bluuebunny/crossref_metadata_2025 huggingface dataset:
Indoor photovoltaic energy harvesting based on semiconducting π-conjugated polymers and oligomeric materials toward future IoT applications
Authors: Hwang Sunbin , Yasuda Takuma
Published: November 2022

With the advancement of artificial intelligence computing systems that can collect, analyze, and utilize metadata from our activities and surrounding environments, establishing self-powered electronic systems/networks supported by energy harvesters is strongly desired. With the lowering of power consumption in contemporary IoT electronics such as wireless sensors, indoor organic photovoltaic devices (iOPVs), which can be driven under ambient indoor light, have recently attracted significant interest as self-sustainable eco-friendly power sources. iOPVs based on organic semiconductors have unique advantages, such as light weight, flexibility, solution processability, and feasibility of low-temperature mass production. Additionally, the spectral tunability and high optical absorptivity of organic semiconductors make iOPVs more effective as energy harvesters in indoor lighting environments. With recent intensive research effort, iOPVs have realized the delivery of high power conversion efficiencies exceeding 25% with output power densities of several tens to a hundred μW cm−2, which are sufficient to drive various low-power electronics compatible with the IoT. This review article focuses on recent progress in iOPVs based on π-conjugated polymers and oligomeric materials and outlines their fundamental principles and characterization techniques.
High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression
Authors: Veggiani G. , Villaseñor R. , Martyn G. D. , Tang J. Q. , Krone M. W. , Gu J. , Chen C. , Waters M. L. , Pearce K. H. , Baubec T. , Sidhu S. S.
Published: November 2022

Histone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies on the use of antibodies, but these suffer from lot-to-lot variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and develop a general strategy for enhancing the affinity of chromodomains of the human Cbx protein family. Our strategy allows us to develop powerful probes for genome-wide binding analysis and live-cell imaging. Furthermore, we use optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.
Brownian reservoir computing realized using geometrically confined skyrmion dynamics
Authors: Raab Klaus , Brems Maarten A. , Beneke Grischa , Dohi Takaaki , Rothörl Jan , Kammerbauer Fabian , Mentink Johan H. , Kläui Mathias
Published: November 2022

Reservoir computing (RC) has been considered as one of the key computational principles beyond von-Neumann computing. Magnetic skyrmions, topological particle-like spin textures in magnetic films are particularly promising for implementing RC, since they respond strongly nonlinearly to external stimuli and feature inherent multiscale dynamics. However, despite several theoretical proposals that exist for skyrmion reservoir computing, experimental realizations have been elusive until now. Here, we propose and experimentally demonstrate a conceptually new approach to skyrmion RC that leverages the thermally activated diffusive motion of skyrmions. By confining the electrically gated and thermal skyrmion motion, we find that already a single skyrmion in a confined geometry suffices to realize nonlinearly separable functions, which we demonstrate for the XOR gate along with all other Boolean logic gate operations. Besides this universality, the reservoir computing concept ensures low training costs and ultra-low power operation with current densities orders of magnitude smaller than those used in existing spintronic reservoir computing demonstrations. Our proposed concept is robust against device imperfections and can be readily extended by linking multiple confined geometries and/or by including more skyrmions in the reservoir, suggesting high potential for scalable and low-energy reservoir computing.
Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks
Authors: Guo Zhiye , Liu Jian , Skolnick Jeffrey , Cheng Jianlin
Published: November 2022

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict intra-chain residue-residue distances of monomers accurately, but few methods can accurately predict inter-chain residue-residue distances of complexes. We develop a deep learning method CDPred (i.e., Complex Distance Prediction) based on the 2D attention-powered residual network to address the gap. Tested on two homodimer datasets, CDPred achieves the precision of 60.94% and 42.93% for top L/5 inter-chain contact predictions (L: length of the monomer in homodimer), respectively, substantially higher than DeepHomo’s 37.40% and 23.08% and GLINTER’s 48.09% and 36.74%. Tested on the two heterodimer datasets, the top Ls/5 inter-chain contact prediction precision (Ls: length of the shorter monomer in heterodimer) of CDPred is 47.59% and 22.87% respectively, surpassing GLINTER’s 23.24% and 13.49%. Moreover, the prediction of CDPred is complementary with that of AlphaFold2-multimer.
Effectiveness of a third BNT162b2 mRNA COVID-19 vaccination during pregnancy: a national observational study in Israel
Authors: Guedalia Joshua , Lipschuetz Michal , Calderon-Margalit Ronit , Cohen Sarah M. , Goldman-Wohl Debra , Kaminer Tali , Melul Eli , Shefer Galit , Sompolinsky Yishai , Walfisch Asnat , Yagel Simcha , Beharier Ofer
Published: November 2022

The Centers for Disease Control (CDC) recommend a third dose of COVID-19 vaccine for pregnant women, although data regarding effectiveness during pregnancy are lacking. This national, population-based, historical cohort study of pregnant women in Israel, delivering between August 1, 2021 and March 22, 2022, aims to analyze and compare the third and second doses’ vaccine effectiveness in preventing COVID-19-related hospitalizations during pregnancy during two COVID-19 waves (Delta variant in the summer of 2021 and Omicron, BA.1, variant in the winter of 2022). Time-dependent Cox proportional-hazards regression models estimate the hazard ratios (HR) and 95% confidence intervals (CI) for COVID-related outcomes according to vaccine dose, and vaccine effectiveness as 1-HR. Study includes 82,659 and 33,303 pregnant women from the Delta and Omicron waves, respectively. Compared with the second dose, the third dose effectively prevents overall hospitalizations with SARS-CoV-2 infections, with estimated effectiveness of 92% (95% CI 83–96%) during Delta, and enhances protection against significant disease during Omicron, with effectiveness of 92% (95% CI 26–99%), and 48% (95% CI 37–57%) effectiveness against hospitalization overall. A third dose of the BNT162b2 mRNA COVID-19 vaccine during pregnancy, given at least 5 months after the second vaccine dose, enhances protection against adverse COVID-19-related outcomes.
Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
Authors: Edgar Robert C.
Published: November 2022

Multiple sequence alignments are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is to construct one alignment by some preferred method and use it in further analysis; however, undetected alignment bias can be problematic. I describe Muscle5, a novel algorithm which constructs an ensemble of high-accuracy alignment with diverse biases by perturbing a hidden Markov model and permuting its guide tree. Confidence in an inference is assessed as the fraction of the ensemble which supports it. Applied to phylogenetic tree estimation, I show that ensembles can confidently resolve topologies with low bootstrap according to standard methods, and conversely that some topologies with high bootstraps are incorrect. Applied to the phylogeny of RNA viruses, ensemble analysis shows that recently adopted taxonomic phyla are probably polyphyletic. Ensemble analysis can improve confidence assessment in any inference from an alignment.
Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis
Authors: Zhong Zhenhui , Wang Yafei , Wang Ming , Yang Fan , Thomas Quentin Angelo , Xue Yan , Zhang Yaxin , Liu Wanlu , Jami-Alahmadi Yasaman , Xu Linhao , Feng Suhua , Marquardt Sebastian , Wohlschlegel James A. , Ausin Israel , Jacobsen Steven E.
Published: November 2022

Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
Authors: Wallen Zachary D. , Demirkan Ayse , Twa Guy , Cohen Gwendolyn , Dean Marissa N. , Standaert David G. , Sampson Timothy R. , Payami Haydeh
Published: November 2022

Parkinson’s disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association, network analysis to identify polymicrobial clusters, and functional profiling. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature; and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.
Selective retention of virus-specific tissue-resident T cells in healed skin after recovery from herpes zoster
Authors: Laing Kerry J. , Ouwendijk Werner J. D. , Campbell Victoria L. , McClurkan Christopher L. , Mortazavi Shahin , Elder Waters Michael , Krist Maxwell P. , Tu Richard , Nguyen Nhi , Basu Krithi , Miao Congrong , Schmid D. Scott , Johnston Christine , Verjans Georges M. G. M. , Koelle David M.
Published: November 2022

Herpes zoster is a localized skin infection caused by reactivation of latent varicella-zoster virus. Tissue-resident T cells likely control skin infections. Zoster provides a unique opportunity to determine if focal reinfection of human skin boosts local or disseminated antigen-specific tissue-resident T cells. Here, we show virus-specific T cells are retained over one year in serial samples of rash site and contralateral unaffected skin of individuals recovered from zoster. Consistent with zoster resolution, viral DNA is largely undetectable on skin from day 90 and virus-specific B and T cells decline in blood. In skin, there is selective infiltration and long-term persistence of varicella-zoster virus-specific T cells in the rash site relative to the contralateral site. The skin T cell infiltrates express the canonical tissue-resident T cell markers CD69 and CD103. These findings show that zoster promotes spatially-restricted long-term retention of antigen-specific tissue-resident T cells in previously infected skin.
Releasing chemical energy in spatially programmed ferroelectrics
Authors: Hu Yong , Gottfried Jennifer L. , Pesce-Rodriguez Rose , Wu Chi-Chin , Walck Scott D. , Liu Zhiyu , Balakrishnan Sangeeth , Broderick Scott , Guo Zipeng , Zhang Qiang , An Lu , Adlakha Revant , Nouh Mostafa , Zhou Chi , Chung Peter W. , Ren Shenqiang
Published: November 2022

Chemical energy ferroelectrics are generally solid macromolecules showing spontaneous polarization and chemical bonding energy. These materials still suffer drawbacks, including the limited control of energy release rate, and thermal decomposition energy well below total chemical energy. To overcome these drawbacks, we report the integrated molecular ferroelectric and energetic material from machine learning-directed additive manufacturing coupled with the ice-templating assembly. The resultant aligned porous architecture shows a low density of 0.35 g cm−3, polarization-controlled energy release, and an anisotropic thermal conductivity ratio of 15. Thermal analysis suggests that the chlorine radicals react with macromolecules enabling a large exothermic enthalpy of reaction (6180 kJ kg−1). In addition, the estimated detonation velocity of molecular ferroelectrics can be tuned from 6.69 ± 0.21 to 7.79 ± 0.25 km s−1 by switching the polarization state. These results provide a pathway toward spatially programmed energetic ferroelectrics for controlled energy release rates.
Accurate and efficient band-gap predictions for metal halide perovskites at finite temperature
Authors: Wang Haiyuan , Tal Alexey , Bischoff Thomas , Gono Patrick , Pasquarello Alfredo
Published: November 2022

We develop a computationally efficient scheme to accurately determine finite-temperature band gaps for metal halide perovskites belonging to the class ABX3 (A = Rb, Cs; B = Ge, Sn, Pb; and X = F, Cl, Br, I). First, an initial estimate of the band gap is provided for the ideal crystalline structure through the use of a range-separated hybrid functional, in which the parameters are determined non-empirically from the electron density and the high-frequency dielectric constant. Next, we consider two kinds of band-gap corrections to account for spin-orbit coupling and thermal vibrations including zero-point motions. In particular, the latter effect is accounted for through the special displacement method, which consists in using a single distorted configuration obtained from the vibrational frequencies and eigenmodes, thereby avoiding lengthy molecular dynamics. The sequential consideration of both corrections systematically improves the band gaps, reaching a mean absolute error of 0.17 eV with respect to experimental values. The computational efficiency of our scheme stems from the fact that only a single calculation at the hybrid-functional level is required and that it is sufficient to evaluate the corrections at the semilocal level of theory. Our scheme is thus convenient for the screening of large databases of metal halide perovskites, including large-size systems.
Vibrationally resolved optical excitations of the nitrogen-vacancy center in diamond
Authors: Jin Yu , Govoni Marco , Galli Giulia
Published: November 2022

A comprehensive description of the optical cycle of spin defects in solids requires the understanding of the electronic and atomistic structure of states with different spin multiplicity, including singlet states which are particularly challenging from a theoretical standpoint. We present a general framework, based on spin-flip time-dependent density function theory, to determine the excited state potential energy surfaces of the many-body singlet states of spin defects; we then predict the vibrationally resolved absorption spectrum between singlet shelving states of a prototypical defect, the nitrogen-vacancy center in diamond. Our results, which are in very good agreement with experiments, provide an interpretation of the measured spectra and reveal the key role of specific phonons in determining absorption processes, and the notable influence of non-adiabatic interactions. The insights gained from our calculations may be useful in defining strategies to improve infrared-absorption-based magnetometry and optical pumping schemes. The theoretical framework developed here is general and applicable to a variety of other spin defects and materials.
Medicine and health of 21st Century: Not just a high biotech-driven solution
Authors: Assidi Mourad , Buhmeida Abdelbaset , Budowle Bruce
Published: November 2022

Many biotechnological innovations have shaped the contemporary healthcare system (CHS) with significant progress to treat or cure several acute conditions and diseases of known causes (particularly infectious, trauma). Some have been successful while others have created additional health care challenges. For example, a reliance on drugs has not been a panacea to meet the challenges related to multifactorial noncommunicable diseases (NCDs)—the main health burden of the 21st century. In contrast, the advent of omics-based and big data technologies has raised global hope to predict, treat, and/or cure NCDs, effectively fight even the current COVID-19 pandemic, and improve overall healthcare outcomes. Although this digital revolution has introduced extensive changes on all aspects of contemporary society, economy, firms, job market, and healthcare management, it is facing and will face several intrinsic and extrinsic challenges, impacting precision medicine implementation, costs, possible outcomes, and managing expectations. With all of biotechnology’s exciting promises, biological systems’ complexity, unfortunately, continues to be underestimated since it cannot readily be compartmentalized as an independent and segregated set of problems, and therefore is, in a number of situations, not readily mimicable by the current algorithm-building proficiency tools. Although the potential of biotechnology is motivating, we should not lose sight of approaches that may not seem as glamorous but can have large impacts on the healthcare of many and across disparate population groups. A balanced approach of “omics and big data” solution in CHS along with a large scale, simpler, and suitable strategies should be defined with expectations properly managed.
MRI biomarkers of freezing of gait development in Parkinson’s disease
Authors: Sarasso Elisabetta , Basaia Silvia , Cividini Camilla , Stojkovic Tanja , Stankovic Iva , Piramide Noemi , Tomic Aleksandra , Markovic Vladana , Stefanova Elka , Kostic Vladimir S. , Filippi Massimo , Agosta Federica
Published: November 2022

This study investigated longitudinal clinical, structural and functional brain alterations in Parkinson’s disease patients with freezing of gait (PD-FoG) and in those developing (PD-FoG-converters) and not developing FoG (PD-non-converters) over two years. Moreover, this study explored if any clinical and/or MRI metric predicts FoG development. Thirty PD-FoG, 11 PD-FoG-converters and 11 PD-non-converters were followed for two years. Thirty healthy controls were included at baseline. Participants underwent clinical and MRI visits. Cortical thickness, basal ganglia volumes and functional network graph metrics were evaluated at baseline and over time. In PD groups, correlations between baseline MRI and clinical worsening were tested. A ROC curve analysis investigated if baseline clinical and MRI measures, selected using a stepwise model procedure, could differentiate PD-FoG-converters from PD-non-converters. At baseline, PD-FoG patients had widespread cortical/subcortical atrophy, while PD-FoG-converters and non-converters showed atrophy in sensorimotor areas and basal ganglia relative to controls. Over time, PD-non-converters accumulated cortical thinning of left temporal pole and pallidum without significant clinical changes. PD-FoG-converters showed worsening of disease severity, executive functions, and mood together with an accumulation of occipital atrophy, similarly to PD-FoG. At baseline, PD-FoG-converters relative to controls and PD-FoG showed higher global and parietal clustering coefficient and global local efficiency. Over time, PD-FoG-converters showed reduced parietal clustering coefficient and sensorimotor local efficiency, PD-non-converters showed increased sensorimotor path length, while PD-FoG patients showed stable graph metrics. Stepwise prediction model including dyskinesia, postural instability and gait disorders scores and parietal clustering coefficient was the best predictor of FoG conversion. Combining clinical and MRI data, ROC curves provided the highest classification power to predict the conversion (AUC = 0.95, 95%CI: 0.86–1). Structural MRI is a useful tool to monitor PD progression, while functional MRI together with clinical features may be helpful to identify FoG conversion early.
Plethora of tunable Weyl fermions in kagome magnet Fe3Sn2 thin films
Authors: Ren Zheng , Li Hong , Sharma Shrinkhala , Bhattarai Dipak , Zhao He , Rachmilowitz Bryan , Bahrami Faranak , Tafti Fazel , Fang Shiang , Ghimire Madhav Prasad , Wang Ziqiang , Zeljkovic Ilija
Published: November 2022

Interplay of magnetism and electronic band topology in unconventional magnets enables the creation and fine control of novel electronic phenomena. In this work, we use scanning tunneling microscopy and spectroscopy to study thin films of a prototypical kagome magnet Fe3Sn2. Our experiments reveal an unusually large number of densely-spaced spectroscopic features straddling the Fermi level. These are consistent with signatures of low-energy Weyl fermions and associated topological Fermi arc surface states predicted by theory. By measuring their response as a function of magnetic field, we discover a pronounced evolution in energy tied to the magnetization direction. Electron scattering and interference imaging further demonstrates the tunable nature of a subset of related electronic states. Our experiments provide a direct visualization of how in-situ spin reorientation drives changes in the electronic density of states of the Weyl fermion band structure. Combined with previous reports of massive Dirac fermions, flat bands, and electronic nematicity, our work establishes Fe3Sn2 as an interesting platform that harbors an extraordinarily wide array of topological and correlated electron phenomena.
Impaired neutralizing antibodies and preserved cellular immunogenicity against SARS-CoV-2 in systemic autoimmune rheumatic diseases
Authors: Intapiboon Porntip , Uae-areewongsa Parichat , Ongarj Jomkwan , Sophonmanee Ratchanon , Seepathomnarong Purilap , Seeyankem Bunya , Surasombatpattana Smonrapat , Pinpathomrat Nawamin
Published: November 2022

Reports on vaccine immunogenicity in patients with systemic autoimmune rheumatic diseases (SARDs) have been inconclusive. Here, we report the immunogenicity of heterologous prime-boost with an inactivated vaccine followed by an adenoviral vector vaccine in patients with SARDs using anti-RBD antibodies, neutralizing capacity against Omicron BA.2 [plaque-reduction neutralization test (PRNT)], T cell phenotypes, and effector cytokine production at 4 weeks after vaccination. SARD patients had lower median (IQR) anti-RBD-IgG levels and neutralizing function against the Omicron BA.2 variant than the healthy group (p = 0.003, p = 0.004, respectively). T cell analysis revealed higher levels of IFN-γ- and TNF-α-secreting CD4 + T cells (p < 0.001, p = 0.0322, respectively) in SARD patients than in the healthy group. Effector cytokine production by CD8 + T cells was consistent with Th responses. These results suggest that this vaccine regimen revealed mildly impaired humoral response while preserving cellular immunogenicity and may be an alternative for individuals for whom mRNA vaccines are contraindicated.
Two-component vaccine consisting of virus-like particles displaying hepatitis C virus envelope protein 2 oligomers
Authors: Prentoe Jannick , Janitzek Christoph M. , Velázquez-Moctezuma Rodrigo , Soerensen Andreas , Jørgensen Thomas , Clemmensen Stine , Soroka Vladislav , Thrane Susan , Theander Thor , Nielsen Morten A. , Salanti Ali , Bukh Jens , Sander Adam F.
Published: November 2022

Development of B-cell-based hepatitis C virus (HCV) vaccines that induce broadly neutralizing antibodies (bNAbs) is hindered by extensive sequence diversity and low immunogenicity of envelope glycoprotein vaccine candidates, most notably soluble E2 (sE2). To overcome this, we employed two-component approaches using self-assembling virus-like particles (cVLPs; component 1), displaying monomeric or oligomeric forms of HCV sE2 (sE2mono or sE2oligo; component 2). Immunization studies were performed in BALB/c mice and the neutralizing capacity of vaccine-induced antibodies was tested in cultured-virus-neutralizations, using HCV of genotypes 1–6. sE2-cVLP vaccines induced significantly higher levels of NAbs (p = 0.0065) compared to corresponding sE2 vaccines. Additionally, sE2oligo-cVLP was superior to sE2mono-cVLP in inducing bNAbs. Interestingly, human monoclonal antibody AR2A had reduced binding in ELISA to sE2oligo-cVLP compared with sE2mono-cVLP and competition ELISA using mouse sera from vaccinated animals indicated that sE2oligo-cVLP induced significantly less non-bNAbs AR2A (p = 0.0043) and AR1B (p = 0.017). Thus, cVLP-displayed oligomeric sE2 shows promise as an HCV vaccine candidate.
Heat transfer analysis in a non-Newtonian hybrid nanofluid over an exponentially oscillating plate using fractional Caputo–Fabrizio derivative
Authors: Ul Haq Sami , Mahmood Naveed , Jan Saeed Ullah , Sehra  , Khan Ilyas , Mohamed Abdullah
Published: November 2022

In this paper, we have been study a hybrid nanofluid over an exponentially oscillating vertical flat plate. Therefore the fractional derivatives definition of Caputo–Fabrizio approach is applied to transform the classical model for this hybrid nanofluid to fractional model. Together with an oscillating boundary motion, therefore the heat transfer is cause as a result of the buoyancy force produce due temperature differences between the plate and the fluid. The dimensionless classical model is generalized by transforming it to the time fractional model using Caputo–Fabrizio time fractional derivative. Exact analytical solutions are obtained by using Laplace transform method to the set of dimensionless fractional governing equations, containing the momentum and energy equations subjected to the boundary and initial conditions. Numerical computations and graphical illustrations are used to checked the results of the Caputo–Fabrizio time-fractional parameter, the second-grade parameter, the magnetic parameter and the Grashof numbers on the velocity field. An assessment for time spin-off is shown graphically of integer order versus fractional-order for these non-Newtonian hybrid nanofluid through Mathcad software. The fluid velocity increases for increasing the value of the fractional parameter, second-grade parameter and Grashof number. Also for increasing the values of the MHD parameter the fluid velocity decreases.
Synergistic activity of pomegranate rind extract and Zn (II) against Candida albicans under planktonic and biofilm conditions, and a mechanistic insight based upon intracellular ROS induction
Authors: Celiksoy Vildan , Moses Rachael L. , Sloan Alastair J. , Moseley Ryan , Heard Charles M.
Published: November 2022

Candida albicans (C. albicans) is an opportunistic pathogen, which causes superficial infection and can lead to mortal systemic infections, especially in immunocompromised patients. The incidence of C. albicans infections is increasing and there are a limited number of antifungal drugs used in treatment. Therefore, there is an urgent need for new and alternative antifungal drugs. Pomegranate rind extract (PRE) is known for its broad-spectrum antimicrobial activities, including against C. albicans and recently, PRE and Zn (II) have been shown to induce synergistic antimicrobial activity against various microbes. In this study, the inhibitory activities of PRE, Zn (II) and PRE in combination with Zn (II) were evaluated against C. albicans. Antifungal activities of PRE and Zn (II) were evaluated using conventional microdilution methods and the interaction between these compounds was assessed by in vitro checkerboard and time kill assays in planktonic cultures. The anti-biofilm activities of PRE, Zn (II) and PRE in combination with Zn (II) were assessed using confocal laser scanning microscopy, with quantitative analysis of biofilm biomass and mean thickness analysed using COMSTAT2 analysis. In addition, antimicrobial interactions between PRE and Zn (II) were assayed in terms reactive oxygen species (ROS) production by C. albicans. PRE and Zn (II) showed a potent antifungal activity against C. albicans, with MIC values of 4 mg/mL and 1.8 mg/mL, respectively. PRE and Zn (II) in combination exerted a synergistic antifungal effect, as confirmed by the checkerboard and time kill assays. PRE, Zn (II) and PRE and Zn (II) in combination gave rise to significant reductions in biofilm biomass, although only PRE caused a significant reduction in mean biofilm thickness. The PRE and Zn (II) in combination caused the highest levels of ROS production by C. albicans, in both planktonic and biofilm forms. The induction of excess ROS accumulation in C. albicans may help explain the synergistic activity of PRE and Zn (II) in combination against C. albicans in both planktonic and biofilm forms. Moreover, the data support the potential of the PRE and Zn (II) combination as a novel potential anti-Candida therapeutic system.
Validation of suitable reference genes by various algorithms for gene expression analysis in Isodon rubescens under different abiotic stresses
Authors: Lian Conglong , Zhang Bao , Yang Jingfan , Lan JinXu , Yang Hao , Guo Kaihua , Li Jingjing , Chen Suiqing
Published: November 2022

Isodon rubescens (Hemsley) H. Hara (Lamiaceae) is a traditional Chinese medicine plant that has been used to treat various human diseases. Oridonin is one of the main active ingredients, and the route of its molecular biosynthesis remains to be determined. The study of gene expression patterns can provide clues toward the understanding of its biological functions. The selection of suitable reference genes for normalizing target gene expression is the first steps in any quantitative real-time PCR (RT-qPCR) gene expression study. Therefore, validation of suitable reference genes is necessary for obtaining reliable results in RT-qPCR analyses of I. rubescens. Here, 12 candidate reference genes were chosen, and their expression stability in different tissues of I. rubescens and in leaves under different abiotic stresses (NaCl, dehydration, SA, MeJA, and ABA) was evaluated using the ∆Ct, NormFinder, GeNorm, BestKeeper, and RankAggreg statistical tools. Analysis using the comprehensive tools of RankAggreg algorithm showed that GADPH, 18S and eIF were stably expressed in different tissues; UBQ, Apt, and HIS; Cycl, UBQ, and PP2A; GADPH, 18S, and eIF; eIF, UBQ, and PP2A; TUB, Cycl, and UBQ; were the best three candidate reference genes for the samples of Dehydration, NaCl, SA, MeJA, and ABA treatment, respectively. While for the concatenated sets of ND (NaCl and dehydration) and SMA (SA, MeJA, and ABA), UBQ, HIS, and TUA; UBQ, eIF and Apt were the three appropriate candidate reference genes, respectively. In addition, the expression patterns of HMGR in different tissues and under different treatments were used to confirm the reliability of the selected reference genes, indicating that the use of an inappropriate reference gene as the internal control will cause results with a large deviation. This work is the first study on the expression stability of reference genes in I. rubescens and will be particularly useful for gene functional research in this species.
Novel 3D video action recognition deep learning approach for near real time epileptic seizure classification
Authors: Karácsony Tamás , Loesch-Biffar Anna Mira , Vollmar Christian , Rémi Jan , Noachtar Soheyl , Cunha João Paulo Silva
Published: November 2022

Seizure semiology is a well-established method to classify epileptic seizure types, but requires a significant amount of resources as long-term Video-EEG monitoring needs to be visually analyzed. Therefore, computer vision based diagnosis support tools are a promising approach. In this article, we utilize infrared (IR) and depth (3D) videos to show the feasibility of a 24/7 novel object and action recognition based deep learning (DL) monitoring system to differentiate between epileptic seizures in frontal lobe epilepsy (FLE), temporal lobe epilepsy (TLE) and non-epileptic events. Based on the largest 3Dvideo-EEG database in the world (115 seizures/+680,000 video-frames/427GB), we achieved a promising cross-subject validation f1-score of 0.833±0.061 for the 2 class (FLE vs. TLE) and 0.763 ± 0.083 for the 3 class (FLE vs. TLE vs. non-epileptic) case, from 2 s samples, with an automated semi-specialized depth (Acc.95.65%) and Mask R-CNN (Acc.96.52%) based cropping pipeline to pre-process the videos, enabling a near-real-time seizure type detection and classification tool. Our results demonstrate the feasibility of our novel DL approach to support 24/7 epilepsy monitoring, outperforming all previously published methods.
Lentinan improves intestinal inflammation and gut dysbiosis in antibiotics-induced mice
Authors: Ji Xiuyu , Su Le , Zhang Ping , Yue Qiulin , Zhao Chen , Sun Xin , Li Kunlun , Liu Xinli , Zhang Song , Zhao Lin
Published: November 2022

Gut microbiota dysbiosis is already a global problem after antibiotic overuse. This study was to investigate the therapeutic effect of lentinan and the mechanism of recovery of intestinal inflammation on broad-spectrum antibiotic-driven gut microbial dysbiosis in mice. Gut microbiota was elucidated by the Illumina MiSeq platform. Gas chromatography/mass spectrometry was used to investigate short-chain fatty acid content. Colon histology, expression of tight-junction associated proteins and pro-inflammatory cytokines levels were evaluated. The results showed that the gut microbiota of diversity and richness were reduced and various taxonomic levels of the gut microbiota were perturbed after antibiotics gavage. The abundance of Firmicutes and Bacteroidetes shifted to Proteobacteria and increased the relative abundance of harmful microbiota (Parabacteroides and Klebsiella) post-antibiotics, whereas lentinan administration reversed the dysbiosis and increased beneficial microbiota, including S24-7, Lactobacillus, Oscillospira, Ruminococcus and Allobaculum. The concentrations of propionic acid and butyric acid were significantly increased by treatment with lentinan. And lentinan improved colon tissue morphology and reduced pro-inflammatory cytokines via altering NF-κB signaling pathway in antibiotic-driven gut microbial dysbiosis mice. Taken together, the results proved that lentinan can be used as a prebiotic and the result provided a theoretical basis for improving the clinical treatment of broad-spectrum antibiotics side effects.
Independent effects of acute normobaric hypoxia and hypobaric hypoxia on human physiology
Authors: Rosales Alejandro M. , Shute Robert J. , Hailes Walter S. , Collins Christopher W. , Ruby Brent C. , Slivka Dustin R.
Published: November 2022

The purpose of this study was to examine the effects of acute normobaric (NH, decreased FiO2) and hypobaric (HH, 4200 m ascent) hypoxia exposures compared to sea level (normobaric normoxia, NN). Tissue oxygenation, cardiovascular, and body fluid variables measured during rest and a 3-min step-test following 90-min exposures (NH, HH, NN). Muscle oxygenated hemoglobin (O2Hb) decreased, and muscle deoxygenated hemoglobin (HHb) increased environmentally independent from rest to exercise (p < 0.001). During exercise, brain O2Hb was lower at HH compared to NN (p = 0.007), trending similarly with NH (p = 0.066), but no difference between NN and NH (p = 0.158). During exercise, HR at NH (141 ± 4 beats·min−1) and HH (141 ± 3 beats·min−1) were higher than NN (127 ± 44 beats·min−1, p = 0.002), but not each other (p = 0.208). During exercise, stroke volume at HH (109.6 ± 4.1 mL·beat−1) was higher than NH (97.8 ± 3.3 mL·beat−1) and NN (99.8 ± 3.9 mL·beat−1, p ≤ 0.010) with no difference between NH and NN (p = 0.481). During exercise, cardiac output at NH (13.8 ± 0.6 L) and HH (15.5 ± 0.7 L) were higher than NN (12.6 ± 0.5 L, p ≤ 0.006) with HH also higher than NH (p = 0.001). During acute hypoxic stimuli, skeletal muscle maintains oxygenation whereas the brain does not. These differences may be mediated by environmentally specific cardiovascular compensation. Thus, caution is advised when equating NH and HH.
The intrafollicular concentration of leptin as a potential biomarker to predict oocyte maturity in in-vitro fertilization
Authors: Hong Kun-Jing , Lin Jun-Jie , Lin Liang-Hua , Lai Tsung-Hsuan
Published: November 2022

Oocyte maturity is critical to the development potential of the embryo and pregnancy outcomes in natural and in-vitro fertilization (IVF). In IVF, oocyte maturity is typically evaluated using morphological criteria, although such assessment remains highly subjective. To identify reliable biomarkers of oocyte maturity, this study investigates the relationship between follicular cytokine concentrations and oocyte maturity in IVF patients with different ovarian reserves. In this prospective study, follicular fluid was collected during oocyte retrieval and the concentrations of cytokines involved in ovarian folliculogenesis were determined. Follicular fluid cytokine concentrations were compared between participants in three groups according to serum anti-Mullerian hormone (AMH) concentration, as follows: low AMH, < 2 ng/mL; normal AMH, 2–5 ng/mL; and high AMH, > 5 ng/mL. Pearson's correlation coefficient analysis showed that the number of mature oocytes correlated positively and strongly with serum AMH level (r = 0.719; p < 0.01). The leptin concentration in follicular fluid was significantly higher in women with normal AMH level than in those with low or high levels. ROC curve analysis showed that the follicular fluid levels of leptin (area under ROC curve, 0.829; 95% confidence interval, 0.659–0.998; p < 0.01) and SCF (area under ROC curve, 0.706; 95% confidence interval, 0.491–0.921; p = 0.087) were the best predictors of oocyte maturity. At an optimal cut-off value of 16 ng/mL, leptin had positive predictive value (sensitivity) up to 70% and negative predictive value (specificity) of 91% for indicating oocyte maturity. The concentration of leptin in follicular fluid is closely related to ovarian reserve and may serve as a biomarker to predict oocyte maturity.
Novel methods for wind speeds prediction across multiple locations
Authors: Gaidai Oleg , Xu Jingxiang , Yan Ping , Xing Yihan , Wu Yu , Zhang Fuxi
Published: November 2022

This article provides two unique methodologies that may be coupled to study the dependability of multidimensional nonlinear dynamic systems. First, the structural reliability approach is well suited for multidimensional environmental and structural reactions and is either measured or numerically simulated over sufficient time, yielding lengthy ergodic time series. Second, a unique approach to predicting extreme values has technical and environmental implications. In the event of measurable environmental loads, it is also feasible to calculate the probability of system failure, as shown in this research. In addition, traditional probability approaches for time series cannot cope effectively with the system's high dimensionality and cross-correlation across dimensions. It is common knowledge that wind speeds represent a complex, nonlinear, multidimensional, and cross-correlated dynamic environmental system that is always difficult to analyze. Additionally, global warming is a significant element influencing ocean waves throughout time. This section aims to demonstrate the efficacy of the previously mentioned technique by applying a novel method to the Norwegian offshore data set for the greatest daily wind cast speeds in the vicinity of the Landvik wind station. This study aims to evaluate the state-of-the-art approach for extracting essential information about the extreme reaction from observed time histories. The approach provided in this research enables the simple and efficient prediction of failure probability for the whole nonlinear multidimensional dynamic system.
Elucidating the genetic architecture of DNA methylation to identify promising molecular mechanisms of disease
Authors: Ma Jiantao , Joehanes Roby , Liu Chunyu , Keshawarz Amena , Hwang Shih-Jen , Bui Helena , Tejada Brandon , Sooda Meera , Munson Peter J. , Demirkale Cumhur Y. , Courchesne Paul , Heard-Costa Nancy L. , Pitsillides Achilleas N. , Feolo Mike , Sharopova Nataliya , Vasan Ramachandran S. , Huan Tianxiao , Levy Daniel
Published: November 2022

DNA methylation commonly occurs at cytosine-phosphate-guanine sites (CpGs) that can serve as biomarkers for many diseases. We analyzed whole genome sequencing data to identify DNA methylation quantitative trait loci (mQTLs) in 4126 Framingham Heart Study participants. Our mQTL mapping identified 94,362,817 cis-mQTLvariant-CpG pairs (for 210,156 unique autosomal CpGs) at P < 1e−7 and 33,572,145 trans-mQTL variant-CpG pairs (for 213,606 unique autosomal CpGs) at P < 1e−14. Using cis-mQTL variants for 1258 CpGs associated with seven cardiovascular disease (CVD) risk factors, we found 104 unique CpGs that colocalized with at least one CVD trait. For example, cg11554650 (PPP1R18) colocalized with type 2 diabetes, and was driven by a single nucleotide polymorphism (rs2516396). We performed Mendelian randomization (MR) analysis and demonstrated 58 putatively causal relations of CVD risk factor-associated CpGs to one or more risk factors (e.g., cg05337441 [APOB] with LDL; MR P = 1.2e−99, and 17 causal associations with coronary artery disease (e.g. cg08129017 [SREBF1] with coronary artery disease; MR P = 5e−13). We also showed that three CpGs, e.g., cg14893161 (PM20D1), are putatively causally associated with COVID-19 severity. To assist in future analyses of the role of DNA methylation in disease pathogenesis, we have posted a comprehensive summary data set in the National Heart, Lung, and Blood Institute’s BioData Catalyst.
Estimation of electrical transformer parameters with reference to saturation behavior using artificial hummingbird optimizer
Authors: Kotb Mohamed F. , El-Fergany Attia A. , Gouda Eid A.
Published: November 2022

This paper offers an efficient tool to define the unknown parameters of electrical transformers. The proposed methodology is developed based on artificial hummingbird optimizer (AHO) to generate the best values of the transformer’s unknown parameters. At initial stage, the parameters’ extraction of the transformer electrical equivalent is adapted as an optimization function along with the associated operating inequality constraints. In which, the sum of absolute errors (SAEs) among many variables from nameplate data of transformers is decided to be minimized. Two test cases of 4 kVA and 15 kVA transformers ratings are demonstrated to indicate the ability of the AHO compared to other recent challenging optimizers. The proposed AHO achieves the lowest SAE’s value than other competing algorithms. At advanced stage of this effort, the capture of percentage of loading to achieve maximum efficiency is ascertained. At later stage, the performance of transformers utilizing the extracted parameters cropped by the AHO to investigate the principal behavior at energization of these transformer units is made. At the end, it can be confirmed that the AHO produces best values of transformer parameters which help much in achieving accurate simulations for steady-state and inrush behaviors.
Facial asymmetry in dogs with fear and aggressive behaviors towards humans
Authors: Siniscalchi Marcello , d’Ingeo Serenella , Minunno Michele , Quaranta Angelo
Published: November 2022

There is now scientific evidence that, in dogs, distinctive facial actions are produced in response to different emotionally-arousing stimuli suggesting a relationship between lateralized facial expressions and emotional states. Although in humans, relationships between facial asymmetry and both emotional and physiological distress have been reported, there are currently no data on the laterality of dogs’ facial expressions in response to social stimuli with respect to canine behavioral disorders. The aim of the present work was to investigate the facial asymmetries of dogs with fear and aggressive behavior towards humans during two different emotional situations: (1) while the dogs were alone in the presence of their owners and (2) during the approach of an unfamiliar human being. Overall, our results demonstrated high levels of asymmetries in facial expressions of dogs displaying fear and aggressive behaviors towards humans indicating that measuring facial asymmetries in dogs could prove to be a useful non-invasive tool for investigating physiology-based behavioral disorders.
Chaotic systems with variable indexs for image encryption application
Authors: Yan Minxiu , Jie Jingfeng , Zhang Ping
Published: November 2022

A new chaotic system is obtained by changing the number of unknown parameters. The dynamical behavior of the chaotic system is investigated by the exponential change of the single unknown parameter and the state variable in the nonlinear term of the system. The structure of the newly constructed chaotic system is explored. When the number of the same state variables in the nonlinear term of the chaotic system varies, the system’s dynamic behavior undergoes complex changes. Moreover, with the exponential change of a single-state variable in a three-dimensional system, the system maintains the chaotic attractor while the state of the attractor changes. On this basis, the Lyapunov exponent, bifurcation diagram, complexity, and 0–1 test are used to compare and analyze this phenomenon. Through circuit simulations, the chaotic characteristics of the system under different conditions are further verified; this provides a theoretical basis for the hardware implementation of the new system. Finally, the new chaotic system is applied to an image encryption system with the same encryption and decryption processes. The comparison shows improved encryption and decryption characteristics of image encryption systems.