bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics of Meningococcal Serogroup C-Specific Functional Antibody Levels Up to 15 Years after a Single Immunization with a Meningococcal Serogroup C Conjugate Vaccine during Adolescence
Authors: Stoof Susanne P. , van Ravenhorst Mariëtte B. , van Rooijen Debbie M. , de Voer Richarda M. , van der Klis Fiona R. M. , Boland Greet J. , Sanders Elisabeth A. M. , Berbers Guy A. M. , Teunis Peter F. 
Published: November 2016

ABSTRACT

Adolescent vaccination is now considered the key factor for offering direct protection against meningococcal disease but also for reducing carriage and transmission and, in this way, establishing herd protection. This study estimated age-dependent patterns in functional meningococcal serogroup C (MenC) antibody kinetics after primary MenC conjugate (MenCC) vaccination in adolescents. Serum samples (
n
= 1,676) were drawn from 2006 to 2011 from individuals aged 9 to 18 years at the time of primary MenCC vaccination in 2002. Functional antibody levels were measured with a serum bactericidal antibody assay (SBA) using rabbit complement. SBA titers gradually declined with time. Up to 9 years after primary vaccination, SBA titers were estimated to be higher in individuals who were aged 13 to 18 years at priming than in those who were aged 9 to 10 years at priming. Based on a linear mixed model, the higher functional antibody levels with age seem to be due to the achievement of higher peak levels upon vaccination rather than to lower rates of decline. It is estimated that 35 to 50% of individuals who received a single primary MenCC vaccination at an age of 9 to 18 years in 2002 will still have sufficient protective antibody levels 15 years later. Using a linear mixed model based on cohort data for a single dated serum sample per person, we were able to estimate the level of protection against MenC up to 15 years after a single vaccination. The current study shows that analysis of antibody kinetics can be done using cross-sectional serology data and is therefore relevant for future serosurveillance studies.
Draft Genome Sequence of the Fungus
Penicillium solitum
NJ1
Authors: Yin Guohua , Zhang Yuliang , Pennerman Kayla K. , Hua Sui Sheng T. , Yu Jiujiang , Guo Anping , Liu Zhixin , Bennett Joan W. 
Published: November 2016

ABSTRACT

Penicillium solitum
is one of the most prevalent species causing postharvest decay of pomaceous fruits during storage. Here, we report the draft genome of
P. solitum
strain NJ1, received as a transfer of a strain originally identified as
P. griseofulvum
by classical means.
Near-Complete Genome Sequence of
Thalassospira
sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm
Authors: Woo Hannah L. , O'Dell Kaela B. , Utturkar Sagar , McBride Kathryn R. , Huntemann Marcel , Clum Alicia , Pillay Manoj , Palaniappan Krishnaveni , Varghese Neha , Mikhailova Natalia , Stamatis Dimitrios , Reddy T. B. K. , Ngan Chew Yee , Daum Chris , Shapiro Nicole , Markowitz Victor , Ivanova Natalia , Kyrpides Nikos , Woyke Tanja , Brown Steven D. , Hazen Terry C. 
Published: November 2016

ABSTRACT

Thalassospira
sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium's ability to degrade recalcitrant organics such as lignin.
Genome Sequence of Salegentibacter salarius KCTC 12974, Isolated from a Marine Solar Saltern of the Yellow Sea in South Korea
Authors: Xu Yongle , Liu Jihua , Zheng Qiang , Liu Yanting , Jiao Nianzhi 
Published: November 2016

ABSTRACT

Salegentibacter salarius
KCTC 12974 is isolated from a marine solar saltern of the Yellow Sea in South Korea. Here, we report the draft genome sequence of
Salegentibacter salarius
KCTC 12974. Various glycoside hydrolase genes in even numbers in the genome reflect the ecological adaption of KCTC 12974 to its habitat.
Draft Genome Sequence of Lysinibacillus xylanilyticus SR-86
Authors: Loscar Michael E. , Huptas Christopher , Wenning Mareike , Sieber Volker , Schmid Jochen 
Published: November 2016

ABSTRACT

Lysinibacillus xylanilyticus
belongs to the family
Bacillaceae
and was first described in 2010 with the type strain
L. xylanilyticus
XDB9. It is able to both degrade xylan and use it as the sole carbon source. Here, we describe the 4.8-Mb genome of the strain
L. xylanilyticus
SR-86, which was isolated from organic waste.
Complete Genome Sequence of the Probiotic Strain Lactobacillus salivarius LPM01
Authors: Chenoll Empar , Codoñer Francisco M. , Martinez-Blanch Juan F. , Acevedo-Piérart Marcelo , Ormeño M. Loreto , Ramón Daniel , Genovés Salvador 
Published: November 2016

ABSTRACT

Lactobacillus salivarius
LPM01 (DSM 22150) is a probiotic strain able to improve health status in immunocompromised people. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insights into its functional activity and safety assessment.
Draft Genome Sequences of Two “
Haemophilus quentini
” Isolates Recovered from Two Different Patients' Blood Cultures
Authors: Eshaghi Alireza , Soares Deidre , Tsang Raymond , Richardson David , Kus Julianne V. , Patel Samir N. 
Published: November 2016

ABSTRACT

Here, we present the draft genome sequences of two strains (K068 and C860) of the genospecies “
Haemophilus quentini
.” The isolates were recovered from blood cultures of a newborn neonate and an elderly patient with septicemia in Ontario, Canada.
Draft Genome Sequence of Salmonella enterica subsp.
diarizonae
Serovar 61:k:1,5,(7) Strain CRJJGF_00165 (Phylum
Gammaproteobacteria
)
Authors: Gupta Sushim K. , McMillan Elizabeth A. , Jackson Charlene R. , Desai Prerak T. , Porwollik Steffen , McClelland Michael , Hiott Lari M. , Humayoun Shaheen B. , Barrett John B. , Frye Jonathan G. 
Published: November 2016

ABSTRACT

Here, we report a 4.78-Mb draft genome sequence of the
Salmonella enterica
subsp.
diarizonae
serovar 61:k:1,5,(7) strain CRJJGF_00165 [also called
S. enterica
subsp. IIIb serovar 61:k:1,5,(7) strain CRJJGF_00165], isolated from ground beef in 2007.
Infectious Bursal Disease Virus Activates c-Src To Promote α4β1 Integrin-Dependent Viral Entry by Modulating the Downstream Akt-RhoA GTPase-Actin Rearrangement Cascade
Authors: Ye Chengjin , Han Xinpeng , Yu Zhaoli , Zhang Enli , Wang Lijuan , Liu Hebin 
Published: November 2016

ABSTRACT

While the entry of infectious bursal disease virus (IBDV) is initiated by the binding of the virus to the two major receptors integrin and HSP90, the signaling events after receptor binding and how they contribute to virus entry remain elusive. We show here that IBDV activates c-Src by inducing the phosphorylation of the Y416 residue in c-Src both in DF-1 chicken fibroblasts and
in vivo
in the bursa of Fabricius from specific-pathogen-free (SPF) chickens. Importantly, inactivated IBDV fails to stimulate c-Src Y416 phosphorylation, and a very virulent IBDV strain induces a much higher level of c-Src Y416 phosphorylation than does an attenuated strain. Inhibition of c-Src activation by an Src kinase inhibitor or expression of a c-Src dominant negative mutant results in a significant decrease in the internalization of IBDV but has little effect on virus adhesion. Furthermore, short hairpin RNA (shRNA) downregulation of integrin, either the α4 or β1 subunit, but not HSP90 remarkably attenuates IBDV-induced c-Src Y416 phosphorylation, resulting in a decrease in IBDV internalization but not virus adhesion. Moreover, interestingly, inhibition of either c-Src downstream of the phosphatidylinositol 3-kinase (PI3K)/Akt-RhoA signaling cascade or actin rearrangement leads to a significant decrease in IBDV internalization irrespective of the IBDV-induced high levels of c-Src phosphorylation. Cumulatively, our results suggest a novel feed-forward model whereby IBDV activates c-Src for benefiting its cell entry via an integrin-mediated pathway by the activation of downstream PI3K/Akt-RhoA signaling and cytoskeleton actin rearrangement.

IMPORTANCE
While IBDV-caused immunosuppression is highly related to viral invasion, the molecular basis of the cellular entry of IBDV remains elusive. In this study, we demonstrate that IBDV activates c-Src by inducing the phosphorylation of the Y416 residue in c-Src to promote virus internalization but not virus adhesion. The ability to induce the level of c-Src Y416 phosphorylation correlates with the pathogenicity of an IBDV strain. IBDV-induced c-Src Y416 activation is α4β1 integrin but not HSP90 dependent and involves the activation of the downstream PI3K/Akt-RhoA GTPase-actin rearrangement cascade. Thus, our findings provide new insights into the IBDV infection process and the potential for c-Src as a candidate target for the development of IBDV therapeutic drugs.
The Norovirus NS3 Protein Is a Dynamic Lipid- and Microtubule-Associated Protein Involved in Viral RNA Replication
Authors: Cotton Ben T. , Hyde Jennifer L. , Sarvestani Soroush T. , Sosnovtsev Stanislav V. , Green Kim Y. , White Peter A. , Mackenzie Jason M. 
Published: November 2016

ABSTRACT

Norovirus (NoV) infections are a significant health burden to society, yet the lack of reliable tissue culture systems has hampered the development of appropriate antiviral therapies. Here we show that the NoV NS3 protein, derived from murine NoV (MNV), is intimately associated with the MNV replication complex and the viral replication intermediate double-stranded RNA (dsRNA). We observed that when expressed individually, MNV NS3 and NS3 encoded by human Norwalk virus (NV) induced the formation of distinct vesicle-like structures that did not colocalize with any particular protein markers to cellular organelles but localized to cellular membranes, in particular those with a high cholesterol content. Both proteins also showed some degree of colocalization with the cytoskeleton marker β-tubulin. Although the distribution of MNV and NV NS3s were similar, NV NS3 displayed a higher level of colocalization with the Golgi apparatus and the endoplasmic reticulum (ER). However, we observed that although both proteins colocalized in membranes counterstained with filipin, an indicator of cholesterol content, MNV NS3 displayed a greater association with flotillin and stomatin, proteins known to associate with sphingolipid- and cholesterol-rich microdomains. Utilizing time-lapse epifluorescence microscopy, we observed that the membrane-derived vesicular structures induced by MNV NS3 were highly motile and dynamic in nature, and their movement was dependent on intact microtubules. These results begin to interrogate the functions of NoV proteins during virus replication and highlight the conserved properties of the NoV NS3 proteins among the seven
Norovirus
genogroups.

IMPORTANCE
Many mechanisms involved in the replication of norovirus still remain unclear, including the role for the NS3 protein, one of seven nonstructural viral proteins, which remains to be elucidated. This study reveals that murine norovirus (MNV) NS3 is intimately associated with the viral replication complex and dsRNA. We observed that the NS3 proteins of both MNV and Norwalk virus (NV) induce prominent vesicular structures and that this formation is dependent on microtubules and cellular cholesterol. Thus, this study contributes to our understanding of protein function within different
Norovirus
genogroups and expands a growing knowledge base on the interaction between positive-strand RNA [(+)RNA] viruses and cellular membranes that contribute to the biogenesis of virus-induced membrane organelles. This study contributes to our understanding of viral protein function and the ability of a viral protein to recruit specific cellular organelles and lipids that enable replication.
Inhibition of Human Cytomegalovirus pUL89 Terminase Subunit Blocks Virus Replication and Genome Cleavage
Authors: Wang Yan , Mao Lili , Kankanala Jayakanth , Wang Zhengqiang , Geraghty Robert J. 
Published: November 2016

ABSTRACT
The human cytomegalovirus terminase complex cleaves concatemeric genomic DNA into unit lengths during genome packaging and particle assembly. This process is an attractive drug target because cleavage of concatemeric DNA is not required in mammalian cell DNA replication, indicating that drugs targeting the terminase complex could be safe and selective. One component of the human cytomegalovirus terminase complex, pUL89, provides the endonucleolytic activity for genome cleavage, and the domain responsible is reported to have an RNase H-like fold. We hypothesize that the pUL89 endonuclease activity is inhibited by known RNase H inhibitors. Using a novel enzyme-linked immunosorbent assay (ELISA) format as a screening assay, we found that a hydroxypyridonecarboxylic acid compound, previously reported to be an inhibitor of human immunodeficiency virus RNase H, inhibited pUL89 endonuclease activity at low-micromolar concentrations. Further characterization revealed that this pUL89 endonuclease inhibitor blocked human cytomegalovirus replication at a relatively late time point, similarly to other reported terminase complex inhibitors. Importantly, this inhibitor also prevented the cleavage of viral genomic DNA in infected cells. Taken together, these results substantiate our pharmacophore hypothesis and validate our ligand-based approach toward identifying novel inhibitors of pUL89 endonuclease.

IMPORTANCE
Human cytomegalovirus infection in individuals lacking a fully functioning immune system, such as newborns and transplant patients, can have severe and debilitating consequences. The U.S. Food and Drug Administration-approved anti-human cytomegalovirus drugs mainly target the viral polymerase, and resistance to these drugs has appeared. Therefore, anti-human cytomegalovirus drugs from novel targets are needed for use instead of, or in combination with, current polymerase inhibitors. pUL89 is a viral ATPase and endonuclease and is an attractive target for anti-human cytomegalovirus drug development. We identified and characterized an inhibitor of pUL89 endonuclease activity that also inhibits human cytomegalovirus replication in cell culture. pUL89 endonuclease, therefore, should be explored as a potential target for antiviral development against human cytomegalovirus.
Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its
Wolbachia
Endosymbiont
Authors: Bennuru Sasisekhar , Cotton James A. , Ribeiro Jose M. C. , Grote Alexandra , Harsha Bhavana , Holroyd Nancy , Mhashilkar Amruta , Molina Douglas M. , Randall Arlo Z. , Shandling Adam D. , Unnasch Thomas R. , Ghedin Elodie , Berriman Matthew , Lustigman Sara , Nutman Thomas B. 
Published: November 2016

ABSTRACT

Onchocerciasis (river blindness) is a neglected tropical disease that has been successfully targeted by mass drug treatment programs in the Americas and small parts of Africa. Achieving the long-term goal of elimination of onchocerciasis, however, requires additional tools, including drugs, vaccines, and biomarkers of infection. Here, we describe the transcriptome and proteome profiles of the major vector and the human host stages (L1, L2, L3, molting L3, L4, adult male, and adult female) of
Onchocerca volvulus
along with the proteome of each parasitic stage and of its
Wolbachia
endosymbiont (
w
Ov). In so doing, we have identified stage-specific pathways important to the parasite’s adaptation to its human host during its early development. Further, we generated a protein array that, when screened with well-characterized human samples, identified novel diagnostic biomarkers of
O. volvulus
infection and new potential vaccine candidates. This immunomic approach not only demonstrates the power of this postgenomic discovery platform but also provides additional tools for onchocerciasis control programs.

IMPORTANCE
The global onchocerciasis (river blindness) elimination program will have to rely on the development of new tools (drugs, vaccines, biomarkers) to achieve its goals by 2025. As an adjunct to the completed genomic sequencing of
O. volvulus
, we used a comprehensive proteomic and transcriptomic profiling strategy to gain a comprehensive understanding of both the vector-derived and human host-derived parasite stages. In so doing, we have identified proteins and pathways that enable novel drug targeting studies and the discovery of novel vaccine candidates, as well as useful biomarkers of active infection.
Study protocol for a randomised controlled trial of brief, habit-based, lifestyle advice for cancer survivors: exploring behavioural outcomes for the Advancing Survivorship Cancer Outcomes Trial (ASCOT)
Authors: Beeken Rebecca J , Croker Helen , Heinrich Maggie , Smith Lee , Williams Kate , Hackshaw Allan , Hines John , Machesney Michael , Krishnaswamy Madhavan , Cavanagh Sharon , Roylance Rebecca , Hill Alison , Pritchard-Jones Kathy , Wardle Jane , Fisher Abigail 
Published: November 2016

IntroductionPositive health behaviours such as regular physical activity and a healthy diet have significant effects on cancer outcomes. There is a need for simple but effective behaviour change interventions with the potential to be implemented within the cancer care pathway. Habit-based advice encourages repetition of a behaviour in a consistent context so that the behaviour becomes increasingly automatic in response to a specific contextual cue. This approach therefore encourages long-term behaviour change and can be delivered through printed materials. ‘Healthy Habits for Life’ is a brief intervention based on habit theory, and incorporating printed materials plus a personally tailored discussion, that has been designed specifically for patients with a diagnosis of cancer. The aim of this trial was to test the effect of ‘Healthy Habits for Life’ on a composite health behaviour risk index (CHBRI) over 3 months in patients with a diagnosis of breast, colorectal or prostate cancer.Method and analysisA 2-arm, individually randomised controlled trial in patients with breast, colorectal and prostate cancer. Patients will be recruited over 18 months from 7 National Health Service Trusts in London and Essex. Following baseline assessments and allocation to intervention or usual care, patients are followed up at 3 and 6 months. The primary outcome will be change in CHBRI at 3 months. Maintenance of any changes over 6 months, and changes in individual health behaviours (including dietary intake, physical activity, alcohol consumption and smoking status) will also be explored.Ethics and disseminationEthical approval was obtained through the National Research Ethics Service Committee South Central—Oxford B via the Integrated Research Application System (reference number 14/SC/1369). Results of this study will be disseminated through peer-reviewed publications and scientific presentations.Trial registration number17421871.
Is famine exposure during developmental life in rural Bangladesh associated with a metabolic and epigenetic signature in young adulthood? A historical cohort study
Authors: Finer S , Iqbal M S , Lowe R , Ogunkolade B W , Pervin S , Mathews C , Smart M , Alam D S , Hitman G A 
Published: November 2016

ObjectivesFamine exposure in utero can ‘programme’ an individual towards type 2 diabetes and obesity in later life. We sought to identify, (1) whether Bangladeshis exposed to famine during developmental life are programmed towards diabetes and obesity, (2) whether this programming was specific to gestational or postnatal exposure windows and (3) whether epigenetic differences were associated with famine exposure.DesignA historical cohort study was performed as part of a wider cross-sectional survey. Exposure to famine was defined through birth date and historical records and participants were selected according to: (A) exposure to famine in postnatal life, (B) exposure to famine during gestation and (C) unexposed.SettingMatlab, a rural area in the Chittagong division of Bangladesh.ParticipantsYoung adult men and women (n=190) recruited to a historical cohort study with a randomised subsample included in an epigenetic study (n=143).Outcome measuresPrimary outcome measures of weight, body mass index and oral glucose tolerance tests (0 and 120 min glucose). Secondary outcome measures included DNA methylation using genome-wide and targeted analysis of metastable epialleles sensitive to maternal nutrition.ResultsMore young adults exposed to famine in gestation were underweight than those postnatally exposed or unexposed. In contrast, more young adults exposed to famine postnatally were overweight compared to those gestationally exposed or unexposed. Underweight adults exposed to famine in gestation in utero were hyperglycaemic following a glucose tolerance test, and those exposed postnatally had elevated fasting glucose, compared to those unexposed. Significant differences in DNA methylation at seven metastable epialleles (VTRNA2-1, PAX8, PRDM-9, near ZFP57, near BOLA, EXD3) known to vary with gestational famine exposure were identified.ConclusionsFamine exposure in developmental life programmed Bangladeshi offspring towards diabetes and obesity in adulthood but gestational and postnatal windows of exposure had variable effects on phenotype. DNA methylation differences were replicated at previously identified metastable epialleles sensitive to periconceptual famine exposure.
Prevalence of papillomavirus in Brazil: a systematic review protocol
Authors: Colpani Verônica , Bidinotto Augusto Bacelo , Falavigna Maicon , Giozza Silvana Pereira , Benzaken Adele Schwartz , Pimenta Cristina , Maranhão Ana Goretti Kalume , Domingues Carla Magda Allan Santos , Hammes Luciano Serpa , Wendland Eliana M 
Published: November 2016

IntroductionHuman papillomavirus (HPV) infection is a cause of premalignant and malignant cancer in the lower genital and digestive tracts. In Brazil, there have been no prevalence studies that included a nationwide sample, and the prevalence of HPV has not been determined in many regions.MethodsWe will search the EMBASE, LILACS, MEDLINE, Web of Science and SciELO databases and previously published review articles to identify original research articles assessing HPV prevalence of the perineal (cervical, penile and anal) and oral areas. No exclusion criteria related to language or publication date will apply. 2 reviewers will independently screen for eligibility and perform data extraction. Discrepancies will be resolved through consensus; the opinion of a third reviewer will be sought as necessary. Relevant measures and data about study and population characteristics will be extracted from the included studies. Where possible, study prevalence will be pooled using a random-effects meta-analysis. The methodological quality of the studies will be assessed using an adapted version of the NIH ‘Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies’. The overall quality of evidence will be assessed using Grading of Recommendations Assessment, Development and Evaluation (GRADE).Ethics and disseminationWe expect to estimate the prevalence of perineal and oral HPV infection in the general population as well as the prevalence of HPV infection in individuals with premalignant and malignant lesions in Brazil and its 5 geographic regions. This systematic review does not require ethical approval.Trial registration numberCRD42016032751.