bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of Clostridium butyricum Strain DSM 10702, a Promising Producer of Biofuels and Biochemicals
Authors: Xin Bo , Tao Fei , Wang Yu , Gao Chao , Ma Cuiqing , Xu Ping 
Published: August 2013

ABSTRACT

Clostridium butyricum
strains have been considered promising producers of biofuels and biochemicals, such as hydrogen, butanol, butyric acid, and 1,3-propanediol. Here, we present a 4.59-Mb assembly of the genome sequence of DSM 10702 (VPI 3266), a type strain of
C. butyricum
.
Genome Sequence of the Polyphosphate-Accumulating Organism
Arthrobacter
sp. Strain PAO19 Isolated from Maize Rhizosphere Soil
Authors: Li Xiaolong , Yuan Hongli , Yang Jinshui , Li Baozhen 
Published: August 2013

ABSTRACT

Arthrobacter
sp. strain PAO19 is a polyphosphate-accumulating organism isolated from maize rhizosphere soil. Here we report its genome sequence, which may shed light on its role in phosphate removal from water bodies. To our knowledge, this is the first genome announcement of a polyphosphate-accumulating strain of the genus
Arthrobacter
.
Cutaneous Infection Caused by a Novel Francisella sp
Authors: Respicio-Kingry Laurel B. , Byrd Lori , Allison Ashley , Brett Meghan , Scott-Waldron Christine , Galliher Karen , Hannah Paul , Mead Paul , Petersen Jeannine M. 
Published: August 2013

ABSTRACT

A 69-year-old patient presented with a tender, thickly crusted skin lesion of 1 week's duration. A bacterial culture swab taken from the underlying granular tissue yielded a pure isolate of a Gram-negative coccobacillus, presumptively identified as a novel
Francisella
species via 16S rRNA and multilocus gene sequence analysis.
Parvoviral Left-End Hairpin Ears Are Essential during Infection for Establishing a Functional Intranuclear Transcription Template and for Efficient Progeny Genome Encapsidation
Authors: Li Lei , Cotmore Susan F. , Tattersall Peter 
Published: August 2013

ABSTRACT

The 121-nucleotide left-end telomere of Minute Virus of Mice (MVM) can be folded into a Y-shaped hairpin with short axial ears that are highly conserved within genus
Parvovirus
. To explore their potential role(s) during infection, we constructed infectious plasmid clones that lacked one or other ear. Although these were nonviable when transfected into A9 cells, excision of the viral genome and DNA amplification appeared normal, and viral transcripts and proteins were expressed, but progeny virion production was minimal, supporting the idea of a potential role for the ears in genome packaging. To circumvent the absence of progeny that confounded further analysis of these mutants, plasmids were transfected into 293T cells both with and without an adenovirus helper construct, generating single bursts of progeny. These virions bound to A9 cells and were internalized but failed to initiate viral transcription, protein expression, or DNA replication. No defects in mutant virion stability or function could be detected
in vitro
. Significantly, mutant capsid gene expression and DNA replication could be rescued by coinfection with wild-type virions carrying a replication-competent, capsid-gene-replacement vector. To pinpoint where such complementation occurred, prior transfection of plasmids expressing only MVM nonstructural proteins was explored. NS1 alone, but not NS2, rescued transcription and protein expression from both P4 and P38 promoters, whereas NS1 molecules deleted for their C-terminal transactivation domain did not. These results suggest that the mutant virions reach the nucleus, uncoat, and are converted to duplex DNA but require an intact left-end hairpin structure to form the initiating transcription complex.
Effectiveness and cost-effectiveness of a universal parenting skills programme in deprived communities: multicentre randomised controlled trial
Authors: Simkiss D E , Snooks H A , Stallard N , Kimani P K , Sewell B , Fitzsimmons D , Anthony R , Winstanley S , Wilson L , Phillips C J , Stewart-Brown S 
Published: August 2013

ObjectiveTo evaluate the effectiveness and cost utility of a universally provided early years parenting programme.DesignMulticentre randomised controlled trial with cost-effectiveness analysis.SettingEarly years centres in four deprived areas of South Wales.ParticipantsFamilies with children aged between 2 and 4 years. 286 families were recruited and randomly allocated to the intervention or waiting list control.InterventionThe Family Links Nurturing Programme (FLNP), a 10-week course with weekly 2 h facilitated group sessions.Main outcome measuresNegative and supportive parenting, child and parental well-being and costs assessed before the intervention, following the course (3 months) and at 9 months using standardised measures.ResultsThere were no significant differences in primary or secondary outcomes between trial arms at 3 or 9 months. With ‘+’ indicating improvement, difference in change in negative parenting score at 9 months was +0.90 (95%CI −1.90 to 3.69); in supportive parenting, +0.17 (95%CI −0.61 to 0.94); and 12 of the 17 secondary outcomes showed a non-significant positive effect in the FLNP arm. Based on changes in parental well-being (SF-12), the cost per quality-adjusted life year (QALY) gained was estimated to be £34 913 (range 21 485–46 578) over 5 years and £18 954 (range 11 664–25 287) over 10 years. Probability of cost per QALY gained below £30 000 was 47% at 5 years and 57% at 10 years. Attendance was low: 34% of intervention families attended no sessions (n=48); only 47% completed the course (n=68). Also, 19% of control families attended a parenting programme before 9-month follow-up.ConclusionsOur trial has not found evidence of clinical or cost utility for the FLNP in a universal setting. However, low levels of exposure and contamination mean that uncertainty remains.Trial registrationThe trial is registered with Current Controlled TrialsISRCTN13919732.
Association between daily antiretroviral pill burden and treatment adherence, hospitalisation risk, and other healthcare utilisation and costs in a US medicaid population with HIV
Authors: Cohen Calvin J , Meyers Juliana L , Davis Keith L 
Published: August 2013

ObjectivesLower pill burden leads to improved antiretroviral therapy (ART) adherence among HIV patients. Simpler dosing regimens have not been widely explored in real-world populations. We retrospectively assessed ART adherence, all-cause hospitalisation risk and costs, and other healthcare utilisation and costs in Medicaid enrollees with HIV treated with ART as a once-daily single-tablet regimen (STR) or two or more pills per day (2+PPD).DesignPatients with an HIV diagnosis from 2005 to 2009 receiving complete ART (ie, two nucleoside/nucleotide reverse transcriptase inhibitors plus a third agent) for ≥60 days as STR or 2+PPD were selected and followed until the first of (1) discontinuation of the complete ART, (2) loss of enrolment or (3) end of database. Adherence was measured using the medication possession ratio. Monthly all-cause healthcare utilisation and costs were observed from regimen initiation until follow-up end.ResultsOf the 7381 patients who met inclusion criteria, 1797 were treated with STR and 5584 with 2+PPD. STR patients were significantly more likely to reach 95% adherence and had fewer hospitalisations than 2+PPD patients (both p<0.01). STR patients had mean (SD) total monthly costs of $2959 ($4962); 2+PPD patients had $3544 ($5811; p<0.001). Hospital costs accounted for 53.8% and pharmacy costs accounted for 32.5% of this difference. Multivariate analyses found that STR led to a 23% reduction in hospitalisations and a 17% reduction in overall healthcare costs. ART adherence appears to be a key mechanism mediating hospitalisation risk, as patients with ≥95% adherence (regardless of regimen type) had a lower hospitalisation rate compared with <95% adherence.ConclusionsWhile it was expected that STR patients would have lower pharmacy costs, we also found that STR patients had fewer hospitalisations and lower hospital costs than 2+PPD patients, resulting in significantly lower total healthcare costs for STR patients.
Pulmonary arterial hypertension associated with connective tissue disease: meta-analysis of clinical trials
Authors: Kuwana Masataka , Watanabe Hiroshi , Matsuoka Nobushige , Sugiyama Naonobu 
Published: August 2013

ObjectivesFew studies have focused on pulmonary arterial hypertension (PAH) associated with connective tissue diseases (CTDs). The optimal treatment for CTD-PAH has yet to be established.DesignMeta-analysis of the data from evaluations of treatment for PAH generally (19 studies) and CTD-PAH specifically (nine studies) to compare the effects of pulmonary vasodilative PAH agents. MEDLINE, EMBASE and BIOSIS were searched. English-language full-text articles published between January 1990 and August 2012 were eligible.SettingInternational.ParticipantsPatients with PAH generally (n=3073) and CTD-PAH specifically (n=678).Primary outcome measureExercise capacity (6 min walk distance, 6 MWD).ResultsPatients with PAH (all forms) had mean age 32–55 years (women, 61–87%); CTD-PAH patients had mean age 45–55 years (women, 74–95%). Overall estimate of mean change in 6 MWD from baseline (95% CI) for the active treatment group versus the control group in all patients with PAH was 34.6 m (27.4–41.9 m). Pooled mean differences from the results for patients receiving placebo by subgroup of patients receiving phosphodiesterase (PDE)-5 inhibitors, endothelin receptor antagonists (ERAs) and prostacyclin (PGI2) analogues were 22.4–45.5, 39.5–44.2 and 12.4–64.9 m, respectively. Overall estimate of mean difference between changes in 6 MWD in patients with CTD-PAH was 34.2 m (23.3–45.0 m). Pooled mean differences by subgroup of patients receiving PDE-5 inhibitors, ERAs and PGI2analogues in patients with CTD-PAH were 37.0–47.1, 14.1–21.7 and 21.0–108.0 m, respectively. ERAs were less effective in patients with CTD-PAH than all-form patients with PAH: 14.1 m (−4.4–32.6 m) vs 39.5 m (19.5–59.6 m) for bosentan and 21.7 m (2.2–41.3 m) vs 44.2 m (30.2–58.2 m) for ambrisentan.ConclusionsAll three types of PAH agent are effective. However, ERAs may be a less effective choice against CTD-PAH; further studies are needed. Limitations include the limited number of studies for some agents and for patients with CTD-PAH.
Objects of temporary contraception: an exploratory study of women's perspectives in Karachi, Pakistan
Authors: Marvi Kamyla , Howard Natasha 
Published: August 2013

ObjectivesTo explore perspectives of three modern contraceptive objects, using anemicapproach, among women in a low-income community in Karachi, Pakistan.DesignA qualitative interview study design was employed, using qualitative content analysis with an inductive approach and manual thematic coding.SettingShah Faisal Colony, Karachi.Participants20 women, potential contraceptive users of reproductive age and living within a health centre catchment, were purposively selected to provide a similar number of non-users (n=5), contraceptive injection users (n=7), pill users (n=4), and intrauterine device users (n=4). One interview was excluded because it was not recorded. No other exclusion criteria were used.Primary and secondary outcome measuresThe primary outcome was interpretation of potency and effects of selected family planning objects. Secondary outcome measures were knowledge of family planning and description of therapeutic approaches used and preferred.ResultsAwareness of family planning was high. Women described different therapeutic approaches, stating they generally preferred modern medicine for contraception as it was fastest and most powerful. They reported that fear of some contraceptive objects, particularly injections and intrauterine contraceptive devices, influenced their choices. Women explained their perceptions of how the heating effects of contraceptives could cause unwanted side effects including menstrual irregularities, weight gain and weakness, leading to disease.ConclusionsMost women wanted family planning, but remained dissatisfied with the available contraceptives and their effects. While women reported that they relied on modern medicine for contraception, their descriptions of how contraceptives affected their health relied on the hot–cold explanatory idiom of traditional medicine.
The impact of chronic untreated hyperglycaemia on the long-term stability of paraoxonase 1 (PON1) and antioxidant status in human sera
Authors: Macharia Muiruri , Kengne Andre P , Blackhurst Diane M , Erasmus Rajiv T , Matsha Tandi E 
Published: August 2013

AimsParaoxonase 1 (PON1) is increasingly measured on samples that have been stored for extended durations. The impact of storage and baseline conditions on the stability of the enzyme is however not well documented. We investigated the influence of hyperglycaemia on the stability of PON1 activity and antioxidant status in human sera stored for 12 months.MethodsBlood was collected from 60 individuals aged 35–80 years with chronic hyperglycaemia (HbA1c≥6.5%) or normoglycaemia (HbA1c<6.5%) in Cape Town. At baseline and after 12 months at −80°C, levels of PON1 activity (paraoxoase and arylesterase), antioxidant activity (ferric reducing antioxidant power (FRAP) and Trolox equivalent antioxidant capacity (TEAC)) and lipid peroxidation (malondialdehyde and oxidised low density lipoprotein (ox-LDL)) were measured and compared.ResultsIn normoglycaemic samples, 12-month storage led to minor alterations of <10% for the six target variables. In hyperglycaemic samples, alterations ranged from 13% for AREase activity to about 23% for ox-LDLs indicating a twofold to fourfold difference between the two groups in the variables assessed. Changes in levels of FRAP, TEAC and ox-LDL were both statistically and clinically significant. Furthermore, there was evidence of significant statistical interaction by baseline glycaemic status on the alteration of FRAP, TEAC, thiobarbituric acid reactive substances and ox-LDL, but not for PON1 activity.ConclusionsThe results indicate that baseline glycaemic status may contribute to a decline in the stability of antioxidant activity and extent of lipid peroxidation but not PON activity.
Inequalities in self-rated health in Japan 1986–2007 according to household income and a novel occupational classification: national sampling survey series
Authors: Hiyoshi Ayako , Fukuda Yoshiharu , Shipley Martin J , Brunner Eric J 
Published: August 2013

BackgroundJapan, for the past two decades, has seen economic stagnation and substantial social change. We examined whether health inequalities increased over this period.MethodsUsing eight triennial waves of a series of large nationally representative surveys between 1986 and 2007 (n=398 303), temporal trends in relative and slope indices of inequality (RII, SII, respectively) were tested based on self-rated health in relation to theory-based social class and household income.ResultsAge-standardised prevalence of self-rated fair or poor health showed V-shaped time trends in both sexes with the lowest prevalence in early/mid-1990s. In 1986, RII and SII in household social class and income were significant for both sexes. In men, RII and SII according to income showed significant narrowing of temporal trends in poor health (−1.4% and −0.1% annually, respectively), but these were stable in women. After multilevel multiple imputation for missing income data, the findings in men were not altered but narrowing trends became evident and significant in women (−1% and −0.1% annually, respectively). Inequality indices for social class remained constant over the study period in both sexes.ConclusionsRelative and absolute health inequalities for social class and income based on self-rated fair or poor health narrowed or remained stable between 1986 and 2007, despite the economic stagnation and adverse social changes. Overall population health across socioeconomic groups initially improved but then worsened. The positive finding regarding the health inequality trend seen in the Japanese context is informative for the wider international community during this period of economic uncertainty.
Social determinants of mental health: a Finnish nationwide follow-up study on mental disorders
Authors: Paananen Reija , Ristikari Tiina , Merikukka Marko , Gissler Mika 
Published: August 2013

BackgroundMost mental disorders start in childhood and adolescence. Risk factors are prenatal and perinatal, genetic as well as environmental and family related. Research evidence is, however, insufficient to explain the life-course development of mental disorders. This study aims to provide evidence on factors affecting mental health in childhood and adolescence.Data and methodsThe 1987 Finnish Birth Cohort covers all children born in Finland in 1987 (N=59 476) who were followed up until the age of 21 years. The study covers detailed health, social welfare and sociodemographic data of the cohort members and their parents from Finnish registers.ResultsAltogether, 7578 (12.7%) cohort members had had a diagnosed mental disorder. Several prenatal, perinatal and family-related risk factors for mental disorders were found, with sex differences. The main risk factors for mental disorders were having a young mother (OR 1.30 (1.16 to 1.47)), parents’ divorce (OR 1.33 (1.26 to1.41)), death of a parent (OR 1.27 (1.16 to 1.38)), parents’ short education (OR 1.23(1.09 to 1.38)), childhood family receiving social assistance (OR 1.61 (1.52 to 1.71)) or having a parent treated at specialised psychiatric care (OR 1.47 (1.39 to 1.55)). Perinatal problem (OR 1.11 (1.01 to 1.22)) and prenatal smoking (OR 1.09 (1.02 to 1.16)) were risk factors for mental disorders, even after controlling for background factors. Elevated risk was seen if the cohort member had only basic education (OR 3.37 (3.14 to 3.62)) or had received social assistance (OR 2.45 (2.30 to 2.60)).ConclusionsMental disorders had many social risk factors which are interlinked. Although family difficulties increased the risk for mental disorders, they were clearly determined by the cohort member's low education and financial hardship. This study provides evidence for comprehensive preventative and supporting efforts. Families with social adversities and with parental mental health problems should be supported to secure children's development.
SIGWEB annual report
Authors: Harper Simon 
Published: August 2013

The last year has been an exciting one for SIGWEB. From the sponsorship of six Web Conference, to that of Cooperating Conferences; from the increase in student travel sponsorship (to $30,000pa), to our increasing volunteer effort; the SIG has been at work at all levels of our domain.
We have forged links with multiple (≈20) conferences and workshops across our field, focusing on new contribution awards and broadening participation of the SIG, while still maintaining our low membership dues. In short, it has been an active and productive year.
We have increased membership numbers (to 561). But, we have an increasing funds balance (to $703,000), and are still increasing the amount we have to spend on each member, from $618 last year to $800 this year; with member benefits of: Reduced rates at SIGWEB sponsored, co-sponsored, and co-operating events; Free access to ACM DL content of events sponsored by SIGWEB; Reduced subscription rates to New Review of Hypermedia and Multimedia; Free subscription to the SIGWEB members email list, with calls, advance and final event programs; and news of interest to the community posted regularly; we still have an excellent membership offering.
In short SIGWEB has successfully expanded its range of conference sponsorships, is working hard on membership and volunteer development and benefits, and is financially healthy with a solid leadership.
Src Family Kinases as Novel Therapeutic Targets to Treat Breast Cancer Brain Metastases
Authors: Zhang Siyuan , Huang Wen-Chien , Zhang Lin , Zhang Chenyu , Lowery Frank J. , Ding Zhaoxi , Guo Hua , Wang Hai , Huang Suyun , Sahin Aysegul A. , Aldape Kenneth D. , Steeg Patricia S. , Yu Dihua 
Published: August 2013

Abstract
Despite better control of early-stage disease and improved overall survival of patients with breast cancer, the incidence of life-threatening brain metastases continues to increase in some of these patients. Unfortunately, other than palliative treatments there is no effective therapy for this condition. In this study, we reveal a critical role for Src activation in promoting brain metastasis in a preclinical model of breast cancer and we show how Src-targeting combinatorial regimens can treat HER2+ brain metastases in this model. We found that Src was hyperactivated in brain-seeking breast cancer cells derived from human cell lines or from patients' brain metastases. Mechanistically, Src activation promoted tumor cell extravasation into the brain parenchyma via permeabilization of the blood–brain barrier. When combined with the EGFR/HER2 dual-targeting drug lapatinib, an Src-targeting combinatorial regimen prevented outgrowth of disseminated breast cancer cells through the induction of cell-cycle arrest. More importantly, this combinatorial regimen inhibited the outgrowth of established experimental brain metastases, prolonging the survival of metastases-bearing mice. Our results provide a rationale for clinical evaluation of Src-targeting regimens to treat patients with breast cancer suffering from brain metastasis. Cancer Res; 73(18); 5764–74. ©2013 AACR.
Integrative Genomics Analysis Identifies Candidate Drivers at 3q26-29 Amplicon in Squamous Cell Carcinoma of the Lung
Authors: Wang Jing , Qian Jun , Hoeksema Megan D. , Zou Yong , Espinosa Allan V. , Rahman S.M. Jamshedur , Zhang Bing , Massion Pierre P. 
Published: August 2013

AbstractPurpose: Chromosome 3q26-29 is a critical region of genomic amplification in lung squamous cell carcinomas (SCC). Identification of candidate drivers in this region could help uncover new mechanisms in the pathogenesis and potentially new targets in SCC of the lung.Experimental Design: We conducted a meta-analysis of seven independent datasets containing a total of 593 human primary SCC samples to identify consensus candidate drivers in 3q26-29 amplicon. Through integrating protein–protein interaction network information, we further filtered for candidates that may function together in a network. Computationally predicted candidates were validated using RNA interference (RNAi) knockdown and cell viability assays. Clinical relevance of the experimentally supported drivers was evaluated in an independent cohort of 52 lung SCC patients using survival analysis.Results: The meta-analysis identified 20 consensus candidates, among which four (SENP2, DCUN1D1, DVL3, and UBXN7) are involved in a small protein–protein interaction network. Knocking down any of the four proteins led to cell growth inhibition of the 3q26-29–amplified SCC. Moreover, knocking down of SENP2 resulted in the most significant cell growth inhibition and downregulation of DCUN1D1 and DVL3. Importantly, a gene expression signature composed of SENP2, DCUN1D1, and DVL3 stratified patients into subgroups with different response to adjuvant chemotherapy.Conclusion: Together, our findings show that SENP2, DCUN1D1, and DVL3 are candidate driver genes in the 3q26-29 amplicon of SCC, providing novel insights into the molecular mechanisms of disease progression and may have significant implication in the management of SCC of the lung. Clin Cancer Res; 19(20); 5580–90. ©2013 AACR.