bluuebunny/crossref_metadata_2025 huggingface dataset:
An automated pipette puller for fabrication of glass micropipettes
Authors: Tamizhanban R. , Sreejith K. R. , Jayanth G. R.
Published: May 2014

Glass micropipettes are versatile probing tools for performing micro- and nano-manipulation tasks. This paper presents the design and development of an automated pipette puller system for fabrication of glass micropipettes. The pipette puller employs a new strategy for fabrication of micropipettes that enables achieving independent control of their taper, tip diameter, and bend-angle, and also facilitates theoretical derivation of simple, approximate relationships between the pipette shape and the pulling parameters. Subsequently, the design and fabrication of the pipette puller is described, which include that of the pipette heating system, the mechanical motion stages, and the control electronics of the pipette puller. The fabricated pipette puller is experimentally evaluated to demonstrate control of the taper, tip diameter, and the bend-angle of the micropipette. Further, the dependence of the taper and tip diameter on the pulling parameters is evaluated and is shown to be in alignment with the proposed theoretical relationships.
Turbulence driven by precession in spherical and slightly elongated spheroidal cavities
Authors: Goto Susumu , Matsunaga Arihiro , Fujiwara Masahiro , Nishioka Michio , Kida Shigeo , Yamato Masahiro , Tsuda Shinya
Published: May 2014

Motivated by the fascinating fact that strong turbulence can be sustained in a weakly precessing container, we conducted a series of laboratory experiments on the flow in a precessing spherical cavity, and in a slightly elongated prolate spheroidal cavity with a minor-to-major axis ratio of 0.9. In order to determine the conditions required to sustain turbulence in these cavities, and to investigate the statistics of the sustained turbulence, we developed an experimental technique to conduct high-quality flow visualizations as well as measurements via particle image velocimetry on a turntable and by using an intense laser. In general, flows in a precessing cavity are controlled by two non-dimensional parameters: the Reynolds number Re (or its reciprocal, the Ekman number) which is defined by the cavity size, spin angular velocity, and the kinematic viscosity of the confined fluid, and the Poincaré number Po, which is defined by the ratio of the magnitude of the precession angular velocity to that of the spin angular velocity. However, our experiments show that the global flow statistics, such as the mean velocity field and the spatial distribution of the intensity of the turbulence, are almost independent of Re, and they are determined predominantly by Po, whereas the instability of these global flow structures is governed by Re. It is also shown that the turbulence statistics are most likely similar in the two cavities due to the slight difference between their shapes. However, the condition to sustain the unsteady flows, and therefore the turbulence, differs drastically depending on the cavity shape. Interestingly, the asymmetric cavity, i.e., the spheroid, requires a much stronger precession than a sphere to sustain such unsteady flows. The most developed turbulence for a given Re is generated in these cavities when 0.04 ≲ Po ≲ 0.1. In such cases, the sustained turbulence is always accompanied by vigorous large-scale vortical structures, and shearing motions around these large-scale vortices create smaller-scale turbulent vortices. The spatial average of the Taylor-length based Reynolds number of the turbulence in the precessing sphere is about \documentclass[12pt]{minimal}\begin{document}$0.15\sqrt{Re}$\end{document}0.15Re for Po = 0.1.
Distribution of charge carrier transport properties in organic semiconductors with Gaussian disorder
Authors: Lorrmann Jens , Ruf Manuel , Vocke David , Dyakonov Vladimir , Deibel Carsten
Published: May 2014

The charge carrier drift mobility in disordered semiconductors is commonly graphically extracted from time-of-flight (TOF) photocurrent transients yielding a single transit time. However, the term transit time is ambiguously defined and fails to deliver a mobility in terms of a statistical average. Here, we introduce an advanced computational procedure to evaluate TOF transients, which allows to extract the whole distribution of transit times and mobilities from the photocurrent transient, instead of a single value. This method, extending the work of Scott et al. (Phys. Rev. B 46, 8603 (1992)), is applicable to disordered systems with a Gaussian density of states and its accuracy is validated using one-dimensional Monte Carlo simulations. We demonstrate the superiority of this new approach by comparing it to the common geometrical analysis of hole TOF transients measured on poly(3-hexyl thiophene-2,5-diyl). The extracted distributions provide access to a very detailed and accurate analysis of the charge carrier transport. For instance, not only the mobility given by the mean transit time but also the mean mobility can be calculated. Whereas the latter determines the macroscopic photocurrent, the former is relevant for an accurate determination of the energetic disorder parameter σ within the Gaussian disorder model. σ derived by using the common geometrical method is, as we show, underestimated instead.
Gyrokinetic theory of electrostatic lower-hybrid drift instabilities in a current sheet with guide field
Authors: Tummel K. , Chen L. , Wang Z. , Wang X. Y. , Lin Y.
Published: May 2014

A kinetic electrostatic eigenvalue equation for the lower-hybrid drift instability (LHDI) in a thin Harris current sheet with a guide field is derived based on the gyrokinetic electron and fully kinetic ion(GeFi) description. Three-dimensional nonlocal analyses are carried out to investigate the influence of a guide field on the stabilization of the LHDI by finite parallel wavenumber, k∥. Detailed stability properties are first analyzed locally, and then as a nonlocal eigenvalue problem. Our results indicate that at large equilibrium drift velocities, the LHDI is further destabilized by finite k∥ in the short-wavelength domain. This is demonstrated in a local stability analysis and confirmed by the peak in the eigenfunction amplitude. We find the most unstable modes localized at the current sheet edges, and our results agree well with simulations employing the GeFi code developed by Lin et al. [Plasma Phys. Controlled Fusion 47, 657 (2005); Plasma Phys. Controlled Fusion 53, 054013 (2011)].
Modeling of divertor geometry effects in China fusion engineering testing reactor by SOLPS/B2-Eirene
Authors: Zhao M. L. , Chen Y. P. , Guo H. Y. , Ye M. Y. , Tendler M. , Li G. Q. , Luo Z. P.
Published: May 2014

The China Fusion Engineering Testing Reactor (CFETR) is currently under design. The SOLPS/B2-Eirene code package is utilized for the design and optimization of the divertor geometry for CFETR. Detailed modeling is carried out for an ITER-like divertor configuration and one with relatively open inner divertor structure, to assess, in particular, peak power loading on the divertor target, which is a key issue for the operation of a next-step fusion machine, such as ITER and CFETR. As expected, the divertor peak heat flux greatly exceeds the maximum steady-state heat load of 10 MW/m2, which is a limit dictated by engineering, for both divertor configurations with a wide range of edge plasma conditions. Ar puffing is effective at reducing divertor peak heat fluxes below 10 MW/m2 even at relatively low densities for both cases, favoring the divertor configuration with more open inner divertor structure.
Zonal flow dynamics in the double tearing mode with antisymmetric shear flows
Authors: Mao Aohua , Li Jiquan , Liu Jinyuan , Kishimoto Yasuaki
Published: May 2014

The generation dynamics and the structural characteristics of zonal flows are investigated in the double tearing mode (DTM) with antisymmetric shear flows. Two kinds of zonal flow oscillations are revealed based on reduced resistive magnetohydrodynamics simulations, which depend on the shear flow amplitudes corresponding to different DTM eigen mode states, elaborated by Mao et al. [Phys. Plasmas 20, 022114 (2013)]. For the weak shear flows below an amplitude threshold, vc, at which two DTM eigen states with antisymmetric or symmetric magnetic island structure are degenerated, the zonal flows grow oscillatorily in the Rutherford regime during the nonlinear evolution of the DTMs. It is identified that the oscillation mechanism results from the nonlinear interaction between the distorted islands and the zonal flows through the modification of shear flows. However, for the medium shear flows above vc but below the critical threshold of the Kelvin-Helmholtz instability, an oscillatory growing zonal flow occurs in the linear phase of the DTM evolution. It is demonstrated that the zonal flow oscillation originates from the three-wave mode coupling or a modulation instability pumped by two DTM eigen modes with the same frequency but opposite propagating direction. With the shear flows increasing, the amplitude of zonal flow oscillation increases first and then decreases, whilst the oscillation frequency as twice of the Doppler frequency shift increases. Furthermore, impacts of the oscillatory zonal flows on the nonlinear evolution of DTM islands and the global reconnection are also discussed briefly.
Advanced properties of extended plasmas for efficient high-order harmonic generation
Authors: Ganeev R. A. , Suzuki M. , Kuroda H.
Published: May 2014

We demonstrate the advanced properties of extended plasma plumes (5 mm) for efficient harmonic generation of laser radiation compared with the short lengths of plasmas (∼0.3–0.5 mm) used in previous studies. The harmonic conversion efficiency quadratically increased with the growth of plasma length. The studies of this process along the whole extreme ultraviolet range using the long plasma jets produced on various metal surfaces, particularly including the resonance-enhanced laser frequency conversion and two-color pump, are presented. Such plasmas could be used for the quasi-phase matching experiments by proper modulation of the spatial characteristics of extended ablating area and formation of separated plasma jets.
A super-compact metamaterial absorber cell in L-band
Authors: Cao Z. X. , Yuan F. G. , Li L. H.
Published: May 2014

A super-compact metamaterial absorber (SMA) unit cell in L band (1–2 GHz) is proposed, which is composed of a pair of electric ring resonator (ERR) and its complementary ERR (CERR) with a high dielectric substrate sandwiched in between. The CERR has a cross sectional area where approximately the etched copper foil in ERR is now retained, and the remaining region is now etched. In contract with quarter-wavelength (λ/4) thickness which is required for conventional absorbers, the largest in-plane dimension and thickness of the SMA cell are only λ/33 and λ/250, respectively, leading to a super compact cell volume. While traditionally the long straight wire is introduced in electric-LC resonators for increasing inductance, the CERR achieves similar inductance with much shorter lengths. Thus, its cell dimensions can be drastically reduced without compromising its performance. In addition, simulations together with an automated phase correction algorithm show that the SMA is a type of metamaterial possessing simultaneous negative electric permittivity (NEP) and negative magnetic permeability (NMP). Further the SMA has a very large imaginary part of the NEP and NMP, resulting in significantly large imaginary part of the refractive index at resonant frequency. These properties are well suited to design excellent absorbers. In addition, numerical results demonstrate that the maximum absorption coefficient of the SMA can reach greater than 99% at resonant frequency, and the full-width half-maximum is roughly 1% of the operating frequency, and a wide incident angle of ±49° over 90% absorption. Meanwhile, it is pointed out that this type of absorber is rather sensitive to polarization characteristic of the incident electromagnetic wave.
Full control of quadruple quantum dot circuit charge states in the single electron regime
Authors: Delbecq M. R. , Nakajima T. , Otsuka T. , Amaha S. , Watson J. D. , Manfra M. J. , Tarucha S.
Published: May 2014

We report the realization of an array of four tunnel coupled quantum dots in the single electron regime, which is the first required step toward a scalable solid state spin qubit architecture. We achieve an efficient tunability of the system but also find out that the conditions to realize spin blockade readout are not as straightforwardly obtained as for double and triple quantum dot circuits. We use a simple capacitive model of the series quadruple quantum dots circuit to investigate its complex charge state diagrams and are able to find the most suitable configurations for future Pauli spin blockade measurements. We then experimentally realize the corresponding charge states with a good agreement to our model.
Effect of Tb3+ concentration on the optical and vibrational properties of YBO3 tri-doped with Eu3+, Ce3+, and Tb3+
Authors: Sohal S. , Nazari M. , Zhang X. , Hassanzadeh E. , Kuryatkov V. V. , Chaudhuri J. , Hope-Weeks L. J. , Huang J. Y. , Holtz M.
Published: May 2014

Structural and optical studies are reported of yttrium orthoborate YBO3 when tri-doped with Eu3+, Ce3+, and Tb3+, focusing on the role of terbium concentration. Incorporation of Tb3+ affects emission properties for photoluminescence (PL) excited by near ultraviolet light. For constant cerium and europium concentrations, increasing the Tb3+ results in diminished PL from the Ce3+ and Tb3+ color centers. Simultaneously, the PL excitation bands related to both Ce3+ and Tb3+ increase in intensity for red emission from the Eu3+. Results are consistent with a Ce3+ → (Tb3+)n → Eu3+ energy transfer scheme, where (Tb3+)n denotes a chain incorporating n terbium ions. A high red to orange PL intensity ratio is obtained, ranging from 1.34 to 2.09. Raman vibrational bands show a systematic change, with Tb3+ concentration, in the B3O9 ring terminal oxygen bending mode coordinated with the yttrium site where dopant ions substitute. The structural changes are interpreted as variations in the local neighborhood of these sites in the YBO3:Ce3+,Tb3+,Eu3+ crystal structure.
High critical-current density with less anisotropy in BaFe2(As,P)2 epitaxial thin films: Effect of intentionally grown c-axis vortex-pinning centers
Authors: Sato Hikaru , Hiramatsu Hidenori , Kamiya Toshio , Hosono Hideo
Published: May 2014

We report herein a high and isotropic critical-current density Jc for BaFe2(As,P)2 epitaxial films. The isotropy of Jc with respect to the magnetic-field direction was improved significantly by decreasing the film growth rate to 2.2 Å/s. The low growth rate served to preferentially align dislocations along the c-axis, which work well as c-axis vortex-pinning centers. Because of the intentional introduction of effective pinning, the absolute Jc at 9 T was larger than that obtained for other iron-based superconductors and conventional alloy superconducting wires.
Room temperature resistive state switching with hysteresis in GdMnO3 thin film with low threshold voltage
Authors: Nath Rajib , Raychaudhuri A. K. , Mukovskii Ya. M. , Andreev N. , Chichkov Vladimir
Published: May 2014

In this paper, we report a room temperature resistive state switching with hysteresis, in a thin film of GdMnO3 grown on NdGaO3 substrate. The switched states have a resistance ratio ≈103. The switching is unipolar in nature, with a low set voltage <3 V, while the reset voltage <0.3 V. The switching occurs between a high resistance polaronic insulating state and a low resistance metallic state. The resistance state transition has been ascribed to an electronic mechanism that originates from co-existing phases (created by charge disproportionation) that can undergo a percolative transition enabled by the applied bias.
PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM
Authors: Ghanat Bari Mehrab , Ma Xuepo , Zhang Jianqiu
Published: May 2014

Motivation: In liquid chromatography–mass spectrometry/tandem mass spectrometry (LC-MS/MS), it is necessary to link tandem MS-identified peptide peaks so that protein expression changes between the two runs can be tracked. However, only a small number of peptides can be identified and linked by tandem MS in two runs, and it becomes necessary to link peptide peaks with tandem identification in one run to their corresponding ones in another run without identification. In the past, peptide peaks are linked based on similarities in retention time (rt), mass or peak shape after rt alignment, which corrects mean rt shifts between runs. However, the accuracy in linking is still limited especially for complex samples collected from different conditions. Consequently, large-scale proteomics studies that require comparison of protein expression profiles of hundreds of patients can not be carried out effectively.

Method: In this article, we consider the problem of linking peptides from a pair of LC-MS/MS runs and propose a new method, PeakLink (PL), which uses information in both the time and frequency domain as inputs to a non-linear support vector machine (SVM) classifier. The PL algorithm first uses a threshold on an rt likelihood ratio score to remove candidate corresponding peaks with excessively large elution time shifts, then PL calculates the correlation between a pair of candidate peaks after reducing noise through wavelet transformation. After converting rt and peak shape correlation to statistical scores, an SVM classifier is trained and applied for differentiating corresponding and non-corresponding peptide peaks.

Results:  PL is tested in multiple challenging cases, in which LC-MS/MS samples are collected from different disease states, different instruments and different laboratories. Testing results show significant improvement in linking accuracy compared with other algorithms.

Availability and implementation: M files for the PL alignment method are available at http://compgenomics.utsa.edu/zgroup/PeakLink

Contact:  Michelle.Zhang@utsa.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
compcodeR—an R package for benchmarking differential expression methods for RNA-seq data
Authors: Soneson Charlotte
Published: May 2014

Summary:  compcodeR is an R package for benchmarking of differential expression analysis methods, in particular, methods developed for analyzing RNA-seq data. The package provides functionality for simulating realistic RNA-seq count datasets, an interface to several of the most commonly used differential expression analysis methods and extensive functionality for evaluating and comparing different approaches on real and simulated data.

Availability and implementation:  compcodeR is available from http://www.bioconductor.org/packages/release/bioc/html/compcodeR.html

Contact:  Charlotte.Soneson@isb-sib.ch or charlottesoneson@gmail.com
Modelling the interaction between the host immune response, bacterial dynamics and inflammatory damage in comparison with immunomodulation and vaccination experiments
Authors: Jarrett Angela M. , Cogan N.G. , Shirtliff M.E.
Published: May 2014

The immune system is a complex system of chemical and cellular interactions that responds quickly to queues that signal infection and then reverts to a basal level once the challenge is eliminated. Here, we present a general, four-component model of the immune system's response to a Staphylococcal aureus (S. aureus) infection, using ordinary differential equations. To incorporate both the infection and the immune system, we adopt the style of compartmenting the system to include bacterial dynamics, damage and inflammation to the host, and the host response. We incorporate interactions not previously represented including cross-talk between inflammation/damage and the infection and the suppression of the anti-inflammatory pathway in response to inflammation/damage. As a result, the most relevant equilibrium of the system, representing the health state, is an all-positive basal level. The model is able to capture eight different experimental outcomes for mice challenged with intratibial osteomyelitis due to S. aureus, primarily involving immunomodulation and vaccine therapies. For further validation and parameter exploration, we perform a parameter sensitivity analysis which suggests that the model is very stable with respect to variations in parameters, indicates potential immunomodulation strategies and provides a possible explanation for the difference in immune potential for different mouse strains.
Factors Associated With Cancer Incidence and With All-Cause Mortality After Cancer Diagnosis Among Human Immunodeficiency Virus-Infected Persons During the Combination Antiretroviral Therapy Era
Authors: Patel Pragna , Armon Carl , Chmiel Joan S. , Brooks John T. , Buchacz Kate , Wood Kathy , Novak Richard M.
Published: May 2014

Background.  Little is known about survival and factors associated with mortality after cancer diagnosis among persons infected with human immunodeficiency virus (HIV).

Methods.  Using Poisson regression, we analyzed incidence rates of acquired immune deficiency syndrome (AIDS)-defining cancers (ADC), non-AIDS-defining infection-related cancers (NADCI), and non-AIDS-defining noninfection-related cancers (NADCNI) among HIV Outpatient Study participants seen at least twice from 1996–2010. All-cause mortality within each cancer category and by calendar period (1996–2000, 2001–2005, 2006–2010) were examined using Kaplan-Meier survival methods and log-rank tests. We identified risk factors for all-cause mortality using multivariable Cox proportional hazard models.

Results.  Among 8350 patients, 627 were diagnosed with 664 cancers. Over the 3 time periods, the age- and sex-adjusted incidence rates for ADC and NADCNI declined (both P < .001) and for NADCI did not change (P = .13). Five-year survival differed by cancer category (ADC, 54.5%; NADCI, 65.8%; NADCNI, 65.9%; P = .018), as did median CD4 cell count (107, 241, and 420 cells/mm3; P < .001) and median log10 viral load (4.1, 2.3, and 2.0 copies/mL; P < .001) at cancer diagnosis, respectively. Factors independently associated with increased mortality for ADC were lower nadir CD4 cell count (hazard ratio [HR] = 3.02; 95% confidence interval [CI], 1.39–6.59) and detectable viral load (≥400 copies/mL; HR = 1.72 [95% CI, 1.01–2.94]) and for NADCNI, age (HR = 1.50 [95% CI, 1.16–1.94]), non-Hispanic black race (HR = 1.92 [95% CI, 1.15–3.24]), lower nadir CD4 cell count (HR = 1.77 [95% CI, 1.07–2.94]), detectable viral load (HR = 1.96 [95% CI, 1.18–3.24]), and current or prior tobacco use (HR = 3.18 [95% CI, 1.77–5.74]).

Conclusions.  Since 1996, ADC and NADCNI incidence rates have declined. Survival after cancer diagnosis has increased with concomitant increases in CD4 cell count in recent years. Advances in HIV therapy, including early initiation of combination antiretroviral therapy, may help reduce mortality risk among HIV-infected persons with cancer.
Rates of Pneumococcal Disease in Adults With Chronic Medical Conditions
Authors: Shea Kimberly M. , Edelsberg John , Weycker Derek , Farkouh Raymond A. , Strutton David R. , Pelton Stephen I.
Published: May 2014

Background.  Although it is widely accepted that adults with immunocompromising conditions are at greatly increased risk of pneumococcal infection, the extent of risk among immunocompetent adults with chronic medical conditions is less certain, particularly in the current era of universal vaccination of children with pneumococcal conjugate vaccines.

Methods.  We conducted a retrospective cohort study using data from 3 healthcare claims repositories (2006–2010) to compare rates of pneumococcal disease in immunocompetent adults with chronic medical conditions (“at-risk”) and immunocompromised adults (“high-risk”), with rates in adults without these conditions (“healthy”). Risk profiles and episodes of pneumococcal disease—all-cause pneumonia, pneumococcal pneumonia, and invasive pneumococcal disease (IPD)—were ascertained from diagnosis, procedure, and drug codes.

Results.  Rates of all-cause pneumonia among at-risk persons aged 18–49 years, 50–64 years, and ≥65 years were 3.2 (95% confidence interval [CI], 3.1–3.2), 3.1 (95% CI, 3.1–3.1), and 3.0 (95% CI, 3.0–3.0) times the rates in age-matched healthy counterparts, respectively. We idetified rheumatoid arthritis, systemic lupus erythematosus, Crohn's disease, and neuromuscular or seizure disorders as additional at-risk conditions for pneumococcal disease. Among persons with at-risk conditions, the rate of all-cause pneumonia substantially increased with the accumulation of concurrent at-risk conditions (risk stacking): among persons 18–49 years, rate ratios increased from 2.5 (95% CI, 2.5–2.5) in those with 1 at-risk condition to 6.2 (95% CI, 6.1–6.3) in those with 2 conditions, and to 15.6 (95% CI, 15.3–16.0) in those with ≥3 conditions. Findings for pneumococcal pneumonia and IPD were similar.

Conclusions.  Despite widespread use of pneumococcal conjugate vaccines, rates of pneumonia and IPD remain disproportionately high in adults with at-risk conditions, including those with conditions not currently included in the Advisory Committee on Immunization Practices’ guidelines for prevention and those with multiple at-risk conditions.
Endothelial Activation and Repair During Hantavirus Infection: Association with Disease Outcome
Authors: Connolly-Andersen Anne-Marie , Thunberg Therese , Ahlm Clas
Published: May 2014

Background.  Endothelial activation and dysfunction play a central role in the pathogenesis of sepsis and viral hemorrhagic fevers. Hantaviral disease is a viral hemorrhagic fever and is characterized by capillary dysfunction, although the underlying mechanisms for hantaviral disease are not fully elucidated.

Methods.  The temporal course of endothelial activation and repair were analyzed during Puumala hantavirus infection and associated with disease outcome and a marker for hypoxia, insulin-like growth factor binding protein 1 (IGFBP-1). The following endothelial activation markers were studied: endothelial glycocalyx degradation (syndecan-1) and leukocyte adhesion molecules (soluble vascular cellular adhesion molecule 1, intercellular adhesion molecule 1, and endothelial selectin). Cytokines associated with vascular repair were also analyzed (vascular endothelial growth factor, erythropoietin, angiopoietin, and stromal cell-derived factor 1).

Results.  Most of the markers we studied were highest during the earliest phase of hantaviral disease and associated with clinical and laboratory surrogate markers for disease outcome. In particular, the marker for glycocalyx degradation, syndecan-1, was significantly associated with levels of thrombocytes, albumin, IGFBP-1, decreased blood pressure, and disease severity.

Conclusions.  Hantaviral disease outcome was associated with endothelial dysfunction. Consequently, the endothelium warrants further investigation when designing future medical interventions.
Gender, Competitiveness, and Career Choices *
Authors: Buser Thomas , Niederle Muriel , Oosterbeek Hessel
Published: May 2014

Gender differences in competitiveness have been hypothesized as a potential explanation for gender differences in education and labor market outcomes. We examine the predictive power of a standard laboratory experimental measure of competitiveness for the later important choice of academic track of secondary school students in the Netherlands. Although boys and girls display similar levels of academic ability, boys choose substantially more prestigious academic tracks, where more prestigious tracks are more math- and science-intensive. Our experimental measure shows that boys are also substantially more competitive than girls. We find that competitiveness is strongly positively correlated with choosing more prestigious academic tracks even conditional on academic ability. Most important, we find that the gender difference in competitiveness accounts for a substantial portion (about 20%) of the gender difference in track choice.
Lysinibacillus halotolerans sp. nov., isolated from saline-alkaline soil
Authors: Kong Delong , Wang Yanwei , Zhao Bingqiang , Li Yanting , Song Jinlong , Zhai Yi , Zhang Chi , Wang Huimin , Chen Xiaorong , Zhao Bin , Ruan Zhiyong
Published: May 2014

A novel aerobic, halotolerant bacterium, designated strain LAM612T, was isolated from saline-alkaline soil samples from Lingxian County, Shandong Province, China. Cells of strain LAM612T were Gram-reaction-positive, endospore-forming, motile and rod-shaped. The optimal temperature and pH for growth were 35 °C and pH 6.0, respectively. Strain LAM612T could grow in the presence of up to 10 % (w/v) NaCl. The genomic DNA G+C conten was 36.4 mol% as detected by the T
m method. Comparative analysis of 16S rRNA gene sequences revealed that LAM612T was closely related to

Lysinibacillus sinduriensis

KACC 16611T (98.0 %),

L. chungkukjangi

KACC 16626T (97.5 %),

L. massiliensis

KCTC 13178T (97.4 %),

L. xylanilyticus

KACC 15113T (97.2 %),

L. macroides

DSM 54T (97.0 %) and

L. manganicus

DSM 26584T (96.5 %). The DNA–DNA hybridization values between strain LAM612T and its closest relatives ranged from 20.6 % to 41.9 %. The major fatty acids of strain LAM612T were iso-C15 : 0 (40.8 %), iso-C16 : 0 (15.2 %) and anteiso-C15 : 0 (10.8 %). The cell-wall peptidoglycan content was A4α (l-Lys–d-Asp). The predominant menaquinone was MK-7 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, five unknown glycolipids and an unknown lipid. Based on the DNA–DNA hybridization results and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM612T could be distinguished from the recognized species of the genus

Lysinibacillus

, and was suggested to represent a novel species of this genus, for which the name Lysinibacillus halotolerans sp. nov. is proposed. The type strain is LAM612T ( = ACCC 00718T = JCM 19611T).
Disintegrin-like domain of glycoprotein B regulates Kaposi’s sarcoma-associated herpesvirus infection of cells
Authors: Walker Lia R. , Hussein Hosni A. M. , Akula Shaw M.
Published: May 2014

Kaposi's sarcoma-associated herpesvirus (KSHV) glycoprotein B (gB) is a lytic structural protein expressed on the envelope of mature virions and on the membrane of cells supporting lytic infection. In addition to this viral glycoprotein’s interaction with integrins via its RGD (Arg-Gly-Asp) motif, KSHV gB possesses a disintegrin-like domain (DLD), which binds integrins as well. Prior to this study, there has been minimal research involving the less common integrin-binding motif, DLD, of gB as it pertains to herpesvirus infection. By using phage display peptide library screening and molecular biology techniques, the DLD of KSHV gB was shown to interact specifically with non-RGD binding α9β1 integrins. Similarly, monitoring wild-type infection confirmed α9β1:DLD interactions to be critical to successful KSHV infection of human foreskin fibroblast (HFF) cells and human dermal microvascular endothelial cells (HMVEC-d) compared with 293 cells. To further demonstrate the importance of the DLD of gB in KSHV infection, two recombinant virus constructs were generated using a bacterial artificial chromosome (BAC) system harbouring the KSHV genome (BAC36): BAC36ΔD-KSHV (lacking a functionally intact DLD of gB and containing an introduced tetracycline cassette) and BAC36.T-KSHV (containing an intact DLD sequence and an introduced tetracycline cassette). Accordingly, BAC36ΔD-KSHV presented significantly lower infection rates in HFF and HMVEC-d cells compared with the comparable infection rates achieved by wild-type BAC36-KSHV and BAC36.T-KSHV. Thus, the present report has delineated a critical role for the DLD of gB in KSHV infection, which may lead to a broader knowledge regarding the sophisticated mechanisms utilized by virus-encoded structural proteins in KSHV entry and infection.
Mycoplasma stress response: adaptive regulation or broken brakes?
Authors: Mazin Pavel V , Fisunov Gleb Y , Gorbachev Alexey Y , Altukhov Ilya A , Semashko Tatiana A , Alexeev Dmitry G , Govorun Vadim M
Published: May 2014

The avian bacterial pathogen Mycoplasma gallisepticum is a good model for transcriptional regulation studies due to its small genome and relative simplicity. In this study, we used RNA-Seq experiments combined with MS-based proteomics to accurately map coding sequences (CDSs), transcription start sites (TSSs) and transcription terminators (TTs) and to decipher their roles in stress-induced transcriptional responses. We identified 1061 TSSs at an FDR (false discovery rate) of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters, which are surrounded by A/T-rich sequences and rarely accompanied by a -35 element. Our analysis revealed the pronounced complexity of the operon structure: on average, each coding operon has one internal TSS and TT in addition to the primary ones. Our new transcriptomic approach based on the intervals between the two closest transcription initiators and/or terminators allowed us to identify two classes of TTs: strong, unregulated and hairpin-containing TTs and weak, heat shock-regulated and hairpinless TTs. Comparing the gene expression levels under different conditions (such as heat, osmotic and peroxide stresses) revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the structure of the core promoter plays a major role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the suppression of hairpinless TTs leads to widespread, seemingly non-functional transcription.
Spatial variation in water loss predicts terrestrial salamander distribution and population dynamics
Authors: Peterman W.E. , Semlitsch R.D.
Published: May 2014

Many patterns observed in ecology, such as species richness, life history variation, habitat use, and distribution have physiological underpinnings. For many ectothermic organisms temperature relations shape these patterns, but for terrestrial amphibians, water balance may supersede temperature as the most critical physiologically-limiting factor. Many amphibian species have little resistance to water loss, which restricts them to moist microhabitats and may significantly affect foraging, dispersal, and courtship. Using plaster models as surrogates for terrestrial plethodontid salamanders, we measured water loss under ecologically-relevant field conditions to estimate the duration of surface activity time across the landscape. Surface activity time was significantly affected by topography, solar exposure, canopy cover, maximum air temperature, and time since rain. Spatially, surface activity times were highest in ravine habitats and lowest on ridges. Surface activity time was a significant predictor of salamander abundance, as well as a predictor of successful recruitment; the probability of a juvenile salamander occupying an area with high surface activity time was two times greater than an area with limited predicted surface activity. Our results suggest that survival, recruitment, or both are demographic processes that are affected by water loss and the ability of salamanders to be surface active. Results from our study extend our understanding of plethodontid salamander ecology, emphasize the limitations imposed by their unique physiology, and highlight the importance of water loss to spatial population dynamics. These findings are timely to understanding the effects that fluctuating temperature and moisture conditions predicted for future climates will have on plethodontid salamanders.
Case of primary cutaneous peripheral T‐cell lymphoma, not otherwise specified, with characteristics of follicular helper T cells
Authors: Takaki Machiko , Inozume Takashi , Matsuzawa Takamitsu , Ando Noriko , Yamaguchi Miyuki , Harada Kazutoshi , Kawamura Tatsuyoshi , Shibagaki Naotaka , Shimada Shinji
Published: May 2014

We report a case of an 88‐year‐old woman with a decalvant, erythematous, ulcerated tumor extending from the right temporal to occipital region. Histopathological analysis revealed a dense infiltration of medium‐to‐large‐sized atypical cells throughout the entire dermis. The result of immunohistochemical analysis showed that the infiltrating T cells expressed programmed death‐1 (PD‐1), Bcl‐6 and CXCL13. Flow cytometry analysis showed that CD4+ PD‐1hi T cells also expressed CD10, inducible T‐cell co‐stimulator and CXCR5. On the basis of the clinical appearance and the histopathological findings, we diagnosed the patient with primary cutaneous peripheral T‐cell lymphoma, not otherwise specified. Recently, the concept of primary cutaneous follicular helper T (TFH)‐cell lymphoma was proposed, and in this case, tumor cells clearly expressed TFH‐cell markers. Therefore, we considered this case to be a variant of the entity. Although this entity is still provisional, this case supports the new concept.
Successful use of intravenous cyclophosphamide pulse therapy for interstitial lung disease in a patient with systemic sclerosis on hemodialysis
Authors: Takahashi Takehiro , Asano Yoshihide , Sunaga Ryo , Ichimura Yohei , Taniguchi Takashi , Yamamoto Mizuho , Tamaki Zenshiro , Takekoshi Tomonori , Mitsui Hiroshi , Sugaya Makoto , Ohse Takamoto , Sato Shinichi
Published: May 2014

Interstitial lung disease and scleroderma renal crisis are major complications of systemic sclerosis, which occasionally coexist in patients with the diffuse cutaneous subtype. We herein report a case of diffuse cutaneous systemic sclerosis under hemodialysis due to a previous history of scleroderma renal crisis, whose interstitial lung disease was effectively and safely treated with a half dose of i.v. cyclophosphamide pulse. The dose of cyclophosphamide and the timing of hemodialysis leading to efficacy and low toxicity are discussed.
Oral S‐1 in advanced cutaneous squamous cell carcinoma
Authors: Teramoto Yukiko , Nakamura Yasuhiro , Yamada Katsuhiro , Yamamoto Akifumi
Published: May 2014

Squamous cell carcinoma (SCC) is the second most common type of skin cancer in Japan, and its incidence has been increasing in recent years. Early diagnosis and complete excision can provide a high cure rate. However, advanced cases of SCC showing local invasion, regional lymph node metastasis or distant metastasis are not curative and are difficult to treat with surgery alone. Some chemotherapy regimens have been used for treating advanced cutaneous SCC. However, almost all these regimens require intravenous administration and result in serious toxicities in elderly people. We gave S‐1, a novel oral chemotherapeutic agent, for six patients with advanced cutaneous SCC. Three patients achieved complete response and one achieved partial response. Two patients showed stable disease. The overall response rate was 66.7% (four of six patients), and the disease control rate was 100%. Two of six patients developed grade 3 anaemia. Oral S‐1 treatment is safe and effective for treating advanced cutaneous SCC. However, a prospective trial is necessary to confirm the effectiveness of oral S‐1 for advanced cutaneous SCC.
Clinical profiles of Stevens–Johnson syndrome among Thai patients
Authors: Limpawattana Panita , Choonhakarn Charoen , Kongbunkiat Kannikar
Published: May 2014

The objective of this study was to demonstrate the clinical profiles of Stevens–Johnson syndrome (SJS) in Thai patients, and to compare those clinical features between younger and older patients. Medical records of all patients with SJS who were admitted to Srinagarind Hospital Medical School, Khon Kaen, Thailand, from January 2002 to December 2014 were reviewed. Epidemiological features, etiologies, treatment and clinical outcomes were collected. There were 45 patients with SJS during the 10‐year period. Females were the majority (57.8%) and the median age was 49 years. Hepatitis was the most frequent complication (67.5%). Phenytoin (15.6%), sulfonamide drugs (15.6%) and allopurinol (13.3%) were implicated as leading causes of SJS. Steroids were prescribed in 37 cases (82.2%). The mortality rate was 4.4%. Comparing older patients to younger patients, allopurinol appeared to be the main instigating drug to develop SJS with an odds ratio of 5.6 (95% confidence interval, 2.8–10.6). In conclusion, clinical features of Thai patients with SJS were similar to other reports. Allopurinol had the strongest association with SJS in older patients as compared to the younger ones.
Case of generalized pustular psoriasis with end‐stage renal disease successfully treated with granulocyte monocyte apheresis in combination with hemodialysis
Authors: Mabuchi Tomotaka , Manabe Yasuaki , Yamaoka Hanako , Ota Tami , Kato Masayuki , Ikoma Norihiro , Kusakabe Yoshiyuki , Komaba Hirotaka , Ozawa Akira
Published: May 2014

Granulocyte monocyte apheresis (GMA) is an extracorporeal apheresis instrument that removes activated neutrophils and monocytes. Generalized pustular psoriasis (GPP) is characterized by neutrophil infiltration into the epidermis that causes Kogoj's spongiotic pustule. Thus, GMA is one of the useful therapies for GPP, and it was approved for the treatment in 2012 in Japan. Herein, we report a case of GPP with end‐stage renal disease (ESRD) successfully treated with GMA in combination with hemodialysis (HD). A 54‐year‐old Japanese female visited our outpatient clinic because of erythema with pustules on her trunk and extremities over the past 4 months. Histopathological examination showed an intraepidermal pustule filled with numerous neutrophils and spongiosis. These findings led to the diagnosis of GPP. She had ESRD and had been treated with HD twice a week for approximately 4 years. During maintenance HD twice a week, weekly GMA was started at Tokai University Hospital. The skin symptoms disappeared after five administrations of GMA. We suggest that GMA is an effective therapy for GPP patients with ESRD who are treated with HD.
Spatial Variability in Litterfall, Litter Standing Crop and Litter Quality in a Tropical Rain Forest Region
Authors: Parsons Scott A. , Congdon Robert A. , Shoo Luke P. , Valdez‐Ramirez Vanessa , Williams Stephen E.
Published: May 2014

Understanding the spatial variability in plant litter processes is essential for accurate comprehension of biogeochemical cycles and ecosystem function. We assessed spatial patterns in litter processes from local to regional scales, at sites throughout the wet tropical rain forests of northern Australia. We aimed to determine the controls (e.g., climate, soil, plant community composition) on annual litter standing crop, annual litterfall rate and in situ leaf litter decomposability. The level of spatial variance in these components, and leaf litter N, P, Ca, lignin, α‐cellulose and total phenolics, was determined from within the scale of subregion, to site (1 km transects) to local/plot (~30 m2). Overall, standing crop was modeled with litterfall and its chemical composition, in situ decomposability, soil Na, and topography (r2 = 0.69, 36 plots). Litterfall was most closely aligned with plant species richness and stem density (negative correlation); leaf decomposability with leaf‐P and lignin, soil Na, and dry season moisture (r2 = 0.89, 40 plots). The predominant scale of variability in litterfall rates was local (plot), while litter standing crop and α‐cellulose variability was more evenly distributed across spatial scales. Litter decomposability, N, P and phenolics were more aligned with subregional differences. Leaf litter C, lignin and Ca varied most at the site level, suggesting more local controls. We show that variability in litter quality and decomposability are more easily accounted for spatially than litterfall rates, which vary widely over short distances possibly in response to idiosyncratic patterns of disturbance.
Rotation thromboelastometry and the hypercoagulable state in Cushing's syndrome
Authors: Alves Coelho Maria Caroline , Vieira Neto Leonardo , Kasuki Leandro , Wildemberg Luiz Eduardo , dos Santos Camila Vicente , Castro Gizele , Gouvêa Glauber , Veloso Orlando Carlos Gloria , Gadelha Telma , Gadelha Mônica R.
Published: May 2014

Introduction

Rotation thromboelastometry (ROTEM®) can be used for hypercoagulability evaluation. Cushing's syndrome (CS) is associated with hypercoagulability; however, ROTEM® has never been evaluated in this setting.

Objective

To evaluate hypercoagulability in CS using ROTEM® and to correlate these parameters with coagulation markers and with the presence of deep vein thrombosis.

Design and methods

Thirty patients with active CS (26 women) and 30 controls matched for age, sex, body mass index, diabetes mellitus, arterial hypertension, ABO blood group and smoking were included. We measured levels of activated partial thromboplastin time (aPTT), platelets, fibrinogen, D‐dimer, factor VIII (FVIII), von Willebrand factor (vWF) and C‐reactive protein. ROTEM® was used to evaluate the intrinsic (INTEM), extrinsic (EXTEM) and fibrinogen (FIBTEM) pathways. Doppler ultrasonography was performed to search for lower limbs deep vein thrombosis.

Results

INTEM clotting time using ROTEM® was shorter in patients than in controls (P = 0·04). Other ROTEM® parameters were not different. Mean aPTT was shorter in patients than in controls (P = 0·001). The FVIII, vWF and D‐dimer levels were higher in patients than in controls (P = 0·001, 0·001 and 0·02, respectively). Obese CS patients presented higher levels of platelets and alterations in maximum clot formation (MCF), alpha angle and maximum speed of clot formation of INTEM (P = 0·03, 0·02 and 0·02, respectively) and an increase in the MCF of FIBTEM (P = 0·02). No deep vein thrombosis was found.

Conclusions

Although FVIII and vWF were abnormal in CS patients, only the initiation clot formation was different in the ROTEM® methodology and no deep vein thrombosis was found.
The Cultural Politics of Childhood: Public Policies in Post‐authoritarian Chile
Authors: Solar Ana Vergara Del
Published: May 2014

This article offers an interpretation of the cultural politics of childhood during the second decade of post‐authoritarian democracy in Chile (2001–2010), as sustained by the discourse of public policies in this area. I understand cultural politics as the combination of cultural contexts, social practices and political processes through which childhood is constructed in different societies and different times James and James (2008b). I develop a ‘textual’ analysis focusing on the discourse of the most recent official governmental policy document on childhood, which is still in force, as well as a ‘contextual’ analysis that examines the historical relationship between the state, public policies and childhood in different periods of Chile's history as a republic.
Echocardiography and Cardiac MRI in Mutation‐Negative Hypertrophic Cardiomyopathy in an Older Patient: A Case Defining the Need for ICD
Authors: Rodriguez Fatima , Degnan Kathleen O. , Seidman Christine E. , Mangion Judy R.
Published: May 2014

We report the case of a 67‐year‐old man with hypertrophic cardiomyopathy who presented for a second opinion about implantable cardio‐defibrillator (ICD) placement after a witnessed syncopal episode. Despite his older age, being mutation‐negative, and having a maximal septal thickness of 2.2 cm on echocardiography, he demonstrated rapid progression of myocardial fibrosis on cardiac MRI, correlating to ventricular tachyarrhythmias and syncope. We review the role of echocardiography and cardiac MRI in optimizing medical care for such patients who may not otherwise meet criteria for an ICD placement or further interventions.