bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allocation of Klebsiella pneumoniae Bloodstream Isolates into Four Distinct Groups byompK36Typing in a Taiwanese University Hospital
Authors: Yan Jing-Jou , Zheng Po-Xing , Wang Ming-Cheng , Tsai Shu-Huei , Wang Li-Rong , Wu Jiunn-Jong 
Published: July 2015

ABSTRACTThe OmpK36 porin plays a role in carbapenem resistance and may contribute to bacterial virulence inKlebsiella pneumoniae. This study aimed to investigate the characteristics of different groups ofK. pneumoniaeseparated byompK36typing. Among 226 nonduplicateK. pneumoniaebloodstream isolates collected at a Taiwanese hospital in 2011, fourompK36types, designated types A, B, C, and D, were identified by PCR in 61, 28, 100, and 36 isolates, respectively; 1 isolate was untypeable. Statistical analysis showed significantly higher rates of antimicrobial resistance (all tested antibiotics except meropenem), extended-spectrum β-lactamases or DHA-1 (47.5% together), Qnr-type quinolone resistance determinants (50.8%), and IncFIIA-type plasmids (49.2%) in group A than in others. Seventeen isolates were identified as belonging to 3 international high-risk clones (4 sequence type 11 [ST11], 10 ST15, and 3 ST147 isolates); all isolates but 1 ST15 isolate were classified in group A. The significant characteristics of group C were hypermucoviscosity (62.0%) and a higher virulence gene content. This group included all serotype K1 (n= 30), K2 (n= 25), and K5 (n= 3) isolates, 6 of 7 K57 isolates, all isolates of major clones associated with pyogenic liver abscesses (29 ST23, 11 ST65, 5 ST86, 7 ST373, and 1 ST375 isolates), and 16 (94.1%) of 17 isolates causing bacteremic liver abscesses. Twelve (42.9%) of the group B isolates were responsible for bacteremic biliary tract infections. Group D was predominant (83.3%) among 12 K20 isolates. This study suggests that most clinicalK. pneumoniaeisolates can be allocated into four groups with distinct characteristics based onompK36types.
Direct Detection of Erythromycin-Resistant Bordetella pertussis in Clinical Specimens by PCR
Authors: Wang Zengguo , Han Ruijun , Liu Ying , Du Quanli , Liu Jifeng , Ma Chaofeng , Li Hengxin , He Qiushui , Yan Yongping 
Published: July 2015

ABSTRACT

Resistance of
Bordetella pertussis
to erythromycin has been increasingly reported. We developed an allele-specific PCR method for rapid detection of erythromycin-resistant
B. pertussis
directly from nasopharyngeal (NP) swab samples submitted for diagnostic PCR. Based on the proven association of erythromycin resistance with the A2047G mutation in the 23S rRNA of
B. pertussis
, four primers, two of which were designed to be specific for either the wild-type or the mutant allele, were used in two different versions of the allele-specific PCR assay. The methods were verified with results obtained by PCR-based sequencing of 16 recent
B. pertussis
isolates and 100 NP swab samples submitted for diagnostic PCR. The detection limits of the two PCR assays ranged from 10 to 100 fg per reaction for both erythromycin-susceptible and -resistant
B. pertussis
. Two amplified fragments of each PCR, of 286 and 112 bp, respectively, were obtained from a mutant allele of the isolates and/or NP swab samples containing
B. pertussis
DNAs. For the wild-type allele, only a 286-bp fragment was visible when the allele-specific PCR assay 1 was performed. No amplification was found when a number of non-
Bordetella
bacterial pathogens and NP swab samples that did not contain the DNAs of
B. pertussis
were examined. This assay can serve as an alternative for PCR-based sequencing, especially for local laboratories in resource-poor countries.
Innate Immune Activity Correlates with CD4 T Cell-Associated HIV-1 DNA Decline during Latency-Reversing Treatment with Panobinostat
Authors: Olesen Rikke , Vigano Selena , Rasmussen Thomas A. , Søgaard Ole S. , Ouyang Zhengyu , Buzon Maria , Bashirova Arman , Carrington Mary , Palmer Sarah , Brinkmann Christel R. , Yu Xu G. , Østergaard Lars , Tolstrup Martin , Lichterfeld Mathias 
Published: July 2015

ABSTRACT

The pharmaceutical reactivation of dormant HIV-1 proviruses by histone deacetylase inhibitors (HDACi) represents a possible strategy to reduce the reservoir of HIV-1-infected cells in individuals treated with suppressive combination antiretroviral therapy (cART). However, the effects of such latency-reversing agents on the viral reservoir size are likely to be influenced by host immune responses. Here, we analyzed the immune factors associated with changes in proviral HIV-1 DNA levels during treatment with the potent HDACi panobinostat in a human clinical trial involving 15 cART-treated HIV-1-infected patients. We observed that the magnitude, breadth, and cytokine secretion profile of HIV-1-specific CD8 T cell responses were unrelated to changes in HIV-1 DNA levels in CD4 T cells during panobinostat treatment. In contrast, the proportions of CD3
−
CD56
+
total NK cells and CD16
+
CD56
dim
NK cells were inversely correlated with HIV-1 DNA levels throughout the study, and changes in HIV-1 DNA levels during panobinostat treatment were negatively associated with the corresponding changes in CD69
+
NK cells. Decreasing levels of HIV-1 DNA during latency-reversing treatment were also related to the proportions of plasmacytoid dendritic cells, to distinct expression patterns of interferon-stimulated genes, and to the expression of the
IL28B
CC genotype. Together, these data suggest that innate immune activity can critically modulate the effects of latency-reversing agents on the viral reservoir and may represent a target for future immunotherapeutic interventions in HIV-1 eradication studies.

IMPORTANCE
Currently available antiretroviral drugs are highly effective in suppressing HIV-1 replication, but the virus persists, despite treatment, in a latent form that does not actively express HIV-1 gene products. One approach to eliminate these cells, colloquially termed the “shock-and-kill” strategy, focuses on the use of latency-reversing agents that induce active viral gene expression in latently infected cells, followed by immune-mediated killing. Panobinostat, a histone deacetylase inhibitor, demonstrated potent activities in reversing HIV-1 latency in a recent pilot clinical trial and reduced HIV-1 DNA levels in a subset of patients. Interestingly, we found that innate immune factors, such as natural killer cells, plasmacytoid dendritic cells, and the expression patterns of interferon-stimulated genes, were most closely linked to a decline in the HIV-1 DNA level during treatment with panobinostat. These data suggest that innate immune activity may play an important role in reducing the residual reservoir of HIV-1-infected cells.
Bub1 in Complex with LANA Recruits PCNA To Regulate Kaposi's Sarcoma-Associated Herpesvirus Latent Replication and DNA Translesion Synthesis
Authors: Sun Zhiguo , Jha Hem Chandra , Robertson Erle S. 
Published: July 2015

ABSTRACT

Latent DNA replication of Kaposi's sarcoma-associated herpesvirus (KSHV) initiates at the terminal repeat (TR) element and requires
trans
-acting elements, both viral and cellular, such as ORCs, MCMs, and latency-associated nuclear antigen (LANA). However, how cellular proteins are recruited to the viral genome is not very clear. Here, we demonstrated that the host cellular protein, Bub1, is involved in KSHV latent DNA replication. We show that Bub1 constitutively interacts with proliferating cell nuclear antigen (PCNA) via a highly conserved PIP box motif within the kinase domain. Furthermore, we demonstrated that Bub1 can form a complex with LANA and PCNA in KSHV-positive cells. This strongly indicated that Bub1 serves as a scaffold or molecular bridge between LANA and PCNA. LANA recruited PCNA to the KSHV genome via Bub1 to initiate viral replication in S phase and interacted with PCNA to promote its monoubiquitination in response to UV-induced damage for translesion DNA synthesis. This resulted in increased survival of KSHV-infected cells.

IMPORTANCE
During latency in KSHV-infected cells, the viral episomal DNA replicates once each cell cycle. KSHV does not express DNA replication proteins during latency. Instead, KSHV LANA recruits the host cell DNA replication machinery to the replication origin. However, the mechanism by which LANA mediates replication is uncertain. Here, we show that LANA is able to form a complex with PCNA, a critical protein for viral DNA replication. Furthermore, our findings suggest that Bub1, a spindle checkpoint protein, serves as a scaffold or molecular bridge between LANA and PCNA. Our data further support a role for Bub1 and LANA in PCNA-mediated cellular DNA replication processes as well as monoubiquitination of PCNA in response to UV damage. These data reveal a therapeutic target for inhibition of KSHV persistence in malignant cells.
Virulence and Fitness Determinants of Uropathogenic
Escherichia coli
Authors: Subashchandrabose Sargurunathan , Mobley Harry L. T. 
Published: July 2015

ABSTRACT

Urinary tract infection (UTI) caused by uropathogenic
Escherichia coli
(UPEC) is a major global public health concern. Increasing antibiotic resistance found in clinical UPEC isolates underscores the immediate need for development of novel therapeutics against this pathogen. Better understanding of the fitness and virulence mechanisms that are integral to the pathogenesis of UTI will facilitate identification of novel strategies to prevent and treat infection with UPEC. Working towards that goal, the global UPEC research community has made great strides at unraveling various virulence and fitness genes. Here, we summarize major findings on virulence and fitness determinants that enable UPEC to successfully survive and colonize the urinary tract of mammalian hosts. Major sections of this chapter are devoted to the role of iron acquisition systems, metabolic pathways, fimbriae, flagella, toxins, biofilm formation, capsule, and strain-specific genes in the initiation and progression of UTIs. Transcriptomes of UPEC during experimental UTI in a murine model and naturally occurring UTI in women are compared to elucidate virulence mechanisms specifically involved in human UTI. Capitalizing on the advances in molecular pathogenesis research by translating these findings will help develop better clinical strategies for prevention and management of UTIs.
Retrospective study using MRI to measure depths of acupuncture points in neck and shoulder region
Authors: Chou Pei-Chi , Huang Yu-Chuen , Hsueh Chun-Jen , Lin Jaung-Geng , Chu Heng-Yi 
Published: July 2015

ObjectivesThere are safety issues associated with acupuncture treatment. Previous studies regarding needling depth of acupuncture points revealed inconsistent results due to vague depth definition, acupuncture point localisation and measuring tools. The objective of this study is to find and compare the differences of the mean depths of 11 acupuncture points in the neck and shoulder region between subjects, with variables including gender and body mass index (BMI).SettingThis study was conducted at a single medical center in Taiwan.ParticipantsThree hundred and ninety-four participants were included in this study. Participants were grouped according to gender and BMI. Acupuncture points were localised by WHO standard and measured by MRI.Outcome measuresThe distance from the needle insertion point (surface of the skin) to any tissues that would cause possible/severe complications.ResultsMean depths of 11 points were obtained in groups of different BMI and gender. Mean depths of all participants regardless of BMI and gender are as follows, in centimetres: GB21=5.6, SI14=5.2, SI15=8.8, GV15=4.9, GV16=4.6, GB20=5.0, ST9=1.6, SI16=1.8, SI17=2.4, TE16=3.1, LI18=1.3. Participants with higher BMI had greater measured depths in both gender groups. Male participants had larger mean depths than female participants regardless of BMI except in SI17 and LI18. When taking BMI into consideration, depths in male participants are greater than in female participants in most of the points except the following: GB21, TE16 in obesity group; ST9 in underweight and obesity group; SI16 in ideal body weight, overweight and obesity group; SI17, LI18 in each group.ConclusionsParticipants with higher BMI had greater measured depths and males tended to have greater depths in most of the points. Clinical practitioners are recommended to consider this information to prevent complications when applying acupuncture treatment to their patients.
Prevalence and determinants of excessive daytime sleepiness in hypertensive patients: a cross-sectional study in Douala, Cameroon
Authors: Mbatchou Ngahane Bertrand Hugo , Nganda Motto Malea , Dzudie Anastase , Luma Henry , Kamdem Félicité , Ngote Henri Roger , Monkam Yves , Kuaban Christopher 
Published: July 2015

ObjectiveTo determine the prevalence and determinants of excessive daytime sleepiness (EDS) among a group of sub-Saharan Africans living with hypertension.DesignA cross-sectional study.SettingCardiology outpatient unit of the Douala General Hospital in Cameroon.ParticipantsPatients aged 15 years and over, being followed for hypertension between 1st January and 31st July 2013. Patients with unstable heart failure, stroke and head trauma were excluded.Main outcome measureEDS was the outcome of interest. It was defined as an Epworth sleeping scale greater or equal to 10. Logistic regression was used to identify factors associated with EDS.ResultsA total of 411 patients participated in this study, with a sex ratio (male/female) of 0.58 and a mean age of 55.56 years. No patient was underweight and the mean body mass index was 30 kg/m2. Controlled blood pressure was found in 92 (22.4%) patients. The prevalence of EDS was 62.78% (95% CI 58.08 to 67.47). The factors independently associated with EDS were: type 2 diabetes (OR 2.51; 95% CI 1 to 6.29), obesity (OR 2.75; 95% CI 1.52 to 4.97), snoring (OR 7.92; 95% CI 4.43 to 14.15) and uncontrolled blood pressure (OR 4.34; 95% CI 2.24 to 8.40).ConclusionsA significant proportion of hypertensive patients suffer from EDS and present a high risk of sleep apnoea. Preventive measures targeted on weight loss, type 2 diabetes and snoring should be considered among these patients.
The persistent clustering of adult body mass index by school attended in adolescence
Authors: Evans Clare Rosenfeld , Lippert Adam M , Subramanian SV 
Published: July 2015

BackgroundIt is well known that adolescent body mass index (BMI) shows school-level clustering. We explore whether school-level clustering of BMI persists into adulthood.MethodsMultilevel models nesting young adults in schools they attended as adolescents are fit for 3 outcomes: adolescent BMI, self-report adult BMI and measured adult BMI. Sex-stratified and race/ethnicity-stratified (black, Hispanic, white, other) analyses were also conducted.ResultsSchool-level clustering (wave 1 intraclass correlation coefficient (ICC)=1.3%) persists over time (wave 4 ICC=2%), and results are comparable across stratified analyses of both sexes and all racial/ethnic groups (except for Hispanics when measured BMIs are used). Controlling for BMI in adolescence partially attenuates this effect.ConclusionsSchool-level clustering of BMI persists into young adulthood. Possible explanations include the salience of school environments in establishing behaviours and trajectories, the selection of adult social networks that resemble adolescent networks and reinforce previous behaviours, and characteristics of school catchment areas associated with BMI.
Arran Field: a complex heterolithic reservoir on the margins of the Forties Fan System
Authors: Collins Jamie , Kenyon-Roberts Steve , Cullen Brian , White Jason , Bordas-Le Floch Nathalie , Downey John 
Published: July 2015

Abstract

The Arran Field contains gas-condensate accumulated within the Paleocene Forties Sandstone Member of the Sele Formation. It is located along the margin of the medial Forties turbidite depositional system, on the eastern flank of the Central Graben's Eastern Trough. The field comprises a low-relief southern extension (Arran South) from a high-relief northern closure (Arran North) around a salt diapir. The eastern margin of the field represents the pinch-out of the Forties Sandstone Member against the Jaeren High. As part of the field development planning, a comprehensive re-evaluation of subsurface data was undertaken. A thorough understanding of the reservoir distribution and turbidite architectures was vital to ensure that the appropriate elements were captured within the reservoir model. This was achieved through a thorough integration and multidisciplinary interpretation of all available data including seismic, core, petrophysical and analogue data. These data indicate that the best quality Forties Sandstone Member reservoir consists of stacked, elongate, amalgamated and non-amalgamated fairway sandstone bodies. These thick-bedded and sand-dominated reservoir units pass laterally into, and are extensively interbedded with, linked debrites, heterolithic low-density turbidite lobe fringe deposits, slumps, and debris flows, along with hemipelagic and turbiditic shales. A seismic shale volume (
V
shale
), derived from inverted pre-SDM data, together with reflection seismic data, were used to identify and map intra-reservoir depositional lobe geometries. These show large-scale, lobe-like depositional bodies which migrated laterally over time and onlapped on to the Jaeren High to the east. Within these, smaller-scale elongated lobe bodies, generally derived from the NW, are interpreted from layer-parallel extractions of the seismic
V
shale
volume. Possible slump units were also identified, predominantly derived from the edges of the Arran North salt diapir, suggesting that the basin floor topography was mobile during deposition. The seismic
V
shale
volume was used to condition the static facies model, utilizing probability relationships between the seismic data and core facies at the wells, providing a soft linkage between the data and models developed. Core, analogue data and facies interpretations from the seismic data were utilized to ensure that appropriate reservoir body geometries and spatial relationships were maintained in the static model and allowed key reservoir heterogeneities to be captured. This integrated approach also supported analysis of reservoir uncertainties, with specific focus on the vertical and lateral reservoir connectivity within this lobe-dominated reservoir.
Reservoir geology of the Paleocene Forties Sandstone Member in the Fram discovery, UK Central North Sea
Authors: Jones David W. , Large Samantha , McQueen Alan , Helmi Ahmed 
Published: July 2015

Abstract
The Fram discovery, located in the UK Central North Sea, comprises the Paleocene-aged Forties Sandstone Member with an oil rim and primary gas-cap trapped within a four-way dip closure around a pierced salt diapir. The Forties Sandstone Member reservoir at Fram is characterized by very-fine- to fine-grained sandstones interbedded with shales with post-depositional small-scale slumping and sand injection, interpreted to be the product of high-density turbidity currents and debris flows. Deposition was in an overall distal and marginal, basin-floor lobe environment. The Forties reservoir interval is considered to comprise a series of offset-stacked, turbidite lobes characterized by a systematic variation from axial amalgamated sandstone facies to more distal, marginal and thinner-bedded heterolithic sandstone facies, producing an overall sheet-like reservoir architecture. The Forties reservoir at Fram is thinner and poorer when compared with more proximal parts of the Forties submarine fan system, and reservoir quality is strongly controlled by sedimentary facies. The architecture of the reservoir is expected to result in poorer vertical, but greater lateral, stratigraphic continuity when compared with more channelized Forties reservoirs such as the Nelson and Forties fields further to the north. A key step in understanding and characterizing the Fram reservoir was the appraisal drilling in 2009, which included coring, comprehensive wireline logging, formation pressure data acquisition and a drill stem production test. This paper provides an overview of the Fram reservoir geology and demonstrates how integration of data acquired in the 2009 29/3c-8,8z appraisal wells with 3D seismic datasets, existing E&A wells and analogues has helped to improve reservoir characterization and identify the major subsurface uncertainties needing to be addressed during the field-development planning.
CSG-Ed
Authors: Weikle Dee A. B. 
Published: July 2015

Computer science faculty have been taught to develop software, crunch through difficult math problems and generally work to be objective about how to solve a problem defined in most cases by a specification. Those who are able to excel at these tasks and continue through the more difficult and theoretical versions are most often the ones who become professors. Likely the professors of computing classes in college have never had an education course or philosophy course, never mind teaching one. The ACM 2013 guidelines not only challenge computer science professors to teach writing throughout the curriculum, but to also break with the old assumption that computing is value-neutral. This session describes a set of entry-level lesson plans for presenting and discussing three different aspects of the social impact of computing appropriate for incorporation into an entry-level general education course. Inspired by previous SIGCAS sessions on ethics in computing, the specific topics are 1) professional codes for software developers and how they relate to student value systems, 2) a single source network router case used to illustrate stakeholder identification, and 3) a very small "service" project using Wikipedia. Each of these lesson plans are presented as a separate set of learning outcomes, a basic lesson plan with tips on presenting the material, an assignment to go along with the lesson plan and a short rubric for grading the assignment. All of these lesson plans have been used multiple times with success in a college general education computing class. These lesson plans were distributed at the workshop. The lessons and accompanying materials are available from the instructor on request.
A combined list of learning outcomes includes: 1) Seeing software engineering and coding as a profession with associated responsibilities and expectations, 2) Understanding the impact computing devices and components in our infrastructure have on our daily lives, including technical aspects of a network 3) Identifying stakeholders in a case study and the importance of a global perspective in policy-making, 4) Understanding the power and vulnerabilities of Wikipedia while contributing some content to this community project, 5) Writing short logical essays to convey an opinion in a convincing manner.
Mitochondrial DNA in Tumor Initiation, Progression, and Metastasis: Role of Horizontal mtDNA Transfer
Authors: Berridge Michael V. , Dong Lanfeng , Neuzil Jiri 
Published: July 2015

Abstract
Mitochondrial DNA (mtDNA), encoding 13 out of more than 1,000 proteins of the mitochondrial proteome, is of paramount importance for the bioenergetic machinery of oxidative phosphorylation that is required for tumor initiation, propagation, and metastasis. In stark contrast to the widely held view that mitochondria and mtDNA are retained and propagated within somatic cells of higher organisms, recent in vitro and in vivo evidence demonstrates that mitochondria move between mammalian cells. This is particularly evident in cancer where defective mitochondrial respiration can be restored and tumor-forming ability regained by mitochondrial acquisition. This paradigm shift in cancer cell biology and mitochondrial genetics, concerning mitochondrial movement between cells to meet bioenergetic needs, not only adds another layer of plasticity to the armory of cancer cells to correct damaged mitochondria, but also points to potentially new therapeutic approaches. Cancer Res; 75(16); 3203–8. ©2015 AACR.