bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequences of Thalassobacter Strains 1CONIMAR09 and 16PALIMAR09, Two Members of the Roseobacter Lineage Isolated from Coastal Areas of the Mediterranean Sea around Mallorca Island
Authors: Mas-Lladó Maria , Piña-Villalonga Joana Maria , Brunet-Galmés Isabel , Nogales Balbina , Bosch Rafael 
Published: March 2015

ABSTRACT
We report the draft genome sequence of two new members of the Roseobacter lineage, Thalassobacter strains 1CONIMAR09 and 16PALIMAR09, which were isolated from the seawater coast of Mallorca Island. Each genome harbored putative genes for obtaining energy by chemolithotrophy and making aerobic anoxygenic photosynthesis.
Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes
Authors: Kotak Malini , Isanapong Jantiya , Goodwin Lynne , Bruce David , Chen Amy , Han Cliff S. , Huntemann Marcel , Ivanova Natalia , Land Miriam L. , Nolan Matt , Pati Amrita , Woyke Tanja , Rodrigues Jorge L. M. 
Published: March 2015

ABSTRACT

The Opitutaceae bacterium strain TAV5, a member of the phylum
Verrucomicrobia
, was isolated from the wood-feeding termite hindgut. We report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.
Genome Sequences of Five Disinfectant-Resistant Listeria monocytogenes Strains from Two Iberian Pork-Processing Plants
Authors: López-Alonso Victoria , Ortiz Sagrario , Martínez-Suárez Joaquín V. 
Published: March 2015

ABSTRACT

We announce the draft genome sequences of five
Listeria monocytogenes
strains from two Iberian pork-processing plants located in Spain that were distinguished by their resistance to benzalkonium chloride. These strains seem highly adapted to the meat-processing environment according to their persistence and transmission capabilities.
Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8
Authors: Zschüttig Anke , Auerbach Christian , Meltke Simone , Eichhorn Christin , Brandt Manuela , Blom Jochen , Goesmann Alexander , Jarek Michael , Scharfe Maren , Zimmermann Kurt , Wassenaar Trudy M. , Gunzer Florian 
Published: March 2015

ABSTRACT

The complete genome of probiotic
Escherichia coli
strain G3/10 is presented here. In addition, the probiotic
E. coli
strains G1/2, G4/9, G5, G6/7, and G8 are presented in draft form. These six strains together comprise the probiotic product Symbioflor 2 (DSM 17252).
Infection with Bartonella henselae in a Danish Family
Authors: Maggi Ricardo G. , Balakrishnan Nandhakumar , Bradley Julie M. , Breitschwerdt Edward B. 
Published: March 2015

ABSTRACT

Bartonella
species constitute emerging, vector-borne, intravascular pathogens that produce long-lasting bacteremia in reservoir-adapted (natural host or passive carrier of a microorganism) and opportunistic hosts. With the advent of more sensitive and specific diagnostic tests, there is evolving microbiological evidence supporting concurrent infection with one or more
Bartonella
spp. in more than one family member; however, the mode(s) of transmission to or among family members remains unclear. In this study, we provide molecular microbiological evidence of
Bartonella henselae
genotype San Antonio 2 (SA2) infection in four of six Danish family members, including a child who died of unknown causes at 14 months of age.
Dynamic Interaction of Stress Granules, DDX3X, and IKK-α Mediates Multiple Functions in Hepatitis C Virus Infection
Authors: Pène Véronique , Li Qisheng , Sodroski Catherine , Hsu Ching-Sheng , Liang T. Jake 
Published: March 2015

ABSTRACT

The ubiquitous ATP-dependent RNA helicase DDX3X is involved in many cellular functions, including innate immunity, and is a pivotal host factor for hepatitis C virus (HCV) infection. Recently, we showed that DDX3X specifically recognizes the HCV 3′ untranslated region (UTR), leading to the activation of IKK-α and a cascade of lipogenic signaling to facilitate lipid droplet biogenesis and viral assembly (Q. Li, V. Pene, S. Krishnamurthy, H. Cha, and T. J. Liang, Nat Med
19:
722–729, 2013,
http://dx.doi.org/10.1038/nm.3190
). The interaction of DDX3X with HCV core protein seems to be dispensable for its proviral role. In this study, through systematic imaging and biochemical and virologic approaches, we identified a dynamic association between DDX3X and various cellular compartments and viral elements mediating multiple functions of DDX3X in productive HCV infection. Upon HCV infection, the HCV 3′UTR interacts with DDX3X and IKK-α, which redistribute to speckle-like cytoplasmic structures shown to be stress granules (SGs). As viral proteins accumulate in infected cells, DDX3X granules together with SG-associated proteins redistribute and colocalize with HCV core protein around lipid droplets (LDs). IKK-α, however, does not relocate to the LD but translocates to the nucleus. In HCV-infected cells, various HCV nonstructural proteins also interact or colocalize with DDX3X in close proximity to SGs and LDs, consistent with the tight juxtaposition of the replication complex and the assembly site at the surface of LDs. Short interfering RNA (siRNA)-mediated silencing of DDX3X and multiple SG components markedly inhibits HCV infection. Our data suggest that DDX3X initiates a multifaceted cellular program involving dynamic associations with HCV RNA and proteins, IKK-α, SG, and LD surfaces for its crucial role in the HCV life cycle.

IMPORTANCE
DDX3X is a proviral host factor for HCV infection. Recently, we showed that DDX3X binds to the HCV 3′UTR, activating IKK-α and cellular lipogenesis to facilitate viral assembly (Q. Li et al., Nat Med
19:
722–729, 2013,
http://dx.doi.org/10.1038/nm.3190
). Here, we report associations of DDX3X with various cellular compartments and viral elements that mediate its multiple functions in the HCV life cycle. Upon infection, the HCV 3′UTR redistributes DDX3X and IKK-α to speckle-like cytoplasmic structures shown to be SGs. Subsequently, interactions between DDX3X, SG, and HCV proteins facilitate the translocation of DDX3X-SG complexes to the LD surface. HCV nonstructural proteins are shown to colocalize with DDX3X in close proximity to SGs and LDs, consistent with the tight juxtaposition of the HCV replication complex and assembly site at the LD surface. Our data demonstrate that DDX3X initiates a multifaceted cellular program involving dynamic associations with HCV elements, IKK-α, SGs, and LDs for its critical role in HCV infection.
B Virus (Macacine herpesvirus 1) Glycoprotein D Is Functional but Dispensable for Virus Entry into Macaque and Human Skin Cells
Authors: Perelygina Ludmila , Patrusheva Irina , Vasireddi Mugdha , Brock Nicole , Hilliard Julia 
Published: March 2015

ABSTRACT

Glycoprotein D (gD) plays an essential role in cell entry of many simplexviruses. B virus (
Macacine herpesvirus 1
) is closely related to herpes simplex virus 1 (HSV-1) and encodes gD, which shares more than 70% amino acid similarity with HSV-1 gD. Previously, we have demonstrated that B virus gD polyclonal antibodies were unable to neutralize B virus infectivity on epithelial cell lines, suggesting gD is not required for B virus entry into these cells. In the present study, we confirmed this finding by producing a B virus mutant, BV-ΔgDZ, in which the gD gene was replaced with a
lacZ
expression cassette. Recombinant plaques were selected on complementing VD60 cells expressing HSV-1 gD. Virions lacking gD were produced in Vero cells infected with BV-ΔgDZ. In contrast to HSV-1, B virus lacking gD was able to infect and form plaques on noncomplementing cell lines, including Vero, HEp-2, LLC-MK2, primary human and macaque dermal fibroblasts, and U373 human glioblastoma cells. The gD-negative BV-ΔgDZ also failed to enter entry-resistant murine B78H1 cells bearing a single gD receptor, human nectin-1, but gained the ability to enter when phenotypically supplemented with HSV-1 gD. Cell attachment and penetration rates, as well as the replication characteristics of BV-ΔgDZ in Vero cells, were almost identical to those of wild-type (wt) B virus. These observations indicate that B virus can utilize gD-independent cell entry and transmission mechanisms, in addition to generally used gD-dependent mechanisms.

IMPORTANCE
B virus is the only known simplexvirus that causes zoonotic infection, resulting in approximately 80% mortality in untreated humans or in lifelong persistence with the constant threat of reactivation in survivors. Here, we report that B virus lacking the gD envelope glycoprotein infects both human and monkey cells as efficiently as wild-type B virus. These data provide evidence for a novel mechanism(s) utilized by B virus to gain access to target cells. This mechanism is different from those used by its close relatives, HSV-1 and -2, where gD is a pivotal protein in the virus entry process. The possibility remains that unidentified receptors, specific for B virus, permit virus entry into target cells through gD-independent pathways. Understanding the molecular mechanisms of B virus entry may help in developing rational therapeutic strategies for the prevention and treatment of B virus infection in both macaques and humans.
Bacterial infections in patients with type 1 diabetes: a 14-year follow-up study
Authors: Simonsen Johan R , Harjutsalo Valma , Järvinen Asko , Kirveskari Juha , Forsblom Carol , Groop Per-Henrik , Lehto Markku 
Published: March 2015

ObjectiveThis study explored the annual occurrence/incidence of bacterial infections, and their association with chronic hyperglycemia and diabetic nephropathy, in patients with type 1 diabetes.DesignIn a register-based follow-up study, we investigated the frequency of bacterial infections in patients with type 1 diabetes (n=4748) and age-matched and sex-matched non-diabetic control (NDC) subjects (n=12 954) using nationwide register data on antibiotic drug prescription purchases and hospital discharge diagnoses, collected between 1996 and 2009. Diabetic nephropathy was classified based on the urinary albumin excretion rate (AER).ResultsThe hospitalization rate due to bacterial infections was higher in patients with diabetes compared with NDCs (rate ratio (RR) 2.30 (95% CI 2.11 to 2.51)). The rate correlated with the severity of diabetic nephropathy: RR for microalbuminuria was 1.23 (0.94 to 1.60), 1.97 (1.49 to 2.61) for macroalbuminuria, 11.2 (8.1 to 15.5) for dialysis, and 6.72 (4.92 to 9.18) for kidney transplant as compared to patients with diabetes and normal AER. The annual number of antibiotic purchases was higher in patients with diabetes (1.00 (1.00 to 1.01)) as compared with NDCs (0.47 (0.46 to 0.47)), RR=1.71 (1.65 to 1.77). Annual antibiotic purchases were 1.18-fold more frequent in patients with microalbuminuria, 1.29-fold with macroalbuminuria, 2.43-fold with dialysis, and 2.74-fold with kidney transplant as compared to patients with normal AER. Each unit of increase in glycated hemoglobin was associated with a 6–10% increase in the number of annual antibiotic purchases.ConclusionsThe incidence of bacterial infections was significantly higher in patients with type 1 diabetes compared with age-matched and sex-matched NDC subjects, and correlated with the severity of diabetic nephropathy in inpatient and outpatient settings.
Associations between source of information about sex and sexual health outcomes in Britain: findings from the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3)
Authors: Macdowall Wendy , Jones Kyle G , Tanton Clare , Clifton Soazig , Copas Andrew J , Mercer Catherine H , Palmer Melissa J , Lewis Ruth , Datta Jessica , Mitchell Kirstin R , Field Nigel , Sonnenberg Pam , Johnson Anne M , Wellings Kaye 
Published: March 2015

ObjectivesTo examine variation in source of information about sexual matters by sociodemographic factors, and associations with sexual behaviours and outcomes.DesignCross-sectional probability sample survey.SettingBritish general population.Participants3408 men and women, aged 17–24 years, interviewed from 2010–2012 for third National Survey of Sexual Attitudes and Lifestyles.Main outcome measuresMain source of information (school, a parent, other); age and circumstances of first heterosexual intercourse; unsafe sex and distress about sex in past year; experience of sexually transmitted infection (STI) diagnoses, non-volitional sex or abortion (women only) ever.ResultsCiting school was associated with younger age, higher educational level and having lived with both parents. Citing a parent was associated, in women, with lower educational level and having lived with one parent. Relative to other sources, citing school was associated with older age at first sex (adjusted HR 0.73 (95% CI 0.65 to 0.83) men, 0.73 (0.65 to 0.82) women), lower likelihood of unsafe sex (adjusted OR 0.58 (0.44 to 0.77) men, 0.69 (0.52 to 0.91) women) and previous STI diagnosis (0.55 (0.33 to 0.91) men, 0.58 (0.43 to 0.80) women) and, in women, with lower likelihood of lack of sexual competence at first sex; and experience of non-volitional sex, abortion and distress about sex. Citing a parent was associated with lower likelihood of unsafe sex (0.53 (0.28 to 1.00) men; 0.69 (0.48 to 0.99) women) and, in women, previous STI diagnosis.ConclusionsGaining information mainly from school was associated with lower reporting of a range of negative sexual health outcomes, particularly among women. Gaining information mainly from a parent was associated with some of these, but fewer cited parents as a primary source. The findings emphasise the benefit of school and parents providing information about sexual matters and argue for a stronger focus on the needs of men.
Introduction of a new electronic medical weekend handover at Tunbridge Wells Hospital
Authors: Vithlani Rohan 
Published: March 2015

AbstractEffective handover between shifts is vital to protect patient safety and assist doctors with clinical governance. Poor quality, or inadequate handover can lead to serious harm for both patients and doctors. The weekend medical handover system among junior doctors at Tunbridge Wells Hospital in Pembury, UK was cumbersome, inadequate and poor, restricting the ability to provide good patient care. 78.6% of doctors felt that the introduction of an electronic weekend handover system would address the issues in order to improve communication between the medical teams and thus improve patient care. A five week trial of an excel based electronic weekend handover system was conducted. 87.5% of the doctors surveyed felt that the new electronic weekend handover was better or significantly better than the old paper based handover system.The effectiveness rating of the weekend medical handover, with 1 (least effective) - 10 (most effective), rose from 6.14 to 7.31 after introduction of the electronic weekend medical handover system. As a result, this project has become part of the junior doctors medical induction, ensuring permanence of electronic weekend medical handover. This project takes a step towards improved patient safety as well improving the working conditions for junior doctors in a busy acute medical unit. There is always a need to refine and optimise systems and though this project is not perfect, it is a step toward electronic handover that is available now and free of cost.
Testing implications of varying targets forBordetella pertussis: comparison of the FilmArray Respiratory Panel and the FocusB. pertussisPCR assay
Authors: Jerris Robert C , Williams Sally R , MacDonald Heather J , Ingebrigtsen Danielle R , Westblade Lars F , Rogers Beverly B 
Published: March 2015

BackgroundThe FilmArray Respiratory Panel (RP) detects multiple pathogens, includingBordetella pertussis.The multiplex PCR system is appropriate for a core laboratory or point of care due to ease of use. The purpose of this study is to compare the analytical sensitivity of the FilmArray RP, which targets the promoter region of theB. pertussistoxin gene, with the Focus real-time PCR assay, which targets the insertion sequence IS481.MethodsSeventy-one specimens from patients aged 1 month to 18 years, which had tested positive forB. pertussisusing the Focus assay, were analysed using the FilmArray RP.ResultsForty-six specimens were positive forB. pertussisby both the Focus and the FilmArray RP assays. Twenty-five specimens were negative forB. pertussisusing the FilmArray RP assay, but positive using the Focus assay.ConclusionsThe FilmArray RP assays will detect approximately 1/3 less cases ofB. pertussisthan the Focus assay.
CEACAM1-3S Drives Melanoma Cells into NK Cell-Mediated Cytolysis and Enhances Patient Survival
Authors: Ullrich Nico , Heinemann Anja , Nilewski Elena , Scheffrahn Inka , Klode Joachim , Scherag André , Schadendorf Dirk , Singer Bernhard B. , Helfrich Iris 
Published: March 2015

Abstract
CEACAM1 is a widely expressed multifunctional cell–cell adhesion protein reported to serve as a poor prognosis marker in melanoma patients. In this study, we examine the functional and clinical contributions of the four splice isoforms of CEACAM1. Specifically, we present in vitro and in vivo evidence that they affect melanoma progression and immune surveillance in a negative or positive manner that is isoform specific in action. In contrast with isoforms CEACAM1-4S and CEACAM1-4L, expression of isoforms CEACAM1-3S and CEACAM1-3L is induced during disease progression shown to correlate with clinical stage. Unexpectedly, overall survival was prolonged in patients with advanced melanomas expressing CEACAM1-3S. The favorable effects of CEACAM1-3S related to enhanced immunogenicity, which was mediated by cell surface upregulation of NKG2D receptor ligands, thereby sensitizing melanoma cells to lysis by natural killer cells. Conversely, CEACAM1-4L downregulated cell surface levels of the NKG2D ligands MICA and ULBP2 by enhanced shedding, thereby promoting malignant character. Overall, our results define the splice isoform-specific immunomodulatory and cell biologic functions of CEACAM1 in melanoma pathogenesis. Cancer Res; 75(9); 1897–907. ©2015 AACR.
Phase I Trial of Arginine Deprivation Therapy with ADI-PEG 20 Plus Docetaxel in Patients with Advanced Malignant Solid Tumors
Authors: Tomlinson Benjamin K. , Thomson James A. , Bomalaski John S. , Diaz Monica , Akande Taiwo , Mahaffey Nichole , Li Tianhong , Dutia Mrinal P. , Kelly Karen , Gong I-Yeh , Semrad Thomas , Gandara David R. , Pan Chong-Xian , Lara Primo N. 
Published: March 2015

Abstract
Purpose: This phase I study examined the toxicity and tolerability of pegylated arginine deiminase (ADI-PEG 20) in combination with docetaxel in patients with advanced solid malignancies.
Experimental Design: Eligible patients had histologically proven advanced solid malignancies, with any number of prior therapies, Zubrod performance status 0–2, and adequate organ function. Patients received ADI-PEG 20 weekly intramuscular injection ranging from 4.5 to 36 mg/m2 and up to 10 doses of docetaxel (75 mg/m2) every 3 weeks. Primary endpoints were safety, toxicity, and a recommended phase II dose. Circulating arginine levels were measured before each cycle. Tumor response was measured as a secondary endpoint every 6 weeks on study.
Results: Eighteen patients received a total of 116 cycles of therapy through four dose levels of ADI-PEG 20. A single dose-limiting toxicity (grade 3 urticarial rash) was observed at the 1st dose level, with no additional dose-limiting toxicities observed. Hematologic toxicities were common with 14 patients experiencing at least one grade 3 to 4 leukopenia. Fatigue was the most prevalent toxicity reported by 16 patients. Arginine was variably suppressed with 10 patients achieving at least a 50% reduction in baseline values. In 14 patients with evaluable disease, four partial responses (including 2 patients with PSA response) were documented, and 7 patients had stable disease.
Conclusions: ADI-PEG 20 demonstrated reasonable toxicity in combination with docetaxel. Promising clinical activity was noted, and expansion cohorts are now accruing for both castrate-resistant prostate cancer and non–small cell lung cancer at a recommended phase II dose of 36 mg/m2. Clin Cancer Res; 21(11); 2480–6. ©2015 AACR.
From Histones to Ribosomes: A Chromatin Regulator Tangoes with Translation
Authors: Rothbart Scott B. , Dickson Bradley M. , Strahl Brian D. 
Published: March 2015

Abstract
Summary: Histone lysine methylation is a critical regulator of chromatin-templated processes such as gene transcription and DNA repair, and is dynamically controlled by enzymes that write and erase this posttranslational modification. Although histone methylation has been well studied, the functions of nonhistone lysine methylation and its regulatory enzymes, particularly outside the nucleus, are poorly defined. In this issue of Cancer Discovery, Van Rechem and colleagues shed light on a new role for the lysine demethylase KDM4A as a regulator of protein translation and identify a single-nucleotide polymorphism in the KDM4A gene as a candidate biomarker for mTOR inhibitor therapy. Cancer Discov; 5(3); 228–30. ©2015 AACR.
See related article by Van Rechem and colleagues, p. 245
See related article by Van Rechem and colleagues, p. 255
Aberrant Cytokine Production by Nonmalignant Cells in the Pathogenesis of Myeloproliferative Tumors and Response to JAK Inhibitor Therapies
Authors: Belver Laura , Ferrando Adolfo A. 
Published: March 2015

Abstract
Summary: Kleppe and colleagues use detailed cytokine profiling analyses to investigate the role of aberrant proinflammatory cytokine secretion in the pathogenesis of myeloproliferative neoplasms. Their analyses implicate constitutive activation of STAT3 in both malignant and nonmalignant bone marrow cell populations as a driver of aberrant cytokine secretion and as a cellular target mediating the therapeutic activity of ruxolitinib. Cancer Discov; 5(3); 234–6. ©2015 AACR.
See related article by Kleppe and colleagues, p. 316
Plasma fibrin clot phenotype independently affects intracoronary thrombus ultrastructure in patients with acute myocardial infarction
Authors: Bogaert Jan , Sadowski Marcin , Woznicka Olga , Doulaptsis Konstantinos , Ntoumpanaki Maria , Zabczyk Michal , Nessler Jadwiga , Undas Anetta , Zalewski Jaroslaw 
Published: March 2015

summaryDeterminants of intracoronary thrombus (ICT) composition in patients with ST-elevation myocardial infarction (STEMI) are largely unknown. We sought to investigate whether plasma fibrin phenotype and platelet reactivity affect ICT ultrastructure. We assessed the content of fibrin, platelets and erythrocytes including polyhedrocytes by scanning electron microscopy on the surface and inside ICT aspirated from 80 STEMI patients within 12 hours since chest pain onset. Plasma fibrin clot permeability (Ks), which indicates the average pore size, lysis time (t50 %), platelet reactivity index (PRI) and ADP-induced platelet aggregation (ADP5,20μM) were evaluated on admission. All patients received aspirin and 45 (56.3 %) 600 mg of clopidogrel, 80 (60–120) min prior to aspiration. Higher content of fibrin (61.6 vs 34.3 %, P< 0.0001) and platelets (8.2 vs 4.8 %, P=0.018) and lower erythrocyte content (15.8 vs 42.9 %, P< 0.0001) were found on ICT surface compared with its inner part. After adjustment for fibrinogen, in both ICT parts fibrin content was correlated with Ks (r≤-0.55, P< 0.0001) and t50% (r≥ 0.29, P≤ 0.02) but not with PRI and ADP5,20μM. Polyhedrocytes were observed in 16 (20 %) patients and their large amount expressed as ≥ 50 % fields of view covered by polyhedrocytes was associated with the lower PRI values (40 vs 69 %, P=0.015), but not Ks or t50%. By multivariate regression, Ks (β=-0.62, P< 0.0001), clopidogrel pretreatment (β=-0.36, P< 0.001), ischemia time (β=0.19, P=0.044) and family history (β=0.18, P=0.049) independently predicted fibrin content in the whole ICT (R2=0.65, P< 0.0001). Formation of denser plasma fibrin clots is independently associated with high fibrin content within the ICT in STEMI.