bluuebunny/crossref_metadata_2025 huggingface dataset:
A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics
Authors: Zhang Zhijun , Liu Xinzijian , Chen Zifei , Zheng Haifeng , Yan Kangyu , Liu Jian
Published: July 2017

We show a unified second-order scheme for constructing simple, robust, and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB algorithm that has been recently investigated. We show that the scheme is also useful for other types of thermostats, such as the Andersen thermostat and Nosé-Hoover chain, regardless of whether the thermostat is deterministic or stochastic. In addition to analytical analysis, two 1-dimensional models and three typical real molecular systems that range from the gas phase, clusters, to the condensed phase are used in numerical examples for demonstration. Accuracy may be increased by an order of magnitude for estimating coordinate-dependent properties in molecular dynamics (when the same time interval is used), irrespective of which type of thermostat is applied. The scheme is especially useful for path integral molecular dynamics because it consistently improves the efficiency for evaluating all thermodynamic properties for any type of thermostat.
Structural study of Na2O–B2O3–SiO2 glasses from molecular simulations using a polarizable force field
Authors: Pacaud Fabien , Delaye Jean-Marc , Charpentier Thibault , Cormier Laurent , Salanne Mathieu
Published: July 2017

Sodium borosilicate glasses Na2O–B2O3–SiO2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO4 and BO4 (BIV) and triangular BO3 (BIII). One of the salient features of these compounds is the change of the BIII/BIV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of BIII/BIV with respect to the composition and the temperature.
Theoretical study of resonance formation in microhydrated molecules. II. Thymine-(H2O)n, n = 1,2,3,5
Authors: Sieradzka Agnieszka , Gorfinkiel Jimena D.
Published: July 2017

We have investigated the effect of microsolvation on the low-lying pure shape π* resonances of thymine. Static-exchange R-matrix calculations for elastic electron scattering from microhydated thymine, i.e., Thy-(H2O)n with n = 1,2,3,5 are discussed. We look at the additive effect of water molecules hydrogen-bonding to thymine. The results for Thy-(H2O)5 show that both π* resonances appear at lower energy in the cluster than in isolated thymine, but that the energy shift is different for each resonance. We discuss how our results could help explain the quenching of hydrogen loss in dissociative electron attachment of microhydrated thymine recently recorded experimentally.
Mesh-type acoustic vector sensor
Authors: Zalalutdinov M. K. , Photiadis D. M. , Szymczak W. G. , McMahon J. W. , Bucaro J. A. , Houston B. H.
Published: July 2017

Motivated by the predictions of a theoretical model developed to describe the acoustic flow force exerted on closely spaced nano-fibers in a viscous medium, we have demonstrated a novel concept for a particle velocity-based directional acoustic sensor. The central element of the concept exploits the acoustically induced normal displacement of a fine mesh as a measure of the collinear projection of the particle velocity in the sound wave. The key observations are (i) the acoustically induced flow force on an individual fiber within the mesh is nearly independent of the fiber diameter and (ii) the mesh-flow interaction can be well-described theoretically by a nearest neighbor coupling approximation. Scaling arguments based on these two observations indicate that the refinement of the mesh down to the nanoscale leads to significant improvements in performance. The combination of the two dimensional nature of the mesh together with the nanoscale dimensions provides a dramatic gain in the total length of fiber exposed to the flow, leading to a sensitivity enhancement by orders of magnitude. We describe the fabrication of a prototype mesh sensor equipped with optical readout. Preliminary measurements carried out over a considerable bandwidth together with the results of numerical simulations are in good agreement with the theory, thus providing a proof of concept.
Electrohydrodynamic generation of millimetric drops and control of electrification
Authors: Yun Sungchan
Published: July 2017

We report a simple method for millimetric drop generation by electrohydrodynamic (EHD) detachment using a conventional nozzle-ring device. The EHD detachment method provides distinct features of uniform-size and controlled electrification of millimetric drops. The drop dynamics of detachment and shape oscillation are recorded using a high-speed camera and analyzed for several dc voltages applied to the electrode. Experimental studies show that an oscillation frequency can be closely related to the amount of electric charge, which can be explained based on both effective interfacial tension and inviscid Rayleigh and Lamb frequency. Furthermore, we present a concept to generate a neutral drop by adjusting the duration time of a pulse signal and discuss a drop oscillation induced by the detachment. This study can provide potential implications for drop manipulation, such as transporting, merging, and mixing, in microfluidic platforms.
Computational ghost imaging of hot objects in long-wave infrared range
Authors: Liu Hong-Chao , Zhang Shuang
Published: July 2017

Ghost imaging (GI) is an intriguing imaging modality to obtain the object information from the correlation calculations of spatial intensity fluctuations. In this letter, we report the computational GI of hot objects in the long-wave infrared range both in experiment and simulation. Without employing an independent light source, we reconstruct thermal images of objects only based on the intensity correlations of their thermal radiation at room temperature. By comparing different GI reconstruction algorithms, we demonstrate that GI with compressive sensing can efficiently obtain the thermal object information only with a single-pixel infrared camera, which might be applied to night-vision, environmental sensing, military detection, etc.
Analysis of spectra of 3s-3p and 3p-3d transitions of highly-charged copper ions
Authors: Su M. G. , Min Q. , He S. Q. , Wu L. , Sun R. , Ding X. B. , Sun D. X.
Published: July 2017

Beam-foil excited spectra in the range of 160–360 Å from highly charged copper ions were identified with the aid of the National Institute of Standards and Technology Atomic Spectra Database and theoretical calculations with Cowan and Flexible Atomic Code (FAC) calculations. Spectra arising from 3s-3p and 3p-3d transitions of Cu13+–Cu22+ ions were considered. The ion fraction at an ion beam energy of 110 MeV was estimated from the equilibrium charge distribution of the fast ion beams after passing through the solid. The corresponding simulated spectra were in good agreement with the experimental result. Our Cowan and FAC calculation results should be useful for further spectral identification and lifetime measurements of highly charged copper ions.
Effect of coupling agents on the dielectric properties and energy storage of Ba0.5Sr0.5TiO3/P(VDF-CTFE) nanocomposites
Authors: Wu Peixuan , Zhang Min , Wang Han , Tang Hui , Bass Patrick , Zhang Lin
Published: July 2017

Dielectric materials with high electric energy density and low dielectric loss are critical for electric applications in modern electronic and electrical power systems. To obtain desirable dielectric properties and energy storage, nanocomposites using Ba0.5Sr0.5TiO3 (BST) as the filler and poly(vinylidene fluoride-chlorotrifluoroethylene) as the matrix material are prepared with a uniform microstructure by using a newly developed process that combines the bridge-linked action of a coupling agent, solution casting, and a hot-pressing method. When a proper amount of coupling agent is used to modify the surface of the nanoparticles, the composite exhibits a higher dielectric constant and a more uniform microstructure. A dielectric constant of 95, dielectric loss of 0.25, and energy density of 2.7 J/cm3 is obtained in the nanocomposite with 30 vol.% of BST and 15 wt.% of coupling agent. The results suggest that the energy storage ability of the composites could be improved by the surface modification of the fillers and from the interface compatibility between the fillers and the polymer matrix.
Differences on meat colour and composition between ‘Landrace × Large White’ and ‘Iberian’ pigs under identical nutritional and management conditions
Authors: Palma-Granados Patricia , Haro Ana , Lara Luis , Aguilera José F. , Nieto Rosa , Seiquer Isabel
Published: July 2017

In pig production, factors such as nutritional system and genotype affect quality characteristics of meat. This study was aimed to evaluate differences in nutritional composition and colour of meat between Iberian (IB) and Landrace × Large White (LLW) pigs reared under identical nutrition and management conditions. Nutrient composition, mineral content, fatty acid profile and instrumental colour of two muscles (longissimus thoracis and biceps femoris) were examined at two growing stages (50- and 115-kg weight). Significant differences were found in relation to genotype. IB muscles contained higher amounts of intramuscular fat, dry matter, monounsaturated fatty acids, iron and zinc, and were redder (higher a* value) and with less colour saturation (lower hue angle), than those from LLW pigs. Significant relationships between colour coordinates with the mineral content and the lipid profile of muscles were found: redness was mainly linked to iron, zinc and monounsaturated fatty acids levels, whereas yellowness was positively related with copper, polyunsaturated fatty acids and linoleic acid level. The results of the present study support that muscles from the IB pig genotype have special characteristics, which may enhance the overall quality of meat compared with conventional or high-lean porcine breeds, even under identical management system, due to its particular fat composition and colour attributes.
Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth
Authors: Reimers Alexandra-M. , Knoop Henning , Bockmayr Alexander , Steuer Ralf
Published: July 2017

Significance

Cyanobacteria are important players in Earth’s biogeochemical cycles and a promising resource for the synthesis of renewable raw materials. Of particular interest are the cellular organization that enables fast growth and the corresponding intracellular limits on growth rates. Here, we develop a constraint-based computational model of phototrophic growth to investigate the optimal allocation of cellular resources in a diurnal light environment. The model-derived optimal metabolite partitioning during diurnal growth is in qualitative agreement with recent experimental data. Our results suggest that phototrophic metabolism at fast growth rates is highly optimized and strongly dependent on the timing characteristics of enzyme synthesis. Furthermore, we demonstrate that the experimentally observed pattern of glycogen accumulation is in agreement with predictions based on optimal resource allocation.
Catalysis and chemical mechanisms of calcite dissolution in seawater
Authors: Subhas Adam V. , Adkins Jess F. , Rollins Nick E. , Naviaux John , Erez Jonathan , Berelson William M.
Published: July 2017

Significance

The experimental system described here provides constraints on the relative balance of gross dissolution and precipitation fluxes contributing to the observed net dissolution rate of calcite in seawater. We show that our dissolution rates fit well within a framework that accounts for the geometry of the dissolving mineral surface. We further show that carbonic anhydrase (CA) catalyzes calcite dissolution, which implicates the hydration of aqueous

CO
2

as a rate-limiting step for calcite dissolution in seawater. The presence of carbonic anhydrase in carbonate-rich environments such as coral reefs or sinking marine particles is poorly understood. However, our findings suggest that CA activity would significantly enhance the rate at which alkalinity is cycled between solids and seawater in these environments.
Interest in using Mobile Technology to Help Self-Manage Alcohol use among Persons Living with the Human Immunodeficiency Virus: A Florida Cohort Cross-Sectional Study
Authors: Sharpe J. Danielle , Zhou Zhi , Escobar-Viera César G. , Morano Jamie P. , Lucero Robert J. , Ibañez Gladys E. , Hart Mark , Cook Christa L. , Cook Robert L.
Published: July 2017

Background

Alcohol consumption at hazardous levels is more prevalent and associated with poor health outcomes among persons living with the human immunodeficiency virus (HIV; PLWH). Although PLWH are receptive to using technology to manage health issues, it is unknown whether a cell phone app to self-manage alcohol use would be acceptable among PLWH who drink. The objectives of this study were to determine factors associated with interest in an app to self-manage drinking and to identify differences in baseline mobile technology use among PLWH by drinking level.

Methods

The study population included 757 PLWH recruited from 2014 to 2016 into the Florida Cohort, an ongoing cohort study investigating the utilization of health services and HIV care outcomes among PLWH. Participants completed a questionnaire examining demographics, substance use, mobile technology use, and other health behaviors. Multivariable logistic regression was used to identify factors significantly associated with interest in an app to self-manage drinking. We also determined whether mobile technology use varied by drinking level.

Results

Of the sample, 40% of persons who drink at hazardous levels, 34% of persons who drink at nonhazardous levels, and 19% of persons who do not drink were interested in a self-management app for alcohol use. Multivariable logistic regression analysis indicated that nonhazardous drinking (adjusted odds ratio [AOR] = 1.78; confidence interval [CI 95%]: 1.10–2.88) and hazardous drinking (AOR = 2.58; CI: 1.60–4.16) were associated with interest, controlling for age, gender, education, and drug use. Regarding mobile technology use, most of the sample reported smartphone ownership (56%), text messaging (89%), and at least one cell phone app (69%).

Conclusions

Regardless of drinking level, overall mobile technology use among PLWH was moderate, whereas PLWH who consumed alcohol expressed greater interest in a cell phone app to self-manage alcohol use. This indicates that many PLWH who drink would be interested in and prepared for a mobile technology–based intervention to reduce alcohol consumption.
The distribution of class numbers in a special family of real quadratic fields
Authors: Dahl Alexander , Lamzouri Youness
Published: July 2017

We investigate the distribution of class numbers in the family of real quadratic fields

Q

(

d

)

\mathbb {Q}(\sqrt {d})

corresponding to fundamental discriminants of the form

d
=
4

m
2

+
1

d=4m^2+1

, which we refer to as Chowla’s family. Our results show a strong similarity between the distribution of class numbers in this family and that of class numbers of imaginary quadratic fields. As an application of our results, we prove that the average order of the number of quadratic fields in Chowla’s family with class number

h
h

is

(
log
⁡
h
)

/

2
G

(\log h)/2G

, where

G
G

is Catalan’s constant. With minor modifications, one can obtain similar results for Yokoi’s family of real quadratic fields

Q

(

d

)

\mathbb {Q}(\sqrt {d})

, which correspond to fundamental discriminants of the form

d
=

m
2

+
4

d=m^2+4

.
Asymptotic analysis of second order nonlocal Cahn-Hilliard-type functionals
Authors: Dal Maso Gianni , Fonseca Irene , Leoni Giovanni
Published: July 2017

In this paper the study of a nonlocal second order Cahn–Hilliard-type singularly perturbed family of functions is undertaken. The kernels considered include those leading to Gagliardo fractional seminorms for gradients. UsingΓ\Gammaconvergence the integral representation of the limit energy is characterized leading to an anisotropic surface energy on interfaces separating different phases.
UV radiation-induced SUMOylation of DDB2 regulates nucleotide excision repair
Authors: Han Chunhua , Zhao Ran , Kroger John , He Jinshan , Wani Gulzar , Wang Qi-En , Wani Altaf A
Published: July 2017

Subunit 2 of DNA damage-binding protein complex (DDB2) is an early sensor of nucleotide excision repair (NER) pathway for eliminating DNA damage induced by UV radiation (UVR) and cisplatin treatments of mammalian cells. DDB2 is modified by ubiquitin and poly(ADP-ribose) (PAR) in response to UVR, and these modifications play a crucial role in regulating NER. Here, using immuno-analysis of irradiated cell extracts, we have identified multiple post-irradiation modifications of DDB2 protein. Interestingly, although the DNA lesions induced by both UVR and cisplatin are corrected by NER, only the UV irradiation, but not the cisplatin treatment, induces any discernable DDB2 modifications. We, for the first time, show that the appearance of UVR-induced DDB2 modifications depend on the binding of DDB2 to the damaged chromatin and the participation of functionally active 26S proteasome. The in vitro and in vivo analysis revealed that SUMO-1 conjugations comprise a significant portion of these UVR-induced DDB2 modifications. Mapping of SUMO-modified sites demonstrated that UVR-induced SUMOylation occurs on Lys-309 residue of DDB2 protein. Mutation of Lys-309 to Arg-309 diminished the DDB2 SUMOylation observable both in vitro and in vivo. Moreover, K309R mutated DDB2 lost its function of recruiting XPC to the DNA damage sites, as well as the ability to repair cyclobutane pyrimidine dimers following cellular UV irradiation. Taken together, our results indicate that DDB2 is modified by SUMOylation upon UV irradiation, and this post-translational modification plays an important role in the initial recognition and processing of UVR-induced DNA damage occurring within the context of chromatin.
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read
Authors: Austin Christopher M. , Tan Mun Hua , Harrisson Katherine A. , Lee Yin Peng , Croft Laurence J. , Sunnucks Paul , Pavlova Alexandra , Gan Han Ming
Published: July 2017

One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ~1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.
Cerebral Aneurysm Size and Distal Intracranial Hemodynamics: An Assessment of Flow and Pulsatility Index Using Quantitative Magnetic Resonance Angiography
Authors: Hussein Ahmed E , Brunozzi Denise , Shakur Sophia F , Ismail Rahim , Charbel Fady T , Alaraj Ali
Published: July 2017

BACKGROUND

The relationship between cerebral aneurysm size and risk of rupture is well documented, but the impact of aneurysms on distal intracranial hemodynamics is unknown.

OBJECTIVE

To examine the relationship between aneurysm size and distal intracranial hemodynamics prior to treatment.

METHODS

Patients seen at our institution between 2006 and 2015 with cerebral aneurysms within the internal carotid artery (ICA) segments (proximal to ICA terminus) were retrospectively reviewed. Patients were included if the aneurysm was unruptured, and were excluded if a contralateral aneurysm was present. Flows within bilateral ICAs and middle cerebral arteries (MCA) were measured prior to any treatment using quantitative magnetic resonance angiography. Pulsatility index (PI = [systolic − diastolic flow velocity]/mean flow velocity) within each vessel was then calculated. Hemodynamic parameters were analyzed with respect to aneurysm size.

RESULTS

Forty-two patients were included. Mean aneurysm size was 13.5 mm (range 2-40 mm). There was a significant correlation between aneurysm size and ipsilateral MCA PI (P = .006; r = 0.441), MCAipsilateral/ICAipsilateral PI ratio (P = .003; r = 0.57), and MCAipsilateral/MCAcontralateral PI ratio (P = .008; r = 0.43). Mean PI in the ipsilateral ICA was 0.38 (range 0.17-0.77) and ipsilateral MCA was 0.31 (range 0.08-0.83), and mean PI in contralateral ICA was 0.35 (range 0.19-0.57) and MCA was 0.30 (range 0.07-0.89).

CONCLUSION

Larger aneurysm size correlates with higher ipsilateral MCA PI, demonstrating that aneurysms affect distal intracranial hemodynamics.
Direct Root Penetration and Rhizome Vascular Colonization by Fusarium oxysporum f. sp. cubense are the Key Steps in the Successful Infection of Brazil Cavendish
Authors: Li Chunqiang , Yang Jinghao , Li Wenbin , Sun Jianbo , Peng Ming
Published: July 2017

Fusarium wilt of banana, which is caused by Fusarium oxysporum f. sp. cubense, is one of the most serious diseases of banana. F. oxysporum f. sp. cubense race 1 (Foc1) and race 4 (Foc4) are the most prevalent pathogens of banana cultivars in the world. To understand the differences in the infection processes between Foc1 and Foc4, green fluorescent protein-tagged strains of F. oxysporum f. sp. cubense tropical race 4 (FocTR4) and Foc1 were used to inoculate ‘Brazil Cavendish’ banana. At 2 days postinoculation (dpi), it was observed that the spores and hyphae of both Foc1 and Foc4 attached to the root hairs and root epidermis. At 3 dpi, the hyphae of both Foc1 and Foc4 were found in the vascular tissues of roots. However, Foc4 was observed in the parenchymal cells of banana root, whereas Foc1 was not found in parenchymal cells at 7 dpi. Furthermore, few Foc1 hyphae were observed in a few xylems whereas many more Foc4 hyphae were present in many xylems and phloems. Foc4 was observed in the vascular tissues of banana rhizomes, whereas no Foc1 was found in rhizomes 2 months after inoculation. The attachment process in F. oxysporum f. sp. cubense infection was further studied with scanning electron microscopy. Foc4 was observed to penetrate into banana roots from the intercellular space of the epidermis and wounds, whereas Foc1 mainly penetrated from the wounds but not from the intercellular space of the epidermis. Therefore, direct root penetration and rhizome vascular colonization by F. oxysporum f. sp. cubense are the key steps in the successful infection of Brazil Cavendish.
The Afya Bora Fellowship: An Innovative Program Focused on Creating an Interprofessional Network of Leaders in Global Health
Authors: Green Wendy M. , Farquhar Carey , Mashalla Yohana
Published: July 2017

Problem

Most current health professions education programs are focused on the development of clinical skills. As a result, they may not address the complex and interconnected nature of global health. Trainees require relevant clinical, programmatic, and leadership skills to meet the challenges of practicing in an increasingly globalized environment.

Approach

To develop health care leaders within sub-Saharan Africa, the Afya Bora Consortium developed a one-year fellowship for medical doctors and nurses. Fellows from nine institutions in the United States and sub-Saharan Africa participate in 12 learning modules focused on leadership development and program management. Classroom-based training is augmented with an experiential apprenticeship component.

Outcomes

Since 2011, 100 fellows have graduated from the program. During their apprenticeships, fellows developed projects beneficial to their development and to host organizations. The program has developed fellows’ skills in leadership, lent expertise to local organizations, and built knowledge in local contexts. Most fellows have returned to their countries of origin, thus building local capacity. U.S.-based fellows examine global health challenges from regional perspectives and learn from sub-Saharan African experts and peers.

Next Steps

The Consortium provides ongoing support to alumni through career development awards and alumni network engagement with current and past fellow cohorts. The Consortium expanded from its initial network of five countries to six and continues to seek opportunities for geographical and institutional expansion.
Establishing Obstetric Anesthesiology Practice Guidelines in the Republic of Armenia
Authors: Yuill Gordon , Amroyan Ashot , Millar Simon , Vardapetyan Emil , Habib Ashraf S. , Owen Medge D.
Published: July 2017

Background

Disparity exists in anesthesia practices between high- and low-to-middle income countries, and awareness has been raised within the global health community to improve the standards of anesthesia care and patient safety. The establishment of international collaborations and appropriate practice guidelines may help address clinical care deficiencies. This report’s aim was to assess the impact of a multiyear collaboration on obstetric anesthesia practices in the Republic of Armenia.

Methods

An invited multinational team of physicians conducted six visits to Armenia between 2006 and 2015 to observe current practice and establish standards of obstetric anesthesia care. The Armenian Society of Anaesthesiologists and Intensive Care specialists collected data on the numbers of vaginal delivery, cesarean delivery, and neuraxial anesthesia use in maternity units during the period. Data were analyzed with the Fisher exact or chi-square test, as appropriate.

Results

Neuraxial anesthesia use for cesarean delivery increased significantly (P < 0.0001) in all 10 maternity hospitals within the capital city of Yerevan. For epidural labor analgesia, there was sustained or increased use in only two hospitals. For hospitals located outside the capital city, there was a similar increase in the use of neuraxial anesthesia for cesarean delivery that was greater in hospitals that were visited by an external team (P < 0.0001); however, use of epidural labor analgesia was not increased significantly. Over the course of the collaboration, guidelines for obstetric anesthesia were drafted and approved by the Armenian Ministry of Health.

Conclusions

Collaboration between Armenian anesthesiologists and dedicated visiting physicians to update and standardize obstetric anesthesia practices led to national practice guidelines and sustained improvements in clinical care in the Republic of Armenia.
Prevention of Ankle Sprain Injuries in Youth Soccer and Basketball: Effectiveness of a Neuromuscular Training Program and Examining Risk Factors
Authors: Owoeye Oluwatoyosi B. A. , Palacios-Derflingher Luz M. , Emery Carolyn A.
Published: July 2017

Objectives:

The primary objective of this study was to examine the effectiveness of a neuromuscular training (NMT) warm-up program in reducing the risk of ankle sprain injury (ASI) in youth soccer and basketball. The secondary objective included the evaluation of risk factors for ASI.

Study Design:

Secondary analysis of pooled data from 5 studies.

Participants:

Male and female youth (11-18 years) soccer and basketball players (n = 2265) in Alberta, Canada.

Outcome Measures:

Ankle sprain injury was the primary outcome and was recorded using a validated prospective injury surveillance system consistent in all studies. The primary exposure of interest was NMT warm-up, which included aerobic, strength, agility, and balance components. Multivariable Poisson regression, controlling for clustering by team and offset for exposure hours, was used to estimate incidence rate ratios (IRRs) with 95% confidence intervals (CIs), with considerations for confounding and effect modification and evaluating all covariates as potential risk factors.

Results:

A total of 188 ASIs were reported in 171 players. Neuromuscular training significantly reduced the risk of ASI [IRR = 0.68 (95% CI; 0.46-0.99)]. Independent risk factors for ASI included previous ASI [IRR = 1.98 (95% CI; 1.38-2.81)] and participation in basketball versus soccer [IRR = 1.83 (95% CI; 1.18-2.85)]. Sex, age, body mass index, and previous lower extremity injury (without previous ASI) did not predict ASI (P > 0.05).

Conclusions:

Exposure to an NMT program is significantly protective for ASI in youth soccer and basketball. Risk of ASI in youth basketball is greater than soccer, and players with a history of ASI are at greater risk.
Trends in Hysteropexy and Apical Support for Uterovaginal Prolapse in the United States from 2002 to 2012
Authors: Madsen Annetta M. , Raker Christina , Sung Vivian W.
Published: July 2017

Objectives

Our objective was to describe trends in hysteropexy and apical support for uterovaginal prolapse (UVP) from 2002 to 2012 in the United States. We identified patient and hospital variables associated with hysteropexy and apical support.

Methods

We used the Nationwide Inpatient Sample and International Classification of Diseases, Ninth Revision codes to identify a population of women 18 years or older with UVP undergoing pelvic organ prolapse surgery from January 1, 2002, to December 31, 2012. Procedures were categorized as (1) hysteropexy, (2) obliterative with uterine preservation, (3) hysterectomy with apical support, (4) hysterectomy without apical support, and (5) other reconstruction without apical support. Categories were dichotomized into those with and without apical support. We used survey weights to obtain nationally representative estimates; χ2 and linear and logistic regression compared procedure groups.

Results

An estimated 815,184 hospital discharges of pelvic organ prolapse procedures for UVP occurred from 2002 to 2012. During this time, hysteropexies increased from 1.81% to 5.00% (P < 0.0001). From 2002 to 2012, hysterectomies with apical support increased (10.07% to 32.51%, P < 0.0001), hysterectomy without apical support decreased (27.14% to 17.12%, P < 0.0001), and reconstruction without apical support decreased (59.07% to 40.48%, P < 0.0001). In most recent years 2011 to 2012, 60% of women with UVP underwent inpatient surgery without an apical procedure. Age 52 years or older, Medicare payment, Northeast region, and urban teaching hospitals were associated with increased odds of apical support for UVP (P < 0.001 for all).

Conclusions

Hysteropexy significantly increased in the United States from 2002 to 2012, although the overall proportion remains low. While hysterectomy without apical support is decreasing, approximately 60% of inpatient procedures performed for UVP do not address the apex.
Direct and trans-generational effects of male and female gut microbiota in
Drosophila melanogaster
Authors: Morimoto Juliano , Simpson Stephen J. , Ponton Fleur
Published: July 2017

There is increasing evidence of the far-reaching effects of gut bacteria on physiological and behavioural traits, yet the fitness-related consequences of changes in the gut bacteria composition of sexually interacting individuals remain unknown. To address this question, we manipulated the gut microbiota of fruit flies,
Drosophila melanogaster
, by monoinfecting flies with either
Acetobacter pomorum
(
AP
) or
Lactobacillus plantarum
(
LP
)
.
Re-inoculated individuals were paired in all treatment combinations.
LP-
infected males had longer mating duration and induced higher short-term offspring production in females compared with
AP
-infected males. Furthermore, females of either re-inoculation state mated with
AP-
infected males were more likely to have zero offspring after mating, suggesting a negative effect of
AP
on male fertility
.
Finally, we found that the effects of male and female gut bacteria interacted to modulate their daughters', but not sons' body mass, revealing a new trans-generational effect of parental gut microbiota. In conclusion, this study shows direct and trans-generational effects of the gut microbiota on mating and reproduction.
Aerodynamic modelling of a Cretaceous bird reveals thermal soaring capabilities during early avian evolution
Authors: Serrano Francisco José , Chiappe Luis María
Published: July 2017

Several flight modes are thought to have evolved during the early evolution of birds. Here, we use a combination of computational modelling and morphofunctional analyses to infer the flight properties of the raven-sized, Early Cretaceous birdSapeornis chaoyangensis—a likely candidate to have evolved soaring capabilities. Specifically, drawing information from (i) mechanical inferences of the deltopectoral crest of the humerus, (ii) wing shape (i.e. aspect ratio), (iii) estimations of power margin (i.e. difference between power required for flight and available power from muscles), (iv) gliding behaviour (i.e. forward speed and sinking speed), and (v) palaeobiological evidence, we conclude thatS. chaoyangensiswas a thermal soarer with an ecology similar to that of living South American screamers. Our results indicate that as early as 125 Ma, some birds evolved the morphological and aerodynamic requirements for soaring on continental thermals, a conclusion that highlights the degree of ecological, functional and behavioural diversity that resulted from the first major evolutionary radiation of birds.
Group choices seemingly at odds with individual preferences
Authors: Laurent Salazar Michel-Olivier , Nicolis Stamatios C. , Calvo Martín Mariano , Sempo Grégory , Deneubourg Jean-Louis , Planas-Sitjà Isaac
Published: July 2017

Numerous studies have focused on the influence of the social environment and the interactions between individuals on the collective decision-making of groups. They showed, for example, that attraction between individuals is at the origin of an amplification of individual preferences. These preferences may concern various environmental cues such as biomolecules that convey information about the environment such as vanillin, which, for some insects, is an attractant. In this study, we analysed how the social context of the cockroaches of the speciesPeriplaneta americanamodifies preferences when individuals are offered two shelters, of which one is vanillin scented. One of the principal results of our study is that isolated individuals stay longer and more frequently in a vanillin-scented shelter, while groups choose more frequently the unscented one. Moreover, the proportion of sheltered insects is larger when the group selects the unscented shelter. Our experimental results and theoretical model suggest that the individual preference is not inverted when insects are in a group but, rather, the response to vanillin decreases the attraction between individuals. As a result, aggregation is favoured in the unscented shelter, leading therefore to a collective inversion.
Simulated seal scarer sounds scare porpoises, but not seals: species-specific responses to 12 kHz deterrence sounds
Authors: Mikkelsen Lonnie , Hermannsen Line , Beedholm Kristian , Madsen Peter Teglberg , Tougaard Jakob
Published: July 2017

Acoustic harassment devices (AHD) or ‘seal scarers’ are used extensively, not only to deter seals from fisheries, but also as mitigation tools to deter marine mammals from potentially harmful sound sources, such as offshore pile driving. To test the effectiveness of AHDs, we conducted two studies with similar experimental set-ups on two key species: harbour porpoises and harbour seals. We exposed animals to 500 ms tone bursts at 12 kHz simulating that of an AHD (Lofitech), but with reduced output levels (source peak-to-peak level of 165 dB re 1 µPa). Animals were localized with a theodolite before, during and after sound exposures. In total, 12 sound exposures were conducted to porpoises and 13 exposures to seals. Porpoises were found to exhibit avoidance reactions out to ranges of 525 m from the sound source. Contrary to this, seal observations increased during sound exposure within 100 m of the loudspeaker. We thereby demonstrate that porpoises and seals respond very differently to AHD sounds. This has important implications for application of AHDs in multi-species habitats, as sound levels required to deter less sensitive species (seals) can lead to excessive and unwanted large deterrence ranges on more sensitive species (porpoises).
Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations
Authors: Nguyen Lan Huong , Holmes Susan
Published: July 2017

Background

Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous process, often unknown. Estimating data points’ ‘natural ordering’ and their corresponding uncertainties can help researchers draw insights about the mechanisms involved.

Results

We introduce a Bayesian Unidimensional Scaling (BUDS) technique which extracts dominant sources of variation in high dimensional datasets and produces their visual data summaries, facilitating the exploration of a hidden continuum. The method maps multivariate data points to latent one-dimensional coordinates along their underlying trajectory, and provides estimated uncertainty bounds. By statistically modeling dissimilarities and applying a DiSTATIS registration method to their posterior samples, we are able to incorporate visualizations of uncertainties in the estimated data trajectory across different regions using confidence contours for individual data points. We also illustrate the estimated overall data density across different areas by including density clouds. One-dimensional coordinates recovered by BUDS help researchers discover sample attributes or covariates that are factors driving the main variability in a dataset. We demonstrated usefulness and accuracy of BUDS on a set of published microbiome 16S and RNA-seq and roll call data.

Conclusions

Our method effectively recovers and visualizes natural orderings present in datasets. Automatic visualization tools for data exploration and analysis are available at:https://nlhuong.shinyapps.io/visTrajectory/.
Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies
Authors: Fernández Rosa , Edgecombe Gregory D. , Giribet Gonzalo
Published: July 2017

The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda–Pauropoda grouping (named Dignatha). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids. We provide a summary state-of-the-art Myriapoda Tree of Life at the ordinal level, the resolution of which has been improved by phylogenomics.
In Rift Valley settings with a feedback loop, assortative mating for versatility predicts hominin brain enlargement in some detail
Authors: Calvin William H.
Published: July 2017

Hominin procedures for fire-starting, sharpening rocks, and softening roots by pounding or chopping require sustained attention for hours; shade is sought in the brush fringe bordering a grassland. Clustering these more versatile adults, while others are away hunting and gathering, provides a setup for assortative mating. This can lengthen attention span, enhance versatility and, with it, brain size. The rate of enlargement is accelerated by a boom-and-bust cycle in their meat supply, predicting the observed initiation of enlargement at −2.3 myr in the Rift Valley once boom-prone grazers evolved from the mixed feeders. Several months after lightning created a burn scar back in the brush, the new grassland enables a population boom for those grazers that discover it. Several decades later as brush regrows, they are pushed back. Their hominin followers, wicked in from the grassland’s shady fringe, boom together with the burn-scar grazers. They then follow their meat supply back to the main population. This creates an amplifying feedback loop, shiftingHomogene frequencies centrally. Brush fires are so frequent that the cosmic ray mutation rate becomes enlargement’s rate-limiter, consistent with 460 cm3/myr remaining constant during many climate shifts. The apparent tripling of enlargement rate in the last 0.2 myr vanished when the non-ancestors were omitted. AsianHomo erectusenlargement lags the ancestral trend line by 0.5 myr. Neanderthals lag somewhat less but have a late size spurt after the −70 kyrHomo sapiensOut of Africa, suggesting enlargement genes were acquired via interbreeding.
Integrated analysis of single cell transcriptomic data across conditions, technologies, and species
Authors: Butler Andrew , Satija Rahul
Published: July 2017

Single cell RNA-seq (scRNA-seq) has emerged as a transformative tool to discover and define cellular phenotypes. While computational scRNA-seq methods are currently well suited for experiments representing a single condition, technology, or species, analyzing multiple datasets simultaneously raises new challenges. In particular, traditional analytical workflows struggle to align subpopulations that are present across datasets, limiting the possibility for integrated or comparative analysis. Here, we introduce a new computational strategy for scRNA-seq alignment, utilizing common sources of variation to identify shared subpopulations between datasets as part of our R toolkit Seurat. We demonstrate our approach by aligning scRNA-seq datasets of PBMCs under resting and stimulated conditions, hematopoietic progenitors sequenced across two profiling technologies, and pancreatic cell ‘atlases’ generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across datasets, and can identify subpopulations that could not be detected by analyzing datasets independently. We anticipate that these methods will serve not only to correct for batch or technology-dependent effects, but also to facilitate general comparisons of scRNA-seq datasets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

Availability

Installation instructions, documentation, and tutorials are available athttp://www.satijalab.org/seurat
VolcanoR - web service to produce volcano plots and do basic enrichment analysis
Authors: Naumov Vladimir , Balashov Ivan , Lagutin Vadim , Borovikov Pavel , Alexeev Alexey
Published: July 2017

Summary: We introduce VolcanoR - web based tool to analyse results of differential gene expression. It takes a table containing gene name p-value and foldChange as input data. It can produce publication quality volcano plots, apply different p-value and fold change thresholds and do basic GeneOntology and KEGG enrichment analysis with selected gene set. For now it supports H.sapiens, R.norvegicus and M.musclus.

Availability and Implementation: VolcanoR is wtitten using R Shiny framework. It is publically available athttp://volcanor.bioinf.suor stand-alone application, that can be downloaded athttps://github.com/vovalive/volcanoR

Contact:looongdog@gmail.com
Abnormal Speech Motor Control in Individuals with 16p11.2 Deletions
Authors: Demopoulos Carly , Kothare Hardik , Mizuiri Danielle , Henderson-Sabes Jennifer , Fregeau Brieana , Tjernagel Jennifer , Houde John , Sherr Elliott H. , Nagarajan Srikantan S.
Published: July 2017

Speech and motor deficits are highly prevalent (>70%) in individuals with the 600 kb BP4-BP5 16p11.2 deletion; however, the mechanisms that drive these deficits are unclear, limiting our ability to target interventions and advance treatment. This study examined fundamental aspects of speech motor control in participants with the 16p11.2 deletion. To assess capacity for control of voice, we examined how accurately and quickly subjects changed the pitch of their voice within a trial to correct for a transient perturbation of the pitch of their auditory feedback. When compared to sibling controls, 16p11.2 deletion carriers show an over-exaggerated pitch compensation response to unpredictable mid-vocalization pitch perturbations. We also examined sensorimotor adaptation of speech by assessing how subjects learned to adapt their sustained productions of formants (speech spectral peak frequencies important for vowel identity), in response to consistent changes in their auditory feedback during vowel production. Deletion carriers show reduced sensorimotor adaptation to sustained vowel identity changes in auditory feedback. These results together suggest that 16p11.2 deletion carriers have fundamental impairments in the basic mechanisms of speech motor control and these impairments may partially explain the deficits in speech and language in these individuals.