bluuebunny/crossref_metadata_2025_split huggingface dataset:
A stochastic model for tumor geometry evolution during radiation therapy in cervical cancer
Authors: Liu Yifang , Chan Timothy C. Y. , Lee Chi‐Guhn , Cho Young‐Bin , Islam Mohammad K. 
Published: February 2014

Purpose:To develop mathematical models to predict the evolution of tumor geometry in cervical cancer undergoing radiation therapy.Methods:The authors develop two mathematical models to estimate tumor geometry change: a Markov model and an isomorphic shrinkage model. The Markov model describes tumor evolution by investigating the change in state (either tumor or nontumor) of voxels on the tumor surface. It assumes that the evolution follows a Markov process. Transition probabilities are obtained using maximum likelihood estimation and depend on the states of neighboring voxels. The isomorphic shrinkage model describes tumor shrinkage or growth in terms of layers of voxels on the tumor surface, instead of modeling individual voxels. The two proposed models were applied to data from 29 cervical cancer patients treated at Princess Margaret Cancer Centre and then compared to a constant volume approach. Model performance was measured using sensitivity and specificity.Results:The Markov model outperformed both the isomorphic shrinkage and constant volume models in terms of the trade‐off between sensitivity (target coverage) and specificity (normal tissue sparing). Generally, the Markov model achieved a few percentage points in improvement in either sensitivity or specificity compared to the other models. The isomorphic shrinkage model was comparable to the Markov approach under certain parameter settings. Convex tumor shapes were easier to predict.Conclusions:By modeling tumor geometry change at the voxel level using a probabilistic model, improvements in target coverage and normal tissue sparing are possible. Our Markov model is flexible and has tunable parameters to adjust model performance to meet a range of criteria. Such a model may support the development of an adaptive paradigm for radiation therapy of cervical cancer.
Computer‐aided detection of clustered microcalcifications in multiscale bilateral filtering regularized reconstructed digital breast tomosynthesis volume
Authors: Samala Ravi K. , Chan Heang‐Ping , Lu Yao , Hadjiiski Lubomir , Wei Jun , Sahiner Berkman , Helvie Mark A. 
Published: February 2014

Purpose:Develop a computer‐aided detection (CADe) system for clustered microcalcifications in digital breast tomosynthesis (DBT) volume enhanced with multiscale bilateral filtering (MSBF) regularization.Methods:With Institutional Review Board approval and written informed consent, two‐view DBT of 154 breasts, of which 116 had biopsy‐proven microcalcification (MC) clusters and 38 were free of MCs, was imaged with a General Electric GEN2 prototype DBT system. The DBT volumes were reconstructed with MSBF‐regularized simultaneous algebraic reconstruction technique (SART) that was designed to enhance MCs and reduce background noise while preserving the quality of other tissue structures. The contrast‐to‐noise ratio (CNR) of MCs was further improved with enhancement‐modulated calcification response (EMCR) preprocessing, which combined multiscale Hessian response to enhance MCs by shape and bandpass filtering to remove the low‐frequency structured background. MC candidates were then located in the EMCR volume using iterative thresholding and segmented by adaptive region growing. Two sets of potential MC objects, cluster centroid objects and MC seed objects, were generated and the CNR of each object was calculated. The number of candidates in each set was controlled based on the breast volume. Dynamic clustering around the centroid objects grouped the MC candidates to form clusters. Adaptive criteria were designed to reduce false positive (FP) clusters based on the size, CNR values and the number of MCs in the cluster, cluster shape, and cluster based maximum intensity projection. Free‐response receiver operating characteristic (FROC) and jackknife alternative FROC (JAFROC) analyses were used to assess the performance and compare with that of a previous study.Results:Unpaired two‐tailedt‐test showed a significant increase (p < 0.0001) in the ratio of CNRs for MCs with and without MSBF regularization compared to similar ratios for FPs. For view‐based detection, a sensitivity of 85% was achieved at an FP rate of 2.16 per DBT volume. For case‐based detection, a sensitivity of 85% was achieved at an FP rate of 0.85 per DBT volume. JAFROC analysis showed a significant improvement in the performance of the current CADe system compared to that of our previous system (p = 0.003).Conclusions:MBSF regularized SART reconstruction enhances MCs. The enhancement in the signals, in combination with properly designed adaptive threshold criteria, effective MC feature analysis, and false positive reduction techniques, leads to a significant improvement in the detection of clustered MCs in DBT.
A new correction method serving to eliminate the parabola effect of flatbed scanners used in radiochromic film dosimetry
Authors: Poppinga D. , Schoenfeld A. A. , Doerner K. J. , Blanck O. , Harder D. , Poppe B. 
Published: February 2014

Purpose:The purpose of this study is the correction of the lateral scanner artifact, i.e., the effect that, on a large homogeneously exposed EBT3 film, a flatbed scanner measures different optical densities at different positions along thex axis, the axis parallel to the elongated light source. At constant dose, the measured optical densitiy profiles along this axis have a parabolic shape with significant dose dependent curvature. Therefore, the effect is shortly called the parabola effect. The objective of the algorithm developed in this study is to correct for the parabola effect. Any optical density measured at given position x is transformed into the equivalent optical density c at the apex of the parabola and then converted into the corresponding dose via the calibration of c versus dose.Methods:For the present study EBT3 films and an Epson 10000XL scanner including transparency unit were used for the analysis of the parabola effect. The films were irradiated with 6 MV photons from an Elekta Synergy accelerator in a RW3 slab phantom. In order to quantify the effect, ten film pieces with doses graded from 0 to 20.9 Gy were sequentially scanned at eight positions along thex axis and at six positions along the z axis (the movement direction of the light source) both for the portrait and landscape film orientations. In order to test the effectiveness of the new correction algorithm, the dose profiles of an open square field and an IMRT plan were measured by EBT3 films and compared with ionization chamber and ionization chamber array measurement.Results:The parabola effect has been numerically studied over the whole measuring field of the Epson 10000XL scanner for doses up to 20.9 Gy and for both film orientations. The presented algorithm transforms any optical density at positionx into the equivalent optical density that would be measured at the same dose at the apex of the parabola. This correction method has been validated up to doses of 5.2 Gy all over the scanner bed with 2D dose distributions of an open square photon field and an IMRT distribution.Conclusions:The algorithm presented in this study quantifies and corrects the parabola effect of EBT3 films scanned in commonly used commercial flatbed scanners at doses up to 5.2 Gy. It is easy to implement, and no additional work steps are necessary in daily routine film dosimetry.
Complete Genome Sequence of Porcine Encephalomyocarditis Virus from an Aardvark in China
Authors: Chang Hongtao , Chen Lu , Zhao Jun , Wang Xinwei , Yang Xia , Yao Huixia , Wang Chuanqing 
Published: February 2014

ABSTRACT
A strain of encephalomyocarditis virus, HNXX13, was isolated from an aardvark in central China. The complete genome was sequenced and analyzed, and phylogenetic analysis suggests that HNXX13 belongs to encephalomyocarditis virus group 1.
Draft Genome Sequence of Bacillus subtilis Type Strain B7-S, Which Converts Ferulic Acid to Vanillin
Authors: Chen Peng , Li Suyue , Yan Lei , Wang Ningbo , Yan Xiaojuan , Li Hongyu 
Published: February 2014

ABSTRACT

The
Bacillus subtilis
type strain B7-S was obtained through induction with ferulic acid. Here, we present the draft genome of strain B7-S, which contains 5,313,924 bp, with a G+C content of 35.8%, 5,135 protein-coding genes, and 40 tRNA-encoding genes.
The Complete Genome Sequence of Pseudomonas putida NBRC 14164
T
Confirms High Intraspecies Variation
Authors: Ohji Shoko , Yamazoe Atsushi , Hosoyama Akira , Tsuchikane Keiko , Ezaki Takayuki , Fujita Nobuyuki 
Published: February 2014

ABSTRACT

Pseudomonas putida
has attracted much interest for its environmental, industrial, biotechnological, and clinical importance. Here, we report the complete genome sequence of the type strain
P. putida
NBRC 14164. This genome sequence will assist to further elucidate the molecular mechanisms of the characteristic traits among strains belonging to the species
P. putida
.
Draft Genome Sequence of Root-Colonizing Bacterium
Bacillus
sp. Strain PTS-394
Authors: Qiao Junqing , Liu Youzhou , Liang Xuejie , Hu Yonghong , Du Yan 
Published: February 2014

ABSTRACT

Here, we report the high-quality draft genome sequence of
Bacillus
sp. strain PTS-394, isolated from the rhizosphere of tomatoes grown on Putuo Mountain (Xiamen, Fujian province, China), which exhibited excellent colonization ability on plant roots. The 4.0-Mb genome uncovered the mechanism for its potential root colonization ability and may provide novel insights into plant-bacterium interactions.
Draft Genome Sequence of an Anaerobic, Thermophilic Bacterium, Thermoanaerobacterium aotearoense SCUT27, Isolated from a Hot Spring in China
Authors: Ai Hongxia , Zhang Junjie , Yang Mingjun , Yu Pingru , Li Shuang , Zhu Mingjun , Dong Hui , Wang Shengyue , Wang Jufang 
Published: February 2014

ABSTRACT

Thermoanaerobacterium aotearoense
SCUT27, isolated from a hot spring in China, is a strictly anaerobic, thermophilic bacterium capable of degrading xylan and converting both pentose and hexose to ethanol with high yields. Here, we report the draft genome sequence of SCUT27, which reveals insights into the mechanisms of carbon source coutilization and xylan degradation in this thermophilic microorganism.
Metagenomic Sequence of Prokaryotic Microbiota from an Intermediate-Salinity Pond of a Saltern in Isla Cristina, Spain
Authors: Fernández Ana B. , León María José , Vera Blanca , Sánchez-Porro Cristina , Ventosa Antonio 
Published: February 2014

ABSTRACT
Marine salterns are artificial multipond systems designed for the commercial production of salt by evaporation of seawater. We report here the metagenomic sequence of the prokaryotic microbiota of a pond with intermediate salinity (21% total salts) of a saltern located in Isla Cristina, Huelva, southwest Spain.
Genome Sequence of the Oleaginous Yeast
Rhodotorula glutinis
ATCC 204091
Authors: Paul Debarati , Magbanua Zenaida , Arick Mark , French Todd , Bridges Susan M. , Burgess Shane C. , Lawrence Mark L. 
Published: February 2014

ABSTRACT

Rhodotorula glutinis
ATCC 204091 is an oleaginous oxidative red yeast that can accumulate lipids to >50% of its biomass when grown with appropriate carbon and nitrogen ratios. It produces a red pigment consisting of useful antioxidants, such as carotenoids, torulene, and torularhodin, when cultivated under carbon-deficient conditions.
Genome Sequence of the Basidiomycetous Fungus
Pseudozyma aphidis
DSM70725, an Efficient Producer of Biosurfactant Mannosylerythritol Lipids
Authors: Lorenz Stefan , Guenther Michael , Grumaz Christian , Rupp Steffen , Zibek Susanne , Sohn Kai 
Published: February 2014

ABSTRACT

Pseudozyma aphidis
is an efficient producer of mannosylerythritol lipids exceeding concentrations of >100 g/liter from renewable feed stocks. Additionally, a biosurfactant cellobiose lipid is also secreted during nitrogen limitation. Here, we describe the sequencing of
P. aphidis
to unravel the genomic basis of biosurfactant metabolism in
P. aphidis
.
Whole-Genome Sequence of Sungri/96 Vaccine Strain of Peste des Petits Ruminants Virus
Authors: Siddappa Manjunath , Gandham Ravi Kumar , Sarsani Vishal , Mishra Bishnu Prasad , Mishra Bina , Joshi C. G. , Sahoo A. P. , Tiwari A. K. , Janga Sarath Chandra 
Published: February 2014

ABSTRACT
We report the complete genome sequence of the Sungri/96 vaccine strain of peste des petits ruminants virus (PPRV). The whole-genome nucleotide sequence has 89 to 99% identity with the available PPRV genome sequences in the NCBI database. This study helps to understand the epidemiological and molecular characteristics of the Sungri/96 strain.
Draft Genome Sequence of Tomitella biformata AHU 1821
T
, Isolated from a Permafrost Ice Wedge in Alaska
Authors: Funo Kentaro , Kitagawa Wataru , Tanaka Michiko , Sone Teruo , Asano Kozo , Kamagata Yoichi 
Published: February 2014

ABSTRACT

Tomitella biformata
AHU 1821
T
was isolated and cultured from a permafrost ice wedge, aged presumably about 25,000 years, in the Fox permafrost tunnel (64.952°N 147.617°W), Alaska. These genome data provide the basis for investigating
T. biformata
AHU 1821
T
, identified as a long-term survivor of the extremely cold and closed environment.
Genome Sequences of Streptococcus thermophilus Strains MTH17CL396 and M17PTZA496 from Fontina, an Italian PDO Cheese
Authors: Treu Laura , Vendramin Veronica , Bovo Barbara , Campanaro Stefano , Corich Viviana , Giacomini Alessio 
Published: February 2014

ABSTRACT

Here is presented the whole-genome sequences of
Streptococcus thermophilus
strains MTH17CL396 and M17PTZA496, isolated from fontina protected designation of origin (PDO) cheese in the Valle d'Aosta Region (Italy).
S. thermophilus
is a lactic acid bacterium widely present in dairy products, and these are the first publicly available genome sequences of
S. thermophilus
strains isolated from cheese.
Draft Genome Sequence of Serratia marcescens Strain LCT-SM166, a Space Flight Strain with a Specific Carbon Source Utilization Pattern
Authors: Wang Yajuan , Du Yu , Yuan Yanting , Guo Yinghua , Wang Junfeng , Li Tianzhi , Chang De , Liu Yan , Jiang Xuege , Dai Wenkui , Liu Changting 
Published: February 2014

ABSTRACT

Serratia marcescens
has been detected in space habitats. To explore the influence of the space flight environment on this bacterium, we investigated the genome sequence of LCT-SM166, which was isolated after space flight and has a specific carbon source utilization pattern.
Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512
T
, Isolated from the Gut of a Termite
Authors: Yuki Masahiro , Oshima Kenshiro , Suda Wataru , Sakamoto Mitsuo , Iida Toshiya , Hattori Masahira , Ohkuma Moriya 
Published: February 2014

ABSTRACT

Here we report the draft genome sequence of
Bacteroides reticulotermitis
strain JCM 10512
T
, a xylanolytic and cellulolytic bacterium isolated from the gut of a wood-feeding termite. The genome information will facilitate the study of this strain for biomass degradation and adaptation to the gut environment.
Draft Genome Sequence of the Sulfonamide Antibiotic-Degrading
Microbacterium
sp. Strain C448
Authors: Martin-Laurent Fabrice , Marti Romain , Waglechner Nicholas , Wright Gerard D. , Topp Edward 
Published: February 2014

ABSTRACT

We report the draft genome sequence of
Microbacterium
sp. strain C448, isolated from agricultural soil with a decade of exposure to veterinary antibiotics on the basis of using sulfamethazine and other antibiotics as the sole sources of carbon. The genome sequence revealed that strain C448 harbors several antibiotic resistance genes, including
sulI
.
Comparing dietary patterns of depressed patients versus healthy people in a case control protocol
Authors: Khosravi Maryam , Sotoudeh Gity , Raisi Firoozeh , Majdzadeh Reza , Foroughifar Tahereh 
Published: February 2014

IntroductionMajor depressive disorder is the leading cause of disability around the world. Because of the high rate of medication discontinuation by patients and the risk of recurrence, factors such as nutrition could be useful for the prevention or treatment of depression. The relationship between depression and dietary patterns has been reported in a few studies but with controversial results. Therefore, we have decided to study the possible effects of cultural, social, racial, geographic and environmental conditions on this relationship in an Iranian population.Methods and analysisIn our case control protocol, 110 cases and 220 controls will be individually matched based on age, sex and area of residence. New cases of depression, based on the criteria of the Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV), will be recruited from two psychiatric clinics in Tehran. Interviewers will then go to each patient's home and invite qualified individuals to participate in the study as controls. Food intakes of all participants will be obtained by semiquantitative food frequency questionnaires covering the past year; these will be transformed into actual food intake (g/day). Dietary patterns will be determined by the principal components method. Conditional logistic regression, as a multivariate analysis, will be used for assessing the relationship between dietary patterns and depression, taking into consideration the potential role of different variables. The results may help to identify differences in dietary patterns between depressed and healthy people.Ethics and disseminationThe study protocol has been approved by ethics committee of Tehran University of Medical Sciences. At the beginning of the study, a written informed consent form will be signed and dated by subjects and investigators. The results will be published in due time.
Social media interventions for diet and exercise behaviours: a systematic review and meta-analysis of randomised controlled trials
Authors: Williams Gillian , Hamm Michele P , Shulhan Jocelyn , Vandermeer Ben , Hartling Lisa 
Published: February 2014

ObjectivesTo conduct a systematic review of randomised controlled trials (RCTs) examining the use of social media to promote healthy diet and exercise in the general population.Data sourcesMEDLINE, CENTRAL, ERIC, PubMed, CINAHL, Academic Search Complete, Alt Health Watch, Health Source, Communication and Mass Media Complete, Web of Knowledge and ProQuest Dissertation and Thesis (2000–2013).Study eligibility criteriaRCTs of social media interventions promoting healthy diet and exercise behaviours in the general population were eligible. Interventions using social media, alone or as part of a complex intervention, were included.Study appraisal and synthesisStudy quality was assessed using the Cochrane Risk of Bias Tool. We describe the studies according to the target populations, objectives and nature of interventions, outcomes examined, and results and conclusions. We extracted data on the primary and secondary outcomes examined in each study. Where the same outcome was assessed in at least three studies, we combined data in a meta-analysis.Results22 studies were included. Participants were typically middle-aged Caucasian women of mid-to-high socioeconomic status. There were a variety of interventions, comparison groups and outcomes. All studies showed a decrease in programme usage throughout the intervention period. Overall, no significant differences were found for primary outcomes which varied across studies. Meta-analysis showed no significant differences in changes in physical activity (standardised mean difference (SMD) 0.13 (95% CI −0.04 to 0.30), 12 studies) and weight (SMD −0.00 (95% CI −0.19 to 0.19), 10 studies); however, pooled results from five studies showed a significant decrease in dietary fat consumption with social media (SMD −0.35 (95% CI −0.68 to −0.02)).ConclusionsSocial media may provide certain advantages for public health interventions; however, studies of social media interventions to date relating to healthy lifestyles tend to show low levels of participation and do not show significant differences between groups in key outcomes.
A non-experimental study of oral anticoagulation therapy initiation before and after national patient safety goals
Authors: Beadles Christopher A , Hassmiller Lich Kristen , Viera Anthony J , Greene Sandra B , Brookhart M Alan , Weinberger Morris 
Published: February 2014

ObjectivesThe Joint Commission revised its National Patient Safety Goals (NPSGs) to include oral anticoagulation therapy (OAT) in 2008. We sought to examine the effect of including OAT in The Joint Commission's NPSGs on historically low rates of OAT initiation for individuals with incident atrial fibrillation (AF).SettingSoutheastern state in the USA.ParticipantsNorth Carolina State Health Plan claims data from 944 500 individuals enrolled between 1 January 2006 and 31 December 2010, supplemented with data from the Area Resource File and Online Survey, Certification and Reporting data network. We evaluated OAT initiation before and after the 2008 NPSGs revisions in a retrospective cohort new user design with an AF intervention group and two control groups: a positive control—patients estimated to be at very high risk of thromboembolism (mechanical heart valve and pulmonary embolism); and a negative control—patients with very low perceived risk of thromboembolism (paroxysmal AF). We developed multivariable models using a difference-in-difference parameterisation. Effects were estimated with generalised estimating equations.Primary outcome measureOAT initiation, a binary outcome defined as having a prescription drug claim for warfarin within 30 days of the index claim.ResultsOAT initiation was low (26.8%) for eligible individuals with incident AF in 2006–2008 but increased after NPSGs implementation (31.7%, p=0.022). OAT initiation was high but decreased in the positive control group (67.5% vs 62.0%, p=0.003). Multivariate analysis resulted in a relative 11% (95% CI (4% to 18%), p<0.01) increase in OAT initiation for incident AF patients.ConclusionsWe document a substantial increase in guideline concordant OAT initiation in incident AF after the establishment of NPSGs, suggesting that regulatory healthcare agency initiatives can influence clinical practice.
Healthcare-seeking behaviour in rural Ethiopia: evidence from clinical vignettes
Authors: Mebratie Anagaw D , Van de Poel Ellen , Yilma Zelalem , Abebaw Degnet , Alemu Getnet , Bedi Arjun S 
Published: February 2014

ObjectivesTo investigate the determinants of healthcare-seeking behaviour using five context-relevant clinical vignettes. The analysis deals with three issues: whether and where to seek modern care and when to seek care.SettingThis study is set in 96 villages located in four main regions of Ethiopia. The participants of this study are 1632 rural households comprising 9455 individuals.Primary and secondary outcome measuresProbability of seeking modern care for symptoms related to acute respiratory infections/pneumonia, diarrhoea, malaria, tetanus and tuberculosis. Conditional on choosing modern healthcare, where to seek care (health post, health centre, clinic and hospital). Conditional on choosing modern healthcare, when to seek care (seek care immediately, the next day, after 2 days, between 3 days to 1 week, a week or more).ResultsWe find almost universal preference for modern care. Foregone care ranges from 0.6% for diarrhoea to 2.5% for tetanus. There is a systematic relationship between socioeconomic status and choice of providers mainly for adult-related conditions with households in higher consumption quintiles more likely to seek care in health centres, private/Non-Government Organization (NGO) clinics as opposed to health posts. Delays in care-seeking behaviour are apparent mainly for adult-related conditions and among poorer households.ConclusionsThe analysis suggests that the lack of healthcare utilisation is not driven by the inability to recognise health problems or due to a low perceived need for modern care.