bluuebunny/crossref_metadata_2025 huggingface dataset:
Two uptake hydrogenases differentially interact with the aerobic respiratory chain during mycobacterial growth and persistence
Authors: Cordero Paul R.F. , Grinter Rhys , Hards Kiel , Cryle Max J. , Warr Coral G. , Cook Gregory M. , Greening Chris
Published: September 2019

Aerobic soil bacteria metabolize atmospheric hydrogen (H2) to persist when nutrient sources are limited. This process is the primary sink in the global H2cycle and supports the productivity of microbes in oligotrophic environments. To mediate this function, bacteria possess [NiFe]-hydrogenases capable of oxidising H2to subatmospheric concentrations. The soil saprophyteMycobacterium smegmatishas two such [NiFe]-hydrogenases, designated Huc and Hhy, which belong to different phylogenetic subgroups. Huc and Hhy exhibit similar characteristics: both are oxygen-tolerant, oxidise H2to subatmospheric concentrations, and enhance survival during hypoxia and carbon limitation. These shared characteristics pose the question: Why doesM. smegmatisrequire two hydrogenases mediating a seemingly similar function? In this work we resolve this question by showing that Huc and Hhy are differentially expressed, localised, and integrated into the respiratory chain. Huc is active in late exponential and early stationary phase, supporting energy conservation during mixotrophic growth and the transition into dormancy. In contrast, Hhy is most active during long-term persistence, providing energy for maintenance processes when carbon sources are depleted. We show that Huc and Hhy are obligately linked to the aerobic respiratory chain via the menaquinone pool and are differentially affected by respiratory uncouplers. Consistent with their distinct expression profiles, Huc and Hhy interact differentially with the terminal oxidases of the respiratory chain. Huc exclusively donates electrons to, and possibly physically associates with, the proton pumping cytochromebcc-aa3supercomplex. In contrast, the more promiscuous Hhy can also provide electrons to the cytochromebdoxidase complex. These data demonstrate that, despite their similar characteristics, Huc and Hhy perform distinct functions during mycobacterial growth and survival.
Decoding the transcriptional response to ischemic stroke in young and aged mouse brain
Authors: Androvic Peter , Kirdajova Denisa Belov , Tureckova Jana , Zucha Daniel , Rohlova Eva , Abaffy Pavel , Kriska Jan , Anderova Miroslava , Kubista Mikael , Valihrach Lukas
Published: September 2019

Ischemic stroke is one of the leading causes of mortality and major healthcare and economic burden. It is a well-recognized disease of aging, yet it is unclear how the age-dependent vulnerability occurs and what are the underlying mechanisms. To address these issues, we performed a comprehensive RNA-Seq analysis of aging, ischemic stroke and their interaction using a model of permanent middle cerebral artery occlusion (MCAO) in 3 and 18 month old female mice. We assessed differential gene expression across injury status and age, estimated cell type proportion changes, assayed the results against a range of transcriptional signatures from the literature and performed unsupervised co-expression analysis, identifying modules of genes with varying response to injury. We uncovered selective vulnerability of neuronal populations and increased activation of type-I interferon (IFN-I) signaling and several other inflammatory pathways in aged mice. We extended these findings via targeted expression analysis in tissue as well as acutely purified cellular populations to show differential temporal dynamics of IFN-I signaling between age groups and contribution of individual cell types. Together, these results paint a picture of ischemic stroke as a complex age-related disease and provide insights into interaction of aging and stroke on cellular and molecular level.

Graphical summary
Copy number motifs expose genome instability type and predict driver events and disease outcome in breast cancer
Authors: Pladsen Arne V. , Nilsen Gro , Rueda Oscar M. , Aure Miriam R. , Borgan Ørnulf , Liestøl Knut , Vitelli Valeria , Frigessi Arnoldo , Langerød Anita ,   OSBREAC, Mathelier Anthony , Engebråten Olav , Wedge David C. , Van Loo Peter , Caldas Carlos , Børresen-Dale Anne-Lise , Russnes Hege G. , Lingjærde Ole Christian
Published: September 2019

Tumor evolution is dependent on and constrained by the genotypes emerging from genome instability. We hypothesized that non-site-specific copy number motifs would correlate with underlying replication defects and also with tumor and patient fate. Six feature detectors were defined to characterize and score the local spatial behaviour of a copy number profile. By accumulating scores across genomic regions, a low-dimensional representation of the tumor genome was obtained. The proposed Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied to 2384 breast tumors from three breast cancer cohorts, revealing distinct copy number motifs in established molecular subtypes. A prognostic index combining the features predicted breast cancer specific survival better than both the genomic instability index (GII) and all commonly used clinical stratifications. CARMA offers effective comparison of tumor subgroups and extracts biologically and clinically relevant features from allele-specific copy number profiles.
The effect of wrist posture on extrinsic finger muscle activity during single joint movements
Authors: Beringer Carl R. , Mansouri Misagh , Fisher Lee E. , Collinger Jennifer L. , Munin Michael C. , Boninger Michael L. , Gaunt Robert A.
Published: September 2019

Wrist posture impacts the muscle lengths and moment arms of the extrinsic finger muscles that cross the wrist. As a result, the electromyographic (EMG) activity associated with digit movement at different wrist postures may also change. Therefore, we sought to quantify the posture-dependence of extrinsic finger muscle activity. Fine-wire bipolar electrodes were inserted in the extrinsic hand muscles of able-bodied subjects to record EMG activity during wrist and finger movements in various postures. EMG activity of all the recorded finger muscles were significantly different (p<.05, ANOVA) when performing the same movement in five different wrist postures. EMG activity varied by up to 70%, with the highest levels of activity observed in finger extensors when the wrist was extended. Similarly, finger flexors were most active when the wrist was flexed. For the finger flexors, EMG variations with wrist posture were most prominent for index finger muscles, while the EMG activity of all finger extensor muscles were similarly modulated. The extrinsic finger muscles also showed significant activity during wrist movements with the digits held still regardless of finger posture, suggesting that they may play a role in generating torque during wrist movements. Finally, we developed a pair of generalized classifiers that show that finger muscle EMG can be used to predict wrist posture. These results may impact the design of biomimetic control algorithms for myoelectric prosthetic hands, but further work in transradial amputees is necessary to determine whether this phenomenon persists after amputation.
MetroNome — a visual data exploration platform for integrating human genotypic and phenotypic data across diseases
Authors: Stolte Christian , Shi Kevin , Lapchyk Nina , Novod Nathaniel , Abhyankar Avinash , Ostrow Lyle W. , Phatnani Hemali , Bloom Toby
Published: September 2019

MetroNome is a web-based visual data exploration platform which integrates de-identified genomic, transcriptomic, and phenotypic data sets. Users can define and compare cohorts constructed from multimodal data and share the data and analyses with outside tools. MetroNome’s interactive visualization and analysis tools allow researchers to quickly form and explore novel hypotheses. The deidentified data is linked back to the source biosample inventories in multiple biobanks, enabling researchers to further investigate new ideas using the most relevant samples.
The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in Arabidopsis thaliana
Authors: Wu Zhiqiang , Waneka Gus , Sloan Daniel B.
Published: September 2019

The mechanisms of sequence divergence in angiosperm mitochondrial genomes have long been enigmatic. In particular, it is difficult to reconcile the rapid divergence of intergenic regions that can make non-coding sequences almost unrecognizable even among close relatives with the unusually high levels of sequence conservation found in genic regions. It has been hypothesized that different mutation/repair mechanisms act on genic and intergenic sequences or alternatively that mutational input is relatively constant but that selection has strikingly different effects on these respective regions. To test these alternative possibilities, we analyzed mtDNA divergence within Arabidopsis thaliana, including variants from the 1001 Genomes Project and changes accrued in published mutation accumulation (MA) lines. We found that base-substitution frequencies are relatively similar for intergenic regions and synonymous sites in coding regions, whereas indel and nonsynonymous substitutions rates are greatly depressed in coding regions, supporting a conventional model in which mutation/repair mechanisms are consistent throughout the genome but differentially filtered by selection. Most types of sequence and structural changes were undetectable in 10-generation MA lines, but we found significant shifts in relative copy number across mtDNA regions for lines grown under stressed vs. benign conditions. We confirmed quantitative variation in copy number across the A. thaliana mitogenome using both whole-genome sequencing and droplet digital PCR, further undermining the classic but oversimplified model of a circular angiosperm mtDNA structure. Our results suggest that copy number variation is one of the most rapidly evolving features in angiosperm mtDNA, even outpacing rearrangements in these notoriously structurally diverse genomes.
SimBSI: An open-source Simulink library for developing closed-loop brain signal interfaces in animals and humans
Authors: Ojeda Alejandro , Buscher Nathalie , Balasubramani Pragathi , Maric Vojislav , Ramanathan Dhakshin , Mishra Jyoti
Published: September 2019

Objective

A promising application of BCI technology is in the development of personalized therapies that can target neural circuits linked to mental or physical disabilities. Typical BCIs, however, offer limited value due to simplistic designs and poor understanding of the conditions being treated. Building BCIs on more solid grounds may require the characterization of the brain dynamics supporting cognition and behavior at multiple scales, from single-cell and local field potential (LFP) recordings in animals to non-invasive electroencephalography (EEG) in humans. Despite recent efforts, a unifying software framework to support closed-loop studies in both animals and humans, is still lacking. The objective of this paper is to develop such a neurotechnology software framework.

Approach

Here we develop the Simulink for Brain Signal Interfaces library (SimBSI). Simulink is a mature graphical programming environment within MATLAB that has gained traction for processing electrophysiological data. SimBSI adds to this ecosystem: 1) advanced human EEG source imaging, 2) cross-species multimodal data acquisition based on the Lab Streaming Layer library, and 3) a graphical experimental design platform.

Main results

We used several examples to demonstrate the capabilities of the library, ranging from simple signal processing, to online EEG source imaging, cognitive task design, and closed-loop neuromodulation. We further demonstrate the simplicity of developing a sophisticated experimental environment for rodents within this environment.

Significance

With the SimBSI library we hope to aid BCI practitioners of dissimilar backgrounds in the development of, much needed, single and cross-species closed-loop neuroscientific experiments. These experiments may provide the necessary mechanistic data for BCIs to become effective therapeutic tools.
Deep Augmented Multiview Clustering
Authors: Mariappan Ragunathan , Liu Jiang , Rajan Vaibhav
Published: September 2019

We develop a deep learning based method to cluster arbitrary collections of matrices. Our method co-clusters each matrix in the input collection and also associates clusters across matrices thereby enabling discovery of cluster chains. We present preliminary findings on a clinical dataset.
What about the environment?
Authors: Nesselhauf Lucas , Fleuchaus Ruth , Theuvsen Ludwig
Published: September 2019

Purpose

Fungus-resistant grape varieties (FRGVs) are the key to more environment-friendly wine growing. This paper aims to examine whether German consumers are willing to buy environment-friendly wines. The study focuses on reducing the amount of fungicides applied and the improvement of the carbon footprint, which are both related to the FRGVs . Furthermore, a cluster analysis leads to more insights into the consumer groups that are open to environment-friendly wine.

Design/methodology/approach

A choice experiment was conducted among 1,500 German wine drinkers with the following attributes: “reduction of pesticides”, “reduction of carbon emissions”,“familiarity with the grape variety”,“organic certification”, the slogan “better for the environment” and“price”. The individual-level, part-worth utilities were estimated using the Hierarchical Bayes method. The Ward’s method was used to cluster the individual-level, part-worth utilities. The participants’ wine involvement and environmentalism are used to further analyse the sample.

Findings

The most important attribute is “price”, followed by the “familiarity with the grape variety” and the “reduction of pesticides” and of “carbon emissions”. The least important attribute is “better for the environment”. The cluster analysis results in three clusters: the green-minded, the traditionalists and the price-minded.

Practical implications

The insights about the consumer acceptance of environment-friendly wines can be used to market these wines more effectively to consumers.

Originality/value

This is the first study that combines a choice experiment with attributes that are derived from the benefits of fungus-resistant grape varieties.
Comparing “parallel passages” in digital archives
Authors: Harris Martyn , Levene Mark , Zhang Dell , Levene Dan
Published: September 2019

Purpose

The purpose of this paper is to present a language-agnostic approach to facilitate the discovery of “parallel passages” stored in historic and cultural heritage digital archives.

Design/methodology/approach

The authors explore a novel, and relatively simple approach, using a character-based statistical language model combined with a tailored version of the Basic Local Alignment Tool to extract exact and approximate string patterns shared between groups of documents.

Findings

The approach is applicable to a wide range of languages, and compensates for variability in the text of the documents as a result of differences in dialect, authorship, language change over time and errors due to inaccurate transcriptions and optical character recognition errors as a result of the digitisation process.

Research limitations/implications

A number of case studies demonstrate that the approach is practical and generalisable to a wide range of archives with documents in different languages, domains and of varying quality.

Practical implications

The approach described can be applied to any digital archive of modern and contemporary texts. This makes the approach applicable to digital archives recording historic texts, but also those composed of more recent news articles, for example.

Social implications

The analysis of “parallel passages” enables researchers to quantify the presence and extent of text-reuse in a collection of documents, which can provide useful data on author style, text genres and cultural contexts.

Originality/value

The approach is novel and addresses a need by humanities researchers for tools that can identify similar documents and local similarities represented by shared text sequences in a potentially vast large archive of documents. As far as the authors are aware, there are no tools currently exist that provide the same level of tolerance to the language of the documents.
Competences desired among educational leaders of technical education degree institutions
Authors: Sharma Payal , Pandher Jagwinder Singh
Published: September 2019

Purpose

This study aims to identify and classify various competences and competencies that educational leaders should essentially possess.

Design/methodology/approach

The systematic review of the literature was conducted to identify various competences of educational leaders in the institutions. Later, an empirical research was conducted. The data were analyzed through confirmatory factor analysis (CFA) using AMOS 20.0 to classify these competences according to their relative importance considering natural gaps in standardized beta (ß) values. In all, 96 administrators of 35 technical institutions of Punjab (India) offering engineering and management programs and 93 veteran educational experts had responded in a survey.

Findings

The results of the study identified five competences: pedagogical, leadership, innovative, research and evaluation competences. The competencies “help others in improvement and not blame circumstances”, “set high benchmarks” and “align class activities with learning objectives” have qualified among the “most important” competencies for the educational leaders.

Research limitations/implications

The sample was specific to one state. There may be the chances of response bias in a few situations. Therefore, there are few reservations in generalizing the findings.

Practical implications

The study has several implications for both the faculty and the technical education degree institutes. The study provides a link between the characteristics and competencies of educational leaders. This study also contributes in terms of mapping of these competencies while recruitment of the faculty to test whether the candidates possess the potential of becoming educational leaders.

Originality/value

The administrators can test these competencies in their faculty for the purpose of identifying both the educational leaders within their institutes and the potential educational leaders in future by assessing “requisite” and “important” competencies.
Problem-based learning in the Irish SME workplace
Authors: O'Brien Emma , McCarthy John , Hamburg Ileana , Delaney Yvonne
Published: September 2019

Purpose

This paper aims to explore how in Irish small- and medium-sized enterprises (SMEs), problem-based learning (PBL) could possibly provide a paradigm which addresses two key research objectives: What are the learning needs and challenges faced by Irish SMEs? and How could PBL satisfy these needs through integrating formal and informal learning?

Design/methodology/approach

An action research methodology was adopted using Lewin’s (1994) action research cycle. In the reconnaissance stage, surveys and focus groups were conducted with a purposive research sample of Irish SMEs regarding their learning needs and challenges. Based on these results, a plan was formulated to adapt the traditional PBL model into a workplace PBL model (wPBL). Lastly, the wPBL model was implemented and evaluated in 42 SMEs.

Findings

The research identified several specific learning needs for SMEs, namely, learning that is cost-effective, tailored to the company and its challenges, immediately applied, demonstrates a tangible outcome (is measurable), organically fostering a learning culture, addresses knowledge gaps, continuous, develops communication, team work, problem-solving and technical skills. The traditional PBL model was adapted into a wPBL model to meet the above learning needs of SMEs. It was found that the wPBL model had the potential to address long-standing company problems (making it cost-effective), facilitate continuous learning and develop horizontal and transversal skills such as problem-solving and communication.

Originality/value

Much of the learning that takes place in SMEs is incidental or informal, and often does not contribute to the long-term sustainability of the organisation. This paper aims to propose a practical framework using wPBL to structure incidental and informal learning in SMEs so that it provides an immediate benefit to the company. To date, there has been little research into the application of PBL outside higher education, and the paper proposes a framework to assist the transition of PBL to a workplace environment.
An integrated EFT‐contextual approach for couples therapy: suggested model and ideas for practice
Authors: Coppola Jennifer L.
Published: September 2019

Attachment theory (Bowlby, 1988) and contextual therapy (Boszormenyi‐Nagy and Krasner, 1986) have conceptual commonalities relative to dialogue, trust, and creating new relational realities (Diamond, Siqueland and Diamond, 2003; Greenberg and Johnson, 2010; Hughes, 2007). Linking Emotionally Focused Couples Therapy (EFT) (Greenberg and Johnson, 2010) and contextual therapy has also been conceptually proposed for couples therapy (Lyness, 2003). Both EFT and contextual therapy centre trust and dialogue as primary relational resources for change (Boszormenyi‐Nagy and Krasner, 1986; Greenberg and Johnson, 2010). This article suggests integrating EFT and contextual therapy within couples therapy. A proposed integrated couples therapy model outlines EFT process steps and contextual therapy principles. Rationale for integration and suggested interventions are discussed. Case studies of two examples of this integrated couples therapy are included for illustration.

Practitioner points

EFT and contextual therapy are distinct and yet converge on the constructs of trust, dialogue, reciprocal care and risk taking

An integration of EFT and contextual therapy begins with EFT enactments, then infuses the intervention of multidirected partiality

Family of origin work on entitlements may enhance attachment‐based enactments in an integrated EFT and contextual therapy approach
Navigating the Shifting Terrain of US Health Care Reform—Medicare for All, Single Payer, and the Public Option
Authors: OBERLANDER JONATHAN
Published: September 2019

Policy Points

“Medicare for All” is an increasingly common term in US health care reform debates, yet widespread confusion exists over its meaning.

The various meanings of Medicare for All and other related terms reflect divergent political and philosophical assumptions about the preferred direction of health care reform, as well as the hybrid structure of the current Medicare program.
Application of Deep Learning in Food: A Review
Authors: Zhou Lei , Zhang Chu , Liu Fei , Qiu Zhengjun , He Yong
Published: September 2019

Deep learning has been proved to be an advanced technology for big data analysis with a large number of successful cases in image processing, speech recognition, object detection, and so on. Recently, it has also been introduced in food science and engineering. To our knowledge, this review is the first in the food domain. In this paper, we provided a brief introduction of deep learning and detailedly described the structure of some popular architectures of deep neural networks and the approaches for training a model. We surveyed dozens of articles that used deep learning as the data analysis tool to solve the problems and challenges in food domain, including food recognition, calories estimation, quality detection of fruits, vegetables, meat and aquatic products, food supply chain, and food contamination. The specific problems, the datasets, the preprocessing methods, the networks and frameworks used, the performance achieved, and the comparison with other popular solutions of each research were investigated. We also analyzed the potential of deep learning to be used as an advanced data mining tool in food sensory and consume researches. The result of our survey indicates that deep learning outperforms other methods such as manual feature extractors, conventional machine learning algorithms, and deep learning as a promising tool in food quality and safety inspection. The encouraging results in classification and regression problems achieved by deep learning will attract more research efforts to apply deep learning into the field of food in the future.
Evaluation of Tilmicosin Contamination in Eggs Following Its Administration to Laying Hens and Subsequent Assessment of Dietary Risks to Chinese Consumers
Authors: Ji Xiaofeng , Yang Hua , Wang Jianmei , Zhou Wei , Wang Xiaoli , Qian Mingrong
Published: September 2019

In the present study, we analyzed the tilmicosin residues in eggs as well as the dietary risks posed by the residual drug to Chinese consumers. Tilmicosin was administrated to laying hens via drinking water in doses of 100 mg/L and 300 mg/L (dose 1 and dose 2) for 5 days. Its residues distribution within egg matrices were detected using a QuEChERS method coupled with liquid chromatography–tandem mass spectrometry (LC‐MS/MS). The results indicated that the tilmicosin residue was the highest in the whole eggs and yolks on day 2 after medication and in the whites on day 5 of drug administration for dose 1 and dose 2 with the residues (µg/kg) being the following: 73.4 and 444.3 in the whole eggs; 152.0 and 1141.1 in the yolks; and 48.8 and 277.6 in the whites, respectively. During withdrawal phase, the tilmicosin levels declined to less than the limit of detection (LOD) after 29 days and 49 days for the whole eggs, after 24 days and 44 days for the yolks, and after 19 days and 49 days for the whites for doses 1 and 2, respectively. An assessment of the dietary risk for Chinese consumers revealed that the hazard quotients (HQ) values for tilmicosin consumption were less than 1 for dose 1 and greater than 1 for dose 2, with children (2 to 7 years) and adult males (over 65 years) being the high‐risk groups. These results suggest that the possible risk associated with tilmicosin contamination in eggs should not be ignored since the accidental or occasional misuse of tilmicosin in the case of egg‐laying hens may occur from time to time, particularly on small farms.

Practical Application

The modified QuEChERS method was used to analyze the tilmicosin residues in egg matrices and a subsequent dietary exposure assessment for Chinese consumers was performed, which can serve as a reference for the food safety risk posed by antibiotic misuse in egg layers.
The Incidental Pundit: Who Talks Politics with Whom, and Why?
Authors: Minozzi William , Song Hyunjin , Lazer David M. J. , Neblo Michael A. , Ognyanova Katherine
Published: September 2019

Informal discussion plays a crucial role in democracy, yet much of its value depends on diversity. We describe two models of political discussion. The purposive model holds that people typically select discussants who are knowledgeable and politically similar to them. The incidental model suggests that people talk politics for mostly idiosyncratic reasons, as by‐products of nonpolitical social processes. To adjudicate between these accounts, we draw on a unique, multisite, panel data set of whole networks, with information about many social relationships, attitudes, and demographics. This evidence permits a stronger foundation for inferences than more common egocentric methods. We find that incidental processes shape discussion networks much more powerfully than purposive ones. Respondents tended to report discussants with whom they share other relationships and characteristics, rather than based on expertise or political similarity, suggesting that stimulating discussion outside of echo chambers may be easier than previously thought.
Tenofovir disoproxil fumarate reduces hepatocellular carcinoma, decompensation and death in chronic hepatitis B patients with cirrhosis
Authors: Liu Ken , Choi Jonggi , Le An , Yip Terry Cheuk‐Fung , Wong Vincent Wai‐Sun , Chan Stephen Lam , Chan Henry Lik‐Yuen , Nguyen Mindie H. , Lim Young‐Suk , Wong Grace Lai‐Hung
Published: September 2019

Background

Lamivudine and entecavir reduce hepatic events and death in chronic hepatitis B (CHB) patients with cirrhosis, but the impact of tenofovir disoproxil fumarate (TDF) is less well studied.

Aim

To investigate the effectiveness of TDF therapy in CHB patients with cirrhosis.

Methods

We studied TDF‐treated and untreated CHB patients with cirrhosis from three tertiary centres. TDF cohort included consecutive patients who received TDF for ≥12 months while the untreated cohort were historical controls receiving routine clinical care prior to the availability of anti‐viral therapy. The primary outcome was 5‐year cumulative probability of hepatocellular carcinoma (HCC) with secondary outcomes being hepatic decompensation and death or liver transplantation (LT).

Results

A total of 1088 (291 untreated and 797 TDF‐treated) patients were included in the study. Five‐year cumulative probabilities in untreated vs TDF‐treated cohorts were 14.9% vs 9.8% for HCC (P = .07), 22.3% vs 5.9% for decompensation (P < .01) and 13.1% vs 1.1% for death or LT (P < .01) respectively. On multivariable Cox regression, TDF treatment was independently associated with reduced risks of HCC (adjusted hazard ratio [aHR] 0.46, P < .01), decompensating events (aHR 0.28, P = .01) and death or LT (aHR 0.06, P < .01). On sensitivity analyses, these risk reductions with TDF treatment were consistently demonstrated regardless of severity of liver disease and prior anti‐viral treatment. TDF treatment led to sustained improvements in most validated prognostic scores for predicting HCC, decompensation and death.

Conclusions

Compared to untreated patients, TDF treatment reduces the risks of HCC, hepatic decompensation and death in CHB patients with cirrhosis at 5 years.
Prevalence, characteristics, and satisfaction of women with a birth plan in The Netherlands
Authors: Jolles Myrthe W. , de Vries Marieke , Hollander Martine H. , van Dillen Jeroen
Published: September 2019

Background

The use of birth plans to facilitate shared decision making in childbirth is widely recommended by international agencies and by the Dutch Integrated Birth Care protocol (2016). This study evaluated the use of birth plans in The Netherlands.

Methods

A retrospective study was conducted during 2017 in a Dutch academic hospital. Women who gave birth after 33 weeks of gestational age were included (N = 1159). Medical records were searched for a birth plan, either a note or attached file. Socio‐demographic, relevant medical and obstetrical characteristics fulfilling criteria for secondary care, and postpartum satisfaction were collected and related to birth plans. Postpartum satisfaction was scored on a scale from 0 to 10. The “net promoter score” (NPS), a quality of care indicator, was also computed. For analysis, independent t test, chi‐square test, ANOVA, and two‐way between ANOVA were used.

Results

A birth plan was noted in the medical records of 34.7% of women. Women with a birth plan were on average older, primiparous, of Dutch ethnicity, and more likely to have a complicated medical history, psychological condition, or fertility treatment. The mean postpartum satisfaction score was 8.28 and the NPS for customer satisfaction was 36.1, falling in the good range. No significant differences in postpartum satisfaction related to birth plans were found.

Conclusions

Although birth plans are recommended for every pregnant woman, this is not everyday practice yet. The purpose of birth plans, to facilitate shared decision making, is therefore not fully realized. Implementation strategies are needed to increase adoption of birth plans for every woman.
Intelligent analysis and data visualisation for teacher assistance tools: The case of exploratory learning
Authors: Mavrikis Manolis , Geraniou Eirini , Gutierrez Santos Sergio , Poulovassilis Alexandra
Published: September 2019

While it is commonly accepted that Learning Analytics (LA) tools can support teachers' awareness and classroom orchestration, not all forms of pedagogy are congruent to the types of data generated by digital technologies or the algorithms used to analyse them. One such pedagogy that has been so far underserved by LA is exploratory learning, exemplified by tools such as simulators, virtual labs, microworlds and some interactive educational games. This paper argues that the combination of intelligent analysis of interaction data from such an Exploratory Learning Environment (ELE) and the targeted design of visualisations has the benefit of supporting classroom orchestration and consequently enabling the adoption of this pedagogy to the classroom. We present a case study of LA in the context of an ELE supporting the learning of algebra. We focus on the formative qualitative evaluation of a suite of Teacher Assistance tools. We draw conclusions relating to the value of the tools to teachers and reflect with transferable lessons for future related work.

Practitioner Notes

What is already known about this topic

Learning Analytics (LA) tools can support teachers' orchestration but most of the work so far has focus mostly on instructionist pedagogies or Computer‐Supported Collaborative Learning.

Exploratory Learning Environments (ELEs) encourage students to freely explore a domain and follow a variety of solutions and have the potential to lead to more engagement and deeper learning.

The freedom in ELEs introduces orchestration challenges that hinder the adoption of such pedagogies in classroom.

What this paper adds

A set of usage scenarios for LA tools for exploratory environments derived from teacher input and design and methodological guidelines based on a reflection from the study.

Showcases a suite of Teacher Assistance tools purposefully designed for teachers' orchestration requirements during Exploratory Learning.

Empirical evidence of the perceived usefulness of these tools and feedback from a large number of teachers thanks to a methodology of re‐using previously collected classroom data.

Implications for practice and/or policy

A methodology for involving teachers in the design and evaluation of LA.

Highlights teacher training needs for LA.

Teachers should be provided with tools that help them orchestrate different activities including ones with digital tools underpinned by a constructionist pedagogy.
In patients with a positive family history of familial adenomatous polyposis can the condition be diagnosed from the presence of congenital hypertrophy of the retinal pigment epithelium detected via an eye examination: A systematic review
Authors: Rehan Shahzaib , Aye Kyaw
Published: September 2019

In classic familial adenomatous polyposis (FAP) adenomas become malignant. Congenital hypertrophy of the retinal pigment epithelium (CHRPE) is a retinal pigmented lesion and is the earliest and most common potential extraintestinal manifestation of FAP. This review aims to summarize and analyse all of the published data on CHRPE in patients with classic FAP and then ascertain whether these patients should undergo a relatively cheap and non‐invasive dilated fundus examination to screen for CHRPE. Adhering to Preferred Reporting Items for Systematic Reviews and Meta Analyses guidelines our database search identified 102 relevant articles of which 13 were selected for further analysis. The percentage of FAP patients with CHRPE was found to be 80.00%, whereas the percentage of at‐risk patients with CHRPE was 31.12%. Despite various statistically significant findings, CHRPE alone cannot be used as a surrogate for diagnosing FAP in those with a positive family history. The authors advocate a combined approach of eye examinations, colonoscopy and genetic testing.
The homozygous variant c.245G > A/p.G82D in PNPLA2 is associated with arrhythmogenic cardiomyopathy phenotypic manifestations
Authors: Rao Man , Guo Guangran , Li Mengmeng , Chen Shi , Chen Kai , Chen Xiao , Song Jiangping , Hu Shengshou
Published: September 2019

Arrhythmogenic cardiomyopathy (ACM) is a familial cardiomyopathy featured by fibrofatty replacement of cardiomyocytes. Responsible genetic factors are not discernible in approximately one‐third of ACM probands. To investigate this further, we performed whole genome sequencing in 14 mutation‐negative ACM probands who underwent cardiac transplantation, and we identified one ACM proband with a rare homozygous missense variant in PNPLA2 (c.245G > A, p.G82D), a rate‐limiting enzyme that hydrolyzes triglycerides into fatty acids and diacylglycerol. Bioinformatic analysis suggested that this missense variant may lead to loss of function and therefore impair lipid catabolism. Genetic screening in this proband's family also inferred that the homozygous variant cosegregated with disease. To validate the pathogenicity of this variant and confirm its association with ACM, we established a knockin mouse model carrying the orthologous human homozygous PNPLA2 variant. Interestingly, mice with the homozygous variant presented with arrhythmias and significant cardiac dysfunction at 12 weeks, whereas heterozygous mice were not affected. Moreover, those homozygous mice suffered sudden death and/or heart failure by the age of 14 weeks. Pathological examination showed that extensive lipogenesis in cardiomyocytes and cardiac fibrosis were prominent in the myocardium. Herein, our data demonstrated that the homozygous missense variant PNPLA2 (c.245G > A, p.G82D) associated with a recessive form of ACM.
Revectorization‐Based Soft Shadow Mapping
Authors: Macedo M. C. F. , Apolinário A. L. , Agüero K. A.
Published: September 2019

In this paper, we present revectorization‐based soft shadow mapping, an algorithm that enables the rendering of visually plausible anti‐aliased soft shadows in real time. In revectorization‐based shadow mapping, shadow silhouettes are anti‐aliased and filtered on the basis of a discontinuity space. By replacing the filtering step of the theoretical framework of the percentage‐closer soft shadow algorithm by a revectorization‐based filtering algorithm, we are able to provide anti‐aliasing mainly for near contact shadows or small penumbra sizes generated from low‐resolution shadow maps. Moreover, we present a screen‐space variant of our technique that generates visually plausible soft shadows with an overhead of only in processing time, when compared to the fastest soft shadow algorithms proposed in the literature, but that introduces shadow overestimation artefacts in the final rendering.
Framework for quantifying population responses to disturbance reveals that coastal birds are highly resilient to hurricanes
Authors: Field Christopher R. , Ruskin Katharine J. , Cohen Jonathan B. , Hodgman Thomas P. , Kovach Adrienne I. , Olsen Brian J. , Shriver W. Gregory , Elphick Chris S.
Published: September 2019

Changes in the frequency and severity of extreme weather may introduce new threats to species that are already under stress from gradual habitat loss and climate change. We provide a probabilistic framework that quantifies potential threats by applying concepts from ecological resilience to single populations. Our approach uses computation to compare disturbance–impacted projections to a population's normal range of variation, quantifying the full range of potential impacts. We illustrate this framework with projection models for coastal birds, which are commonly depicted as vulnerable to disturbances, especially hurricanes and oil spills. We found that populations of coastal specialists are resilient to extreme disturbances, with high resistance to the effects of short‐term reductions in vital rates and recovery within 20 years. Applying the general framework presented here across disturbance‐prone species and ecosystems would improve understanding of population resilience and generate specific projections of resilience that are needed for effective conservation planning.
Defining a spectrum of integrative trait‐based vegetation canopy structural types
Authors: Fahey Robert T. , Atkins Jeff W. , Gough Christopher M. , Hardiman Brady S. , Nave Lucas E. , Tallant Jason M. , Nadehoffer Knute J. , Vogel Christoph , Scheuermann Cynthia M. , Stuart‐Haëntjens Ellen , Haber Lisa T. , Fotis Alexander T. , Ricart Raleigh , Curtis Peter S.
Published: September 2019

Vegetation canopy structure is a fundamental characteristic of terrestrial ecosystems that defines vegetation types and drives ecosystem functioning. We use the multivariate structural trait composition of vegetation canopies to classify ecosystems within a global canopy structure spectrum. Across the temperate forest sub‐set of this spectrum, we assess gradients in canopy structural traits, characterise canopy structural types (CST) and evaluate drivers and functional consequences of canopy structural variation. We derive CSTs from multivariate canopy structure data, illustrating variation along three primary structural axes and resolution into six largely distinct and functionally relevant CSTs. Our results illustrate that within‐ecosystem successional processes and disturbance legacies can produce variation in canopy structure similar to that associated with sub‐continental variation in forest types and eco‐climatic zones. The potential to classify ecosystems into CSTs based on suites of structural traits represents an important advance in understanding and modelling structure–function relationships in vegetated ecosystems.
Early Life Stress in Adolescent Migraine and the Mediational Influence of Symptoms of Depression and Anxiety in a Canadian Cohort
Authors: Hammond Nicole G. , Orr Serena L. , Colman Ian
Published: September 2019

Objective

This study sought to examine the association between early life stressors and adolescent headache in the Canadian population, and the potential mediating influence of symptoms of depression and anxiety.

Background

Early life stress or adverse childhood experiences have a well‐documented association with migraine and headache in adulthood, as do symptoms of depression and anxiety. However, there is limited evidence examining the relationship between early life environmental stressors and adolescent headache, and a lack of longitudinal research. Family‐level factors including parenting behaviors and parental influences such as maternal distress have been implicated in pediatric chronic pain.

Methods

This study used data from 2313 respondents of the National Longitudinal Survey of Children and Youth, followed prospectively from age 0 to 1 years at baseline (1994/1995) until age 14 to 15 years (2008/2009). The relationships between 4 measures of early life family level stressors, and outcomes of incident health professional‐diagnosed migraine and self‐reported, unclassified frequent headache (>1 per week) were examined. We conducted a series of mediation analyses of the indirect effect (IE) of family‐level stressors on headache outcomes through symptoms of depression and anxiety in late childhood. The IE and 95% bias‐corrected confidence interval (CIBC) were estimated using maximum likelihood logistic regression methods (log odds scale).

Results

The proportion of respondents with incident migraine and frequent headache was 3.1% and 11.1%, respectively. There were no direct associations between distal early life family‐level factors and adolescent headache. Symptoms of depression‐ and anxiety‐mediated relationships between family dysfunction (IE 0.0181, 95% CIBC 0.0001‐0.0570), punitive parenting (IE 0.0241, 95% CIBC 0.0015‐0.0633), parental depressive symptomatology (IE 0.0416, 95% CIBC 0.0017‐0.0861), and incident migraine but not frequent headache. Indirectly, presence of family dysfunction, punitive parenting, and higher parental depressive symptomatology in early life were associated with a greater likelihood of migraine in adolescence, through greater symptoms of depression and anxiety in late childhood.

Conclusions

Findings provide support for the influence of early life family‐level factors on prospective risk of developing migraine, through symptoms of depression and anxiety. Addressing family dynamics in clinical practice may reduce unnecessary stress‐related burdens on children and adolescents, which could lead to improvements in their somatic complaints.
Timing and development of sedimentation of the Cleaverville Formation and a post‐accretion pull‐apart system in the Cleaverville area, coastal Pilbara Terrane, Pilbara, Western Australia
Authors: Kiyokawa Shoichi , Aihara Yuhei , Takehara Mami , Horie Kenji
Published: September 2019

In the Cleaverville area of Western Australia, the Regal, Dixon Island, and Cleaverville Formations preserve a Mesoarchean lower‐greenschist‐facies volcano‐sedimentary succession in the coastal Pilbara Terrane. These formations are distributed in a rhomboidal‐shaped area and are unconformably overlain by two narrowly distributed shallow‐marine sedimentary sequences: the Sixty‐Six Hill and Forty‐Four Hill Members of the Lizard Hills Formation. The former member is preserved within the core of the Cleaverville Syncline and the latter formed along the northeast‐trending Eighty‐Seven Fault. Based on the metamorphic grade and structures, two deformation events are recognized: D1 resulted in folding caused by a collisional event, and D2 resulted in regional sinistral strike‐slip deformation. A previous study reported that the Cleaverville Formation was deposited at 3020 Ma, after the Prinsep Orogeny (3070–3050 Ma). Our SHRIMP U–Pb zircon ages show that: (i) graded volcaniclastic–felsic tuff within the black shale sequence below the banded iron formation in the Cleaverville Formation yields an age of (3 114 ±14) Ma; (ii) the youngest zircons in sandstones of the Sixty‐Six Hill Member, which unconformably overlies pillow basalt of the Regal Formation, yield ages of 3090–3060 Ma; and (iii) zircons in sandstones of the Forty‐Four Hill Member show two age peaks at 3270 Ma and 3020 Ma. In this way, the Cleaverville Formation was deposited at 3114–3060 Ma and was deformed at 3070–3050 Ma (D1). Depositional age of the Cleaverville Formation is at least 40–90 Myr older than that proposed in previous studies and pre‐dates the Prinsep Orogeny (3070–3050 Ma). After 3020 Ma, D2 resulted in the formation of a regional strike‐slip pull‐apart basin in the Cleaverville area. The lower‐greenschist‐facies volcano‐sedimentary rocks are distributed only within this basin structure. This strike‐slip deformation was synchronous with crustal‐scale sinistral shear deformation (3000–2930 Ma) in the Pilbara region.