bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence for Lactobacillus helveticus CNRZ 32, an Industrial Cheese Starter and Cheese Flavor Adjunct
Authors: Broadbent Jeff R. , Hughes Joanne E. , Welker Dennis L. , Tompkins Thomas A. , Steele James L. 
Published: August 2013

ABSTRACT

Lactobacillus helveticus
is a lactic acid bacterium widely used in the manufacture of cheese and for production of bioactive peptides from milk proteins. We present the complete genome sequence for
L. helveticus
CNRZ 32, a strain particularly recognized for its ability to reduce bitterness and accelerate flavor development in cheese.
Complete Genome Sequence Analysis of a Reassortant Strain of Bluetongue Virus Serotype 16 from Italy
Authors: Lorusso Alessio , Costessi Adalberto , Pirovano Walter , Marcacci Maurilia , Cammà Cesare , Savini Giovanni 
Published: August 2013

ABSTRACT
The complete genome sequence of a reassortant field strain of bluetongue virus serotype 16 (BTV-16), isolated from cattle in the Apulia region of Italy in 2002, has been determined by Illumina sequencing. Sequence comparisons of segment 1 (Seg-1) to Seg-10, except Seg-5, show that BTV-16 strain ITL2002 belongs to the major eastern topotype of BTV.
Full Genome Sequence of Egg Drop Syndrome Virus Strain FJ12025 Isolated from Muscovy Duckling
Authors: Fu Guanghua , Chen Hongmei , Huang Yu , Cheng Longfei , Fu Qiuling , Shi Shaohua , Wan Chunhe , Chen Cuiteng , Lin Jiansheng 
Published: August 2013

ABSTRACT
Egg drop syndrome virus (EDSV) strain FJ12025 was isolated from a 9-day-old Muscovy duckling. The results of the sequence showed that the genome of strain FJ12025 is 33,213 bp in length, with a G+C content of 43.03%. When comparing the genome sequence of strain FJ12025 to that of laying duck original strain AV-127, we found 50 single-nucleotide polymorphisms (SNPs) between the two viral genome sequences. A genomic sequence comparison of FJ12025 and AV-127 will help to understand the phenotypic differences between the two viruses.
Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31
Authors: Mondy Samuel , Lalouche Ouaghlis , Dessaux Yves , Faure Denis 
Published: August 2013

ABSTRACT

Agrobacterium tumefaciens
strain WRT31 is a quorum-sensing signal-degrading bacterium that has been isolated from the rhizosphere of tobacco plants. This strain belongs to
A. tumefaciens
genomovar G1, is avirulent on various putative host plants, devoid of Ti plasmid, and contains the
blcC
gene encoding a gamma-butyrolactonase.
Complete Genome Sequence of the Arcobacter butzleri Cattle Isolate 7h1h
Authors: Merga J. Yvette , Winstanley Craig , Williams Nicola J. , Yee Emma , Miller William G. 
Published: August 2013

ABSTRACT

Arcobacter butzleri
strain 7h1h was isolated in the United Kingdom from the feces of a clinically healthy dairy cow. The genome of this isolate was sequenced to completion. Here, we present the annotation and analysis of the completed 7h1h genome, along with a comparison of this genome to the existing
A. butzleri
genomes.
Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179
T
, Isolated from Human Intestine
Authors: Cousin Sylvie , Creno Sophie , Ma Laurence , Clermont Dominique , Loux Valentin , Bizet Chantal , Bouchier Christiane 
Published: August 2013

ABSTRACT

We report the draft genome sequence of the strain
Lactobacillus hominis
CRBIP 24.179
T
, isolated from a human clinical sample. The total length of the 28 contigs is about 1.9 Mb, with a G+C content of 37% and 1,983 coding sequences.
Dimerization of the Pseudomonas aeruginosa Translocator Chaperone PcrH Is Required for Stability, Not Function
Authors: Tomalka Amanda G. , Zmina Stephanie E. , Stopford Charles M. , Rietsch Arne 
Published: August 2013

ABSTRACT

Type III secretion systems rely on hydrophobic translocator proteins that form a pore in the host cell membrane to deliver effector proteins into targeted host cells. These translocator proteins are stabilized in the cytoplasm and targeted for export with the help of specific chaperone proteins. In
Pseudomonas aeruginosa
, the chaperone of the pore-forming translocator proteins is PcrH. Although all translocator chaperones dimerize, the location of the dimerization interface is in dispute. Moreover, it has been reported that interfering with dimerization interferes with chaperone function. However, binding of
P. aeruginosa
chaperone PcrH to its cognate secretion substrate, PopD, results in dissociation of the PcrH dimer
in vitro
, arguing that dimerization of PcrH is likely not important for substrate binding or targeting translocators for export. We demonstrate that PcrH dimerization occurs
in vivo
in
P. aeruginosa
and used a genetic screen to identify a dimerization mutant of PcrH. The mutant protein is fully functional in that it can both stabilize PopB and PopD in the cytoplasm and promote their export via the type III secretion system. The location of the mutation suggests that the dimerization interface of PcrH mirrors that of the
Yersinia
homolog SycD and not the dimerization interface that had previously been reported for PcrH based on crystallographic evidence. Finally, we present data that the dimerization mutant of PcrH is less stable than the wild-type protein in
P. aeruginosa
, suggesting that the function of dimerization is stabilization of PcrH in the absence of its cognate cargo.
Posttranscriptional Self-Regulation by the Lyme Disease Bacterium's BpuR DNA/RNA-Binding Protein
Authors: Jutras Brandon L. , Jones Grant S. , Verma Ashutosh , Brown Nicholas A. , Antonicello Alyssa D. , Chenail Alicia M. , Stevenson Brian 
Published: August 2013

ABSTRACTBacteria require explicit control over their proteomes in order to compete and survive in dynamic environments. The Lyme disease spirocheteBorrelia burgdorferiundergoes substantial protein profile changes during its cycling between vector ticks and vertebrate hosts. In an effort to understand regulation of these transitions, we recently isolated and functionally characterized the borrelial nucleic acid-binding protein BpuR, a PUR domain-containing protein. We now report that this regulatory protein governs its own synthesis through direct interactions withbpuRmRNA.In vitroandin vivotechniques indicate that BpuR binds with high affinity and specificity to the 5′ region of its message, thereby inhibiting translation. This negative feedback could permit the bacteria to fine-tune cellular BpuR concentrations. These data add to the understanding of this newly described class of prokaryotic DNA- and RNA-binding regulatory proteins.
Probing Bacterial Metabolism during Infection Using High-Resolution Transcriptomics
Authors: Jorth Peter , Trivedi Urvish , Rumbaugh Kendra , Whiteley Marvin 
Published: August 2013

ABSTRACT

A fundamental aspect of most infectious diseases is the need for the invading microbe to proliferate in the host. However, little is known about the metabolic pathways required for pathogenic microbes to colonize and persist in their hosts. In this study, we used RNA sequencing (RNA-seq) to generate a high-resolution transcriptome of the opportunistic pathogen
Aggregatibacter actinomycetemcomitans
in vivo
. We identified 691
A. actinomycetemcomitans
transcriptional start sites and 210 noncoding RNAs during growth
in vivo
and as a biofilm
in vitro
. Compared to
in vitro
biofilm growth on a defined medium, ∼14% of the
A. actinomycetemcomitans
genes were differentially regulated
in vivo
. A disproportionate number of genes coding for proteins involved in metabolic pathways were differentially regulated
in vivo
, suggesting that
A. actinomycetemcomitans
in vivo
metabolism is distinct from
in vitro
growth. Mutational analyses of differentially regulated genes revealed that formate dehydrogenase H and fumarate reductase are important
A. actinomycetemcomitans
fitness determinants
in vivo
. These results not only provide a high-resolution genomic analysis of a bacterial pathogen during
in vivo
growth but also provide new insight into metabolic pathways required for
A. actinomycetemcomitans
in vivo
fitness.
Social participation in older adults with joint pain and comorbidity; testing the measurement properties of the Dutch Keele Assessment of Participation
Authors: Hermsen Lotte A H , Terwee Caroline B , Leone Stephanie S , van der Zwaard Babette , Smalbrugge Martin , Dekker Joost , van der Horst Henriëtte E , Wilkie Ross 
Published: August 2013

ObjectiveThe Keele Assessment of Participation (KAP) questionnaire measures person-perceived participation in 11 aspects of life. Participation allows fulfilment of valued life activities and social roles, which are important to older adults. Since we aimed to use the KAP in a larger Dutch cohort, we examined the measurement properties of KAP in a Dutch sample of older adults with joint pain and comorbidity.DesignCohort study.SettingA community-based sample in Amsterdam, the Netherlands and North Staffordshire, UK.ParticipantsParticipants were aged 65 years and over, had at least two chronic diseases (identified through general practice consultation) and reported joint pain on most days (questionnaire). The Dutch cohort provided baseline data (n=407), follow-up data at 6 months (n=364) and test–retest data 2 weeks after 6 months (n=122). The UK cohort provided comparable data (n=404).Outcome measuresThe primary outcome was person-perceived participation, as measured with the KAP. The measurement properties examined were the following: structural validity (factor analysis), internal consistency (Cronbach's α), reliability (intraclass correlation coefficients; ICC), construct validity (hypothesis testing), responsiveness (hypothesis testing and area under the curve) and cross-cultural validity (differential item functioning; DIF).ResultsFactor analysis revealed two domains: KAPd1: ‘participation in basic activities’ and KAPd2: ‘participation in complex activities’, with Cronbach's α of 0.74 and 0.57 and moderate test–retest reliability: ICC of 0.63 and 0.57, respectively. Further analyses of KAPd1 showed poor construct validity and responsiveness. Despite the uniform DIF in item ‘interpersonal relations’, the total KAPd1 score seemed comparable between the Dutch and UK sample.ConclusionsOnly KAP domain ‘participation in basic activities’ showed good internal consistency and sufficient reliability. KAPd2 lacks sufficient measurement properties for application in studies, although items may be used as single items. Further development of the concept ‘participation’ may help the development and validation of instruments to measure participation.
Facilitating and inhibiting factors for long-term involvement of patients at outcome conferences—lessons learnt from a decade of collaboration in OMERACT: a qualitative study
Authors: de Wit Maarten , Abma Tineke , Koelewijn-Van Loon Marije , Collins Sarah , Kirwan John 
Published: August 2013

ObjectiveSeveral studies have provided insights into the conditions for successful patient involvement in health research. We recently demonstrated that long-term engagement with people with rheumatic conditions in international outcome research led to significant changes in the research agenda in the field of rheumatology. This article explores facilitating and inhibiting factors for long-term involvement of patients as collaborative partners at five Outcome Measures in Rheumatology (OMERACT) conferences.DesignResponsive evaluation, starting with a thematic document analysis of conference proceedings and the grey literature, followed by 38 qualitative interviews. Interview transcripts were subjected to inductive content analysis.Setting5 international OMERACT conferences between 2002 and 2012.ParticipantsPatient delegates (n=16) and professional delegates representing researchers (n=14), pharmaceutical industry and regulators (n=2).ResultsCombined review of the document analysis and interview data revealed five main facilitators and three main barriers. Patient engagement as full participants at OMERACT conferences was enhanced by: strong leadership commitment and the presence of change agents, a clear selection procedure, an inclusive consensus-based conference design, individualised and self-organised support, an interactive and encouraging moderation style during discussion groups. Barriers were related to the intensity of the conference programme, scepticism among researchers and doubts about the representativeness of the patient group.ConclusionsThis study concludes that developing a sustainable structure for funding, selection and support of patient delegates, as well as adjusting conference design and moderation style, contributes not only towards facilitating direct dialogue between all stakeholders but also towards enhancing mutual understanding and the successful incorporation of the patient perspective in an outcome conference such as OMERACT.
Regional and socioeconomic disparities in the treatment of unruptured cerebral aneurysms in the USA: 2000–2010
Authors: Bekelis Kimon , Missios Symeon , Labropoulos Nicos 
Published: August 2013

BackgroundThe Institute of Medicine called attention to the pervasive differences in treatments and outcomes between ethnic groups. We sought to highlight the geographic and racial disparities in access to treatment for unruptured cerebral aneurysms.MethodsWe performed a retrospective cohort study involving patients with unruptured cerebral aneurysms from 2000 to 2010, registered in the National Inpatient Sample (NIS) database. Primary outcomes were those patients receiving treatment and the ratio of untreated to treated aneurysms per state. The purpose of this study was to determine if there were geographic and racial disparities in access to treatment of unruptured cerebral aneurysms based on the NIS. Logistic regression and analysis of variance (ANOVA) techniques were used.ResultsThere were 57 418 patients diagnosed with unruptured aneurysms (mean age 61.4 years, 70.5% females), with 18 231 undergoing treatment. Males (OR 0.67, 95% CI 0.64 to 0.71, p<0.0001), Asian (OR 0.88, 95% CI 0.81 to 0.96, p=0.003), Hispanic (OR 0.76, 95% CI 0.65 to 0.90, p=0.001), African American (OR 0.57, 95% CI 0.53 to 0.62, p<0.0001), and patients without insurance (OR 0.76, 95% CI 0.67 to 0.87, p<0.0001) were associated with decreased chance of treatment. The opposite was true for lower Charlson Comorbidity Index (OR 3.03, 95% CI 2.71 to 3.39, p<0.0001), coverage by Medicaid (OR 1.12, 95% CI 1.03 to 1.23, p=0.012), or private insurance (OR 1.92, 95% CI 1.80 to 2.04, p<0.0001), and lower income (OR 1.22, 95% CI 1.15 to 1.31, p<0.0001). Significant regional variability was observed among the different states (p=0.006, ANOVA), with Maryland being an outlier.ConclusionsBased on the NIS database, the rate of treatment of unruptured cerebral aneurysms varies according to sex, race, and region.
Education forms the tender mind
Authors: Gardner-Thorpe Christopher 
Published: August 2013

Abstract
In the early days of the development of a more formal approach to academic geology many natural philosophers, now better known as scientists, were men (rarely women) with inquisitive minds who encapsulated the field of what we now call the sciences. Thus medical practitioners, clergymen and others were enquiring into the natural world. One such was James Parkinson who was a doctor, geologist and keen moral philosopher. The area of Hoxton in East London where he lived his whole life has been redeveloped since then. Some of James’s interests are discussed here and the multiple interrelationships of medicine and geology within his family are illustrated.
Extraction of financial information from online business reports
Authors: Simmons Lakisha L. , Conlon Sumali J. 
Published: August 2013

CAINES, Content Analysis and INformation Extraction System, employs a semantic based information extraction (IE) methodology through a design science approach to extract unstructured text from the Web. Our system was knowledge-engineered and tested on an active business database by experts who use the database regularly to perform their job functions. We believe that by heavily involving business experts, we are able to advance our thinking about IS research. CAINES extracts information to meet three objectives that were deemed important by our experts: (1) understand what current market conditions impacted the growth of certain balance sheets (2) summarize management's discussion of potential risks and uncertainties (3) identify significant financial activities including mergers, acquisitions, and new business segments. These objectives were developed based on the advice of financial experts who regularly analyze financial reports.
A total of 21 online business reports from the EDGAR database, each averaging about 100 pages long, were used in this study. Based on financial expert opinions, extraction rules were created to extract information from financial reports. Using CAINES, one can extract information about global and domestic market conditions, market condition impacts, and information about the business outlook. User testing of CAINES resulted in recall of 85.91%, precision of 87.16%, and an F-measure of 86.46%. Speed with CAINES was also greater than manually extracting information. Users agreed that CAINES quickly and easily extracts unstructured information from financial reports on the EDGAR database. This study highlights the significance of creating a semantic based IE system that addresses practical business issues and solves a true business problem with the knowledge of business experts.
The p90 RSK Family Members: Common Functions and Isoform Specificity
Authors: Lara Romain , Seckl Michael J. , Pardo Olivier E. 
Published: August 2013

Abstract
The p90 ribosomal S6 kinases (RSK) are implicated in various cellular processes, including cell proliferation, survival, migration, and invasion. In cancer, RSKs modulate cell transformation, tumorigenesis, and metastasis. Indeed, changes in the expression of RSK isoforms have been reported in several malignancies, including breast, prostate, and lung cancers. Four RSK isoforms have been identified in humans on the basis of their high degree of sequence homology. Although this similarity suggests some functional redundancy between these proteins, an increasing body of evidence supports the existence of isoform-based specificity among RSKs in mediating particular cellular processes. This review briefly presents the similarities between RSK family members before focusing on the specific function of each of the isoforms and their involvement in cancer progression. Cancer Res; 73(17); 5301–8. ©2013 AACR.
Therapeutic PD-1 Pathway Blockade Augments with Other Modalities of Immunotherapy T-Cell Function to Prevent Immune Decline in Ovarian Cancer
Authors: Duraiswamy Jaikumar , Freeman Gordon J. , Coukos George 
Published: August 2013

AbstractThe tumor microenvironment mediates induction of the immunosuppressive programmed cell death-1 (PD-1) pathway, and targeted interventions against this pathway can help restore antitumor immunity. To gain insight into these responses, we studied the interaction between PD-1 expressed on T cells and its ligands (PD-1:PD-L1, PD-1:PD-L2, and PD-L1:B7.1), expressed on other cells in the tumor microenvironment, using a syngeneic orthotopic mouse model of epithelial ovarian cancer (ID8). Exhaustion of tumor-infiltrating lymphocytes (TIL) correlated with expression of PD-1 ligands by tumor cells and tumor-derived myeloid cells, including tumor-associated macrophages (TAM), dendritic cells, and myeloid-derived suppressor cells (MDSC). When combined with GVAX or FVAX vaccination (consisting of irradiated ID8 cells expressing granulocyte macrophage colony—stimulating factor or FLT3 ligand) and costimulation by agonistic α-4-1BB or TLR 9 ligand, antibody-mediated blockade of PD-1 or PD-L1 triggered rejection of ID8 tumors in 75% of tumor-bearing mice. This therapeutic effect was associated with increased proliferation and function of tumor antigen-specific effector CD8+ T cells, inhibition of suppressive regulatory T cells (Treg) and MDSC, upregulation of effector T-cell signaling molecules, and generation of T memory precursor cells. Overall, PD-1/PD-L1 blockade enhanced the amplitude of tumor immunity by reprogramming suppressive and stimulatory signals that yielded more powerful cancer control. Cancer Res; 73(23); 6900–12. ©2013 AACR.
The G-Protein–Coupled Receptor CLR Is Upregulated in an Autocrine Loop with Adrenomedullin in Clear Cell Renal Cell Carcinoma and Associated with Poor Prognosis
Authors: Nikitenko Leonid L. , Leek Russell , Henderson Stephen , Pillay Nischalan , Turley Helen , Generali Daniele , Gunningham Sarah , Morrin Helen R. , Pellagatti Andrea , Rees Margaret C.P. , Harris Adrian L. , Fox Stephen B. 
Published: August 2013

Abstract
Purpose: The G-protein–coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) and its ligand peptide adrenomedullin (encoded by ADM gene) are implicated in tumor angiogenesis in mouse models but poorly defined in human cancers. We therefore investigated the diagnostic/prognostic use for CLR in human tumor types that may rely on adrenomedullin signaling and in clear cell renal cell carcinoma (RCC), a highly vascular tumor, in particular.
Experimental Design: In silico gene expression mRNA profiling microarray study (n = 168 tumors) and cancer profiling cDNA array hybridization (n = 241 pairs of patient-matched tumor/normal tissue samples) were carried out to analyze ADM mRNA expression in 13 tumor types. Immunohistochemistry on tissue microarrays containing patient-matched renal tumor/normal tissues (n = 87 pairs) was conducted to study CLR expression and its association with clinicopathologic parameters and disease outcome.
Results: ADM expression was significantly upregulated only in RCC and endometrial adenocarcinoma compared with normal tissue counterparts (P &lt; 0.01). CLR was localized in tumor cells and vessels in RCC and upregulated as compared with patient-matched normal control kidney (P &lt; 0.001). Higher CLR expression was found in advanced stages (P &lt; 0.05), correlated with high tumor grade (P &lt; 0.01) and conferred shorter overall survival (P &lt; 0.01).
Conclusions: In human tissues ADM expression is upregulated in cancer type–specific manner, implicating potential role for adrenomedullin signaling in particular in RCC, where CLR localization suggests autocrine/paracrine mode for adrenomedullin action within the tumor microenvironment. Our findings reveal previously unrecognized CLR upregulation in an autocrine loop with adrenomedullin in RCC with potential application for this GPCR as a target for future functional studies and drug development. Clin Cancer Res; 19(20); 5740–8. ©2013 AACR.