bluuebunny/crossref_metadata_2025_split huggingface dataset:
QTL for maize grain yield identified by QTL mapping in six environments and consensus loci for grain weight detected by meta‐analysis
Authors: Pan Limei , Yin Zengqi , Huang Yaqun , Chen Jingtang , Zhu Liying , Zhao Yongfeng , Guo Jinjie 
Published: October 2017

AbstractGrain yield is the most important and complicated trait in maize. In this study, a total of 498 recombinant inbred lines (RIL) derived from a biparental cross of two elite inbred lines, 178 and P53, were grown in six different environments. Quantitative trait locus (QTL) mapping was conducted for three grain yield component traits (100 grain weight, ear weight and kernel weight per plant). Subsequently, meta‐analysis was performed after a comprehensive review of the research on QTL mapping for grain weight (100, 300 and 1000) using BioMercator V4.2. In total, 62 QTLs were identified for 100 grain weight, ear weight and kernel weight per plant in six environments. Forty‐three meta‐QTLs (MQTLs) were detected by meta‐analysis. A total of 13 candidate genes homologous to eight functionally characterized rice genes were found, and four candidate genes were located in the two hot spot regions of MQTL1.5 and MQTL2.3. Our results suggest that the combination of literature collection, meta‐analysis and homologous blast searches can offer abundant information for further fine mapping, marker‐assisted selection (MAS) breeding and map‐based cloning for maize.
Generation and analysis of expressed sequence tag sequences from a soft‐seeded pomegranate cDNA library
Authors: Zhang Shuiming , Chen Lei , Huang Rong , Isha Abdurazak , Dong Lili 
Published: October 2017

AbstractThe cultivation of soft‐seeded pomegranate is an important direction in pomegranate breeding. To comprehensively understand the molecular mechanisms involved in the formation of soft‐seeded pomegranate (Punica granatum. var. Hongmanaozi), we established an expressed sequence tag (EST) resource. Two thousand valid sequences were generated, from which 907 unigenes were obtained after initial assembly using the clustalx program. Among these unigenes, 51 showed no similarity to any protein in the public databases, 433 matched with proteins of unknown function, and 423 matched with proteins of known or putative functions. The 423 unigenes were further classified into 13 categories. Among these categories, protein synthesis, cell structure, protein destination and storage, secondary metabolism, signal transduction and transporters accounted for 8%, 8%, 4%, 7%, 6% and 17%, respectively. We also successfully developed 10 highly polymorphic expressed sequence tag‐simple sequence repeat (EST‐SSR) markers for pomegranate. The results provide a new tool for future activities in pomegranate breeding.
Reliable and sensitive physical testing of elite trapeze sailors
Authors: Bay J. , Bojsen‐Møller J. , Nordsborg N. B. 
Published: October 2017

It was investigated whether a newly developed discipline‐specific test for elite‐level trapeze sailors is reliable and sensitive. Furthermore, the physical demands of trapeze sailing were examined. In part 1, 9 national team athletes were accustomed to a simulated sailing test, which subsequently was completed on 4 occasions to determine test reliability and sensitivity to manipulations in body weight. Rope‐pulling mean power output (MPO), oxygen consumption (VO2), heart rate (HR), and blood lactate values were acquired in all trials. In part 2, 6 sailors completed on‐water racing with concurrent measurements of VO2, HR, and blood lactate. VO2max was determined during an incremental treadmill running test. Typical error, minimal difference, and ICC for average MPO in the test were 1.3%, 1.7%, and 0.99%, respectively. Adding 4 kg of external body weight caused a decrease in average MPO (270 ± 45W vs 265 ± 45W, P < .05) and an increase in VO2 (2.44 ± 0.23 L·min−1 vs 2.55 ± 0.26 L·min−1, P < .01). VO2, HR, and blood lactate during on‐water sailing were 54.5% ± 7.2% VO2max, 75.1% ± 3.1% HRmax, and 5.8 ± 2.7 mmol·L−1, respectively. However, VO2 and HR were substantially higher for periods of the race as peak values were 83.5% ± 11.4% and 89.9% ± 1.7% of max, respectively. In conclusion, the present test is reliable and sensitive, thus providing a sailing‐specific alternative to traditional physical testing of elite trapeze sailors. Additionally, on‐water racing requires moderate aerobic energy production, although oxygen consumption can approach maximal levels for short periods of time.
Who accesses surgery at district level in sub‐Saharan Africa? Evidence from Malawi and Zambia
Authors: Gajewski Jakub , Dharamshi Rachel , Strader Michael , Kachimba John , Borgstein Eric , Mwapasa Gerald , Cheelo Mweene , McCauley Tracey , Bijlmakers Leon , Brugha Ruairi 
Published: October 2017

AbstractObjectivesTo examine age and gender distribution for the most common types of surgery in Malawi and Zambia.MethodsData were collected from major operating theatres in eight district hospitals in Malawi and nine in Zambia. Raw data on surgical procedures were coded by specialist surgeons for frequency analyses.ResultsIn Malawi female surgical patients had a mean age of 25 years, with 91% aged 16–40 years. Females accounted for 85%, and obstetric cases for 75%, of all surgical patients. In Zambia, female surgical patients had a mean age of 26, with 75% aged 16–40 years. They accounted for 55% of all cases, 34% being obstetric. Male surgical patients in Malawi were on average older (33 years) than in Zambia (23 years). General surgical cases in men and women, respectively, had a median age of 42 and 32 in Malawi and 26 and 30 in Zambia. The median age of trauma patients was 12 in males and 10 in females in both countries. Children aged 0–15 years accounted for 64–65% of all trauma cases in Malawi and 57–58% in Zambia, with peak incidences in 6‐ to 10‐year‐olds.ConclusionsWomen of reproductive (16–45 years) mainly undergoing Caesarean sections and children aged 0–15 years who accounted for two‐thirds of trauma cases are the main patient populations undergoing surgery at district hospitals in Zambia and Malawi. Verification and analysis of routine hospital data, across 10–30% of districts countrywide, demonstrated the need to prioritise quality assurance in surgery and anaesthesia, and preventive interventions in children.
Complete Genome Sequence of
Porphyrobacter
sp. Strain CACIAM 03H1, a Proteobacterium Obtained from a Nonaxenic Culture of Microcystis aeruginosa
Authors: Castro Wendel de Oliveira , Lima Alex Ranieri Jerônimo , Moraes Pablo Henrique Gonçalves , Siqueira Andrei Santos , Aguiar Délia Cristina Figueira , Baraúna Anna Rafaella Ferreira , Martins Luisa Carício , Fuzii Hellen Thais , Couto Danielle Costa Carrara , Francês Regiane Silva Kawasaki , Silva de Lima Clayton Pereira , Vianez-Júnior João Lídio Silva Gonçalves , Nunes Márcio Roberto Teixeira , Dall’Agnol Leonardo Teixeira , Gonçalves Evonnildo Costa 
Published: October 2017

ABSTRACT

Here, we present a complete genome sequence and annotation of
Porphyrobacter
sp. strain CACIAM 03H1, which was obtained from a nonaxenic culture of
Microcystis aeruginosa
, a cyanobacterium isolated from an Amazonian freshwater environment.
Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates from Humans with Long-Term Swine Contact
Authors: Hau Samantha J. , Bayles Darrell O. , Alt David P. , Davies Peter R. , Haan Jisun S. , Nicholson Tracy L. 
Published: October 2017

ABSTRACT

Humans have been found to harbor livestock-associated methicillin-resistant
Staphylococcus aureus
(LA-MRSA) isolates. LA-MRSA isolates are considered adapted to colonizing livestock and less pathogenic in humans than their hospital- and community-acquired counterparts. Here, we present nine LA-MRSA sequence type 5 isolates from veterinarians with long-term swine contact.
The BvgAS Regulon of
Bordetella pertussis
Authors: Moon Kyung , Bonocora Richard P. , Kim David D. , Chen Qing , Wade Joseph T. , Stibitz Scott , Hinton Deborah M. 
Published: October 2017

ABSTRACT

Nearly all virulence factors in
Bordetella pertussis
are activated by a master two-component system, BvgAS, composed of the sensor kinase BvgS and the response regulator BvgA. When BvgS is active, BvgA is phosphorylated (BvgA~P), and virulence-activated genes (
vag
s) are expressed [Bvg(+) mode]. When BvgS is inactive and BvgA is not phosphorylated, virulence-repressed genes (
vrg
s) are induced [Bvg(−) mode]. Here, we have used transcriptome sequencing (RNA-seq) and reverse transcription-quantitative PCR (RT-qPCR) to define the BvgAS-dependent regulon of
B. pertussis
Tohama I. Our analyses reveal more than 550 BvgA-regulated genes, of which 353 are newly identified. BvgA-activated genes include those encoding two-component systems (such as
kdpED
), multiple other transcriptional regulators, and the extracytoplasmic function (ECF) sigma factor
brpL
, which is needed for type 3 secretion system (T3SS) expression, further establishing the importance of BvgA~P as an apex regulator of transcriptional networks promoting virulence. Using
in vitro
transcription, we demonstrate that the promoter for
brpL
is directly activated by BvgA~P. BvgA-FeBABE cleavage reactions identify BvgA~P binding sites centered at positions −41.5 and −63.5 in
bprL
. Most importantly, we show for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the
B. pertussis
Bvg(−) mode. These include genes for fatty acid and lipid metabolism, sugar and amino acid transporters, pyruvate dehydrogenase, phenylacetic acid degradation, and the glycolate/glyoxylate utilization pathway. Our results suggest that metabolic changes in the Bvg(−) mode may be participating in bacterial survival, transmission, and/or persistence and identify over 200 new
vrg
s that can be tested for function.

IMPORTANCE
Within the past 20 years, outbreaks of whooping cough, caused by
Bordetella pertussis
, have led to respiratory disease and infant mortalities, despite good vaccination coverage. This is due, at least in part, to the introduction of a less effective acellular vaccine in the 1990s. It is crucial, then, to understand the molecular basis of
B. pertussis
growth and infection. The two-component system BvgA (response regulator)/BvgS (histidine kinase) is the master regulator of
B. pertussis
virulence genes. We report here the first RNA-seq analysis of the BvgAS regulon in
B. pertussis
, revealing that more than 550 genes are regulated by BvgAS. We show that genes for multiple and varied metabolic pathways are highly regulated in the Bvg(−) mode (absence of BvgA phosphorylation). Our results suggest that metabolic changes in the Bvg(−) mode may be participating in bacterial survival, transmission, and/or persistence.
More than Enzymes That Make or Break Cyclic Di-GMP—Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of
Escherichia coli
Authors: Sarenko Olga , Klauck Gisela , Wilke Franziska M. , Pfiffer Vanessa , Richter Anja M. , Herbst Susanne , Kaever Volkhard , Hengge Regine 
Published: October 2017

ABSTRACT

The bacterial second messenger bis-(3′-5′)-cyclic diguanosine monophosphate (c-di-GMP) ubiquitously promotes bacterial biofilm formation. Intracellular pools of c-di-GMP seem to be dynamically negotiated by diguanylate cyclases (DGCs, with GGDEF domains) and specific phosphodiesterases (PDEs, with EAL or HD-GYP domains). Most bacterial species possess multiple DGCs and PDEs, often with surprisingly distinct and specific output functions. One explanation for such specificity is “local” c-di-GMP signaling, which is believed to involve direct interactions between specific DGC/PDE pairs and c-di-GMP-binding effector/target systems. Here we present a systematic analysis of direct protein interactions among all 29 GGDEF/EAL domain proteins of
Escherichia coli
. Since the effects of interactions depend on coexpression and stoichiometries, cellular levels of all GGDEF/EAL domain proteins were also quantified and found to vary dynamically along the growth cycle. Instead of detecting specific pairs of interacting DGCs and PDEs, we discovered a tightly interconnected protein network of a specific subset or “supermodule” of DGCs and PDEs with a coregulated core of five hyperconnected hub proteins. These include the DGC/PDE proteins representing the c-di-GMP switch that turns on biofilm matrix production in
E. coli
. Mutants lacking these core hub proteins show drastic biofilm-related phenotypes but no changes in cellular c-di-GMP levels. Overall, our results provide the basis for a novel model of local c-di-GMP signaling in which a single strongly expressed master PDE, PdeH, dynamically eradicates global effects of several DGCs by strongly draining the global c-di-GMP pool and thereby restricting these DGCs to serving as local c-di-GMP sources that activate specific colocalized effector/target systems.

IMPORTANCE
c-di-GMP signaling in bacteria is believed to occur via changes in cellular c-di-GMP levels controlled by antagonistic and potentially interacting pairs of diguanylate cyclases (DGCs) and c-di-GMP phosphodiesterases (PDEs). Our systematic analysis of protein-protein interaction patterns of all 29 GGDEF/EAL domain proteins of
E. coli
, together with our measurements of cellular c-di-GMP levels, challenges both aspects of this current concept. Knocking out distinct DGCs and PDEs has drastic effects on
E. coli
biofilm formation without changing the cellular c-di-GMP level. In addition, rather than generally coming in interacting DGC/PDE pairs, a subset of DGCs and PDEs operates as central interaction hubs in a larger "supermodule," with other DGCs and PDEs behaving as “lonely players” without contacts to other c-di-GMP-related enzymes. On the basis of these data, we propose a novel concept of “local” c-di-GMP signaling in bacteria with multiple enzymes that make or break the second messenger c-di-GMP.
GWAS on prolonged gestation (post-term birth): analysis of successive Finnish birth cohorts
Authors: Schierding William , Antony Jisha , Karhunen Ville , Vääräsmäki Marja , Franks Steve , Elliott Paul , Kajantie Eero , Sebert Sylvain , Blakemore Alex , Horsfield Julia A , Järvelin Marjo-Riitta , O’Sullivan Justin M , Cutfield Wayne S 
Published: October 2017

BackgroundGestation is a crucial timepoint in human development. Deviation from a term gestational age correlates with both acute and long-term adverse health effects for the child. Both being born preterm and post-term, that is, having short and long gestational ages, are heritable and influenced by the prenatal and perinatal environment. Despite the obvious heritable component, specific genetic influences underlying differences in gestational age are poorly understood.MethodsWe investigated the genetic architecture of gestational age in 9141 individuals, including 1167 born post-term, across two Northern Finland cohorts born in 1966 or 1986.ResultsHere we identify one globally significant intronic genetic variant within the ADAMTS13 gene that is associated with prolonged gestation (p=4.85×10−8). Additional variants that reached suggestive levels of significance were identified within introns at the ARGHAP42 and TKT genes, and in the upstream (5’) intergenic regions of the B3GALT5 and SSBP2 genes. The variants near the ADAMTS13, B3GALT5, SSBP2 and TKT loci are linked to alterations in gene expression levels (cis-eQTLs). Luciferase assays confirmed the allele specific enhancer activity for the BGALT5 and TKT loci.ConclusionsOur findings provide the first evidence of a specific genetic influence associated with prolonged gestation. This study forms a foundation for a better understanding of the genetic and long-term health risks faced by induced and post-term individuals. The long-term risks for induced individuals who have a previously overlooked post-term potential may be a major issue for current health providers.
mtDNA copy number associated with age of onset in familial amyloid polyneuropathy
Authors: Santos Diana , Santos Maria João , Alves-Ferreira Miguel , Coelho Teresa , Sequeiros Jorge , Alonso Isabel , Oliveira Pedro , Sousa Alda , Lemos Carolina , Grazina Manuela 
Published: October 2017

BackgroundTransthyretin-related familial amyloid polyneuropathy (TTR-FAP Val30Met) shows a wide variation in age-at-onset (AO) between generations and genders, as in Portuguese families, where women display a later onset and a larger anticipation (>10 years). Mitochondrial DNA (mtDNA) copy number was assessed to clarify whether it has a modifier effect on AO variability in Portuguese patients.MethodsThe mtDNA copy number of 262 samples (175 Val30Met TTR carriers and 87 controls (proven Val30Val)) was quantified by quantitative real-time PCR. Statistical analysis was performed using IBM SPSS V.23 software.ResultsThis study shows that Val30Met TTR carriers have a significantly higher (p<0.001) mean mtDNA copy number than controls. Furthermore, the highest mtDNA copy number mean was observed in early-onset patients (AO <40 years). Importantly, early-onset offspring showed a significant increase (p=0.002) in the mtDNA copy number, when compared with their late AO parents.ConclusionsThe present findings suggest, for the first time, that mtDNA copy number may be associated with earlier events and may therefore be further explored as a potential biomarker for follow-up of TTR-FAP Val30Met carriers.
Nodulation and nitrogen accumulation in pulses vary with species, cultivars, growth stages, and environments
Authors: Hossain Zakir , Wang Xiaoyu , Hamel Chantal , Gan Yantai 
Published: October 2017

Biological N2-fixation underpins the role of pulse crops in the development of sustainable cropping systems, but it is uncertain how nodulation and N accumulation may differ with pulse species, cultivars, and environments. This 3 yr field study investigated nodulation at the early and late flowering stages and seed and straw N uptake for chickpea (Cicer arietinum L.), dry bean (Phaseolus vulgaris L.), faba bean (Vicia faba L.), field pea (Pisum sativum L.), and lentil (Lens culinaris Medik.). At early flowering, all pulses except dry bean had more nodules in the wetter (2010) than drier year (2009). Faba bean had the most nodules followed by field pea and chickpea, while the nodulation varied with plant growth stages and environments. For both pea and lentil, more nodules were observed at early flowering, but higher nodule biomass was obtained at late flowering. Chickpea had higher nodule biomass at late than early flowering but number of nodules varied with year. Seed N uptake was highest in field pea, whereas straw N uptake was highest in faba bean. Our results suggest a possibility of improving pulse N2-fixation by targeting nodule numbers and nodule biomass, although the outcome of plant N uptake will vary with environments.
Indium–gallium–zinc–oxide thin-film transistor with a planar split dual-gate structure
Authors: Liu Yu-Rong , Liu Jie , Song Jia-Qi , Lai Pui-To , Yao Ruo-He 
Published: October 2017

An amorphous indium–gallium–zinc–oxide (a-IGZO) thin-film transistor (TFT) with a planar split dual gate (PSDG) structure has been proposed, fabricated and characterized. Experimental results indicate that the two independent gates can provide dynamical control of device characteristics such as threshold voltage, sub-threshold swing, off-state current and saturation current. The transconductance extracted from the output characteristics of the device increases from [Formula: see text] to [Formula: see text] for a change of control gate voltage from −2 V to 2 V, and thus the device could be used in a variable-gain amplifier. A significant advantage of the PSDG structure is its flexibility in controlling the device performance according to the need of practical applications.
AUTOMATED IDENTIFICATION OF CORONARY ARTERY DISEASE FROM SHORT-TERM 12 LEAD ELECTROCARDIOGRAM SIGNALS BY USING WAVELET PACKET DECOMPOSITION AND COMMON SPATIAL PATTERN TECHNIQUES
Authors: OH SHU LIH , ADAM MUHAMMAD , TAN JEN HONG , HAGIWARA YUKI , SUDARSHAN VIDYA K. , KOH JOEL EN WEI , CHUA KUANG CHUA , CHUA KOK POO , TAN RU SAN , NG EDDIE Y. K. 
Published: October 2017

The occlusion of the coronary arteries commonly known as coronary artery disease (CAD) restricts the normal blood circulation required to the heart muscles, thus results in an irreversible myocardial damage or death (myocardial infarction). Clinically, electrocardiogram (ECG) is performed as a primary diagnostic tool to capture these cardiac activities and detect the presence of CAD. However, the use of computer-aided techniques can reduce the visual burden and manual time required for the analysis of complex ECG signals in order to identify the CAD affected subjects from normal ones. Therefore, in this study, a novel computer-aided technique is proposed using 2[Formula: see text]s of 12 lead ECG signals for the identification of CAD affected patients. Each of the 2[Formula: see text]s 12 lead ECG signal beats (3791 normal and 12308 CAD ECG signal beats) are implemented with four levels of wavelet packet decomposition (WPD) to obtain various coefficients. Using the fourth-level coefficients obtained for each lead ECG signal beat, new 2[Formula: see text]s. ECG signal beats are reconstructed. Later, the reconstructed signals are split into two-fold data sets, in which one set is used for acquiring common spatial pattern (CSP) filter and the other for obtaining features vector (vice versa). The obtained features are one by one fed into k-nearest neighbors (KNN) classifier for automated classification. The proposed system yielded maximum average classification results of 99.65% accuracy, 99.64% sensitivity and 99.7% specificity using 10 features. Our proposed algorithm is highly efficient and can be used by the clinicians as an aiding system in their CAD diagnosis, thus, assisting in faster treatment and avoiding the progression of CAD condition.
A solver-aided language for test input generation
Authors: Ringer Talia , Grossman Dan , Schwartz-Narbonne Daniel , Tasiran Serdar 
Published: October 2017

Developing a small but useful set of inputs for tests is challenging. We show that a domain-specific language backed by a constraint solver can help the programmer with this process. The solver can generate a set of test inputs and guarantee that each input is
different
from other inputs in a way that is useful for testing.

This paper presents Iorek: a tool that empowers the programmer with the ability to express to any SMT solver what it means for inputs to be different. The core of Iorek is a rich language for constraining the set of inputs, which includes a novel bounded enumeration mechanism that makes it easy to define and encode a flexible notion of difference over a recursive structure. We demonstrate the flexibility of this mechanism for generating strings.
We use Iorek to test real services and find that it is effective at finding bugs. We also build Iorek into a random testing tool and show that it increases coverage.