bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Authors: Collins Ben C. , Hunter Christie L. , Liu Yansheng , Schilling Birgit , Rosenberger George , Bader Samuel L. , Chan Daniel W. , Gibson Bradford W. , Gingras Anne-Claude , Held Jason M. , Hirayama-Kurogi Mio , Hou Guixue , Krisp Christoph , Larsen Brett , Lin Liang , Liu Siqi , Molloy Mark P. , Moritz Robert L. , Ohtsuki Sumio , Schlapbach Ralph , Selevsek Nathalie , Thomas Stefani N. , Tzeng Shin-Cheng , Zhang Hui , Aebersold Ruedi
Published: September 2016

Quantitative proteomics employing mass spectrometry has become an indispensable tool in basic and applied life science research. Methods based on data-dependent acquisition have proved extremely valuable for qualitative proteome analysis but historically have struggled to achieve reproducible quantitative data if large sample cohorts are comparatively analyzed. Targeted proteomics, most commonly implemented as selected reaction monitoring, has emerged as a powerful alternative and succeeded in providing a data independent approach for reproducible quantitative proteomics data but is limited in the number of proteins quantified. SWATH-MS is a recently introduced technique consisting of a data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, specificity) achieved in targeted proteomics but on the scale of thousands of proteins. While previous SWATH-MS studies have shown high intra-lab reproducibility, this has not been evaluated on an inter-lab basis. In this multi-laboratory evaluation study using data from 11 sites worldwide, we have demonstrated that using SWATH-MS we can consistently detect and quantify more than 4,000 proteins from HEK293 cells and that the quantitative protein data generated across laboratories is reproducible. Using synthetic peptide dilution series, we have shown that the sensitivity, dynamic range and reproducibility established with SWATH-MS methods are also uniformly achieved across labs. This study demonstrates that SWATH-MS is a reproducible and accurate technique that can be confidently deployed for large-scale protein quantification in life science research.
Phylo-Node: a molecular phylogenetic toolkit using Node.js
Authors: O’Halloran Damien M.
Published: September 2016

Background: Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis.

Results: To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines.

Conclusions: phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node
3D chromatin structure estimation through a constraint-enhanced score function
Authors: Caudai Claudia , Salerno Emanuele , Zoppè Monica , Tonazzini Anna
Published: September 2016

Based on experimental techniques of the typeChromosome Conformation Capture(3C), several methods have been proposed in the literature to estimate the structure of the nuclear dna in homogeneous populations of cells. Many of these methods transform contact frequencies into Euclidean distances between pairs of chromatin fragments, and then reconstruct the structure by solving a distance-to-geometry problem. To avoid the drawbacks of this strategy, we propose to abandon the frequency-distance translation and adopt a recursive multiscale procedure, where the chromatin fibre is modelled by a new kind of modified bead chain, the data are suitably partitioned at each scale, and the resulting partial structures are estimated independently of each other and then connected again to rebuild the whole chain.

We propose a new score function to generate the solution space: it includes a data-fit part that does not require target distances, and a penalty part, which enforcessoftgeometric constraints on the solution, coherent with known physical and biological constraints. The relative weights of the two parts are balanced automatically at each scale and each subchain treated. Since it is reasonable to expect that many different structures fit any 3c-type data set, we sample the solution space by simulated annealing, with no search for an absolute optimum. A set of different solutions with similar scores is thus generated. The procedure can be managed through a minimum set of parameters, independent of both the scale and the particular genomic segment being treated. The user is thus allowed to control the solutions easily and effectively. The partition of the fibre, along with several intrinsically parallel parts, make this method computationally efficient.

We report some results obtained with the new method and code, tested against real data, that support the reliability of our method and the biological plausibility of our solutions.
Sequence biases in CLIP experimental data are incorporated in protein RNA-binding models
Authors: Orenstein Yaron , Hosur Raghavendra , Simmons Sean , Bienkoswka Jadwiga , Berger Bonnie
Published: September 2016

We report a newly-identified bias in CLIP data that results from cleaving enzyme specificity. This bias is inadvertently incorporated into standard peak calling methods [1], which identify the most likely locations where proteins bind RNA. We further show how, in downstream analysis, this bias is incorporated into models inferred by the state-of-the-art GraphProt method to predict protein RNA-binding. We call for both experimental controls to measure enzyme specificities and algorithms to identify unbiased CLIP binding sites.
CEO succession: what we know and where to go?
Authors: Cragun Ormonde R. , Nyberg Anthony J. , Wright Pat M.
Published: September 2016

Purpose

The purpose of this paper is to conduct a comprehensive analysis and synthesis of the splintered chief executive officer (CEO) succession literature and provide a unifying future research agenda.

Design/methodology/approach

This review content analyzes 227 relevant articles published after 1994. These articles examine the causes, process, replacement, and consequences of CEO succession.

Findings

The review develops a comprehensive typology, identifies gaps in the literature, and proposes opportunities for future research. For instance, the CEO succession literature can be classified along four primary dimensions: when, how, who, and consequences. These four primary dimensions are further explained by ten secondary factors and 30 tertiary components. Research opportunities include: enlarging the data pool to expand the repertoire of firms studied, incorporating the CEO’s perspective, and integrating CEO succession research with literatures in selection, turnover, and human capital theory.

Practical implications

Through integrating research across research domains, future research will be able to better predict when CEO succession will occur, how to avoid unwanted CEO succession, how to better implement CEO succession, and how to minimize negative aspects and maximize positive aspects of CEO succession for the firm and the CEO, as well as understand the consequences of CEO selection, and help move toward and understanding of how to prevent poor performance, and retain high performing CEOs.

Originality/value

This is the first comprehensive review since 1994. It creates a typology to guide and categorize future research, and shows ways to incorporate relevant, but often ignored literatures (e.g. human resources, psychology, decision making, and human capital).
Time to change: a review of organisational culture change in health care organisations
Authors: Johnson Anya , Nguyen Helena , Groth Markus , Wang Karyn , Ng Ju Li
Published: September 2016

Purpose

The culture of an organization shapes the attitudes and behaviors of employees and plays a key role in driving organizational outcomes. Yet, it is enormously challenging to manage or change. The purpose of this paper is to review the recent literature on culture change interventions in health care organizations to identify the common themes underpinning these interventions.

Design/methodology/approach

The paper is developed from an extensive review of the literature on culture change interventions in health care from 2005 to 2015, building on previous reviews and highlighting examples of good practice.

Findings

All culture change interventions included in the review used processes and techniques that can be classified into Lewin’s (1951) three stage model of change. These include providing evidence for the need for change through data, a range of successful change strategies, and strategies for embedding the culture change into business as usual.

Practical implications

There is no “one size fits all” recipe for culture change. Rather, attention to context with key features including diagnosis and evaluation of culture, a combination of support from leaders and others in the organization, and strategies to embed the culture change are important for the change process to happen.

Originality/value

The authors provide an important insight into the key principles and features of culture change interventions to provide practitioners with guidance on the process within health care and other organizations.
Effects of pre‐ and post‐dispersal temperature on primary and secondary dormancy dynamics in contrasting genotypes of Arabidopsis thaliana (Brassicaceae)
Authors: Coughlan Jennifer M. , Saha Anamika , Donohue Kathleen
Published: September 2016

Germination is determined by the depth of primary dormancy and the dynamics of secondary dormancy induction. We assess how dark imbibition at cool temperatures influences primary dormancy breakage and secondary dormancy induction, and how the depth of primary dormancy influences secondary dormancy induction. We manipulated primary dormancy by maturing seeds at two temperatures (‘pre‐dispersal’) known to induce different levels of primary dormancy, and by employing genotypes that differ in primary dormancy. To assess primary dormancy breakage and secondary dormancy induction, seeds of each genotype and maturation treatment were imbibed in the dark at one of four temperatures (‘post‐dispersal’) for one of three durations. Germination proportions were recorded. Seed‐maturation condition and genotype influenced the degree of primary dormancy breakage in response to dark stratification and in the optimal temperature for dormancy breakage. Secondary dormancy induction was strongest in cool‐matured seeds and seeds stratified at warmer temperatures for longer durations. These effects were consistent across genotypes. Maturation temperature influenced the expression of genetic variation for primary but not secondary dormancy, which showed little genetic variation. Seed‐maturation temperature influenced primary and secondary dormancy induction by dark imbibition, and it also influenced the expression of genetic variation for temperature‐dependent dormancy breakage. Cool seed‐maturation induced primary dormancy in a genotype‐specific manner and enhanced secondary dormancy induction. Post‐dispersal temperature also influenced primary dormancy breakage and secondary dormancy induction. The observed interactions between primary and secondary dormancy, and between pre‐ and post‐dispersal temperature, are expected to influence life‐history expression in nature.
A novel regulatory circuit to control indole biosynthesis protects Escherichia coli from nitrosative damages during the anaerobic respiration of nitrate
Authors: Lai Yong , Xu Zeling , Yan Aixin
Published: September 2016

Indole is a widely distributed microbial secondary metabolite. It mediates a broad range of physiological processes in both its producing and surrounding species. Yet, indole biosynthesis during the anaerobiosis of bacteria remains largely uncharacterized. Here, we find that while indole production is promoted during fermentation and anaerobic respiration of fumarate and trimethylamine N‐oxide in E. coli, its biosynthesis is repressed during anaerobic respiration of nitrate especially during exponential growth. We show that expression of the indole biosynthetic operon tnaCAB is repressed under this condition by the two component systems NarXL and NarPQ in the global regulator FNR dependent manner. During stationary growth phase of nitrate respiration, indole biosynthesis is derepressed. However, cellular indole concentration remains low. We demonstrate that this is due to the rapid conversion of indole into mutagenic indole nitrosative derivatives under this condition. Consistent with this, a supplement of exogenous indole during nitrate respiration causes elevated mutation frequencies in E. coli cells lacking the detoxifying efflux genes mdtEF, and ectopic over‐expression of tnaAB genes decreases the fitness of E. coli to this physiological condition. Together, these results suggest that indole production is tuned to the bioenergetics activities of E. coli to facilitate its adaptation and fitness.
Income Mobility and Income Inequality in Scottish Agriculture
Authors: Allanson Paul , Kasprzyk Kalina , Barnes Andrew P.
Published: September 2016

The paper explores the distributional consequences of farm income mobility in Scotland, focusing on the extent to which farm income inequality is a chronic as opposed to a temporary phenomenon and on the nature of the dynamic processes driving changes in farm income inequality over time. The empirical results reveal that the majority of farm income inequality was long‐run or structural in nature, reflecting differences in both farm business size and farm‐specific factors such as land quality, managerial ability and business structures. Evidence of absolute convergence in farm incomes is explained by short‐run adjustments towards equilibrium or target incomes conditional upon prices, technology and farm business size, with farm business growth conditional upon survival found to have had no significant redistributive effect.
Hepatic resection for hepatocellular carcinoma in cirrhotic patients with portal hypertension
Authors: Zakaria Hazem M. , Gad Emad H. , Nada Ali , Abdelaleem Anwar A. , Maher Doha , Abdel Samea Mohammad E. , Sabry Alyaa
Published: September 2016

Aim

Hepatic resection (HR) in cirrhotic patients with hepatocellular carcinoma (HCC) and portal hypertension (PHT) is not recommended, according to international guidelines. The aim of the present study was to determine the outcome of HR for HCC in cirrhotic patients with PHT.

Methods

The present study was a single institutional, retrospective study of 170 Child–Pugh class A cirrhotic patients who underwent HR for HCC from 2011 to July 2015. The patients were divided into two groups, according to the presence and absence of PHT.

Results

PHT was present in 91 patients (53.5 per cent). The postoperative morbidity was insignificantly higher in patients with PHT than patients without PHT (31.9 per cent vs 25.3 per cent, respectively, P = 0.36). Patients with PHT showed 90‐day perioperative mortality (3.3 per cent), which was similar to patients without PHT (2.5 per cent). In the subgroup analysis, the 1‐, 3‐ and 5‐year overall survival for patients with limited HR was 90.3 per cent, 74.3 per cent and 66.2 per cent, respectively, for patients with PHT, and 93.9 per cent, 80.9 per cent and 73.6 per cent, respectively, for patients without PHT, without a significant statistical difference (P = 0.38).

Conclusion

HR in Child–Pugh class A cirrhotic patients with PHT is a safe and effective procedure with good short‐ and long‐term outcomes in comparison to patients without PHT, especially those with limited liver resection.
The Evolution of Out‐of‐Hospital Medical Costs to and through Retirement
Authors: Johar Meliyanni
Published: September 2016

This paper shows how the cost of out‐of‐hospital medical services and prescription drugs change as Australians enter and live through retirement. We use a sample of over 65,000 retired individuals aged forty‐five and over, and extract their Medicare claims for period 2005–2014. Analysing the expenditure distribution for up to eight years after retirement, the result shows that expenditure on medical services continues to increase while pharmaceutical expenditure declines for most retirees. Partially retired individuals have higher medical service cost but lower pharmaceutical cost, while those retiring prior to Age Pension age have slower growth in medical service and pharmaceutical costs.
Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe
Authors: Iso‐Touru T. , Tapio M. , Vilkki J. , Kiseleva T. , Ammosov I. , Ivanova Z. , Popov R. , Ozerov M. , Kantanen J.
Published: September 2016

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P‐value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding.
Scripting Dissent: US Abortion Laws, State Power, and the Politics of Scripted Speech
Authors: Buchbinder Mara
Published: September 2016

Abortion laws offer a point of entry for “the state” to intervene in intimate clinical matters. In this article, I explore the various uses of scripts and scripting in state‐mandated abortion counseling following the implementation of North Carolina's (2011) Woman's “Right to Know” Act. The law mandates that women receive counseling with specific, state‐prescribed information at least 24 hours prior to an abortion. Drawing on interviews with abortion providers in North Carolina, I analyze how the meaning of scripting shifts across different clinical and bureaucratic contexts and show that abortion providers perceived themselves to be scripted by “the state” even though their words were not explicitly chosen by lawmakers. Thus, rather than viewing the law merely as a product of North Carolina legislative activity, I argue that abortion providers also help to create the law, and its social and moral power, by interpreting and enacting it. However, abortion providers also revealed creative strategies for “scripting dissent” from the law—that is, rejecting, challenging, or otherwise subverting the state's ideological message. This demonstrates that the linguistic force of the script stretches beyond its textual meaning to encompass the way it is performed within a particular context and how it is sometimes used for unexpected ends. [abortion, reproduction, biopolitics, the state, law, medicine, United States]
Systematic review with meta‐analysis: the risk of mother‐to‐child transmission of hepatitis B virus infection in sub‐Saharan Africa
Authors: Keane E. , Funk A. L. , Shimakawa Y.
Published: September 2016

Background

The risk of mother‐to‐child transmission of hepatitis B virus (HBV) has been quoted as 70–90% among women positive for hepatitis B surface antigen (HBsAg) and e antigen (HBeAg), and 5–30% among HBsAg‐positive HBeAg‐negative women. These risks are derived from Asia; little is known about sub‐Saharan Africa.

Aim

To determine the risk of mother‐to‐child transmission in sub‐Saharan Africa, according to maternal HBeAg and type of prophylaxis.

Methods

We searched Medline, Global Health, Embase, African Journals Online and African Index Medicus. We included observational or interventional studies that enrolled infants of HBV‐infected women, and that tested for HBsAg or HBV DNA between 3 and 12 months of age.

Results

Fifteen articles from 11 African countries were included. Among HBeAg‐positive women, the pooled risk was 38.3% (95% CI: 7.0–74.4%) without prophylaxis, which was significantly lower than the lower bound of 70–90% risk in the literature (P = 0.007). Among HBeAg‐negative women, the pooled risk was 4.8% (95% CI: 0.1–13.3%) without prophylaxis, which lays within the lower range of the 5–30% risk in Asia. By extrapolating the pooled transmission risks to the number of births to infectious mothers, an estimated 1% of newborns (n = 367 250) are annually infected with HBV at birth in sub‐Saharan Africa.

Conclusions

Compared to Asia, the risk of mother‐to‐child transmission is low in sub‐Saharan Africa. However, the annual number of infants perinatally infected with HBV is twice the number of incident paediatric HIV infections in sub‐Saharan Africa (n = 190 000). This highlights the importance of preventing mother‐to‐child transmission of HBV in sub‐Saharan Africa, which has been long neglected.
Population pharmacokinetics of daptomycin in adult patients undergoing continuous renal replacement therapy
Authors: Xu Xiaoying , Khadzhynov Dmytro , Peters Harm , Chaves Ricardo L. , Hamed Kamal , Levi Micha , Corti Natascia
Published: September 2016

Aim

The objective of this population pharmacokinetic (PK) analysis was to provide guidance for the dosing interval of daptomycin in patients undergoing continuous renal replacement therapy (CRRT).

Methods

A previously published population PK model for daptomycin was updated with data from patients undergoing continuous veno‐venous haemodialysis (CVVHD; n = 9) and continuous veno‐venous haemodiafiltration (CVVHDF; n = 8). Model‐based simulations were performed to compare the 24 h AUC, Cmax and Cmin of daptomycin following various dosing regimens (4, 6, 8, 10, and 12 mg kg−1 every [Q] 24 h and Q48 h), with the safety and efficacy exposure references for Staphylococcus aureus bacteraemia/right‐sided infective endocarditis.

Results

The previously developed daptomycin structural population PK model could reasonably describe data from the patients on CRRT. The clearance in patients undergoing CVVHDF and CVVHD was estimated at 0.53 and 0.94 l h−1, respectively, as compared with 0.75 l h−1 in patients with creatinine clearance (CrCl) ≥ 30 ml min−1. Daptomycin Q24 h dosing in patients undergoing CRRT resulted in optimal exposure for efficacy, with AUC comparable to that in patients with CrCl ≥ 30 ml min−1. In contrast, Q48 h dosing was associated with considerably lower AUC24–48h in all patients for doses up to 12 mg kg−1 and is therefore inappropriate.

Conclusions

Q24 h dosing of daptomycin up to 12 mg kg−1 provides comparable drug exposure in patients on CVVHD and in those with CrCl ≥ 30 ml min−1. Daily daptomycin use up to 8 mg kg−1 doses are appropriate for patients on CVVHDF, but higher doses may increase the risk of toxicity.
Pharmacokinetics of neratinib during coadministration with lansoprazole in healthy subjects
Authors: Keyvanjah Kiana , DiPrimeo Daniel , Li Ai , Obaidi Mohammad , Swearingen Dennis , Wong Alvin
Published: September 2016

Aims

To evaluate the effect of lansoprazole, a proton‐pump inhibitor, on the absorption, pharmacokinetics, and safety of neratinib, a pan‐HER tyrosine kinase inhibitor, in healthy subjects.

Methods

This was an open‐label, two‐period, fixed‐sequence study. Fifteen healthy adult subjects received a single oral dose of neratinib 240 mg (Period 1), followed by a washout period, then oral lansoprazole 30 mg once daily for 7 days and a single dose of neratinib 240 mg on Day 5 (Period 2). Pharmacokinetic sampling was performed for 72 h following each neratinib dose. Plasma neratinib concentration–time data were analysed using noncompartmental methods. Geometric mean ratios for AUC0–t, AUC0–inf, and peak plasma concentrations (Cmax) for neratinib plus lansoprazole vs. neratinib were used to assess the magnitude of the drug–drug interaction if the 90% confidence intervals were outside 80.00–125.00%.

Results

Neratinib geometric least‐squares mean (LSM) Cmax was reduced from 84.5 ng ml−1 with neratinib alone to 24.5 ng ml−1 with neratinib plus lansoprazole. The extent of exposure to neratinib was also decreased: geometric LSM AUC0–t was 1478 ng ml−1 h with neratinib vs. 426 ng ml−1 h with neratinib plus lansoprazole, and geometric LSM AUC0–inf was 1557 ng ml−1 h vs. 542 ng ml−1 h, respectively. Mean t½ was similar with both treatments (approximately 14 h). Geometric mean ratios 90% confidence intervals for AUC0–t, AUC0–inf and Cmax fell outside the prespecified equivalence range (80.0–125.0%). Treatment‐emergent adverse events, all mild, were reported by five (33%) subjects.

Conclusions

Coadministration of lansoprazole with neratinib reduced the rate and extent of neratinib exposure in healthy subjects.
Unravelling the adiponectin paradox: novel roles of adiponectin in the regulation of cardiovascular disease
Authors: Woodward Lavinia , Akoumianakis Ioannis , Antoniades Charalambos
Published: September 2016

Adipose tissue (AT) has recently been identified as a dynamic endocrine organ secreting a wide range of adipokines. Adiponectin is one such hormone, exerting endocrine and paracrine effects on the cardiovascular system. At a cellular and molecular level, adiponectin has anti‐inflammatory, antioxidant and anti‐apoptotic roles, thereby mitigating key mechanisms underlying cardiovascular disease (CVD) pathogenesis. However, adiponectin expression in human AT as well as its circulating levels are increased in advanced CVD states, and it is actually considered by many as a ‘rescue hormone’. Due to the complex mechanisms regulating adiponectin's biosynthesis in the human AT, measurement of its levels as a biomarker in CVD is highly controversial, given that adiponectin exerts protective effects on the cardiovascular system but at the same time its increased levels flag advanced CVD. In this review article, we present the involvement of adiponectin in CVD pathogenesis and we discuss its role as a clinical biomarker.

Linked Articles

This article is part of a themed section on Targeting Inflammation to Reduce Cardiovascular Disease Risk. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.22/issuetoc and http://onlinelibrary.wiley.com/doi/10.1111/bcp.v82.4/issuetoc
Mutations of SGO2 and CLDN14 collectively cause coincidental Perrault syndrome
Authors: Faridi R. , Rehman A.U. , Morell R.J. , Friedman P.L. , Demain L. , Zahra S. , Khan A.A. , Tohlob D. , Assir M.Z. , Beaman G. , Khan S.N. , Newman W.G. , Riazuddin S. , Friedman T.B.
Published: September 2016

Perrault syndrome (PS) is a genetically heterogeneous disorder characterized by primary ovarian insufficiency (POI) in females and sensorineural hearing loss in males and females. In many PS subjects, causative variants have not been found in the five reported PS genes. The objective of this study was to identify the genetic cause of PS in an extended consanguineous family with six deaf individuals. Whole exome sequencing (WES) was completed on four affected members of a large family, and variants and co‐segregation was confirmed by Sanger sequencing. All hearing impaired individuals, including the proband, are homozygous for a pathogenic variant of CLDN14, but this only explains the deafness. The PS proband is also homozygous for a frameshift variant (c.1453_1454delGA, p.(Glu485Lysfs*5)) in exon 7 of SGO2 encoding shugoshin 2, which is the likely cause of her concurrent ovarian insufficiency. In mouse, Sgol2a encoding shugoshin‐like 2a is necessary during meiosis in both sexes to maintain the integrity of the cohesin complex that tethers sister chromatids. Human SGO2 has not previously been implicated in any disorder, but in this case of POI and perhaps others, it is a candidate for unexplained infertility.
Accounting for imperfect observation and estimating true species distributions in modelling biological invasions
Authors: Mang Thomas , Essl Franz , Moser Dietmar , Karrer Gerhard , Kleinbauer Ingrid , Dullinger Stefan
Published: September 2016

The documentation of biological invasions is often incomplete with records lagging behind the species’ actual spread to a spatio‐temporally heterogeneous extent. Such imperfect observation bears the risk of underestimating the already realised distribution of the invading species, misguiding management efforts and misjudging potential future impacts. In this paper, we develop a hierarchical modelling framework which disentangles the determinants of the invasion and observation processes, models spatio‐temporal heterogeneity in detection patterns, and infers the actual, yet partly undocumented distribution of the species at any particular time. We illustrate the model with a case study application to the invasion of common ragweed Ambrosia artemisiifolia in Austria. The invasion part of the model reconstructs the historical spread of this species across a grid of ∼ 6 × 6 km2 cells as driven by spatio‐temporal variation in physical site conditions, propagule production, dispersal, and ‘background’ introductions from unknown sources. The observation part models the detection of the species’ occurrences based on heterogeneous sampling efforts, human population density, and estimated local invasion level. We fitted the hierarchical model using a Bayesian inference approach with parameters estimated by Markov chain Monte Carlo (MCMC). The actual spread of A. artemisiifolia concentrated on the climatically well‐suited lowlands and was mainly driven by spatio‐temporal propagule pressure from source cells with long‐distance dispersal occurring rather frequently. Annual detection probabilities were estimated to vary between about 1 and up to 28%, depending mainly on sampling intensity. The model suggested that by 2005 about half of the actual distribution of the species was not yet documented. Our hierarchical model offers a flexible means to account for imperfect observation and spatio‐temporal variability in detection efficiency. Inferences can be used to disentangle aspects of the invasion dynamics itself from patterns of data collection, develop improved future surveying schemes, and design more efficient invasion management strategies.
Weak functional response to agricultural landscape homogenisation among plants, butterflies and birds
Authors: Jonason Dennis , Ekroos Johan , Öckinger Erik , Helenius Juha , Kuussaari Mikko , Tiainen Juha , Smith Henrik G. , Lindborg Regina
Published: September 2016

Measures of functional diversity are expected to predict community responses to land use and environmental change because, in contrast to taxonomic diversity, it is based on species traits rather than their identity. Here, we investigated the impact of landscape homogenisation on plants, butterflies and birds in terms of the proportion of arable field cover in southern Finland at local (0.25 km2) and regional (> 10 000 km2) scales using four functional diversity indices: functional richness, functional evenness, functional divergence and functional dispersion. No uniform response in functional diversity across taxa or scales was found. However, in all cases where we found a relationship between increasing arable field cover and any index of functional diversity, this relationship was negative. Butterfly functional richness decreased with increasing arable field cover, as did butterfly and bird functional evenness. For butterfly functional evenness, this was only evident in the most homogeneous regions. Butterfly and bird functional dispersion decreased in homogeneous regions regardless of the proportion of arable field cover locally. No effect of landscape heterogeneity on plant functional diversity was found at any spatial scale, but plant species richness decreased locally with increasing arable field cover. Overall, species richness responded more consistently to landscape homogenisation than did the functional diversity indices, with both positive and negative effects across species groups. Functional diversity indices are in theory valuable instruments for assessing effects of land use scenarios on ecosystem functioning. However, the applicability of empirical data requires deeper understanding of which traits reliably capture species’ vulnerability to environmental factors and of the ecological interpretation of the functional diversity indices. Our study provides novel insights into how the functional diversity of communities changes in response to agriculturally derived landscape homogenisation; however, the low explanatory power of the functional diversity indices hampers the ability to reliably anticipate impacts on ecosystem functioning.
Spatial extinction or persistence: landscape‐temperature interactions perturb predator–prey dynamics
Authors: Salt Jason L. , Bulit Celia , Zhang Wei , Qi Hongli , Montagnes David J. S.
Published: September 2016

Recognising that species interact across a range of spatial scales, we explore how landscape structure interacts with temperature to influence persistence. Specifically, we recognise that few studies indicate thermal shifts as the proximal cause of species extinctions; rather, species interactions exacerbated by temperature result in extinctions. Using microcosm‐based experiments, as models of larger landscape processes, we test hypotheses that would be problematic to address through field work. A text‐book predator–prey system (the ciliatesDidiniumandParamecium) was used to compare three landscapes: an unfragmented landscape subjected to uniform temperatures (10, 20, 30°C); a fragmented landscape (potentially hosting metapopulations) subjected to these three temperatures; and a fragmented landscape subjected to a spatial temperature gradient (∼ 10 to 30°C) – despite the prevalence of natural temperature ecoclines this is the first time such an analysis has been conducted. Initial thermal response‐analysis (growth, mortality, and movement measured between 10 and 30°C) suggested that as temperature increased, the predator might drive the prey to extinction. Thermal preferences (measured at 5 temperatures between 10 and 30°C), indicated that both predator and prey preferred warmer temperatures, with the predator exhibiting the stronger preference, suggesting that cooler regions might act as a prey‐refuge. The landscape level observations, however, did not entirely support the predictions. First, in the unfragmented landscape, increased temperature led to extinctions, but at the highest temperature (where the predator growth can be reduced) the prey survived. Second, at high temperatures the fragmented landscape failed to host metapopulations that would allow predator–prey persistence. Third, the thermal ecocline did not provide heterogeneity that improved stability; rather it forced both species to occupy a smaller realized space, leading toward extinctions. These findings reveal that temperature‐impacted rates and temperature preferences combine to drive predator–prey dynamics and persistence across landscapes.
The value of coarse species range maps to inform local biodiversity conservation in a global context
Authors: Maréchaux Isabelle , Rodrigues Ana S. L. , Charpentier Anne
Published: September 2016

Range maps of thousands of species, compiled and made freely available by the International Union for Conservation of Nature, are being increasingly applied to support spatial conservation planning. However, their coarse nature makes them prone to commission and omission errors, and they lack information on the variations in abundance within species’ distributions, calling into question their value to inform decisions at the fine scales at which conservation often takes place. Here, we tested if species ranges can reliably be used to estimate the responsibility of sites for the global conservation of species. We defined ‘specific responsibility’ as the fraction of a species’ population within a given site, considering it useful for prioritising species within sites; and defined ‘overall responsibility’ as the sum of specific responsibility across species within a site, assuming it informative of priorities among sites. Taking advantage of an exceptionally detailed dataset on the distribution and abundance of bird species at a near‐continental scale – a level of information rarely available to local decision‐makers – we created a benchmark against which we tested estimates of responsibility derived from range maps. We investigated approaches for improving these estimates by complementing range maps with plausibly available local data. We found that despite their coarse nature, range maps provided good estimates of sites’ overall responsibility, but relatively poor estimates of specific responsibility. Estimates were improved by combining range maps with local species lists or local abundance data, easily available through local surveys on the sites of interest, or simulated expert knowledge. Our results suggest that combining range maps with local data is a promising route for improving the effectiveness of local conservation decisions at contributing to reducing global biodiversity losses. This is all the more urgent in hyper‐diverse poorly‐known regions where conservation‐relevant decisions must proceed despite a paucity of biodiversity data.
Reversal learning strategy in adolescence is associated with prefrontal cortex activation
Authors: Boehme Rebecca , Lorenz Robert C. , Gleich Tobias , Romund Lydia , Pelz Patricia , Golde Sabrina , Flemming Eva , Wold Andrew , Deserno Lorenz , Behr Joachim , Raufelder Diana , Heinz Andreas , Beck Anne
Published: September 2016

Adolescence is a critical maturation period for human cognitive control and executive function. In this study, a large sample of adolescents (n = 85) performed a reversal learning task during functional magnetic resonance imaging. We analyzed behavioral data using a reinforcement learning model to provide individually fitted parameters and imaging data with regard to reward prediction errors (PE). Following a model‐based approach, we formed two groups depending on whether individuals tended to update expectations predominantly for the chosen stimulus or also for the unchosen one. These groups significantly differed in their problem behavior score obtained using the child behavior checklist (CBCL) and in a measure of their developmental stage. Imaging results showed that dorsolateral striatal areas covaried with PE. Participants who relied less on learning based on task structure showed less prefrontal activation compared with participants who relied more on task structure. An exploratory analysis revealed that PE‐related activity was associated with pubertal development in prefrontal areas, insula and anterior cingulate. These findings support the hypothesis that the prefrontal cortex is implicated in mediating flexible goal‐directed behavioral control.
Decreased photosynthesis and growth with reduced respiration in the model diatom Phaeodactylum tricornutum grown under elevated CO2 over 1800 generations
Authors: Li Futian , Beardall John , Collins Sinéad , Gao Kunshan
Published: September 2016

Studies on the long‐term responses of marine phytoplankton to ongoing ocean acidification (OA) are appearing rapidly in the literature. However, only a few of these have investigated diatoms, which is disproportionate to their contribution to global primary production. Here we show that a population of the model diatom Phaeodactylum tricornutum, after growing under elevated CO2 (1000 μatm, HCL, pHT: 7.70) for 1860 generations, showed significant differences in photosynthesis and growth from a population maintained in ambient CO2 and then transferred to elevated CO2 for 20 generations (HC). The HCL population had lower mitochondrial respiration, than did the control population maintained in ambient CO2 (400 μatm, LCL, pHT: 8.02) for 1860 generations. Although the cells had higher respiratory carbon loss within 20 generations under the elevated CO2, being consistent to previous findings, they downregulated their respiration to sustain their growth in longer duration under the OA condition. Responses of phytoplankton to OA may depend on the timescale for which they are exposed due to fluctuations in physiological traits over time. This study provides the first evidence that populations of the model species, P. tricornutum, differ phenotypically from each other after having been grown for differing spans of time under OA conditions, suggesting that long‐term changes should be measured to understand responses of primary producers to OA, especially in waters with diatom‐dominated phytoplankton assemblages.
Association between polypharmacy and cognitive impairment in an elderly Japanese population residing in an urban community
Authors: Niikawa Hirotoshi , Okamura Tsuyoshi , Ito Kae , Ura Chiaki , Miyamae Fumiko , Sakuma Naoko , Ijuin Mutsuo , Inagaki Hiroki , Sugiyama Mika , Awata Shuichi
Published: September 2016

Aim

Polypharmacy is a serious medical problem among older adults. Polypharmacy can cause adverse drug reactions and is associated with frailty. Several drugs, particularly psychotropic medications, can cause cognitive impairment. Recent research also suggests that polypharmacy can cause cognitive impairment. We investigated the prevalence of polypharmacy, and examined the association between polypharmacy and cognitive impairment in a large sample of community‐dwelling older adults in Japan.

Methods

A questionnaire covering sociodemographic variables was sent to all residents aged ≥65 years in an urban residential district of Tokyo, Japan (n = 7682). Next, 3000 individuals were randomly selected as study participants. A trained nurse and researcher interviewed participants in their own homes to obtain information about cognitive status, prescribed medications, and current medical history. Cognitive status was assessed using the Mini‐Mental State Examination. Polypharmacy was defined as treatment with six or more prescribed medications.

Results

Of the 1270 respondents who completed an interview, 1152 were included in the analysis of medications. The prevalence of polypharmacy was 28.0% (n = 323). When the older adults in the medications analysis were stratified by Mini‐Mental State Examination scores, polypharmacy was present in 48.3% of those scoring <24, and 25.7% of those scoring ≥24 (χ2 = 26.76, P < 0.001). After controlling for potential confounding factors (including psychotropic medications), a multivariate logistic regression analysis showed an association between polypharmacy and cognitive impairment (odds ratio 1.83, 95% confidence interval 1.10–3.02; P = 0.019).

Conclusions

Polypharmacy was associated with cognitive impairment among urban community‐dwelling older adults. Geriatr Gerontol Int 2017; 17: 1286–1293.
Formation and Dehydration Enthalpy of Potassium Hexaniobate
Authors: Sahu Sulata K. , Boatner Lynn A. , Navrotsky Alexandra
Published: September 2016

The formation energetics of hydrous and dehydrated potassium hexaniobates are investigated using high‐temperature oxide melt solution calorimetry. The enthalpies of formation of K4Nb6O17 and K4Nb6O17·3H2O from oxides are (−864.42 ± 10.63) and (−899.32 ± 11.48) kJ/mol, respectively. The formation enthalpy of K4Nb6O17 from elements is (−7289.64 ± 12.50) kJ/mol, and of K4Nb6O17·3H2O is (−8181.94 ± 13.24) kJ/mol. The enthalpy of dehydration (ΔHdehy) for the reaction K4Nb6O17·3H2O (xl, 25°C) = K4Nb6O17 (xl, 25°C) + 3H2O (l, 25°C) is endothermic and is 34.60 ± 7.56 kJ/mol. The ΔHdehy per mole of water, 11.53 ± 2.52 kJ/mol, indicates the water molecules in K4Nb6O17·3H2O are not just physically adsorbed, but loosely bonded in the K4Nb6O17 phase, presumably in specific interlayer sites. The loss of this water near 100°C on heating is consistent with the weak bonding of water.
Models Proposed to Explain the Electrical Conductivity of Polymer‐Derived Silicon Carbide Fibers
Authors: Hu Tianjiao , Li Xiaodong , Pu Wenjing , Chu Zengyong , Li Gongyi , Wang Qinghua
Published: September 2016

Two types of silicon carbide fibers (SiCf) were prepared employing different pyrolysis techniques. The relationship between the microstructure and the electrical resistivity of the fibers was investigated. The results indicated that the carbon layer present on the fiber surface acted as the main conductive phase in the SiCf obtained by direct pyrolysis, whereas a free carbon phase determined the conductivity of the SiCf prepared by the preheated pyrolysis method. A core‐shell model and a general effective media (GEM) theory were proposed to explain the conductivity of different types of SiCf. Quantitative analysis based on these models indicated an electrical resistivity of ~10−2 Ω·cm for the carbon layer on the surface of SiCf obtained by direct pyrolysis. The electrical resistivity and the percolation threshold of the free carbon in SiCf prepared by the preheated pyrolysis method were 10−1 Ω·cm and 11.3% respectively.
The Influence of Physical Properties of ZnO Films on the Efficiency of Planar ZnO/Perovskite/P3HT Solar Cell
Authors: Qiu Zhiwen , Yuan Shuai , Gong Haibo , Zhang Hailiang , Qiu Xiaofeng , Luo Ting , Cao Bingqiang
Published: September 2016

ZnO thin films prepared by pulsed laser deposition at low temperature are utilized as the electron transport layer in CH3NH3PbI3−xClx‐based perovskite solar cells with a planar heterojunction structure. Oxygen pressure greatly influences the transparent and conductive properties of ZnO films, which are extremely important as electron transport layer for the perovskite solar cells. The transparent and conductive properties of the films under different oxygen pressures are studied by ultraviolet‐visible spectrophotometer and Hall effect measurement system. Through controlling the oxygen pressure, transparent ZnO films with high conductivity are grown and adopted as electron transport layer for planar perovskite solar cell with a power conversion efficiency of 6.3%. After further surface modification of ZnO electron transport layer with [6,6]‐phenyl‐C61‐butyric acid methyl ester, the efficiency of the planar solar cell increases to 7.5%.