bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated fluence map optimization based on fuzzy inference systems
Authors: Dias Joana , Rocha Humberto , Ventura Tiago , Ferreira Brígida , Lopes Maria do Carmo 
Published: February 2016

Purpose:The planning of an intensity modulated radiation therapy treatment requires the optimization of the fluence intensities. The fluence map optimization (FMO) is many times based on a nonlinear continuous programming problem, being necessary for the planner to define a priori weights and/or lower bounds that are iteratively changed within a trial‐and‐error procedure until an acceptable plan is reached. In this work, the authors describe an alternative approach for FMO that releases the human planner from trial‐and‐error procedures, contributing for the automation of the planning process.Methods:The FMO is represented by a voxel‐based convex penalty continuous nonlinear model. This model makes use of both weights and lower/upper bounds to guide the optimization process toward interesting solutions that are able to satisfy all the constraints defined for the treatment. All the model's parameters are iteratively changed by resorting to a fuzzy inference system. This system analyzes how far the current solution is from a desirable solution, changing in a completely automated way both weights and lower/upper bounds. The fuzzy inference system is based on fuzzy reasoning that enables the use of common‐sense rules within an iterative optimization process. The method is built in two stages: in a first stage, an admissible solution is calculated, trying to guarantee that all the treatment planning constraints are being satisfied. In this first stage, the algorithm tries to improve as much as possible the irradiation of the planning target volumes. In a second stage, the algorithm tries to improve organ sparing, without jeopardizing tumor coverage.Results:The proposed methodology was applied to ten head‐and‐neck cancer cases already treated in the Portuguese Oncology Institute of Coimbra (IPOCFG) and signalized as complex cases. IMRT treatment was considered, with 7, 9, and 11 equidistant beam angles. It was possible to obtain admissible solutions for all the patients considered and with no human planner intervention. The results obtained were compared with the optimized solution using a similar optimization model but with human planner intervention. For the vast majority of cases, it was possible to improve organ sparing and at the same time to assure better tumor coverage.Conclusions:Embedding a fuzzy inference system into FMO allows human planner reasoning to be used in the guidance of the optimization process toward interesting regions in a truly automated way. The proposed methodology is capable of calculating high quality plans within reasonable computational times and can be an important contribution toward fully automated radiation therapy treatment planning.
Draft Genome Sequence of Mycobacterium tuberculosis KT-0204, Isolated in South Korea
Authors: Yun Mi-ran , Han Seung Jung , Yoo Won Gi , Kwon Taesoo , Lee Sanghyun , Lee Jong Seok , Kim Dae-Won 
Published: February 2016

ABSTRACT

Here, we describe the draft genome sequence of
Mycobacterium tuberculosis
KT-0204, non-Beijing family. This sequence will reveal genes related to the evolution and adaptation of
M. tuberculosis
KT-0204 in human hosts.
Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin
Authors: Patel Bharat K. C. , Te'o Valentino Setoa Junior 
Published: February 2016

ABSTRACT

The genome sequence of
Caloramator mitchellensis
strain VF08, a rod-shaped, heterotrophic, strictly anaerobic bacterium isolated from the free-flowing waters of a Great Artesian Basin (GAB) bore well located in Mitchell, an outback Queensland town in Australia, is reported here. The analysis of the 2.42-Mb genome sequence indicates that the attributes of the genome are consistent with its physiological and phenotypic traits.
Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing
Authors: Ham Claire , Morris Clare , Berry Neil 
Published: February 2016

ABSTRACT
The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays.
Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract
Authors: Mignolet Johann , Fontaine Laetitia , Kleerebezem Michiel , Hols Pascal 
Published: February 2016

ABSTRACT

The human commensal bacterium
Streptococcus salivarius
plays a major role in the equilibrium of microbial communities of the digestive tract. Here, we report the first complete genome sequence of a
Streptococcus salivarius
strain isolated from the small intestine, namely, HSISS4. Its circular chromosome comprises 1,903 coding sequences and 2,100,988 nucleotides.
Draft Whole-Genome Sequence of Haemophilus ducreyi Strain AUSPNG1, Isolated from a Cutaneous Ulcer of a Child from Papua New Guinea
Authors: Gangaiah Dharanesh , Marinov Georgi K. , Roberts Sally A. , Robson Jenny , Spinola Stanley M. 
Published: February 2016

ABSTRACT

Haemophilus ducreyi
has recently emerged as a leading cause of cutaneous ulcers in the yaws-endemic areas of Papua New Guinea and other South Pacific islands. Here, we report the draft genome sequence of the
H. ducreyi
strain AUSPNG1, isolated from a cutaneous ulcer of a child from Papua New Guinea.
Draft Genome Sequence of Coccoid Lactobacillus equigenerosi NRIC 0697
T
Isolated from the Gastrointestinal Tracts of Healthy Thoroughbreds
Authors: Toh Hidehiro , Nakano Akiyo , Nguyen Co Thi Kim , Mimura Iyo , Arakawa Kensuke , Tashiro Kosuke , Kikusui Takefumi , Morita Hidetoshi 
Published: February 2016

ABSTRACT

Lactobacillus equi
generosi NRIC 0697
T
was isolated from the gastrointestinal tracts of healthy thoroughbreds. This strain produced unique spherical or oval cells, which is rare in the genus
Lactobacillus
. Here, we report the draft genome sequence of this strain.
Complete Closed Genome Sequences of Salmonella enterica subsp.
enterica
Serotypes Anatum, Montevideo, Typhimurium, and Newport, Isolated from Beef, Cattle, and Humans
Authors: Harhay Dayna M. , Bono James L. , Smith Timothy P. L. , Fields Patricia I. , Dinsmore Blake A. , Santovenia Monica , Kelley Christy M. , Wang Rong , Harhay Gregory P. 
Published: February 2016

ABSTRACT

Salmonella enterica
spp. are a diverse group of bacteria with a wide range of virulence potential. To facilitate genome comparisons across this virulence spectrum, we present eight complete closed genome sequences of four
S. enterica
serotypes (Anatum, Montevideo, Typhimurium, and Newport), isolated from various cattle samples and from humans.
Draft Genome Sequence of Actinomyces odontolyticus subsp.
actinosynbacter
Strain XH001, the Basibiont of an Oral TM7 Epibiont
Authors: McLean Jeffrey S. , Liu Quanhui , Bor Batbileg , Bedree Joseph K. , Cen Lujia , Watling Michael , To Thao T. , Bumgarner Roger E. , He Xuesong , Shi Wenyuan 
Published: February 2016

ABSTRACT

Here, we present the draft genome sequence of
Actinomyces odontolyticus
subsp.
actinosynbacter
strain XH001, isolated from the human oral cavity. Uniquely, it was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the first cultivated member of “
Candidatus
Saccharibacteria” (formerly candidate phylum TM7).
Draft Genome Sequences of Sarcina ventriculi Strains Isolated from Wild Japanese Macaques in Yakushima Island
Authors: Ushida Kazunari , Tsuchida Sayaka , Ogura Yoshitoshi , Hayashi Tetsuya , Sawada Akiko , Hanya Goro 
Published: February 2016

ABSTRACTWe report the draft genome sequences ofSarcina ventriculistrains 14 and 17, both isolated from feces of wild Yakushima macaques (Macaca fuscatayakui). These genomic sequences will be helpful for the phylogenetic consideration of the familyClostridiaceaeand understanding of the contribution of intestinal microbiota to the survival of Yakushima macaques.
Dietary sources and sodium intake in a sample of Australian preschool children
Authors: O'Halloran Siobhan A , Grimes Carley A , Lacy Kathleen E , Nowson Caryl A , Campbell Karen J 
Published: February 2016

ObjectivesTo assess dietary sodium intake and the food sources of sodium in a sample of Australian preschool children.DesignCross-sectional.SettingMothers were followed up when children were approximately 3.5 years of age after participating in a cluster randomised controlled trial: the Melbourne Infant Feeding Activity and Nutrition Trial Program.Participants251 Australian children aged 3.5±0.19 (SD) years.Primary and secondary outcome measuresThe average daily sodium intake was determined using three unscheduled 24 h dietary recalls. The contributions of food groups, core, discretionary and processed foods to daily sodium intake were assessed.ResultsThe average sodium intake was 1508±495 (SD) mg/day, (salt equivalent 3.9±1.3 (SD) g/day) and 87% of children exceeded the Australian Upper Level of Intake (UL) for sodium of 1000 mg/day (salt equivalent 2.6 g/day). Main food sources of sodium were cereal/cereal products (25%), milk products (19%), meat, poultry/game (17%) and cereal-based products (15%). Core foods contributed 65%, and discretionary foods 35% of total daily sodium intake, and within the total diet, minimally processed, processed, processed culinary ingredient and ultraprocessed foods contributed 16%, 35%, 1% and 48% of sodium, respectively.ConclusionsWithin this sample, most children exceeded the recommended UL for sodium. Core and ultraprocessed foods were key sources of sodium which suggests that reductions in the sodium content of these foods are required to reduce sodium intake in young children. These data also provide further support for public health campaigns that seek to reduce consumption of energy-dense, nutrient-poor foods.
HIV testing among men who have sex with men in Tijuana, Mexico: a cross-sectional study
Authors: Pines Heather A , Goodman-Meza David , Pitpitan Eileen V , Torres Karla , Semple Shirley J , Patterson Thomas L 
Published: February 2016

ObjectivesHIV testing is critical to the delivery of comprehensive HIV prevention and care services, yet coverage of sexual minorities by HIV testing programmes remains insufficient in many low- and middle-income countries, including Mexico. The objective of this study was to identify the prevalence and correlates of HIV testing among men who have sex with men (MSM) in Tijuana, Mexico.MethodsWe conducted a cross-sectional study (2012–2013) among 189 MSM recruited via respondent-driven sampling (RDS). RDS-weighted logistic regression was used to identify correlates of prior HIV testing.ResultsRDS-adjusted prevalence of prior and recent (≤12 months) HIV testing was 63.5% (95% CI 51.9% to 73.5%) and 36.8% (95% CI 25.4% to 46.4%), respectively. Prior HIV testing was positively associated with older age (adjusted OR (AOR)=1.09, 95% CI 1.04 to 1.15), being born in Tijuana (AOR=2.68, 95% CI 1.05 to 6.86), higher levels of education (AOR=2.65, 95% CI 1.08 to 6.53), identifying as homosexual or gay (AOR=3.73, 95% CI 1.48 to 9.42), being more ‘out’ about having sex with men (AOR=1.28, 95% CI:1.02 to 1.62), and a history of sexual abuse (AOR=3.24, 95% CI 1.06 to 9.86). Prior HIV testing was negatively associated with reporting more condomless anal intercourse acts (past 2 months) (AOR=0.95, 95% CI 0.92 to 0.98) and greater internalised homophobia (AOR=0.92, 95% CI 0.86 to 0.99).ConclusionsOur findings indicate an urgent need for expanded HIV testing services for MSM in Tijuana. Innovative, non-stigmatising, confidential HIV testing interventions targeted at young, less educated, migrant and non-gay identifying MSM may facilitate HIV testing and timely linkage to HIV care and treatment within this population.
The decay τ → K−π0ντ in the Nambu–Jona-Lasinio model
Authors: Volkov M. K. , Pivovarov A. A. 
Published: February 2016

In this paper, the width of the decay [Formula: see text] is calculated in the framework of the Nambu–Jona-Lasinio (NJL) model. The contributions of the intermediate vector [Formula: see text] and scalar [Formula: see text] mesons are taken into account. It is shown that the main contribution to the width of this decay is given by the subprocesses with the intermediate [Formula: see text]-boson and vector [Formula: see text] meson. The scalar channel with the intermediate [Formula: see text] meson gives an insignificant contribution. In Appendix A, it is shown that the contribution of the subprocess with the intermediate [Formula: see text] meson is negligible as well. The obtained results are in satisfactory agreement with the experimental data.
The sedimentation of Suminagashi-like floating clay patterns at El Chichón crater lake (Chiapas, Mexico)
Authors: Rouwet D. , Iorio M. 
Published: February 2016

Abstract
This study describes the traditional Japanese Suminagashi paper marbling technique in an unusual, non-artistic way based on observations in nature (El Chichón crater lake, Chiapas, Mexico) and supported by physical processes such as wave action and Marangoni flow. It is the first time that these seemingly unrelated phenomena are linked. We show how clays floating on the surface of the El Chichón crater lake bear a strong resemblance to Suminagashi patterns. Clays rise from the lake bottom by vigorous bubbling of gases or thermal convection. After floating on the water surface due to capillary forces, the clays are transported towards the lake shore by wind-generated waves. The clay-covered lake surface is subject to Marangoni flow when the lake becomes very shallow (a few centimetres) near the lake shore. The flat lake bottom and the dynamic alternation between retreat and incurrence of the lake shore consequently result in the precipitation of the clay patterns, preserving the Suminagashi-like designs in the lake sediments. Recognition of similar patterns in the sedimentary record could indicate the presence of a shallow sedimentary environment in the past, possibly pointing to a heated crater lake.
Blood Pressure Is a Major Modifiable Risk Factor Implicated in Pathogenesis of Intraplaque Hemorrhage
Authors: Sun Jie , Canton Gador , Balu Niranjan , Hippe Daniel S. , Xu Dongxiang , Liu Jin , Hatsukami Thomas S. , Yuan Chun 
Published: February 2016

Objective—
Effective prevention and management strategies of intraplaque hemorrhage (IPH) remain elusive because of our limited knowledge regarding its contributing factors. This hypothesis-generating study aimed to investigate associations between cardiovascular risk factors and IPH for improved understanding of the pathogenesis of IPH.

Approach and Results—

Asymptomatic subjects with 16% to 79% stenosis on ultrasound underwent carotid magnetic resonance imaging using a large-coverage, 3-dimensional magnetic resonance imaging protocol. Individual plaques (maximum thickness >1.5 mm) in bilateral carotid arteries were identified, and presence of IPH was determined. From 80 subjects, 176 de novo plaques were measured, of which 38 (21.6%) contained IPH. Blood pressure (BP), primarily low diastolic BP, was associated with IPH in multivariate analysis adjusted for age, sex, and plaque size (odds ratio with 95% confidence interval per 10-mm Hg increase: 0.51 [0.30–0.88]), which was little changed after adjusting for antihypertensive use and systemic atherosclerosis. Antiplatelet use was associated with IPH in age and sex-adjusted models (
P
=0.018), for which a trend remained after considering plaque size and past medical history (odds ratio for aspirin alone versus none: 3.1 [0.66–14.8]; odds ratio for clopidogrel or dual therapy versus none: 5.3 [0.80–35.0];
P
=0.083).

Conclusions—
Low diastolic BP was independently associated with IPH, which was not attributed to treatment difference or BP changes from systemic atherosclerosis. Hemodynamic changes from lowering diastolic BP may be the pathophysiological link. Prospective serial studies are needed to assess whether BP and antiplatelet use are associated with the development of new or repeated IPH.
Imaging and Baseline Predictors of Cognitive Performance in Minor Ischemic Stroke and Patients With Transient Ischemic Attack at 90 Days
Authors: Mandzia Jennifer L. , Smith Eric E. , Horton Myles , Hanly Patrick , Barber Philip A. , Godzwon Catherine , Donaldson Emily , Asdaghi Negar , Patel Shiel , Coutts Shelagh B. 
Published: February 2016

Background and Purpose—
Few studies have examined predictors of cognitive impairment after minor ischemic stroke and transient ischemic attack (TIA). We examined clinical and imaging features associated with worse cognitive performance at 90 days.

Methods—

TIA or patients with minor stroke underwent neuropsychological testing 90 days post event.
Z
scores were calculated for cognitive tests, and then grouped into domains of executive function (EF), psychomotor processing speed (PS), and memory. White matter hyperintensity and diffusion-weighted imaging volumes were measured on baseline magnetic resonance imaging. Ninety-day outcomes included modified Rankin Scale (mRS) and Centre for Epidemiological Studies Depression Scale (CES-D) score.

Results—

Ninety-two patients were included, 76% male, 54% TIA, and mean age 65.1±12.0. Sixty-four percent were diffusion-weighted imaging positive. Median domain
z
scores were not significantly different from published norms (
P
>0.05): memory −0.03, EF −0.12, and PS −0.05. Patient performance ≥1 SD below normal was 20% on memory, 16% on PS, and 17% on EF. Cognitive scores did not differ by diagnosis (stroke versus TIA), stroke pathogenesis, presence of obstructive sleep apnea, and diffusion-weighted imaging or white matter hyperintensity volumes. In multivariable analyses, lower EF was associated with previous cortical infarct on magnetic resonance imaging (
P
=0.03), mRS score of >1;
P
=0.0003 and depressive symptoms (CES-D ≥16;
P
=0.03). Lower PS scores were associated with previous cortical infarct (
P
=0.02), acute bilateral positive diffusion-weighted imaging (
P
=0.02), mRS score of >1 (
P
=0.003), and CES-D ≥16 (
P
=0.03).

Conclusions—
Despite average-range cognitive performance in this TIA and population with minor stroke, we found associations of EF and PS with evidence of previous stroke, postevent disability, and depression.
BAECC: A Field Campaign to Elucidate the Impact of Biogenic Aerosols on Clouds and Climate
Authors: Petäjä Tuukka , O’Connor Ewan J. , Moisseev Dmitri , Sinclair Victoria A. , Manninen Antti J. , Väänänen Riikka , von Lerber Annakaisa , Thornton Joel A. , Nicoll Keri , Petersen Walt , Chandrasekar V. , Smith James N. , Winkler Paul M. , Krüger Olaf , Hakola Hannele , Timonen Hilkka , Brus David , Laurila Tuomas , Asmi Eija , Riekkola Marja-Liisa , Mona Lucia , Massoli Paola , Engelmann Ronny , Komppula Mika , Wang Jian , Kuang Chongai , Bäck Jaana , Virtanen Annele , Levula Janne , Ritsche Michael , Hickmon Nicki 
Published: February 2016

Abstract
During Biogenic Aerosols—Effects on Clouds and Climate (BAECC), the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Program deployed the Second ARM Mobile Facility (AMF2) to Hyytiälä, Finland, for an 8-month intensive measurement campaign from February to September 2014. The primary research goal is to understand the role of biogenic aerosols in cloud formation. Hyytiälä is host to the Station for Measuring Ecosystem–Atmosphere Relations II (SMEAR II), one of the world’s most comprehensive surface in situ observation sites in a boreal forest environment. The station has been measuring atmospheric aerosols, biogenic emissions, and an extensive suite of parameters relevant to atmosphere–biosphere interactions continuously since 1996. Combining vertical profiles from AMF2 with surface-based in situ SMEAR II observations allows the processes at the surface to be directly related to processes occurring throughout the entire tropospheric column. Together with the inclusion of extensive surface precipitation measurements and intensive observation periods involving aircraft flights and novel radiosonde launches, the complementary observations provide a unique opportunity for investigating aerosol–cloud interactions and cloud-to-precipitation processes in a boreal environment. The BAECC dataset provides opportunities for evaluating and improving models of aerosol sources and transport, cloud microphysical processes, and boundary layer structures. In addition, numerical models are being used to bridge the gap between surface-based and tropospheric observations.
Strengthening of the Tropopause Inversion Layer during the 2009 Sudden Stratospheric Warming: A MERRA-2 Study
Authors: Wargan Krzysztof , Coy Lawrence 
Published: February 2016

Abstract
The behavior of the tropopause inversion layer (TIL) during the 2009 sudden stratospheric warming (SSW) is analyzed using NASA’s Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2), and short-term simulations with the MERRA-2 general circulation model. Consistent with previous studies, it is found that static stability in a shallow layer above the polar tropopause sharply increases following the SSW, leading to a strengthening of the high-latitude TIL. Simultaneously, the height of the thermal tropopause decreases by around 1 km. Similar behavior is also detected during other major SSW events between the years 2004 and 2013. Using an ensemble of general circulation model forecasts initialized from MERRA-2, it is demonstrated that the primary cause of the strengthening of the TIL is an increased convergence of the vertical component of the stratospheric residual circulation in response to an SSW-induced acceleration of the mean downward motion between 75° and 90°N. In addition, ~6% of the strengthening in 2009 is attributed to an enhanced anticyclonic circulation at the tropopause. A preliminary analysis indicates that during other recent SSW events there was a significant increase in the convergence of the vertical residual wind velocity throughout the middle and lower stratosphere. The static stability increase simulated by the model during the 2009 SSW is 60%–80% of that seen in MERRA-2. The underestimate is traced back to a tendency for the forecasts to underestimate the resolved planetary wave forcing on the stratosphere compared to the reanalysis.