bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes
Authors: Fernandes Daniel , Sirak Kendra , Novak Mario , Finarelli John , Byrne John , Connolly Edward , Carlsson Jeanette EL , Ferretti Edmondo , Pinhasi Ron , Carlsson Jens 
Published: September 2016

ABSTRACTThomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison's grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent's DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as “forced homozygote approach”. The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.
Harnessing Big Data for Systems Pharmacology
Authors: Xie Lei , Draizen Eli J. , Bourne Philip E. 
Published: September 2016

AbstractSystems pharmacology aims to holistically understand genetic, molecular, cellular, organismal, and environmental mechanisms of drug actions through developing mechanistic or predictive models. Data-driven modeling plays a central role in systems pharmacology, and has already enabled biologists to generate novel hypotheses. However, more is needed. The drug response is associated with genetic/epigenetic variants and environmental factors, is coupled with molecular conformational dynamics, is affected by possible off-targets, is modulated by the complex interplay of biological networks, and is dependent on pharmacokinetics. Thus, in order to gain a comprehensive understanding of drug actions, systems pharmacology requires integration of models across data modalities, methodologies, organismal hierarchies, and species. This imposes a great challenge on model management, integration, and translation. Here, we discuss several upcoming issues in systems pharmacology and potential solutions to them using big data technology. It will allow systems pharmacology modeling to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable.
Baptists in Burma: collaboratively mapping missionary archives
Authors: Finnell Joshua 
Published: September 2016

Purpose
– The purpose of this case study is to discuss and analyze the process of developing and sustaining a multi-institutional digital humanities projects across several institutions.

Design/methodology/approach
– This case study will provide an overview of a multi-institutional digital humanities project from the planning phase to implementation. In particular, this case study will discuss identifying institutional partners, collaborating with a design, designing for curricular integration and best practices for sustaining a project of this size and scope.

Findings
– Sustainable collaboration develops slowly over time. Communication and consensus-building are key components to completing and sustaining a multi-institutional digital project. Scalable design is a crucial step in planning for project expansion.

Originality/value
– Though many journal articles articulate “best practices” for collaboration among geographically dispersed institutions, very few case studies discuss “best practices” within the context of project development, from initial idea to completion.
Classification of Opium by UPLC‐Q‐TOF Analysis of Principal and Minor Alkaloids
Authors: Liu Cuimei , Hua Zhendong , Bai Yanping 
Published: September 2016

AbstractOpium is the raw material for the production of heroin, and the characterization of opium seizures through laboratory analysis is a valuable tool for law enforcement agencies to trace clandestine opium production and trafficking. In this work, a method for opium profiling based on the relative content of five principal and 14 minor opium alkaloids was developed and validated. UPLC‐Q‐TOF was adopted in alkaloid analysis for its high selectivity and sensitivity, which facilitated the sample preparation and testing. The authentic sample set consisted of 100 “Myanmar” and 45 “Afghanistan” opium seizures; based on the data set of the 19 alkaloid variables in them, a partial least squares discriminant analysis classification model was successfully achieved. Minor alkaloids were found to be vitally important for opium profiling, although combined use of both principal and minor alkaloids resulted in the best geographical classification result. The developed method realized a simple and accurate way to differentiate opium from Myanmar and Afghanistan, which may find wide application in forensic laboratories.
Auditor Choice and Its Implications for Group‐Affiliated Firms
Authors: Fang Junxiong , Pittman Jeffrey , Zhang Yinqi , Zhao Yuping 
Published: September 2016

AbstractWe examine which of two opposing financial reporting incentives that group‐affiliated firms experience shapes their accounting transparency evident in auditor choice. In one direction, complex group structure and intragroup transactions enable controlling shareholders to pursue diversionary activities that they later hide by distorting reported earnings. In the other direction, as outside investors price‐protect against potential expropriation, controlling shareholders may be eager to improve financial reporting quality in order to alleviate agency costs. To empirically clarify whether group affiliation affects company insiders' incentives to address minority shareholders' concerns over agency costs, we examine auditor selection of group firms relative to stand‐alone firms. In comparison to nongroup firms, our evidence implies that group firms are more likely to appoint Top 10 audit firms in China, especially when their controlling shareholders have stronger incentives to improve external monitoring of the financial reporting process. After isolating group firms, we find that the presence of a Top 10 auditor translates into higher earnings and disclosure quality, higher valuation implications for related‐party transactions, and cheaper equity financing, implying that these firms benefit from engaging a high‐quality auditor. In additional analysis consistent with our predictions, we find that group firms that are Top 10 clients pay higher audit fees and their controlling shareholders are more constrained against meeting earnings benchmarks through intragroup transactions and siphoning corporate resources at the expense of minority investors. Collectively, our evidence supports the narrative that insiders in firms belonging to business groups weigh the costs and benefits stemming from auditor choice.
Trophic cascades in 3D: network analysis reveals how apex predators structure ecosystems
Authors: Wallach Arian D. , Dekker Anthony H. , Lurgi Miguel , Montoya Jose M. , Fordham Damien A. , Ritchie Euan G. 
Published: September 2016

Summary

Trophic cascade theory predicts that apex predators structure ecosystems by regulating mesopredator and herbivore abundance and behaviour. Studies on trophic cascades have typically focused on short linear chains of species interactions. A framework that integrates more realistic and complex interactions is needed to make broader predictions on ecosystem structuring.

Network analysis is used to study food webs and other types of species interaction networks. These often comprise large numbers of species but rarely account for multiple interaction types and strengths. Here, we develop an intermediate complexity theoretical framework that allows specification of multiple interaction types and strengths for the study of trophic cascades. This ecological network is designed to suit data typically derived from field‐based studies. The trophic cascade network contains fewer nodes than food webs, but provides semi‐weighted directional links that enable different types of interactions to be included in a single model.

We use this trophic cascade network model to explore how an apex predator shapes ecosystem structure in an Australian arid ecosystem. We compared two networks that contrasted in the dominance of an apex predator, the dingo (Canis dingo), using published results ranking the direction and strength of key interactions. Nodes and links interacted dynamically to shape these networks. We examined how changes to an apex predator population affect ecosystem structure through their direct and indirect influences on different components of this ecological community.

Under strong apex predator influence, the network structure was denser and more complex, even and top‐down driven; and dingo predation and soil commensalism formed denser interactive modules. Under weak apex predator influence (e.g. reflecting predator control), the resulting network structure was frayed, with mesopredator predation and grazing forming modules.

Our study demonstrates that networks of intermediate complexity can provide a powerful tool for elucidating potential ecosystem‐wide effects of apex predators and predicting the consequences of management interventions such as predator control. Integrating trophic cascades, with their array of complex interactions, with the three‐dimensional structure of ecological networks, has the potential to reveal ‘ecological architecture’ that neither captures on its own.
Anti‐ageing active ingredients from herbs and nutraceuticals used in traditional Chinese medicine: pharmacological mechanisms and implications for drug discovery
Authors: Shen Chun‐Yan , Jiang Jian‐Guo , Yang Li , Wang Da‐Wei , Zhu Wei 
Published: September 2016

Ageing, an unanswered question in the medical field, is a multifactorial process that results in a progressive functional decline in cells, tissues and organisms. Although it is impossible to prevent ageing, slowing down the rate of ageing is entirely possible to achieve. Traditional Chinese medicine (TCM) is characterized by the nourishing of life and its role in anti‐ageing is getting more and more attention. This article summarizes the work done on the natural products from TCM that are reported to have anti‐ageing effects, in the past two decades. The effective anti‐ageing ingredients identified can be generally divided into flavonoids, saponins, polysaccharides, alkaloids and others. Astragaloside, Cistanche tubulosa acteoside, icariin, tetrahydrocurcumin, quercetin, butein, berberine, catechin, curcumin, epigallocatechin gallate, gastrodin, 6‐Gingerol, glaucarubinone, ginsenoside Rg1, luteolin, icarisid II, naringenin, resveratrol, theaflavin, carnosic acid, catalpol, chrysophanol, cycloastragenol, emodin, galangin, echinacoside, ferulic acid, huperzine, honokiol, isoliensinine, phycocyanin, proanthocyanidins, rosmarinic acid, oxymatrine, piceid, puerarin and salvianolic acid B are specified in this review. Simultaneously, chemical structures of the monomers with anti‐ageing activities are listed, and their source, model, efficacy and mechanism are also described. The TCMs with anti‐ageing function are classified according to their action pathways, including the telomere and telomerase, the sirtuins, the mammalian target of rapamycin, AMP‐activated kinase and insulin/insulin‐like growth factor‐1 signalling pathway, free radicals scavenging and the resistance to DNA damage. Finally, Chinese compound prescription and extracts related to anti‐ageing are introduced, which provides the basis and the direction for the further development of novel and potential drugs.Linked ArticlesThis article is part of a themed section on Principles of Pharmacological Research of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.11/issuetoc
Does Bank Institutional Setting Affect Board Effectiveness? Evidence from Cooperative and Joint‐Stock Banks
Authors: D'Amato Antonio , Gallo Angela 
Published: September 2016

AbstractManuscript TypeEmpiricalResearch Question/IssueDo cooperative banks suffer from board deficiencies less frequently and severely than joint‐stock banks? To answer this question, we analyze banks operating in Italy during the period 2006–2012 to examine whether the governing bodies of cooperative banks are less effective in carrying out their duties than those of joint‐stock banks. Deficiencies in the governing body are measured by sanctions imposed by the supervisory authority.Research Findings/InsightsFindings revealed that the boards of directors of cooperative banks were sanctioned more often than board of directors of joint‐stock banks. Furthermore, board turnover mediates the relationship between the cooperative status and board deficiencies.Theoretical/Academic ImplicationsThis study provides empirical evidence in support of the weakness of corporate governance in cooperative banks. Methodologically, our approach is novel in that we adopt a measure of board effectiveness/deficiency based on an independent third‐party perspective (supervisory authority) that is not biased by the different objective function of the two types of banks.Practitioner/Policy ImplicationsThe findings have several policy and managerial implications. We contribute to the ongoing debate on the proposal for flexible regulation of corporate governance for cooperative banks and emphasize that policy‐makers and regulators should rethink the corporate governance structures of cooperative banks. In particular, the study reveals how board turnover should be carefully monitored to reduce board deficiencies at the bank level.
Allergic rhinitis, rhinoconjunctivitis, and eczema: prevalence and associated factors in children
Authors: Singh Sheetu , Sharma Bharat Bhushan , Salvi Sundeep , Chhatwal Jugesh , Jain Kailash Chandra , Kumar Lata , Joshi Mohan Keshav , Pandramajal Suresh Babu , Awasthi Shally , Bhave Sheila , Rego Sylvan , Sukumaran Thevaruparambil Unny , Khatav Vasant A. , Singh Virendra , Sharma Surendra Kumar , Sabir Mohammed 
Published: September 2016

AbstractObjectiveWe aim to describe the data collected from India during phase 3 of the International study of asthma and allergy in childhood (ISAAC) study. Prevalence, severity, and population characteristics associated with rhinitis, rhinoconjunctivitis, and eczema were assessed.MethodsChildren from two age groups (6‐7 and 13‐14 years) were included in the study as per the ISAAC protocol. The symptoms of allergy and associated features were assessed using a questionnaire.ResultsThe prevalence of allergic rhinitis among the 6‐7 years age group was 11.3%, while it was 24.4% in the 13‐14 years age group. The prevalence of allergic rhinoconjunctivitis was 3.9% in the 6‐7 years age group and 10.9% in the 13‐14 years age group. The prevalence of eczema was 2.8% in the 6‐7 years age group and 3.7% in the 13‐14 years age group. The passage of trucks near home, parental smoking, use of paracetamol, use of antibiotics, cooking with firewood, and television watching were associated with allergic rhinitis, rhinoconjunctivitis, and eczema. Maternal smoking was the strongest of all the associated features for allergic rhinitis, rhinoconjunctivitis, and eczema, especially in the 6‐7 years age group (odds ratio: 1.9, 95% CI: 1.5‐2.4; odds ratio: 2.9, 95% CI, 2.2‐3.9; and odds ratio: 3.5, 95% CI: 2.6‐4.8, respectively).ConclusionAllergic conditions like allergic rhinitis, rhinoconjunctivitis, and eczema are prevalent among Indian children and are associated with environmental tobacco smoke, paracetamol use, antibiotic use, television watching, and outdoor and indoor air pollution.
Exploring the evolutionary origins of overimitation: a comparison across domesticated and non‐domesticated canids
Authors: Johnston Angie M. , Holden Paul C. , Santos Laurie R. 
Published: September 2016

AbstractWhen learning from others, human children tend to faithfully copy – or ‘overimitate’ – the actions of a demonstrator, even when these actions are irrelevant for solving the task at hand. We investigate whether domesticated dogs (Canis familiaris) and dingoes (Canis dingo) share this tendency to overimitate in three experiments. In Experiment 1, dogs and dingoes had the opportunity to solve a puzzle after watching an ostensive demonstrator who used both a relevant action and an irrelevant action. We find clear evidence against overimitation in both species. In contrast to human children (Horner & Whiten, 2005), dogs and dingoes used the irrelevant action less often across trials, suggesting that both species were filtering out the irrelevant action as they gained experience with the puzzle (like chimpanzees; Horner & Whiten, 2005). Experiments 2 and 3 provide further evidence against overimitation, demonstrating that both species’ behavior is better characterized by individual exploration than overimitation. Given that both species, particularly dogs, show human‐like social learning in other contexts, these findings provide additional evidence that overimitation may be a unique aspect of human social learning. A video abstract of this article can be viewed at: https://youtu.be/g2mRniJZ7aU.
Comparing single‐ and dual‐process models of memory development
Authors: Hayes Brett K. , Dunn John C. , Joubert Amy , Taylor Robert 
Published: September 2016

AbstractThis experiment examined single‐process and dual‐process accounts of the development of visual recognition memory. The participants, 6–7‐year‐olds, 9–10‐year‐olds and adults, were presented with a list of pictures which they encoded under shallow or deep conditions. They then made recognition and confidence judgments about a list containing old and new items. We replicated the main trends reported by Ghetti and Angelini () in that recognition hit rates increased from 6 to 9 years of age, with larger age changes following deep than shallow encoding. Formal versions of the dual‐process high threshold signal detection model and several single‐process models (equal variance signal detection, unequal variance signal detection, mixture signal detection) were fit to the developmental data. The unequal variance and mixture signal detection models gave a better account of the data than either of the other models. A state‐trace analysis found evidence for only one underlying memory process across the age range tested. These results suggest that single‐process memory models based on memory strength are a viable alternative to dual‐process models for explaining memory development.
Autophagy activation involved in hypoxic‐ischemic brain injury induces cognitive and memory impairment in neonatal rats
Authors: Xu Ying , Tian Ye , Tian Yue , Li Xingyue , Zhao Ping 
Published: September 2016

AbstractHypoxic‐ischemic brain injury (HIBI) in neonates can lead to lifelong cognitive and memory impairment, but protective strategies are lacking at present. It has been demonstrated that autophagy plays a critical role in HIBI, while the function of autophagy in cognitive and memory impairment induced by HIBI in neonates has not been tested. In this study, we tested the impact of autophagy on the impairment of cognitive function and memory in HIBI neonatal rats by using a Morris water maze and investigated its possible mechanisms, which were established as HIBI model by ligating the left common carotid artery in neonatal rats, followed by 2‐h hypoxia. The expression of microtubule‐associated protein 1 light chain 3 (LC3)‐II increased in HI group 24 h after HI in neonatal rats, while Sequestosome 1 (P62/SQSTM1), phosphorylated cAMP‐response element‐binding protein (p‐CREB) decreased (compared with the sham group, p < 0.05), which were shown in the same left hippocampus CA3 region by immunofluorescence analysis. Brain injury of neonatal rats was aggravated significantly at 7 day after HI, coinciding with the results of Morris water maze. An autophagy inhibitor, 3‐methyladenine (3‐MA) pretreatment significantly attenuated the increase of LC3II and the loss of P62/SQSTM1 and p‐CREB, ameliorated neuronal death, and improved the results of Morris water maze. Our results demonstrate that HIBI in neonatal rats induced excessive autophagy flux, which aggravated brain injury and induced cognitive and memory impairment during adolescence. Inhibition of autophagy reversed the results partly and improved the function of spatial learning and memory by attenuating the reduction of p‐CREB. The use of autophagy modulators in the immature brain would create new opportunities for protective strategies clinically in the future.
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Metabolic profile of injured human spinal cord determined using surface microdialysis
Authors: Chen Suliang , Phang Isaac , Zoumprouli Argyro , Papadopoulos Marios C. , Saadoun Samira 
Published: September 2016

AbstractThe management of patients having traumatic spinal cord injury would benefit from understanding and monitoring of spinal cord metabolic states. We hypothesized that the metabolism of the injured spinal cord could be visualized using Kohonen self‐organizing maps. Sixteen patients with acute, severe spinal cord injuries were studied. Starting within 72 h of the injury, and for up to a week, we monitored the injury site hourly for tissue glucose, lactate, pyruvate, glutamate, and glycerol using microdialysis as well as intraspinal pressure and spinal cord perfusion pressure. A Kohonen map, which is an unsupervised, self‐organizing topology‐preserving neural network, was used to analyze 3366 h of monitoring data. We first visualized the different spinal cord metabolic states. Our data show that the injured cord assumes one or more of four metabolic states. On the basis of their metabolite profiles, we termed these states near‐normal, ischemic, hypermetabolic, and distal. We then visualized how patients’ intraspinal pressure and spinal cord perfusion pressure affect spinal cord metabolism. This revealed that for more than 60% of the time, spinal cord metabolism is patient‐specific; periods of high intraspinal pressure or low perfusion pressure are not associated with specific spinal cord metabolic patterns. Finally, we determined relationships between spinal cord metabolism and neurological status. Patients with complete deficits have shorter periods of near‐normal spinal cord metabolic states (7 ± 4% vs. 58 ± 12%, p < 0.01, mean ± standard error) and more variable injury site metabolic responses (metabolism spread in 70 ± 11 vs. 40 ± 6 hexagons, p < 0.05), compared with patients who have incomplete neurological deficits. We conclude that Kohonen maps allow us to visualize the metabolic responses of the injured spinal cord and may thus aid us in treating patients with acute spinal cord injuries.
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