bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supplementary comparisons of COOMET in the field of measurements of liquids kinematical viscosity COOMET.M.V-S2
Authors: Demyanov A A , Tsurko A A 
Published: May 2017

In the comparisons three Newtonian liquid samples were used with nominal values of 20 mm2/s 100 mm2/s and 1000 mm2/s ('20', '100' and '1000', respectively) at 20 °C. Each NMI presented results of measurements values kinematic viscosity samples, uncertainty and uncertainty budget.
The purpose of these comparisons was confirmation of measurement and calibration capabilities (CMC) of the relevant NMI.
As a reference the values of kinematic viscosity reference samples were taken as average values of measurement results obtained in the research laboratory of the national standards and research in the field of measurements of viscosity and density of the D I Mendeleev Institute for Metrology (VNIIM, RF), as a participant in international comparisons CCM.V-K1, BIPM.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
BioMake: a GNU make-compatible utility for declarative workflow management
Authors: Holmes Ian H , Mungall Christopher J 
Published: May 2017

Abstract

Motivation
The Unix ‘make’ program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program.

Results
We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog.

Availability and implementation
BioMake is available for MacOSX and Linux systems from https://github.com/evoldoers/biomake under the BSD3 license. The only dependency is SWI-Prolog (version 7), available from http://www.swi-prolog.org/.

Supplementary information
Feature table comparing BioMake to similar tools. Supplementary data are available at Bioinformatics online.
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana
Authors: Nowell Reuben W. , Elsworth Ben , Oostra Vicencio , Zwaan Bas J. , Wheat Christopher W. , Saastamoinen Marjo , Saccheri Ilik J. , van't Hof Arjen E. , Wasik Bethany R. , Connahs Heidi , Aslam Muhammad L. , Kumar Sujai , Challis Richard J. , Monteiro Antónia , Brakefield Paul M. , Blaxter Mark 
Published: May 2017

Abstract
The mycalesine butterfly Bicyclus anynana, the “Squinting bush brown,” is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (~×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).
How supernovae launch galactic winds?
Authors: Fielding Drummond , Quataert Eliot , Martizzi Davide , Faucher-Giguère Claude-André 
Published: May 2017

Abstract
We use idealized three-dimensional hydrodynamic simulations of global galactic discs to study the launching of galactic winds by supernovae (SNe). The simulations resolve the cooling radii of the majority of supernova remnants (SNRs) and thus self-consistently capture how SNe drive galactic winds. We find that SNe launch highly supersonic winds with properties that agree reasonably well with expectations from analytic models. The energy loading ($\eta _{\rm E}= \dot{E}_{\rm wind}/ \dot{E}_{\rm SN}$) of the winds in our simulations are well converged with spatial resolution while the wind mass loading ($\eta _{\rm M}= \dot{M}_{\rm wind}/\dot{M}_\star$) decreases with resolution at the resolutions we achieve. We present a simple analytic model based on the concept that SNRs with cooling radii greater than the local scaleheight break out of the disc and power the wind. This model successfully explains the dependence (or lack thereof) of ηE (and by extension ηM) on the gas surface density, star formation efficiency, disc radius and the clustering of SNe. The winds our simulations are weaker than expected in reality, likely due to the fact that we seed SNe preferentially at density peaks. Clustering SNe in time and space substantially increases the wind power.
SODA: prediction of protein solubility from disorder and aggregation propensity
Authors: Paladin Lisanna , Piovesan Damiano , Tosatto Silvio C. E. 
Published: May 2017

Abstract
Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility. It has been trained and benchmarked on two different datasets. The comparison to other recently published methods shows that SODA has state-of-the-art performance and is particularly well suited to predict mutations decreasing solubility. The method is fast, returning results for single mutations in seconds. A usage example estimating the full repertoire of mutations for a human germline antibody highlights several solubility hotspots on the surface. The web server, complete with RESTful interface and extensive help, can be accessed from URL: http://protein.bio.unipd.it/soda.
Bipolar Cutting Method: Another Technique for Harvesting Donor Artery With Histological Investigation
Authors: Tokugawa Joji , Ogura Kanako , Yatomi Kenji , Kudo Kentaro , Hishii Makoto , Tanikawa Rokuya , Kamiyama Hiroyasu 
Published: May 2017

Abstract

BACKGROUND
Safe and appropriate harvesting of the donor scalp vessel is the first key procedure in any type of bypass surgery.

OBJECTIVE
To use the so-called bipolar cutting method to harvest donor arteries, in which the donor arteries are skeletonized with bipolar cautery. The surgical procedure and the preparation of the equipment of the bipolar cutting method are described. The surgical results and histological assessment are presented.

METHODS
The bipolar generator was set at 50 Malis units in the coagulation mode. Under the surgical microscope, the surrounding tissue of the donor artery was divided and coagulated with the bipolar forceps. The donor artery was completely skeletonized to provide adequate length. After the recipient artery was chosen and the anastomosis site was decided, the distal end of the donor artery was cut to the appropriate length. The remnant fragment of the donor artery was histologically investigated for any damage to the arterial wall. The specimen was cut longitudinally to observe the entire length of the arterial wall and stained with hematoxylin and eosin and elastica van Gieson.

RESULTS
A total of 30 bypass surgeries were performed and 38 histological specimens were obtained between February 2015 and June 2016. The success rate of the bypass was 96%. No arterial wall damage such as thermal injury or dissection of the wall was recognized in any of the specimens.

CONCLUSION
The bipolar cutting method is a useful and safe method for harvesting donor scalp artery.
Radial Artery Fascial Flow-Through Free Flap for Combined Revascularization in Moyamoya Disease
Authors: Russin Jonathan , Carey Joseph 
Published: May 2017

Abstract

BACKGROUND
Free flaps are commonly used by other surgical subspecialties for soft tissue reconstruction and revascularization. Cranial applications of these flaps have been limited to only a single case report.

OBJECTIVE
To present a new technique for combined revascularization in moyamoya disease using a flow-through free flap.

METHODS
Data were obtained from an Institutional Review Board-approved, prospectively maintained database with informed consent from the patient.

RESULTS
A 28-yr-old patient presented with progressive stenosis of the proximal anterior cerebral artery resulting in ischemic infarcts. Direct revascularization of the anterior cerebral artery territory and indirect revascularization of the middle cerebral artery with a large vascularized fascial pedicle was performed.

CONCLUSION
Flow-through free flaps offer a unique combination of revascularization and a large vascularized pedicle. This technique highlights the application of these flaps for revascularization in moyamoya disease and the value of multidisciplinary collaboration. Revascularization will likely play an increasing role in the open surgical treatment of cerebrovascular disease. We believe that flow-through free flaps will be a contribution to the future of revascularization in neurosurgery.
Properties of molecular gas in galaxies in the early and mid stages of interaction. II. Molecular gas fraction
Authors: Kaneko Hiroyuki , Kuno Nario , Iono Daisuke , Tamura Yoichi , Tosaki Tomoka , Nakanishi Kouichiro , Sawada Tsuyoshi 
Published: May 2017

Abstract
We have investigated properties of the interstellar medium in interacting galaxies in early and mid stages using mapping data of 12CO(J = 1–0) and H i. Assuming the standard CO–H2 conversion factor, we found no difference in molecular gas mass, atomic gas mass, and total gas mass (the sum of atomic and molecular gas mass) between interacting galaxies and isolated galaxies. However, interacting galaxies have a higher global molecular gas fraction $f_{\rm {mol}}^{\rm {global}}$ (the ratio of molecular gas mass to total gas mass averaged over a whole galaxy) at 0.71 ± 0.15 than isolated galaxies (0.52 ± 0.18). The distribution of the local molecular gas fraction fmol, the ratio of the surface density of molecular gas to that of the total gas, is different from the distribution in typical isolated galaxies. By a pixel-to-pixel comparison, isolated spiral galaxies show a gradual increase in fmol along the surface density of total gas until it is saturated at 1.0, while interacting galaxies show no clear relation. We performed pixel-to-pixel theoretical model fits by varying metallicity and external pressure. According to the model fitting, external pressure can explain the trend of fmol in the interacting galaxies. Assuming half of the standard CO–H2 conversion factor for interacting galaxies, the results of pixel-to-pixel theoretical model fitting get worse than adopting the standard conversion factor, although $f_{\rm {mol}}^{\rm {global}}$ of interacting galaxies (0.62 ± 0.17) becomes the same as in isolated galaxies. We conclude that external pressure occurs due to the shock prevailing over a whole galaxy or due to collisions between giant molecular clouds even in the early stage of the interaction. The external pressure accelerates an efficient transition from atomic gas to molecular gas. Regarding the chemical timescale, high fmol can be achieved at the very early stage of interaction even if the shock induced by the collision of galaxies ionizes interstellar gas.
Neurophysiologic Correlates of Ketamine Sedation and Anesthesia
Authors: Vlisides Phillip E. , Bel-Bahar Tarik , Lee UnCheol , Li Duan , Kim Hyoungkyu , Janke Ellen , Tarnal Vijay , Pichurko Adrian B. , McKinney Amy M. , Kunkler Bryan S. , Picton Paul , Mashour George A. 
Published: May 2017

Abstract

Background
Previous studies have demonstrated inconsistent neurophysiologic effects of ketamine, although discrepant findings might relate to differences in doses studied, brain regions analyzed, coadministration of other anesthetic medications, and resolution of the electroencephalograph. The objective of this study was to characterize the dose-dependent effects of ketamine on cortical oscillations and functional connectivity.

Methods
Ten healthy human volunteers were recruited for study participation. The data were recorded using a 128-channel electroencephalograph during baseline consciousness, subanesthetic dosing (0.5 mg/kg over 40 min), anesthetic dosing (1.5 mg/kg bolus), and recovery. No other sedative or anesthetic medications were administered. Spectrograms, topomaps, and functional connectivity (weighted and directed phase lag index) were computed and analyzed.

Results
Frontal theta bandwidth power increased most dramatically during ketamine anesthesia (mean power ± SD, 4.25 ± 1.90 dB) compared to the baseline (0.64 ± 0.28 dB), subanesthetic (0.60 ± 0.30 dB), and recovery (0.68 ± 0.41 dB) states; P < 0.001. Gamma power also increased during ketamine anesthesia. Weighted phase lag index demonstrated theta phase locking within anterior regions (0.2349 ± 0.1170, P < 0.001) and between anterior and posterior regions (0.2159 ± 0.1538, P < 0.01) during ketamine anesthesia. Alpha power gradually decreased with subanesthetic ketamine, and anterior-to-posterior directed connectivity was maximally reduced (0.0282 ± 0.0772) during ketamine anesthesia compared to all other states (P < 0.05).

Conclusions
Ketamine anesthesia correlates most clearly with distinct changes in the theta bandwidth, including increased power and functional connectivity. Anterior-to-posterior connectivity in the alpha bandwidth becomes maximally depressed with anesthetic ketamine administration, suggesting a dose-dependent effect.
Epidemiologic Surveillance of Teenage Birth Rates in the United States, 2006–2012
Authors: Amin Raid , Decesare Julie Zemaitis , Hans Jennifer , Roussos-Ross Kay 
Published: May 2017

OBJECTIVE:
To investigate the geographic variation in the average teenage birth rates by county in the contiguous United States.

METHODS:
Data from the National Center for Health Statistics were used in this retrospective cohort to count the total number of live births to females aged 15–19 years by county between 2006 and 2012. Software for disease surveillance and spatial cluster analysis was used to identify clusters of high or low teenage births in counties or areas of greater than 100,000 teenage females. The analysis was then adjusted for percentage of poverty and high school diploma achievement.

RESULTS:
The unadjusted analysis identified the top 10 clusters of teenage births. The cluster with the highest rate was a city and the surrounding 40 counties, demonstrating an average teen birth rate of 67 per 1,000 females in the age range, 87% higher than the rate in the contiguous United States. Adjustments for poverty rates and high school diploma achievement shifted the top clusters to other areas.

CONCLUSION:
Despite an overall national decline in the teenage birth rate, clusters of elevated teenage birth rates remain. These clusters are not random and remain higher than expected when adjusted for poverty and education. This data set provides a framework to focus targeted interventions to reduce teenage birth rates in this high-risk population.
Maternal Racial and Ethnic Disparities in Neonatal Birth Outcomes With and Without Assisted Reproduction
Authors: Crawford Sara , Joshi Nikhil , Boulet Sheree L. , Bailey Marie A. , Hood Maria-Elena , Manning Susan E. , McKane Patricia , Kirby Russell S. , Kissin Dmitry M. , Jamieson Denise J. ,   for the States Monitoring Assisted Reproductive Technology (SMART) Collaborative
Published: May 2017

OBJECTIVE:
To explore disparities in prematurity and low birth weight (LBW) by maternal race and ethnicity among singletons conceived with and without assisted reproductive technology (ART).

METHODS:
We performed a retrospective cohort study using resident birth certificate data from Florida, Massachusetts, and Michigan linked with data from the National ART Surveillance System from 2000 to 2010. There were 4,568,822 live births, of which 64,834 were conceived with ART. We compared maternal and ART cycle characteristics of singleton liveborn neonates using χ2 tests across maternal race and ethnicity groups. We used log binomial models to explore associations between maternal race and ethnicity and LBW and preterm birth by ART conception status.

RESULTS:
The proportion of liveborn neonates conceived with ART differed by maternal race and ethnicity (P<.01). It was smallest among neonates of non-Hispanic black (0.3%) and Hispanic women (0.6%) as compared with neonates of non-Hispanic white (2.0%) and Asian or Pacific Islander women (1.9%). The percentages of LBW or preterm singletons were highest for neonates of non-Hispanic black women both for non-ART (11.3% and 12.4%) and ART (16.1% and 19.1%) -conceived neonates. After adjusting for maternal factors, the risks of LBW or preterm birth for singletons born to non-Hispanic black mothers were 2.12 [95% confidence interval (CI) 2.10–2.14] and 1.56 (95% CI 1.54–1.57) times higher for non-ART neonates and 1.87 (95% CI 1.57–2.23) and 1.56 (95% CI 1.34–1.83) times higher for ART neonates compared with neonates of non-Hispanic white women. The adjusted risk for LBW was also significantly higher for ART and non-ART singletons born to Hispanic (adjusted relative risk [RR] 1.26, 95% CI 1.09–1.47 and adjusted RR 1.15, 95% CI 1.13–1.16) and Asian or Pacific Islander (adjusted RR 1.39, 95% CI 1.16–1.65 and adjusted RR 1.55, 95% CI 1.52–1.58) women compared with non-Hispanic white women.

CONCLUSION:
Disparities in adverse perinatal outcomes by maternal race and ethnicity persisted for neonates conceived with and without ART.
Minimally Invasive Hysterectomy and Power Morcellation Trends in a West Coast Integrated Health System
Authors: Zaritsky Eve , Tucker Lue-Yen , Neugebauer Romain , Chou Tatiana , Flanagan Tracy , Walter Andrew J. , Raine-Bennett Tina 
Published: May 2017

OBJECTIVE:
To examine trends in minimally invasive hysterectomy and power morcellation use over time and associated clinical characteristics.

METHODS:
We conducted a trend analysis and retrospective cohort study of all women 18 years of age and older undergoing hysterectomy for benign conditions at Kaiser Permanente Northern California collected from electronic health records. Generalized estimating equations and Cochran–Armitage testing were used to assess the primary outcomes, hysterectomy incidence, and proportion of hysterectomies by surgical route and power morcellation. Logistic regression analysis was used to assess secondary outcomes, clinical characteristics, and complications associated with surgical route.

RESULTS:
There were 31,971 hysterectomies from 2008 to 2015; the incidence decreased slightly from 2.86 (95% confidence interval [CI] 2.85–2.87) to 2.60 (95% CI 2.59–2.61) per 1,000 women (P<.001). Minimally invasive hysterectomies increased from 39.8% to 93.1%, almost replacing abdominal hysterectomies entirely (P<.001). Vaginal hysterectomies decreased slightly from 26.6% to 23.4% (P<.001). The proportion of nonrobotic laparoscopic hysterectomies with power morcellation increased steadily from 3.7% in 2008 to a peak of 11.4% in 2013 and decreased to 0.02% in 2015 (P<.001). Robot-assisted laparoscopic hysterectomies remained a small proportion of all hysterectomies comprising 7.8% of hysterectomies in 2015. Women with large uteri (greater than 1,000 g) were more likely to receive abdominal hysterectomies than minimally invasive hysterectomy (adjusted relative risk 11.62, 95% CI 9.89–13.66) and laparoscopic hysterectomy with power morcellation than without power morcellation (adjusted relative risk 5.74, 95% CI 4.12–8.00). Laparoscopic supracervical hysterectomy was strongly associated with power morcellation use (adjusted relative risk 43.89, 95% CI 37.55–51.31).

CONCLUSION:
A high minimally invasive hysterectomy rate is primarily associated with uterine size and can be maintained without power morcellation.
Changes in Myomectomy Practice After the U.S. Food and Drug Administration Safety Communication on Power Morcellation
Authors: Stentz Natalie C. , Cooney Laura G. , Sammel Mary , Shah Divya K. 
Published: May 2017

OBJECTIVE:
To examine the association between the 2014 U.S. Food and Drug Administration (FDA) safety communication on power morcellation and surgical approach and morbidity after myomectomy.

METHODS:
In this retrospective cohort study, data were abstracted from the American College of Surgeons National Surgical Quality Improvement Program database on 3,160 myomectomies between April 2012 and December 2013 (pre-FDA) and 4,378 between April 2014 and December 2015 (post-FDA). Aims were to 1) compare rates of abdominal and laparoscopic myomectomy pre-FDA and post-FDA (primary outcome), 2) directly compare the morbidity of abdominal and laparoscopic myomectomy during each time period (secondary outcome 1), and 3) compare the morbidity after all myomectomies performed pre-FDA and post-FDA (secondary outcome 2). Adjusted means, odds ratios, and rate ratios with 95% confidence intervals were calculated using linear, logistic, and Poisson regression, respectively, adjusting for age, race, ethnicity, body mass index, and myoma burden.

RESULTS:
Myomectomies performed post-FDA were more likely to be abdominal (60.0%, 95% confidence interval [CI] 58.6–61.5%) than laparoscopic (40.0%, 95% CI 38.5–41.4%) as compared with myomectomies pre-FDA, which were equally divided between surgical approaches (49.1% abdominal, 95% CI 47.4–50.9% compared with 50.9% laparoscopic, 95% CI 49.1–52.6%; P<.001). When directly compared with laparoscopic myomectomy, abdominal myomectomy was associated with longer hospitalizations, higher readmission rates, and greater morbidity both pre-FDA and post-FDA (P<.05, all comparisons). Adjusted models demonstrated shorter operative times post-FDA for all myomectomies (P<.001), although composite morbidity was similar between myomectomies performed pre-FDA and post-FDA (P=.809).

CONCLUSIONS:
The FDA safety communication on power morcellation was associated with an 11% absolute increase in the use of abdominal myomectomy. Although morbidity is consistently higher after abdominal as compared with laparoscopic myomectomy, the increased reliance on abdominal myomectomy post-FDA did not result in clinically significant changes in morbidity in this cohort.
Premature Thelarche and the PURA Syndrome
Authors: Rezkalla Joshua , Von Wald Tiffany , Hansen Keith A. 
Published: May 2017

BACKGROUND:
Premature thelarche is a self-limited condition characterized by Tanner stage II–III breast development in girls younger than 8 years of age with no evidence of advancing puberty. Evaluation concentrates on excluding central or peripheral causes of precocious puberty.

CASE:
A girl aged 2 years 4 months with profound hypotonia and delayed developmental milestones presented with Tanner II breast development, elevated follicle-stimulating hormone levels, suppressed luteinizing hormone level, normal growth and skeletal development, and prepubertal uterine length and ovarian volume. Monitoring until 8 years of age revealed no pubertal progression. Whole exome sequencing at 8 years revealed an autosomal-dominant mutation in the purine-rich element-binding protein A (PURA) gene. Previous patients with PURA syndrome have had pituitary dysfunction and precocious puberty.

CONCLUSION:
Purine-rich element-binding protein A syndrome can be associated with premature thelarche.