bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate estimation of cell composition in bulk expression through robust integration of single-cell information
Authors: Jew Brandon , Alvarez Marcus , Rahmani Elior , Miao Zong , Ko Arthur , Sul Jae Hoon , Pietiläinen Kirsi H. , Pajukanta Päivi , Halperin Eran 
Published: June 2019

AbstractWe present Bisque, a tool for estimating cell type proportions in bulk expression. Bisque implements a regression-based approach that utilizes single-cell RNA-seq (scRNA-seq) data to generate a reference expression profile and learn gene-specific bulk expression transformations to robustly decompose RNA-seq data. These transformations significantly improve decomposition performance compared to existing methods when there is significant technical variation in the generation of the reference profile and observed bulk expression. Importantly, compared to existing methods, our approach is extremely efficient, making it suitable for the analysis of large genomic datasets that are becoming ubiquitous. When applied to subcutaneous adipose and dorsolateral prefrontal cortex expression datasets with both bulk RNA-seq and single-nucleus RNA-seq (snRNA-seq) data, Bisque was able to replicate previously reported associations between cell type proportions and measured phenotypes across abundant and rare cell types. Bisque requires a single-cell reference dataset that reflects physiological cell type composition and can further leverage datasets that includes both bulk and single cell measurements over the same samples for improved accuracy. We further propose an additional mode of operation that merely requires a set of known marker genes. Bisque is available as an R package at: https://github.com/cozygene/bisque.
Primary human chondrocytes respond to compression with plasma membrane receptors and by microtubule activation: a phosphoproteomic study
Authors: Zignego Donald L. , Hilmer Jonathan K. , Bothner Brian , Schell William J. , June Ronald K. 
Published: June 2019

AbstractChondrocytes are responsible for maintaining the cartilage that helps joints like the knee and hip bear load and move smoothly. These cells typically respond to physiological compression with pathways consistent with matrix synthesis, and chondrocyte mechanotransduction is essential for tissue and joint homeostasis. In osteoarthritis (OA), chondrocyte mechanotransduction appears to be dysregulated, yet many pathways and mechanisms of osteoarthritic chondrocyte mechanotransduction remain poorly understood. The objective of this study is to document the phosphoproteomic responses of primary osteoarthritic chondrocytes to physiological sinusoidal compression. Here we show that OA chondrocytes respond to physiological compression by first activating proteins consistent with cytoskeletal remodeling and decreased transcription, and then later activating proteins for transcription. These results show that several microtubule-related proteins respond to compression, as well as proteins related to calcium signaling, which has previously been extensively shown in chondrocytes. Our results demonstrate that compression is a relevant physiological stimulus for osteoarthritic chondrocytes. We anticipate these data to be a starting point for more sophisticated analysis of both normal and osteoarthritic chondrocyte mechanotransduction. For example, finding differences in compression-induced phosphoproteins between normal and OA cells may lead to druggable targets to restore homeostasis to diseased joints.
Inherited duplications ofPPP2R3Bpromote naevi and melanoma via a novelC21orf91-driven proliferative phenotype
Authors: Polubothu Satyamaanasa , Al-Olabi Lara , Lionarons Daniël A , Harland Mark , Thomas Anna C , Horswell Stuart , Hunt Lilian , Wlodarchak Nathan , Aguilera Paula , Brand Sarah , Bryant Dale , Beales Philip , Carrera Cristina , Chen Hui , Elgar Greg , Harwood Catherine A , Howell Michael , Jenkins Dagan , Larue Lionel , Loughlin Sam , MacDonald Jeff , Malvehy Josep , Barberan Sara Martin , Martins da Silva Vanessa , Molina Miriam , Morrogh Deborah , Moulding Dale , Nsengimana Jérémie , Pittman Alan , Puig-Butillé Juan-Anton , Parmar Kiran , Sebire Neil J , Scherer Stephen , Stadnik Paulina , Stanier Philip , Tell Gemma , Waelchli Regula , Zarrei Mehdi , Zecchin Davide , Puig Susana , Bataille Véronique , Xing Yongna , Healy Eugene , Moore Gudrun E , Di Wei-Li , Newton-Bishop Julia , Downward Julian , Kinsler Veronica A 
Published: June 2019

AbstractThe majority of the heredity of melanoma remains unexplained, however inherited copy number changes have not yet been systematically studied. The genetic environment is highly relevant to treatment stratification, and new gene discovery is therefore desirable. Using an unbiased whole genome screening approach for copy number we identify here a novel melanoma predisposing factor, familial duplications of genePPP2R3B, encoding a regulatory unit of critical phosphatase PP2A. Significant correlation between expression ofPPP2R3Bin tumour tissue and survival in a large melanoma cohort was confirmed, and associated with a non-immunological expression profile. Mechanistically, construction and extensive characterization of a stable, inducible cellular model forPPP2R3Boverexpression revealed induction of pigment cell switching towards proliferation and away from migration. Importantly, this was independent of the known microphthalmia-associated transcription factor(MITF)-controlled pigment cell phenotype switch, and was instead driven by uncharacterised geneC21orf91. Bioinformatic studies point toC21orf91as a novel target ofMITF,and therefore a potential hub in the control of phenotype switching in melanoma. This study identifies novel germline copy number variants inPPP2R3Bpredisposing to melanocytic neoplasia, and uncovers a new potential therapeutic targetC21orf91in the control of pigment cell proliferation.
Autonomous drones are a viable tool for acoustic bat surveys
Authors: August Tom , Moore Tom 
Published: June 2019

AbstractAcoustic surveys of bats are currently limited by the detection range of ultrasound microphones. This makes it difficult to survey bats at height, over water, or in other hard to reach locations. Drones, also known as UAVs or UASs, are becoming more affordable and feature rich, resulting in more uptake in conservation, primarily for aerial imagery. In this paper we address current limitations to acoustic bat surveys by developing three autonomous drones for surveying bats; a plane, quadcopter and boat. All three are capable of moving autonomously from one waypoint to another while carrying a bat detector to record bats and are all low cost (under US$950) with large operational ranges that make them suited to aerial transect work.Initial testing highlighted ultrasound noise generated by the drones as a major issue for recording bats from these systems. This was mitigated through iterative design of the microphone placement and the vehicles themselves. Subsequent testing in real world settings, in the presence of bats, demonstrated that bats could be recorded under autonomous navigation and that the ultrasound interference could be reduced to a negligible level.Autonomous drones offer an exciting new tool in the tool box of bat workers and researchers. They allow us to study areas previously inaccessible on foot, as well as at heights that have previously been inaccessible. We also discuss current limitations to this technology, including legal considerations, hidden costs and potential impacts on bat behaviour.
Identifying Combinations of Cancer Drivers in Individual Patients
Authors: Klein Michael I. , Cannataro Vincent L. , Townsend Jeffrey P. , Stern David F. , Zhao Hongyu 
Published: June 2019

ABSTRACTIdentifying the subset of genetic alterations present in individual tumors that are essential and collectively sufficient for cancer initiation and progression would advance the development of effective personalized treatments. We present CRSO for inferring the combinations of alterations, i.e., rules, that cooperate to drive tumor formation in individual patients. CRSO prioritizes rules by integrating patient-specific passenger probabilities for individual alterations along with information about the recurrence of particular combinations throughout the population. We present examples in glioma, liver cancer and melanoma of significant differences in patient outcomes based on rule assignments that are not identifiable by consideration of individual alterations.
RFID-based tracking and monitoring approach of real-time data in production workshop
Authors: Li Xixing , Du Baigang , Li Yibing , Zhuang Kejia 
Published: June 2019

Purpose
In practical workshop production process, there are many production emergencies, e.g. new manufacturing tasks, facilities failure and tasks change. On one hand, it results in poor timeliness and reliability of real-time production data collection, acquisition and transmission; on the other hand, it increases the difficulty of real-time data tracking and monitoring. This paper aims to develop a novel RFID-based tracking and monitoring approach of real-time data in production workshop (TMrfid) to solve them.

Design/methodology/approach
At first, a three-layer model of real-time data based on RFID has been constructed, which contains RFID-based integrated acquisition center; “RFID & Cloud-service-rules”-based calculation and analysis center; and “RFID & Ontology-knowledge-base”-based monitoring and scheduling center. Then, a targeted analysis and evaluation method of TMrfid with feasibility, quality and performance has been proposed. Finally, a prototype platform of a textile machinery manufacturing enterprise has been built to verify the effective of TMrfid.

Findings
The effectiveness of TMrfid is verified by applying two groups of actual experimental data from the case enterprise, the results show that TMrfid can promote the efficiency, reliability and feasibility of tacking and monitoring of real-time data in production workshop.

Originality/value
RFID-based tracking and monitoring approach of real-time data in production workshop has been developed to solve the data information transmission and sharing problem. Three analysis and evaluation approaches have been introduced to solve the un-standardized evaluation problem of RFID application. A prototype platform of a textile machinery manufacturing enterprise has been constructed.
Design and optimization of a low voltage RF switch MEMS capacitance using genetic algorithm and Taguchi method
Authors: Ardehshiri Alireza , Karimi Gholamreza , Dehdasht-Heydari Ramin 
Published: June 2019

Purpose
This paper aims to design, optimize and simulate the Radio Frequency (RF) micro electromechanical system (MEMS) Switch which is stimulated by electrostatically voltage.

Design/methodology/approach
The geometric structure of the switch was extracted based on the design of Taguchi-based experiment using the mathematical programming and obtaining objective function by the genetic meta-heuristic algorithm.

Findings
The RF parameters of the switch were calculated for the design of Taguchi-based S11 = −5.649 dB and S21 = −46.428 dB at the working frequency of 40 GHz. The pull-in voltage of the switch was 2.8 V and the axial residual stress of the proposed design was obtained 28 MPa and the design of Taguchi-based S11 = −4.422 dB and S21 = −48.705dB at the working frequency of 40 GHz. The pull-in voltage of the switch was 2.5 V and the axial residual stress of the proposed design was obtained 25 MPa.

Originality/value
A novel complex strategy in the design and optimization of capacitive RF switch MEMS modeling is proposed.
Numerical modeling of the simultaneous propagation of multiple hydraulic fractures with fluid lags
Authors: Zeng Qinglei , Liu Zhanli , Wang Tao , Gao Yue , Zhuang Zhuo 
Published: June 2019

PurposeThe purpose of this paper is to develop a numerical method to model the simultaneous propagation of multiple hydraulic fractures (HFs) with fluid lags driven from a horizontal wellbore.Design/methodology/approachFracture propagation in solid medium is modeled with the extended finite element method and fluid flow is modeled with finite volume method. Three iteration loops are introduced to solve the nonlinear system within each time increment, i.e. a Newtonian iteration to solve the solid-fluid coupling system, a Picard iteration to determine fluid front positions and a secant iteration to update fracture lengths.FindingsThe propagation of one single HF with a fluid lag is simulated and agrees well with semi-analytical solutions or other numerical results in the literature. The simultaneous propagation of two HFs are then investigated, which demonstrates the ability of the proposed method in capturing the hydraulic fracturing process with multiple fractures and fluid lags.Originality/valueWith the proposed method, one can simulate the simultaneous propagation of multiple HFs with fluid lags, which play a significant role during early-time propagation or when the confinement stress is relatively low (shallow HFs). Solid deformation and fracturing, fluid flow in fractures and in the wellbore are fully coupled, and three iteration loops are introduced to solve the nonlinear system.
Cooperation as a vehicle for innovation: a study of the effects of firm size and industry type
Authors: Cristo-Andrade Silveli , Franco Mário José 
Published: June 2019

Purpose
Based on firms’ need to remain competitive and dynamic in a scenario of constant change, the purpose of this paper is to compare the actors involved in cooperation for innovation between Brazilian small- and medium-sized enterprises (SMEs) and large firms (LFs), and also in two industries/sectors, manufacturing and services.

Design/methodology/approach
To achieve this objective, the database chosen was PINTEC, with data available from 1998 to 2014. The statistical analyses performed were binary logistic regression, descriptive statistics of the variables, correlation matrix and the difference of means.

Findings
The empirical evidence show that the firm’s characteristics (SME or LF) favour the use of one type of cooperation for innovation or another, highlighting SMEs’ proximity to their clients and LFs’ structures, tending to belong to business groups and having links to training centres and technical assistance networks.

Research limitations/implications
The theoretical contribution of this study lies in the evidence that types of cooperation for innovation can vary according to firm size and the type of industry/sector, and the practical contribution lies in pointing out the importance of clients for SMEs, and for LFs the importance of business groups, technical assistance and professional training centres. The importance of suppliers in cooperation for innovation stands out in the service sector, and that of clients in the manufacturing sector.

Originality/value
This study shows that the types of cooperation to innovation can vary according to firm size and type of sector, in an emerging market and with low rates of innovation. It is emphasized that most research on the subject has been carried out in developed countries or emerging Asian ones. Therefore, this study is innovative because it shows particularities of the Brazilian market that can subsequently be observed in other emerging markets.
Identifying counterfeit brand logos: on the importance of the first and last letters of a logotype
Authors: Pathak Abhishek , Velasco Carlos , Calvert Gemma Anne 
Published: June 2019

PurposeCounterfeiting is a menace in the emerging markets and many successful brands are falling prey to it. Counterfeit brands not only deceive consumers but also fuel a demand for lower priced replicas, both of which can devalue the bona-fide brand. But can consumers accurately identify a counterfeit logo? This paper aims to explore this question and examines the accuracy and speed with which a consumer can identify a counterfeit (vs original) logo.Design/methodology/approachSeven popular brand logos were altered by transposing and substituting the first and last letters of the logotypes. Consumers then classified the logos as counterfeit (vs original) across two experiments.FindingsParticipants were faster and more accurate in identifying a counterfeit logo when the first letter (vs last letter) of a logotype was manipulated, thus revealing last letter manipulations of a brand’s logotype to be more deceptive.Research limitations/implicationsThis paper comments only on the manipulation of logotypes but not of logo symbols. Similarly, findings may not be generalizable across languages which are read from right to left.Practical implicationsCounterfeit trade is already a multibillion dollar industry. Understanding the key perceptual differentiators between a counterfeit (vs original) logo can be insightful for both consumers and firms alike.Originality/valueResearch available on objective measures of similarities (vs dissimilarities) between counterfeit (vs original) brand logos is limited. This paper contributes by examining the ability of consumers to discriminate between counterfeit (vs original) logos at different levels of visual similarity.
Brownian models effect on turbulent fluid flow and heat transfer and entropy generation of water/boehmite alumina nanofluid inside enclosure
Authors: Mozafari Behrouz , Abbasian Arani Ali Akbar , Sheikhzadeh Ghanbar Ali , Salimi Mahmoud 
Published: June 2019

Purpose
The purpose of this paper is to study the effects of using different Brownian models on natural and mixed convection fluid flow and heat transfer inside the square enclosure filled with the AlOOH–water nanofluid.

Design/methodology/approach
Due to fulfill of this demand, five different models for the effective thermal conductivity and viscosity of the nanofluid are considered. The following results are presented for the
Ra=107 to 1010 and
Ri=0.01 to 100, whereas the volume fraction of the nanoparticles is varied from
φ = 0.01 to 0.04.

Findings
According to the obtained results, increasing of Rayleigh number and reduction of Richardson number leads to the higher values of the average Nusselt number and entropy generation. Also, it is realized that, variation trend of the average Nusselt number and entropy generation in all cases is increasing by growing the volume fraction. It is found that the obtained average Nusselt numbers and entropy generations with Koo and Kleinstreuer are the highest among all the studied cases, and it is followed by Patel, Vajjha and Das, Corcione and Maxwell–Brinkman models, respectively.

Originality/value
Based on the results of present investigation, the Nusselt number difference predicted between the Maxwell–Brinkman model (as constant-property model) and Koo and Kleinstreuer model is about 7.84 per cent at 0.01 per cent volume fraction and 5.47 per cent at 0.04 per cent volume fraction for the Rayleigh number equal to 107. The entropy generation difference predicted between the two above studied model is about 8.05 per cent at 0.01 per cent volume fraction and 5.86 per cent at 0.04 per cent volume fraction for the Rayleigh number equal to 107. It is observed that using constant-property model has a significant difference in the obtained results with the results of other variable-property models.
An efficient space-time operator-splitting method for high-dimensional vector-valued Allen–Cahn equations
Authors: Sun Yunxia , Xiao Xufeng , Gao Zhiming , Feng Xinlong 
Published: June 2019

Purpose
The purpose of this paper is to propose an efficient space-time operator-splitting method for the high-dimensional vector-valued Allen–Cahn (AC) equations. The key of the space-time operator-splitting is to devide the complex partial differential equations into simple heat equations and nolinear ordinary differential equations.

Design/methodology/approach
Each component of high-dimensional heat equations is split into a series of one-dimensional heat equations in different spatial directions. The nonlinear ordinary differential equations are solved by a stabilized semi-implicit scheme to preserve the upper bound of the solution. The algorithm greatly reduces the computational complexity and storage requirement.

Findings
The theoretical analyses of stability in terms of upper bound preservation and mass conservation are shown. The numerical results of phase separation, evolution of the total free energy and total mass conservation show the effectiveness and accuracy of the space-time operator-splitting method.

Practical implications
Extensive 2D/3D numerical tests demonstrated the efficacy and accuracy of the proposed method.

Originality/value
The space-time operator-splitting method reduces the complexity of the problem and reduces the storage space by turning the high-dimensional problem into a series of 1D problems. We give the theoretical analyses of upper bound preservation and mass conservation for the proposed method.
Gender and business owner satisfaction
Authors: Li Wenxuan , Marshall Maria I. 
Published: June 2019

Purpose
The purpose of this paper is to investigate how the factors associated with role satisfaction in farm and non-farm family businesses differ by gender of the business owner.

Design/methodology/approach
The data used are from a 30-minute telephone survey of owners of farm and non-farm family businesses in Indiana, Illinois, Michigan and Ohio. The sample consists of 627 small- and medium-size family businesses. Three ordered probit regressions are used to analyze role satisfaction.

Findings
Women’s participation in management and the number of family members in management are positively associated with women’s role satisfaction, while tension from resource competition is negatively associated with role satisfaction. In contrast, men’s role satisfaction is increased through high family business functioning and profit.

Practical implications
There is no difference in the level of role satisfaction between men and women when one controls for the owner, family and business characteristics. However, there is a difference in the factors that drive role satisfaction between men and women. This may be driven, in part, by what their roles are vis-à-vis the financial aspects of the business. Male and female business owners seem to focus on different aspects of their family business to achieve role satisfaction.

Originality/value
This paper determines the impact of gender on the role satisfaction of business owners of farm and non-farm family businesses in four Midwestern states. It identifies the different factors associated with role satisfaction for female and male family business owners based on their actual roles.