bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships
Authors: Andersson Alma , Larsson Ludvig , Stenbeck Linnea , Salmén Fredrik , Ehinger Anna , Wu Sunny , Al-Eryani Ghamdan , Roden Daniel , Swarbrick Alex , Borg Åke , Frisén Jonas , Engblom Camilla , Lundeberg Joakim 
Published: July 2020

ABSTRACTIn the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra-and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. We integrate and spatially map tumor-associated types from single cell data to find: segregated epithelial cells, interactions between B and T-cells and myeloid cells, co-localization of macrophage and T-cell subsets. A model is constructed to infer presence of tertiary lymphoid structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define novel interactions between tumor-infiltrating cells in breast cancer and provide tools generalizing across tissues and diseases.
Combinatorial deployment of F-actin regulators to build complex 3D actin structuresin vivo
Authors: Xie Yi , Blankenship J. Todd 
Published: July 2020

SUMMARYDespite extensive studies on the actin regulators that direct microfilament dynamics, how these regulators are combinatorially utilized in organismal tissues to generate 3D structures is an unresolved question. Here, we present an in-depth characterization of cortical actin cap dynamics and their regulation in vivo. We identify rapid phases of initiation, expansion, duplication and disassembly and examine the functions of 7 different Actin and/or Nucleator Regulators (ANRPs) in guiding these behaviors. We find ANRPs provide distinct but cooperative activities in building actin cap morphologies – specifically, while DPod1 is a major regulator of actin intensities, Cortactin is required for continued cortical growth, while Coronin functions in both growth and intensity and is required for Cortactin localization to the cap periphery. Unexpectedly, cortical actin populations recovermore rapidlyafter regulator disruption, suggestive of a potential deep competition for limited G-actin pools, and we measurein vivoArp2/3 recruitment efficiencies through an ectopic relocalization strategy. Our results illustrate how the coordination of multiple actin regulators can orchestrate organized and dynamic actin structures in anin vivosystem.
miRNA activity inferred from single cell mRNA expression
Authors: Nielsen Morten Muhlig , Pedersen Jakob Skou 
Published: July 2020

AbstractHigh throughput single-cell RNA sequencing (scRNAseq) can provide mRNA expression profiles for thousands of cells. However, miRNAs cannot currently be studied at the same scale. By exploiting that miRNAs bind well-defined sequence motifs and typically down-regulate target genes, we show that motif enrichment analysis can be used to derive miRNA activity estimates from scRNAseq data.Motif enrichment analyses have traditionally been used to derive binding motifs for regulatory factors, such as miRNAs or transcription factors, that have an effect on gene expression. Here we reverse its use. By starting from the miRNA seed site, we derive a measure of activity for miRNAs in single cells. We first establish the approach on a comprehensive set of bulk TCGA cancer samples (n=9,679), with paired mRNA and miRNA expression profiles, where many miRNAs show a strong correlation with measured expression. By downsampling we show that the method can be used to estimate miRNA activity in sparse data comparable to scRNAseq experiments. We then analyze a human and a mouse scRNAseq data set, and show that for several miRNA candidates, including liver specific miR-122 and muscle specific miR-1 and miR-133a, we obtain activity measures supported by the literature. The methods are implemented and made available in the miReact software. Our results demonstrate that miRNA activities can be estimated at the single cell level. This allows insights into the dynamics of miRNA activity across a range of fields where scRNAseq is applied.
Discriminative Bayesian Serology: Counting Without Cutoffs
Authors: Christian Murray , Murrell Ben 
Published: July 2020

AbstractDuring the emergence of a pandemic, we need to estimate the prevalence of a disease using serological assays whose characterization is incomplete, relying on limited validation data. This introduces uncertainty for which we need to account.In our treatment, the data take the form of continuous assay measurements of antibody response to antigens (eg. ELISA), and fall into two groups. Thetraining dataincludes the confirmed positive or negative infection status for each sample. Thepopulation dataincludes only the assay measurements, and is assumed to be a random sample from the population from which we estimate the seroprevalence.We use the training data to model the relationship between assay values and infection status, capturing both individual-level uncertainty in infection status, as well as uncertainty due to limited training data. We then estimate the posterior distribution over population prevalence, additionally capturing uncertainty due to finite samples.Finally, we introduce a means to pool information over successive time points, using a Gaussian process, which dramatically reduces the variance of our estimates.The methodological approach we here describe was developed to support the longitudinal characterization of the seroprevalence of COVID-19 in Stockholm, Sweden.
A population of CD4+T cells with a naïve phenotype stably polarized to the TH1 lineage
Authors: Lo Jonathan W. , de Mucha Maria Vila , Roberts Luke B. , Garrido-Mesa Natividad , Hertweck Arnulf , Neves Joana F. , Stolarczyk Emilie , Henderson Stephen , Jackson Ian , Howard Jane K. , Jenner Richard G. , Lord Graham M. 
Published: July 2020

AbstractT-bet is the lineage-specifying transcription factor for CD4+T helper type 1 (TH1) cells. T-bet has also been found in other CD4+T cell subsets, including TH17 cells and TREG, where it modulates their functional characteristics. However, we lack information on when and where T-bet is expressed during T cell differentiation and how this impacts T cell function. To address this, we traced the ontogeny of T-bet-expressing cells using a fluorescent fate-mapping mouse line. We demonstrate that T-bet is expressed in a subset of CD4+T cells with naïve cell surface markers and that this novel cell population is phenotypically and functionally distinct from conventional naïve CD4+T cells. These cells are also distinct from previously described populations of memory phenotype and stem cell-like T cells. Naïve-like T-bet-experienced cells are polarised to the TH1 lineage, predisposed to produce IFNγ upon cell activation, and resist repolarisation to other lineagesin vitroandin vivo. These results demonstrate that lineage-specifying factors can function to polarise T cells in the absence of canonical markers of T cell activation and that this has an impact on the subsequent T helper response.
Cortico-subcortical functional connectivity profiles of resting-state networks in marmosets and humans
Authors: Hori Yuki , Schaeffer David J. , Yoshida Atsushi , Cléry Justine C. , Hayrynen Lauren K. , Gati Joseph S. , Menon Ravi S. , Everling Stefan 
Published: July 2020

AbstractUnderstanding the similarity of cortico-subcortical networks topologies between humans and nonhuman primate species is critical to study the origin of network alternations underlying human neurological and neuropsychiatric diseases. The New World common marmoset (Callithrix jacchus) has become popular as a non-human primate model for human brain function. Most marmoset connectomic research, however, has exclusively focused on cortical areas, with connectivity to subcortical networks less extensively explored. In this study, we aimed to first isolate patterns of subcortical connectivity with cortical resting-state networks (RSNs) in awake marmosets using resting-state functional magnetic resonance imaging (RS-fMRI), then to compare these networks to those in humans using connectivity fingerprinting. While we could match several marmoset and human RSNs based on their functional fingerprints, we also found a few striking differences, for example strong functional connectivity of the default mode network with the superior colliculus in marmosets that was much weaker in humans. Together, these findings demonstrate that many of the core cortico-subcortical networks in humans are also present in marmosets, but that small, potentially functionally relevant differences exist.
The use of self-reflection for enhanced enterprise education: a case study
Authors: Clarke Andrew Paul , Cornes Clare , Ferry Natalie 
Published: July 2020

PurposeA case study was undertaken to evaluate the use of self-reflection in enterprise education in a UK university, where the taught content was tailored to ensure relevance to the students who were from a variety of subject disciplines.Design/methodology/approachEnterprise taught content was established in masters level 7 programmes across a range of subject disciplines. Taught content was designed using problem based learning, and evaluated using self-reflective methodologies. The paper reflects on the current position of enterprise education and asks the research question of whether the use of self-reflective teaching methodologies are valid for enterprise education.FindingsResults suggest that the students appreciated the introduction of enterprise into their course and in the main did not view it as disjointed or irrelevant to their wider aims. More so, the students commented favourably towards the integration of enterprise into their primary discipline, and noted an enhanced learning experience because of this integration.Research limitations/implicationsFor the University: A novel approach to enterprise teaching has been developed at a UK university, focusing on teaching non-business students how to be more valuable to a business within their degree subject context. This has empowered the students with an enhanced understanding of commercial issues and increased employability (Rae 2007; Huq and Gilbert 2017). This has also led to enhanced relationships with industry and given students a wider understanding of their degree area.Practical implicationsFor the educator: The use of self-reflective teaching methodologies (Hayward 2000) are noted to be vital in order to deliver enterprise education in a way that is relevant to the student cohort body. By reflecting on one’s teaching style and delivery method, the authors were able to engage non-business students in enterprise education, and receive a high level of student satisfaction. It is noted that self-reflection was a valuable process for delivery to each degree discipline. By employing problem based learning and self-reflective teaching methodologies, an increased synergy between the business taught elements and the science subjects was created.Originality/valueThis approach is shown to empower the students with an enhanced understanding of commercial issues and an increased employability. This has led to enhanced relationships between academia and industry, and given students a wider understanding of their degree area; the enhanced relationships with industry offer students a wider commercial understanding of their degree area. A gap in the current knowledge base in enterprise education has been identified: enterprise education with the aim of educating the student to be more valuable to a business as opposed to starting a business. The use of self-reflective methodologies has offered a novel approach to enterprise teaching in a UK university.
Third-grade non-Newtonian fluid flow and heat transfer in two coaxial pipes with a variable radius ratio with magnetic field
Authors: Javanmard Mohsen , Taheri Mohammad Hasan , Askari Nematollah , Öztop Hakan F. , Abu-Hamdeh Nidal 
Published: July 2020

Purpose
The purpose of this paper is to investigate the hydromagnetic third-grade non-Newtonian fluid flow and heat transfer between two coaxial pipes with a variable radius ratio.

Design/methodology/approach
To solve the approximate nonlinear and linear problems with variable coefficients, a trial function was applied. Methods include collocation, least square and Galerkin that can be applied for obtaining these coefficients.

Findings
It is revealed that an increase of the non-Newtonian parameter, Hartmann number, and radius ratio leads to an augmentation of the absolute value of the dimensionless velocity, temperature, velocity gradient, and temperature gradient of about 10-60%. Further, the augmentation of Bi1 reduces the absolute value of the dimensionless temperature profile and dimensionless temperature gradient about three to four times; hence, the dimensionless heat transfer rate reduces. However, the growth of Bi2 has a contrary impact. Besides, the increase of Pr and Ec leads to an increase in the dimensionless temperature profile and dimensionless temperature gradient; therefore, the dimensionless heat transfer rate increases.

Originality/value
The convection heat transfer on the walls of the pipes is considered, and the nonlinear coupled momentum and energy equations are solved using the least squared method and collocation methods, respectively.
Free convection and thermal radiation of nanofluid inside nonagon inclined cavity containing a porous medium influenced by magnetic field with variable direction in the presence of uniform heat generation/absorption
Authors: Massoudi Mohamed Dhia , Ben Hamida Mohamed Bechir , Almeshaal Mohammed A. 
Published: July 2020

Purpose
The purpose of this paper is to study the natural convection and radiation heat transfer inside Nonagon inclined cavity with variable heated source length, which contains a porous medium saturated with nanofluid in the presence of uniform heat generation or absorption under the effect of uniform magnetic field with variable direction. The shape factor of nano particles is taking account for the model of nanofluid.

Design/methodology/approach
This study is established in two-dimensional space. The 2D numerical study is effectuated with Comsol Multiphysics based on the on the finite element method. The 2D equation system is exposed on dimensionless form taking into account the boundary conditions.

Findings
Results obtained show that the convection heat transfer is ameliorated with the augmentation of heated source length. The convection heat transfer is enhanced by increasing Rayleigh, Darcy numbers and the heated source length; however, it is reduced by rising Hartmann number. The presence of radiation parameter lead to improve the convection heat transfer in the presence of both uniform heat generation/absorption. The average Nusselt number reaches a maximum for an inclination of cavity γ = 45° and a minimum for γ = 60°. Both the increase of the shape factor of nano particles and the solid fraction of nano particles improve the convection heat transfer.

Originality/value
Different studies have been realized to study the heat transfer inside cavity contains porous medium saturated with nanofluid under magnetic field effect. In this work, the Nonagon geometric of cavity studied has never been studied. In addition, the effect of radiation parameter with relation of the shape factor of nanoparticles in the presence of uniform heat generation/absorption on the heat transfer performance have never been investigated. Also, the effect of magnetic field direction with relation of the inclination cavity on heat transfer performance.
Similarities and differences between virtual and actual pants
Authors: Zulkifli Siti Zulaikha Binti , Kim KyoungOk , Takatera Masayuki 
Published: July 2020

PurposeThis study aimed to clarify the criteria for subjective evaluation of the similarities and differences between virtual and actual pants and propose a quantitative evaluation method for those similarities and differences based on geometric features related to the evaluation.Design/methodology/approachUsing patterns, we made five pairs of actual pants for a dummy in five fabrics. We simulated virtual pants with a 3-D simulator. Sensory evaluation was conducted with images of the virtual and actual pants: 20 participants compared the images based on a questionnaire. For the structure of evaluation, the authors undertook analysis of variance and principal component analysis. The actual and virtual pants were geometrically compared using the 3-D scanned data. To investigate the relationship between quantitative and sensory evaluation, the authors calculated the correlation coefficients.FindingsThe authors found that subjects perceived the differences between actual and simulated pants. When comparing the virtual and actual pants, the criteria for the differences were the silhouette from the front view, hem width, waist and wrinkles. Using differences in the hem width, it would be possible to evaluate the differences between actual and simulated pants. Roughness and smoothness of the silhouette also affected evaluation.Originality/valueThe authors clarified the evaluation criteria for the similarities and differences between virtual and actual pants. The authors proposed a quantitative evaluation method for the similarities and differences between virtual and actual garment based on our criteria. This study will be of benefit to 3-D simulator users and developers.
Response surface optimization of cotton tufts opening degree using Box–Behnken designs
Authors: Alkhateeb Weaam Jameel 
Published: July 2020

PurposeThis study aims to investigate the effect of process parameters of blow room machines on openness degree and quality of cotton tufts in a blow room.Design/methodology/approachFor this purpose, an experimental Box–Behnken design (BBD) was used, and the process parameters were the angles of the grid bars underneath the opening rollers of CVT3 beaters and the distance between feed roller of the first opening roller of CVT3.FindingsIt was found that the cotton tuft openness increased by increasing the angles of grid bars and by decreasing the distance between the feed roller and first opening roller on CVT3 beater. Further, the optimization procedure showed that an optimum value of cotton tuft openness (in laser method) was determined for specific levels of the process parameters.Originality/valueThe originality of this investigation is that it showed the individual effects and interactions of the most important factors in two tufting machines instead of only one machine. This study is important because it helps cotton yarn spinners to improve the quality of the final yarns by optimizing the levels of tuft openness which in turn improves fiber cleaning.
Color fastness of fabrics after dyeing with fungal dyes
Authors: Hernández Vicente , Galleguillos Felipe , Sagredo Nicole , Machuca Ángela 
Published: July 2020

PurposeThe study aims to test the color fastness of wool and linen fabrics dyed by simple immersion in ethanol dissolutions of fungal dyes.Design/methodology/approachEthanol dissolutions ofTalaromyces australisandPenicillium murcianumdyes were prepared to a concentration of 0.3% and used to dye wool and linen samples by immersion. Color fastness to washing, dry cleaning, wet and dry rubbing, perspiration and light, were tested according to AATCC standards.FindingsColor fastness reached acceptable results at dry cleaning and wet and dry rubbing by crocking but did not performed well at laundering, perspiration and light exposure. Results indicate that ethanol dissolutions of tested dyes had better affinity for wool fabrics than linen, but the dyeing method requires further improvements to be considered attractive for full scale applications.Originality/valueIn this work sustainability of fabrics dyeing is improved by using natural pigments produced by filamentous fungi and a method to dye that requires no increment of temperature and mordants.
Exploring the antecedents of organizational resilience practices – A transactive memory systems approach
Authors: Cotta Diogo , Salvador Fabrizio 
Published: July 2020

PurposeThe purpose of this paper was to explore individual- and firm-level antecedents of the ability of a manufacturing firm's personnel to collaborate and integrate knowledge for organizational resilience practices.Design/methodology/approachThe authors apply hierarchical regression analysis to study a sample of 192 European industrial equipment manufacturers. Data for each firm are collected from surveys of two key informants in each firm, as well as from public sources.FindingsFirms' personnel’s ability to integrate information and knowledge for organizational resilience practices was positively related with the extent of the head of manufacturing's network of personal contacts inside the firm. This effect was stronger in firms with more formalized job descriptions and clearly defined roles. The head of manufacturing's orientation to teamwork and cooperation impacted this ability only in firms that did not financially incentivize cooperation. The authors also found that cooperation incentives and role formalization directly relate to firms' personnel’s ability to integrate information and knowledge for organizational resilience practices.Originality/valueThe study proposes to study organizational resilience practices through a transactive memory systems lens. The study is also the first to link characteristics of individual managers to firm-level resilience practices by examining the antecedents of firms' ability to integrate information and knowledge to recover from operational disruptions. Furthermore, the study serves to enhance the knowledge of resilience practices by examining the role of firm-level antecedents and their interplay with characteristics of individual managers.
Performance measures of parallel tandem open queueing network
Authors: Priya Banu , P. Rajendran 
Published: July 2020

Purpose
The authors consider parallel four-state tandem open queueing network. The queue capacity is infinite. Passenger arrival rate is Poisson distribution and service rate is exponential distribution. The queue is constructed in the form of tandem queue, and each and every queue of tandem queue is single server (M/M/1) queue. In tandem queue, passengers will leave the system once they receive service from both the states. The purpose of this paper is to provide performance analysis for four-state tandem open queue network, and a governing equation is formulated with the help of transition diagram. Using Burke theorem, the authors formulated equation for average number of passenger in the system, average waiting time of passenger in the system, average number of passenger in the queue and average waiting time of passenger in the queue.

Design/methodology/approach
This paper used Burke’s theorem.

Findings
In this paper, performance analysis is done for parallel four-state tandem open queueing network and performance measure solved using Burkes theorem formula. K. Sreekanth et al. has done performance analysis for single tandem queue with three states. In this paper, the authors have done performance analysis for two tandem queues parallel with four states. This four-state tandem open queueing network is suitable for real world applications. This paper can extend for more number of service states and multi-server states according to the application, and in such case, the authors have to prove and explain with numerical examples. This analysis is more useful for the applications such as airports, railway stations, bus-stands and banks.

Originality/value
In this paper, parallel four-state tandem open queueing network and performance measure has been solved using Burke’s theorem formula.