bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibroblast growth factor (FGF), FGF receptor (FGFR), and cyclin D1 (CCND1) DNA methylation in head and neck squamous cell carcinomas is associated with transcriptional activity, gene amplification, human papillomavirus (HPV) status, and sensitivity to tyrosine kinase inhibitors
Authors: Bao Yilin , Gabrielpillai Jennis , Dietrich Jörn , Zarbl Romina , Strieth Sebastian , Schröck Friederike , Dietrich Dimo 
Published: December 2021

AbstractBackgroundDysregulation of fibroblast growth factor receptor (FGFR)signaling pathway has been observed in head and neck squamous cell carcinoma (HNSCC) and is a promising therapeutic target for selective tyrosine kinase inhibitors (TKIs). Potential predictive biomarkers for response to FGFR-targeted therapies are urgently needed. Understanding the epigenetic regulation of FGF pathway related genes, i.e. FGFRs, FGFs, andCCND1, could enlighten the way towards biomarker-selected FGFR-targeted therapies.MethodsWe performed DNA methylation analysis of the encoding genesFGFR1, FGFR2,FGFR3, FGFR4, FGF1-14,FGF16-23, andCCND1at single CpG site resolution (840 CpG sites) employing The Cancer Genome Research Atlas (TCGA) HNSCC cohort comprisingN = 530 tumor tissue andN = 50 normal adjacent tissue samples. We correlated DNA methylation to mRNA expression with regard to human papilloma virus (HPV) and gene amplification status. Moreover, we investigated the correlation of methylation with sensitivity to the selective FGFR inhibitors PD 173074 and AZD4547 inN = 40 HPV(−) HNSCC cell lines.ResultsWe found sequence-contextually nuanced CpG methylation patterns in concordance with epigenetically regulated genes. High methylation levels were predominantly found in the promoter flank and gene body region, while low methylation levels were present in the central promoter region for most of the analyzed CpG sites. FGFRs, FGFs, andCCND1methylation differed significantly between tumor and normal adjacent tissue and was associated with HPV and gene amplification status.CCND1promoter methylation correlated withCCND1amplification.For most of the analyzed CpG sites, methylation levels correlated to mRNA expression in tumor tissue. Furthermore, we found significant correlations of DNA methylation of specific CpG sites with response to the FGFR1/3–selective inhibitors PD 173074 and AZD4547, predominantly within the transcription start site ofCCND1.ConclusionsOur results suggest an epigenetic regulation ofCCND1, FGFRs, and FGFs via DNA methylation in HNSCC and warrants further investigation of DNA methylation as a potential predictive biomarker for response to selective FGFR inhibitors in clinical trials.
What evidence exists on the impact of anthropogenic radiofrequency electromagnetic fields on animals and plants in the environment? A systematic map protocol
Authors: Karipidis Ken , Brzozek Chris , Bhatt Chhavi Raj , Loughran Sarah , Wood Andrew 
Published: December 2021

Abstract
Background
Exposure to radiofrequency (RF) electromagnetic fields (EMF), particularly from telecommunications sources, is one of the most common and fastest growing anthropogenic factors on the environment. In many countries, humans are protected from excessive RF EMF exposure by safety standards that are based on guidelines by the International Commission on Non-Ionizing Radiation Protection (ICNIRP). The ICNIRP guidelines are based on knowledge of how RF EMF affects the human body, however, there are currently no recognised international guidelines to specifically protect animals and plants. Whether the ICNIRP guidelines for humans is adequate to provide protection to the environment is a subject of active debate. This systematic map will collate all the available evidence on whether anthropogenic RF EMF has a negative effect on plants and animals in the environment. The map will also identify gaps in knowledge, recommend future research and inform environmental and radiation protection authorities.

Methods
The proposed systematic map will include peer-reviewed and grey literature published in English. The EMF—Portal, PubMed and Web of Science databases will be searched using a search string prepared by the review team and tested for comprehensiveness against a list of known relevant reviews. Once duplicates are removed, retrieved articles will be screened in three stages: title, abstract, and full text. Studies will be selected with a subject population of all plants and animals, with exposures to anthropogenic RF EMF (frequency range 100 kHz–300 GHz) compared to no or lower-level exposure, and for all outcomes related to the studied populations. Kappa statistic tests will be conducted at each stage to ensure consistency of decision-making regarding the predefined inclusion/exclusion criteria. Eligible studies will then proceed to the data extraction phase, which will extract meta-data such as bibliographic information, taxonomic information, RF EMF exposure data, outcome(s), sample size, etc. The extracted data will then be organised into a systematic map and the findings summarised by cross-tabulating key meta-data variables in heat maps, charts or other data visualization methods. The systematic map will identify gaps in knowledge, priorities for future research and potential subtopics for further analysis and/or systematic review.
Global survey to assess preferences when attending virtual orthodontic learning sessions: optimising uptake from virtual lectures
Authors: Mheissen Samer , Almuzian Mohammed , Wertheimer Mark B. , Khan Haris 
Published: December 2021

Abstract
Objectives
Understanding the issues concerning the conducting of virtual orthodontic learning sessions (VOLSs) is essential. This study aims to identify attendees- and host-related aspects that could optimise learning and uptake from the VOLSs.

Methodology
Fourteen pre-validated questions were anonymously and electronically sent to 3000 orthodontic residents and specialists globally. The survey included demographic questions and questions to gauge attendees' engagement, memorising, and motivation-related factors. Reminders were sent at two-week intervals to non-respondents. The survey was closed when the sample size was met. Descriptive and inferential statistics were performed.

Results
593 orthodontic residents and specialists (294 males and 299 females), primarily junior orthodontists and residents aged between 25 and 35 years of age, completed the survey. Post-VOLS recording was highly requested by the participants (8.84/10, 95% CI 8.67–9.00) with no significant influence of demographics on this trend (p > 0.05). Most of the participants were in favour of short post-VOLSs feedback (6.79/10 95% CI 6.58–6.99) with significant differences (p = 0.048) between participants from different regions of the world. The average number of screenshots taken was 6.1 per lecture. The learners’ interests in attending on-line lectures were mainly to learn new clinical orthodontic tips (96.8%).

Conclusion
Implementing a short feedback survey after VOLSs, the provision of recording, and the provision of certificates of attendance need to be considered.
Extrusion-based additive manufacturing of fungal-based composite materials using the tinder fungus Fomes fomentarius
Authors: Chen Huaiyou , Abdullayev Amanmyrat , Bekheet Maged F. , Schmidt Bertram , Regler Isabel , Pohl Carsten , Vakifahmetoglu Cekdar , Czasny Mathias , Kamm Paul H. , Meyer Vera , Gurlo Aleksander , Simon Ulla 
Published: December 2021

Abstract
Background
Recent efforts in fungal biotechnology aim to develop new concepts and technologies that convert renewable plant biomass into innovative biomaterials. Hereby, plant substrates become metabolized by filamentous fungi to transform them into new fungal-based materials. Current research is thus focused on both understanding and optimizing the biology and genetics underlying filamentous fungal growth and on the development of new technologies to produce customized fungal-based materials.

Results
This manuscript reports the production of stable pastes, composed of Fomes fomentarius mycelium, alginate and water with 71 wt.% mycelium in the solid content, for additive manufacturing of fungal-based composite materials. After printing complex shapes, such as hollow stars with up to 39 mm in height, a combination of freeze-drying and calcium-crosslinking processes allowed the printed shapes to remain stable even in the presence of water. The printed objects show low bulk densities of 0.12 ± 0.01 g/cm3 with interconnected macropores.

Conclusions
This work reports for the first time the application of mycelium obtained from the tinder fungus F. fomentarius for an extrusion-based additive manufacturing approach to fabricate customized light-weight 3D objects. The process holds great promise for developing light-weight, stable, and porous fungal-based materials that could replace expanded polystyrene produced from fossil resources.
Role of liver biopsy versus non-invasive biomarkers for diagnosis of significant fibrosis and cirrhosis: a web-based survey
Authors: Alboraie Mohamed , Khairy Marwa , Elsharkawy Aisha , Asem Noha , El Kassas Mohamed , Elgendy Abdelaleem A. , Nagdy Hanaa , Shady Zakarya , Eliwa Ahmed , El-Ansary Amira R. , Ibrahem Mohamed , Allam Mahmoud A. , Elsherif Abdelhalim , Elghamry Fathy , Hassan Fuad , Hassany Mohamed , Esmat Gamal ,   On behalf of the Egyptian Liver Fibrosis Study Group
Published: December 2021

Abstract
Background
Liver biopsy is the standard reference for staging hepatic fibrosis. Non-invasive methods for assessment of hepatic fibrosis and cirrhosis are becoming increasingly popular.

Objective
We aimed at exploring the change in practice regarding the use of liver biopsy and non-invasive methods for staging hepatic fibrosis and cirrhosis among hepatologists.

Methods
We performed a survey-based study that recruited hepatologists from various Egyptian institutions. Physicians were deemed eligible if they had a degree in internal medicine with hepatology as a subspecialty. We utilized an online-based survey that assessed the acceptability and reliability of liver biopsy, serum biomarkers, and radiological tools for evaluating liver fibrosis and cirrhosis.

Results
A total of 573 responses were retrieved (response rate = 80.3%). Out of them, 58% were having more than 15 years of experience as a hepatologist.
Liver biopsy is still considered the gold standard for assessment of hepatic fibrosis and cirrhosis by 61% of participants. Liver biopsy was accepted by 44% of their patients. 84% reported the need for a more practical alternative to liver biopsy to assess disease progression or response to treatment. 78.34% of participants know serum biomarkers, 84.08% reported that they were acceptable by their patients, 37.79% thought they are reliable. 95.4% were familiar with radiological methods of non-invasive assessment of hepatic fibrosis, 89.1% reported that radiological methods were acceptable by their patients, 62% think that they are reliable and 78% reported they were applicable in clinical practice. Sixty-five percent think that combining non-invasive methods is better than using a single method. Forty percent of participants thought that radiological methods are easier to use for assessment of hepatic fibrosis followed by a combination of non-invasive methods, serum biomarkers, and liver biopsy respectively.

Conclusion
In conclusion, liver biopsy is still considered the most reliable method for evaluation and staging of liver cirrhosis by hepatologists in Egyptian institutions, despite the modest acceptance by the patients. Nonetheless, non-invasive methods are gaining acceptance by Egyptian physicians and patients, and most of them consider these methods as reliable and applicable tools for predicting the course of liver cirrhosis.
Mobile Audio Recording Technology to Promote Informed Decision Making in Advanced Prostate Cancer
Authors: Kwon Daniel H. , Karthikeyan Sneha , Chang Alison , Borno Hala T. , Koshkin Vadim S. , Desai Arpita , Bose Rohit , Friedlander Terence , Rodvelt Tammy , Li Patricia , Small Eric J. , Aggarwal Rahul R. , Belkora Jeffrey 
Published: December 2021

PURPOSE: Men with metastatic castration-resistant prostate cancer increasingly encounter complex treatment decisions. Consultation audio recordings and summaries promote patient informed decision making but are underutilized. Mobile recording software applications may increase access. Little is known regarding the feasibility of implementation in clinical encounters. METHODS: We conducted a mixed-methods pilot study in men with progressive metastatic castration-resistant prostate cancer. We instructed patients to use a mobile software application to record an oncology visit. Patients could share the recording with our patient scribing program to receive a written summary. We assessed feasibility and acceptability with postvisit surveys. We measured patient-reported helpfulness of the intervention in decision making and change in Decisional Conflict Scale–informed subscale. We conducted semistructured interviews to explore implementation and analyzed transcripts using thematic analysis. RESULTS: Across 20 patients, 18 (90%) recorded their visits. Thirteen of 18 (72%) listened to the recording, and 14 of 18 (78%) received a summary. Eighteen of 20 (90%) visits were telehealth. Fourteen patients (70% of all 20; 78% of 18 question respondents) found the application easy to use. Nine patients (50% of 18 recording patients; 90% of 10 question respondents) reported that the recording helped treatment decision making. Decisional conflict decreased from baseline to 1-week postvisit (47.4-28.5, P < .001). Interviews revealed benefits, facilitators, contextual factors, and technology and patient-related barriers to recordings and summaries. CONCLUSION: In this single-institution academic setting, a mobile application for patients to record consultations was a feasible, acceptable, and potentially valued intervention that improved decision making in the telehealth setting. Studies in larger, diverse populations are needed.
Roles of GARCH and ARCH effects on the stability in stock market crash
Authors: Li Hai-Feng , Xing Dun-Zhong , Huang Qian , Li Jiang-Cheng 
Published: December 2021

Abstract
We theoretically stochastically simulate and empirically analyze the escape process of stock market price non-equilibrium dynamics under the influence of GARCH and ARCH effects, and explore the impact of ARCH and GARCH effects on stock market stability. Based on the nonlinear GARCH model of econophysics, and combined with GARCH and ARCH effects of volatility, we propose a delay stochastic monostable potential model. We use the mean escape time, or mean hitting time, as an indicator for measuring price stability, as first introduced in Valenti D. et al., Phys. Rev. E, 97 (2018) 062307. Based on the comparative analysis of actual Chinese A-share data, the theoretical and empirical findings of this paper are as follows: 1) The theoretical simulation results and actual data are consistent. 2) There exist optimal GARCH and ARCH effects maximally enhancing stock market stability.
Towards high-performance near-infrared photodetectors based on SnS nanowires
Authors: Gu C. F. , Cheng Y. C. , Dai Q. Y. , Liu D. Q. , Lv W. L. , Xv S. N. , Sun L. , Peng Y. Q. , Shu H. B. 
Published: December 2021

AbstractCompared with bulk structures, semiconductor nanowires exhibit a higher surface-to-volume ratio, as well as unique electrical and optical properties. Due to its narrow band gap, tin (ii) sulfide (SnS) nano wire is a promising candidate for constructing near-infrared (NIR) photodetectors. Uniformly distributed and well-aligned SnS nanowires were grown on a mica substrate by chemical vapor deposition, and NIR photodetectors with Au (Au-device) and Al (Al-device) as the electrode were fabricated and characterized. Compared to the Au-device, the Al-device achieved higher photodetectivity due to reduced dark current. More importantly by incorporating a photosensitive lead phthalocyanine (PbPc) film into the Al-device, both responsivity and detectivity could be apparently improved, especially at weak light intensities. Under a weak light intensity of 0.79 mW/cm2the photoresponsivity and specific detectivity were improved fromandJones to 0.96 A/W andJones, respectively.
Controllable molecule waves in the femtosecond regime
Authors: Zhou Shuo , Zhao Jun-Fei , Wang Lei 
Published: December 2021

Abstract
We investigate the nonautonomous molecule waves of the inhomogeneous Hirota equation describing the propagation of femtosecond pulses in inhomogeneous fibers. By employing the characteristic line analysis, the breather molecules of the inhomogeneous Hirota equation under different cases of dispersion and nonlinear modulation are obtained. We find that the inhomogeneous coefficients d
2(z) and d
3(z) have influences on the distance between constituent pulses. In addition, we introduce the state transitions to the nonautonomous breather molecules and reveal that there is no full-transition mode for the inhomogeneous Hirota equation.
Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival
Authors: Kubinyecz Oana , Santos Fatima , Drage Deborah , Reik Wolf , Eckersley-Maslin Melanie A. 
Published: December 2021

ABSTRACT
Zygotic genome activation (ZGA) represents the initiation of transcription following fertilisation. Despite its importance, we know little of the molecular events that initiate mammalian ZGA in vivo. Recent in vitro studies in mouse embryonic stem cells have revealed developmental pluripotency associated 2 and 4 (Dppa2/4) as key regulators of ZGA-associated transcription. However, their roles in initiating ZGA in vivo remain unexplored. We reveal that Dppa2/4 proteins are present in the nucleus at all stages of preimplantation development and associate with mitotic chromatin. We generated conditional single and double maternal knockout mouse models to deplete maternal stores of Dppa2/4. Importantly, Dppa2/4 maternal knockout mice were fertile when mated with wild-type males. Immunofluorescence and transcriptome analyses of two-cell embryos revealed that, although ZGA took place, there were subtle defects in embryos that lacked maternal Dppa2/4. Strikingly, heterozygous offspring that inherited the null allele maternally had higher preweaning lethality than those that inherited the null allele paternally. Together, our results show that although Dppa2/4 are dispensable for ZGA transcription, maternal stores have an important role in offspring survival, potentially via epigenetic priming of developmental genes.
WASp controls oriented migration of endothelial cells to achieve functional vascular patterning
Authors: Rosa André , Giese Wolfgang , Meier Katja , Alt Silvanus , Klaus-Bergmann Alexandra , Edgar Lowell T. , Bartels-Klein Eireen , Collins Russell T. , Szymborska Anna , Coxam Baptiste , Bernabeu Miguel O. , Gerhardt Holger 
Published: December 2021

ABSTRACT
Endothelial cell migration and proliferation are essential for the establishment of a hierarchical organization of blood vessels and optimal distribution of blood. However, how these cellular processes are quantitatively coordinated to drive vascular network morphogenesis remains unknown. Here, using the zebrafish vasculature as a model system, we demonstrate that the balanced distribution of endothelial cells, as well as the resulting regularity of vessel calibre, is a result of cell migration from veins towards arteries and cell proliferation in veins. We identify the Wiskott-Aldrich Syndrome protein (WASp) as an important molecular regulator of this process and show that loss of coordinated migration from veins to arteries upon wasb depletion results in aberrant vessel morphology and the formation of persistent arteriovenous shunts. We demonstrate that WASp achieves its function through the coordination of junctional actin assembly and PECAM1 recruitment and provide evidence that this is conserved in humans. Overall, we demonstrate that functional vascular patterning in the zebrafish trunk is established through differential cell migration regulated by junctional actin, and that interruption of differential migration may represent a pathomechanism in vascular malformations.
A novel role for PRL in regulating epithelial cell density by inducing apoptosis at confluence
Authors: Lohani Sweksha , Funato Yosuke , Akieda Yuki , Mizutani Kiyohito , Takai Yoshimi , Ishitani Tohru , Miki Hiroaki 
Published: December 2021

ABSTRACT
Maintaining proper epithelial cell density is essential for the survival of multicellular organisms. Although regulation of cell density through apoptosis is well known, its mechanistic details remain elusive. Here, we report the involvement of membrane-anchored phosphatase of regenerating liver (PRL), originally known for its role in cancer malignancy, in this process. In epithelial Madin–Darby canine kidney cells, upon confluence, doxycycline-induced expression of PRL upregulated apoptosis, reducing cell density. This could be circumvented by artificially reducing cell density via stretching the cell-seeded silicon chamber. Moreover, small interfering RNA-mediated knockdown of endogenous PRL blocked apoptosis, leading to greater cell density. Mechanistically, PRL promoted apoptosis by upregulating the translation of E-cadherin and activating the TGF-β pathway. Morpholino-mediated inhibition of PRL expression in zebrafish embryos caused developmental defects, with reduced apoptosis and increased epithelial cell density during convergent extension. Overall, this study revealed a novel role for PRL in regulating density-dependent apoptosis in vertebrate epithelia.
This article has an associated First Person interview with the first author of the paper.
Thermoregulatory morphodynamics of honeybee swarm clusters
Authors: Peters Jacob M. , Peleg Orit , Mahadevan L. 
Published: December 2021

ABSTRACT
During reproductive swarming, honeybee clusters of more than 10,000 individuals that hang from structures in the environment (e.g. tree branches) are exposed to diurnal variations in ambient temperature for up to a week. Swarm clusters collectively modulate their morphology in response to these variations (i.e. expanding/contracting in response to heating/cooling) to maintain their internal temperature within a tolerable range and to avoid exhausting their honey stores prematurely. To understand the spatiotemporal aspects of thermoregulatory morphing, we measured the change in size, shape and internal temperature profiles of swarm clusters in response to dynamic temperature ramp perturbations. Swarm clusters showed a two-fold variation in their volume/density when heated from 15°C to 30°C. However, they did not reach an equilibrium size or shape when held at 30°C for 5 h, long after the core temperature of the cluster had stabilized. Furthermore, the changes in cluster shape and size were hysteretic, contracting in response to cooling faster than expanding in response to heating. Although the base contact diameter of the cluster increased continuously when the swarm was heated, the change in length of the swarm (base to tip) over time was non-monotonic. Consequently, the aspect ratio of the swarm fluctuated continuously even when held at a constant temperature. Taken together, our results quantify the hysteretic and anisotropic morphological responses of swarm clusters to ambient temperature variations while suggesting that both mechanical constraints and heat transfer govern their thermoregulatory morphodynamics.