bluuebunny/crossref_metadata_2025_split huggingface dataset:
A NOVEL UNBIASED SEED-BASED RNAi SCREEN IDENTIFIES SMALL RNAs THAT INHIBIT ANDROGEN SIGNALING AND PROSTATE CANCER CELL GROWTH
Authors: Corbin Joshua M , Georgescu Constantin , Wang Lin , Wren Jonathan D , Bieniasz Magdalena , Xu Chao , Asch Adam S , Ruiz-Echevarría Maria J 
Published: September 2022

ABSTRACTBlocking androgen receptor signaling is the mainstay of therapy for advanced prostate cancer (PCa). However, acquired resistance to single agents targeting this pathway results in the development of lethal castration resistant PCa. Combination therapy approaches represent a promising strategy for the treatment of advanced disease. Here we explore a therapeutic strategy for PCa based on the ability of sh/siRNAs to function essentially as miRNAs and, via seed sequence complementarity, induce RNA interference of numerous targets simultaneously. We developed a library that contained shRNAs with all possible seed sequence combinations to identify those ones that most potently reduce cell growth and viability when expressed in PCa cells. Validation of some of these RNAi sequences indicated that the toxic effect is associated with seed sequence complementarity to the 3’-UTR of AR coregulatory and essential genes. In fact, expression of siRNAs containing the identified toxic seed sequences led to global inhibition of AR-mediated gene expression and reduced expression of cell cycle genes. When tested in mice, the toxic shRNAs also inhibited castration resistant PCa and exhibited therapeutic efficacy in pre-established tumors. This multi-targeted RNAi approach may be a promising therapeutic strategy for PCa.
Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing during epigenetic reprogramming in pollen
Authors: Ichino Lucia , Picard Colette L. , Yun Jaewon , Chotai Meera , Wang Shuya , Lin Evan Kai , Papareddy Ranjith K. , Xue Yan , Jacobsen Steven E. 
Published: September 2022

SUMMARYSilencing of transposable elements (TEs) drove the evolution of numerous redundant mechanisms of transcriptional regulation. Arabidopsis MBD5, MBD6, and SILENZIO act as TE repressors downstream of DNA methylation. Here we show via single-nucleus RNA-seq of developing male gametophytes that these repressors are critical for TE silencing in the pollen vegetative cell, which undergoes epigenetic reprogramming causing chromatin decompaction to support fertilization by sperm cells. Instead, other silencing mutants (met1, ddm1, mom1, morc) show loss of silencing in all pollen nucleus types and somatic cells. We found that TEs repressed by MBD5/6 gain accessibility in wild-type vegetative nuclei despite remaining silent, suggesting that loss of DNA compaction makes them sensitive to loss of MBD5/6. Consistently, crossing mbd5/6 to histone 1 mutants, which have decondensed chromatin in leaves, reveals derepression of MBD5/6-dependent TEs in leaves. MBD5/6 and SILENZIO thus act as a silencing system especially important when chromatin compaction is compromised.
Structural basis of Norrin recognition by Lgr4/5/6
Authors: Chang Tao-Hsin , Harlos Karl , Hsieh Fu-Lien , Jones E. Yvonne 
Published: September 2022

AbstractLgr4/5/6 have been identified as stem cell markers and canonical Wnt signalling enhancers via complexing with R-spondin and Rnf43/Znrf3. Lgr4/5/6 have been reported to interact with Norrin, a cystine-knot growth factor that activates Wnt signalling via binding to Frizzled4 cysteine-rich domain (Fz4CRD). Norrin–Fz4 signalling axis regulates central nervous system vascularization. However, the molecular basis of Norrin and Lgr4/5/6 recognition remains lacking. Here, we present the structure of Norrin in complex with an ectodomain variant of Lgr4 (Norrin–Lgr4ECD), revealing a 2:2 stoichiometry. Our analyses show that residues of Lgr4/5/6ECD for Norrin binding are highly conserved. Structural comparisons of Norrin–Lgr4ECD with Rspo1– Lgr4ECD and Norrin–Fz4CRD complexes reveal that Norrin binding site on Lgr4 overlaps with Rspo1 binding site on Lgr4 and Fz4 binding site on Norrin overlaps with Lgr4 binding site on Norrin. The present work opens new avenues to elucidate the function of Norrin–Lgr4/5/6 signalling axis.
Stress vesicles are induced by acute mechanical force and precede the commitment of epidermal stem cells to terminal differentiation
Authors: Huang Sixia , Kuri Paola , Zou Jonathan , Blanco Adriana , Marshall Maxwell , Rice Gabriella , Prouty Stephen , Dentchev Tzvete , Doepner Miriam , Boerckel Joel D. , Capell Brian C. , Ridky Todd W. , Rompolas Panteleimon 
Published: September 2022

AbstractThe skin has a pronounced ability to adapt to physical changes in the environment by exhibiting plasticity at the cellular level. Transient mechanical deformations applied to the skin are accommodated without permanent changes to tissue structure. However, sustained physical stress induces long-lasting alterations in the skin, which are mediated by shifts in the fates of epidermal stem cells. To investigate this phenomenon, we implemented two-photon intravital imaging to capture the responses of epidermal cells when an acute mechanical force is applied to the live skin. We show that mechanical stress induces the formation of intracellular vesicles in epidermal stem cells, which are filled with extracellular fluid and gradually enlarge, causing the deformation of the cell nucleus. By lineage tracing analysis we demonstrate that the degree of nuclear deformation is linked to cell fate. Utilizing a fluorescentin vivoreporter, to capture intracellular calcium dynamics, we show that mechanical force induces a sustained increase in intracellular calcium within basal epidermal stem cells. Conditional deletion of Piezo1, a mechanosensitive ion channel, alters intracellular calcium dynamics and increases the number of stress vesicles in epidermal stem cells. Using a human skin xenograft model, we show that stress vesicles are a conserved phenomenon in mammalian skin. This study uncovers stress vesicles as key manifestations of the mechanism that regulates the fate of epidermal stem cells under conditions of mechanical stress, in which Piezo1 and calcium dynamics are also involved.
Detyrosination enrichment on microtubule subsets is established by the interplay between a stochastically-acting enzyme and microtubule stability
Authors: Tang Qing , Sensale Sebastian , Bond Charles , Qiao Andy , Hugelier Siewert , Arab Arian , Arya Gaurav , Lakadamyali Melike 
Published: September 2022

AbstractMicrotubules in cells consist of functionally diverse subpopulations carrying distinct post-translational modifications (PTMs). Akin to the histone code, the tubulin code regulates a myriad of microtubule functions ranging from intracellular transport to chromosome segregation. Yet, how individual PTMs only occur on subsets of microtubules to contribute to microtubule specialization is not well understood. In particular, microtubule detyrosination, which is the removal of the C-terminal tyrosine on α-tubulin subunits, marks the stable population of microtubules and modifies how microtubules interact with other microtubule-associated proteins to regulate a wide range of cellular processes. Previously, we found that, in certain cell types, only a small subpopulation of microtubules is highly enriched with the detyrosination mark (∼30%) and that detyrosination spans most of the length of a microtubule, often adjacent to a completely tyrosinated microtubule. How the activity of a cytosolic detyrosinase, Vasohibin (VASH) leads to only a small subpopulation of highly detyrosinated microtubules is unclear. Here, using quantitative super-resolution microscopy, we visualized nascent microtubule detyrosination events in cells consisting of 1-3 detyrosinated α-tubulin subunits after Nocodazole washout. Microtubule detyrosination accumulates slowly and in a disperse pattern across the microtubule length. By visualizing single molecules of VASH in live cells, we found that VASH engages with microtubules stochastically on a short time scale suggesting limited removal of tyrosine per interaction, consistent with the super-resolution results. Combining these quantitative imaging results with simulations incorporating parameters from our experiments, we propose a stochastic model for cells to establish a subset of detyrosinated microtubules via a detyrosination-stabilization feedback mechanism.
in vivo RNA structural probing of guanine and uracil nucleotides in yeast
Authors: Xiao Kevin , Ghalei Homa , Khoshnevis Sohail 
Published: September 2022

AbstractRNAs have critical catalytic or regulatory functions in the cell and play significant roles in many steps of gene expression regulation. RNA structure can be essential for its cellular function. Therefore, methods to investigate the structure of RNA in vivo are of great importance for understanding the role of cellular RNAs. RNA structural probing is an indirect method to probe the three-dimensional structure of RNA by analyzing the reactivity of different nucleotides to chemical modifications. The chemical modifications can target either the RNA backbone or the Watson-Crick face of nucleotides. The selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) can probe the ribose sugar in all unpaired RNA nucleotides. In contrast, Dimethyl sulfate (DMS) alkylates adenine and cytosine and reports on base pairing context but is not reactive to guanine (G) or uracil (U). Recently, new compounds were used to modify Gs and Us in the plant model system Oryza sativa and in the prokaryotic organisms Bacillus subtilis and Echerichia coli, as well as human cells. To complement the scope of RNA structural probing by chemical modifications in the model organism yeast, we analyzed the effectiveness of guanine modification by a family of aldehyde derivatives, the glyoxal family, in Saccharomyces cerevisiae and Candida albicans. We also explored the effectiveness of uracil modification by carbodiimide N-cyclohexyl-N-(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate (CMCT) in vivo. We show that among the glyoxal family, phenylglyoxal (PGO) is the best guanine probe for structural probing in S. cerevisiae and C. albicans. We also demonstrate uracil modification by CMCT in S. cerevisiae in vivo. Further, we show that PGO treatment does not affect the processing of different RNA species in the cell and is not toxic for the cells under the conditions we have established for RNA structural probing. Our results provide the conditions for in vivo probing the reactivity of guanine and uracil in RNA structures in yeast and offer a valuable tool for studying RNA structure and function in two widely used yeast model systems.
In situtargeted mutagenesis of gut bacteria
Authors: Brödel Andreas K , Charpenay Loïc , Galtier Matthieu , Fuche Fabien J , Terrasse Rémi , Poquet Chloé , Arraou Marion , Prevot Gautier , Spadoni Dalila , Hessel Edith M , Fernandez-Rodriguez Jesus , Duportet Xavier , Bikard David 
Published: September 2022

AbstractMicrobiome research is revealing a growing number of bacterial genes that impact our health. While CRISPR-derived tools have shown great success in editing disease-driving genes in human cells, we currently lack the tools to achieve comparable success for bacterial targets. Here we engineer a phage-derived particle to deliver a base editor and modifyE. colicolonizing the mouse gut. This was achieved using a non-replicative DNA payload, preventing maintenance and dissemination of the payload, while allowing for an editing efficiency of up to 99.7% of the target bacterial population. The editing of a β-lactamase gene resulted in the stable maintenance of edited bacteria in the mouse gut at least 42 days after treatment. By enabling thein situmodification of bacteria directly in the gut, our approach offers a novel avenue to investigate the function of bacterial genes and provides an opportunity to develop novel microbiome-targeted therapies.
Single-particle tracking reveals heterogeneous PIEZO1 diffusion
Authors: Ly Alan T. , Freites J. Alfredo , Bertaccini Gabriella A. , Evans Elizabeth L. , Dickinson George D. , Tobias Douglas J. , Pathak Medha M. 
Published: September 2022

ABSTRACTThe mechanically-activated ion channel PIEZO1 is critical to numerous physiological processes, and is activated by diverse mechanical cues. The channel is gated by membrane tension and has been found to be mobile in the plasma membrane. We employed single particle tracking (SPT) of endogenous, tdTomato-tagged PIEZO1 using Total Internal Reflection Fluorescence Microscopy in live cells. Application of SPT unveiled a surprising heterogeneity of diffusing PIEZO1 subpopulations, which we labeled “mobile” and “immobile”. We sorted these trajectories into the two aforementioned categories using trajectory spread. To evaluate the effects of the plasma membrane composition on PIEZO1 diffusion, we manipulated membrane composition by depleting or supplementing cholesterol, or by adding margaric acid to stiffen the membrane. To examine effects of channel activation on PIEZO1 mobility, we treated cells with Yoda1, a PIEZO1 agonist, and GsMTx-4, a channel inhibitor. We collected thousands of trajectories for each condition, and found that cholesterol removal and Yoda1 incubation increased the channel’s propensity for mobility. Conversely, we found that GsMTx-4 incubation and cholesterol supplementation resulted in a lower chance of mobile trajectories, whereas margaric acid incubation did not have a significant effect on PIEZO1 mobility. The “mobile” trajectories were analyzed further by fitting the time-averaged mean-squared displacement as a function of lag time to a power-law model, revealing mobile PIEZO1 puncta exhibit anomalous subdiffusion. These studies illuminate the fundamental properties governing PIEZO1 diffusion in the plasma membrane and set the stage to determine how cellular processes and interactions may influence channel activity and mobility.SIGNIFICANCEPIEZO1 is a mechanically-activated ion channel that regulates a number of physiological processes. Here we examine a fundamental biophysical property of PIEZO1 - its movement in the plasma membrane. We find that the mobility of PIEZO1 is surprisingly heterogeneous, with some PIEZO1 puncta showing high mobility and some displaying very limited mobility. Cholesterol depletion from the plasma membrane increases PIEZO1 mobility while cholesterol supplementation decreases mobility. Yoda1 treatment increases PIEZO1 mobility whereas GsMTx-4 treatment decreases channel mobility.
An empirical study on the use of a facial emotion recognition system in guidance counseling utilizing the technology acceptance model and the general comfort questionnaire
Authors: Gom-os Dhong Fhel K. , Yong Kelvin Y. 
Published: September 2022

PurposeThe goal of this study is to test the real-world use of an emotion recognition system.Design/methodology/approachThe researchers chose an existing algorithm that displayed high accuracy and speed. Four emotions: happy, sadness, anger and surprise, are used from six of the universal emotions, associated by their own mood markers. The mood-matrix interface is then coded as a web application. Four guidance counselors and 10 students participated in the testing of the mood-matrix. Guidance counselors answered the technology acceptance model (TAM) to assess its usefulness, and the students answered the general comfort questionnaire (GCQ) to assess their comfort levels.FindingsResults from TAM found that the mood-matrix has significant use for the guidance counselors and the GCQ finds that the students were comfortable during testing.Originality/valueNo study yet has tested an emotion recognition system applied to counseling or any mental health or psychological transactions.
Prioritization of risks associated with the implementation of project-based learning concept in engineering institutions
Authors: Pasi Bhaveshkumar Nandanram , Dongare Pallavi Vivek , Rawat Suman Joshi 
Published: September 2022

PurposeThis research article aims to prioritize the risks associated with the implementation of the project-based learning (PBL) concept in engineering institutions and develop possible strategies for risk management.Design/methodology/approachIn this research article, various risks associated with the implementation of the PBL concept in engineering institutions are discovered by taking inputs from academicians and performing a literature survey of peer-reviewed journal articles. Then, identified risks are prioritized by using the Technique for Order Preference by Similarity to the Ideal Solution (TOPSIS) method. Finally, the risk mitigation strategies are developed.FindingsFrom the literature survey, 11 risks associated with the implementation of the PBL concept are identified. The TOPSIS method resulted in group dynamics risk and faculty training risk as the top two risks in the implementation of the PBL concept, whereas anxiety risk and poor prior learning experience risk are relatively low-ranked risks.Research limitations/implicationsThe outcome of the research is based on the responses received through questionnaires. There are other methods also available for risk analysis, which are beyond this study.Practical implicationsThe outcome of this research work will help the implementer of the PBL concept to effectively deal with the risks involved in implementing the PBL concept in engineering institutions by adopting strategies.Originality/valueThis research paper gives an idea about risks associated with the PBL implementation in engineering institutions. Also, this paper uses TOPSIS method for ranking of identified risks.
Remote sensing to assess the risk for cultural heritage: forecasting potential collapses due to rainfall in historic fortifications
Authors: Moreno Mónica , Ortiz Rocío , Ortiz Pilar 
Published: September 2022

PurposeHeavy rainfall is one of the main causes of the degradation of historic rammed Earth architecture. For this reason, ensuring the conservation thereof entails understanding the factors involved in these risk situations. The purpose of this study is to research three past events in which rainfall caused damage and collapse to historic rammed Earth fortifications in Andalusia in order to analyse whether it is possible to prevent similar situations from occurring in the future.Design/methodology/approachThe three case studies analysed are located in the south of Spain and occurred between 2017 and 2021. The hazard presented by rainfall within this context has been obtained from Art-Risk 3.0 (Registration No. 201999906530090). The vulnerability of the structures has been assessed with the Art-Risk 1 model. To characterise the strength, duration, and intensity of precipitation events, a workflow for the statistical use of GPM and GSMaP satellite resources has been designed, validated, and tested. The strength of the winds has been evaluated from data from ground-based weather stations.FindingsGSMaP precipitation data is very similar to data from ground-based weather stations. Regarding the three risk events analysed, although they occurred in areas with a torrential rainfall hazard, the damage was caused by non-intense rainfall that did not exceed 5 mm/hour. The continuation of the rainfall for several days and the poor state of conservation of the walls seem to be the factors that triggered the collapses that fundamentally affected the restoration mortars.Originality/valueA workflow applied to vulnerability and hazard analysis is presented, which validates the large-scale use of satellite images for past and present monitoring of heritage structure risk situations due to rain.
Minority dissent, social acceptance and conflict transformation in multiparty systems
Authors: Curșeu Petru Lucian , Schruijer Sandra G.L. 
Published: September 2022

Purpose
This study aims to investigate the role of minority dissent (MD) as an antecedent for task (TC) and relationship conflict (RC) in groups engaged in multiparty collaboration. The authors hypothesized that MD triggers both TC and RC and that the association between MD and RC is mediated by TC. Moreover, the authors hypothesized that the positive association between MD and RC is attenuated by social acceptance, while the positive association between TC and RC is attenuated by trust.

Design/methodology/approach
The authors have tested the hypotheses in 36 groups comprising in total 145 professionals that attended a two-day workshop on working across organizational boundaries and who filled in three surveys during a multiparty simulation. The authors used multilevel mediation analyses to test the hypotheses.

Findings
The results generally supported the role of MD as an antecedent for both TC and RC as well as the mediating role of TC in the relationship between MD and RC. The attenuating role of social acceptance in the relationship between MD and RC was fully supported, while the attenuating role of trust in the relationship between TC and RC was not supported.

Research limitations/implications
This study is based on a rather small sample and used a cross-lagged data collection design, and no causal claims can be derived from the findings. Behavioral multiparty simulations create a realistic context in which the authors investigate the dynamics of conflict transformation and explore the interplay of MD, TC and RC.

Social implications
As nowadays, multiparty systems are engaged in dealing with important societal challenges and because RC is detrimental for collaborative effectiveness, the results have important implications for facilitating effective collaboration in such complex systems.

Originality/value
This study makes an important contribution to the literature on conflict in multiparty systems by showing that as an antecedent of intragroup conflict, MD can have both a beneficial as well as a detrimental impact on the conflict dynamics of multiparty systems. It points out the importance of social acceptance as a buffer against the detrimental role of MD.
Government data openness and knowledge management: configurational patterns for national competitiveness
Authors: Ham Juyeon , Koo Yunmo , Lee Jae Nam 
Published: September 2022

PurposeIn the data economy era, despite the tremendous effort of governments to actively provide and use open data, its effect on national performance such as competitiveness differs widely from country to country. A sufficient knowledge base and its appropriate management are important to effectively derive the potential value from open data. A country can implement multiple and equally viable means to effectively align open data with knowledge management, which lead to high national performance. However, previous studies lack consideration of the possibility of these various configurations. To fill the research gap, this study aims to investigate the configurational patterns constituted by government data openness and knowledge management for national competitiveness.Design/methodology/approachFrom the open innovation perspective, this study collected data from the global reports of 76 countries and examined them through fuzzy-set qualitative comparative analysis (fsQCA).FindingsFour configurational patterns are identified, namely, coupled (outbound-focused)-, coupled (inbound-focused)-, inbound-focused-, and outbound-focused national competitiveness.Originality/valueThis study provides a foundation that enables researchers to build a holistic and balanced perspective that can manage open government data and develop knowledge management capability.