bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing wetland climate change vulnerability for wetland management decision support using the hydrogeological landscape framework: application in the Australian Capital Territory
Authors: Cowood A. L. , Young J. , Dowling T. I. , Moore C. L. , Muller R. , MacKenzie J. , Littleboy M. , Nicholson A. T.
Published: September 2018

The hydrogeological landscape (HGL) framework provides a landscape characterisation method that identifies areas of similar physical, hydrogeological, hydrological, chemical and biological properties, referred to as HGL units. The underlying principle of the HGL framework is that water distribution and movement is controlled by climate, landform, geology, regolith, soil and vegetation properties. By understanding the patterns of variability in the setting and controls of atmospheric, surface and groundwater systems for a given landscape, the developed HGL units, and associated landscape element-based management areas, can be used for hazard assessment and natural resource management centred on water availability, quality, sustainability and associated ecological systems. Existing wetland frameworks also demonstrate that it is the hydrogeomorphological or hydrogeological characteristics of the landscape that will determine the variability in water inputs and outputs for a wetland water balance, a principle shared with the HGL framework. It is therefore logical that HGL units and management areas can be used as planning units for wetland hazard assessment and management. This paper presents an assessment of climate change vulnerability for 1296 wetlands across the Australian Capital Territory using indicators representing current anthropogenic pressure, future ecological change and future hydrological change. The use of management areas for the hazard assessment allows understanding of the patterns of variability in the chosen indicators and hazard assessment outcomes specifically for the areas to be managed. This approach allows consideration of the landscape setting when identifying suitable locations to undertake on-ground management actions to address the hazards identified.
Axonal plasticity associated with perceptual learning in adult macaque primary visual cortex
Authors: van Kerkoerle Timo , Marik Sally A. , Meyer zum Alten Borgloh Stephan , Gilbert Charles D.
Published: September 2018

Significance

Perceptual learning is a form of memory involving improvement in the ability to detect or discriminate between sensory stimuli. Encoding learned information requires plasticity of cortical circuits. Physiological studies have suggested that even the earliest stages in sensory cortical processing show functional changes associated with perceptual improvements. Previously, we have shown experience-dependent change in cortical circuits associated with retinal lesions that can account for functional adaptation to CNS lesions. Here, we have studied whether these changes are also associated with normal visual experience, specifically with perceptual learning. We found that during the course of perceptual learning axon collaterals in primary visual cortex (V1) undergo sprouting and pruning, suggesting how V1 is engaged in encoding learned information.
From personal narrative to global call for action
Authors: Mustafa Balsam
Published: September 2018

This paper examines personal narratives and how they change according to the context in which they are narrated. In particular, it argues that personal narratives change as they are mediated by various discourses, genres and modes, as well as by the peculiarities that emerge when speaking and writing in different languages and when undertaking translation. It uses a case-study approach to analyse the different narratives told by Islamic State’s Yezidi female survivor, and United Nations Goodwill ambassador, Nadia Murad, in different contexts in 2014 and in2015. In 2014, when two Western mass media outlets interviewed Murad, her narrative was compacted and less detailed. This shifted in December2015when Murad testified about her ordeal before the Security Council. Mediated by the discourse of the latter and by the genre of testimony, Murad’s narrative became more detailed, and transformed from a description of a personal suffering into a call for action.
Moving music for moving source texts
Authors: Naranjo Sánchez Beatriz
Published: September 2018

Based on previous findings about the role of music as an emotional stimulus, as well as the potential benefits of music-driven emotional engagement in written production and creative behaviour, the present study investigates the impact of emotional background music on translation quality and creativity. A translation experiment in two different conditions (music vs. silence) was conducted in a controlled environment. Participants translated two literary texts of opposing emotional contents (happy vs. sad) while they listened to an emotionally-matching soundtrack. Statistical analysis of within- and between-group comparisons only revealed conclusive results for the sad condition, showing a positive effect of sad music on translation creativity and a negative effect on accuracy.
Severn Sound Remedial Action Plan: The friendly little monster
Authors: Sherman R. Keith , Whittam Robert , Cayley Julie
Published: September 2018

The Severn Sound Remedial Action Plan began as a federal-provincial initiative and became a “friendly little monster” when the community of small urban centers and rural townships took their responsibility seriously and became fully committed to the restoration of Severn Sound as a “toxic hot-spot” on the Great Lakes. Severn Sound is a complex of bays and inlets in south-eastern Georgian Bay. The Area of Concern was listed in 1985 because of eutrophication and habitat loss. This article will explore the changes in organizational structure supporting Remedial Action Plan development and implementation from an external federal-provincial program to a local organization supported by a variety of partners. Key principles of funding the remedial actions and administration of the local Severn Sound Environmental Association will be highlighted. This transition led to successful implementation and ultimate delisting of the Area of Concern in 2003. Following delisting, creative local partnership agreements and financing were arranged to continue long-term implementation and to meet emerging environmental challenges.
Introduction
Authors: Marten James
Published: September 2018

Although the biological facts of being a child have remained largely the same, philosophers and theologians, reformers and policymakers, educators and scholars have, over the last few centuries, come to varying conclusions about the meaning of childhood and the place of children in society. Childhood is a social construction, shaped by local conditions, beliefs, and needs, as well as time. As a result, it is important that while children are a relatively unchanging fact of life, childhood is a constantly shifting concept. The Introduction explains that there are many histories of childhood, although a few general concepts and facts loosely bind them together.
1. Introduction to Africa and its politics
Authors: Taylor Ian
Published: September 2018

Africa is a continent of over a billion people, yet questions of underdevelopment, malgovernance, and a form of political life based upon patronage are characteristic of many African states. ‘Introduction to Africa and its politics’ explains that the core questions underpinning this VSI centre on how politics is typically practised on the continent; the nature of the state in Africa; and what accounts for Africa’s underdevelopment. This VSI aims to appraise sub-Saharan Africa’s recent political history, examining post-colonial political structures, the impact of colonialism, and the form and nature of post-colonial states. The type of politics practised in many African states continues to be hostile to genuine nation building and broad-based, sustainable development.
3. The transfer of power and the colonial legacy
Authors: Taylor Ian
Published: September 2018

Colonialism profoundly transformed African political, economic, and social structures. The exploitation of Africa’s labour and natural resources for the benefit of the metropoles was to have intense implications for the continent as it emerged towards independence in the 1960s as, in most cases, the foundations necessary for the construction of sovereign, economically viable, and politically stable African states did not exist. ‘The transfer of power and the colonial legacy’ describes how the European powers left most of their colonial possessions unprepared for self-rule. The key colonial legacy was economic, which massively influenced the political realm. Initial state and nation building encouraged the centralization of power and creation of political monopolies.
4. The primacy of patronage politics
Authors: Taylor Ian
Published: September 2018

A great number of post-colonial African countries, bounded by formal frontiers and with an international presence at various international institutions such as the United Nations, function quite differently from conventional understandings of what a formal state is and should do. ‘The primacy of patronage politics’ explains that to understand African politics, the concept of neo-patrimonialism must be considered. Neo-patrimonialism is where patronage, clientelism, and rent-seeking exist, but where the structures of a modern state are also in place. In general, post-colonial African leaders have relied on coercive control and patronage through capturing power over the state, rather than through constructing a functioning impartial administration.
6. The role of identity in African politics
Authors: Taylor Ian
Published: September 2018

‘The role of identity in African politics’ explains that identity politics are symptoms of Africa’s underdevelopment, not the cause, and the prominence of such political mobilization reflects much deeper structural problems facing many post-colonial states. Before the colonial era, African societies were based on notions of identity, such as the family, ancestral lineage, the clan, or the community. Colonial rule forced together different communities (some of which were traditionally hostile to each other) and was mainly responsible for producing the situation found today where very few nation states exist. Colonial authorities concretized differences among and between the subjugated and the de-colonization period further contributed to the politicization of identity.
7. The military in African politics
Authors: Taylor Ian
Published: September 2018

Since the 1960s, there have been more than 200 coups—extra-constitutional or forced changes in government—in Africa, with around half of them being successful. The period between the 1960s and 1990s was characterized by Cold War machinations, economic crises, and the growing de-legitimization of many post-colonial regimes. The majority of coups were followed by the formation of some type of military government, but after this diverse outcomes resulted. ‘The military in African politics’ outlines the nature of military rule and why there were so many coups. The fragility of the state and its tenuous hold on legitimacy, accentuated by the behaviour of those in power, is of critical importance.
Sociology: A Very Short Introduction
Authors: Bruce Steve
Published: September 2018

Drawing on studies of social class, crime and deviance, education, work in bureaucracies, and changes in religious and political organizations, Sociology: A Very Short Introduction explores the tension between the individual’s place in society and society’s role in shaping the individual, and demonstrates the value of sociology for understanding the modern world. It outlines the unique vision of sociology and shows that much social theory is actually philosophy or literary theory. It discusses the continuing arguments for social egalitarianism, considering issues such as gay marriage, women in combat roles, and the 2010 Equality Act to debunk contemporary arguments against parity, and looks at the likely consequences for society as gender divisions are increasingly questioned.
Causes and consequences
Authors: Bruce Steve
Published: September 2018

One of the ways that sociology differs from common sense is in challenging the image of ourselves as authors of our own thoughts and actions. If there is to be any explanation of human behaviour, there must be regular patterns to life and those regularities will be partly caused by forces outside our control and cognition. ‘Causes and consequences’ explains that if we wish to understand what people are doing and why, we must be interested in their motives and intentions, in how they see the world. But if we wish to understand why the world is as it is, we need to be concerned with unintended and unanticipated consequences.
6. The Blessed Virgin Mary
Authors: Yarrow Simon
Published: September 2018

The Blessed Virgin Mary is pre-eminent among Christian saints. Her giving birth to Jesus the God-man distinguishes her from other women, even as it draws attention to that experience uniquely distinguishing women from men: childbirth. ‘The Blessed Virgin Mary’ shows how this delicate partitioning of empathetic possibilities in the veneration of Mary, intimately grounded in biology and played out through ideas of gender difference, has stimulated profound and sometimes conflicted religious emotions in men and women. St Mary presents a conundrum to Christian theology: a virgin mother, a Jew who became a Christian, a redeemer of humanity from Eve’s sins, a human who gave birth to God, and the Queen of Heaven.
Epidemiology of Diabetic Foot Infection in the Metro-Detroit Area With a Focus on Independent Predictors for Pathogens Resistant to Recommended Empiric Antimicrobial Therapy
Authors: Henig Oryan , Pogue Jason M , Cha Raymond , Kilgore Paul E , Hayat Umar , Ja’ara Mahmoud , Ali Raza Muhamad , Mahboob Salman , Pansare Rahul , Deeds Kathryn , Joarder Bushra , Kandala Hyndavi , Dhar Sorabh , Kaye Keith S
Published: September 2018

Background

The polymicrobial nature of diabetic foot infection (DFI) and the emergence of antimicrobial resistance have complicated DFI treatment. Current treatment guidelines for deep DFI recommend coverage of methicillin-resistant Staphylococcus aureus (MRSA) and susceptible Enterobacteriaceae. This study aimed to describe the epidemiology of DFI and to identify predictors for DFI associated with multidrug-resistant organisms (MDROs) and pathogens resistant to recommended treatment (PRRT).

Methods

Adult patients admitted to Detroit Medical Center from January 2012 to December 2015 with DFI and positive cultures were included. Demographics, comorbidities, microbiological history, sepsis severity, and antimicrobial use within 3 months before DFI were obtained retrospectively. DFI-PRRT was defined as a DFI associated with a pathogen resistant to both vancomycin and ceftriaxone. DFI-MDRO pathogens included MRSA in addition to PRRT.

Results

Six-hundred forty-eight unique patients were included, with a mean age of 58.4 ± 13.7 years. DFI-MDRO accounted for 364 (56%) of the cohort, and 194 (30%) patients had DFI-PRRT. Independent predictors for DFI-PRRT included history of PRRT in a diabetic foot ulcer, antimicrobial exposure in the prior 90 days, peripheral vascular disease, and chronic kidney disease. Long-term care facility residence was independently associated with DFI due to ceftriaxone-resistant Enterobacteriaceae, and recent hospitalization was an independent predictor of DFI due to vancomycin-resistant Enterococcus.

Conclusions

An unexpectedly high prevalence of DFI-PRRT pathogens was identified. History of the same pathogen in a prior diabetic foot ulcer and recent antimicrobial exposure were independent predictors of DFI-PRRT and should be considered when selecting empiric DFI therapy.
A Connectomic Atlas of the Human Cerebrum—Chapter 2: The Lateral Frontal Lobe
Authors: Baker Cordell M , Burks Joshua D , Briggs Robert G , Conner Andrew K , Glenn Chad A , Morgan Jake P , Stafford Jordan , Sali Goksel , McCoy Tressie M , Battiste James D , O’Donoghue Daniel L , Sughrue Michael E
Published: September 2018

In this supplement, we show a comprehensive anatomic atlas of the human cerebrum demonstrating all 180 distinct regions comprising the cerebral cortex. The location, functional connectivity, and structural connectivity of these regions are outlined, and where possible a discussion is included of the functional significance of these areas. In part 2, we specifically address regions relevant to the lateral frontal lobe.
A Connectomic Atlas of the Human Cerebrum—Chapter 5: The Insula and Opercular Cortex
Authors: Baker Cordell M , Burks Joshua D , Briggs Robert G , Conner Andrew K , Glenn Chad A , Robbins Justin M , Sheets John R , Sali Goksel , McCoy Tressie M , Battiste James D , O’Donoghue Daniel L , Sughrue Michael E
Published: September 2018

In this supplement, we build on work previously published under the Human Connectome Project. Specifically, we show a comprehensive anatomic atlas of the human cerebrum demonstrating all 180 distinct regions comprising the cerebral cortex. The location, functional connectivity, and structural connectivity of these regions are outlined, and where possible a discussion is included of the functional significance of these areas. In part 5, we specifically address regions relevant to the insula and opercular cortex.
A Connectomic Atlas of the Human Cerebrum—Chapter 9: The Occipital Lobe
Authors: Baker Cordell M , Burks Joshua D , Briggs Robert G , Stafford Jordan , Conner Andrew K , Glenn Chad A , Sali Goksel , McCoy Tressie M , Battiste James D , O’Donoghue Daniel L , Sughrue Michael E
Published: September 2018

In this supplement, we build on work previously published under the Human Connectome Project. Specifically, we seek to show a comprehensive anatomic atlas of the human cerebrum demonstrating all 180 distinct regions comprising the cerebral cortex. The location, functional connectivity, and structural connectivity of these regions are outlined, and where possible a discussion is included of the functional significance of these areas. In part 9, we specifically address regions relevant to the occipital lobe and the visual system.
A Connectomic Atlas of the Human Cerebrum—Chapter 10: Tractographic Description of the Superior Longitudinal Fasciculus
Authors: Conner Andrew K , Briggs Robert G , Rahimi Meherzad , Sali Goksel , Baker Cordell M , Burks Joshua D , Glenn Chad A , Battiste James D , Sughrue Michael E
Published: September 2018

The superior longitudinal fasciculus/arcuate white matter complex (SLF/AC) is the largest and most complex white matter tract of the human cerebrum with multiple inter-linked connections encompassing multiple cognitive functions such as language, attention, memory, emotion, and visuospatial function. However, little is known regarding the overall connectivity of this complex. Recently, the Human Connectome Project parcellated the human cortex into 180 distinct regions. Utilizing diffusion spectrum magnetic resonance imaging tractography coupled with the human cortex parcellation data presented earlier in this supplement, we aim to describe the macro-connectome of the SLF/AC in relation to the linked parcellations present within the human cortex. The purpose of this study is to present this information in an indexed, illustrated, and tractographically aided series of figures and tables for anatomic and clinical reference.
A Connectomic Atlas of the Human Cerebrum—Chapter 15: Tractographic Description of the Uncinate Fasciculus
Authors: Briggs Robert G , Rahimi Meherzad , Conner Andrew K , Sali Goksel , Baker Cordell M , Burks Joshua D , Glenn Chad A , Battiste James D , Sughrue Michael E
Published: September 2018

In this supplement, we show a comprehensive anatomic atlas of the human cerebrum demonstrating all 180 distinct regions comprising the cerebral cortex. The location, functional connectivity, and structural connectivity of these regions are outlined, and where possible a discussion is included of the functional significance of these areas. In this chapter, we specifically address the regions integrating to form the uncinate fasciculus.
Police Cybercrime Training: Perceptions, Pedagogy, and Policy
Authors: Cockcroft Tom , Shan-A-Khuda Mohammad , Schreuders Z Cliffe , Trevorrow Pip
Published: September 2018

Cybercrime presents numerous issues for police organizations. A key challenge is to understand how best to impart relevant skills and knowledge about cybercrime throughout the organization to enable police officers to react appropriately to such incidents. This article is drawn from research undertaken as part of the CARI Project, a major study into the effectiveness of cybercrime investigation within a large UK police force funded by the Police Knowledge Fund. As part of the needs assessment for the above project, concerns were raised about the effectiveness of existing training arrangements in facilitating the development of cyber skills within police officers. The present research, based on survey data, explored the effectiveness of different training styles as perceived by those who had undertaken cyber training. The research found that officers perceived some modes of training as more effective than others and highlighted some of the organizational contexts that impact negatively on the delivery of effective cyber training. The findings are presented within a context, informed by existing literature, that acknowledges wider debates surrounding the pedagogy of police learning and the organizational challenges of developing cyber skills within police officers. The authors believe that the findings will have relevance to police training policy both in the UK and in the wider international context.
New applications of sonoelastography in rheumatology: where are we now?
Authors: Martins-Rocha Teresa , Azzolin Irene , Serban Teodora , Massazza Giuseppe , Iagnocco Annamaria
Published: September 2018

Ultrasound elastography (UE) is a non-invasive imaging method that allows the assessment of tissue elastic property. Different UE techniques are currently available (i.e. strain UE and acoustic radiation force impulse UE), with several potential clinical applications. Recent studies investigated the role of UE in two systemic rheumatic diseases and psoriasis. This research added interesting information to the already known applications of UE in the assessment of tendinopathies. In SS, acoustic radiation force impulse UE has shown a potential role in the diagnosis of the disease, with lower sensitivity than and similar specificity to salivary gland histology. In SSc, a potential use of UE in screening pre-clinical disease has been reported. In psoriasis, the use of strain UE in evaluating treatment response has been highlighted. UE is a promising tool in rheumatology, with a potential role in the evaluation of various tissues and pathologies.
Medial Approach for Total Elbow Arthroplasty: A New Surgical Technique for Tumor Resection and Joint Replacement
Authors: Vajapey Sravya , Mayerson Joel L.
Published: September 2018

Total elbow arthroplasty (TEA) is a procedure that has become more frequently performed in the United States in the recent years. One of the most common complications associated with this procedure is related to the surgical approach. All the approaches described to date in the literature have been posterior approaches to the elbow. Depending on how the extensor mechanism is approached, there is usually some loss of range of motion and extension strength postoperatively. In addition a significant amount of physical therapy is often necessary in order to achieve maximal postoperative range of motion. We describe for the first time a medial approach to the elbow/distal humerus for TEA that preserves full range of motion and extension strength. Although this approach may not be appropriate for all patients undergoing TEA, it is quite useful in procedures requiring a wide field of exposure of the elbow joint such as malignant neoplasms or extensively comminuted distal humerus fractures.
A Novel Technique to Remove Posterior Intra-Articular Bodies Within the Hip Through an Anterior Approach
Authors: Davis Elissa S. , Strotman Patrick K. , Killen Cameron , Lack William D.
Published: September 2018

Removal of foreign and loose bodies form the hip joint classically involves arthroscopic approaches or surgical dislocation of the hip. However, traumatic injuries associated with loose or foreign bodies are often best treated via an anterior approach. Retrieving intra-articular foreign bodies through an anterior approach can be challenging even for the most experienced surgeon. We describe 2 cases of hip intra-articular foreign body removal through an anterior approach utilizing a Satinsky vascular clamp under fluoroscopic guidance.
Overachieving Municipalities in Public Health: A Machine-learning Approach
Authors: Chiavegatto Filho Alexandre Dias Porto , dos Santos Hellen Geremias , do Nascimento Carla Ferreira , Massa Kaio , Kawachi Ichiro
Published: September 2018

Background:

Identifying successful public health ideas and practices is a difficult challenge towing to the presence of complex baseline characteristics that can affect health outcomes. We propose the use of machine learning algorithms to predict life expectancy at birth, and then compare health-related characteristics of the under- and overachievers (i.e., municipalities that have a worse and better outcome than predicted, respectively).

Methods:

Our outcome was life expectancy at birth for Brazilian municipalities, and we used as predictors 60 local characteristics that are not directly controlled by public health officials (e.g., socioeconomic factors).

Results:

The highest predictive performance was achieved by an ensemble of machine learning algorithms (cross-validated mean squared error of 0.168), including a 35% gain in comparison with standard decision trees. Overachievers presented better results regarding primary health care, such as higher coverage of the massive multidisciplinary program Family Health Strategy. On the other hand, underachievers performed more cesarean deliveries and mammographies and had more life-support health equipment.

Conclusions:

The findings suggest that analyzing the predicted value of a health outcome may bring insights about good public health practices.
The Association Between Childhood Leukemia and Population Mixing
Authors: Berrie Laurie , Ellison George T.H. , Norman Paul D. , Baxter Paul D. , Feltbower Richard G. , Tennant Peter W.G. , Gilthorpe Mark S.
Published: September 2018

Background:

Studies investigating the population-mixing hypothesis in childhood leukemia principally use two analytical approaches: (1) nonrandom selection of areas according to specific characteristics, followed by comparisons of their incidence of childhood leukemia with that expected based on the national average; and (2) regression analyses of region-wide data to identify characteristics associated with the incidence of childhood leukemia. These approaches have generated contradictory results. We compare these approaches using observed and simulated data.

Methods:

We generated 10,000 simulated regions using the correlation structure and distributions from a United Kingdom dataset. We simulated cases using a Poisson distribution with the incidence rate set to the national average assuming the null hypothesis that only population size drives the number of cases. Selection of areas within each simulated region was based on characteristics considered responsible for elevated infection rates (population density and inward migration) and/or elevated leukemia rates. We calculated effect estimates for 10,000 simulations and compared results to corresponding observed data analyses.

Results:

When the selection of areas for analysis is based on apparent clusters of childhood leukemia, biased assessments occur; the estimated 5-year incidence of childhood leukemia ranged between zero and eight per 10,000 children in contrast to the simulated two cases per 10,000 children, similar to the observed data. Performing analyses on region-wide data avoids these biases.

Conclusions:

Studies using nonrandom selection to investigate the association between childhood leukemia and population mixing are likely to have generated biased findings. Future studies can avoid such bias using a region-wide analytical strategy. See video abstract at, http://links.lww.com/EDE/B431.
Testing Differential Associations Between Smoking and Chronic Disease Across Socioeconomic Groups
Authors: de Mestral Carlos , Bell Steven , Stamatakis Emmanuel , Batty G. David
Published: September 2018

Background:

For the same quantity of cigarettes smoked, relative to more affluent people, socioeconomically disadvantaged people have higher levels of smoking biomarkers. This may be ascribed to inhaling cigarette smoke more deeply and more frequently and/or choosing higher tar-containing brands. We investigated whether this increased tobacco load, as captured using cotinine measurements, is associated with a greater risk of mortality in lower social groups.

Methods:

We used Cox proportional hazards models stratified by socioeconomic position to calculate hazard ratios in a pooled sample of 15 English and Scottish prospective cohort studies (N = 81,476).

Results:

During a mean (SD) follow-up of 10.3 (4.4) years, 8234 deaths occurred. Risk of total mortality (hazard ratio; 95% confidence interval) for smokers relative to never-smokers in the high (2.5; 2.1, 3.1), intermediate (2.1; 1.8, 2.4), and low (2.0; 1.9, 2.2) educational groups did not differ markedly (P for interaction=0.61). Similar findings emerged when using cause-specific outcomes and occupational social class and housing tenure as socioeconomic indices.

Conclusion:

Contrary to our hypothesis, we found no indication that chronic disease mortality associated with smoking was higher in disadvantaged people.
The Impact of Nurses' Uniforms on Nurse-Patient Interactions
Authors: Tam Wai Yi , Ng Deborah Li Li , Kowitlawakul Yanika
Published: September 2018

OBJECTIVES

The aim of this study was to explore patients' perceptions toward the nursing uniforms used in a hospital in Singapore and how different uniforms impact nurse-patient interactions.

BACKGROUND

Nursing uniforms act as a form of nonverbal communication. However, implications of the increasing variety of nursing uniforms on patients' perceptions of nurses and nurse-patient interactions are unexplored.

METHODS

An exploratory qualitative study design using semistructured interviews was adopted for the study. Twenty-one patients agreed to be interviewed. An audio recorder was used during data collection. The thematic analysis method was used for data analysis.

RESULTS

Four major themes were identified: identity, subjectivity, suitability, and inconsequential. Nurses' uniform was regarded as a representation of identity. Suitability of the uniform for nurses was a main concern for patients. However, nurses' uniforms were inconsequential to nurse-patient interactions.

CONCLUSION

Patients' perceptions of nurses' uniforms were highly subjective and have no substantial impact on nurse-patient interactions.
V-Mart, a Virtual Reality Grocery Store
Authors: Levy Charles E. , Miller David M. , Akande Christiana A. , Lok Benjamin , Marsiske Michael , Halan Shivahankar
Published: September 2018

Objective

This study examined the potential usability, relevance, and acceptability of V-Mart, a virtual reality grocery store as an assessment and intervention tool for veterans with mild traumatic brain injury.

Design

Six focus groups were conducted for a 2-yr period to assess perceptions from the following three key stakeholders: therapists, veterans with neither mild traumatic brain injury nor posttraumatic stress disorder, and veterans with mild traumatic brain injury with or without posttraumatic stress disorder (mild traumatic brain injury/posttraumatic stress disorder). The System Usability Scale was applied as an objective measure of usability. Transcripts from the six focus groups were subjected to thematic analyses using the constant, comparative method.

Results

The focus groups indicated that V-Mart was perceived as highly usable, relevant, and acceptable. Early technical problems were resolved satisfactorily. Therapists indicated that they would use an application such as V-Mart if it were available. The veterans with neither mild traumatic brain injury nor posttraumatic stress disorder felt that it was realistic and likely to be useful, as did the veterans with mild traumatic brain injury/posttraumatic stress disorder. The System Usability Scale mean follow-up scores ranged from 71.4 to 86.0, surpassing the threshold for acceptable usability in health care settings.

Conclusions

Focus group and System Usability Scale data indicate that the V-Mart has great potential as an assessment tool and intervention for veterans with mild traumatic brain injury/posttraumatic stress disorder. Further development and clinical trials are warranted.
Metformin induces lipogenic differentiation in myofibroblasts to reverse mouse and human lung fibrosis
Authors: Kheirollahi Vahid , Wasnick Roxana M. , Biasin Valentina , Vazquez-Armendariz Ana Ivonne , Chu Xuran , Moiseenko Alena , Weiss Astrid , Wilhelm Jochen , Zhang Jin-San , Kwapiszewska Grazyna , Herold Susanne , Schermuly Ralph T. , Seeger Werner , Günther Andreas , Bellusci Saverio , Agha Elie El
Published: September 2018

Idiopathic pulmonary fibrosis is a fatal, incurable lung disease in which the intricate alveolar network of the human lung is progressively replaced by fibrotic scars, eventually leading to respiratory failure. Myofibroblasts are the effector cells that lead to abnormal deposition of extracellular matrix proteins and therefore mediate fibrotic disease not only in the lung but also in other organs. Emerging literature suggests a correlation between fibrosis and metabolic alterations in IPF. In this study, we show that the first-line antidiabetic drug, metformin, exerts potent antifibrotic effects in the lung by modulating metabolic pathways, inhibiting TGFβ1 action, suppressing collagen formation, activating PPARγ signaling and inducing lipogenic differentiation in lung myofibroblasts derived from human patients. Using genetic lineage tracing in a murine model of lung fibrosis, we show that metformin alters the fate of myofibroblasts and accelerates fibrosis resolution by inducing myofibroblast-tolipofibroblast transdifferentiation. Detailed pathway analysis showed that the reduction of collagen synthesis was largely AMPK-dependent, whereas the transdifferentiation of myo- to lipofibroblasts occurred in a BMP2-PPARγ-dependent fashion and was largely AMPK-independent. Our data report an unprecedented role for metformin in lung fibrosis, thus warranting further therapeutic evaluation.
Thesaurus: quantifying phosphoprotein positional isomers
Authors: Searle Brian C. , Lawrence Robert T. , MacCoss Michael J. , Villén Judit
Published: September 2018

Proteins can be phosphorylated at neighboring sites resulting in different functional states, and studying the regulation of these sites has been challenging. Here we present Thesaurus, a search engine that detects new positional isomers using site-specific fragment ions from parallel reaction monitoring and data independent acquisition mass spectrometry experiments. We apply Thesaurus to analyze phosphorylation events in the PI3K/AKT signaling pathway and show neighboring sites with distinct quantitative profiles, indicating regulation by different kinases.
Chemical depletion of phagocytic immune cells reveals dual roles of mosquito hemocytes in Anopheles gambiae anti-Plasmodium immunity
Authors: Kwon Hyeogsun , Smith Ryan C.
Published: September 2018

Mosquito innate immunity is comprised of both cellular and humoral factors that provide protection from invading pathogens. Immune cells, known as hemocytes, have been intricately associated with these immune responses through direct roles in phagocytosis and immune signaling. Recent studies have implicated hemocytes as integral determinants of anti-Plasmodium immunity, yet little is known regarding the specific mechanisms by which hemocytes limit malaria parasite survival. With limited genetic tools to enable their study, we employed a chemical-based treatment widely used for macrophage depletion in mammalian systems for the first time in an invertebrate organism. Upon its application in Anopheles gambiae, we observe distinct populations of phagocytic immune cells that are significantly depleted, causing high mortality following bacterial challenge and an increased intensity of malaria parasite infection. Through these studies, we demonstrate that phagocytes are required for mosquito complement recognition of invading ookinetes, as well as the production of prophenoloxidases that limit oocyst survival. Through these experiments, we also define specific sub-types of phagocytic immune cells in An. gambiae, providing new insights beyond the morphological characteristics that traditionally define mosquito hemocyte populations. Together, this study provides the first definitive insights into the dual roles of mosquito phagocytes in limiting malaria parasite survival, and illustrates the use of clodronate liposomes as an important advancement in the study of invertebrate immunity.
Differential expression and homotypic enrichment of a classic Cadherin directs tissue-level contractile asymmetry during neural tube closure
Authors: Hashimoto Hidehiko , Munro Edwin
Published: September 2018

Embryos pattern force generation at tissue boundaries during morphogenesis, but how they do so remains poorly understood. Here we show how tissue-specific expression of the type II cadherin, Cadherin2 (hereafter Cad2), patterns actomyosin contractility along the neural/epidermal (Ne/Epi) boundary to drive zippering and neural tube closure in the basal chordate,Ciona robusta. Cad2 is differentially expressed and homotypically enriched in neural cells along the Ne/Epi boundary, where RhoA and Myosin are activated during zipper progression. Equalizing Cad2 expression across the Ne/Epi boundary inhibits RhoA/Myosin activation and zipper progression, while creating ectopic Cad2 expression boundaries is sufficient to direct RhoA/Myosin activity to those boundaries. We show that Cad2 polarizes RhoA activity by sequestering the Rho GTPase activating protein, Gap21/23, to homotypic junctions, which in turn redirects RhoA/Myosin activity to heterotypic Ne/Epi junctions. By activating Myosin II along Ne/Epi junctions ahead of zipper and inhibiting Myosin II at new Ne/Ne junctions behind zipper, Cad2 promotes tissue level contractile asymmetry to drive zipper progression.
The impact of a reduced calorie, macronutrient diet change on Caucasian males in relation to genotypes associated with obesity, increased BMI and dietary response
Authors: Ellis L , Collins C.
Published: September 2018

Obesity is a growing crisis within the 1st world and the causes of obesity are well studied: a lack of physical activity combined with an increased calorie intake. This energy imbalance leads to fat accumulation leading to eventual obesity. Whilst the cause may appear clear, the options of lifestyle change and/or diet planning that is efficient with effective sustainability has been harder to come by. Genetic variants linked to obesity may hold clues on how to best customise a diet plan to an individual leading to an easier to change lifestyle with better sustainability. This study aimed to find correlations with a diet change that decreased kcal intake by 200kcal per day with a macronutrient alteration (decreased carbohydrates and increased unsaturated fat) and genetic components to discover responders and non-responders. Within the study group of Caucasian males the genes TCF7L2, TFAP2B, PPARG2 and FTO all impacted the response of the dietary intervention. In conclusion it would be prudent to consider DNA analysis as part of a battery of diet and lifestyle tests to personalise a sustainable and effective lifestyle/dietary intervention to help control weight.
Pathway analysis of GWAS loci identifies novel drug targets and repurposing opportunities
Authors: Jhamb Deepali , Magid-Slav Michal , Hurle Mark R. , Agarwal Pankaj
Published: September 2018

Genome-wide association studies (GWAS) have made considerable progress and there is emerging evidence that genetics-based targets can lead to 28% more launched drugs. However, translating the results of GWAS for drug discovery remains challenging. We analyzed 1,589 GWAS across 1,456 protein interaction pathways to translate these often, imprecise genetic loci into therapeutic hypotheses for 182 diseases. We validate these pathway-based genetic targets by testing if current drug targets are enriched in the pathway space of the same indication. Remarkably, 30% of diseases have significantly more targets in these pathways than expected by chance; the comparable number for GWAS alone (without using pathway analysis) is zero. Although pathway analysis is routine for GWAS, this study shows that the routine analysis can often enrich for drug targets, by performing a systematic global analysis to translate genetic findings into therapeutic hypotheses for new drug discovery and repositioning opportunities for current drugs.
The diurnal transcriptional landscape of the microalga Tetradesmus obliquus
Authors: Carreres Benoit M. , León-Saiki G. Mitsue , Schaap Peter J. , Remmers Ilse M. , van der Veen Douwe , Martins dos Santos Vitor A.P. , Wijffels René H. , Martens Dirk E. , Suarez-Diez Maria
Published: September 2018

Tetradesmus obliquus is a promising oleaginous microalga. We functionally annotated its genome and characterized the transcriptional landscape of T. obliquus adapted to 16:8h light dark (LD) cycles in turbidostat culture conditions at very high temporal resolution (1h intervals). Revealing a cycle of cellular events, six distinct expression profiles were obtained, each with transcriptional phenotypes correlating with measurements of biochemical composition.

The impact of starch deficiency was studied using the starchless mutant slm1. Significant changes in the transcriptional landscape were observed. Starch deficiency resulted in incapacity to supply energy during dark period, resulting in early or late time shift for energy demanding processes. Our study provides new perspectives on the role of starch and the adaptation to LD cycles of oleaginous microalgae.
Molecular Screening of Familial Hypercholesterolemia in the Icelandic Population
Authors: Kellogg Greg , Thorsson Bolli , Cai Ying , Wisotzkey Robert , Pollock Andrew , Akana Matthew , Fox Rebecca , Jansen Michael , Gudmundsson Elias F. , Patel Bonny , Chang Chihyu , Jaremko Malgorzata , Emilsson Valur , Gudnason Vilmundur , Puig Oscar
Published: September 2018

Familial hypercholesterolemia (FH) is a monogenic disease characterized by a lifelong exposure to high LDL-C levels that can lead to early onset coronary heart disease (CHD). The main causes of FH identified to date include loss-of-function mutations in LDLR or APOB, or gain-of-function mutations in PCSK9. Early diagnosis and genetic testing of FH suspects is critical for improved prognosis of affected individuals as lipid lowering treatments are effective in preventing CHD related morbidity and mortality. In the present manuscript, we developed a comprehensive next generation sequencing (NGS) panel which we applied on two different resources of FH in the Icelandic population: 62 subjects from 23 FH families with known or unknown culprit mutations, and a population-based sampling of 315 subjects selected for total cholesterol levels above the 95th percentile cut-point. The application of the NGS panel revealed significant diagnostic yields in identifying pathogenic LDLR mutations in both family and population-based genetic testing.
Process-specific somatic mutation distributions vary with three-dimensional genome structure
Authors: Akdemir Kadir C. , Le Victoria T. , Killcoyne Sarah , King Devin A. , Li Ya-Ping , Tian Yanyan , Inoue Akira , Amin Samir , Robinson Frederick S. , Herrera Rafael E. , Lynn Erica J. , Chan Kin , Seth Sahil , Klimczak Leszek J. , Gerstung Moritz , Gordenin Dmitry A. , O’Brien John , Li Lei , Verhaak Roel G. , Campbell Peter , Fitzgerald Rebecca , Morrison Ashby J. , Dixon Jesse R. , Andrew Futreal P.
Published: September 2018

Somatic mutations arise during the life history of a cell. Mutations occurring in cancer driver genes may ultimately lead to the development of clinically detectable disease. Nascent cancer lineages continue to acquire somatic mutations throughout the neoplastic process and during cancer evolution (Martincorena and Campbell, 2015). Extrinsic and endogenous mutagenic factors contribute to the accumulation of these somatic mutations (Zhang and Pellman, 2015). Understanding the underlying factors generating somatic mutations is crucial for developing potential preventive, therapeutic and clinical decisions. Earlier studies have revealed that DNA replication timing (Stamatoyannopoulos et al., 2009) and chromatin modifications (Schuster-Böckler and Lehner, 2012) are associated with variations in mutational density. What is unclear from these early studies, however, is whether all extrinsic and exogenous factors that drive somatic mutational processes share a similar relationship with chromatin state and structure. In order to understand the interplay between spatial genome organization and specific individual mutational processes, we report here a study of 3000 tumor-normal pair whole genome datasets from more than 40 different human cancer types. Our analyses revealed that different mutational processes lead to distinct somatic mutation distributions between chromatin folding domains. APOBEC- or MSI-related mutations are enriched in transcriptionally-active domains while mutations occurring due to tobacco-smoke, ultraviolet (UV) light exposure or a signature of unknown aetiology (signature 17) enrich predominantly in transcriptionally-inactive domains. Active mutational processes dictate the mutation distributions in cancer genomes, and we show that mutational distributions shift during cancer evolution upon mutational processes switch. Moreover, a dramatic instance of extreme chromatin structure in humans, that of the unique folding pattern of the inactive X-chromosome leads to distinct somatic mutation distribution on X chromosome in females compared to males in various cancer types. Overall, the interplay between three-dimensional genome organization and active mutational processes has a substantial influence on the large-scale mutation rate variations observed in human cancer.
goCTF: Geometrically optimized CTF determination for single-particle cryo-EM
Authors: Su Min
Published: September 2018

Preferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to reliably determine the global focus gradient. A novel strategy of determining contrast transfer function (CTF) parameters from a sector of the signal preserved power spectrum is applied to increase reliability. Subsequently, per-particle based local focus refinement is conducted in an iterative manner to further improve the defocus accuracy. Novel diagnosis methods using a standard deviation defocus plot and goodness fitting heatmap have also been proposed to evaluate CTF fitting quality prior to 3D refinement. In a benchmark study, goCTF processed a published single-particle cryo-EM dataset for influenza hemagglutinin trimer collected at a 40-degree specimen tilt. The resulting 3D reconstruction map was improved from 4.1Å to 3.7Å resolution. The goCTF program is built on the open-source code of CTFFIND4, which adopts a consistent user interface ease of use.