bluuebunny/crossref_metadata_2025_split huggingface dataset:
DivergentIn vitroMIC Characteristics and underlying isogenic mutations in host-specializedPseudomonas aeruginosa
Authors: Qin Xuan , Greninger Alexander L , Zhou Chuan , Adler Amanda , Yuan Shuhua , Zerr Danielle M. 
Published: March 2017

AbstractClinical isolates ofPseudomonas aeruginosa (Pa)from patients with cystic fibrosis (CF) are known to differ from those associated with infections of non-CF hosts in colony morphology, drug susceptibility patterns, and genomic hypermutability. AlthoughPaisolates from CF have long been recognized for their overall higher resistance rate calculated generally by reduced “percent susceptible”, this study takes the approach to compare and contrast Etest MIC distributions between two distinct cohorts of clinical strains (n=224 from 56 CF patients and n=130 from 68 non-CF patients respectively) isolated in 2013. Logarithmic transformed MIC (logMIC) values of 11 antimicrobial agents were compared between the two groups. CF isolates tended to produce heterogeneous and widely dispersed MICs compared to non-CF isolates. By applying a test for equality of variances, we were able to confirm that the MICs generated from CF isolates against 9 out of the 11 agents were significantly more dispersed than those from non-CF (p<0.02-<0.001). Quantile-quantiles plots indicated little agreement between the two cohorts of isolates. Based on whole genome sequencing of 19 representative CFPaisolates, divergent gain- or loss-of-function mutations in efflux and porin genes and their regulators between isogenic or intra-clonal associates were evident. Not one, not a few, but the net effect all adaptive mutational changes in the genomes of CFPa, both shared and unshared between isogenic strains, are responsible for the divergent heteroresistance patterns. Moreover, the isogenic variations are suggestive of a bacterial syntrophic lifestyle when “lockedȍ inside a host focal airway environment over prolonged periods.Significance statementBacterial heteroresistance is associated with niche specialized organisms interacting with host species for prolonged period of time, medically characterized by “chronic focal infections”. A prime example is found inPseudomonas aeruginosaisogenic/non-homogeneous isolates from patient airways with cystic fibrosis. The development of pseudomonal polarizing MICsin vitroto many actively used antimicrobial agents among isogenic isolates and “Eagle-type” heteroresistance patterns are common and characteristic. Widespread isogenic gene lesions were evident for defects in drug transporters, DNA mismatch repair, and many other structural or cellular functions—a result of pseudomonal symbiotic response to host selection. Co-isolation of extremely susceptible and resistant isogenicPastrains suggests intra-airway evolution of a multicellular syntrophic bacterial lifestyle, which has laboratory interpretation and clinical treatment implications.
Dynein dynamics at the microtubule plus-ends and cortex during division in theC. eleganszygote
Authors: Rodriguez-Garcia Ruddi , Chesneau Laurent , Pastezeur Sylvain , Roul Julien , Tramier Marc , Pécréaux Jacques 
Published: March 2017

AbstractDuring asymmetric cell division, dynein generates forces, which position the spindle to reflect polarity and ensure correct daughter cell fates. The transient cortical localization of dynein raises the question of its targeting. We found that it accumulates at the microtubule plus-ends like in budding yeast, indirectly hitch-hiking on EBP-2EB1likely via dynactin. Importantly, this mechanism, which modestly accounts for cortical forces, does not transport dynein, which displays the same binding/unbinding dynamics as EBP-2EB1. At the cortex, dynein tracks can be classified as having either directed or diffusive-like motion. Diffusive-like tracks reveal force-generating dyneins. Their densities are higher on the posterior tip of the embryos, where GPR-1/2LGNconcentrate, but their durations are symmetric. Since dynein flows to the cortex are non-polarized, we suggest that this posterior enrichment increases dynein binding, thus accounts for the force imbalance reflecting polarity, and supplements the regulation of mitotic progression via the non-polarized detachment rate.
Identifying drivers of parallel evolution: A regression model approach
Authors: Bailey Susan F. , Guo Qianyun , Bataillon Thomas 
Published: March 2017

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution, however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce several statistical models to examine the contributions of mutation and selection heterogeneity to shaping parallel evolutionary changes at the gene-level. Using this framework we analyze published data from forty experimentally evolvedSaccharomyces cerevisiaepopulations. We can partition the effects of a number of genomic variables into those affecting patterns of parallel evolution via effects on the rate of arising mutations, and those affecting the retention versus loss of the arising mutations (i.e. selection). Our results suggest that gene-to-gene heterogeneity in both mutation and selection, associated with gene length, recombination rate, and number of protein domains drive parallel evolution at both synonymous and nonsynonymous sites. While there are still a number of parallel changes that are not well described, we show that allowing for heterogeneous rates of mutation and selection can provide improved predictions of the prevalence and degree of parallel evolution.Data archival locationDryad, doi to be included later
Comparison of village dog and wolf genomes highlights the pivotal role of the neural crest in dog domestication
Authors: Pendleton Amanda L. , Shen Feichen , Taravella Angela M. , Emery Sarah , Veeramah Krishna R. , Boyko Adam R. , Kidd Jeffrey M. 
Published: March 2017

AbstractBackgroundDogs (Canis lupus familiaris) were domesticated from gray wolves between 10-40 kya in Eurasia, yet details surrounding the process of domestication remain unclear. The vast array of phenotypes exhibited by dogs mirror other domesticated animal species, a phenomenon known as the Domestication Syndrome. Here, we use signatures persisting in the dog genome to identify genes and pathways altered by the intensive selective pressures of domestication.ResultsWe identified 246 candidate domestication regions containing 10.8Mb of genome sequence and 178 genes through whole-genome SNP analysis of 43 globally distributed village dogs and 10 wolves. Comparisons with ancient dog genomes suggest that these regions reflect signatures of domestication rather than breed formation. The strongest hit is located in theRetinoic Acid-Induced 1(RAI1) gene, mutations of which cause Smith-Magenis syndrome. The identified regions contain a significant enrichment of genes linked to neural crest cell migration, differentiation and development. Read depth analysis suggests that copy number variation played a minor role in dog domestication.ConclusionOur results indicate that phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development, are determined by genes which act early in embryogenesis. These differences are all phenotypes of the Domestication Syndrome, which can be explained by decreases in neural crest cells at these sites. We propose that initial selection during early dog domestication was for behavior, a trait also influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
Unaware processing of tools in the neural system for object-directed action representation
Authors: Tettamanti Marco , Conca Francesca , Falini Andrea , Perani Daniela 
Published: March 2017

AbstractThe hypothesis that the brain constitutively encodes observed manipulable objects for the actions they afford is still debated. Yet, crucial supporting evidence demonstrating that such visuo-motor embodiment occurs even without awareness has hitherto not been provided. In this fMRI study, we reliably instantiated unaware visual perception conditions by means of Continuous Flash Suppression, and found consistent activation in the target visuo-motor, action representation system, specifically for manipulable versus non-manipulable objects
Sorting & Sequencing Flies by Size: Identification of novel TOR regulators and Parameters for Successful Sorting
Authors: Strassburger Katrin , Zöller Tanja , Sandmann Thomas , Leible Svenja , Kerr Grainne , Boutros Michael , Teleman Aurelio A. 
Published: March 2017

AbstractAs DNA sequencing throughput increases, novel strategies for discovering genes that affect traits of interest become available. One strategy starts with a population of animals and selects individuals over multiple generations for a particular trait. Subsequent whole genome sequencing should identify loci affecting this trait. We apply this strategy by sorting flies for wing length over 18 generations, obtaining two populations that differ in wing length by 20%. Flies with longer wings had increased overall body sizes and elevated TOR activity, suggesting that genetic variation targets TOR signaling to influence body size. High-throughput sequencing of big and small flies identified thousands of single nucleotide polymorphisms that differed between the two populations, leading us to identify five novel regulators of TOR signaling. Surprisingly, stochastic simulations of the process show that large fractions of the genetic differences between the big and small flies are probably biological false positives, selected by chance by random drift. We employ these computer simulations to identify experimental setup parameters to improve the signal-to-noise ratio for successfully running sort-and-sequence experiments – a resource which will hopefully be useful for the community.
Vegetally localized Vrtn functions as a novel repressor to modulatebmp2btranscription during dorsoventral patterning in zebrafish
Authors: Shao Ming , Wang Min , Ge Yi-Wen , Zhang Yan-Jun , Shi De-Li 
Published: March 2017

ABSTRACTThe vegetal pole cytoplasm represents a critical source of maternal signals for patterning the primary dorsoventral axis of the early embryo. Vegetally localized dorsal determinants are essential for the formation of the Spemann organizer, which expresses both bone morphogenetic proteins and their antagonists. The extracellular regulation of BMP signalling activity has been well characterized, however, transcriptional regulation ofbmpgenes along the dorsoventral axis remains largely unknown. Here, we report a novel mode of maternal regulation of BMP signalling in the lateral and ventral regions by analyzing the unexpected dorsalizing effect following vegetal yolk ablation experiment. We identified Vrtn as a novel vegetally localized maternal factor displaying dorsalizing activity. It functions as a novel transcriptional repressor to regulatebmp2bexpression in the marginal region. Mechanistically, Vrtn bindsbmp2bupstream sequence and inhibits its transcription independently of maternal Wnt/ß-catenin signalling. By creatingvrtnloss-of-function mutation and analyzing maternal-zygotic mutant embryos, we further showed that Vrtn is required for the formation of dorsoventral axis. Our work thus unveils a novel maternal mechanism regulating BMP gradient during dorsoventral specification.
The acute toxicity of Oxydemeton-methyl in zebrafish
Authors: Jia Guofeng , Liu Xiecheng 
Published: March 2017

AbstractOxydemeton-methyl, is an organothiophosphate insecticide, which is widely used in agricultural and urban pest controls. It exists in the environment and a large amount bioaccumulation in the wildlife due to its strong water solubility and mobility. Although its potentially harmful effect on animals and humans, few studies have focused on the oxydemeton-methyl pollution in the environment. Zebrafish have been used for many years to valuate the pollution status of water and toxicity of chemicals. In the present study, we aimed to investigate the effect of oxydemeton-methyl on the expression level of liver microsomal cytochrome P450, on the activity of NADPH-P450 reductase and reactive oxygen species (ROS) generation in zebrafish. Adult male and female zebrafish were treated with different concentration of oxydemeton-methyl (10, 50, 100 μM) for 5, 10, 20 and 30 days. We found that the oxydemeton-methyl exposure significantly increased the P450 levels and the activity of NAPDH-P450 reductase. ROS generation and the DNA damage were augmented in a dose-dependent manner in the zebrafish. These results indicated that oxydemeton-methyl is able to induce strong oxidative stress and hence highly toxic to the zebrafish.
Integrated Structure-Transcription analysis of small molecules reveals widespread noise in drug-induced transcriptional responses and a transcriptional signature for drug-induced phospholipidosis
Authors: Sirci Francesco , Napolitano Francesco , Pisonero-Vaquero Sandra , Carrella Diego , Medina Diego L. , di Bernardo Diego 
Published: March 2017

AbstractWe performed an integrated analysis of drug chemical structures and drug-induced transcriptional responses. We demonstrated that a network representing 3D structural similarities among 5,452 compounds can be used to automatically group together drugs with similar scaffolds and mode-of-action. We then compared the structural network to a network representing transcriptional similarities among a subset of 1,309 drugs for which transcriptional response were available in the Connectivity Map dataset. Analysis of structurally similar, but transcriptionally different, drugs sharing the same mode of action (MOA) enabled us to detect and remove weak and noisy transcriptional responses, greatly enhancing the reliability and usefulness of transcription-based approaches to drug discovery and drug repositioning. Analysis of transcriptionally similar, but structurally different drugs with unrelated MOA, led us to the identification of a “toxic” transcriptional signature indicative of lysosomal stress (lysosomotropism) and lipid accumulation (phospholipidosis) partially masking the target-specific transcriptional effects of these drugs. We further demonstrated by High Content Screening that this transcriptional signature is caused by the activation of the transcription factor TFEB, a master regulator of lysosomal biogenesis and autophagy. Our results show that chemical structures and transcriptional profiles provide complementary information and that combined analysis can lead to new insights on on- and off-target effects of small molecules.
Benchmarking towards excellence in higher education
Authors: Tasopoulou Konstantina , Tsiotras George 
Published: March 2017

Purpose
The purpose of this paper is to investigate the extent to which higher education institutions can benefit from the implementation of benchmarking practices. Thus, the aim of this research is to point out the structure and applications of quality improvement, by providing evidence for understanding the implementation of benchmarking as a competing tool for excellence in higher education institutions.

Design/methodology/approach
The methodology followed in this paper is based on a method approach, including both qualitative and quantitative analysis. Research is based on 20 case studies of universities committed to excellence around the world. Data collection was accomplished by a well-designed questionnaire on how quality improvement can be accomplished through benchmarking practices.

Findings
The findings of this research indicate that benchmarking can improve academic excellence by means of comparison and assessment. The study finds that process performance measurements can bring considerable outcomes of enhancement, improvement and transformation in higher education systems.

Practical implications
This research on benchmarking in higher education institutions provides exemplar standpoints and practices for the pursuit of excellence in educational organizations, in order to gain additional knowledge and paradigm on quality improvement that can lead to excellence. Considering the population of rankings worldwide, the main idea is linked to benchmarking and the acceptance of being compared to others in the sector.

Originality/value
The value of this paper lies in the identification and presentation of several ideas and tools which can successfully be applied to higher education institutions in order to achieve excellence by using benchmarking practices.
The effect of supply chain integration on technical innovation in Jordan
Authors: Ayoub Heba Fawzi , Abdallah Ayman Bahjat , Suifan Taghreed S. 
Published: March 2017

Purpose
The purpose of this paper is to investigate the effect of supply chain integration (SCI) in terms of supplier integration, customer integration, and internal integration on knowledge management (KM) and technical innovation (TI). The study also investigates the effect of KM on TI. Furthermore, the mediating effect of KM on the relationship between SCI and TI is investigated.

Design/methodology/approach
Study model and hypotheses were developed based on literature review. The study is based on survey data collected from 217 Jordanian manufacturing companies in electrical, electronics, machinery, and mechanical appliances industries. Exploratory factor analysis and confirmatory factor analysis were applied to assess construct validity. Direct and indirect effects were tested using structural equation modeling and bootstrap re-sampling technique.

Findings
The results reveal that supplier integration and customer integration have positive effects on KM and TI, while internal integration has not. Also, KM has a positive effect on TI. In addition, KM mediates supplier integration-TI and customer integration-TI relationships, while does not mediate internal integration-TI relationship.

Originality/value
Most existing studies examined the effect of KM on SCI and supply chain management. This study argues and empirically demonstrates that SCI contributes to KM capability of manufacturing companies. Moreover, this is one of the first studies to investigate the mediating role of KM on SCI-TI relationship. The paper provides evidence that external integration is superior to internal integration in enhancing KM and TI.
Measuring efficiency drivers and productive slacks in UK auditing firms
Authors: Wanke Peter , Barros Carlos , Azad Md. Abul Kalam 
Published: March 2017

Purpose
The purpose of this paper is to measure the efficiency and the productive slacks of a sample of major UK auditing firms between 2005 and 2012.

Design/methodology/approach
Using the bootstrapping technique as the cornerstone method, DEA estimates were computed, allowing the test for differences in the levels of efficiency and in the potentials for decreasing inputs and increasing outputs. Then, neural networks were combined with DEA estimates to model, with effective predictive ability, the drivers of auditing firms’ performance.

Findings
The findings indicate an ambiguous impact of regulatory policies on efficiency levels. Results also indicate an eventual capacity shortfall, since the most important productive resource does not seem to cope with demand growth in the future.

Originality/value
This paper aims to focus on efficiency, complementing previous research in the UK that focuses on productivity, and helps in establishing a decision-support system to slack evaluation.
Strategic CSR: a panacea for profit and altruism?
Authors: Fontana Enrico 
Published: March 2017

PurposeThis e-book sheds light on the concept of strategic corporate social responsibility (CSR) in supply chains within a developing country context. This paper aims to investigate cognitive antecedents as well as behavioral consequences of corporate executives toward investing in strategic CSR. Moreover, it displays if and how strategic CSR contributes to creating performance benefits for the supplier.Design/methodology/approachThis study is qualitative and exploratory in its nature. After drafting a five-dimensional framework from extant literature, it empirically elaborates on a case-study analysis based on primary data gathered through semi-structured interviews on ten executives (i.e. top executives, directors, owners) in large-size supplier companies within the Bangladeshi ready-made garment (RMG) supply chain.FindingsFirst, it highlights altruism and performance as being cognitively and theoretically espoused in strategic CSR; yet, one appears to oust the other. Second, it demonstrates that if CSR-driven investments allow for a competitive positional betterment, as for suppliers in the Bangladeshi RMG industry, profit-driven CSR diffuses at the expense of altruism. Third, it confirms CSR’s strategic role as necessary but not sufficient for competitive advantage, delivering insights on suppliers’ future posturevis-à-visCSR in the Bangladeshi RMG supply chains.Research limitations/implicationsThe e-book investigates strategic CSR’s struggle to maintain a balance between moral and profit-maximization motives at the cognitive level but being paradoxically required in supply chains. A limitation,inter alia, entails the focus on the horizontal perspective of the sample and the RMG supply chain.Originality/valueThe e-book provides valuable theoretical and practical insights by capitalizing on unique data retrieved from the Bangladeshi supply chain.
Naini Papers: capacity dilemma
Authors: Ganguly Kunal K. , Rai Siddharth 
Published: March 2017

Subject area
The subject area of the case is operations management and capacity planning. The case adopts different operation strategies to use the idle capacity.

Study level/applicability
The case study is suitable for discussion in masters level classes. The case explains the situation of a company which is fighting for its survival. The case reveals the alternative operations strategies it applies to maximize its capacity utilization and reduce its costs.

Case overview
The case describes a paper producing company which is earning low margins. The company’s capacity remains unused during the off-seasons. The company then plans to share its capacity with another dying industry. Both the companies plan to cooperate and share resources. However, there are other attractive alternatives too and the dilemma situations leave the gap for continuous discussions.

Expected learning outcomes
The case aims at providing potential alternatives to the students and initiating healthy discussions. The students will be able to understand the capacity utilization dilemmas and applicability of the operations strategy concept in practice.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 9: Operations and Logistics.