bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplexed single-cell profiling of post-perturbation transcriptional responses to define cancer vulnerabilities and therapeutic mechanism of action
Authors: McFarland James M. , Paolella Brenton R. , Warren Allison , Geiger-Schuller Kathryn , Shibue Tsukasa , Rothberg Michael , Kuksenko Olena , Jones Andrew , Chambers Emily , Dionne Danielle , Bender Samantha , Wolpin Brian M. , Ghandi Mahmoud , Tirosh Itay , Rozenblatt-Rosen Orit , Roth Jennifer A. , Golub Todd R. , Regev Aviv , Aguirre Andrew J. , Vazquez Francisca , Tsherniak Aviad 
Published: December 2019

AbstractAssays to study cancer cell responses to pharmacologic or genetic perturbations are typically restricted to using simple phenotypic readouts such as proliferation rate or the expression of a marker gene. Information-rich assays, such as gene-expression profiling, are generally not amenable to efficient profiling of a given perturbation across multiple cellular contexts. Here, we developed MIX-Seq, a method for multiplexed transcriptional profiling of post-perturbation responses across a mixture of samples with single-cell resolution, using SNP-based computational demultiplexing of single-cell RNA-sequencing data. We show that MIX-Seq can be used to profile responses to chemical or genetic perturbations across pools of 100 or more cancer cell lines, and combine it with Cell Hashing to further multiplex additional experimental conditions, such as multiple post-treatment time points or drug doses. Analyzing the high-content readout of scRNA-seq reveals both shared and context-specific transcriptional response components that can identify drug mechanism of action and can be used to predict long-term cell viability from short-term transcriptional responses to treatment.
Using nonthermal plasma treatment to improve quality and durability of hydrophilic coatings on hydrophobic polymer surfaces
Authors: Learn Greg D. , Lai Emerson J. , von Recum Horst A. 
Published: December 2019

AbstractLow surface energy substrates, which include many polymers in medicine/industry, present challenges toward achieving uniform, adherent, durable coatings, thus limiting intended coating function. Examples include hydrophobic polymers such as polypropylene, polyethylene, polytetrafluoroethylene, and polydimethylsiloxane. These inert materials are used in various biomedical implants due to favorable bulk properties despite perhaps unfavorable surface properties. The capability to coat such materials holds great value as the surface heavily influences biological response and implant function in vivo. Likewise, paint/ink coatings are often necessary on these same plastics, as their final appearance can be critical for automotive, packaging, and consumer products. Substrate exposure to nonthermal plasma was explored here as a means to improve quality of coatings, specifically cyclodextrin-based polyurethanes previously explored for biomedical applications such as controlled drug delivery and anti-biofouling, upon otherwise incompatible polypropylene substrates. Plasma treatment was found to increase wettability and oxygen content on substrate surfaces. These plasma-induced surface alterations were associated with enhanced coating uniformity, and improved coating/substrate adherence – determined to derive partly from interfacial covalent bond formation. Findings demonstrate the utility of plasma-based surface activation as a strategy to improve coating quality on polymeric substrates, and reveal insights regarding mechanisms by which plasma improves polymer coating adherence.
Sex-based mutational landscape confers sensitivity to checkpoint blockade immunotherapy in cutaneous melanoma
Authors: Jia Mingming , Chi Tian 
Published: December 2019

AbstractAnti-programmed cell death protein 1 (PD-1) therapy provided superior benefits in skin cutaneous melanoma (SKCM), but only a minority of patients responded. As SKCM had sex-based immunological differences, we sought to explore the potential interactions between sex and clinical responses to anti-PD-1 therapy in SKCM. We found that sex had significant effects on anti-PD-1 therapy. Tumor mutation burden (TMB) and neoantigen burden significantly correlated with the clinical responses to anti-PD-1 therapy only in males. Meanwhile, we recruited The Cancer Genome Atlas (TCGA) database to explore sex-based differences of the tumor microenvironment (TME) in SKCM. We observed that males with high TMB, especially in conjunction with interferon-gamma (IFN-γ) signaling, significantly correlated with increased PD-L1 expression, major histocompatibility complex (MHC) class I gene expression, and the infiltration of cytotoxic T lymphocytes (CTLs). In addition, TMB and anti-PD-1 efficacy in SKCM each correlated with homologous recombination repair (HRR) gene BRCA2 mutations, but only in males. Taken together, these data revealed that in SKCM, high TMB correlated with prominent immunotherapeutic TME only in males, and that gender should be taken into account when predicting the efficacy of anti-PD-1 therapy for SKCM.
Brain computation by assemblies of neurons
Authors: Papadimitriou Christos H. , Vempala Santosh S. , Mitropolsky Daniel , Collins Michael , Maass Wolfgang 
Published: December 2019

AbstractAssemblies are large populations of neurons believed to imprint memories, concepts, words and other cognitive information. We identifya repertoire of operationson assemblies. These operations correspond to properties of assemblies observed in experiments, and can be shown, analytically and through simulations, to be realizable by generic, randomly connected populations of neurons with Hebbian plasticity and inhibition. Operations on assemblies include: projection (duplicating an assembly by creating a new assembly in a downstream brain area); reciprocal projection (a variant of projection also entailing synaptic connectivity from the newly created assembly to the original one); association (increasing the overlap of two assemblies in the same brain area to reflect cooccurrence or similarity of the corresponding concepts); merge (creating a new assembly with ample synaptic connectivity to and from two existing ones); and pattern-completion (firing of an assembly, with some probability, in response to the firing of some but not all of its neurons). Our analytical results establishing the plausibility of these operations are proved in a simplified mathematical model of cortex: a finite set of brain areas each containingnexcitatory neurons, withrandomconnectivity that is both recurrent (within an area) and afferent (between areas). Within one area and at any time, onlykof thenneurons fire — an assumption that models inhibition and serves to define both assemblies and areas — while synaptic weights are modified by Hebbian plasticity, as well as homeostasis. Importantly, all neural apparatus needed for the functionality of the assembly operations is created on the fly through the randomness of the synaptic network, the selection of thekneurons with the highest synaptic input, and Hebbian plasticity, without any special neural circuits assumed to be in place. Assemblies and their operations constitute a computational model of the brain which we call theAssembly Calculus, occupying a level of detail intermediate between the level of spiking neurons and synapses, and that of the whole brain. As with high-level programming languages, a computation in the Assembly Calculus (that is, a coherent sequence of assembly operations accomplishing a task) can ultimately be reduced — “compiled down” — to computation by neurons and synapses; however, it would be far more cumbersome and opaque to represent the same computation that way. The resulting computational system can be shown, under assumptions, to be in principle capable of carrying out arbitrary computations. We hypothesize that something like it may underlie higher human cognitive functions such as reasoning, planning, and language. In particular, we propose a plausible brain architecture based on assemblies for implementing the syntactic processing of language in cortex, which is consistent with recent experimental results.
Mechanical cell competition in heterogeneous epithelial tissues
Authors: Murphy R. J. , Buenzli P. R. , Baker R. E. , Simpson M. J. 
Published: December 2019

AbstractMechanical cell competition is important during tissue development, cancer invasion, and tissue ageing. Heterogeneity plays a key role in practical applications since cancer cells can have different cell stiffness and different proliferation rates than normal cells. To study this phenomenon, we propose a one-dimensional mechanical model of heterogeneous epithelial tissue dynamics that includes cell-length-dependent proliferation and death mechanisms. Proliferation and death are incorporated into the discrete model stochastically and arise as source/sink terms in the corresponding continuum model that we derive. Using the new discrete model and continuum description, we explore several applications including the evolution of homogeneous tissues experiencing proliferation and death, and competition in a heterogeneous setting with a cancerous tissue competing for space with an adjacent normal tissue. This framework allows us to postulate new mechanisms that explain the ability of cancer cells to outcompete healthy cells through mechanical differences rather than by having some intrinsic proliferative advantage. We advise when the continuum model is beneficial and demonstrate why naively adding source/sink terms to a continuum model without considering the underlying discrete model may lead to incorrect results.
The effectiveness of game dynamics in cooperation networks
Authors: Silva Luciano Francisco Silveira da , Verschoore Jorge Renato , Bortolaso Ingridi Vargas , Brambilla Flávio Régio 
Published: December 2019

PurposeIn line with the recent adoption of game dynamics to promote motivation and engagement in business contexts, the purpose of this paper is to analyze how gamification tools (i.e. points, levels, challenges, badges and ranking) are used to manage cooperation networks.Design/methodology/approachTo develop this purpose, an exploratory case study is conducted on the RedeMac Qualifying Program as a set of tools to enhance customer service in RedeMac, a cooperation network of hardware stores in southern Brazil.FindingsThe results showed the motivating role of gamification in engaging associates to the network’s decisions. The findings also indicated the effectiveness of points and badges in engaging members and highlighted opportunities to apply tools of challenge. In addition, the paper argues about the constraints for ranking in cooperation networks.Research limitations/implicationsThe study reinforces literature assumptions that stand for the motivating potential of points, levels, badges and challenges. However, the case study highlighted the constraints to adopt the ranking tool in cooperation networks.Practical implicationsFrom the managerial point of view, the study informs managers about the adoption of gamification tools to promote motivation and engagement of associates in cooperation networks, facilitating the achievement of collective goals.Originality/valueIn spite of the growth of empirical literature in applying gamification to business contexts, there are no reports of research about the adoption of gamification tools on cooperative relations in a network organization.
El bueno, El malo y El FeoEfectividad organizacional en los procesos de recursos humanos
Authors: Gaytán-Jiménez María de Guadalupe GG , López-Hernández Carlos Eduardo , Cordero-Estefan Jaqueline 
Published: December 2019

Learning outcomes
Se espera que los estudiantes logren: Identificar los requisitos previos y básicos a un proceso de institucionalización. Priorizar procesos estratégicos de recursos humanos como base para el crecimiento de la empresa. Analizar la importancia de las etapas en la gestión de recursos humanos. Definir las áreas de oportunidad y sus respectivos planes de acción. Proponer las habilidades de liderazgo que requiere un líder

Case overview/synopsis
Tramuntana® es una agencia de viajes que destaca por ser un servicio de primer nivel, promovida por sus propios clientes. Su fundador desea institucionalizar la empresa. El principal problema al que se enfrenta para crecer y consolidarse es mantener sus recursos humanos y que no pueden ser retenidos, por lo tanto, no tienen una estructura sólida.

Complexity academic level
Escuela de pregrado y posgrado de negocios y educación ejecutiva

Supplementary materials
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Subject code
CSS 1: Accounting and Finance
Expert recommendation in community question answering: a review and future direction
Authors: Yang Zhengfa , Liu Qian , Sun Baowen , Zhao Xin 
Published: December 2019

PurposeThis paper aims to make it convenient for those who have only just begun their research into Community Question Answering (CQA) expert recommendation, and for those who are already concerned with this issue, to ease the extension of our understanding with future research.Design/methodology/approachIn this paper, keywords such as “CQA”, “Social Question Answering”, “expert recommendation”, “question routing” and “expert finding” are used to search major digital libraries. The final sample includes a list of 83 relevant articles authored in academia as well as industry that have been published from January 1, 2008 to March 1, 2019.FindingsThis study proposes a comprehensive framework to categorize extant studies into three broad areas of CQA expert recommendation research: understanding profile modeling, recommendation approaches and recommendation system impacts.Originality/valueThis paper focuses on discussing and sorting out the key research issues from these three research genres. Finally, it was found that conflicting and contradictory research results and research gaps in the existing research, and then put forward the urgent research topics.
Achieving SME performance through individual entrepreneurial orientation
Authors: Fatima Tehreem , Bilal Ahmad Raza 
Published: December 2019

PurposeThis study has advanced the role of individual entrepreneurial orientation (IEO) as a precedent of small and medium-sized enterprises (SMEs) performance in the emerging economies. This study aims to use the action regulation theory (ART) to show that active social networking of SME owners acts as a conduit in the above-mentioned relationship and how the social skills of SME owners improve their ability to leverage on entrepreneurial orientation and strengthen their social networking.Design/methodology/approachA three-wave time-lagged survey approach was deployed to collect data from SME owners in the service and manufacturing sector of Pakistan through cluster sampling. The analysis of results was carried out by Models 1 and 4 of Hayes (2017) PROCESS macro.FindingsThe findings revealed a positive association in the IEO of SME owners and their performance through a partial mediating role of active social networking. Furthermore, SME owners’ social skills played a moderating role in linking IEO of SME owners and active development of social networks.Originality/valueBased on ART, this study has targeted a scantly examined psychological perspective in SME performance research and it has shown that by having entrepreneurial orientation and social skills, SME owners can develop active social networks that are an important yet neglected performance precursor in the emerging economy of Pakistan.
Empowerment and organizational identification
Authors: Ertürk Alper , Albayrak Taner 
Published: December 2019

Purpose
The purpose of this paper is to explore the mechanism through which perceived empowerment practices in a firm influence employees’ organizational identification. Specifically, the authors posit the mediating role of leader‒member exchange (LMX) and the moderating role of leader trustworthiness in the relationship.

Design/methodology/approach
Data were collected through survey from 236 white-collar employees working in 20 private companies in Turkey. The authors tested the model using hierarchical regression and conditional process analysis.

Findings
Findings of this study are as follows: first, LMX mediates the relationship between empowerment practices and organizational identification, second, leader integrity, a dimension of trustworthiness, moderates the relationship between empowerment practices and LMX and the relationship between LMX and organizational identification and, third, leader integrity moderates the indirect effect of empowerment practices on organizational identification via LMX. These direct and indirect effects are stronger when leaders have higher integrity than when they have lower integrity.

Originality/value
This study enhances the understanding of the mechanism through which empowerment practices influence employees’ organizational identification.
Land‐use change affects size spectra, energy flux and ecosystem functions in litter and soil invertebrates
Authors: Ehnes Roswitha B. 
Published: December 2019

AbstractIn Focus: Potapov, A. M., Klarner, B., Sandmann, D., Widyastuti, R. and Scheu, S. (2019). Linking size spectrum, energy flux and trophic multifunctionality in soil food webs of tropical land‐use systems. Journal of Animal Ecology, 88, 1845–1859. https://doi.org/10.1111/1365-2656.13027Potapov et al. (2019) advance our understanding of the various levels of the consequences of human impact on ecosystems. They examine the communities of litter and soil invertebrates in four different forests (from rainforest to oil palm plantations). Data on abundance, body masses and trophic guild in litter and soil invertebrates are expanded to a study towards biodiversity, biomass, energy flux and ecosystem functions. Their results show that size spectra are affected differently for decomposers, herbivores, omnivores and predators. Most of these groups decrease in abundance with increasing land use, and only large decomposers increase strongly. Moreover, creating trophic‐group food webs for litter and soil invertebrates of each forest demonstrates the changes in energy flux and ecosystem functions. With their study, Potapov et al. (2019) present new insights into ecosystem functions and the sensitivity of communities to changes in land use.
Decadal changes in masting behaviour of oak trees with rising temperature
Authors: Shibata Mitsue , Masaki Takashi , Yagihashi Tsutomu , Shimada Takuya , Saitoh Takashi 
Published: December 2019

Abstract

Decadal changes in masting behaviour—directional changes in seed production with fluctuations on a decadal time‐scale—are attracting widespread attention in the context of global climate change. However, our mechanistic understanding of the effects of climate on seed production on a decadal scale is unsatisfactory, partly because of the insufficient statistical analyses of long‐term data on masting.

We detected decadal changes in masting behaviour in the Japanese oak Quercus crispula based on long‐term data (38 years: 1980–2017) from the Kitakami Mountains of Japan. The moving average of seed production in a 20‐year sliding window increased, whereas the coefficient of variation decreased. A wavelet power spectrum, as well as a second‐order log‐linear autoregressive (AR) model showed that masting intervals shortened from 3‐ or 4‐year cycle to a 2‐year cycle.

The moving average of seed production increased linearly as the moving average of temperature increased. Temporal variations of the two AR model coefficients as a function of temperature were well described by concave curves.

Synthesis. By conducting the statistical analyses of a long‐term seed production dataset, we obtained significant evidence of decadal changes in the masting behaviour of the Japanese oak and showed that the shortening of the masting interval was associated with rising temperature. A resource allocation shift and an environmental veto were discussed as possible mechanisms underlying the decadal change.
Fatal and Nonfatal Rip Saw Injuries
Authors: Handlosová Klára , Klabal Ondřej , Dokoupil Marek , Vojtek Vladimír , Uvíra Matěj , Handlos Petr 
Published: December 2019

AbstractThis paper deals with a fatal stab wound suffered by a 29‐year‐old man and nonfatal injuries of 35‐year‐old and 67‐year‐old saw operators. Rip saw is a machine that is specially designed for making a rip cut, a cut made parallel to the direction of the wood grain. Rip‐saw‐related injuries mostly occur when a person is struck by the cutting material, which usually involves splinters of irregular shape and diameter. When the splinter strikes the body diagonally, the injuries may include abrasions, lacerations, and cut wounds; in situations where the victim is struck directly, the most common injuries are oval‐ or star‐shaped stab wounds with a varying width of abrasions around the wounds. Therefore, such injuries may come across as injuries produced by a knife‐like instrument, which is an added difficulty in the interpretation of such injuries.
Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish
Authors: Pochardt Meredith , Allen Jennifer M. , Hart Ted , Miller Sophie D. L. , Yu Douglas W. , Levi Taal 
Published: December 2019

AbstractAlthough environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental‐DNA‐based indices of abundance for long‐term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark‐recapture population estimates for eulachon (Thaleichthys pacificus) and “eDNA rates” which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark‐recapture population estimate, explaining 84.96% and 92.53% of the deviance, respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark‐recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark‐recapture is infeasible.