bluuebunny/crossref_metadata_2025 huggingface dataset:
How cryo‐electron microscopy and X‐ray crystallography complement each other
Authors: Wang Hong‐Wei , Wang Jia‐Wei
Published: August 2016

With the ability to resolve structures of macromolecules at atomic resolution, X‐ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo‐EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X‐ray crystallography and cryo‐EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms.
An Approach for Embedding Critical Thinking in Second Language Paragraph Writing
Authors: Chason Lisa , Loyet Dianne , Sorenson Luann , Stoops Anastasia
Published: August 2016

Writing textbooks for English language learners frequently teach a paragraph pattern that is limited to topic sentence, support, and concluding sentence. Although beginning second language (L2) writers benefit from having a structured way to organize their ideas, as they advance, this type of writing can sound trite and uncritical. To provide a deeper understanding of how L2 learners can develop critical thinking skills in paragraph writing, this article presents empirical research on intermediate to advanced L2 writers enrolled in an 8‐week intensive English program where they were taught how to use theTBSIR(topic, bridge, support, interpretation, return) framework. Using a double‐blind rating approach, the study reveals that instruction inTBSIRpositively impacts writing quality regardless of native language, suggesting that a writing framework with a rubric that includes critical thinking criteria provides developing writers with the guidance they need to move from banal and formulaic writing to more analytic and thoughtful prose.
Characterization of an α-amino-ɛ-caprolactam racemase with broad substrate specificity from Citreicella sp. SE45
Authors: Payoungkiattikun Wisarut , Okazaki Seiji , Ina Atsutoshi , H-Kittikun Aran , Asano Yasuhisa
Published: August 2016

α-Amino-ε-caprolactam (ACL) racemizing activity was detected in a putative dialkylglycine decarboxylase (EC 4.1.1.64) from Citreicella sp. SE45. The encoding gene of the enzyme was cloned and transformed in Escherichia coli BL21 (DE3). The molecular mass of the enzyme was shown to be 47.4 kDa on SDS–polyacrylamide gel electrophoresis. The enzymatic properties including pH and thermal optimum and stabilities were determined. This enzyme acted on a broad range of amino acid amides, particularly unbranched amino acid amides including l-alanine amide and l-serine amide with a specific activity of 17.5 and 21.6 U/mg, respectively. The K  m and V  max values for d- and l-ACL were 5.3 and 2.17 mM, and 769 and 558 μmol/min.mg protein, respectively. Moreover, the turn over number (K  cat) and catalytic efficiency (K  cat/K  m) of purified ACL racemase from Citreicella sp. SE45 using l-ACL as a substrate were 465 S−1 and 214 S−1mM−1, respectively. The new ACL racemase from Citreicella sp. SE45 has a potential to be used as the biocatalytic application.
Effects of long‐term experimental warming on plants and soil microbes in a cool temperate semi‐natural grassland in Japan
Authors: Suzuki Mayuko , Suminokura Nobuhiko , Tanami Kenta , Yoshitake Shinpei , Masuda Shingo , Tomotsune Mitsutoshi , Koizumi Hiroshi
Published: August 2016

To clarify the effects of long‐term warming on ecosystem matter cycling, we conducted an in situ 7‐year experimental warming (2009–2015) using infrared heaters in a cool temperate semi‐natural grassland in Japan. We measured plant aboveground biomass, soil total C and N, soil inorganic N (NH4+‐N and NO3−‐N), and soil microbial biomass for 7 years (2009–2015). We also measured heterotrophic respiration for 2 years (2013–2014) and assessed net N mineralization and nitrification in 2015. We found that warming immediately increased plant aboveground biomass, but this effect ceased in 2013. However, the soil microbial biomass was continuously depressed by warming. Soil inorganic N concentrations in warmed plots substantially increased in the later years of the experiment (2013–2015) and the potential net N mineralization rate was also higher than in the earlier years. In contrast, heterotrophic respiration decreased with warming in 2013–2014. Our observations indicate that long‐term warming has a contrasting effect on plants and soil microbes. In addition, the warming could have different effects on subterranean C and N cycling. To enhance the accuracy of estimation of future climate change, it is essential to continuously observe the warming effects on ecosystems and to focus on the change in subterranean C and N cycling.
Investigation on the laser ablation of SiC ceramics using micro‐Raman mapping technique
Authors: Fu Chaoli , Yang Yong , Huang Zhengren , Liu Guiling , Zhang Hui , Jiang Fang , Wei Yuquan , Jiao Zheng
Published: August 2016

Research on the laser ablation behavior of SiC ceramics has great significance for the improvement of their anti-laser ability as high-performance mirrors in space and lasers, or the laser surface micro-machining technology as electronic components in micro-electron mechanical systems (MEMS). In this work, the laser ablation of SiC ceramics has been performed by using laser pulses of 12 ns duration at 1064 nm. The laser induced damage threshold (LIDT) below 0.1 J/cm2 was obtained by 1-on-1 mode and its damage morphology appeared in the form of “burning crater” with a clear boundary. Micro-Raman mapping technique was first introduced in our study on the laser ablation mechanisms of SiC surface by identifying physical and chemical changes between uninjured and laser-ablated areas. It has been concluded that during the ablation process, SiC surface mainly underwent decomposition to the elemental Si and C, accompanied by some transformation of crystal orientation. The oxidation of SiC also took place but only in small amount on the edges of target region, while there was no hint of SiO2 in the center with higher energy density, maybe because of deficiency of O2 atmosphere in the ablated area, elimination of SiO2 by carbon at 1505 °C, or evaporating at 2230 °C.
How does gatekeeper training improve suicide prevention for elderly people in nursing homes? A controlled study in 24 centres
Authors: Chauliac N. , Brochard N. , Payet C. ,   The EGEE (Étude Gatekeepers en EHPAD) study group, Margue Y. , Bordin P. , Depraz P. , Dumont A. , Kroupa E. , Pacaut-Troncin M. , Polo P. , Straub S. , Boissin J. , Burtin C. , Montoya G. , Rivière A. , Didier C. , Fournel C. , Durand C. , Barrellon M. , Amigues O. , Brosson A. , Mahé E. , Haxaire O. , Bonnot C. , Defaux M. , Rougier D. , Gaultier A. , Gutierrez A. , Pozo M. , Lefèvre V. , Nier A. , Bolzan S. , Liautaud M. , Barbosa S. , Garcia S. , Anfreville A. , Mazille S. , Durantet C. , Morlon M. , Gaboriau C. , Halbert C. , Cholvy M. , Milinkovich P. , Martin L. , Maury-Abello L. , Toulier B. , Kerleguer V. , Gabriel S. , Duclos A. , Terra J.-L.
Published: August 2016

Background

The death rate due to suicide in elderly people is particularly high. As part of suicide selective prevention measures for at-risk populations, the WHO recommends training “gatekeepers”.

Methods

In order to assess the impact of gatekeeper training for members of staff, we carried out a controlled quasi-experimental study over the course of one year, comparing 12 nursing homes where at least 30% of the staff had undergone gatekeeper training with 12 nursing homes without trained staff. We collected data about the residents considered to be suicidal, their management further to being identified, as well as measures taken at nursing home level to prevent suicide.

Results

The two nursing home groups did not present significantly different characteristics. In the nursing homes with trained staff, the staff were deemed to be better prepared to approach suicidal individuals. The detection of suicidal residents relied more on the whole staff and less on the psychologist alone when compared to nursing homes without trained staff. A significantly larger number of measures were taken to manage suicidal residents in the trained nursing homes. Suicidal residents were more frequently referred to the psychologist. Trained nursing homes put in place significantly more suicide prevention measures at an institutional level.

Conclusions

Having trained gatekeepers has an impact not only for the trained individuals but also for the whole institution where they work, both in terms of managing suicidal residents and routine suicide prevention measures.
Host government impact on the logistics performance of international humanitarian organisations
Authors: Dube N. , Van der Vaart T. , Teunter R.H. , Van Wassenhove L.N.
Published: August 2016

Host governments severely impact international relief operations. An openness to assistance can lead to the timely delivery of aid whereas a reluctance to receive assistance can have devastating consequences. With lives at stake and no time to lose in humanitarian crises, understanding the host government's impact on the logistics performance of international humanitarian organisations (IHOs) is crucial. In this paper, we present an in‐depth multiple‐case study that explores this aspect. Results show that host government actions are explained by their dependency on IHOs and the levels of tensions between their interests (i.e., conflicting strategic goals). In addition, a host government's regulatory and enforcement capabilities are important for ensuring that they can safeguard their interests. We derive four stances that host governments can adopt in regulating logistics‐related activities: non‐restrictive, opportunistic, selectively accommodating and uncompromising. Each of these has different implications for the logistics performance of IHOs.
Initial Validation of the Sexual Pleasure Scale in Clinical and Non-Clinical Samples of Partnered Heterosexual People
Authors: Pascoal Patrícia M. , Sanchez Diana T. , Raposo Catarina Fonseca , Pechorro Pedro
Published: August 2016

Introduction

Sexual pleasure is a central aspect of human sexuality; however, no validated measurements exist that assess sexual pleasure. We present a preliminary validation study of the psychometric properties of a Sexual Pleasure Scale (SPS), based on the three items developed by Sanchez, Crocker and Boike to measure sexual pleasure. The SPS is a brief and easy-to-implement instrument that assesses the extent of sexual pleasure experienced from sexual relationships, sexual activities, and sexual intimacy.

Aim

To assess the validity of the SPS in a subgroup of patients diagnosed with sexual dysfunction (n = 89) and a non-clinical community sample (n = 188) of Portuguese men and women.

Methods

We provide an initial examination of the reliability (eg, Cronbach α), convergent validity (eg, with measurements of sexual satisfaction), and divergent validity (eg, with measurements of body satisfaction) of the SPS.

Main Outcome Measures

The survey included a sociodemographic questionnaire and a set of questionnaires to test the psychometric properties of the SPS.

Results

The reliability study showed a high Cronbach value (α = 0.94). Convergent validity of the SPS with the measurements described showed mostly moderate to high statistically significant positive correlations, whereas the criterion-related validity showed the expected low non-significant correlation. The results also showed that the SPS shows strong sensitivity to discriminate people with from those without sexual problems.

Conclusion

Results from the clinical population indicate that the SPS has good psychometric qualities and is a reliable measurement of sexual pleasure with applicability in clinical practice and clinical research but shows little variability within the community sample.
Is Risk of Artificial Urethral Sphincter Cuff Erosion Higher in Patients with Penile Prosthesis?
Authors: Sundaram Varun , Cordon Billy H. , Hofer Matthias D. , Morey Allen F.
Published: August 2016

Introduction

Frequently encountered morbidities after prostatectomy include stress urinary incontinence and erectile dysfunction. Patients with severe disease may undergo placement of both a penile prosthesis (PP) and an artificial urethral sphincter (AUS).

Aim

We hypothesized that concomitant PP may promote AUS cuff erosion by impaired corporal blood flow and/or direct pressure on the cuff. The aim of this study was to compare the rate of AUS cuff erosion in patients with and without a PP.

Methods

We reviewed 366 AUS operations at our tertiary center between 2007 and 2015 with a mean follow-up of 41 months (range 6–104). Included in the analysis were first-time AUS cuff erosions. Patients with recurrent erosions, AUS revisions, and iatrogenic erosions were excluded. In a separate analysis, we analyzed AUS explantations for all causes. Cohorts were compared by demographic information, preoperative characteristics, and rates of erosion and explantation.

Main Outcome Measures

Erosion confirmed by cystourethroscopy and explantation of the AUS for all causes.

Results

Among 366 AUS surgeries at a mean follow-up of 41 months, there were 248 (67.8%) AUS alone cases compared to 118 (32.2%) AUS and PP cases (AUS/PP). Sixty-two patients met exclusion criteria for first-time cuff erosion. Among 304 evaluable AUS patients, we found a significantly higher rate of erosion in the AUS/PP group (11/95, 11.6%) compared to the AUS alone group (9/209, 4.3%, P = .037). When examining explantations for all causes in the entire cohort (n = 366), we observed a significantly higher rate of device removal, (20/118, 17%) in the AUS/PP group compared to the AUS group (23/248, 9.2%, P = .044).

Conclusion

AUS/PP patients appear to have a higher risk of AUS cuff erosion and explantation compared to men with AUS alone.
Blood Pressure, Sexual Activity, and Dysfunction in Women with Hypertension: Baseline Findings From the Systolic Blood Pressure Intervention Trial (SPRINT)
Authors: Foy Capri G. , Newman Jill C. , Berlowitz Dan R. , Russell Laurie P. , Kimmel Paul L. , Wadley Virginia G. , Thomas Holly N. , Lerner Alan J. , Riley William T. ,   SPRINT Study Research Group
Published: August 2016

Introduction

Sexual function, an important component of quality of life, is gaining increased research and clinical attention in older women with hypertension.

Aim

To assess the association between systolic blood pressure (SBP) and other variables, and sexual activity and sexual dysfunction in hypertensive women.

Methods

Baseline analysis of 635 women participants of a larger randomized clinical trial of 9361 men and women.

Main Outcome Measures

Self-reported sexual activity (yes/no), and sexual function using the Female Sexual Function Inventory (FSFI).

Results

452 participants (71.2%) reported having no sexual activity during the previous 4 weeks. The mean (SD) FSFI score for sexually active participants was 25.3 (6.0), and 52.6% of the sample reported a FSFI score ≤26.55 designating sexual dysfunction. In logistic regression models, SBP was not significantly associated with sexual activity (AOR = 1.002; P > .05). Older age (AOR = 0.95, P < .05), and lower education (AOR for < high school vs college degree = 0.29, P < .05) were associated with lower odds of being sexually active, as was living alone versus living with others (AOR = 0.56, P < .05). Higher weekly alcohol consumption was associated with increased odds of being sexually active (AOR = 1.39; P < .05). In logistic regression models among sexually active participants, SBP was not associated with sexual dysfunction (AOR = 1.01; P > .05). Higher depressive symptoms from the Patient Health Questionnaire-9 (PHQ-9) was associated with higher odds of sexual dysfunction (AOR = 1.24, P < .05), as was increased number of physical comorbidities (AOR = 1.25, P < .05). Diuretic use was associated with lower odds of being sexually active in participants with chronic kidney disease (AOR = 0.33, P < .05).

Conclusion

Younger age, higher education, living with others, and higher weekly alcohol consumption were significantly associated with higher odds of being sexually active in a sample of middle-aged and older women with hypertension. Increased depressive symptoms and increased physical comorbidities were significantly associated with increased odds of sexual dysfunction. SBP was not significantly associated with sexual activity or sexual dysfunction.
The Role of Somatic Symptoms in Sexual Medicine: Somatization as Important Contextual Factor in Male Sexual Dysfunction
Authors: Fanni Egidia , Castellini Giovanni , Corona Giovanni , Boddi Valentina , Ricca Valdo , Rastrelli Giulia , Fisher Alessandra Daphne , Cipriani Sarah , Maggi Mario
Published: August 2016

Introduction

An important feature of somatic symptom disorder is the subjective perception of the physical symptoms and its maladaptive interpretation. Considering that psychological distress is often expressed through somatic symptoms, it is possible that they underlie at least a part of the symptoms in subjects complaining of sexual dysfunction. Nevertheless, studies on the impact of somatoform disorders in sexual dysfunction are scanty.

Aim

To define the psychological, relational, and organic correlates of somatic symptoms in a large sample of patients complaining of sexual problems.

Methods

A consecutive series of 2833 men (mean age 50.2 ± 13.5 years) was retrospectively studied.

Main Outcome Measures

Somatic symptoms were assessed using the “somatized anxiety symptoms” subscale of the Middlesex Hospital Questionnaire (MHQ-S). Several clinical, biochemical, psychological, and relational parameters were studied. Patients were interviewed with the previously validated Structured Interview on Erectile Dysfunction (SIEDY), and ANDROTEST (a structured interview for the screening of hypogonadism in patients with sexual dysfunction).

Results

Among the 2833 patients studied, subjects scoring higher on somatic symptoms were older, more obese, reporting unhealthy lifestyle (current smoking, alcohol consumption), and a lower education (all P < .05). Moreover, they reported a general impairment of their sexuality more often, including erectile problems (spontaneous or sexual-related), low sexual desire, decreased frequency of intercourse, and perceived reduction of ejaculate volume (all P < .005). Interestingly, we observed a significant association between MHQ-S scoring with a reduced testosterone level and hypogonadism symptoms (both P < .05). Finally, we found a significant association between somatic symptoms and both SIEDY Scales 1 (organic domain of ED) and 3 (intrapsychic domain of ED) (both P < .0001).

Conclusion

The present study demonstrates that the presence of somatic symptoms can represent an important contextual factor in the determination of or in the exacerbation of male sexual dysfunction. High levels of somatic symptoms in subjects with sexual dysfunction can be related to the sexual symptom itself. The consequences of this pattern have great clinical relevance in a sexual medicine setting, considering their severe impact on sexuality.
High Triglycerides Predicts Arteriogenic Erectile Dysfunction and Major Adverse Cardiovascular Events in Subjects with Sexual Dysfunction
Authors: Corona Giovanni , Cipriani Sarah , Rastrelli Giulia , Sforza Alessandra , Mannucci Edoardo , Maggi Mario
Published: August 2016

Introduction

The atherogenic role of triglycerides (TG) remains controversial. The aim of the present study is to analyze the contribution of TG in the pathogenesis of erectile dysfunction (ED) and to verify the value of elevated TG in predicting major adverse cardiovascular events (MACE).

Methods

An unselected series of 3,990 men attending our outpatient clinic for sexual dysfunction was retrospectively studied. A subset of this sample (n = 1,687) was enrolled in a longitudinal study.

Main Outcome Measures

Several clinical, biochemical, and instrumental (penile color Doppler ultrasound; PCDU) factors were evaluated.

Results

Among the patients studied, after adjustment for confounders, higher TG levels were associated with arteriogenic ED and a higher risk of clinical and biochemical hypogonadism. Conversely, no association between TG and other sexual dysfunctions was observed. When pathological PCDU parameters—including flaccid acceleration (<1.17 m/sec2) or dynamic peak systolic velocity (PSV <35 cm/sec)—were considered, the negative association between impaired penile flow and higher TG levels was confirmed, even when subjects taking lipid-lowering drugs or those with diabetes were excluded from the analysis (OR = 6.343 [1.243;32.362], P = .026 and 3.576 [1.104;11.578]; P = .34 for impaired acceleration and PSV, respectively). Similarly, when the same adjusted models were applied, TG levels were associated with a higher risk of hypogonadism, independently of the definition criteria (OR = 2.892 [1.643;5.410], P < .0001 and 4.853 [1.965;11.990]; P = .001 for total T <12 and 8 nM, respectively). In the longitudinal study, after adjusting for confounders, elevated TG levels (upper quartile: 162–1686 mg/dL) were independently associated with a higher incidence of MACE (HR = 2.469 [1.019;5.981]; P = .045), when compared to the rest of the sample.

Conclusion

Our data suggest an association between elevated TG and arteriogenic ED and its cardiovascular (CV) risk stratification. Whether the use of TG lowering drugs might improve ED and its associated CV risk must be confirmed through specific trials.
Preserved Erectile Function in the Aged Transgenic Rat Harboring Human Tissue Kallikrein 1
Authors: Luan Yang , Ruan Yajun , Wang Tao , Zhuan Li , Wen Zheng , Chen Ruibao , Zhang Yan , Cui Kai , Yang Jun , Wang Shaogang , Liu Jihong , Ye Zhangqun , Wang Daowen
Published: August 2016

Introduction

Human tissue kallikrein 1 (hKLK1) has enormous potential for the protection of vasodilation and endothelial function in the cardiovascular system. Our previous study proved the decreased expression of kallikrein 1 in the corpus cavernosum (CC) of aged rats, but the role of kallikrein 1 in age-related erectile dysfunction remains unknown.

Aim

To explore the effect and underlying mechanisms of hKLK1 on age-related erectile dysfunction.

Methods

Male wild-type Sprague-Dawley rats (WTR) and transgenic rats harboring the hKLK1 gene (TGR) were fed to 4 and 27 months of age, respectively, and divided into four groups: young WTR (yWTR) as the control, young TGR (yTGR), aged WTR (aWTR), and aged TGR (aTGR). Rats' erectile function was evaluated by the cavernous nerve electrostimulation method. Then, CCs were collected for verification of hKLK1 followed by measurement of nitric oxide (NO)-cyclic guanosine monophosphate (cGMP) and RhoA-Rho-kinase (ROCK) signaling activities. Masson trichrome staining and terminal deoxynucleotidyl transferase 2′-deoxyuridine 5′-triphosphate nick end labeling assay were conducted to evaluate penile fibrosis and apoptosis.

Main Outcome Measures

Erectile response, NO-cGMP and RhoA-ROCK pathway-related indices, ratio of smooth muscle to collagen, and apoptosis index.

Results

The hKLK1 alleviated the decrease of erectile function in the aWTR group. Endothelial NO synthase (eNOS) and phospho-eNOS(Ser1177) expressions, NO synthase activity, and NO and cGMP levels were decreased, whereas phospho-eNOS(Thr495), L-type Ca2+ channel, RhoA, ROCK1, ROCK2, and transforming growth factor β1 proteins were increased in the CCs of the aWTR group compared with the control yWTR group. These changes were obviously mitigated in the aTGR group. Moreover, hKLK1 prevented the sharp decrease of the ratio of smooth muscle to collagen and the increase of the apoptosis index in the CCs of the aWTR group.

Conclusion

These results suggest that hKLK1 could play a preventive role in age-related erectile dysfunction by activation of the NO-cGMP pathway and inhibition of the RhoA-ROCK pathway and by antitissue fibrotic and apoptotic effects.
Quantile regression to characterize solanezumab effects in Alzheimer's disease trials
Authors: Chen Yun‐Fei , Ma Xiwen , Sundell Karen , Alaka Karla , Schuh Kory , Raskin Joel , Dean Robert A.
Published: August 2016

Introduction

In two solanezumab trials for mild‐to‐moderate Alzheimer's disease (AD) dementia, 27% of patients had biomarker confirmation of amyloid status. Of these, approximately 25% of mild patients and approximately 10% of moderate patients were amyloid negative and, as a group, did not exhibit clinical progression typical of AD. This post‐hoc analysis describes a statistical surrogate for amyloid status.

Methods

Quantile regression was used to examine solanezumab treatment effects at fixed percentiles of varying degrees of clinical progression, with lowest percentiles (minimal progression atypical of AD) and higher percentiles acting as surrogates for amyloid negativity or positivity, respectively.

Results

In mild patients, solanezumab treatment effect was greater in higher percentiles of progression and less in lowest percentiles (AD‐atypical). In moderate patients, solanezumab did not show effects across most percentiles.

Discussion

Results are compatible with design of the ongoing solanezumab EXPEDITION 3 trial that limits patients to those with mild AD dementia and evidence of amyloid pathology.
New Flood Model Offers National Streamflow Coverage
Authors: Wendel JoAnna
Published: August 2016

The model, released by the National Weather Service, will provide neighborhood-level flood forecasting.
Angiotensin-(1–7) decreases the expression of collagen I via TGF-β1/Smad2/3 and subsequently inhibits fibroblast–myofibroblast transition
Authors: Zhou Jian Ping , Tang Wei , Feng Yun , Li Ning , Gu Chen Juan , Li Qing Yun , Wan Huan Ying
Published: August 2016

Previous studies have shown that the RAS (renin–angiotensin system) might participate in airway remodelling in asthma. As a main component of the RAS, Ang-(1–7) [angiotensin-(1–7)] has been reported in few studies regarding its protective effect on asthma. However, the functional roles and relevant signalling pathways of Ang-(1–7) have not been well illustrated. In the present study, we analysed the effect of Ang-(1–7) on AngII (angiotensin II)-induced HLF (human lung fibroblast)–MF (myofibroblast) transition by detecting Col-I (collagen type I), TGF-β1 (transforming growth factor-β1) and α-SMA (α-smooth muscle actin) expression. We explored further the possible signalling pathways involved in HLF–MF transition. Our results showed that Ang-(1–7) could down-regulate the expression of Col-I, α-SMA and TGF-β1/Smad2/3 (all P<0.05). A significant decrease was found in phosphorylation of PI3K (phosphoinositide 3-kinase), Akt, p38-MAPK (mitogen-activated protein kinase) and JNK (c-Jun N-terminal kinase) signalling pathways during HLF–MF transition (all P<0.05). Our data suggests that Ang-(1–7) decreases the expression of Col-I via TGF-β1/Smad2/3 and subsequently inhibits HLF–MF transition.
Full-wave feasibility study of anti-radar diagnostic of magnetic field based on O-X mode conversion and oblique reflectometry imaging
Authors: Meneghini Orso , Volpe Francesco A.
Published: August 2016

An innovative millimeter wave diagnostic is proposed to measure the local magnetic field and edge current as a function of the minor radius in the tokamak pedestal region. The idea is to identify the direction of minimum reflectivity at the O-mode cutoff layer. Correspondingly, the transmissivity due to O-X mode conversion is maximum. That direction, and the angular map of reflectivity around it, contains information on the magnetic field vector B at the cutoff layer. Probing the plasma with different wave frequencies provides the radial profile of B. Full-wave finite-element simulations are presented here in 2D slab geometry. Modeling confirms the existence of a minimum in reflectivity that depends on the magnetic field at the cutoff, as expected from mode conversion physics, giving confidence in the feasibility of the diagnostic. The proposed reflectometric approach is expected to yield superior signal-to-noise ratio and to access wider ranges of density and magnetic field, compared with related radiometric techniques that require the plasma to emit electron Bernstein waves. Due to computational limitations, frequencies of 10-20 GHz were considered in this initial study. Frequencies above the edge electron-cyclotron frequency (f > 28 GHz here) would be preferable for the experiment, because the upper hybrid resonance and right cutoff would lie in the plasma, and would help separate the O-mode of interest from spurious X-waves.
A fiber-coupled displacement measuring interferometer for determination of the posture of a reflective surface
Authors: Mao Shuai , Hu Peng-Cheng , Ding Xue-Mei , Tan Jiu-Bin
Published: August 2016

A fiber-coupled displacement measuring interferometer capable of determining of the posture of a reflective surface of a measuring mirror is proposed. The newly constructed instrument combines fiber-coupled displacement and angular measurement technologies. The proposed interferometer has advantages of both the fiber-coupled and the spatially beam-separated interferometer. A portable dual-position sensitive detector (PSD)-based unit within this proposed interferometer measures the parallelism of the two source beams to guide the fiber-coupling adjustment. The portable dual PSD-based unit measures not only the pitch and yaw of the retro-reflector but also measures the posture of the reflective surface. The experimental results of displacement calibration show that the deviations between the proposed interferometer and a reference one, Agilent 5530, at two different common beam directions are both less than ±35 nm, thus verifying the effectiveness of the beam parallelism measurement. The experimental results of angular calibration show that deviations of pitch and yaw with the auto-collimator (as a reference) are less than ±2 arc sec, thus proving the proposed interferometer’s effectiveness for determination of the posture of a reflective surface.
CRDS with a VECSEL for broad-band high sensitivity spectroscopy in the 2.3 μm window
Authors: Čermák P. , Chomet B. , Ferrieres L. , Vasilchenko S. , Mondelain D. , Kassi S. , Campargue A. , Denet S. , Lecocq V. , Myara M. , Cerutti L. , Garnache A.
Published: August 2016

The integration of an industry ready packaged Sb-based Vertical-External-Cavity Surface-Emitting-Laser (VECSEL) into a Cavity Ring Down Spectrometer (CRDS) is presented. The instrument operates in the important 2.3 μm atmospheric transparency window and provides a high sensitivity (minimum detectable absorption of 9 × 10−11 cm−1) over a wide spectra range. The VECSEL performances combine a large continuous tunability over 120 cm−1 around 4300 cm−1 together with a powerful (∼5 mW) TEM00 diffraction limited beam and linewidth at MHz level (for 1 ms of integration time). The achieved performances are illustrated by high sensitivity recordings of the very weak absorption spectrum of water vapor in the region. The developed method gives potential access to the 2-2.7 μm range for CRDS.
Asymmetric bursting of Taylor bubble in inclined tubes
Authors: Rana Basanta Kumar , Das Arup Kumar , Das Prasanta Kumar
Published: August 2016

In the present study, experiments have been reported to explain the phenomenon of approach and collapse of an asymmetric Taylor bubble at free surface inside an inclined tube. Four different tube inclinations with horizontal (30°, 45°, 60° and 75°) and two different fluids (water and silicon oil) are considered for the experiment. Using high speed imaging, we have investigated the approach, puncture, and subsequent liquid drainage for re-establishment of the free surface. The present study covers all the aspects in the collapse of an asymmetric Taylor bubble through the generation of two films, i.e., a cap film which lies on top of the bubble and an asymmetric annular film along the tube wall. Retraction of the cap film is studied in detail and its velocity has been predicted successfully for different inclinations and fluids. Film drainage formulation considering azimuthal variation is proposed which also describes the experimental observations well. In addition, extrapolation of drainage velocity pattern beyond the experimental observation limit provides insight into the total collapse time of bubbles at different inclinations and fluids.
Direct numerical simulation of double-diffusive gravity currents
Authors: Penney Jared , Stastna Marek
Published: August 2016

This paper presents three-dimensional direct numerical simulations of laboratory-scale double-diffusive gravity currents. Flow is governed by the incompressible Navier-Stokes equations under the Boussinesq approximation, with salinity and temperature coupled to the equations of motion using a nonlinear approximation to the UNESCO equation of state. The effects of vertical boundary conditions and current volume are examined, with focus on flow pattern development, current propagation speed, three-dimensionalization, dissipation, and stirring and mixing. It was observed that no-slip boundaries cause the gravity current head to take the standard lobe-and-cleft shape and encourage both a greater degree and an earlier onset of three-dimensionalization when compared to what occurs in the case of a free-slip boundary. Additionally, numerical simulations with no-slip boundary conditions experience greater viscous dissipation, stirring, and mixing when compared to similar configurations using free-slip conditions.
Generation of electric fields and currents by neutral flows in weakly ionized plasmas through collisional dynamos
Authors: Dimant Y. S. , Oppenheim M. M. , Fletcher A. C.
Published: August 2016

In weakly ionized plasmas neutral flows drag plasma across magnetic field lines generating intense electric fields and currents. An example occurs in the Earth's ionosphere near the geomagnetic equator. Similar processes take place in the Solar chromosphere and magnetohydrodynamic generators. This paper argues that not all convective neutral flows generate electric fields and currents and it introduces the corresponding universal criterion for their formation, ∇×(U×B)≠∂B/∂t, where U is the neutral flow velocity, B is the magnetic field, and t is time. This criterion does not depend on the conductivity tensor, σ̂. For many systems, the displacement current, ∂B/∂t, is negligible making the criterion even simpler. This theory also shows that the neutral-dynamo driver that generates E-fields and currents plays the same role as the DC electric current plays for the generation of the magnetic field in the Biot-Savart law.
Development of a 6-DoF motion system for realizing a linear datum for geometric measurements
Authors: Wang Shaokai , Cui Jiwen , Tan Jiubin , Liu Yongmeng
Published: August 2016

In order to further improve the linear datum based geometric measurement accuracy and expand the measurement range, a 6-DoF motion system is developed for realizing a linear datum in the form of motion trajectory of the contact point (CP) of an absolute displacement measurement probe. This linear datum is established based on the concept of coordinate measurement and it does not contain straightness error in theory. The 6-DoF motion system consists of a 6-DoF fine stage and a 1-DoF coarse stage. The probe is moved by the 6-DoF fine stage which is magnetically noncontact supported and parallelly noncontact actuated. A CP-centred 6-DoF metrology model and a CP-centred 6-DoF motion model are established for elimination of Abbe error and on-line compensation of motion error of CP, respectively. 1-DoF coarse stage is controlled with relative position between two stages to extend the limited motion range of 6-DoF fine stage along the linear datum. Effectiveness of the metrology and motion models is verified through experiment. Straightness error of a 91.5 mm long line of an optical flat is measured by the proposed system and a commercial Fizeau interferometer. Comparison shows a consistency with standard deviation of 11 nm. Another experiment indicates that the proposed system could be used to realize a linear datum within a range of 220 mm with a repeatability of standard deviation of 7 nm.
Tune-out wavelengths for helium atom in plasma environments
Authors: Kar Sabyasachi , Wang Yu-Shu , Wang Yang , Jiang Zishi
Published: August 2016

We investigate the effect of plasma screening on the tune-out wavelengths for helium atom using correlated exponential wave function within the framework of Debye shielding approach. The pseudostate summation technique has been used to calculate the dynamic dipole polarizability for the states (2 1S, 3 1S, 2 3S, 3 3S) of helium embedded in plasma environments. In a free-atomic system, our calculated results are in agreement with available theoretical and experimental predictions. The tune-out wavelengths show interesting behavior as functions of screening parameter.
Human mucosal-associated invariant T cells contribute to antiviral influenza immunity via IL-18–dependent activation
Authors: Loh Liyen , Wang Zhongfang , Sant Sneha , Koutsakos Marios , Jegaskanda Sinthujan , Corbett Alexandra J. , Liu Ligong , Fairlie David P. , Crowe Jane , Rossjohn Jamie , Xu Jianqing , Doherty Peter C. , McCluskey James , Kedzierska Katherine
Published: August 2016

Significance

Mucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes with potent antibacterial reactivity. In this study, we investigated whether MAIT cells also contribute to immunity against influenza A viruses. Compared with those who succumbed, hospitalized patients who recovered from severe avian H7N9 influenza infection had higher numbers of MAIT cells. Subsequent in vitro analysis established that MAIT cells from healthy donors are indirectly activated by influenza infection via an IL-18–dependent (but not IL-12–dependent) mechanism requiring the involvement of CD14
+
monocytes. Our findings highlight the potential for MAIT cells to promote protective immunity in human influenza.
Prevalence, Awareness, Treatment, and Control of Hypertension in the Southern Cone of Latin America
Authors: Rubinstein Adolfo L. , Irazola Vilma E. , Calandrelli Matias , Chen Chung-Shiuan , Gutierrez Laura , Lanas Fernando , Manfredi Jose A. , Mores Nora , Poggio Rosana , Ponzo Jacqueline , Seron Pamela , Bazzano Lydia A. , He Jiang
Published: August 2016

BACKGROUND

Hypertension is the leading global preventable risk factor for premature death. While hypertension prevalence has been declining in high-income countries, it has increased continuously in low- and middle-income countries.

METHODS

We conducted a cross-sectional survey in 7,524 women and men aged 35–74 years from randomly selected samples in 4 cities (Bariloche and Marcos Paz, Argentina; Temuco, Chile; and Pando-Barros Blancos, Uruguay) in 2010–2011. Three blood pressure (BP) measurements were obtained by trained observers using a standard mercury sphygmomanometer. Hypertension was defined as a mean systolic BP ≥140mm Hg and/or diastolic BP ≥90mm Hg and/or use of antihypertensive medications.

RESULTS

An estimated 42.5% of the study population (46.6% of men and 38.7% of women) had hypertension and an estimated 32.5% (36.0% of men and 29.4% of women) had prehypertension. Approximately 63.0% of adults with hypertension (52.5% of men and 74.3% of women) were aware of their disease condition, 48.7% (36.1% of men and 62.1% of women) were taking prescribed medications to lower their BP, and only 21.1% of all hypertensive patients (13.8% of men and 28.9% of women) and 43.3% of treated hypertensive patients (38.1% of men and 46.5% of women) achieved BP control.

CONCLUSIONS

This study indicates that the prevalence of hypertension is high while awareness, treatment, and control are low in the general population in the Southern Cone of Latin America. These data call for bold actions at regional and national levels to implement effective, practical, and sustainable intervention programs aimed to improve hypertension prevention, detection, and control.
STAMS: STRING-assisted module search for genome wide association studies and application to autism
Authors: Hillenmeyer Sara , Davis Lea K. , Gamazon Eric R. , Cook Edwin H. , Cox Nancy J. , Altman Russ B.
Published: August 2016

Motivation: Analyzing genome wide association data in the context of biological pathways helps us understand how genetic variation influences phenotype and increases power to find associations. However, the utility of pathway-based analysis tools is hampered by undercuration and reliance on a distribution of signal across all of the genes in a pathway. Methods that combine genome wide association results with genetic networks to infer the key phenotype-modulating subnetworks combat these issues, but have primarily been limited to network definitions with yes/no labels for gene-gene interactions. A recent method (EW_dmGWAS) incorporates a biological network with weighted edge probability by requiring a secondary phenotype-specific expression dataset. In this article, we combine an algorithm for weighted-edge module searching and a probabilistic interaction network in order to develop a method, STAMS, for recovering modules of genes with strong associations to the phenotype and probable biologic coherence. Our method builds on EW_dmGWAS but does not require a secondary expression dataset and performs better in six test cases.

Results: We show that our algorithm improves over EW_dmGWAS and standard gene-based analysis by measuring precision and recall of each method on separately identified associations. In the Wellcome Trust Rheumatoid Arthritis study, STAMS-identified modules were more enriched for separately identified associations than EW_dmGWAS (STAMS P-value 3.0 × 10−4; EW_dmGWAS- P-value = 0.8). We demonstrate that the area under the Precision-Recall curve is 5.9 times higher with STAMS than EW_dmGWAS run on the Wellcome Trust Type 1 Diabetes data.

Availability and Implementation: STAMS is implemented as an R package and is freely available at https://simtk.org/projects/stams.

Contact:  rbaltman@stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments
Authors: Vrahatis Aristidis G. , Balomenos Panos , Tsakalidis Athanasios K. , Bezerianos Anastasios
Published: August 2016

Summary: DEsubs is a network-based systems biology R package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customized framework with a broad range of operation modes at all stages of the subpathway analysis, enabling so a case-specific approach. The operation modes include pathway network construction and processing, subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render DEsubs a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level drug targets and biomarkers for complex diseases.

Availability and Implementation: DEsubs is implemented as an R package following Bioconductor guidelines: http://bioconductor.org/packages/DEsubs/.

Contact:  tassos.bezerianos@nus.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Switching to Raltegravir From a Virologically Effective Boosted Protease Inhibitor Regimen: A Comparative Effectiveness Analysis From the French Hospital Database on HIV (FHDH-ANRS CO4)
Authors: Potard Valérie , Simon Anne , Lacombe Jean-Marc , Parienti Jean-Jacques , Costagliola Dominique
Published: August 2016

Background.  In individuals with viral load (VL) suppression on a boosted protease inhibitor (PI) regimen, a switch to raltegravir (RAL) can be an option in case of comorbidities, but the SWITCHMRK trials challenged this strategy. Here, among individuals with VL suppression on a boosted PI, we compared outcomes between those who continued on the same regimen and those who switched to RAL.

Methods.  In this cohort study from the French Hospital Database on HIV, each individual who switched to RAL was matched with up to 3 individuals who continued PI, were being followed up during the calendar period of the switch, and had the same duration of VL suppression (both ±6 months). The primary endpoint was a composite endpoint of hospitalization, or AIDS event or death, and secondary endpoints the immunovirologic responses. To control for measured confounders, the inverse probability treatment weighting (IPTW) method was applied to estimate hazards ratios between the 2 groups.

Results.  We matched 282 RAL switchers with 838 nonswitchers. Although several variables differed significantly between the groups, including a higher prevalence of comorbidities in the RAL group, the IPTW method yielded standardized differences <10% for all variables. After IPTW, there was no difference in the risk of hospitalization or AIDS event or death between the 2 groups (13.6% and 10.5%, respectively; hazard ratio, 1.16 [95% confidence interval, .74–1.83]) and no difference in the likelihood of virologic failure or CD4 cell gain.

Conclusions.  In individuals with controlled VL on a boosted PI regimen who switched to RAL, none of the endpoints differed with nonswitchers after IPTW.
Cell cycle arrest caused by MEK/ERK signaling is a mechanism for suppressing growth of antigen-hyperstimulated effector T cells
Authors: Ohtsuka Shizuka , Ogawa Shuhei , Wakamatsu Ei , Abe Ryo
Published: August 2016

Suppression of T-cell growth is an important mechanism for establishment of self-tolerance and prevention of unwanted prolonged immune responses that may cause tissue damage. Although negative selection of potentially self-reactive T cells in the thymus as well as in peripheral tissues has been extensively investigated and well documented, regulatory mechanisms to dampen proliferation of antigen-specific effector T cells in response to antigen stimulation remain largely unknown. Thus, in this work, we focus on the identification of growth suppression mechanisms of antigen-specific effector T cells. In order to address this issue, we investigated the cellular and molecular events in growth suppression of an ovalbumin (OVA)-specific T-cell clone after stimulation with a wide range of OVA-peptide concentrations. We observed that while an optimal dose of peptide leads to cell cycle progression and proliferation, higher doses of peptide reduced cell growth, a phenomenon that was previously termed high-dose suppression. Our analysis of this phenomenon indicated that high-dose suppression is a consequence of cell cycle arrest, but not Fas–Fas ligand-dependent apoptosis or T-cell anergy, and that this growth arrest occurs in S phase, accompanied by reduced expression of CDK2 and cyclin A. Importantly, inhibition of MEK/ERK activation eliminated this growth suppression and cell cycle arrest, while it reduced the proliferative response to optimal antigenic stimulation. These results suggest that cell cycle arrest is the major mechanism regulating antigen-specific effector T-cell expansion, and that the MEK/ERK signaling pathway has both positive and negative effects, depending on the strength of antigenic stimulation.