bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Wood Canker Caused by Botryosphaeria dothidea, Diplodia seriata, Neofusicoccum parvum, and Lasiodiplodia theobromae on Grapevine in Turkey
Authors: Akgul D. S. , Savas N. G. , Eskalen A. 
Published: October 2013

The Aegean region (western Turkey) is the center of table, raisin, and wine grape cultivation. During the 2012 growing season, wood canker symptoms were observed in vineyards in Manisa city. Symptoms adjacent to pruning wounds, including shoot dieback and wedge-shaped wood discolorations observed in cross section, were among the most prevalent symptoms of the vines. To identify the causal agents, symptomatic woody tissues were surface disinfested with 95% ethanol and flame-sterilized and the discolored outer bark was cut away. The internal tissues (0.5 cm2) were excised from cankers of vines and plated onto potato dextrose agar amended with tetracycline (0.01%) (PDA-tet). The most frequently isolated fungi, based on general growth pattern, speed of growth, and colony color, resembled species in the Botryosphaeriaceae family. According to morphological characteristics, four different groups have been identified based on visual discrimination. After DNA extraction, ribosomal DNA fragments (ITS1-5.8S-ITS2) (2) amplified with ITS4 and ITS5 primers were sequenced and sequences were compared with those deposited in NCBI GenBank database. Four different Botryosphaeriaceae isolates were identified, including Botryosphaeria dothidea (MBAi25AG), Diplodia seriata (MBAi23AG), Lasiodiplodia theobromae (MBAi28AG), and Neofusicoccum parvum (MBAi27AG) (Accession Nos. KF182329, KF182328, KF182331, and KF182330, respectively) with species nomenclature based on Crous et al. (1). Pathogenicity tests were conducted under greenhouse conditions (24°C, 16/8-h day/night, 70% RH) on 1-year-old own rooted grapevine (Vitis vinifera) cv. Sultana Seedless seedlings using one isolate from each of the Botryosphaeriaceae species specified above. Stems of grapevine seedlings were wounded by removing bark with 4-mm cork borer and fresh mycelial plugs were inoculated into the holes and covered with Parafilm. Sterile PDA plugs were placed into the wounds of control seedlings. Five vines were inoculated per isolate. The experiment was repeated twice. After 4 months of incubation, grapevine seedlings were examined for the extent of vascular discoloration and recovery of fungal isolates. Mean lesion lengths on wood tissues were 85.3, 17.2, 13.9, and 13.1 mm for N. parvum, B. dothidea, L. theobromae, and D. seriata, and 6.3 mm for control. Each fungal isolate was successfully re-isolated from inoculated seedlings to fulfill Koch's postulates. To our knowledge, this is the first report of multiple species in the Botryosphaeriaceae causing wood canker and dieback on grapevine in Turkey. These results are significant because Botryosphaeriaceae species are known causal agents of grapevine trunk disease worldwide (3). References: (1) P. W. Crous et al. Stud. Mycol. 55:235, 2006. (2) B. Slippers et al. Mycologia 96:83, 2004. (3) J. R. Urbez-Torres. Phytopathol. Mediterr. 50:S5, 2011.
Structure and dynamic behavior of Toll‐like receptor 2 subfamily triggered by malarial glycosylphosphatidylinositols of Plasmodium falciparum
Authors: Durai Prasannavenkatesh , Govindaraj Rajiv Gandhi , Choi Sangdun 
Published: October 2013

Proinflammatory responses by Toll‐like receptors (TLRs) to malaria infection are considered to be a significant factor in suppressing pathogen growth and in disease control. The key protozoan parasite Plasmodium falciparum causes malaria through glycosylphosphatidylinositols (GPIs), which induce the host immune response mainly via TLR2 signalling. Experimental studies have suggested that malarial GPIs from P. falciparum are recognized by the TLR2 subfamily. However, the interaction site and their involvement in the activation mechanism are still unknown. A better understanding of the detailed structure of the TLR–GPI interaction is important for the design of more effective anti‐malarial therapeutics. We used a molecular docking method to predict the binding regions of malarial GPIs with the TLR2 subfamily members. We also employed molecular dynamics simulations and principal component analysis to understand ligand‐induced conformational changes of the TLR2 subfamily. We observed the expected structural changes upon ligand binding, and significant movements were found in loop regions located in the ligand‐binding site of the TLR2 subfamily. We further propose that the binding modes of malarial GPIs are similar to lipopeptides, and that the lipid portions of the ligands could play an essential role in selective dimerization of the TLR2 subfamily.
Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus
Sensu Lato
Authors: Van der Auwera Géraldine A. , Feldgarden Michael , Kolter Roberto , Mahillon Jacques 
Published: October 2013

ABSTRACT

Bacillus cereus
sensu lato
is a species complex that includes the anthrax pathogen
Bacillus anthracis
and other bacterial species of medical, industrial, and ecological importance. Their phenotypes of interest are typically linked to large plasmids that are closely related to the anthrax plasmids pXO1 and pXO2. Here, we present the draft genome sequences of 94 isolates of
B. cereus
sensu lato
, which were chosen for their plasmid content and environmental origins.
Identification of a Novel Strain of Human Papillomavirus from Children with Diarrhea in China
Authors: Yu Jie-mei , Ao Yuan-yun , Zhao Guoyan , Li Li-li , Wang David , Duan Zhao-jun 
Published: October 2013

ABSTRACT
A highly divergent human papillomavirus (HPV) strain, HPV-L55, was identified in fecal samples from children hospitalized with diarrhea in China. The L1 gene of HPV-L55 shares <75% identity with previously reported HPVs, indicating that this virus represents a novel type of HPV. Phylogenetic analysis classified this virus as a member of the gammapapillomaviruses.
Full-Genome Sequence of a Reassortant H1N1 Swine Influenza Virus Isolated from Pigs in Italy
Authors: Chiapponi Chiara , Baioni Laura , Luppi Andrea , Moreno Ana , Castellan Alberto , Foni Emanuela 
Published: October 2013

ABSTRACT
In this study, the full-genome sequence of a novel reassortant H1N1 swine influenza virus (SIV) is reported. The isolate has a hemagglutinin (HA) gene of the pandemic H1N1 influenza virus, but it carries the seven genome segments of the avian-origin H1N1 SIV currently circulating in European pig farms.
Genome Sequence of Streptococcus parauberis Strain KCTC11980, Isolated from Diseased
Paralichthys olivaceus
Authors: Park Myoung Ae , Kwon Mun Gyeong , Hwang Jee Youn , Jung Sung Hee , Kim Dong-Wook , Park Jin-Young , Kim Ji-Sun , Na Yun-Jeong , Kim Min-Young , Kim Dae-Soo , Chae Sung-Hwa , Seo Jung Soo 
Published: October 2013

ABSTRACT

Streptococcus parauberis
is a coccoid, nonmotile, alpha-hemolytic, Gram-positive bacterium of the
Streptococcaceae
family.
Streptococcus parauberis
strain KCTC11980 was isolated from the kidney of a diseased olive flounder collected from an aquaculture farm on Jeju Island in 2010. The 2.12-Mb genome sequence consists of 44 large contigs in 16 scaffolds and contains 2,214 predicted protein-coding genes, with a G+C content of 35.4%.
Draft Genome Sequence of Vibrio coralliilyticus Strain OCN008, Isolated from Kāne‘ohe Bay, Hawai‘i
Authors: Ushijima Blake , Videau Patrick , Aeby Greta S. , Callahan Sean M. 
Published: October 2013

ABSTRACT

Vibrio coralliilyticus
is a Gram-negative bacterium found in seawater and is associated with diseased marine organisms. Strains of
V. coralliilyticus
have been shown to infect coral from multiple genera. We report the draft genome sequence of
V. coralliilyticus
strain OCN008, the third
V. coralliilyticus
genome to be sequenced.
Whole-Genome Sequence of the Clinical Strain Corynebacterium argentoratense DSM 44202, Isolated from a Human Throat Specimen
Authors: Bomholt Christina , Glaub Alina , Gravermann Kerstin , Albersmeier Andreas , Brinkrolf Karina , Rückert Christian , Tauch Andreas 
Published: October 2013

ABSTRACT

Corynebacterium argentoratense
is part of the human skin microbiota and is occasionally detected in the upper respiratory tract of patients suffering from tonsillitis. The complete DNA sequence of the type strain DSM 44202 comprises 2,031,902 bp, yielding the smallest genome sequenced thus far for a corynebacterium associated with humans.
Draft Genome Sequence of a Neisseria meningitidis Serogroup C Isolate of Sequence Type 11 Linked to an Outbreak among Men Who Have Sex with Men
Authors: Veyrier Frédéric J. , Hong Eva , Deghmane Ala-Eddine , Taha Muhamed-Kheir 
Published: October 2013

ABSTRACT

Meningococcal disease occurs as sporadic cases in developed countries, with the occasional emergence of new clones of
Neisseria meningitidis
. Here, we report the genome sequence of
N. meningitidis
strain LNP27256, an isolate of sequence type 11 linked to a recent outbreak among men who have sex with men in Europe.
Genome Sequence of the Quorum-Sensing-Signal-Producing Nonpathogen Agrobacterium tumefaciens Strain P4
Authors: Mondy Samuel , Lalouche Ouaghlis , Dessaux Yves , Faure Denis 
Published: October 2013

ABSTRACT

Agrobacterium tumefaciens
P4 is a quorum-sensing-signal-producing bacterium that has been isolated from the tobacco rhizosphere. This strain belongs to genomospecies 1 of the
A. tumefaciens
complex; it is avirulent on various putative host plants, devoid of the Ti plasmid, and contains a
luxI
homolog on the At plasmid.
Draft Genome Sequence of Pasteurella multocida A:3 Strain 671/90
Authors: Lainson Frederick A. , Dagleish Mark P. , Fontaine Michael C. , Bayne Colin , Hodgson J. Christopher 
Published: October 2013

ABSTRACT

Pasteurella multocida
serogroup A is commonly isolated from nasal swabs of clinically healthy calves and also from diseased lung tissue in bovine pneumonia. Here, we report the draft genome sequence of the virulent strain
P. multocida
671/90, which has been characterized previously in experimental infections of calves and mice.
Bibliographic review of research publications on access to and use of medicines in low-income and middle-income countries in the Eastern Mediterranean Region: identifying the research gaps
Authors: Rashidian Arash , Jahanmehr Nader , Jabbour Samer , Zaidi Shehla , Soleymani Fatemeh , Bigdeli Maryam 
Published: October 2013

ObjectivesWe assessed the situation of academic publications on access to and use of medicines (ATM) in low-income and middle-income countries (LMICs) of the Eastern Mediterranean Region (EMR). We aimed to inform priority setting for research on ATM in the region.DesignBibliographic review of published studies.SettingLMICs in EMR.Inclusion criteriaPublications on ATM issues originating from or focusing on EMR LMICs covering the period 2000–2011. Publications involving multinational studies were included if at least one eligible country had been included in the study.Information sources and data extractionWe conducted comprehensive searches of the PubMed, Social Science Citation Index and Science Citation Index. We used the WHO ATM framework for data extraction and synthesis. We analysed the data according to the ATM issues, health system levels, year of publication and the countries of origin or focus of the studies.Results151 articles met the inclusion criteria. Most articles (77%) originated from LMICs in EMR, suggesting that the majority of evidence on ATM in the region is home-grown. Over 60% of articles were from Iran, Pakistan, Jordan and Lebanon (in order of volume), while we found no studies assessing ATM in Somalia, Djibouti and South Sudan, all low-income countries. Most studies focused on the rational use of medicines, while affordability and financing received limited attention. There was a steady growth over time in the number of ATM publications in the region (r=0.87).ConclusionsThere is a growing trend, over the years, of more studies from the region appearing in international journals. There is a need for further research on the financing and affordability aspects of ATM in the region. Cross-border issues and the roles of non-health sectors in access to medicines in the region have not been explored widely.
A pragmatic randomised controlled trial of ‘PhysioDirect’ telephone assessment and advice services for patients with musculoskeletal problems: economic evaluation
Authors: Hollinghurst Sandra , Coast Joanna , Busby John , Bishop Annette , Foster Nadine E , Franchini Angelo , Grove Sean , Hall Jeanette , Hopper Cherida , Kaur Surinder , Montgomery Alan A , Salisbury Chris 
Published: October 2013

ObjectivesTo compare the cost-effectiveness of PhysioDirect with usual physiotherapy care for patients with musculoskeletal problems.Design(1) Cost-consequences comparing cost to the National Health Service (NHS), to patients, and the value of lost productivity with a range of outcomes. (2) Cost-utility analysis comparing cost to the NHS with Quality-Adjusted Life Years (QALYs).SettingFour physiotherapy services in England.ParticipantsAdults (18+) referred by their general practitioner or self-referred for physiotherapy.InterventionsPhysioDirect involved telephone assessment and advice followed by face-to-face care if needed. Usual care patients were placed on a waiting list for face-to-face care.Primary and secondary outcomesPrimary clinical outcome: physical component summary from the SF-36v2 at 6 months. Also included in the cost-consequences: Measure Yourself Medical Outcomes Profile; a Global Improvement Score; response to treatment; patient satisfaction; waiting time. Outcome for the cost-utility analysis: QALYs.Results2249 patients took part (1506 PhysioDirect; 743 usual care). (1) Cost-consequences: there was no evidence of a difference between the two groups in the cost of physiotherapy, other NHS services, personal costs or value of time off work. Outcomes were also similar. (2) Cost-utility analysis based on complete cases (n=1272). Total NHS costs, including the cost of physiotherapy were higher in the PhysioDirect group by £19.30 (95% CI −£37.60 to £76.19) and there was a QALY gain of 0.007 (95% CI −0.003 to 0.016). The incremental cost-effectiveness ratio was £2889 and the net monetary benefit at λ=£20 000 was £117 (95% CI −£86 to £310).ConclusionsPhysioDirect may be a cost-effective alternative to usual physiotherapy care, though only with careful management of staff time. Physiotherapists providing the service must be more fully occupied than was possible under trial conditions: consideration should be given to the scale of operation, opening times of the service and flexibility in the methods used to contact patients.
THE LARGE HADRON COLLIDER 2008–2013
Authors: MYERS STEPHEN 
Published: October 2013

The Large Hadron Collider (LHC) was first suggested (in a documented way) in 1983 (S. Myers and W. Schnell, Preliminary performance estimates for a LEP proton collider, LEP Note 440, April 1983) as a possible future hadron collider to be installed in the 27 km "LEP" tunnel. More than 30 years later the collider has been operated successfully with beam for three years with spectacular performance and has discovered the long-sought-after Higgs boson. The LHC is the world's largest and most energetic particle collider. It took many years to plan and build this large complex machine which promises exciting, new physics results for many years to come. I describe the LHC design objectives, review some of the more relevant beam effects, define the major accelerator components and parameters, and finally give an overview of the commissioning and operational performance since the initial turn on of the collider. The latter will include the major accident which took place in September 2008 and the subsequent repair and redesign of the faulty components. The first attempt to circulate beam in the LHC in September 2008 were initially very successful. However, after only nine days of preliminary beam commissioning, on 19 September 2008, disaster struck: the last octant was being ramped up in preparation for high energy operation when a magnet interconnect failed and the enormous energy stored in the superconducting magnets was released in an uncontrolled way and damaged around 600 m of the LHC installed equipment. The next 14 months were crucial for the machine. A crash programme for the repair of the damaged sector was initiated as well as in depth studies to understand the cause of the failure and make design changes which would ensure that such an accident could never reoccur in the future. In this paper, the story of the four years of the intensive activity since the accident is described starting with the repair of the damaged area and followed by the three very successful years of beam operation.
Prognostic and Predictive Blood-Based Biomarkers in Patients with Advanced Pancreatic Cancer: Results from CALGB80303 (Alliance)
Authors: Nixon Andrew B. , Pang Herbert , Starr Mark D. , Friedman Paula N. , Bertagnolli Monica M. , Kindler Hedy L. , Goldberg Richard M. , Venook Alan P. , Hurwitz Herbert I. ,   for the Alliance for Clinical Trials In Oncology
Published: October 2013

Abstract
Purpose: CALGB80303 was a phase III trial of 602 patients with locally advanced or metastatic pancreatic cancer comparing gemcitabine/bevacizumab versus gemcitabine/placebo. The study found no benefit in any outcome from the addition of bevacizumab to gemcitabine. Blood samples were collected and multiple angiogenic factors were evaluated and then correlated with clinical outcome in general (prognostic markers) and with benefit specifically from bevacizumab treatment (predictive markers).
Experimental Design: Plasma samples were analyzed via a novel multiplex ELISA platform for 31 factors related to tumor growth, angiogenesis, and inflammation. Baseline values for these factors were correlated with overall survival (OS) using univariate Cox proportional hazard regression models and multivariable Cox regression models with leave-one-out cross validation. Predictive markers were identified using a treatment by marker interaction term in the Cox model.
Results: Baseline plasma was available from 328 patients. Univariate prognostic markers for OS were identified including: Ang2, CRP, ICAM-1, IGFBP-1, TSP-2 (all P &lt; 0.001). These prognostic factors were found to be highly significant, even after adjustment for known clinical factors. Additional modeling approaches yielded prognostic signatures from multivariable Cox regression. The gemcitabine/bevacizumab signature consisted of IGFBP-1, interleukin-6, PDGF-AA, PDGF-BB, TSP-2; whereas the gemcitabine/placebo signature consisted of CRP, IGFBP-1, PAI-1, PDGF-AA, P-selectin (both P &lt; 0.0001). Finally, three potential predictive markers of bevacizumab efficacy were identified: VEGF-D (P &lt; 0.01), SDF1 (P &lt; 0.05), and Ang2 (P &lt; 0.05).
Conclusion: This study identified strong prognostic markers for pancreatic cancer patients. Predictive marker analysis indicated that plasma levels of VEGF-D, Ang2, and SDF1 significantly predicted for benefit or lack of benefit from bevacizumab in this population. Clin Cancer Res; 19(24); 6957–66. ©2013 AACR.
BH3 Profiling Discriminates Response to Cytarabine-Based Treatment of Acute Myelogenous Leukemia
Authors: Pierceall William E. , Kornblau Steven M. , Carlson Nicole E. , Huang Xuelin , Blake Noel , Lena Ryan , Elashoff Michael , Konopleva Marina , Cardone Michael H. , Andreeff Michael 
Published: October 2013

Abstract
As acute myelogenous leukemia (AML) patient response to cytarabine-based standard-of-care treatment is variable, stratification into subgroups by biomarker-predicted response may lead to improved clinical outcomes. Here, we assess cell mitochondrial depolarization to proapoptotic signaling BH3-only peptides as a surrogate for the function of Bcl-2 family proteins to address clinical response to cytarabine-based therapy in patients with AML (N = 62). Peripheral blood mononuclear cell (PBMC) or bone marrow aspirate specimens were obtained from newly diagnosed patients with AML, viably preserved, and assayed by flow cytometry following BH3 profile assay with individual BH3 peptides. Mann–Whitney analysis indicates biomarker correlation with response to induction therapy: Notably, BIM priming was highly significant (P = 2 × 10−6) with a compelling sensitivity/specificity profile [area under curve (AUC) = 0.83; 95% confidence interval (CI), 0.73–0.94; P = 2 × 10−10]. Multivariate analysis indicates improved profiles for BIM readout + patient age (AUC = 0.89; 95% CI, 0.81–0.97) and BIM + patient age + cytogenetic status (AUC = 0.91; 95% CI, 0.83–0.98). When patients were stratified by cytogenetic status, BIM readout was significant for both intermediate (P = 0.0017; AUC = 0.88; 95% CI, 0.71–1.04) and unfavorable (P = 0.023; AUC = 0.79; 95% CI, 0.58–1.00) risk groups, demonstrating predictive power independent of cytogenetics. Additional analyses of secondary clinical endpoints displayed correlation between overall survival (P = 0.037) and event-free survival (P = 0.044) when patients were stratified into tertiles by BIM peptide response. Taken together, these results highlight the potential utility of BH3 profiling in personalized diagnostics of AML by offering actionable information for patient management decisions. Mol Cancer Ther; 12(12); 2940–9. ©2013 AACR.
A Proangiogenic Signature Is Revealed in FGF-Mediated Bevacizumab-Resistant Head and Neck Squamous Cell Carcinoma
Authors: Gyanchandani Rekha , Ortega Alves Marcus V. , Myers Jeffrey N. , Kim Seungwon 
Published: October 2013

Abstract
Resistance to antiangiogenic therapies is a critical problem that has limited the utility of antiangiogenic agents in clinical settings. However, the molecular mechanisms underlying this resistance have yet to be fully elucidated. In this study, we established a novel xenograft model of acquired resistance to bevacizumab. To identify molecular changes initiated by the tumor cells, we performed human-specific microarray analysis on bevacizumab-sensitive and -resistant tumors. Efficiency analysis identified 150 genes upregulated and 31 genes downregulated in the resistant tumors. Among angiogenesis-related genes, we found upregulation of fibroblast growth factor-2 (FGF2) and fibroblast growth factor receptor-3 (FGFR3) in the resistant tumors. Inhibition of the FGFR in the resistant tumors led to the restoration of sensitivity to bevacizumab. Furthermore, increased FGF2 production in the resistant cells was found to be mediated by overexpression of upstream genes phospholipase C (PLCg2), frizzled receptor-4 (FZD4), chemokine [C-X3-C motif] (CX3CL1), and chemokine [C-C motif] ligand 5 (CCL5) via extracellular signal-regulated kinase (ERK). In summary, our work has identified an upregulation of a proangiogenic signature in bevacizumab-refractory HNSCC tumors that converges on ERK signaling to upregulate FGF2, which then mediates evasion of anti-VEGF therapy. These findings provide a new strategy on how to enhance the therapeutic efficacy of antiangiogenic therapy.
Implications: Novel xenograft model leads to the discovery of FGF as a promising therapeutic target in overcoming the resistance of antiangiogenic therapy in HNSCC. Mol Cancer Res; 11(12); 1585–96. ©2013 AACR.