bluuebunny/crossref_metadata_2025 huggingface dataset:
Semi-Automated Identification of Ontological Labels in the Biomedical Literature with goldi
Authors: Cole Christopher B. , Patel Sejal , French Leon , Knight Jo
Published: September 2016

Recent growth in both the scale and the scope of large publicly available ontologies has spurred the development of computational methodologies which can leverage structured information to answer important questions. However, ontological labels, or “terms” have thus far proved difficult to use in practice; text mining, one crucial aspect of electronically understanding and parsing the biomedical literature, has historically had difficulty identifying “terms” in literature. In this article, we present goldi, an open source R package whose goal it is to identify terms of variable length in free form text. It is available athttps://github.com/Chris1221/goldior through CRAN. The algorithm works through identifying words or synonyms of words present in individual terms and comparing the number of present words to an acceptance function for decision making. In this article we present the theoretical rationale behind the algorithm, as well as practical advice for its usage applied to Gene Ontology term identification and quantification. We additionally detail the options available and describe their respective computational efficiencies.
Retroviral origins of theCaenorhabditis elegansorphan gene F58H7.5
Authors: Kapulkin Wadim J
Published: September 2016

This work describes the results of the genome-scale analysis of endogenous retrovirus insertions in twoC. elegansisolates: the prototype N2 (Bristol) and CB4856 (Hawaii). In total thirteen, identification of potentially replication competent, endogenous retroviral elements is described. Ten elements were identified as conserved between N2 and CB4856 by the reciprocal match of paired LTRs. The description focuses on the particular endogenous retrovirus insertion wich is identified on the proximal arm of the chromosome IV (located at positions IV: 912,948 – 921,658 and IV: 899,767 – 908,485 of the N2 and CB4856 respectively). In both isolates the inserted provirus is flanked by the predicted long terminal repeats (LTR)s of the length of 415 bp and of identical sequence. Provided the absolute LTR sequence identity this particular provirus represents insertion acquired prior to split from the common ancestor, suggesting this insertion event is evolutionary recent. The identified insertion of the endogenous retrovirus embeds the orphan gene F58H7.5, specific toC. eleganslineage. This unprecedented example establishes that in the evolutionary pastC. elegans, had acquired the gene of the retroviral origins presumably via mechanisms involving the RNA intermediate.

Importance

This work describes the retroviral origins ofC. elegansorphan gene F58H7.5. Presented work implies that in the evolutionary past theC. eleganshave acquired new gene as a result of the infection event.C. elegansis presently regarded as genetic model organism widely used in genetic research. The genome ofC. eleganshave been sequenced nearly 20 years ago. This unprecedented example establishes that in the evolutionary past C. elegans genome, had acquired the gene of the retroviral origins presumably via mechanisms involving the RNA intermediate.
What have single-molecule studies taught us about gene expression?
Authors: Chen Huimin , Larson Daniel R.
Published: September 2016

The production of a single mRNA is the result of many sequential steps, from docking of transcription factors to polymerase initiation, elongation, splicing, and, finally, termination. Much of our knowledge about the fundamentals of RNA synthesis and processing come from ensemble in vitro biochemical measurements. Single-molecule approaches are very much in this same reductionist tradition but offer exquisite sensitivity in space and time along with the ability to observe heterogeneous behavior and actually manipulate macromolecules. These techniques can also be applied in vivo, allowing one to address questions in living cells that were previously restricted to reconstituted systems. In this review, we examine the unique insights that single-molecule techniques have yielded on the mechanisms of gene expression.
Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM)
Authors: Gosselin Pauline , Rando Gianpaolo , Fleury-Olela Fabienne , Schibler Ueli
Published: September 2016

The discovery of transcription factors (TFs) controlling pathways in health and disease is of paramount interest. We designed a widely applicable method, dubbed barcorded synthetic tandem repeat promoter screening (BC-STAR-PROM), to identify signal-activated TFs without any a priori knowledge about their properties. The BC-STAR-PROM library consists of ∼3000 luciferase expression vectors, each harboring a promoter (composed of six tandem repeats of synthetic random DNA) and an associated barcode of 20 base pairs (bp) within the 3′ untranslated mRNA region. Together, the promoter sequences encompass >400,000 bp of random DNA, a sequence complexity sufficient to capture most TFs. Cells transfected with the library are exposed to a signal, and the mRNAs that it encodes are counted by next-generation sequencing of the barcodes. This allows the simultaneous activity tracking of each of the ∼3000 synthetic promoters in a single experiment. Here we establish proof of concept for BC-STAR-PROM by applying it to the identification of TFs induced by drugs affecting actin and tubulin cytoskeleton dynamics. BC-STAR-PROM revealed that serum response factor (SRF) is the only immediate early TF induced by both actin polymerization and microtubule depolymerization. Such changes in cytoskeleton dynamics are known to occur during the cell division cycle, and real-time bioluminescence microscopy indeed revealed cell-autonomous SRF–myocardin-related TF (MRTF) activity bouts in proliferating cells.
Exploring talenting: talent management as a collective endeavour
Authors: Gold Jeff , Oldroyd Tony , Chesters Ed , Booth Amanda , Waugh Adrian
Published: September 2016

Purpose

This paper seeks to show appreciation for the collective endeavour of work practices based on varying degrees of dependence, interdependence and mutuality between at least two people. Such dependencies have to be concerned with how talent is used and how this use is an interaction between people, a process called talenting. The aim of this paper is to provide a method to explore talenting.

Design/methodology/approach

The paper provides a brief overview of recent debates relating to talent management (TM). This paper argues that TM seldom pays attention to work practices where performance is frequently a collective endeavour. A mapping method is explained to identify work practices and obtain narrative data. This paper provides a case to explore talenting in West Yorkshire Police.

Findings

In total, 12 examples are found and 3 are presented showing the value of various forms of dependency to achieve outcomes.

Research limitations/implications

TM needs to move beyond employment practices to work practices. There is a need to close the gap between traditional TM employment practices, usually individually focused, and work practices which are most likely to require a collective endeavour.

Practical implications

There needs be ongoing appreciation of talenting to add to TM activities.

Social implications

This paper recognises a more inclusive approach to TM based on work performance.

Originality/value

This paper, to the best of the authors’s knowledge, is probably the first enquiry of its kind.
Determinants of intention of using mortgage in financing home ownership in Bauchi, Nigeria
Authors: Usman Hamza , Lizam Mohd
Published: September 2016

Purpose

This paper aims to evaluate the bane of home ownership in Nigeria through mortgage financing by examining the determinants of intention of using mortgage in financing home ownership.

Design/methodology/approach

The paper adopted a survey quantitative research design. A total of 235 valid questionnaires randomly distributed were retrieved from 300 potential homeowners who were the sample of the research. Partial least squares-structural equation modeling was used for data analysis and hypotheses testing.

Findings

The findings revealed that religious perception on mortgage was the most significant determinant of intention of using mortgage in financing home-ownership. Subjective norms and perceived behavioral control also have significant effect on intention of using mortgage financing. However, attitude and familiarity/knowledge of mortgage were found not to have a significant effect on intention of using mortgage financing. The determinants cumulatively determined 77.6 per cent (R2 = 0.776) of the variance in intention of using mortgage in financing home ownership.

Practical implications

The research contributed to knowledge and has practical implications to policy makers, mortgage institutions, investors and the society.

Originality/value

The paper uniquely explores the bane of home-ownership through mortgage financing by examining potential home-owners’ intention of using mortgage financing. To authors’ knowledge, this is the first paper to evaluate intention of using mortgage financing, at least in Nigeria.
Challenges in and recommendations for working with international students with first-episode psychosis: a descriptive case series
Authors: Lee Connie , Marandola Gina , Malla Ashok , Iyer Srividya
Published: September 2016

Purpose

The purpose of this paper is to present a series of cases of international students being treated in a specialized early intervention service for first-episode psychosis (FEP), describing the particular challenges that arise in this process, and to provide recommendations addressing these challenges.

Design/methodology/approach

Two researchers independently reviewed the charts of seven international students and discussed them with their treating clinicians. Recurring themes were identified through an iterative process of discussion and consensus.

Findings

Four themes were identified which demonstrated specific challenges faced by international students being treated for FEP: difficulty maintaining student visa status, limited social and family support, financial and health insurance issues, and service disengagement.

Originality/value

The study suggests that international students with FEP may present with numerous and unique challenges, thereby requiring special attention in their treatment. Although these are preliminary findings based on a small case series, the findings can inform recommendations for mental health services in cities with a sizeable international student population and guide future research on this topic.
An agile robot taping system – modeling, tool design, planning and execution
Authors: Yuan Qilong , Chen I-Ming , Lembono Teguh Santoso
Published: September 2016

Purpose

Taping, covering objects with masking tapes, is a common process before conducting surface treatments such as plasma spraying and painting. Manual taping is tedious and takes a lot of effort of the workers. This paper aims to introduce an automatic agile robotic system and corresponding algorithm to do the surface taping.

Design/methodology/approach

The taping process is a special process which requires correct tape orientation and proper allocation of the masking tape for the coverage. This paper discusses on the design of the novel automatic system consisting of a robot manipulator, a rotating platform, a 3D scanner and a specially designed novel taping end-effectors. Meanwhile, the taping path planning to cover the region of interests is introduced.

Findings

Currently, cylindrical and freeform surfaces have been tested. With improvements on new sets of taping tools and more detailed taping method, taping of general surfaces can be conducted using such system in future.

Originality/value

The introduced taping path planning method is a novel method first talking about the mathematical model of the taping process. Such taping solution with the taping tool and the taping methodology can be combined as a very useful and practical taping package to replace the work of human in such tedious and time-consuming works.
Robots collaboration for wearable products lifetime testing
Authors: Mao Hank , Peng Lawrence , Liu Zigui , Zhen Yongkang , Kurwa Murad
Published: September 2016

Purpose

The purpose of this paper is to find a practical and effective way to test wearing product lifetime with two SCARA robots.

Design/methodology/approach

The paper designs a mathematical model to simulate human motion, calculate the coordinate trajectory, then implement with two SCARA robots.

Findings

The two-robot testing platform for wrist band is an effective and precise simulation method and is feasible to deploy in mass production.

Originality/value

The paper introduces a way for apply robots in wearing product lifetime testing which is novel, practical and effective.
Requirements for building an ontology for autonomous robots
Authors: Bayat Behzad , Bermejo-Alonso Julita , Carbonera Joel , Facchinetti Tullio , Fiorini Sandro , Goncalves Paulo , Jorge Vitor A.M. , Habib Maki , Khamis Alaa , Melo Kamilo , Nguyen Bao , Olszewska Joanna Isabelle , Paull Liam , Prestes Edson , Ragavan Veera , Saeedi Sajad , Sanz Ricardo , Seto Mae , Spencer Bruce , Vosughi Amirkhosro , Li Howard
Published: September 2016

Purpose

IEEE Ontologies for Robotics and Automation Working Group were divided into subgroups that were in charge of studying industrial robotics, service robotics and autonomous robotics. This paper aims to present the work in-progress developed by the autonomous robotics (AuR) subgroup. This group aims to extend the core ontology for robotics and automation to represent more specific concepts and axioms that are commonly used in autonomous robots.

Design/methodology/approach

For autonomous robots, various concepts for aerial robots, underwater robots and ground robots are described. Components of an autonomous system are defined, such as robotic platforms, actuators, sensors, control, state estimation, path planning, perception and decision-making.

Findings

AuR has identified the core concepts and domains needed to create an ontology for autonomous robots.

Practical implications

AuR targets to create a standard ontology to represent the knowledge and reasoning needed to create autonomous systems that comprise robots that can operate in the air, ground and underwater environments. The concepts in the developed ontology will endow a robot with autonomy, that is, endow robots with the ability to perform desired tasks in unstructured environments without continuous explicit human guidance.

Originality/value

Creating a standard for knowledge representation and reasoning in autonomous robotics will have a significant impact on all R&A domains, such as on the knowledge transmission among agents, including autonomous robots and humans. This tends to facilitate the communication among them and also provide reasoning capabilities involving the knowledge of all elements using the ontology. This will result in improved autonomy of autonomous systems. The autonomy will have considerable impact on how robots interact with humans. As a result, the use of robots will further benefit our society. Many tedious tasks that currently can only be performed by humans will be performed by robots, which will further improve the quality of life. To the best of the authors’knowledge, AuR is the first group that adopts a systematic approach to develop ontologies consisting of specific concepts and axioms that are commonly used in autonomous robots.
A comparison of industrial robots interface: force guidance system and teach pendant operation
Authors: Rodamilans Guilherme Boulhosa , Villani Emília , Trabasso Luís Gonzaga , Oliveira Wesley Rodrigues de , Suterio Ricardo
Published: September 2016

Purpose

This paper aims to propose an evaluation method to compare two different Human–Robot Interaction (HRI) solutions that can be used for on-line programming in an industrial context: a force guidance system and the traditional teach pendant operation.

Design/methodology/approach

The method defines three evaluation criteria (agility, accuracy and learning) and describes an experimental approach based on the analysis of variance to verify the performance of guidance systems according to these criteria. This method is used in this paper to compare the traditional teach pendant interface with an implementation of a force guidance system based on the use of an external force/torque sensor.

Findings

The application of the proposed method to an off-the-shelf industrial robot shows that the force guidance system has a better performance according to the agility criterion. Both solutions have a similar performance for the accuracy criterion, with a limit of about 2 mm in the achieved position accuracy. Regarding the learning criterion, the authors cannot affirm that any of the methods has an improved agility when the operator repeats the tasks.

Practical implications

This work supports the selection of guidance systems to be used in on-line programming of industrial applications. It shows that the force guidance system is an option potentially faster than the teach pendant when the required positioning accuracy is greater than 2 mm.

Originality/value

The new method proposed in this paper can be applied to a large range of robots, not being limited to commercial available collaborative robots. Furthermore, the method is appropriate to accomplish further investigations in HRI not only to compare programming methods but also to evaluate guidance systems approaches or robot control systems.
Robots poised to revolutionise agriculture
Authors: Bogue Robert
Published: September 2016

Purpose

This paper aims to provide details of a number of recent and significant agricultural robot research and development activities.

Design/methodology/approach

Following an introduction, this first provides a brief overview of agricultural robot research. It then discusses a number of specific activities involving robots for precision weed control and fertiliser application. A selection of harvesting robots and allied technological developments is then considered and is followed by concluding comments.

Findings

Agricultural robots are the topic of an extensive research and development effort. Several autonomous robots aimed at precision weed control and fertiliser application have reached the pre-production stage. Equally, harvesting robots are at an advanced stage of development. Both classes exploit state-of-the-art machine vision and image processing technologies which are the topic of a major research effort. These developments will contribute to the forecasted rapid growth in the agricultural robot markets during the next decade.

Originality/value

Robots are expected to play a significant role in meeting the ever increasing demand for food, and this paper provides details of some recent agricultural robot research and development activities.
The Pransky interview: Professor Jacob Rosen, Co-Founder of Applied Dexterity and ExoSense
Authors: Pransky Joanne
Published: September 2016

Purpose

The following article is a “Q&A interview” conducted by Joanne Pransky of Industrial Robot journal as a method to impart the combined technological, business and personal experience of a prominent, robotic industry engineer-turned-entrepreneur regarding the evolution, commercialization and challenges of bringing a technological invention to market. The paper aims to discuss these issues.

Design/methodology/approach

The interviewee is Jacob Rosen, a Professor of Medical Robotics at the Department of Mechanical and Aerospace Engineering, University of California, Los Angeles (UCLA), where he directs the Bionics Lab. Professor Rosen is also the Director of Surgical Robotics Engineering at the UCLA School of Medicine’s Center for Advanced Surgical and Interventional Technology and has joint appointments at UCLA’s Department of Surgery and UCLA’s Department of Bioengineering. Professor Rosen is the co-founder of the companies Applied Dexterity, ExoSense and SPI. As a pioneer in medical robotics devices and technologies, Professor Rosen describes his unique approaches and philosophies.

Findings

Dr Rosen received his BSc degree in Mechanical Engineering, MSc and PhD degrees in Biomedical Engineering from Tel-Aviv University in 1987, 1993 and 1997, respectively. From 1987 to 1992, he served as an officer in the Israeli Defense Forces studying human–machine interfaces. From 1993 to 1997, he was a research associate at Tel-Aviv University, as well as held a position at a startup company developing innovative orthopedic spine/pelvis implants. From 2001-2013, he held faculty positions at the University of Washington and at University of California, Santa Cruz.

Originality/value

Dr Rosen developed several key systems in the field of medical robotics, such as the Blue and the Red Dragon, for minimally invasive surgical skill evaluation; RAVEN, a surgical robotic system for telesurgery; and several generations of upper and lower limb exoskeletons including the Exo-UL7 – a dual arm wearable robotic system. He is a co-author of 100 manuscripts in the field of medical robotics and a co-author and co-editor of two books entitled “Surgical Robotics – Systems, Applications, and Visions” and “Redundancy in Robot Manipulators and Multi-robot systems” published by Springer. Professor Rosen has filed eight different patent applications and also works as an expert witness and consultant on design, patent protection & litigation and malpractice regarding surgical robotics.
How was competitive advantage sustained in management consultancies during change
Authors: Seyed Kalali Nader , Heidari Ali
Published: September 2016

Purpose

The purpose of this paper is to study the process in which dynamic capabilities renewed operational capabilities to sustain competitive advantage in management consulting firms of Iran during a period of drastic environmental changes.

Design/methodology/approach

Using a grounded theory building approach, comparative longitudinal case analyses were conducted in consultancies of Iran. The research was based on a deep study of documents, observations and interviews with managers and employees of 14 consulting firms.

Findings

It was found that during a period of environmental changes there was a relationship between dynamic capabilities and competitive advantage, but this relationship was mediated by the role of marketing and technological capabilities of a firm. It was also found that trust-building capabilities of the consulting firms moderate the relationship between dynamic and operational capabilities. The research explores homogeneity and heterogeneity of dynamic capabilities among consultancies too.

Originality/value

This research shows that under changing environmental conditions, dynamic capabilities of consultancies can become a source of competitive advantage. Moreover, it discusses whether dynamic capabilities are idiosyncratic or are best practices. It also explains the role of trust-building capabilities of consulting firms in moderating the relationship between dynamic and operational capabilities in the particular environment of Iran.
Modified Dufourmentel flap, easy to design and tailor to the defect
Authors: Imafuku Keisuke , Hata Hiroo , Yamaguchi Yasuyuki , Inamura Yuka , Kitamura Shinya , Yanagi Teruki , Shimizu Hiroshi
Published: September 2016

How to close skin defects is one of the most important considerations for skin surgeons. Rhomboid flaps are used for many types of skin defect. Such flaps, represented by the Limberg and Dufourmentel flaps, are widely used at any region of the body because they are composed of straight lines and are easy to draw. However, these valuable techniques have the disadvantage of being prone to dog‐ears at a particular area of the flap. Therefore, our talented predecessors have modified these flaps in order to resolve the problems. The modified flaps they designed were difficult to draw because the modified designs were curvy and along esthetic lines. It is difficult for trainees to draw these flaps. To address this issue, we have developed newly modified rhomboid flaps that are based on the Dufourmentel flap. This flap is different from the Dufourmentel flap in omitting the top half of the diamond above the circle. Thus, the tension on the skin decreases and dog‐ears are less likely to occur. In addition, our flaps are geometric and easily drawn even by novices. We believe our flap will be a promising option for closing skin defects at any site.
Reproduction by seed and clonality in plants: correlated syndromes or independent strategies?
Authors: Herben Tomáš , Tackenberg Oliver , Klimešová Jitka
Published: September 2016

We examine the relationships of traits of seed reproduction to traits of clonal growth and bud banks. Although there are a number of functional differences between these sets of traits underlying two different modes of reproduction, they both constitute a response to ecological gradients, which makes them potentially interdependent.

We performed phylogenetic regressions of seed traits and traits of bud banks and clonal growth across the Central European flora. We took Ellenberg indicator values and indices of responses to disturbance as information on the positions of species optima along important ecological gradients.

The analyses show that there are almost no relationships between these two groups of traits. This contrasts with the existence of strong correlations within these groups of traits which indicate specific syndromes of seed reproduction and of clonality. Both seed traits and traits of bud banks and clonal growth show fairly strong phylogenetic conservatism.

The absence of correlations between individual groups of traits is at least partly due to the fact that each trait group shows relationships to different parameters of species' niches. Bud bank traits are determined by the disturbance niche of the species, clonal traits by soil and climatic factors, while seed traits show only weak correlations with the examined environmental factors if phylogeny is taken into account.

Synthesis. The absence of integrated syndromes that would cover both seed reproduction and clonality across the flora implies that there are no selective forces that would affect both trait groups simultaneously. Clonal and bud bank traits are more tightly linked to species' niches, presumably because they are selected by local population processes only, in contrast to seed traits, which play a role also in dispersal. As the phylogenetic conservatism of clonal traits is almost as strong as the phylogenetic conservatism of seed traits, these traits do not serve as an evolutionarily more flexible alternative to seed reproduction.
Organ donation agency: A discourse analysis of correspondence between donor and organ recipient families
Authors: Galasiński Dariusz , Sque Magi
Published: September 2016

Studies about the psychosocial issues concerning organ donation and transplantation tend to focus on the experiences of donor or recipient families. Little is known about the part played by correspondence exchanged between these two groups; in particular how they perceive the agency of organ donation. This is the first analysis to address the representation of the act of donation from the viewpoint of both donor and recipient families through interrogation of archived correspondence data, using linguistic techniques. The data was drawn from a collection of letters, from fourUSAorgan procurement organisations, exchanged between donor and transplant recipient families. Donor families consistently linguistically ascribed agency and accountability for donation to the person who died, the donor. For the recipient families, on the other hand, the ‘giver’ was mainly implied, ambiguous or ascribed to the donor family.
Language profiles of poor comprehenders in English and French
Authors: D'Angelo Nadia , Chen Xi
Published: September 2016

This study explored components of language comprehension (vocabulary, grammar, and higher‐level language) skills for poor comprehenders in French immersion. We identified three groups of bilingual comprehenders (poor, average, and good) based on English reading performance and compared their language comprehension skills in English L1 and French L2. We also identified and compared English skills for three groups of monolingual comprehenders from English‐stream programmes. Among both bilingual and monolingual learners, poor comprehenders performed significantly lower than good comprehenders on English vocabulary, morphological awareness, and inference. Bilingual poor comprehenders also differed from average comprehenders on English morphological awareness and inference. Similar results were found in French for the bilingual learners. Lower scores on French vocabulary and morphological awareness distinguished between bilingual poor and good comprehenders. Additionally, weaknesses in French semantics and inference distinguished between bilingual poor and good comprehenders and bilingual poor and average comprehenders. These results suggest that poor comprehenders share remarkably similar language characteristics in L1 and L2.
Fast‐track surgery for uncomplicated appendicitis in children: a matched case–control study
Authors: Cundy Thomas P. , Sierakowski Kyra , Manna Alexandra , Cooper Celia M. , Burgoyne Laura L. , Khurana Sanjeev
Published: September 2016

Background

Standardized post‐operative protocols reduce variation and enhance efficiency in patient care. Patients may benefit from these initiatives by improved quality of care. This matched case–control study investigates the effect of a multidisciplinary criteria‐led discharge protocol for uncomplicated appendicitis in children.

Methods

Key protocol components included limiting post‐operative antibiotics to two intravenous doses, avoidance of intravenous opioid analgesia, prompt resumption of diet, active encouragement of early ambulation and nursing staff autonomy to discharge patients that met assigned criteria. The study period was from August 2015 to February 2016. Outcomes were compared with a historical control group matched for operative approach.

Results

Outcomes for 83 patients enrolled to our protocol were compared with those of 83 controls. There was a 29.2% reduction in median post‐operative length of stay in our protocol‐based care group (19.6 versus 27.7 h; P < 0.001). The rate of discharges within 24 h improved from 12 to 42%. There was no significant difference in complication rate (4.8 versus 7.2%; P = 0.51). Mean oral morphine dose equivalent per kilogram requirement was less than half (46%) that of control group patients (P < 0.001). Mean number of ondansetron doses was also significantly lower. Projected annual direct cost savings following protocol implementation was AUD$77 057.

Conclusion

Implementation of a criteria‐led discharge protocol at our hospital decreased length of stay, reduced variation in care, preserved existing low morbidity, incurred substantial cost savings, and safely rationalized opioid and antiemetic medication. These protocols are inexpensive and offer tangible benefits that are accessible to all health care settings.
Assessing quality of care in oesophago‐gastric cancer surgery in Australia
Authors: Burton Paul R. , Ooi Geraldine J. , Shaw Kalai , Smith Andrew I. , Brown Wendy A. , Nottle Peter D.
Published: September 2016

Background

Outcomes of oesophago‐gastric cancer are poor and highly variable between centres. It is important that complex multimodal treatments are applied optimally. Low case volumes at Australian centres mean that the analysis of crude outcomes is an inadequate assessment of overall quality of care. Detailed analysis across a range of quality domains offers the opportunity to measure performance.

Methods

We compared data from the UK National Oesophago‐gastric Cancer Audit 2010 with the prospective Alfred Hospital oesophago‐gastric cancer database.

Results

There were 314 Alfred and 17 279 UK patients identified. The volume of patients assessed by the Alfred was equal to the second highest quartile in the UK trust (4–5 new cases per month). Case ascertainment was better, capturing 84% of all oesophago‐gastric cancer within the Alfred prospective audit (P < 0.001). The use of staging CT and PET scans was more common among Alfred patients (99% versus 89%, P < 0.01 and 83.8% versus 17%, P < 0.01, respectively). More patients embarked on a curative pathway (P < 0.01), with greater use of neo‐adjuvant therapies. Acceptable lymph node yields were less in oesophagectomies (88.2% versus 96.2%, P < 0.01) and similar in gastrectomies (77.4% versus 74.6%, P = 0.61). Higher overall complications were observed in Alfred patients (P < 0.01), predominantly due to respiratory complications. Perioperative mortality after resection and 1‐year survival was similar.

Conclusions

Comparing a range of quality domains as a means of identifying areas of deficiency is feasible. This allows for contemporaneous improvements in service quality and may be more appropriate in the Australian setting than focusing on volume.
The expression of SFRP1, SFRP3, DVL1, and DVL2 proteins in testicular germ cell tumors
Authors: Fabijanovic Dora , Zunic Iris , Martic Tamara Nikuseva , Skenderi Faruk , Serman Ljiljana , Vranic Semir
Published: September 2016

Germ cell tumors of the testis are a heterogeneous group of neoplasms that affect male adolescents and young adults. Wnt signaling pathway components have been shown to be actively involved in normal and malignant germ cell differentiation and progression. In this study, we aimed to explore the expression patterns of the secreted frizzled‐related protein (SFRP) and Disheveled protein family (DVL) in a subset of testicular germ cell tumors. Eighty‐five formalin‐fixed, paraffin‐embedded tissue samples of the primary germ cell tumors of the testis were stained against SFRP1, SFRP3, DVL1, and DVL2 proteins using immunohistochemistry. SFRP1 and SFRP3 exhibited lower expression in both seminomas and mixed/non‐seminomatous tumors, compared with atrophic/benign tissue (p < 0.001). SFRP3 expression was lower than SFRP1 expression within the seminoma group (p = 0.004), but not within the mixed/non‐seminomatous group (p = 0.409). The majority of the tested cases (27/28, 96%) exhibited low DVL1 protein expression (median 0%, range 0–90%). In contrast, 20 out of 22 tested cases (91%) exhibited strong expression of DVL2 protein (median 80%, range 0–100%). No significant difference in DVL1 and DVL2 protein expression was observed between seminomas and mixed/non‐seminomatous tumors (p = 0.68 and 0.29). The secreted frizzled‐related protein and disheveled protein family members appear to be actively involved in the pathogenesis of primary testicular germ cell tumors.
Estimating plant abundances from crown cover and forest structure data reveals size‐dependent patterns of rarity in subtropical Australia
Authors: McCarthy James K. , Mokany Karel , Dwyer John M.
Published: September 2016

Aims

Accurate field quantification of stem counts is time consuming and laborious, especially in ecosystems containing many small individuals where counts are immense. There are many large, long‐term data sets worldwide that include various measures of woody plant abundance, such as crown cover, that are faster and easier to measure than true counts of individuals. Quantifying the number of individuals allows in‐depth research into various topics including functional ecology, carbon accounting, conservation and metabolic theory. Here we test the accuracy of predicting the abundance of individual woody plants from cover and forest structure measures, and explore the implications of refined abundance measures for understanding the rarity of woody plant species across southeast Queensland.

Location

Southeast Queensland (SEQ), Australia.

Methods

To supplement an existing data set of 1251 sites with measured crown covers for woody plants in various strata, we sampled stem counts in an additional 30 sites, forming a calibration data set. We ensured that these 30 sites covered the environmental variation in the study area. Generalized additive mixed effects models were used to predict stem counts for all woody plants in the original data set from their crown cover and forest structure values and a site‐level variable accounting for water balance. We used these refined abundance data to investigate relationships between local and regional abundance for different size classes.

Results

Stem densities increased with crown cover in a non‐linear fashion; slowing once crown cover reached ca. 5% for shrubs and ca. 50% for trees, depending on their maximum potential height. Using the predicted stem count data, we found that shrubs were more locally abundant than trees, but less regionally abundant. Larger trees (>20 m maximum potential height) showed a negative relationship between local and regional abundance; there was no significant relationship between other size classes.

Conclusions

Our study demonstrates how crown cover can be converted to stem counts using a calibration data set and flexible mixed‐effects models. This enables further ecological analysis at a fraction of the investment required to re‐survey. Analyses of abundances revealed that tree species are less locally abundant than smaller woody species, likely due to space filling constraints, but more regionally abundant.
Sequential Multiple Assignment Randomization Trials with Enrichment Design
Authors: Liu Ying , Wang Yuanjia , Zeng Donglin
Published: September 2016

Sequential multiple assignment randomization trial (SMART) is a powerful design to study Dynamic Treatment Regimes (DTRs) and allows causal comparisons of DTRs. To handle practical challenges of SMART, we propose a SMART with Enrichment (SMARTER) design, which performs stage-wise enrichment for SMART. SMARTER can improve design efficiency, shorten the recruitment period, and partially reduce trial duration to make SMART more practical with limited time and resource. Specifically, at each subsequent stage of a SMART, we enrich the study sample with new patients who have received previous stages’ treatments in a naturalistic fashion without randomization, and only randomize them among the current stage treatment options. One extreme case of the SMARTER is to synthesize separate independent single-stage randomized trials with patients who have received previous stage treatments. We show data from SMARTER allows for unbiased estimation of DTRs as SMART does under certain assumptions. Furthermore, we show analytically that the efficiency gain of the new design over SMART can be significant especially when the dropout rate is high. Lastly, extensive simulation studies are performed to demonstrate performance of SMARTER design, and sample size estimation in a scenario informed by real data from a SMART study is presented.
Estimation of Diagnostic Accuracy of a Combination of Continuous Biomarkers Allowing for Conditional Dependence Between the Biomarkers and the Imperfect Reference-Test
Authors: García Barrado Leandro , Coart Els , Burzykowski Tomasz
Published: September 2016

Estimating biomarker-index accuracy when only imperfect reference-test information is available is usually performed under the assumption of conditional independence between the biomarker and imperfect reference-test values. We propose to define a latent normally-distributed tolerance-variable underlying the observed dichotomous imperfect reference-test results. Subsequently, we construct a Bayesian latent-class model based on the joint multivariate normal distribution of the latent tolerance and biomarker values, conditional on latent true disease status, which allows accounting for conditional dependence. The accuracy of the continuous biomarker-index is quantified by the AUC of the optimal linear biomarker-combination. Model performance is evaluated by using a simulation study and two sets of data of Alzheimer's disease patients (one from the memory-clinic-based Amsterdam Dementia Cohort and one from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database). Simulation results indicate adequate model performance and bias in estimates of the diagnostic-accuracy measures when the assumption of conditional independence is used when, in fact, it is incorrect. In the considered case studies, conditional dependence between some of the biomarkers and the imperfect reference-test is detected. However, making the conditional independence assumption does not lead to any marked differences in the estimates of diagnostic accuracy.
Randomised trial of early infant circumcision performed by clinical officers and registered nurse midwives using the Mogen clamp in Rakai, Uganda
Authors: Kankaka Edward N. , Murungi Teddy , Kigozi Godfrey , Makumbi Frederick , Nabukalu Dorean , Watya Stephen , Kighoma Nehemiah , Nampijja Resty , Kayiwa Daniel , Nalugoda Fred , Serwadda David , Wawer Maria , Gray Ronald H.
Published: September 2016

Objectives

To assess the safety and acceptability of early infant circumcision (EIC) provided by trained clinical officers (COs) and registered nurse midwives (RNMWs) in rural Uganda.

Subjects and Methods

We conducted a randomised trial of EIC using the Mogen clamp provided by newly trained COs and RNMWs in four health centres in rural Rakai, Uganda. The trial was registered with clinicaltrials.gov # NCT02596282. In all, 501 healthy neonates aged 1–28 days with normal birth weight and gestational age were randomised to COs (n = 256) and RNMWs (n = 245) for EIC, and were followed‐up at 1, 7 and 28 days.

Results

In all, 701 mothers were directly invited to participate in the trial, 525 consented to circumcision (74.9%) and 23 were found ineligible on screening (4.4%). The procedure took an average of 10.5 min. Adherence to follow‐up was >90% at all scheduled visits. The rates of moderate/severe adverse events were 2.4% for COs and 1.6% for RNMWs (P = 0.9). All wounds were healed by 28 days after circumcision. Maternal satisfaction with the procedure was 99.6% for infants circumcised by COs and 100% among infants circumcised by RNMWs.

Conclusions

EIC was acceptable in this rural Ugandan population and can be safely performed by RNMWs who have direct contact with the mothers during pregnancy and delivery. EIC services should be made available to parents who are interested in the service.
Implications of different population model structures for management of threatened plants
Authors: Regan Helen M. , Bohórquez Clara I. , Keith David A. , Regan Tracey J. , Anderson Kurt E.
Published: September 2016

Population viability analysis (PVA) is a reliable tool for ranking management options for a range of species despite parameter uncertainty. No one has yet investigated whether this holds true for model uncertainty for species with complex life histories and for responses to multiple threats. We tested whether a range of model structures yielded similar rankings of management and threat scenarios for 2 plant species with complex postfire responses. We examined 2 contrasting species from different plant functional types: an obligate seeding shrub and a facultative resprouting shrub. We exposed each to altered fire regimes and an additional, species‐specific threat. Long‐term demographic data sets were used to construct an individual‐based model (IBM), a complex stage‐based model, and a simple matrix model that subsumes all life stages into 2 or 3 stages. Agreement across models was good under some scenarios and poor under others. Results from the simple and complex matrix models were more similar to each other than to the IBM. Results were robust across models when dominant threats are considered but were less so for smaller effects. Robustness also broke down as the scenarios deviated from baseline conditions, likely the result of a number of factors related to the complexity of the species’ life history and how it was represented in a model. Although PVA can be an invaluable tool for integrating data and understanding species’ responses to threats and management strategies, this is best achieved in the context of decision support for adaptive management alongside multiple lines of evidence and expert critique of model construction and output.
SLEEPWALKING THROUGH SCHOOL: NEW EVIDENCE ON SLEEP AND ACADEMIC ACHIEVEMENT
Authors: Sabia Joseph J. , Wang Kurt , Cesur Resul
Published: September 2016

Policymakers advocating for later school starting times argue that increased sleep duration may generate important schooling benefits. Using data from the National Longitudinal Study of Adolescent Health, this study examines the relationship between sleep duration and academic performance, while carefully controlling for difficult‐to‐measure characteristics at the family and individual levels. We find that increased sleep time is associated with improvements in classroom concentration as well as increased educational attainment. However, we also find evidence of diminishing returns to increased sleep. We estimate an “academic optimum” number of sleep hours of, on average, 8.5 hours per night. Turning to sleep quality, we find that the onset of insomnia‐like symptoms is associated with diminished contemporaneous academic concentration, but little change in long‐run educational attainment. (JEL I12)
Angioimmunoblastic T‐cell lymphoma with a clonal plasma cell proliferation that underwent immunoglobulin isotype switch in the skin, coinciding with cutaneous disease progression
Authors: Suárez Ana E. , Artiga M.J. , Santonja Carlos. , Montes‐Moreno Santiago , De Pablo P. , Requena Luis , Piris Miguel A. , Rodríguez‐Pinilla Socorro M.
Published: September 2016

Plasma cell proliferations in specific cutaneous lesions of angioimmunoblastic T‐cell lymphoma(AITL) are very uncommon. Here, we report a case of clonal plasma cell proliferation in skin with heavy‐chain‐immunoglobulin‐isotype‐switch after cutaneous disease progression. Histopathologically, initial plaque lesions were suggestive of marginal‐zone B‐cell‐lymphoma. Nevertheless, this 77‐year‐old lady was diagnosed with AITL after the progression of skin lesions from plaques to nodular tumors. A lymph node biopsy confirmed the diagnosis. Both cutaneous specimens showed a polymorphic cellular infiltrate with atypical T‐cell‐lymphocytes arranged in a pseudonodular pattern that expressed CD3, PD1 and BCL6, with patchy expression of CD30. Interestingly, a slight IgG‐Lambda plasma cell component was seen at the periphery of the infiltrate in the first specimen which increased in number in the later nodular lesion, showing not only Lambda light chain restriction and IgG but also IgG4. PCR studies for IgH and TCR genes showed an IgH clonal peak on both skin lesions but not on lymph node biopsy. On the contrary, the same clonal TCR peak was found in the three specimens. Neoplastic follicular helper T‐cells within cutaneous‐specific microenvironment could be responsible for the modulation of the immunoglobulin isotype class switch change. Further studies are needed to support this hypothesis.
ENTRY BARRIERS, COMPETITION, AND TECHNOLOGY ADOPTION
Authors: Fang Lei
Published: September 2016

I build a model of technology adoption to study the quantitative effect of entry barriers on total factor productivity (TFP). In my model, incumbent firms choose technologies that are sufficiently productive to deter entry from a potential competitor. I show that higher entry barriers help to deter entry and lead to the choice of less productive technologies. A novelty of my work is that I use a direct measure of entry barriers. I find that reducing entry barriers from their average level in the poorest 30% of countries to their U.S. level leads to a sizeable increase in aggregate TFP of 12%. (JEL O11, O43)