bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skeletal muscle gene expression dysregulation in long-term spaceflights and aging is clock-dependent
Authors: Malhan Deeksha , Yalçin Müge , Schoenrock Britt , Blottner Dieter , Relógio Angela 
Published: April 2023

AbstractThe circadian clock regulates cellular and molecular processes in mammals across all tissues including skeletal muscle, one of the largest organs in the human body. Dysregulated circadian rhythms are characteristic of aging and crewed spaceflight, associated with, for example, musculoskeletal atrophy. Molecular insights into spaceflight-related alterations of circadian regulation in skeletal muscle are still missing. Here, we investigated potential functional consequences of clock disruptions on skeletal muscle using published omics datasets obtained from spaceflights and other clock-altering, external (fasting and exercise), or internal (aging) conditions on Earth. Our analysis identified alterations of the clock network and skeletal muscle-associated pathways, as a result of spaceflight duration in mice, which resembles aging-related gene expression changes observed in humans on Earth (e.g., ATF4 downregulation, associated with muscle atrophy). Furthermore, according to our results, external factors such as exercise or fasting lead to molecular changes in the core-clock network, which may compensate for the circadian disruption observed during spaceflights. Thus, maintaining circadian functioning is crucial to ameliorate unphysiological alterations and musculoskeletal atrophy reported among astronauts.
Dopamine facilitates the translation of physical exertion into assessments of effort
Authors: Padmanabhan Purnima , Casamento-Moran Agostina , Kim Aram , Gonzalez Anthony J. , Pantelyat Alexander , Roemmich Ryan T. , Chib Vikram S. 
Published: April 2023

AbstractOur assessments of effort are critically shaped by experiences of exertion. However, it is unclear how the nervous system transforms physical exertion into assessments of effort. Availability of the neuromodulator dopamine influences features of motor performance and effort-based decision-making. To test dopamine’s role in the translation of effortful exertion into assessments of effort, we had participants with Parkinson’s disease, in dopamine depleted (OFF dopaminergic medication) and elevated (ON dopaminergic medication) states, exert levels of physical exertion and retrospectively assess how much effort they exerted. In a dopamine-depleted state, participants exhibited increased exertion variability and over-reported their levels of exertion, compared to the dopamine-supplemented state. Increased exertion variability was associated with less accurate effort assessment and dopamine had a protective influence on this effect, reducing the extent to which exertion variability corrupted assessments of effort. Our findings provide an account of dopamine’s role in the translation of features of motor performance into judgments of effort, and a potential therapeutic target for the increased sense of effort observed across a range of neurologic and psychiatric conditions.
Regulation of human trophoblast gene expression by endogenous retroviruses
Authors: Frost Jennifer M. , Amante Samuele M. , Okae Hiroaki , Jones Eleri M. , Ashley Brogan , Lewis Rohan M. , Cleal Jane K. , Caley Matthew P. , Arima Takahiro , Maffucci Tania , Branco Miguel R. 
Published: April 2023

AbstractThe placenta is a fast-evolving organ with large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programs. Here we assess the contribution of transposable elements to human trophoblast gene expression as enhancers or promoters. Using epigenomic data from primary human trophoblast and trophoblast stem-cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential expression in trophoblast. These largely primate-specific elements are associated with inter-species gene expression differences and are bound by transcription factors with key roles in placental development. Using genetic editing, we demonstrate that several elements act as transcriptional enhancers of important placental genes, such as CSF1R and PSG5. We also identify an LTR10A element that regulates ENG expression, affecting secretion of soluble endoglin, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.
Synthesis of innovative and sustainable gelatin@graphene oxide-crosslinked-zirconium silicate@gelatin nanobiosorbent for effective biosorption of basic fuchsin dye
Authors: Mahmoud Mohamed E. , Nabil Gehan M. , Elsayed Sarah M. , Rashad Amal R. 
Published: April 2023

AbstractMost dye stuffs and coloring materials are mainly categorized as hazardous pollutants in water effluents due to their nature as non-biodegradable, highly toxic and extremely carcinogenic. For this reason, rapid and efficient eradication of waste dyes from wastewaters before discharging into water streams must be accomplished by an acceptable approach as adsorption technique. Therefore, the present study is aimed and devoted to synthesize a novel nanobiosorbent from three different constituents, gelatin (Gel) as a sustainable natural product, graphene oxide (GO) as an example of highly stable carbonaceous material and zirconium silicate (ZrSiO4) as an example of combined metal oxides for the formation of Gel@GO-F-ZrSiO4@Gel by using formaldehyde (F) as a cross-linkage reagent. Several characterization techniques as FT-IR were employed to identify the incorporated surface reactive Functionalities in Gel@GO-F-ZrSiO4@Gel as –OH, =NH, –NH2, –COOH and C=O, etc. The morphology for particle shape and size of Gel@GO-F-ZrSiO4@Gel were confirmed from the SEM and TEM analyses providing 15.75- 32.79 nm. The surface area was determined by the BET and found to correspond to 219.46 m2 g-1. Biosorptive removal of basic fuchsin (BF) pollutant as an example of a widely applicable dye in various activities was monitored and optimized under the influence of pH (2–10), reaction time (1–30 min), initial BF pollutant concentration (5–100 mg L−1), nanobiosorbent dosage (5–60 mg), temperature (30–60 °C) and interfering ions. The maximum biosorptive removal values of BF dye were established as 96.0 and 95.2% using 5 and 10 mg L−1, respectively at the recommended pH 7 condition. The Thermodynamic parameters demonstrated that the BF dye adsorption onto Gel@GO-F-ZrSiO4@Gel was taken place via spontaneous and endothermic reaction. Chemisorption is the predominant adsorption mechanism by forming multilayers upon nonhomogeneous surface in accordance with Freundlich model hypothesis. The applicability of the optimized Gel@GO-F-ZrSiO4@Gel in biosorptive removal of BF pollutant from real water sample was successfully accomplished by the batch technique. Thus, this study clearly shows that Gel@GO-F-ZrSiO4@Gel exhibited significant influences on remediation of industrial effluents containing BF pollutant with superior efficiency.
Machine learning unifies flexibility and efficiency of spinodal structure generation for stochastic biomaterial design
Authors: Wang Zhuo , Dabaja Rana , Chen Lei , Banu Mihaela 
Published: April 2023

AbstractPorous biomaterials design for bone repair is still largely limited to regular structures (e.g. rod-based lattices), due to their easy parameterization and high controllability. The capability of designing stochastic structure can redefine the boundary of our explorable structure–property space for synthesizing next-generation biomaterials. We hereby propose a convolutional neural network (CNN) approach for efficient generation and design of spinodal structure—an intriguing structure with stochastic yet interconnected, smooth, and constant pore channel conducive to bio-transport. Our CNN-based approach simultaneously possesses the tremendous flexibility of physics-based model in generating various spinodal structures (e.g. periodic, anisotropic, gradient, and arbitrarily large ones) and comparable computational efficiency to mathematical approximation model. We thus successfully design spinodal bone structures with target anisotropic elasticity via high-throughput screening, and directly generate large spinodal orthopedic implants with desired gradient porosity. This work significantly advances stochastic biomaterials development by offering an optimal solution to spinodal structure generation and design.
Channel activity of SARS-CoV-2 viroporin ORF3a inhibited by adamantanes and phenolic plant metabolites
Authors: Fam Marina Sherif , Sedky Christine Adel , Turky Nancy Osama , Breitinger Hans-Georg , Breitinger Ulrike 
Published: April 2023

AbstractSARS-CoV-2 has been responsible for the major worldwide pandemic of COVID-19. Despite the enormous success of vaccination campaigns, virus infections are still prevalent and effective antiviral therapies are urgently needed. Viroporins are essential for virus replication and release, and are thus promising therapeutic targets. Here, we studied the expression and function of recombinant ORF3a viroporin of SARS-CoV-2 using a combination of cell viability assays and patch-clamp electrophysiology. ORF3a was expressed in HEK293 cells and transport to the plasma membrane verified by a dot blot assay. Incorporation of a membrane-directing signal peptide increased plasma membrane expression. Cell viability tests were carried out to measure cell damage associated with ORF3a activity, and voltage-clamp recordings verified its channel activity. The classical viroporin inhibitors amantadine and rimantadine inhibited ORF3a channels. A series of ten flavonoids and polyphenolics were studied. Kaempferol, quercetin, epigallocatechin gallate, nobiletin, resveratrol and curcumin were ORF3a inhibitors, with IC50values ranging between 1 and 6 µM, while 6-gingerol, apigenin, naringenin and genistein were inactive. For flavonoids, inhibitory activity could be related to the pattern of OH groups on the chromone ring system. Thus, the ORF3a viroporin of SARS-CoV-2 may indeed be a promising target for antiviral drugs.
Ultra-thin Ag/Si heterojunction hot-carrier photovoltaic conversion Schottky devices for harvesting solar energy at wavelength above 1.1 µm
Authors: Su Zih-Chun , Chang Chung-Han , Jhou Jia-Ci , Lin Hsin-Ting , Lin Ching-Fuh 
Published: April 2023

AbstractTraditional silicon solar cells can only absorb the solar spectrum at wavelengths below 1.1 μm. Here we proposed a breakthrough in harvesting solar energy below Si bandgap through conversion of hot carriers generated in the metal into a current using an energy barrier at the metal–semiconductor junction. Under appropriate conditions, the photo-excited hot carriers can quickly pass through the energy barrier and lead to photocurrent, maximizing the use of excitation energy and reducing waste heat consumption. Compared with conventional silicon solar cells, hot-carrier photovoltaic conversion Schottky device has better absorption and conversion efficiency for an infrared regime above 1.1 μm, expands the absorption wavelength range of silicon-based solar cells, makes more effective use of the entire solar spectrum, and further improves the photovoltaic performance of metal–silicon interface components by controlling the evaporation rate, deposition thickness, and annealing temperature of the metal layer. Finally, the conversion efficiency 3.316% is achieved under the infrared regime with a wavelength of more than 1100 nm and an irradiance of 13.85 mW/cm2.
A simple method to make, trap and deform a vesicle in a gel
Authors: Tapie Pierre , Prevost Alexis M. , Montel Lorraine , Pontani Léa-Laetitia , Wandersman Elie 
Published: April 2023

AbstractWe present a simple method to produce giant lipid pseudo-vesicles (vesicles with an oily cap on the top), trapped in an agarose gel. The method can be implemented using only a regular micropipette and relies on the formation of a water/oil/water double droplet in liquid agarose. We characterize the produced vesicle with fluorescence imaging and establish the presence and integrity of the lipid bilayer by the successful insertion of $$\alpha $$
α
-Hemolysin transmembrane proteins. Finally, we show that the vesicle can be easily mechanically deformed, non-intrusively, by indenting the surface of the gel.
New compartment model for COVID-19
Authors: Odagaki Takashi 
Published: April 2023

AbstractThe SIR or susceptible-infected-recovered model is the standard compartment model for understanding epidemics and has been used all over the world for COVID-19. While the SIR model assumes that infected patients are identical to symptomatic and infectious patients, it is now known that in COVID-19 pre-symptomatic patients are infectious and there are significant number of asymptomatic patients who are infectious. In this paper, population is separated into five compartments for COVID-19; susceptible individuals (S), pre-symptomatic patients (P), asymptomatic patients (A), quarantined patients (Q) and recovered and/or dead patients (R). The time evolution of population in each compartment is described by a set of ordinary differential equations. Numerical solution to the set of differential equations shows that quarantining pre-symptomatic and asymptomatic patients is effective in controlling the pandemic.
Food system actor perspectives on future-proofing European food systems through plant breeding
Authors: Stetkiewicz S. , Menary J. , Nair A. , Rufino M. , Fischer A. R. H. , Cornelissen M. , Guichaoua A. , Jorasch P. , Lemarié S. , Nanda A. K. , Wilhelm R. , Davies J. A. C. 
Published: April 2023

AbstractCrop improvement is a key innovation area in the pursuit of sustainable food systems. However, realising its potential requires integration of the needs and priorities of all agri-food chain stakeholders. In this study, we provide a multi-stakeholder perspective on the role of crop improvement in future-proofing the European food system. We engaged agri-business, farm- and consumer-level stakeholders, and plant scientists through an online survey and focus groups. Four of each group’s top five priorities were shared and related to environmental sustainability goals (water, nitrogen and phosphorus efficiency, and heat stress). Consensus was identified on issues including considering existing alternatives to plant breeding (e.g. management strategies), minimising trade-offs, and addressing geographical variation in needs. We conducted a rapid evidence synthesis on the impacts of priority crop improvement options, highlighting the urgent need for further research examining downstream sustainability impacts to identify concrete targets for plant breeding innovation as a food systems solution.
Suboptimal controller design of global active noise control system for various acoustic environments
Authors: Jeong Ikchae , Park Youngjin 
Published: April 2023

AbstractConventional active noise control (ANC) systems in enclosed spaces are not easy to implement experimentally because they require a large number of microphones to measure sound pressure in global areas. Even if such systems are possible, if there are any changes in the locations of noise sources or surrounding objects, or if ANC system moves to another enclosed space, an expensive and time-consuming experimental calibration is again required. Implementation of global ANC in enclosed spaces is thus difficult. Therefore, we designed a global ANC system that can be used in various acoustic environments. The main idea involves suboptimal open-loop controller design in the free field. By using an open-loop controller, a controller calibrated once can be used in various acoustic environments. A controller designed in the free field derive a suboptimal solution without bias toward a specific acoustic environment. For controller design in the free field, we propose an experimental calibration approach in which the arrangement and the number of control speakers and microphones are determined by the frequency range and radiation pattern of the noise source. We conducted simulations and experiments to show that the designed controller in the free field is sufficiently effective in other enclosed spaces.
Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart
Authors: Botos Marius Alexandru , Arora Prateek , Chouvardas Panagiotis , Mercader Nadia 
Published: April 2023

AbstractZebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signaling pathways and gene regulatory networks in the zebrafish heart regeneration process. This process has been studied in response to different types of injuries namely: ventricular resection, ventricular cryoinjury, and genetic ablation of cardiomyocytes. However, there exists no database to compare injury specific and core cardiac regeneration responses. Here, we present a meta-analysis of transcriptomic data of regenerating zebrafish hearts in response to these three injury models at 7 days post injury (7dpi). We reanalyzed 36 samples and analyzed the differentially expressed genes (DEG) followed by downstream Gene Ontology Biological Processes (GO:BP) analysis. We found that the three injury models share a common core of DEG encompassing genes involved in cell proliferation, the Wnt signaling pathway and genes that are enriched in fibroblasts. We also found injury-specific gene signatures for resection and genetic ablation, and to a lower extent the cryoinjury model. Finally, we present our data in a user-friendly web interface that displays gene expression signatures across different injury types and highlights the importance to consider injury-specific gene regulatory networks when interpreting the results related to cardiac regeneration in the zebrafish. The analysis is freely available at: https://mybinder.org/v2/gh/MercaderLabAnatomy/PUB_Botos_et_al_2022_shinyapp_binder/HEAD?urlpath=shiny/bus-dashboard/.
Myopia prediction for children and adolescents via time-aware deep learning
Authors: Huang Junjia , Ma Wei , Li Rong , Zhao Na , Zhou Tao 
Published: April 2023

AbstractThis is a retrospective analysis. Quantitative prediction of the children’s and adolescents’ spherical equivalent based on their variable-length historical vision records. From October 2019 to March 2022, we examined uncorrected visual acuity, sphere, astigmatism, axis, corneal curvature and axial length of 75,172 eyes from 37,586 children and adolescents aged 6–20 years in Chengdu, China. 80% samples consist of the training set, the 10% form the validation set and the remaining 10% form the testing set. Time-Aware Long Short-Term Memory was used to quantitatively predict the children’s and adolescents’ spherical equivalent within two and a half years. The mean absolute prediction error on the testing set was 0.103 ± 0.140 (D) for spherical equivalent, ranging from 0.040 ± 0.050 (D) to 0.187 ± 0.168 (D) if we consider different lengths of historical records and different prediction durations. Time-Aware Long Short-Term Memory was applied to captured the temporal features in irregularly sampled time series, which is more in line with the characteristics of real data and thus has higher applicability, and helps to identify the progression of myopia earlier. The overall error 0.103 (D) is much smaller than the criterion for clinically acceptable prediction, say 0.75 (D).
Computational screening of FDA-approved drugs to identify potential TgDHFR, TgPRS, and TgCDPK1 proteins inhibitors against Toxoplasma gondii
Authors: Gharibi Zahra , Shahbazi Behzad , Gouklani Hamed , Nassira Hoda , Rezaei Zahra , Ahmadi Khadijeh 
Published: April 2023

AbstractToxoplasma gondii (T. gondii) is one of the most successful parasites in the world, because about a third of the world's population is seropositive for toxoplasmosis. Treatment regimens for toxoplasmosis have remained unchanged for the past 20 years, and no new drugs have been introduced to the market recently. This study, performed molecular docking to identify interactions of FDA-approved drugs with essential residues in the active site of proteins of T. gondii Dihydrofolate Reductase (TgDHFR), Prolyl-tRNA Synthetase (TgPRS), and Calcium-Dependent Protein Kinase 1 (TgCDPK1). Each protein was docked with 2100 FDA-approved drugs using AutoDock Vina. Also, the Pharmit software was used to generate pharmacophore models based on the TgDHFR complexed with TRC-2533, TgPRS in complex with halofuginone, and TgCDPK1 in complex with a bumped kinase inhibitor, RM-1–132. Molecular dynamics (MD) simulation was also performed for 100 ns to verify the stability of interaction in drug–protein complexes. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis evaluated the binding energy of selected complexes. Ezetimibe, Raloxifene, Sulfasalazine, Triamterene, and Zafirlukast drugs against the TgDHFR protein, Cromolyn, Cefexim, and Lactulose drugs against the TgPRS protein, and Pentaprazole, Betamethasone, and Bromocriptine drugs against TgCDPK1 protein showed the best results. These drugs had the lowest energy-based docking scores and also stable interactions based on MD analyses with TgDHFR, TgPRS, and TgCDPK1 drug targets that can be introduced as possible drugs for laboratory investigations to treat T. gondii parasite infection.
Longitudinal trajectory of vascular age indices and cardiovascular risk factors: a repeated-measures analysis
Authors: Watanabe Daiki , Gando Yuko , Murakami Haruka , Kawano Hiroshi , Yamamoto Kenta , Morishita Akie , Miyatake Nobuyuki , Miyachi Motohiko 
Published: April 2023

AbstractThis study aimed to identify the modifiable cardiovascular risk factors associated with longitudinal changes, which are nine functional and structural biological vascular aging indicators (BVAIs), to propose an effective method to prevent biological vascular aging. We conducted a longitudinal study of 697 adults (a maximum of 3636 BVAI measurements) who were, at baseline, aged between 26 and 85 years and whose BVAIs were measured at least twice between 2007 and 2018. The nine BVAIs were measured using vascular testing and an ultrasound device. Covariates were assessed using validated questionnaires and devices. During the mean follow-up period of 6.7 years, the average number of BVAI measurements ranged from 4.3 to 5.3. The longitudinal analysis showed a moderate positive correlation between the common carotid intima-media thickness (IMT) and chronological age in both men (r = 0.53) and women (r = 0.54). In the multivariate analysis, BVAIs were associated with factors such as age, sex, residential area, smoking status, blood clinical chemistry test levels, number of comorbidities, physical fitness, body mass, physical activity, and dietary intake. The IMT is the most useful BVAI. Our findings suggest that modifiable cardiovascular risk factors are associated with longitudinal changes in BVAI as represented by IMT.