bluuebunny/crossref_metadata_2025 huggingface dataset:
Review of Christopher F. Baum's An Introduction to Stata Programming, Second Edition
Authors: Schechter Clyde
Published: November 2018

In this article, I review An Introduction to Stata Programming, Second Edition, by Christopher F. Baum (2016 [Stata Press]).
Eq5dds: A Command to Analyze the Descriptive System of EQ-5D Quality-of-life Instrument
Authors: Ramos-Goñi Juan Manuel , Ramallo-Fariña Yolanda
Published: November 2018

In this article, we describe the eq5dds command, which presents the results of a descriptive system using individuals’ responses for mobility, self care, usual activities, pain or discomfort, anxiety or depression, and visual analog scale from the EQ-5D health-related quality-of-life instrument (in its 3L and 5L versions). The command presents each of the tables and the figures recommended in the official user guide of the instrument (developed by the EuroQol Group).
Estimating Survival Functions after Stcox with Time-varying Coefficients
Authors: Ruhe Constantin
Published: November 2018

In many applications of the Cox model, the proportional-hazards assumption is implausible. In these cases, the solution to nonproportional hazards usually consists of modeling the effect of the variable of interest and its interaction effect with some function of time. Although Stata provides a command to implement this interaction in stcox, it does not allow the typical visualizations using stcurve if stcox was estimated with the tvc() option. In this article, I provide a short workaround that estimates the survival function after stcox with time-dependent coefficients. I introduce and describe the scurve_tvc command, which automates this procedure and allows users to easily visualize survival functions for models with time-varying effects.
Creating HTML or Markdown Documents from within Stata using Webdoc
Authors: Jann Ben
Published: November 2018

In this article, I discuss the use of webdoc for creating HTML or Markdown documents from within Stata. The webdoc command provides a way to embed HTML or Markdown code directly in a do-file and automate the integration of results from Stata in the final document. The command can be used, for example, to create a webpage documenting your data analysis, including all Stata output and graphs. More generally, the command can be used to create and maintain a website that contains results computed by Stata.
Capturing a Stata Dataset and Releasing it into REDcap
Authors: Lirette Seth T. , Seals Samantha R. , Blackshear Chad , May Warren
Published: November 2018

With technology advances, researchers can now capture data using web-based applications. One such application, Research Electronic Data Capture (REDCap), allows for data entry from any computer with an Internet connection. As the use of REDCap has increased in popularity, we have observed the need to easily create data dictionaries and data collection instruments for REDCap. The command presented in this article, redcapture, demonstrates one method to create a REDCap-ready data dictionary using a loaded Stata dataset, illustrated by examples of starting from an existing dataset or completely starting from scratch.
Introducing the StataStan Interface for Fast, Complex Bayesian Modeling Using Stan
Authors: Grant Robert L. , Carpenter Bob , Furr Daniel C. , Gelman Andrew
Published: November 2018

In this article, we present StataStan, an interface that allows simulation-based Bayesian inference in Stata via calls to Stan, the flexible, open-source Bayesian inference engine. Stan is written in C++, and Stata users can use the commands stan and windowsmonitor to run Stan programs from within Stata. We provide a brief overview of Bayesian algorithms, details of the commands available from Statistical Software Components, considerations for users who are new to Stan, and a simple example. Stan uses a different algorithm than bayesmh, BUGS, JAGS, SAS, and MLwiN. This algorithm provides considerable improvements in efficiency and speed. In a companion article, we give an extended comparison of StataStan and bayesmh in the context of item response theory models.
Rdrobust: Software for Regression-discontinuity Designs
Authors: Calonico Sebastian , Cattaneo Matias D. , Farrell Max H. , Titiunik Rocío
Published: November 2018

We describe a major upgrade to the Stata (and R) rdrobust package, which provides a wide array of estimation, inference, and falsification methods for the analysis and interpretation of regression-discontinuity designs. The main new features of this upgraded version are as follows: i) covariate-adjusted bandwidth selection, point estimation, and robust bias-corrected inference, ii) cluster–robust bandwidth selection, point estimation, and robust bias-corrected inference, iii) weighted global polynomial fits and pointwise confidence bands in regression-discontinuity plots, and iv) several new bandwidth selection methods, including different bandwidths for control and treatment groups, coverage error-rate optimal bandwidths, and optimal bandwidths for fuzzy designs. In addition, the upgraded package has superior performance because of several numerical and implementation improvements. We also discuss issues of backward compatibility and provide a companion R package with the same syntax and capabilities.
A Combined Test for a Generalized Treatment Effect in Clinical Trials with a Time-to-event Outcome
Authors: Royston Patrick
Published: November 2018

Most randomized controlled trials with a time-to-event outcome are designed and analyzed assuming proportional hazards of the treatment effect. The sample-size calculation is based on a log-rank test or the equivalent Cox test. Nonproportional hazards are seen increasingly in trials and are recognized as a potential threat to the power of the log-rank test. To address the issue, Royston and Parmar (2016, BMC Medical Research Methodology 16: 16) devised a new “combined test” of the global null hypothesis of identical survival curves in each trial arm. The test, which combines the conventional Cox test with a new formulation, is based on the maximal standardized difference in restricted mean survival time (RMST) between the arms. The test statistic is based on evaluations of RMST over several preselected time points. The combined test involves the minimum p-value across the Cox and RMST-based tests, appropriately standardized to have the correct null distribution. In this article, I outline the combined test and introduce a command, stctest, that implements the combined test. I point the way to additional tools currently under development for power and sample-size calculation for the combined test.
Estimating Responsiveness Scores Using Rscore
Authors: Cerulli Giovanni
Published: November 2018

rscore computes unit-specific responsiveness scores using an iterated random-coefficient regression approach. The model fit by rscore considers a regression of a response variable y, that is, outcome, on a series of factors (or regressors) x, that is, varlist, by assuming a different reaction (or “responsiveness”) of each unit to each factor contained in x. rscore allows for i) ranking units according to the obtained level of the responsiveness score; ii) detecting more influential factors in driving unit performance; and iii) studying the distribution (heterogeneity) of factors’ responsiveness scores across units. Also, rscore offers useful graphical representation of results. We provide two illustrative applications of the model: the first is on a cross-section, and the second is on a longitudinal dataset.
Randomization Inference with Stata: A Guide and Software
Authors: Heß Simon
Published: November 2018

Randomization inference or permutation tests are only sporadically used in economics and other social sciences—this despite a steep increase in randomization in field and laboratory experiments that provide perfect experimental setups for applying randomization inference. In the context of causal inference, such tests can handle problems often faced by applied researchers, including issues arising in the context of small samples, stratified or clustered treatment assignments, or nonstandard randomization techniques. Standard statistical software packages have either no implementation of randomization tests or very basic implementations. Whenever researchers use randomization inference, they regularly code individual program routines, risking inconsistencies and coding mistakes. In this article, I show how randomization inference can best be conducted in Stata and introduce a new command, ritest, to simplify such analyses. I illustrate this approach's usefulness by replicating the results in Fujiwara and Wantchekon (2013, American Economic Journal: Applied Economics 5: 241–255) and running simulations. The applications cover clustered and stratified assignments, with varying cluster sizes, pairwise randomization, and the computation of nonapproximate p-values. The applications also touch upon joint hypothesis testing with randomization inference.
validscale: A Command to Validate Measurement Scales
Authors: Perrot Bastien , Bataille Emmanuelle , Hardouin Jean-Benoit
Published: November 2018

Subjective measurement scales are used to measure nonobservable respondent characteristics in several fields such as clinical research, educational sciences, or psychology. To be useful, the scores resulting from the questionnaire must be validated; that is, they must provide the psychometric properties validity, reliability, and sensitivity. In this article, we present the validscale command, which carries out the required statistical analyses to validate a subjective measurement scale. We have also developed a dialog box, and validscale will soon be implemented online with Numerics by Stata.
Assessing the Health Economic Agreement of Different Data Sources
Authors: Gallacher Daniel , Achana Felix
Published: November 2018

In this article, we present a simple-to-use framework for assessing the agreement of cost-effectiveness endpoints generated from different sources of data. The aim of this package is to enable the rapid assessment of routine data for use in cost-effectiveness analyses. By quantifying the comparability of routine data with “gold-standard” trial data, we inform decisions on the suitability of routine data for cost-effectiveness analysis. The rapid identification of informative routine data will increase the opportunity for economic analyses and potentially reduce the cost and burden of collecting patient-reported data in clinical trials.
Linear Dynamic Panel-data Estimation Using Maximum Likelihood and Structural Equation Modeling
Authors: Williams Richard , Allison Paul D. , Moral-Benito Enrique
Published: November 2018

Panel data make it possible both to control for unobserved confounders and to include lagged, endogenous regressors. However, trying to do both simultaneously leads to serious estimation difficulties. In the econometric literature, these problems have been addressed by using lagged instrumental variables together with the generalized method of moments, while in sociology the same problems have been dealt with using maximum likelihood estimation and structural equation modeling. While both approaches have merit, we show that the maximum likelihood–structural equation models method is substantially more efficient than the generalized method of moments method when the normality assumption is met and that the former also suffers less from finite sample biases. We introduce the command xtdpdml, which has syntax similar to other Stata commands for linear dynamic panel-data estimation. xtdpdml greatly simplifies the structural equation model specification process; makes it possible to test and relax many of the constraints that are typically embodied in dynamic panel models; allows one to include time-invariant variables in the model, unlike most related methods; and takes advantage of Stata's ability to use full-information maximum likelihood for dealing with missing data. The strengths and advantages of xtdpdml are illustrated via examples from both economics and sociology.
Attrition Diagrams for Clinical Trials and Meta-analyses in Stata
Authors: Righolt Christiaan H. , Mahmud Salaheddin M.
Published: November 2018

In this article, we present attrition, a suite of commands to simplify the maintenance and documentation of implemented exclusion criteria and attrition conditions using standard Stata facilities and to generate an attrition diagram. attrition can be used, both from the command line and in do-files, to keep the diagram up to date with the analysis it documents. Six subcommands (set, exclude, count, tab, list, graph) allow the diagram to be constructed in a versatile way.
Group Sequential Clinical Trial Designs for Normally Distributed Outcome Variables
Authors: Grayling Michael J. , Wason James M. S. , Mander Adrian P.
Published: November 2018

In a group sequential clinical trial, accumulated data are analyzed at numerous time points to allow early decisions about a hypothesis of interest. These designs have historically been recommended for their ethical, administrative, and economic benefits. In this article, we first discuss a collection of new commands for computing the stopping boundaries and required group size of various classical group sequential designs, assuming a normally distributed outcome variable. Then, we demonstrate how the performance of several designs can be compared graphically.
Biological Effects of Continuous Low-Dose-Rate Irradiation in Silkworms and Mice: Growth Promotion and Tumor Transplantability
Authors: Nakashima Masahiro , Sugie Chikao , Wang Zhen , Kondo Takuhito , Manabe Yoshihiko , Murai Taro , Shibamoto Yuta
Published: November 2018

A previous study showed that continuous low-dose-rate irradiation promoted the growth of silkworm larvae. This study aimed to confirm that finding, determine the optimal dose rate for growth promotion, and compare low- and high-dose-rate irradiation in silkworms, while also investigating the effects of the radiation-emitting sheet on growth and tumor transplantability in mice. Silkworm eggs were placed on low-dose-emitting sheets with 4 different dose rates (γ-ray rate: 1.7 -22.4 μSv/hour) or on control sheets. The other groups of silkworm larvae received single whole-body X-irradiation (0.1-50 Gy), and subsequent body weight changes were monitored. Starting at 3 weeks old, Balb/c mice were bred on the same sheets, and body weight change was measured. Seven weeks later, the mice were used to investigate the transplantability of EMT6 tumor cells cultured in vitro. The silkworms bred on the 13.4- and 22.4-μSv/hour sheets became larger than the control. Single 50-Gy irradiation suppressed the growth of silkworms. An increase in the time to EMT6 tumor development was observed in low-dose-rate-irradiated mice. This study confirmed growth promotion of silkworms by continuous low-dose radiation and demonstrated growth suppression at a high dose rate. Growth promotion was not observed in mice; further studies using higher dose-rate sheets may be warranted.
Design and bearing characteristics of planetary roller screws based on aerospace high-load conditions
Authors: Zu Li , Zhang Zhou , Gao Liang
Published: November 2018

Under the background of the rapid development of today’s aerospace industry, the bearing characteristics of planetary roller screw drive under high overload conditions are studied. Designing a high-load, high-performance precision planetary roller screw drive is of practical and significant. An axially spaced RV type planetary roller screw with a single nut is designed under aerospace conditions. Under the conditions of the aerospace working load and efficiency, the parameters and structures of the planetary roller screw are completed. Based on this, the bearing characteristics of the planetary roller screw are studied and the equivalent finite element model of the planetary roller screw is analyzed. Those analyses include stress and strain, elastic–plastic properties, transmission efficiency, and dynamic load capacity. The results show that the design of planetary roller screw meets the design requirements for aerospace conditions. And the results can provide a basis for the design and manufacture of planetary roller screws under high loads.
Evoked hypoalgesia is accompanied by tonic pain and immune cell infiltration in the dorsal root ganglia at late stages of diabetic neuropathy in mice
Authors: Agarwal Nitin , Helmstädter Johanna , Rojas Daniel R , Bali Kiran K , Gangadharan Vijayan , Kuner Rohini
Published: November 2018

Diabetic peripheral neuropathy is a major debilitating late complication of diabetes, which significantly reduces the quality of life in patients. Diabetic peripheral neuropathy is associated with a wide spectrum of sensory abnormalities, where in loss of sensation or hypoalgesia to applied external stimuli is paradoxically accompanied by debilitating tonic spontaneous pain. In numerous studies on animal models of diabetic peripheral neuropathy, behavioural measurements have been largely confined to analysis of evoked withdrawal to mechanical and thermal stimuli applied to dermatomes, whereas spontaneous, on-going pain has not been widely studied. In the Streptozotocin model of type 1 diabetes, we employed the Conditioned Place Preference test to assess tonic pain. Our results indicate that both phases, that is, early evoked hypersensitivity (i.e. 5–7 weeks post-Streptozotocin) as well as late stage hypoalgesia (i.e. 17–20 weeks post-Streptozotocin) are accompanied by significant tonic pain in mice with diabetic peripheral neuropathy. We also report on the temporal relation between on-going pain and neuropathological changes in the dorsal root ganglia of mice with diabetic peripheral neuropathy up to 6 months post-Streptozotocin. Neither early hypersensitivity nor late hypoalgesia were associated with markers of cellular stress in the dorsal root ganglia. Whereas significant neutrophil infiltration was observed in the dorsal root ganglia over both early and late stages post-Streptozotocin, T-cell infiltration in the dorsal root ganglia was prominent at late stages post-Streptozotocin. Thus, longitudinal analyses reveal that similar to patients with chronic diabetic peripheral neuropathy, mice show tonic pain despite sensory loss after several months in the Streptozotocin model, which is accompanied by neuroimmune interactions in the dorsal root ganglia.
Diagnostic utility of the Active Compression Test for the superior labrum anterior posterior tear: A systematic review
Authors: Davis Cody , Immormino Jenna , Higgins Brendan M , Clark Kyle , Engebose Samuel , Garcia Alessandra N , Cook Chad E
Published: November 2018

Background

The Active Compression Test has been proposed to have high diagnostic accuracy for superior labrum anterior to posterior tears. The aim of this systematic review was to compile the available evidence for this test and evaluate its diagnostic accuracy.

Methods

The databases PubMed, Embase, Cochrane, CINAHL, and SCOPUS were searched for case control, diagnostic studies that evaluated the Active Compression Test between 1999 (date of test introduction) and February 2018. Two independent review authors screened the search results, assessed the risk of bias using QUADAS-2, and extracted the data.

Results

Eighteen studies (pooled sample = 3091) were included in this review. Twelve out of 18 studies either had high or unclear risk of bias (66.6%). Results from the pooled analysis of all 18 studies provided that the Active Compression Test is more sensitive (71.5: 95% CI = 68.8, 74.0) than specific (51.9: 95% CI = 50.7, 53.1) and only marginally influenced posttest probability from a pretest probability of 31.7–40.72% with a positive finding and a pretest probability of 31.7–20.33% with a negative finding.

Discussion

The Active Compression Test has both limited screening and confirmation ability; therefore, we do not advocate for its use in clinical decision making.
Genetic Diversity of Dominant Plant Species in Tropical Land-Use Systems in Sumatra, Indonesia
Authors: Breidenbach Natalie , Rahayu Sri , Siregar Iskandar Z. , Siregar Ulfah J. , Hamzah  , Finkeldey Reiner
Published: November 2018

Biodiversity hotspots like tropical lowland rainforests in Sumatra are threatened by the agricultural expansion, which increases the deforestation rate in Indonesia, which is highest worldwide. Main land-use change drivers in Indonesia include the production of rubber and palm oil, both of which lead to a high forest conversion rate. In the remaining and degraded forest patches, species diversity has declined and species composition has been altered. Effects of habitat fragmentation and land-use change on genetic structure were frequently investigated at the species level and compared across plant species, but not for plant communities. In addition, the effect of land-use change on the genetic structure of plants has not yet been investigated. Using Amplified Fragment Length Polymorphism marker, the genetic diversity of 112 dominant plant species was assessed in four different land-use systems in Sumatra: old growth tropical lowland rainforest, jungle rubber, rubber plantation, and oil palm plantation. The four systems were investigated in two regions with four replicates, respectively. Because of different species compositions, characterized by different life history traits, forest and jungle rubber plots showed the highest diversity level, while oil palm and rubber plantations showed the lower diversity levels. The two intensively managed plantation systems showed similar genetic diversity levels as the tree dominated systems but are dominated by mainly alien species. This indicates that oil palm and rubber plantations could not be identified as habitats of conservational value. The newly introduced collection and analysis approach presents a universally applicable method to investigate different ecosystems in their plant genetic diversity to support the identification of habitats with high conservational value.
Caroli’s-type ductal plate malformation and a portosystemic shunt in a 4-month-old kitten
Authors: Roberts Madeleine L , Rine Stacy , Lam Amy
Published: November 2018

Case summary

A 4-month-old neutered male Russian Blue kitten had a 4 week history of hypersalivation and failure to thrive. In addition, there was a 2 week history of soft tissue swelling on the ventral abdomen, which had failed to improve with antimicrobial therapy. There were no significant physical examination or neurological deficits on examination; however, the cat had a quiet demeanour for its age. Postprandial bile acids were increased (32 µmol/l; reference interval <25 µmol/l). An abdominal CT scan revealed changes consistent with an extrahepatic portosystemic shunt and inflammation of fat of the ventral abdominal body wall. Surgical biopsy and culture of the subcutaneous swelling identified non-infectious steatitis. Ten weeks following initial presentation, surgical exploration, liver biopsy and ligation of the portosystemic shunt were performed. Liver biopsy was submitted to the Anatomical Pathology Laboratory of Cornell University Animal Health Diagnostic Center, New York, USA. Histopathology revealed a ductal plate malformation (Caroli’s type), as well as changes consistent with a portosystemic shunt.

Relevance and novel information

Ductal plate malformations are rarely described in the veterinary literature. To our knowledge this is the first reported case of Caroli’s-type malformation in a cat. There are no biochemical changes that allow for differentiation of ductal plate malformations from other hepatopathies. Liver biopsy is required for a definitive diagnosis.
Seismic Response of Embankment Dams Based on Recorded Strong-Motion Data in Japan
Authors: Park DongSoon , Kishida Tadahiro
Published: November 2018

It is important to investigate strong-motion time series recorded at dams to understand their complex seismic responses. This paper develops a strong-motion database recorded at existing embankment dams and analyzes correlations between dam dynamic responses and ground-motion parameters. The Japan Commission on Large Dams database used here includes 190 recordings at the crests and foundations of 60 dams during 54 earthquakes from 1978 to 2012. Seismic amplifications and fundamental periods from recorded time series were computed and examined by correlation with shaking intensities and dam geometries. The peak ground acceleration (PGA) at the dam crest increases as the PGA at the foundation bedrock increases, but their ratio gradually decreases. The fundamental period broadly increases with the dam height and PGA at the foundation bedrock. The nonlinear dam response becomes more apparent as the PGA at the foundation bedrock becomes >0.2 g. The prediction models of these correlations are proposed for estimating the seismic response of embankment dams, which can inform the preliminary design stage.
A Candidate Proxy to be used in Intensity-Based Triggering Mechanism for Parametric CAT-Bond Insurance: Istanbul Case Study
Authors: Mousavi Mehdi , Akkar Sinan , Erdik Mustafa
Published: November 2018

We study the suitability of average peak ground acceleration ( PGA) as a ground-motion proxy for parametric catastrophe bond (CAT bond) design. We tie the selection of PGA (as a triggering parameter for CAT bonds) to computational convenience (fast retrieval from the recorded ground motion) and loss correlation (optimum monetary return on the investor side). Our case studies advocate that PGA, as a candidate ground-motion proxy, can be used confidently for parametric CAT bonds, particularly applications associated with dense coverage of seismic networks. It is still a compelling ground-motion proxy even if the seismic network coverage is sparse, provided that the accelerometric stations are deployed in the vicinity of assets that financially represent the most significant portion of the insured building stock. We establish an event-based risk model of the Istanbul city (via Monte Carlo simulations) to depict the rationale behind our proposition and compare its performance with other competing (more sophisticated) proxies in terms of accelerometric network density and spatial distribution as well as the different risk levels used in risk management.
Modeling epigenetic modifications in renal development and disease with organoids and genome editing
Authors: Hurtado del Pozo Carmen , Garreta Elena , Izpisúa Belmonte Juan Carlos , Montserrat Nuria
Published: November 2018

Understanding epigenetic mechanisms is crucial to our comprehension of gene regulation in development and disease. In the past decades, different studies have shown the role of epigenetic modifications and modifiers in renal disease, especially during its progression towards chronic and end-stage renal disease. Thus, the identification of genetic variation associated with chronic kidney disease has resulted in better clinical management of patients. Despite the importance of these findings, the translation of genotype–phenotype data into gene-based medicine in chronic kidney disease populations still lacks faithful cellular or animal models that recapitulate the key aspects of the human kidney. The latest advances in the field of stem cells have shown that it is possible to emulate kidney development and function with organoids derived from human pluripotent stem cells. These have successfully recapitulated not only kidney differentiation, but also the specific phenotypical traits related to kidney function. The combination of this methodology with CRISPR/Cas9 genome editing has already helped researchers to model different genetic kidney disorders. Nowadays, CRISPR/Cas9-based approaches also allow epigenetic modifications, and thus represent an unprecedented tool for the screening of genetic variants, epigenetic modifications or even changes in chromatin structure that are altered in renal disease. In this Review, we discuss these technical advances in kidney modeling, and offer an overview of the role of epigenetic regulation in kidney development and disease.
Distribution of Toxoplasma gondii IgM and IgG antibody seropositivity among age groups and gestational periods in pregnant women
Authors: Sadiqui Shahida , Shah Syed Rafiq Hussain , Almugadam Babiker Saad , Shakeela Qismat , Ahmad Shehzad
Published: November 2018

Background: Toxoplasmosis is a globally distributed parasitic disease. The present study aimed to estimate the prevalence and geographic distribution of toxoplasmosis, as well assess the risk of animal contact in disease development and determine the percentage of toxoplasmois-associated IgM and IgG seropositivity among different age groups. In addition, it aimed to estimate the proportion of toxoplasma IgM seropositivity among pregnancy trimesters.

Methods: A total of 500 pregnant women were included in this study. From each participant, a 5-ml venous blood sample was collected and centrifuged to obtain serum that was tested for Toxoplasma gondii IgM and IgG antibodies using immunochromatographic testing and ELISA.

Results: The overall seroprevalence of toxoplasmosis was 24.8%, with rates of acute infection of 8%. Among positive cases in every trimester, 54.34% of first trimester positive cases had a serologic marker of acute toxoplasmosis. Out of the 40 pregnant women with previous history of cow/buffalo contact and toxoplasmosis, 40% were seropositive for toxoplasma IgM; and out of 30 women with prior history of dog contact, 16.66% had serological marker of acute toxoplasmosis.

Conclusions: In this study, there is a high prevalence of toxoplasmosis and contact with domestic animals is a risk factor for this illness. Therefore, it is necessary to test every pregnant women for toxoplasmosis and distinguish the type of infection, as well as the conduction of public health education programs to generate the awareness.
RNA interactomics: recent advances and remaining challenges
Authors: Schönberger Brigitte , Schaal Christoph , Schäfer Richard , Voß Björn
Published: November 2018

Tight regulation of cellular processes is key to the development of complex organisms but also vital for simpler ones. During evolution, different regulatory systems have emerged, among them RNA-based regulation that is carried out mainly by intramolecular and intermolecular RNA–RNA interactions. However, methods for the transcriptome-wide detection of these interactions were long unavailable. Recently, three publications described high-throughput methods to directly detect RNA duplexes in living cells. This promises to enable in-depth studies of RNA-based regulation and will narrow the gaps in our understanding of RNA structure and function. In this review, we highlight the benefits of these methods and their commonalities and differences and, in particular, point to methodological shortcomings that hamper their wider application. We conclude by presenting ideas for how to overcome these problems and commenting on the prospects we see in this area of research.
Inflammatory cell expression of Toll-like receptor-2 (TLR2) within refractory periapical granuloma.
Authors: Chen Eric , Bakr Mahmoud M. , Firth Norman , Love Robert M.
Published: November 2018

Background: Toll-like receptor-2 (TLR2) is highly important within the immune system. Characterization of the expression of TLR2 within inflammatory cells in periapical lesions could help in diagnosis and management of refractory cases. The aim of the study is identification of Toll-like receptor (TLR2) through immunohistochemical and immunofluroscence expression in inflammatory cells within refractory periapical granuloma cases.

Methods: Eight cases of refractory periapical granuloma were selected out of 772 cases. Histological examination and immunohistochemical staining with polyclonal rabbit antihuman TLR2, monoclonal mouse antihuman CD38, CD68 and CD83 primary antibodies, as well as immunofluorescence staining with goat anti-rabbit TLR2, donkey anti-mouse CD38, CD68 and CD83 primary antibodies was conducted. Positive controls, negative controls and experimental sections with no primary antibody were included in the study. Qualitative analysis and double immunofluorescence technique was used to characterize the TLR+ cells.

Results: In periapical granuloma, lymphocytes (CD38 cells) expressed the most amount of TLR reactivity followed by macrophages (CD68 cells), and odontogenic epithelial cells. Neutrophils, red blood cells (RBCs) and collagen ground substance were negative to TLR2. 

Conclusion: TLR2 was highly expressed by lymphocytes and plasma cells indicative of their major role in the inflammatory process and antigen recognition in refractory periapical granuloma. Dendritic cells expressing TLR2 were low in number suggesting a minor role in sustaining these lesions.
Metachronous or synchronous male breast and prostate cancers a duality to lookout for.
Authors: Mukendi Alain Mwamba , Van Den Berg Eunice , Pather Sugeshnee , Padayachee Rushen Siva
Published: November 2018

Introduction: Breast cancer is well known as the stereotypical women's cancer, and prostate cancer represents the well-known stereotypical male counterpart. While prostate cancer carries the potential to metastasize to the breast, the synchronous or metachronous co-occurrence of primary breast and primary prostate cancers is quite unusual. Prostate cancer in men of African descent may have its own behavior with regards to its relationship with male breast cancer.

Case presentation:

Case 1: A 64 year old male presented to Chris Hani Baragwanath Hospital (CHBAH) with a 2 years history of a painless left breast lump. A core biopsy was confirmed breast carcinoma. Tamoxifen was started but, due to disease progression, he underwent left modified radical mastectomy followed by chemotherapy. Prostate biopsy was done for raised Prostate Specific Antigen (PSA) and suspicious prostate on digital rectal examination. A prostatic adenocarcinoma was subsequently diagnosed with bone metastasis on bone scan. He was started on Androgen deprivation therapy and followed up every 3 months.

Case 2: A 68 year old male presented to CHBAH with a 1 year history of a painless right breast lump. A core biopsy confirmed breast cancer. Tamoxifen was started, followed by right modified radical mastectomy and chemotherapy for disease progression. A raised PSA and suspicious prostate on digital rectal examination prompted a prostate biopsy revealing a prostatic adenocarcinoma. Bone scan was negative for metastasis. He is currently on 3 monthly Androgen deprivation therapy and awaiting radiation.

Conclusion: This clinical practice article not only presents this exceptionally rare duality but highlights that both cancers can coexist either as sporadic conditions, or as a result of genetic mutations. Thus, we suggest that men with prostate cancer be screened clinically, biochemically and genetically for breast cancer and vice versa.
Development of an e-learning programme to improve knowledge of interprofessional education
Authors: O'Hara Clare , Trotter Lana , Olsen Carl , Stinson Donna , McCutcheon Karen
Published: November 2018

Evidence has highlighted the importance of interprofessional education in relation to the promotion of collaborative team working and the ultimate reduction in communication errors between health professionals. The establishment of interprofessional education in undergraduate healthcare programmes prepares students for interprofessional collaboration, which is vital to the delivery of safe patient care. Using a logic model approach an interprofessional education e-learning programme was developed and made available to healthcare students to undertake during their clinical practice experiences. This article describes how a logic model process was used to develop and implement this interprofessional education e-learning programme for use by undergraduate healthcare students.
Self-confidence and attitude of acute care nurses to the presence of family members during resuscitation
Authors: Rafiei Hossein , Senmar Mojtaba , Mostafaie Mohammad Reza , Goli Zeinab , Avanaki Sedighe Nasiri , Abbasi Leila , Mafi Mohamad Hossein
Published: November 2018

Aim:

the present study aimed to assess the relationship between attitude to the presence of family members during cardiopulmonary resuscitation and confidence of acute care nurses in performing cardiopulmonary resuscitation in the presence of family.

Methods:

this descriptive-analytical study was conducted on nurses working in acute care units (intensive care unit, coronary care unit, and emergency department) in Iran in 2017. A total of 150 nurses entered the study by convenience sampling. Data were collected on nurses' attitude towards the presence of family scale and nurses' self-confidence in presence of family scale.

Results:

of the 150 participants, 48 (32%) were men and 102 (68%) were women. Total mean score of attitude was 67±10.4 (obtained scores by nurses ranged from 32 to 100). Total mean score of self-confidence was 53.86 ±11.7 (obtained scores by nurses ranged from 23 to 81). Pearson correlation test showed a significant negative relationship between nurses' attitude toward presence of family members during cardiopulmonary resuscitation and their self-confidence (rr=-0.45, p=0.001).

Conclusion:

the present study showed that nurses with a higher self-confidence have a more positive attitude toward presence of family members during cardiopulmonary resuscitation. Given the importance of the subject, it should be considered by nursing managers and planners.
A qualitative study of nursing staff experiences of delirium in the hospice setting
Authors: Waterfield Kerry , Weiand Donna , Dewhurst Felicity , Kiltie Rachel , Pickard Jonathan , Karandikar Ulka , MacCormick Fiona , Vidrine Jen , Rowley Grace , Coulter Paul , Lee Mark , Frew Katie
Published: November 2018

Background:

Delirium is a common condition occurring in 13–42% of people admitted to palliative care units and up to 88% of these patients are at the end of their lives. It is frequently unrecognised and distressing to all those affected—patients, families and health professionals. In addition, there is considerable uncertainty surrounding its trajectory and optimal management, both of which can be inconsistent.

Aims:

This study aims to explore the experience of nursing staff who are caring for patients with delirium in the hospice environment and understand any potential barriers to its management.

Methods:

Semistructured interviews using emotional touchpoints were conducted with 12 nurses and six healthcare assistants in three hospices in North East England. Data was analysed using interpretative phenomenological analysis.

Findings:

The results highlighted gaps in knowledge and understanding in the management of delirium. The results demonstrated delirium had significant emotional effects, which were associated with uncertainty in managing the condition and the impact of this uncertainty on the relationship between staff and patients.

Conclusion:

This study highlights the emotional impact of caring for patients with delirium. Future work is needed to address the areas of uncertainty identified and ascertain how to best support nursing staff in these challenges.
An ethnographic study in nursing homes in Iran
Authors: Shahrki Sedigheh Khodabandeh , Abazari Farokh , Nayer Nahid Dehghan , Pouraboli Batool
Published: November 2018

Background:

The approach of death is an undeniable part of ageing and death is the most important concern for elderly people who live in nursing homes. This study examines describes how care home residents feel when they recognise that they are close to death.

Aims:

The aim of this study was to explore the experiences of elderly residents who are dying in nursing homes as well as their caregivers toward death in an Iranian context.

Methods:

A focused ethnographic research design was chosen. The research sample consisted of 25 nursing home staff—three nurses, 18 healthcare assistants, two administrators, a social worker and a psychologist—and 10 elderly people in two nursing homes in Iran. Data was collected through field notes, observations and semistructured, in-depth interviews. Data was analysed using thematic analysis.

Findings:

There were two main themes of: seeking the embrace of a calm death; and waiting for death. Within these, four subthemes were identified.

Conclusion:

The perceptions of the participants originated from the nursing home culture and their beliefs in eternal life. Training staff about the cultural needs of dying people and end-of-life care would be the most effective way to improve the experience of dying for nursing home residents.
Physico-chemical characterization of hybridized graphene and boron-nitride layers
Authors: MartÃ­nez-Alanis Paulina Raquel , Alvarez de la Paz Antonio , Santamaria Ruben
Published: November 2018

New materials can be created by modifying matter. In this work we characterize graphene and boron-nitride (BN) layers after doping them with BN and carbon dimers, respectively, in diï¬€erent amounts and with diï¬€erent spatial distributions. We provide the energetic description, electron density features, molecular electrostatic potential maps, net charge populations, and the speeds of propagating waves on the hybridized layers. We show the possibility of designing molecular electrostatic potentials from a spatially controlled doping. A strategy is illustrated on a BN hybrid layer with the adsorption of DNA nucleic acid bases.
Tackling domestic abuse locally: paradigms, ideologies and the political tensions of multi-agency working
Authors: Davies Pamela
Published: November 2018

The British government’s strategy to tackle violence against women and girls cements an approach seeking to prevent and protect. Within this context, local initiatives to tackle domestic abuse have proliferated. This article draws on an evaluation of an innovative multi-agency tasking and coordination (MATAC) approach to tackling serial perpetrators. Though the evaluation showed positive outcomes, tensions surfaced within this holistic strategy. In reflecting on the shifting economic and political context in which local agenda setting and commissioning is occurring, perceived concerns about victim safety are reported. Where initiatives have a heightened focus on perpetrators, and in the effort to responsibilise, there are tensions around safeguarding and risk. These are discussed with reference to divergent political cultures and translations of the problem of tackling domestic abuse.
Women Like That: a poetic exploration into the complexities of intimate partner abuse
Authors: Walker Amelia
Published: November 2018

‘Women Like That’ is a poem written after overhearing a stranger say, in reference to domestic abuse, that they couldn’t understand ‘why women like that don’t just get out’. It is based on my personal experiences and, as such, responds to contemporary calls for first-person accounts that go beyond the contemporarily dominant social narratives around intimate partner abuse. The poem is here presented with a contextualising statement that discusses how the poem may be seen to reflect findings and arguments drawn from contemporary scholarly work around intimate partner abuse. The contextualising statement particularly considers contemporary research into issues of coercive control, why some abusees stay or defer leaving, and the challenges of moving forward.
Leukocyte Nucleus Reveals a Linear Order of Chromosomes Separated in Two Parental Genomes That Favors the Process of Gene Activation
Authors: Chaudhuri Jyoti P. , Karamanov Sultan , Scott Liliana , Liehr Thomas , Walther Joachim U.
Published: November 2018

Analysis of trisomy 8 cells and the chromosome-specific fluorescence in situ hybridization (FISH) signals on the ring-shaped nucleus of a neutrophil reveal that homologue chromosomes orient in diametrical opposition to each other. This positioning results in a separation of the two haploid sets of parental chromosomes organized as two exclusive groups. These two groups impart the nucleus a symmetry that fortifies immune protection by accelerating chemotaxis. The ring form of the nucleus is a legacy of the orientation of chromosomes as a rosette during metaphase and telophase stages. A dual control maintains this spatial order: (1) chromosomes are tethered to the centriole all through the cell cycle, and (2) during their circular orientation in telophase the chromosomes bind to each other with lamins, which reorganize the nuclear membrane of the daughter nuclei, generating an additional anchorage. Here, chromosomes serve as temporary packets to assure proper distribution of the nuclear DNA during mitosis. The remainder time of the cell cycle the chromosomes are chained together across the telomeres, allowing a continuous sequence of genes of the two genomes, maternal and paternal, thus facilitating easy reading of the gene sequence. Exceptions to these orders are either physiological and temporary, or pathological and disease causing.
Increased Ferritin Concentration and Risk of Atrial Fibrillation and Heart Failure in Men and Women: Three Studies of the Danish General Population Including 35799 Individuals
Authors: Mikkelsen Lise Fischer , Nordestgaard Børge G , Schnohr Peter , Ellervik Christina
Published: November 2018

BACKGROUND

Moderately increased plasma ferritin, as a biomarker of iron overload, has been associated with higher rates of cardiovascular death and heart failure. However, the association of moderately increased plasma ferritin with risk of atrial fibrillation in the general population is unknown.

METHODS

We examined the association of plasma ferritin concentrations with risk of atrial fibrillation and heart failure in metaanalyses of 35799 men and women from 3 studies of the Danish general population: the Copenhagen City Heart Study, the Danish General Suburban Population Study, and the Copenhagen General Population Study.

RESULTS

Multivariable adjusted fixed effects odds ratios for atrial fibrillation were 1.23 (95% CI, 1.05–1.44; P = 0.005) in men for ferritin concentration ≥300 μg/L vs <300 μg/L, 1.13 (95% CI, 0.93–1.38; P = 0.22) in women for ≥200 μg/L vs <200 μg/L, and 1.19 (95% CI, 1.06–1.35; P = 0.005) in both sexes combined (Psex interaction = 0.52). Corresponding fixed effects odds ratios for heart failure were 1.16 (95% CI, 0.98–1.37; P = 0.08) in men, 0.86 (95% CI, 0.67–1.10; P = 0.23) in women, and 1.05 (95% CI, 0.91–1.21; P = 0.45) in both sexes combined (Psex interaction = 0.05). Multivariable adjusted fixed effects odds ratio for atrial fibrillation per step increase in ferritin concentrations was 1.13 (95% CI, 1.06–1.21; Ptrend = 0.0005) in both sexes combined (Psex interaction = 0.59); the corresponding value for heart failure was 1.03 (95% CI, 0.95–1.11; Ptrend = 0.47) (Psex interaction = 0.08). In sensitivity analyses, there was no evidence of U-shaped relationships between plasma ferritin concentrations and risk of atrial fibrillation or heart failure in men or women.

CONCLUSIONS

Increased ferritin concentration is associated with increased risk of atrial fibrillation in the general population.
Identifying and Eliminating Laboratory Contamination by Topical Testosterone Therapeutics
Authors: Genzen Jonathan R , La'ulu Sonia L , Wyness Sara P , Scholes Kelly L , Signorelli Heather N , Greer Ryan W
Published: November 2018

Many prescription and over-the-counter drugs are available as topical formulations. Contamination of clinical laboratory workspaces by topical drugs may increase the risk of potential interference with diagnostic testing. An example of localized workspace contamination attributed to a topical hormonal drug (testosterone, T) is presented to highlight significant challenges in identifying and resolving this potential problem. Investigation included precision studies, instrument service and parts replacement, instrument replacement, airflow analysis, environmental dust sampling, and the development of customized methods for workspace monitoring and cleaning. Laboratory policies and procedures were also revised to minimize future risk.