bluuebunny/crossref_metadata_2025 huggingface dataset:
Angle-/temperature-dependence of Raman scattering in layered NbSe3 crystal
Authors: Chen Haiping , Ma Zehao , Shao Yanjie , Rehman Zia ur , Zhang Ke , He Qun , Song Li
Published: September 2017

Distinguishing the lattice vibrational modes of different Raman peaks and further studying the temperature-dependent behaviour of the different Raman modes are fundamental subjects for Raman spectroscopy of single crystal. Herein, we conducted a comprehensive study of angle- and temperature-dependant Raman scattering behaviour in high-crystalline NbSe3 layers prepared by chemical vapour transport method. The polarization experiments performed on NbSe3’s (100) crystal surface revealed that the Raman peaks could be clearly identified as Ag and Bg vibrational modes, indicating significantly anisotropic structure. Meanwhile, the effect of charge density wave (CDW) transition on the lattice vibrational behaviour was studied by investigating temperature-dependent Raman scattering spectra above and below the CDW transition temperature. It was observed that Raman shifts versus temperature for the four prominent Raman peaks of NbSe3 which belonged to Ag vibrational mode exhibited linear softening behaviour as the temperature increased from 83k to 293k. The temperature coefficient of Raman peaks fitted by Grüneisen model further confirmed the anharmonicity of the lattice in NbSe3 crystal, suggesting that the changes of ionic positions across the CDW transition has small effect on its Raman scattering behaviour.
Energetics of pure and doped helium droplets - application to interpreting pick-up experiments
Authors: Dutra Matthew , Hinde Robert
Published: September 2017

We use helium density functional theory to calculate the energies of spherically symmetric 4He helium droplets both with and without heteroatom dopants. Self-consistent calculations using an imaginary time propagation method are used to compute structural and energetic properties of these droplets ranging in size from 50 to 9500 atoms. Particular attention is given to the solvation energies of the resident dopant atoms, as these values play an important role in experimental superfluid helium calorimetry techniques. We also suggest a method of predicting new droplet size distributions following dopant pickup using the chemical potential values obtained from our calculations.
Spontaneous formation of highly periodic nano-ripples in inclined deposition of Mo/Si multilayers
Authors: Voronov D. L. , Gawlitza P. , Braun S. , Padmore H. A.
Published: September 2017

We investigated the growth of Mo/Si multilayers (ML) deposited using a highly collimated flux of ion-beam sputtered particles for a wide range of deposition angles. Growth of the multilayers at normal and moderately inclined deposition is dominated by surface relaxation resulting in smooth interfaces of the multilayer stack. The first signs of interface roughening are observed at a deposition angle of 45° with respect to the normal to the substrate surface. At an oblique angle of 55°, the ML interfaces undergo fast progressive roughening from the substrate to the top of the ML stack, leading to the formation of ripples which are perpendicular to the deposition flux direction. Deposition of the multilayer at an angle of 65° results in a highly periodic lateral ripple structure with a period of 10 nm. The mature ripple pattern forms during growth of only the first few layers and then stabilizes. The ripples propagate through the whole ML stack with almost no changes in frequency and amplitude, resulting in a highly periodic bulk array composed of silicon and molybdenum nano-rods closely packed in a 6-fold symmetric lattice. We present a simple model for the ripple growth, which gives results that are in good agreement with experimental data.
Sharp improvement of flashover strength from composite micro-textured surfaces
Authors: Huo Yankun , Liu Wenyuan , Ke Changfeng , Chang Chao , Chen Changhua
Published: September 2017

A composite micro-textured surface structure is proposed and demonstrated to enhance the surface flashover strength of polymer insulators used in vacuum. The structure is fabricated in two stages, with periodic triangular grooves of approximately 210 μm in width formed in the first stage and micro-holes of approximately 2 μm coated on the inner surface of grooves in the second. The aim is to exploit the synergistic effects between the grooves and micro-holes to suppress the secondary electron yield to obtain a better flashover performance. To acquire insulators with the composite micro-textured surface, the CO2 laser processing technique is applied to treat the surface of the PMMA insulators. The test results show that the flashover voltages of the insulators with the two-stage fabricated structure increase by 150% compared with the untreated samples in the best state. Compared with the traditional macro-groove structures on insulators, the proposed composite micro-textured insulators exhibit a better surface flashover performance.
Determination of charge transport activation energy and injection barrier in organic semiconductor devices
Authors: Züfle S. , Altazin S. , Hofmann A. , Jäger L. , Neukom M. T. , Brütting W. , Ruhstaller B.
Published: September 2017

Charge carrier transport in organic semiconductor devices is thermally activated with characteristic activation energies in the range of 0.2–0.6 eV, leading to strongly temperature-dependent behaviour. For designing efficient organic semiconductor materials and devices, it is therefore indispensable to understand the origin of these activation energies. We propose that in bilayer organic light-emitting diodes (OLEDs) employing a polar electron transport layer, as well as in metal-insulator-semiconductor (MIS) devices, the hole injection barrier Einj and the hole mobility activation energy Eμ can be decoupled from each other if temperature-dependent capacitance-frequency (C-f-T) and MIS-CELIV (charge extraction by linearly increasing voltage) experiments are combined. While the C-f-T signal contains information of both injection and transport, the CELIV current is expected to be insensitive to the electrode injection properties. We employ numerical drift-diffusion simulations to investigate the accuracy of this analytical parameter extraction approach and to develop criteria for its validity. We show that the implicit assumption of constant charge density and field profiles leads to systematic errors in determining the activation energies. Thus, one should be aware of the intrinsic limitations of the analytical Arrhenius fit, and for more accurate parameter determination a full drift-diffusion modelling is advised. Applying the analytical method to a standard bilayer OLED, we find that the total activation energy of 0.5 eV for the hole current can be split into contributions of ≈0.25 eV each for injection barrier and mobility. Finally, we also discuss the broader applicability of this method for other device stacks and material combinations.
Electron mobility limited by optical phonons in wurtzite InGaN/GaN core-shell nanowires
Authors: Liu W. H. , Qu Y. , Ban S. L.
Published: September 2017

Based on the force-balance and energy-balance equations, the optical phonon-limited electron mobility in InxGa1-xN/GaN core-shell nanowires (CSNWs) is discussed. It is found that the electrons tend to distribute in the core of the CSNWs due to the strong quantum confinement. Thus, the scattering from first kind of the quasi-confined optical (CO) phonons is more important than that from the interface (IF) and propagating (PR) optical phonons. Ternary mixed crystal and size effects on the electron mobility are also investigated. The results show that the PR phonons exist while the IF phonons disappear when the indium composition x < 0.047, and vice versa. Accordingly, the total electron mobility μ first increases and then decreases with indium composition x, and reaches a peak value of approximately 3700 cm2/(V·s) when x = 0.047. The results also show that the mobility μ increases as increasing the core radius of CSNWs due to the weakened interaction between the electrons and CO phonons. The total electron mobility limited by the optical phonons exhibits an obvious enhancement as decreasing temperature or increasing line electron density. Our theoretical results are expected to be helpful to develop electronic devices based on CSNWs.
Design and verification of monopole patch antenna systems to generate orbital angular momentum waves
Authors: Liu Dandan , Gui Liangqi , Zhou Cong , Zhang Zixiao , Chen Han , Jiang Tao
Published: September 2017

Monopole patch antenna systems, which can generate orbital angular momentum (OAM) waves at 2.4GHz, are proposed in this paper. The proposed antenna systems have advantages of simple planar structure and small size of antenna element. Design, simulation, fabrication and measurement of the proposed antenna systems are presented. Two feeding networks, which constitute the proposed antenna systems with monopole patch antenna array, are designed to generate modes 1 and 2 of OAM waves. The antenna systems for both modes are shown to be effective in generating OAM waves of modes 1 and 2 from both simulation and three types of measurement: radiation pattern, phase distribution and phase gradient. Simulation and measurement results of radiation pattern and phase distribution have shown very close results. Phase gradient measurement results has verified that the generated waves from the antenna systems are indeed OAM waves.
Enhanced optical nonlinearities in CMOS-compatible ultra-silicon-rich nitride photonic crystal waveguides
Authors: Sahin E. , Ooi K. J. A. , Chen G. F. R. , Ng D. K. T. , Png C. E. , Tan D. T. H.
Published: September 2017

We present the design, fabrication, and characterization of photonic crystal waveguides (PhCWs) on an ultra-silicon-rich nitride (USRN) platform, with the goal of augmenting the optical nonlinearities. The design goals are to achieve an optimized group index curve on the PhCW band edge with a non-membrane PhCW with symmetric SiO2 undercladding and overcladding, so as to maintain back-end CMOS compatibility and better structural robustness. Linear optical characterization, as well as nonlinear optical characterization of PhCWs on ultra-silicon-rich nitride is performed at the telecommunication wavelengths. USRN's negligible two-photon absorption and free carrier losses at the telecommunication wavelengths ensure that there is no scaling of two-photon related losses with the group index, thus maintaining a high nonlinear efficiency. Self-phase modulation experiments are performed using a 96.6 μm PhCW. A 1.5π phase shift is achieved with an input peak power of 2.5 W implying an effective nonlinear parameter of 1.97 × 104 (W m)−1. This nonlinear parameter represents a 49× enhancement in the nonlinear parameter from the slow light effect, in good agreement with expected scaling from the measured group index.
Effects of common dietary fatty acids on milk yield and concentrations of fat and fatty acids in dairy cattle
Authors: Dorea J. R. R. , Armentano L. E.
Published: September 2017

The objective of the present article was to summarise the effects of five common dietary fatty acids (C16:0, C18:0, C18:1, C18:2 and C18:3) on the major milk fat groups (<C16, C16 and C18). Forty published papers were reviewed to evaluate the effect of adding free fat or oil supplements rich in C16 and C18 fatty acids on the response of milk fat secretion and composition. From those 40 studies, 21 were used to investigate the effect of total dietary concentration of C16:0, C18:0, C18:1, C18:2 and C18:3 on milk secretion or concentrations of milk <C16, C16 and C18 fatty acid groups. The results indicated that C16 supplementation increased total milk fatty acids, mainly by increasing milk C16 yield, without affecting milk <C16 and C18 yield. Supplements rich in unsaturated fatty acid decreased total milk fatty acid by inhibiting secretion of milk fatty acids shorter than C18, with linoleic acid being the most inhibitory. Mixtures of feed fatty acid (C16:0 + C18:0 and C16:0 + C18:1) did not significantly affect total milk fatty acid yield. According to regression of milk C16 yield on dietary fatty acid, endogenous C16 contributes ~80% of total milk C16, but this proportion varies with the level and type of dietary fatty acid fed. Milk mid-infrared analysis can be used to routinely measure the presence of milk <C16 fatty acid, the concentration of which provides a good indicator of inhibition of milk fatty acid secretion. In contrast, measurement of total milk fat content is less effective as a diagnostic tool due to the masking effect of the exogenous supply of C16 and C18 dietary fatty acids.
Evaluation of knowledge and utility of the 2014 Australian sexually transmissible infection and HIV testing guidelines for asymptomatic men who have sex with men among general practitioners in Sydney
Authors: Templeton David J. , Adam Phillipe C. G. , Varma Rajesh , Read Phillip , Bourne Chistopher , Kao Shih-Chi ,   on behalf of the Sexually Transmissible Infections in Gay Men Action Group (STIGMA)
Published: September 2017

The Australian sexually transmissible infection and HIV testing guidelines for asymptomatic men who have sex with men were updated in 2014. An evaluation study targeting Sydney-based general practitioners was conducted among 85 clinicians. Respondents with knowledge of guideline recommendations were significantly more likely to feel comfortable asking men who have sex with men about their sexual history (98.1% vs 81.3%, P = 0.039), and to recommend at least annual testing (94.0% vs 68.8%, P = 0.015), 3-month retesting after chlamydia or gonorrhoea treatment (96.2% vs 73.3%, P = 0.017) and syphilis testing with routine HIV monitoring bloods (90.2% vs 57.1%, P = 0.037). Familiarity with the guidelines was associated with a range of positive outcomes on general practitioners’ clinical practice. Novel approaches are required to ensure more widespread distribution of future guidelines.
Evolutionary diversification of protein–protein interactions by interface add-ons
Authors: Plach Maximilian G. , Semmelmann Florian , Busch Florian , Busch Markus , Heizinger Leonhard , Wysocki Vicki H. , Merkl Rainer , Sterner Reinhard
Published: September 2017

Significance

Proteins adopt no more than a thousand folds, and the number of different protein–protein interface geometries is restricted to around 1,000, too. Given this limited structural repertoire, it has remained elusive how hundreds of thousands of specific protein–protein interactions evolved and how unspecific interactions are avoided. We report on a strategy to solve this dilemma, which is the integration of additional structural elements at the interface periphery that guarantee specificity. We named these elements “interface add-ons” to reflect the benefit they provide to protein interfaces, as software add-ons do to web browsers or as additional bits turn a master key into a special key.
Expressing conditionality in Mandarin
Authors: Chen Weiying , Evers-Vermeul Jacqueline
Published: September 2017

After a broad overview of Mandarin Chinese conditionality marking, this paper presents a corpus-based analysis of two conditional connectives,rúguǒandzhǐyào(both translatable as ‘if’), from a syntactic and a cognitive perspective. We examine their use in narrative and informative texts along four parameters: clause order, position of the connective within the clause, domain, and counterfactuality. For all parameters, the two connectives displayed robust profiles across genres. Both connectives preferred an antecedent-consequent clause order. They displayed flexibility in their position, behaving like adverbs, withrúguǒshowing a stronger preference for the pre-subject position thanzhǐyào. In terms of domains,zhǐyàohas a stronger preference for content conditionals thanrúguǒ, which is also frequently used in the epistemic domain. In our data, onlyrúguǒwas used meta-metaphorically and in counterfactuals. We argue that both connectives can be translated with ‘if’, butzhǐyàoalso matches ‘so/as long as’.
West Germanic monosyllabic lengthening and Gothic breaking as partially Proto-Germanic developments
Authors: Hill Eugen
Published: September 2017

The paper deals with two Germanic sound changes which are traditionally believed to postdate the disintegration of the Proto-Germanic parent language. The lengthening in several monosyllables, attested in West Germanic languages, is usually believed to be an innovation of this branch. The so-called Gothic breaking is similarly thought of as belonging exclusively to East Germanic. The paper shows that there is evidence suggesting a Proto-Germanic age for parts of both sound changes, in particular for a lengthening in monosyllabic words ending in PGmc *-r and for a lowering of PGmc *i if followed by *r. Proto-Germanic possessed at least three pronoun-based place adverbs formed with PGmc *-r, cf. Gothƕar‘where’ fromƕa-‘what’,þar‘there’ fromþa-‘that’ andhēr‘here’ fromhi-‘this here’. The vocalism of these adverbs did not match that of the corresponding pronouns on two points. First, the vowels of the adverbs were probably long. Second, the close PGmc *ẹ̄ (Gothē, OHGia) of ‘here’ did not match PGmc *i in the corresponding pronoun. The paper assumes that the long vowels of the place adverbs emerged by a lengthening of etymologically short vowels in monosyllablic words ending in PGmc *-r. The timbre difference between PGmc *ẹ̄ in ‘here’ and PGmc *i in the corresponding pronoun for ‘this here’ is accounted for by a lowering of PGmc *i before *r. Both postulated developments must have been operating already in Proto-Germanic times but the lowering must have chronologically preceded the lengthening. The paper introduces the data supporting the assumptions made and discusses the apparent counterevidence.
Comparison of two types of low-transformation-temperature weld metals based on solidification mode
Authors: Feng Zhong-Yuan , Di Xin-Jie , Wu Shi-Pin , Zhang Zhi , Liu Xiao-Qian , Wang Dong-Po
Published: September 2017

Two types of low-transformation-temperature weld metals were devised, one associated with primary austenite solidification, the other primary ferrite solidification. The martensite start temperature of both low-transformation-temperature weld metals was about 125°C. Experimental results showed that low-transformation-temperature weld microstructure associated with primary austenite solidification was martensite with 8.0% retained austenite, whereas that one related to primary ferrite solidification primarily consisted of martensite and δ-ferrite. Accordingly, both welded joints had little distinction between distortion and residual stress, indicating that weld metal associated with primary ferrite solidification played the same function as primary austenite solidification on residual stress reduction. Moreover, the low-transformation-temperature weld metal associated with primary ferrite solidification had higher tensile strength and hardness than that based on primary austenite solidification.
SecA mediates cotranslational targeting and translocation of an inner membrane protein
Authors: Wang Shuai , Yang Chien-I , Shan Shu-ou
Published: September 2017

Protein targeting to the bacterial plasma membrane was generally thought to occur via two major pathways: cotranslational targeting by signal recognition particle (SRP) and posttranslational targeting by SecA and SecB. Recently, SecA was found to also bind ribosomes near the nascent polypeptide exit tunnel, but the function of this SecA–ribosome contact remains unclear. In this study, we show that SecA cotranslationally recognizes the nascent chain of an inner membrane protein, RodZ, with high affinity and specificity. In vitro reconstitution and in vivo targeting assays show that SecA is necessary and sufficient to direct the targeting and translocation of RodZ to the bacterial plasma membrane in an obligatorily cotranslational mechanism. Sequence elements upstream and downstream of the RodZ transmembrane domain dictate nascent polypeptide selection by SecA instead of the SRP machinery. These findings identify a new route for the targeting of inner membrane proteins in bacteria and highlight the diversity of targeting pathways that enables an organism to accommodate diverse nascent proteins.
Carbon tax effects on the poor: a SAM-based approach
Authors: Chapa Joana , Ortega Araceli
Published: September 2017

A SAM-based price model for Mexico is developed in order to assess the effects of the carbon tax, which was part of the fiscal reform approved in 2014. The model is formulated based on a social accounting matrix (SAM) that distinguishes households by the official poverty condition and geographical area. The main results are that the sector that includes coke, refined petroleum and nuclear fuel shows the highest price increase due to the direct impact of the carbon tax; in addition, air transport and inland transport are the most affected sectors, in an indirect manner, because both employ inputs from the former sector. Also, it is found that welfare diminishes more in the rural strata than in the urban one. In the urban area, the carbon tax is regressive: the negative impact of carbon tax on family welfare is greater on the poorest families.
Factors Associated With Medical School Graduates’ Intention to Work With Underserved Populations: Policy Implications for Advancing Workforce Diversity
Authors: Garcia Andrea N. , Kuo Tony , Arangua Lisa , Pérez-Stable Eliseo J.
Published: September 2017

Purpose

Given projected U.S. physician shortages across all specialties that will likely impact underserved areas disproportionately, the authors sought to explore factors most correlated with medical school graduates’ intention to work with underserved populations (IWUP).

Method

Data from the 2010–2012 Association of American Medical Colleges Medical School Graduation Questionnaire (n = 40,846) were analyzed. Variables (demographics, career preference, debt burden, intention to enter loan forgiveness programs) were examined using chi-square tests and logistic regression models.

Results

Respondents included 49.5% (20,228/40,846) women, 16.6% (6,771/40,837) underrepresented minorities (URMs), and 32.4% (13,034/37,342) with primary care intent. The median educational debt was $160,000. Respondents who were women (adjusted odds ratio [aOR] 1.59, 95% confidence interval [CI] 1.49, 1.70), URMs (aOR 2.50, 95% CI 2.30, 2.72), intended to enter loan forgiveness programs (aOR 2.44, 95% CI 2.26, 2.63), intended to practice primary care (aOR 1.65, 95% CI 1.54, 1.76), and intended to emphasize nonclinical careers (aOR 1.23, 95% CI 1.11, 1.37) had greater odds of reporting IWUP. Among those who chose specialties and careers with a nonclinical emphasis, and among those with greater burdens of educational and consumer debt, URMs were nearly twice as likely as other minorities and whites to report IWUP.

Conclusions

Findings suggest physician characteristics that may be associated with filling workforce gaps in underserved areas. Restructuring financial incentive programs to support physician leaders and specialists with characteristics associated with IWUP may complement similar policies in primary care and could have key impacts on health equity in underserved areas.
Upper Eyelid Splitting to Facilitate the Insertion of Glaucoma Drainage Devices
Authors: Provencher Lorraine M. , Carter Keith D. , Nerad Jeffrey A. , Alward Wallace L.M.
Published: September 2017

Purpose:

To describe a new application for vertical splitting of the upper eyelid, a technique traditionally used for orbital access, to facilitate glaucoma drainage device (GDD) implantation in patients with poor surgical exposure.

Methods:

Case series.

Cases:

We present a case of Möbius syndrome with complete restriction of the extraocular muscles, followed by a case of cicatricial narrowing of the palpebral fissures due to chronic allergic dermatitis. Both patients had severe, medically uncontrolled glaucoma, but poor surgical exposure precluded implantation of a GDD. Both cases underwent vertical splitting of the upper eyelid, which allowed for adequate exposure of the superior globe quadrants and successful implantation of a GDD.

Conclusions:

A variety of congenital or acquired conditions result in narrowing of the palpebral fissure or restriction of extraocular motility. When these patients have concurrent advanced glaucoma, inadequate surgical exposure can impede necessary surgical intervention. Use of a vertical upper eyelid split technique allows for access to the superior globe and facilitates implantation of a GDD.
Costs and Trends in Utilization of Low-value Services Among Older Adults With Commercial Insurance or Medicare Advantage
Authors: Carter Elizabeth A. , Morin Pamela E. , Lind Keith D.
Published: September 2017

Background:

Overutilization of low-value services (unnecessary or minimally beneficial tests or procedures) has been cited as a large contributor to the high costs of health care in the United States.

Objectives:

To analyze trends in utilization of low-value services from 2009 to 2014 among commercial and Medicare Advantage (MA) enrollees 50 and older.

Research Design:

A retrospective analysis of deidentified claims obtained from the OptumLab Data Warehouse.

Subjects:

Adults 50 and older enrolled in commercial plans and adults 65 and older enrolled in MA plans between 2009 and 2014.

Measures:

Costs and utilization of 16 low-value services in the following categories: cancer screening, imaging, and invasive procedures.

Results:

The most commonly performed low-value service was imaging of the head for syncope, at rates of 33%–39% in commercial enrollees and 45% in MA enrollees. The least common service was peripheral artery stenting (<1%) in commercial enrollees, and laminectomy (0.15% in 2009) and renal artery stenting in MA enrollees (0.07% in 2014). Renal artery stenting decreased by roughly 75% over the study period, the largest decrease in utilization, with ∼$30 million and $10 million in reduced spending for commercial and MA plans and enrollees, respectively. Spending on these services in 2014 totaled $317.6 million for commercial and $100.8 million for MA health plans.

Conclusions:

Clinicians, researchers, and policymakers should strive to reach consensus on methods for more reliably and accurately identifying low-value service utilization. Greater consistency would facilitate monitoring use of low-value services and changing clinical practice patterns over time.
Hip Fracture in the Frail Elderly
Authors: Atkinson Smith Mary , Acker Kristi , Torres Lisa
Published: September 2017

With the projected increase of an aging population in the upcoming decades, coupled with increasing elderly longevity, the incidence of hip fractures among this vulnerable population is expected to grow. Current evidence reveals high mortality rates within 6 months to 1 year among frail elderly patients who suffer hip fracture. In addition, the presence of multiple chronic conditions negatively impacts mortality rates in this vulnerable population. The purpose of this article is to discuss both the importance of integrating early palliative care and the appropriateness for hospice referral among frail elderly hip fracture patients. Moreover, the role nurses' play in early recognition of the need for palliative and/or hospice services among this vulnerable population will be explored.
Rituximab Experience in Patients With Long-standing Systemic Sclerosis–Associated Interstitial Lung Disease
Authors: Sari Alper , Guven Denizcan , Armagan Berkan , Erden Abdulsamet , Kalyoncu Umut , Karadag Omer , Apras Bilgen Sule , Ertenli Ihsan , Kiraz Sedat , Akdogan Ali
Published: September 2017

Objectives

The objective of this study was to report the experience with rituximab treatment in a case series of patients with long-standing systemic sclerosis–associated interstitial lung disease (SSc-ILD).

Methods

We reviewed the charts of 197 SSc patients. Fourteen patients who received rituximab for SSc-ILD participated in this analysis. Pulmonary function tests, high-resolution thorax computed tomography and modified Rodnan skin scores were evaluated at baseline and end of the follow-up.

Results

Median age was 53.2 years (interquartile range, 46.8–55.5 years), and median disease duration was 9.1 years (interquartile range, 5.1–13.6 years). At the end of median follow-up (15 months), although the median forced vital capacity value increased compared with baseline, the change was not statistically significant (52.5 vs. 58.0, P = 0.065). Forced vital capacity was improved in 4 patients and stabilized in 10 patients. High-resolution computed tomography was stable in 7 patients and worsened in 3 patients. Modified Rodnan skin scores remained stable at the end of follow-up (8.0 vs. 6.0, P = 0.6).

Conclusions

The improvement or stabilization of pulmonary disease was observed in most SSc patients with longer disease duration and worse pulmonary function. Rituximab might be useful in this patient group who is resistant to conventional immunosuppressive treatments.
An Enrichment Strategy Yields Seven Novel Single Nucleotide Polymorphisms Associated With Mortality and Altered Th17 Responses Following Blunt Trauma
Authors: Schimunek Lukas , Namas Rami A. , Yin Jinling , Liu Dongmei , Barclay Derek , el-Dehaibi Fayten , Abboud Andrew , Lindberg Haley , Zamora Ruben , Billiar Timothy R. , Vodovotz Yoram
Published: September 2017

Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single-nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397. Of these, 13 patients were non-survivors and the remaining 384 were survivors. All 397 DNA samples were amplified, fragmented, and examined for 551,839 SNPs using the Illumina Infinium CoreExome-24 v1.1 BeadChip (Illumina). To enrich for likely important SNPs, we initially compared SNPs of the 13 non-survivors versus 13 matched survivors, who were matched algorithmically for injury severity score (ISS), age, and gender ratio. This initial enrichment yielded 126 SNPs; a further comparison to the haplotypes of the remaining 371 survivors yielded a final total of 7 SNPs that distinguished survivors from non-survivors. Furthermore, severely injured survivors with the same seven SNPs as non-survivor exhibited distinct inflammatory responses from similarly injured survivors without those SNPs, and specifically had evidence of altered Th17 cell phenotypes based on computational modeling. These studies suggest an interaction among genetic polymorphism, injury severity, and initial inflammatory responses in driving trauma outcomes.
Microvesicle Subsets in Sepsis Due to Community Acquired Pneumonia Compared to Faecal Peritonitis
Authors: Lashin Hazem M.S. , Nadkarni Suchita , Oggero Silvia , Jones Hefin R. , Knight Julian C. , Hinds Charles J. , Perretti Mauro
Published: September 2017

Rationale:

Microvesicles (MV) act as a nonsoluble means of intercellular communication, with effector roles in disease pathogenesis and potentially as biomarkers. Previously, we reported that neutrophil MV expressing alpha-2-macroglobulin (A2MG) are protective in experimental sepsis and associate with survival in a small cohort of patients with sepsis due to community acquired pneumonia (CAP).

Objectives:

To characterize MV profiles in sepsis due to CAP or fecal peritonitis (FP) and determine their relation to outcome. To investigate the effects of novel sepsis treatments (granulocyte-macrophage colony stimulating factor (GM-CSF) and interferon-ϒ (IFN-γ)) on MV production and functions in vitro.

Methods:

Flow cytometry analysis of MV identified the cell of origin and the proportion of A2MG expression in the plasma of patients with sepsis secondary to CAP (n = 60) or FP (n = 40) and compared with healthy volunteers (HV, n = 10). The association between MV subsets and outcome was examined. The ability of GM-CSF and IFN-γ on A2MG+ve MV production from whole blood was examined together with the assessment of their effect on neutrophil and endothelial functions.

Results:

Circulating cell-derived and A2MG+ve MV were higher in CAP compared with FP and HV. A2MG+ve MV were higher in survivors of CAP, but not in FP. GM-CSF and IFN-γ enhanced A2MG+ve MV production, with these MV eliciting pathogen clearance in vitro.

Conclusions:

Plasma MV profiles vary according to the source of infection. A2MG+ve MV are associated with survival in CAP but not FP. We propose specific MV subsets as novel biomarkers in sepsis and potential effector for some of the actions of experimental therapeutic interventions.
Mini-review: Perfluorocarbons, Oxygen Transport, and Microcirculation in Low Flow States: in Vivo and in Vitro Studies
Authors: Torres Filho Ivo P.
Published: September 2017

Thein vivostudy of microvascular oxygen transport requires accurate and challenging measurements of several mass transfer parameters. Although recommended, blood flow and oxygenation are typically not measured in many studies where treatments for ischemia are tested. Therefore, the aim of this communication is to briefly review cardinal aspects of oxygen transport, and the effects of perfluorocarbon (PFC) treatment on blood flow and oxygenation based mostly on studies performed in our laboratory. As physiologically relevant events in oxygen transport take place at the microvascular level, we implemented the phosphorescence quenching technique coupled with noninvasive intravital videomicroscopy for quantitative evaluation of these eventsin vivo. Rodent experimental models and various approaches have been used to induce ischemia, including hemorrhage, micro- and macroembolism, and microvessel occlusion. Measurements show decrease in microvascular blood flow as well as intravascular and tissue oxygen partial pressure (PO2) after these procedures. To minimize or reverse the effects of ischemia and hypoxia, artificial oxygen carriers such as different PFCs were tested. Well-defined endpoints such as blood flow and tissue PO2were measured because they have significant effect on tissue survival and outcome. In several cases, enhancement of flow and oxygenation could be demonstrated. Similar results were foundin vitro: PFC emulsion mixed with blood (from healthy donors and sickle cell disease patients) enhanced oxygen transport. In summary, PFCs may provide beneficial effects in these models by mechanisms at the microvascular level including facilitated diffusion and bubble reabsorption leading to improved blood flow and oxygenation.
Spectropolarimetry of stripped-envelope supernovae: observations and modelling
Authors: Tanaka Masaomi
Published: September 2017

Spectropolarimetry is one of the most powerful methods to study the multi-dimensional geometry of supernovae (SNe). We present a brief summary of the spectropolarimetric observations of stripped-envelope core-collapse SNe. Observations indicate that stripped-envelope SNe generally have a non-axisymmetric ion distribution in the ejecta. Three-dimensional clumpy geometry nicely explains the observed properties. A typical size of the clumps deduced from observations is relatively large:

25% of the photosphere. Such a large-scale clumpy structure is similar to that observed in Cassiopeia A, and suggests that large-scale convection or standing accretion shock instability takes place at the onset of the explosion.

This article is part of the themed issue ‘Bridging the gap: from massive stars to supernovae’.
Bridging the gap: from massive stars to supernovae
Authors: Maund Justyn R. , Crowther Paul A. , Janka Hans-Thomas , Langer Norbert
Published: September 2017

Almost since the beginning, massive stars and their resultant supernovae have played a crucial role in the Universe. These objects produce tremendous amounts of energy and new, heavy elements that enrich galaxies, encourage new stars to form and sculpt the shapes of galaxies that we see today. The end of millions of years of massive star evolution and the beginning of hundreds or thousands of years of supernova evolution are separated by a matter of a few seconds, in which some of the most extreme physics found in the Universe causes the explosive and terminal disruption of the star. Key questions remain unanswered in both the studies of how massive stars evolve and the behaviour of supernovae, and it appears the solutions may not lie on just one side of the explosion or the other or in just the domain of the stellar evolution or the supernova astrophysics communities. The need to view massive star evolution and supernovae as continuous phases in a single narrative motivated the Theo Murphy international scientific meeting ‘Bridging the gap: from massive stars to supernovae’ at Chicheley Hall, UK, in June 2016, with the specific purpose of simultaneously addressing the scientific connections between theoretical and observational studies of massive stars and their supernovae, through engaging astronomers from both communities.

This article is part of the themed issue ‘Bridging the gap: from massive stars to supernovae’.
Multi-system manifestations of Mycoplasma pneumoniae infection in a young patient
Authors: Al Busaidi Ibrahim , Al-Amin Mohammed , Ibrahim Shadin , Balkhair Abdullah , Gaifer Zied
Published: September 2017

Introduction.
Mycoplasma pneumoniae is a small cell-wall-lacking bacterium that belongs to the mycoplasma (Mollicutes) prokaryote micro-organisms. It is a common cause of both upper and lower respiratory tract infections in all age groups. Respiratory illness is the most common manifestation of M. pneumoniae infection; however, extrapulmonary involvement may be present or predominant. The skin, mucus membranes, central nervous system, cardiovascular system, haematopoietic system, kidneys and musculoskeletal system are the most commonly involved extrapulmonary sites. Immune thrombocytopenia purpura has been reported as a rare haematological manifestation of mycoplasma infection. Here, we report, with a literature review, the case of a young adult with M. pneumoniae infection, presenting with acute febrile illness, myringitis, erythema multiforme, mild Raynaud’s phenomenon symptoms and severe thrombocytopenia.

Case presentation. Our patient was a 24-year-old healthy man who presented to an emergency department with acute febrile illness, upper respiratory tract infection symptoms, myringitis, erythema multiforme skin lesions, severe thrombocytopenia, and pale and cold hands. Mycoplasma serology suggested acute M. pneumoniae infection. The patient had a complete resolution of symptoms and gradual recovery from the thrombocytopenia after a course of anti-Mycoplasma therapy with azithromycin. Our case illustrates the multi-system involvement of M. pneumoniae infection.

Conclusion.
M. pneumoniae is a frequent cause of upper and lower respiratory tract infections in children and young adults. Multi-system involvement including the skin, vascular and haematological systems in young adults with upper or lower respiratory tract infection, as in our patient, should raise the suspicion of Mycoplasma infection. Our case also illustrates an excellent clinical response and recovery from thrombocytopenia shortly after anti-Mycoplasma antimicrobial therapy.
Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017
Authors:   The ZIKAVAT Collaboration, Asher Jason , Barker Christopher , Chen Grace , Cummings Derek , Chinazzi Matteo , Daniel-Wayman Shelby , Fischer Marc , Ferguson Neil , Follman Dean , Elizabeth Halloran M. , Johansson Michael , Kugeler Kiersten , Kwan Jennifer , Lessler Justin , Longini Ira M. , Merler Stefano , Monaghan Andrew , y Piontti Ana Pastore , Perkins Alex , Rebecca Prevots D. , Reiner Robert , Rossi Luca , Rodriguez-Barraquer Isabel , Siraj Amir S. , Sun Kaiyuan , Vespignani Alessandro , Zhang Qian
Published: September 2017

Numerous Zika virus vaccines are being developed. However, identifying sites to evaluate the efficacy of a Zika virus vaccine is challenging due to the general decrease in Zika virus activity. We compare results from three different modeling approaches to estimate areas that may have increased relative risk of Zika virus transmission during 2017. The analysis focused on eight priority countries (i.e., Brazil, Colombia, Costa Rica, Dominican Republic, Ecuador, Mexico, Panama, and Peru). The models projected low incidence rates during 2017 for all locations in the priority countries but identified several subnational areas that may have increased relative risk of Zika virus transmission in 2017. Given the projected low incidence of disease, the total number of participants, number of study sites, or duration of study follow-up may need to be increased to meet the efficacy study endpoints.
Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
Authors: Duchene Sebastian , Duchene David , Geoghegan Jemma , Dyson Zoe Anne , Hawkey Jane , Holt Kathryn E
Published: September 2017

Background: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale.
Results: We compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart.
Conclusions: Hybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates.
Convergent mutations and single nucleotide variants in mitochondrial genomes of modern humans and Neanderthals
Authors: Ferreira Renata C. , Rodrigues Camila R. , Broach James R. , Briones Marcelo R. S.
Published: September 2017

Genetic contributions of Neanderthals to the modern human genome have been evidenced by comparison of present-day human genomes with paleogenomes suggesting that the Neanderthal introgression is higher in Asians and Europeans and lower in Africans. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic Anatomically Modern Humans (AMH). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain potential 66 Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs) being 36 in coding regions of which 7 are nonsynonymous. Also, 7 N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer’s disease, Parkinson’s disease and 2 N-SNVs are associated with intelligence quotient. Based on recombination tests, Principal Component Analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes we conclude that convergent evolution due to homoplasy and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
Modified penetrance of coding variants bycis-regulatory variation shapes human traits
Authors: Castel Stephane E. , Cervera Alejandra , Mohammadi Pejman , Aguet François , Reverter Ferran , Wolman Aaron , Guigo Roderic , Iossifov Ivan , Vasileva Ana , Lappalainen Tuuli
Published: September 2017

Coding variants represent many of the strongest associations between genotype and phenotype, however they exhibit inter-individual differences in effect, known as variable penetrance. In this work, we study howcis-regulatory variation modifies the penetrance of coding variants in their target gene. Using functional genomic and genetic data from GTEx, we observed that in the general population, purifying selection has depleted haplotype combinations that lead to higher penetrance of pathogenic coding variants. Conversely, in cancer and autism patients, we observed an enrichment of haplotype combinations that lead to higher penetrance of pathogenic coding variants in disease implicated genes, which provides direct evidence that regulatory haplotype configuration of causal coding variants affects disease risk. Finally, we experimentally demonstrated that a regulatory variant can modify the penetrance of a coding variant by introducing a Mendelian SNP using CRISPR/Cas9 on distinct expression haplotypes and using the transcriptome as a phenotypic readout. Our results demonstrate that joint effects of regulatory and coding variants are an important part of the genetic architecture of human traits, and contribute to modified penetrance of disease-causing variants.
Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants inSchizosaccharomyces pombe
Authors: Brown Simon David , Jarosinska Olga Dorota , Lorenz Alexander
Published: September 2017

Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast,Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events. We determined how mutants of homologous recombination factors genetically interact withhop1, studied the role(s) of the HORMA domain of Hop1, and characterized a bio-informatically predicted interactor of Hop1, Aho1 (SPAC688.03c). Our observations indicate that in fission yeast, Hop1 does require its HORMA domain to support wild-type levels of meiotic recombination and localization to meiotic chromatin. Furthermore, we show thathop1Δonly weakly interacts genetically with mutants of homologous recombination factors, and in fission yeast likely has no major role beyond break formation and promoting inter-homolog events. We speculate that after the evolutionary loss of the synaptonemal complex, Hop1 likely has become less important for modulating recombination outcome during meiosis in fission yeast, and that this led to a concurrent rewiring of genetic pathways controlling meiotic recombination.