bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient-derived organoids as a platform for modeling a patient’s response to chemoradiotherapy in esophageal cancer
Authors: Karakasheva Tatiana A. , Gabre Joel T. , Sachdeva Uma M. , Cruz-Acuña Ricardo , Lin Eric W. , DeMarshall Maureen , Falk Gary W. , Ginsberg Gregory G. , Yang Zhaohai , Kim Michele M. , Diffenderfer Eric S. , Pitarresi Jason R. , Li Jinyang , Muir Amanda B. , Hamilton Kathryn E. , Nakagawa Hiroshi , Bass Adam J. , Rustgi Anil K. 
Published: October 2021

Abstract3D patient-derived organoids (PDOs) have been utilized to evaluate potential therapies for patients with different cancers. However, the use of PDOs created from treatment-naive patient biopsies for prediction of clinical outcomes in patients with esophageal cancer has not yet been reported. Herein we describe a pilot prospective observational study with the goal of determining whether esophageal cancer PDOs created from treatment naive patients can model or predict clinical outcomes. Endoscopic biopsies of treatment-naive patients at a single tertiary care center were used to generate esophageal cancer PDOs, which were treated with standard-of-care chemotherapy, gamma-irradiation, and newer non-standard approaches, such as proton beam therapy or two small molecule inhibitors. Clinical outcomes of patients following neoadjuvant treatment were compared to their in vitro PDO responses, demonstrating the PDO’s ability to mirror clinical response, suggesting the value of PDOs in prediction of clinical response to new therapeutic approaches. Future prospective clinical trials should test the use of pre-treatment PDOs to identify specific, targeted therapies for individual patients with esophageal adenocarcinoma.
Grip strength as a predictor of depressive symptoms among vulnerable elderly Europeans with musculoskeletal conditions
Authors: Marconcin Priscila , Marques Adilson , Henriques-Neto Duarte , Gouveia Élvio R. , Ferrari Gerson , Peralta Miguel , Ihle Andreas 
Published: October 2021

AbstractThe present study aimed to investigate the grip strength (GS) discrimination capacity and cutoffs points for depressive symptoms among vulnerable elderly individuals with musculoskeletal conditions. The Survey of Health, Aging, and Retirement in Europe wave 6 was analyzed. GS was measured by a handgrip dynamometer, and EURO-D scale was used to assess depressive symptoms. GS cutoff values for depressive symptoms were calculated using the receiver operating characteristics curve. 2206 participants, mean age 74.0 (73.7–74.3), 78.8% with osteoarthritis/other rheumatism, enrolled in the study. Sensitivity varies between 0.44 (men, ≥ 85 years) and 0.82 (men, 75–84 years), and specificity varying between 0.35 (women, 75–84 years) and 0.70 (men 75–84 years). GS is associated with depressive symptoms just for women and it is not possible to use a GS cutoff point for screening depressive symptoms for vulnerable men and women with musculoskeletal conditions over the age of 65 years.
Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1
Authors: Xue Shu-Wen , Tian Yue-Xin , Pan Jin-Cheng , Liu Ya-Ni , Ma Yan-Ling 
Published: October 2021

AbstractPseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His217-His222-Asp372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C7-C8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C7-O and C8-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.
The evaluation of novel oral vaccines based on self-amplifying RNA lipid nanparticles (saRNA LNPs), saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum to neutralize SARS-CoV-2 variants alpha and delta
Authors: Keikha Reza , Hashemi-Shahri Seyed Mohammad , Jebali Ali 
Published: October 2021

AbstractThe aim of this study was to present and evaluate novel oral vaccines, based on self-amplifying RNA lipid nanparticles (saRNA LNPs), saRNA transfected Lactobacillus plantarum LNPs,
and saRNA transfected Lactobacillus plantarum, to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants alpha and delta. After invitro evaluation of the oral vaccines on HEK293T/17 cells, we found that saRNA LNPs, saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum could express S-protein at both mRNA and protein levels. In the next step, BALB/c mice were orally vaccinated with saRNA LNPs, saRNA transfected Lactobacillus plantarum LNPs, and saRNA transfected Lactobacillus plantarum at weeks 1 and 3. Importantly, a high titer of IgG and IgA was observed by all of them, sharply in week 6 (P < 0.05). In all study groups, their ratio of IgG2a/IgG1 was upper 1, indicating Th1-biased responses. Wild-type viral neutralization assay showed that the secreted antibodies in vaccinated mice and recovered COVID-19 patients could neutralize SARS-COV-2 variants alpha and delta. After oral administration of oral vaccines, biodistribution assay was done. It was found that all of them had the same biodistribution pattern. The highest concentration of S-protein was seen in the small intestine, followed by the large intestine and liver.
Influence of psychostimulants and opioids on epigenetic modification of class III histone deacetylase (HDAC)-sirtuins in glial cells
Authors: Sivalingam Kalaiselvi , Doke Mayur , Khan Mansoor A. , Samikkannu Thangavel 
Published: October 2021

AbstractSubstance abuse affects the central nervous system (CNS) and remains a global health problem. Psychostimulants, such as cocaine and methamphetamine (METH), and opioids affect neuronal function and lead to behavioral impairments via epigenetic modification. Epigenetic changes occur via classical pathways, especially the class III histone deacetylase (HDAC)-sirtuin (SIRT) family, that act as cellular sensors to regulate energy homeostasis and coordinate cellular responses to maintain genome integrity. However, SIRT family (1–7)-associated neurodegeneration has not been elucidated in the context of energy metabolism. The present study examined the effects of psychostimulants, such as cocaine and METH, and opioids, such as morphine, on SIRT family (1–7) [class I, II, III and IV] expression and cellular translocation-mediated dysfunction in astrocytes and microglial cells. The “nootropic” drug piracetam played a preventative role against psychostimulant- and opioid-induced SIRT (1–7) expression in astrocytes. These results indicate that cocaine, METH, and morphine affected deacetylation and cellular function, and these changes were prevented by piracetam in astrocytes.
Automated image segmentation method to analyse skeletal muscle cross section in exercise-induced regenerating myofibers
Authors: Rahmati Masoud , Rashno Abdolreza 
Published: October 2021

AbstractSkeletal muscle is an adaptive tissue with the ability to regenerate in response to exercise training. Cross-sectional area (CSA) quantification, as a main parameter to assess muscle regeneration capability, is highly tedious and time-consuming, necessitating an accurate and automated approach to analysis. Although several excellent programs are available to automate analysis of muscle histology, they fail to efficiently and accurately measure CSA in regenerating myofibers in response to exercise training. Here, we have developed a novel fully-automated image segmentation method based on neutrosophic set algorithms to analyse whole skeletal muscle cross sections in exercise-induced regenerating myofibers, referred as MyoView, designed to obtain accurate fiber size and distribution measurements. MyoView provides relatively efficient, accurate, and reliable measurements for CSA quantification and detecting different myofibers, myonuclei and satellite cells in response to the post-exercise regenerating process. We showed that MyoView is comparable with manual quantification. We also showed that MyoView is more accurate and efficient to measure CSA in post-exercise regenerating myofibers as compared with Open-CSAM, MuscleJ, SMASH and MyoVision. Furthermore, we demonstrated that to obtain an accurate CSA quantification of exercise-induced regenerating myofibers, whole muscle cross-section analysis is an essential part, especially for the measurement of different fiber-types. We present MyoView as a new tool to quantify CSA, myonuclei and satellite cells in skeletal muscle from any experimental condition including exercise-induced regenerating myofibers.
Genome-wide identification and expression analysis of the JAZ gene family in turnip
Authors: Jia Kai , Yan Cunyao , Zhang Jing , Cheng Yunxia , Li Wenwen , Yan Huizhuan , Gao Jie 
Published: October 2021

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.
Direct SARS-CoV-2 infection of the human inner ear may underlie COVID-19-associated audiovestibular dysfunction
Authors: Jeong Minjin , Ocwieja Karen E. , Han Dongjun , Wackym P. Ashley , Zhang Yichen , Brown Alyssa , Moncada Cynthia , Vambutas Andrea , Kanne Theodore , Crain Rachel , Siegel Noah , Leger Valerie , Santos Felipe , Welling D. Bradley , Gehrke Lee , Stankovic Konstantina M. 
Published: October 2021

Abstract
Background
COVID-19 is a pandemic respiratory and vascular disease caused by SARS-CoV-2 virus. There is a growing number of sensory deficits associated with COVID-19 and molecular mechanisms underlying these deficits are incompletely understood.

Methods
We report a series of ten COVID-19 patients with audiovestibular symptoms such as hearing loss, vestibular dysfunction and tinnitus. To investigate the causal relationship between SARS-CoV-2 and audiovestibular dysfunction, we examine human inner ear tissue, human inner ear in vitro cellular models, and mouse inner ear tissue.

Results
We demonstrate that adult human inner ear tissue co-expresses the angiotensin-converting enzyme 2 (ACE2) receptor for SARS-CoV-2 virus, and the transmembrane protease serine 2 (TMPRSS2) and FURIN cofactors required for virus entry. Furthermore, hair cells and Schwann cells in explanted human vestibular tissue can be infected by SARS-CoV-2, as demonstrated by confocal microscopy. We establish three human induced pluripotent stem cell (hiPSC)-derived in vitro models of the inner ear for infection: two-dimensional otic prosensory cells (OPCs) and Schwann cell precursors (SCPs), and three-dimensional inner ear organoids. Both OPCs and SCPs express ACE2, TMPRSS2, and FURIN, with lower ACE2 and FURIN expression in SCPs. OPCs are permissive to SARS-CoV-2 infection; lower infection rates exist in isogenic SCPs. The inner ear organoids show that hair cells express ACE2 and are targets for SARS-CoV-2.

Conclusions
Our results provide mechanistic explanations of audiovestibular dysfunction in COVID-19 patients and introduce hiPSC-derived systems for studying infectious human otologic disease.
A two-dimensional polymer memristor based on conformational changes with tunable resistive switching behaviours
Authors: Song Yaru , Feng Guangyuan , Wu Lingli , Zhang Enbing , Sun Chenfang , Fa Dejuan , Liang Qiu , Lei Shengbin , Yu Xi , Hu Wenping 
Published: October 2021

A resistive switching memory device based on a 2DPTPAK+TAPB film with the conformational change mechanism was prepared and the memory behaviors can be adjusted by the degree of conformational changes.
Zn(NH3)CO3: a “three-in-one” UV nonlinear optical crystal built by a polar molecule bonding strategy
Authors: Tang Hong-Xin , Shui Qi-Rui , Fu Rui-Biao , Zhou Zi-Qi , Bao Wen-Xiu , Ma Zu-Ju , Wu Xin-Tao 
Published: October 2021

Centimeter-sized Zn(NH3)CO3 is a “three-in-one” UV nonlinear optical crystal, featuring a Chinese-knot-like framework and great optical performance.
Fuzzy model‐based multi‐objective dynamic programming with modified particle swarm optimization approach for the balance control of bicycle robot
Authors: Sun Yiyong , Zhao Haotian , Chen Zhang , Zheng Xudong , Zhao Mingguo , Liang Bin 
Published: October 2021

AbstractExisting studies for the balance control of unmanned bicycle robots only consider constant forward velocity and a single optimal objective that cannot be applied to the complex motion situation. To balance the bicycle robot with time‐varying forward velocity, only with the steering actuator, the multiple objective optimal balance control issue is studied here. A fuzzy state‐space model under different forward velocities is firstly offered based on the non‐linear Euler–Lagrange model. Based on this, a closed‐loop equation under a fuzzy controller is verified. To regulate the feedback gain of the fuzzy controller, a modified particle swarm optimization (MPSO) algorithm with two stages is proposed. In the MPSO's second stage, a novel objective fitness function, consisting of multiple objectives and combining the conventional Hurwitz stability analysis criterium, is designed. Procedures for the MPSO dynamic programming approach are presented. By two examples, the efficiency of the MPSO algorithm, for time‐varying and time‐constant velocity situations, and faster capacity for iteration convergence, are examined.
A novel deep reinforcement learning enabled agent for pumped storage hydro‐wind‐solar systems voltage control
Authors: Huang Qin , Hu Weihao , Zhang Guozhou , Cao Di , Liu Zhou , Huang Qi , Chen Zhe 
Published: October 2021

AbstractWith the large‐scale penetration of wind and solar energies in the power system, the randomness of this renewable energy increases the non‐linear characteristics and uncertainty of the system, which causes a mismatch between renewable energy generation and load demand and it will badly affect the bus voltage control of distribution network. In this context, this study applies pumped storage hydroelectric (PSH) which tracks the load variation rapidly, operate flexibly and reliably to balance the power of the system to minimize the bus voltage deviation. Moreover, to obtain the optimal control policy of PSH, a deep‐reinforcement‐learning algorithm, that is, deep deterministic policy gradient, is utilized to train the agent to address the continuous transformation of the pumped storage hydro‐wind‐solar (PSHWS) system. The performance of a well‐trained agent was evaluated on the IEEE 30‐bus power system. Simulation results show that the proposed method achieves an improvement of 21.8% in cumulative deviation per month, which implies that it can keep the system operating in a safe voltage range more effectively.
A review of power system predictive failure model for resilience enhancement against hurricane events
Authors: Omogoye Okeolu Samuel , Folly Komla Agbenyo , Awodele Kehinde Oladayo 
Published: October 2021

AbstractNatural events such as hurricanes usually cause unimaginable destruction to the electric power system infrastructures across the globe leading to large‐scale power outages. While the transmission network offers relatively high resilience to the hurricane extreme wind speed intensity (HEWSI), the distribution power system network (DPSN) is always the worst hit. To enhance the DPSN against hurricane events, both the pre‐ and post‐event power system resilience enhancement techniques can be reviewed, and their limitations improved. Handling hurricane risks proactively for effective recovery plans requires rigorous techniques for locating and estimating the number of system component's damage causing outages on a DPSN. A review of the resilience evaluation methodologies utilized for a proactive statistical system component's failure predictive model is presented in this paper. As a contribution, this article presents the current practices, the problems, and points out the future research directions for a statistical system components’ line outage predictive model that can greatly enhance the DPSN against hurricane events for short‐term operational planning.
Photoprocessing of H2S on dust grains
Authors: Cazaux S. , Carrascosa H. , Muñoz Caro G. M. , Caselli P. , Fuente A. , Navarro-Almaida D. , Riviére-Marichalar P. 
Published: October 2021

Context. Sulfur is a biogenic element used as a tracer of the evolution of interstellar clouds to stellar systems. However, most of the expected sulfur in molecular clouds remains undetected. Sulfur disappears from the gas phase in two steps. The first depletion occurs during the translucent phase, reducing the gas-phase sulfur by 7–40 times, while the following freeze-out step occurs in molecular clouds, reducing it by another order of magnitude. This long-standing question awaits an explanation.
Aims. The aim of this study is to understand under what form the missing sulfur is hiding in molecular clouds. The possibility that sulfur is depleted onto dust grains is considered.
Methods. Experimental simulations mimicking H2S ice UV photoprocessing in molecular clouds were conducted at 8 K under ultra-high vacuum. The ice was subsequently warmed up to room temperature. The ice was monitored using infrared spectroscopy, and the desorbing molecules were measured by quadrupole mass spectrometry in the gas phase. Theoretical Monte Carlo simulations were performed for interpretation of the experimental results and extrapolation to the astrophysical and planetary conditions.
Results. H2S2 formation was observed during irradiation at 8 K. Molecules H2Sx with x > 2 were also identified and found to desorb during warm-up, along with S2 to S4 species. Larger Sx molecules up to S8 are refractory at room temperature and remained on the substrate forming a residue. Monte Carlo simulations were able to reproduce the molecules desorbing during warming up, and found that residues are chains of sulfur consisting of 6–7 atoms.
Conclusions. Based on the interpretation of the experimental results using our theoretical model, it is proposed that S+ in translucent clouds contributes notoriously to S depletion in denser regions by forming long S chains on dust grains in a few times 104 yr. We suggest that the S2 to S4 molecules observed in comets are not produced by fragmentation of these large chains. Instead, they probably come either from UV photoprocessing of H2S-bearing ice produced in molecular clouds or from short S chains formed during the translucent cloud phase.
Stellar populations with MEGARA: The inner regions of NGC 7025
Authors: Chamorro-Cazorla M. , Gil de Paz A. , Castillo-Morales A. , Dullo B. T. , Gallego J. , Carrasco E. , Iglesias-Páramo J. , Cedazo R. , García-Vargas M. L. , Pascual S. , Cardiel N. , Pérez-Calpena A. , Gómez-Álvarez P. , Martínez-Delgado I. , Catalán-Torrecilla C. 
Published: October 2021

Context. This paper aims to determine the capabilities of the MEGARA spectrograph at the Gran Telescopio Canarias (GTC), which is an optical integral-field unit, for studying stellar populations. We also aim to exploit its combination of high spectral (R ∼ 6000, 12 000 and 20 000) and spatial (0.62″) resolution within its 12″​​.5 × 11″​​.3 field of view. We do this by analysing the commissioning data of the nearby S0a galaxy NGC 7025.
Aims. We establish a systematic method through which we can determine the properties of the stellar populations in the observations made with MEGARA, more specifically, within the MEGADES legacy project. For this paper in particular, we determine the properties of the stellar populations of NGC 7025.
Methods. We used MEGARA observations of galaxy NGC 7025 that were taken during the commissioning phase of the instrument. We applied different approaches to estimate the properties of the stellar populations with the highest possible certainty. In addition to the specific study of NGC 7025 and in the context of the MEGADES survey, we have carried out a number of tests to determine the expected errors (including potential biases) in these star formation history (SFH) derivations as a function of these parameters, namely spectral setup, signal-to-noise ratio, σ, and the SFH itself.
Results. All the studies we conduct (both full spectral fitting and absorption line indices) of the stellar populations of NGC 7025 indicate that the stars that form its bulge have supersolar metallicity and considerably old ages (∼10 Gyr) in general. Using three different combinations of MEGARA spectral setups, we determined that the bulge of NGC 7025 has smild negative mass-weighted age gradient. For the more detailed SFH, our results indicate that in addition to a rather constant star formation at early epochs, a peak in the formation history of the stars in the bulge is also found 3.5–4.5 Gyr ago. This partly explains the mass-weighted age gradients we measured.
Conclusions. The scenario presented in NGC 7025 is that of an isolated galaxy under secular evolution that about 3.5–4.5 Gyr ago likely experienced a minor merger (mass ratio 1/10) that induced an increase in star formation and also perturbed the morphology of its outer disc. In addition to these specific results for NGC 7025, we report different lessons learned for the ongoing exploitation of the MEGADES survey with the GTC, such as the need to obtain combined observations in the LR-B + LR-V setups and a signal-to-noise ratio of at least 20 per Å.