bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy, limitations and cost-efficiency of eDNA-based community survey in tropical frogs
Authors: Bálint Miklós , Nowak Carsten , Márton Orsolya , Pauls Steffen U. , Wittwer Claudia , Jose Luis Aramayo B. , Schulze Arne , Chambert Thierry , Cocchiararo Berardino , Jansen Martin 
Published: August 2017

AbstractRapid environmental change in highly biodiverse tropical regions demands efficient biomonitoring programs. While existing metrics of species diversity and community composition rely on encounter-based survey data, eDNA recently emerged as alternative approach. Costs and ecological value of eDNA-based methods have rarely been evaluated in tropical regions, where high species richness is accompanied by high functional diversity (e.g. the use of different microhabitats by different species and life-stages). We first tested whether estimation of tropical frogs’ community structure derived from eDNA data is compatible with expert field assessments. Next we evaluated whether eDNA is a financially viable solution for biodiversity monitoring in tropical regions. We applied eDNA metabarcoding to investigate frog species occurrence in five ponds in the Chiquitano dry forest region in Bolivia and compared our data with a simultaneous visual and audio encounter survey (VAES). We found that taxon lists and community structure generated with eDNA and VAES correspond closely, and most deviations are attributable to different species’ life histories. Cost efficiency of eDNA surveys was mostly influenced by the richness of local fauna and the number of surveyed sites: VAES may be less costly in low-diversity regions, but eDNA quickly becomes more cost-efficient in high-diversity regions with many sites sampled. The results highlight that eDNA is suitable for large-scale biodiversity surveys in high-diversity areas if life history is considered, and certain precautions in sampling, genetic analyses and data interpretation are taken. We anticipate that spatially extensive, standardized eDNA biodiversity surveys will quickly emerge in the future.
Stochastic processes dominate the within and between host evolution of influenza virus
Authors: McCrone John T. , Woods Robert J. , Martin Emily T. , Malosh Ryan E. , Monto Arnold S. , Lauring Adam S. 
Published: August 2017

AbstractThe global evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define the dynamics of influenza A virus populations in human hosts through next generation sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected over 5 seasons from individuals in a prospective community-based cohort, they are broadly representative of natural human infections with seasonal viruses. We used viral sequence data from 35 serially sampled individuals to estimate a within host effective population size of 30-70 and an in vivo mutation rate of 4x10−5per nucleotide per cellular infectious cycle. These estimates are consistent across several models and robust to the models' underlying assumptions. We also identified 43 epidemiologically linked and genetically validated transmission pairs. Maximum likelihood optimization of multiple transmission models estimates an effective transmission bottleneck of 1-2 distinct genomes. Our data suggest that positive selection of novel viral variants is inefficient at the level of the individual host and that genetic drift and other stochastic processes dominate the within and between host evolution of influenza A viruses.
PANOPLY:Omics-guided drug prioritization method tailored to an individual patient
Authors: Kalari Krishna R. , Sinnwell Jason P. , Thompson Kevin J. , Tang Xiaojia , Carlson Erin E. , Yu Jia , Vedell Peter T. , Ingle James N. , Weinshilboum Richard M. , Boughey Judy C. , Wang Liewei , Goetz Matthew P. , Suman Vera 
Published: August 2017

ABSTRACTPurposeThe majority of cancer patients receive treatments that are minimally informed by omics data. We propose a precision medicine computational framework (PANOPLY:Precision cancer genomic report: single sample inventory) to identify and prioritize drug targets and cancer therapy regimens.MethodsThe PANOPLY approach integrates clinical data with germline and somatic features obtained from multi-omics platforms, and apply machine learning, and network analysis approaches in the context of the individual patient and matched controls. The PANOPLY workflow employs four steps (i) selection of matched controls to the case of interest (ii) identification of case-specific genomic events (iii) identification of suitable drugs using the driver-gene network and random forest analyses and (iv) provide an integrated multi-omics case report of the patient with prioritization of anti-cancer drugs.ResultsThe PANOPLY workflow can be executed on a stand-alone virtual machine and is also available for download as an R package. We applied the method to an institutional breast cancer neoadjuvant chemotherapy study which collected clinical and genomic data as well as patient-derived xenografts (PDXs) to investigate the prioritization offered by PANOPLY. In a chemotherapy-resistant PDX model, we found that that the prioritized drug, olaparib, was more effective than placebo in treating the tumor (P < 0.05). We also applied PANOPLY to in-house and publicly accessible multi-omics tumor datasets with therapeutic response or survival data available.ConclusionPANOPLY shows promise as a means to prioritize drugs based on clinical and multi-omics data for an individual cancer patient. Additional studies are needed to confirm this approach.
Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem
Authors: Noor Mohd Ezhar Mohd , Fadaak Sharifah Noor Emilia Syed Jamil , Isa Mohd Noor Mat , Bakar Mohd Faizal Abu , Abdullah Muhd Danish-Daniel 
Published: August 2017

AbstractTropical freshwater lake such as Tasik Kenyir are underrepresented among the growing number of environmental metagenomic data sets. In Tasik Kenyir, water from two different sites, pristine and disturbed areas were sampled. After the filtration process, genomic DNA from both sites were extracted using Meta-G-nome DNA isolation kit and shotgun metagenomic sequencing was carried out on Illumina HiSeq2500 Desktop Sequencer (Illumina, Inc.). Raw data were then trimmed and assembled using Metagenomic Assembler program, MetaVelvet. Data analysis was carried out using software Blast2GO (BioBam Bioinformatic S.L). The total number of sequence reads was 189,158 from TKS1.5m (disturbed area) and 246,577 from TKS2.5m (pristine area).The results indicate that sequence reads of microbial species were presence at disturbed area near the aquaculture zone was lower than the sequence reads of microbial species were presence at pristine area. When compared to archaea, both samples were dominated by bacteria (more than 90%) suggesting that bacteria are absolutely dominant in the prokaryotic communities in the freshwater samples. The lake appears to contain a mixture of autotrophs and heterotrophs capable of performing main biogeochemical cycles like nitrogen fixation byKlebsiellasp for TKS1.5m andPontibactersp. for TKS2.5m. and carbon fixation by heterotrophicAlcaligenessp. andShewanella decolorationiin TKS1.5m, and byPantoeasp. in TKS2.5m. Present study will advance our understanding of the importance of freshwater microbial communities for ecosystem and human health.
Metabolomic profiling reveals effects of marein on energy metabolism in HepG2 cells
Authors: Jiang Baoping , Le Liang , Hu Keping , Xu Lijia , Xiao Peigen 
Published: August 2017

AbstractPrevious studies have suggested thatCoreopsis tinctoriaimproves insulin resistance in rats fed with high-fat diet. But little is known about the antidiabetic effects of marein which is the main component ofC. tinctoria. This study investigated the effects of ethyl acetate extract ofC. tinctoria(AC) on insulin resistance (IR) in rats fed a high-fat diet. High glucose and fat conditions cause a significant increase in blood glucose, insulin, serum TC,TG and LDL-C, leading to an abnormal IR in rats. However, treatment with AC protects against HFD-induced IR by improving fasting serum glucose and lipid homeostasis. High glucose conditions cause a significant decrease in glycogen synthesis and increases PEPCK and G6Pase protein levels and Krebs-cycle-related enzymes levels, leading to an abnormal metabolic state in HepG2 Cells. However, treatment with Marein improves IR by increasing glucose uptake and glycogen synthesis and by downregulating PEPCK and G6Pase protein levels. The statistical analysis of HPLC/MS data demonstrates that Marein restores the normal metabolic state. The results show that AC ameliorates IR in rats and Marein has the potential effect in improving IR by ameliorating glucose metabolic disorders.AbbreviationsACethyl acetate extract ofCoreopsis tinctoriaTCATricarboxylic acidHepG2hepatocellular carcinoma cell line2-NBDG2-(N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino)-2-deoxyglucoseG6Paseglucose-6-phosphatasePEPCKphosphoenolpyruvate carboxykinaseIRinsulin resistanceHFDhigh-fat dietSDHAsuccinate dehydrogenase flavoprotein subunitACO2aconitase 2IDH2isocitrate dehydrogenase 2CScitrate synthaseFHfumarate hydrataseMDH2malate dehydrogenaseDLSTdihydrolipoamide S-succinyltransferase
Breaking the Deadlock of Molecular Chaperones
Authors: Luengo Tania Morán , Kityk Roman , Mayer Matthias P. , Rüdiger Stefan G. D. 
Published: August 2017

AbstractProtein folding in the cell requires ATP-driven chaperone machines. It is poorly understood, however, how these machines fold proteins. Here we propose that the conserved Hsp70 and Hsp90 chaperones support formation of the folding nucleus by providing a gradient of decreasing hydrophobicity. Early on the folding pathway Hsp70 uses its highly hydrophobic binding pocket to recover a stalled, unproductive folding intermediate. The aggressive nature of Hsp70 action, however, blocks productive folding by grabbing hydrophobic, core-forming segments. This precludes on-pathway nucleation at high, physiological Hsp70 levels. Transfer to the less hydrophobic Hsp90 enables the intermediate to resume forming its folding nucleus. Subsequently, the protein enters a spontaneous folding trajectory towards its native state, independent of the ATPase activities of both Hsp70 and Hsp90. Our findings provide a general mechanistic concept for chaperoned protein folding.
From foodwebs to gene regulatory networks (GRNs) - weak repressions by microRNAs confer system stability
Authors: Chen Yuxin , Shen Yang , Allesina Stefano , Wu Chung-I 
Published: August 2017

AbstractMore than 30% of mRNAs are repressed by microRNAs (miRNAs) but most repressions are too weak to have a phenotypic consequence. The diffuse actions have been a central conundrum in understanding the functions of miRNAs. By applying the May-Wigner theory used in foodweb studies, we show that i) weak repressions cumulatively enhance the stability of gene regulatory network (GRN), and ii) broad and weak repressions confer greater stability than a few strong ones. Transcriptome data show that yeast cells, which do not have miRNAs, use strong and non-specific mRNA degradation to stabilize their GRN; in contrast, human cells use miRNAs to increase degradation more modestly and selectively. Simulations indicate that miRNA repressions should be distributed broadly to >25% of mRNAs, in agreement with observations. As predicted, extremely highly expressed genes are avoided and transcription factors are preferred by miRNAs. In conclusion, the diffuse repression by miRNAs is likely a system-level strategy for enhancing GRN stability. This stability control may be the mechanistic basis of “canalization” (i.e., developmental homeostasis within each species), sometimes hypothesized to be a main function of miRNAs.
Searching for Correlated Conformational Dynamics: Analysis of the NMR Relaxation Dispersions with Akaike's Information Theory and Hierarchical Clustering
Authors: Kovrigin Evgenii L. 
Published: August 2017

ABSTRACT:In this manuscript, I am proposing an approach for identification of correlated exchange in proteins via analysis of the NMR relaxation dispersion data. For a set of spins experiencing exchange, every relaxation dispersion datasets is fit individually and then—globally while paired with every other dataset. The corrected Akaike’ s Information Criteria (AICc) for individual and global fits are used to evaluate the likelihood of two spins to report on the same dynamic event. Application of hierarchical cluster analysis reveals correlated spin groups using the difference in AICcs as a measure of similarity within the pairs. This approach to detection of correlated dynamics is independent of accuracy of best-fit parameters rendering it less sensitive to experimental noise. High throughput and the absence of the operator bias might make it applicable to a relatively lower quality NMR relaxation dispersion data from large and poorly soluble systems.
Analyzing the agile manufacturing barriers using fuzzy DEMATEL
Authors: Potdar Pavan Kumar , Routroy Srikanta , Behera Astajyoti 
Published: August 2017

Purpose
The purpose of this paper is to identify and analyze the agile manufacturing barriers (AMBs) for establishing a cause and effect relationship among them.

Design/methodology/approach
A methodology is proposed using fuzzy decision-making trial and evaluation laboratory (DEMATEL) to capture multiple experts’ qualitative judgments for mitigating the impact of the AMBs. In order to validate the proposed methodology, it is applied to an Indian automobile manufacturing company.

Findings
Out of 36 AMBs identified through literature review, 20 AMBs are found to be relevant to the case company. Five AMBs (i.e. lack of resource reconfiguration, inefficient conflicting management styles, imperfect market knowledge, inadequate information handling and improper strategic plan) were identified as significant cause group where the case company has to put efforts and resources. Also the impact relationship matrix for each AMB has been developed to visualize its interactions (i.e. influencing and influenced) among other AMBs.

Research limitations/implications
The results obtained are specific to the Indian automobile manufacturing company and it cannot be generalized for every manufacturing company or any other sector. However, the proposed approach can be a basis and provide a platform to understand and analyze the interactions between AMBs.

Practical implications
The proposed methodology will show the appropriate areas for allocating efforts and resources to mitigate the impact of AMBs for successful implementation of agile manufacturing.

Originality/value
According to the authors’ knowledge, no work is reported in the literature that proposes a framework using fuzzy DEMATEL for the analysis of AMBs in Indian automobile manufacturing company.
Supplier selection for a sustainable supply chain
Authors: Faisal Mohd. Nishat , Al-Esmael Bader , Sharif Khurram Jahangir 
Published: August 2017

Purpose
The purpose of this paper is to integrate the “triple bottom line (3BL)” approach in the supplier selection decision. It also aims to consider the feedback effect of the decision on strategic factors that determine the future viability of the firm in the market.

Design/methodology/approach
A multi-criteria decision model is developed that considers simultaneously the impact of three dimensions of 3BL approach and their sub-dimensions on the supplier selection decision. The proposed model is evaluated for a large white goods manufacturer using the analytic network process (ANP) approach.

Findings
The ANP considers the impact of variables, sub-variables, and their interdependencies simultaneously. The outcome of the model is the relative priorities for the firms considered as potential suppliers.

Practical implications
This research was conducted in one of the largest developing economies. The impact of integrating sustainability would be widespread due to the huge market in which the company operates. The results of this research can provide support to the decision makers in arriving at an optimal decision considering all sustainability dimensions.

Originality/value
The novelty of the approach lies in the application of multi-criteria model integrating sustainability dimensions with a feedback effect for supplier selection. The case company would benefit by showing its commitment toward environment and social responsibility leading to improved brand image and sustainable business.
High-performance benchmarking of manufacturing processes with object-based modeling
Authors: Zhou Xing , Kohl Holger 
Published: August 2017

Purpose
The purpose of this paper is to guide companies in conducting benchmarking studies of their manufacturing processes by viewing across industries, locations and products. In particular, the proposed framework can help corporate decision makers in terms of production footprint and site location studies. The level of benchmarking performance can be measured by evaluating defined benchmarking evaluation profiles.

Design/methodology/approach
This paper develops a tool to operationalize value-added manufacturing processes for benchmarking evaluations. In this context, an object-oriented database structure has been developed for the business areas such as product development, manufacturing and assembly. This paper focuses on manufacturing processes. Furthermore, a framework for applying high-performance benchmarking has been developed and applied in a case study.

Findings
This paper shows that object class-oriented modeling approach can be applied to manufacturing processes. The higher the degree of independence in terms of locations, industry sectors and products, the more powerful thus a higher performance of benchmarking is achieved. The performance level of benchmarking has been defined by proving and demonstrating higher and lower performance levels. The high-performance benchmarking tool has been successfully applied to a production footprint case study.

Originality/value
This paper takes up the superiority of process benchmarking that has been the focus of numerous research papers on benchmarking techniques in the past. The potential of process benchmarking has been enhanced and operationalized as a tool. A classification logic for benchmarking evaluation profiles has been developed and integrated in the overall tool set. The model helps decision makers to configure their benchmarking studies tailored to their strategic entrepreneurial questions and to guide them to achieve a higher benchmarking performance level.
Modeling the CSR barriers in manufacturing industries
Authors: Goyal Praveen , Kumar Divesh 
Published: August 2017

PurposeThe purpose of this paper is to identify and rank the various barriers of the CSR implementation in Indian manufacturing companies. Further, this paper also studies interaction of different barriers.Design/methodology/approachThe study was carried out using an interpretive structural modeling (ISM) approach to analyze the interaction among different barriers for corporate social responsibility (CSR) implementation in manufacturing companies in the Indian context.FindingsIn the present study, ten CSR implementation barriers were identified through an extensive literature review followed by the expert’s opinion. The present study outlines that lack of money and consumer’s passive attitude towards CSR are the major barriers in CSR implementation in Indian manufacturing companies. On the other hand, top management commitment, lack of knowledge about CSR and lack of skills for CSR implementation are barriers which occur due to the investment required in term of time and consumer’s passive attitude.Originality/valueThe present study is helpful to both academicians and practitioners by providing a model of CSR barriers. This study is important in the context of India which is a developing economy and this development is exerting pressure on the corporations to adopt CSR in their practices. This ISM-based model of barriers of CSR implementation in the manufacturing sector will help practitioners and managers to have enhanced knowledge about these barriers and to concentrate on important barriers to implement CSR activities in their organizations in an efficient manner.
Simultaneous evaluation of efficiency, input effectiveness, and output effectiveness
Authors: Shabani Amir , Faramarzi Gholam Reza , Farzipoor Saen Reza , Khodakarami Mohsen 
Published: August 2017

Purpose
The purpose of this paper is to develop a data envelopment analysis (DEA) technique that simultaneously measures efficiency and effectiveness to provide a comprehensive appraisal of the productivity. Additionally, an algorithm is recommended to determine targets that are used for measuring effectiveness.

Design/methodology/approach
In this paper, for measuring productivity, a new methodology based on non-parametric mathematical DEA technique was presented. The proposed procedure is able to compute the efficiency input effectiveness, and output effectiveness, simultaneously.

Findings
By comparing with previous models, the authors’ proposed integrated model generates more detailed results and has more discriminating power.

Originality/value
To the best of the authors knowledge, there is not any study in which a non-parametric mathematical approach measures productivity through simultaneous combining of the effectiveness, including input effectiveness, and output effectiveness, and the efficiency.
Exploring adolescent-parent interaction strategies for accessing alcohol at home
Authors: Dresler Emma , Whitehead Dean , Weaver Kelly 
Published: August 2017

PurposeThe purpose of this paper is to determine the extent to which youth have ready access to alcohol and the extent to which immediate family influence affects consumption.Design/methodology/approachThis qualitative descriptive exploratory study undertook semi-structured peer-group interviews with 20 participants from four New Zealand high schools. The interviews centred on exploring the “general” experiences of youth related to alcohol access – but with a focus on alcohol access “at home” and the parental role.FindingsThe study confirmed that the home unit was the main source of alcohol for most youth and parents were the most common source of provision. Parents provided financial access to alcohol by giving their child money to purchase it themselves through older family members or friends. It was also found that youth used negotiation strategies with their parents to influence their consumer purchases of alcohol.Research limitations/implicationsYouth frequently used strategies such as pressure tactics, exchange tactics, ingratiating tactics and consultation tactics to influence their family’s decision-making process and to pressure their parents into supplying them with alcohol.Practical implicationsIt is important to recognise the role that family play as “gatekeepers” for readily allowing access and supplying youth with alcohol – and the reasons for doing so.Social implicationsAlcohol plays an important part in many societies. It is important to understand how young people consume and access alcohol – particularly when the family plays a major role in access and consumption.Originality/valueMany studies have been conducted in relation to youth and alcohol consumption. Very few, as far as we can tell, explore the role of the family from the young consumers’ perspective and especially from a qualitative narrative perspective.