bluuebunny/crossref_metadata_2025 huggingface dataset:
Finite Element Method Based Three-Dimensional Thermal Tomography for Disease Diagnosis of Human Body
Authors: Jin Chao , He Zhi-Zhu , Liu Jing
Published: May 2016

A finite element method (FEM)-based thermal approach to reconstruct the disease-associated heat source distribution has been developed. The congruent relationship between the heat sources and the observed temperature is established from the FEM solution matrix. The regularization method based parameter iteration algorithm is further developed to solve the inverse bioheat transfer problems. Typical simulations on sphere model and real digital human head have been performed to validate the feasibility and efficacy of the current method. In addition, the regularization parameter is optimized to speed up the reconstruction process and reduce the thermal noises. All the results indicate that both the heat source distribution and three-dimensional (3D) temperature field within the biological body were successfully reconstructed with acceptable accuracy.
Magnetoreflection spectroscopy of monolayer transition-metal dichalcogenide semiconductors in pulsed magnetic fields
Authors: Stier Andreas V. , McCreary Kathleen M. , Jonker Berend T. , Kono Junichiro , Crooker Scott A.
Published: May 2016

The authors describe recent experimental efforts to perform polarization-resolved optical spectroscopy of monolayer transition-metal dichalcogenide semiconductors in very large pulsed magnetic fields to 65 T. The experimental setup and technical challenges are discussed in detail, and temperature-dependent magnetoreflection spectra from atomically thin tungsten disulphide are presented. The data clearly reveal not only the valley Zeeman effect in these two-dimensional semiconductors but also the small quadratic exciton diamagnetic shift from which the very small exciton size can be directly inferred. Finally, the authors present model calculations that demonstrate how the measured diamagnetic shifts can be used to constrain estimates of the exciton binding energy in this new family of monolayer semiconductors.
MRI texture features as biomarkers to predict MGMT methylation status in glioblastomas
Authors: Korfiatis Panagiotis , Kline Timothy L. , Coufalova Lucie , Lachance Daniel H. , Parney Ian F. , Carter Rickey E. , Buckner Jan C. , Erickson Bradley J.
Published: May 2016

Purpose:

Imaging biomarker research focuses on discovering relationships between radiological features and histological findings. In glioblastoma patients, methylation of the O6‐methylguanine methyltransferase (MGMT) gene promoter is positively correlated with an increased effectiveness of current standard of care. In this paper, the authors investigate texture features as potential imaging biomarkers for capturing the MGMT methylation status of glioblastoma multiforme (GBM) tumors when combined with supervised classification schemes.

Methods:

A retrospective study of 155 GBM patients with known MGMT methylation status was conducted. Co‐occurrence and run length texture features were calculated, and both support vector machines (SVMs) and random forest classifiers were used to predict MGMT methylation status.

Results:

The best classification system (an SVM‐based classifier) had a maximum area under the receiver‐operating characteristic (ROC) curve of 0.85 (95% CI: 0.78–0.91) using four texture features (correlation, energy, entropy, and local intensity) originating from the T2‐weighted images, yielding at the optimal threshold of the ROC curve, a sensitivity of 0.803 and a specificity of 0.813.

Conclusions:

Results show that supervised machine learning of MRI texture features can predict MGMT methylation status in preoperative GBM tumors, thus providing a new noninvasive imaging biomarker.
Dosimetric comparison of stopping power calibration with dual‐energy CT and single‐energy CT in proton therapy treatment planning
Authors: Zhu Jiahua , Penfold Scott N.
Published: May 2016

Purpose:

The accuracy of proton dose calculation is dependent on the ability to correctly characterize patient tissues with medical imaging. The most common method is to correlate computed tomography (CT) numbers obtained via single‐energy CT (SECT) with proton stopping power ratio (SPR). CT numbers, however, cannot discriminate between a change in mass density and change in chemical composition of patient tissues. This limitation can have consequences on SPR calibration accuracy. Dual‐energy CT (DECT) is receiving increasing interest as an alternative imaging modality for proton therapy treatment planning due to its ability to discriminate between changes in patient density and chemical composition. In the current work we use a phantom of known composition to demonstrate the dosimetric advantages of proton therapy treatment planning with DECT over SECT.

Methods:

A phantom of known composition was scanned with a clinical SECT radiotherapy CT‐simulator. The phantom was rescanned at a lower X‐ray tube potential to generate a complimentary DECT image set. A set of reference materials similar in composition to the phantom was used to perform a stoichiometric calibration of SECT CT number to proton SPRs. The same set of reference materials was used to perform a DECT stoichiometric calibration based on effective atomic number. The known composition of the phantom was used to assess the accuracy of SPR calibration with SECT and DECT. Intensity modulated proton therapy (IMPT) treatment plans were generated with the SECT and DECT image sets to assess the dosimetric effect of the imaging modality. Isodose difference maps and root mean square (RMS) error calculations were used to assess dose calculation accuracy.

Results:

SPR calculation accuracy was found to be superior, on average, with DECT relative to SECT. Maximum errors of 12.8% and 2.2% were found for SECT and DECT, respectively. Qualitative examination of dose difference maps clearly showed the dosimetric advantages of DECT imaging, compared to SECT imaging for IMPT dose calculation for the case investigated. Quantitatively, the maximum dose calculation error in the SECT plan was 7.8%, compared to a value of 1.4% in the DECT plan. When considering the high dose target region, the root mean square (RMS) error in dose calculation was 2.1% and 0.4% for SECT and DECT, respectively.

Conclusions:

DECT‐based proton treatment planning in a commercial treatment planning system was successfully demonstrated for the first time. DECT is an attractive imaging modality for proton therapy treatment planning owing to its ability to characterize density and chemical composition of patient tissues. SECT and DECT scans of a phantom of known composition have been used to demonstrate the dosimetric advantages obtainable in proton therapy treatment planning with DECT over the current approach based on SECT.
Grating‐based x‐ray differential phase contrast imaging with twin peaks in phase‐stepping curves—phase retrieval and dewrapping
Authors: Yang Yi , Xie Huiqiao , Cai Weixing , Mao Hui , Tang Xiangyang
Published: May 2016

Purpose:

X‐ray differential phase contrast CT implemented with Talbot interferometry employs phase‐stepping to extract information of x‐ray attenuation, phase shift, and small‐angle scattering. Since inaccuracy may exist in the absorption grating G2 due to an imperfect fabrication, the effective period of G2 can be as large as twice the nominal period, leading to a phenomenon of twin peaks that differ remarkably in their heights. In this work, the authors investigate how to retrieve and dewrap the phase signal from the phase‐stepping curve (PSC) with the feature of twin peaks for x‐ray phase contrast imaging.

Methods:

Based on the paraxial Fresnel–Kirchhoff theory, the analytical formulae to characterize the phenomenon of twin peaks in the PSC are derived. Then an approach to dewrap the retrieved phase signal by jointly using the phases of the first‐ and second‐order Fourier components is proposed. Through an experimental investigation using a prototype x‐ray phase contrast imaging system implemented with Talbot interferometry, the authors evaluate and verify the derived analytic formulae and the proposed approach for phase retrieval and dewrapping.

Results:

According to theoretical analysis, the twin‐peak phenomenon in PSC is a consequence of combined effects, including the inaccuracy in absorption grating G2, mismatch between phase grating and x‐ray source spectrum, and finite size of x‐ray tube's focal spot. The proposed approach is experimentally evaluated by scanning a phantom consisting of organic materials and a lab mouse. The preliminary data show that compared to scanning G2 over only one single nominal period and correcting the measured phase signal with an intuitive phase dewrapping method that is being used in the field, stepping G2 over twice its nominal period and dewrapping the measured phase signal with the proposed approach can significantly improve the quality of x‐ray differential phase contrast imaging in both radiograph and CT.

Conclusions:

Using the phase retrieval and dewrapping methods proposed to deal with the phenomenon of twin peaks in PSCs and phase wrapping, the performance of grating‐based x‐ray differential phase contrast radiography and CT can be significantly improved.
Non-stationary Bayesian estimation of parameters from a body cover model of the vocal folds
Authors: Hadwin Paul J. , Galindo Gabriel E. , Daun Kyle J. , Zañartu Matías , Erath Byron D. , Cataldo Edson , Peterson Sean D.
Published: May 2016

The evolution of reduced-order vocal fold models into clinically useful tools for subject-specific diagnosis and treatment hinges upon successfully and accurately representing an individual patient in the modeling framework. This, in turn, requires inference of model parameters from clinical measurements in order to tune a model to the given individual. Bayesian analysis is a powerful tool for estimating model parameter probabilities based upon a set of observed data. In this work, a Bayesian particle filter sampling technique capable of estimating time-varying model parameters, as occur in complex vocal gestures, is introduced. The technique is compared with time-invariant Bayesian estimation and least squares methods for determining both stationary and non-stationary parameters. The current technique accurately estimates the time-varying unknown model parameter and maintains tight credibility bounds. The credibility bounds are particularly relevant from a clinical perspective, as they provide insight into the confidence a clinician should have in the model predictions.
A simulation framework for auditory discrimination experiments: Revealing the importance of across-frequency processing in speech perception
Authors: Schädler Marc René , Warzybok Anna , Ewert Stephan D. , Kollmeier Birger
Published: May 2016

A framework for simulating auditory discrimination experiments, based on an approach from Schädler, Warzybok, Hochmuth, and Kollmeier [(2015). Int. J. Audiol. 54, 100–107] which was originally designed to predict speech recognition thresholds, is extended to also predict psychoacoustic thresholds. The proposed framework is used to assess the suitability of different auditory-inspired feature sets for a range of auditory discrimination experiments that included psychoacoustic as well as speech recognition experiments in noise. The considered experiments were 2 kHz tone-in-broadband-noise simultaneous masking depending on the tone length, spectral masking with simultaneously presented tone signals and narrow-band noise maskers, and German Matrix sentence test reception threshold in stationary and modulated noise. The employed feature sets included spectro-temporal Gabor filter bank features, Mel-frequency cepstral coefficients, logarithmically scaled Mel-spectrograms, and the internal representation of the Perception Model from Dau, Kollmeier, and Kohlrausch [(1997). J. Acoust. Soc. Am. 102(5), 2892–2905]. The proposed framework was successfully employed to simulate all experiments with a common parameter set and obtain objective thresholds with less assumptions compared to traditional modeling approaches. Depending on the feature set, the simulated reference-free thresholds were found to agree with—and hence to predict—empirical data from the literature. Across-frequency processing was found to be crucial to accurately model the lower speech reception threshold in modulated noise conditions than in stationary noise conditions.
Acoustic firearm discharge detection and classification in an enclosed environment
Authors: Luzi Lorenzo , Gonzalez Eric , Bruillard Paul , Prowant Matthew , Skorpik James , Hughes Michael , Child Scott , Kist Duane , McCarthy John E.
Published: May 2016

Two different signal processing algorithms are described for detection and classification of acoustic signals generated by firearm discharges in small enclosed spaces. The first is based on the logarithm of the signal energy. The second is a joint entropy. The current study indicates that a system using both signal energy and joint entropy would be able to both detect weapon discharges and classify weapon type, in small spaces, with high statistical certainty.
Physical Activity and Cognitive Trajectories in Schoolchildren
Authors: López-Vicente Mónica , Forns Joan , Esnaola Mikel , Suades-González Elisabet , Álvarez-Pedrerol Mar , Robinson Oliver , Júlvez Jordi , Garcia-Aymerich Judith , Sunyer Jordi
Published: May 2016

Purpose:

The evidence regarding the role of physical activity (PA) habits on cognitive development in children is still scarce. Our study aimed to assess the association between PA habits and cognitive growth patterns, including working memory (WM) and inattentiveness in a large sample of primary schoolchildren.

Method:

This study included 2,897 children between 7 and 10 years old. WM was measured using the n-back task (2- and 3-back) and inattentiveness was measured using the attentional network task (ANT) on four occasions during one year. Parents completed a questionnaire with data about the extracurricular exercise of their child, commuting to school and other sociodemographic information at the first visit.

Results:

Exercising twice per week or more was associated with better 2-back, 3-back and inattentiveness scores at baseline, as compared with the once per week or less category. Active commuting for more than 50 min was associated with better 3-back scores at baseline, as compared with passive commuting. No consistent associations were found between PA and cognitive growth.

Conclusion:

Overall, although children with high levels of PA performed better in cognitive tasks at baseline, PA levels had no clear effects on cognitive growth trajectories.
The CHANGE! Project: Changes in Body Composition and Cardiorespiratory Fitness in 10- to 11-Year-Old Children After Completing the CHANGE! Intervention
Authors: Dagger Rebecca M. , Davies Ian G. , Mackintosh Kelly A. , Stone Genevieve L. , George Keith P. , Fairclough Stuart J. , Boddy Lynne M.
Published: May 2016

Purpose: To assess the effects of the Children’s Health, Activity and Nutrition: Get Educated! intervention on body size, body composition, and peak oxygen uptake in a subsample of 10- to 11-year-old children. Methods: Sixty children were recruited from 12 schools (N = 6 intervention) to take part in the CHANGE! subsample study. Baseline, postintervention, and follow-up measures were completed in October 2010, March–April 2011, and June–July 2011, respectively. Outcome measures were body mass index z score, waist circumference, body composition assessed using dual-energy X-ray absorptiometry (baseline and follow-up only), and peak oxygen uptake. Results: Significant differences in mean trunk fat mass (control = 4.72 kg, intervention = 3.11 kg, P = .041) and trunk fat % (control = 23.08%, intervention = 17.75%, P = .022) between groups were observed at follow-up. Significant differences in waist circumference change scores from baseline to follow-up were observed between groups (control = 1.3 cm, intervention = −0.2 cm, P = .023). Favorable changes in body composition were observed in the intervention group; however, none of these changes reached statistical significance. No significant differences in peak oxygen uptake were observed. Conclusions: The results of the present study suggest the multicomponent curriculum intervention had small to medium beneficial effects on body size and composition health outcomes.
Impact of a School-Based Intervention Protocol—ACORDA Project—On Adipokines in an Overweight and Obese Pediatric Population
Authors: Nascimento Henrique , Alves Ana Inês , Medeiros Ana Filipa , Coimbra Susana , Catarino Cristina , Bronze-da-Rocha Elsa , Costa Elísio , Rocha-Pereira Petronila , Silva Gustavo , Aires Luísa , Seabra André , Mota Jorge , Mansilha Helena Ferreira , Rêgo Carla , Santos-Silva Alice , Belo Luis
Published: May 2016

Purpose:

There are few reliable studies assessing the effect of physical exercise (PE) on adipokines levels at young ages. Our objective was to study the effects of regular PE on plasma adipokines in pediatric overweight and obesity.

Method:

117 overweight and obese children and adolescents (47% females; 10.2 years) participated in an 8-month longitudinal study divided in two groups: PE group (n = 80), engaged in an after-school PE program; control group (n = 37), with no PE program. Plasma lipids, C-reactive protein (CRP), adiponectin, resistin, leptin, IL-6, IL-1beta, TNF-alpha, insulin and glucose levels were determined.

Results:

contrarily to the control group, the PE group presented reductions in body mass index z-score (BMIzsc) and body fat percentage that were accompanied by an improvement in lipid profile and insulin resistance, a reduction in CRP and TNF-alpha and an increase in adiponectin levels. The reductions in BMIzsc were inversely correlated with changes in adiponectin (r=−0.329, p = .003) and positively correlated with changes in percentage body fat (r = .262, p = .032), triglycerides (r = .228, p = .042) and leptin (r = .285, p = .010).

Conclusion:

Moderate reductions in adiposity improve proinflammatory status in obese children and adolescents. A more substantial reduction in BMIzsc was associated with a greater increment in adiponectin and reduction in leptin.
Waist-to-Height Ratio, Aerobic Fitness, and Cardiometabolic Risk in Hispanic Children From Low-Income U.S. Schools
Authors: Burns Ryan D. , Brusseau Timothy A. , Fang Yi , Fu You , Hannon James C.
Published: May 2016

Purpose:

The purpose of this study was to examine the relationships among waist-to-height ratio (WHtR), aerobic fitness, and cardio-metabolic risk factors in Hispanic children from low-income U.S. schools.

Method:

Participants were 198 Hispanic children from low-income schools (Mean age = 10.3 ± 0.5 years; 119 girls, 79 boys). Waist circumference, height, and cardio-metabolic blood markers were collected in a fasted state. Estimated VO2 Peak scores were also collected. Multilevel generalized mixed effects models were employed to examine the independent effect of WHtR and aerobic fitness classification on a child meeting recommended levels for each cardio-metabolic blood marker.

Results:

A child having a WHtR < 0.5 related to meeting recommended levels for HDL cholesterol (OR = 3.25, p < .01), triglycerides (OR = 2.94, p < .01), glucose (OR = 3.42, p < .01), and related to a lower continuous Mean Arterial Pressure (MAP) score (β = −8.5 mmHg, p < .01). Aerobic fitness classification only independently related to meeting recommended levels for HDL cholesterol (OR = 2.94, p = .010).

Conclusion:

Having a WHtR < 0.5 independently associated with favorable cardio-metabolic blood markers and thus serves as an effective screening tool for cardio-metabolic risk in Hispanic children from low-income schools.
The Effect of Handcycle Ergometer Exercise on Glucose Tolerance in Ambulatory and Non-Ambulatory Adolescents
Authors: Short Kevin R. , Teague April M. , Klein Jake C. , Malm-Buatsi Elizabeth , Frimberger Dominic
Published: May 2016

Purpose:

Whole body or leg exercise before a meal can increase insulin sensitivity, but it is unclear whether the same can occur with upper body exercise since a smaller muscle mass is activated. We measured the impact of a single session of handcycle exercise on glucose tolerance and insulin sensitivity.

Methods:

Nonambulatory (Non-Amb) adolescents with spina bifida or cerebral palsy (4F/3M), or ambulatory peers (Control, 4F/7M) completed 2 glucose tolerance tests on separate days, preceded by either rest or a 35-min bout of moderate-to-vigorous intermittent handcycle exercise.

Results:

The Non-Amb group had higher body fat (mean ± SD: 38 ± 12%, Control: 24 ± 9, p = .041) but similar VO2peak (17.7 ± 6.1 ml/kg/min, Control: 21.1 ± 7.9). Fasting glucose and insulin were normal for all participants. Compared with the rest trial, exercise resulted in a reduction in glucose area under the curve (11%, p = .008) without a significant group x trial interaction and no difference in the magnitude of change between groups. Insulin sensitivity was increased 16% (p = .028) by exercise in the Control group but was not significantly changed in the Non-Amb group.

Conclusion:

A single bout of handcycle exercise improves glucose tolerance in adolescents with and without mobility limitations and could therefore help maintain or improve metabolic health.
Electron-scale measurements of magnetic reconnection in space
Authors: Burch J. L. , Torbert R. B. , Phan T. D. , Chen L.-J. , Moore T. E. , Ergun R. E. , Eastwood J. P. , Gershman D. J. , Cassak P. A. , Argall M. R. , Wang S. , Hesse M. , Pollock C. J. , Giles B. L. , Nakamura R. , Mauk B. H. , Fuselier S. A. , Russell C. T. , Strangeway R. J. , Drake J. F. , Shay M. A. , Khotyaintsev Yu. V. , Lindqvist P.-A. , Marklund G. , Wilder F. D. , Young D. T. , Torkar K. , Goldstein J. , Dorelli J. C. , Avanov L. A. , Oka M. , Baker D. N. , Jaynes A. N. , Goodrich K. A. , Cohen I. J. , Turner D. L. , Fennell J. F. , Blake J. B. , Clemmons J. , Goldman M. , Newman D. , Petrinec S. M. , Trattner K. J. , Lavraud B. , Reiff P. H. , Baumjohann W. , Magnes W. , Steller M. , Lewis W. , Saito Y. , Coffey V. , Chandler M.
Published: May 2016

Probing magnetic reconnection in space

Magnetic reconnection occurs when the magnetic field permeating a conductive plasma rapidly rearranges itself, releasing energy and accelerating particles. Reconnection is important in a wide variety of physical systems, but the details of how it occurs are poorly understood. Burch
et al.
used NASA's Magnetospheric Multiscale mission to probe the plasma properties within a reconnection event in Earth's magnetosphere (see the Perspective by Coates). They find that the process is driven by the electron-scale dynamics. The results will aid our understanding of magnetized plasmas, including those in fusion reactors, the solar atmosphere, solar wind, and the magnetospheres of Earth and other planets.

Science
, this issue p.
10.1126/science.aaf2939
; see also p.
1176
Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (
Anser indicus
) Feces on the Qinghai-Tibet Plateau
Authors: Wang Wen , Zheng Si-Si , Sun Hao , Cao Jian , Yang Fang , Wang Xue-Lian , Li Lai-Xing
Published: May 2016

Bacillus megaterium
is a soil-inhabiting Gram-positive bacterium that is routinely used in industrial applications for recombinant protein production and bioremediation. Studies involving
Bacillus megaterium
isolated from waterfowl are scarce. Here, we report a 6.26-Mbp draft genome sequence of
Bacillus megaterium
BHG1.1, which was isolated from feces of a bar-headed goose.
Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Strain from the
H
30Rx Subclone of Sequence Type 131 from a Patient with Recurrent Urinary Tract Infections, Closely Related to a Lethal Urosepsis Isolate from the Patient's Sister
Authors: Johnson Timothy J. , Aziz Maliha , Liu Cindy M. , Sokurenko Evgeni , Kisiela Dagmara I. , Paul Sandip , Andersen Paal , Johnson James R. , Price Lance B.
Published: May 2016

We report here the complete genome sequence, including five plasmid sequences, of
Escherichia coli
sequence type 131 (ST131) strain JJ1887. The strain was isolated in 2007 in the United States from a patient with recurrent cystitis, whose caregiver sister died from urosepsis caused by a nearly identical strain.
Whole-Genome Sequence of Salmonella enterica Serovar Enteritidis Phage Type 4, Isolated from a Brazilian Poultry Farm
Authors: Milanez Guilherme Paier , Nascimento Leandro Costa , Tirabassi Adriane Holtz , Zuanaze Marcelo , Rodrigues Dália Prazeres , Pereira Gonçalo Amarante Guimarães , Brocchi Marcelo
Published: May 2016

The draft genome of
Salmonella enterica
serovar Enteritidis phage type 4 (PT4) strain IOC4647/2004, isolated from a poultry farm in São Paulo state, was obtained with high-throughput Illumina sequencing platform, generating 4,173,826 paired-end reads with 251 bp. The assembly of 4,804,382 bp in 27 scaffolds shows strong similarity to other
S
. Enteritidis strains.
Complete Genome Sequence of
Algoriphagus
sp. Strain M8-2, Isolated from a Brackish Lake
Authors: Muraguchi Yusuke , Kushimoto Koya , Ohtsubo Yoshiyuki , Suzuki Tomohiro , Dohra Hideo , Kimbara Kazuhide , Shintani Masaki
Published: May 2016

Algoriphagus
sp. strain M8-2 was isolated from a brackish lake, Lake Sanaru, in Hamamatsu, Japan, as a filterable bacterium through a 0.22-µm-pore-size membrane filter. We report here the complete nucleotide sequence of the M8-2 genome (a 3,882,610-bp chromosome).
Complete Genome Sequence of a Chicken Embryo Fibroblast-Adapted Attenuated Infectious Bursal Disease Virus Isolate from India
Authors: Senthilkumar T. M. A. , Priyadharsini C. V. , Raja P. , Kumanan K.
Published: May 2016

Infectious bursal disease virus is an avian pathogen that causes huge morbidity and mortality in the poultry sector all over the world. Here, we report the full-length genome sequence of an Indian strain, MB11/ABT/MVC/2016, isolated from a commercial broiler flock. This is a first report of a complete genome sequence of infectious bursal disease virus from India.
Genome Sequencing of Foot-and-Mouth Disease Virus Type O Isolate GRE/23/94
Authors: King David J. , Knowles Nick J. , Freimanis Graham L. , King Donald P.
Published: May 2016

The complete genome of a foot-and-mouth disease type O virus originating from an epidemic in Greece in 1994 is reported. This virus belongs to the Middle East-South Asia topotype.
Complete Genome Sequence of
Labrenzia
sp. Strain CP4, Isolated from a Self-Regenerating Biocathode Biofilm
Authors: Wang Zheng , Eddie Brian J. , Malanoski Anthony P. , Hervey W. Judson , Lin Baochuan , Strycharz-Glaven Sarah M.
Published: May 2016

Here, we present the complete genome sequence of
Labrenzia
sp. strain CP4, isolated from an electricity-consuming marine biocathode biofilm.
Labrenzia
sp. strain CP4 consists of a circular 5.2 Mbp chromosome and an 88 Kbp plasmid.
Complete Mitochondrial Genome Sequence of the Pezizomycete
Pyronema confluens
Authors: Nowrousian Minou
Published: May 2016

The complete mitochondrial genome of the ascomycete
Pyronema confluens
has been sequenced. The circular genome has a size of 191 kb and contains 48 protein-coding genes, 26 tRNA genes, and two rRNA genes. Of the protein-coding genes, 14 encode conserved mitochondrial proteins, and 31 encode predicted homing endonuclease genes.
Draft Genome Sequence of Lampenflora Chlorobium limicola Strain Frasassi in a Sulfidic Cave System
Authors: Mansor Muammar , Macalady Jennifer L.
Published: May 2016

The draft genome sequence of
Chlorobium limicola
strain Frasassi was assembled from metagenomic sequencing of a green mat in an artificially lighted aquarium inside the Frasassi caves in Italy. The genome is 2.08 Mbp in size and contains the necessary genes for anoxygenic photosynthesis and CO
2
fixation.
Draft Genome Sequences of Four Plant Probiotic
Bacillus
Strains
Authors: Jeong Haeyoung , Park Seung-Hwan , Choi Soo-Keun
Published: May 2016

Here, we report the whole-genome sequences of four
Bacillus
strains that exhibit plant probiotic activities. Three of them are the type strains of
Bacillus endophyticus
, “
Bacillus gaemokensis
,” and
Bacillus trypoxylicola
, and the other,
Bacillus
sp. strain KCTC 13219, should be reclassified into a species belonging to the genus
Lysinibacillus
.
Complete Genome Sequences of Zika Virus Strains Isolated from the Blood of Patients in Thailand in 2014 and the Philippines in 2012
Authors: Ellison D. W. , Ladner J. T. , Buathong R. , Alera M. T. , Wiley M. R. , Hermann L. , Rutvisuttinunt W. , Klungthong C. , Chinnawirotpisan P. , Manasatienkij W. , Melendrez M. C. , Maljkovic Berry I. , Thaisomboonsuk B. , Ong-ajchaowlerd P. , Kaneechit W. , Velasco J. M. , Tac-An I. A. , Villa D. , Lago C. B. , Roque V. G. , Plipat T. , Nisalak A. , Srikiatkhachorn A. , Fernandez S. , Yoon I. K. , Haddow A. D. , Palacios G. F. , Jarman R. G. , Macareo L. R.
Published: May 2016

Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, Zika virus/
Homo sapiens
-tc/THA/2014/SV0127-14 and Zika virus/
H. sapiens
-tc/PHL/2012/CPC-0740, isolated from the blood of patients collected in Thailand, 2014, and the Philippines, 2012, respectively. Sequencing and phylogenetic analysis showed that both strains belong to the Asian lineage.
Draft Genome Sequence of
Cutaneotrichosporon curvatus
DSM 101032 (Formerly
Cryptococcus curvatus
), an Oleaginous Yeast Producing Polyunsaturated Fatty Acids
Authors: Hofmeyer Thomas , Hackenschmidt Silke , Nadler Florian , Thürmer Andrea , Daniel Rolf , Kabisch Johannes
Published: May 2016

Cutaneotrichosporon curvatus
DSM 101032 is an oleaginous yeast that can be isolated from various habitats and is capable of producing substantial amounts of polyunsaturated fatty acids. Here, we present the first draft genome sequence of any
C. curvatus
species.
Draft Genome Sequence of Hydrocarbon-Degrading Staphylococcus saprophyticus Strain CNV2, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil Refinery, Guwahati, Assam, India
Authors: Mukherjee Arghya , Chettri Bobby , Langpoklakpam James S. , Singh Arvind K. , Chattopadhyay Dhrubajyoti
Published: May 2016

Here, we report the 2.6 Mb draft genome sequence of hydrocarbon-degrading
Staphylococcus saprophyticus
strain CNV2, isolated from oil-contaminated soil in Guwahati, India. CNV2 contains 2,545 coding sequences and has a G+C content of 33.2%. This is the first report of the genome sequence of an
S. saprophyticus
adapted to an oil-contaminated environment.
Complete Genome Sequence of Staphylococcus aureus MCRF184, a Necrotizing Fasciitis-Causing Methicillin-Sensitive Sequence Type 45
Staphylococcus
Strain
Authors: Aswani Vijay , Mau Bob , Shukla Sanjay K.
Published: May 2016

We report here the complete genome sequence of a highly virulent methicillin-sensitive
Staphylococcus aureus
strain
,
MCRF184, belonging to sequence type 45. This staphylococcal strain was isolated from a surgical biopsy specimen from a patient with necrotizing fasciitis.
Complete Genome Sequences of Five Zika Virus Isolates
Authors: Ladner Jason T. , Wiley Michael R. , Prieto Karla , Yasuda Chadwick Y. , Nagle Elyse , Kasper Matthew R. , Reyes Daniel , Vasilakis Nikolaos , Heang Vireak , Weaver Scott C. , Haddow Andrew , Tesh Robert B. , Sovann Ly , Palacios Gustavo
Published: May 2016

Zika virus is an emerging human pathogen of great concern due to putative links to microcephaly and Guillain-Barre syndrome. Here, we report the complete genomes, including the 5′ and 3′ untranslated regions, of five Zika virus isolates, one from the Asian lineage and four from the African lineage.
First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508
T
Authors: Poehlein Anja , Friedrich Ines , Krüger Larissa , Daniel Rolf
Published: May 2016

The moderately thermophilic bacterium
Clostridium tepidiprofundi
is Gram-positive and belongs to clostridial cluster I. It was isolated from a hydrothermal vent chimney. Substrates utilized by
C. tepidiprofundi
include casein, peptone, tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome consists of one replicon (3.06 Mb).
Seroprevalence and correlates ofToxoplasma gondiiinfection in Yoremes (Mayos) in Mexico: a cross-sectional study
Authors: Alvarado-Esquivel Cosme , Rascón-Careaga Antonio , Hernández-Tinoco Jesús , Corella-Madueño María Alba Guadalupe , Sánchez-Anguiano Luis Francisco , Aldana-Madrid María Lourdes , Almada-Balderrama Gerardo Javier , Nuñez-Aguirre Alan Daniel , Liesenfeld Oliver
Published: May 2016

Objectives

We sought to determine the prevalence of anti-Toxoplasma gondiiantibodies in Yoremes and to identify associations ofT. gondiiexposure with sociodemographic, clinical and behavioural characteristics of Yoremes.

Design

A cross-sectional survey.

Setting

Yoremes were enrolled in the locality of Tierra Blanca in the municipality of Navojoa in Sonora State, Mexico.

Participants

We studied 200 Yoremes (Mayos); they are an indigenous ethnic group living in a coastal region in northwestern Mexico.

Primary and secondary outcome measures

We assessed the prevalence of anti-ToxoplasmaIgG and IgM antibodies in participants using enzyme-linked immunoassays. We used a standardised questionnaire to obtain the characteristics of Yoremes. The association ofT. gondiiexposure and Yoremes’ characteristics was assessed by bivariate and multivariate analyses.

Results

Of the 200 Yoremes studied (mean age: 31.50±18.43 years), 26 (13.0%) were positive for anti-T. gondiiIgG antibodies and 19 (73.1%) of them were also positive for anti-T. gondiiIgM antibodies. Seroprevalence ofT. gondiiinfection did not vary with sex, educational level, occupation or socioeconomic status. In contrast, multivariate analysis of sociodemographic and behavioural characteristics showed thatT. gondiiexposure was associated with increasing age (OR=1.02; 95% CI 1.00 to 1.04; p=0.03) and consumption of squirrel meat (OR=4.99; 95% CI 1.07 to 23.31; p=0.04). Furthermore, seroprevalence ofT. gondiiinfection was significantly higher in Yoremes with a history of lymphadenopathy (p=0.03) and those suffering from frequent abdominal pain (p=0.03). In women,T. gondiiexposure was associated with a history of caesarean sections (p=0.03) and miscarriages (p=0.02).

Conclusions

We demonstrate, for the first time, serological evidence ofT. gondiiexposure among Yoremes in Mexico. Results suggest that infection withT. gondiimight be affecting the health of Yoremes. Results may be useful for an optimal design of preventive measures againstT. gondiiinfection.
Association between fluid intake and kidney function, and survival outcomes analysis: a nationwide population-based study
Authors: Wu Li-Wei , Chen Wei-Liang , Liaw Fang-Yih , Sun Yu-Shan , Yang Hui-Fang , Wang Chung-Ching , Lin Chien-Ming , Tsao Yu-Tzu
Published: May 2016

Objectives

Fluid intake, one of the most common daily activities, has not been well studied in chronic kidney disease (CKD) populations, and clinical outcomes are rarely addressed. The aim of this nationwide study is to explore the influence of daily fluid intake on cardiovascular and all-cause mortality and its association with renal function.

Design

Observational cohort study.

Participants

In all, 2182 participants aged more than 20 years participated in the Third National Health and Nutrition Examination Survey (1988–1994).

Main outcome measures

Survival outcomes in patients with or without CKD, using multiple variable adjusted Cox proportional hazard models.

Results

In a longitudinal survey with a median follow-up length of 15.4 years, 1080 participants died and 473 cardiovascular deaths were recorded. For all-cause mortality in the CKD group, individuals in the highest quartile of fluid intake (≧3.576 L/day) had better survival outcomes than those in the lowest quartile of fluid intake (≤2.147 L/day) (p=0.029) after adjustment of several pertinent variables.

Conclusions

Although the interpretation of this observational study was limited by the failure to identify the compositions of ingested fluids, adequate hydration may offer some advantages in patients with CKD. However, the underlying pathophysiological mechanisms of the responses of normal and injured kidneys to chronic changes in fluid consumption warrant further investigation.
Layperson mouth-to-mask ventilation using a modified I-gel laryngeal mask after brief onsite instruction: a manikin-based feasibility trial
Authors: Schälte Gereon , Bomhard Lilli-Theresa , Rossaint Rolf , Coburn Mark , Stoppe Christian , Zoremba Norbert , Rieg Annette
Published: May 2016

Objective

The intention of this manikin-based trial was to evaluate whether laypersons are able to operate an I-gel laryngeal mask (I-gel) modified for mouth-to-mask ventilation after receiving brief on-site instruction.

Setting

Entrance hall of a university hospital and the city campus of a public technical university, using a protected manikin scenario.

Methods

Laypersons were handed a labelled, mouthpiece-integrated I-gel laryngeal mask and a corresponding instruction chart and were asked to follow the printed instructions.

Outcome measures

The overall process was analysed and evaluated according to quality and duration.

Results

Data from 100 participants were analysed. Overall, 79% of participants were able to effectively ventilate the manikin, 90% placed the laryngeal mask with the correct turn and direction, 19% did not position the mask deep enough and 85% believed that their inhibition threshold for performing resuscitation was lowered. A significant reduction in reluctance before and after the trial was found (p<0.0001). A total of 35% of participants had concerns about applying first aid in an emergency. Former basic life support (BLS) training significantly reduced the time of insertion (19.6 s, 95% CI 17.8 to 21.5, p=0.0004) and increased overall success (p=0.0096).

Conclusions

Laypersons were able to manage mouth-to-mask ventilation in the manikin with a reasonable success rate after receiving brief chart-based on-site instructions using a labelled I-gel mask. Positioning the mask deep enough and identifying whether the manikin was successfully ventilated were the main problems observed. A significant reduction in reluctance towards initialising BLS by using a modified supraglottic airway device (SAD) may lead to better acceptance of bystander resuscitation in laypersons, supporting the introduction of SADs into BLS courses and the stocking of SADs in units with public automatic external defibrillators.
Out-of-hours antibiotic prescription after screening with C reactive protein: a randomised controlled study
Authors: Rebnord Ingrid Keilegavlen , Sandvik Hogne , Batman Mjelle Anders , Hunskaar Steinar
Published: May 2016

Objective

To evaluate the effect of preconsultation C reactive protein (CRP) screening on antibiotic prescribing and referral to hospital in Norwegian primary care settings with low prevalence of serious infections.

Design

Randomised controlled observational study at out-of-hours services in Norway.

Setting

Primary care.

Participants

401 children (0–6 years) with fever and/or respiratory symptoms were recruited from 5 different out-of-hours services (including 1 paediatric emergency clinic) in 2013–2015.

Intervention

Data were collected from questionnaires and clinical examination results. Every third child was randomised to a CRP test before the consultation; for the rest, the doctor ordered a CRP test if considered necessary.

Outcome measures

Main outcome variables were prescription of antibiotics and referral to hospital.

Results

In the group pretested with CRP, the antibiotic prescription rate was 26%, compared with 22% in the control group. In the group pretested with CRP, 5% were admitted to hospital, compared with 9% in the control group. These differences were not statistically significant. The main predictors for ordering a CRP test were parents' assessment of seriousness of the illness and the child's temperature. Paediatricians ordered CRP tests less frequently than did other doctors (9% vs 56%, p<0.001).

Conclusions

Preconsultation screening with CRP of children presenting to out-of-hours services with fever and/or respiratory symptoms does not significantly affect the prescription of antibiotics or referral to hospital.

Trial registration number

NCT02496559; Results.
Sleep extension increases IGF-I concentrations before and during sleep deprivation in healthy young men
Authors: Chennaoui Mounir , Arnal Pierrick J. , Drogou Catherine , Sauvet Fabien , Gomez-Merino Danielle
Published: May 2016

Sleep deprivation is known to suppress circulating trophic factors such as insulin-like growth factor (IGF)-I and brain-derived neurotrophic factor (BDNF). This experiment examined the effect of an intervention involving 6 nights of extended sleep before total sleep deprivation on this catabolic profile. In a randomized crossover design, 14 young men (age range: 26–37 years) were either in an extended (EXT; time in bed: 2100–0700 h) or habitual (HAB: 2230–0700 h) sleep condition, followed by 3 days in the laboratory with blood sampling at baseline (B), after 24 h of sleep deprivation (24h-SD), and after 1 night of recovery sleep (R). In the EXT condition compared with the HAB condition, free IGF-I levels were significantly higher at B, 24h-SD, and R (P < 0.001), and those of total IGF-I at B and 24h-SD (P < 0.05). EXT did not influence growth hormone, IGF binding protein 3, BDNF, insulin, and glucose levels. The only effect of 24 h of sleep deprivation was for insulin levels, which were significantly higher after R compared with B. In a healthy adult, additional sleep over 1 week increased blood concentrations of the anabolic factor IGF-I before and during 24 h of sleep deprivation and after the subsequent recovery night without effects on BDNF. With further research, these findings may prove to be important in guiding effective lifestyle modifications to limit physical or cognitive deficits associated with IGF-I decrease with age.
Investigating the behaviour of typical and designed wall-to-floor connections in light-frame wood stud wall structures subjected to blast loading
Authors: Viau Christian , Doudak Ghasan
Published: May 2016

The performance of light-frame wood stud walls under simulated blast loading has so far been limited to investigating the behaviour of structural elements with idealized boundary conditions. The current study investigates, experimentally and analytically, whether walls with prescriptive connection detailing for low and high seismic and wind regions are capable of resisting blast loadings such that the walls’ ultimate capacity can be reached. The study also investigates the behaviour of different connections with various design capacity levels to develop failure in the stud wall system rather than in the connection. A total of ten full-scale walls with different boundary conditions were tested dynamically. The results showed that typical prescriptive connection detailing did not perform adequately. Designed connections performed well, but the findings show that basing the connection design solely on capacity may be inadequate. Single degree-of-freedom modelling may only be utilized if damage in the connections is limited.
Safety evaluation of unconventional outside left-turn lane using automated traffic conflict techniques
Authors: Guo Yanyong , Sayed Tarek , Zaki Mohamed H. , Liu Pan
Published: May 2016

The objective of this study is to evaluate the safety impacts of unconventional outside left-turn lane at signalized intersections. New designed unconventional outside left-turn lanes are increasingly used at signalized intersections in urban areas in China. The unconventional outside left-turn lane design allows an exclusive left-turn lane to be located to the right of through lanes to improve the efficiency and increase the capacity of left-turn movements. However, the design also raises some concerns regarding potential negative safety impacts. The evaluation is conducted using an automated video-based traffic conflict technique. The traffic conflicts approach provides better understanding of collision contributing factors and the failure mechanism that leads to road collisions. Traffic conflicts are automatically detected and time to collision is calculated based on the analysis of the vehicles’ positions in space and time. Video data are collected from a signalized intersection in Nanjing, China, where both traditional inside and unconventional outside left-turn lanes are installed on two intersection approaches. The other two approaches have only inside left-turn lanes. The study compared frequency and severity of conflict for left-turning vehicles as well as the percentage of vehicles involved in conflicts from the inside and outside left-turn lanes. The results show that the intersection approaches with outside left-turn lanes had considerably more conflicts compared to approaches without outside left-turn lanes. As well, the approaches with outside left-turn lanes had significantly higher conflict severity than the approaches without outside left-turn lanes. As such, it is recommended that the trade-off between the improved mobility and negative safety impact of outside left-turn lanes be carefully considered before recommending their installation.
A global review of the spatial, taxonomic, and temporal scope of freshwater fisheries hydroacoustics research
Authors: Pollom Riley A. , Rose George A.
Published: May 2016

This review assessed the status and scope of freshwater hydroacoustic fisheries research in global aquatic ecosystems with emphasis on (i) geographical and spatial scope, (ii) taxonomic range at the species and family levels (restricted to bony fishes of the Actinopterygii and Sarcopterygii), and (iii) temporal scope. Hydroacoustic measures have been used by ecologists and managers of freshwater systems for several decades, with major progress in technology and methods in recent years. A literature review indicated 296 research contributions that employed hydroacoustics to study freshwater fisheries in 294 different aquatic ecosystems. Spatially, hydroacoustics research in freshwater systems have thus far been concentrated in developed countries, particularly in North America and Northern and Central Europe (83% of the studies reviewed here). Most studies were small in spatial scale and short-term, with 80% including only a single body of water and 63% conducted over a single year or season (75% spanning less than two years). In addition, effects of fish morphology and behavior on acoustic target strength (TS) and taxonomic identification are not well parameterized, with only 21 species receiving empirical study of TS. Despite progress, the present study reveals gaps in the knowledge needed for wider applications to management. These include larger biogeographical and temporal scales of study and further empirical research on TS and taxonomic identification. Recent advances in size rather than species-based methods and theory offer potential solutions to this issue but require further investigation. We conclude with recommendations for systematic hydroacoustic research to enable more effective monitoring, management, and conservation of fisheries and freshwater ecosystems.
TBA type equations and tropical curves
Authors: Filippini Sara Angela , Stoppa Jacopo
Published: May 2016

The Joyce integrable system and the corresponding Bridgeland–Toledano-Laredo connections are fundamental objects associated with suitable abelian categories or, more generally, with a class of continuous families of stability data. We offer an overview of some of our work, mostly joint with M. Garcia Fernandez, focusing on equations of TBA type as a useful tool in the analysis of these objects and their deformations, and as a means to establish a connection with tropical geometry.
Investigating the cohomological dimensions of ℳg
Authors: Mondello Gabriele
Published: May 2016

We discuss the problem of determining the de Rham, Dolbeault and algebraic cohomological dimension of [Formula: see text], focusing on possible strategies of attack and then concentrating on exhaustion functions. In the final section, we explain how these techniques can be employed to provide a nontrivial upper bound for the Dolbeault cohomological dimension of [Formula: see text].