bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond ENL norms in ELF use
Authors: Alptekin Cem
Published: July 2016

This article presents a cognitively-oriented account of the qualitative differences between ENL (English as a native language) and ELF (English as a lingua franca) users. Based on the declarativeprocedural model of second language acquisition, it examines the linguistic and sociolinguistic implications of ELF users’ dependence on their declarative memory system, with its corresponding explicit knowledge and controlled processes of cognition subserving the production of their output in English. In contrast, it points to ENL speakers’ output being sustained by both their procedural and declarative memory systems, with their corresponding implicit and explicit knowledge types that interact through automatic and controlled processes. Given the differences in the underlying cognitive resources and processes in output production, it concludes that the prevailing practice of assessing ELF users’ output in relation to ENL norms is simply irrelevant.
‘Qualified’? A framework for comparing ELT teacher preparation courses
Authors: Stanley Phiona , Murray Neil
Published: July 2016

There is no standard way via which to measure the ‘qualified’ English language teacher in a way that is meaningful to institutions seeking to employ teaching staff. This is significant given that candidates may differ markedly in their language competence, knowledge about language, methodological skills and ability to explain and justify their praxis and operate in intercultural spaces. In this article, we propose a framework, based on Bourdieu’s (1986) ‘forms of capital’, with a view to helping stakeholders articulate and evaluate teachers’ skills. To demonstrate how this framework might be used, we apply it to two English language teacher qualifications that have wide professional currency: CELTA courses and Masters degrees in ELT/Applied Linguistics.
The problematic of second language errors
Authors: Hamid M. Obaidul , Doan Linh Dieu
Published: July 2016

The significance of errors in explicating Second Language Acquisition (SLA) processes led to the growth of error analysis in the 1970s which has since maintained its prominence in English as a second/foreign language (L2) research. However, one problem with this research is errors are often taken for granted, without problematising them and their identification. Against this background, the present study aimed to: (a) measure L2 English teachers’ ability to interpret L2 learner intentions in idiosyncratic expressions, and (b) bring to light factors that facilitate error identification. Findings show that: (1) there is a significant difference between L2 students’ intentions and teachers’ interpretations of those intentions; and (2) L2 English teachers’ knowledge of students’ L1 is not an advantage in error detection. Teacher interview data were drawn on to explicate text interpretation, reconstruction and error identification, suggesting implications for L2 research and pedagogy.
First results with 3-strap ICRF antennas in ASDEX Upgrade
Authors: Bobkov V. , Braun F. , Dux R. , Herrmann A. , Faugel H. , Fünfgelder H. , Kallenbach A. , Neu R. , Noterdaeme J.-M. , Ochoukov R. , Pütterich Th. , Tuccilo A. , Tudisco O. , Wang Y. , Yang Q.
Published: July 2016

The 3-strap antennas in ASDEX Upgrade allow ICRF operation with low tungsten (W) content in the confined plasma with W-coated antenna limiters. With the 3-strap antenna configuration, the local W impurity source at the antenna is drastically reduced and the core W concentration is similar to that of the boron coated 2-strap antenna at a given ICRF power. Operation of the 3-strap antennas with the power ratio between the central and the outer straps of

1.5
:
1

and

2
:
1

is adopted to minimize the ICRF-specific W release.
Optimization of x-ray emission from under-critical CH foam coated gold targets by laser irradiation
Authors: Shang Wanli , Yu Ruizhen , Zhang Wenhai , Yang Jiamin
Published: July 2016

Under-critical CH foam coated gold targets benefit laser-to-x-ray emission because CH plasma inhibits gold plasma expansion, which leads to higher gold plasma density and temperature. Conversely, the CH foam partially absorbs the incident laser energy, which lowers laser absorption into the gold plasma. An analytical model is built to solve the laser collisional deposition fraction in the CH foam layer. The optimization of x-ray emission from under-critical CH foam coated gold targets by laser irradiation is obtained numerically with different CH foam densities and thicknesses. The plasma and x-ray emission properties are investigated. It is found that different CH thicknesses lead to different increase mechanisms for x-ray emission. The x-ray spectrum distributions show that most of the x-ray emission increases occur with photon energy less than 2000 eV.
Extended magneto-hydro-dynamic model for neoclassical tearing mode computations
Authors: Maget Patrick , Février Olivier , Garbet Xavier , Lütjens Hinrich , Luciani Jean-Francois , Marx Alain
Published: July 2016

A self-consistent fluid model for describing neoclassical tearing modes in global magneto-hydro-dynamic simulations is presented. It is illustrated by its application to a simple toroidal configuration unstable to the (2, 1) tearing mode. The island saturation is verified to increase with the bootstrap current fraction. New features that are specific to this model are evidenced, like the unsteady saturated state of the island, and its deformation to a droplet shape, when the magnetic Prandtl number is not too high. Synthetic diagnostics demonstrate that diamagnetic and neoclassical effects should have in this case a measurable impact on the signature of magnetic islands.
Stabilization of the vertical instability by non-axisymmetric coils
Authors: Turnbull A.D. , Reiman A.H. , Lao L.L. , Cooper W.A. , Ferraro N.M. , Buttery R.J.
Published: July 2016

In a published Physical Review Letter (Reiman 2007 Phys. Rev. Lett. 99 135007), it was shown that axisymmetric (or vertical) stability can be improved by placing a set of parallelogram coils above and below the plasma oriented at an angle to the constant toroidal planes. The physics of this stabilization can be understood as providing an effective additional positive stability index. The original work was based on a simplified model of a straight tokamak and is not straightforwardly applicable to a finite aspect ratio, strongly shaped plasma such as in DIII-D. Numerical calculations were performed in a real DIII-D -like configuration to provide a proof of principal that 3-D fields can, in fact raise the elongation limits as predicted. A four field period trapezioid-shaped coil set was developed in toroidal geometry and 3D equilibria were computed using trapezium coil currents of

10
 
k
A

,

100
 
k
A

, and

500
 
k
A

. The ideal magnetohydrodynamics growth rates were computed as a function of the conformal wall position for the

n
 
=
 
0

symmetry-preserving family. The results show an insignificant relative improvement in the stabilizing wall location for the two lower coil current cases, of the order of 10−3 and less. In contrast, the marginal wall position is increased by 7% as the coil current is increased to

500
 
k
A

, confirming the main prediction from the original study in a real geometry case. In DIII-D the shift in marginal wall position of 7% would correspond to being able to move the existing wall outward by 5 to 10 cm. While the predicted effect on the axisymmetric stability is real, it appears to require higher coil currents than could be provided in an upgrade to existing facilities. Additional optimization over the pitch of the coils, the number of field periods and the coil positions, as well as plasma parameters, such as the internal inductivity

ℓ

i

,

β

, and

q

95

would mitigate this but seem unlikely to change the conclusion.
Hydrodynamic limit of granular gases to pressureless Euler in dimension 1
Authors: Jabin Pierre-Emmanuel , Rey Thomas
Published: July 2016

We investigate the behavior of granular gases in the limit of small Knudsen number, that is, very frequent collisions. We deal with the strongly inelastic case in one dimension of space and velocity. We are able to prove the convergence toward the pressureless Euler system. The proof relies on dispersive relations at the kinetic level, which leads to the so-called Oleinik property at the limit.
deBGA: read alignment with de Bruijn graph-based seed and extension
Authors: Liu Bo , Guo Hongzhe , Brudno Michael , Wang Yadong
Published: July 2016

Motivation: As high-throughput sequencing (HTS) technology becomes ubiquitous and the volume of data continues to rise, HTS read alignment is becoming increasingly rate-limiting, which keeps pressing the development of novel read alignment approaches. Moreover, promising novel applications of HTS technology require aligning reads to multiple genomes instead of a single reference; however, it is still not viable for the state-of-the-art aligners to align large numbers of reads to multiple genomes.

Results: We propose de Bruijn Graph-based Aligner (deBGA), an innovative graph-based seed-and-extension algorithm to align HTS reads to a reference genome that is organized and indexed using a de Bruijn graph. With its well-handling of repeats, deBGA is substantially faster than state-of-the-art approaches while maintaining similar or higher sensitivity and accuracy. This makes it particularly well-suited to handle the rapidly growing volumes of sequencing data. Furthermore, it provides a promising solution for aligning reads to multiple genomes and graph-based references in HTS applications.

Availability and Implementation: deBGA is available at: https://github.com/hitbc/deBGA .

Contact:  ydwang@hit.edu.cn

Supplementary information : Supplementary data are available at Bioinformatics online.
Icarus: visualizer for
de novo
assembly evaluation
Authors: Mikheenko Alla , Valin Gleb , Prjibelski Andrey , Saveliev Vladislav , Gurevich Alexey
Published: July 2016

Summary : Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus—a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application.

Availability and Implementation:  http://cab.spbu.ru/software/icarus

Contact:  aleksey.gurevich@spbu.ru

Supplementary information:  Supplementary data are available at Bioinformatics online.
Addressing Authorship Issues Prospectively: A Heuristic Approach
Authors: Roberts Laura Weiss
Published: July 2016

Collaborative writing in academic medicine gives rise to more richly informed scholarship, and yet challenging ethical issues surrounding authorship are commonly encountered. International guidelines on authorship help clarify whether individuals who have contributed to a completed scholarly work have been correctly included as authors, but these guidelines do not facilitate intentional and proactive authorship planning or decisions regarding authorship order.

In this Commentary, the author presents a heuristic approach to help collaborators clarify, anticipate, and resolve practical and ethically important authorship issues as they engage in the process of developing manuscripts. As this approach illustrates, assignment of authorship should balance work effort and professional responsibility, reflecting the effort and intellectual contribution and the public accountability of the individuals who participate in the work. Using a heuristic approach for managing authorship issues prospectively can foster an ethical, collaborative writing process in which individuals are properly recognized for their contributions.
Aseptic loosening of uncemented femoral components in long-term hemodialysis patients: a systematic review of the literature
Authors: Hess Shane R. , Saper Michael G. , Taunt Charles J.
Published: July 2016

Background:

The purpose of this study was to determine if reliable cementless fixation in hip arthroplasty can be achieved in patients on long-term hemodialysis.

Methods:

A systematic review was conducted with an emphasis on aseptic loosening of femoral components in total hip arthroplasty and hemiarthroplasty. Studies were analyzed using the Methodological Index for Nonrandomized Studies (MINORS) instrument and the Center for Evidence-Based Medicine’s Levels of Evidence Scale. Six lower-quality cases series were included.

Results:

Rates of radiographic evidence of loosening and revision caused by aseptic loosening ranged from 0% to 100%. Data pooling could not be performed because of heterogeneity of the studies included.

Conclusions:

It appears that patients with end-stage renal disease have bone stock suitable for cementless fixation. However, the varying outcomes reported in the literature reflect that the factors leading to early loosening of femoral components in dialyzed patients still remain unclear.
Does malunion in multiple planes predict worse functional outcomes in distal radial fractures?
Authors: Cantlon Matthew B. , Marcano Alejandro I. , Lee James , Egol Kenneth A.
Published: July 2016

Background:

The objective of this study was to investigate whether the total number of radiographic malalignments after distal radial fracture was associated with poor clinical outcome.

Methods:

Over a 7-year period, 382 patients who sustained a distal radial fracture were enrolled in a prospectively collected database and met our inclusion criteria. Patients were followed for a mean of 11 mo. Radiographs were taken and analyzed at each follow-up interval. Patients were divided in three groups, those with normal radiographic alignment (group 1), those with one abnormal measurement (group 2), and those with two or more abnormal measurements (group 3). Each patient was assessed for the Disabilities of the Arm Shoulder and Hand (DASH) and Short Form-36 (SF36) clinical outcome scores, along with functional parameters.

Results:

Thirty-four percent of patients had at least one abnormal radiographic measurement after initial reduction, 21% at short-term, and 24% at long-term follow-up. The long-term DASH was low (18.17 and 12.12 in groups 2 and 3, respectively) and the SF36 was correspondingly high (77.36 and 80.45 in groups 2 and 3, respectively). No individual radiographic measurement of wrist deformity or a combination of these was significantly correlated to any of the clinical outcome scores or functional parameters.

Conclusions:

Our data confirm reports from previous studies that no single radiographic measurement was correlated with clinical or functional outcomes. Moreover, if analyzed in combination, malalignment in multiple planes did not result in a higher association with worse outcomes.
Mid-term Results of Femoral and Tibial Osteotomies and Fassier-Duval Nailing in Children With Osteogenesis Imperfecta
Authors: Azzam Khalid A. , Rush Eric T. , Burke Bridget R. , Nabower Aleisha M. , Esposito Paul W.
Published: July 2016

Background:

Patients with osteogenesis imperfecta (OI) have significant burden of both fractures and bony deformities. The present approach to care in this disorder is a combination of surgical care with intramedullary rod fixation, cyclic bisphosphonate therapy, and rehabilitation with goal of maximizing patient function and quality of life.

Methods:

Retrospective chart review identified 58 children with OI who had realignment osteotomies with Fassier-Duval (FD) intramedullary nailing of the lower extremity by a single surgeon. This is a consecutive series treated between 2003 and 2010. Postoperatively, patients were followed up clinically and radiologically. Motor function was assessed using the Brief Assessment of Motor Function score and the walking scale subset of the Gillette Functional Assessment Questionnaire.

Results:

Fifty-eight patients had 179 lower extremity FD intramedullary rods placed. This technique allowed for intervention on multiple long bones, with 29% having bilateral femur and tibial rodding in the same procedure. Revisions were required in 53% of patients, which occurred at a mean time of 52 months after initial rodding surgery. In most cases, revision surgery was related to patient growth and subsequent fracture, although rod migration did occur in a minority of patients. Nonunion or incomplete union was 14.5% in this series. Bisphosphonate infusion was not postponed after surgical procedures. Patients had improvement in mobility status at the latest follow-up.

Conclusions:

This series lends evidence to the medium-term utility of FD intramedullary rods as an effective and less invasive platform for stabilization and correction of deformity in long bones of patients with OI. Relatively low blood loss and relatively short hospitalizations were noted. Nonunion rate was comparable with existing literature noting that our patients did not have postsurgical postponement of bisphosphonate therapy.

Level of Evidence:

Therapeutic study to investigate the results of treatment with FD rods. Retrospective case series model of Level IV evidence quality.
Development of a Tobacco Cessation Clinical Decision Support System for Pediatric Emergency Nurses
Authors: Mahabee-Gittens E. Melinda , Dexheimer Judith W. , Gordon Judith S.
Published: July 2016

Almost 50% of children who visit the pediatric emergency department are exposed to tobacco smoke. However, pediatric emergency nurses do not routinely address this issue. The incorporation of a clinical decision support system into the electronic health record may improve the rates of tobacco exposure screening and interventions. We used a mixed-methods design to develop, refine, and implement an evidence-based clinical decision support system to help nurses screen, educate, and assist caregivers to quit smoking. We included an advisory panel of emergency department experts and leaders and focus and user groups of nurses. The prompts include the following: (1) “Ask” about child smoke exposure and caregiver smoking; (2) “Advise” caregivers to reduce their child’s smoke exposure by quitting smoking; (3) “Assess” interest; and (4) “Assist” caregivers to quit. The clinical decision support system was created to reflect nurses’ suggestions and was implemented in five busy urgent care settings with 38 nurses. The nurses reported that the system was easy to use and helped them to address caregiver smoking. The use of this innovative tool may create a sustainable and disseminable model for prompting nurses to provide evidence-based tobacco cessation treatment.
Visuomotor Function in School-Age Children with Single-Suture Craniosynostosis
Authors: Wallace Erin R. , Collett Brent R. , Kapp-Simon Kathleen , Starr Jacqueline R. , Birgfeld Craig , Speltz Matthew L.
Published: July 2016

Objective:

Previous studies have shown that infants and young children with single-suture craniosynostosis (SSC) perform more poorly on tests of visuomotor function than children without SSC. However, previous studies are limited by small sample sizes and little is known about the persistence of visuomotor problems into the school-age years. The aim of this study was to compare visuomotor function in children with and without SSC at the beginning of elementary school.

Methods:

The study included 179 children with SSC (cases) and 183 children without SSC (controls). Visuomotor function was measured by the NEPSY-II Arrows, the Purdue Pegboard Test, and the Beery-Buktenica Developmental Test of visual-motor integration. Case-control differences were estimated using linear regression, adjusted for age, sex, socioeconomic status, and maternal IQ.

Results:

Cases scored more poorly on all measures of visuomotor function, although the magnitude of case-control differences varied across measures. The greatest differences were observed for the Purdue Pegboard Test, with an average adjusted difference of −0.2 to −0.4 SD points (p-values ranged from .008 to .05). Case-control differences were small in magnitude for other measures of visuomotor function, ranging from −0.01 to −0.1 SD points (p-values ranged from .22 to .88).

Conclusion:

Children with SSC experienced deficits in manual dexterity into the school-age years but were similar to children without SSC on measures of visual processing. These findings advocate for the assessment of fine-motor function as part of school readiness evaluations in children with SSC.
Biomarkers of Hepatic Fibrosis in Chronic Hepatitis C
Authors: Tanwar Sudeep , Trembling Paul M. , Hogan Brian J. , Parkes Julie , Harris Scott , Grant Paul , Nastouli Eleni , Ocker Mathias , Wehr Klaus , Herold Christoph , Neureiter Daniel , Schuppan Detlef , Rosenberg William M.
Published: July 2016

Background:

Advancing fibrosis is regarded as the most important factor when stratifying patients with chronic hepatitis C for retreatment.

Goals:

(1) To compare the performance of 10 biomarkers of fibrosis, including patented tests, among patients with chronic hepatitis C and treatment failure; and (2) to assess the impact on biomarker performance of using 2 different assays of hyaluronic acid (HA).

Study:

For 80 patients, liver histology (Metavir) was compared with biomarker scores using sera obtained within 6 months of liver biopsy (indirect biomarkers: AST:ALT ratio, APRI, Forns index, FIB-4, Fibrometer V3G; direct biomarkers: ELF, Fibrospect II, Hyaluronic acid-HA, Fibrometer V2G, Hepascore). Direct biomarker scores were calculated using 2 validated assays for HA (ELISA and radiometric).

Results:

Using the ELISA assay for HA to calculate the direct panels, all 10 of the biomarkers exhibited comparable overall discriminatory performance (unweighted Obuchowski measure, ordROC 0.92-0.94, P-value>0.05) except AST:ALT ratio and APRI (ordROC 0.86-0.88, P-value<0.05). For the detection of moderate (F2-4) and advanced (F3-4) fibrosis, the AUROC of Fibrometer 2G were significantly higher than AST:ALT ratio and APRI but none of the other biomarkers. Good correlation was observed between the 2 HA assays (intraclass correlation coefficient=0.873) with the ELISA assay exhibiting superior diagnostic performance (ordROC 0.92 vs. 0.88, P-value=0.003). Importantly, the performance of many of the direct biomarkers at their diagnostic thresholds was heavily influenced by the choice of HA assay.

Conclusions:

Although many biomarkers exhibited good diagnostic performance for the detection of advancing fibrosis, our results indicate that diagnostic performance may be significantly affected by the selection of individual component assays.
Point-of-Care Virologic Testing to Improve Outcomes of HIV-Infected Children in Zambia: A Clinical Trial Protocol
Authors: Chibwesha Carla J. , Ford Catherine E. , Mollan Katie R. , Stringer Jeffrey S. A.
Published: July 2016

Introduction:

In the absence of early infant diagnosis (EID) and immediate antiretroviral therapy (ART), some 50% of untreated HIV-infected infants die before age 2. Conventional EID requires sophisticated instruments that are typically placed in centralized or reference laboratories. In low-resource settings, centralized systems often lead to result turnaround times of several months, long delays in diagnosis, and adverse outcomes for HIV-infected children. Our clinical trial tests the effectiveness of a new point-of-care (POC) diagnostic technology to identify HIV-infected infants and start providing them life-saving ART as soon as possible.

Methods and Design:

The study uses a randomized, controlled design to test whether the Alere q platform for HIV DNA polymerase chain reaction (PCR) testing improves outcomes of HIV-infected children in Zambia. We aim to enroll 2867 HIV-exposed infants aged 4–12 weeks and to follow those who are HIV infected for 12 months as they receive HIV care at 6 public health facilities in Lusaka. The trial's primary endpoint is the proportion of HIV-infected infants in each study arm who start ART and remain alive, in care, and virally suppressed 12 months after their diagnostic blood draw.

Discussion:

Our trial will provide evidence for the incremental benefit of implementing a POC EID strategy in low-resource settings where only off-site PCR services are currently available. The results will be useful in guiding future decisions regarding investments in POC virologic testing as part of overall pediatric AIDS mitigation strategies in sub-Saharan Africa.

Trial Registration:

clinicaltrials.gov NCT02682810.
Modeling the Cost-Effectiveness of Home-Based HIV Testing and Education (HOPE) for Pregnant Women and Their Male Partners in Nyanza Province, Kenya
Authors: Sharma Monisha , Farquhar Carey , Ying Roger , Krakowiak Daisy , Kinuthia John , Osoti Alfred , Asila Victor , Gone Molly , Mark Jennifer , Barnabas Ruanne V.
Published: July 2016

Introduction:

Women in sub-Saharan Africa face a 2-fold higher risk of HIV acquisition during pregnancy and postpartum and the majority do not know the HIV status of their male partner. Home-based couple HIV testing for pregnant women can reduce HIV transmission to women and infants while increasing antiretroviral therapy (ART) coverage in men. However, the cost-effectiveness of this program has not been evaluated.

Methods:

We modeled the health and economic impact of implementing a home-based partner education and HIV testing (HOPE) intervention for pregnant women and their male partners in a region of Western Kenya (formally Nyanza Province). We used data from the HOPE randomized clinical trial conducted in Kisumu, Kenya, to parameterize a mathematical model of HIV transmission. We conducted an in-country microcosting of the HOPE intervention (payer perspective) to estimate program costs as well as a lower cost scenario of task-shifting to community health workers.

Results:

The incremental cost of adding the HOPE intervention to standard antenatal care was $31–37 and $14–16 USD per couple tested with program and task-shifting costs, respectively. At 60% coverage of male partners, HOPE was projected to avert 6987 HIV infections and 2603 deaths in Nyanza province over 10 years with an incremental cost-effectiveness ratio (ICER) of $886 and $615 per disability-adjusted life year averted for the program and task-shifting scenario, respectively. ICERs were robust to changes in intervention coverage, effectiveness, and ART initiation and dropout rates.

Conclusions:

The HOPE intervention can moderately decrease HIV-associated morbidity and mortality by increasing ART coverage in male partners of pregnant women. ICERs fall below Kenya's per capita gross domestic product ($1358) and are therefore considered cost-effective. Task-shifting to community health workers can increase intervention affordability and feasibility.
Patient and Provider Satisfaction With a Comprehensive Strategy to Improve Prevention of Mother-to-Child HIV Transmission Services in Rural Nigeria
Authors: Boehmer Angie , Audet Carolyn M. , Blevins Meridith , Gebi Usman I. , Wester C. William , Vermund Sten H. , Aliyu Muktar H.
Published: July 2016

Background:

High mother-to-child HIV transmission rates in Nigeria are coupled with a critical shortage of trained health personnel, dearth of infrastructure, and low levels of male involvement in HIV care. This study evaluated maternal and provider satisfaction with services for prevention of mother-to-child transmission within the context of an implementation science cluster-randomized trial that included task shifting to lower-cadre workers, male engagement, point-of-care CD4+ cell counts, and integrated mother–infant care.

Methods:

Patient and clinician satisfaction were measured at 6 control and 6 intervention sites using a 5-point Likert scale. Patient satisfaction was assessed at 6 weeks postpartum through a 22-item scale about the provider's ability to explain the health problem, time spent with the clinician, and motivation to follow prescribed treatment. Provider satisfaction was assessed through a 12-item scale about motivation, compensation, and training, with 4 additional questions about the impact of task shifting on job satisfaction to intervention arm providers.

Results:

We measured satisfaction among 340 mothers (intervention n = 160; control n = 180) and 60 providers (intervention n = 36; control n = 24). Total patient satisfaction (maximum 5) was higher in the intervention than control arm [median (interquartile range) = 4.61 (4.22–4.79) vs. 3.84 (3.22–4.22), respectively; P < 0.001]. Provider satisfaction was generally high, and was similar between the intervention and the control arms [median (interquartile range) = 3.60 (3.37–3.91) vs. 3.50 (3.08–4.25), respectively; P = 0.69]. Provider satisfaction dropped when questions on newly acquired provider roles were included [3.47 (3.25–3.72)]. Patient and provider satisfaction were not associated with uptake of antiretroviral therapy or mother–infant retention at 6 and 12 weeks postpartum.

Conclusions:

Satisfaction was higher among patients at intervention sites, and provider satisfaction decreased when newly assigned roles were factored in. Task shifting should include training and supportive oversight to ensure comfort with assigned tasks.
Option B+ in Mozambique: Formative Research Findings for the Design of a Facility-Level Clustered Randomized Controlled Trial to Improve ART Retention in Antenatal Care
Authors: Napúa Manuel , Pfeiffer James T. , Chale Falume , Hoek Roxanne , Manuel Joao , Michel Cathy , Cowan Jessica G. , Cowan James F. , Gimbel Sarah , Sherr Kenneth , Gloyd Stephen , Chapman Rachel R.
Published: July 2016

Introduction:

With the rollout of “Option B+” in Mozambique in 2013, initial data indicated major challenges to early retention in antiretroviral therapy (ART) among HIV-positive pregnant women. We sought to develop and test a pilot intervention in 6 large public clinics in central Mozambique to improve retention of mothers starting ART in antenatal care. The results from the formative research from this study described here were used to design the intervention.

Methods:

The research was initiated in early 2013 and completed in early 2014 in each of the 6 study clinics and consisted of (1) patient flow mapping and measurement of retention through collection of health systems data from antenatal care registries, pharmacy registries, ART clinic databases, (2) workforce assessment and measurement of patient waiting times, and (3) patient and worker individual interviews and focus groups.

Results:

Coverage of HIV testing and ART initiation were over 90% at all sites, but retention at 30-, 60-, and 90-day pharmacy refill visits was very low ranging from only 5% at 1 site to 30% returning at 90 days. These data revealed major systemic bottlenecks that contributed to poor adherence and retention in the first month after ART initiation. Long wait times, short consultations, and poor counseling were identified as barriers.

Conclusions:

Based on these findings, we designed an intervention with these components: (1) workflow modification to redefine nurse tasks, shift tasks to community health workers, and enhance patient tracking and (2) an adherence and retention package to systematize active patient follow-up, ensure home visits by community health workers, use text messaging, and intensify counseling by health staff. This intervention is currently under evaluation using a stepped wedge design.
The zinc sensing receptor, ZnR/GPR39, triggers metabotropic calcium signalling in colonocytes and regulates occludin recovery in experimental colitis
Authors: Sunuwar Laxmi , Medini Michal , Cohen Limor , Sekler Israel , Hershfinkel Michal
Published: July 2016

Impaired epithelial barrier function is a hallmark of inflammatory bowel diseases, such as colitis, contributing to diarrhoea and perpetuating inflammation. We show that the zinc sensing receptor, ZnR/GPR39, triggers intracellular Ca
2+
signalling in colonocytes thereby inducing occludin expression. Moreover, ZnR/GPR39 is essential for epithelial barrier recovery in the dextran sodium sulfate (DSS) ulcerative colitis model. Loss of ZnR/GPR39 results in increased susceptibility to DSS-induced inflammation, owing to low expression of the tight junction protein occludin and impaired epithelial barrier. Recovery of wild-type (WT) mice from the DSS insult was faster than that of ZnR/GPR39 knockout (KO) mice. Enhanced recovery of the epithelial layer and increased crypt regeneration were observed in WT mice compared with ZnR/GPR39 KO, suggesting that ZnR/GPR39 is promoting epithelial barrier integrity following DSS insult. Indeed, cell proliferation and apical expression of occludin, following the DSS-induced epithelial erosion, were increased in WT tissue but not in ZnR/GPR39 KO tissue. Importantly, survival following DSS treatment was higher in WT mice compared with ZnR/GPR39 KO mice. Our results support a direct role for ZnR/GPR39 in promoting epithelial renewal and barrier function following DSS treatment, thereby affecting the severity of the disease. We suggest ZnR/GPR39 as a novel therapeutic target that can improve epithelial barrier function in colitis.

This article is part of the themed issue ‘Evolution brings Ca
2+
and ATP together to control life and death’.
Intertwining extracellular nucleotides and their receptors with Ca2+in determining adult neural stem cell survival, proliferation and final fate
Authors: Lecca Davide , Fumagalli Marta , Ceruti Stefania , Abbracchio Maria P.
Published: July 2016

In the central nervous system (CNS), during both brain and spinal cord development, purinergic and pyrimidinergic signalling molecules (ATP, UTP and adenosine) act synergistically with peptidic growth factors in regulating the synchronized proliferation and final specification of multipotent neural stem cells (NSCs) to neurons, astrocytes or oligodendrocytes, the myelin-forming cells. Some NSCs still persist throughout adulthood in both specific ‘neurogenic’ areas and in brain and spinal cord parenchyma, retaining the potentiality to generate all the three main types of adult CNS cells. Once CNS anatomical structures are defined, purinergic molecules participate in calcium-dependent neuron-to-glia communication and also control the behaviour of adult NSCs. After development, some purinergic mechanisms are silenced, but can be resumed after injury, suggesting a role for purinergic signalling in regeneration and self-repair also via the reactivation of adult NSCs. In this respect, at least three different types of adult NSCs participate in the response of the adult brain and spinal cord to insults: stem-like cells residing in classical neurogenic niches, in particular, in the ventricular–subventricular zone (V-SVZ), parenchymal oligodendrocyte precursor cells (OPCs, also known as NG2-glia) and parenchymal injury-activated astrocytes (reactive astrocytes). Here, we shall review and discuss the purinergic regulation of these three main adult NSCs, with particular focus on how and to what extent modulation of intracellular calcium levels by purinoceptors is mandatory to determine their survival, proliferation and final fate.

This article is part of the themed issue ‘Evolution brings Ca2+and ATP together to control life and death’.
General calibration of microbial growth in microplate readers
Authors: Stevenson Keiran , McVey Alexander F. , Clark Ivan B.N. , Swain Peter S. , Pilizota Teuta
Published: July 2016

Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from antibiotic efficacy studies, studies of growth under different nutritional or stress environments, to studies of different mutant strains, including those harbouring synthetic circuits. OD measurements are performed under the assumption that the OD value obtained is proportional to the cell number, i.e. the concentration of the sample. However, the assumption holds true in a limited range of conditions and calibration techniques that determine that range are currently missing. Here we present a set of calibration procedures and considerations that are necessary to successfully estimate the cell concentration from OD measurements.
Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models
Authors: He Zhangyi , Beaumont Mark , Fu Feng
Published: July 2016

The Wright-Fisher model and its extensions are of central importance in population genetics, and so far, they have formed the basis of most theoretical and applied population genetic research. In the present work, we explore the effect that the ordering of natural selection and population regulation in the life cycle has on the resulting population dynamics under the Wright-Fisher model, especially for the evolution of one- and two-locus systems. With weak natural selection, the details of how to order natural selection and population regulation in the life cycle do not matter in the Wright-Fisher model and its diffusion approximation. By contrast, we show that when there is strong natural selection and the population is in linkage disequilibrium, there can be appreciable differences in the resulting population dynamics under the Wright-Fisher model, depending on whether natural selection occurs before or after population regulation in the life cycle. We argue that this effect may be of significance in natural populations subject to gene migration and local selection.

F.Y. supported in part by EPSRC Grant EP/I028498/1.
Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies
Authors: Song Minsun , Wheeler William , Caporaso Neil E. , Landi Maria Teresa , Chatterjee Nilanjan
Published: July 2016

Background

Genome-wide association studies (GWAS) are now routinely imputed for untyped SNPs based on various powerful statistical algorithms for imputation trained on reference datasets. The use of predicted allele count for imputed SNPs as the dosage variable is known to produce valid score test for genetic association.

Methods

In this paper, we investigate how to best handle imputed SNPs in various modern complex tests for genetic association incorporating gene-environment interactions. We focus on case-control association studies where inference in an underlying logistic regression model can be performed using alternative methods that rely on varying degree on an assumption of gene-environment independence in the underlying population. As increasingly large scale GWAS are being performed through consortia effort where it is preferable to share only summary-level information across studies, we also describe simple mechanisms for implementing score-tests based on standard meta-analysis of “one-step” maximum-likelihood estimates across studies.

Results

Applications of the methods in simulation studies and a dataset from genome-wide association study of lung cancer illustrate ability of the proposed methods to maintain type-I error rates for underlying testing procedures. For analysis of imputed SNPs, similar to typed SNPs, retrospective methods can lead to considerable efficiency gain for modeling of gene-environment interactions under the assumption of gene-environment independence.

Conclusions

Proposed methods allow valid analysis of imputed SNPs in case-control studies of gene-environment interaction using alternative strategies that had been earlier available only for genotyped SNPs.
Three-dimensional nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction
Authors: Meng Yifei , Zuo Jian-Min
Published: July 2016

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can be extended to multiphase nanocrystalline materials as well. Thus, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.
3,4-Dimethoxybenzaldehyde
Authors: Ronde Erik de , Brugman Sander J.T. , Koning Niels , Tinnemans Paul , Vlieg Elias
Published: July 2016

In the title compound, C9H10O3, one of the methoxy C atoms deviates from the plane of the aromatic ring by 0.337 (2) Å. Crystallization was hindered by oiling out in various solvents. The crystal contains neither hydrogen bonds nor aromatic π–π stacking.
Bis(2,2′:6′,2′′-terpyridine-κ3N,N′,N′′)nickel(II) bis(perchlorate) hemihydrate
Authors: Anderer Carolin , Näther Christian , Bensch Wolfgang
Published: July 2016

In the title compound, [Ni(C15H11N3)2](ClO4)2·0.5H2O, the Ni2+cation is coordinated by two terpyridine ligands to form a discrete complex and the coordination polyhedron can be described as a slightly distorted octahedron. It crystallizes as a hemihydrate with two perchlorate anions to compensate the charges. In the crystal, one of the two crystallographically independent perchlorate anions is involved in O—H...O hydrogen bonding to the water molecules, where two inversion-related water molecules link two inversion-related perchlorate anions into a ring with anR42(12) loop. The O-atom position of the water molecule is only half occupied,i.e.only half of the anions are involved in hydrogen bonding. A similar arrangement of two anions is also observed for the second crystallographically independent perchlorate anion but no water molecules are located between the anions. The cationic complex and the perchlorate anions are additionally linked by a number of weak C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. The crystal structure of the monohydrate of the same complex has been reported [Bakeret al.(1995).Aust. J. Chem.48, 1373–1378].
2-(4,6-Dimethyl-1-benzofuran-3-yl)acetic acid
Authors: Ramprasad N. , Gowda Ramakrishna , Gowda K.V. Arjuna , Basanagouda Mahantesha
Published: July 2016

In the title compound, C12H12O3, the dihedral angle between the planes of the carboxylic acid group and the benzofuran ring system (r.m.s. deviation = 0.012 Å) is 76.53 (10)°. In the crystal, carboxylic acid inversion dimers linked by pairs of O—H...O hydrogen bonds generateR22(8) loops. C—H...O interactions link the dimers into (101) sheets.
The interaction effect of job redesign and job satisfaction on employee performance
Authors: Siengthai Sununta , Pila-Ngarm Patarakhuan
Published: July 2016

Purpose

– The purpose of this paper is to examine the effect of job redesign as well as that of the interaction effect of job redesign and job satisfaction on employee performance.

Design/methodology/approach

– The qualitative research method is used, i.e., in-depth interviews, to validate the questionnaire which is modified based on the well-established Job Diagnostic Survey instrument. A large-scale questionnaire survey was conducted in 2012 taking the hotel and resort industry and the banking industry in Thailand as its research sites. Multiple regression analysis was used to analyse the survey data obtained from 295 sample respondent managers.

Findings

– It is found that job redesign is significantly and inversely related to employee performance. Meanwhile job satisfaction is found to be positively and significantly related to employee performance. Moreover, the interaction effect between job redesign and job satisfaction is found to be positively and significantly related to employee performance. Furthermore, when controlled for demographic characteristics of sample respondents, it is found that being in the age group of 37-47 years old is significantly and inversely related to employee performance. These findings suggest that when firms implement job redesign, it is likely that it will negatively influence employee performance in the first stage of change. Hence, firms should try to enhance employee job satisfaction while implementing job redesign so that the job redesign will result in improved employee performance. The findings suggest that implementing job redesign without concerned employees experiencing job satisfaction or merely implementing job redesign can result in a possible decreased employee performance. These findings also suggest that any proposed job redesign will be an effective HR strategy to significantly mobilize employee performance only when firms ensure that the implementation of job redesign involves the concerned employees and enhances their job satisfaction.

Originality/value

– Job redesign by itself is found to have a significant negative effect on employee performance while job satisfaction is found to always positively and significantly influence employee performance. This study ascertains the positive interaction effect of job redesign and job satisfaction for employee performance improvement. These findings suggest that job satisfaction positively moderates the effect of job redesign on employee performance.
Measuring the use of human resources practices and employee attitudes
Authors: Kampkötter Patrick , Mohrenweiser Jens , Sliwka Dirk , Steffes Susanne , Wolter Stefanie
Published: July 2016

Purpose

– The purpose of this paper is to introduce a new data source available for researchers with interest in human resources management (HRM) and personnel economics, the Linked Personnel Panel (LPP).

Design/methodology/approach

– The LPP is a longitudinal and representative employer-employee data set covering establishments in Germany and a subset of their workforce and is designed for quantitative empirical human resource research.

Findings

– The LPP employee survey applies a number of established scales to measure job characteristics and job perceptions, personal characteristics, employee attitudes towards the organization and employee behaviour. This paper gives an overview of both the employer and employee survey and outlines the definitions, origins, and statistical properties of the scales used in the individual questionnaire.

Practical implications

– The paper describes how researchers can access the data.

Originality/value

– First, the data set combines employer and employee surveys that can be matched to each other. Second, it can also be linked to a number of additional administrative data sets. Third, the LPP covers a wide range of firms and workers from different backgrounds. Finally, because of its longitudinal dimension, the LPP should facilitate the study of causal effects of HRM practices.