bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Primed Adaptation in theEscherichia colitype I-E CRISPR-Cas System
Authors: Stringer Anne M. , Cooper Lauren A. , Kadaba Sujatha , Shrestha Shailab , Wade Joseph T. 
Published: February 2020

ABSTRACTCRISPR-Cas systems are bacterial immune systems that target invading nucleic acid. The hallmark of CRISPR-Cas systems is the CRISPR array, a genetic locus that includes short sequences known as “spacers”, that are derived from invading nucleic acid. Upon exposure to an invading nucleic acid molecule, bacteria/archaea with functional CRISPR-Cas systems can add new spacers to their CRISPR arrays in a process known as “adaptation”. In type I CRISPR-Cas systems, which represent the majority of CRISPR-Cas systems found in nature, adaptation can occur by two mechanisms: naïve and primed. Here, we show that, for the archetypal type I-E CRISPR-Cas system fromEscherichia coli, primed adaptation occurs at least 1,000 times more efficiently than naïve adaptation. By initiating primed adaptation on theE. colichromosome, we show that spacers can be acquired across distances of >100 kb from the initially targeted site, and we identify multiple factors that influence the efficiency with which sequences are acquired as new spacers. Thus, our data provide insight into the mechanism of primed adaptation.[This paper has been peer reviewed, with Ailong Ke (Cornell University) serving as the editor. Reviews and point-by-point response, and a marked-up version of the edited manuscript are provided as supplementary files.]
Altered hippocampal place cell representation and theta rhythmicity following moderate prenatal alcohol exposure
Authors: Harvey Ryan E. , Berkowitz Laura E. , Savage Daniel D. , Hamilton Derek A. , Clark Benjamin J. 
Published: February 2020

SummaryPrenatal alcohol exposure (PAE) leads to profound deficits in spatial memory and synaptic and cellular alterations to the hippocampus that last into adulthood. Neurons in the hippocampus, called place cells, discharge as an animal enters specific places in an environment, establish distinct ensemble codes for familiar and novel places, and are modulated by local theta rhythms. Spatial memory is thought to critically depend on the integrity of hippocampal place cell firing. We therefore tested the hypothesis that hippocampal place cell firing is impaired after PAE by performing in-vivo recordings from the hippocampi (CA1 and CA3) of moderate PAE and control adult rats. Our results show that hippocampal CA3 neurons from PAE rats have reduced spatial tuning. Secondly, CA1 and CA3 neurons from PAE rats are less likely to orthogonalize their firing between directions of travel on a linear track and between contexts in an open arena compared to control neurons. Lastly, reductions in the number of hippocampal place cells exhibiting significant theta rhythmicity and phase precession were observed which may suggest changes to hippocampal microcircuit function. Together, the reduced spatial tuning and sensitivity to context provides a neural systems-level mechanism to explain spatial memory impairment after moderate PAE.
DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers
Authors: Boža Vladimír , Perešíni Peter , Brejová Broňa , Vinař Tomáš 
Published: February 2020

AbstractMotivationOxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.ResultsWe have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or pre-filtering of results for more detailed analysis (i.e. filtering out human DNA from human–pathogen runs).Availability and ImplementationDeepNano-blitz has been developed and tested on Linux and is available under MIT license athttps://github.com/fmfi-compbio/deepnano-blitzContactvladimir.boza@fmph.uniba.sk
Longitudinal analysis of naturally acquired antibodies to PfEMP1 CIDR domain variants and their association with malaria protection
Authors: Obeng-Adjei Nyamekye , Larremore Daniel B. , Turner Louise , Ongoiba Aissata , Li Shanping , Doumbo Safiatou , Yazew Takele B. , Kayentao Kassoum , Miller Louis H. , Traore Boubacar , Pierce Susan K. , Buckee Caroline O. , Lavstsen Thomas , Crompton Peter D. , Tran Tuan M. 
Published: February 2020

ABSTRACTMalaria pathogenicity is determined, in part, by the adherence ofPlasmodium falciparuminfected erythrocytes to the microvasculature mediated via specific interactions between PfEMP1 variant domains to host endothelial receptors. Naturally acquired antibodies against specific PfEMP1 variants can play an important role in clinical protection against malaria. We evaluated IgG responses against a repertoire of PfEMP1 CIDR domain variants to determine the rate and order of variant-specific antibody acquisition and their association with protection against febrile malaria in a prospective cohort study conducted in an area of intense, seasonal malaria transmission. Using longitudinal data, we found that IgG to the pathogenic domain variants CIDRα1.7 and CIDRα1.8 were acquired the earliest. Furthermore, IgG to CIDRγ3 was associated with reduced prospective risk of febrile malaria and recurrent malaria episodes. Future studies will need to validate these findings in other transmission settings and determine the functional activity of these naturally acquired CIDR variant-specific antibodies.
Selection-driven tumor evolution involving non-cell growth promotion leads to patterns of clonal expansion consistent with neutrality interpretation
Authors: Edwards Jack , Marusyk Andriy , Basanta David 
Published: February 2020

SummaryCancers are the result of eco-evolutionary processes fueled by heritable phenotypic diversification and driven by environmentally dependent selection. As space represents a key growth-limiting ecological resource, the ability to gain and explore this resource is likely to be under strong selection. Using agent-based computational modeling, we explored the consequences of the interplay between phenotypic strategies centered on gaining access to new space through cell-extrinsic degradation of extracellular matrix barriers and the exploitation of this resource through maximizing cell proliferation. While cell proliferation is a cell-intrinsic property, newly accessed space represents a public good, which can benefit both producers and non-producers. We found that that this interplay results in ecological succession, enabling emergence of large, heterogenous, and highly proliferative populations. Even though in our simulations both remodeling and proliferation strategies were under strong positive selection, their interplay led to sub-clonal architecture that could be interpreted as evidence for neutral evolution, warranting cautious interpretation of inferences from sequencing of cancer genomes.
How does group differences in motion scrubbing affect false positives in functional connectivity studies?
Authors: Eklund Anders , Nichols Thomas E. , Afyouni Soroosh , Craddock Cameron 
Published: February 2020

AbstractAnalyzing resting state fMRI data is difficult due to a weak signal and several noise sources. Head motion is also a major problem and it is common to apply motion scrubbing, i.e. to remove time points where a subject has moved more than some pre-defined motion threshold. A problem arises if one cohort on average moves more than another, since the remaining temporal degrees of freedom are then different for the two groups. The effect of this is that the uncertainty of the functional connectivity estimates (e.g. Pearson correlations) are different for the two groups, but this is seldom modelled in resting state fMRI. We demonstrate that group differences in motion scrubbing can result in inflated false positives, depending on how the temporal auto correlation is modelled when performing the Fisher r-to-z transform.
Massively Parallel Analysis of Human 3′ UTRs Reveals that AU-Rich Element Length and Registration Predict mRNA Destabilization
Authors: Siegel David A. , Tonqueze Olivier Le , Biton Anne , Zaitlen Noah , Erle David J. 
Published: February 2020

AbstractAU-rich elements (AREs) are 3′ UTR cis-regulatory elements that regulate the stability of mRNAs. Consensus ARE motifs have been determined, but little is known about how differences in 3′ UTR sequences that conform to these motifs affect their function. Here we use functional annotation of sequences from 3′ UTRs (fast-UTR), a massively parallel reporter assay (MPRA), to investigate the effects of 41,288 3′ UTR sequence fragments from 4,653 transcripts on gene expression and mRNA stability. The library included 9,142 AREs, and incorporated a set of fragments bearing mutations in each ARE. Our analyses demonstrate that the length of an ARE and its registration (the first and last nucleotides of the repeating ARE motif) have significant effects on gene expression and stability. Based on this finding, we propose improved ARE classification and concomitant methods to categorize and predict the effect of AREs on gene expression and stability. Our new approach explains 64±13% of the contribution of AREs to the stability of human 3′ UTRs in Jurkat cells and predicts ARE activity in an unrelated cell type. Finally, to investigate the advantages of our general experimental design for annotating 3′ UTR elements we examine other motifs including constitutive decay elements (CDEs), where we show that the length of the CDE stem-loop has a significant impact on steady-state expression and mRNA stability. We conclude that fast-UTR, in conjunction with our analytical approach, can produce improved yet simple sequence-based rules for predicting the activity of human 3′ UTRs containing functional motifs.
Customer aggression and service sabotage
Authors: Goussinsky Ruhama 
Published: February 2020

Purpose
The purpose of this study aims to investigate the independent and combined moderating effects of social sharing and rumination on the relationship between customer aggression and service sabotage.

Design/methodology/approach
Two samples of service providers were recruited: a sample of face-to-face service employees from various organizations (N = 481) and a sample of call center employees (N = 122). Data were collected using self-reported questionnaires and the research hypotheses were tested using hierarchical regression analyses.

Findings
The impact of customer aggression on service sabotage was exacerbated by rumination in Sample 1 and although failing to reach significance (0.08), the same pattern of interaction was observed in Sample 2. The results lend support to the existence of a three-way interaction effect between customer aggression, social sharing and rumination. Specifically, the positive relationship between customer aggression and service sabotage was stronger for employees who reported high levels of both social sharing and rumination compared to employees who reported high levels of social sharing but low levels of rumination.

Practical implications
Implementing stress-management training intended to help service employees avoid using maladaptive coping strategies when confronted with mistreatment can serve to reduce employees’ engagement in retaliatory behaviors directed against customers.

Originality/value
The study’s findings provide one potential explanation for the mixed findings in the literature on social sharing and suggest that sharing of emotions for coping with customer aggression may become a maladaptive strategy for individuals who tend to engage in ruminative thinking whereas it may be a helpful coping choice for individuals who do not.
Adapting a Lean leadership-training program within a health care organization through cocreation
Authors: Ingelsson Pernilla , Bäckström Ingela , Snyder Kristen 
Published: February 2020

Purpose
The purpose of this paper is to describe and evaluate a Lean leadership-training program within the health-care sector. A training program developed through a cocreative process with the intent of enhancing the possibilities for a context-specific adaption of Lean.

Design/methodology/approach
A cocreated leadership-training program, executed over a period of one year, is described both as a model development process and as the final training program. The program was evaluated through reflective discussions and feedback as well as a written final evaluation of the program from participants in the program.

Findings
The evaluation shows that the objectives of the training program were met, at least among the participants who attended the whole program. Using a cocreative process when developing and realizing a leadership-training program enhances the possibilities for an organization to adapt Lean to its own context. One condition for this approach to be successful is that the expectations of both the organization and the university need to be in focus through the whole process. In addition, the executive team needs to be continuously engaged and create conditions for the organization to realize the potential benefits of the training program.

Originality/value
This paper highlights the challenge when applying Lean in a health-care organization but also describes a way to address Lean training and learning in this context.
Optimal location of UPQC for power quality improvement: novel hybrid approach
Authors: Gaddala Kaladhar , Raju P. Sangameswara 
Published: February 2020

PurposeIn general, the optimal reactive power compensation could drastically enhance the performance of distributed network by the reduction of power loss and by enhancement of line loadability and voltage profile. Till now, there exist various reactive power compensation models including capacitor placement, joined process of on-load tap changer and capacitor banks and integration of DG. Further, one of the current method is the allocation of distribution FACTS (DFACTS) device. Even though, the DFACTS devices are usually used in the enhancement of power quality, they could be used in the optimal reactive power compensation with more effectiveness.Design/methodology/approachThis paper introduces a power quality enhancement model that is based on a new hybrid optimization algorithm for selecting the precise unified power quality conditioner (UPQC) location and sizing. A new algorithm rider optimization algorithm (ROA)-modified particle swarm optimization (PSO) in fitness basis (RMPF) is introduced for this optimal selections.FindingsThrough the performance analysis, it is observed that as the iteration increases, there is a gradual minimization of cost function. At the 40th iteration, the proposed method is 1.99 per cent better than ROA and genetic algorithm (GA); 0.09 per cent better than GMDA and WOA; and 0.14, 0.57 and 1.94 per cent better than Dragonfly algorithm (DA), worst solution linked whale optimization (WS-WU) and PSO, respectively. At the 60th iteration, the proposed method attains less cost function, which is 2.07, 0.08, 0.06, 0.09, 0.07 and 1.90 per cent superior to ROA, GMDA, DA, GA, WS-WU and PSO, respectively. Thus, the proposed model proves that it is better than other models.Originality/valueThis paper presents a technique for optimal placing and sizing of UPQC. To the best of the authors’ knowledge, this is the first work that introduces RMPF algorithm to solve the optimization problems.
An integrated approach for three-dimensional capacitated vehicle routing problem considering time windows
Authors: Ayough Ashkan , Khorshidvand Behrooz , Massomnedjad Negah , Motameni Alireza 
Published: February 2020

Purpose
As a critical problem in sophisticated distribution systems, vehicle routing plays a pivotal role in dealing with time windows and capacities constraints. The purpose of this paper is to addresses a new integrated model to incorporate both three-dimensional and time windows aspects of the routing problem. First, capacitated vehicle routing decisions are made subject to a soft time interval to meet the customers’ demands. Afterward, these decisions are entered into the three-dimensional loading problem.

Design/methodology/approach
The problem is solved using generalized algebraic modeling system software in small-size problems. The problem is NP-hard and requires an efficient solution methodology. For this purpose, a hybrid algorithm has been proposed to solve the large-size problems. The efficiency of this algorithm is checked by making comparisons with exact solutions for small and medium size test problems, and with the related literature for large size problems.

Findings
The numerical experiments show that the proposed model covers more effectively the broader aspects of the transportation problem. Furthermore, the proposed algorithm supports competitive and satisfactory results by giving reasonable outputs in comparison with previous studies.

Originality/value
The main purpose of this integration is to achieve minimum total transportation costs, which cannot be guaranteed without applying two referred constraints, simultaneously.
Trust and dynamic governance mechanisms in the university-industry R&D alliances
Authors: Ruangpermpool Somchai , Igel Barbara , Siengthai Sununta 
Published: February 2020

PurposeThis paper aims to examine how the dynamic interplay of governance mechanisms of the university-firm R&D alliance reduces obstacles and enables the successful commercialization of research collaboration output.Design/methodology/approachA longitudinal case research and retrospective strategy were used to collect relevant data and information in the four university-and-firm alliance teams collaborating on R&D projects in Thailand during 2008-2014. In-depth interviews and meetings were conducted with representatives of all partners and R&D project teams.FindingsThe authors found that formal and informal control mechanisms act as complementary forms of governance. The informal control (trust) serves as the frame of intentions whether the formal control is interpreted as a guideline or a commitment. Both formal and informal control mechanisms must be put in place to successfully and sustainably develop collaborative research into a commercial product.Research limitations/implicationsThis study investigated four Thai government-funded research collaboration teams from a single industry. It would be worth investigating such research collaboration in other industries and those without any government funding.Originality/valueThis study applied an exploratory case research method which is rarely used in research on R&D alliance teams. It generates cross-functional insights on how to build trust in such R&D context, especially in an emerging economy.
The role of ICT infrastructure, innovation and globalization on economic growth in OECD countries, 1996-2017
Authors: Kurniawati Meta Ayu 
Published: February 2020

PurposeThe rapid development of information and communication technology (ICT) over the past decade has enabled heterogeneous economic sectors to be more integrated, leading to a significant effect on nation’s growth across OECD countries. The objective of this study is to estimate the short run and long run inter-linkages among ICT, innovation technology, globalization, and economic growth for the period 1996-2017 in OECD countries.Design/methodology/approachThis research provides some sophisticated methodologies by using principal component analysis to construct ICT and innovation indices and follow up by employing the panel cointegration test, pooled mean group regression, fully modified ordinary least squares and dynamic ordinary least squares as sophisticated estimation techniques, panel Granger causality and forecast error variance decomposition to examine the robustness of the causal association in the findings.FindingsThe empirical results herein suggest that ICT, innovation and globalization positively contribute to economic growth, while the causality findings reveal strong endogenous relationships among both ICT mobile and internet use, innovation development, globalization and economic growth in both short and long run. The findings further imply that OECD countries have yet to promote economic growth from ICT infrastructure expansion, the enlargement of technology innovation and the spread of globalization.Practical implicationsThe particular policy recommendation is to reinforce the investment and establishment of a reliable ICT infrastructure as well as innovation technology to create sustained economic growth in this progressively interconnected world.Originality/valueThis study is valuable from policy and decision-makers’ perspective, as it highlights the significance of ICT infrastructure development, innovation enlargement and globalization to elevate the economic growth in OECD countries.
The nexus between supply chain analytic, innovation and robustness capability
Authors: Shamout Mohamed Dawood 
Published: February 2020

PurposeBy drawing on knowledge-based view, this paper aims to test causal model linking supply chain analytics, innovation, robustness capability and firm age. More specifically, the mediating role of supply chain innovation on supply chain analytics and robustness capability link and the moderating role of firm age.Design/methodology/approachSurvey data were procured from companies operating in the United Arab Emirates using a simple random sampling technique. The obtained data were analyzed with variance-based structural equation modeling (PLS-SEM).FindingsThe findings from PLS-SEM revealed that supply chain innovation fully mediate supply chain analytics and robustness capability associations. Findings from multi-group analysis (MGA) denote that firm age did not moderate any of the paths of the research model. Suggesting that the associations are similar for old, mid-aged and younger firms.Originality/valueThis work demonstrates that supply chain analytic is valuable tool that can foster innovation and robustness in supply chain. This work is among the first to scrutinize the variation among old, mid-aged and younger firms in supply chain analytics research stream. The paper concludes with implications for theory and practice.