bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Testosterone Synthesis and Conversion on Serum Testosterone Levels in Obese Men
Authors: Xu Xiaolin , Wang Lei , Luo Dandan , Zhang Meijie , Chen Shuhong , Wang Yupeng , Zheng Dongmei , Feng Li , Gao Ling , Yu Chunxiao , Guan Qingbo
Published: August 2018

Obesity is associated with decreased testosterone levels in males. Testosterone is synthesized by testosterone synthetic enzymes, which are stimulated by luteinizing hormone (LH). Testosterone can also be converted to estradiol via the aromatase. The objective of this study was to examine the factors related to testosterone synthesis and conversion, and to systematically evaluate the key processes that influence testosterone levels in male obesity. Three hundred and two male subjects (aged 25–45 years old) were divided according to BMI into normal weight (18.5–23.9 kg/m2), overweight (24–27.9 kg/m2), and obese (≥28 kg/m2) groups; or divided following WHR into non-abdominal obesity and abdominal obesity groups (WHR: ≥0.9). Male C57BL/6 mice were divided into normal diet (ND) and high-fat diet (HFD)-induced obesity group. Serum sex hormones and aromatase levels were measured using ELISAs. Testosterone synthetic enzymes in the testes were measured by qRT-PCR. The testosterone levels in obese men and abdominal obesity men were lower than normal men. In abdominal obesity men serum LH levels were decreased and associated with testosterone levels after multivariate regression analysis. Serum aromatase levels were increased in abdominal obesity males. In mice, compared to the ND group, the HFD group had decreased steroidogenic acute regulatory protein (StAR). However, aromatase levels in subcutaneous adipose tissue were higher in the ND group than HFD group. In conclusion, according to this study decreased testicular synthesis function and the conversion of testosterone may explain the reduction in testosterone levels in male obesity, and the decrease of testicular synthesis may change first.
Evolution of Retrograde Transvenous Obliteration Techniques
Authors: Molvar Christopher , Patel Mihir
Published: August 2018

Gastric variceal hemorrhage is a life-threatening complication of portal hypertension with a poorer prognosis compared with esophageal variceal hemorrhage. The presence of an infradiaphragmatic portosystemic shunt, often a gastrorenal shunt, allows for treatment with retrograde transvenous obliteration (RTO). RTO is an evolving treatment strategy, which includes balloon-assisted RTO, plug-assisted RTO, and coil-assisted RTO, for both gastric variceal hemorrhage and hepatic encephalopathy. RTO techniques are less invasive than transjugular intrahepatic portosystemic shunt creation, with the benefit of improved hepatic function, but at the expense of increased portal pressure. This article discusses the techniques of RTO, including patient eligibility, as well as technical and clinical outcomes, including adverse events.
Is Cord Blood Bilirubin Level a Reliable Predictor for Developing Significant Hyperbilirubinemia?
Authors: Dogan Caner , Okmen Zeynep , Gulec Seda , Aktas Selma
Published: August 2018

Objective We aimed to investigate whether cord blood bilirubin (CBB) level could be used to identify the newborns at a high risk of developing hyperbilirubinemia.

Study Design Total and direct serum bilirubin level were evaluated from umbilical cord blood of newborns. We checked blood groups and Rh status of all mothers and determined blood groups and direct Coombs test (DC) of newborns born to mothers whose blood group was O type or Rh negative to determine the maternal–fetal blood group or Rh incompatibility.

Results A total of 418 newborns were included, and phototherapy (PT) was required in 17 newborns. The cutoff value of CBB for predicting the occurrence of significant hyperbilirubinemia requiring PT was 1.67 mg/dL, with a sensitivity of 82% and specificity of 99%. The mean CBB level in babies receiving PT was 2.4 ± 0.9 mg/dL. When blood group, CBB level, DC, gender, and mode of delivery were assigned as possible risk factors, multıvariate analysis showed ABO, Rh incompatibility, and CBB level increased the risk of PT requirement.

Conclusion CBB could be useful to determine newborns at a risk of developing hyperbilirubinemia and prevent developing severe complications due to delay in diagnosis.
Association of Fetal Fraction of Cell-Free DNA and Hypertensive Disorders of Pregnancy
Authors: Koelper Nathanael , Sammel Mary , Dugoff Lorraine , Bender Whitney
Published: August 2018

Objective The objective of this study is to examine the relationship between fetal fraction and hypertensive disorders of pregnancy.

Study Design This is a retrospective cohort study of women with singleton pregnancies who had cell-free DNA (cfDNA) screening at 10 to 20 weeks of gestation. The primary outcome was the development of gestational hypertension (gHTN), preeclampsia (PEC), and PEC with severe features. Multinomial logistic regression was performed to assess the relationship between fetal fraction and pregnancy outcomes of interest while controlling for potential confounders.

Results Among 2,701 women meeting inclusion criteria, 387 (14.3%) were diagnosed with hypertensive disorders of pregnancy. First-trimester fetal fraction was significantly lower in women diagnosed with hypertensive disorders of pregnancy (10.9 vs. 12.4, p < 0.0001). An increased risk of gHTN and PEC, PEC with severe features with delivery > 34 weeks, and PEC with severe features with delivery ≤ 34 weeks was seen with lower first-trimester fetal fractions (odds ratio [OR]: 0.55, 95% confidence interval [CI] [0.36–0.83], p = 0.005; OR: 0.59, 95% CI [0.35–0.99], p = 0.048; and OR: 0.27, 95% CI [0.08–0.96], p = 0.044). The relationship between fetal fraction and hypertensive disorders of pregnancy was not statistically significant after adjusting for maternal age, race, body mass index, and chronic hypertension.

Conclusion Fetal fraction of cfDNA at 10 to 20 weeks of gestation was not associated with the development of hypertensive disorders of pregnancy.
The Association between Depressive State and Maternal Cognitive Function in Postpartum Women
Authors: Sheiner Eyal , Wainstock Tamar , Attias Monic , Walfisch Asnat , Mazor Elad
Published: August 2018

Objective Maternal amnesia is a transitional cognitive impairment occurring during pregnancy and the postpartum period. We evaluated the prevalence and extent of this suggested cognitive decline and the role of postpartum depression.

Study Design A cross-sectional study was performed in women during the immediate postpartum period. Eligible women completed the Edinburgh Postnatal Depression Scale (EPDS). Cognitive function was assessed using an objective neurocognitive test (Symbol Digit Modalities Test, SDMT90, and SDMT4) and a subjective self-estimation questionnaire (Attention Function Index [AFI]).

Results A total of 120 women completed the study questionnaires; 33.3% (40 women) exhibited signs of postpartum depression (EPDS ≥10). The subjective AFI test results correlated with the objective SDMT90 test results (r
2 = 0.2, p = 0.039). Depressed mothers scored significantly lower in the subjective AFI test (67.69 ± 12.01 in the study vs. 79.05 ± 14.3 in the comparison group; p < 0.001) and nearly significantly lower in the objective SDMT test (p = 0.057). In the multi-variable model, maternal depression was independently associated with the subjective AFI score (β  = −13.7; 95% confidence interval [CI]: −19.1 to −8.2, p < 0.001) but not with the objective SDMT score (β = −3.48; 95% CI −8.3 to 1.3, p = 0.15), while controlling for maternal age, gestational age, and ethnicity.

Conclusion Postpartum depression is common and appears to predominantly affect maternal self-assessment of cognitive ability, rather than a true cognitive impairment.
Risk Factors Linked to Central Catheter-Associated Thrombosis in Critically Ill Infants in the Neonatal Intensive Care Unit
Authors: Lambert Isabella , Tarima Sergey , Uhing Michael , Cohen Susan
Published: August 2018

Objective Our study identified risk factors for the development of clinically identifiable catheter-associated thrombosis (CT).

Study Design We performed a retrospective cohort study of neonates in whom a central catheter was present. A total of 1,475 catheters were identified in 766 patients during a 36-month study period. The odds ratio (OR) of thrombi formation in catheterized neonates was modeled using simple (single predictor) and multiple (multiple predictors) logistic regressions as well as simple and multiple Cox's proportional hazard models.

Result The incidence of CT was 1.17 per 100 neonates. Unadjusted factors including age at insertion, history of surgery before or during line placement, cholestasis, femoral location, and line size significantly increased the OR or hazards ratio (HR) of developing thrombi formation. In multiple logistic and Cox's regression analyses, three factors continued to be significantly associated with OR or HR of thrombi formation: line size, femoral location, and cholestasis.

Conclusion We conclude that clinically identifiable CT is rare in the neonatal population. Furthermore, catheter-specific characteristics are predictive for CT and require further investigation.
Side Effects of Phototherapy on Neonates
Authors: Procianoy Renato , Silveira Rita , Faulhaber Fabrízia
Published: August 2018

Phototherapy in neonates for treatment of pathological jaundice is an effective therapeutic tool that is widely used in neonatal units. Over the past years, a greater concern has emerged about the effects on the immune and inflammatory system and its potential genotoxic and side effects, especially the late ones, possibly associated with childhood diseases, showing that this treatment is not as harmless as previously believed. Numerous studies assessing these possible adverse effects of phototherapy on neonates have been published over the past years. Through this review, we seek to analyze what we know about the side effects of phototherapy in the neonatal period. The main causes of jaundice, phototherapy techniques, acute and late side effects, and effects on the immune and inflammatory system were reviewed. It was concluded that phototherapy is not a treatment free of side effects and further studies need to be conducted to elucidate its harmful effects on neonates.
Implementation of Updated Hearing Screen Guidelines in a Level IV NICU—A Quality Improvement Project
Authors: Patel Jasminkumar , Park Nesha , Manimtim Winston , George Lovya
Published: August 2018

Hearing loss is the most common congenital birth defect. In 2007, American Academy of Pediatrics updated the hearing screen guidelines to recommend hearing screen by 1 month of age, diagnostic evaluation by 3 months, and early interventions by 6 months. Early interventions have been shown to improve developmental outcome in children with hearing loss. Infants admitted to the neonatal intensive care unit (NICU) are at higher risk for hearing loss. For infants born before 34 weeks' gestation, there are no guidelines for initial hearing screen. Although auditory brain stem response can be reliably performed at 32 to 34 weeks, in most NICUs, they are screened prior to discharge per universal hearing screen guidelines. In high-risk infants, often with prolonged hospitalization, this leads to missed opportunity for early detection and implementation of early intervention services. Using quality improvement methodology, an updated hearing screen algorithm was developed and implemented in our level IV NICU along with an electronic medical record tool to improve the process of identifying infants meeting criteria for hearing screen.
Individual liberty and the importance of the concept of the people
Authors: Queiroz Regina
Published: August 2018

Through publically agreed laws that correspond to a common set of public restrictions, the ‘people as a sovereign body’ serves to protect against violations of individual liberty and despotic power. Where no such common body exists, individuals are deprived of this protection. In such cases, individuals must obey without liberty, while those in power command under a state of license. Neoliberal theorists maintain that any common personality, with its corresponding set of public and arbitrary positive and negative restrictions on liberty, undermines individual liberty. Neoliberal theory only allows for private restrictions on liberty. Against these neoliberal assumptions, we argue that rejecting public restrictions on liberty does not promote individual liberty. To the contrary, it creates conditions in which free individuals become servile and political inequality becomes entrenched, where citizens are divided into those who obey and those who command. Tracing the consequences of neoliberalism, we argue that unless we take seriously both the people as a political category and the right to equal and reciprocal coercion, individual liberty will be at risk. The article argues that neoliberalism ultimately leads to the total exclusion of certain citizensunder the veil of full liberty. With the vanishing of the people’s will comesthe utter disappearance of certain citizens, who live in a spontaneous society as if they were stateless or lawless persons. To better understand the connections between the rejection of the concept of the people, private restrictions on liberty and the fostering of the servile citizen, this paper considers the political philosophy of Hayek and Nozick. It also considers key ideas from Locke and Kant—theorists who, despite the differences between their philosophical perspectives, and despite the fact that they both provided crucial inspiration for Hayek’s political economy and Nozick’s libertarianism, stressed the protective role of the people with regard to individual liberty.
How much different are thermochemical properties of enantiomers and their racemates? Thermochemical properties of enantiopure and racemate of methyl- and butyl lactates
Authors: Verevkin Sergey P. , Emel‘yanenko Vladimir N. , Pimerzin Andrey A. , Yermalayeu Andrei V.
Published: August 2018

This work is a contribution to the molecular understanding of the thermodynamic properties of the chiral compounds. A comprehensive thermochemical study of the liquid enantiopure and racemate pairs of optically active alkyl lactates has been performed. Vapor pressures of DL-(±)-, L-(−)-methyl-, and DL-(±)-, L-(−)-n-butyl esters of lactic acid were measured by the transpiration method. The liquid phase standard molar enthalpies of formation of these esters were measured by using the high-precision combustion calorimetry. The standard molar enthalpies of vaporization of alkyl lactates at 298.15 K were derived from vapor pressure temperature dependencies. Thermochemical data of these compounds were collected, evaluated, and tested for internal and external consistency. The high-level G4 quantum-chemical method was used for mutual validation of the experimental and theoretical gas phase enthalpies of formation of alkyl lactates. A critical review of the available thermochemical data for the liquid and crystalline enantiopure and racemate pairs of optically active compounds has been performed. Useful general trends in energetics of sublimation, vaporization, and formation of optically active compounds have been revealed. This knowledge is required for evaluation of new and already available experimental data for the chiral compounds, and it can be helpful to assess volatility or feasibility of processes to separate enantiomers.
Deformation behaviors of Au nanotubes under torsion by molecular dynamics simulations
Authors: Hwang Yeong-Maw , Pan Cheng-Tang , Lu Ying-Xu , Jian Sheng-Rui , Juang Jenh-Yih
Published: August 2018

In this study, the mechanical deformation behaviors of Au nanotubes (Au-NTs) under torsional stress are investigated using molecular dynamics (MD) simulations. The inter-atomic interaction is modeled using the embedded-atom potential. In particular, the effects of loading rate, thickness and length of the nanotube, as well as the thermal effects were systematically explored. The results indicated that higher loading rate, longer length and thinner wall thickness all led to a larger value of critical torsional angle (θcr), which signifies the onset of plastic deformation. On the other hand, θcr decreases with increasing temperature in all simulated results. Moreover, the torsional buckling deformation behavior and geometrical instability are found to strongly depend on the length of Au-NTs, the applied strain rate and temperature with vastly different underlying mechanisms.
Asymptotic analysis of resonances of small volume high contrast linear and nonlinear scatterers
Authors: Meklachi Taoufik , Moskow Shari , Schotland John C.
Published: August 2018

We consider the asymptotic analysis of the resonances of high contrast small volume scatterers for linear and nonlinear scalar waves. The resonance problem is formulated as a nonlinear eigenvalue problem. We derive asymptotic formulae for linear scatterers and nonlinear scatterers of the Kerr type. Our results are illustrated with numerical examples.
Acceleration of oxidation process of iron in supercritical water containing dissolved oxygen by the formation of H2O2
Authors: Zhang Caili , Li Jianguo , Zhang Zhuxia , Dong Nan , Wang Jian , Liu Ying , Ling Lixia , Han Peide
Published: August 2018

To improve fuel use and energy-conversion efficiency and reduce the emission of pollutants, oxygenation is now deemed an effective chemical treatment of water in supercritical and ultra-supercritical power plants. Supercritical water with dissolved oxygen significantly enhances the oxidation rate of steels in the main steam pipeline and super-heater header. However, at the atomic scale, the mechanism of metal oxidation in supercritical water containing dissolved oxygen is unknown and has not been investigated by simulation. In this work, the oxidation of iron in supercritical water containing dissolved oxygen is studied by ab initio molecular dynamics and first principles calculations. The results indicate that dissolved oxygen in supercritical water dramatically accelerates the oxidation of iron. With the help of oxygen, the decomposition of water occurs on the iron surface, thereby producing more iron oxides and iron hydroxides. Additionally, hydrogen peroxide (H2O2) forms as an intermediate product, instantaneously decomposing to form iron hydroxides, and this is another reason for the enhancement in the oxidation of steel by supercritical water containing dissolved oxygen. Based on the results from ab initio molecular dynamics, we develop herein typical models of water molecules and oxygen molecules reacting directly on the iron surface and then carry out first-principles calculations. The results show that water decomposes on the iron surface only with the assistance of adjacent oxygen molecules and in the absence of surrounding water molecules. This investigation deepens our understanding of the oxidation mechanism of metal in supercritical water containing dissolved oxygen. The ideas and methods implemented in this work can also be used to study other materials exposed to supercritical water involving oxygen.
DNA molecules deviate from shortest trajectory when driven through hydrogel
Authors: Guan Juan , Chen Kejia , Jee Ah-Young , Granick Steve
Published: August 2018

Dynamic fluorescence-based single-molecule imaging of λ-DNA molecules driven through agarose hydrogels by DC electric fields reveals that passage through the hydrogel (98.5% water content) induces mobility orthogonal to the external field. Tortuous paths followed by the DNA molecules, which are heavily entangled in the hydrogel mesh as their contour length is nearly 100 times the hydrogel mesh size of 200 nm, cause them to appear to diffuse orthogonal to the driving force. The higher the driving field, from 2 to 16 V/cm, the higher the off-axis dispersion is, over the same time interval. We measure the off-axis displacement distribution over 3 orders of magnitude of probability density and find a master curve after normalizing for time (t) elapsed, but the power of time for normalizing increases with the external field, from t0.25 to t0.6 with increasing field. Comparing trajectories over the same distance traveled in the electric field direction, we observe whereas for the highest field strengths DNA molecules come closest to taking the shortest trajectory between two points in space, deviations from the shortest trajectory grow larger and larger (up to 40% larger) as one approaches the case of small yet finite external field strength.
Universal rotation of nanowires in static uniform electric fields in viscous dielectric liquids
Authors: Farain K. , Esfandiar A. , Moshfegh A. Z.
Published: August 2018

The wide utilization of nanomanipulation as a promising approach in microorganisms, nanoelectromechanical systems, and assembly of nanostructures remarks the importance of nanostructures' motion in electric fields. Here, we study the rotational dynamics of metallic and non-metallic nanowires (NWs) in a static uniform electric field in viscous dielectric liquids. For metallic NWs, it has been theoretically shown that the electric field-induced rotation is practically independent of the geometrical dimensions and the electrical properties of NWs. Our experimental results for suspended silver (Ag) NWs in microscope oil are perfectly in agreement with this model. However, in the case of TiO2 NWs, as an example of non-metallic NWs, we surprisingly observe the exact same electromechanical torque as metallic Ag NWs under the same experimental conditions. This is mainly explained by NWs' high aspect-ratio which allows one to ignore the non-axial component of the electric field inside the NWs. Therefore, all high-aspect-ratio metallic Ag and non-metallic TiO2 NWs demonstrate an identical rotational speed in the same dielectric liquid and electric field. This result can be used for the controllable alignment or synchronous rotation of an ensemble of different types of NWs for hybrid and advanced devices.
Flow structure and evaporation behavior of an acoustically levitated droplet
Authors: Kobayashi K. , Goda A. , Hasegawa K. , Abe Y.
Published: August 2018

We experimentally investigate the flow structure and evaporation behavior of a droplet in an ∼19 kHz single-axis acoustic levitator. Decane, nonane, octane, heptane, hexane, and pentane are used as test fluids to investigate the effect of saturated vapor pressure on the internal and external flow fields. Under low saturated vapor pressure (decane and nonane), the direction of the external flow is away from the surface of the droplet. However, at a relatively higher saturated vapor pressure (octane, heptane, hexane, and pentane), the direction of the external flow is toward the surface of the droplet, with vortices forming near the droplet surface. For droplets with a low saturated vapor pressure (decane, nonane, octane, and heptane), the internal flow is similar to that in the case of rigid body rotation. Finally, under high saturated vapor pressure (hexane and pentane), the internal flow is an unsteady 3D complex flow. The experimental results indicate that the vapor concentration distribution around a levitated droplet surface correlates closely with changes in the external and internal flows.
Using Laser-Induced Rydberg Spectroscopy diagnostic for direct measurements of the local electric field in the edge region of NSTX/NSTX-U: Modeling
Authors: Reymond L. , Diallo A. , Vekselman V.
Published: August 2018

We discuss a novel diagnostic allowing direct measurements of the local electric field in the edge region of NSTX/NSTX-U. This laser based diagnostic’s principle consists of depleting the naturally populated n = 3 level to a Rydberg state—sensitive to electric fields—that will result in a suppression of part of the Dα emission. We refer to this approach as Laser-Induced Rydberg Spectroscopy. It is shown that the local electric field can be measured through the Stark induced resonances observed as dips in the Dα emission. Using forward-modeling of simulated absorption spectra, we show precisions reaching ±2 kV m−1 in regions with a local electric field of 15 kV m−1.
Three-dimensional magnetohydrodynamic (MHD) flow of Maxwell nanofluid containing gyrotactic micro-organisms with heat source/sink
Authors: Ali Aamir , Sulaiman M. , Islam S. , Shah Zahir , Bonyah Ebenezer
Published: August 2018

This paper discusses the three-dimensional flow of Maxwell nanofluid containing gyrotactic micro-organisms over a stretching surface. The effects of magnetic field and heat source/sink are also considered. Theory of microorganisms is utilized to stabilize the suspended nanoparticles through bioconvection induced by the effects of buoyancy forces. HAM (homotopy analysis method) is used to acquire analytic solution for the governing nonlinear equations. The effects of Deborah number, Hartmann number, mixed convection parameter, buoyancy ratio parameter, bioconvection Rayeigh number, stretching ratio parameter, brownian diffusion and thermophoresis diffusion parameters, Prandtl number, Lewis number, micro-organisms concentration difference parameter, bioconvection Peclet number and the bioconvection Lewis number on velocity, temperature, density of motile microorganisms and nanoparticle concentration are discussed graphically. The local Nusselt, Sherwood and motile micro-organisms numbers are also analyzed graphically. The reduction of the boundary layer thickness and velocity due to magnetic field is noted. The heat source/sink parameter have opposite effects on the temperature profile. We found that In comparison to the case of heat sink the thermal boundary layer thickness and temperature increases in the case of heat source.
A practical wide-field Raman imaging method with high spectral and spatial resolution
Authors: Li Haibo , Luo Wenhua , Li Gan , Zhang Guangfeng , Zhang Pengcheng , Li Changmao , Gu Yuejiao
Published: August 2018

Raman imaging has a great advantage in characterizing inhomogeneous systems. A practical wide-field Raman imaging platform is developed that shows major improvements on imaging speed, sensitivity, and resolution. Different from the traditional Raman imaging systems using the wavelength-fixed lasers and the chromatic dispersion devices, this system adopts an inverted architecture, integrated with a tunable laser and the wavelength-fixed filters. Owing to the high transmission of the fixed filters, the imaging sensitivity can be improved 5-10 times in comparison to the present wide-field Raman imaging setups using liquid-crystal tunable filters. Via combining with the high-power tunable laser, Raman images could be obtained in minutes and the Raman shift of the images could be tuned easily and accurately. The resolution of this system can reach 1.5 cm−1 in the spectrum and 490 nm in space, which could provide more fingerprint details of the analytes. This effective Raman imaging method allowing us to see chemical spatial variations on microscale is anticipated to be widely applied in scientific research fields.
Preface: Special Topic on Enhanced Sampling for Molecular Systems
Authors: Laio Alessandro , Panagiotopoulos Athanassios Z. , Zuckerman Daniel M.
Published: August 2018

This special topic highlights recent developments in enhanced sampling methods for molecular-level simulations of chemical and biological systems. These methods are designed to enable more efficient exploration of phase space and extend the time scales that can be explored by simulations.
Progress in integrating natural and social science in marine ecosystem-based management research
Authors: Alexander K. A. , Hobday A. J. , Cvitanovic C. , Ogier E. , Nash K. L. , Cottrell R. S. , Fleming A. , Fudge M. , Fulton E. A. , Frusher S. , Kelly R. , MacLeod C. K. , Pecl G. T. , van Putten I. , Vince J. , Watson R. A.
Published: August 2018

Climate change, in combination with population growth, is placing increasing pressure on the world’s oceans and their resources. This is threatening sustainability and societal wellbeing. Responding to these complex and synergistic challenges requires holistic management arrangements. To this end, ecosystem-based management (EBM) promises much by recognising the need to manage the ecosystem in its entirety, including the human dimensions. However, operationalisation of EBM in the marine environment has been slow. One reason may be a lack of the inter-disciplinary science required to address complex social–ecological marine systems. In the present paper, we synthesise the collective experience of the authors to explore progress in integrating natural and social sciences in marine EBM research, illustrating actual and potential contributions. We identify informal barriers to and incentives for this type of research. We find that the integration of natural and social science has progressed at most stages of the marine EBM cycle; however, practitioners do not yet have the capacity to address all of the problems that have led to the call for inter-disciplinary research. In addition, we assess how we can support the next generation of researchers to undertake the effective inter-disciplinary research required to assist with operationalising marine EBM, particularly in a changing climate.
The LeuT-fold neurotransmitter:sodium symporter MhsT has two substrate sites
Authors: Quick Matthias , Abramyan Ara M. , Wiriyasermkul Pattama , Weinstein Harel , Shi Lei , Javitch Jonathan A.
Published: August 2018

Significance

The crystal structure of the human serotonin transporter (hSERT) features a drug bound not only in the primary site, but also simultaneously in a second site, thereby supporting the existence of two binding sites in neurotransmitter:sodium symporters (NSSs) as we demonstrated previously for the bacterial NSS homolog LeuT. Here, we provide evidence that MhsT, another NSS homolog, can simultaneously bind substrate molecules both in its primary substrate (S1) site and in its secondary substrate (S2) site. As in LeuT, substrate binding to both the S1 and S2 sites of MhsT is critical for transport, providing further support for a mechanistic model in which the allosteric interaction between the two substrate sites is a key element of Na
+
-coupled symport.
Solving high-dimensional partial differential equations using deep learning
Authors: Han Jiequn , Jentzen Arnulf , E Weinan
Published: August 2018

Significance

Partial differential equations (PDEs) are among the most ubiquitous tools used in modeling problems in nature. However, solving high-dimensional PDEs has been notoriously difficult due to the “curse of dimensionality.” This paper introduces a practical algorithm for solving nonlinear PDEs in very high (hundreds and potentially thousands of) dimensions. Numerical results suggest that the proposed algorithm is quite effective for a wide variety of problems, in terms of both accuracy and speed. We believe that this opens up a host of possibilities in economics, finance, operational research, and physics, by considering all participating agents, assets, resources, or particles together at the same time, instead of making ad hoc assumptions on their interrelationships.
Patient–physician gender concordance and increased mortality among female heart attack patients
Authors: Greenwood Brad N. , Carnahan Seth , Huang Laura
Published: August 2018

Significance

A large body of medical research suggests that women are less likely than men to survive traumatic health episodes like acute myocardial infarctions. In this work, we posit that these difficulties may be partially explained, or exacerbated, by the gender match between the patient and the physician. Findings suggest that gender concordance increases a patient’s probability of survival and that the effect is driven by increased mortality when male physicians treat female patients. Empirical extensions indicate that mortality rates decrease when male physicians practice with more female colleagues or have treated more female patients in the past.
Isolating the roles of movement and reproduction on effective connectivity alters conservation priorities for an endangered bird
Authors: Robertson Ellen P. , Fletcher Robert J. , Cattau Christopher E. , Udell Bradley J. , Reichert Brian E. , Austin James D. , Valle Denis
Published: August 2018

Significance

Animal movement has captured the interest of biologists over the past century. Although animal movement is increasingly well understood, it is unclear how postmovement reproduction varies across landscapes despite its important role in many ecological and evolutionary processes. We address this problem by isolating the roles of movement and postmovement reproduction for connecting local populations using 9 years of data on an endangered bird across its entire geographic range. Our findings highlight the important role that postmovement reproduction can play for connecting animal populations across landscapes.
Natural and managed watersheds show similar responses to recent climate change
Authors: Ficklin Darren L. , Abatzoglou John T. , Robeson Scott M. , Null Sarah E. , Knouft Jason H.
Published: August 2018

Significance

Climate change is expected to alter streamflow volume and variability in watersheds throughout the world, which will have impacts on agricultural, aquatic, and urban environments. Human modifications such as the building of reservoirs and the extraction of water for agricultural and urban uses, however, are thought to mask climate-induced changes in streamflow. Using observed streamflow data from over 3,000 sites from 1981 to 2015, this work identifies negative trends in streamflow throughout the southern and western portions of the United States and positive trends across the eastern portion of the United States and Canada. Within these regions, streamflow trends from human-modified sites are similar to unimpacted sites, indicating that the signal of climate change is apparent in all streamflow systems.
Five-S-isotope evidence of two distinct mass-independent sulfur isotope effects and implications for the modern and Archean atmospheres
Authors: Lin Mang , Zhang Xiaolin , Li Menghan , Xu Yilun , Zhang Zhisheng , Tao Jun , Su Binbin , Liu Lanzhong , Shen Yanan , Thiemens Mark H.
Published: August 2018

Significance

Anomalous sulfur isotopic compositions preserved in sedimentary rocks older than ∼2.5 billion years have been widely interpreted as the products of UV photolysis of sulfur dioxide in an anoxic atmosphere and used to track the history of primitive Earth and evolution of early life. In this study, we present strong observational evidence that there is an additional process that produces similar anomalous sulfur isotope signatures. This previously unknown origin not only offers a tool for quantifying the present-day atmospheric sulfur budget and evaluating its influences on climate and public health but also implies that anomalous sulfur isotopic compositions in some of the oldest rocks on Earth might have been produced in a way different from that previously thought.
Lithium metal stripping beneath the solid electrolyte interphase
Authors: Shi Feifei , Pei Allen , Boyle David Thomas , Xie Jin , Yu Xiaoyun , Zhang Xiaokun , Cui Yi
Published: August 2018

Significance

This study explores the stripping of lithium anodes under various current densities and in different liquid electrolyte systems. We discovered nanovoid formation between the lithium and the solid electrolyte interphase (SEI). Lithium polarization behavior has been systematically investigated with a three-electrode system and ultramicroelectrode. The diffusion and migration of lithium cations across the SEI have been determined to be the main contributors to the stripping overpotential. Two modes of stripping are proposed based on the passivation condition of lithium: stripping on passivated lithium and pitting on lithium after SEI layer breakdown. The present work provides a mechanistic explanation of Coulombic efficiency decay under high charging current density. We also demonstrate that metallurgical factors greatly accelerate the local dissolution of lithium.
Robust nanoscopy of a synaptic protein in living mice by organic-fluorophore labeling
Authors: Masch Jennifer-Magdalena , Steffens Heinz , Fischer Joachim , Engelhardt Johann , Hubrich Jasmine , Keller-Findeisen Jan , D’Este Elisa , Urban Nicolai T. , Grant Seth G. N. , Sahl Steffen J. , Kamin Dirk , Hell Stefan W.
Published: August 2018

Significance

In vivo fluorescence microscopy with resolution well beyond the diffraction limit entails complexities that challenge the attainment of sufficient image brightness and contrast. These challenges have so far hampered investigations of the nanoscale distributions of synaptic proteins in the living mouse. Here, we describe a combination of stimulated emission depletion microscopy and endogenous protein labeling, providing high-quality in vivo data of the key scaffolding protein PSD95 at the postsynaptic membrane, which frequently appeared in extended distributions rather than as isolated nanoclusters. Operating in the far-red to near-IR wavelength range, this combination promises reduced photostress compared with prior in vivo nanoscopy at much shorter wavelengths.
Volatile element evolution of chondrules through time
Authors: Mahan Brandon , Moynier Frédéric , Siebert Julien , Gueguen Bleuenn , Agranier Arnaud , Pringle Emily A. , Bollard Jean , Connelly James N. , Bizzarro Martin
Published: August 2018

Significance

We present time-anchored elemental abundance data for some of the Solar System’s first solids by tracking Pb−Pb dated chondrule compositions. Volatile element contents generally rise, while redox conditions (based on chondrule Mn/Na ratios) decline beginning ∼1 My after Solar System formation (∼4,567 Ma). These results reflect a continued rise in volatile element contents and their fugacities during chondrule recycling, and early water influx to the inner Solar System followed by its express removal. These observations support the early formation of Mars under oxidizing condition and Earth’s protracted growth under more reducing conditions in an environment increasing in volatile contents with time, while also calling into question the coupling of water and volatile elements during Solar System evolution.
Third DWF1 paralog in Solanaceae, sterol Δ
24
-isomerase, branches withanolide biosynthesis from the general phytosterol pathway
Authors: Knoch Eva , Sugawara Satoko , Mori Tetsuya , Poulsen Christian , Fukushima Atsushi , Harholt Jesper , Fujimoto Yoshinori , Umemoto Naoyuki , Saito Kazuki
Published: August 2018

Significance

Withanolides form a major class of plant steroids with unique side-chain modifications. Withanolides are one of the main active components in an Indian Ayurvedic medicinal plant, ashwagandha, which has been used for over 3,000 y. Because of their highly diversified structures, withanolides are promising pharmacological compounds with proven antiinflammatory and anticancer properties. We identified a sterol Δ
24
-isomerase (24ISO) catalyzing the first committed step in the biosynthesis of withanolides and related compounds. Identification of 24ISO paves the way for targeted manipulations to increase withanolide yields and as a starting point to elucidate the downstream pathway of yet-unknown withanolide biosynthesis. This study also demonstrates how the evolution of enzymes catalyzing double-bond modifications of triterpene side chains lead to diversity in structures and functions.
Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion
Authors: Löber Ulrike , Hobbs Matthew , Dayaram Anisha , Tsangaras Kyriakos , Jones Kiersten , Alquezar-Planas David E. , Ishida Yasuko , Meers Joanne , Mayer Jens , Quedenau Claudia , Chen Wei , Johnson Rebecca N. , Timms Peter , Young Paul R. , Roca Alfred L. , Greenwood Alex D.
Published: August 2018

Significance

Endogenous retroviruses (ERVs) are proviral sequences that result from host germ-line invasion by exogenous retroviruses. The majority of ERVs are degraded. Using the koala retrovirus (KoRV) as a model system, we demonstrate that recombination with an ancient koala retroelement disables KoRV, and that recombination occurs frequently and early in the invasion process. Recombinant KoRVs (recKoRVs) are then able to proliferate in the koala germ line. This may in part explain the generally degraded nature of ERVs in vertebrate genomes and suggests that degradation via recombination is one of the earliest processes shaping retroviral genomic invasions.
When did
Homo sapiens
first reach Southeast Asia and Sahul?
Authors: O’Connell James F. , Allen Jim , Williams Martin A. J. , Williams Alan N. , Turney Chris S. M. , Spooner Nigel A. , Kamminga Johan , Brown Graham , Cooper Alan
Published: August 2018

Anatomically modern humans (
Homo sapiens
, AMH) began spreading across Eurasia from Africa and adjacent Southwest Asia about 50,000–55,000 years ago (
ca
. 50–55 ka). Some have argued that human genetic, fossil, and archaeological data indicate one or more prior dispersals, possibly as early as 120 ka. A recently reported age estimate of 65 ka for Madjedbebe, an archaeological site in northern Sahul (Pleistocene Australia–New Guinea), if correct, offers what might be the strongest support yet presented for a pre–55-ka African AMH exodus. We review evidence for AMH arrival on an arc spanning South China through Sahul and then evaluate data from Madjedbebe. We find that an age estimate of >50 ka for this site is unlikely to be valid. While AMH may have moved far beyond Africa well before 50–55 ka, data from the region of interest offered in support of this idea are not compelling.
Cargo transport shapes the spatial organization of a microbial community
Authors: Shrivastava Abhishek , Patel Visha K. , Tang Yisha , Yost Susan Connolly , Dewhirst Floyd E. , Berg Howard C.
Published: August 2018

Significance

We describe a situation in which bacteria typical of the human oral microbiome are organized spatially by gliding cells, species of
Capnocytophaga
, that move backward and forward over the substratum. The mobile adhesins that pull the cells over the substratum also attach to cells of nonmotile bacterial species, which are carried up and down the motile cells as cargo. The synchronized transport of nonmotile cargo bacteria helps to shape a polymicrobial community.
The voltage-gated sodium channel pore exhibits conformational flexibility during slow inactivation
Authors: Chatterjee Soumili , Vyas Rajan , Chalamalasetti Sreevatsa V. , Sahu Indra D. , Clatot Jérôme , Wan Xiaoping , Lorigan Gary A. , Deschênes Isabelle , Chakrapani Sudha
Published: August 2018

Slow inactivation in voltage-gated sodium channels (NaVs) directly regulates the excitability of neurons, cardiac myocytes, and skeletal muscles. Although NaV slow inactivation appears to be conserved across phylogenies—from bacteria to humans—the structural basis for this mechanism remains unclear. Here, using site-directed labeling and EPR spectroscopic measurements of membrane-reconstituted prokaryotic NaV homologues, we characterize the conformational dynamics of the selectivity filter region in the conductive and slow-inactivated states to determine the molecular events underlying NaV gating. Our findings reveal profound conformational flexibility of the pore in the slow-inactivated state. We find that the P1 and P2 pore helices undergo opposing movements with respect to the pore axis. These movements result in changes in volume of both the central and intersubunit cavities, which form pathways for lipophilic drugs that modulate slow inactivation. Our findings therefore provide novel insight into the molecular basis for state-dependent effects of lipophilic drugs on channel function.
Earing prediction of AA 2008-T4 with anisotropic Drucker yield function based on the second and third stress invariants
Authors: Zhang Saijun , Lou Yanshan , Yoon Jeong Whan
Published: August 2018

This paper applies anisotropic Drucker yield function [14] (Lou and Yoon, 2018, Int. J. Plasticity 101, 125-55) to predict earing profile after cup deep drawing of AA 2008-T4. The new yield function is implemented into ABAQUS/Explicit using semi-implicit integration algorithm to calculate the increment of plastic strain. Both associated and non-associated flow rules are incorporated in this study. The predicted anisotropy and cup height profile are compared with the experimental results and those predicted from the Hill48, Yld91 and Yld2004-18p yield functions. It is observed that the earing profile predicted from the new yield function shows high accuracy. The computation time is also compared to investigate the computation cost of different yield functions. The comparison reveals that it takes the shortest time for the Hill48 function, the anisotropic Drucker yield function reduces 30%∼40% of computation cost compared with the Yld91 and Yld2004-18p functions. It is concluded from the simulation of cup deep drawing that the new yield function can provide high accurate numerical analysis of plastic deformation for anisotropic metals with competitive computation cost.
Impact of similarity metrics on single-cell RNA-seq data clustering
Authors: Kim Taiyun , Chen Irene Rui , Lin Yingxin , Wang Andy Yi-Yang , Yang Jean Yee Hwa , Yang Pengyi
Published: August 2018

Advances in high-throughput sequencing on single-cell gene expressions [single-cell RNA sequencing (scRNA-seq)] have enabled transcriptome profiling on individual cells from complex samples. A common goal in scRNA-seq data analysis is to discover and characterise cell types, typically through clustering methods. The quality of the clustering therefore plays a critical role in biological discovery. While numerous clustering algorithms have been proposed for scRNA-seq data, fundamentally they all rely on a similarity metric for categorising individual cells. Although several studies have compared the performance of various clustering algorithms for scRNA-seq data, currently there is no benchmark of different similarity metrics and their influence on scRNA-seq data clustering. Here, we compared a panel of similarity metrics on clustering a collection of annotated scRNA-seq datasets. Within each dataset, a stratified subsampling procedure was applied and an array of evaluation measures was employed to assess the similarity metrics. This produced a highly reliable and reproducible consensus on their performance assessment. Overall, we found that correlation-based metrics (e.g. Pearson’s correlation) outperformed distance-based metrics (e.g. Euclidean distance). To test if the use of correlation-based metrics can benefit the recently published clustering techniques for scRNA-seq data, we modified a state-of-the-art kernel-based clustering algorithm (SIMLR) using Pearson’s correlation as a similarity measure and found significant performance improvement over Euclidean distance on scRNA-seq data clustering. These findings demonstrate the importance of similarity metrics in clustering scRNA-seq data and highlight Pearson’s correlation as a favourable choice. Further comparison on different scRNA-seq library preparation protocols suggests that they may also affect clustering performance. Finally, the benchmarking framework is available at http://www.maths.usyd.edu.au/u/SMS/bioinformatics/software.html.
Global importance of RNA secondary structures in protein-coding sequences
Authors: Fricke Markus , Gerst Ruman , Ibrahim Bashar , Niepmann Michael , Marz Manja
Published: August 2018

Motivation

The protein-coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base-pairing.

Results

We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein-coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.

Supplementary information

Supplementary data are available at Bioinformatics online.