bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractParkinson’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

AbstractHerpes 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

AbstractChemical 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

AbstractWe 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

AbstractA 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

AbstractMany 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

AbstractThis 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

AbstractInterplay 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

AbstractReports 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

AbstractDevelopment 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

AbstractIn 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

AbstractCandida 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

AbstractIsodon 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.