bluuebunny/crossref_metadata_2025 huggingface dataset:
Curriculum design for research-led teaching: Molecule to Malady
Authors: Cain Helen , Strugnell Richard , Hollande Frederic
Published: April 2016

Modern medicine is increasingly characterised by a personalised approach to treatment through producing therapies that target specific biological processes. When planning the new Bachelor of Biomedicine (BBiomed) degree, one of two completely new undergraduate courses crafted as part of the ‘Melbourne Curriculum’ introduced by The University of Melbourne in 2008, the paradigm that medical interventions should be evidence-based and driven by a molecular understanding of the cause of disease was a key design parameter. Our intention in developing the curriculum for Biomedicine: Molecule to Malady (M2M), a third-year compulsory capstone subject of this new BBiomed degree, was to enhance the ability of students to apply their core cross-disciplinary knowledge to unfamiliar problems in translational medicine by having expert clinicians/researchers explain the scientific reasoning applied to the development of disease interventions in their specialist areas.
Effects of amino acid mutations in the pore-forming domain of the hemolytic lectin CEL-III
Authors: Nagao Tomonao , Masaki Risa , Unno Hideaki , Goda Shuichiro , Hatakeyama Tomomitsu
Published: April 2016

The hemolytic lectin CEL-III forms transmembrane pores in the membranes of target cells. A study on the effect of site-directed mutation at Lys405 in domain 3 of CEL-III indicated that replacements of this residue by relatively smaller residues lead to a marked increase in hemolytic activity, suggesting that moderately destabilizing domain 3 facilitates formation of transmembrane pores through conformational changes.
To the question about the states of workability for automatic control systems with complicated structure
Authors: Kuznetsov P A , Kovalev I V , Losev V V , Kalinin A O , Murygin A V
Published: April 2016

The article discusses the reliability of automated control systems. Analyzes the approach to the classification systems for health States. This approach can be as traditional binary approach, operating with the concept of "serviceability", and other variants of estimation of the system state. This article provides one such option, providing selective evaluation of components for the reliability of the entire system. Introduced description of various automatic control systems and their elements from the point of view of health and risk, mathematical method of determining the transition object from state to state, they differ from each other in the implementation of the objective function. Explores the interplay of elements in different States, the aggregate state of the elements connected in series or in parallel. Are the tables of various logic States and the principles of their calculation in series and parallel connection. Through simulation the proposed approach is illustrated by finding the probability of getting into the system state data in parallel and serially connected elements, with their different probabilities of moving from state to state. In general, the materials of article will be useful for analyzing of the reliability the automated control systems and engineering of the highly-reliable systems. Thus, this mechanism to determine the State of the system provides more detailed information about it and allows a selective approach to the reliability of the system as a whole. Detailed results when assessing the reliability of the automated control systems allows the engineer to make an informed decision when designing means of improving reliability.
Pediatric orthopedic surgical simulation at Boston Children’s Hospital
Authors: Bae Donald S. , Waters Peter M.
Published: April 2016

Orthopedic surgical simulation has become an increasing valuable means for optimizing patient care, promoting patient safety, improving education, and fostering clinical research. The purpose of this review was to discuss the rationale for simulation training, describe current simulation efforts within the Department of Orthopaedic Surgery at Boston Children’s Hospital, and provide an example of how these simulation efforts touch both patient care and clinical research.
Acute distal biceps rupture in an adolescent weightlifter on chronic steroid suppression: a case report
Authors: Ding David Y. , LaMartina Joey A. , Zhang Alan L. , Pandya Nirav K.
Published: April 2016

Distal biceps tendon ruptures are uncommon events in the adult population and exceedingly rare in the adolescent population. To the best of our knowledge, this is the first and only report of a distal biceps tendon rupture in an adolescent with a history of chronic corticosteroid suppression. We present a case of a 17-year-old male on chronic corticosteroid suppression who underwent a successful distal biceps tendon repair after an acute rupture following weightlifting. At the 1-year follow-up, the patient reports full range of motion and strength, and is able to return to his preinjury activity level with sports and weightlifting. Acute distal biceps ruptures are uncommon injuries in the pediatric population, but may occur in conjunction with chronic corticosteroid use. Anatomic repair, when possible, can restore function and strength. Level of Evidence: level IV, case report
Postoperative Symptomatic Anterior Spinal Epidural Hematoma
Authors: González-Diaz Rafael , Auñon-Martin Ismael , Ortega-Garcia Francisco Javier , da Rocha Rui Miguel Reis
Published: April 2016

Study Design.

A case report.

Objective.

We describe a technique to drain a thoracic and cervical postoperative epidural hematoma causing paraplegia after anterior cervical discectomy and fusion.

Summary of Background Data.

Postoperative compressive spinal epidural hematoma (SEH) is a devastating complication and early diagnosis and treatment is essential. The most commonly accepted treatment is decompression and drainage of hematoma.

Methods.

A 65-year-old male with a degenerative disc disease located at C4-C5, C5-C6, and C6-C7 levels with disc herniation underwent a standard anterior cervical decompression and fusion at C4-C5-C6-C7. Three hours after the procedure, the patient started complaining of progressive paraplegia and affectation of upper extremity. A magnetic resonance imaging (MRI) revealed a postoperative SEH extending from C3 to T6, causing compression.

To resolve this unusual complication, a new surgery was performed. An anterior approach through the previous one was performed, and a C6 corpectomy was done. The anterior epidural hematoma was drained with an elastic urinary catheter. At the end of the surgery, a tricortical iliac crest autograft was placed between C5-C7 and the plate was placed as previously.

Results.

The patient recovered tactile and vibratory senses, as well as motor function in both hands 12 hours after the second procedure. The complete drainage of the hematoma was MRI-verified the first postoperative day.

The patient was discharged from the hospital presenting a complete sensitive recovery and a 3/5 of muscle recovery. At one year, the patient made a full recovery and was able to walk unassisted.

Conclusion.

The treatment of choice in SEH is the early decompression as complete as possible, usually with the same approach or at the level of major compression. In rare cases like this, we recommend the use of an elastic catheter to complete hematoma drainage, distant from the surgical wound.

Level of Evidence: N/A
Does Early Surgical Decompression in Cauda Equina Syndrome Improve Bladder Outcome?
Authors: DeLong W. Bradford , Polissar Nayak L. , Neradilek Moni B. , Laam Leslie A.
Published: April 2016

Study Design and Objectives.

This study by Srikandarajah et al is a retrospective cohort study of 200 CES patients. Although parts of the study appear to be well done we identified serious problems that impacted their conclusions.

Summary of Background Data.

There is strong consensus that patients with incomplete cauda equina syndrome (CESI) should be operated upon expeditiously to prevent progression to CES with urinary retention (CESR). There is controversy concerning optimal timing of surgery in patients who have entered CESR. Some studies conclude urgent surgery for CESR does nothing to improve chance of recovery; others conclude surgery should be done within a 48 or 24-hours window after onset of bladder paralysis. Srikandarajah et al concluded that in CESI patients, decompressive surgery within 24 hours of onset of autonomic symptoms reduces bladder dysfunction at follow-up. In CESR patients, “no statistically significant difference in outcome was observed” regarding timing of surgery.

Methods.

We analyzed the methods used by Srikandarajah et al to collect and analyze their data.

Results.

The primary problem with their study is that it does not consider deterioration to CESR that occurs in CESI patients over time. We also found serious problems with the methods, implementation (including numeric errors), and interpretation of the statistical analysis.

Conclusion.

The authors’ conclusion that in CESR patients, “no statistically significant difference in outcome was observed” regarding timing of surgery is not justified as a representation of their findings, because absence of statistical significance does not mean acceptance of the null hypothesis of “no effect”. Their numeric results do show elevated risk of delay. We do not want to detract from the basic importance of this study, because it emphasizes the importance of operating expeditiously on patients with CESI. However, the authors’ conclusions are compromised by the methodological problems.

Level of Evidence: N/A
Defining Sepsis Mortality Clusters in the United States*
Authors: Moore Justin Xavier , Donnelly John P. , Griffin Russell , Howard George , Safford Monika M. , Wang Henry E.
Published: April 2016

Objectives:

In the United States, sepsis is a major public health problem accounting for over 200,000 annual deaths. The aims of this study were to identify U.S. counties with high sepsis mortality and to assess the community characteristics associated with increased sepsis mortality.

Design:

We performed a descriptive analysis of 2003 through 2012 Compressed Mortality File data. We defined sepsis deaths as deaths associated with an infection, classified according to the International Classification of Diseases, 10th Version.

Setting:

Three thousand one hundred and eight counties in the contiguous U.S. counties, excluding Hawaii and Alaska.

Measurements and Main Results:

Using geospatial autocorrelation methods, we defined county-level sepsis mortality as strongly clustered, moderately clustered, and nonclustered. We approximated the mean crude, age-adjusted, and community-adjusted sepsis mortality rates nationally and for clustering groups. We contrasted demographic and community characteristics between clustering groups. We performed logistic regression for the association between strongly clustered counties and community characteristics. Among 3,108 U.S. counties, the age-adjusted sepsis mortality rate was 59.6 deaths per 100,000 persons (95% CI, 58.9–60.4). Sepsis mortality was higher in the Southern U.S. and clustered in three major regions: Mississippi Valley, Middle Georgia, and Central Appalachia. Among 161 (5.2%) strongly clustered counties, age-adjusted sepsis mortality was 93.1 deaths per 100,000 persons (95% CI, 90.5–95.7). Strongly clustered sepsis counties were more likely to be located in the south (92.6%; p < 0.001), exhibit lower education, higher impoverished population, without medical insurance, higher medically uninsured rates, and had higher unemployment rates (p < 0.001).

Conclusions:

Sepsis mortality is higher in the Southern United States, with three regional clusters: “Mississippi Valley,” “Middle Georgia,” and “Central Appalachia”: Regions of high sepsis mortality are characterized by lower education, income, employment, and insurance coverage.
Emergency Cerclage: Outcomes, Patient Selection, and Operative Considerations
Authors: NAQVI MARIAM , BARTH WILLIAM H.
Published: April 2016

Emergency cerclage refers to a cerclage placed during the second trimester in a woman noted to have painless cervical dilation. Although randomized-controlled trials are limited, observational studies suggest an improvement in neonatal outcomes in selected patients undergoing an emergency cerclage. Labor and chorioamniontis are contraindications for cerclage placement. Advanced dilation (>3 to 4 cm) and a later gestational age (22 to 24 wk) are associated with poorer outcomes. This chapter reviews the indications, outcomes and perioperative management strategies for cerclage placement in this setting.
Risk Management and Medico-Legal Issues in Breast Cancer
Authors: WARD CHARLES J. , GREEN VICTORIA L.
Published: April 2016

Breast cancer is a leading source of malpractice claims for radiologists and gynecologists. Delay in or failure to diagnosis was the second most common cause for allegations of malpractice and failure to diagnosis breast cancer accounted for the majority of these claims. The amount paid in indemnity for such claims was only second to claims paid for neurologically impaired newborns. Issues involved in documentation and communication are reviewed with a focus on specific medical legal cases. Obstetrician gynecologists must remain cognizant of the potential for liability.
Controversies in Screening Mammography
Authors: SWAIN MONIQUE , JEUDY MYRLENE , PEARLMAN MARK D.
Published: April 2016

The utility and effectiveness of screening mammography in diagnosing breast cancer at earlier stages and reducing disease-specific mortality remain controversial especially as to when to start and stop routine mammographic screening, and whether mammograms should be performed annually or biennially in average-risk women. This manuscript will analyze the available moderate and high-quality data to analyze both the benefits (lives saved and life-years saved) and inconveniences/harms (additional views, extra biopsies/overdiagnosis, and overtreatment of ductal carcinoma in situ) of different mammography screening guidelines to assist the practitioner in counseling their patients in clinical practice.
Differentiated Vulvar Intraepithelial Neoplasia: What Criteria Do We Use in Practice?
Authors: Reutter Jason C. , Walters Ruth A. , Selim M. Angelica
Published: April 2016

Objectives

We sought to recognize the working diagnostic criteria for differentiated vulvar intraepithelial neoplasia (dVIN) among expert pathologists in the field. We also sought the frequency of definitive diagnosis, terminology of equivocal lesions, and views on dVIN’s biological significance.

Methods

Respondents ranked 26 histological and 8 ancillary studies and 5 clinical findings as “essential,” “nonessential but strongly supports diagnosis,” “possibly supports diagnosis,” “weighs against diagnosis” or “uncertain significance or noncontributory.” Consensus was defined as 75% agreement. They were asked about diagnosing dVIN on partially sampled lesions, terminology for uncertain lesions, frequency of diagnosis of dVIN relative to uncertain lesions, and if dVIN a is a precursor to an invasion.

Results

Twenty-three completed the survey. Only “basal layer atypia” met consensus (86%) as essential. Consensus criteria for being at least strongly supportive of dVIN were “basal layer hyperchromasia,” “presence of basal layer mitoses,” and “large keratinocytes with abundant eosinophilic cytoplasm.” Only “block-like positivity with p16” or positive HPV specific studies weighed against the diagnosis by consensus. Approximately 87% diagnosed dVIN on partially sampled lesions. Squamous cell hyperplasia with atypia was the most frequent terminology used for uncertain lesions; 87% felt dVIN is a precursor to invasion.

Conclusions

Only basal layer atypia was considered diagnostically essential by consensus. Additional criteria that strongly support the diagnosis include changes affecting the basal layer and abundant eosinophilic keratinocytic cytoplasm. There was no consensus on ancillary study findings to confirm dVIN. Most would diagnose dVIN on a partial sample. Most consider dVIN a precursor to invasion.
Correlation Between Aeroallergen Levels and New Diagnosis of Eosinophilic Esophagitis in New York City
Authors: Fahey Lisa , Robinson Guy , Weinberger Kate , Giambrone Ashley E. , Solomon Aliza B.
Published: April 2016

Objective:

The relation between food allergies and eosinophilic esophagitis (EoE) is well established. Aeroallergens may also contribute to the development of EoE; however, there are limited data to support or refute this hypothesis. The objectives of this pilot study were to determine whether there is a seasonal variation in the onset of symptoms and/or diagnosis of EoE and whether these variations correlate with a specific pollen concentration within New York City.

Methods:

We performed a retrospective chart review to identify all pediatric patients at New York Presbyterian Weill Cornell Medical Center diagnosed with EoE between 2002 and 2012. Sixty‐six patients were identified and 28 were excluded. Cases were classified by both date of initial symptoms and date of histologic diagnosis. Pollen counts from a certified New York City counting station and the percentage of EoE cases were collated monthly and seasonally and compared.

Results:

There was a seasonal variation in onset of symptoms and diagnosis of EoE, with the highest number of patients reporting onset of symptoms of EoE in July to September, and those being diagnosed with EoE in October to December. There was a seasonal correlation between peak levels of grass pollen and peak onset of EoE symptoms, which were both highest in July to September. The diagnosis of EoE peaked one season later.

Conclusions:

The study findings suggest that there is a correlation between specific aeroallergens and both the onset of symptoms and time of diagnosis of patients with EoE.
Facilitators and Hindrances of Implementing Colorectal Cancer Screening Intervention Among Vietnamese Americans
Authors: Sin Mo-Kyung , Yip Mei-Po , Kimura Amanda , Tu Shin-Ping
Published: April 2016

Background:

Little is published about the factors that facilitate and hinder the intervention implementation process.

Objective:

The aim of this study was to examine factors that facilitated and hindered the implementation of a culturally appropriate colorectal cancer screening intervention targeting Vietnamese Americans in a Federally Qualified Health Center located in the Puget Sound area of Washington.

Methods:

Three focus group discussions (2 during the implementation phase and 1 during the maintenance phase) with the medical assistants (N = 13) who were the intervention implementation agents were conducted at the Federally Qualified Health Center. Three research team members independently analyzed the data using content analysis and then compared for agreement. We reread and recoded the transcripts until consensus was reached. The themes were clustered by similar codes and categorized into 4 groups, each including facilitators and hindrances of implementation: identification of implementation agents, implementation environment, intervention recipients, and the colorectal cancer screening intervention.

Results:

Facilitators included medical assistants’ high motivation with a positive attitude toward the intervention, team approach, and simplicity of the intervention, whereas hindrances included lack of time, forgetfulness, staff turnover, and language barriers.

Conclusion:

The findings emphasized the importance of supporting implementation agents to ensure effective intervention program implementation.

Implications for Practice:

Oncology nurses need to particularly take into consideration the evidence-based findings when planning any intervention programs.
Posttraumatic Stress Disorder Symptoms and Social and Occupational Functioning of People With Schizophrenia
Authors: Ng Lauren C. , Petruzzi Liana J. , Greene M. Claire , Mueser Kim T. , Borba Christina P.C. , Henderson David C.
Published: April 2016

This study sought to clarify the contribution of posttraumatic stress disorder (PTSD) to interpersonal and occupational functioning in people with schizophrenia. Self-report questionnaires and semistructured interviews were used to evaluate PTSD and brain injury, positive symptoms, depression, substance abuse, occupational and social functioning, and intelligence. Multiple regressions assessed the relationship between predictors and functional impairment. Posttraumatic stress disorder symptoms were present in 76% of participants, with 12% of participants meeting diagnostic criteria for PTSD. Participants with PTSD had higher rates of depression and more severe positive symptoms. Results of multiple regressions indicated that PTSD symptoms were the only significant predictor of patient-rated interpersonal and occupational functioning. Posttraumatic stress disorder symptoms were not associated with interviewer-rated interpersonal or occupational functioning or employment. While more research is needed, screening and treatment for exposure to traumatic events and PTSD symptoms might be indicated for individuals with schizophrenia. Availability of PTSD assessment and evidence-based treatments for people with schizophrenia is a crucial and often unmet health service need.
Single Viral Load Measurements Overestimate Stable Viral Suppression Among HIV Patients in Care: Clinical and Public Health Implications
Authors: Marks Gary , Patel Unnati , Stirratt Michael J. , Mugavero Michael J. , Mathews William C. , Giordano Thomas P. , Crepaz Nicole , Gardner Lytt I. , Grossman Cynthia , Davila Jessica , Sullivan Meg , Rose Charles E. , O'Daniels Christine , Rodriguez Allan , Wawrzyniak Andrew J. , Golden Matthew R. , Dhanireddy Shireesha , Ellison Jacqueline , Drainoni Mari-Lynn , Metsch Lisa R. , Cachay Edward R.
Published: April 2016

Background:

The HIV continuum of care paradigm uses a single viral load test per patient to estimate the prevalence of viral suppression. We compared this single-value approach with approaches that used multiple viral load tests to examine the stability of suppression.

Methods:

The retrospective analysis included HIV patients who had at least 2 viral load tests during a 12-month observation period. We assessed the (1) percent with suppressed viral load (<200 copies/mL) based on a single test during observation, (2) percent with suppressed viral loads on all tests during observation, (3) percent who maintained viral suppression among patients whose first observed viral load was suppressed, and (4) change in viral suppression status comparing first with last measurement occasions. Prevalence ratios compared demographic and clinical subgroups.

Results:

Of 10,942 patients, 78.5% had a suppressed viral load based on a single test, whereas 65.9% were virally suppressed on all tests during observation. Of patients whose first observed viral load was suppressed, 87.5% were suppressed on all subsequent tests in the next 12 months. More patients exhibited improving status (13.3% went from unsuppressed to suppressed) than worsening status (5.6% went from suppressed to unsuppressed). Stable suppression was less likely among women, younger patients, black patients, those recently diagnosed with HIV, and those who missed ≥1 scheduled clinic visits.

Conclusions:

Using single viral load measurements overestimated the percent of HIV patients with stable suppressed viral load by 16% (relative difference). Targeted clinical interventions are needed to increase the percent of patients with stable suppression.
Nonclotted Blood Patch Technique Reduces Pneumothorax and Chest Tube Placement Rates After Percutaneous Lung Biopsies
Authors: Clayton Joshua D. , Elicker Brett M. , Ordovas Karen G. , Kohi Maureen P. , Nguyen Janet , Naeger David M.
Published: April 2016

Purpose:

The aim of this study was to determine whether autologous nonclotted blood patch decreases pneumothorax and chest tube placement rates in computed tomography–guided biopsies of the lung.

Materials and Methods:

Percutaneous computed tomography–guided lung biopsies performed over a period of 6 years were retrospectively reviewed to determine the overall rates of pneumothorax and chest tube placement and rates before and after the autologous nonclotted blood patch procedure was instituted as a departmental policy. The effect of the intervention was only assessed in patients in whom a blood patch could be applied, therefore only when the needle traversed an aerated lung and only when the needle remained in the lung at the end of the study.

Results:

There was a statistically significant decrease in both the rate of pneumothorax [28% (69/245) vs. 42% (80/189); P=0.002] and chest tube placement [4% (10/245) vs. 16% (30/189); P<0.001] in patients who received nonclotted blood patch versus those who did not. Blood patch was performed in 222/312 (71%) eligible patients after the introduction of the blood patch policy. After policy introduction, there was a decreased rate of pneumothorax, with a rate of 32% (101/312) versus 40% (49/122) (P=0.12) and a statistically significant decrease in departmental chest tube placement rates of 6% (20/312) versus 16% (20/122) (P=0.001).

Conclusions:

Nonclotted autologous blood patch for percutaneous lung biopsy resulted in significantly decreased pneumothorax and chest tube placement rates in our patient population.
Fundamentals of cutting
Authors: Williams J. G. , Patel Y.
Published: April 2016

The process of cutting is analysed in fracture mechanics terms with a view to quantifying the various parameters involved. The model used is that of orthogonal cutting with a wedge removing a layer of material or chip. The behaviour of the chip is governed by its thickness and for large radii of curvature the chip is elastic and smooth cutting occurs. For smaller thicknesses, there is a transition, first to plastic bending and then to plastic shear for small thicknesses and smooth chips are formed. The governing parameters are tool geometry, which is principally the wedge angle, and the material properties of elastic modulus, yield stress and fracture toughness. Friction can also be important. It is demonstrated that the cutting process may be quantified via these parameters, which could be useful in the study of cutting in biology.
Dental abrasion as a cutting process
Authors: Lucas Peter W. , Wagner Mark , Al-Fadhalah Khaled , Almusallam Abdulwahab S. , Michael Shaji , Thai Lidia A. , Strait David S. , Swain Michael V. , van Casteren Adam , Renno Waleed M. , Shekeban Ali , Philip Swapna M. , Saji Sreeja , Atkins Anthony G.
Published: April 2016

A mammalian tooth is abraded when a sliding contact between a particle and the tooth surface leads to an immediate loss of tooth tissue. Over time, these contacts can lead to wear serious enough to impair the oral processing of food. Both anatomical and physiological mechanisms have evolved in mammals to try to prevent wear, indicating its evolutionary importance, but it is still an established survival threat. Here we consider that many wear marks result from a cutting action whereby the contacting tip(s) of such wear particles acts akin to a tool tip. Recent theoretical developments show that it is possible to estimate the toughness of abraded materials via cutting tests. Here, we report experiments intended to establish the wear resistance of enamel in terms of its toughness and how friction varies. Imaging via atomic force microscopy (AFM) was used to assess the damage involved. Damage ranged from pure plastic deformation to fracture with and without lateral microcracks. Grooves cut with a Berkovich diamond were the most consistent, suggesting that the toughness of enamel in cutting is 244 J m
−2
, which is very high. Friction was higher in the presence of a polyphenolic compound, indicating that this could increase wear potential.
Cutting science in biology and engineering
Authors: Williams J. G. , Atkins A. G. , Charalambides M. N. , Lucas P. W.
Published: April 2016

On 26–27 October 2015, the Theo Murphy international scientific meeting on ‘Cutting science in biology and engineering’ was held at the Kavli Royal Society Centre, Chicheley Hall, Buckinghamshire, UK. The meeting was organized by Professor Gordon Williams FREng FRS, Professor Tony Atkins FREng, Professor Peter Lucas and Dr Maria Charalambides and it was enabled through the Royal Society scientific programme. It connected scientists from diverse backgrounds and disciplines including Biology and Mechanical Engineering from around the world.
Inferring intrinsic and extrinsic noise from a dual fluorescent reporter
Authors: van Nimwegen Erik
Published: April 2016

Dual fluorescent reporter constructs, which measure gene expression from two identical promoters within the same cell, allow total gene expression noise to be decomposed into an extrinsic component, roughly associated with cell-to-cell fluctuations in cellular component concentrations, and intrinsic noise, roughly associated with inherent stochasticity of the biochemical reactions involved in gene expression [1]. A recent paper by Fu and Pachter presented frequentist statistical estimators for intrinsic and extrinsic noise using data from dual reporters [2]. For comparison, I here present results of a Bayesian analysis of this problem. I show that the orthodox estimators suffer from pathologies such as predicting negative values for a manifestly non-negative quantity, i.e. variance, and show that the Bayesian estimators do not suffer from such pathologies. In addition, I show that the Bayesian analysis automatically identifies that optimal estimates of intrinsic and extrinsic noise depend on a subtle combination of two statistics of the data, allowing for accuracies that are up to twice the accuracy of the orthodox estimators in some parameter regimes.

I hope up this little worked out example contrasting orthodox statistical analysis based on ad hoc estimators with estimators resulting from a Bayesian analysis, will be educational for others in the field. I distribute a Mathematica Notebook with this paper that allows users to easily reproduce all results and figures of the paper.
Mortality Selection in a Genetic Sample and Implications for Association Studies
Authors: Domingue Benjamin W. , Belsky Daniel W. , Harrati Amal , Conley Dalton , Weir David , Boardman Jason
Published: April 2016

Mortality selection is a general concern in the social and health sciences. Recently, existing health and social science cohorts have begun to collect genomic data. Causes of selection into a genomic dataset can influence results from genomic analyses. Selective non-participation, which is specific to a particular study and its participants, has received attention in the literature. But mortality selection—the very general phenomenon that genomic data collected at a particular age represents selective participation by only the subset of birth cohort members who have survived to the time of data collection—has been largely ignored. Here we test the hypothesis that such mortality selection may significantly alter estimates in polygenetic association studies of both health and non-health traits. We demonstrate mortality selection into genome-wide SNP data collection at older ages using the U.S.-based Health and Retirement Study (HRS). We then model the selection process. Finally, we test whether mortality selection alters estimates from genetic association studies. We find evidence for mortality selection. Healthier and more socioeconomically advantaged individuals are more likely to survive to be eligible to participate in the genetic sample of the HRS. Mortality selection leads to modest drift in estimating time-varying genetic effects, a drift that is enhanced when estimates are produced from data that has additional mortality selection. There is no general solution for correcting for mortality selection in a birth cohort prior to entry into a longitudinal study. We illustrate how genetic association studies using HRS data can adjust for mortality selection from study entry to time of genetic data collection by including probability weights that account for mortality selection. Mortality selection should be investigated more broadly in genetically-informed samples from other cohort studies.
Hybrid reciprocal lattice: application to layer stress determination in GaAlN/GaN(0001) systems with patterned substrates
Authors: Domagała Jarosław Z. , Morelhão Sérgio L. , Sarzyński Marcin , Maździarz Marcin , Dłużewski Paweł , Leszczyński Michał
Published: April 2016

Epitaxy of semiconductors is a process of tremendous importance in applied science and in the optoelectronics industry. The control of defects introduced during epitaxial growth is a key point in manufacturing devices of high efficiency and durability. In this work, it is demonstrated how useful hybrid reflections are for the study of epitaxial structures with anisotropic strain gradients due to patterned substrates. High accuracy in detecting and distinguishing elastic and plastic relaxations is one of the greatest advantages of measuring this type of reflection, as well as the fact that the method can be exploited in a symmetric reflection geometry on a commercial high-resolution diffractometer.
A crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualization
Authors: Junius Niels , Oksanen Esko , Terrien Maxime , Berzin Christophe , Ferrer Jean-Luc , Budayova-Spano Monika
Published: April 2016

Many instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.
Crystal structure of ketopantoate reductase fromThermococcus kodakarensiscomplexed with NADP+
Authors: Aikawa Yoshiki , Nishitani Yuichi , Tomita Hiroya , Atomi Haruyuki , Miki Kunio
Published: April 2016

Coenzyme A (CoA) plays pivotal roles in a variety of metabolic pathways in all organisms. The biosynthetic pathway of CoA is strictly regulated by feedback inhibition. In the hyperthermophilic archaeonThermococcus kodakarensis, ketopantoate reductase (KPR), which catalyzes the NAD(P)H-dependent reduction of 2-oxopantoate, is a target of feedback inhibition by CoA. The crystal structure of KPR fromT. kodakarensis(Tk-KPR) complexed with CoA and 2-oxopantoate has previously been reported. The structure provided an explanation for the competitive inhibition mechanism. Here, further biochemical analyses of Tk-KPR and the crystal structure of Tk-KPR in complex with NADP+are reported. A mutational analysis implies that the residues in the binding pocket cooperatively contribute to the recognition of CoA. The structure reveals the same dimer architecture as the Tk-KPR–CoA–2-oxopantoate complex. Moreover, the positions of the residues involved in the dimer interaction are not changed by the binding of CoA and 2-oxopantoate, suggesting individual conformational changes of Tk-KPR monomers.
Structural and functional insights into the stationary-phase survival protein SurE, an important virulence factor ofBrucella abortus
Authors: Tarique K. F. , Abdul Rehman S. A. , Devi S. , Tomar Priya , Gourinath S.
Published: April 2016

The stationary-phase survival protein SurE fromBrucella abortus(BaSurE) is a metal-dependent phosphatase that is essential for the survival of this bacterium in the stationary phase of its life cycle. Here, BaSurE has been biochemically characterized and its crystal structure has been determined to a resolution of 1.9 Å. BaSurE was found to be a robust enzyme, showing activity over wide ranges of temperature and pH and with various phosphoester substrates. The active biomolecule is a tetramer and each monomer was found to consist of two domains: an N-terminal domain, which forms an approximate α + β fold, and a C-terminal domain that belongs to the α/β class. The active site lies at the junction of these two domains and was identified by the presence of conserved negatively charged residues and a bound Mg2+ion. Comparisons of BaSurE with its homologues have revealed both common features and differences in this class of enzymes. The number and arrangement of some of the equivalent secondary structures, which are seen to differ between BaSurE and its homologues, are responsible for a difference in the size of the active-site area and the overall oligomeric state of this enzyme in other organisms. As it is absent in mammals, it has the potential to be a drug target.
(4-Aminosulfonylphenyl)[(2-oxidonaphthalen-1-yl)imino]azanium
Authors: Benosmane A. , Rouag D. A. , Mili A. , Merazig H. , Benaouida M. A.
Published: April 2016

The crystal structure of the title compound, C16H13N3O3S, shows that the two independent zwitterions in the asymmetric unit are approximately planar. Intramolecular N—H...O hydrogen bonds occur and the aromatic rings have atransconfiguration with respect to the azo double bond. In the crystal, the molecules are linkedviaN—H...O hydrogen bonds and π–π stacking, forming a three-dimensional supramolecular network, the π–π stacking interactions between adjacent benzene and naphthalene rings having centroid-to-centroid distances of 3.764 (3) and 3.775 (3) Å.
Climate change perception and choice of adaptation strategies
Authors: Tesfaye Wondimagegn , Seifu Lemma
Published: April 2016

Purpose

– The purpose of this paper is to analyze smallholder farmers’ perceptions of climate change and its adverse effects, identify major adaptation strategies used by farmers and analyze the factors that influence the choice of adaptation strategy by smallholder farmers in eastern Ethiopia.

Design/methodology/approach

– The study was based on a cross-sectional survey of 296 sample households selected from three districts in east Ethiopia. Data were collected with the aid of a semi-structured questionnaire and review of literature, documents and databases.

Findings

– The study provides empirical evidence that majority of farmers in the study area are aware of climate change patterns and their adverse effect on income, food security, diversity, forest resources, food prices and crop and livestock diseases. In response to these adverse effects, major adaptation strategies used by farmers include cultivating different crops, planting different crop varieties, changing planting dates, use of soil and water conservation techniques, conservation agriculture practices and engaging in non-farm income activities. Choice of adaptation strategies are influenced by gender of household head, household size, farm size, distance from market and number of farm plots.

Practical implications

– The study suggests that developing more effective climate change adaptation strategies need support from the government. Such an effort needs provision of the necessary resources such as credit, information and extension services on climate change adaptation strategies and technologies, and investing in climate smart and resilient projects.

Originality/value

– The study adopts multivariate probit model that models farmers’ simultaneous adaptation choice behavior which has been rarely addressed by previous researches.
Anticipatory adaptation and the role of decadal climate information in rural African livelihood systems
Authors: Nyamwanza Admire M. , New Mark
Published: April 2016

Purpose

– This study aims to explore the utility of anticipatory adaptation to climate variability and related livelihood sensitivities in rural African contexts using the case of Mbire district situated in the mid-Zambezi valley region of Zimbabwe. The provision of decadal climate information (up to ten years), as part of an anticipatory adaptation package, is at the centre of analysis.

Design/methodology/approach

– The study used semi-structured and key informant interviews, with a total of 45 semi-structured interviews being conducted with randomly selected long-term communal farmers in the case study area. Whilst data from semi-structured interviews was arranged in Microsoft Excel, thematic analysis was used in analyzing all data.

Findings

– Anticipatory adaptation and decadal climate projections are shown to potentially enhance flexibility in adaptation planning vis- à-vis responding to climate variability and other challenges, as well as reduce chances of maladaptation in responding to climate challenges in the context of multiple and reinforcing stresses and shocks.

Originality/value

– Anticipatory adaptation, with its three main pillars of future analysis, flexibility of strategies and proactive action, is emerging as key in assisting adaptation planning, the harnessing of opportunities and decision-making vis- à-vis responding to climate uncertainties and related livelihood sensitivities. Yet there have not been much empirically grounded analyses in understanding the role of anticipatory adaptation in rural Africa. This study therefore adds to evidence-based analyses towards understanding the role and utility of anticipatory adaptation in local communities in Africa.
A guide to clarifying evidence in Australian child forensic interviews
Authors: Burrows Kimberlee S. , Powell Martine B. , Benson Mairi
Published: April 2016

Purpose

– Interviewing victims of child sex abuse requires considerable care in order to minimise error. Due to children’s heightened suggestibility any question asked of a child could potentially incite error that could undermine the witness’s credibility. A focus group was conducted in order to facilitate the development of guidance for interviewers around the circumstances in which it is necessary to ask children follow-up questions in an interview. The paper aims to discuss these issues.

Design/methodology/approach

– Seven Crown prosecutors representing every Australian state and territory (with the exception of one small state) were issued with 25 hypothetical narrative accounts of child abuse and asked to indicate what information, if any, required follow-up in the child’s narrative. Their responses and rationale for requiring following up in some cases and not others were discussed.

Findings

– Thematic analysis revealed three recommendations to guide questioning: whether the case involved identification or recognition evidence; the presence of contextual features that may influence the witness’s memory, or that should trigger a particular line of questioning; and whether the information can or should be sought at a later stage by the trial prosecutor, rather than by the interviewer.

Practical implications

– The recommendations are discussed within the context of their implications for interviewing, that is, how each recommendation could be implemented in practice.

Originality/value

– The present study extends prior literature by elucidating principles to guide decision making across interview topic areas. The need for such guidance is highlighted by research suggesting that topics such as offender identity, offence time and place, and witnesses are a source of overzealous questioning in interviews.
A SWOT analysis of reliability centered maintenance framework
Authors: Gupta Gajanand , Mishra Rajesh P
Published: April 2016

Purpose

– The purpose of this paper is to use well-established methodology strengths, weaknesses, opportunities and threats (SWOT) analysis – in order to identify the important factors for reliability centered maintenance (RCM) implementation.

Design/methodology/approach

– The paper demonstrates a SWOT analysis for different 19 frameworks of RCM to make a strategic decision for implementing RCM in different organizations. The various 19 frameworks are grouped together into three clusters, namely Group A, Group B and Group C based on their qualitative or theoretical, quantitative and practical approach, respectively.

Findings

– The strengths and weaknesses are identified by internal factors while the opportunities and threats are identified by external factors of an organization for each group of frameworks. Also, it was observed that each group of frameworks has a unique set of strengths and weaknesses.

Research limitations/implications

– In this paper, the SWOT analysis for RCM implementation is limited to the comparison of various 19 RCM frameworks which are available in literatures and based on internal or external factors of an organization.

Practical implications

– The SWOT analysis also suggests that the implementation of RCM is not an easy task for any practitioner and one should weigh in all the opportunities and threats before arriving at any strategic decision.

Originality/value

– A unique approach applied to analysis the frameworks of RCM. The SWOT analysis of various RCM frameworks will help the practitioner to take any strategic decision for RCM implementation in an organization.
Representation of replacement rules in the form of a matrix
Authors: Golovin Sergey
Published: April 2016

Purpose

– The purpose of this paper is to represent replacement policies (rules) in the form of a matrix. Visualization of replacement rules is useful for maintenance records. Matrix representation is more effective than the verbal description usually provided, as it allows better understanding of the specifics of the different replacement rules without careful research of their mathematical models.

Design/methodology/approach

– This approach employs mathematical models to investigate the simple conditions (requirements) for replacement of system component with illustrative examples. When comparing the different replacement rules a cost structure is applied to takes into account the nature and technology of disassembly assembly actions for the repair unit.

Findings

– Representation of replacement rules in the matrix form is useful when describing planned replacement models, opportunity replacement models, group replacement models and others, as well as computer modeling of the renewal process. Forming simple conditions for the replacement of system components ensures the total average repair cost is minimized. These conditions can be applied in the early stages of creating a maintenance program for the machine.

Practical implications

– Replacement matrices can be specified in a technical manual for maintenance of machines to achieve reliable operation and to reduce repair costs. Replacement matrices can be put into practical use for maintenance records and may be included in the maintenance procedures library of CMMSs. Developed in the paper, the replacement matrix, the conditions for replacement of system components and the cost structure will help engineers to make decisions at the time of repair for assembly units.

Originality/value

– Proposed in the paper is a new approach to the visualization of the replacement rules and cost structure which simplifies the analysis of options for repair actions. The proposed technique contributes to the record of maintenance actions and the decision making process for replacement.