bluuebunny/crossref_metadata_2025 huggingface dataset:
Disturbance amplification in boundary layers over thin wall films
Authors: Saha Sandeep , Page Jacob , Zaki Tamer A.
Published: February 2016

In single-fluid boundary layers, streaks can amplify at sub-critical Reynolds numbers and initiate early transition to turbulence. Introducing a wall film of different viscosities can appreciably alter the stability of the base flow and, in particular, the transient growth of the perturbation streaks. The formalism of seminorms is used to identify optimal disturbances which maximize the kinetic energy in the two-fluid flow. An examination of optimal growth over a range of viscosity ratios of the film relative to the outer flow reveals three distinct regimes of amplification, each associated with a particular combination of the eigenfunctions. In order to elucidate the underlying amplification mechanisms, a model problem is formulated: An initial value problem is solved using an eigenfunction expansion and is used to compute the evolution of pairs of eigenfunctions. By appropriately selecting the pair, the initial value problem qualitatively reproduces the temporal evolution of the optimal disturbance, and provides an unambiguous explanation of the dynamics. Two regimes of transient growth are attributed to the evolution of the interface mode along with free-stream vortical modes; the third regime is due to the evolution of the interface and a discrete mode. The results demonstrate that a lower-viscosity film can effectively reduce the efficacy of the lift-up mechanism and, as a result, transient growth of disturbances. However, another mechanism of amplification of wall-normal vorticity arises due to the deformation of the two-fluid interface and becomes dominant below a critical viscosity ratio.
Pressure-induced ferroelectric to paraelectric transition in LiTaO3 and (Li,Mg)TaO3
Authors: Yamanaka Takamitsu , Nakamoto Yuki , Takei Fumihiko , Ahart Muhtar , Mao Ho-kwang , Hemley Russell J.
Published: February 2016

X-ray powder diffraction and Raman scattering of LiTaO3 (LT) and (Li,Mg)TaO3 (LMT) have been measured under pressure up to 46 GPa. Above 30 GPa, the ferroelectric rhombohedral phase (R3c, Z = 6) of LiTaO3 transforms to a paraelectric orthorhombic phase (Pnma with Z = 4) with a large hysteresis. Rietveld profile fitting analysis shows that the Li-O bond is compressed and approaches that of Ta-O with pressure. The cation distribution analysis of the orthorhombic perovskite structure shows that Li and Ta are located in the octahedral 8-fold coordination sites. Difference Fourier |Fobs(hkl)| - |Fcal(hkl)| maps of LiTaO3 and (Li,Mg)TaO3 indicate polarization in the c axis direction and a more distinct electron density distribution around the Ta position for (Li,Mg)TaO3 compared to LiTaO3. The observed effective charges indicate that for (Li,Mg)TaO3 without vacancies Ta5+ becomes less ionized as a function of Mg substitution. Considering both site occupancy and effective charge analysis, Ta5+ is reduced to Ta4.13+. Mg2+ and O2- change to Mg1.643+ and O1.732 -, respectively. The space- and time-averaged structures of the dynamical vibration of atoms can be elucidated from the electron density analysis by difference Fourier and temperature factors T(hkl) in the structure refinement. The refinement of the temperature factor is consistent with the cation distribution assuming full stoichiometry. The residual electron density induced from the excess electron in (Li,Mg)TaO3 indicates more electrons around the Ta site, as confirmed by the effective charge analysis. Raman spectra of LiTaO3 and (Li,Mg)TaO3 show notable changes over the measured pressure range. Raman peaks centered at 250 cm−1 and 350 cm−1 at ambient pressure merge above 8 GPa, which we associate with the diminishing of difference in distances between Li-O and Ta-O bonds with pressure in both materials. Raman spectra show significant changes at 28 GPa and 33 GPa for LT and LMT, respectively, due to the structural transition from R3c to Pnma consistent with the x-ray diffraction results.
Coupling of isotropic and directional interactions and its effect on phase separation and self-assembly
Authors: Audus Debra J. , Starr Francis W. , Douglas Jack F.
Published: February 2016

The interactions of molecules and particles in solution often involve an interplay between isotropic and highly directional interactions that lead to a mutual coupling of phase separation and self-assembly. This situation arises, for example, in proteins interacting through hydrophobic and charged patch regions on their surface and in nanoparticles with grafted polymer chains, such as DNA. As a minimal model of complex fluids exhibiting this interaction coupling, we investigate spherical particles having an isotropic interaction and a constellation of five attractive patches on the particle’s surface. Monte Carlo simulations and mean-field calculations of the phase boundaries of this model depend strongly on the relative strength of the isotropic and patch potentials, where we surprisingly find that analytic mean-field predictions become increasingly accurate as the directional interactions become increasingly predominant. We quantitatively account for this effect by noting that the effective interaction range increases with increasing relative directional to isotropic interaction strength. We also identify thermodynamic transition lines associated with self-assembly, extract the entropy and energy of association, and characterize the resulting cluster properties obtained from simulations using percolation scaling theory and Flory-Stockmayer mean-field theory. We find that the fractal dimension and cluster size distribution are consistent with those of lattice animals, i.e., randomly branched polymers swollen by excluded volume interactions. We also identify a universal functional form for the average molecular weight and a nearly universal functional form for a scaling parameter characterizing the cluster size distribution. Since the formation of branched clusters at equilibrium is a common phenomenon in nature, we detail how our analysis can be used in experimental characterization of such associating fluids.
Electronic topological transitions in Nb3X (X = Al, Ga, In, Ge, and Sn) under compression investigated by first principles calculations
Authors: Sreenivasa Reddy P. V. , Kanchana V. , Vaitheeswaran G. , Modak P. , Verma Ashok K.
Published: February 2016

First principles electronic structure calculations of A-15 type Nb3X (X = Al, Ga, In, Ge, and Sn) compounds are performed at ambient and high pressures. Mechanical stability is confirmed in all the compounds both at ambient as well as under compression from the calculated elastic constants. We have observed four holes and two electron Fermi surfaces (FS) for all the compounds studied and FS nesting feature is observed at M and along X-Γ in all the compounds. A continuous change in the FS topology is observed under pressure in all the compounds which is also reflected in the calculated elastic constants and density of states under pressure indicating the Electronic topological transitions (ETT). The ETT observed at around 21.5 GPa, 17.5 GPa in Nb3Al and Nb3Ga are in good agreement with the anomalies observed by the experiments.
Generation of pressures over 40 GPa using Kawai-type multi-anvil press with tungsten carbide anvils
Authors: Ishii T. , Shi L. , Huang R. , Tsujino N. , Druzhbin D. , Myhill R. , Li Y. , Wang L. , Yamamoto T. , Miyajima N. , Kawazoe T. , Nishiyama N. , Higo Y. , Tange Y. , Katsura T.
Published: February 2016

We have generated over 40 GPa pressures, namely, 43 and 44 GPa, at ambient temperature and 2000 K, respectively, using Kawai-type multi-anvil presses (KMAP) with tungsten carbide anvils for the first time. These high-pressure generations were achieved by combining the following pressure-generation techniques: (1) precisely aligned guide block systems, (2) high hardness of tungsten carbide, (3) tapering of second-stage anvil faces, (4) materials with high bulk modulus in a high-pressure cell, and (5) high heating efficiency.
Application of generalized Snoek's law over a finite frequency range: A case study
Authors: Rozanov Konstantin N. , Koledintseva Marina Y.
Published: February 2016

Generalized Snoek's law proposed in an integral form by Acher and coauthors is a useful tool for investigation of high-frequency properties of magnetic materials. This integral law referred to as Acher's law allows for evaluating the ultimate performance of RF and microwave devices which employ magnetic materials. It may also be helpful in obtaining useful information on the structure and morphology of the materials. The key factor in practical application of Acher's law is an opportunity to employ either measured or calculated data available over a finite frequency range. The paper uses simple calculations to check the applicability of Acher's law in cases when the frequency range is limited and the magnetic loss peak is comparatively wide and has a distorted shape. The cases of large magnetic damping, pronounced skin effect, and inhomogeneity of the material are considered. It is shown that in most cases calculation of the integral through fitting of actual magnetic frequency dispersion by the Lorentzian dispersion law results in accurate estimations of the ultimate high-frequency performance of magnetic materials.
Control of threshold voltage in E-mode and D-mode GaN-on-Si metal-insulator-semiconductor heterostructure field effect transistors by in-situ fluorine doping of atomic layer deposition Al2O3 gate dielectrics
Authors: Roberts J. W. , Chalker P. R. , Lee K. B. , Houston P. A. , Cho S. J. , Thayne I. G. , Guiney I. , Wallis D. , Humphreys C. J.
Published: February 2016

We report the modification and control of threshold voltage in enhancement and depletion mode AlGaN/GaN metal-insulator-semiconductor heterostructure field effect transistors through the use of in-situ fluorine doping of atomic layer deposition Al2O3. Uniform distribution of F ions throughout the oxide thickness are achievable, with a doping level of up to 5.5 × 1019 cm−3 as quantified by secondary ion mass spectrometry. This fluorine doping level reduces capacitive hysteretic effects when exploited in GaN metal-oxide-semiconductor capacitors. The fluorine doping and forming gas anneal also induces an average positive threshold voltage shift of between 0.75 and 1.36 V in both enhancement mode and depletion mode GaN-based transistors compared with the undoped gate oxide via a reduction of positive fixed charge in the gate oxide from +4.67 × 1012 cm−2 to −6.60 × 1012 cm−2. The application of this process in GaN based power transistors advances the realisation of normally off, high power, high speed devices.
Type-II vertical-external-cavity surface-emitting laser with Watt level output powers at 1.2 μm
Authors: Möller C. , Fuchs C. , Berger C. , Ruiz Perez A. , Koch M. , Hader J. , Moloney J. V. , Koch S. W. , Stolz W.
Published: February 2016

Semiconductor laser characteristics based on type-II band-aligned quantum well heterostructures for the emission at 1.2 μm are presented. Ten “W”-quantum wells consisting of GaAs/(GaIn)As/Ga(AsSb)/(GaIn)As/GaAs are arranged as resonant periodic gain in a vertical-external-cavity surface-emitting laser. Its structure is analyzed by X-ray diffraction, photoluminescence, and reflectance measurements. The laser's power curves and spectra are investigated. Output powers at Watt level are achieved, with a maximum output power of 4 W. It is confirmed that laser operation only involves the type-II transition. A blue shift of the material gain is observed while the modal gain exhibits a red shift.
Crystalline anisotropy of shock-induced phenomena: Omni-directional multiscale shock technique
Authors: Shimamura Kohei , Misawa Masaaki , Ohmura Satoshi , Shimojo Fuyuki , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: February 2016

We propose an omni-directional multiscale shock technique (OD-MSST) to study the shock waves in an arbitrary direction of crystalline materials, atomistically based on the molecular dynamics simulation method. Using OD-MSST, we found transitions from elastic to shear-banding to plastic behaviors for a model covalent crystal. In addition to such a shock “phase diagram,” a transition from inter-molecular to intra-molecular mechanochemical reaction pathways was found as a function of crystallographic orientation in an energetic van der Waals crystal.
Adsorption of CO molecules on doped graphene: A first-principles study
Authors: Wang Weidong , Zhang Yuxiang , Shen Cuili , Chai Yang
Published: February 2016

As a typical kinds of toxic gases, CO plays an important role in environmental monitoring, control of chemical processes, space missions, agricultural and medical applications. Graphene is considered a potential candidate of gases sensor, so the adsorption of CO molecules on various graphene, including pristine graphene, Nitrogen-doped graphene (N-doped graphene) and Aluminum-doped graphene (Al-doped graphene), are studied by using first-principles calculations. The optimal configurations, adsorption energies, charge transfer, and electronic properties including band structures, density of states and differential charge density are obtained. The adsorption energies of CO molecules on pristine graphene and N-doped graphene are −0.01 eV, and −0.03 eV, respectively. In comparison, the adsorption energy of CO on Al-doped graphene is much larger, −2.69 eV. Our results also show that there occurs a large amount of charge transfer between CO molecules and graphene sheet after the adsorption, which suggests Al-doped graphene is more sensitive to the adsorption of CO than pristine graphene and N-doped graphene. Therefore, the sensitivity of gases on graphene can be drastically improved by introducing the suitable dopants.
Perceptions and correlates of pubic hair removal and grooming among college-aged women: a mixed methods approach
Authors: DeMaria Andrea L. , Sundstrom Beth , McInnis Stephanie M. , Rogers Emily
Published: February 2016

Background
Although much is known about behavioural indicators of pubic hair removal, current research lacks deeper cognitive reasoning and understanding through utilising quantitative and qualitative methodologies. The purpose of this study was to: (1) describe and understand pubic hair removal behaviours using a quantitative survey; and (2) examine the relationship between pubic hair removal, sexual behaviours and genital self-image using in-depth interviews. Methods: Data were collected from women aged 18–24 years living in the United States. Overall, 663 participants completed an online survey and 53 completed in-depth interviews. Questions asked related to pubic hair removal and sexual history. Results: Participants removed hair for hygiene, comfort and sensation purposes, which was a personal decision influenced by family, friends and the media. Race, pubic hair removal initiation age, genital image and sexual behaviours were significantly related to pubic hair removal. Conclusions: Data from this study prove that further education regarding safe pubic hair removal methods is needed, especially for those who initiate pubic hair removal and sexual behaviours concurrently.
Corrigendum to: Road and traffic factors correlated to wildlife–vehicle collisions in Galicia (Spain)
Authors: Valero Enrique , Picos Juan , Lagos Laura , Álvarez Xana
Published: February 2016

Context
Wildlife–vehicle collisions (WVC) are one of the major risk factors for the safety of drivers, as well as a great danger to wildlife that moves through the territory. In recent decades, given the growth of these accidents, some researches emerged to understand what are the main causes of this phenomenon and find the best solutions for implementation and try to solve this problem.

Aims
The aim of the present study was to analyse the road and traffic characteristics of road segments with a high occurrence of WVC in north-western Spain, specifically, the collisions with wild ungulates (roe deer and wild boar).

Methods
A nearest-neighbour analysis was used to analyse the spatial distribution of the WVC spots, and so as to identify these hotspots of accidents, we performed a hotspot analysis using the routine nearest-neighbour hierarchical cluster. Then, we calculated the WVC density of each road segment (KP). The existence of differences in the values of variables between high and low accident densities was analysed using a Mann–Whitney U-test for the continuous variables, and a ?2-test for the categorical ones. Then, multiple logistic regression analysis was used to identify which variables could predict the existence of KPs with a high density of WVC.

Key results
Our results showed that the daily traffic volume, the width of the road, the number of lanes and speed limit affect whether a particular road marker has a high or low density of WVC.

Conclusions
We conclude that high WVC is frequently characterised by wider lanes and shoulders, as well as gentler slopes, whereas in the sections with narrower roads and a shorter curvature radius, there are some conditions (low visibility and speed reduction) that reduce the probability of having an accident with ungulates. However, the speed at which it is possible to drive on a given road section is closely related to the occurrence of WVC.

Implications
These findings emphasise the importance of including mitigation measures in the decision-making when planning and designing infrastructure.
Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma
Authors: Lissanu Deribe Yonathan , Shi Yanxia , Rai Kunal , Nezi Luigi , Amin Samir B. , Wu Chia-Chin , Akdemir Kadir C. , Mahdavi Mozhdeh , Peng Qian , Chang Qing Edward , Hornigold Kirsti , Arold Stefan T. , Welch Heidi C. E. , Garraway Levi A. , Chin Lynda
Published: February 2016

Significance

Mutations in the PI3K/PTEN/Akt signaling pathway occur frequently across multiple tumor types. These mutations primarily serve to activate PI-3 and Akt kinases. PREX2 is a guanine nucleotide exchanger for Rac1 that is significantly mutated in melanoma and pancreatic ductal adenocarcinoma. Here we report that a mouse model of a truncating PREX2 mutation shows accelerated melanoma development in the context of mutant NRAS. Truncating PREX2 mutations have increased Rac1 guanine nucleotide exchange factor activity, and tumors harboring these mutations have elevated PI3K/Akt pathway activation and reduced expression of critical negative cell cycle regulators leading to increased cell proliferation. This work provides evidence for a previously unidentified mechanism of activating Rac1, the PI3K pathway, and regulation of cell cycle progression in melanoma.
The relationship between non-symbolic multiplication and division in childhood
Authors: McCrink Koleen , Shafto Patrick , Barth Hilary
Published: February 2016

Children without formal education in addition and subtraction are able to perform multi-step operations over an approximate number of objects. Further, their performance improves when solving approximate (but not exact) addition and subtraction problems that allow for inversion as a shortcut (e.g., a + b − b = a). The current study examines children's ability to perform multi-step operations, and the potential for an inversion benefit, for the operations of approximate, non-symbolic multiplication and division. Children were trained to compute a multiplication and division scaling factor (*2 or /2, *4 or /4), and were then tested on problems that combined two of these factors in a way that either allowed for an inversion shortcut (e.g., 8*4/4) or did not (e.g., 8*4/2). Children's performance was significantly better than chance for all scaling factors during training, and they successfully computed the outcomes of the multi-step testing problems. They did not exhibit a performance benefit for problems with the a* b/ b structure, suggesting that they did not draw upon inversion reasoning as a logical shortcut to help them solve the multi-step test problems.
How gender-expectancy affects the processing of “them”
Authors: Doherty Alice , Conklin Kathy
Published: February 2016

How sensitive is pronoun processing to expectancies based on real-world knowledge and language usage? The current study links research on the integration of gender stereotypes and number-mismatch to explore this question. It focuses on the use of them to refer to antecedents of different levels of gender-expectancy (low– cyclist, high– mechanic, known– spokeswoman). In a rating task, them is considered increasingly unnatural with greater gender-expectancy. However, participants might not be able to differentiate high-expectancy and gender-known antecedents online because they initially search for plural antecedents (e.g., Sanford & Filik), and they make all-or-nothing gender inferences. An eye-tracking study reveals early differences in the processing of them with antecedents of high gender-expectancy compared with gender-known antecedents. This suggests that participants have rapid access to the expected gender of the antecedent and the level of that expectancy.
Functional screen identifies regulators of murine hematopoietic stem cell repopulation
Authors: Holmfeldt Per , Ganuza Miguel , Marathe Himangi , He Bing , Hall Trent , Kang Guolian , Moen Joseph , Pardieck Jennifer , Saulsberry Angelica C. , Cico Alba , Gaut Ludovic , McGoldrick Daniel , Finkelstein David , Tan Kai , McKinney-Freeman Shannon
Published: February 2016

Understanding the molecular regulation of hematopoietic stem and progenitor cell (HSPC) engraftment is paramount to improving transplant outcomes. To discover novel regulators of HSPC repopulation, we transplanted >1,300 mice with shRNA-transduced HSPCs within 24 h of isolation and transduction to focus on detecting genes regulating repopulation. We identified 17 regulators of HSPC repopulation: Arhgef5, Armcx1, Cadps2, Crispld1, Emcn, Foxa3, Fstl1, Glis2, Gprasp2, Gpr56, Myct1, Nbea, P2ry14, Smarca2, Sox4, Stat4, and Zfp521. Knockdown of each of these genes yielded a loss of function, except in the cases of Armcx1 and Gprasp2, whose loss enhanced hematopoietic stem cell (HSC) repopulation. The discovery of multiple genes regulating vesicular trafficking, cell surface receptor turnover, and secretion of extracellular matrix components suggests active cross talk between HSCs and the niche and that HSCs may actively condition the niche to promote engraftment. We validated that Foxa3 is required for HSC repopulating activity, as Foxa3−/− HSC fails to repopulate ablated hosts efficiently, implicating for the first time Foxa genes as regulators of HSPCs. We further show that Foxa3 likely regulates the HSC response to hematologic stress. Each gene discovered here offers a window into the novel processes that regulate stable HSPC engraftment into an ablated host.
Regulation of ENaC trafficking in rat kidney
Authors: Frindt Gustavo , Gravotta Diego , Palmer Lawrence G.
Published: February 2016

The epithelial Na channel (ENaC) forms a pathway for Na+ reabsorption in the distal nephron, and regulation of these channels is essential for salt homeostasis. In the rat kidney, ENaC subunits reached the plasma membrane in both immature and fully processed forms, the latter defined by either endoglycosidase H–insensitive glycosylation or proteolytic cleavage. Animals adapted to a low-salt diet have increased ENaC surface expression that is specific for the mature forms of the subunit proteins and is similar (three- to fourfold) for α, β, and γENaC. Kidney membranes were fractionated using differential centrifugation, sucrose-gradient separation, and immunoabsorption. Endoplasmic reticulum membranes, isolated using an antibody against calnexin, expressed immature γENaC, and the content decreased with Na depletion. Golgi membranes, isolated with an antibody against the cis-Golgi protein GM130, expressed both immature and processed γENaC; Na depletion increased the content of processed γENaC in this fraction by 3.8-fold. An endosomal compartment isolated using an antibody against Rab11 contained both immature and processed γENaC; the content of processed subunit increased 2.4-fold with Na depletion. Finally, we assessed the content of γENaC in the late endocytic compartments indirectly using urinary exosomes. All of the γENaC in these exosomes was in the fully cleaved form, and its content increased by 4.5-fold with Na depletion. These results imply that stimulation of ENaC surface expression results at least in part from increased rates of formation of fully processed subunits in the Golgi and subsequent trafficking to the apical membrane.
Thermally stable yttrium–scandium oxide high-k dielectrics deposited by a solution process
Authors: Hu Wenbing , Frost Bradley , Peterson Rebecca L
Published: February 2016

We investigated the thermal stability of electrical properties in ternary alloy (Y
x
Sc1−x
)2O3 high-k oxides as a function of yttrium fraction, x. The yttrium–scandium oxide dielectric films are deposited using a facile ink-based process. The oxides have a stoichiometry-dependent relative dielectric constant of 26.0 to 7.7 at 100 kHz, low leakage current density of 10−8 A·cm−2, high breakdown field of 4 MV⋅cm−1, and interface trap density of 1012 cm−2·eV−1 with silicon. Compared with binary oxides, ternary alloys exhibit less frequency dispersion of the dielectric constant and a higher crystallization temperature. After crystallization is induced through a 900 °C anneal, ternary (Y0.6Sc0.4)2O3 films maintain their low leakage current and high breakdown field. In contrast, the electrical performance of the binary oxides significantly degrades following the same treatment. The solution-processed ternary oxide dielectrics demonstrated here may be used as high-k gate insulators in complementary metal-oxide semiconductor (CMOS) technologies, in novel electronic material systems and devices, and in printed, flexible thin film electronics, and as passivation layers for high power devices. These oxides may also be used as insulators in fabrication process flows that require a high thermal budget.
Learning from Inflation Experiences
*
Authors: Malmendier Ulrike , Nagel Stefan
Published: February 2016

How do individuals form expectations about future inflation? We propose that individuals overweight inflation experienced during their lifetimes. This approach modifies existing adaptive learning models to allow for age-dependent updating of expectations in response to inflation surprises. Young individuals update their expectations more strongly than older individuals since recent experiences account for a greater share of their accumulated lifetime history. We find support for these predictions using 57 years of microdata on inflation expectations from the Reuters/Michigan Survey of Consumers. Differences in experiences strongly predict differences in expectations, including the substantial disagreement between young and old individuals in periods of highly volatile inflation, such as the 1970s. It also explains household borrowing and lending behavior, including the choice of mortgages.
Wealth Inequality in the United States since 1913: Evidence from Capitalized Income Tax Data *
Authors: Saez Emmanuel , Zucman Gabriel
Published: February 2016

This paper combines income tax returns with macroeconomic household balance sheets to estimate the distribution of wealth in the United States since 1913. We estimate wealth by capitalizing the incomes reported by individual taxpayers, accounting for assets that do not generate taxable income. We successfully test our capitalization method in three micro datasets where we can observe both income and wealth: the Survey of Consumer Finance, linked estate and income tax returns, and foundations’ tax records. We find that wealth concentration was high in the beginning of the twentieth century, fell from 1929 to 1978, and has continuously increased since then. The top 0.1% wealth share has risen from 7% in 1978 to 22% in 2012, a level almost as high as in 1929. Top wealth-holders are younger today than in the 1960s and earn a higher fraction of the economy’s labor income. The bottom 90% wealth share first increased up to the mid-1980s and then steadily declined. The increase in wealth inequality in recent decades is due to the upsurge of top incomes combined with an increase in saving rate inequality. We explain how our findings can be reconciled with Survey of Consumer Finances and estate tax data.
Phytopathogen Genome Announcement: Draft Genome Sequences of 62 Pseudomonas syringae Type and Pathotype Strains
Authors: Thakur Shalabh , Weir Bevan S. , Guttman David S.
Published: February 2016

Pseudomonas syringae is a diverse species-complex that includes many important crop pathogens. Here, we report the draft genomes of 62 type and pathotype strains, which provide a genomic reference for the diversity of this species complex and will contribute to the elucidation of the genomic basis of pathogenicity and host specificity.
MucR Is Required for Transcriptional Activation of Conserved Ion Transporters to Support Nitrogen Fixation of Sinorhizobium fredii in Soybean Nodules
Authors: Jiao Jian , Wu Li Juan , Zhang Biliang , Hu Yue , Li Yan , Zhang Xing Xing , Guo Hui Juan , Liu Li Xue , Chen Wen Xin , Zhang Ziding , Tian Chang Fu
Published: February 2016

To achieve effective symbiosis with legume, rhizobia should fine-tune their background regulation network in addition to activating key genes involved in nodulation (nod) and nitrogen fixation (nif). Here, we report that an ancestral zinc finger regulator, MucR1, other than its paralog, MucR2, carrying a frameshift mutation, is essential for supporting nitrogen fixation of Sinorhizobium fredii CCBAU45436 within soybean nodules. In contrast to the chromosomal mucR1, mucR2 is located on symbiosis plasmid, indicating its horizontal transfer potential. A MucR2 homolog lacking the frameshift mutation, such as the one from S. fredii NGR234, can complement phenotypic defects of the mucR1 mutant of CCBAU45436. RNA-seq analysis revealed that the MucR1 regulon of CCBAU45436 within nodules exhibits significant difference compared with that of free-living cells. MucR1 is required for active expression of transporters for phosphate, zinc, and elements essential for nitrogenase activity (iron, molybdenum, and sulfur) in nodules but is dispensable for transcription of key genes (nif/fix) involved in nitrogen fixation. Further reverse genetics suggests that S. fredii uses high-affinity transporters to meet the demand for zinc and phosphate within nodules. These findings, together with the horizontal transfer potential of the mucR homolog, imply an intriguing evolutionary role of this ancestral regulator in supporting nitrogen fixation.
Providing Anesthesia Care in Resource-limited Settings
Authors: Ariyo Promise , Trelles Miguel , Helmand Rahmatullah , Amir Yama , Hassani Ghulam Haidar , Mftavyanka Julien , Nzeyimana Zenon , Akemani Clemence , Ntawukiruwabo Innocent Bagura , Charles Adelin , Yana Yanang , Moussa Kalla , Kamal Mustafa , Suma Mohamed Lamin , Ahmed Mowlid , Abdullahi Mohamed , Wong Evan G. , Kushner Adam , Latif Asad
Published: February 2016

AbstractAbstract

Médecins Sans Frontières (MSF; Doctors Without Borders) anesthesia providers include physician anesthesiologists, nurse anesthetists, and local nurses trained by MSF to provide anesthesia. A standardized set of essential equipment and medications is provided for each mission to enable anesthesia care delivery and management of potential complications. A retrospective review of anesthetic procedures performed at MSF facilities from 2008 until 2014 found that a wide range of anesthesia procedures can be carried out safely in resource-limited settings with resources such as those provided by MSF.

Background

Anesthesia is integral to improving surgical care in low-resource settings. Anesthesia providers who work in these areas should be familiar with the particularities associated with providing care in these settings, including the types and outcomes of commonly performed anesthetic procedures.

Methods

The authors conducted a retrospective analysis of anesthetic procedures performed at Médecins Sans Frontières facilities from July 2008 to June 2014. The authors collected data on patient demographics, procedural characteristics, and patient outcome. The factors associated with perioperative mortality were analyzed.

Results

Over the 6-yr period, 75,536 anesthetics were provided to adult patients. The most common anesthesia techniques were spinal anesthesia (45.56%) and general anesthesia without intubation (33.85%). Overall perioperative mortality was 0.25%. Emergent procedures (0.41%; adjusted odds ratio [AOR], 15.86; 95% CI, 2.14 to 115.58), specialized surgeries (2.74%; AOR, 3.82; 95% CI, 1.27 to 11.47), and surgical duration more than 6 h (9.76%; AOR, 4.02; 95% CI, 1.09 to 14.88) were associated with higher odds of mortality than elective surgeries, minor surgeries, and surgical duration less than 1 h, respectively. Compared with general anesthesia with intubation, spinal anesthesia, regional anesthesia, and general anesthesia without intubation were associated with lower perioperative mortality rates of 0.04% (AOR, 0.10; 95% CI, 0.05 to 0.18), 0.06% (AOR, 0.26; 95% CI, 0.08 to 0.92), and 0.14% (AOR, 0.29; 95% CI, 0.18 to 0.45), respectively.

Conclusions

A wide range of anesthetics can be carried out safely in resource-limited settings. Providers need to be aware of the potential risks and the outcomes associated with anesthesia administration in these settings.
External Rotation Predicts Outcomes After Closed Glenohumeral Joint Reduction With Botulinum Toxin Type A in Brachial Plexus Birth Palsy
Authors: Greenhill Dustin A. , Wissinger Kevin , Trionfo Arianna , Solarz Mark , Kozin Scott H. , Zlotolow Dan A.
Published: February 2016

Background:

Few studies have investigated outcomes after adjunct botulinum toxin type A (BTX-A) injections into the shoulder internal rotator muscles during shoulder closed reduction and spica cast immobilization in children with brachial plexus birth palsy. The purpose of this study was to report success rates after treatment and identify pretreatment predictors of success.

Methods:

Children with brachial plexus birth palsy who underwent closed glenohumeral joint reduction with BTX-A and casting were included. Minimum follow-up was 1 year. Included patients did not receive concomitant shoulder surgery nor undergo microsurgery within 8 months. Records were reviewed for severity of palsy, age, physical examination scores, passive external rotation (PER), and subsequent orthopaedic procedures (repeat injections, repeat reduction, shoulder tendon transfers, and humeral osteotomy). Treatment success was defined in 3 separate ways: no subsequent surgical reduction, no subsequent closed or surgical reduction, and no subsequent procedure plus adequate external rotation.

Results:

Forty-nine patients were included. Average age at time of treatment was 11.5 months. Average follow-up was 21.1 months (range, 1 to 9 y). Thirty-two patients (65%) required repeat reduction (closed or surgical). Only 16% of all patients obtained adequate active external rotation without any subsequent procedure. Increased PER (average 41±14 degrees, odds ratio=1.21, P=0.01) and Active Movement Scale external rotation (average 1.3, odds ratio=2.36, P=0.02) predicted optimal treatment success. Limited pretreatment PER (average −1±17 degrees) was associated with treatment failure. Using the optimal definition for success, all patients with pretreatment PER>30 degrees qualified as successes and all patients with PER<15 degrees were treatment failures.

Conclusions:

Pretreatment PER>30 degrees can help identify which patients are most likely to experience successful outcomes after shoulder closed reduction with BTX-A and cast immobilization. However, a large proportion of these patients will still have mild shoulder subluxation or external rotation deficits warranting subsequent intervention.

Level of Evidence:

Level IV—therapeutic.
Pre-ESRD Care and Mortality in Incident ESRD Patients With Multiple Myeloma
Authors: Cobb Jason , Plantinga Laura , Luthi Jean-Christophe , Lynch Janet R. , Huff Edwin D. , Mohan Sumit , McClellan William M.
Published: February 2016

Objectives:

The relationship between mortality and pre-ESRD (end-stage renal disease) nephrology care in incident ESRD patients with multiple myeloma (MM) as the primary cause of renal failure has not been examined.

Materials and Methods:

Among 439,206 incident US hemodialysis patients with MM as the primary cause of ESRD (June 1, 2005 to May 31, 2009) identified using the US Renal Data System, adjusted odds ratios (OR) for reported pre-ESRD nephrology care for ESRD due to MM (n=4561) versus other causes (n=434,645) were calculated. The association of pre-ESRD nephrology care with subsequent mortality in MM-ESRD patients was examined.

Results:

MM-ESRD patients were less likely to have any predialysis nephrology care in the year before initiation of dialysis (34.8% vs. 58.5%; OR=0.38; 95% confidence interval [CI], 0.34-0.43) compared with patients with ESRD due to other causes. MM-ESRD patients compared with others were more likely to have catheters on first dialysis (91.8% vs. 75.6%; OR=4.15; 95% CI, 3.54-4.86). Incident MM-ESRD patients receiving predialysis care for ≥6 months had significantly lower 1-year mortality (hazard ratio 0.89; 95% CI, 0.82-0.97 and 0.88; 95% CI, 0.80-0.96, respectively), relative to those without this care. A catheter for dialysis access was associated with a 1.6-fold increase in 1-year mortality in incident MM-ESRD (hazard ratio 1.55; 95% CI, 1.32-1.83).

Conclusions:

MM-ESRD patients were less likely to have predialysis nephrology care and more likely to use catheters on first dialysis. However, predialysis care is independently associated with lower mortality in MM-ESRD patients. Predialysis care should be prioritized in MM patients approaching ESRD.
Disseminated Histoplasmosis in Patients Receiving Tumor Necrosis Factor-α Inhibitors
Authors: Bogorodskaya Milana , El Chakhtoura Nadim G. , Salata Robert A.
Published: February 2016

Since their introduction in the late 1990s, tumor necrosis factor (TNF)-α inhibitors have proven effective in the treatment of several inflammatory disorders, and their use has become increasingly common. Tumor necrosis factor-α blockade is nonetheless associated with an increase in the risk of infection by intracellular, granuloma-forming pathogens, such as Histoplasma capsulatum. We performed a query of our medical records for all cases of disseminated histoplasmosis in patients receiving TNF-α inhibitors between the years 1999 and 2014 at University Hospitals Case Medical Center in Cleveland, Ohio, an area of moderate histoplasmosis endemicity. A total of 357 cases of disseminated histoplasmosis were identified, 8 (2.2%) of whom were receiving TNF-α inhibitor therapy at the time of diagnosis. Five patients were receiving infliximab, and 3 were receiving adalimumab. All patients had generalized, nonspecific presenting symptoms, and all but one had a complete response to antifungal treatment and the cessation of the inciting TNF-α inhibitor. Five of the patients eventually resumed TNF-α inhibitor therapy a year after their initial diagnosis with disseminated histoplasmosis. The only patient who succumbed to the infection had a delayed diagnosis. The increasing use of TNF-α inhibitors should come with an increased awareness of its association with opportunistic infections including disseminated histoplasmosis and by other endemic fungi. This case series highlights the importance of early diagnosis of such infections to achieve a favorable outcome. Further research will need to focus on determining the best long-term treatment strategies in managing these patients after the resolution of the acute infection.
The Lived Experience of Jordanian Parents in a Neonatal Intensive Care Unit: A Phenomenological Study
Authors: Abuidhail Jamila , Al-Motlaq Mohammad , Mrayan Lina , Salameh Taghreed
Published: February 2016

Background:

Many international studies in the field of neonatal nursing have identified parental stress, coping difficulties, support issues, and various other experiences that are related to the birth of a preterm infant. However, no studies have assessed the interrelated issues of parental stress, social support, satisfaction, and nursing support in neonatal intensive care units (NICUs) in Jordan.

Purpose:

This study describes the lived experiences, needs in relation to care, and support systems of parents whose neonates were admitted to the NICU.

Methods:

A qualitative design using a phenomenological approach was used to explore the experiences of Jordanian parents who gave birth to neonates in the NICU setting. Participants were recruited from the NICUs of government, teaching, and private hospitals. Data were collected using semistructured interviews that were conducted with parents in a suitable place. Ten participants were interviewed: eight mothers and two fathers. After interviews were transcribed, the methodology suggested by van Manen (1990) was used to analyze the data.

Results:

The shock, worry, and anxiety experienced by parents; the influences of NICU admission on the experiences of parents and families; the information and assistance required and received by parents from healthcare professionals; and the emotions and satisfaction of parents were the main themes that emerged from the study to reflect the lived experience of parents of neonates in the NICU.

Conclusions/Implications for Practice:

The parents in this study were satisfied with the healthcare process in the NICUs, even when this care did not fulfill their expectations or needs for their infants. Nurses in the NICUs must develop interventions and strategies that minimize the stress experienced by parents and that support the emotional capacity of parents to deal with this stressful situation.
SOX2 Expression in Cervical Intraepithelial Neoplasia Grade 3 (CIN3) and Superficially Invasive (Stage IA1) Squamous Carcinoma of the Cervix
Authors: Stewart Colin J.R. , Crook Maxine
Published: February 2016

The transcription factor SOX2 plays an important role in tissue development and differentiation. In the neoplastic context, SOX2 has been shown to potentiate tumor invasion, and increased SOX2 immunoreactivity has been demonstrated in a variety of epithelial and nonepithelial malignancies often correlating with adverse prognosis. There are limited data on SOX2 expression in cervical squamous neoplasia and in particular, no studies have compared staining in cervical intraepithelial neoplasia (CIN)3 and in superficially invasive (Stage IA1) squamous cell carcinomas (SCC). We examined SOX2 expression in 12 cervical biopsies showing CIN3 only and 30 specimens with an initial diagnosis of Stage IA1 SCC; 7 of the latter samples did not demonstrate residual invasive foci in the study slides but all showed CIN3. There was variable staining in CIN3 without stromal invasion but CIN3 adjacent to SCC was more often SOX2 positive with 70% cases showing diffuse staining. CIN within endocervical crypts often showed more extensive SOX2 expression and in some cases staining was restricted to areas of crypt involvement. In contrast to CIN, most SCCs were SOX2 negative and there was often an abrupt loss of expression at the tumor-stromal interface. In summary, CIN3 usually showed increased SOX2 expression compared with normal epithelium, particularly in areas of endocervical crypt involvement and adjacent to superficially invasive SCC. However, most invasive tumor cells were unstained suggesting downregulation of SOX2 during the initial stages of the invasive process. Progression of cervical squamous neoplasia may involve cyclical alterations in SOX2 activity.
Growth Hormone Therapy Accelerates Axonal Regeneration, Promotes Motor Reinnervation, and Reduces Muscle Atrophy following Peripheral Nerve Injury
Authors: Tuffaha Sami H. , Budihardjo Joshua D. , Sarhane Karim A. , Khusheim Mohammed , Song Diana , Broyles Justin M. , Salvatori Roberto , Means Kenneth R. , Higgins James P. , Shores Jaimie T. , Cooney Damon S. , Hoke Ahmet , Lee W. P. Andrew , Brandacher Gerald
Published: February 2016

Background:

Therapies to improve outcomes following peripheral nerve injury are lacking. Prolonged denervation of muscle and Schwann cells contributes to poor outcomes. In this study, the authors assess the effects of growth hormone therapy on axonal regeneration, Schwann cell and muscle maintenance, and end-organ reinnervation in rats.

Methods:

Male Sprague-Dawley rats underwent sciatic nerve transection and repair and femoral nerve transection without repair and received either daily subcutaneous growth hormone (0.4 mg/day) or no treatment (n = 8 per group). At 5 weeks, the authors assessed axonal regeneration within the sciatic nerve, muscle atrophy within the gastrocnemius muscle, motor endplate reinnervation within the soleus muscle, and Schwann cell proliferation within the denervated distal femoral nerve.

Results:

Growth hormone–treated animals demonstrated greater percentage increase in body mass (12.2 ± 1.8 versus 8.5 ± 1.5; p = 0.0044), greater number of regenerating myelinated axons (13,876 ± 2036 versus 8645 ± 3279; p = 0.0018) and g-ratio (0.64 ± 0.11 versus 0.51 ± 0.06; p = 0.01), greater percentage reinnervation of motor endplates (75.8 ± 8.7 versus 38.2 ± 22.6; p = 0.0008), and greater muscle myofibril cross-sectional area (731.8 ± 157 μm versus 545.2 ± 144.3 μm; p = 0.027).

Conclusions:

In male rats, growth hormone therapy accelerates axonal regeneration, reduces muscle atrophy, and promotes muscle reinnervation. Growth hormone therapy may also maintain proliferating Schwann cells in the setting of prolonged denervation. These findings suggest potential for improved outcomes with growth hormone therapy after peripheral nerve injuries.
Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments
Authors: Gorter Florien A. , Scanlan Pauline D. , Buckling Angus
Published: February 2016

Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium
Pseudomonas fluorescens
and its viral parasite bacteriophage Φ2. We coevolved replicate populations of bacteria and phages at three different temperatures, and determined their performance against coevolutionary partners from the same and different temperatures. Crucially, we measured performance at different assay temperatures, which allowed us to disentangle adaptation to biotic and abiotic habitat components. Our results show that bacteria and phages are more resistant and infectious, respectively, at the temperature at which they previously coevolved, confirming that local adaptation to abiotic conditions can play a crucial role in determining parasite infectivity and host resistance. Our work underlines the need to assess host–parasite interactions across multiple relevant abiotic environments, and suggests that microbial adaption to local temperatures can create ecological barriers to dispersal across temperature gradients.