bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorylation of an HP1-like protein is a prerequisite for heterochromatin body formation in
Tetrahymena
DNA elimination
Authors: Kataoka Kensuke , Noto Tomoko , Mochizuki Kazufumi
Published: July 2016

Significance

In various eukaryotes, heterochromatin is cytologically visible because multiple heterochromatic loci are assembled into higher order structures called heterochromatin bodies. Although heterochromatin bodies are dynamically assembled and disassembled during development, aging, and carcinogenesis, their role and the mechanism of formation remain to be clarified. In this report, by investigating the role of the heterochromatin body component Jub4p in the de novo heterochromatin body formation process in the ciliated protozoan
Tetrahymena
, we reveal that the phosphorylation and subsequent dephosphorylation of the Heterochromatin Protein 1-like protein Pdd1p are prerequisites for heterochromatin body formation and the following programmed DNA elimination. This study demonstrates the biochemical and biological importance of a temporally ordered phosphorylation–dephosphorylation cycle of a heterochromatin component in heterochromatin body formation.
Do women with smaller breasts perform better in long‐distance running?
Authors: Brown Nicola , Scurr Joanna
Published: July 2016

Literature has established that a range of physiological, biomechanical, and training variables influence marathon performance. The influence of anthropometric characteristics has also received attention. However, despite major marathons exceeding 40,000 participants and approximately a third of these runners being female, no data exist on the influence of the breast on running performance. This cross‐sectional study aimed to explore the impact of breast mass on marathon finish time. One hundred and sixty‐eight of 321 female marathon runners contacted completed an on‐line survey focusing on marathon performance during the 2012 London marathon. Participants were categorised as smaller (<500 g, 54%) or larger breasted (>500 g, 46%). Regression analysis identified that 24% of marathon performance variance could be explained by body mass index (BMI), but breast mass improved the model to explain 28% of performance variation. The model determined that for women with 32/34 or 36/38 underband each increase in cup size equates to a performance decrement of 4.6 min or 8.6 min, equivalent to 34.4 min difference between a woman with 36A compared to 36DD breast size. Larger breasted runners had greater BMIs, completed less marathons and had slower marathon finish times (316 ± 48 min) compared to smaller breasted runners (281 ± 51 min). Twenty‐five per cent less larger breasted women finished in the fastest quartile. These results suggest that differences in breast mass are an important factor for female athletes and should be considered in future research in this area.
A predictive model for the tokamak density limit
Authors: Teng Q. , Brennan D.P. , Delgado-Aparicio L. , Gates D.A. , Swerdlow J. , White R.B.
Published: July 2016

The Greenwald density limit, found in all tokamak experiments, is reproduced for the first time using a phenomenologically correct model with parameters in the range of experiments. A simple model of equilibrium evolution and local power balance inside the island has been implemented to calculate the radiation-driven thermo-resistive tearing mode growth and explain the density limit. Strong destabilization of the tearing mode due to an imbalance of local Ohmic heating and radiative cooling in the island predicts the density limit within a few percent. The density limit is found to be a local edge limit and weakly dependent on impurity densities. Results are robust to a substantial variation in model parameters within the range of experiments.
Towards understanding the differences in irradiation effects of He, Ne and Ar plasma by investigating the physical origin of their clustering in tungsten
Authors: Kong Xiang-Shan , You Yu-wei , Li Xiang-yan , Wu Xuebang , Liu C.S. , Chen Jun-Ling , Luo G.-N.
Published: July 2016

While inert gas seeding to improve energy confinement has been successfully applied in many tokamak experiments, questions remain as to the irradiation effects of inert gases on tungsten. In this paper, we have systematically investigated the clustering behaviors of the inert gas atoms He, Ne and Ar in plasma-facing tungsten using first-principles calculations. Small interstitial clusters, He
m
, Ne
m
, and Ar
m
, can form due to the attraction between the atoms and tend to expand along the (1 1 0) planes. The inert gas clusters induce strong lattice distortions and so it is energetically favorable for a self-interstitial atom to be emitted from the clusters when the numbers of atoms are above six, three, three for He
m
, Ne
m
, and Ar
m
respectively. The clustering behaviors can be well explained by the intrinsic repulsive interaction between the inert gas atoms and the attractive interaction coming from the reduced valence-electron density by interstitial inert gas atoms. Compared to He, the much greater attraction between the Ne/Ar atoms and the lower trigger condition of ‘self-trapping process’ for Ne/Ar clusters provide a reasonable explanation for the difference of irradiation effects on tungsten between He and Ne/Ar plasmas, i.e. Ne/Ar plasmas cannot result in the formation of holes/bubbles and fiber-form nanostructures on tungsten surface under the same irradiation conditions as He plasma.
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network
Authors: Zhao Zhehuan , Yang Zhihao , Luo Ling , Lin Hongfei , Wang Jian
Published: July 2016

Motivation: Detecting drug-drug interaction (DDI) has become a vital part of public health safety. Therefore, using text mining techniques to extract DDIs from biomedical literature has received great attentions. However, this research is still at an early stage and its performance has much room to improve.

Results: In this article, we present a syntax convolutional neural network (SCNN) based DDI extraction method. In this method, a novel word embedding, syntax word embedding, is proposed to employ the syntactic information of a sentence. Then the position and part of speech features are introduced to extend the embedding of each word. Later, auto-encoder is introduced to encode the traditional bag-of-words feature (sparse 0–1 vector) as the dense real value vector. Finally, a combination of embedding-based convolutional features and traditional features are fed to the softmax classifier to extract DDIs from biomedical literature. Experimental results on the DDIExtraction 2013 corpus show that SCNN obtains a better performance (an F-score of 0.686) than other state-of-the-art methods.

Availability and Implementation: The source code is available for academic use at http://202.118.75.18:8080/DDI/SCNN-DDI.zip.

Contact:  yangzh@dlut.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Motif comparison based on similarity of binding affinity profiles
Authors: Lambert Samuel A. , Albu Mihai , Hughes Timothy R. , Najafabadi Hamed S.
Published: July 2016

Summary: Measuring motif similarity is essential for identifying functionally related transcription factors (TFs) and RNA-binding proteins, and for annotating de novo motifs. Here, we describe Motif Similarity Based on Affinity of Targets (MoSBAT), an approach for measuring the similarity of motifs by computing their affinity profiles across a large number of random sequences. We show that MoSBAT successfully associates de novo ChIP-seq motifs with their respective TFs, accurately identifies motifs that are obtained from the same TF in different in vitro assays, and quantitatively reflects the similarity of in vitro binding preferences for pairs of TFs.

Availability and implementation: MoSBAT is available as a webserver at mosbat.ccbr.utoronto.ca, and for download at github.com/csglab/MoSBAT.

Contact:  t.hughes@utoronto.ca or hamed.najafabadi@mcgill.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
WALT: fast and accurate read mapping for bisulfite sequencing
Authors: Chen Haifeng , Smith Andrew D. , Chen Ting
Published: July 2016

Whole-genome bisulfite sequencing (WGBS) has emerged as the gold-standard technique in genome-scale studies of DNA methylation. Mapping reads from WGBS requires unique considerations that make the process more time-consuming than in other sequencing applications. Typical WGBS data sets contain several hundred million reads, adding to this analysis challenge. We present the WALT tool for mapping WGBS reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup compared with the most efficient methods currently available. Although many existing WGBS mappers slow down with read length, WALT improves in speed. Importantly, these speed gains do not sacrifice accuracy.

Availability and implementation

WALT is available under the GPL v3 license, and downloadable from https://github.com/smithlabcode/walt.

Contact

andrewds@usc.edu or tingchen@usc.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Anesthesia Technique and Mortality after Total Hip or Knee Arthroplasty
Authors: Perlas Anahi , Chan Vincent W. S. , Beattie Scott
Published: July 2016

Background

This propensity score–matched cohort study evaluates the effect of anesthetic technique on a 30-day mortality after total hip or knee arthroplasty.

Methods

All patients who had hip or knee arthroplasty between January 1, 2003, and December 31, 2014, were evaluated. The principal exposure was spinal versus general anesthesia. The primary outcome was 30-day mortality. Secondary outcomes were (1) perioperative myocardial infarction; (2) a composite of major adverse cardiac events that includes cardiac arrest, myocardial infarction, or newly diagnosed arrhythmia; (3) pulmonary embolism; (4) major blood loss; (5) hospital length of stay; and (6) operating room procedure time. A propensity score–matched-pair analysis was performed using a nonparsimonious logistic regression model of regional anesthetic use.

Results

We identified 10,868 patients, of whom 8,553 had spinal anesthesia and 2,315 had general anesthesia. Ninety-two percent (n = 2,135) of the patients who had general anesthesia were matched to similar patients who did not have general anesthesia. In the matched cohort, the 30-day mortality rate was 0.19% (n = 4) in the spinal anesthesia group and 0.8% (n = 17) in the general anesthesia group (risk ratio, 0.42; 95% CI, 0.21 to 0.83; P = 0.0045). Spinal anesthesia was also associated with a shorter hospital length of stay (5.7 vs. 6.6 days; P < 0.001).

Conclusions

The results of this observational, propensity score–matched cohort study suggest a strong association between spinal anesthesia and lower 30-day mortality, as well as a shorter hospital length of stay, after elective joint replacement surgery.
Topical versus intravenous tranexamic acid use in total knee arthroplasty
Authors: Arntson Zach , Ferguson Adam , Markel David C.
Published: July 2016

Background:

Topical or intravenous application of tranexamic acid (TXA) during total knee arthroplasty has been shown to reduce postoperative bleeding and transfusion rates. The objective of this study was to compare the efficacy and safety of topical and intravenous TXA at a single institution.

Methods:

Four hundred and eighty-two patients were reviewed retrospectively, with 166 patients included as a non-TXA control group, and 70 in the topical TXA group and 48 in the intravenous TXA group. The primary outcomes were transfusion rates and blood loss calculated from the difference between preoperative and postoperative hemoglobin levels. Thromboembolic complications were recorded up to 90 days postoperatively.

Results:

After TXA use, the mean hemoglobin levels were significantly higher in the topical (10.5 g/dL) and intravenous TXA groups (10.4 g/dL) when compared to the control group (9.6 g/dL) (P<0.001). This resulted in ∼18% less blood loss postoperatively when comparing both the intravenous and topical cohorts. The transfusion rate for the control group (12.7%; 21/166) was higher than rates for the intravenous (2.1%; 1/48) and topical (4.3%; 3/70) TXA cohorts (P=0.023). There were no differences in complication rates among cohorts.

Conclusions:

During cemented total knee arthroplasty, both topical and intravenous application of TXA resulted in significant reductions in postoperative bleeding and transfusion rates. There were no statistically significant changes in complication rates in either treatment group compared with the control group. Both topical and intravenous TXA appeared safe and effective in reducing postoperative bleeding and transfusion rates in cemented total knee arthroplasty.
Alarming consequences – autoinflammatory disease spectrum due to mutations in proline-serine-threonine phosphatase-interacting protein 1
Authors: Holzinger Dirk , Roth Johannes
Published: July 2016

Purpose of review

To give an overview about the expanding spectrum of autoinflammatory diseases due to mutations in proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1) and new insights into their pathogenesis.

Recent findings

In addition to classical pyogenic sterile arthritis, pyoderma gangrenosum, and acne (PAPA) syndrome, PSTPIP1-associated myeloid-related proteinemia inflammatory (PAMI) syndrome has been described as a distinct clinical phenotype of PSTPIP1-associated inflammatory diseases (PAID) and other entities are emerging. In addition to dysregulation of IL-1ß release from activated PAPA monocytes that requires NLR family, pyrin domain containing 3 (NLRP3), PSTPIP1 mutations have an general impact on cellular dynamics of cells of the innate immune system. In addition, overwhelming expression and release of the alarmins myeloid-related protein (MRP) 8 and 14 by activated phagocytes and keratinocytes, which promote innate immune mechanisms in a Toll like receptor (TLR) 4-dependent manner, are a characteristic feature of these diseases and form a positive feed-back mechanism with IL-1ß.

Autoinflammatory diseases due to PSTPIP1 mutations are not restricted to the classical PAPA phenotype but might present with other distinct clinical features. MRP8/14 serum levels are a hallmark of PAPA and PAMI and can be used as screening tool to initiate targeted genetic testing in suspected cases. The feedback mechanism of IL-1ß and MRP-alarmin release may offer novel targets for future therapeutic approaches.
Filler Rhinoplasty Evaluated by Anthropometric Analysis
Authors: Youn Sung Hwan , Seo Kyle K.
Published: July 2016

BACKGROUND

There are no reports of objectively evaluating the efficacy of filler rhinoplasty by anthropometric techniques.

OBJECTIVE

To objectively demonstrate the effectiveness of filler rhinoplasty by anthropometric analysis.

MATERIALS AND METHODS

A total of 242 patients who revisited the clinic within 2 months of undergoing hyaluronic acid filler rhinoplasty were analyzed based on the injection site, injected volume, and the change in anthropometry.

RESULTS

Among the 242 patients, 112 (46.3%) were in the nasal dorsum augmentation group, 8 (3.3%) were in the tip rotation group, and 122 (50.4%) were in the whole nose augmentation group. Average injection volume was 1 ± 0.4 mL for nasal dorsum and 0.9 ± 0.3 mL for tip rotation, whereas 1.6 ± 0.5 mL was used for whole nose augmentation. On follow-up, the radix height, nasofrontal angle, and nasolabial angle (NLA) had increased by 78.3%, 5.7 ± 4.1°, and 9.4 ± 4.5°, respectively, whereas the modified nasofacial angle had decreased by 1.9 ± 2.9°. Three cases (1.2%) of vascular complications were encountered.

CONCLUSION

Filler rhinoplasty is a simple and effective treatment modality producing outcomes comparable with surgical augmentation rhinoplasty. Among various anthropometric measurements, the nasal radix height was the most useful for evaluating dorsum augmentation, whereas the NLA was the best for nasal tip rotation.
The More Things Change, the More They Stay the Same
Authors: Miller Lisa A.
Published: July 2016

Thirty years ago, the inaugural issue of The Journal of Perinatal & Neonatal Nursing was published and the entire perinatal portion of the journal was devoted to electronic fetal monitoring (EFM). This article provides a historical perspective on EFM in perinatal care since the 1980s by exploring the similarities and differences of the state of the science presented in that first issue. Both EFM and intermittent auscultation are discussed.
Trends in Perinatal Care and Implications for Frontline Nurse Leaders
Authors: Crenshaw Jeannette T. , Adams Ellise D. , Amis Debby
Published: July 2016

The perinatal trends presented in this article are based on recent topics from conferences, journals, the media, as well as from input from perinatal nurses. Trends in patient care are influenced by evidence known for decades, new research, emerging and innovative concepts in healthcare, patient and family preferences, and the media. Trends discussed in this article are rethinking the due date, birth outside the hospital setting, obstetric hospitalists as birth attendants, nitrous oxide for pain in childbirth, hydrotherapy and waterbirth in the hospital setting, delayed cord clamping, disrupters of an optimal infant microbiome, skin-to-skin care during cesarean surgery, and breast-sleeping and the breast-feeding dyad. In addition, the authors developed implications for perinatal nurses related to each trend. The goal is to stimulate reflection on evidence that supports or does not support current practice and to stimulate future research by discussing some of the current trends that may influence the care that perinatal nurses provide during the birthing year.
Birth Environments
Authors: Adams Ellise D.
Published: July 2016

A woman has many important decisions to make once discovering a pregnancy. One of those decisions with significant implications is where the birth will take place. The primary consideration for the majority of pregnant women when making a decision about birth environment is safety. However, other factors such as attitudes of family and friends, religious reasons, and confidence in the body's ability to give birth play a factor in the choice of birth environment. It is recommended that birth attendants use the process of shared decision making to assist pregnant women in making choices related to the birth environment. This process empowers the pregnant woman and provides a woman-centered and evidence-based approach to choices related to obstetrical care.
Shared Decision Making
Authors: Klassa Patricia J. , Dendrinos Susan , Penn Annette , Radke Judith
Published: July 2016

Birth is an intimate moment in a woman's life, and healthcare providers play a pivotal role in pregnant women having safe and memorable birth experiences. Utilizing the shared decision-making model during the prenatal period involves listening to the voices of identified high-risk patients and giving them options for care during labor and birth. “Through the Patient's Eyes” is an innovative program that evolved from the care planning process for these identified high-risk obstetric patients who are invited back postpartum to describe to the team birth through “their” eyes. Through this program, the team learned that compassionate care comes from truly listening to pregnant women and their families and that nurses play a pivotal role as educators and advocates. Sharing birth stories with the staff who cared for them not only had a positive effect on the staff but also many women described profound healing afterward.
Educational Changes to Support Advanced Practice Nursing Education
Authors: LeFlore Judy L. , Thomas Patricia E.
Published: July 2016

Educational factors limit the number of advanced practice registered nurse (APRN) graduates to meet the growing workforce demands. Healthcare dynamics are necessitating a shift in how nursing education envisions, creates, and implements clinical learning opportunities. The current clinical education model in APRN programs continues to be the same as it was 45 years ago when the student numbers were much smaller. New approaches in graduate nursing education are needed to address the shortage of APRNs in primary and acute care areas. Determining competency based on the number of clinical hours can be inefficient, ineffective, and costly and limits the ability to increase capacity. Little research exists in graduate nursing education to support the effectiveness and efficiency of current hours of clinical required for nurse practitioner students. Simulation and academic-practice partnership models can offer innovative approaches to nurse practitioner education for clinical training, with the goal of producing graduates who can provide safe, quality care within the complex practice-based environment of the nation's evolving healthcare system.
Single-Site Cannulation Venovenous Extracorporeal CO2 Removal as Bridge to Lung Volume Reduction Surgery in End-Stage Lung Emphysema
Authors: Redwan Bassam , Ziegeler Stephan , Semik Michael , Fichter Joachim , Dickgreber Nicolas , Vieth Volker , Ernst Erik Christian , Fischer Stefan
Published: July 2016

Lung volume reduction surgery (LVRS) is an important treatment option for end-stage lung emphysema in carefully selected patients. Here, we first describe the application of low-flow venovenous extracorporeal CO2 removal (LFVV-ECCO2R) as bridge to LVRS in patients with end-stage lung emphysema experiencing severe hypercapnia caused by acute failure of the breathing pump. Between March and October 2015, n = 4 patients received single-site LFVV-ECCO2R as bridge to LVRS. Indication for extracorporeal lung support was severe hypercapnia with respiratory acidosis and acute breathing pump failure. Two patients required continuous mechanical ventilation over a temporary tracheostomy and were bed ridden. The other two patients were nearly immobile because of severe dyspnea at rest. Length of preoperative ECCO2R was 14 (1–42) days. All patients underwent unilateral LVRS. Anatomical resection of the right (n = 3) or left (n = 1) upper lobe was performed. Postoperatively, both patients with previous mechanical ventilatory support were successfully weaned. ECCO2R in patients with end-stage lung emphysema experiencing severe hypercapnia caused by acute breathing pump failure is a safe and effective bridging tool to LVRS. In such patients, radical surgery leads to a significant improvement of the performance status and furthermore facilitates respiratory weaning from mechanical ventilation.
Reporting Guidelines for Health Care Simulation Research
Authors: Cheng Adam , Kessler David , Mackinnon Ralph , Chang Todd P. , Nadkarni Vinay M. , Hunt Elizabeth A. , Duval-Arnould Jordan , Lin Yiqun , Cook David A. , Pusic Martin , Hui Joshua , Moher David , Egger Matthias , Auerbach Marc
Published: July 2016

Introduction

Simulation-based research (SBR) is rapidly expanding but the quality of reporting needs improvement. For a reader to critically assess a study, the elements of the study need to be clearly reported. Our objective was to develop reporting guidelines for SBR by creating extensions to the Consolidated Standards of Reporting Trials (CONSORT) and Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statements.

Methods

An iterative multistep consensus-building process was used on the basis of the recommended steps for developing reporting guidelines. The consensus process involved the following: (1) developing a steering committee, (2) defining the scope of the reporting guidelines, (3) identifying a consensus panel, (4) generating a list of items for discussion via online premeeting survey, (5) conducting a consensus meeting, and (6) drafting reporting guidelines with an explanation and elaboration document.

Results

The following 11 extensions were recommended for CONSORT: item 1 (title/abstract), item 2 (background), item 5 (interventions), item 6 (outcomes), item 11 (blinding), item 12 (statistical methods), item 15 (baseline data), item 17 (outcomes/estimation), item 20 (limitations), item 21 (generalizability), and item 25 (funding). The following 10 extensions were recommended for STROBE: item 1 (title/abstract), item 2 (background/rationale), item 7 (variables), item 8 (data sources/measurement), item 12 (statistical methods), item 14 (descriptive data), item 16 (main results), item 19 (limitations), item 21 (generalizability), and item 22 (funding). An elaboration document was created to provide examples and explanation for each extension.

Conclusions

We have developed extensions for the CONSORT and STROBE Statements that can help improve the quality of reporting for SBR.
A 2-Year Evaluation of Quality of Life Outcomes of Patients With Pelvic Organ Prolapse Treated With an Elevate Prolapse Repair System
Authors: Buca Danilo Italo Pio , Leombroni Martina , Falò Eleonora , Bruno Matteo , Santarelli Alessandro , Frondaroli Franco , Liberati Marco , Fanfani Francesco
Published: July 2016

Objectives

To evaluate 2-year quality of life of women with pelvic organ prolapse submitted to prosthetic correction with Elevate.

Methods

We enrolled 116 consecutive patients with a stage ≥ to 2 prolapse. The Prolapse Quality of Life questionnaire was administered in the preoperative time and after 2 years of follow-up. The statistical results were obtained by using the SPSS Advanced Statistical™ 11.0 Software.

Results

Patient's quality of life improved substantially following prosthetic vaginal surgery. In particular, a clear improvement in the “general state of patients health” (P < 0.05), and a reduction in the daily physical, social, and psychological quality of life (P < 0.05) connected to the prolapse of pelvic organ were observed. Furthermore, a significant reduction in the percentage of patients with urinal disturbances (86.2% preoperative vs 20.7% postoperative; P < 0.05), and an improvement in patient's relations with their partners with 12 patients resuming sexual activity were found.

Conclusions

This study demonstrates that prosthetic vaginal correction represents a long-term efficient clinical instrument for women with symptomatic pelvic organ prolapse. It also achieves a resolution for urinary symptomatology and embarrassment, social limitation, physical and psychological difficulties of women, which, in great part, resulted in many overcoming surgical therapy, worried about fixed outcomes.
Pink-beam focusing with a one-dimensional compound refractive lens
Authors: Dufresne Eric M. , Dunford Robert W. , Kanter Elliot P. , Gao Yuan , Moon Seoksu , Walko Donald A. , Zhang Xusheng
Published: July 2016

The performance of a cooled Be compound refractive lens (CRL) has been tested at the Advanced Photon Source (APS) to enable vertical focusing of the pink beam and permit the X-ray beam to spatially overlap with an 80 µm-high low-density plasma that simulates astrophysical environments. Focusing the fundamental harmonics of an insertion device white beam increases the APS power density; here, a power density as high as 500 W mm−2was calculated. A CRL is chromatic so it does not efficiently focus X-rays whose energies are above the fundamental. Only the fundamental of the undulator focuses at the experiment. A two-chopper system reduces the power density on the imaging system and lens by four orders of magnitude, enabling imaging of the focal plane without any X-ray filter. A method to measure such high power density as well as the performance of the lens in focusing the pink beam is reported.
Real-time image-content-based beamline control for smart 4D X-ray imaging
Authors: Vogelgesang Matthias , Farago Tomas , Morgeneyer Thilo F. , Helfen Lukas , dos Santos Rolo Tomy , Myagotin Anton , Baumbach Tilo
Published: July 2016

Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensionalin situ,in vivoandoperandotomography and laminography.
Polarized proton spin density images the tyrosyl radical locations in bovine liver catalase
Authors: Zimmer Oliver , Jouve Hélène M. , Stuhrmann Heinrich B.
Published: July 2016

A tyrosyl radical, as part of the amino acid chain of bovine liver catalase, supports dynamic proton spin polarization (DNP). Finding the position of the tyrosyl radical within the macromolecule relies on the accumulation of proton polarization close to it, which is readily observed by polarized neutron scattering. The nuclear scattering amplitude due to the polarization of protons less than 10 Å distant from the tyrosyl radical is ten times larger than the amplitude of magnetic neutron scattering from an unpaired polarized electron of the same radical. The direction of DNP was inverted every 5 s, and the initial evolution of the intensity of polarized neutron scattering after each inversion was used to identify those tyrosines which have assumed a radical state. Three radical sites, all of them close to the molecular centre and the haem, appear to be equally possible. Among these is tyr-369, the radical state of which had previously been proven by electron paramagnetic resonance.
Indirect Fourier transform in the context of statistical inference
Authors: Muthig Michael , Prévost Sylvain , Orglmeister Reinhold , Gradzielski Michael
Published: July 2016

Inferring structural information from the intensity of a small-angle scattering (SAS) experiment is an ill-posed inverse problem. Thus, the determination of a solution is in general non-trivial. In this work, the indirect Fourier transform (IFT), which determines the pair distance distribution function from the intensity and hence yields structural information, is discussed within two different statistical inference approaches, namely a frequentist one and a Bayesian one, in order to determine a solution objectively From the frequentist approach the cross-validation method is obtained as a good practical objective function for selecting an IFT solution. Moreover, modern machine learning methods are employed to suppress oscillatory behaviour of the solution, hence extracting only meaningful features of the solution. By comparing the results yielded by the different methods presented here, the reliability of the outcome can be improved and thus the approach should enable more reliable information to be deduced from SAS experiments.
Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C β-lactamases AmpC BER and CMY-10
Authors: Na Jung-Hyun , Cha Sun-Shin
Published: July 2016

AmpC BER is an extended substrate spectrum class C β-lactamase with a two-amino-acid insertion in the R2 loop compared with AmpC EC2. The crystal structures of AmpC BER (S64A mutant) and AmpC EC2 were determined. Structural comparison of the two proteins revealed that the insertion increases the conformational flexibility of the R2 loop. Two citrate molecules originating from the crystallization solution were observed in the active site of the S64A mutant. One citrate molecule makes extensive interactions with active-site residues that are highly conserved among class C β-lactamases, whereas the other one is weakly bound. Based on this structural observation, it is demonstrated that citrate, a primary metabolite that is widely used as a food additive, is a competitive inhibitor of two class C β-lactamases (AmpC BER and CMY-10). Consequently, the data indicate enhancement of the flexibility of the R2 loop as an operative strategy for molecular evolution of extended-spectrum class C β-lactamases, and also suggest that the citrate scaffold is recognized by the active sites of class C β-lactamases.
Managers’ motives for investing in HR practices and their implications for public service motivation
Authors: Gould-Williams Julian Seymour
Published: July 2016

Purpose

– The purpose of this paper is to explain how approaches to human resource management may contribute to the development of public service motivation (PSM). Three different approaches to managing people are outlined, namely, the “high performance”, “high commitment” and “high involvement”. Relevant theories are then used to predict the outcomes and relevance of the different approaches when promoting PSM in public sector organisations.

Design/methodology/approach

– This is a theoretical paper.

Findings

– This paper provides the first theoretical explanations for the relationships between human resource (HR) practices and PSM in public sector organisations.

Originality/value

– This paper explains how the same HR practices may have different employee outcomes depending on managers’ motivations for implementing them.
From compliance to commitment
Authors: Prysmakova Palina
Published: July 2016

Purpose

– Building on institutional theories, the purpose of this paper is to test the relationship of organizational centralization and public service motivation (PSM), and to explore country’s centralization effect on it.

Design/methodology/approach

– The quantitative analysis of 390 responses from 42 social care and labor market public service providers operating in two countries with opposite administrative regimes – decentralized Poland and centralized Belarus.

Findings

– The Polish sample confirms previous observations. Organizational centralization correlates with PSM, while PMS dimensions do not act in concert. In contrast to others, self-sacrifice is positively associated with increased centralization. A country’s context has a strong mediating effect. The Belarusian sample revealed no relationship between organizational centralization and PSM. Because the main difference with Poland lies in the politico-administrative organization of the public sector, the findings suggest further examination of the county’s centralization effects. Democracy is not an imperative for higher PSM. Belarusian employees scored higher than the Polish on attraction to public service. Centralization of state administration does not necessarily indicate higher centralization in separate executive units. Polish organizations scored similar or higher on the questions of organizational centralization.

Research limitations/implications

– Context factors correlate differently with separate PSM dimensions, therefore, researchers should always look at PSM as a complex concept. Robust assertions about country’s centralization effect will require further tests on a larger sample of countries with different administrative regimes.

Practical implications

– Human resource (HR) managers in decentralized Poland could modify employees’ PSM behavior by altering the centralization level of an organization. In highly centralized Belarus, employees’ PSM is less responsive to centralization changes, thus, HR managers should recruit individuals with the initially high PSM.

Originality/value

– First PSM study with the primary data collected in a non-democratic country; first study to simultaneously address centralization on organizational and country levels.
Dynamic range boxes – a robust nonparametric approach to quantify size and overlap of n‐dimensional hypervolumes
Authors: Junker Robert R. , Kuppler Jonas , Bathke Arne C. , Schreyer Manuela L. , Trutschnig Wolfgang
Published: July 2016

n‐dimensional hypervolumes are commonly applied in ecology and evolutionary studies to describe and compare niches, trait spaces characterizing phenotypes or the functional composition of communities. Classical ecological surveys, modern analytical tools and the establishment of online data bases will produce large multivariate data sets, which demands robust statistical tools to analyse and interpret hypervolumes.

Existing approaches often have weaknesses; for example, they rely on multivariate normally or elliptically distributed data, perform poorly in higher dimensions, or their outputs vary arbitrarily with parameter choice. Here we introduce dynamic range boxes as a robust nonparametric approach to quantify size and overlap of n‐dimensional hypervolumes.

Dynamic range boxes (implemented in the r package dynRB) improve the concept of multivariate range boxes by accounting for the distribution of the data within their range, while still no assumptions on the underlying distributions are needed. In addition to calculating the whole n‐dimensional hypervolume, the package dynRB also provides functions for a coordinate‐wise analysis and interpretation of the data.

The concept of dynamic range boxes reliably computes sizes and overlaps of n‐dimensional hypervolumes, which makes dynamic range boxes readily applicable for a broad range of data sets to answer questions related to various disciplines.
Slow pupillary light responses in infants at high risk of cerebral palsy were associated with periventricular leukomalacia and neurological outcome
Authors: Hamer Elisa G. , Vermeulen R. Jeroen , Dijkstra Linze J. , Hielkema Tjitske , Kos Claire , Bos Arend F. , Hadders‐Algra Mijna
Published: July 2016

Aim

Having observed slow pupillary light responses (PLRs) in infants at high risk of cerebral palsy, we retrospectively evaluated whether these were associated with specific brain lesions or unfavourable outcomes.

Methods

We carried out neurological examinations on 30 infants at very high risk of cerebral palsy five times until the corrected age of 21 months, classifying each PLR assessment as normal or slow. The predominant reaction during development was determined for each infant. Neonatal brain scans were classified based on the type of brain lesion. Developmental outcome was evaluated at 21 months of corrected age with a neurological examination, the Bayley Scales of Infant Development Second Edition and the Infant Motor Profile.

Results

Of the 30 infants, 16 developed cerebral palsy. Predominantly slow PLRs were observed in eight infants and were associated with periventricular leukomalacia (p = 0.007), cerebral palsy (p = 0.039), bilateral cerebral palsy (p = 0.001), poorer quality of motor behaviour (p < 0.0005) and poorer cognitive outcome (p = 0.045).

Conclusion

This explorative study suggested that predominantly slow PLR in infants at high risk of cerebral palsy were associated with periventricular leukomalacia and poorer developmental outcome. Slow PLR might be an expression of white matter damage, resulting in dysfunction of the complex cortico‐subcortical circuitries.
Comparative study of CD4 and CD45RO T cells and CD20 B cells in cerebrospinal fluid of syphilitic meningitis and tuberculous meningitis patients
Authors: Yu Nian , Zhang Qiao‐quan , Zhang Kang , Xie Yuan , Zhu Hai‐qing , Lin Xing‐jian , Di Qing
Published: July 2016

This study was to investigate the differences of lymphocyte in the cerebrospinal fluid (CSF) of patients with syphilis meningitis (SM) and tuberculous meningitis (TBM) for new diagnostic insights. Totally, 79 cases of SM and 45 cases of TBM were enrolled. In the CSF, the CD4, CD45RO or CD20 positive lymphocytes were detected by immunohistochemistry. The proportion of CD4 T cells in the CSF lymphocytes in patients with SM was significantly higher than that in patients with TBM (p < 0.05). After medical therapy, there was a significantly decline trend of the CD4 T‐cell proportion in both groups (p < 0.05). The proportion of CD45RO T cells in CSF lymphocytes of patients with SM was less than that of patients with TBM (p < 0.05). After medical therapy, the positive ratio of CD45RO T cells was increased in the CSF of both group patients (p < 0.05). The proportion of CD20B cells in the CSF lymphocytes was not obviously different between the two groups during every stage. In conclusion, there are strong differences of CD4 and CD45RO T‐cell ratio, but not the CD20 B cells in the meningitis. CD4 and CD45RO T cells in CSF are a useful complement in differentially diagnosing SM and TBM; it contributes to further understand the pathogenesis and prognosis of SM and TBM.
Timor‐Leste's demographic challenges for environment, peace and nation building
Authors: Hosgelen Merve , Saikia Udoy
Published: July 2016

Timor‐Leste's nation‐building process faces significant demographic challenges because of its current and prospective population dynamics. Based on the 2010 census data this paper projects the demographic structure of Timor‐Leste by 2030 and discusses the impact of the same on peace, development and environmental sustainability. This paper projects that Timor‐Leste's population will increase from 1.06 million in 2010 to 1.82 million in 2030, and because of a slow decline in total fertility rates, its population characteristics will remain that of a very youthful country with an extraordinarily high dependency ratio. Timor‐Leste will have extremely high proportion of excess labour, high concentration of uneducated and jobless youth in small urban areas and an ever‐increasing demand on natural resources in the next two decades. In the context of poor performing domestic economy, very low formal sector employment and weak environmental governance, these challenges may well contribute to social conflict which is evident in the nation's recent past. This paper is an attempt to reflect upon the implications of Timor‐Leste's population dynamics by 2030 on urbanisation, economy (labour market) and the environment which tend to have a strong relationship with social stability.
Sparking development or consuming the countryside? Lao charcoal commodity networks in the Mekong Region
Authors: Barney Keith
Published: July 2016

One of the unexpected outcomes of increased regional integration in southern Laos has been a boom in household production and roadside sale of wood charcoal. This paper develops an ethnographically informed analysis of charcoal as a socially embedded market, providing insights into the sociopolitical relations of access, legal and extra‐legal regulations, and the distribution of rents that characterise this trade. Contrary to some assumptions about charcoal as a necessarily exploitative commodity, this paper points to some of the advantageous income smoothing opportunities that charcoal presents for many rural Lao households and detail the complex ways in which charcoal production can relate to forest sustainability and degradation. The paper elaborates a perspective of entrepreneurial Lao charcoal communities, energetically utilising locally available natural resources, for direct cash income. Charcoal production networks also connect everyday household livelihoods in Laos to large‐scale extractive industry, in ways that have been arguably underemphasised previously. At the same time, the charcoal trade highlights the structural limits to notions of smallholder agency and local participation in commodified market relations, within broader political‐economic contexts decidedly shaped through uneven development, and accumulation through dispossession.
Efficacy of system l amino acid transporter 1 inhibition as a therapeutic target in esophageal squamous cell carcinoma
Authors: Ohshima Yasuhiro , Kaira Kyoichi , Yamaguchi Aiko , Oriuchi Noboru , Tominaga Hideyuki , Nagamori Shushi , Kanai Yoshikatsu , Yokobori Takehiko , Miyazaki Tatsuya , Asao Takayuki , Tsushima Yoshito , Kuwano Hiroyuki , Ishioka Noriko S.
Published: July 2016

System l amino acid transporter 1 (LAT1) is highly expressed in various types of human cancer, and contributes to cancer growth and survival. Recently, we have shown that LAT1 expression is closely related to the growth and aggressiveness of esophageal cancer, and is an independent marker of poor prognosis. However, it remains unclear whether LAT1 inhibition could suppress esophageal cancer growth. In this study, we investigated the tumor‐suppressive effects of the inhibition of LAT1. Both LAT1 and CD98, which covalently associates to LAT1 on the membrane, were expressed in human esophageal cancer cell lines KYSE30 and KYSE150. Quantitative PCR analysis showed that the expression of LAT1 was much higher than other subtypes of LAT. A selective inhibitor of LAT, 2‐aminobicyclo‐(2,2,1)‐heptane‐2‐carboxylic acid (BCH), suppressed cellular uptake of l‐14C‐leucine and cell proliferation in a dose‐dependent manner. It also suppressed phosphorylation of mammalian target of rapamycin, 4E‐BP1, and p70S6K protein, and induced cell cycle arrest at G1 phase. These results suggest that suppression of both mammalian target of rapamycin signaling and cell cycle progression is involved in BCH‐induced growth inhibition. In tumor‐bearing mice, daily treatment with BCH significantly delayed tumor growth and decreased glucose metabolism, indicating that LAT1 inhibition potentially suppresses esophageal cancer growth in vivo. Thus, our results suggest that LAT1 inhibition could be a promising molecular target for the esophageal cancer therapy.
Discovery of neurotrophic agents based on hydroxycinnamic acid scaffold
Authors: Hosseini Razieh , Moosavi Fatemeh , Rajaian Hamid , Silva Tiago , Magalhães e Silva Diogo , Soares Pedro , Saso Luciano , Edraki Najmeh , Miri Ramin , Borges Fernanda , Firuzi Omidreza
Published: July 2016

The number of people affected by neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease is rapidly increasing owing to the global increase in life expectancy. Small molecules with neurotrophic effects have great potential for management of these neurological disorders. In this study, different (C1–C12) alkyl ester derivatives of hydroxycinnamic acids (HCAs) were synthesized (a total of 30 compounds). The neurotrophic capacity of the test compounds was examined by measuring promotion of survival in serum‐deprived conditions and enhancement of nerve growth factor (NGF)‐induced neurite outgrowth in PC12 neuronal cells. p‐Coumaric, ferulic, and sinapic acids and their esters did not alter cell survival, while caffeic acid and all its alkyl esters, especially decyl and dodecyl caffeate, significantly promoted neuronal survival at 25 μm. Methyl, ethyl, propyl, and butyl caffeate esters also significantly enhanced NGF‐induced neurite outgrowth, among which the most effective ones were propyl and butyl esters, which at 5 μm led to 25‐ and 22‐fold increases in the number of neurites, respectively. The findings of the docking study suggested phosphatidylinositol 3‐kinase (PI3K) as the potential molecular target. In conclusion, our findings demonstrate that alkyl esters of caffeic acid can be useful as scaffolds for the discovery of therapeutic agents for neurodegenerative diseases.