bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rethinking glottal midline detection
Authors: Kist Andreas M. , Zilker Julian , Gómez Pablo , Schützenberger Anne , Döllinger Michael 
Published: November 2020

AbstractA healthy voice is crucial for verbal communication and hence in daily as well as professional life. The basis for a healthy voice are the sound producing vocal folds in the larynx. A hallmark of healthy vocal fold oscillation is the symmetric motion of the left and right vocal fold. Clinically, videoendoscopy is applied to assess the symmetry of the oscillation and evaluated subjectively. High-speed videoendoscopy, an emerging method that allows quantification of the vocal fold oscillation, is more commonly employed in research due to the amount of data and the complex, semi-automatic analysis. In this study, we provide a comprehensive evaluation of methods that detect fully automatically the glottal midline. We used a biophysical model to simulate different vocal fold oscillations, extended the openly available BAGLS dataset using manual annotations, utilized both, simulations and annotated endoscopic images, to train deep neural networks at different stages of the analysis workflow, and compared these to established computer vision algorithms. We found that classical computer vision perform well on detecting the glottal midline in glottis segmentation data, but are outperformed by deep neural networks on this task. We further suggest GlottisNet, a multi-task neural architecture featuring the simultaneous prediction of both, the opening between the vocal folds and the symmetry axis, leading to a huge step forward towards clinical applicability of quantitative, deep learning-assisted laryngeal endoscopy, by fully automating segmentation and midline detection.
MicroRNA retrocopies generated via L1-mediated retrotransposition in placental mammals help to reveal how their parental genes were transcribed
Authors: Pan Cheng-Tsung , Lin Yeong-Shin 
Published: November 2020

AbstractIn mammalian genomes, most retrocopies emerged via the L1 retrotransposition machinery. The hallmarks of an L1-mediated retrocopy, i.e., the intronlessness, the presence of a 3′ poly-A tail, and the TSDs at both ends, were frequently used to identify retrotransposition events. However, most previous studies only focused on protein-coding genes as their possible parental sources and thus only a few retrocopies derived from non-coding genes were reported. Remarkably, none of them was from microRNAs. Here in this study, we found several retrocopies generated from the mir-302–367 cluster gene (MIR302CHG), and identified a novel alternatively spliced exon encoding mir-302a. The other recognized microRNA retrotransposition events are primate-specific with mir-373 and mir-498 as their parental genes. The 3′ poly-A tracts of these two retrocopy groups were directly attached to the end of the microRNA precursor homologous regions, which suggests that their parental transcripts might alternatively terminate at the end of mir-373 and mir-498. All the three parental microRNAs are highly expressed in specific tissues with elevated retrotransposon activity, such as the embryonic stem cells and the placenta. This might be the reason that our first microRNA retrocopy findings were derived from these three microRNA genes.
TRPM2 promotes autophagic degradation in vascular smooth muscle cells
Authors: Zhao Qiannan , Li Jingxuan , Ko Wing-Hung , Kwan Yiu-Wa , Jiang Liwen , Sun Lei , Yao Xiaoqiang 
Published: November 2020

AbstractTransient receptor potential channel M2 (TRPM2) is a Ca2+-permeable channel that is activated by reactive oxygen species (ROS). In many cell types, ROS activate TRPM2 to induce excessive Ca2+ influx, resulting in Ca2+ overload and consequent cell death. Recent studies suggest that TRPM2 may also regulate autophagy in pericytes and cancer cells by acting on the early step of autophagy, i.e. autophagic induction. However, there is no report on the role of TRPM2 in autophagic degradation, which is the late stage of autophagy. In the present study, we found abundant TRPM2 expression in lysosomes/autolysosomes in the primary cultured mouse aortic smooth muscle cells (mASMCs). Nutrient starvation stimulated autophagic flux in mASMCs mainly by promoting autophagic degradation. This starvation-induced autophagic degradation was reduced by TRPM2 knockout. Importantly, starvation-induced lysosomal/autolysosomal acidification and cell death were also substantially reduced by TRPM2 knockout. Taken together, the present study uncovered a novel mechanism that lysosomal TRPM2 facilitates lysosomal acidification to stimulate excessive autolysosome degradation and consequent cell death.
Modeling the effects of hyaluronic acid degradation on the regulation of human astrocyte phenotype using multicomponent interpenetrating polymer networks (mIPNs)
Authors: Jimenez-Vergara Andrea C. , Van Drunen Rachel , Cagle Tyler , Munoz-Pinto Dany J. 
Published: November 2020

AbstractHyaluronic acid (HA) is a highly abundant component in the extracellular matrix (ECM) and a fundamental element to the architecture and the physiology of the central nervous system (CNS). Often, HA degradation occurs when an overreactive inflammatory response, derived from tissue trauma or neurodegenerative diseases such as Alzheimer’s, causes the ECM in the CNS to be remodeled. Herein, we studied the effects of HA content as a key regulator of human astrocyte (HAf) reactivity using multicomponent interpenetrating polymer networks (mIPNs) comprised of Collagen I, HA and poly(ethylene glycol) diacrylate. The selected platform facilities the modulation of HA levels independently of matrix rigidity. Total astrocytic processes length, number of endpoints, the expression of the quiescent markers: Aldehyde Dehydrogenase 1 Family Member L1 (ALDH1L1) and Glutamate Aspartate Transporter (GLAST); the reactive markers: Glial Fibrillary Acidic Protein (GFAP) and S100 Calcium-Binding Protein β (S100β); and the inflammatory markers: Inducible Nitric Oxide Synthase (iNOS), Interleukin 1β (IL-1β) and Tumor Necrosis Factor Alpha (TNFα), were assessed. Cumulatively, our results demonstrated that the decrease in HA concentration elicited a reduction in the total length of astrocytic processes and an increase in the expression of HAf reactive and inflammatory markers.
A novel noninvasive approach for evaluating work of breathing indices in a developmental rat model using respiratory inductance plethysmography
Authors: Zhu Yan , Aghai Zubair H. , Betal Suhita Gayen Nee , Favara Michael , Fong Gina , Rahman Tariq , Shaffer Thomas H. 
Published: November 2020

AbstractPulmonary function testing (PFT) is an important component for evaluating the outcome of experimental rodent models of respiratory diseases. Respiratory inductance plethysmography (RIP) provides a noninvasive method of PFT requiring minimal cooperation. RIP measures work of breathing (WOB) indices including phase angle (Ф), percent rib cage (RC %), breaths per minute (BPM), and labored breathing index (LBI) on an iPad. The aim of this study was to evaluate the utility of a recently developed research instrument, pneuRIP, for evaluation of WOB indices in a developmental rat model. Sprague Dawley rats (2 months old) were commercially acquired and anaesthetised with isoflurane. The pneuRIP system uses two elastic bands: one band (RC) placed around the rib cage under the upper armpit and another band (AB) around the abdomen. The typical thoracoabdominal motion (TAM) plot showed the abdomen and rib cage motion in synchrony. The plots of phase angle and LBI as a function of data point number showed that values were within the range. The distribution for phase angle and LBI was within a narrow range. pneuRIP testing provided instantaneous PFT results. This study demonstrated the utility of RIP as a rapid, noninvasive approach for evaluating treatment interventions in the rodent model.
Recurrent SARS-CoV-2 RNA positivity after COVID-19: a systematic review and meta-analysis
Authors: Azam Mahalul , Sulistiana Rina , Ratnawati Martha , Fibriana Arulita Ika , Bahrudin Udin , Widyaningrum Dian , Aljunid Syed Mohamed 
Published: November 2020

AbstractPresent study aimed to estimate the incidence of recurrent SARS-CoV-2 RNA positivity after recovery from COVID-19 and to determine the factors associated with recurrent positivity. We searched the PubMed, MedRxiv, BioRxiv, the Cochrane Library, ClinicalTrials.gov, and the World Health Organization International Clinical Trials Registry for studies published to June 12, 2020. Studies were reviewed to determine the risk of bias. A random-effects model was used to pool results. Heterogeneity was assessed using I2. Fourteen studies of 2568 individuals were included. The incidence of recurrent SARS-CoV-2 positivity was 14.8% (95% confidence interval [CI] 11.44–18.19%). The pooled estimate of the interval from disease onset to recurrence was 35.4 days (95% CI 32.65–38.24 days), and from the last negative to the recurrent positive result was 9.8 days (95% CI 7.31–12.22 days). Patients with younger age and a longer initial illness were more likely to experience recurrent SARS-CoV-2 positivity, while patients with diabetes, severe disease, and a low lymphocyte count were less likely to experience. Present study concluded that the incidence of recurrent SARS-CoV-2 positivity was 14.8% suggesting further studies must be conducted to elucidate the possibility of infectious individuals with prolonged or recurrent RNA positivity.
Quantifying human mobility behaviour changes during the COVID-19 outbreak in the United States
Authors: Pan Yixuan , Darzi Aref , Kabiri Aliakbar , Zhao Guangchen , Luo Weiyu , Xiong Chenfeng , Zhang Lei 
Published: November 2020

AbstractSince the first case of the novel coronavirus disease (COVID-19) was confirmed in Wuhan, China, social distancing has been promoted worldwide, including in the United States, as a major community mitigation strategy. However, our understanding remains limited in how people would react to such control measures, as well as how people would resume their normal behaviours when those orders were relaxed. We utilize an integrated dataset of real-time mobile device location data involving 100 million devices in the contiguous United States (plus Alaska and Hawaii) from February 2, 2020 to May 30, 2020. Built upon the common human mobility metrics, we construct a Social Distancing Index (SDI) to evaluate people’s mobility pattern changes along with the spread of COVID-19 at different geographic levels. We find that both government orders and local outbreak severity significantly contribute to the strength of social distancing. As people tend to practice less social distancing immediately after they observe a sign of local mitigation, we identify several states and counties with higher risks of continuous community transmission and a second outbreak. Our proposed index could help policymakers and researchers monitor people’s real-time mobility behaviours, understand the influence of government orders, and evaluate the risk of local outbreaks.
The earliest diverging extant scleractinian corals recovered by mitochondrial genomes
Authors: Seiblitz Isabela G. L. , Capel Kátia C. C. , Stolarski Jarosław , Quek Zheng Bin Randolph , Huang Danwei , Kitahara Marcelo V. 
Published: November 2020

AbstractEvolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging “Basal” lineage remains poorly studied compared to “Robust” and “Complex” corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas
Authors: Tran Paul M. H. , Tran Lynn K. H. , Nechtman John , dos Santos Bruno , Purohit Sharad , Satter Khaled Bin , Dun Boying , Kolhe Ravindra , Sharma Suash , Bollag Roni , She Jin-Xiong 
Published: November 2020

AbstractGliomas are currently classified through integration of histology and mutation information, with new developments in DNA methylation classification. However, discrepancies exist amongst the major classification methods. This study sought to compare transcriptome-based classification to the established methods. RNAseq and microarray data were obtained for 1032 gliomas from the TCGA and 395 gliomas from REMBRANDT. Data were analyzed using unsupervised and supervised learning and other statistical methods. Global transcriptomic profiles defined four transcriptomic glioma subgroups with 91.4% concordance with the WHO-defined mutation subtypes. Using these subgroups, 168 genes were selected for the development of 1000 linear support vector classifiers (LSVC). Based on plurality voting of 1000 LSVC, the final ensemble classifier confidently classified all but 17 TCGA gliomas to one of the four transcriptomic profile (TP) groups. The classifier was validated using a gene expression microarray dataset. TP1 cases include IDHwt, glioblastoma high immune infiltration and cellular proliferation and poor survival prognosis. TP2a is characterized as IDHmut-codel, oligodendrogliomas with high tumor purity. TP2b tissue is mostly composed of neurons and few infiltrating malignant cells. TP3 exhibit increased NOTCH signaling, are astrocytoma and IDHmut-non-codel. TP groups are highly concordant with both WHO integrated histology and mutation classification as well as methylation-based classification of gliomas. Transcriptomic profiling provides a robust and objective method to classify gliomas with high agreement to the current WHO guidelines and may provide additional survival prediction to the current methods.
Continuous and non-invasive thermography of mouse skin accurately describes core body temperature patterns, but not absolute core temperature
Authors: van der Vinne Vincent , Pothecary Carina A. , Wilcox Sian L. , McKillop Laura E. , Benson Lindsay A. , Kolpakova Jenya , Tam Shu K. E. , Krone Lukas B. , Fisk Angus S. , Wilson Tatiana S. , Yamagata Tomoko , Cantley James , Vyazovskiy Vladyslav V. , Peirson Stuart N. 
Published: November 2020

AbstractBody temperature is an important physiological parameter in many studies of laboratory mice. Continuous assessment of body temperature has traditionally required surgical implantation of a telemeter, but this invasive procedure adversely impacts animal welfare. Near-infrared thermography provides a non-invasive alternative by continuously measuring the highest temperature on the outside of the body (Tskin), but the reliability of these recordings as a proxy for continuous core body temperature (Tcore) measurements has not been assessed. Here, Tcore (30 s resolution) and Tskin (1 s resolution) were continuously measured for three days in mice exposed to ad libitum and restricted feeding conditions. We subsequently developed an algorithm that optimised the reliability of a Tskin-derived estimate of Tcore. This identified the average of the maximum Tskin per minute over a 30-min interval as the optimal way to estimate Tcore. Subsequent validation analyses did however demonstrate that this Tskin-derived proxy did not provide a reliable estimate of the absolute Tcore due to the high between-animal variability in the relationship between Tskin and Tcore. Conversely, validation showed that Tskin-derived estimates of Tcore reliably describe temporal patterns in physiologically-relevant Tcore changes and provide an excellent measure to perform within-animal comparisons of relative changes in Tcore.
ZnAl nano layered double hydroxides for dual functional CRISPR/Cas9 delivery and enhanced green fluorescence protein biosensor
Authors: Rabiee Navid , Bagherzadeh Mojtaba , Ghadiri Amir Mohammad , Salehi Ghazal , Fatahi Yousef , Dinarvand Rassoul 
Published: November 2020

AbstractEvaluation of the effect of different parameters for designing a non-viral vector in gene delivery systems has great importance. In this manner, 2D crystals, precisely layered double hydroxides, have attracted the attention of scientists due to their significant adjustability and low-toxicity and low-cost preparation procedure. In this work, the relationship between different physicochemical properties of LDH, including pH, size, zeta potential, and synthesis procedure, was investigated and optimized for CRISPR/Cas9 delivery and reverse fluorescence response to the EGFP. In this manner, ZnAl LDH and ZnAl HMTA LDH were synthesized and characterized and applied in the HEK-293 cell line to deliver CRISPR/Cas9. The results were optimized by different characterizations as well as Gel Electrophoresis and showed acceptable binding ability with the DNA that could be considered as a promising and also new gold-standard for the delivery of CRISPR/Cas9. Also, the relationship of the presence of tertiary amines (in this case, hexamethylenetetramine (HMTA) as the templates) in the structure of the ZnAl LDH, as well as the gene delivery application, was evaluated. The results showed more than 79% of relative cell viability in most of the weight ratios of LDH to CRISPR/Cas9; fully quenching the fluorescence intensity of the EGFP/LDH in the presence of 15 µg mL−1 of the protoporphyrins along with the detection limit of below 2.1 µg mL−1, the transfection efficiency of around 33% of the GFP positive cell for ZnAl LDH and more than 38% for the ZnAl LDH in the presence of its tertiary amine template.
3D printable biomimetic rod with superior buckling resistance designed by machine learning
Authors: Challapalli Adithya , Li Guoqiang 
Published: November 2020

AbstractOur mother nature has been providing human beings with numerous resources to inspire from, in building a finer life. Particularly in structural design, plenteous notions are being drawn from nature in enhancing the structural capacity as well as the appearance of the structures. Here plant stems, roots and various other structures available in nature that exhibit better buckling resistance are mimicked and modeled by finite element analysis to create a training database. The finite element analysis is validated by uniaxial compression to buckling of 3D printed biomimetic rods using a polymeric ink. After feature identification, forward design and data filtering are conducted by machine learning to optimize the biomimetic rods. The results show that the machine learning designed rods have 150% better buckling resistance than all the rods in the training database, i.e., better than the nature’s counterparts. It is expected that this study opens up a new opportunity to design engineering rods or columns with superior buckling resistance such as in bridges, buildings, and truss structures.
Very Large Array observations of the mini-halo and AGN feedback in the Phoenix cluster
Authors: Timmerman R. , van Weeren R. J. , McDonald M. , Ignesti A. , McNamara B. R. , Hlavacek-Larrondo J. , Röttgering H. J. A. 
Published: November 2020

Context. The relaxed cool-core Phoenix cluster (SPT-CL J2344-4243) features an extremely strong cooling flow, as well as a mini halo. Strong star formation in the brightest cluster galaxy indicates that active galactic nucleus (AGN) feedback has been unable to inhibit this cooling flow.
Aims. We aim to study the strong cooling flow in the Phoenix cluster by determining the radio properties of the AGN and its lobes. In addition, we used spatially resolved radio observations to investigate the origin of the mini halo.
Methods. We present new multifrequency Very Large Array 1–12 GHz observations of the Phoenix cluster, which resolve the AGN and its lobes in all four frequency bands as well as the mini-halo in the L and S bands.
Results. Using our L-band observations, we measure the total flux density of the radio lobes at 1.5 GHz to be 7.6 ± 0.8 mJy, and the flux density of the mini halo to be 8.5 ± 0.9 mJy. Using high-resolution images in the L and X bands, we produced the first spectral index maps of the lobes from the AGN and find the spectral indices of the northern and southern lobes to be −1.35 ± 0.07 and −1.30 ± 0.12, respectively. Similarly, using L- and S-band data, we mapped the spectral index of the mini halo, and obtain an integrated spectral index of α = −0.95 ± 0.10.
Conclusions. We find that the mini halo is most likely formed by turbulent re-acceleration powered by sloshing in the cool core due to a recent merger. In addition, we find that the feedback in the Phoenix cluster is consistent with the picture that stronger cooling flows are to be expected for massive clusters such as this one, as these may feature an underweight supermassive black hole due to their merging history. Strong time variability of the AGN on Myr timescales may help explain the disconnection between the radio and the X-ray properties of the system. Finally, a small amount of jet precession of the AGN likely contributes to the relatively low intracluster medium re-heating efficiency of the mechanical feedback.
Experience of practices of urban territorial Planning of Belarus
Authors: Panchenko Tatyana 
Published: November 2020

Rapid urbanization is one of the most significant global trends in an increasingly interconnected world. This means a new global approach to assessing the role of cities in the economy, climate change, use and consumption of natural resources as well as their contribution to social and innovative development. Globalization and large-scale urbanization, combined with smart technologies, are rapidly changing the world around us, the structure of economic activity and the way people live. After the publication in 1987 the report “Our Common Future” by the UN World Commission on Environment and Development, the conference in Rio de Janeiro in 1992 and other international initiatives by 2008 declarations, framework directives, strategies and methodologies for sustainable development and the creation of “green” economy were adopted.
Taking into account the historically high level of urbanization in our country (70.08% of the population lives in cities) [1], in recent years, legislative instruments of the local (city) level, aimed at using the tools of integrated territorial planning, have begun to form. The article describes the experience of urban territorial planning practices in Novogrudok, Polotsk, Novopolotsk and Brest for which local strategic documents of a new type have now been developed: “Green Urban Development Plans” and the Concept of Smart Sustainable Development.