bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence determinants of human gene regulatory elements
Authors: Sahu Biswajyoti , Hartonen Tuomo , Pihlajamaa Päivi , Wei Bei , Dave Kashyap , Zhu Fangjie , Kaasinen Eevi , Lidschreiber Katja , Lidschreiber Michael , Daub Carsten O. , Cramer Patrick , Kivioja Teemu , Taipale Jussi 
Published: March 2021

AbstractDNA determines where and when genes are expressed, but the full set of sequence determinants that control gene expression is not known. To obtain a global and unbiased view of the relative importance of different sequence determinants in gene expression, we measured transcriptional activity of DNA sequences that are in aggregate ∼100 times longer than the human genome in three different cell types. We show that enhancers can be classified to three main types: classical enhancers1, closed chromatin enhancers and chromatin-dependent enhancers, which act via different mechanisms and differ in motif content. Transcription factors (TFs) act generally in an additive manner with weak grammar, with classical enhancers increasing expression from promoters by a mechanism that does not involve specific TF-TF interactions. Few TFs are strongly active in a cell, with most activities similar between cell types. Chromatin-dependent enhancers are enriched in forkhead motifs, whereas classical enhancers contain motifs for TFs with strong transactivator domains such as ETS and bZIP; these motifs are also found at transcription start site (TSS)-proximal positions. However, some TFs, such as NRF1 only activate transcription when placed close to the TSS, and others such as YY1 display positional preference with respect to the TSS. TFs can thus be classified into four non-exclusive subtypes based on their transcriptional activity: chromatin opening, enhancing, promoting and TSS determining factors – consistent with the view that the binding motif is the only atomic unit of gene expression.
Stonewall prevents expression of testis-enriched genes and binds to insulator elements inD. melanogaster
Authors: Zinshteyn Daniel , Barbash Daniel A 
Published: March 2021

AbstractGermline stem cells (GSCs) are the progenitor cells of the germline for the lifetime of an animal. InDrosophila, these cells reside in a cellular niche that is required for both their maintenance (self-renewal) and differentiation (asymmetric division resulting in a daughter cell that differs from the GSC). The stem cell-daughter cell transition is tightly regulated by a number of processes, including an array of proteins required for genome stability. The germline stem-cell maintenance factor Stonewall (Stwl) associates with heterochromatin, but its molecular function is poorly understood. We performed RNA-Seq onstwlmutant ovaries and found significant derepression of many transposon families but not heterochromatic genes. We also discovered that testis-enriched genes, including the differentiation factorbgcnand a large testis-specific cluster on chromosome 2, are upregulated or ectopically expressed instwlmutant ovaries. Surprisingly, we also found that RNAi knockdown ofstwlin somatic S2 cells results in ectopic expression of these genes.Using parallel ChIP-Seq and RNA-Seq experiments in S2 cells, we discovered that Stwl binds upstream of transcription start sites and localizes to heterochromatic sequences. We also find that Stwl is enriched at repetitive sequences associated with telomeres. Finally, we identify Stwl binding motifs that are shared with known insulator binding proteins. We propose that Stwl affects gene regulation by binding insulators and establishing chromatin boundaries.
Fronto-medial theta coordinates posterior maintenance of working memory content
Authors: Ratcliffe Oliver , Shapiro Kimron , Staresina Bernhard P. 
Published: March 2021

AbstractHow does the human brain manage multiple bits of information to guide goal-directed behaviour? Successful working memory (WM) functioning has consistently been linked to oscillatory power in the theta frequency band (4-8 Hz) over fronto-medial cortex (fronto-medial theta, FMT). Specifically, FMT is thought to reflect the mechanism of an executive sub-system that coordinates maintenance of memory contents in posterior regions. However, direct evidence for the role of FMT in controlling specific WM content is lacking. Here we collected high-density Electroencephalography (EEG) data whilst participants engaged in load-varying WM tasks and then used multivariate decoding methods to examine WM content during the maintenance period. Higher WM load elicited a focal increase in FMT. Importantly, decoding of WM content was driven by posterior/parietal sites, which in turn showed load-induced functional theta coupling with fronto-medial cortex. Finally, we observed a significant slowing of FMT frequency with increasing WM load, consistent with the hypothesised broadening of a theta ‘duty cycle’ to accommodate additional WM items. Together these findings demonstrate that frontal theta orchestrates posterior maintenance of WM content. Moreover, the observed frequency slowing elucidates the function of FMT oscillations by specifically supporting phase-coding accounts of WM.Significance StatementHow does the brain juggle the maintenance of multiple items in working memory (WM)? Here we show that increased WM demands increase theta power (4-8 Hz) in fronto-medial cortex. Interestingly, using a machine learning approach, we found that the content held in WM could be read out not from frontal, but from posterior areas. These areas were in turn functionally coupled with fronto-medial cortex, consistent with the idea that frontal cortex orchestrates WM representations in posterior regions. Finally, we observed that holding an additional item in WM leads to significant slowing of the frontal theta rhythm, supporting computational models that postulate longer ‘duty cycles’ to accommodate additional WM demands.
Ultrastructural plasma membrane asymmetries in tension and curvature promote yeast cell fusion
Authors: Muriel Olivia , Michon Laetitia , Kukulski Wanda , Martin Sophie G 
Published: March 2021

AbstractCell-cell fusion is central to the process of fertilization for sexual reproduction. This necessitates the remodeling of peri-cellular matrix or cell wall material and the merging of plasma membranes. In walled fission yeastS. pombe, the fusion of P and M cells during sexual reproduction relies on the fusion focus, an actin structure that concentrates glucanase-containing secretory vesicles for local cell wall digestion necessary for membrane fusion. Here, we present a correlative light and electron microscopy (CLEM) quantitative study of a large dataset of 3D tomograms of the fusion site, which revealed the ultrastructure of the fusion focus as an actin-containing, vesicle-dense structure excluding other organelles. Unexpectedly, the data revealed asymmetries between the two gametes: M-cells exhibit a taut and convex plasma membrane that progressively protrudes into P-cells, which exhibit a more slack, wavy plasma membrane. These asymmetries are relaxed upon plasma membrane fusion, with observations of ramified pores that may result from multiple initiations or inhomogeneous expansion. We show that P-cells have a higher exo-to endocytosis ratio than M-cells, and that local reduction in exocytosis abrogates membrane waviness and compromises cell fusion significantly more in P-than M-cells. Reciprocally, reduction of turgor pressure specifically in M-cells prevents their protrusions into P-cells and delays cell fusion. Thus, asymmetric membrane conformations, which result from differential turgor pressure and exocytosis/endocytosis ratios between mating types, favor cell-cell fusion.
The mechanosensitive Ca2+-permeable ion channel PIEZO1 promotes satellite cell function in skeletal muscle regeneration
Authors: Hirano Kotaro , Tsuchiya Masaki , Takabayashi Seiji , Nagao Kohjiro , Kitajima Yasuo , Ono Yusuke , Nonomura Keiko , Mori Yasuo , Umeda Masato , Hara Yuji 
Published: March 2021

AbstractMuscle satellite cells (MuSCs), myogenic stem cells in skeletal muscle, play an essential role in muscle regeneration. During the regeneration process, cues from the surrounding microenvironment are critical for the proliferation and function of MuSCs. However, the mechanism by which mechanical stimuli from the MuSCs niche is converted into biochemical signals to promote muscle regeneration is yet to be determined. Here, we show that PIEZO1, a calcium ion (Ca2+)-permeable cation channel that is activated by membrane tension, mediates the spontaneous Ca2+influx to controls the regenerative function of MuSCs. Our genetically engineering approach in mice revealed that PIEZO1 is functionally expressed in MuSCs, and the conditional deletion ofPiezo1in MuSCs delays myofiber regeneration after myofiber injury, which is at least in part due to the growth defect in MuSCs via the reduction in RhoA-mediated actomyosin formation. Thus, we provide the first evidence in MuSCs that PIEZO1, abona fidemechanosensitive ion channel, promotes the proliferative and regenerative function during skeletal muscle regeneration.
Transcription Factor NF-κB Unravels Nucleosomes
Authors: Stormberg Tommy , Filliaux Shaun , Baughman Hannah E. R. , Komives Elizabeth A. , Lyubchenko Yuri L. 
Published: March 2021

AbstractNF-κB is a transcription factor responsible for activating hundreds of genes in mammalian organisms. To accomplish its function, NF-κB must interact with DNA occupied by nucleosomes, but how this interaction occurs is unclear. Here we used Atomic Force Microscopy to characterize complexes of NF-κB with nucleosomes assembled on different DNA templates. The assembly of NF-κB-nucleosome complexes leads to a substantial decrease of DNA wrapping efficiency. Mapping of the nucleosomes did not reveal displacement of under-wrapped nucleosomes from their original position, suggesting that unravelling involves dissociation of one or both flanks of the nucleosomes. We discovered two binding modes of NF-κB associated with nucleosome unraveling - NF-κB bound to the nucleosome core and to the DNA flanks and propose models explaining the interaction of NF-κB with the nucleosome. We speculate that NF-κB can function as a pioneer factor enhancing its ability to facilitate rapid transcriptional response to cell stress.
Dynamic movement primitives based cloud robotic skill learning for point and non-point obstacle avoidance
Authors: Lu Zhenyu , Wang Ning 
Published: March 2021

Purpose
Dynamic movement primitives (DMPs) is a general robotic skill learning from demonstration method, but it is usually used for single robotic manipulation. For cloud-based robotic skill learning, the authors consider trajectories/skills changed by the environment, rebuild the DMPs model and propose a new DMPs-based skill learning framework removing the influence of the changing environment.

Design/methodology/approach
The authors proposed methods for two obstacle avoidance scenes: point obstacle and non-point obstacle. For the case with point obstacles, an accelerating term is added to the original DMPs function. The unknown parameters in this term are estimated by interactive identification and fitting step of the forcing function. Then a pure skill despising the influence of obstacles is achieved. Using identified parameters, the skill can be applied to new tasks with obstacles. For the non-point obstacle case, a space matching method is proposed by building a matching function from the universal space without obstacle to the space condensed by obstacles. Then the original trajectory will change along with transformation of the space to get a general trajectory for the new environment.

Findings
The proposed two methods are certified by two experiments, one of which is taken based on Omni joystick to record operator’s manipulation motions. Results show that the learned skills allow robots to execute tasks such as autonomous assembling in a new environment.

Originality/value
This is a new innovation for DMPs-based cloud robotic skill learning from multi-scene tasks and generalizing new skills following the changes of the environment.
Radiation heat transfer within a solar system considering nanofluid flow inside the absorber tube
Authors: Ebrahimpour Zahra , Sheikholeslami Mohsen , Farshad Seyyed Ali , Shafee Ahmad 
Published: March 2021

Purpose
This paper aims to model solar unit equipped with mirrors with numerical simulation. To augment the efficiency of system, absorber pipe was equipped with fins and nanomaterial was used as carrier fluid. Existence of secondary reflector results in better optical efficiency.

Design/methodology/approach
Finite volume approach is used for modeling which is done in two steps. The first one is done to achieve the heat flux distribution and second step to model turbulent flow inside the pipe. Verification has been presented for calculation of important functions (f and Nu). Outputs reveal the impacts of fin height (HF), number of fin (NF), inlet temperature (Tin) and velocity on irreversibility, thermal treatment.

Findings
Surface temperature decreases by 0.498, 0.07 and 0.017% with intensify of Re, HF and NF, respectively, when other factors were minimum. With augment of Tin, wall temperature increases about 9.87%. Given NF = 8, HF = 3 mmm, growth of Re makes Darcy factor to decrease about 28.28%, but it augments the Nu by 2.63%. Nu augments with rise of NF and HF about 2.63 and 7.66%. Irreversibility reduces about 29.5 and 11.65% with augment of NF and HF, respectively.

Originality/value
Numerical simulations for solar unit equipped with mirrors were reported in this modeling. To augment the efficiency of system, absorber pipe was equipped with fins and nanomaterial was used as carrier fluid. Existence of secondary reflector results in better optical efficiency. Finite volume approach is used for modeling which is done in two steps. The first one is done to achieve the heat flux distribution and second step to model turbulent flow inside the pipe. Verification has been presented for calculation of important functions (f and Nu). Outputs reveal the impacts of fin height (HF), number of fin (NF), inlet temperature (Tin) and velocity on irreversibility, thermal treatment.
Mixed convective stagnation point flow of a hybrid nanofluid toward a vertical cylinder
Authors: Khashi'ie Najiyah Safwa , Arifin Norihan M. , Merkin John H. , Yahaya Rusya Iryanti , Pop Ioan 
Published: March 2021

PurposeThe purpose of this paper is to numerically analyze the stagnation point flow of Cu-Al2O3/water hybrid nanofluid with mixed convection past a flat plate and circular cylinder.Design/methodology/approachThe similarity equations that reduced from the boundary layer and energy equations are solved using the bvp4c solver. The duality of solutions is observed within the specific range of the control parameters, namely, mixed convection parameterλ, curvature parameterγand nanoparticles volumetric concentrationϕ1for alumina, while for copperϕ2. The stability analysis is also designed to justify the particular solutions’ stability. Additionally, the idea to obtain the solution for large value ofλandγis also presented in this paper.FindingsTwo solutions exist in opposing and assisting flows up to a critical valueλcwhereλclies in the opposing region. An upsurge of the curvature parameter tends to extend the critical value (delay the separation process), whilst increase the heat transfer performance of the working fluid. Meanwhile, the application of hybrid Cu-Al2O3/water nanofluid also can decelerate the separation of laminar boundary layer flow and produce higher heat transfer rate than the Cu–water nanofluid and pure water.Originality/valueThe results are new and original. This study benefits to the other researchers, specifically in the observation of the fluid flow characteristics and heat transfer rate of the hybrid nanofluid. Also, this paper features with the mathematical formulation for the solution with large values ofλandγ.
Listening to your employees: analyzing opinions from online reviews of hotel companies
Authors: Shi Xiaolin (Crystal) , Chen Zixi 
Published: March 2021

Purpose
This study aims to examine the factors influencing hotel employee satisfaction and explores the different sentiments expressed in these factors in online reviews by hotel type (premium versus economy) and employment status (current versus former).

Design/methodology/approach
A total of 78,535 online reviews by employees of 29 hotel companies for the period of 2011-2019 were scraped from Indeed.com. Structural topic modeling (STM) and sentiment analysis were used to extract topics influencing employee satisfaction and examine differences in sentiments in each topic.

Findings
Results showed that employees of premium hotels expressed more positive sentiments in their reviews than employees of economy hotels. The STM results demonstrated that 20 topics influenced employee satisfaction, the top three of which were workplace bullying and dirty work (18.01%), organizational support (16.29%) and career advancement (8.88%). The results indicated that the sentiments in each topic differed by employment status and hotel type.

Practical implications
Rather than relying on survey data to explore employee satisfaction, hotel industry practitioners can analyze employees’ online reviews to design action plans.

Originality/value
This study is one of only a few to use online reviews from an employment search engine to explore hotel employee satisfaction. This study found that workplace bullying and dirty work heavily influenced employee satisfaction. Moreover, analysis of the comments from previous employees identified antecedents of employees’ actual turnover behavior but not their turnover intention.
First-generation Ethiopian immigrants and beliefs about physical activity
Authors: Alemu Brook T. , Carlisle Kristy L. , Abate Sara N. 
Published: March 2021

Purpose
While several studies have examined the attitudes, perceptions and beliefs of physical activity in different immigrant groups, little is known in this area among the first-generation Ethiopian immigrant population who lives in the USA. The purpose of this paper is to explore the behavioral, normative and control beliefs of physical activity among first-generation Ethiopian immigrants living in the DC-Metro area.

Design/methodology/approach
The study used semi-structured interviews, focus group discussions and unobtrusive observation. Three structural themes and six textural themes were identified from the three forms of data collections. Qualitative data analysis including topics, categories and pattern analysis were conducted using phenomenological techniques.

Findings
Findings highlighted similarities to the theory of planned behavior with regard to attitudes, subjective norms and perceived behavioral control. Consistent with the literature, several salient behavioral determinants of physical activity that could affect participants’ decision-making were identified in the current pilot study. Increased longevity, mental well-being, improved sleep and improved metabolism were listed as the most common benefits of physical activity. Lack of time, family responsibility, neighborhood safety, location of the gym, lack of awareness and social and economic stressors were the major barriers to engage in physical activity. Implications for service providers and future research are discussed.

Practical implications
This study supported the need for future research into the social aspects of physical activity, as well as barriers to physical activity, including time, family responsibility, culture, income and neighborhood safety.

Originality/value
To the best of the authors’ knowledge, this is the first study exploring the behavioral, normative and control beliefs of physical activity among first-generation Ethiopian immigrants. To understand the beliefs, desires and barriers to physical activity in this population subgroup, the authors examined the behavioral, normative and control beliefs of regular moderate-intensity physical activity using the theory of planned behavior as a conceptual framework. As health education researchers, it is their responsibility to develop theory-driven policies and interventions to promote a healthy lifestyle among these underserved populations.
Spatial decision support for social hybrid organizations: siting new social supermarkets in Austria
Authors: Lienbacher Eva , Koschinsky Julia , Holweg Christina , Vallaster Christine 
Published: March 2021

PurposeIncreasingly complex societal challenges call for new, innovative solutions that social hybrid business models can provide. Social supermarkets (SSMs) are one example offering access to affordable food to people living in poverty while reducing food waste of nearby retailers. Finding the “right” location is an essential part of this retail marketing strategy. However, limited research has attempted to investigate the specific conditions of locational planning for hybrid and nonprofit retail organizations. This paper illustrates the case of Austria where SSMs are well established.Design/methodology/approachA GIS-based white space analysis was carried out to identify potential neighborhoods or rural areas for new social supermarkets with sufficient nearby demand, supply and no existing SSMs. The empirical parameters for this spatial analysis can be transferred to European countries with similar ecosystems. The authors collected a unique data set of 79 (2014) and 88 SSMs (2019) and 4,665 (2014) and 4,211 (2019) food retailers as (potential) suppliers to SSMs. To determine demand, the authors relied on small-scale integrated wage and income tax data and unemployment rates (2011) from Statistics Austria.FindingsOverall, Austria has very good spatial access to grocery stores, including to SSMs. SSM access increased especially in the capital of Vienna between 2014 and 2019. The GIS-based white space analysis identified several other regions where residents have a high demand for affordable food with sufficient potential suppliers of surplus food but no SSM yet. Neighborhood-level findings are released as part of a publicly accessible spatial decision support system.Originality/valueThe methodology allowed a specific definition of the key areas of relevance by matching the demand for SSMs, calculated as the number of people with low incomes in the respective regions in Austria, with the supply of SSMs, calculated as the amount of potential food loss prevention by nearby retail stores. These parameters have proven to help in identifying the white spaces and therefore can be used in Austria and other European countries with similar ecosystems.