bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial dysfunction is signaled to the integrated stress response by OMA1, DELE1 and HRI
Authors: Guo Xiaoyan , Aviles Giovanni , Liu Yi , Tian Ruilin , Unger Bret A. , Lin Yu-Hsiu T. , Wiita Arun P. , Xu Ke , Correia M. Almira , Kampmann Martin 
Published: July 2019

AbstractIn mammalian cells, mitochondrial dysfunction triggers the integrated stress response (ISR), in which eIF2α phosphorylation upregulates the transcription factor ATF4. However, how mitochondrial stress is relayed to the ISR is unknown. We found that HRI is the eIF2α kinase necessary and sufficient for this relay. Using an unbiased CRISPRi screen, we identified factors upstream of HRI: OMA1, a mitochondrial stress-activated protease, and DELE1, a little-characterized protein we found to be associated with the inner mitochondrial membrane. Mitochondrial stress stimulates the OMA1-dependent cleavage of DELE1, leading to its accumulation in the cytosol, where it interacts with HRI and activates its eIF2α kinase activity. Blockade of the OMA1-DELE1-HRI pathway is beneficial during some, but not all types of mitochondrial stress, and leads to an alternative response that induces specific molecular chaperones. Therefore, this pathway is a potential therapeutic target enabling fine-tuning of the ISR for beneficial outcomes in diseases involving mitochondrial dysfunction.
Testing the ability of species distribution models to infer variable importance
Authors: Smith Adam B. , Santos Maria J. 
Published: July 2019

AbstractModels of species’ distributions and niches are frequently used to infer the importance of range- and niche-defining variables. However, the degree to which these models can reliably identify important variables and quantify their influence remains unknown. Here we use a series of simulations to explore how well models can 1) discriminate between variables with different influence and 2) calibrate the magnitude of influence relative to an “omniscient” model. To quantify variable importance, we trained generalized additive models (GAMs), Maxent, and boosted regression trees (BRTs) on simulated data and tested their sensitivity to permutations in each predictor. Importance was inferred by calculating the correlation between permuted and unpermuted predictions, and by comparing predictive accuracy of permuted and unpermuted predictions using AUC and the Continuous Boyce Index. In scenarios with one influential and one uninfluential variable, models were unable to discriminate reliably between variables in conditions that are normally challenging for generating accurate predictions: training occurrences <8-64; prevalence >0.5; small spatial extent; environmental data with coarse resolution when spatial autocorrelation is low; and correlation between environmental variables where |r| >0.7. When two variables influenced the distribution equally, importance was underestimated when species had narrow or intermediate niche breadth. Interactions between variables in how they shaped the niche did not affect inferences about their importance. When variables acted unequally, the effect of the stronger variable was overestimated. GAMs and Maxent discriminated between variables more reliably than BRTs, but no algorithm was consistently well-calibrated vis-à-vis the omniscient model. Algorithm-specific measures of importance like Maxent’s change-in-gain metric were less robust than the permutation test. Overall, high predictive accuracy did not connote robust inferential capacity. As a result, requirements for reliably measuring variable importance are likely more stringent than for creating models with high predictive accuracy.
Pathfinder: open source software for analyzing spatial navigation search strategies
Authors: Cooke Matthew B. , O’Leary Timothy P. , Harris Phelan , Brown Richard E. , Snyder Jason S. 
Published: July 2019

AbstractSpatial navigation is a universal behavior that varies depending on goals, experience and available sensory stimuli. Spatial navigational tasks are routinely used to study learning, memory and goal-directed behavior, in both animals and humans. One popular paradigm for testing spatial memory is the Morris water maze, where subjects learn the location of a hidden platform that offers escape from a pool of water. Researchers typically express learning as a function of the latency to escape, though this reveals little about the underlying navigational strategies. Recently, a number of studies have begun to classify water maze search strategies in order to clarify the precise spatial and mnemonic functions of different brain regions, and to identify which aspects of spatial memory are disrupted in disease models. However, despite their usefulness, strategy analyses have not been widely adopted due to the lack of software to automate analyses. To address this need we developed Pathfinder, an open source application for analyzing spatial navigation behaviors. In a representative dataset, we show that Pathfinder effectively characterizes the development of highly-specific spatial search strategies as male and female mice learn a standard spatial water maze. Pathfinder can read data files from commercially- and freely-available software packages, is optimized for classifying search strategies in water maze paradigms, but can also be used to analyze 2D navigation by other species, and in other tasks, as long as timestamped xy coordinates are available. Pathfinder is simple to use, can automatically determine pool and platform geometry, generates heat maps, analyzes navigation with respect to multiple goal locations, and can be updated to accommodate future developments in spatial behavioral analyses. Given these features, Pathfinder may be a useful tool for studying how navigational strategies are regulated by the environment, depend on specific neural circuits, and are altered by pathology.
Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching
Authors: Wouters Jasper , Kalender-Atak Zeynep , Minnoye Liesbeth , Spanier Katina I. , De Waegeneer Maxime , González-Blas Carmen Bravo , Mauduit David , Davie Kristofer , Hulselmans Gert , Najem Ahmad , Dewaele Michael , Rambow Florian , Makhzami Samira , Christiaens Valerie , Ceyssens Frederik , Ghanem Ghanem , Marine Jean-Christophe , Poovathingal Suresh , Aerts Stein 
Published: July 2019

AbstractMelanoma is notorious for its cellular heterogeneity, which is at least partly due to its ability to transition between alternate cell states. Similarly to EMT, melanoma cells with a melanocytic phenotype can switch to a mesenchymal-like phenotype. However, scattered emerging evidence indicates that additional, intermediate state(s) may exist. In order to search for such new melanoma states and decipher their underlying gene regulatory network (GRN), we extensively studied ten patient-derived melanoma cultures by single-cell RNA-seq of >39,000 cells. Although each culture exhibited a unique transcriptome, we identified shared gene regulatory networks that underlie the extreme melanocytic and mesenchymal cell states, as well as one (stable) intermediate state. The intermediate state was corroborated by a distinct open chromatin landscape and governed by the transcription factors EGR3, NFATC2, and RXRG. Single-cell migration assays established that this “transition” state exhibits an intermediate migratory phenotype. Through a dense time-series sampling of single cells and dynamic GRN inference, we unraveled the sequential and recurrent arrangement of transcriptional programs at play during phenotype switching that ultimately lead to the mesenchymal cell state. We provide the scRNA-Seq data with 39,263 melanoma cells on our SCope platform and the ATAC-seq data on a UCSC hub to jointly serve as a resource for the melanoma field. Together, this exhaustive analysis of melanoma cell state diversity indicates that additional states exists between the two extreme melanocytic and mesenchymal-like states. The GRN we identified may serve as a new putative target to prevent the switch to mesenchymal cell state and thereby, acquisition of metastatic and drug resistant potential.
Single-cell in vivo imaging reveals light-initiated circadian oscillators in zebrafish
Authors: Wang Haifang , Yang Zeyong , Li Xingxing , Huang Dengfeng , Yu Shuguang , He Jie , Li Yuanhai , Yan Jun 
Published: July 2019

AbstractCircadian clock is a cell-autonomous time-keeping mechanism established gradually during embryonic development. Here we generated a transgenic zebrafish line carrying a destabilized fluorescent protein driven by the promoter of a core clock gene, nr1d1, to report in vivo circadian rhythm at the single-cell level. By time-lapse imaging of this fish line, we observed the sequential initiation of the reporter expression starting at photoreceptors in pineal gland then spreading to cells in other brain regions. Even within pineal gland, we found heterogeneous onset of nr1d1 expression in which each cell undergoes circadian oscillation superimposed over cell-type specific developmental trajectory. Furthermore, we found that single-cell expression of nr1d1 showed synchronous circadian oscillation under light-dark cycle. Remarkably, single-cell oscillations were lost in animals raised under constant darkness while developmental trend still persists. It suggests that light exposure in early clock development initializes cellular clocks rather than synchronizes existing individual oscillators as previously believed.
Data-driven integration of hippocampal CA1 synapse physiology in silico
Authors: Ecker András , Romani Armando , Sáray Sára , Káli Szabolcs , Migliore Michele , Mercer Audrey , Markram Henry , Muller Eilif , Ramaswamy Srikanth 
Published: July 2019

AbstractThe anatomy and physiology of synaptic connections in rodent hippocampal CA1 have been exhaustively characterized in recent decades. Yet, the resulting knowledge remains disparate and difficult to reconcile. Here, we present a data-driven approach to integrate the current state-of-the-art knowledge on the synaptic anatomy and physiology of rodent hippocampal CA1, including axo-dendritic innervation patterns, number of synapses per connection, quantal conductances, neurotransmitter release probability, and short-term plasticity into a single coherent resource. First, we undertook an extensive literature review of paired-recordings of hippocampal neurons and compiled experimental data on their synaptic anatomy and physiology. The data collected in this manner is sparse and inhomogeneous due to the diversity of experimental techniques used by different labs, which necessitates the need for an integrative framework to unify these data. To this end, we extended a previously developed workflow for the neocortex to constrain a unifying in silico reconstruction of the synaptic physiology of CA1 connections. Our work identifies gaps in the existing knowledge and provides a complementary resource towards a more complete quantification of synaptic anatomy and physiology in the rodent hippocampal CA1 region.
A flexible resource investment problem based on project splitting for aircraft moving assembly line
Authors: Ren Yifei , Lu Zhiqiang 
Published: July 2019

Purpose
In response to the station design and flexible resources allocation of the aircraft moving assembly line, a new problem named flexible resource investment problem based on project splitting (FRIP_PS), which minimizes total cost of resources with a given deadline are proposed in this paper.

Design/methodology/approach
First, a corresponding mathematical model considering project splitting is constructed, which needs to be simultaneously determined together with job scheduling to acquire the optimized project scheduling scheme and resource configurations. Then, an integrated nested optimization algorithm including project splitting policy and job scheduling policy is designed in this paper. In the first stage of the algorithm, a heuristic algorithm designed to get the project splitting scheme and then in the second stage a genetic algorithm with local prospective scheduling strategy is adopted to solve the flexible resource investment problem.

Findings
The heuristic algorithm of project splitting gets better project splitting results through the job shift selection strategy and meanwhile guides the algorithm of the second stage. Furthermore, the genetic algorithm solves resources allocation and job schedule through evaluation rules which can effectively solve the delayed execution of jobs because of improper allocation of flexible resources.

Originality/value
This paper represents a new extension of the resource investment problem based on aircraft moving assembly line. An effective integrated nested optimization algorithm is proposed to specify station splitting scheme, job scheduling scheme and resources allocation in the assembly lines, which is significant for practical engineering applications.
Factors affecting environmental citizenship behaviour
Authors: Chua Kean Boon , Quoquab Farzana , Mohammad Jihad 
Published: July 2019

Purpose
The purpose of this paper is to examine the factors that affect paddy farmers’ environmental citizenship behaviour (ECB) in the context of agrochemical purchase. To achieve this objective, a theoretical framework has been developed based on value-belief-norm (VBN) theory.

Design/methodology/approach
Data were obtained from 251 farmers using a survey method. Partial lease square structural equation modelling (PLS-SEM) was used to examine the hypothetical model.

Findings
The results of PLS analysis confirm the direct and mediating effect of the causal sequences of the variables in the VBN model.

Originality/value
Given the limited number of studies in a non-western context, this study examines and confirms the applicability of the VBN theory in predicting ECB in a Malaysian context.
A modified method for solving non-linear time and space fractional partial differential equations
Authors: Saeed Umer , Umair Muhammad 
Published: July 2019

Purpose
The purpose of the paper is to extend the differential quadrature method (DQM) for solving time and space fractional non-linear partial differential equations on a semi-infinite domain.

Design/methodology/approach
The proposed method is the combination of the Legendre polynomials and differential quadrature method. The authors derived and constructed the new operational matrices for the fractional derivatives, which are used for the solutions of non-linear time and space fractional partial differential equations.

Findings
The fractional derivative of Lagrange polynomial is a big hurdle in classical DQM. To overcome this problem, the authors represent the Lagrange polynomial in terms of shifted Legendre polynomial. They construct a transformation matrix which transforms the Lagrange polynomial into shifted Legendre polynomial of arbitrary order. Then, they obtain the new weighting coefficients matrices for space fractional derivatives by shifted Legendre polynomials and use these in conversion of a non-linear fractional partial differential equation into a system of fractional ordinary differential equations. Convergence analysis for the proposed method is also discussed.

Originality/value
Many engineers can use the presented method for solving their time and space fractional non-linear partial differential equation models. To the best of the authors’ knowledge, the differential quadrature method has never been extended or implemented for non-linear time and space fractional partial differential equations.
Identifying the preference of buyers of single-family homes in Dammam, Saudi Arabia
Authors: Bin Mohanna Ameen , Alqahtany Ali 
Published: July 2019

PurposeThe purpose of this study is to identify the preferred characteristics of buyers of single-family homes in Saudi Arabia with an emphasis on the city of Dammam.Design/methodology/approachData were collected using face-to-face structured interviews conducted from November 2016 to May 2017 with 177 owners of single-family homes that were purchased between 2010 and the first quarter of 2017.FindingsThe findings indicate that homes can be divided into three types: villas, detached duplexes and semi-detached duplexes. Also, more than three-quarters of the respondents purchased their homes through mortgages from either lenders or the government. It seems we find that the advantages of the detached duplex, particularly its privacy level, over other types of single-family homes induce homebuyers to choose this home type.Originality/valueIn this study, the authors analyze housing preferences among various segments of the Saudi society, in the city of Dammam, to understand the housing supply in Saudi Arabia. Only a few studies have investigated the preferences of homebuyers in Saudi Arabia. Below the authors provide a literature review, discuss data and methods and results, as well as provide concluding remarks.
Inequality, concentration of wealth and ownership structure of Islamic banks
Authors: Farooq Mohammad Omar , Meer Fouad , Iqbal Basit 
Published: July 2019

PurposeAn important Islamic imperative is prevention of concentration of wealth among a few so that wealth circulates widely to enhance shared prosperity. In contemporary economic discourse, inequality and concentration of wealth have emerged as among key causes of instability and crisis. Unfortunately, although Islamic finance has emerged as a Shari’ah-compliant industry, it does not seem to be connected with the Islamic concern about inequality and concentration of wealth. This paper aims to explore the issues of inequality and concentration of wealth in the context of Islamic finance.Design/methodology/approachThis paper addresses a number of queries: Are Islamic banks, as the dominant component of the industry, helping to improve inequality and concentration of wealth and thus offer a better framework to deal with instability and crisis? Is the ownership structure of Islamic banks conducive to meeting the Islamic imperative regarding inequality and concentration of wealth? Using secondary data, this research illuminates the pertinent issues in light of the experience of Bahrain as one of the hubs of Islamic banking and finance.FindingsThe paper finds that the ownership pattern of Islamic banks in Bahrain lends credence to the entrenched, not-so-unexpected concentration of wealth.Research limitations/implicationsThis study is based on data of one country. Further studies on other countries will help illuminate the relevant patterns and issues.Practical implicationsInequality and concentration of wealth are among central economic issues in contemporary economic discourse. Because of the significant impact of such inequality and concentration, societies need to be more aware of these impacts and devise ways to address it.Social implicationsInequality and concentration of wealth have fundamental social implications, as the issues of poverty, deprivation, exploitation, etc. are inseparable from concentration of wealth (accompanied by concentration of power), and widening wealth gap can cause or induce major socio-political upheaval.Originality/valueAlthough inequality and concentration of wealth are robust fields of inquiry, this might be the first work addressing the issue of concentration of wealth in the context of Islamic finance in general and Islamic banking in particular.
Motivating factors in a teacher’s research and developmental activities and their impact on effective quality teaching in higher education institutions
Authors: Chakraborty Debarun , Biswas Wendrila 
Published: July 2019

PurposeResearch and development pursuits have always been an integral part of a teacher’s professional development. Today, the higher educational institutes (HEIs) are chiefly prioritizing and providing a sustained support toward research-based and research-oriented learning. But as revealed by the broad outlines of the entire scenario, a fall in research productivity and developmental attempts is witnessed among the faculties of higher educational establishments. To put it succinctly, the motivating aspects that reinforce such activities are not adequately taken care of and have thwarted their progression. The purpose of this paper is to delve deep and explore the factors that inspire teachers toward an enriched research and learning, which equally gets reflected in their teaching practices.Design/methodology/approachThis is a descriptive research with a cross-sectional survey on faculties from different HEIs of West Bengal. A questionnaire has been designed with a five-point Likert scale to draw the primary data. Convenience sampling technique has been utilized. Exploratory factor analysis and confirmatory factor analysis have been performed with structural equation modeling on the hypothesized research model through AMOS.FindingsThe major findings of the research have revealed that improved research and development activities of faculties had an immense impact on their teaching quality. The level and accessibility of infrastructure posits a strong influence in augmenting a teacher’s research and developmental endeavors. Working climate influences teachers’ research activities as well their teaching adroitness.Research limitations/implicationsResults may vary when an extensive study is conducted on teachers of HEIs of two or more states or of the country as a whole. Suppression of the real underlying facts by few respondents may affect the result to a small extent.Practical implicationsWhen faculties orient themselves toward research intensive learning and teaching, the students actively get involved in a platform of greater interaction. It elevates their persistence level, intellectual curiosity, critical thinking and cognitive skills. Research-based teaching is also instrumental in honing their analytical skills, promoting creativity.Originality/valueThe study identified a vital role of the higher education institutes in motivating the faculties toward research-based teaching. There is a dearth of empirical research in identifying the factors that enrich the learning patterns and research activities of the teachers. Thus, it can prove to be a constructive study if implemented.
Dual perspectives on learning analytics in higher education
Authors: Parrish Andrea Harkins , Richman Laila J. 
Published: July 2019

Purpose
In higher education, the authors serve multiple stakeholders with varying perspectives on the institution’s learning analytic system. The purpose of this paper is to highlight dual perspectives within the learning analytics (LA) system in one institution: that of an administrator responsible for college-wide improvement, and a faculty member responsible for programmatic improvement.

Design/methodology/approach
This manuscript provides a critical perspective with dual sets of experiences and viewpoints. This approach allows close examination of each perspective within the context of the existing literature, as the authors examine transitions in the use of LA.

Findings
These viewpoints offer insight into the interpretation of LA through the lens of various roles. In examining these viewpoints, the authors offer three actionable steps for other institutions who seek to implement.

Practical implications
These actionable steps offer a starting point for other institutions to engage in conversations related to the adoption of LA for continuous improvement across levels and roles. Relevant implications for various parties are discussed, with an emphasis on how administrators within the university system may support faculty to incorporate LA as part of their scholarly and teaching responsibilities.

Originality/value
Few studies have examined the perspectives of multiple stakeholders within an institution. Here the authors have presented these dual perspectives in order to further the dialogue between university administration and faculty as analytic systems become more widespread. Through this dialogue, the authors see increased opportunities for all stakeholders to better understand their role in LA.