bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of DNA methylation dynamics in desiccation and salinity stress responses in rice cultivars
Authors: Rajkumar Mohan Singh , Shankar Rama , Garg Rohini , Jain Mukesh 
Published: February 2019

AbstractDNA methylation is an epigenetic mark that controls gene expression in response to internal and environmental cues. In this study, we sought to understand the role of DNA methylation in response to desiccation and salinity stresses in three rice cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) via bisulphite sequencing. We identified DNA methylation patterns in different genomic/genic regions and analysed their correlation with gene expression. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. However, methylation in other sequence contexts and genic regions was negatively correlated with gene expression. DNA methylation was found to be most dynamic in CHH context under stress condition(s) in the rice cultivars. The expression profiles of genes involved inde-novomethylation were correlated with methylation dynamics. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stress, respectively, were correlated with higher expression of abiotic stress response related genes. Our results suggest an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. This study provides useful resource of DNA methylomes that can be integrated with other data to understand abiotic stress response in rice.HighlightBisulphite sequencing revealed single base resolution DNA methylation, and cultivar-specific differential methylation patterns and correlation with gene expression that control desiccation and salinity stress response in the rice cultivars.
Sustained Ca2+mobilizations: a quantitative approach to predict their importance in cell-cell communication and wound healing
Authors: Lee Yoonjoo , Kim Min Tae , Rhodes Garrett , Sack Kelsey , Son Sung Jun , Rich Celeste B. , Kolachalama Vijaya B. , Gabel Christopher V , Trinkaus-Randall Vickery 
Published: February 2019

AbstractEpithelial wound healing requires the coordination of cells to migrate as a unit over the basement membrane after injury. To understand the process of this coordinated movement, it is critical to study the dynamics of cell-cell communication. We developed a method to characterize the injury-induced sustained Ca2+mobilizations that travel between cells for periods of time up to several hours. These events of communication are concentrated along the wound edge and are reduced in cells further away from the wound. Our goal was to delineate the role and contribution of these sustained mobilizations and using MATLAB analyses, we determined the probability of cell-cell communication events in in vitro models and ex vivo organ culture models. We demonstrated that the injury response was complex and represented the activation of a number of receptors. In addition, we found that pannexin channels mediated the cell-cell communication and motility. Furthermore, the sustained Ca2+mobilizations are associated with changes in cell morphology and motility during wound healing. The results demonstrate that both purinoreceptors and pannexins regulate the sustained Ca2+mobilization necessary for cell-cell communication in wound healing.
A multi-scale coevolutionary approach to predict interactions between protein domains
Authors: Croce Giancarlo , Gueudré Thomas , Cuevas Maria Virginia Ruiz , Keidel Victoria , Figliuzzi Matteo , Szurmant Hendrik , Weigt Martin 
Published: February 2019

AbstractInteracting proteins and protein domains coevolve on multiple scales, from their correlated presence across species, to correlations in amino-acid usage. Genomic databases provide rapidly growing data for variability in genomic protein content and in protein sequences, calling for computational predictions of unknown interactions. We first introduce the concept ofdirect phyletic couplings, based on global statistical models of phylogenetic profiles. They strongly increase the accuracy of predicting pairs of related protein domains beyond simpler correlation-based approaches like phylogenetic profiling (80% vs. 30-50% positives out of the 1000 highest-scoring pairs). Combined with the direct coupling analysis of inter-protein residue-residue coevolution, we provide multi-scale evidence for direct but unknown interaction between protein families. An in-depth discussion shows these to be biologically sensible and directly experimentally testable. Negative phyletic couplings highlight alternative solutions for the same functionality, including documented cases of convergent evolution. Thereby our work proves the strong potential of global statistical modeling approaches to genome-wide coevolutionary analysis, far beyond the established use for individual protein complexes and domain-domain interactions.Author summaryInteractions between proteins and their domains are at the basis of almost all biological processes. To complement labor intensive and error-prone experimental approaches to the genome-scale characterization of such interactions, we propose a computational approach based upon rapidly growing protein-sequence databases. To maintain interaction in the course of evolution, proteins and their domains are required to coevolve: evolutionary changes in the interaction partners appear correlated across several scales, from correlated presence-absence patterns of proteins across species, up to correlations in the amino-acid usage. Our approach combines these different scales within a common mathematical-statistical inference framework, which is inspired by the so-called direct coupling analysis. It is able to predict currently unknown, but biologically sensible interaction, and to identify cases of convergent evolution leading to alternative solutions for a common biological task. Thereby our work illustrates the potential of global statistical inference for the genome-scale coevolutionary analysis of interacting proteins and protein domains.
A machine learning tool for interpreting differences in cognition using brain features
Authors: Azevedo Tiago , Passamonti Luca , Lió Pietro , Toschi Nicola 
Published: February 2019

AbstractPredicting variability in cognition traits is an attractive and challenging area of research, where different approaches and datasets have been implemented with mixed results. Some powerful Machine Learning algorithms employed before are difficult to interpret, while other algorithms are easy to interpret but might not be as powerful. To improve understanding of individual cognitive differences in humans, we make use of the most recent developments in Machine Learning in which powerful prediction models can be interpreted with confidence. We used neuroimaging data and a variety of behavioural, cognitive, affective and health measures from 905 people obtained from the Human Connectome Project (HCP). As a main contribution of this paper, we show how one could interpret the neuroanatomical basis of cognition, with recent methods which we believe are not yet fully explored in the field. By reducing neuroimages to a well characterised set of features generated from surface-based morphometry and cortical myelin estimates, we make the interpretation of such models easier as each feature is self-explanatory. The code used in this tool is available in a public repository: https://github.com/tjiagoM/interpreting-cognition-paper-2019
A new approach for performance assessment of parallel and non-bottleneck machines in a dynamic job shop environment
Authors: Faccio Maurizio , Nedaei Mojtaba , Pilati Francesco 
Published: February 2019

Purpose
The current study aims to propose a new analytical approach by considering energy consumption (EC), maximum tardiness and completion time as the primary objective functions to assess the performance of parallel, non-bottleneck and multitasking machines operating in dynamic job shops.

Design/methodology/approach
An analytical and iterative method is presented to optimize a novel dynamic job shop under technical constraints. The machine’s performance is analyzed by considering the setup energy. An optimization model from initial processing until scheduling and planning is proposed, and data sets consisting of design parameters are fed into the model.

Findings
Significant variations of EC and tardiness are observed. The minimum EC was calculated to be 141.5 hp.s when the defined decision variables were constantly increasing. Analysis of the optimum completion time has shown that among all studied methods, first come first served (FCFS), earliest due date (EDD) and shortest processing time (SPT) have resulted in the least completion time with a value of 20 s.

Originality/value
Considerable amount of energy can be dissipated when parallel, non-bottleneck and multitasking machines operate in lower-power modes. Additionally, in a dynamic job shop, adjusting the trend and arrangement of decision variables plays a crucial role in enhancing the system’s reliability. Such issues have never caught the attention of scientists for addressing the aforementioned problems. Therefore, with these underlying goals, this paper presents a new approach for evaluating and optimizing the system’s performance, considering different objective functions and technical constraints.
Mental health law under review: messages from English safeguarding adults reviews
Authors: Manthorpe Jill , Martineau Stephen 
Published: February 2019

Purpose
The purpose of this paper is to examine safeguarding adults reviews (SARs) that refer to mental health legislation in order to contribute to the review of English mental health law (2018).

Design/methodology/approach
Searches of a variety of sources were conducted to compile a list of relevant SARs. These are summarised and their contexts assessed for what they reveal about the use and coherence of mental health legislation.

Findings
The interaction of the statutes under consideration, in particular the Mental Health Act (MHA) 1983, the Mental Capacity Act (MCA) 2005, together with the Care Act 2014, presents challenges to practitioners and the efficacy of their application is variable.

Research limitations/implications
In light of the absence of a duty to report SARs to a national register, it is possible that relevant SARs were missed in the search phase of this research, meaning that the results do not present a complete picture.

Practical implications
Examining cases where use of legislative provisions in mental health has been found wanting or legislation may not be easily implemented may inform initiatives to increase understanding of the law in this area.

Originality/value
This paper’s originality and value lie in its focus on mental health legislation as discussed in SARs at a time when both the MHA 1983 and the MCA 2005 are the focus of attention for reform.
Police legitimacy: perspectives of migrants and non-migrants in Australia
Authors: Schermuly Allegra Clare , Forbes-Mewett Helen 
Published: February 2019

Purpose
This paper is drawn from a larger study investigating community perceptions of police legitimacy in the Monash Local Government Area (LGA), in the Australian state of Victoria. Monash had seen declining results in the official government survey in the indicators that assessed police legitimacy over the preceding decade. The purpose of this paper is to explore the perceptions of both migrant and non-migrant participants to understand the role of migrant status in influencing assessments of police legitimacy in Monash LGA.

Design/methodology/approach
Through six focus groups, 18 interviews and one e-mail response with 31 individuals, perceptions of Victoria Police among the communities of Monash were collated and analysed.

Findings
One of the key findings of the study was that ethnic diversity and/or migrant status of community members were a key factor raised in response to questions about community perceptions of the legitimacy of Victoria Police in Monash LGA. Demographic change had been significant in Monash LGA over the preceding decade, including increasing ethnic diversity in the population and a shift in migration patterns from predominantly European to migrants from East and South Asia. In this paper, the authors suggest that the migrant status of Monash residents was a key factor that both migrant and non-migrant participants thought influenced perceptions of the police. Accordingly, because migrants make up a significant cohort of Australia’s population, we afford due attention to this previously overlooked topic.

Practical implications
The practical implications of this paper are as follows: existing Victoria Police partnerships in the Monash community should be continued and expanded where possible; Victoria Police should also prioritise partnerships with large, new migrant communities, for example, Monash’s Chinese communities; orientation for new migrants to Victoria around the criminal justice system, including Victoria Police, would help new migrants be more aware of their rights and what to expect of law enforcement in their new host country; police should continue to increase representation of ethnic diversity in the force via recruitment of greater numbers of ethnically diverse police members.

Originality/value
Although there have been previous Australian studies on migrant status as a factor in perceptions of criminal justice (see Murphy and Cherney, 2011, 2012; Hong Chui and Kwok-Yin Cheng, 2014), the paper identifies a distinct narrative around migrants’ views of Victoria Police which the authors believe warrant further investigation using an example from a local context. Furthermore, most research in this field has been quantitative. The current study provides additional new insights through an in-depth qualitative approach.
Phylogenetic structure of wildlife assemblages shapes patterns of infectious livestock diseases in Africa
Authors: Wang Yingying X. G. , Matson Kevin D. , Prins Herbert H. T. , Gort Gerrit , Awada Lina , Huang Zheng Y. X. , de Boer Willem F. 
Published: February 2019

Abstract

Host species diversity can affect disease risk, but the precise nature of this effect is disputed. To date, most studies on the diversity–disease relationships have focused on host species richness and single diseases, ignoring phylogenetic diversity and disease richness.

We first evaluated the effects of wildlife assemblage variables (i.e. species richness of wild ungulates and carnivores, phylogenetic structure) and livestock host density on the regional occurrence of 19 individual livestock diseases in Africa. We then explored the relationships between wildlife assemblage variables and the total disease burden (measured as disease richness) at regional scale across the entire continent of Africa.

Our results suggest that wild ungulate and carnivore species richness had a positive relationship with disease richness, but no relationship with disease occurrence. When controlling for host species richness, standardized phylogenetic divergence was negatively correlated with both disease richness and disease occurrence while standardized phylogenetic richness was positively correlated with disease occurrences.

Our results suggest that the phylogenetic structure of the surrounding wildlife assemblage can shape patterns of livestock diseases in Africa. Species richness alone is apparently inadequate for analyses of disease–diversity relationships, and this shortfall might partly account for current disagreements over the importance of the dilution effect. Future studies on this topic should strive to include parameters that take host phylogeny into account.

A plain language summary is available for this article.
Antioxidant and Antiproliferative Activities of Modified Polysaccharides Originally Isolated from Morchella Angusticepes Peck
Authors: Tang Yu , Chen Jinlong , Li Fuhua , Yang Yaxuan , Wu Surui , Ming Jian 
Published: February 2019

AbstractPolysaccharides extracted from Morchella angusticepes Peck (PMEP) were chemically modified to obtain sulfated, carboxymethylated, and acetyled derivatives. Results showed that the acetyled derivatives with the degree of substitution (0.40 ± 0.07) exerted higher antioxidant ability than native polysaccharides, demonstrating inhibitory effects on growth of human hepatoma cells (EC50 = 0.710 ± 0.002 mg/mL) and human colon cancer cells (EC50 = 1.229 ± 0.008 mg/mL). It indicated that the acetylation was a favorable way to enhance the bioactivities of PMEP.Practical ApplicationPolysaccharides extracted from Morchella angusticepes Peck (PMEP) have many health‐promoting properties. Chemical modifications could improve the bioactivities of polysaccharides. We demonstrated that acetylation enhanced the cellular antioxidant and antiproliferative activities of PMEP. The results support further research that explores clinical utility, and may justify ex vivo and in vivo designs toward that end.
Treat‐to‐target in rheumatoid arthritis: Evaluating the patient perspective using the Patient Opinion Real‐Time Anonymous Liaison system: The RA T2T PORTAL study
Authors: Benham Helen , Rutherford Merrin , Kirby Sandra , Stebbings Simon , White Douglas , Sim Dalice , Harrison Andrew 
Published: February 2019

AbstractObjectivesTo determine the level of agreement among patients with rheumatoid arthritis (RA) with the principles and recommendations of the treat‐to‐target (T2T) initiative in New Zealand (NZ) and to further explore specific patient opinions via online iterative surveys.MethodsParticipants with RA were recruited from rheumatology clinics in NZ and invited to receive and reply to surveys administered via the Patient Opinion Real‐Time Anonymous Liaison (PORTAL) system. An enrolment survey recorded demographics, disease duration and treatment and then RA T2T surveys were administered weekly. A Likert scale 1‐5 measured agreement with the principles and recommendations and further surveys explored responses of interest identified by investigators from each prior survey.ResultsOne hundred and ninety patients consented to participate in PORTAL and 132 in the RA T2T surveys. Level of agreement with RA T2T principles was: 93.3% to 99.3% and to the recommendations: 77.3%‐100%. The lowest level of agreement 77.3% was with recommendation 8, 3 monthly treatment adjustment, and the highest was 100% agreement with recommendation 10, shared decision‐making. Patients agreed less with low disease activity as the target compared with remission (91.4% and 98%). Despite high‐level agreement for the use of a disease activity score (95.7%), 23% did not feel the individual components reflected their disease control. Patients rated difficulty coping, erosions on imaging, health‐related quality of life and pain all significantly higher than C‐reactive protein as indicators of worsening arthritis.ConclusionsDespite a high level of patient agreement with RA T2T this study highlights the importance of patient engagement in the RA T2T process to individualize therapy adjustments, make shared decisions and decide on targets that accurately reflect disease control according to patients.
Knockout of receptor for advanced glycation end‐products attenuates age‐related renal lesions
Authors: Teissier Thibault , Quersin Valentine , Gnemmi Viviane , Daroux Maité , Howsam Mike , Delguste Florian , Lemoine Cécile , Fradin Chantal , Schmidt Ann‐Marie , Cauffiez Christelle , Brousseau Thierry , Glowacki François , Tessier Frédéric J. , Boulanger Eric , Frimat Marie 
Published: February 2019

AbstractPro‐aging effects of endogenous advanced glycation end‐products (AGEs) have been reported, and there is increasing interest in the pro‐inflammatory and ‐fibrotic effects of their binding to RAGE (the main AGE receptor). The role of dietary AGEs in aging remains ill‐defined, but the predominantly renal accumulation of dietary carboxymethyllysine (CML) suggests the kidneys may be particularly affected. We studied the impact of RAGE invalidation and a CML‐enriched diet on renal aging. Two‐month‐old male, wild‐type (WT) and RAGE−/− C57Bl/6 mice were fed a control or a CML‐enriched diet (200 μg CML/gfood) for 18 months. Compared to controls, we observed higher CML levels in the kidneys of both CML WT and CML RAGE−/− mice, with a predominantly tubular localization. The CML‐rich diet had no significant impact on the studied renal parameters, whereby only a trend to worsening glomerular sclerosis was detected. Irrespective of diet, RAGE−/− mice were significantly protected against nephrosclerosis lesions (hyalinosis, tubular atrophy, fibrosis and glomerular sclerosis) and renal senile apolipoprotein A‐II (ApoA‐II) amyloidosis (p < 0.001). A positive linear correlation between sclerosis score and ApoA‐II amyloidosis score (r = 0.92) was observed. Compared with old WT mice, old RAGE−/− mice exhibited lower expression of inflammation markers and activation of AKT, and greater expression of Sod2 and SIRT1. Overall, nephrosclerosis lesions and senile amyloidosis were significantly reduced in RAGE−/− mice, indicating a protective effect of RAGE deletion with respect to renal aging. This could be due to reduced inflammation and oxidative stress in RAGE−/− mice, suggesting RAGE is an important receptor in so‐called inflamm‐aging.
Delirium management: Let's get physical? A systematic review and meta‐analysis
Authors: Haley Melanie Nance , Casey Penelope , Kane Richard Youlten , Dārziņš Pēteris , Lawler Katherine 
Published: February 2019

ObjectiveTo investigate whether physical training (alone or in a multi‐component intervention) is effective in preventing delirium or improving outcomes for adult patients with delirium in the hospital setting.MethodsA systematic review, qualitative synthesis and meta‐analysis of randomised controlled trials identified by searches of electronic databases, combining key concepts of delirium and physical training (the target intervention). Outcomes were incidence of delirium (for prevention trials) and delirium duration, delirium severity and hospital outcomes (for management trials).ResultsSeven trials were included, five of which were multi‐component. The odds of developing delirium were lower for patients who received physical training compared with a control intervention [odds ratio 0.46 (95% confidence interval 0.32‐0.65), P < 0.01] (moderate‐quality evidence). There was insufficient evidence to draw conclusions about managing established delirium.ConclusionsStrategies incorporating physical training appear to prevent delirium in the hospital setting. More research is required regarding management of established delirium.
Time to recurrence after surgical excision of atypical fibroxanthoma‐updated systematic review and meta‐analysis
Authors: Phan Kevin , Onggo James 
Published: February 2019

AbstractAtypical fibroxanthoma (AFX) remains a rare cutaneous dermally based fibrohistiocytic tumour with high rates of local recurrence. Mohs micrographic surgery (MMS) and wide local excision (WLE) with margins 1–2 cm are two surgical options. It is unclear whether timing of recurrence following surgical excision of AFX differs according to technique. A systematic review and meta‐analysis were performed according to PRISMA guidelines. There was a total of 188 MMS cases and 783 WLE cases. The pooled proportion of MMS cases of recurrence is 6.6% (95% CI 3.6–11.9%), compared with WLE 11.3% (95% CI 7.1–16.5%), which was not significantly different (P = 0.12) Pooled time to recurrence of MMS for AFX to be 14.2 (95% CI 11.6–16.8%) months, compared to 13.3 (95% CI 9.99–16.6%) months (P = 0.86). Our findings suggest that recurrence rates are similar between MMS and WLE techniques and that timing of recurrence is similar regardless of surgical technique employed.