bluuebunny/crossref_metadata_2025 huggingface dataset:
bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays
Authors: Wang Kevin YX , Menzies Alexander M , Silva Ines P , Wilmott James S , Yan Yibing , Wongchenko Matthew , Kefford Richard F , Scolyer Richard A , Long Georgina V , Tarr Garth , Mueller Samuel , Yang Jean YH
Published: December 2017

Motivation: Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes are important tools in Gene Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene set selection bias induced during the construction of these platforms.

Results: We propose bcGST, a bias-corrected Gene Set Test by introducing bias correction terms in the contingency table needed for calculating the Fisher’s Exact Test (FET). The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and TCGA cancer studies.

Availability: The bcGST method is made available as a Shiny web application at http://shiny.maths.usyd.edu.au/bcGST/

Contact:kevin.wang@sydney.edu.au
MSAC: Compression of multiple sequence alignment files
Authors: Deorowicz Sebastian , Walczyszyn Joanna , Debudaj-Grabysz Agnieszka
Published: December 2017

Motivation

Bioinformatics databases grow rapidly and achieve values hardly to imagine a decade ago. Among numerous bioinformatics processes generating hundreds of GB is multiple sequence alignments of protein families. Its largest database, i.e., Pfam, consumes 40–230 GB, depending of the variant. Storage and transfer of such massive data has become a challenge.

Results

We propose a novel compression algorithm, MSAC (Multiple Sequence Alignment Compressor), designed especially for aligned data. It is based on a generalisation of the positional Burrows–Wheeler transform for non-binary alphabets. MSAC handles FASTA, as well as Stockholm files. It offers up to six times better compression ratio than other commonly used compressors, i.e., gzip. Performed experiments resulted in an analysis of the influence of a protein family size on the compression ratio.

Availability

MSAC is available for free at https://github.com/refresh-bio/msac and http://sun.aei.polsl.pl/REFRESH/msac.

Contact

sebastian.deorowicz@polsl.pl

Supplementary material

Supplementary data are available at the publisher Web site.
Whisper: Read sorting allows robust mapping of sequencing data
Authors: Deorowicz Sebastian , Debudaj-Grabysz Agnieszka , Gudyś Adam , Grabowski Szymon
Published: December 2017

Motivation

Mapping reads to a reference genome is often the first step in a sequencing data analysis pipeline. Mistakes made at this computationally challenging stage cannot be recovered easily.

Results

We present Whisper, an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement. Employing task and data parallelism as well as storing temporary data on disk result in superior time efficiency at reasonable memory requirements. Whisper excels at large NGS read collections, in particular Illumina reads with typical WGS coverage. The experiments with real data indicate that our solution works in about 15% of the time needed by the well-known Bowtie2 and BWA-MEM tools at a comparable accuracy (validated in variant calling pipeline).

Availability

Whisper is available for free from https://github.com/refresh-bio/Whisper or http://sun.aei.polsl.pl/REFRESH/Whisper/

Contact

sebastian.deorowicz@polsl.pl

Supplementary information

Supplementary data are available at publisher Web site.
Decoding the gene co-expression network underlying the ability of Gevuina avellana Mol. to live in diverse light conditions
Authors: Ostria-Gallardo E , Ranjan A , Ichihashi Y , Corcuera LJ , Sinha NR
Published: December 2017

Gevuina avellana Mol. (Proteaceae) is a typical tree from the South American temperate rainforest. Although this species mostly regenerates in shaded understories, it exhibits an exceptional ecological breadth, being able to live under a wide range of light conditions. Here we studied the genetic basis regulating physiological acclimation of the photosynthetic responses of G. avellana under contrasting light conditions.

We analyzed carbon assimilation and light energy used for photochemical process in plants acclimated to contrasting light conditions. Also, we used a transcriptional profile of leaf primordia from G. avellana saplings growing under different light environments to identify the gene co-expression network underpinning photosynthetic performance and light-related processes.

The photosynthetic parameters revealed optimal performance regardless of light conditions. Strikingly, the mechanism involved in dissipation of excess light energy showed no significant differences between high and low-light acclimated plants. The gene co-expression network defined a community structure consistent with the photochemical responses, including genes involved mainly in assembly and functioning of photosystems, photoprotection, and retrograde signaling.

Our ecophysiological genomics approach provides an understanding of the molecular regulatory mechanisms that allows this tree to have an optimal balance between photochemical, photoprotective and antioxidant performance in the diverse light habitats it encounters in nature.
Scaling of G1 duration with population doubling time by a cyclin inSaccharomyces cerevisiae
Authors: Blank Heidi M. , Callahan Michelle , Pistikopoulos Ioannis P.E. , Polymenis Aggeliki O. , Polymenis Michael
Published: December 2017

The longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells the length of the G1 phase (TG1) regressed on Tdwith a slope of ≈0.75, while in the yeastSaccharomyces cerevisiaethe slope was slightly smaller, at ≈0.60. On the other hand, cell size was not strongly associated with Tdor TG1in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short uORF in theCLN3transcript. Cln3p was also necessary for the proper scaling between TG1and Td. In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1and Td. These data reveal fundamental scaling relations between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relations in yeast and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.
A new recommendation system on the basis of consumer initiative decision based on an associative classification approach
Authors: Yin Chengxin , Guo Yan , Yang Jianguo , Ren Xiaoting
Published: December 2017

Purpose

The purpose of this paper is to improve the customer satisfaction by offering online personalized recommendation system.

Design/methodology/approach

By employing an innovative associative classification method, this paper is able to predict a customer’s pleasure during the online while-recommending process. Consumers can make an active decision to recommended products. Based on customer’s characteristics, a product will be recommended to the potential buyer if the model predicts that he/she will click to view the product. That is, he/she is satisfied with the recommended product. Finally, the feasibility of the proposed recommendation system is validated through a Taobao shop.

Findings

The results of the experimental study clearly show that the online personalized recommendation system maximizes the customer’s satisfaction during the online while-recommending process based on an innovative associative classification method on the basis of consumer initiative decision.

Originality/value

Conventionally, customers are considered as passive recipients of the recommendation system. However, customers are tired of the recommendation system, and they can do nothing sometimes. This paper designs a new recommendation system on the basis of consumer initiative decision. The proposed recommendation system maximizes the customer’s satisfaction during the online while-recommending process.
Exploring the sustainable logistics innovation process
Authors: Björklund Maria , Forslund Helena
Published: December 2017

Purpose

The development of more sustainable logistics calls for innovative thinking. In order to accelerate the development in the field, there is a need for increased understanding of the process behind successful implementation of sustainable logistics innovations (SLI). The purpose of this paper is to explore the SLI process, in order to identify critical factors, challenges as well as actors involved.

Design/methodology/approach

A multiple-case study in six Swedish retailers and logistics service providers (LSPs), successful in SLI implementations, was conducted. Both within-case and cross-case analyses were applied.

Findings

The SLI process consists of five phases. The positive relationship between formalisation and SLI success is supported. Critical activities and challenges not known from literature were found in each phase. Examples are the use of logistics and customer KPIs, quickness, developing simple concepts, using a sustainability business case template and selecting where to test SLIs. Some phases are involving many internal and external actors, while others involve few internal actors. Customers are not particularly involved, and retailers involve their LSP suppliers.

Research limitations/implications

This study addresses the lack of empirical research in logistics innovation and has bridged the gap of innovation studies in other companies than in LSPs. Furthermore it has combined two developing areas, sustainable innovation and logistics innovation, into SLI. A number of critical activities and challenges, and complex patterns for actors’ involvement in the SLI process phases are explored as insights from particular cases; these results could be analytically generalised to theory.

Practical implications

The practical implications lie in guiding managers who wish to improve sustainability and innovativeness in logistics and, consequently, business success. Knowledge from successful companies about which phases to go through in which sequence, which challenges that can be expected and who to include in the SLI process could imply that more companies focus on SLI.

Social implications

Knowledge on how to include sustainability in a clear innovation process, e.g., by making strong business cases, should imply an accelerated development of sustainable logistics in society.

Originality/value

This study addresses the lack of empirically-based research in logistics innovation and expands the concept to retailers.
Decision-making models for promoting consumption of low energy-intensive broadband terminal products in the Chinese telecommunication industry
Authors: Liu Qing , Zhao Senlin , Zhu Qinghua
Published: December 2017

Purpose

The purpose of this paper is to extend game analysis to explore decision-making mechanisms for promoting a specific type of products, low energy consumption for individual one while the total energy consumption is huge due to the high quantity of sales, that is, low for individual and high for total (LIHT) in terms of energy consumption.

Design/methodology/approach

Game models are developed to compare decisions of optimal prices for newly developed and environmentally friendly (NDEF) and regular products as well as associated sales quantity, profits, carbon emissions under different governmental policies, along with a case of low energy-intensive broadband terminal products in the Chinese telecommunication industry under the carbon tax and subsidy policies.

Findings

For both NDEF and regular products, optimal prices decrease under the subsidy policy while both increase under the tax policy. Manufacturers’ decision of optimal prices is highly relevant with unit carbon tax/subsidy and the consumers’ preference. Both the tax and subsidy policies can improve consumption of NDEF products while the subsidy policy can be more effective at the current initial stage.

Research limitations/implications

This paper provides decision support for manufacturers to promote sustainable consumption of LIHT products. Research ideas on models development and solutions for optimal prices can be applied to other LIHT products.

Practical implications

The results provide insights for governments on how to effectively evaluate and motivate sustainable consumption for LIHT products.

Originality/value

This paper first explores how to motivate sustainable consumption of LIHT products by developing models, examining effectiveness of potential governmental policies as well as associated carbon emissions.
Understanding the determinants of business intelligence system adoption stages
Authors: Puklavec Borut , Oliveira Tiago , Popovič Aleš
Published: December 2017

Purpose

The purpose of this paper is to provide a better understanding of the determinants of business intelligence system (BIS) adoption stages. It develops and empirically tests a conceptual model for assessing the determinants of BIS diffusion on the evaluation, adoption, and use stages in the context of small and medium enterprises (SMEs).

Design/methodology/approach

Drawing on data from 181 SMEs the influence of technological, organizational, and environmental factors on BIS adoption stages were analyzed using the PLS-SEM method.

Findings

The paper provides empirical insights about how technological, organizational, and environmental factors affect individual BIS adoption stages.

Practical implications

The paper includes implications for managers and solution providers to understand the influence of various determinants to more effectively conclude the adoption process.

Originality/value

This study represents important progress in the theoretical understanding of the role of technological, organizational, and environmental factors across the different BIS adoption stages.
Setting-up material handling network in manufacturing systems using graph theory
Authors: Gupta Shashank , Gupta Piyush
Published: December 2017

Purpose

Material handling (MH) is an important facility in any manufacturing system. It facilitates the transport of in-process material from one workstation (WS) to another. MH devices do imply incurring capital costs and, therefore, minimizing their deployment without compromising on smooth material flow will ensure savings in addition to the optimal use of productive shop floor space and, avoid space cluttering. The purpose of this paper is to evaluate the minimal network that connects all the WSs, therefore ensuring economic and safe manufacturing operations.

Design/methodology/approach

Graph theoretical approach and Prim’s algorithm for minimal spanning tree is used to evaluate the minimal span of the MH devices. The algorithm is initialized by translating the graph of WSs into a distance matrix to evaluate the minimal MH network.

Findings

The minimal length of the MH devices is evaluated for a typical case study.

Research limitations/implications

The step-by step methodology explained in the manuscript acts as a good guide for practicing operational managers. The shortcoming of the methodology is that, it presumes the use of modular MH devices that will need to be reconfigured based on dynamic changes to the manufacturing system.

Practical implications

The methodology is explained in detail to enable the practicing managers to use it for designing their MH networks in any manufacturing system.

Originality/value

There is no evidence to indicate the use of minimal spanning tree algorithm for design of MH networks in a manufacturing system. This paper attempts to fill this gap.
Calendar anomaly: unique evidence from the Indian stock market
Authors: Harshita Harshita , Singh Shveta , Yadav Surendra S.
Published: December 2017

Purpose

The purpose of this paper is to ascertain the monthly seasonality in the Indian stock market after taking into consideration the market features of leptokurtosis, volatility clustering and the leverage effect.

Design/methodology/approach

Augmented Dickey-Fuller, Phillips-Perron and Kwaitkowski-Phillips-Schmidt-Shin tests are deployed to check stationarity of the series. Autocorrelation function, partial autocorrelation function and Ljung-Box statistics are employed to check the applicability of volatility models. An exponential generalized auto regressive conditionally heteroskedastic model is deployed to test the seasonality, where the conditional mean equation is a switching model with dummy variables for each month of the year.

Findings

Though the financial year in India stretches from April to March, the stock market exhibits a November effect (returns in November are the highest). Cultural factors, misattribution bias and liquidity hypothesis seem to explain the phenomenon.

Research limitations/implications

The paper endeavors to provide a review of possible explanations behind month-of-the-year effect documented in literature in the past four decades. Further, the unique evidence from the Indian stock market supports the argument in the literature that monthly seasonality, by nature, may not be a consistent/robust phenomenon. Therefore, it needs to be examined from time to time.

Originality/value

As the seasonality in the stock market and resultant anomalies are dynamic phenomena, the paper reports the current seasonality/anomalies prevalent in the Indian market. This would aid investors in designing short-term investment portfolios (based on anomalies present) in order to earn abnormal returns.
Change in mental health collaborative care attitudes and practice in Australia
Authors: Murphy Barbara , Gibbs Chris , Hoppe Kate , Ratnaike Deepika , Lovelock Harry
Published: December 2017

Purpose

The Mental Health Professionals Network (MHPN) was established to support and enhance collaborative care among health professionals working in primary mental healthcare. The MHPN has two primary arms: face-to-face network meetings and online webinars. The purpose of this paper is to investigate attitudinal and practice changes amongst health professionals after participation in MHPN’s network meetings.

Design/methodology/approach

In April 2016, an online survey was e-mailed to health professionals who had attended at least one network meeting during 2015. The survey asked about practice changes across seven key areas relating to increased awareness of and interaction with professionals from other disciplines. Interdisciplinary differences were investigated using the χ2 statistic (p<0.05).

Findings

A total of 1,375 health professionals participated in the survey. For each of the seven practice changes investigated, between 74 and 92 per cent of respondents had made the change. Those who attended more network meetings were significantly more likely to have made changes. General practitioners were significantly more likely than other professionals to have made changes.

Research limitations/implications

Attendance at MHPN network meetings has a positive impact on health professionals’ attitudes and practices towards a more collaborative approach to mental healthcare.

Originality/value

MHPN is a unique, national platform successfully delivering opportunities for interdisciplinary professional development in the primary mental health sector. The model is unique, cost-effective, practitioner driven and transferable to other settings.
Are academic libraries utilized to produce engaged alumni?
Authors: Griffith Andrew S. , Kealty Ceire
Published: December 2017

Purpose

The purpose of this paper is to explain the relationship alumni may have with their institution’s library and its effect on student success, which, in turn, produces more engaged alumni.

Design/methodology/approach

This paper provides a base interaction model that describes this relationship.

Findings

Libraries are well positioned to not only engage current students but to establish the foundation for these students to become engaged alumni.

Originality/value

This base relationship model may help with advocating for secure funds of libraries and/or a higher priority for fundraising.
Agency in advanced liberal services: grounding sociological knowledge in homeless people's accounts
Authors: Parsell Cameron , Clarke Andrew
Published: December 2017

This paper aims to understand how people who are homeless respond to advanced liberal social services that endeavour to promote their autonomy and responsible actions. We prioritize the experiences and positions of people who are homeless, and what agentic action means to them. Sociological literature is selective about what accounts are deemed agentic. Agency is associated with accounts that resist or subvert dominant neoliberal framings of homelessness as failure of individuals. When people experiencing homelessness or poverty themselves foreground autonomy or responsibility, sociologists treat them as cultural dopes who have internalized neoliberal discourse. Our analysis is driven by an ethnographic study in an Australian homelessness shelter. We demonstrate how people who are homeless neither outright reject nor completely embrace advanced liberal practices to influence their actions and promote autonomy. People engaged in relational reasoning. Paternalist and advanced liberal social services were both lauded and rejected for their capacities and limitations to realize a good life. We contribute to the discussion for sociology to value people's accounts and experiences, rather than broader social process explaining their accounts. From the perspectives of people who are homeless, we show that just because something appears neoliberal does not mean it should be automatically rejected.
The Capitalisation of CAP Payments into Land Rental Prices: A Panel Sample Selection Approach
Authors: Guastella Gianni , Moro Daniele , Sckokai Paolo , Veneziani Mario
Published: December 2017

The empirical literature suggests that farmland prices and rents capitalise agricultural subsidies and that the 2003 reform of the EU Common Agricultural Policy, which decoupled subsidies from production and attached them to land, may have increased the extent of the phenomenon. Employing a farm‐level dataset, the Farm Accountancy Data Network (FADN) for Italy, we investigate this issue while accounting for selectivity, endogeneity and unobserved individual heterogeneity. To understand the impact of the reform we compare the estimates of capitalisation rate for decoupled payments with those for coupled payments. After correcting for unobserved individual heterogeneity and selectivity, our results reveal no capitalisation of coupled payments and only limited capitalisation of decoupled area payments into farmland rents in Italy.
Genetic variation and potential coinfection of Wolbachia among widespread Asian citrus psyllid (Diaphorina citri Kuwayama) populations
Authors: Chu Chia‐Ching , Hoffmann Mark , Braswell W. Evan , Pelz‐Stelinski Kirsten S.
Published: December 2017

Wolbachia can profoundly influence the survival, reproduction, and defenses of insect hosts. These interactions could potentially be harnessed for managing pests or insect‐transmitted diseases. Diaphorina citri Kuwayama is a phloem‐feeding pest capable of transmitting the putative causal agent of citrus greening, Candidatus Liberibacter asiaticus (CLas). Like many insects, D. citri is also infected with Wolbachia (wDi). Recent studies indicate that the relative abundance of wDi could be associated with the abundance of CLas, and that wDi may contribute to regulating expression of phage lytic cycle genes in CLas, suggesting the need for better understanding of wDi biology in general. This study investigated the genetic diversity of wDi among D. citri in populations spanning eleven countries and two U.S. territories. Six Wolbachia genes, wsp, coxA, fbpA, ftsZ, gatB, and hcpA, were sequenced and compared across samples. Two prevalent wDi strains were identified across the samples, and screening of clone libraries revealed possible coinfection of wDi strains in specific populations. D. citri mitochondrial cytochrome oxidase subunit I gene (mtCOI) were more divergent between D. citri populations that were infected with different wDi strains or had different infection statuses (single infection vs. coinfection). While we could not eliminate the possibility that maternal transmission may contribute to such patterns, it is also possible that wDi may induce cytoplasmic incompatibility in their host. These findings should contribute to the understanding of wDi population ecology, which may facilitate manipulation of this endosymbiont for management of citrus greening disease worldwide.
Detecting Deception in Our Research Participants: Are Your Participants Who You Think They Are?
Authors: McCaul Mary E. , Wand Gary S.
Published: December 2017

There is increasing awareness of the potential negative impacts of participant deception on research, including possibly undermining reliability and reproducibility of study findings. These deceptive individuals set their personal interests above the rules of study participation, thereby jeopardizing data quality as well as placing themselves and others at risk. The costs of participant deception are numerous. Overall, it reduces statistical power and may even result in false conclusions about efficacy and safety. To date, most studies have not utilized sufficient methods to detect rule‐breaking subjects. The purpose of this article is to bring to the attention of alcohol and other drug researchers issues involving deceptive participants. The review will suggest alcohol‐specific as well as more general strategies to identify and thereby minimize enrollment of these deceptive participants. Specifically, we will identify strategies that are employed in different phases of human alcohol research and advance approaches that may be helpful to the field in reducing these contaminants. As a field, we need to be more proactive in identifying the deceptive participant even at the cost of more burdensome study enrollment. In light of the systemic nature and multipronged damage that this emerging pattern of deception inflicts on clinical research, it is imperative that we each assume greater responsibility for our role in mitigating this source of research contamination.
The associations between psychotic experiences and substance use and substance use disorders: findings from the World Health Organization World Mental Health surveys
Authors: Degenhardt Louisa , Saha Sukanta , Lim Carmen C. W. , Aguilar‐Gaxiola Sergio , Al‐Hamzawi Ali , Alonso Jordi , Andrade Laura H. , Bromet Evelyn J. , Bruffaerts Ronny , Caldas‐de‐Almeida José Miguel , de Girolamo Giovanni , Florescu Silvia , Gureje Oye , Haro Josep M. , Karam Elie G. , Karam Georges , Kovess‐Masfety Viviane , Lee Sing , Lepine Jean‐Pierre , Makanjuola Victor , Medina‐Mora Maria E. , Mneimneh Zeina , Navarro‐Mateu Fernando , Piazza Marina , Posada‐Villa José , Sampson Nancy A. , Scott Kate M. , Stagnaro Juan Carlos , Ten Have Margreet , Kendler Kenneth S. , Kessler Ronald C. , McGrath John J. ,   on behalf of the WHO World Mental Health Survey Collaborators
Published: December 2017

Background and aims

Prior research has found bidirectional associations between psychotic experiences (PEs) and selected substance use disorders. We aimed to extend this research by examining the bidirectional association between PEs and various types of substance use (SU) and substance use disorders (SUDs), and the influence of antecedent mental disorders on these associations.

Design, setting, participants and measurements

We used data from the World Health Organization World Mental Health surveys. A total of 30 902 adult respondents across 18 countries were assessed for (a) six types of life‐time PEs, (b) a range of types of SU and DSM‐IV SUDs and (c) mental disorders using the Composite International Diagnostic Interview. Discrete‐time survival analyses based on retrospective age‐at‐onset reports examined the bidirectional associations between PEs and SU/SUDs controlling for antecedent mental disorders.

Findings

After adjusting for demographics, comorbid SU/SUDs and antecedent mental disorders, those with prior alcohol use disorders [odds ratio (OR) = 1.6, 95% confidence interval (CI) = 1.2–2.0], extra‐medical prescription drug use (OR = 1.5, 95% CI = 1.1–1.9), alcohol use (OR = 1.4, 95% CI = 1.1–1.7) and tobacco use (OR = 1.3, 95% CI = 1.0–1.8) had increased odds of subsequent first onset of PEs. In contrast, those with temporally prior PEs had increased odds of subsequent onset of tobacco use (OR = 1.5, 95% CI = 1.2–1.9), alcohol use (OR = 1.3, 95% CI = 1.1–1.6) or cannabis use (OR = 1.3, 95% CI = 1.0–1.5) as well as of all substance use disorders (ORs ranged between 1.4 and 1.5). There was a dose response relationship between both count and frequency of PEs and increased subsequent odds of selected SU/SUDs.

Conclusions

Associations between psychotic experiences (PEs) and substance use/substance use disorders (SU/SUDs) are often bidirectional, but not all types of SU/SUDs are associated with PEs. These findings suggest that it is important to be aware of the presence of PEs within those with SUDs or at risk of SUDs, given the plausibility that they may each impact upon the other.
The effect of forest canopy and flood disturbance on New Zealand stream food web structure and robustness
Authors: Canning A. D. , Death R. G. , Gardner E. M.
Published: December 2017

The effects of disturbance on communities have been a focus of both theoretical and empirical inquiries for many years. Food web stability is hypothesized to be affected by disturbance and the nature of the energy pathways (i.e. allochthonous or autochthonous) of a community. In this study, we investigated whether food webs at paired sites, one in forest and the other in grassland, in ten New Zealand streams along a disturbance gradient differ in their topological structure and robustness. Food web robustness (an indicator of web resistance) assesses the ease with which secondary extinctions permeate the food web following an initial random extinction (disturbance). We found that neither the nature of the energy source nor physical disturbance affected structural metrics or web robustness. As stream systems, particularly in New Zealand, are exposed to regular, unpredictable and dramatic physical disturbance from flooding, it may simply be that the floods result in generalist species dominating and increasing robustness irrespective of the energy source.
Hyperbaric oxygen therapy: An alternative treatment for radiation‐induced cutaneous ulcers
Authors: Fernández Canedo Inés , Padilla España Laura , Francisco Millán Cayetano José , Repiso Jiménez Juan Bosco , Pérez Delgado Manuel , de Troya Martín Magdalena
Published: December 2017

Radiotherapy is a widely recognised treatment for non‐melanoma skin cancer. We report three cases of radiation‐induced skin ulcers in which hyperbaric oxygen therapy was administered in 90‐min sessions, 5 days a week at 2.4 absolute atmospheres in a multiplace hyperbaric chamber. Hyperbaric oxygen therapy is an outpatient treatment that does not displace other classical treatments and may be used as an adjunct therapy.
Estimation of dietary threonine requirement using plasma amino acid concentrations in mature thoroughbreds
Authors: Yoshida Tatsuyuki , Ohta Yoshiyuki
Published: December 2017

The experiment was conducted to estimate dietary threonine (Thr) requirement using plasma amino acid concentrations as a criterion in mature thoroughbreds. Four adult thoroughbreds were used, and a 4 × 4 Latin square design was used for four dietary Thr levels. Plasma Thr concentration was constant until 0.41%, and then increased rapidly with increasing dietary Thr levels. The Thr requirement was estimated to be 67% of lysine with plasma Thr concentration at four Thr levels.
Expression, distribution and function of kinin B1 receptor in the rat diabetic retina
Authors: Hachana Soumaya , Bhat Menakshi , Sénécal Jacques , Huppé‐Gourgues Frédéric , Couture Réjean , Vaucher Elvire
Published: December 2017

Background and Purpose

The kinin B1 receptor contributes to vascular inflammation and blood‐retinal barrier breakdown in diabetic retinopathy (DR). We investigated the changes in expression, cellular localization and vascular inflammatory effect of B1 receptors in retina of streptozotocin diabetic rats.

Experimental Approach

The distribution of B1 receptors on retinal cell types was investigated by immunocytochemistry. Effects of B1 receptor agonist, R‐838, and antagonist, R‐954, on retinal leukocyte adhesion, gene expression of kinin and VEGF systems, B1 receptor immunoreactivity, microgliosis and capillary leakage were measured. Effect of B1 receptor siRNA on gene expression was also assessed.

Key Results

mRNA levels of the kinin and VEGF systems were significantly enhanced at 2 weeks in streptozotocin (STZ)‐retina compared to control‐retina and were further increased at 6 weeks. B1 receptor mRNA levels remained increased at 6 months. B1 receptor immunolabelling was detected in vascular layers of the retina, on glial and ganglion cells. Intravitreal R‐838 amplified B1 and B2 receptor gene expression, B1 receptor levels (immunodetection), leukostasis and vascular permeability at 2 weeks in STZ‐retina. Topical application (eye drops) of R‐954 reversed these increases in B1 receptors, leukostasis and vascular permeability. Intravitreal B1 receptor siRNA inhibited gene expression of kinin and VEGF systems in STZ‐retina. Microgliosis was unaffected by R‐838 or R‐954 in STZ‐retina.

Conclusion and Implications

Our results support the detrimental role of B1 receptors on endothelial and glial cells in acute and advanced phases of DR. Topical application of the B1 receptor antagonist R‐954 seems a feasible therapeutic approach for the treatment of DR.
2‐anilino‐4‐amino‐5‐aroylthiazole‐type compound AS7128 inhibits lung cancer growth through decreased iASPP and p53 interaction
Authors: Cheng Hao‐Wei , Chein Rong‐Jie , Cheng Ting‐Jen , Wu Pei‐Shan , Wu Hsin‐Yi , Hung Pei‐Fang , Wang Chia‐Jen , Hsu Yuan‐Ling , Wong Jau‐Min , Yuan Ang , Wong Chi‐Huey , Yang Pan‐Chyr , Pan Szu‐Hua
Published: December 2017

Lung cancer is the leading cause of cancer‐related death worldwide. Thus, developing novel therapeutic agents has become critical for lung cancer treatment. In this study, compound AS7128 was selected from a 2‐million entry chemical library screening and identified as a candidate drug against non‐small cell lung cancer in vitro and in vivo. Further investigation indicated that AS7128 could induce cell apoptosis and cell cycle arrest, especially in the mitosis stage. In addition, we also found that iASPP, an oncogenic protein that functionally inhibits p53, might be associated with AS7128 through mass identification. Further exploration indicated that AS7128 treatment could restore the transactivation ability of p53 and, thus, increase the expressions of its downstream target genes, which are related to cell cycle arrest and apoptosis. This occurs through disruption of the interactions between p53 and iASPP in cells. Taken together, AS7128 could bind to iASPP, disrupt the interaction between iASPP and p53, and result in cell cycle arrest and apoptosis. These findings may provide new insight for using iASPP as a therapeutic target for non‐small cell lung cancer treatment.
Case‐based surveillance study in judicial districts in Turkey: Child sexual abuse sample from four provinces
Authors: Sofuoglu Zeynep , Cankardas Nalbantcilar Sinem , Oral Resmiye , Ince Basak
Published: December 2017

Child sexual abuse is a universal public health problem. Although studies have reported that 11% to 37% of children have been sexually abused in Turkey, no accurate information is available. Thus, this study aims to investigate child sexual abuse cases registered in legal databases in select provinces in Turkey to improve our epidemiological understanding of regionally reported cases. The sample of this study consists of child sexual abuse cases filed with courthouses in four provinces in Turkey under Articles 103 and 104 of the Turkish Criminal Law, between October 2010 and October 2011. Retrospective review of these case files revealed 1,005 cases, 86% female, and 45.7% both sexually abused and exposed to other forms of abuse. Sexual abuse was often accompanied by physical abuse. Regarding the relationship of the perpetrator to the victim, 14.3% of perpetrators were found to be family members. There was also a significant relationship between child's gender and perpetrator's relationship to the victim; boys were abused mostly by strangers (55.7%) and girls by their peers (54.9%).
Two‐year observational study of deferiprone in superficial siderosis
Authors: Kessler Remi A. , Li Xu , Schwartz Kateryna , Huang Hwa , Mealy Maureen A. , Levy Michael
Published: December 2017

Introduction

Superficial siderosis is a rare, neurodegenerative disease caused by toxic accumulation of hemosiderin on the surface of the brain and the spinal cord, most commonly from chronic subarachnoid hemorrhage.

Aims

The aim of this study was to assess the clinical and radiological outcomes of superficial siderosis patients using deferiprone, a cell permeant iron chelator. Subjects obtained pre‐ and post‐treatment brain MRIs and weekly laboratory tests. Osirix software was used to develop a method of quantifying hemosiderin deposition. Three‐dimensional whole brain images of gradient echo images were rendered and compared by dividing the mean T2 hyperintensity to the maximal cerebrospinal fluid signal.

Results

A total of 38 subjects completed the study, of which clinical and radiological data were available for 30. The average age was 64 years (range 37‐86), 53% were male, 94% were white. Nineteen subjects (63%) reported either no progression of disease or an improvement in at least one neurological domain, with 40% of patients reporting a stabilization in hearing function and 30% reporting stable or improved coordination and walking. By MRI, there was an overall mean increase in T2 hyperintensity of the whole brain of 1%‐13% over the 2‐year time period in half of patients, indicating a reduction hemosiderosis. There were no cases of agranulocytosis, and declines of white blood cells counts and neutrophils averaged <10%. Fatigue was the most common side effect.

Conclusion

This is the first long‐term prospective study of superficial siderosis on the iron chelator, deferiprone. MRI quantification of hemosiderin appears to demonstrate a measurable reduction in half of patients and this correlated with a stabilized or improving disease course. A future placebo‐controlled trial is necessary to determine whether deferiprone is an effective therapy for superficial siderosis.
Isolated coarctation of the aorta in the fetus: A diagnostic challenge
Authors: Kailin Joshua A. , Santos Alexia B. , Yilmaz Furtun Betul , Sexson Tejtel S. Kristen , Lantin‐Hermoso Regina
Published: December 2017

Isolated coarctation of the aorta (CoA) is estimated by the Centers for Disease Control and Prevention to account for 4%–6% of all congenital heart disease (CHD) in the United States, with a reported prevalence of ~4 per 10 000 live births. Prenatal recognition of coarctation is important as it may improve neonatal survival and reduce morbidity. However, despite advances in imaging and the trend toward detailed aortic arch assessment as part of a comprehensive fetal echocardiogram, isolated CoA may still elude prenatal detection, with potentially lethal consequences if the diagnosis is not suspected and the patent ductus arteriosus (PDA) closes spontaneously in postnatal life. The purpose of this review is to outline the methods of antenatal aortic arch evaluation in the current era, discuss “red flags” that raise the suspicion for CoA, including associated anomalies and serve as a repository of the most up to date information regarding its diagnosis in utero and its perinatal management. Other aortic arch abnormalities, such as interrupted aortic arch, or CoA associated with complex single ventricles, are not included in this review.
A brief history of fetal echocardiography and its impact on the management of congenital heart disease
Authors: Maulik Dev , Nanda Navin C. , Maulik Devika , Vilchez Gustavo
Published: December 2017

Congenital heart disease (CHD), the most common congenital malformation, is associated with adverse outcome. Development of fetal echocardiography has made prenatal diagnosis of CHD a reality, and in the process revolutionized its management. This historical review briefly narrates this development over the decades focusing on the emergence of the primary modalities of fetal echocardiography comprised of the time‐motion mode, two‐dimensional B‐mode, spectral Doppler, color Doppler, and three‐ and four‐dimensional cardiac imaging. Collaboration between clinicians and engineers has been central to these advances. Also discussed are the accuracy and impact of fetal echocardiography on the management of CHD, and especially its role in the prenatal diagnosis of critical CHD in individualizing the management and improving the outcome. Despite these advances, most cases of CHD are not identified prenatally, emphasizing the continuing need for further technological and educational innovation and improvement.
A long‐term habitat fragmentation experiment leads to morphological change in a species of carabid beetle
Authors: EVANS MALDWYN J. , BANKS SAM C. , BARTON PHILIP S. , DAVIES KENDI F. , DRISCOLL DON A.
Published: December 2017

1. Habitat fragmentation and transformation are key drivers of species declines in landscapes. Most of the current understanding of species' responses to environmental change originates from studies of populations and communities. However, phenotypic variation offers another key aspect of species responses and could provide additional insights into the functional drivers of population change.

2. The goal of this study was to address this gap by exploring the morphological changes of a species of carabid beetle (Notonomus resplendens) with a known population response to the Wog Wog Habitat Fragmentation Experiment in Australia. We measured morphological traits associated with body size, head width, and dispersal ability. We quantified patterns of morphological variation over time and between nativeEucalyptusforest fragments and the surrounding pine plantation matrix and the continuous intact nativeEucalyptusforest controls.

3. We found sexually dimorphic morphological changes in response to the experimental treatments. Males increased in size, had larger legs and had smaller interocular widths in the matrix in both the short and long terms. Conversely, females became comparatively smaller and had increased interocular widths in the same treatments. Effects in the fragments were similar to those in the matrix, but exhibited more uncertainty.

4. Our results demonstrate that species can show morphological change in response to environmental change over very short time periods. We demonstrate that using both population and morphological data allows stronger inferences about the mechanisms behind species responses to environmental change.
Systematic review of infectious events with the Bruton tyrosine kinase inhibitor ibrutinib in the treatment of hematologic malignancies
Authors: Tillman Benjamin F. , Pauff James M. , Satyanarayana Gowri , Talbott Mahsa , Warner Jeremy L.
Published: December 2017

Objective

Ibrutinib is an irreversible inhibitor of Bruton tyrosine kinase (BTK) in B lymphocytes as well as other kinases including interleukin‐2‐inducible T‐cell kinase (ITK) in CD4+ Th2 regulatory T cells. Increased infections have been observed in patients taking ibrutinib. The overall incidence has not been systematically evaluated.

Methods

The published literature and conference abstracts of prospective clinical trials using ibrutinib in hematologic malignancies were identified and reviewed using PubMed, Google Scholar, and HemOnc.org per PRISMA guidelines. Infectious events with a focus on pneumonia were collated per the Common Terminology Criteria for Adverse Events Version 4.03 grading.

Results

Infectious complications are common, occurring in 56% of patients taking single‐agent ibrutinib and 52% of those on combination therapy. Approximately one in 5 patients developed pneumonia, which was the major contributor to a 2% rate of death from infections. Many of the cases of pneumonia were due to opportunistic pathogens.

Conclusions

Ibrutinib use requires prudent consideration of the impacts on host immunity. We identified a high rate of serious adverse infectious events within prospective clinical trials. Data suggest a role of both BTK and ITK inhibition for the increased events. There was considerable variability in the reporting of adverse events between trials, journals, and conference reports.
Disease and treatment characteristics of polycythemia vera patients in Belgium: Results from a scientific survey
Authors: Devos Timothy , Beguin Yves , Noens Lucien , Van Eygen Koen , Zachée Pierre , Mineur Philippe , Knoops Laurent , Doyen Chantal , Theunissen Koen , Benghiat Fleur Samantha , Reusens Michael , Pluymers Wim
Published: December 2017

Objective

The current survey aimed to gather predefined disease parameters and treatment strategies to characterize the polycythemia vera (PV) patient population in Belgium.

Methods

Cross‐sectional data from PV patients, seen at least once between May 2014 and May 2015 at 10 sites in Belgium, were collected in aggregated form and analyzed descriptively and quantitatively.

Results

Data from 343 PV patients were collected. Of these, 174 (50.7%) were male and 256 (74.6%) were ≥60 years of age. Ninety‐two (26.8%) had a prior history of thrombotic events. Considerable proportions of patients had increased hematological parameters (hematocrit > 45% [31.2%], leukocytes > 10 × 109/L [33.3%], and platelet > 400 × 109/L [38.2%]). Most patients had non‐palpable spleen (284, 87.7%) and no phlebotomies during the past 6 months (197, 57.4%). Low‐dose aspirin was given as thrombosis prophylaxis in 249 (72.6%) patients, while 232 (67.6%) received hydroxyurea (HU) as cytoreductive treatment. Forty‐one patients (12.0%) were reported as resistant and/or intolerant to HU. Seventeen patients (5.0%) received ruxolitinib in the context of clinical trials.

Conclusion

This survey provides better insight into the characteristics of Belgian PV patients and currently used treatment strategies. It shows that 232 (67.6%) PV patients continue to receive HU despite being potentially HU‐resistant.