bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Role for SIRT2-Dependent Histone H3K18 Deacetylation in Bacterial Infection
Authors: Eskandarian Haig A. , Impens Francis , Nahori Marie-Anne , Soubigou Guillaume , Coppée Jean-Yves , Cossart Pascale , Hamon Mélanie A. 
Published: August 2013

Bacterial Subversion TacticsIntracellular bacterial pathogens such asListeria monocytogenescan change host cell transcription programs to promote infection.Eskandarianet al.(1238858) found that during infection, theListeriaeffector protein InlB promoted the movement of a host protein deacetylase, SIRT2, from its normal location in the cytosol to the nucleus. In the nucleus, SIRT2 helped to repress a number of host cell genes by deacetylating one of their associated histones. In mice, reduced levels of SIRT2 impaired bacterial infection.
Molecular Epidemiology of Clostridium difficile Infection in a Major Chinese Hospital: an Underrecognized Problem in Asia?
Authors: Hawkey Peter M. , Marriott Clare , Liu Wen En , Jian Zi Juan , Gao Qian , Ling Thomas Kin Wah , Chow Viola , So Erica , Chan Raphael , Hardy Katie , Xu Li , Manzoor Susan 
Published: August 2013

ABSTRACT

Clostridium difficile
infection is almost unrecognized in mainland China. We have undertaken a study in a large Chinese teaching hospital in Changsha, Hunan, China, to identify cases of
C. difficile
, record patient characteristics, and define the molecular epidemiology with respect to ribotype distribution and cross-infection. Between April 2009 and February 2010, we examined fecal samples from 70 hospitalized patients with diarrhea who were receiving or had received antibiotics within the previous 6 weeks. Clinical information was collected and the samples were cultured for
C. difficile
retrospectively. Isolates were ribotyped, and multiple-locus variable-number tandem-repeat assay (MLVA) subtyping was performed on clusters of the same ribotype. The mean age of patients from whom
C. difficile
was cultured was 58 years, with only 4/21 patients aged >65 years. All patients, with a single exception, had received a third-generation cephalosporin and/or a quinolone antibiotic. Twenty-one isolates of
C. difficile
were recovered, and seven different ribotypes were identified, the dominant types being 017 (48%), 046 (14%), and 012 (14%). We identified two clusters of cross-infection with indistinguishable isolates of ribotype 017, with evidence of spread both within and between wards. We have identified
C. difficile
as a possibly significant problem, with cross-infection and a distinct ribotype distribution, in a large Chinese hospital.
C. difficile
may be underrecognized in China, and further epidemiological studies across the country together with the introduction of routine diagnostic testing are needed to ascertain the size of this potentially significant problem.
Subtyping Clinical Specimens of Influenza A Virus by Use of a Simple Method To Amplify RNA Targets
Authors: Wang Jingjing , Tai Warren , Angione Stephanie L. , John Amrita R. , Opal Steven M. , Artenstein Andrew W. , Tripathi Anubhav 
Published: August 2013

ABSTRACT

This work presents the clinical application of a robust and unique approach for RNA amplification, called a simple method for amplifying RNA targets (SMART), for the detection and identification of subtypes of H1N1 pandemic, H1N1 seasonal, and H3N2 seasonal influenza virus. While all the existing amplification techniques rely on the diffusion of two molecules to complex RNA structures, the SMART achieves fast and efficient amplification via single-molecule diffusion. The SMART utilizes amplifiable single-stranded DNA (ssDNA) probes, which serve as reporter molecules for capturing specific viral RNA (vRNA) sequences and are subsequently separated on a microfluidic chip under zero-flow conditions. The probe amplification and detection are performed using an isothermal (41°C) amplification scheme via a modified version of nucleic acid sequence-based amplification (NASBA). In our study, 116 consecutive, deidentified, clinical nasopharyngeal swab samples were analyzed independently in a blinded fashion using the SMART, reverse transcription-PCR (RT-PCR), antigen (Ag) testing, and viral culture. The SMART was shown to have a limit of detection (LOD) of approximately 10
5
vRNA copies/ml, corresponding with a time-to-positivity (TTP) value of 70 min for real-time detection. The SMART correctly detected influenza virus in 98.3% of the samples with a subtyping accuracy of 95.7%. This work demonstrates that the SMART represents a highly accurate diagnostic platform for the detection and subtyping of influenza virus in clinical specimens and offers significant advantages over the current commercially available diagnostic tools.
PCR and Electrospray Ionization Mass Spectrometry for Detection of Persistent Enterococcus faecalis in Cerebrospinal Fluid following Treatment of Postoperative Ventriculitis
Authors: Farrell John J. , Tsung Andrew J. , Flier Lisa , Martinez Derek L. , Beam Sarah B. , Chen Clifford , Lowery Kristin S. , Sampath Rangarajan , Bonomo Robert A. 
Published: August 2013

ABSTRACT

We describe the use of PCR and electrospray ionization followed by mass spectrometry (PCR/ESI-MS) to evaluate “culture-negative” cerebrospinal fluid (CSF) from a 67-year-old man who developed postoperative bacterial ventriculitis following a suboccipital craniotomy for resection of an ependymoma in the 4th ventricle. CSF samples were obtained on seven occasions, beginning in the operating room at the time of insertion of a right ventriculoperitoneal shunt (VPS) and continuing until his death, 6 weeks later. During the course of the illness, two initial CSF specimens taken before the initiation of antimicrobial treatment were notable for growth of
Enterococcus faecalis
. Once antimicrobial treatment was initiated, all CSF cultures were negative. PCR/ESI-MS detected genetic evidence of
E. faecalis
in all CSF samples, but the level of detection (LOD) decreased once antimicrobial treatment was initiated. When our patient returned with symptoms of meningitis 3 days after the completion of antibiotic treatment, CSF cultures remained negative, but PCR/ESI-MS again found genetic evidence for
E. faecalis
at levels comparable to the pretreatment levels seen initially. This unique case and these findings suggest that determination of CSF LOD by PCR/ESI-MS may be a very sensitive indicator of persistent infection in patients on antibiotic therapy for complex CNS infections and may have relevance for treatment duration and assessment of persistent or recurrent infection at the completion of therapy.
Cell-Based Screening Assay for Antiviral Compounds Targeting the Ability of Herpesvirus Posttranscriptional Regulatory Proteins To Stabilize Viral mRNAs
Authors: Verma Dinesh , Kim Eun A , Swaminathan Sankar 
Published: August 2013

ABSTRACT

Each human herpesvirus expresses a multifunctional regulatory protein that is essential for lytic viral replication. A cell-based assay targeting the function of these proteins was developed based on the finding that Epstein-Barr virus (EBV) SM and Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 stabilize specific target mRNAs. Both proteins facilitate the accumulation of lytic transcripts by incompletely characterized posttranscriptional mechanisms. SM and ORF57 exhibit target gene specificity and enhance the accumulation of certain EBV and KSHV mRNAs that are poorly expressed in their absence. Conversely, SM- and ORF57-independent viral and cellular transcripts accumulate efficiently, and their expression does not respond to SM or ORF57. Fusion of an ORF57-responsive transcript to ORF57-independent transcripts demonstrated that ORF57 dependence is
cis
-dominant. EBV SM also enhanced the accumulation of such fused mRNA transcripts. These data suggest that the coding regions of specific viral transcripts confer instability even when fused to heterologous genes. The findings were used to develop a reporter assay that measures EBV SM function in rescuing the expression of poorly expressed transcripts by posttranscriptional mechanisms. The assay represents a method for the screening of small interfering RNAs (siRNAs) and compounds to investigate the mechanism of action of SM and its homologs and potentially to aid in the discovery of novel antiviral agents.
Preferential HIV Infection of CCR6
+
Th17 Cells Is Associated with Higher Levels of Virus Receptor Expression and Lack of CCR5 Ligands
Authors: Alvarez Yelina , Tuen Michael , Shen Guomiao , Nawaz Fatima , Arthos James , Wolff Martin J. , Poles Michael A. , Hioe Catarina E. 
Published: August 2013

ABSTRACT

Th17 cells are enriched in the gut mucosa and play a critical role in maintenance of the mucosal barrier and host defense against extracellular bacteria and fungal infections. During chronic human immunodeficiency virus (HIV) infection, Th17 cells were more depleted compared to Th1 cells, even when the patients had low or undetectable viremia. To investigate the differential effects of HIV infection on Th17 and Th1 cells, a culture system was used in which CCR6
+
CD4
+
T cells were sorted from healthy human peripheral blood and activated in the presence of interleukin 1β (IL-1β) and IL-23 to drive expansion of Th17 cells while maintaining Th1 cells. HIV infection of these cultures had minimal effects on Th1 cells but caused depletion of Th17 cells. Th17 loss correlated with greater levels of virus-infected cells and cell death. In identifying cellular factors contributing to higher susceptibility of Th17 cells to HIV, we compared Th17-enriched CCR6
+
and Th17-depleted CCR6
−
CD4 T cell cultures and noted that Th17-enriched CCR6
+
cells expressed higher levels of α4β7 and bound HIV envelope in an α4β7-dependent manner. The cells also had greater expression of CD4 and CXCR4, but not CCR5, than CCR6
−
cells. Moreover, unlike Th1 cells, Th17 cells produced little CCR5 ligand, and transfection with one of the CCR5 ligands, MIP-1β (CCL4), increased their resistance against HIV. These results indicate that features unique to Th17 cells, including higher expression of HIV receptors and lack of autocrine CCR5 ligands, are associated with enhanced permissiveness of these cells to HIV.
Follow-up of the air pollution and the human male-to-female ratio analysis in São Paulo, Brazil: a times series study
Authors: Miraglia Simone Georges El Khouri , Veras Mariana Matera , Amato-Lourenço Luis Fernando , Rodrigues-Silva Fernando , Saldiva Paulo Hilário Nascimento 
Published: July 2013

ObjectivesIn order to assess if ambient air pollution in urban areas could be related to alterations in male/female ratio this study objectives to evaluate changes in ambient particulate matter (PM10) concentrations after implementation of pollution control programmes in São Paulo city and the secondary sex ratio (SRR).Design and methodsA time series study was conducted. São Paulo’s districts were stratified according to the PM10concentrations levels and were used as a marker of overall air pollution. The male ratio was chosen to represent the secondary sex ratio (SSR=total male birth/total births). The SSR data from each area was analysed according to the time variation and PM10concentration areas using descriptive statistics. The strength association between annual average of PM10concentration and SSR was performed through exponential regression, and it was adopted as a statistical significance level of p<0.05.ResultsThe exponential regression showed a negative and significant association between PM10and SSR. SSR varied from 51.4% to 50.7% in São Paulo in the analysed period (2000–2007). Considering the PM10average concentration in São Paulo city of 44.72 μg/m3in the study period, the SSR decline reached almost 4.37%, equivalent to 30 934 less male births.ConclusionsAmbient levels of PM10are negatively associated with changes in the SSR. Therefore, we can speculate that higher levels of particulate pollution could be related to increased rates of female births.
Use of health services following self-harm in urban versus suburban and rural areas: a national cross-sectional study
Authors: Fadum Elin Anita , Stanley Barbara , Rossow Ingeborg , Mork Erlend , Törmoen Anita J , Mehlum Lars 
Published: July 2013

ObjectivesThis study examines whether there is a difference between urban versus suburban and rural adolescents in their use of health services following two types of self-harm distinguished as self-harm with or without suicide intent.SettingA nationwide cross-sectional school survey of 11 406 Norwegian adolescents aged 13–19 years in 73 Norwegian junior and senior high schools.ParticipantsAdolescents who reported self-harm and provided valid responses to a follow-up question about having received subsequent help or treatment (n=959) were included in the study. Adolescents were divided into urban versus suburban and rural depending on: (1) the location of municipalities where they attended school and (2) the place of residence. Associations between urban versus suburban and rural areas and the use of health services following self-harm were assessed in those who self-harmed with and without suicide intent.Primary outcome measureUse of health services following self-harm.Results1 in 4 adolescents reported using health services following self-harm. Adolescents reporting self-harm with suicide intent were more likely to use health services than those who self-harmed without suicide intent. Following self-harm without suicide intent, adolescents in urban areas were four times more likely to use health services than adolescents in suburban and rural areas. There was no statistically significant area difference in the use of health services following self-harm with suicide intent.ConclusionsThis study found a geographical variation in the use of health services following self-harm without suicide intent, but not following self-harm with suicide intent. Differences in perception of self-harm and help-seeking behaviour between areas and different accessibility to services are suggested as possible explanations. There is a need to better understand how the interplay between individual characteristics and accessibility to services influences adolescents’ use of health services following self-harm. We suggest that multilevel models are a valuable approach to achieve this goal.
Issues for palliative medicine doctors surrounding the withdrawal of non-invasive ventilation at the request of a patient with motor neurone disease: a scoping study
Authors: Faull Christina , Rowe Haynes Cassy , Oliver David 
Published: July 2013

BackgroundNon-invasive ventilation (NIV) is beneficial for respiratory failure in motor neurone disease (MND) but some patients may wish to stop the intervention. Guidance from the National Institute for Health and Care Excellence recommends that research is needed on NIV withdrawal. There is little in the literature focusing on the issues doctors face when withdrawing NIV in this group.AimTo identify issues and challenges that palliative medicine doctors encounter in relation to the withdrawal of NIV in MND patients.MethodAn electronic questionnaire was sent to members of the Association of Palliative Medicine of Great Britain and Ireland. Participants rated how practically, emotionally and ethically challenging they found the process of NIV withdrawal.Results76 doctors responding had been directly involved in withdrawal of NIV at the request of a patient with MND. A high percentage rated the practical, ethical and emotional challenges as 7 or more on a 0–10 scale. Thematic analysis of the free text revealed some common difficulties. Lack of guidance on practical aspects of withdrawal, poor advance care planning and the need to support all involved to prevent conflict were recurrent themes. Statements relating to the emotional burden were diverse but suggest many palliative care doctors feel significant personal impact.ConclusionsThe withdrawal of NIV in patients with MND appears to pose considerable challenges to palliative medicine doctors; emotionally, practically and to a lesser extent ethically. Development of guidelines and a clear ethical statement of conduct may help but emotional issues appear more complex.
The application of outcrop-based research boreholes for reservoir modelling: potential, challenges and pitfalls
Authors: Luthi S. M. , Flint S. S. 
Published: July 2013

Abstract
Research boreholes drilled in outcrop studies of reservoir analogues can have two distinctly different objectives. One is to assess how the sequences observed on outcrops are represented in cores and wireline logs, an exercise that can form an important link between data retrieved from actual reservoirs and observations made on outcrops. The second objective is to obtain information on the lateral and vertical extensions of the exposed rock types and possible changes in lithofacies beyond the limits of exposure. This can provide improved insights into the three-dimensional (3D) architecture of the system and the 3D distribution of reservoir rock types. Additional information gained from research boreholes concerns lithofacies types prone to weathering such as shales; cores are generally less weathered than outcrops and therefore provide a fresher and often more representative appearance. Electrical borehole images are found to be particularly useful as they have a large dynamic range that makes subtle sedimentary structures more visible, and their 3D nature allows accurate determination of directional structures such as cross-bedding. The costs and logistics of drilling research boreholes are important issues to consider before embarking on such projects.
Proof-Directed Parallelization Synthesis by Separation Logic
Authors: Botinčan Matko , Dodds Mike , Jagannathan Suresh 
Published: July 2013

We present an analysis which takes as its input a sequential program, augmented with annotations indicating potential parallelization opportunities, and a sequential proof, written in separation logic, and produces a correctly synchronized parallelized program and proof of that program. Unlike previous work, ours is not a simple independence analysis that admits parallelization only when threads do not interfere; rather, we insert synchronization to preserve dependencies in the sequential program that might be violated by a naïve translation. Separation logic allows us to parallelize fine-grained patterns of resource usage, moving beyond straightforward points-to analysis. The sequential proof need only represent shape properties, meaning we can handle complex algorithms without verifying every aspect of their behavior.
Our analysis works by using the sequential proof to discover dependencies between different parts of the program. It leverages these discovered dependencies to guide the insertion of synchronization primitives into the parallelized program, and to ensure that the resulting parallelized program satisfies the same specification as the original sequential program, and exhibits the same sequential behavior. Our analysis is built using frame inference and abduction, two techniques supported by an increasing number of separation logic tools.
Zombie memory: Extending memory lifetime by reviving dead blocks
Authors: Azevedo Rodolfo , Davis John D. , Strauss Karin , Gopalan Parikshit , Manasse Mark , Yekhanin Sergey 
Published: July 2013

Zombie is an endurance management framework that enables a variety of error correction mechanisms to extend the lifetimes of memories that suffer from bit failures caused by wearout, such as phase-change memory (PCM). Zombie supports both single-level cell (SLC) and multi-level cell (MLC) variants. It extends the lifetime of blocks in working memory pages (primary blocks) by pairing them with spare blocks, i.e., working blocks in pages that have been disabled due to exhaustion of a single block's error correction resources, which would be 'dead' otherwise. Spare blocks adaptively provide error correction resources to primary blocks as failures accumulate over time. This reduces the waste caused by early block failures, making working blocks in discarded pages a useful resource. Even though we use PCM as the target technology, Zombie applies to any memory technology that suffers stuck-at cell failures.
This paper describes the Zombie framework, a combination of two new error correction mechanisms (ZombieXOR for SLC and ZombieMLC for MLC) and the extension of two previously proposed SLC mechanisms (ZombieECP and ZombieERC). The result is a 58% to 92% improvement in endurance for Zombie SLC memory and an even more impressive 11x to 17x improvement for ZombieMLC, both with performance overheads of only 0.1% when memories using prior error correction mechanisms reach end of life.
Surveillance of Second-Degree Relatives from Melanoma Families with a CDKN2A Germline Mutation
Authors: van der Rhee Jasper I. , Boonk Stephanie E. , Putter Hein , Cannegieter Suzanne C. , Flinterman Linda E. , Hes Frederik J. , de Snoo Femke A. , Mooi Wolter J. , Gruis Nelleke A. , Vasen Hans F.A. , Kukutsch Nicole A. , Bergman Wilma 
Published: July 2013

Abstract
Background: Lifetime melanoma risk of mutation carriers from families with a germline mutation in the CDKN2A gene is estimated to be 67%. The necessity to include family members in a melanoma surveillance program is widely endorsed, but there is no consensus on which family members should be invited.
Methods: In a retrospective follow-up study, we investigated the yield of surveillance of first- and second-degree relatives of melanoma and pancreatic cancer patients from 21 families with the “p16-Leiden” CDKN2A mutation. Melanoma incidence rates were compared with the general population.
Results: Three-hundred and fifty-four first-degree relatives and 391 second-degree relatives were included. Forty-five first-degree relatives and 11 second-degree relatives were diagnosed with melanoma. Most (72%) of second-degree relatives diagnosed with melanoma had become a first-degree relative before diagnosis, due to the occurrence of a melanoma in a parent or sibling. Overall, melanoma incidence rate was 2.1 per 1,000 person years [95% confidence interval (CI), 1.2–3.8] in family members still being second-degree relatives at diagnosis, compared with 9.9 per 1,000 person years (95% CI, 7.4–13.3) in first-degree relatives. The standardized morbidity ratio for melanoma of second-degree relatives compared with the general population was 12.9 (95% CI, 7.2–23.4).
Conclusion: Second-degree relatives from families with the p16-Leiden mutation in CDKN2A have a considerably increased melanoma risk compared with the general population.
Impact: This study provides justification for the surveillance of second-degree relatives from families with a CDKN2A germline mutation. Cancer Epidemiol Biomarkers Prev; 22(10); 1771–7. ©2013 AACR.