bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel meta-analysis pipeline of heterogeneous high-throughput gene expression datasets reveals dysregulated interactions and pathways in asthma
Authors: Guo Brandon , Kaushik Abhinav , Nadeau Kari C. 
Published: November 2019

AbstractIntroductionAsthma is a complex and chronic inflammatory disorder with varying degrees of airway inflammation. It affects ∼235 million people worldwide, and about 8% of the United States population. Unlike single-gene disorders, asthma phenotypes are guided by a highly variable combination of genotypes, making it a complex disease to study computationally. Recently, several independent high-throughput gene expression studies in bioinformatics have identified and proposed numerous molecular drivers involved in asthma initiation and progression. However, there is a poor consensus in our understanding of the molecular factors involved in the mechanism of this disease due to inherent genetic heterogeneity. Such an uncertainty in bioinformatics studies have led to a “reproducibility crisis” in the field, where similar analyses can often yield greatly varying results. In this study, we seek to harness heterogeneity in asthma by applying a meta-analysis that explores varying tissue environments.MethodsWe use three publicly-available microarray gene expression datasets, belonging to different tissues in asthma patients, from NCBI’s Gene Expression Omnibus (GEO). As a meta-analysis, we apply a mixed-model effect size test to determine differentially expressed (DE) genes across all three studies. Then, The datasets are pre-processed and subjected to Weighted Gene Co-expression Network Analysis (WGCNA) for identification of functional modules. Using module preservation, we determine modules in asthma that were not preserved in the healthy condition, then combine the three with a Fisher’s test for a set of asthma-unique modules. These modules are explored using functional analysis (i.e. GO term analysis). Using the DE genes as well as known transcription factors, we re-construct Gene Regulatory Networks (GRNs) for each of our shortlisted modules. We then studied the topology of these GRNs using hive plots to reveal underlying dysregulations, paving the way for future analyses.ResultsOur analysis reveals a novel perspective to a key interaction in asthma inflammatory regulation, the CHD4-CCL26 transcription relation. Our hive plot analysis is able to explore this gene interaction beyond the typical “over-expression, under-expression” results from typical bioinformatics studies. We reveal that CCL26, an important regulator of asthma, appears to increase in expression and topological degree in asthma, but loses connection to CHD4, which seems to be characteristic to the asthma disease. Such analysis suggests that the topology of gene networks, above simply expression values, may be key to understanding the nuanced interactions between fundamental biomarkers and drug targets in complex diseases like asthma.
Vascular Territory, White Matter Connections and the Neuroanatomical Basis of Memory Impairment after Stroke
Authors: Wright Paul , O’Sullivan Michael J. 
Published: November 2019

ABSTRACTObjectiveTo investigate neuroanatomical correlates of memory impairment 30-90 days after stroke, including the role of white matter connections in the core circuit for episodic memory.MethodsA cohort of 179 patients with first symptomatic ischaemic stroke were enrolled into a longitudinal cognitive study, STRATEGIC. Verbal and visual memory were assessed at 50±19 (range 22-109) days. Lesion topography was defined by imaging (n=152). In a representative subgroup (n=53), 3T MRI and tractography was used to define patterns of tract injury and microstructure of uninjured tracts.ResultsLesion location, defined by arterial territory, was associated with verbal memory impairment (F(12,164)=2.62, p=0.003), independent of other factors such as age, risk factor status and lesion volume. Independent lesion symptom mapping identified regions of the left posterior temporal white matter, within the left posterior cerebral artery territory, associated specifically with verbal recall. Visual recognition memory was associated with microstructure of the uninjured fornix but not with lesion location.ConclusionsInfarct location strongly influenced verbal recall performance 50 days after stroke. Damage in two locations underpinned this relationship: the thalamus; and within the left PCA territory, where disconnection of parahippocampal white matter projections contributed to verbal memory impairment in some cases. The correlates of early cognitive prognosis were domain-specific with a different pattern of associations with executive function. The association between microstructure of the uninjured fornix and visual memory might reflect the effects of comorbid pathology on hippocampal circuits.
The rice pentatricopeptide repeat protein PPR756 is involved in pollen development by affecting multiple RNA editing in mitochondria
Authors: Zhang Qiannan , Xu Yanghong , Huang Jishuai , Zhang Kai , Xiao Haijun , Qin Xiaojian , Zhu Linlin , Zhu Yingguo , Hu Jun 
Published: November 2019

AbstractIn land plants, the pentatricopeptide repeat (PPR) proteins form a large family involved in post-transcriptional processing of RNA in mitochondria and chloroplasts, which is critical for plant development and evolutionary adaption. Although studies showed a number of PPR proteins generally influence the editing of organellar genes, few of them were characterized in detail in rice. Here, we report a PLS-E subclass PPR protein in rice, PPR756, loss of function of which led to the abolishment of RNA editing events among three mitochondrial genes including atp6, ccmC, and nad7. Their defective C-to-U transformation then resulted in improper amino acid retention which could cause abortive pollen development. Furthermore, PPR756 could bind to the three target genes directly and interact with three OsMORFs (multiple organellar RNA editing factors): OsMORF1, OsMORF8-1, and OsMORF8-2. The knock-out plants of PPR756 exhibited retarded growth and greener leaves during the early vegetative stages, along with sterile pollen and lower seed setting at the reproductive stage. These results established a role for PPR756 in rice development, participating in RNA editing of three various transcripts and cooperating with OsMORFs via an editosome manner in rice.
Collision detection and force control based on the impedance approach and dynamic modelling
Authors: Wang Pengcheng , Zhang Dengfeng , Lu Baochun 
Published: November 2019

Purpose
This paper aims to address the collision problem between robot and the external environment (including human) in an unstructured situation. A new collision detection and torque optimization control method is proposed.

Design/methodology/approach
Firstly, when the collision appears, a second-order Taylor observer is proposed to estimate the residual value. Secondly, the band-pass filter is used to reduce the high-frequency torque modeling dynamic uncertainty. With the estimate information and the torque value, a variable impedance control approach is then synthesized to guarantee that the collision is avoided or the collision will be terminated with different contact models and positions. However, in terms of adaptive linear force error, the variation of the thickness of the boundary layer is controlled by the new proximity function.

Findings
Finally, the experimental results show the better performance of the proposed control method, realizing the force control during the collision process.

Originality/value
Origin approach and origin experiment.
Overcoming the capital investment hurdle in worker-controlled firms
Authors: Major Guy , Preminger Jonathan 
Published: November 2019

Purpose
Both the academic literature and practitioners have long noted the need for an equity investment mechanism for worker-controlled firms that alleviates investor anxieties without undermining internal workplace democracy. The purpose of this paper is to outline one such possible mechanism.

Design/methodology/approach
The proposal locks together the interests of workers and external investors, via non-voting shares with dividends set by a pre-agreed value-added sharing formula. Each worker is paid a base wage, with the average across the firm being a pre-defined multiple of the national minimum wage. Any additional surplus is split into a number of equal “slices”, with each share receiving one slice as its dividend, and the average worker receiving a pre-agreed number of slices as a bonus.

Findings
Workers have an incentive to maximise their own incomes, and in so doing, will also automatically maximise the dividends received by investors, obviating the need for the shares to have normal voting rights. Working on this principle of aligned interests, the authors also discuss reinvestment, worker ownership of non-voting shares and possibilities for a secondary share market. The authors show how this proposal will be a significant step in aligning the interests of investors with owner-workers in a democratic, negotiated way that shares both risk and returns, thus making worker-controlled firms more attractive to equity investment.

Originality/value
In light of the recognised problem of underinvestment in worker-controlled firms and the risk of their degeneration, this paper will interest both academics and practitioners in employee ownership, co-operatives and various forms of workplace democracy.
A two-stage structural equation modeling-neural network approach for understanding and predicting the determinants of m-government service adoption
Authors: Talukder Shamim , Chiong Raymond , Dhakal Sandeep , Sorwar Golam , Bao Yukun 
Published: November 2019

Purpose
Despite the widespread use of mobile government (m-government) services in developed countries, the adoption and acceptance of m-government services among citizens in developing countries is relatively low. The purpose of this study is to explore the most critical determinants of acceptance and use of m-government services in a developing country context.

Design/methodology/approach
The unified theory of acceptance and use of technology (UTAUT) extended with perceived mobility and mobile communication services (MCS) was used as the theoretical framework. Data was collected from 216 m-government users across Bangladesh and analyzed in two stages. First, structural equation modeling (SEM) was used to identify significant determinants affecting users' acceptance of m-government services. In the second stage, a neural network model was used to validate SEM results and determine the relative importance of the determinants of acceptance of m-government services.

Findings
The results show that facilitating conditions and performance expectancy are the two important precedents of behavioral intention to use m-government services, and performance expectancy mediates the relationship between MCS, mobility and the intention to use m-government services.

Research limitations/implications
Academically, this study extended and validated the underlying concept of UTAUT to capture the adoption behavior of individuals in a different cultural context. In particular, MCS might be the most critical antecedent towards mobile application studies. From a practical perspective, this study may provide valuable guidelines to government policymakers and system developers towards the development and effective implementation of m-government systems.

Originality/value
This study has contributed to the existing, but limited, literature on m-government service adoption in the context of a developing country. The predictive modeling approach is an innovative approach in the field of technology adoption.
Rap1‐mediated nucleosome displacement can regulate gene expression in senescent cells without impacting the pace of senescence
Authors: Song Shufei , Perez Javier V. , Svitko William , Ricketts M. Daniel , Dean Elliot , Schultz David , Marmorstein Ronen , Johnson F. Brad 
Published: November 2019

AbstractCell senescence is accompanied, and in part mediated, by changes in chromatin, including histone losses, but underlying mechanisms are not well understood. We reported previously that during yeast cell senescence driven by telomere shortening, the telomeric protein Rap1 plays a major role in reprogramming gene expression by relocalizing hundreds of new target genes (called NRTS, for new Rap1 targets at senescence) to the promoters. This leads to two types of histone loss: Rap1 lowers histone level globally by repressing histone gene expression, and it also causes local nucleosome displacement at the promoters of upregulated NRTS. Here, we present evidence of direct binding between Rap1 and histone H3/H4 heterotetramers, and map amino acids involved in the interaction within the Rap1 SANT domain to amino acids 392–394 (SHY). Introduction of a point mutation within the native RAP1 locus that converts these residues to alanines (RAP1SHY), and thus disrupts Rap1‐H3/H4 interaction, does not interfere with Rap1 relocalization to NRTS at senescence, but prevents full nucleosome displacement and gene upregulation, indicating direct Rap1‐H3/H4 contacts are involved in nucleosome displacement. Consistent with this, the histone H3/H4 chaperone Asf1 is similarly unnecessary for Rap1 localization to NRTS but is required for full Rap1‐mediated nucleosome displacement and gene activation. Remarkably, RAP1SHY does not affect the pace of senescence‐related cell cycle arrest, indicating that some changes in gene expression at senescence are not coupled to this arrest.
A Multifaceted Intervention to Improve Patient Knowledge and Safe Use of Opioids: Results of the ED EMC2 Randomized Controlled Trial
Authors: McCarthy Danielle M. , Curtis Laura M. , Courtney D. Mark , Cameron Kenzie A. , Lank Patrick M. , Kim Howard S. , Opsasnick Lauren A. , Lyden Abbie E. , Gravenor Stephanie J. , Russell Andrea M. , Eifler Morgan R. , Hur Scott I. , Rowland Megan E. , Walton Surrey M. , Montague Enid , Kim Kwang‐Youn A. , Wolf Michael S. 
Published: November 2019

AbstractObjectivesDespite increased focus on opioid prescribing, little is known about the influence of prescription opioid medication information given to patients in the emergency department (ED). The study objective was to evaluate the effect of an Electronic Medication Complete Communication (EMC2) Opioid Strategy on patients’ safe use of opioids and knowledge about opioids.MethodsThis was a three‐arm prospective, randomized controlled pragmatic trial with randomization occurring at the physician level. Consecutive discharged patients at an urban academic ED (>88,000 visits) with new hydrocodone‐acetaminophen prescriptions received one of three care pathways: 1) usual care, 2) EMC2 intervention, or 3) EMC2 + short message service (SMS) text messaging. The ED EMC2 intervention triggered two patient‐facing educational tools (MedSheet, literacy‐appropriate prescription wording [Take‐Wait‐Stop]) and three provider‐facing reminders to counsel (directed to ED physician, dispensing pharmacist, follow‐up physician). Patients in the EMC2 + SMS arm additionally received one text message/day for 1 week. Follow‐up at 1 to 2 weeks assessed “demonstrated safe use” (primary outcome). Secondary outcomes including patient knowledge and actual safe use (via medication diaries) were assessed 2 to 4 days and 1 month following enrollment.ResultsAmong the 652 enrolled, 343 completed follow‐up (57% women; mean ± SD age = 42 ± 14.0 years). Demonstrated safe opioid use occurred more often in the EMC2 group (adjusted odds ratio [aOR] = 2.46, 95% confidence interval [CI] = 1.19 to 5.06), but not the EMC2 + SMS group (aOR = 1.87, 95% CI = 0.90 to 3.90) compared with usual care. Neither intervention arm improved medication safe use as measured by medication diary data. Medication knowledge, measured by a 10‐point composite knowledge score, was greater in the EMC2 + SMS group (β = 0.57, 95% CI = 0.09 to 1.06) than usual care.ConclusionsThe study found that the EMC2 tools improved demonstrated safe dosing, but these benefits did not translate into actual use based on medication dairies. The text‐messaging intervention did result in improved patient knowledge.
Institutions, banking structure and the cost of debt: new international evidence
Authors: Álvarez‐Botas Celia , González Víctor M. 
Published: November 2019

AbstractThis paper analyses the effect of institutions and the structure of the banking system on the cost of debt for a sample of firms from 37 countries. The cost of debt decreases with the rule of law, the protection of creditors’ rights and the weight of banks in the economy. Bank financing and bank concentration have a positive differential effect on the cost of debt in those countries where the financial difficulties of banks are greater. Legal enforcement, the protection of creditors’ rights and the weight of bank financing have a greater influence in countries with a lower degree of economic development.
CEO characteristics: a review of influential publications and a research agenda
Authors: Shen Yun 
Published: November 2019

AbstractThis paper provides a systematic review of literature pertaining to CEO characteristics and firm performance. The CEO of a firm provides critical leadership, social capital, and legitimacy, and as such exerts significant influence on firm performance. By using a bibliographic mapping approach, we identify the fifty‐one most influential publications on CEO characteristics. This field has developed from a few Upper Echelon Theory publications into four distinct categories. We review each of these to identify the main contributions to this research area and to outline research gaps and future research trends.
Peter the great and cataract surgery
Authors: Grzybowski Andrzej , Zimin Igor , Leffler Christopher T. 
Published: November 2019

AbstractTsar Peter Alekseyevich Romanov (1672–1725), often called Peter the Great, modernized Russia in many areas, including in the field of medicine. Peter I attended medical lectures and demonstrations and may have even performed some medical procedures himself. In Paris, he witnessed a cataract couching performed by Englishman John Thomas Woolhouse (1664–1733/4) and requested that Woolhouse train a Russian student in ophthalmology.
Climate severity and land‐cover transformation determine plant community attributes in Colombian dry forests
Authors: González‐M. Roy , Norden Natalia , Posada Juan M. , Pizano Camila , García Hernando , Idárraga‐Piedrahita Álvaro , López‐Camacho René , Nieto Jhon , Rodríguez-M Gina M. , Torres Alba M. , Castaño‐Naranjo Alejandro , Jurado Rubén , Franke‐Ante Rebeca , Galindo-T Robinson , Hernández R. Elkin , Barbosa Adriana , Salgado‐Negret Beatriz 
Published: November 2019

AbstractTropical dry forests (TDF) are known to be resource‐limited due to a marked seasonality in precipitation. However, TDF are also shaped by factors such as solar radiation, wind speed, soil fertility, and land‐cover transformation. Together, these factors may determine different gradients of environmental harshness that are likely to drive changes in plant community attributes. Here, we evaluated the effects of environmental harshness on plant community diversity and structure of Colombian TDF, based on floristic and environmental data from 15 1‐ha permanent plots. We also analyzed these effects on legumes species only (including both deciduous and non‐deciduous species), deciduous species only (including both legumes and non‐legumes species), and on the whole community excluding either legumes or deciduous separately. Drier conditions and higher land‐cover transformation had the strongest negative effects on species diversity, basal area (BA), and canopy height. Soil fertility, on the contrary, did not have a significant effect on any of the evaluated response variables. Interestingly, legumes maintained their diversity and BA along the climatic gradient, while deciduous species were negatively affected by drier conditions and by an increase in secondary vegetation at the landscape level. Our results suggest that although TDF are limited by water availability, land‐cover transformation strongly increases environmental harshness. Yet, both legumes and deciduous species were differentially impacted by climatic and land transformation variables. Thus, to better understand TDF plant community attributes, it is necessary to consider these gradients and to disentangle their effects on different plant functional groups.Abstract in Spanish is available with online material.
Engaging Children in Meaningful Charity: Opening‐up the Spaces within Which Children Learn to Give
Authors: Body Alison , Lau Emily , Josephidou Jo 
Published: November 2019

This paper presents qualitative evidence from an in‐depth, participative action research project with 150 children aged 4–8 years old, exploring their experiences, perceptions and preferences regarding charitable giving. Most children positively engage in charitable giving through home, school and their community; however, less than 20% are aware of the cause area they are being asked to support, and most have little decision‐making in their giving. Children’s willingness to engage increases when they critically examine the cause area and are facilitated to lead on giving decisions, often resulting in increased and sustained efforts to support cause areas that matter to them.
Ecological change in dynamic environments: Accounting for temporal environmental variability in studies of ocean change biology
Authors: Kroeker Kristy J. , Bell Lauren E. , Donham Emily M. , Hoshijima Umihiko , Lummis Sarah , Toy Jason A. , Willis‐Norton Ellen 
Published: November 2019

AbstractThe environmental conditions in the ocean have long been considered relatively more stable through time compared to the conditions on land. Advances in sensing technologies, however, are increasingly revealing substantial fluctuations in abiotic factors over ecologically and evolutionarily relevant timescales in the ocean, leading to a growing recognition of the dynamism of the marine environment as well as new questions about how this dynamism may influence species' vulnerability to global environmental change. In some instances, the diurnal or seasonal variability in major environmental change drivers, such as temperature, pH and seawater carbonate chemistry, and dissolved oxygen, can exceed the changes expected with continued anthropogenic global change. While ocean global change biologists have begun to experimentally test how variability in environmental conditions mediates species' responses to changes in the mean, the extensive literature on species' adaptations to temporal variability in their environment and the implications of this variability for their evolutionary responses has not been well integrated into the field. Here, we review the physiological mechanisms underlying species' responses to changes in temperature,pCO2/pH (and other carbonate parameters), and dissolved oxygen, and discuss what is known about behavioral, plastic, and evolutionary strategies for dealing with variable environments. In addition, we discuss how exposure to variability may influence species' responses to changes in the mean conditions and highlight key research needs for ocean global change biology.