bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uphill energy transfer mechanism for photosynthesis in an Antarctic alga
Authors: Kosugi Makiko , Kawasaki Masato , Shibata Yutaka , Hara Kojiro , Takaichi Shinichi , Moriya Toshio , Adachi Naruhiko , Kamei Yasuhiro , Kashino Yasuhiro , Kudoh Sakae , Koike Hiroyuki , Senda Toshiya 
Published: February 2023

AbstractPrasiola crispa, an aerial green alga, forms layered colonies under the severe terrestrial conditions of Antarctica. Since only far-red light is available at a deep layer of the colony, P. crispa has evolved a molecular system for photosystem II (PSII) excitation using far-red light with uphill energy transfer. However, the molecular basis underlying this system remains elusive. Here, we purified a light-harvesting chlorophyll (Chl)-binding protein complex from P. crispa (Pc-frLHC) that excites PSII with far-red light and revealed its ring-shaped structure with undecameric 11-fold symmetry at 3.13 Å resolution. The primary structure suggests that Pc-frLHC evolved from LHCI rather than LHCII. The circular arrangement of the Pc-frLHC subunits is unique among eukaryote LHCs and forms unprecedented Chl pentamers at every subunit‒subunit interface near the excitation energy exit sites. The Chl pentamers probably contribute to far-red light absorption. Pc-frLHC’s unique Chl arrangement likely promotes PSII excitation with entropy-driven uphill excitation energy transfer.
Molecular mechanisms of coronary artery disease risk at the PDGFD locus
Authors: Kim Hyun-Jung , Cheng Paul , Travisano Stanislao , Weldy Chad , Monteiro João P. , Kundu Ramendra , Nguyen Trieu , Sharma Disha , Shi Huitong , Lin Yi , Liu Boxiang , Haldar Saptarsi , Jackson Simon , Quertermous Thomas 
Published: February 2023

AbstractGenome wide association studies for coronary artery disease (CAD) have identified a risk locus at 11q22.3. Here, we verify with mechanistic studies that rs2019090 andPDGFDrepresent the functional variant and gene at this locus. Further, FOXC1/C2 transcription factor binding at rs2019090 is shown to promotePDGFDtranscription through the CAD promoting allele. With single cell transcriptomic and histology studies withPdgfdknockdown in an SMC lineage tracing male atherosclerosis mouse model we find that Pdgfd promotes expansion, migration, and transition of SMC lineage cells to the chondromyocyte phenotype. Pdgfd also increases adventitial fibroblast and pericyte expression of chemokines and leukocyte adhesion molecules, which is linked to plaque macrophage recruitment. Despite these changes there is no effect ofPdgfddeletion on overall plaque burden. These findings suggest thatPDGFDmediates CAD risk by promoting deleterious phenotypic changes in SMC, along with an inflammatory response that is primarily focused in the adventitia.
Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation
Authors: Bernkopf Marie , Abdullah Ummi B. , Bush Stephen J. , Wood Katherine A. , Ghaffari Sahar , Giannoulatou Eleni , Koelling Nils , Maher Geoffrey J. , Thibaut Loïc M. , Williams Jonathan , Blair Edward M. , Kelly Fiona Blanco , Bloss Angela , Burkitt-Wright Emma , Canham Natalie , Deng Alexander T. , Dixit Abhijit , Eason Jacqueline , Elmslie Frances , Gardham Alice , Hay Eleanor , Holder Muriel , Homfray Tessa , Hurst Jane A. , Johnson Diana , Jones Wendy D. , Kini Usha , Kivuva Emma , Kumar Ajith , Lees Melissa M. , Leitch Harry G. , Morton Jenny E. V. , Németh Andrea H. , Ramachandrappa Shwetha , Saunders Katherine , Shears Deborah J. , Side Lucy , Splitt Miranda , Stewart Alison , Stewart Helen , Suri Mohnish , Clouston Penny , Davies Robert W. , Wilkie Andrew O. M. , Goriely Anne 
Published: February 2023

AbstractFollowing the diagnosis of a paediatric disorder caused by an apparently de novo mutation, a recurrence risk of 1–2% is frequently quoted due to the possibility of parental germline mosaicism; but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk. By combining locus-specific sequencing of multiple tissues to detect occult mosaicism with long-read sequencing to determine the parent-of-origin of the mutation, we show that we can stratify the majority of couples into one of seven discrete categories associated with substantially different risks to future offspring. Among 58 families with a single affected offspring (representing 59 de novo mutations in 49 genes), the recurrence risk for 35 (59%) was decreased below 0.1%, but increased owing to parental mixed mosaicism for 5 (9%)—that could be quantified in semen for paternal cases (recurrence risks of 5.6–12.1%). Implementation of this strategy offers the prospect of driving a major transformation in the practice of genetic counselling.
A general thermodynamics-triggered competitive growth model to guide the synthesis of two-dimensional nonlayered materials
Authors: Zhao Zijing , Fang Zhi , Han Xiaocang , Yang Shiqi , Zhou Cong , Zeng Yi , Zhang Biao , Li Wei , Wang Zhan , Zhang Ying , Zhou Jian , Zhou Jiadong , Ye Yu , Hou Xinmei , Zhao Xiaoxu , Gao Song , Hou Yanglong 
Published: February 2023

AbstractTwo-dimensional (2D) nonlayered materials have recently provoked a surge of interest due to their abundant species and attractive properties with promising applications in catalysis, nanoelectronics, and spintronics. However, their 2D anisotropic growth still faces considerable challenges and lacks systematic theoretical guidance. Here, we propose a general thermodynamics-triggered competitive growth (TTCG) model providing a multivariate quantitative criterion to predict and guide 2D nonlayered materials growth. Based on this model, we design a universal hydrate-assisted chemical vapor deposition strategy for the controllable synthesis of various 2D nonlayered transition metal oxides. Four unique phases of iron oxides with distinct topological structures have also been selectively grown. More importantly, ultra-thin oxides display high-temperature magnetic ordering and large coercivity. MnxFeyCo3-x-yO4 alloy is also demonstrated to be a promising room-temperature magnetic semiconductor. Our work sheds light on the synthesis of 2D nonlayered materials and promotes their application for room-temperature spintronic devices.
Wireless communications sensing and security above 100 GHz
Authors: Jornet Josep M. , Knightly Edward W. , Mittleman Daniel M. 
Published: February 2023

AbstractThe field of sub-terahertz wireless communications is advancing rapidly, with major research efforts ramping up around the globe. To address some of the significant hurdles associated with exploiting these high frequencies for broadband and secure networking, systems will require extensive new capabilities for sensing their environment and manipulating their broadcasts. Based on these requirements, a vision for future wireless systems is beginning to emerge. In this Perspective article, we discuss some of the prominent challenges and possible solutions which are at the forefront of current research, and which will contribute to the architecture of wireless platforms beyond 5G.
Endogenous retroviruses and TDP-43 proteinopathy form a sustaining feedback driving intercellular spread of Drosophila neurodegeneration
Authors: Chang Yung-Heng , Dubnau Josh 
Published: February 2023

AbstractInter-cellular movement of “prion-like” proteins is thought to explain propagation of neurodegeneration between cells. For example, propagation of abnormally phosphorylated cytoplasmic inclusions of TAR-DNA-Binding protein (TDP-43) is proposed to underlie progression of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). But unlike transmissible prion diseases, ALS and FTD are not infectious and injection of aggregated TDP-43 is not sufficient to cause disease. This suggests a missing component of a positive feedback necessary to sustain disease progression. We demonstrate that endogenous retrovirus (ERV) expression and TDP-43 proteinopathy are mutually reinforcing. Expression of either Drosophila mdg4-ERV (gypsy) or the human ERV, HERV-K (HML-2) are each sufficient to stimulate cytoplasmic aggregation of human TDP-43. Viral ERV transmission also triggers TDP-43 pathology in recipient cells that express physiological levels of TDP-43, whether they are in contact or at a distance. This mechanism potentially underlies the TDP-43 proteinopathy-caused neurodegenerative propagation through neuronal tissue.
Real-space imaging of a phenyl group migration reaction on metal surfaces
Authors: Ruan Zilin , Li Baijin , Lu Jianchen , Gao Lei , Sun Shijie , Zhang Yong , Cai Jinming 
Published: February 2023

AbstractThe explorations to extend present chemical synthetic methods are of great importance to simplify synthetic routes of chemical species. Additionally, understanding the chemical reaction mechanisms is critical to achieve controllable synthesis for applications. Here, we report the on-surface visualization and identification of a phenyl group migration reaction of 1,4-dimethyl-2,3,5,6-tetraphenyl benzene (DMTPB) precursor on Au(111), Cu(111) and Ag(110) substrates. With the combination of bond-resolved scanning tunneling microscopy (BR-STM), noncontact atomic force microscopy (nc-AFM) and density functional theory (DFT) calculations, the phenyl group migration reaction of DMTPB precursor is observed, forming various polycyclic aromatic hydrocarbons on the substrates. DFT calculations reveal that the multiple-step migrations are facilitated by the hydrogen radical attack, inducing cleavage of phenyl groups and subsequent rearomatization of the intermediates. This study provides insights into complex surface reaction mechanisms at the single molecule level, which may guide the design of chemical species.
Mutations in Parkinsonism-linked endocytic proteins synaptojanin1 and auxilin have synergistic effects on dopaminergic axonal pathology
Authors: Ng Xin Yi , Wu Yumei , Lin Youneng , Yaqoob Sidra Mohamed , Greene Lois E. , De Camilli Pietro , Cao Mian 
Published: February 2023

AbstractParkinson’s disease (PD) is a neurodegenerative disorder characterized by defective dopaminergic (DAergic) input to the striatum. Mutations in two genes encoding synaptically enriched clathrin-uncoating factors, synaptojanin 1 (SJ1) and auxilin, have been implicated in atypical Parkinsonism. SJ1 knock-in (SJ1-KIRQ) mice carrying a disease-linked mutation display neurological manifestations reminiscent of Parkinsonism. Here we report that auxilin knockout (Aux-KO) mice display dystrophic changes of a subset of nigrostriatal DAergic terminals similar to those of SJ1-KIRQ mice. Furthermore, Aux-KO/SJ1-KIRQ double mutant mice have shorter lifespan and more severe synaptic defects than single mutant mice. These include increase in dystrophic striatal nerve terminals positive for DAergic markers and for the PD risk protein SV2C, as well as adaptive changes in striatal interneurons. The synergistic effect of the two mutations demonstrates a special lability of DAergic neurons to defects in clathrin uncoating, with implications for PD pathogenesis in at least some forms of this condition.
WS22 database, Wigner Sampling and geometry interpolation for configurationally diverse molecular datasets﻿
Authors: Pinheiro Jr Max , Zhang Shuang , Dral Pavlo O. , Barbatti Mario 
Published: February 2023

AbstractMultidimensional surfaces of quantum chemical properties, such as potential energies and dipole moments, are common targets for machine learning, requiring the development of robust and diverse databases extensively exploring molecular configurational spaces. Here we composed the WS22 database covering several quantum mechanical (QM) properties (including potential energies, forces, dipole moments, polarizabilities, HOMO, and LUMO energies) for ten flexible organic molecules of increasing complexity and with up to 22 atoms. This database consists of 1.18 million equilibrium and non-equilibrium geometries carefully sampled from Wigner distributions centered at different equilibrium conformations (either at the ground or excited electronic states) and further augmented with interpolated structures. The diversity of our datasets is demonstrated by visualizing the geometries distribution with dimensionality reduction as well as via comparison of statistical features of the QM properties with those available in existing datasets. Our sampling targets broader quantum mechanical distribution of the configurational space than provided by commonly used sampling through classical molecular dynamics, upping the challenge for machine learning models.
Novel data dependent divider circuit block implementation for complex division and area critical applications
Authors: Patankar Udayan S. , Flores Miguel E. , Koel Ants 
Published: February 2023

AbstractThis article elaborates on the state-of-the-art novel Udayan S. Patankar (USP)-Awadhoot algorithm for distinctive implementation area improvement for area-critical electronic applications. The proposed USP-Awadhoot divider is a digit recurrence class, but it can be flexibly implemented as a restoring or nonrestoring algorithm. The implementation example indicates the use of the Baudhayan-Pythagoras triplet method in association with the proposed USP-Awadhoot divider. The triplet method provides an easy way to generate Mat_Term1, Mat_Term2, and T_Term, which are further utilized with the proposed USP-Awadhoot divider. The USP-Awadhoot divider is implemented in three parts. First is preprocessing circuit stage for executing a dynamic separate scaling operation on input operands, ensuring the inputs are in the correct form. Second is the processing circuit stage for implementing the conversion logic expressed by the Awadhoot matrix, and third is the postprocessing circuit stage for recombining the individual results into the final result. The proposed divider works upto 285 MHz frequency with a power estimation of 3.366 W, also significantly improves the chip area requirements over those of the commercially and noncommercially implemented solutions.
Satellite observation of atmospheric CO2 and water storage change over Iran
Authors: Safaeian Samaneh , Falahatkar Samereh , Tourian Mohammad J. 
Published: February 2023

AbstractLike many other Middle East countries, Iran has been suffering from severe water shortages over the last two decades, as evidenced by significant decline in surface water and groundwater levels. The observed changes in water storage can be attributed to the mutually reinforcing effects of human activities, climatic variability, and of course the climate change. The objective of this study is to analyze the dependency of atmospheric CO2 increase on the water shortage of Iran, for which we investigate the spatial relationship between water storage change and CO2 concentration using large scale satellite data. We conduct our analysis using water storage change data from GRACE satellite and atmospheric CO2 concentration from GOSAT and SCIAMACHY satellites during 2002–2015. To analyze the long-term behavior of time series we benefit from Mann-Kendal test and for the investigation of the relationship between atmospheric CO2 concentration and total water storage we use Canonical Correlation Analysis (CCA) and Regression model. Our Results show that the water storage change anomaly and CO2 concentration are negatively correlated especially in northern, western, southwest (Khuzestan province), and also southeast (Kerman, Hormozgan, Sistan, and Baluchestan provinces) of Iran. CCA results reveal that in the most of northern regions, the decrease in water storage is significantly influenced by the increase of CO2 concentration. The results further show that precipitation in the highland and peaks does not seem to be influenced by the long and short-term variation in CO2 concentration. Besides, our results show that the CO2 concentration is slightly correlated with a weak positive trend in evapotranspiration over agricultural areas. Thus, the indirect effect of CO2 on increasing evapotranspiration is observed spatially in the whole of Iran. The results of the regression model between total water storage change and carbon dioxide (R2 = 0.91)/water discharge/water consumption show that carbon dioxide has the highest effect on total water storage change at large scale. The results of this study will contribute to both water resource management and mitigation plans to achieve the goal of CO2 emission reduction.
Nature-inspired stochastic hybrid technique for joint and individual inversion of DC and MT data
Authors: Sarkar Kuldeep , Mukesh  , Singh Upendra K. 
Published: February 2023

AbstractHere, a new naturally-inspired stochastic nonlinear joint and individual inversion technique for integrating direct current (DC) and magnetotelluric (MT) data interpretation-based simulation of a swarm intelligence combo with specific capabilities for exploitation of the variable weight particle swarm optimizer (vPSO) and exploration of the grey wolf optimizer (GWO), vPSOGWO, is used. They are particularly notable for their capacity for information exchange while hunting for food. Through synthetic MT and DC data contaminated with various sets of random noise, the applicability of the anticipated vPSOGWO algorithm based joint and individual inversion algorithm was assessed. The field examples, collected from diversified different geological terrains, including Digha (West Bengal), India; Sundar Pahari (Jharkhand), India; Puga Valley (Ladakh), India; New Brunswick, Canada; and South Central Australia, have shown the practical application of the proposed algorithm. Further, a Bayesian probability density function (bpdf) for estimating a mean global model and uncertainty assessment in posterior; and a histogram for model resolution assessment have also been created using 1000 inverted models. We examined the inverted outcomes and compared them with results from other cutting-edge methodologies, including the GWO, PSO, genetic algorithm (GA), Levenberg–Marquardt (LM), and ridge-regression (RR). Our findings showed that the current methodology is more effective than the GWO, PSO, GA, LM, and RR techniques at consistently improving the convergence of the global minimum. In contrast to earlier approaches, the current cutting-edge strategy vPSOGWO offers an improved resolution of an additional significant crustal thickness of about 65.68 ± 1.96 km over the Puga Valley, in which the inverted crustal thickness determined by vPSOGWO agrees well with the published crustal thickness over the Puga Valley. The new technology brings simulations closer to genuine models by significantly reducing uncertainty and enhancing model resolution.
Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach
Authors: Średnicka Paulina , Roszko Marek Łukasz , Popowski Dominik , Kowalczyk Monika , Wójcicki Michał , Emanowicz Paulina , Szczepańska Magdalena , Kotyrba Danuta , Juszczuk-Kubiak Edyta 
Published: February 2023

AbstractGut microbiota (GM) plays many key functions and helps maintain the host’s health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC–MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.
Uric acid and risk of pre-eclampsia: results from a large case–control study and meta-analysis of prospective studies
Authors: Colmenares-Mejia Claudia C. , Quintero-Lesmes Doris C. , Bautista-Niño Paula K. , Guío Elizabeth , Paez Maria C. , Beltrán Mónica , Williams David , Gray Kathryn J. , Casas Juan P. , Serrano Norma C. 
Published: February 2023

AbstractTo quantify the association between maternal uric acid levels and pre-eclampsia risk in a large collection of primigravid women. A case–control study (1365 cases of pre-eclampsia and 1886 normotensive controls) was conducted. Pre-eclampsia was defined as blood pressure ≥ 140/90 mmHg and proteinuria ≥ 300 mg/24 h. Sub-outcome analysis included early, intermediate, and late pre-eclampsia. Multivariable analysis for pre-eclampsia and its sub-outcomes was conducted using binary and multinomial logistic regression, respectively. Additionally, a systematic review and meta-analysis of cohort studies measuring uric acid levels < 20 weeks of gestation was performed to rule out reverse causation. There was a positive linear association between increasing uric acid levels and presence of pre-eclampsia. Adjusted odds ratio of pre-eclampsia was 1.21 (95%CI 1.11–1.33) for every one standard deviation increase in uric acid levels. No differences in the magnitude of association were observed between early and late pre-eclampsia. Three studies with uric acid measured < 20 weeks’ gestation were identified, with a pooled OR for pre-eclampsia of 1.46 (95%CI 1.22–1.75) for a top vs. bottom quartile comparison. Maternal uric acid levels are associated with risk of pre-eclampsia. Mendelian randomisation studies would be helpful to further explore the causal role of uric acid in pre-eclampsia.
Validation of an MD simulation approach for electrical field responsive micelles and their application in drug delivery
Authors: Razavi Leila , Raissi Heidar , Farzad Farzaneh 
Published: February 2023

AbstractIn the current work, a new type of micelle is designed that has active connectivity in respond to exterior stimulus and the desired water solubility. Two end-ornamented homopolymers, polystyrene-beta-cyclodextrin (PS-β-CD) and polyethylene oxide-ferrocene (PE-FE), can aggregate as a supramolecular micelle (PS-β-CD/PE-FE) by the guest–host interactions. Our results showed that the Lennard–Jones and hydrophobic interactions are the main powerful forces for the micelle formation process. It was found that the electrical field plays a role as a driving force in the reversible assembly-disassembly of the micellar system. Moreover, for the first time, we examined the PS-β-CD/PE-FE micelle interaction as a drug delivery system with anastrozole (ANS) and mitomycin C (MIC) anti-cancer drugs. The investigation of the total energy between PS-β-CD/PE-FE micelle and drugs predicts the drug adsorption process as favorable (Etotal = − 638.67 and − 259.80 kJ/mol for the Micelle@ANS and Micelle@MIC complexes, respectively). Our results offer a deep understanding of the micelle formation process, the electrical field-respond, and drug adsorption behaviors of the micelle. This simulation study has been accomplished by employing classical molecular dynamics calculation.