bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photo-responsive hydrogel-based re-programmable metamaterials
Authors: Patel Herit , Chen Jiehao , Hu Yuhang , Erturk Alper 
Published: March 2022

Abstract
This paper explored a novel programmable metamaterial using stimuli-responsive hydrogels with a demonstration of bandgap formation and tuning. Specifically, a photo-responsive hydrogel beam that can achieve re-programmable periodicity in geometric and material properties through patterned light irradiation is designed. Hydrogels consist of polymeric networks and water molecules. Many unique properties of hydrogels, including bio-compatibility, stimuli-responsiveness, and low dissipation make them ideal for enabling re-programmable metamaterials for manipulating structural dynamic response and wave propagation characteristics. Bandgap generation and tunability in photo-responsive hydrogel-based metamaterial as well as the effects of system parameters such as light exposure pattern and photo-sensitive group concentration on the bandgap width and center frequency are systematically studied. Along with a finite element model, it is concluded that an increase in light exposure region size reduces both the bandgap width and center frequency, while an increase in the concentration of photo-sensitive group increases bandgap width, attenuation and reduces its center frequency. This work unveils the potential of stimuli-response hydrogels as a new class of low-loss soft metamaterials, unlike most other soft materials that are too lossy to sustain and exploit wave phenomena.
Circular RNAs Expression Profiles and Bioinformatics Analysis in Bronchopulmonary Dysplasia
Authors: Lun Yu , Zuming Yang 
Published: March 2022

Abstract
Background: Bronchopulmonary dysplasia (BPD) is a congenital chronic lung illness characterised by alveolar simplification and abnormal pulmonary microvasculature angiogenesis. Circular RNAs (circRNAs) have recently attracted significant interest due to their function in developing many disorders, but their role in BPD remains largely untapped. The purpose of this work was to discover a profile of circRNA expression related to severe BPD and to anticipate its possible biological activities.Methods: PBMCs were extracted from peripheral blood, and the circRNAs expression profiles in the PBMCs of severe BPD group (n = 3) and control group (n = 3). We identified and grouped significantly differently expressed circRNAs between the two groups. Following that, we used bioinformatics to design a circRNA-miRNA-mRNA network. Gene ontology and the Kyoto Encyclopedia of Genes and Genomes were performed.Results: Among hundreds of circRNAs, 171 were upregulated, and 81 were downregulated (fold change > 1.5, P < 0.05). Using GO and KEGG analyses revealed that circRNA target genes were considerably enriched. These genes are involved in transcription regulation, protein phosphorylation, and cell adhesion. A crosstalk network was developed to investigate the interactions of several components, including four circRNAs, sixteen microRNAs and thirty-seven messenger RNAs. A pathway network identified several critical pathways involved in the pathogenesis and development of BPD. These include the Wnt signalling pathway, the Hippo signalling pathway, and signalling pathways regulating stem cell pluripotency.Conclusions: CircRNAs in the peripheral blood of severe BPD children were considerably changed in the early post-birth period, which may be critical in developing this disease.
Study on temperature of cylindrical wet grinding considering lubrication effect of grinding fluid
Authors: Zheng Yong , Wang Changqing , Zhang Yifei , Meng Fanming 
Published: March 2022

Abstract
The improved cylindrical wet grinding temperature (ICWGT) model considering the lubrication effect of the grinding fluid is established and solved numerically. In doing so, the Newton-Raphson method is used to solve the hydrodynamic pressure of grinding fluid and the fast Fourier transform (FFT) method is employed to accelerate the deformation calculation. Further, the convective heat transfer coefficient (CHTC) is calculated based on the heat transfer theory and the moving heat source method is adopted to obtain the grinding temperature. Meanwhile, the effectiveness of ICWGT is verified through the grinding temperature measurement experiment of alloy steel. Then, the cylindrical wet grinding temperature for alloy steel considering the lubrication effect of grinding fluid are studied and compared at varied grinding process parameter, and some rules are revealed.
NIR-Mediated Drug Release and Tumor Theranostics Using Melanin-Loaded Liposomes
Authors: Kim Min Ah , Lee Chang-Moon 
Published: March 2022

Abstract
Background
Heat generation in a drug delivery carrier by exposure to near-infrared (NIR) light with excellent tissue transmittance is an effective strategy for drug release and tumor therapy. Because liposomes have amphiphilic properties, they are useful as drug carriers. Liposomes are also very suitable for drug delivery strategies using heat generation by NIR laser because lipid bilayers are easily broken by heat. Thermally generated bubbles from liposomes not only induce drug release, but also enable ultrasound imaging.
Methods
Melanin, perfluorohexane (PFH), and 5-fluorouracil (5-FU)-loaded liposomes (melanin@PFH@5-FU-liposomes) that can generate heat and bubble by NIR laser irradiation were prepared by a thin film method. Conversion of light to heat and bubble generation of melanin@PFH@5-FU-liposomes were evaluated using an infrared (IR) thermal imaging camera and an ultrasound imaging system both in vitro and in vivo. To investigate tumor therapeutic effect, NIR laser of 808 nm was used to irradiate tumor site for 10 min after injecting melanin@PFH@5-FU-liposome into tail veins of CT26-bearing mice.
Results
Melanin@PFH@5-FU-liposomes showed a spherical shape with a size of 209.6 ± 4.3 nm. Upon NIR laser irradiation, melanin@PFH@5-FU-liposomes exhibited effective temperature increase both in vitro and in vivo. In this regard, temperature increase caused a phase transition of PFH to induce bubble generation dramatically, resulting in effective drug release behavior and ultrasound imaging. The temperature of the tumor site was increased to 52℃ and contrast was greatly enhanced during ultrasound imaging due to the generation of bubble. More importantly, tumor growth was effectively inhibited by injection of melanin@PFH@5-FU-liposomes with laser irradiation.
Conclusions
Based on intrinsic photothermal properties of melanin and phase transition properties of PFH, melanin@PFH@5-FU-liposomes exhibited effective heat and bubble generation upon NIR laser irradiation. The elevated temperature induced bubble generation, resulting in contrast enhancement of ultrasound imaging. Melanin@PFH@5-FU-liposomes under NIR laser irradiation induced the death of cancer cells, thereby effectively inhibiting tumor growth. These results suggest that melanin@PFH@5-FU-liposomes can be utilized as a promising agent for photothermal tumor therapy and ultrasound imaging.
Beta-receptor blockade attenuates atherosclerosis progression following traumatic brain injury in apolipoprotein E deficient mice
Authors: Eitzman Daniel T. , Venugopal Jessica , Wang Jintao , Su Enming J , Guo Chiao , Lawrence Daniel A. 
Published: March 2022

Abstract
Traumatic brain injury (TBI) is associated with cardiovascular mortality in humans. Enhanced sympathetic activity following TBI may contribute to accelerated atherosclerosis. The effect of beta-adrenergic receptor blockade on atherosclerosis progression induced by TBI was studied in apolipoprotein E deficient mice. Mice were treated with metoprolol or vehicle following TBI or sham operation. Mice treated with metoprolol experienced a reduced heart rate with no difference in blood pressure. Six weeks following TBI, mice were sacrificed for analysis of atherosclerosis. Lesion thickness was analyzed at the level of the aortic valve and found to be increased in mice receiving TBI with vehicle treatment but was reduced in TBI mice receiving metoprolol. The increase in lesion thickness was associated with increased percent macrophage immunostaining area of intima which was also reduced with metoprolol. No effect of metoprolol on lesion thickness or macrophage content was observed in mice receiving only sham operation. In conclusion, accelerated atherosclerosis following TBI is reduced with beta-adrenergic receptor antagonism. Beta blockers may be useful to reduce vascular risk associated with TBI.
Identification and Computational Validation of TolC Derived B- and T- Cell Epitopes for the Development of Pan-Rickettsial Vaccine
Authors: Sankar Sathish , Suganya Subramanian , Venkatesan Arthi 
Published: March 2022

Abstract
Introduction: Rickettsia is vector-borne causing Rickettsial infections with high mortality. Currently, no vaccines are available for the prevention of rickettsioses. The study aims to identify B- and T- cell epitopes to peptides derived from TolC protein of rickettsial group of pathogens. Immunogenic linear B-cell epitopes and MHC class I and II T-cell epitopes predicted from the consensus sequences of TolC protein for each rickettsial species. The putative antigenic epitopes may trigger an effective immune response and prove to be a novel vaccine that protects against all rickettsial infections. Methods: MHC class-I binding T-cell epitopes were predicted along with TAP binding efficiency and proteasomal cleavage sites. Molecular docking study was carried out to investigate the binding affinity between the MHC-I protein molecules with the peptides. The MHC-peptide complex with the highest RMSD score was further used for molecular dynamic simulation study.Results: Three B-cell candidate peptide epitopes were selected, of which epitope IYPEGGAQYSRIRSAKNQTRNSA/VVQ is conserved across both typhus group and spotted fever group of rickettsial species was considered best suitable for candidate vaccine. The peptide epitope KLYEAKITR had a good RMSD score as well as promiscuous binding to 28 different HLA allele supertypes and was considered suitable for the development of subunit peptide vaccine. Conclusion: The B- and T- cell candidate peptide epitopes identified in our study would elicit B- and T-cell immune responses respectively and serve as a novel candidate peptide vaccine.
An Adaptive Stacking Ensemble Approach to Network Inference Outperforms Any Single Method
Authors: Shen Bingran , Coruzzi Gloria , Shasha Dennis 
Published: March 2022

Abstract
This study evaluates both a variety of existing causal inference methods and a variety of ensemble methods. We show that: (i) individual causal network methods vary in their performance across different datasets, so a method that works poorly on one dataset may work well on another; (ii) a Bayesian ensemble method leads overall to better results than using the best single method or any other ensemble method; (iii) for the best results, the Bayesian ensemble method should integrate all methods that satisfy a statistical test of normality on training data. The Bayesian ensemble model easily integrates all kinds of RNA-seq data and priors as well as new and existing inference methods.The paper categorizes and reviews state-of-the-art underlying methods, describes the Bayesian stacking ensemble approach in detail, and presents experimental results. The source code and data used will be available to the community.
Application of docking-based inverse high throughput virtual screening to found phytochemical covalent inhibitors of SARS-CoV-2 main protease, NSP12 and NSP16
Authors: Faletrov Yaroslav V. , Staravoitava Viktoryia A. , Dudko Anastasiya R. , Shkumatov Vladimir M. 
Published: March 2022

Abstract
Computer-aided docking-based inverse high-throughput virtual screening (inv HTVS) was applied for a quick evaluation of compounds as new affine ligands for SARS-CoV-2 proteins. We performed Autodock Vina-based inv HTVS using more than 450 structures of the virus proteins from Protein Data Bank (PDB) and totally ~ 2000 structures of compound with electrophilic motifs (mainly, α,β-unsaturated carbonyls) from Pubchem (CID codes) or Biogem databases. The inv HTVS calculations were semi-automatically organized, run and analyzed using our helper program tool composed of Python scripts and Excel files with macroses. Criteria for binding energy (Ebind, kcal/mol) values (no more than 6.9), distance between thiol groups of cysteine residues and electrophilic groups of the compounds within 0.4 nm (distance criterium) and total number of structures meeting the criteria were used. New in silico interactions were found for Mpro in the cases of such phytochemicals as peperomine E, 15-oxosteviol, zambesiacolactone B, isodehydroeupatundin, 2deoxycucurbitacin and jatrophone. Analogously, potential covalent ligands for NSP12 were found to include ixerin D, xindongnin C, rabdosin B, epinodosin as well as such ligands for NSP16 were found to include anhydroverlotolin-like compound CID325147, mexicanin E, insulicolide B and geoditin A. These and others hits are discussed with respect to their availability and biological properties. Thus, a set of natural compounds were pointed out as potential new covalent inhibitors of SARS-CoV-2 proteins Mpro, Nsp12 and Nsp16. This information could be used for further evaluations as prophylaxis tools or drugs against COVID-19.
Harrison’s Rule Corroborated Among Nomadine Cuckoo Bees (Hymenoptera: Apidae: Nomadinae) : The Role of Body Size in Host-Switching Dynamics
Authors: Lim Kayun , Lee Seunghyun , Orr Michael , Lee Seunghwan 
Published: March 2022

Abstract
Harrison’s rule, that body size is positively correlated between parasites and hosts, has been reported in a range of taxa, but whether the rule is applicable to cleptoparasitic insects is poorly understood. Subfamily Nomadinae, the largest group of cleptoparasitic bees, usurp the nests of a variety of host bees. Within the subfamily, Nomada exploits the most diverse hosts, using at least ten genera from five families. Not only they use diverse hosts, but the nomadine bees are also remarkably diverse in size, making them an ideal model to test Harrison’s rule. Here, we reassess the phylogeny of Nomadinae, including the expanded sampling of the genus Nomada, to explore host shift fluctuations throughout their evolutionary history and test the applicability of Harrison’s rule for the subfamily. Our phylogenetic results are mostly congruent with previous investigations, but we infer the tribe Hexepeolini as a sister taxon to the tribe Nomadini. Additionally, the results reveal discrepancies with the traditional classifications of Nomada. Ancestral state reconstruction of host use indicates that, early in their evolution, parasites used closer relatives, before attacking less related groups later. Lastly, we confirm Harrison’s rule in Nomadinae, supporting that body size dynamics influence the host shifts of cleptoparasitic bees.
In Silico Prediction of Deleterious Non-Synonymous SNPs of Human GABRA2 gene and Altered Protein Structure and Function – A Link to Alcohol Dependence?
Authors: Sankar Sathish , Suganya Subramanian 
Published: March 2022

Abstract
Alcohol Dependence is a serious and common public health problem around the globe. Genetic factors contribute to the risk of alcohol dependence. Mapping and identifying the specific genes that influence alcohol dependence and factors that alter the genetic expression are the thrust areas. Single-nucleotide polymorphisms (SNPs) in GABRA2 are associated with impulsiveness-related traits. The present study looked at non-synonymous SNPs with the potential to affect the structural and functional properties of the protein. The missense variants in the GABRA2 gene from sequences available in the NCBI database were analyzed using different bioinformatics tools. The modeled protein structures of the mutant proteins were compared with the native protein to determine stability changes. The identified deleterious variants were mostly present in the neurotransmitter-gated ion-channel ligand-binding domain and predicted to cause potential structural and functional changes in the protein. Among the 14 mutants, R58T was found to have the highest energy of -19646 KJ/mol, even after energy minimization, when compared with the native structure. The remaining 13 mutants were found to have lower energy values ranging from − 13567 to -13857 KJ/mol and 10 mutants were found in the conserved regions of the protein sequence. With a better understanding of the genetic basis of alcohol dependence, it is possible to pre-screen 'at-risk' individuals and design personalized early intervention, especially among the youth population.
Portuguese Physical Literacy Assessment Questionnaire (PPLA-Q) for adolescents (15-18 years) from grades 10-12: item response theory analysis of the content knowledge questionnaire
Authors: Mota João , Martins João , Onofre Marcos 
Published: March 2022

Abstract

Background: Aims of this study were to assess construct validity (dimensionality and measurement invariance) and reliability of the previously developed Cognitive module of the Portuguese Physical Literacy Assessment – Questionnaire (PPLA-Q). Secondary aims were to assess whether using distractor information was useful for higher precision, and whether a total sum-score has enough precision for applied PE settings.Methods: Parametric Item Response Theory (IRT) models were estimated using a final sample of 508 Portuguese adolescents (Mage= 16, SD = 1 years) studying in public schools in Lisbon. A retest subsample of 73 students, collected 15 days after baseline, was used to calculate Intraclass Correlation Coefficient (ICC) and Svenson’s ordinal paired agreement. Results: A mixed 2-parameter nested logit + graded response model provided the best fit to the data, C2 (21) = 23.92, p = .21; CFI = .98; RMSEAC2= .017 [0,.043] with no misfitting items. Modelling distractor information provided an increase in available information and thus, reliability. There was evidence of differential item functioning in one item in favor of male students, however it did not translate in statistically significant differences at test level (sDTF = -0.06; sDTF% = -0.14). Average score reliability was low (marginal reliability= .60); while adequate reliability was attained in the -2 to -1 θ range. ICC results suggest poor to moderate test-retest reliability (ICC = .56, [.38, .70]); while Svenson’s method resulted in 6 out of 10 items with acceptable agreement (>.70), and 4 remaining items revealing a small individual variability across time points. We found a high correlation (r = .91 [.90,.93]) among sum-score and scores derived from calibrated mixed model.Conclusions: Evidence supports the construct validity of the cognitive module of the PPLA-Q to assess Content Knowledge in the Portuguese PE context for grade 10-12 (15-18 years) adolescents. This test attainted acceptable reliability for distinguishing student with transitional knowledge (between Foundation and Mastery), with further revisions needed to target full spectrum of θ. Its sum-score might be used in applied settings to get a quick overview of student’s knowledge; for precision IRT score is recommended. Further scrutiny of test-retest reliability is warranted in future research, along with the use of 3-parameter logistic models.
Long-term Physical Activity Decreased the Risk of New-onset Hypertension in Type 2 Diabetes Mellitus Patients with Pre-hypertension: A Retrospective Cohort Study
Authors: Zhou Jianmei , Lv Xiaoling , Zhou Rongfang , Wang Bozhong , Wu Qing 
Published: March 2022

Abstract
Background Numerous studies were demonstrated the inverse relationship between all kinds of physical activity (PA) and cardiovascular diseases (CVDs), few of them focus on the new-onset hypertension. Therefore, this study was aimed to determine the impact of long-term PA on the risk of new-onset hypertension in type 2 diabetes mellitus (T2DM) patients with pre-hypertension.Methods A total of 268 T2DM patients with pre-hypertension were recruited between January and December 2015, and followed them up until December 2020. All patients were took PA self-assessment. Demographic, clinical, laboratory, radiologic, treatments, complications, lifestyle and clinical outcomes data were extracted from electronic medical records or collected through a structured interview.Results During 5 year follow-up, the incidence of new-onset hypertension was significantly lower in PA group (15.5% vs 35.4%, p<0.01) when compared to the inactivity group. Logistic regression analysis showed that PA (OR 0.337, 95%CI 0.168 to 0.677, p<0.01), body mass index (BMI) (OR 1.138, 95%CI 1.019 to 1.272, p<0.05) and glycosylated hemoglobin (HbA1C) (OR 1.206, 95%CI 1.006 to 1.446, p<0.05) were associated to the incidence of new-onset hypertension in pre-hypertensive T2DM patients. Subgroup analysis found that for those overweight and blood glucose poor controlled pre-hypertensive T2DM patients, long-term PA were less likely to develop hypertension (overweight: OR 0.187, 95%CI 0.063 to 0.558, p<0.01; glucose poor controlled: OR 0.349, 95%CI 0.138 to 0.880, p<0.05).Conclusion These results suggested that long-term PA might be an important protective factor for new-onset hypertension in overweight and poor blood glucose controlled pre-hypertensive T2DM patients.
Global evidence of rapid urban growth in flood zones since 1985
Authors: Rentschler Jun , Avner Paolo , Marconcini Mattia , Su Rui , Strano Emanuele , Hallegatte Stephane 
Published: March 2022

Abstract
As countries urbanize, human settlements are rapidly expanding into hazardous flood zones. This study provides a global analysis of spatial urbanization patterns and the evolution of flood exposure between 1985 and 2015. Using high-resolution annual data, it shows that settlements across the world grew by 85 percent to over 1.28 million square kilometers. In the same period, settlements exposed to the highest flood hazard level increased by 122 percent. In many regions, risky growth is outpacing safe growth, particularly in East Asia, where high risk settlements have expanded 60 percent faster than safe ones. Developing countries are driving the recent growth of flood exposure: 82 percent of the 36,500 square kilometers of settlements built in the world’s highest-risk zones since 1985 are in low- and middle-income countries. In comparison, recent growth in high-income countries has been relatively slow and safe. These results document a divergence in countries’ exposure to flood hazards. Rather than adapting their exposure to climatic hazards, many countries are actively increasing their exposure.
A familial 16p11.2 microdeletion associated with mental retardation, scoliosis, and genital tract malformation
Authors: Zhang Zhi-Jun , Deng Chun-Lei , Li Yan , Wang Man , He Yun , Zhang Juan-Juan , Xiong Ping-An , Wang Chao-Yun , Wu Jin-Hua , Gong Qi , Zhou Xiao-Hong , Guo Chong 
Published: March 2022

Abstract
Objectives: In this study, we aimed to identify the family members carried the same microdeletion and to discover the symptoms of a familial 16p11.2 microdeletion were greatly different. Case Report: The son, a 6-years-old boy, displayed scoliosis, mental retardation, and language retardation. The mother displayed mild mental retardation, but no scoliosis or language retardation or genital tract malformation. Pedigree research revealed that the mother, her son, and her fetus carried the same 16p11.2 microdeletion through CNV-sequencing, Whole Exon Sequencing, and PCR, but the father was normal. And her fetal displayed no scoliosis by ultrasound. After birth, the baby displayed genital tract malformation, but no scoliosis or mental retardation.Conclusions: This finding uncovered that the symptoms of 16p11.2 microdeletion syndrome are greatly different, even in the same segment microdeletion.