bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants
Authors: Tsyvina Viachaslau , Campo David S. , Sims Seth , Zelikovsky Alex , Khudyakov Yury , Skums Pavel 
Published: May 2018

AbstractMany biological analysis tasks require extraction of families of genetically similar sequences from large datasets produced by Next-generation Sequencing (NGS). Such tasks include detection of viral transmissions by analysis of all genetically close pairs of sequences from viral datasets sampled from infected individuals or studying of evolution of viruses or immune repertoires by analysis of network of intra-host viral variants or antibody clonotypes formed by genetically close sequences. The most obvious naϊeve algorithms to extract such sequence families are impractical in light of the massive size of modern NGS datasets. In this paper, we present fast and scalable k-mer-based framework to perform such sequence similarity queries efficiently, which specifically targets data produced by deep sequencing of heterogeneous populations such as viruses. The tool is freely available for download at https://github.com/vyacheslav-tsivina/signature-sj
RefCell: Multi-dimensional analysis of image-based high-throughput screens based on ‘typical cells’
Authors: Shen Yang , Kubben Nard , Candia Julián , Morozov Alexandre V. , Misteli Tom , Losert Wolfgang 
Published: May 2018

AbstractBackgroundImage-based high-throughput screening (HTS) reveals a high level of heterogeneity in single cells and multiple cellular states may be observed within a single population. Cutting-edge high-dimensional analysis methods are successful in characterizing cellular heterogeneity, but they suffer from the “curse of dimensionality” and non-standardized outputs.ResultsHere we introduce RefCell, a multi-dimensional analysis pipeline for image-based HTS that reproducibly captures cells with typical combinations of features in reference states, and uses these “typical cells” as a reference for classification and weighting of metrics. RefCell quantitatively assesses the heterogeneous deviations from typical behavior for each analyzed perturbation or sample.ConclusionsWe apply RefCell to the analysis of data from a high-throughput imaging screen of a library of 320 ubiquitin protein targeted siRNAs selected to gain insights into the mechanisms of premature aging (progeria). RefCell yields results comparable to a more complex clustering based single cell analysis method, which both reveal more potential hits than conventional average based analysis.
Design of a de novo aggregating antimicrobial peptide and bacterial conjugation delivery system
Authors: Collins Logan T. , Otoupal Peter B. , Courtney Colleen M. , Chatterjee Anushree 
Published: May 2018

AbstractTraditional antibiotics are reaching obsolescence as a consequence of antibiotic resistance; therefore novel antibiotic approaches are needed. A recent non-traditional approach involves formation of protein aggregates as antimicrobials to disrupt bacterial homeostasis. Previous work on protein aggregates has focused on genome mining for aggregation-prone sequences in bacterial genomes rather than on rational design of aggregating antimicrobial peptides. Here, we use a synthetic biology approach to design an artificial gene encoding the first de novo aggregating antimicrobial peptide. This artificial gene,opaL(overexpressed protein aggregator Lipophilic), disrupts bacterial homeostasis by expressing extremely hydrophobic peptides. When this hydrophobic sequence is disrupted by acidic residues, consequent aggregation and antimicrobial effect decreases. Further, to deliver this artificial gene, we developed a probiotic approach using RK2, a broad host range conjugative plasmid, to transferopaLfrom donor to recipient bacteria. We utilize RK2 to mobilize a shuttle plasmid carrying theopaLgene by adding the RK2 origin of transfer. We show thatopaLis non-toxic to the donor, allowing for maintenance and transfer since its expression is under control of a promoter with a recipient-specific T7 RNA polymerase. Upon mating of donor and recipientEscherichia coli, we observe selective growth repression in T7 polymerase expressing recipients. This technique could be used to target desired pathogens by selecting pathogen-specific promoters to controlopaLexpression. This system provides a basis for the design and delivery of novel antimicrobial peptides.ImportanceThe growing threat of antibiotic resistance necessitates new treatment options for bacterial infections that are recalcitrant to traditional antimicrobials. Existing methods usually involve small-molecule compounds which interfere with essential processes in bacterial cells. By contrast, protein aggregates operate by causing widespread disruption of bacterial homeostasis and may provide a new method for combating infections. We used rational design to create and test an aggregating de novo antimicrobial peptide, OpaL. In addition, we employed bacterial conjugation to deliver theopaLgene from donor bacteria to recipient bacteria while using a strain-specific promoter to ensure that OpaL was only expressed in targeted recipients. To the best of our knowledge, this represents the first design for a de novo peptide with aggregation-mediated antimicrobial activity. We envision that OpaL’s design parameters could be used in developing a new class of antimicrobial peptides to help treat antibiotic resistant infections.
Isolation and characterization of antagonistic bacteria with the potential for biocontrol of soil-borne wheat diseases
Authors: Wang Xiaohui , Wang Changdong , Ji Chao , Li Qian , Zhang Jiamiao , Song Xin , Jun Kang Sui , Liu Zhaoyang , Du Jianfeng , Liu Xunli 
Published: May 2018

AbstractBacillus amyloliquefaciens subsp. plantarum XH-9 is a plant-beneficial rhizobacterium that shows good antagonistic potential against phytopathogens by releasing diffusible and volatile antibiotics, and secreting hydrolytic enzymes. Furthermore, the XH-9 strain possesses important plant growth-promoting characteristics, including nitrogen fixation (7.92 ± 1.05 mg/g), phosphate solubilization (58.67 ± 4.20 μg/L), potassium solubilization (10.07 ± 1.26 μg/mL), and the presence of siderophores (4.92 ± 0.46 μg/mL), indole-3-acetic acid (IAA) (7.76 ± 0.51 μg/mL) and 1-aminocyclopropane-1-carboxylic acid deaminase (ACC-deaminase) (4.67 ± 1.21 nmol/[mg•h]). Moreover, the XH-9 strain showed good capacities for wheat, corn, and chili root colonization, which are critical prerequisites for controlling soil-borne diseases as a bio-control agent. Real-time quantitative polymerase chain reaction experiments showed that the amount of Fusarium oxysporum DNA associated with the XH-9 strain after treatment significantly decreased compared with control group. Accordingly, wheat plants inoculated with the XH-9 strain showed significant increases in the plant shoot heights (14.20%), root lengths (32.25%), dry biomass levels (11.93%), and fresh biomass levels (16.28%) relative to the un-inoculated plants. The results obtained in this study suggest that the XH-9 strain has potential as plant-growth promoter and biocontrol agent when applied in local arable land to prevent damage caused by F. oxysporum and other phytopathogens.ImportancePlant diseases, particularly soilborne pathogens, play a significant role in the destruction of agricultural resources. Although these diseases can be controlled to some extent with crop and fungicides, while these measures increase the cost of production, promote resistance, and lead to environmental contamination, so they are being phased out. Plant growth-promoting rhizobacteria are an alternative to chemical pesticides that can play a key role in crop production by means of siderophore and indole-3-acetic acid production, antagonism to soilborne root pathogens, phosphate and potassium solubilization, and nitrogen fixation. These rhizobacteria can also promote a beneficial change in the microorganism community by significantly reducing its pathogenic fungi component. Their use is fully in accord with the principles of sustainability.
Granzyme B is an essential mediator in CD8+ T cell killing ofTheileria parva-infected cells
Authors: Yang Jie , Pemberton Alan , Morrison W. Ivan , Connelley Tim 
Published: May 2018

AbstractThere is established evidence that cytotoxic CD8+ T cells are important mediators of immunity against the bovine intracellular protozoan parasiteT. parva.However, the mechanism by which the specific CD8+ T cells kill parasitized cells is not understood. Although the predominant pathway used by human and murine CD8+ T cells to kill pathogen-infected cells is granule exocytosis, involving release of perforin and granzyme B, there is to date a lack of published information on the biological activities of bovine granzyme B. The present study set out to define the functional activities of bovine granzyme B and determine its role in mediating killing ofT. parva-parasitized cells. DNA constructs encoding functional and non-functional forms of bovine granzyme B were produced and the proteins expressed in Cos-7 cells were used to establish an enzymatic assay to detect and quantify expression of functional granzyme B protein. Using this assay, the levels of killing of differentT. parva-specific CD8+ T cell clones were found to be significantly correlated with levels of granzyme B protein, but not mRNA transcript, expression. Experiments using inhibitors specific for perforin and granzyme B confirmed that CD8+ T cell killing of parasitized cells is dependent on granule exocytosis and specifically granzyme B. Further studies showed that granzyme B-mediated death of parasitized cells is independent of caspases, but involves activation of the pro-apoptotic molecule Bid.
Made in Vietnam
Authors: Phung Minh Thu Thuy , Knoben Joris , Vermeulen Patrick , Tran Dat Tho 
Published: May 2018

PurposeThe purpose of this paper is to simultaneously test the association between three different sources of knowledge (internal, collaborative and regional) and innovation. This study aims to expand the insights by assessing these associations in the context of a rapidly developing and liberalizing economy; Vietnam. By conducting this study with Vietnamese data, the authors can assess whether the association between different sources of knowledge and innovation shows systematic differences to those in advanced economies.Design/methodology/approachIn this study, the authors utilize data from two main sources: The World Bank Enterprise Survey and the Innovation Capabilities Survey. These firm-level surveys comprise non-agricultural formal and private sector firms. For Vietnam, 300 manufacturing firms have been included in the sample. The authors use a series of binary logistic regression models to analyze the data.FindingsThe analyses reveal that internal R&D has a strong positive association with product innovation. In contrast to findings in Western economies, not all kinds of collaborative knowledge sources have a significant association with innovation. Only collaborative knowledge gained from inside the supply chain is positively related to product innovation. Unexpectedly, negative effects from using too much external knowledge were also found.Research limitations/implicationsDue to the cross-sectional nature of the data causality could not be inferred from the study. Moreover, a relatively large number of the measures were dichotomous due the large number of missing observations for more detailed measurements of the variables.Practical implicationsWhen developing their innovation strategy firms in developing countries should take into account that collaborating with partners useful, but only if they collaborate within the supply chain. As such, firms should increase their interaction with suppliers and customers and put their efforts on the development of customized solutions for them.Social implicationsThe Vietnamese Government could implement policies that help to enhance the quality of universities and research institutes. In most developed countries, universities and research institutes are vital sources of knowledge for innovation whereas they are not in Vietnam.Originality/valueThis paper contributes to the growing body of literature on firm-level innovation in developing countries. It identifies several core differences between the drivers of innovation in developed and developing contexts. Surprisingly, a feature that was expected to differ, the negative effect of over-search of external knowledge on innovation, was also found in Vietnam.
Ten commandments of Lean Six Sigma: a practitioners’ perspective
Authors: Antony Jiju , Gupta Sandeep , Sunder M. Vijaya , Gijo E.V. 
Published: May 2018

Purpose
The purpose of this paper is to provide lean and six sigma professionals and researchers of tomorrow with Ten Commandments of Lean Six Sigma (LSS).

Design/methodology/approach
The Ten Commandments of LSS are based on several years’ experience of four authors who act as researchers, LSS Master Black Belts, consultants, practitioners and trainers on various topics of Lean, Six Sigma and general quality management and continuous improvement.

Findings
The Ten Commandments in our opinion include: alignment of LSS initiative with organisational strategy, LSS project selection and prioritisation, selection of top talent for the project execution, leadership for LSS, effective training and design of appropriate curriculum for different LSS roles, development of reward and recognition system, LSS sustainability, Linking LSS with Organisational Learning and Innovation, Linking LSS with Environmental Management System Standards and finally LSS and Big Data.

Research limitations/implications
The key features outlined in this paper are based on the practitioners of LSS. The authors of this article are planning to pursue a global study to critically evaluate these commandments by various practitioners of LSS.

Originality/value
The senior managers and executives of various businesses can use these commandments of LSS as a guide to achieve and sustain competitive advantage.
The teaching of information communication in Namibian schools
Authors: Wilfred Chanakira Tonderayi 
Published: May 2018

Purpose
The study is a survey covering the Ohangwena, Khomas and Otjozondjupa regions highlighting developments in the teaching of information literacy in Namibian schools through the subject Basic Information Science (BIS). This paper aims to provide an update on previous related studies which have been conducted in Namibia led by Nengomasha et al. (2012), Namibia Library Council (NLIC) Report (2007) and Smith et al.’s Baseline Study (2008).

Design/methodology/approach
The main objective of this study is to find reasons for non-compliance in the effective teaching of BIS in Namibian schools focus sing on the three regions. The data collection methods were questionnaires and focus group discussions.

Findings
A major finding from the study is that 80 per cent school principals are supporting the teaching of the subject BIS in the Ohangwena region, while 20 per cent are non-compliant in the teaching of BIS. The compliance levels in the Otjozondjupa region is that 75 per cent school principals support the teaching of BIS whilst 25 per cent school principals are non-compliant. In total, 60 teachers were randomly sampled in the Otjozondjupa region, while 75 school principals out of a population of 157 were also randomly sampled in the Ohangwena region. In the Khomas (100) region, 52 school principals were randomly sampled out of a population of a 108. The study recommends that it is critical for school principals in Namibia to fully support the development of young learners to be critical thinkers for lifelong learning challenges through the teaching of information literacy.

Originality/value
This study is original.
Exploring the dual-role of cognitive heuristics and the moderating effect of gender in microblog information credibility evaluation
Authors: Yin Chunxiao , Sun Yongqiang , Fang Yulin , Lim Kai 
Published: May 2018

Purpose
Although microblogs have become an important information source, the credibility of their postings is still a critical concern due to the open and unregulated nature. To understand the antecedents of microblog information credibility, the purpose of this paper is to investigate the dual-role of cognitive heuristics (i.e. the additivity and bias roles) and the effect of gender differences.

Design/methodology/approach
This study collected data via an online field survey of active microblog users, and a total of 204 valid responses was received.

Findings
This study demonstrates the dual-role of source credibility and vividness, the additivity role of microblog platform credibility, and the bias role of social endorsement. Furthermore, this study also found out gender difference that the additivity role of cognitive heuristics was stronger for men while bias role was stronger for women.

Research limitations/implications
This research enriches the microblog literature by examining the cognitive heuristic determinants as key predictors of microblog information credibility, and contributes to the information credibility literature by identifying and analyzing the dual-role effect of cognitive heuristics and corresponding gender differences.

Practical implications
This study can help organizations better manage their reputation, especially during the reputation crises, and also serves as a reminder to microblog platform operators of the importance of their microblog platform credibility.

Social implications
This study can help organizations better manage their reputation, especially during the reputation crises, and serves as a reminder to the microblog platform operators of the importance of their microblog platform credibility.

Originality/value
This study investigates the dual-role effect of cognitive heuristics (i.e. the additivity role and bias role) and corresponding gender differences that are less touched on before, and thus provides a more nuanced understanding of the more complex effects of cognitive heuristics.
Exploring effective work unit knowledge management (KM): roles of network, task, and KM strategies
Authors: Song Seokwoo , Sun Jonghak 
Published: May 2018

PurposeThis paper aims to explore the potential contribution of inter-unit network structure and intra-unit task environment to the overall knowledge management (KM) effectiveness of an organization through different KM strategies.Design/methodology/approachThe survey method was used to empirically test the hypotheses. The authors administered two survey forms: a member-survey form that obtained responses from members of each work unit and a leader-survey form issued only to the leader of each unit to obtain his/her perception on inter-unit communications.FindingsThe findings indicate that both a unit’s boundary-spanning role and its extensive interaction with other units help promote the unit’s overall KM effectiveness. In addition, the authors found that task variety was significantly related to the use of both personalization and codification of KM strategies in the unit, and that a unit’s KM strategy played a mediating role between intra-unit task characteristics and KM effectiveness.Originality/valueFew studies have attempted to address what makes some work units within an organization more effective in their use of knowledge than others. This study provides an understanding of the influence of inter-unit social network structure on KM effectiveness, as well as the influence of intra-unit task environment and KM strategies on KM effectiveness. The findings suggest that inter-unit knowledge exchange and a unit’s brokering role can be a vital component of a work unit’s KM strategy, and that for successful KM in a work unit, an organization should not only establish appropriate inter-unit relationship but also develop the unit’s own KM strategies.
Hospital unit understaffing and missed treatments: primary evidence
Authors: Metcalf Ashley Y. , Wang Yong , Habermann Marco 
Published: May 2018

Purpose
Hospitals throughout the USA are facing increasing patient demand and employee shortages. This capacity issue has led to understaffing in some hospital areas. The purpose of this paper is to examine the understaffing in hospital-unit respiratory care and the impact to error rates, specifically missed treatments rates. The moderating effects of teamwork and standardized, integrated information systems are also considered.

Design/methodology/approach
Survey methodology is used for data collection of respiratory care managers within hospital units. Regression is used to test the hypotheses in this study.

Findings
The regression results show that higher rates of understaffing are associated with more missed treatments. In addition, both teamwork and integrated information systems are associated with lower missed treatments. Finally, the moderating effect of teamwork is also highly significant within the model while integrated information systems are not a significant moderator.

Practical implications
Managers working within understaffed hospital units can try to reduce missed treatment rates by both integrated information systems and teamwork among employees. Additional benefits can be gained from teamwork due to the indirect effects (moderating effects) as well. This indicates teamwork training can be useful for quality initiatives.

Originality/value
Understaffing is associated with higher missed treatments in hospital units. Standardized, integrated information systems within a hospital are associated with less missed treatments. Furthermore, employee teamwork within a hospital unit is associated with a direct effect on missed treatment rates as well as an indirect effect by weakening the negative impact of understaffing.
Strategic orientation for failure recovery and performance behavior
Authors: Ladeira Wagner Junior , de Oliveira Santini Fernando , da Costa Janaína Raquel Andrade , Ribeiro Lucas Endrigo Severo 
Published: May 2018

Purpose
The purpose of this paper is to analyze the moderating effect of salesperson environmental and goal orientation on the relationship between strategic orientation for failure recovery and performance behavior.

Design/methodology/approach
In total, 287 usable samples were collected from surveying sales representatives. The data were analyzed using structural equation modeling.

Findings
The results indicated that the recovery strategy has a positive and significant impact on performance behavior. However, this relationship can be influenced by high levels of competitiveness to generate a smaller commitment in the sales team in behavioral performance and by the fact that salespeople who have a high learning goal orientation ascribed stronger relationships between the recovery strategy and performance goal.

Originality/value
Academically, this research has several purposes. In the sales area, the authors analyze the strategic orientation for failure recovery. The authors believe that this approach is necessary to improve the scientific quality of the studies in the sales area.