bluuebunny/crossref_metadata_2025_split huggingface dataset:
Craniofacial cartilage organoids from human embryonic stem cells via a neural crest cell intermediate
Authors: Foltz Lauren , Levy Tyler , Possemato Anthony , Grimes Mark 
Published: June 2021

AbstractSevere birth defects or major injuries to the face require surgical reconstruction and rehabilitation. The ability to make bona fide craniofacial cartilage – cartilage of the head and face – from patient-derived induced pluripotent stem cells (iPSCs) to repair these birth defects and injuries has tremendous translational applications, but is not yet possible. The neural crest is the normal developmental pathway for craniofacial cartilage, however, the knowledge of cell signaling pathways that drive neural crest differentiation into craniofacial chondrocytes is limited. Here we describe a differentiation protocol that generated self-organizing craniofacial cartilage organoids from human embryonic stem cells (hESCs) and IPSCs through a neural crest stem cell (NCSC) intermediate. Histological staining of cartilage organoids revealed tissue architecture typical of hyaline cartilage. Organoids were composed of rounded aggregates of glassy, gray matrix that contained scattered small nuclei in lacunae. Mass spectrometry shows that the organoids express robust levels of cartilage markers including aggrecan, perlecan, proteoglycans, and many collagens. Organoids expressed markers indicative of neural crest lineage, as well as growth factors that are candidates for chondrocyte differentiation factors. The data suggest that chondrocyte differentiation is initiated by autocrine loops driven by a combination of secreted growth factors that bind to chondrocyte receptors. Craniofacial cartilage organoids were continuously cultured for one year, reaching up to one centimeter in diameter. The ability to grow craniofacial cartilage from NCSCs provides insights into the cell signaling mechanisms of differentiation into craniofacial cartilage, which lays the groundwork for understanding mechanistic origins of congenital craniofacial anomalies and repairing cartilaginous structures of the head and face.
Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids
Authors: Sancho Rubén , Inda Luis A. , Díaz-Pérez Antonio , Des Marais David L. , Gordon Sean , Vogel John , Lusinska Joanna , Hasterok Robert , Contreras-Moreira Bruno , Catalán Pilar 
Published: June 2021

AbstractUnraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when their progenitor genome sequences are unavailable. The subgenome identification methods cannot adequately retrieve the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate cereals and biofuel grasses. We used a transcriptome-based phylogeny and newly designed subgenome detection algorithms coupled with a comparative chromosome barcoding analysis. Our phylogenomic subgenome detection pipeline was validated in Triticum allopolyploids, which have known progenitor genomes, and was used to infer the identities of three extant and four ‘ghost’ subgenomes in six Brachypodium polyploids (B. mexicanum, B. boissieri, B. retusum, B. phoenicoides, B. rupestre and B. hybridum), of which five contain undescribed homeologous subgenomes. The existence of the seven Brachypodium progenitor genomes in the polyploids was confirmed by their karyotypic barcode profiles. Our results demonstrate that our subgenome detection method is able to uncover the ancestral genomic components of both allo- and autopolyploids.
Integrating ecological monitoring and local ecological knowledge to evaluate conservation outcomes
Authors: Early-Capistrán Michelle María , Solana-Arellano Elena , Abreu-Grobois F. Alberto , Garibay-Melo Gerardo , Seminoff Jeffrey A. , Sáenz-Arroyo Andrea , Narchi Nemer E. 
Published: June 2021

AbstractSuccessful conservation of long-lived species requires reliable understanding of long-term trends and historical baselines. Using a green turtle (Chelonia mydas) foraging aggregation in the northern Gulf of California, Mexico as case study, we integrated scientific monitoring data with historic catch rate reconstructions derived from Local Ecological Knowledge (LEK). Models fit to LEK and monitoring data indicate that turtle abundance is increasing, but only after ~40 years of safeguarding the species’ nesting and foraging habitats in Mexico. However, as population declines occurred 75% faster than increases, and current abundance is at ~60% of historical baseline levels, indicating the need for sustained, long-term conservation actions. This study demonstrates the potential of linking LEK and ecological science to provide critical information for conservation, by establishing reference baselines and gauging population status, while promoting equitable and sustainable futures for local communities.
A multi-tiered map of EMT defines major transition points and identifies vulnerabilities
Authors: Paul Indranil , Bolzan Dante , Youssef Ahmed , Gagnon Keith A. , Hook Heather , Karemore Gopal , Oliphant Michael UJ , Lin Weiwei , Liu Qian , Phanse Sadhna , White Carl , Padhorny Dzmitry , Kotelnikov Sergei , Andrieu Guillaume P. , Chen Christopher S. , Hu Pingzhao , Denis Gerald V. , Kozakov Dima , Raught Brian , Siggers Trevor , Wuchty Stefan , Muthuswamy Senthil K. , Emili Andrew 
Published: June 2021

SummaryEpithelial to mesenchymal transition (EMT) is a complex cellular program proceeding through a hybrid E/M state linked to cancer-associated stemness, migration and chemoresistance. Deeper molecular understanding of this dynamic physiological landscape is needed to define events which regulate the transition and entry into and exit from the E/M state. Here, we quantified >60,000 molecules across ten time points and twelve omic layers in human mammary epithelial cells undergoing TGFβ-induced EMT. Deep proteomic profiles of whole cells, nuclei, extracellular vesicles, secretome, membrane and phosphoproteome defined state-specific signatures and major transition points. Parallel metabolomics showed metabolic reprogramming preceded changes in other layers, while single-cell RNA sequencing identified transcription factors controlling entry into E/M. Covariance analysis exposed unexpected discordance between the molecular layers. Integrative causal modeling revealed co-dependencies governing entry into E/M that were verified experimentally using combinatorial inhibition. Overall, this dataset provides an unprecedented resource on TGFβ signaling, EMT and cancer.
VIQoR: a web service for Visually supervised protein Inference and protein Quantification
Authors: Tsiamis Vasileios , Schwämmle Veit 
Published: June 2021

AbstractMotivationIn quantitative bottom-up mass spectrometry (MS)-based proteomics the reliable estimation of protein concentration changes from peptide quantifications between different biological samples is essential. This estimation is not a single task but comprises the two processes of protein inference and protein abundance summarization. Furthermore, due to the high complexity of proteomics data and associated uncertainty about the performance of these processes, there is a demand for comprehensive visualization methods able to integrate protein with peptide quantitative data including their post-translational modifications. Hence, there is a lack of a suitable tool that provides post-identification quantitative analysis of proteins with simultaneous interactive visualization.ResultsIn this article, we present VIQoR, a user-friendly web service that accepts peptide quantitative data of both labeled and label-free experiments and accomplishes the processes for relative protein quantification, along with interactive visualization modules, including the novel VIQoR plot. We implemented two parsimonious algorithms to solve the protein inference problem, while protein summarization is facilitated by a well established factor analysis algorithm called fast-FARMS followed by a weighted average summarization function that minimizes the effect of missing values. In addition, summarization is optimized by the so-called Global Correlation Indicator (GCI). We test the tool on three publicly available ground truth datasets and demonstrate the ability of the protein inference algorithms to handle degenerate peptides. We furthermore show that GCI increases the accuracy of the quantitative analysis in data sets with replicated design.Availability and implementationVIQoR is accessible at: http://computproteomics.bmb.sdu.dk:8192/app_direct/VIQoR/The source code is available at: https://bitbucket.org/vtsiamis/viqor/Contactveits@bmb.sdu.dkSupplementary informationSupplementary data are available at Bioinformatics online.
The impact of the spatial heterogeneity of resistant cells and fibroblasts on treatment response
Authors: M A Masud , Kim Jae-Young , Pan Cheol-Ho , Kim Eunjung 
Published: June 2021

AbstractA long-standing practice in the treatment of cancer is that of hitting hard with the maximum tolerated dose to eradicate tumors. This continuous therapy, however, selects for resistant cells, leading to the failure of the treatment. A different type of treatment strategy, adaptive therapy, has recently been shown to have a degree of success in both preclinical xenograft experiments and clinical trials. Adaptive therapy is used to maintain a tumor’s volume by exploiting the competition between drug-sensitive and drug-resistant cells with minimum effective drug doses or timed drug holidays. To further understand the role of competition in the outcomes of adaptive therapy, we developed a 2D on-lattice agent-based model. Our simulations show that the superiority of the adaptive strategy over continuous therapy depends on the local competition shaped by the spatial distribution of resistant cells. Cancer cell migration and increased carrying capacity accelerate the progression of the tumor under both types of treatments by reducing the spatial competition. Intratumor competition can also be affected by fibroblasts, which produce microenvironmental factors that promote cancer cell growth. Our simulations show that the spatial architecture of fibroblasts modulates the benefits of adaptive therapy. Finally, as a proof of concept, we simulated the outcomes of adaptive therapy in multiple metastatic sites composed of different spatial distributions of fibroblasts and drug-resistant cell populations.
Proteome of actin stress fibers
Authors: Liu Shiyou , Matsui Tsubasa S. , Kang Na , Deguchi Shinji 
Published: June 2021

AbstractStress fibers (SFs), which are actomyosin structures, reorganize in response to various cues to maintain cellular homeostasis. Currently, the protein components of SFs are only partially identified, limiting our understanding of their responses. Here we isolate SFs from huma fibroblasts HFF-1 to determine with proteomic analysis the whole protein components and how they change with replicative senescence (RS), a state where cells decline in ability to replicate after repeated divisions. We found that at least 263 proteins are associated with SFs, and 101 of them are upregulated with RS, by which SFs become larger in size. Among them, we focused on eEF2 (eukaryotic translation elongation factor 2) as it exhibited upon RS the most significant increase in abundance. We show that eEF2 is critical to the reorganization and stabilization of SFs in senescent fibroblasts. Our findings provide a novel molecular basis for SFs to be reinforced to resist cellular senescence.
Minimal-invasive enhancement of auditory perception by terahertz wave modulation
Authors: Tan Xiaoxuan , Wu Kaijie , Liu Shuang , Chang Chao , Xiong Wei 
Published: June 2021

AbstractHearing impairment is a common disease affecting a substantial proportion of the global population. Currently, the most effective clinical treatment for patients with sensorineural deafness is to implant an artificial electronic cochlea. However, the improvements to hearing perception are variable and limited among healthy subjects. Moreover, cochlear implants have disadvantages, such as crosstalk derived from the currents that spread into non-target tissue between the electrodes. Here, in this work, we describe terahertz wave modulation (THM), a new, minimally invasive technology that can enhance hearing perception in animals by reversible modulation of currents in cochlear hair cells. Using single-cell electrophysiology, guinea pig audiometry, and molecular dynamics simulations (MD), we show that THM can reversibly increase mechano-electrical transducer (MET) currents (∼50% higher) and voltage-gated K+ currents in cochlear hair cells through collective resonance of −C=O groups. In addition, measurement of auditory brainstem response (ABR) in guinea pigs treated with THM indicated a ∼10 times increase in hearing sensitivity. This study thus reports a new method of highly spatially selective hearing enhancement without introducing any exogeneous gene, which has potential applications for treatment of hearing disorders as well as several other areas of neuroscience.
The liverwort Marchantia polymorpha operates a depolarization-activated Slowpoke (SLO) K+ channel that recognises pH changes in the environment
Authors: Sussmilch Frances C. , Böhm Jennifer , Gessner Guido , Maierhofer Tobias , Müller Thomas D. , Heinemann Stefan H. , Becker Dirk , Hedrich Rainer 
Published: June 2021

SUMMARYVoltage-dependent ion channels are a prerequisite for cellular excitability and electrical communication – important traits for multicellular organisms to thrive in a changeable terrestrial environment. Based on their presence in extant embryophytes and closely-related green algae, the first plants to survive on land likely possessed genes encoding channels with homology to large-conductance calcium-activated K+ channels (BK channels from the Slo family) in addition to primary voltage-gated potassium channels from the plant VG-type family (Shaker or Kv channels). While the function and gating of Shaker channels has been characterised in flowering plants, so far knowledge of BK channels has been limited to animal models. In humans, BK-mediated K+ efflux has a critical role in sperm motility and membrane polarisation to enable fertilisation. In the liverwort Marchantia polymorpha, the MpBK2a channel gene is most highly expressed in male reproductive tissue, suggesting that these channels may function in sexual reproduction. We characterised MpBK2a channels and found them to be strongly K+-selective, outward-rectifying, 80-pS channels capable of repolarising the membrane after stimulus-dependent depolarisation. In contrast to its animal counterpart, MpBK2a is insensitive to cytoplasmic Ca2+ variations but effectively gated by pH changes. Given that this plant BK channel is active even in the presence of trace amounts of external K+ and at low pH, the liverwort channel could have stabilised the membrane potential under stressful pre-historic conditions including nutrient-depleted and acid environments as early plant pioneers conquered land.
Effects of isentropic efficiency of turbomachinery components on entropy production for small turbojet engine
Authors: Aygün Hakan 
Published: June 2021

Purpose
Usage of gas turbine engines has increased by day due to rising demand for military and civil applications. This case results in investigating diverse topics related to energy efficiency and irreversibility of these systems. The purpose of this paper is to perform a detailed entropy assessment of turbojet engines for different flight conditions.

Design/methodology/approach
In this study, for small turbojet engines used in unmanned aerial vehicles, parametric cycle analysis is carried out at (sea level-zero Mach (hereinafter phase-I)) and (altitude of 9,000 m- Mach of 0.7 (hereinafter phase-II)). Based on this analysis, variation of performance and thermodynamic parameters with respect to change in isentropic efficiency of the compressor (CIE) and turbine (TIE) is examined at both phases. In this context, the examined ranges for CIE is between 0.78 and 0.88 whereas TIE is between 0.85 and 0.95.

Findings
Increasing isentropic efficiency decreases entropy production of the small turbojet engine. Moreover, the highest entropy production occurs in the combustor in the comparison of other components. Namely, it decreases from 2.81 to 2.69 kW/K at phase-I and decreases from 1.44 to 1.39 kW/K at phase-II owing to rising CIE.

Practical implications
It is thought that this study helps in understanding the relationship between entropy production and the efficiency of components. Namely, the approach used in the current analysis could help decision-makers or designers to determine the optimum value of design variables.

Originality/value
Due to rising isentropic efficiencies of both components, it is observed that specific fuel consumption (SFC) decreases whereas specific thrust (ST) increases. Also, the isentropic efficiency of a compressor affects relatively SFC and ST higher than that of the turbine.
How privacy concerns and cultural differences affect public opinion during the COVID-19 pandemic: a case study
Authors: Xing Yunfei , Li Yuhai , Wang Feng-Kwei 
Published: June 2021

PurposeCOVID-19, an infectious disease first identified in China, has resulted in an ongoing pandemic all over the world. Most of the countries have been experiencing a difficult period during the fighting of this pandemic. The purpose of this study is to explore the effect of privacy concerns and cultural differences on public opinion related to the pandemic. The authors conducted a comparative analysis of public opinion in the US and in China as a case study, in order to determine the results.Design/methodology/approachNational policies on important issues faced during the COVID-19 pandemic in the US and in China were examined through a comparative analysis. The authors used text clustering and visualization to mine public opinion on two popular social media platforms, Twitter and Weibo. From the perspectives of concern for privacy and of national culture, this study combines qualitative and quantitative analysis to discover the acceptance level of national policies by the public in the two countries.FindingsThe anti-pandemic policies and measures of the US and China reflect the different characteristics of their respective political systems and national cultures. When considering the culture of the US, it is hard to establish and enforce a rigorous regulation on either mask wearing in public or home quarantine on the national level. The opinions of US people are diverse, regarding national COVID-19 policies, but they are rather unified on privacy issues. On the other hand, Chinese people show a high acceptance of national policies based on their mask-wearing customs and their culture of collectivism.Originality/valuePrior studies have paid insufficient attention to the ways in which user privacy and cultural difference affect public opinion on national policies between the US and China. This case study that compares public opinion on current and topical issues which are closely bound up with public life shows originality, as it innovatively provides a cross-cultural perspective on the research of public opinion dissemination during emergencies by considering the ongoing COVID-19 pandemic.
CSR during COVID-19: exploring select organizations’ intents and activities
Authors: Ramya S.M. , Baral Rupashree 
Published: June 2021

Purpose
This paper aims to explore the immediate proactive corporate social responsibility (CSR) efforts undertaken by select organizations in India in response to the coronavirus (COVID-19) pandemic and the approach they have adopted toward it.

Design/methodology/approach
Semi-structured interviews were conducted with 27 senior managers across top Bombay Stock Exchange indexed organizations from the manufacturing and services sector in India during the national COVID-19 pandemic lockdown between March and June 2020. Manual content analysis and the Gioia method were used to arrive at the insights.

Findings
Results of the analysis showcase the spirited immediate CSR measures undertaken by the select organizations in the broader interests of the community at large. The study also highlights the need for a paradox approach toward CSR strategy.

Research limitations/implications
Given that the present study adopts an exploratory qualitative research design, the scope for generalization is rather limited.

Practical implications
This paper classifies COVID-19 related initiatives undertaken by selected few top organizations in India and attempts to justify the need to opt for a paradox approach toward CSR strategy.

Originality/value
To the best of the author’s knowledge, this is one of the first few studies to have attempted to put forth a dialog at the intersection of COVID-19 and CSR with rich insights gained from qualitative data collected during India’s intense lockdown period and offering a different perspective with the inclusion of paradox theory into the discussion.
Lyapunov–Krasovskii based FPID controller for LFC in a time-delayed micro-grid system with fuel cell power units
Authors: Sabahi Kamel , Hajizadeh Amin , Tavan Mehdi 
Published: June 2021

Purpose
In this paper, a novel Lyapunov–Krasovskii stable fuzzy proportional-integral-derivative (PID) (FPID) controller is introduced for load frequency control of a time-delayed micro-grid (MG) system that benefits from a fuel cell unit, wind turbine generator and plug-in electric vehicles.

Design/methodology/approach
Using the Lyapunov–Krasovskii theorem, the adaptation laws for the consequent parameters and output scaling factors of the FPID controller are developed in such a way that an upper limit (the maximum permissible value) for time delay is introduced for the stability of the closed-loop MG system. In this way, there is a stable FPID controller, the adaptive parameters of which are bounded. In the obtained adaptation laws and the way of stability analyses, there is no need to approximate the nonlinear model of the controlled system, which makes the implementation process of the proposed adaptive FPID controller much simpler.

Findings
It has been shown that for a different amount of time delay and intermittent resources/loads, the proposed adaptive FPID controller is able to enforce the frequency deviations to zero with better performance and a less amount of energy. In the proposed FPID controller, the increase in the amount of time delay leads to a small increase in the amount of overshoot/undershoot and settling time values, which indicate that the proposed controller is robust to the time delay changes.

Originality/value
Although the designed FPID controllers in the literature are very efficient in being applied to the uncertain and nonlinear systems, they suffer from stability problems. In this paper, the stability of the FPID controller has been examined in applying to the frequency control of a nonlinear input-delayed MG system. Based on the Lyapunov–Krasovskii theorem and using rigorous mathematical analyses, the stability conditions and the adaptation laws for the parameters of the FPID controller have been obtained in the presence of input delay and nonlinearities of the MG system.