3-MCA induction.

Conclusions
The abundant SULT2B1 expression in normal gastric epithelium might maintain epithelial function via the PI3K/AKT signaling pathway and suppress gastric carcinogenesis induced by a carcinogenic agent.
Value of respiratory variation of aortic peak velocity in predicting children receiving mechanical ventilation: a systematic review and meta-analysis
Authors: Wang Xiaoying , Jiang Lulu , Liu Shuai , Ge Yali , Gao Ju 
Published: November 2019

Abstract
Background
Accurate volume assessment is crucial in children under fluid therapy. Over the last decade, respiratory variation of aortic peak velocity (△VPeak) has been applied in intensive care unit and surgeries to help clinicians guide fluid management. The aim of this systematic review and meta-analysis was to test diagnostic performance of △VPeak in predicting fluid responsiveness of ventilated children and to explore the potential factors that influence the accuracy of △VPeak.

Methods
We searched PubMed, Embase, and Cochrane from inception to April 2019 that evaluated association between △VPeak and fluid responsiveness after fluid challenge in children receiving mechanical ventilation. Data synthesis was performed within the bivariate mixed-effects regression model modified for synthesis of diagnostic test data.

Results
Eleven studies with a total of 302 pediatric patients were included in our meta-analysis. The pooled sensitivity and specificity of △VPeak was 0.89 (95%CI = 0.77 to 0.95) and 0.85 (95%CI = 0.77 to 0.91), respectively. The diagnostic odds ratio (DOR) of △VPeak was 48 (95%CI = 15 to 155). SROC yielded an area under the curve of 0.91 (95%CI = 0.88–0.93). The △VPeak cutoff value was nearly conically symmetrical distribution and varied from 7 to 20%. After excluding several extreme studies, most data were centered between 12 and 13%. The medium and mean cutoff values of △VPeak were 12.2% and 12.7%, respectively. In subgroup analysis, compared to total data analysis, △VPeak performed weaker in the younger children group (mean ages < 25 months), with lower area under the summary receiver operating characteristic curve (AUSROC) of 0.80 (0.76 to 0.83), but stronger in the older children group (mean ages > 25 months), with AUSROC of 0.96 (0.94 to 0.97).

Conclusions
Overall, △VPeak has a good ability in predicting fluid responsiveness of children receiving mechanical ventilation, but this ability decreases in younger children (mean age < 25 months). The optimal threshold of △VPeak to predict fluid responsiveness in ventilated children is reliable between 12 and 13%.

Trial registration
The study protocol was registered prospectively on PROSPERO no. CRD42019129361.
A condition for blow-up solutions to discrete p-Laplacian parabolic equations under the mixed boundary conditions on networks
Authors: Chung Soon-Yeong , Choi Min-Jun , Hwang Jaeho 
Published: November 2019

AbstractIn this paper, we investigate the condition
$$(C_{p})\quad \alpha \int _{0}^{u}f(s)\,ds \leq uf(u)+\beta u^{p}+\gamma ,\quad u>0 $$(Cp)α∫0uf(s)ds≤uf(u)+βup+γ,u>0 for some $\alpha >2$α>2, $\gamma >0$γ>0, and $0\leq \beta \leq \frac{ (\alpha -p ) \lambda _{p,0}}{p}$0≤β≤(α−p)λp,0p, where $p>1$p>1, and $\lambda _{p,0}$λp,0 is the first eigenvalue of the discrete p-Laplacian $\Delta _{p,\omega }$Δp,ω. Using this condition, we obtain blow-up solutions to discrete p-Laplacian parabolic equations
$$ \textstyle\begin{cases} u_{t} (x,t )=\Delta _{p,\omega }u (x,t )+f(u(x,t)), & (x,t )\in S\times (0,+\infty ), \\ \mu (z)\frac{\partial u}{\partial _{p} n}(x,t)+\sigma (z) \vert u(x,t) \vert ^{p-2}u(x,t)=0, & (x,t )\in \partial S\times [0,+\infty ), \\ u (x,0 )=u_{0}\geq 0\quad (\mbox{nontrivial}), & x\in S, \end{cases} $${ut(x,t)=Δp,ωu(x,t)+f(u(x,t)),(x,t)∈S×(0,+∞),μ(z)∂u∂pn(x,t)+σ(z)|u(x,t)|p−2u(x,t)=0,(x,t)∈∂S×[0,+∞),u(x,0)=u0≥0(nontrivial),x∈S, on a discrete network S, where $\frac{\partial u}{\partial _{p}n}$∂u∂pn denotes the discrete p-normal derivative. Here μ and σ are nonnegative functions on the boundary ∂S of S with $\mu (z)+\sigma (z)>0$μ(z)+σ(z)>0, $z\in \partial S$z∈∂S. In fact, we will see that condition $(C_{p})$(Cp) improves the conditions known so far.
Rehabilitation of indigenous browse plant species following exclosure established on communal grazing lands in South Tigray, Ethiopia, and implication for conservation
Authors: Atsbha Tesfay , Wayu Solomon , Gebretsadkan Nguse , Gebremariam Tesfay , Giday Tsgehiwet 
Published: November 2019

AbstractBackgroundDespite the wide use of indigenous browse plant species, there is almost no information on the rehabilitation of indigenous browse species following area exclosure (AE) established on communal grazing lands (CGL) in Southern Tigray. The objectives of this study were to assess the rehabilitation of browse plant species following AE establishment on CGL. A total of 61 and 59 plots of 10 × 10 m2size were laid down at 50-m intervals along parallel line transects at AE and GCL, respectively. Data collected on vegetation attributes were subjected to analysis ofttest (unequal variances) using R-software.ResultsThe Shannon diversity index of the browse plant species was 1.25 and 0.81 in AE and CGL, respectively (P < 0.001). The overall population structure of browse plant species in the AE shows a reverse J-shaped population curve and “good” regeneration status, which reveals that the future communities may be sustained. Leaf biomass and basal area of browse plant species were significantly higher in the AE than in CGL (P < 0.001). After exclusion of grazing, AE was found to have positive effects on diversity and aboveground biomass of browse plant species.ConclusionsThe study gives an understanding of the diversity, the pattern of population and regeneration of the browse plant species, which may help in the management and conservation of the species. Our results indicate that grazing exclusion is an effective management strategy to restore browse plant species. We concluded that the establishment of AE had a positive effect on the rehabilitation of browse plant species diversity and improved population structure and regeneration potentials of degraded grazing lands. Long-term monitoring and evaluation systems will be required to gain an informed understanding of the roles played by area exclosures in the rehabilitation and conservation of browse palnt species diversity.
Antecedent cancer in Takotsubo syndrome predicts both cardiovascular and long-term mortality
Authors: Nguyen Thanh H. , Stansborough Jeanette , Ong Gao J. , Surikow Sven , Price Timothy J. , Horowitz John D. 
Published: November 2019

Abstract
Background
Takotsubo syndrome (TTS), primarily an acute myocardial inflammatory condition engendered by catecholamine exposure, is associated with similar long-term mortality rates to those of patients with acute myocardial infarction. However, there is increasing evidence of a nexus between TTS and underlying malignancies:- many patients have antecedent cancer (A/Ca), while incremental risk of late cancer-related death has also been reported.

Purpose
To evaluate potential interactions between A/Ca among TTS patients and both early and late clinical course.

Methods
Three hundred forty-six consecutive TTS patients [aged 69 ± 13 (SD) years, males: 8.2%] were prospectively followed up for a median duration of 4.1 (IQR 2.2–6.4) years. Associations between A/Ca and severity of acute attacks, in-hospital complications and long-term death rates were sought utilising univariate analyses followed by multiple logistic regression analysis.

Results
A/Ca (present in 16.8% of patients) was associated with (i) greater elevation of hs-CRP and NT-proBNP concentrations (p = 0.01 and 0.04, respectively), (ii) more complicated in-hospital clinical course, with major adverse cardiac events (MACE) in 30.9% of patients, compared to 18.2% in non-A/Ca patients (p = 0.04). Long-term all-cause mortality rate was also greater [hazard ratio (HR) = 2.4, p = 0.0001] in A/Ca patients, with an excess cardiovascular (CVS) fatality rate (HR = 3.1, p = 0.001). On multivariate analysis, male gender, peak plasma concentrations of normetanephrine and hs-CRP, early arrhythmias and development of shock, but not A/Ca per se, were all independently associated with increased long-term mortality rate. Furthermore, patients discharged on β-adrenoceptor antagonists (βBl) or angiotensin converting enzyme inhibitors/ angiotensin receptor blockers (ACEi/ARB) had lower long-term mortality rates (β = − 0.2, p = 0.01; β = − 0.14, p = 0.05, respectively).

Conclusions
(1) A/Ca is associated with greater clinical severity of initial TTS attacks and substantially greater long-term CVS-related as well as all-cause mortality.
(2) Post-discharge therapy with either βBl or ACEi/ARB is associated with reductions in long-term mortality rates.
Overall, the current data suggest operation of substantial interactions between neoplasia and TTS, both at the level of pathogenesis and of outcomes.