bluuebunny/crossref_metadata_2025_split huggingface dataset:
CTCF-mediated Chromatin Structures Dictate the Spatio-temporal Propagation of Replication Foci
Authors: Su Qian Peter , Zhao Ziqing Winston , Meng Luming , Ding Miao , Zhang Weiwei , Li Yongzheng , Liu Mengzhu , Li Rongqin , Gao Yi-Qin , Xie Xiaoliang Sunney , Sun Yujie 
Published: January 2019

ABSTRACTMammalian DNA replication is initiated at numerous replication origins, which are clustered into thousands of replication domains (RDs) across the genome. However, it remains unclear whether the replication origins within each RD are activated stochastically. To understand how replication is regulated at the sub-RD level, we directly visualized the spatio-temporal organization, morphology, andin situepigenetic signatures of individual replication foci (RFi) across S-phase using super-resolution stochastic optical reconstruction microscopy (STORM). Importantly, we revealed a hierarchical radial pattern of RFi propagation that reverses its directionality from early to late S-phase, and is diminished upon caffeine treatment or CTCF knockdown. Together with simulation and bioinformatic analyses, our findings point to a ‘CTCF-organized REplication Propagation’ (CoREP) model. The CoREP model suggests a non-random selection mechanism for replication activation mediated by CTCF at the sub-RD level, as well as the critical involvement of local chromatin environment in regulating replication in space and time.
Distribution and characterization of Aegilops cylindrica species from Iran
Authors: Bakhshi Behnam , Aghaei Mohammad Jaffar , Zarifi Eissa , Bihamta Mohammad Reza , Fard Ehsan Mohseni 
Published: January 2019

AbstractJointed goatgrass (Aegilops cylindrica Host; 2n = 4x = 28, CcCcDcDc) is a tetraploid remote relative of bread wheat (Triticum aestivum L; 2n=6x=42, AABBDD) with 2 genomes and 28 chromosomes. The diversity center of this species is in the Fertile Crescent and in central Asia and could also be found in many places in Iran. In this experiment, 359 accessions provided by National Plant Gene Bank of Iran (NPGBI) were used. Based on the geographical distribution, the highest distribution of Ae. cylindrica are from North, West and North West regions of Iran. The distribution data of Ae. cylindrica showed that the distribution centers in Iran are more than those reported in previous studies in Iran. Chromosome counting showed that all Ae. cylindrica accessions are tetraploid (2n=4x=28). Results of factor analysis for 9 morphological chromosome traits showed that karyotypic variation within accessions are related to the length of chromosomes and there is difference between accessions for their total chromosome length, but the karyotype of different accessions were almost the same for the symmetry. Low coefficient of variation in morphological traits as well as symmetric karyotypes of Ae. cylindrica species observed in this study could lead us to more confidently say that Ae. cylindrica could be a recently evolved species among remote relatives of bread wheat.
Whole Aegilops tauschii transcriptome investigation revealed nine novel miRNAs involved in stress response
Authors: Bakhshi Behnam , Fard Ehsan Mohseni 
Published: January 2019

AbstractAegilops tauschii is wild relative of bread wheat. This species has been reported as donor of bread wheat D genome. There are also many reports that mentioned Ae. tauschii importance in biotic and abiotic stress resistance. Thus, it is important to investigate regulatory mechanisms involved in Ae. tauschii stress tolerance. MiRNAs have been reported as essential regulatory elements in stress response. In this study, using ESTs/TSAs databases nine novel miRNA stem-loops have been identified including ata-miRNovel_1 to 9. MiR156, miR168, miR169, miR319, miR397 and miR530 are some miRNA families that their mature miRNAs could be matched with these novel stem-loop miRNAs. We have also observed wheat ESTs/TSAs as similar as Ae. tauschii ESTs/TSAs that could produce new miRNA stem-loops in wheat. These novel miRNA stem-loops could play important role in transcription regulation involved in stress response.
Genetic diversity analysis of an isolate of microsporidia infesting Athetis lepigone
Authors: Zhang Haijian , Song Jian , Yang Yunhe , An Jingjie , Ma Hongxia , Li Yaofa 
Published: January 2019

AbstractIn this study, PCR amplification, cloning and sequencing analysis were adopted to explore genetic diversity of microsporidia (LEP9557) infecting Athetis lepigone. The small subunit ribosomal DNA (SSU rDNA), internal transcribed spacer (ITS) and intergenic spacers (IGS) of ribosomal RNA (rRNA) were cloned from the strain and sequenced. By means of multiple sequence alignment, we found that the three gene regions had different levels of polymorphism. There was greater polymorphism in ITS (74 variable sites) and IGS (55.59%) regions than in the SSU rDNA (17 variable sites). Phylogenetic analysis was performed using Kimura 2-parameter with neighbor joining and the results showed that LEP9557 had a close relationship with Nosema bombycis. Sequences of each clone were submitted to Genbank (Accession number: MF150254-MF150258). All of the results indicated the presence of genetic diversity in LEP9557, which established the foundation for identifying the phylogeny and relationships with other microsporidian strains, and had significant biological meaning for maintaining the survival and population continuity of the strain.
Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space
Authors: Mayalu Michaelle N , Kim Min-Cheol , Asada Harry 
Published: January 2019

AbstractCells interacting through an extracellular matrix (ECM) exhibit emergent behaviors resulting from collective intercellular interaction. In wound healing and tissue development, characteristic compaction of ECM gel is induced by multiple cells that generate tensions in the ECM fibers and coordinate their actions with other cells. Computational prediction of collective cell-ECM interaction based on first principles is highly complex especially as the number of cells increase. Here, we introduce a computationally-efficient method for predicting nonlinear behaviors of multiple cells interacting mechanically through a 3-D ECM fiber network. The key enabling technique is superposition of single cell computational models to predict multicellular behaviors. While cell-ECM interactions are highly nonlinear, they can be linearized accurately with a unique method, termed Dual-Faceted Linearization. This method recasts the original nonlinear dynamics in an augmented space where the system behaves more linearly. The independent state variables are augmented by combining auxiliary variables that inform nonlinear elements involved in the system. This computational method involves a) expressing the original nonlinear state equations with two sets of linear dynamic equations b) reducing the order of the augmented linear system via principal component analysis and c) superposing individual single cell-ECM dynamics to predict collective behaviors of multiple cells. The method is computationally efficient compared to original nonlinear dynamic simulation and accurate compared to traditional Taylor expansion linearization. Furthermore, we reproduce reported experimental results of multi-cell induced ECM compaction.Author summaryCollective behaviors of multiple cells interacting through an ECM are prohibitively complex to predict with a mechanistic computational model due to its highly nonlinear dynamics and high dimensional space. We introduce a methodology where nonlinear dynamics of single cells are superposed to predict collective multi-cellular behaviors through a developed linearization method. We represent nonlinear single cell dynamics with linear state equations by augmenting the independent state variables with a set of auxiliary variables. We then transform the linear augmented state equations to a low-dimensional latent model and superpose the linear latent models of individual cells to predict collective behaviors that emerge from multi-cellular interactions. The method successfully reproduced experimental results of cell-induced ECM compaction.
Review of short-text classification
Authors: Alsmadi Issa , Gan Keng Hoon 
Published: January 2019

PurposeRapid developments in social networks and their usage in everyday life have caused an explosion in the amount of short electronic documents. Thus, the need to classify this type of document based on their content has a significant implication in many applications. The need to classify these documents in relevant classes according to their text contents should be interested in many practical reasons. Short-text classification is an essential step in many applications, such as spam filtering, sentiment analysis, Twitter personalization, customer review and many other applications related to social networks. Reviews on short text and its application are limited. Thus, this paper aims to discuss the characteristics of short text, its challenges and difficulties in classification. The paper attempt to introduce all stages in principle classification, the technique used in each stage and the possible development trend in each stage.Design/methodology/approachThe paper as a review of the main aspect of short-text classification. The paper is structured based on the classification task stage.FindingsThis paper discusses related issues and approaches to these problems. Further research could be conducted to address the challenges in short texts and avoid poor accuracy in classification. Problems in low performance can be solved by using optimized solutions, such as genetic algorithms that are powerful in enhancing the quality of selected features. Soft computing solution has a fuzzy logic that makes short-text problems a promising area of research.Originality/valueUsing a powerful short-text classification method significantly affects many applications in terms of efficiency enhancement. Current solutions still have low performance, implying the need for improvement. This paper discusses related issues and approaches to these problems.
Three challenging trends for marketing strategy – and B2B – doctoral education
Authors: Scheer Lisa 
Published: January 2019

Purpose
The purpose of this paper is to share personal observations regarding three trends that pose challenges for marketing doctoral programs and the development of B2B scholar-researchers.

Design/methodology/approach
The author raises questions and looks to the body of marketing and B2B scholars to seek answers – if they agree that these trends threaten to undermine the strength of marketing doctoral education.

Findings
The study has no findings, just observations and thoughts from a marketing strategy and B2B researcher who has been involved in doctoral education in various ways.

Originality/value
This paper represents only the author’s perspective.
The Volkswagen recovery: leaving scandal in the dust
Authors: Welch James 
Published: January 2019

Purpose
Following the diesel emissions debacle of 2015, Volkswagen Group has rebounded significantly in terms of sales and market value. When examining Volkswagen’s dramatic recovery, it is clear to notice four distinct elements that helped to bring about this rapid turnaround. To push through the public relations nightmare and regain sales traction, Volkswagen embarked on a four-step process that centered on four key words: Replace, Restructure, Redevelop and Rebrand. The purpose of this study is to examine that process.

Design/methodology/approach
This study is a case study examining the performance of Volkswagen Group and their recovery from the 2015 diesel emissions scandal. To achieve their significant turnaround, the company sought to: replace the leadership, restructure the organization, redevelop the strategy and rebrand the product. This study examines those four steps in the recovery process as a model for other firms.

Findings
To try and achieve an unprecedented turnaround, the company sought to: replace the leadership, restructure the organization, redevelop the strategy and rebrand the product. These four strategic elements formed the basis of a newly focused company and continue to push the company forward and further away from the scandal. This four-step process of recovery provides an excellent case study for other firms who may find themselves in the midst of turmoil and crisis.

Originality/value
To push through the public relations nightmare and regain sales traction following their 2015 emissions testing scandal, Volkswagen embarked on a four-step process that centered on four key words: Replace, Restructure, Redevelop and Rebrand. These four strategic elements formed the basis of a newly focused company and continue to push the company forward and further away from the scandal. This four-step process of recovery provides an excellent case study for other firms who may find themselves in the midst of turmoil and crisis.
Secrets of succession: how one family business reached the ninth generation
Authors: Fendri Chamsa , Nguyen Pascal 
Published: January 2019

PurposeThe purpose of this paper is to provide insight into the specific structures and routines of family firms and to highlight their strengths and weaknesses using a case study.Design/methodology/approachThe case describes a French SME in the construction sector that is undergoing succession from the eighth to the ninth generation. Both generations have offered their viewpoints. The succession context allows us to better distinguish what makes a family firm uniquely resilient and what may easily turn into a weakness.FindingsThe case indicates that the trust that family owners have cultivated with employees allows the firm to operate less formally and with less rigid procedures. It also encourages employees to take initiatives and contributes to their greater engagement. On the other hand, it may expose the firm to more structured and well-organized competitors.Research limitations/implicationsThe limitations are those relative to the use of a single case.Practical implicationsSuccession is a delicate process that needs to be well prepared and executed without any haste. It involves retaining the firm’s strengths, such as the social capital that the family has patiently amassed. But it also represents an opportunity to review the firm’s practices and to introduce a good dose of innovation.Originality/valueThe case provides a vivid illustration of what makes family firms so distinctive. Theoretical concepts and empirical findings from the literature are put together in a single consistent picture.
Re-distribution and promotion practices for suboptimal foods – commercial and social initiatives for the reduction of food waste
Authors: Bech-Larsen Tino , Ascheman-Witzel Jessica , Kulikovskaja Viktorija 
Published: January 2019

Purpose
The increased acknowledgement of the problems associated with food waste has triggered a number of social and commercial initiatives for the re-distribution of suboptimal foods (SOFs). This paper aims to explore a variety of such initiatives and discuss their prospects, considering the commercial contingencies of the food supply system.

Design/methodology/approach
The exploration is based on a multi-country study of cases representing three initiatives related to the reduction of waste from SOFs, i.e. social supermarkets (SSMs), food banks and expiration date-based pricing practices. The collected data comprise expert interviews, store-check observations and secondary material; the data are analyzed from a marketing practice perspective.

Findings
The analyses indicate that the distribution and re-distribution of SOFs are moving toward normalization, that the diffusion of expiration date-based pricing through all food retailing formats is likely to continue, that food banks – despite reports of dwindling supplies of SOFs – are likely to increase their expansion and that SSMs face a variety of challenges, e.g. as regards their supply of SOFs and their customers’ preferences for stable assortments.

Originality/value
By synthesizing data from various European implementations of re-distribution practices, this article contributes to the understanding of the viability of such practices. Developing this understanding should benefit social and commercial entrepreneurs, as well as policymakers, when designing and implementing initiatives for the reduction of waste from SOFs.
Pembrolizumab resolves adult ashy dermatosis developing in patients with squamous cell carcinoma of the lung
Authors: Takeda Kana , Fujimura Taku , Tsuchiyama Kenichiro , Lyu Chunbing , Aiba Setsuya 
Published: January 2019

AbstractAshy dermatosis is a rare cutaneous disorder of unknown etiology. We describe a case of adult ashy dermatosis developing in a patient with squamous cell carcinoma of the lung, which was resolved by the administration of pembrolizumab in parallel with multiple vitiligo. Interestingly, immunohistochemical staining revealed that lesional skin of the ashy dermatosis contained cytotoxic T cells and programmed death ligand 1 expressing cells. To our knowledge, this is the first case of adult ashy dermatosis resolved by pembrolizumab.
The diversity of eco‐evolutionary dynamics: Comparing the feedbacks between ecology and evolution across scales
Authors: Brunner Franziska S. , Deere Jacques A. , Egas Martijn , Eizaguirre Christophe , Raeymaekers Joost A. M. 
Published: January 2019

Abstract

Evidence of reciprocal influences between ecological and evolutionary processes (eco‐evolutionary dynamics) is accumulating at different levels of biological organisation, ranging from populations to communities and even ecosystems.

This special feature showcases the state‐of‐the art knowledge on eco‐evolutionary dynamics and dissects the feedback types, the biological and spatial scales as well as the agents of selection underlying the interactions between ecology and evolution.

Theoretical approaches to eco‐evolutionary feedbacks can draw on a wide range of fields and have a long history within evolutionary ecology. The integration of theoretical approaches from quantitative genetics, evolutionary ecology, and metapopulation ecology is necessary to advance our understanding of rapid evolution and associated eco‐evolutionary dynamics.

Empirical studies in this special feature focus on the evolution‐to‐ecology pathway by which evolutionary processes influence ecological dynamics (the direction in eco‐evolutionary dynamics less well studied). Advancing towards the study of complete (i.e. reciprocal) eco‐evolutionary feedbacks requires unravelling both the ecology‐to‐evolution and the evolution‐to‐ecology pathways in isolation and understanding how they are coupled. This endeavour will require a combination of laboratory, semi‐natural (e.g. mesocosm) and field studies.

As the field of eco‐evolutionary dynamics matures, it moves from proof‐of‐principle studies to understanding increasingly complex biological systems. This Special Feature provides necessary tools and approaches, both theoretical and empirical, to achieve this new aim.
Combined effects of seed provenance, plant facilitation and restoration site on revegetation success
Authors: Fedriani Jose M. , Garrote Pedro J. , Calvo Gemma , Delibes Miguel , Castilla Antonio R. , Żywiec Magdalena 
Published: January 2019

Abstract

Plant provenance, plant facilitation and the characteristics of restoration sites are critical determinants of revegetation success. Surprisingly, however, very little is known about how these key factors interact, both with each other and to complex patterns of recruitment in target plant species.

We investigated, for the first time, the potential of combining seed provenance, plant facilitation and restoration site characteristics to guide revegetation efforts. As a model system, we used the Iberian pear (Pyrus bourgaeana) and three potential nurse shrub species. To this end, we completed a comprehensive reciprocal transplant experiment in five P. bourgaeana populations within a fragmented landscape at the Doñana Biosphere Reserve (SW Spain).

There were marked differences among provenances for seedling emergence and growth, as well as for recruitment, but no evidence of local adaptation was found. Shrubs generally had a positive or neutral effect on P. bourgaeana seedling performance with, for example survival underneath shrubs being, on average, twice as high as in open microhabitats. Interestingly, however, the magnitude and even the sign of such plant–plant interactions changed with both sowing locality and seed provenance. For instance, shrubs enhanced seedling survival and recruitment at the end of the study in four of the five sowing localities, whereas it decreased it in the remaining locality. Also, although nurse shrubs lessened seedling size of two provenances, it did not have a significant effect on the other three.

Synthesis and applications. We show how revegetation success can be maximized, not only by selecting the most appropriate plant material, taking advantage of plant facilitative interactions and selecting the right restoration site, but also by using these factors in an integrated fashion. We propose local managers efficiently undertake future revegetation campaigns by mixing seeds from several genetically adequate source populations in numbers weighted according to previously estimated provenance‐specific recruitment successes. Our novel approach can help to guide revegetation of many tree and plant species living in stressful conditions, such as arid, semi‐arid and high mountain habitats.
Pollination by wild bees yields larger strawberries than pollination by honey bees
Authors: MacInnis Gail , Forrest Jessica R. K. 
Published: January 2019

Abstract

A diverse array of wild bee species may provide more effective pollination than the widely employed European honey bee (Apis mellifera L.). High species richness within crop pollinator assemblages has been linked to enhanced fruit and seed yields, but species richness is often confounded with abundance in studies of pollinator communities.

We investigated the effects of bee diversity and species identity on pollen deposition and crop yield in the strawberry (Fragaria × ananassa) variety Jewel through a field experiment that independently manipulated the species richness and abundance of flower visitors. We used a new pollen deposition measurement technique to determine the pollen contribution of individual bees in an assemblage of flower visits. We compared the performance of wild bee species and managed honey bees, as pollinators of strawberry. We also calculated the influence of species richness, visit frequency and visitor identity on fruit mass, using the fruit that developed from each sampled flower.

Species richness of flower visitors did not influence floral pollen loads or strawberry mass. Honey bees and wild bees deposited the same amount of pollen per visited flower. However, strawberries that developed from flowers visited by wild bees were heavier than flowers visited by honey bees. In addition, flowers visited by a combination of wild and honey bees produced strawberries that weighed less than flowers receiving purely WB visits.

Synthesis and applications. Our findings show that honey bee pollination results in lower yields than wild bee pollination in a strawberry crop. Consequently, if managed honey bees in strawberry fields displace wild pollinators, growers may obtain suboptimal yields. Management efforts aimed at the maintenance or enhancement of wild pollinator populations may therefore be a cost‐effective way to increase both crop yield and biodiversity on strawberry farms.