bluuebunny/crossref_metadata_2025_split huggingface dataset:
Particle-templated emulsification for microfluidics-free digital biology
Authors: Hatori Makiko N. , Kim Samuel C. , Abate Adam R. 
Published: April 2018

AbstractThe compartmentalization of reactions in monodispersed droplets is valuable for applications across biology. However, the requirement of microfluidics to partition the sample into monodispersed droplets is a significant barrier that impedes implementation. Here, we introduce particle-templated emulsification, a method to encapsulate samples in monodispersed emulsions without microfluidics. By vortexing a mixture of hydrogel particles and sample solution, we encapsulate the sample in monodispersed emulsions that are useful for most droplet applications. We illustrate the method with ddPCR and single cell culture. The ability to encapsulate samples in monodispersed droplets without microfluidics should facilitate the implementation of compartmentalized reactions in biology.
Transient kinetic analysis of SWR1C-catalyzed H2A.Z deposition unravels the impact of nucleosome dynamics and the asymmetry of stepwise histone exchange
Authors: Singh Raushan K. , Watanabe Shinya , Bilsel Osman , Peterson Craig L. 
Published: April 2018

SUMMARYThe SWR1C chromatin remodeling enzyme catalyzes an ATP-dependent replacement of nucleosomal H2A with the H2A.Z variant, regulating key DNA-mediated processes, such as transcription and DNA repair. Here we investigate the transient kinetic mechanism of the histone exchange reaction employing ensemble FRET, fluorescence correlation spectroscopy (FCS), and the steady state kinetics of ATP hydrolysis. Our studies indicate that SWR1C modulates nucleosome dynamics on both the millisecond and microsecond timescales, poising the nucleosome for the dimer exchange reaction. The transient kinetic analysis of the remodeling reaction performed under single turnover conditions unraveled a striking asymmetry in the ATP-dependent replacement of nucleosomal dimers, promoted by localized DNA translocation. Taken together, our transient kinetic studies identify new intermediates and provide crucial insights into the SWR1C-catalyzed dimer exchange reaction, as well as shedding light on how the mechanics of H2A.Z deposition might contribute to transcriptional regulation in vivo.
Impact of DNA sequencing and analysis methods on 16S rRNA gene bacterial community analysis in dairy products
Authors: Xue Zhengyao , Kable Mary E , Marco Maria L 
Published: April 2018

AbstractDNA sequencing and analysis methods were compared for 16S rRNA V4 PCR amplicon and gDNA mock communities encompassing nine bacterial species commonly found in milk and dairy products. The communities were examined using Illumina MiSeq and Ion Torrent PGM DNA sequencing methods followed by the QIIME 1 (UCLUST) and Divisive Amplicon Denoising Algorithm 2 (DADA2) data analysis pipelines including taxonomic comparisons to the Greengenes and Ribosomal Database Project (RDP) databases. Examination of the PCR amplicon mock community with these methods resulted in Operation Taxonomy Units (OTUs) and Amplicon Sequence Variants (ASVs) that ranged from a low of 13 to high of 118 and were dependent on the DNA sequencing method and read assembly step. The elevated numbers of OTUs and ASVs included assignments to spurious taxa as well as sequence variants of the nine species included in the mock community. Comparisons between the gDNA and PCR amplicon mock communities showed that combining gDNA from the different strains prior to PCR resulted in up to 8.9-fold greater numbers of spurious OTUs and ASVs. However, the DNA sequencing method and initial data assembly steps conferred the largest effects on predictions of bacterial diversity, independent of the mock community type (PCR amplicon or gDNA; Bray-Curtis R2 = 0.88 and weighted Unifrac, R2 = 0.32). Overall, DNA sequencing performed with the Ion Torrent PGM and analyzed with DADA2 and the Greengenes database resulted in the most accurate predictions of the mock community phylogeny, taxonomy, and diversity.ImportanceValidated methods are urgently needed to improve DNA-sequence based assessments of complex bacterial communities. In this study, we used 16S rRNA PCR amplicon and gDNA mock community standards, consisting of nine, dairy-associated bacterial species, to evaluate the most commonly applied 16S rRNA marker gene DNA sequencing and analysis platforms used in evaluating dairy and other bacterial habitats. Our results show that bacterial metataxonomic assessments are largely dependent on the DNA sequencing platform and read curation method used. DADA2 improved sequence annotation compared with QIIME 1, and when combined with the Ion Torrent PGM DNA sequencing platform and the Greengenes database for taxonomic assignment, the most accurate representation of the dairy mock community standards was reached. This approach will be useful for validating sample collection and DNA extraction methods and ultimately investigating bacterial population dynamics in milk and dairy-associated environments.
Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
Authors: Brinkman Arie B. , Nik-Zainal Serena , Simmer Femke , Rodríguez-González F. Germán , Smid Marcel , Alexandrov Ludmil B. , Butler Adam , Martin Sancha , Davies Helen , Glodzik Dominik , Zou Xueqing , Ramakrishna Manasa , Staaf Johan , Ringnér Markus , Sieuwerts Anieta , Ferrari Anthony , Morganella Sandro , Fleischer Thomas , Kristensen Vessela , Gut Marta , van de Vijver Marc J. , Børresen-Dale Anne-Lise , Richardson Andrea L. , Thomas Gilles , Gut Ivo G. , Martens John W.M. , Foekens John A. , Stratton Mike , Stunnenberg Hendrik G. 
Published: April 2018

SUMMARYGlobal loss of DNA methylation and CpG island (CGI) hypermethylation are regarded as key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which can extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. Using whole genome bisulfite sequencing (WGBS) of breast cancers, we comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of variation in DNA methylation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). However, significant repression effects on cancer-genes are negligible as tumor suppressor genes are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin of different cancers and may represent tissue-specific ‘silent’ regions of the genome, which tolerate instability at the epigenetic, transcriptomic and genetic level.
Hematopoietic Stem Cell Dynamics are Regulated by Progenitor Demand: Lessons from a Quantitative Modeling Approach
Authors: Klose Markus , Florian Maria Carolina , Geiger Hartmut , Glauche Ingmar 
Published: April 2018

AbstractThe prevailing view on murine hematopoiesis and on hematopoietic stem cells (HSC) in particular derives from experiments that are related to regeneration after irradiation and HSC transplantation. However, over the past years, different experimental techniques have been developed to investigate hematopoiesis under homeostatic conditions, thereby providing access to proliferation and differentiation rates of hematopoietic stem and progenitor cells in the unperturbed situation. Moreover, it has become clear that hematopoiesis undergoes distinct changes during aging with large effects on HSC abundance, lineage contribution, asymmetry of division and self-renewal potential. However, it is currently not fully resolved how stem and progenitor cells interact to respond to varying demands and how this balance is altered by an aging-induced shift in HSC polarity.Here, we present anin-silicomodel to investigate the dynamics of HSC response to varying demand. By introducing an internal feedback between stem and progenitor cells, the model is suited to consistently describe both hematopoietic homeostasis and regeneration, including the limited regulation of HSCs in the homeostatic situation. The model further explains the age-dependent increase in phenotypic HSCs as a consequence of the cells’ inability to preserve divisional asymmetry.Our model suggests a dynamically regulated population of intrinsically asymmetrically dividing HSCs as suitable control mechanism that adheres with many qualitative and quantitative findings on hematopoietic recovery after stress and aging. The modeling approach thereby illustrates how a mathematical formalism can support the conceptual and the quantitative understanding of regulatory principles in HSC biology.
The Receptor-Like Kinase AtVRLK1 Regulates Secondary Cell Wall Thickening
Authors: Huang Cheng , Zhang Rui , Gui Jinshan , Zhong Yu , Li Laigeng 
Published: April 2018

Abstract
During the growth and development of land plants, some specialized cells, such as tracheary elements, undergo secondary cell wall thickening. Secondary cell walls contain additional lignin, compared with primary cell walls, thus providing mechanical strength and potentially improving defenses against pathogens. However, the molecular mechanisms that initiate wall thickening are unknown. In this study, we identified an Arabidopsis (Arabidopsis thaliana) leucine-rich repeat receptor-like kinase, encoded by AtVRLK1 (Vascular-Related Receptor-Like Kinase1), that is expressed specifically in cells undergoing secondary cell wall thickening. Suppression of AtVRLK1 expression resulted in a range of phenotypes that included retarded early elongation of the inflorescence stem, shorter fibers, slower root growth, and shorter flower filaments. In contrast, up-regulation of AtVRLK1 led to longer fiber cells, reduced secondary cell wall thickening in fiber and vessel cells, and defects in anther dehiscence. Molecular and cellular analyses showed that down-regulation of AtVRLK1 promoted secondary cell wall thickening and up-regulation of AtVRLK1 enhanced cell elongation and inhibited secondary cell wall thickening. We propose that AtVRLK1 functions as a signaling component in coordinating cell elongation and cell wall thickening during growth and development.
The Tomato Mitogen-Activated Protein Kinase SlMPK1 Is as a Negative Regulator of the High-Temperature Stress Response
Authors: Ding Haidong , He Jie , Wu Yuan , Wu Xiaoxia , Ge Cailin , Wang Yijun , Zhong Silin , Peiter Edgar , Liang Jiansheng , Xu Weifeng 
Published: April 2018

Abstract
High-temperature (HT) stress is a major environmental stress that limits plant growth and development. MAPK cascades play key roles in plant growth and stress signaling, but their involvement in the HT stress response is poorly understood. Here, we describe a 47-kD MBP-phosphorylated protein (p47-MBPK) activated in tomato (Solanum lycopersicum) leaves under HT and identify it as SlMPK1 by tandem mass spectrometry analysis. Silencing of SlMPK1 in transgenic tomato plants resulted in enhanced tolerance to HT, while overexpression resulted in reduced tolerance. Proteomic analysis identified a set of proteins involved in antioxidant defense that are significantly more abundant in RNA interference-SlMPK1 plants than nontransgenic plants under HT stress. RNA interference-SlMPK1 plants also showed changes in membrane lipid peroxidation and antioxidant enzyme activities. Furthermore, using yeast two-hybrid screening, we identified a serine-proline-rich protein homolog, SlSPRH1, which interacts with SlMPK1 in yeast, in plant cells, and in vitro. We demonstrate that SlMPK1 can directly phosphorylate SlSPRH1. Furthermore, the serine residue serine-44 of SlSPRH1 is a crucial phosphorylation site in the SlMPK1-mediated antioxidant defense mechanism activated during HT stress. We also demonstrate that heterologous expression of SlSPRH1 in Arabidopsis (Arabidopsis thaliana) led to a decrease in thermotolerance and lower antioxidant capacity. Taken together, our results suggest that SlMPK1 is a negative regulator of thermotolerance in tomato plants. SlMPK1 acts by regulating antioxidant defense, and its substrate SlSPRH1 is involved in this pathway.
The entrepreneurial profile of Brazilian business administration students
Authors: Amaral Marcelo , Toledo Hernandez Cecília , Rodrigues Bastos Marcellus Henrique 
Published: April 2018

Purpose
This study aims to focus on the entrepreneurial education and profile in undergraduate business administration programs in Brazil, particularly in the southern region of the state of Rio de Janeiro. Assuming that the entrepreneurial profile can be developed by teaching and learning processes.

Design/methodology/approach
The research performed qualitative approach through interviews and a quantitative approach using multiple criteria decision-making methods. Data were collected along 2015 in a survey with a population of 412 students from three high education institutions (HEIs) and analyzed using the analytic hierarchy process with ratings.

Findings
The study has found that the key entrepreneurial trait for all groups was the ability to “plan”. Other relevant dimensions were “self-realization”, “innovative” and “leader”. The dimensions “risk taking” and “sociability” were considered not important in the opinion of all groups.

Practical implications
The entrepreneurial profile does not seem to evolve over the four-year college period, thus suggesting a failure of the entrepreneurial education at the three surveyed HEIs to impact the overall perception of students about the requirements for creating and developing new ventures. Actions to revert this trend should be taken.

Originality/value
This research aims to identify differences in perception about the entrepreneurial profile among freshmen and senior undergraduates. The theme is relevant in a knowledge era where academy has to prepare students to be entrepreneurs. Similar studies were done around in Brazil and around the world but no one in the state of Rio de Janeiro, Brazil. The work has a contribution by proposing and applying a method to compare students groups, programs, institutions and countries over time.
An approach to task recommendation in crowdsourcing based on 2-tuple fuzzy linguistic method
Authors: Zhang Xuefeng , Su Jiafu 
Published: April 2018

Purpose
Task recommendation is an important way for workers and requesters to get better outcomes in shorter time in crowdsourcing. This paper aims to propose an approach based on 2-tuple fuzzy linguistic method to recommend tasks to the workers who would be capable of completing and accept them.

Design/methodology/approach
In this paper, worker’s capability-to-complete (CTC) and possibility-to-accept (PTA) for a task needs to be recommended are proposed, measured and aggregated to determine worker’s priority for task recommendation. Therein, the similarity between the recommended task and its similar tasks and worker’s performance on these similar tasks are computed and aggregated to determine worker’s CTC quantitatively. In addition, two factors of worker’s active degree and worker’s preferences to a task category are presented to reflect and determine worker’s PTA. In the process of measuring them, 2-tuple fuzzy linguistic method is used to represent, process and aggregate vague and imprecise information.

Findings
To demonstrate the implementation process and performance of the proposed approach, an illustrative example is conducted on Taskcn, a widely used Chinese online crowdsourcing market. The experimental results show that the proposed approach outperformed the self-selection approach, especially for complex or creative tasks. Moreover, comparing with task recommendation considering worker’s CTC solely, the proposed approach would be better in terms of workers’ response rate. Additionally, the use of linguistic terms and fuzzy linguistic method facilitates the expression of vague and subjective information and makes recommendation process more practical.

Research limitations/implications
In the study, the authors capture alternative workers, collect workers’ behaviors and compute workers’ CTC and PTA manually. However, as the number of tasks and alternative workers grow, the issue, i.e. how to conveniently collect workers’ behaviors and determine their CTC and PTA, becomes conspicuous and needs to be studied further.

Practical implications
The proposed approach provides an alternative way to perform tasks posted in crowdsourcing platforms. It can assist workers to contribute to right tasks, and requesters to get outcomes with high quality more efficiently.

Originality/value
This study proposes an approach to task recommendation in crowdsourcing that integrates workers’ CTC and PTA for the recommended tasks and can deal with vague and imprecise information.
The effects of entrepreneurial orientation dimensions on performance in the tourism sector
Authors: Fadda Nicoletta 
Published: April 2018

Purpose
The purpose of this paper is to examine the influence of entrepreneurial orientation (EO) dimensions on firm performance in the tourism sector. The goal is twofold: on the one hand, the paper aims to test whether EO dimensions are still significant determinants of performance after controlling for possible confounding factors; on the other hand, it aims to address the question of which EO dimension exerts the strongest effect on performance.

Design/methodology/approach
A survey was carried out in the Sardinian accommodation sector in 2012 and 224 questionnaires were collected. The multidimensional EO constructs were adopted.

Findings
The results show that innovativeness, proactiveness and autonomy were significantly associated with tourism firm performance, whereas risk-taking and competitiveness were not.

Research limitations/implications
The results are limited to the Sardinian accommodation context. Self-reported data were used to measure firm performance. Further research works could replicate the analyses using objective firm performance not only in similar touristic destinations but also in other countries and incorporating other industries.

Practical implications
The study suggests educational and managerial implications. Entrepreneurs in the tourism sector should be encouraged to adopt an innovative, autonomous and proactive approach in managing their firms.

Originality/value
The study advances entrepreneurial knowledge in the tourism sector and in particular in the accommodation industry. The multidimensional EO approach has never been adopted among touristic firms. Furthermore, considering that EO research has been overlooked in the country of Italy, this study’s contribution is also providing evidence from an area that has received minimal attention to date.
Horn growth variation and hunting selection of the Alpine ibex
Authors: Büntgen Ulf , Galván Juan D. , Mysterud Atle , Krusic Paul J. , Hülsmann Lisa , Jenny Hannes , Senn Josef , Bollmann Kurt 
Published: April 2018

Abstract

Selective hunting can affect demographic characteristics and phenotypic traits of the targeted species. Hunting systems often involve harvesting quotas based on sex, age and/or size categories to avoid selective pressure. However, it is difficult to assess whether such regulations deter hunters from targeting larger “trophy” animals with longer horns that may have evolutionary consequences.

Here, we compile 44,088 annually resolved and absolutely dated measurements of Alpine ibex (Capra ibex) horn growth increments from 8,355 males, harvested between 1978 and 2013, in the eastern Swiss Canton of Grisons. We aim to determine whether male ibex with longer horns were preferentially targeted, causing animals with early rapid horn growth to have shorter lives, and whether such hunting selection translated into long‐term trends in horn size over the past four decades.

Results show that medium‐ to longer‐horned adult males had a higher probability of being harvested than shorter‐horned individuals of the same age and that regulations do affect the hunters’ behaviour. Nevertheless, phenotypic traits such as horn length, as well as body size and weight, remained stable over the study period.

Although selective trophy hunting still occurs, it did not cause a measurable evolutionary response in Grisons’ Alpine ibex populations; managed and surveyed since 1978. Nevertheless, further research is needed to understand whether phenotypic trait development is coinfluenced by other, potentially compensatory factors that may possibly mask the effects of selective, long‐term hunting pressure.
Rapamycin protects against early brain injury independent of cerebral blood flow changes in a mouse model of subarachnoid haemorrhage
Authors: Sasaki Kazumasu , Yamamoto Shuzo , Mutoh Tatsushi , Tsuru Yoshiharu , Taki Yasuyuki , Kawashima Ryuta 
Published: April 2018

SummaryWe evaluated the neuroprotective role of rapamycin, a mammalian target of rapamycin (mTOR) kinase inhibitor, in cerebral ischaemia and locomotor function in a mouse model of subarachnoid haemorrhage (SAH). Pretreatment with rapamycin, an mTOR kinase inhibitor, resulted in better recovery from cerebral hypoxia early after SAH than control (P < .05), while the values of peak flow velocity in the middle cerebral artery did not change significantly (P > .05). Average distance travelled and the ratio of central‐area distance/total travelled distance determined by open‐field test after day 14 was significantly higher in mice pretreated with rapamycin than in control mice (P < .05). Inhibition of the mTOR pathway could be protective against post‐SAH early brain injury, ameliorating brain tissue hypoxia and locomotor hypoactivity.
Penumbral role of beta blockade on heart rate recovery in heart failure
Authors: Pan Alan 
Published: April 2018

SummaryWe would agree that Heart Rate Variability (HRR) is a measure of parasympathetic activity, which may need to be augmented in chronic management of Heart Failure (HF). A viable next step would be the determination of the relative strength of the sympathetic response versus the decrease of parasympathetic tone in HF, while taking into consideration the suppression of the sympathetic nervous system by virtue of Beta Blockade, which constitutes standard therapy.
Race, Crime, and Criminal Justice
Authors: Fernandes April D. , Crutchfield Robert D. 
Published: April 2018

AbstractFifty years ago, the U.S. President's Commission on Law Enforcement and Administration of Justice under President Johnson did not frequently mention race and ethnicity in its discussion of and recommendations for the criminal justice system, but it did have a lot to say about race and crime. Through the use of arrest rates to measure racial differentials in criminal involvement, the Commission concluded that Blacks commit more crime as a consequence of Black people living in greater numbers in criminogenic “slum” conditions. To address racial differences, the Commission favored the Great Society programs of Johnson's War on Poverty. Contemporary criminologists continue to debate the racial distribution of crime, the causes of crimes, and the best policies to reduce crime and racial differentials. The Commission did not anticipate the current debate among scholars regarding how much racial disproportionality exists in the criminal justice system and its causes and consequences. The policies that led to mass incarceration have been significant drivers of continued criminal justice racial disparity. Those policies are inconsistent with the recommendation in The Challenge of Crime in a Free Society (1967), upending the pursuit of a more fair and just system.