bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential T‐cell responses to a chimeric Plasmodium falciparum antigen; UB05‐09, correlates with acquired immunity to malaria
Authors: Dinga J. N. , Njimoh D. L. , Kiawa B. , Djikeng A. , Nyasa R. B. , Nkuo‐Akenji T. , Pellé R. , Titanji V. P. K. 
Published: March 2016

SummaryThe development of a sterilizing and cost‐effective vaccine against malaria remains a major problem despite recent advances. In this study, it is demonstrated that two antigens of P. falciparum UB05, UB09 and their chimera UB05‐09 can serve as protective immunity markers by eliciting higher T‐cell responses in malaria semi‐immune subjects (SIS) than in frequently sick subjects (FSS) and could be used to distinguish these two groups. UB05, UB09 and UB05‐09 were cloned, expressed in E. coli, purified and used to stimulate PBMCs isolated from 63 subjects in a malaria endemic area, for IFN‐γ production, which was measured by the ELISpot assay. The polymorphism of UB09 gene in the malaria infected population was also studied by PCR/sequencing of the gene in P. falciparum field isolates. All three antigens were preferentially recognized by PBMCs from SIS. IFN‐γ production induced by these antigens correlated with the absence of fever and parasitaemia. UB09 was shown to be relatively well‐conserved in nature. It is concluded that UB05, UB09 and the chimera UB05‐09 posses T‐cell epitopes that are associated with protection against malaria and could thus be used to distinguish SIS from FSS eventhough acute infection with malaria has been shown to reduce cytokine production in some studies. Further investigations of these antigens as potential diagnostic and/or vaccine candidates for malaria are indicated.
Low‐temperature concentration of tellurium and gold in continental red bed successions
Authors: Parnell John , Spinks Samuel , Bellis David 
Published: March 2016

AbstractThere is very little understanding of tellurium (Te) distribution and behaviour in sedimentary rocks. A suite of 15 samples of reduction spheroids (centimetre‐scale pale spheroids in otherwise red rock), including samples from eight localities in Triassic red beds across the British Isles, were mapped for Te using Laser Ablation–Inductively Coupled Plasma–Mass Spectrometry. Almost all showed enrichment in Te in the cores of the spheroids relative to background red bed concentrations, by up to four orders of magnitude. Some were also enriched over background in gold and/or mercury. In one case, discrete telluride minerals were recorded. The data show that Te is mobile and can be concentrated in low‐temperature sedimentary environments, controlled by redox variations. The consistency in enrichment across widely separate localities implies that the enrichment is a normal aspect of red bed diagenesis and so likely to be controlled by a ubiquitous process, such as microbial activity.
Identification of genetic variants associated with maize flowering time using an extremely large multi‐genetic background population
Authors: Li Yong‐xiang , Li Chunhui , Bradbury Peter J. , Liu Xiaolei , Lu Fei , Romay Cinta M. , Glaubitz Jeffrey C. , Wu Xun , Peng Bo , Shi Yunsu , Song Yanchun , Zhang Dengfeng , Buckler Edward S. , Zhang Zhiwu , Li Yu , Wang Tianyu 
Published: March 2016

SummaryFlowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi‐ genetic background population that contained more than 8000 lines under multiple Sino‐United States environments. The population included two nested association mapping (NAM) panels and a natural association panel. Nearly 1 million single‐nucleotide polymorphisms (SNPs) were used in the analyses. Through the parallel linkage analysis of the two NAM panels, both common and unique flowering time regions were detected. Genome wide, a total of 90 flowering time regions were identified. One‐third of these regions were connected to traits associated with the environmental sensitivity of maize flowering time. The genome‐wide association study of the three panels identified nearly 1000 flowering time‐associated SNPs, mainly distributed around 220 candidate genes (within a distance of 1 Mb). Interestingly, two types of regions were significantly enriched for these associated SNPs – one was the candidate gene regions and the other was the approximately 5 kb regions away from the candidate genes. Moreover, the associated SNPs exhibited high accuracy for predicting flowering time.
Large‐scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis
Authors: He Fei , Yoo Shinjae , Wang Daifeng , Kumari Sunita , Gerstein Mark , Ware Doreen , Maslov Sergei 
Published: March 2016

SummaryTranscriptome data sets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta‐analysis of these samples has become routine in the plant research community, it is often hampered by a lack of metadata or differences in annotation styles of different labs. In this study, we carefully selected and integrated 6057 Arabidopsis microarray expression samples from 304 experiments deposited to the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI). Metadata such as tissue type, growth conditions and developmental stage were manually curated for each sample. We then studied the global expression landscape of the integrated data set and found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome, compared with aerial tissues, but the transcriptome of cultured root is more similar to the transcriptome of aerial tissues, as the cultured root samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating the re‐use of plant transcriptome data. As a proof of principle, we applied our automated annotation pipeline to 708 RNA‐seq samples from public repositories and verified the accuracy of our predictions with sample metadata provided by the authors.
3D microwave tomography of the breast using prior anatomical information
Authors: Golnabi Amir H. , Meaney Paul M. , Paulsen Keith D. 
Published: March 2016

Purpose:The authors have developed a new 3D breast image reconstruction technique that utilizes the soft tissue spatial resolution of magnetic resonance imaging (MRI) and integrates the dielectric property differentiation from microwave imaging to produce a dual modality approach with the goal of augmenting the specificity of MR imaging, possibly without the need for nonspecific contrast agents. The integration is performed through the application of a soft prior regularization which imports segmented geometric meshes generated from MR exams and uses it to constrain the microwave tomography algorithm to recover nearly uniform property distributions within segmented regions with sharp delineation between these internal subzones.Methods:Previous investigations have demonstrated that this approach is effective in 2D simulation and phantom experiments and also in clinical exams. The current study extends the algorithm to 3D and provides a thorough analysis of the sensitivity and robustness to misalignment errors in size and location between the spatial prior information and the actual data.Results:Image results in 3D were not strongly dependent on reconstruction mesh density, and the changes of less than 30% in recovered property values arose from variations of more than 125% in target region size—an outcome which was more robust than in 2D. Similarly, changes of less than 13% occurred in the 3D image results from variations in target location of nearly 90% of the inclusion size. Permittivity and conductivity errors were about 5 times and 2 times smaller, respectively, with the 3D spatial prior algorithm in actual phantom experiments than those which occurred without priors.Conclusions:The presented study confirms that the incorporation of structural information in the form of a soft constraint can considerably improve the accuracy of the property estimates in predefined regions of interest. These findings are encouraging and establish a strong foundation for using the soft prior technique in clinical studies, where their microwave imaging system and MRI can simultaneously collect breast exam data in patients.
Draft Genome Sequences of
Streptococcus agalactiae
Serotype Ia and III Isolates from Tilapia Farms in Thailand
Authors: Areechon Nontawith , Kannika Korntip , Hirono Ikuo , Kondo Hidehiro , Unajak Sasimanas 
Published: March 2016

ABSTRACT

Streptococcus agalactiae
serotypes Ia and III were isolated from infected tilapia in cage and pond culture farms in Thailand during 2012 to 2014, in which pathogenicity analysis demonstrated that serotype III showed higher virulence than serotype Ia. Here, we report the draft genome sequencing of piscine
S. agalactiae
serotypes Ia and III.
Complete Genome Sequence of
Alteromonas stellipolaris
LMG 21856, a Budding Brown Pigment-Producing Oligotrophic Bacterium Isolated from the Southern Ocean
Authors: Chen Jigang , Wang Xing , Zhu Sidong , Chen Yong , Yang Jifang 
Published: March 2016

ABSTRACT

Here, we report the complete genome sequence of
Alteromonas stellipolaris
LMG 21856, which was isolated from seawater collected from the Southern Ocean.
A. stellipolaris
LMG 21856 is a budding, psychrotrophic, brown pigment-producing, and oligotrophic bacterium
.
The complete genome of this bacterium contains 4,686,200 bp, with a G+C content of 43.6%.
Genome Sequence of a Fowl Adenovirus Serotype 4 Strain Lethal to Chickens, Isolated from China
Authors: Li Lintao , Luo Ling , Luo Qingping , Zhang Tengfei , Zhao Kang , Wang Honglin , Zhang Rongrong , Lu Qin , Pan Zishu , Shao Huabin , Zhang Wanpo , Wen Guoyuan 
Published: March 2016

ABSTRACT
We report here the complete genome sequence of virulent fowl adenovirus serotype 4 strain HB1510, isolated from a diseased chicken with hydropericardium-hepatitis syndrome in Hubei, China, in 2015. The viral genome is 43,721 bp long, and sequence analysis showed an 11-amino-acid deletion in open reading frame 29 (ORF29).
Fully Closed Genome Sequences of Five Type Strains of the Genus
Cronobacter
and One
Cronobacter sakazakii
Strain
Authors: Moine Deborah , Kassam Mohamed , Baert Leen , Tang Yanjie , Barretto Caroline , Ngom Bru Catherine , Klijn Adrianne , Descombes Patrick 
Published: March 2016

ABSTRACT

Cronobacter
is associated with infant infections and the consumption of reconstituted infant formula. Here we sequenced and closed six genomes of
C. condimenti
T
,
C. muytjensii
T
,
C. universalis
T
,
C. malonaticus
T
,
C. dublinensis
T
, and
C. sakazakii
that can be used as reference genomes in single nucleotide polymorphism (SNP)-based next-generation sequencing (NGS) analysis for source tracking investigations.
First Genome Sequence of a Mexican Multidrug-Resistant
Acinetobacter baumannii
Isolate
Authors: Graña-Miraglia Lucía , Lozano Luis , Castro-Jaimes Semiramis , Cevallos Miguel A. , Volkow Patricia , Castillo-Ramírez Santiago 
Published: March 2016

ABSTRACT

Acinetobacter baumannii
has emerged as an important nosocomial pathogen worldwide. Here, we present the draft genome of the first multidrug-resistant
A. baumannii
isolate, sampled from a tertiary hospital in Mexico City. This genome will provide a starting point for studying the genomic diversity of this species in Mexico.
Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant
Pseudomonas aeruginosa
Strain
Authors: Manivannan Bhavani , Mahalingam Niranjana , Jadhao Sudhir , Mishra Amrita , Nilawe Pravin , Pradeep Bulagonda Eswarappa 
Published: March 2016

ABSTRACT

We present the draft genome assembly of an extensively drug-resistant (XDR)
Pseudomonas aeruginosa
strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.
Draft Genome Sequence of an Endophytic
Actinoplanes
Species, Encoding Uncommon
trans
-Acyltransferase Polyketide Synthases
Authors: Centeno-Leija Sara , Vinuesa Pablo , Rodríguez-Peña Karol , Trenado-Uribe Miriam , Cárdenas-Conejo Yair , Serrano-Posada Hugo , Rodríguez-Sanoja Romina , Sánchez Sergio 
Published: March 2016

ABSTRACT

Actinoplanes
is an endophytic actinobacterium isolated from the medicinal plant
Amphipterygium adstringens
. The strain draft genome sequence reveals a gene cluster involved in the biosynthesis of a hybrid
trans
-acyltransferase (AT) polyketide, an unconventional bioactive metabolite never reported before in the genus
Actinoplanes
.
Complete Genome Sequence of
Arthrobacter
sp. ATCC 21022, a Host for Bacteriophage Discovery
Authors: Russell Daniel A. , Hatfull Graham F. 
Published: March 2016

ABSTRACT

We report the complete genome sequence of
Arthrobacter
sp. ATCC 21022, a strain maintained by ATCC and a commonly used host for bacteriophage isolation and genomic analysis. The strain is prophage-free and CRISPR-free but codes for two predicted restriction-modification systems.
Draft Genome Sequence of
Streptomyces canus
ATCC 12647, a Producer of Telomycin
Authors: Liu Dennis Y. , Li Yongchang , Magarvey Nathan A. 
Published: March 2016

ABSTRACT

We present here the genome sequence of
Streptomyces canus
ATCC 12647, a producer of the antibiotic telomycin, noted for its unique antibacterial activity against cardiolipin. Genomic analysis using the bioinformatics tool PRISM revealed the presence of multiple biosynthetic gene clusters, including those for telomycin and other natural products of potential pharmacological interest.
Whole-Genome Sequence of
Bacillus
sp. SDLI1, Isolated from the Social Bee
Scaptotrigona depilis
Authors: Paludo Camila R. , Ruzzini Antonio C. , Silva-Junior Eduardo A. , Pishchany Gleb , Currie Cameron R. , Nascimento Fábio S. , Kolter Roberto G. , Clardy Jon , Pupo Mônica T. 
Published: March 2016

ABSTRACT

We announce the complete genome sequence of
Bacillus
sp. strain SDLI1, isolated from larval gut of the stingless bee
Scaptotrigona depilis
. The 4.13-Mb circular chromosome harbors biosynthetic gene clusters for the production of antimicrobial compounds.
Draft Genome Sequence of
Streptococcus gordonii
Type Strain CCUG 33482
T
Authors: Salvà-Serra Francisco , Jakobsson Hedvig E. , Thorell Kaisa , Gonzales-Siles Lucia , Hallbäck Erika T. , Jaén-Luchoro Daniel , Boulund Fredrik , Sikora Per , Karlsson Roger , Svensson Liselott , Bennasar Antoni , Engstrand Lars , Kristiansson Erik , Moore Edward R. B. 
Published: March 2016

ABSTRACT

Streptococcus gordonii
type strain CCUG 33482
T
is a member of the
Streptococcus mitis
group, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence of
S. gordonii
CCUG 33482
T
, composed of 41 contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.
Whole-Genome Sequence of
Corynebacterium pseudotuberculosis
262 Biovar
equi
Isolated from Cow Milk
Authors: Araújo Carlos Leonardo de A. , Dias Larissa M. , Veras Adonney A. O. , Alves Jorianne T. C. , Cavalcante Ana Lídia Q. , Dowson Christopher G. , Azevedo Vasco , Ramos Rommel T. J. , Silva Artur , Carneiro Adriana R. 
Published: March 2016

ABSTRACT

We report the complete genome sequence of
Corynebacterium pseudotuberculosis
262, isolated from a bovine host.
C. pseudotuberculosis
is an etiological agent of diseases with medical and veterinary relevance. The genome contains 2,325,749 bp, 52.8% G+C content, 2,022 coding sequences (CDS), 50 pseudogenes, 48 tRNAs, and 12 rRNAs.
Brief strategic therapy for obsessive–compulsive disorder: a clinical and research protocol of a one-group observational study
Authors: Pietrabissa Giada , Manzoni Gian Mauro , Gibson Padraic , Boardman Donald , Gori Alessio , Castelnuovo Gianluca 
Published: March 2016

IntroductionObsessive–compulsive disorder (OCD) is a disabling psychopathology. The mainstay of treatment includes cognitive–behavioural therapy (CBT) and medication management. However, individual suffering, functional impairments as well as the direct and indirect costs associated with the disease remain substantial. New treatment programmes are necessary and the brief strategic therapy (BST) has recently shown encouraging results in clinical practice but no quantitative study has as yet been conducted.Methods and analysisThe clinical effectiveness of the OCD-specific BST protocol will be evaluated in a one-group observational study. Participants will be sequentially recruited from a state community psychotherapy clinic in Dublin, Ireland. Outcome measures will be the Yale-Brown Obsessive Compulsive Scale (Y-BOCS) and the Beck Depression Inventory-II (BDI-II). Data will be collected at baseline, at treatment termination and at 3 month follow-up. The statistical significance of the post-treatment effect will be assessed by the paired-sample Student t test, while clinical significance will be evaluated by means of the equivalence testing method, which will be also used to assess the maintenance of effect at follow-up.Ethics/disseminationThe present study is approved by the Hesed House Ethics Board in Dublin. Findings will enhance the evidence-based knowledge about the clinical effectiveness of BST in treating OCD symptoms, prior to assessing its efficacy in a randomised and controlled clinical trial, and will be disseminated through publication in peer-reviewed journals and conference presentations.
Evaluation of the associations between changes in intraocular pressure and metabolic syndrome parameters: a retrospective cohort study in Japan
Authors: Yokomichi Hiroshi , Kashiwagi Kenji , Kitamura Kazuyoshi , Yoda Yoshioki , Tsuji Masahiro , Mochizuki Mie , Sato Miri , Shinohara Ryoji , Mizorogi Sonoko , Suzuki Kohta , Yamagata Zentaro 
Published: March 2016

ObjectiveThe contributions of highly correlated cardiovascular risk factors to intraocular pressure (IOP) are not clear due to underlying confounding problems. The present study aimed to determine which metabolic syndrome parameters contribute to elevating IOP and to what extent.DesignRetrospective cohort study.SettingA private healthcare centre in Japan.ParticipantsIndividuals who visited a private healthcare centre and underwent comprehensive medical check-ups between April 1999 and March 2009 were included (20 007 in the cross-sectional study and 15 747 in the longitudinal study).Primary and secondary outcome measuresChanges in IOP were evaluated in terms of ageing and changes in metabolic syndrome parameters. Pearson's correlation coefficients and mixed-effects models were used to examine the relationship of changes in IOP with ageing and changes in metabolic syndrome parameters in cross-sectional and longitudinal studies, respectively.ResultsIn the cross-sectional study, IOP was negatively correlated with age and positively correlated with waist circumference, high-density lipoprotein cholesterol (HDL-C) levels, triglyceride levels, systolic blood pressure (SBP), diastolic blood pressure (DBP) and fasting plasma glucose (FPG) levels. In the longitudinal multivariate analysis, the associated IOP changes were −0.12 (p<0.0001) mm Hg with male sex; −0.59 (p<0.0001) mm Hg with 10 years of ageing; +0.42 (p<0.0001) mm Hg with 1 mmol/L increase in HDL-C levels; +0.092 (p<0.0001) mm Hg with 1 mmol/L increase in triglyceride levels; +0.090 (p<0.0001) mm Hg with 10 mm Hg increase in SBP; +0.085 (p<0.0001) mm Hg with 10 mm Hg increase in DBP; and+0.091 (p<0.0001) mm Hg with 1 mmol/L increase in FPG levels.ConclusionsElevation of IOP was related to longitudinal worsening of serum triglyceride levels, blood pressure and FPG and improvement in serum HDL-C levels.
Rehabilitation interventions in children and adults with infectious encephalitis: a systematic review protocol
Authors: Christie Shanice , Chan Vincy , Mollayeva Tatyana , Colantonio Angela 
Published: March 2016

IntroductionMany encephalitis survivors can benefit from rehabilitation. However, there is currently no comprehensive review describing rehabilitation intervention outcomes among children and adults with infectious encephalitis. This is a protocol for a systematic review that will summarise the current literature on outcomes following rehabilitative interventions among children and adults with infectious encephalitis. With a sufficient sample size, a sex-stratified analysis of the findings will also be presented, as variability between male and female patients with neurological disorders, including encephalitis, regarding outcomes after rehabilitative interventions has been noted in the literature.Methods and analysisThis review will systematically search MEDLINE, MEDLINE In-Process, EMBASE, Cochrane Central Register of Controlled Trials, and PsycINFO using the concepts ‘encephalitis’ and ‘rehabilitation’. Grey literature will be searched usingGrey Matters: A practical search tool for evidence-based medicineand the Google search engine. In addition, reference lists of eligible articles will be screened for any relevant studies. 2 reviewers will independently evaluate the retrieved studies based on predetermined eligibility criteria and perform a quality assessment on eligible studies.Ethics and disseminationThe results from this review hold the potential to advance our knowledge on the value of rehabilitative interventions targeting children and adults with infectious encephalitis and any sex differences among patients with regard to rehabilitative intervention outcomes. The authors will publish findings from this review in a peer-reviewed scientific journal (electronic and in-print) and present the results at national and international conferences.Trial registration numberCRD42015029217.