bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Resolution Transcriptomic Analysis of the Adaptive Response of Staphylococcus aureus during Acute and Chronic Phases of Osteomyelitis
Authors: Szafranska Anna K. , Oxley Andrew P. A. , Chaves-Moreno Diego , Horst Sarah A. , Roßlenbroich Steffen , Peters Georg , Goldmann Oliver , Rohde Manfred , Sinha Bhanu , Pieper Dietmar H. , Löffler Bettina , Jauregui Ruy , Wos-Oxley Melissa L. , Medina Eva 
Published: December 2014

ABSTRACT

Osteomyelitis is a difficult-to-eradicate bone infection typically caused by
Staphylococcus aureus
. In this study, we investigated the
in vivo
transcriptional adaptation of
S. aureus
during bone infection. To this end, we determined the transcriptome of
S. aureus
during the acute (day 7) and chronic (day 28) phases of experimental murine osteomyelitis using RNA sequencing (RNA-Seq). We identified a total of 180 genes significantly more highly expressed by
S. aureus
during acute or chronic
in vivo
infection than under
in vitro
growth conditions. These genes encoded proteins involved in gluconeogenesis, proteolysis of host proteins, iron acquisition, evasion of host immune defenses, and stress responses. At the regulatory level,
sarA
and -
R
and
saeR
and -
S
as well as the small RNA RsaC were predominantly expressed by
S. aureus
during
in vivo
infection. Only nine genes, including the genes encoding the arginine deiminase (ADI) pathway and those involved in the stringent response, were significantly more highly expressed by
S. aureus
during the chronic than the acute stage of infection. Analysis by quantitative reverse transcription-PCR (qRT-PCR) of a subset of these
in vivo-
expressed genes in clinical specimens yielded the same results as those observed in the murine system. Collectively, our results show that during acute osteomyelitis,
S. aureus
induced the transcription of genes that mediate metabolic adaptation, immune evasion, and replication. During the chronic phase, however,
S. aureus
switched its transcriptional response from a proliferative to a persistence mode, probably driven by the severe deficiency in nutrient supplies. Interfering with the survival strategies of
S. aureus
during chronic infection could lead to more effective treatments.

IMPORTANCE
The key to the survival success of pathogens during an infection is their capacity to rapidly adjust to the host environment and to evade the host defenses. Understanding how a pathogen redirects and fine-tunes its gene expression in response to the challenges of infection is central to the development of more efficient anti-infective therapies. Osteomyelitis is a debilitating infection of the bone predominantly caused by
S. aureus
. In this study, we evaluated the transcriptional response of
S. aureus
during bone infection. Our results indicate that
S. aureus
reprograms its genetic repertoire during the acute phase of infection to adapt to nutrient availability and to replicate within the host. During the chronic phase,
S. aureus
upregulates a survival genetic program activated in response to nutrient starvation. Thus, we have uncovered key survival pathways of
S. aureus
during acute and chronic osteomyelitis that can be used as therapeutic targets.
Phylodynamic Analysis of Clinical and Environmental Vibrio cholerae Isolates from Haiti Reveals Diversification Driven by Positive Selection
Authors: Azarian Taj , Ali Afsar , Johnson Judith A. , Mohr David , Prosperi Mattia , Veras Nazle M. , Jubair Mohammed , Strickland Samantha L. , Rashid Mohammad H. , Alam Meer T. , Weppelmann Thomas A. , Katz Lee S. , Tarr Cheryl L. , Colwell Rita R. , Morris J. Glenn , Salemi Marco 
Published: December 2014

ABSTRACTPhylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates ofVibrio choleraefrom Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenicV. choleraeO1 isolates, four non-O1/O139 isolates, and a novel nontoxigenicV. choleraeO1 isolate with the classicaltcpAgene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenicV. choleraeO1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy.IMPORTANCECholera, a dehydrating diarrheal disease caused by toxigenic strains of the bacteriumVibrio cholerae, emerged in 2010 in Haiti, a country where there were no available records on cholera over the past 100 years. While devastating in terms of morbidity and mortality, the outbreak provided a unique opportunity to study the evolutionary dynamics ofV. choleraeand its environmental presence. The present study expands on previous work and provides an in-depth phylodynamic analysis inferred from genome-wide single nucleotide polymorphisms of clinical and environmental strains from dispersed geographic settings in Haiti over a 2-year period. Our results indicate that even during such a short time scale,V. choleraein Haiti has undergone evolution and diversification driven by positive selection, which may have implications for understanding the global clinical and epidemiological patterns of the disease. Furthermore, the continued presence of the epidemic strain in Haitian aquatic environments has implications for transmission.
Regulation of the Arginine Deiminase System by ArgR2 Interferes with Arginine Metabolism and Fitness of Streptococcus pneumoniae
Authors: Schulz Christian , Gierok Philipp , Petruschka Lothar , Lalk Michael , Mäder Ulrike , Hammerschmidt Sven 
Published: December 2014

ABSTRACT

Streptococcus pneumoniae
is auxotrophic for arginine, and molecular analysis of the pneumococcal genome showed that the gene encoding an arginine-ornithine antiporter (ArcD) is organized in a cluster together with the
arcABC
genes encoding the arginine deiminase system (ADS) of pneumococci. The ADS consists of the arginine deiminase (AD), the catabolic ornithine carbamoyltransferase (cOCT), and the carbamate kinase (CK). Pneumococcal genomes contain three ArgR-type regulators (ArgR1, ArgR2, and AhrC) that are supposed to be involved in the regulation of arginine metabolism. Here, we identified ArgR2 of TIGR4 as the regulator of the ADS and ArcD. ArgR2 binds to promoter sequences of the
arc
operon, and the deficiency of ArgR2 in TIGR4 abrogates expression of the ADS, including the arginine-ornithine antiporter ArcD. Intranasal infection of mice and real-time bioimaging revealed that deletion of the
arcABCDT
genes attenuates TIGR4. However, the acute-pneumonia model and coinfection experiments indicated that the arginine-ornithine antiporter ArcD is essential to maintain fitness, while the deficiency of ADS enzymes has a minor impact on pneumococcal fitness under
in vivo
conditions. Strikingly,
argR2
mutant TIGR4 outcompeted the wild type in the respiratory tract, suggesting an increase in fitness and further regulatory functions of ArgR2. In contrast to TIGR4, other pneumococci, such as D39, lacking expression of ArgR2, constitutively express the ADS with a truncated nonfunctional AD. On the basis of these results, we propose that the arginine-ornithine antiporter is essential to maintain pneumococcal fitness and that the genes of the ADS cluster are positively regulated in a strain-specific manner by ArgR2.

IMPORTANCE
Pneumococci are the major etiologic agents of community-acquired pneumonia, causing more than 1.5 million deaths annually worldwide. These versatile pathogens are highly adapted to the nutrients provided by the host niches encountered. Physiological fitness is of major importance for colonization of the nasopharyngeal cavity and dissemination during invasive infections. This work identifies the regulator ArgR2 as the activator of the
S. pneumoniae
TIGR4 ADS and the arginine-ornithine transporter ArcD, which is needed for uptake of the essential amino acid arginine. Although ArgR2 activates ArcD expression and uptake of arginine is required to maintain pneumococcal fitness, the deficiency of ArgR2 increases TIGR4 virulence under
in vivo
conditions, suggesting that other factors regulated by ArgR2 counterbalance the reduced uptake of arginine by ArcD. Thus, this work illustrates that the physiological homeostasis of pneumococci is complex and that ArgR2 plays a key role in maintaining bacterial fitness.
Human Papillomavirus E6 Triggers Upregulation of the Antiviral and Cancer Genomic DNA Deaminase APOBEC3B
Authors: Vieira Valdimara C. , Leonard Brandon , White Elizabeth A. , Starrett Gabriel J. , Temiz Nuri A. , Lorenz Laurel D. , Lee Denis , Soares Marcelo A. , Lambert Paul F. , Howley Peter M. , Harris Reuben S. 
Published: December 2014

ABSTRACT

Several recent studies have converged upon the innate immune DNA cytosine deaminase APOBEC3B (A3B) as a significant source of genomic uracil lesions and mutagenesis in multiple human cancers, including those of the breast, head/neck, cervix, bladder, lung, ovary, and other tissues.
A3B
is upregulated in these tumor types relative to normal tissues, but the mechanism is unclear. Because A3B also has antiviral activity in multiple systems and is a member of the broader innate immune response, we tested the hypothesis that human papillomavirus (HPV) infection causes A3B upregulation. We found that
A3B
mRNA expression and enzymatic activity were upregulated following transfection of a high-risk HPV genome and that this effect was abrogated by inactivation of E6. Transduction experiments showed that the E6 oncoprotein alone was sufficient to cause
A3B
upregulation, and a panel of high-risk E6 proteins triggered higher
A3B
levels than did a panel of low-risk or noncancer E6 proteins. Knockdown experiments in HPV-positive cell lines showed that endogenous
E6
is required for
A3B
upregulation. Analyses of publicly available head/neck cancer data further support this relationship, as
A3B
levels are higher in HPV-positive cancers than in HPV-negative cancers. Taken together with the established role for high-risk E6 in functional inactivation of TP53 and published positive correlations in breast cancer between
A3B
upregulation and genetic inactivation of
TP53
, our studies suggest a model in which high-risk HPV E6, possibly through functional inactivation of TP53, causes derepression of
A3B
gene transcription. This would lead to a mutator phenotype that explains the observed cytosine mutation biases in HPV-positive head/neck and cervical cancers.

IMPORTANCE
The innate immune DNA cytosine deaminase APOBEC3B (A3B) accounts for a large proportion of somatic mutations in cervical and head/neck cancers, but nothing is known about the mechanism responsible for its upregulation in these tumor types. Almost all cervical carcinomas and large proportions of head/neck tumors are caused by human papillomavirus (HPV) infection. Here, we establish a mechanistic link between HPV infection and
A3B
upregulation. The E6 oncoprotein of high-risk, but not low-risk, HPV types triggers
A3B
upregulation, supporting a model in which TP53 inactivation causes a derepression of
A3B
gene transcription and elevated A3B enzyme levels. This virus-induced mutator phenotype provides a mechanistic explanation for A3B signature mutations observed in HPV-positive head/neck and cervical carcinomas and may also help to account for the preferential cancer predisposition caused by high-risk HPV isolates.
A usability study of two formats of a shortened systematic review for clinicians
Authors: Perrier Laure , Kealey M Ryan , Straus Sharon E 
Published: December 2014

ObjectiveThe aim of this study was to evaluate the usability of two formats of a shortened systematic review for clinicians.Materials and methodsUsability of the prototypes was assessed using three cycles of iterative testing. 10 participants were asked to complete tasks of locating information or items within two prototypes and ‘think aloud’ while being audio taped. Interviews were also audio recorded and participants completed a systematic usability scale.ResultsRevisions were made between each iteration in order to address issues identified by participants. Finding information relating to the number of studies in the meta-analysis, and locating the number of studies in the entire systematic review were revealed as areas needing attention during the usability evaluation.ConclusionsIterative testing combined with a multifaceted approach to usability testing offered essential insight into aspects of the prototypes that required modifications. Alterations were made in order to create finalised versions of the two shortened systematic review formats.
The association between neighbourhood greenspace and type 2 diabetes in a large cross-sectional study
Authors: Bodicoat Danielle H , O'Donovan Gary , Dalton Alice M , Gray Laura J , Yates Thomas , Edwardson Charlotte , Hill Sian , Webb David R , Khunti Kamlesh , Davies Melanie J , Jones Andrew P 
Published: December 2014

ObjectiveTo investigate the relationship between neighbourhood greenspace and type 2 diabetes.DesignCross-sectional.Setting3 diabetes screening studies conducted in Leicestershire, UK in 2004–2011. The percentage of greenspace in the participant's home neighbourhood (3 km radius around home postcode) was obtained from a Land Cover Map. Demographic and biomedical variables were measured at screening.Participants10 476 individuals (6200 from general population; 4276 from high-risk population) aged 20–75 years (mean 59 years); 47% female; 21% non-white ethnicity.Main outcome measureScreen-detected type 2 diabetes (WHO 2011 criteria).ResultsIncreased neighbourhood greenspace was associated with significantly lower levels of screen-detected type 2 diabetes. The ORs (95% CI) for screen-detected type 2 diabetes were 0.97 (0.80 to 1.17), 0.78 (0.62 to 0.98) and 0.67 (0.49 to 0.93) for increasing quartiles of neighbourhood greenspace compared with the lowest quartile after adjusting for ethnicity, age, sex, area social deprivation score and urban/rural status (Ptrend=0.01). This association remained on further adjustment for body mass index, physical activity, fasting glucose, 2 h glucose and cholesterol (OR (95% CI) for highest vs lowest quartile: 0.53 (0.35 to 0.82); Ptrend=0.01).ConclusionsNeighbourhood greenspace was inversely associated with screen-detected type 2 diabetes, highlighting a potential area for targeted screening as well as a possible public health area for diabetes prevention. However, none of the risk factors that we considered appeared to explain this association, and thus further research is required to elicit underlying mechanisms.Trial registration numberThis study uses data from three studies (NCT00318032,NCT00677937,NCT00941954).
A cross-sectional exploration of the clinical characteristics of disengaged (NEET) young people in primary mental healthcare
Authors: O'Dea Bridianne , Glozier Nicholas , Purcell Rosemary , McGorry Patrick D , Scott Jan , Feilds Kristy-Lee , Hermens Daniel F , Buchanan John , Scott Elizabeth M , Yung Alison R , Killacky Eoin , Guastella Adam J , Hickie Ian B 
Published: December 2014

ObjectiveYouth with mental health problems often have difficulties engaging in education and employment. In Australia, youth mental health services have been widely established with a key aim of improving role functioning; however, there is little knowledge of those who are not engaged in employment, education or training (NEET) and the factors which may influence this. This study aimed to examine NEET status and its correlates in a sample of such youth.DesignCross-sectional data from a longitudinal cohort study.SettingBetween January 2011 and August 2012, young people presenting to one of the four primary mental health centres in Sydney or Melbourne were invited to participate.ParticipantsYoung adults (N=696) aged between 15 and 25 years (M=19.0, SD=2.8), 68% female, 58% (n=404) attendedheadspacein Sydney.MeasuresIndividuals ‘Not in any type of Education, Employment or Training’ in the past month were categorised as NEET. Demographic, psychological and clinical factors alongside disability and functioning were assessed using clinical interview and self-report.ResultsA total of 19% (n=130/696) were NEET. NEETs were more likely to be male, older, have a history of criminal charges, risky cannabis use, higher level of depression, poorer social functioning, greater disability and economic hardship, and a more advanced stage of mental illness than those engaged in education, training or work. Demographics such as postsecondary education, immigrant background and indigenous background, were not significantly associated with NEET status in this sample.ConclusionsOne in five young people seeking help for mental health problems were not in any form of education, employment and training. The commonly observed risk factors did not appear to influence this association, instead, behavioural factors such as criminal offending and cannabis use appeared to require targeted intervention.
Exploring cardiovascular health: the Healthy Life in Suriname (HELISUR) study. A protocol of a cross-sectional study
Authors: Diemer Frederieke S , Aartman Jet Q , Karamat Fares A , Baldew Sergio M , Jarbandhan Ameerani V , van Montfrans Gert A , Oehlers Glenn P , Brewster Lizzy M 
Published: December 2014

IntroductionObesity, hypertension and diabetes are on a dramatic rise in low-income and middle-income countries, and this foretells an overwhelming increase in chronic disease burden from cardiovascular disease. Therefore, rapid action should be taken through preventive population-based programmes. However, in these regions, data on the population distribution of cardiovascular risk factors, and of intermediate and final end points for cardiovascular disease are scarce. The Healthy Life in Suriname (HELISUR) study is a cardiovascular population study in Suriname, which is part of the Caribbean Community. The HELISUR study is dedicated to provide data on risk factors and prevalent cardiovascular disease in the multiethnic population, which is mainly of African and Asian descent.Methods and analysisIn a cross-sectional, observational population-based setting, a random representative sample of 1800 citizens aged between 18 and 70 years will be selected using a cluster household sampling method. Self-reported demographic, socioeconomic and (cardiovascular) health-related data will be collected. Physical examination will include the assessment of cardiovascular risk factors and prevalent cardiovascular disease. In addition, we will study cardiovascular haemodynamics non-invasively, as a novel intermediate outcome. Finally, fasting blood and overnight urine samples will be collected to monitor cardiometabolic risk factors. The main outcome will be descriptive in reporting the prevalence of risk factors and measures of (sub) clinical end organ damage, stratified for ethnicity and sex-age groups.Ethics and disseminationEthical approval has been obtained from the State Secretary of Health. Data analysis and manuscript submission are scheduled for 2016. Findings will be disseminated in peer-reviewed journals, and at national, regional and international scientific meetings. Importantly, data will be presented to Surinamese policymakers and healthcare workers, to develop preventive strategies to combat the rapid rise of cardiovascular disease.
A Pilot Trial Using Lymphocytes Genetically Engineered with an NY-ESO-1–Reactive T-cell Receptor: Long-term Follow-up and Correlates with Response
Authors: Robbins Paul F. , Kassim Sadik H. , Tran Thai L.N. , Crystal Jessica S. , Morgan Richard A. , Feldman Steven A. , Yang James C. , Dudley Mark E. , Wunderlich John R. , Sherry Richard M. , Kammula Udai S. , Hughes Marybeth S. , Restifo Nicholas P. , Raffeld Mark , Lee Chyi-Chia R. , Li Yong F. , El-Gamil Mona , Rosenberg Steven A. 
Published: December 2014

Abstract
Purpose: Although adoptive cell therapy can be highly effective for the treatment of patients with melanoma, the application of this approach to the treatment of other solid tumors has been limited. The observation that the cancer germline (CG) antigen NY-ESO-1 is expressed in 70% to 80% and in approximately 25% of patients with synovial cell sarcoma and melanoma, respectively, prompted us to perform this first-in-man clinical trial using the adoptive transfer of autologous peripheral blood mononuclear cells that were retrovirally transduced with an NY-ESO-1–reactive T-cell receptor (TCR) to heavily pretreated patients bearing these metastatic cancers.
Experimental Design: HLA-*0201 patients with metastatic synovial cell sarcoma or melanoma refractory to standard treatments and whose cancers expressed NY-ESO-1 received autologous TCR-transduced T cells following a lymphodepleting preparative chemotherapy. Response rates using Response Evaluation Criteria in Solid Tumors (RECIST), as well as immunologic correlates of response, are presented in this report.
Results: Eleven of 18 patients with NY-ESO-1+ synovial cell sarcomas (61%) and 11 of 20 patients with NY-ESO-1+ melanomas (55%) who received autologous T cells transduced with an NY-ESO-1–reactive TCR demonstrated objective clinical responses. The estimated overall 3- and 5-year survival rates for patients with synovial cell sarcoma were 38% and 14%, respectively, whereas the corresponding estimated survival rates for patients with melanoma were both 33%.
Conclusions: The adoptive transfer of autologous T cells transduced with a retrovirus encoding a TCR against an HLA-A*0201 restricted NY-ESO-1 epitope can be an effective therapy for some patients bearing synovial cell sarcomas and melanomas that are refractory to other treatments. Clin Cancer Res; 21(5); 1019–27. ©2014 AACR.
Protease-Activated Pore-Forming Peptides for the Treatment and Imaging of Prostate Cancer
Authors: LeBeau Aaron M. , Denmeade Samuel R. 
Published: December 2014

Abstract
A common hallmark of cancers with highly aggressive phenotypes is increased proteolysis in the tumor and the surrounding microenvironment. Prostate cancer has a number of proteases uniquely associated with it that may play various important roles in disease progression. In this report, we utilize the peritumoral proteolytic activity of prostate cancer to activate engineered peptide constructs for the treatment and noninvasive imaging of prostate cancer. Using a modular “propeptide” approach, a cationic diastereomeric pore-forming peptide domain was linked to an inactivating acidic peptide domain. The inactivating acidic peptide domain was engineered to be a cleavable substrate for the secreted serine protease prostate-specific antigen (PSA) or the transmembrane metalloprotease prostate-specific membrane antigen (PSMA). The propeptides were then evaluated in a direct comparison study. Both the PSA and PSMA activated propeptides were found to be cytotoxic to prostate cancer cells in vitro. In vivo, however, treatment of LNCaP and CWR22Rv1 xenografts with the PSMA propeptide resulted in a pronounced cytostatic effect when compared with xenografts treated with the PSA propeptide or the cationic diastereomeric peptide alone. The PSMA activated propeptide also proved to be an effective optical imaging probe in vivo when labeled with a near-infrared fluorophore. These data suggest that protease-activated pore-forming peptides could potentially be used for both imaging and treating prostate cancer. Mol Cancer Ther; 14(3); 659–68. ©2014 AACR.