bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of positive chemotaxis in the protozoan pathogenTrypanosoma brucei
Authors: DeMarco Stephanie F. , Saada Edwin A. , Lopez Miguel A. , Hill Kent L. 
Published: June 2019

AbstractTo complete its infectious cycle, the protozoan parasite,Trypanosoma brucei, must navigate through diverse tissue environments in both its tsetse fly and mammalian hosts. This is hypothesized to be driven by yet unidentified chemotactic cues. Prior work has shown that parasites engaging in social motilityin vitroalter their trajectory to avoid other groups of parasites, an example of negative chemotaxis. However, movement ofT. bruceitoward a stimulus, positive chemotaxis, has so far not been reported. Here we show that upon encounteringE. coli,socially behavingT. bruceiparasites exhibit positive chemotaxis, redirecting group movement toward the neighboring bacterial colony. This response occurs at a distance from the bacteria and involves active changes in parasite motility. By developing a quantitative chemotaxis assay, we show that the attractant is a soluble, diffusible signal dependent on actively growingE. coli. Time-lapse and live video microscopy revealed thatT. bruceichemotaxis involves changes in both group and single cell motility. Groups of parasites change direction of group movement and accelerate as they approach the source of attractant, and this correlates with increasingly constrained movement of individual cells within the group. Identification of positive chemotaxis inT. bruceiopens new opportunities to study mechanisms of chemotaxis in these medically and economically important pathogens. This will lead to deeper insights into how these parasites interact with and navigate through their host environments.ImportanceAlmost all living things need to be able to move, whether it is toward desirable environments or away from danger. For vector-borne parasites, successful transmission and infection require that these organisms be able to sense where they are and use signals from their environment to direct where they go next, a process known as chemotaxis. Here we show thatTrypanosoma brucei, the deadly protozoan parasite that causes African sleeping sickness, can sense and move toward an attractive cue. To our knowledge, this is the first report of positive chemotaxis in these organisms. In addition to describing a new behavior inT. brucei, our findings enable future studies of how chemotaxis works in these pathogens, which will lead to deeper understanding of how they move through their hosts and may lead to new therapeutic or transmission-blocking strategies.
High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification
Authors: Zhu Yi , Weiss Tobias , Zhang Qiushi , Sun Rui , Wang Bo , Wu Zhicheng , Zhong Qing , Yi Xiao , Gao Huanhuan , Cai Xue , Ruan Guan , Zhu Tiansheng , Xu Chao , Lou Sai , Yu Xiaoyan , Gillet Ludovic , Blattmann Peter , Saba Karim , Fankhauser Christian D. , Schmid Michael B. , Rutishauser Dorothea , Ljubicic Jelena , Christiansen Ailsa , Fritz Christine , Rupp Niels J. , Poyet Cedric , Rushing Elisabeth , Weller Michael , Roth Patrick , Haralambieva Eugenia , Hofer Silvia , Chen Chen , Jochum Wolfram , Gao Xiaofei , Teng Xiaodong , Chen Lirong , Wild Peter J. , Aebersold Ruedi , Guo Tiannan 
Published: June 2019

AbstractFormalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between one to 15 years in a biobank and show a high degree of the proteome pattern similarity between two types histological region of small FFPE samples, i.e. punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of certain degree of biological variations. Applying the method to two independent DLBCL cohorts we identified myeloperoxidase (MPO), a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.
PRC1 catalytic activity is central to Polycomb system function
Authors: Blackledge Neil P. , Fursova Nadezda A. , Kelley Jessica R. , Huseyin Miles K. , Feldmann Angelika , Klose Robert J. 
Published: June 2019

SummaryThe Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how its target genes are selected and whether its histone modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. We demonstrate that a mutation widely used to disrupt PRC1 catalysis is hypomorphic, complicating the interpretation of previous studies. To overcome this, we develop a new inducible mutation system in embryonic stem cells that completely ablates PRC1 catalytic activity, revealing that catalysis by PRC1 drives Polycomb chromatin domain formation and higher-order chromatin interactions. In the absence of catalysis, we uncover the primary DNA-based targeting determinants that direct Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling new evidence supporting a PRC1-initiated pathway for Polycomb system function in gene regulation.
Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises
Authors: Sun Mengyi , Zhang Jianzhi 
Published: June 2019

ABSTRACTGene expression noise refers to the variation of the expression level of a gene among isogenic cells in the same environment, and has two sources: extrinsic noise arising from the disparity of the cell state and intrinsic noise arising from the stochastic process of gene expression in the same cell state. Due to the low throughput of the existing method for measuring the two noise components, the architectures of intrinsic and extrinsic expression noises remain elusive. Using allele-specific single-cell RNA sequencing, we here estimate the two noise components of 3975 genes in mouse fibroblast cells. Our analyses verify predicted influences of several factors such as the TATA-box and microRNA targeting on intrinsic and extrinsic noises and reveal gene function-associated noise trends implicating the action of natural selection. These findings unravel differential regulations, optimizations, and biological consequences of intrinsic and extrinsic noises and can aid the construction of desired synthetic circuits.
How neural circuits achieve and use stable dynamics
Authors: Kozachkov Leo , Lundqvist Mikael , Slotine Jean-Jacques , Miller Earl K. 
Published: June 2019

1AbstractThe brain consists of many interconnected networks with time-varying activity. There are multiple sources of noise and variation yet activity has to eventually converge to a stable state for its computations to make sense. We approached this from a control-theory perspective by applying contraction analysis to recurrent neural networks. This allowed us to find mechanisms for achieving stability in multiple connected networks with biologically realistic dynamics, including synaptic plasticity and time-varying inputs. These mechanisms included anti-Hebbian plasticity, synaptic sparsity and excitatory-inhibitory balance. We leveraged these findings to construct networks that could perform functionally relevant computations in the presence of noise and disturbance. Our work provides a blueprint for how to construct stable plastic and distributed networks.
Carbon management framework for sustainable manufacturing using life cycle assessment, IoT and carbon sequestration
Authors: Mishra Shraddha , Singh Surya Prakash 
Published: June 2019

PurposeEmission reduction methodologies alone are not sufficient to mitigate the climatic catastrophes caused due to ongoing carbon emissions. Rather, a bidirectional approach is required to decarbonize the excess carbon in the atmosphere through carbon sequestration along with carbon reduction. Since the manufacturing sector contributes heavily to the ongoing carbon emissions, the purpose of this paper is to propose a framework for carbon emission reduction and carbon sequestration in the context of the manufacturing industry.Design/methodology/approachIn this paper, life cycle assessment (LCA) is employed to track the carbon emission at each stage of the product development life cycle. The pre-requisite for this is the accurate evaluation of the carbon emissions. Therefore, IoT technologies have been employed for collecting real-time data with high credibility to perceive environmental impact caused during the entire life cycle of the product. The total carbon emission calculation is based on the bill of material (BOM)-based LCA of the product to realize the multi-structure (from parts and components to product) as well as multi-stage (from cradle to gate) carbon emission evaluation. Carbon sequestration due to plantation is evaluated using root-shoot ratio and total biomass.FindingsA five interwoven layered structure is proposed in the paper to facilitate the real-time data collection and carbon emission evaluation using BOM-based LCA of products. Further, a carbon neutral coefficient (CNC) is proposed to indicate the state of a firm’s carbon sink and carbon emissions. CNC=1 indicates that the firm is carbon neutral. CNC >1 implies that the firm’s carbon sequestration is more than carbon emissions. CNC <1 indicates that the firm’s carbon emission is more than the carbon sink.Originality/valueThe paper provides a novel framework which integrates the real-time data collection and evaluation of carbon emissions with the carbon sequestration.
Bank institutional setting and risk-taking: the missing role of directors’ education and turnover
Authors: D’Amato Antonio , Gallo Angela 
Published: June 2019

PurposeThis paper aims to analyze the relationship between bank institutional setting and risk-taking by exploring whether board education and turnover are drivers of the risk propensity of cooperative banks compared to joint-stock banks.Design/methodology/approachBased on a comprehensive data set of Italian banks over the 2011-2017 period, this paper examines whether these board characteristics affect the risk propensity of cooperative and joint-stock banks. Bank risk is measured by the Z-index, profit volatility and the ratio of non-performing loans to total gross loans.FindingsThe findings show that cooperatives take less risk than joint-stock banks and have lower board turnover and education. Furthermore, this study finds that while board education mediates the relationship between the cooperative model and bank risk-taking, there is no evidence for board turnover. Thus, the lower educational level of cooperative directors contributes to explaining the lower risk-taking of cooperative banks.ImplicationsThe findings have several implications. In terms of the more general policy debate, the results point to the need to strengthen the governance model for both joint-stock and cooperative banks while supporting the view that a moread hocperspective on the best models and practices for each type of institutional setting would be preferable. In particular, the study reveals how board education’s effects on bank risk-taking should be carefully monitored.Originality/valueThrough a mediation framework, this study provides empirical evidence on the relationship between bank institutional setting (by distinguishing between cooperative and joint-stock banks) and risk-taking behavior by exploring the underlying mechanisms at the board level, which is novel in the literature.
Factors and determinants of value- and business-driven sustainability initiatives in health care organizations: intrinsic differences and extrinsic similarities
Authors: Rodriguez Rocio , Svensson Göran , Høgevold Nils M. , Eriksson David 
Published: June 2019

Purpose
The purpose of this paper is to compare the similarities and differences relating to sustainability initiatives between health-care organizations. The aim is to provide a framework of factors and their determinants to enable a profiling of organizational sustainability initiatives.

Design/methodology/approach
Based on an inductive approach, judgmental sampling was applied to select relevant health-care organizations. Informants were identified according to their knowledge of their organizations’ sustainability initiatives.

Findings
Several factors and their determinants for characterizing differences and similarities were found. The results also reveal that organizational sustainability initiatives are either value-driven or business-driven.

Research limitations/implications
The reported framework of factors and their determinants serves the purpose of profiling organizational sustainability initiatives. Opportunities for further research are provided.

Practical implications
This paper provides managerial guidance for characterizing the differences and similarities with respect to organizational sustainability initiatives in relation to other organizations.

Originality/value
This study establishes a framework for characterizing organizational sustainability initiatives. It also contributes to reveal whether organizational sustainability initiatives are value – or business-driven and considers intrinsic-oriented differences and extrinsic-oriented similarities.
A truck scheduling problem at a cross-docking facility with mixed service mode dock doors
Authors: Vahdani Behnam , Shahramfard Shayan 
Published: June 2019

Purpose
The purpose of this study is truck scheduling and assignment of trucks to the doors simultaneously since these issues were considered mainly separately in the previous research. Also, the door service time and its impact on truck scheduling were not taken into account, so this research endeavors to cover this gap.

Design/methodology/approach
In this research, a novel model has been presented for simultaneous truck scheduling and assignment problem with time window constraints for the arrival and departure of trucks, mixed service mode dock doors and truck queuing. To resolve the developed model, two meta-heuristic algorithms, namely, genetic and imperialist competitive algorithms, are presented.

Findings
The computational results indicate that the proposed framework leads to increased total costs, although it has a more accurate planning; moreover, these indicate that the proposed algorithms have different performances based on the criteria considered for the comparison.

Research limitations/implications
There are some limitations in this research, which can be considered by other researchers to expand the current study, among them the specifications of uncertainty about arrival times of inbound and outbound trucks, number of merchandises which has been loaded on inbound trucks are the main factors. If so, by considering this situation, a realistic scheme about planning of cross docking system would be acquired. Moreover, the capacity of temporary storage has been considered unlimited, so relaxing this limitation can prepare a real and suitable situation for further study. Examining the capacity in the front of each type of doors of cross-dock and executive servers are the other aspects, which could be expanded in the future.

Originality/value
In this study, a mathematical programing model proposed for truck scheduling to minimize total costs including holding, truck tardiness and waiting time for queue of trucks caused by the interference of each carrier’s movement. At the operational levels, this research considered a multi-door cross-docking problem with mixed service mode dock doors and time window constraints for arrival and departure time of trucks. Moreover, M/G/C queue system was developed for truck arrival and servicing of carriers to trucks.
Multi-objective optimization of bending force preset in cold rolling
Authors: Bu He-Nan , Zhou Hong-Gen , Yan Zhu-Wen , Zhang Dian-Hua 
Published: June 2019

PurposeIn the process of cold rolled strip, there is tight coupling between flatness control and gauge control. The variation of the roll gap caused by the change of bending force will lead to the change of rolling force. Furthermore, it can cause a deep impact on the control accuracy of strip exit thickness and exit crown. The purpose of this paper is to improve the accuracy of the bending force preset value for cold rolled strip.Design/methodology/approachIn this paper, the bending force preset control strategy with considering of rolling force was proposed for the first time and the preset objective function of bending force was established on the basis of the two-objective optimization of bending force and rolling force. Meanwhile, the multi-objective intelligent algorithm – INSGA-II – was used to solve the objective function.FindingsThe proposed bending force multi-objective preset model has been tested in a 1,450 mm tandem cold rolling line. The analyzed results of field data show that the deviations of strip exit thickness and exit crown are reduced effectively by using the improved model, and at the same time, more reasonable bending force preset values are obtained, which can enhance the accuracy of flatness preset control.Originality/valueA preset model of bending force with considering flatness and gauge is proposed in this paper and the multi-objective function of bending force preset is established on the basis of the two-objective optimization of bending force and rolling force. The value lies in proposing a new decoupling method of rolling force and bending force.
Developing cybersecurity education and awareness programmes for small- and medium-sized enterprises (SMEs)
Authors: Bada Maria , Nurse Jason R.C. 
Published: June 2019

PurposeThe purpose of this study is to focus on organisation’s cybersecurity strategy and propose a high-level programme for cybersecurity education and awareness to be used when targeting small- and medium-sized enterprises/businesses (SMEs/SMBs) at a city-level. An essential component of an organisation’s cybersecurity strategy is building awareness and education of online threats and how to protect corporate data and services. This programme is based on existing research and provides a unique insight into an ongoing city-based project with similar aims.Design/methodology/approachTo structure this work, a scoping review was conducted of the literature in cybersecurity education and awareness, particularly for SMEs/SMBs. This theoretical analysis was complemented using a case study and reflecting on an ongoing, innovative programme that seeks to work with these businesses to significantly enhance their security posture. From these analyses, best practices and important lessons/recommendations to produce a high-level programme for cybersecurity education and awareness were recommended.FindingsWhile the literature can be informative at guiding education and awareness programmes, it may not always reach real-world programmes. However, existing programmes, such as the one explored in this study, have great potential, but there can be room for improvement. Knowledge from each of these areas can, and should, be combined to the benefit of the academic and practitioner communities.Originality/valueThe study contributes to current research through the outline of a high-level programme for cybersecurity education and awareness targeting SMEs/SMBs. Through this research, literature in this space was examined and insights into the advances and challenges faced by an on-going programme were presented. These analyses allow us to craft a proposal for a core programme that can assist in improving the security education, awareness and training that targets SMEs/SMBs.
Contextual adaptation of omni-channel grocery retailers’ online fulfilment centres
Authors: Eriksson Ebba , Norrman Andreas , Kembro Joakim 
Published: June 2019

Purpose
The purpose of this paper is to investigate how grocery retailers configure their online fulfilment centres (OFC) as they move towards an omni-channel structure and what contextual factors influence their decisions.

Design/methodology/approach
An exploratory case study with three grocery retailers in the Nordic countries was conducted. The study investigates the current OFC configurations and identifies nine important contextual factors.

Findings
This study shows the importance of understanding the changes that omni-channel retailing entails for an OFC configuration. Nine contextual factors were identified. Several of the factors are found in previous theory, but this paper extends the knowledge of how they affect the configuration of an OFC in grocery retail. The changes in, for example, order characteristics create different requirements for picking, packing, sorting and shipping when compared with traditional distribution centres (DC). Although representing a separate flow for online fulfilment, OFC configuration depends on how the other logistics flows from the DC to stores are designed.

Research limitations/implications
To support further theory development, nine contextual factors and their relationship to OFC configurations are proposed.

Practical implications
This study provides managerial value in two ways. First, grocery retailers with one or more OFCs can benchmark existing solutions using the empirical case descriptions. Second, the findings provide grocery retailers with knowledge of how to configure an OFC.

Originality/value
The literature lacks a holistic approach towards how grocery retailers configure their OFCs and what factors affect these decisions. This study provides the first in-depth analysis of how the omni-channel context affects the configuration of all the aspects of an OFC.