bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of 11 different radioisotopes for palliative treatment of bone metastases by computational methods
Authors: Guerra Liberal Francisco D. C. , Tavares Adriana Alexandre S. , Tavares João Manuel R. S. 
Published: October 2014

Purpose:Throughout the years, the palliative treatment of bone metastases using bone seeking radiotracers has been part of the therapeutic resources used in oncology, but the choice of which bone seeking agent to use is not consensual across sites and limited data are available comparing the characteristics of each radioisotope. Computational simulation is a simple and practical method to study and to compare a variety of radioisotopes for different medical applications, including the palliative treatment of bone metastases. This study aims to evaluate and compare 11 different radioisotopes currently in use or under research for the palliative treatment of bone metastases using computational methods.Methods:Computational models were used to estimate the percentage of deoxyribonucleic acid (DNA) damage (fast Monte Carlo damage algorithm), the probability of correct DNA repair (Monte Carlo excision repair algorithm), and the radiation‐induced cellular effects (virtual cell radiobiology algorithm) post‐irradiation with selected particles emitted by phosphorus‐32 (32P), strontium‐89 (89Sr), yttrium‐90 (90Y), tin‐117 (117mSn), samarium‐153 (153Sm), holmium‐166 (166Ho), thulium‐170 (170Tm), lutetium‐177 (177Lu), rhenium‐186 (186Re), rhenium‐188 (188Re), and radium‐223 (223Ra).Results:223Ra alpha particles, 177Lu beta minus particles, and 170Tm beta minus particles induced the highest cell death of all investigated particles and radioisotopes. The cell survival fraction measured post‐irradiation with beta minus particles emitted by 89Sr and 153Sm, two of the most frequently used radionuclides in the palliative treatment of bone metastases in clinical routine practice, was higher than 177Lu beta minus particles and 223Ra alpha particles.Conclusions:223Ra and 177Lu hold the highest potential for palliative treatment of bone metastases of all radioisotopes compared in this study. Data reported here may prompt future in vitro and in vivo experiments comparing different radionuclides for palliative treatment of bone metastases, raise the need for the careful rethinking of the current widespread clinical use of 89Sr and 153Sm, and perhaps strengthen the use of 223Ra and 177Lu in the palliative treatment of bone metastases.
Spatiotemporal filtering of MR‐temperature artifacts arising from bowel motion during transurethral MR‐HIFU
Authors: Schmitt Alain , Mougenot Charles , Chopra Rajiv 
Published: October 2014

Purpose:Transurethral MR‐HIFU is a minimally invasive image‐guided treatment for localized prostate cancer that enables precise targeting of tissue within the gland. The treatment is performed within a clinical MRI to obtain real‐time MR thermometry used as an active feedback to control the spatial heating pattern in the prostate and to monitor for potential damage to surrounding tissues. This requires that the MR thermometry measurements are an accurate representation of the true tissue temperature. The proton resonance frequency shift thermometry method used is sensitive to tissue motion and changes in the local magnetic susceptibility that can be caused by the motion of air bubbles in the rectum, which can impact the performance of transurethral MR‐HIFU in these regions of the gland.Methods:A method is proposed for filtering of temperature artifacts based on the temporal variance of the temperature, using empirical and dynamic positional knowledge of the ultrasonic heating beam, and an estimation of the measurement noise. A two‐step correction strategy is introduced which eliminates artifact‐detected temperature variations while keeping the noise level low through spatial averaging.Results:The filter has been evaluated by postprocessing data from five human transurethral ultrasound treatments. The two‐step correction process led to reduced final temperature standard deviation in the prostate and rectum areas where the artifact was located, without negatively affecting areas distal to the artifact. The performance of the filter was also found to be consistent across all six of the data sets evaluated. The evaluation of the detection criterion parameter M determined that a value of M = 3 achieves a conservative filter with minimal loss of spatial resolution during the process.Conclusions:The filter was able to remove most artifacts due to the presence of moving air bubbles in the rectum during transurethral MR‐HIFU. A quantitative estimation of the filter capabilities shows a systematic improvement in the standard deviation of the corrected temperature maps in the rectum zone as well as in the entire acquired slice.
Criblamydia sequanensis
Harbors a Megaplasmid Encoding Arsenite Resistance
Authors: Bertelli Claire , Goesmann Alexander , Greub Gilbert 
Published: October 2014

ABSTRACT

Criblamydia sequanensis
is an amoeba-resisting bacterium recently isolated from the Seine River. This
Chlamydia-
related bacterium harbors a genome of approximately 3 Mbp and a megaplasmid of 89,525 bp. The plasmid encodes several efflux systems and an operon for arsenite resistance. This first genome sequence within the
Criblamydiaceae
family enlarges our view on the evolution and the ecology of this important bacterial clade largely understudied so far.
Complete Genome Sequences of Lineage III Peste des Petits Ruminants Viruses from the Middle East and East Africa
Authors: Muniraju Murali , Munir Muhammad , Banyard Ashley C. , Ayebazibwe Chrisostom , Wensman Jonas , Zohari Siamak , Berg Mikael , Parthiban AravindhBabu R. , Mahapatra Mana , Libeau Geneviève , Batten Carrie , Parida Satya 
Published: October 2014

ABSTRACT
For the first time, complete genome sequences of four lineage III peste des petits ruminants (PPR) viruses (Oman 1983, United Arab Emirates 1986, Ethiopia 1994, and Uganda 2012) originated from the Middle East and East Africa are reported here. The availability of complete genome sequences from all four lineages (I to IV) of the PPR virus (PPRV) would greatly help in a comprehensive understanding of the molecular evolution and emergence of PPRV.
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant “Thiobacillus prosperus” Type Strain DSM 5130
Authors: Ossandon Francisco J. , Cárdenas Juan Pablo , Corbett Melissa , Quatrini Raquel , Holmes David S. , Watkin Elizabeth 
Published: October 2014

ABSTRACT

“
Thiobacillus prosperus
” is a halotolerant mesophilic acidophile that gains energy through iron and sulfur oxidation. Its physiology is poorly understood. Here, we describe the principal genomic features of the type strain of
T. prosperus
, DSM 5130. This is the first public genome sequence of an acidophilic halotolerant bacterium.
Metagenomics of Ancient Fermentation Pits Used for the Production of Chinese Strong-Aroma Liquor
Authors: Guo Ming-Yi , Huo Dan-Qun , Ghai Rohit , Rodriguez-Valera Francisco , Shen Cai-Hong , Zhang Niang , Zhang Su-Yi , Hou Chang-Jun 
Published: October 2014

ABSTRACT
The complex microbiota of pit mud of solid-state fermentation reactors used for the production of Chinese liquor is responsible for producing one of the oldest distillates in the world. We apply a deep-sequencing approach to characterize the microbiota from pits that have been in use for up to 440 years.
Complete Genome Sequence of Type Strain Pasteurella multocida subsp.
multocida
ATCC 43137
Authors: Davenport K. W. , Daligault H. E. , Minogue T. D. , Bishop-Lilly K. A. , Bruce D. C. , Chain P. S. , Coyne S. R. , Frey K. G. , Jaissle J. , Koroleva G. I. , Ladner J. T. , Lo C. C. , Palacios G. F. , Redden C. L. , Scholz M. B. , Teshima H. , Johnson S. L. 
Published: October 2014

ABSTRACT

Soft-tissue infection by
Pasteurella multocida
in humans is usually associated with a dog- or cat-related injury, and these infections can become aggressive. We sequenced the type strain
P. multocida
subsp.
multocida
ATCC 43137 into a single closed chromosome consisting of 2,271,840 bp (40.4% G+C content), which is currently available in the NCBI GenBank under the accession number CP008918.
Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01
Authors: Minogue T. D. , Daligault H. E. , Davenport K. W. , Bishop-Lilly K. A. , Bruce D. C. , Chain P. S. , Coyne S. R. , Chertkov O. , Freitas T. , Frey K. G. , Jaissle J. , Koroleva G. I. , Ladner J. T. , Palacios G. F. , Redden C. L. , Xu Y. , Johnson S. L. 
Published: October 2014

ABSTRACT

The
Enterobacteriaceae
are environmental and enteric microbes. We sequenced the genomes of two
Enterobacter
reference strains,
E. aerogenes
CDC 6003-71 and
E. cloacae
CDC 442-68, as well as one near neighbor used as an exclusionary reference for diagnostics,
Pantoea agglomerans
CDC UA0804-01. The genome sizes range from 4.72 to 5.55 Mbp and have G+C contents from 54.6 to 55.1%.
Full-Genome Sequence of a Hepatitis B Virus Genotype F1b Clone from a Chronically Infected Chilean Patient
Authors: Hernández Sergio , Venegas Mauricio , Brahm Javier , Villanueva Rodrigo A. 
Published: October 2014

ABSTRACT

The hepatitis B virus (HBV) is a DNA virus belonging to the
Hepadnaviridae
family. Viral isolates have been classified into 10 genotypes, named from A to J, and several subtypes. We report the full-genome sequence from a single molecular clone of HBV genotype F1b, amplified from a chronically infected Chilean patient.
Genome Sequences of Five Oenococcus oeni Strains Isolated from Nero Di Troia Wine from the Same Terroir in Apulia, Southern Italy
Authors: Capozzi Vittorio , Russo Pasquale , Lamontanara Antonella , Orrù Luigi , Cattivelli Luigi , Spano Giuseppe 
Published: October 2014

ABSTRACT

Oenococcus oeni
is the principal lactic acid bacterium responsible for malolactic fermentation in wine. Here, we announce the genome sequences of five
O. oeni
strains isolated from Nero di Troia wine undergoing spontaneous malolactic fermentation, and we report, for the first time, several genome sequences of strains isolated from the same terroir.
Draft Genome Sequences of Two Ulvan-Degrading Isolates, Strains LTR and LOR, That Belong to the
Alteromonas
Genus
Authors: Kopel Moran , Helbert William , Henrissat Bernard , Doniger Tirza , Banin Ehud 
Published: October 2014

ABSTRACT

Here, we report the draft genome sequence of two ulvan-degrading
Alteromonas
spp. isolated from the feces of the sea slug,
Aplysia
. These sequenced genomes display a unique ulvan degradation machinery compared with ulvanolytic enzymes previously identified in
Nonlabens ulvanivorans
.
Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672
Authors: Frey K. G. , Bishop-Lilly K. A. , Daligault H. E. , Davenport K. W. , Bruce D. C. , Chain P. S. , Coyne S. R. , Chertkov O. , Freitas T. , Jaissle J. , Koroleva G. I. , Ladner J. T. , Minogue T. D. , Palacios G. F. , Redden C. L. , Xu Y. , Johnson S. L. 
Published: October 2014

ABSTRACT

A member of the normal human gut microflora,
Providencia stuartii
is of clinical interest due to its role in nosocomial infections of the urinary tract and because it readily acquires antibiotic resistance. Here, we present the complete genome of
P. stuartii
strain ATCC 33672, consisting of a 4.28-Mbp chromosome and a 48.9-kbp plasmid.
Metagenomic Assessment of the Eastern Oyster-Associated Microbiota
Authors: Chauhan Ashvini , Wafula Denis , Lewis Dawn E. , Pathak Ashish 
Published: October 2014

ABSTRACT

Bacteria associated with the Eastern oysters (
Crassostrea virginica
) native to Apalachicola Bay, FL, were investigated using 16S rRNA gene amplicon metagenomic sequencing which revealed that the oyster microbiome was predominated by
Cyanobacteria
and
Proteobacteria
. We also found that the oyster tissues were predominated by the pathogenic and symbiotic
Photobacterium
spp. (formerly known as
Vibrio damsela
e).
Draft Genome Sequences of Three
Smithella
spp. Obtained from a Methanogenic Alkane-Degrading Culture and Oil Field Produced Water
Authors: Tan BoonFei , de Araújo e Silva Renata , Rozycki Trent , Nesbø Camilla , Foght Julia 
Published: October 2014

ABSTRACT

Two draft genomes affiliated with
Smithella
spp. were obtained from a methanogenic alkane-degrading enrichment culture by single-cell sorting and metagenome contig binning, and a third was obtained by single-cell sorting of oil field produced water. Two genomes contained putative
assABC
genes encoding alkylsuccinate synthase, indicating genetic potential for fumarate activation of alkanes.
Electronic health records improve clinical note quality
Authors: Burke Harry B , Sessums Laura L , Hoang Albert , Becher Dorothy A , Fontelo Paul , Liu Fang , Stephens Mark , Pangaro Louis N , O'Malley Patrick G , Baxi Nancy S , Bunt Christopher W , Capaldi Vincent F , Chen Julie M , Cooper Barbara A , Djuric David A , Hodge Joshua A , Kane Shawn , Magee Charles , Makary Zizette R , Mallory Renee M , Miller Thomas , Saperstein Adam , Servey Jessica , Gimbel Ronald W 
Published: October 2014

AbstractBackground and objective The clinical note documents the clinician's information collection, problem assessment, clinical management, and its used for administrative purposes. Electronic health records (EHRs) are being implemented in clinical practices throughout the USA yet it is not known whether they improve the quality of clinical notes. The goal in this study was to determine if EHRs improve the quality of outpatient clinical notes.Materials and methods A five and a half year longitudinal retrospective multicenter quantitative study comparing the quality of handwritten and electronic outpatient clinical visit notes for 100 patients with type 2 diabetes at three time points: 6 months prior to the introduction of the EHR (before-EHR), 6 months after the introduction of the EHR (after-EHR), and 5 years after the introduction of the EHR (5-year-EHR). QNOTE, a validated quantitative instrument, was used to assess the quality of outpatient clinical notes. Its scores can range from a low of 0 to a high of 100. Sixteen primary care physicians with active practices used QNOTE to determine the quality of the 300 patient notes.Results The before-EHR, after-EHR, and 5-year-EHR grand mean scores (SD) were 52.0 (18.4), 61.2 (16.3), and 80.4 (8.9), respectively, and the change in scores for before-EHR to after-EHR and before-EHR to 5-year-EHR were 18% (p&lt;0.0001) and 55% (p&lt;0.0001), respectively. All the element and grand mean quality scores significantly improved over the 5-year time interval.Conclusions The EHR significantly improved the overall quality of the outpatient clinical note and the quality of all its elements, including the core and non-core elements. To our knowledge, this is the first study to demonstrate that the EHR significantly improves the quality of clinical notes.
Implications of an emerging EHR monoculture for hospitals and healthcare systems
Authors: Koppel Ross , Lehmann Christoph U 
Published: October 2014

Abstract
In many hospitals and health systems, a ‘new’ electronic health record means a shift to one vendor: Epic, a vendor that dominates in large and medium hospital markets and continues its success with smaller institutions and ambulatory practices. Our paper examines the implications of this emerging monoculture: its advantages and disadvantages for physicians and hospitals and its role in innovation, professional autonomy, implementation difficulties, workflow, flexibility, cost, data standards, interoperability, and interactions with other information technology (IT) systems.
Association between the ACE insertion/deletion polymorphism and pterygium in Sardinian patients: a population based case–control study
Authors: Demurtas Paolo , Orrù Germano , Coni Pierpaolo , Minerba Luigi , Corrias Michela , Sirigu Paola , Zucca Ignazio , Demurtas Elena , Maxia Cristina , Piras Franca , Murtas Daniela , Lai Simone , Perra Maria Teresa 
Published: October 2014

ObjectiveThe purpose of the study was to examine whether the insertion (I) and/or deletion (D) polymorphism of ACE confers susceptibility to primary pterygium in Sardinian patients in a case–control study.Methods and resultsPolymorphism genotyping was performed by nested PCR using genomic DNA extracted from the whole peripheral blood of participants with (n=251) and without (n=260) pterygium. DD, ID and II genotype frequencies were: 48%, 39% and 13%, respectively, for patients with pterygium, and 15%, 40% and 44%, respectively, for the control group. A statistically significant difference was found between the pterygium and control groups for theACEI/D polymorphism (p<0.001). Moreover, a statistically significant difference was found between the DD and II groups (p<0.01; OR=10.49; 95% CI 6.18 to 17.79), DD+ID versus II group (p<0.01; OR=5.23; 95% CI 3.37 to 8.13) and DD versus ID groups (p<0.01; OR=3.21; 95% CI 2.04 to 5.04).ConclusionsStatistical analysis showed that the DD genotype is associated with an increased risk of developing pterygium, and with a good chance that the D allele may play an important role in the development of disease.
The effect of enhanced public–private partnerships on Maternal, Newborn and child Health Services and outcomes in Nairobi–Kenya: the PAMANECH quasi-experimental research protocol
Authors: Bakibinga Pauline , Ettarh Remare , Ziraba Abdhalah K , Kyobutungi Catherine , Kamande Eva , Ngomi Nicholas , Osindo Jane 
Published: October 2014

IntroductionRapid urbanisation in Kenya has resulted in growth of slums in urban centres, characterised by poverty, inadequate social services and poor health outcomes. The government's initiatives to improve access to quality healthcare for mothers and children are largely limited to public health facilities, which are few and/or inaccessible in underserved areas such as the slums. The ‘Partnership for Maternal, Newborn and Child Health’ (PAMANECH) project is being implemented in two Nairobi slums, Viwandani and Korogocho, to assess the impact of strengthening public–private partnerships for the delivery of healthcare on the health of mothers, newborns and young children in two informal settlements in Kenya.Methods and analysisThis is a quasi-experimental study; our approach is to support private as well as public health providers and the community to enhance access to and demand for quality healthcare services. Key activities include: infrastructural upgrade of selected Private Not-For-Profit health facilities operating in the two slums, building capacity for healthcare providers as well as the Health Management Teams in Nairobi, facilitating provision of supportive supervision by the local health authorities and forming networks of Community Health Volunteers (CHVs) to create demand for health services. To assess the impact of the intervention, the study is utilising multiple data sources using a combination of qualitative and quantitative methods. A baseline survey was conducted in 2013 and an end-line survey will be conducted at least 1 year after full implementation of the intervention. Systematic monitoring and documentation of the intervention is on-going to strengthen the case for causal inference.Ethics and disseminationEthical approval for the study was obtained from the Kenya Medical Research Institute. Key messages from the results will be packaged and widely disseminated through workshops, conference presentations, reports, factsheets and academic publications to facilitate uptake by policymakers.Protocol registration numberKEMRI- NON-SSC-PROTOCOL No. 393.
Functional MRI-guided microsurgery of intracranial arteriovenous malformations: study protocol for a randomised controlled trial
Authors: Zhao Bing , Cao Yong , Zhao Yuanli , Wu Jun , Wang Shuo 
Published: October 2014

IntroductionIntracranial arteriovenous malformations (AVMs) are associated with high morbidity and mortality. Modern microsurgery has improved the results of surgical treatment of AVMs; however, the treatment of AVMs, particularly eloquently located AVMs, still carries a high risk. Functional MRI (fMRI) has been reported to be used for the preoperative evaluation of AVMs in small case series. The purpose is to identify the utility and efficacy of fMRI-guided microsurgery of AVMs in a large randomised controlled trial.Methods and analysisThe study is a prospective, randomised controlled clinical trial. This study will enrol a total of 600 eligible patients. These eligible patients will be randomised to the standard microsurgery group and the fMRI-guided microsurgery group in a 1:1 ratio. Patient baseline characteristics and AVM architecture and characteristics will be described. In the fMRI-guided group, fMRI mapping of an eloquent cortex in all AVMs will be identified. Surgical complications and outcomes at pretreatment, post-treatment, at discharge and at 1-month, 3-month and 6-month follow-up intervals will be analysed using the modified Rankin Scale (mRS). This trial will determine whether fMRI-guided microsurgery could improve outcomes in patients with AVMs and also identify the safety and efficacy of fMRI-guided microsurgery.Ethics and disseminationThe study protocol and written informed consent were reviewed and approved by the Institutional Review Board of Beijing Tiantan Hospital Affiliated to Capital Medical University (ky2012-016-02). Study findings will be disseminated in the printed media.Trial registration numberClinicalTrials.govNCT01758211.
Cardiovascular Disease Population Risk Tool (CVDPoRT): predictive algorithm for assessing CVD risk in the community setting. A study protocol
Authors: Taljaard Monica , Tuna Meltem , Bennett Carol , Perez Richard , Rosella Laura , Tu Jack V , Sanmartin Claudia , Hennessy Deirdre , Tanuseputro Peter , Lebenbaum Michael , Manuel Douglas G 
Published: October 2014

IntroductionRecent publications have called for substantial improvements in the design, conduct, analysis and reporting of prediction models. Publication of study protocols, with prespecification of key aspects of the analysis plan, can help to improve transparency, increase quality and protect against increased type I error. Valid population-based risk algorithms are essential for population health planning and policy decision-making. The purpose of this study is to develop, evaluate and apply cardiovascular disease (CVD) risk algorithms for the population setting.Methods and analysisThe Ontario sample of the Canadian Community Health Survey (2001, 2003, 2005; 77 251 respondents) will be used to assess risk factors focusing on health behaviours (physical activity, diet, smoking and alcohol use). Incident CVD outcomes will be assessed through linkage to administrative healthcare databases (619 886 person-years of follow-up until 31 December 2011). Sociodemographic factors (age, sex, immigrant status, education) and mediating factors such as presence of diabetes and hypertension will be included as predictors. Algorithms will be developed using competing risks survival analysis. The analysis plan adheres to published recommendations for the development of valid prediction models to limit the risk of overfitting and improve the quality of predictions. Key considerations are fully prespecifying the predictor variables; appropriate handling of missing data; use of flexible functions for continuous predictors; and avoiding data-driven variable selection procedures. The 2007 and 2009 surveys (approximately 50 000 respondents) will be used for validation. Calibration will be assessed overall and in predefined subgroups of importance to clinicians and policymakers.Ethics and disseminationThis study has been approved by the Ottawa Health Science Network Research Ethics Board. The findings will be disseminated through professional and scientific conferences, and in peer-reviewed journals. The algorithm will be accessible electronically for population and individual uses.Trial registration numberClinicalTrials.govNCT02267447.