bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting objective function weights from patient anatomy in prostate IMRT treatment planning
Authors: Lee Taewoo , Hammad Muhannad , Chan Timothy C. Y. , Craig Tim , Sharpe Michael B. 
Published: November 2013

Purpose:Intensity‐modulated radiation therapy (IMRT) treatment planning typically combines multiple criteria into a single objective function by taking a weighted sum. The authors propose a statistical model that predicts objective function weights from patient anatomy for prostate IMRT treatment planning. This study provides a proof of concept for geometry‐driven weight determination.Methods:A previously developed inverse optimization method (IOM) was used to generate optimal objective function weights for 24 patients using their historical treatment plans (i.e., dose distributions). These IOM weights were around 1% for each of the femoral heads, while bladder and rectum weights varied greatly between patients. A regression model was developed to predict a patientˈs rectum weight using the ratio of the overlap volume of the rectum and bladder with the planning target volume at a 1 cm expansion as the independent variable. The femoral head weights were fixed to 1% each and the bladder weight was calculated as one minus the rectum and femoral head weights. The model was validated using leave‐one‐out cross validation. Objective values and dose distributions generated through inverse planning using the predicted weights were compared to those generated using the original IOM weights, as well as an average of the IOM weights across all patients.Results:The IOM weight vectors were on average six times closer to the predicted weight vectors than to the average weight vector, usingl2 distance. Likewise, the bladder and rectum objective values achieved by the predicted weights were more similar to the objective values achieved by the IOM weights. The difference in objective value performance between the predicted and average weights was statistically significant according to a one‐sided sign test. For all patients, the difference in rectum V54.3 Gy, rectum V70.0 Gy, bladder V54.3 Gy, and bladder V70.0 Gy values between the dose distributions generated by the predicted weights and IOM weights was less than 5 percentage points. Similarly, the difference in femoral head V54.3 Gy values between the two dose distributions was less than 5 percentage points for all but one patient.Conclusions:This study demonstrates a proof of concept that patient anatomy can be used to predict appropriate objective function weights for treatment planning. In the long term, such geometry‐driven weights may serve as a starting point for iterative treatment plan design or may provide information about the most clinically relevant region of the Pareto surface to explore.
Patient‐specific QA and delivery verification of scanned ion beam at NIRS‐HIMAC
Authors: Furukawa Takuji , Inaniwa Taku , Hara Yousuke , Mizushima Kota , Shirai Toshiyuki , Noda Koji 
Published: November 2013

Purpose:To evaluate a patient‐specific QA program and system for constancy checking of a scanning delivery system developed at the National Institute of Radiological Sciences.Methods:For the patient‐specific QA, all the planned beams are recalculated on a water phantom with treatment planning software (TPS). The recalculated dose distributions are compared with the measured distributions using a 2D ionization chamber array at several depths, and evaluated using gamma index analysis with criteria of 3% and 3 mm and a pass rate of 90%. For the constancy check, the authors developed the multiwire proportional chamber (MWPC), which can record the delivered 2D fluence images in a slice‐by‐slice manner. During irradiation for dosimetric QA with the 2D ionization chamber array and an accordion‐type water phantom, the 2D fluence images are recorded using the MWPC in the delivery system. These recorded images are then compared to those taken in the treatment session to check the constancy check. This analysis also employs gamma index analysis using the same criteria as in the patient‐specific QA. These patient‐specific QA and constancy check evaluations were performed using the data of 122 patients.Results:In the patient‐specific QA, the measured dose distributions agreed well with those calculated by the TPS, and the QA criteria were satisfied in all measurements. The additional check of the fluence comparison ensured the constancy of the delivered field during each treatment irradiation.Conclusions:The authors established a patient‐specific QA program and additional check of delivery constancy in every treatment session. Fluence comparison is a strong tool for constancy checking of the delivery system.
Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota
Authors: Tang Yue , Underwood Anthony , Gielbert Adriana , Woodward Martin J. , Petrovska Liljana 
Published: November 2013

ABSTRACT

The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified
Clostridiales
,
Bacteroidaceae
, and
Lactobacillaceae
species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to
Lactobacillus
spp., 155 belonged to
Clostridium
spp., and 66 belonged to
Streptococcus
spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.
Nanoscale Cell Wall Deformation Impacts Long-Range Bacterial Adhesion Forces on Surfaces
Authors: Chen Yun , Harapanahalli Akshay K. , Busscher Henk J. , Norde Willem , van der Mei Henny C. 
Published: November 2013

ABSTRACT

Adhesion of bacteria occurs on virtually all natural and synthetic surfaces and is crucial for their survival. Once they are adhering, bacteria start growing and form a biofilm, in which they are protected against environmental attacks. Bacterial adhesion to surfaces is mediated by a combination of different short- and long-range forces. Here we present a new atomic force microscopy (AFM)-based method to derive long-range bacterial adhesion forces from the dependence of bacterial adhesion forces on the loading force, as applied during the use of AFM. The long-range adhesion forces of wild-type
Staphylococcus aureus
parent strains (0.5 and 0.8 nN) amounted to only one-third of these forces measured for their more deformable isogenic Δ
pbp4
mutants that were deficient in peptidoglycan cross-linking. The measured long-range Lifshitz-Van der Waals adhesion forces matched those calculated from published Hamaker constants, provided that a 40% ellipsoidal deformation of the bacterial cell wall was assumed for the Δ
pbp4
mutants. Direct imaging of adhering staphylococci using the AFM peak force-quantitative nanomechanical property mapping imaging mode confirmed a height reduction due to deformation in the Δ
pbp4
mutants of 100 to 200 nm. Across naturally occurring bacterial strains, long-range forces do not vary to the extent observed here for the Δ
pbp4
mutants. Importantly, however, extrapolating from the results of this study, it can be concluded that long-range bacterial adhesion forces are determined not only by the composition and structure of the bacterial cell surface but also by a hitherto neglected, small deformation of the bacterial cell wall, facilitating an increase in contact area and, therewith, in adhesion force.
Polysulfides as Intermediates in the Oxidation of Sulfide to Sulfate by Beggiatoa spp
Authors: Berg Jasmine S. , Schwedt Anne , Kreutzmann Anne-Christin , Kuypers Marcel M. M. , Milucka Jana 
Published: November 2013

ABSTRACT

Zero-valent sulfur is a key intermediate in the microbial oxidation of sulfide to sulfate. Many sulfide-oxidizing bacteria produce and store large amounts of sulfur intra- or extracellularly. It is still not understood how the stored sulfur is metabolized, as the most stable form of S
0
under standard biological conditions, orthorhombic α-sulfur, is most likely inaccessible to bacterial enzymes. Here we analyzed the speciation of sulfur in single cells of living sulfide-oxidizing bacteria via Raman spectroscopy. Our results showed that under various ecological and physiological conditions, all three investigated
Beggiatoa
strains stored sulfur as a combination of cyclooctasulfur (S
8
) and inorganic polysulfides (S

n

2−
). Linear sulfur chains were detected during both the oxidation and reduction of stored sulfur, suggesting that S

n

2−
species represent a universal pool of bioavailable sulfur. Formation of polysulfides due to the cleavage of sulfur rings could occur biologically by thiol-containing enzymes or chemically by the strong nucleophile HS
−
as
Beggiatoa
migrates vertically between oxic and sulfidic zones in the environment. Most
Beggiatoa
spp. thus far studied can oxidize sulfur further to sulfate. Our results suggest that the ratio of produced sulfur and sulfate varies depending on the sulfide flux. Almost all of the sulfide was oxidized directly to sulfate under low-sulfide-flux conditions, whereas only 50% was oxidized to sulfate under high-sulfide-flux conditions leading to S
0
deposition. With Raman spectroscopy we could show that sulfate accumulated in
Beggiatoa
filaments, reaching intracellular concentrations of 0.72 to 1.73 M.
Genes Similar to the Vibrio parahaemolyticus Virulence-Related Genes
tdh
,
tlh
, and
vscC2
Occur in Other Vibrionaceae Species Isolated from a Pristine Estuary
Authors: Klein Savannah L. , Gutierrez West Casandra K. , Mejia Diana M. , Lovell Charles R. 
Published: November 2013

ABSTRACT

Detection of the human pathogen
Vibrio parahaemolyticus
often relies on molecular biological analysis of species-specific virulence factor genes. These genes have been employed in determinations of
V. parahaemolyticus
population numbers and the prevalence of pathogenic
V. parahaemolyticus
strains. Strains of the
Vibrionaceae
species
Photobacterium damselae
,
Vibrio diabolicus
,
Vibrio harveyi
, and
Vibrio natriegens
, as well as strains similar to
Vibrio tubiashii
, were isolated from a pristine salt marsh estuary. These strains were examined for the
V. parahaemolyticus
hemolysin genes
tdh
,
trh
, and
tlh
and for the
V. parahaemolyticus
type III secretion system 2α gene
vscC2
using established PCR primers and protocols. Virulence-related genes occurred at high frequencies in non-
V. parahaemolyticus Vibrionaceae
species.
V. diabolicus
was of particular interest, as several strains were recovered, and the large majority (>83%) contained virulence-related genes. It is clear that detection of these genes does not ensure correct identification of virulent
V. parahaemolyticus
. Further, the occurrence of
V. parahaemolyticus
-like virulence factors in other vibrios potentially complicates tracking of outbreaks of
V. parahaemolyticus
infections.
In Silico
Rational Design and Systems Engineering of Disulfide Bridges in the Catalytic Domain of an Alkaline α-Amylase from Alkalimonas amylolytica To Improve Thermostability
Authors: Liu Long , Deng Zhuangmei , Yang Haiquan , Li Jianghua , Shin Hyun-dong , Chen Rachel R. , Du Guocheng , Chen Jian 
Published: November 2013

ABSTRACT

High thermostability is required for alkaline α-amylases to maintain high catalytic activity under the harsh conditions used in textile production. In this study, we attempted to improve the thermostability of an alkaline α-amylase from
Alkalimonas amylolytica
through
in silico
rational design and systems engineering of disulfide bridges in the catalytic domain. Specifically, 7 residue pairs (P35-G426, Q107-G167, G116-Q120, A147-W160, G233-V265, A332-G370, and R436-M480) were chosen as engineering targets for disulfide bridge formation, and the respective residues were replaced with cysteines. Three single disulfide bridge mutants—P35C-G426C, G116C-Q120C, and R436C-M480C—of the 7 showed significantly enhanced thermostability. Combinational mutations were subsequently assessed, and the triple mutant P35C-G426C/G116C-Q120C/R436C-M480C showed a 6-fold increase in half-life at 60°C and a 5.2°C increase in melting temperature compared with the wild-type enzyme. Interestingly, other biochemical properties of this mutant also improved: the optimum temperature increased from 50°C to 55°C, the optimum pH shifted from 9.5 to 10.0, the stable pH range extended from 7.0 to 11.0 to 6.0 to 12.0, and the catalytic efficiency (
k
cat
/

K
m

) increased from 1.8 × 10
4
to 2.4 × 10
4
liters/g · min. The possible mechanism responsible for these improvements was explored through comparative analysis of the model structures of wild-type and mutant enzymes. The disulfide bridge engineering strategy used in this work may be applied to improve the thermostability of other industrial enzymes.
Characterization of Escherichia coli O157:H7 Strains from Contaminated Raw Beef Trim during “High Event Periods”
Authors: Arthur Terrance M. , Bono James L. , Kalchayanand Norasak 
Published: November 2013

ABSTRACT

The development and implementation of effective antimicrobial interventions by the beef processing industry in the United States have dramatically reduced the incidence of beef trim contamination by
Escherichia coli
O157:H7. However, individual processing plants still experience sporadic peaks in contamination rates where multiple
E. coli
O157:H7-positive lots are clustered in a short time frame. These peaks have been referred to as “high event periods” (HEP) of contamination. The results reported here detail the characterization of
E. coli
O157:H7 isolates from 21 HEP across multiple companies and processing plants to gain insight regarding the mechanisms causing these incidents. Strain genotypes were determined by pulsed-field gel electrophoresis, and isolates were investigated for characteristics linking them to human illness. Through these analyses, it was determined that individual HEP show little to no diversity in strain genotypes. Hence, each HEP has one strain type that makes up most, if not all, of the contamination. This is shown to differ from the genotypic diversity of
E. coli
O157:H7 found on the hides of cattle entering processing plants. In addition, it was found that a large proportion (81%) of HEP are caused by strain types associated with human illness. These results pose a potential challenge to the current model for finished product contamination during beef processing.
Genome Sequence of Border Disease Virus Strain JSLS12-01, Isolated from Sheep in China
Authors: Liu Xia , Mao Li , Li Wenliang , Yang Leilei , Zhang Wenwen , Wei Jianzhong , Jiang Jieyuan 
Published: November 2013

ABSTRACT

Border disease virus (BDV) is a recognized virus in the genus
Pestivirus
and causes border disease (BD) in sheep and goats. Here, a novel BDV strain, JSLS12-01, was identified from sheep in Jiangsu Province, China. The complete coding sequence (CDS) was finished, which provides a better understanding of the molecular evolution of BDV isolates.
Draft Genome Sequence of Mycobacterium abscessus subsp.
bolletii
INCQS 00594
Authors: Leão Sylvia Cardoso , Matsumoto Cristianne Kayoko , Viana-Niero Cristina , Ramos Rommel Thiago Jucá , Carneiro Adriana Ribeiro , Barbosa Maria Silvanira , Lima Karla Valéria Batista , Lopes Maria Luiza , Azevedo Vasco , Silva Artur 
Published: November 2013

ABSTRACT

An epidemic of surgical-site infections by a single strain of
Mycobacterium abscessus
subsp.
bolletii
affected >1,700 patients in Brazil from 2004 to 2008. The genome of the epidemic prototype strain
M. abscessus
subsp.
bolletii
INCQS 00594, deposited in the collection of the National Institute for Health Quality Control (INCQS), was sequenced.
Draft Genome Sequence of Beta-Hemolytic Streptococcus iniae KCTC 11634
Authors: Choi Hye Sung , Kwon Mun Gyeong , Kim Myoung Sug , Park Myoung Ae , Kim Dong-Wook , Park Jin-Young , Kim Ji-Sun , Na Yun-Jeong , Kim Min-Young , Kim Dae-Soo , Chae Sung-Hwa , Seo Jung Soo 
Published: November 2013

ABSTRACT

Streptococcus iniae
is a beta-hemolytic, Gram-positive coccus, which affects a broad range of freshwater and marine fish species, causing substantial economic losses in the aquaculture industry worldwide. Thus, it is very important to derive a complete genome sequence of the bacterium to aid in the development of vaccines and methods for preventing fish streptococcosis and zoonotic infections in humans. Here, we present the draft genome sequence of
S. iniae
KCTC 11634 (1,955,615 bp, with a G+C content of 36.6%), which contains 1,868 putative coding sequences.
Draft Genome Sequence of the Clinical Isolate Acinetobacter nosocomialis Strain M2
Authors: Carruthers Michael D. , Harding Christian M. , Baker Beth D. , Bonomo Robert A. , Hujer Kristine M. , Rather Philip N. , Munson Robert S. 
Published: November 2013

ABSTRACT

We report the 3.78-Mbp high-quality draft assembly of the genome from a clinical isolate of
Acinetobacter nosocomialis
called strain M2 (previously known as
Acinetobacter baumannii
strain M2).
Sequence Determination of Burkholderia pseudomallei Strain NCTC 13392 Colony Morphology Variants
Authors: Vipond Julia , Kane Jennifer , Hatch Graham , McCorrison Jamison , Nierman William C. , Losada Liliana 
Published: November 2013

ABSTRACT

Burkholderia pseudomallei
is a biothreat and the causative agent of melioidosis. There are at least seven known colony morphotypes of
B. pseudomallei
that appear to have different virulence properties in animal models. We report the genome sequence of
B. pseudomallei
strain NCTC 13392 and the genomic variations of its eight morphotype derivatives.
Tobacco-stained fingers: a clue for smoking-related disease or harmful alcohol use? A case–control study
Authors: John Gregor , Pasche Sephora , Rothen Nicole , Charmoy Alexia , Delhumeau-Cartier Cécile , Genné Daniel 
Published: November 2013

ObjectiveTobacco stain on fingers is frequent. However, there is scarce description of this clinical sign. We aimed to explore tobacco stain on fingers as a marker of tobacco-related disease independent of cumulative tobacco exposure, and to find behavioural and environmental characteristics associated with those stains.DesignCase–control study.SettingA Swiss community hospital of 180 beds.Participants49 adults presenting tobacco-tars staining on fingers were matched to 49 control smokers by age, gender, height and pack-year (PY).Outcome measuresDocumented smoking-related carcinoma, ischaemic heart disease, peripheral arterial disease, stroke and chronic obstructive pulmonary disease (COPD), also determined by lung function, were compared between groups. Association between harmful alcohol use, mental disorders or unemployment and tar-staining was adjusted for smoking behaviour through conditional logistic regression.ResultsOverall cigarette-related disease was high in the case group (84%), and symptomatic peripheral arterial disease was more frequent compared to controls (OR 3.5, CI 95% 1.1 to 14.6). Smoking-related carcinoma, ischaemic heart disease, stroke and COPD were not statistically different for control smokers. Harmful alcohol use was strongly associated with stains and this association persists after adjustment for smoking unfiltered cigarettes, smoking more than one pack of cigarettes in a day and age at smoking onset (adjusted OR 4.6, CI 95% 1.2 to 17.2). Mental disorders and unemployment were not statistically significant.ConclusionsPatients with tobacco-tar-stained fingers frequently have cigarette-related disease, however statistically not more than control smokers matched for PY, except for symptomatic peripheral arterial disease. This study suggests a link between stained fingers and addictive behaviour or concomitant high alcohol consumption.
‘I'd like to know what causes it, you know, anything I've done?’ Are we meeting the information and support needs of patients with macular degeneration? A qualitative study
Authors: Burton A E , Shaw R L , Gibson J M 
Published: November 2013

ObjectiveTo examine patients’ experiences of information and support provision for age-related macular degeneration (AMD) in the UK.Study designExploratory qualitative study investigating patient experiences of healthcare consultations and living with AMD over 18 months.SettingSpecialist eye clinics at a Birmingham hospital.Participants13 patients diagnosed with AMD.Main outcome measuresAnalysis of patients’ narratives to identify key themes and issues relating to information and support needs.ResultsInformation was accessed from a variety of sources. There was evidence of clear information deficits prior to diagnosis, following diagnosis and ongoing across the course of the condition. Patients were often ill informed and therefore unable to self-advocate and recognise when support was needed, what support was available and how to access support.ConclusionsAMD patients have a variety of information needs that are variable across the course of the condition. Further research is needed to determine whether these experiences are typical and identify ways of translating the guidelines into practice. Methods of providing information need to be investigated and improved for this patient group.
HIGH ENERGY ASTROPHYSICAL MISSIONS IN JAPAN
Authors: TSUNEMI HIROSHI 
Published: November 2013

There are five X-ray astronomy satellites launched from Japan. The latest satellite, Suzaku, was launched in 2005. MAXI is an all sky survey mission in X-ray that was attached to the ISS in 2009. These two are functioning at present. ASTRO-H is the only approved mission in X-ray that will be launched in 2014. There are four X-ray detectors on board ASTRO-H, SXS, SXI, HXI and SGD as well as X-ray telescopes made of thin foil mirrors. Most of the future missions heavily depend on them both in technology and in science. From this point of view, we have to concentrate on ASTRO-H so that we can expand our activities in future. In Japan, the small scientific satellite project is now on-going. Two missions are already allocated while no X-ray mission is approved. DIOS, PolariS, CAST and FFAST are proposed. Here we explain FFAST in detail that will study the evolution of the universe.
MULTIPLE SIGNAL CLASSIFICATION FOR GRAVITATIONAL WAVE BURST SEARCH
Authors: CAO JUNWEI , HE ZHENGQI 
Published: November 2013

This work is mainly focused on the application of the multiple signal classification (MUSIC) algorithm for gravitational wave burst search. This algorithm extracts important gravitational wave characteristics from signals coming from detectors with arbitrary position, orientation and noise covariance. In this paper, the MUSIC algorithm is described in detail along with the necessary adjustments required for gravitational wave burst search. The algorithm's performance is measured using simulated signals and noise. MUSIC is compared with the Q-transform for signal triggering and with Bayesian analysis for direction of arrival (DOA) estimation, using the Ω-pipeline. Experimental results show that MUSIC has a lower resolution but is faster. MUSIC is a promising tool for real-time gravitational wave search for multi-messenger astronomy.