bluuebunny/crossref_metadata_2025_split huggingface dataset:
Programmed cell death 11 modulates but not entirely relies on p53-HDM2 loop to facilitate G2/M transition in colorectal cancer cells
Authors: Ding Li , Xu Yujie , Xu Lin , Zhao Chenhong , Zhang Zhiping , Zhang Jie , Liao Kai , Chen Yuerou , Li Jingwen , Mei Xinyu , Zhang Xinyue 
Published: December 2023

AbstractWe previously described a nucleolar protein RSL1D1 but distributed throughout the nucleus in HCT116 colorectal cancer (CRC) cells to facilitate G1/S transition by inhibiting p53 signaling. Here, we found another nucleolar protein, programmed cell death 11 (PDCD11), also with an “Extra-nucleolar” localization in CRC cells but to regulate G2/M checkpoint. This protein directly interacts with p53 and HDM2 in the nucleoplasm, thereby recruiting p53 to HDM2 for ubiquitination and degradation. The ensuing downregulation of p53 increases the CDK1 level to help the cells pass G2/M checkpoint. Upon DNA damage stress, PDCD11 gains the power to upregulate CDK1 independently of p53. Beyond these, PDCD11 also upregulates CDC25C in a p53-independent manner to dephosphorylate CDK1 to facilitate G2/M transition. Downregulation of PDCD11 greatly reduced cancer cell growth in vitro and in vivo, additionally sensitized cells to DNA damage signals, highlighting that PDCD11 is a crucial driving factor of CRC and a potential target for cancer treatment.
Epigenome-wide association studies of prenatal maternal mental health and infant epigenetic profiles: a systematic review
Authors: Drzymalla Emily , Crider Krista S. , Wang Arick , Marta Gwinn , Khoury Muin J. , Rasooly Danielle 
Published: December 2023

AbstractPrenatal stress and poor maternal mental health are associated with adverse offspring outcomes; however, the biological mechanisms are unknown. Epigenetic modification has linked maternal health with offspring development. Epigenome-wide association studies (EWAS) have examined offspring DNA methylation profiles for association with prenatal maternal mental health to elucidate mechanisms of these complex relationships. The objective of this study is to provide a comprehensive, systematic review of EWASs of infant epigenetic profiles and prenatal maternal anxiety, depression, or depression treatment. We conducted a systematic literature search following PRISMA guidelines for EWAS studies between prenatal maternal mental health and infant epigenetics through May 22, 2023. Of 645 identified articles, 20 fulfilled inclusion criteria. We assessed replication of CpG sites among studies, conducted gene enrichment analysis, and evaluated the articles for quality and risk of bias. We found one repeated CpG site among the maternal depression studies; however, nine pairs of overlapping differentially methylatd regions were reported in at least two maternal depression studies. Gene enrichment analysis found significant pathways for maternal depression but not for any other maternal mental health category. We found evidence that these EWAS present a medium to high risk of bias. Exposure to prenatal maternal depression and anxiety or treatment for such was not consistently associated with epigenetic changes in infants in this systematic review and meta-analysis. Small sample size, potential bias due to exposure misclassification and statistical challenges are critical to address in future efforts to explore epigenetic modification as a potential mechanism by which prenatal exposure to maternal mental health disorders leads to adverse infant outcomes.
Pressure-induced reversal of Peierls-like distortions elicits the polyamorphic transition in GeTe and GeSe
Authors: Fujita Tomoki , Chen Yuhan , Kono Yoshio , Takahashi Seiya , Kasai Hidetaka , Campi Davide , Bernasconi Marco , Ohara Koji , Yumoto Hirokatsu , Koyama Takahisa , Yamazaki Hiroshi , Senba Yasunori , Ohashi Haruhiko , Inoue Ichiro , Hayashi Yujiro , Yabashi Makina , Nishibori Eiji , Mazzarello Riccardo , Wei Shuai 
Published: December 2023

AbstractWhile polymorphism is prevalent in crystalline solids, polyamorphism draws increasing interest in various types of amorphous solids. Recent studies suggested that supercooling of liquid phase-change materials (PCMs) induces Peierls-like distortions in their local structures, underlying their liquid-liquid transitions before vitrification. However, the mechanism of how the vitrified phases undergo a possible polyamorphic transition remains elusive. Here, using high-energy synchrotron X-rays, we can access the precise pair distribution functions under high pressure and provide clear evidence that pressure can reverse the Peierls-like distortions, eliciting a polyamorphic transition in GeTe and GeSe. Combined with simulations based on machine-learned-neural-network potential, our structural analysis reveals a high-pressure state characterized by diminished Peierls-like distortion, greater coherence length, reduced compressibility, and a narrowing bandgap. Our finding underscores the crucial role of Peierls-like distortions in amorphous octahedral systems including PCMs. These distortions can be controlled through pressure and composition, offering potentials for designing properties in PCM-based devices.
Topological electronic structure and spin texture of quasi-one-dimensional higher-order topological insulator Bi4Br4
Authors: Zhao Wenxuan , Yang Ming , Xu Runzhe , Du Xian , Li Yidian , Zhai Kaiyi , Peng Cheng , Pei Ding , Gao Han , Li Yiwei , Xu Lixuan , Han Junfeng , Huang Yuan , Liu Zhongkai , Yao Yugui , Zhuang Jincheng , Du Yi , Zhou Jinjian , Chen Yulin , Yang Lexian 
Published: December 2023

AbstractThe notion of topological insulators (TIs), characterized by an insulating bulk and conducting topological surface states, can be extended to higher-order topological insulators (HOTIs) hosting gapless modes localized at the boundaries of two or more dimensions lower than the insulating bulk. In this work, by performing high-resolution angle-resolved photoemission spectroscopy (ARPES) measurements with submicron spatial and spin resolution, we systematically investigate the electronic structure and spin texture of quasi-one-dimensional (1D) HOTI candidate Bi4Br4. In contrast to the bulk-state-dominant spectra on the (001) surface, we observe gapped surface states on the (100) surface, whose dispersion and spin-polarization agree well with our ab-initio calculations. Moreover, we reveal in-gap states connecting the surface valence and conduction bands, which is a signature of the hinge states inside the (100) surface gap. Our findings provide compelling evidence for the HOTI phase of Bi4Br4. The identification of the higher-order topological phase promises applications based on 1D spin-momentum locked current in electronic and spintronic devices.
Stabilizing ruthenium dioxide with cation-anchored sulfate for durable oxygen evolution in proton-exchange membrane water electrolyzers
Authors: Xue Yanrong , Zhao Jiwu , Huang Liang , Lu Ying-Rui , Malek Abdul , Gao Ge , Zhuang Zhongbin , Wang Dingsheng , Yavuz Cafer T. , Lu Xu 
Published: December 2023

AbstractRuthenium dioxide is the most promising alternative to the prevailing but expensive iridium-based catalysts for the oxygen evolution reaction in proton-exchange membrane water electrolyzers. However, the under-coordinated lattice oxygen of ruthenium dioxide is prone to over-oxidation, and oxygen vacancies are formed at high oxidation potentials under acidic corrosive conditions. Consequently, ruthenium atoms adjacent to oxygen vacancies are oxidized into soluble high-valence derivatives, causing the collapse of the ruthenium dioxide crystal structure and leading to its poor stability. Here, we report an oxyanion protection strategy to prevent the formation of oxygen vacancies on the ruthenium dioxide surface by forming coordination-saturated lattice oxygen. Combining density functional theory calculations, electrochemical measurements, and a suite of operando spectroscopies, we showcase that barium-anchored sulfate can greatly impede ruthenium loss and extend the lifetime of ruthenium-based catalysts during acidic oxygen evolution, while maintaining the activity. This work paves a new way for designing stable and active anode catalysts toward acidic water splitting.
Towards understanding structure–property relations in materials with interpretable deep learning
Authors: Vu Tien-Sinh , Ha Minh-Quyet , Nguyen Duong-Nguyen , Nguyen Viet-Cuong , Abe Yukihiro , Tran Truyen , Tran Huan , Kino Hiori , Miyake Takashi , Tsuda Koji , Dam Hieu-Chi 
Published: December 2023

AbstractDeep learning (DL) models currently employed in materials research exhibit certain limitations in delivering meaningful information for interpreting predictions and comprehending the relationships between structure and material properties. To address these limitations, we propose an interpretable DL architecture that incorporates the attention mechanism to predict material properties and gain insights into their structure–property relationships. The proposed architecture is evaluated using two well-known datasets (the QM9 and the Materials Project datasets), and three in-house-developed computational materials datasets. Train–test–split validations confirm that the models derived using the proposed DL architecture exhibit strong predictive capabilities, which are comparable to those of current state-of-the-art models. Furthermore, comparative validations, based on first-principles calculations, indicate that the degree of attention of the atoms’ local structures to the representation of the material structure is critical when interpreting structure–property relationships with respect to physical properties. These properties encompass molecular orbital energies and the formation energies of crystals. The proposed architecture shows great potential in accelerating material design by predicting material properties and explicitly identifying crucial features within the corresponding structures.
Genetic risk variants in New Yorkers of Puerto Rican and Dominican Republic heritage with Parkinson’s disease
Authors: Miltenberger-Miltenyi Gabriel , Ortega Roberto A. , Domingo Aloysius , Yadav Rachita , Nishiyama Ayumi , Raymond Deborah , Katsnelson Viktoriya , Urval Nikita , Swan Matthew , Shanker Vicki , Miravite Joan , Walker Ruth H. , Bressman Susan B. , Ozelius Laurie J. , Cabassa José C. , Saunders-Pullman Rachel 
Published: December 2023

AbstractThere is a paucity of genetic characterization in people with Parkinson’s disease (PD) of Latino and Afro-Caribbean descent. Screening LRRK2 and GBA variants in 32 New Yorkers of Puerto Rican ethnicity with PD and in 119 non-Hispanic-non-Jewish European PD cases revealed that Puerto Rican participants were more likely to harbor the LRRK2-p.G2019S variant (15.6% vs. 4.2%, respectively). Additionally, whole exome sequencing of twelve Puerto Rican and Dominican PD participants was performed as an exploratory study.
Development and validation of an expanded antibody toolset that captures alpha-synuclein pathological diversity in Lewy body diseases
Authors: Altay Melek Firat , Kumar Senthil T. , Burtscher Johannes , Jagannath Somanath , Strand Catherine , Miki Yasuo , Parkkinen Laura , Holton Janice L. , Lashuel Hilal A. 
Published: December 2023

AbstractThe abnormal aggregation and accumulation of alpha-synuclein (aSyn) in the brain is a defining hallmark of synucleinopathies. Various aSyn conformations and post-translationally modified forms accumulate in pathological inclusions and vary in abundance among these disorders. Relying on antibodies that have not been assessed for their ability to detect the diverse forms of aSyn may lead to inaccurate estimations of aSyn pathology in human brains or disease models. To address this challenge, we developed and characterized an expanded antibody panel that targets different sequences and post-translational modifications along the length of aSyn, and that recognizes all monomeric, oligomeric, and fibrillar aSyn conformations. Next, we profiled aSyn pathology across sporadic and familial Lewy body diseases (LBDs) and reveal heterogeneous forms of aSyn pathology, rich in Serine 129 phosphorylation, Tyrosine 39 nitration and N- and C-terminal tyrosine phosphorylations, scattered both to neurons and glia. In addition, we show that aSyn can become hyperphosphorylated during processes of aggregation and inclusion maturation in neuronal and animal models of aSyn seeding and spreading. The validation pipeline we describe for these antibodies paves the way for systematic investigations into aSyn pathological diversity in the human brain, peripheral tissues, as well as in cellular and animal models of synucleinopathies.
Structural insights into the iron nitrogenase complex
Authors: Schmidt Frederik V. , Schulz Luca , Zarzycki Jan , Prinz Simone , Oehlmann Niels N. , Erb Tobias J. , Rebelein Johannes G. 
Published: December 2023

AbstractNitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO2) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO2, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF3-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [Fe8S9C-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit ‘communication’ and thus the nitrogenase mechanism.
A future for digital public goods for monitoring SDG indicators
Authors: Liang Dong , Guo Huadong , Nativi Stefano , Kulmala Markku , Shirazi Zeeshan , Chen Fang , Kalonji Gretchen , Yan Dongmei , Li Jianhui , Duerler Robert , Luo Lei , Han Qunli , Deng Siming , Wang Yuanyuan , Kong Lingyi , Jelinek Thorsten 
Published: December 2023

AbstractDigital public goods (DPGs), if implemented with effective policies, can facilitate the realization of the United Nations Sustainable Development Goals (SDGs). However, there are ongoing deliberations on how to define DPGs and assure that society can extract the maximum benefit from the growing number of digital resources. The International Research Center of Big Data for Sustainable Development Goals (CBAS) sees DPGs as an important mechanism to facilitate information-driven policy and decision-making processes for the SDGs. This article presents the results of a CBAS survey of 51 respondents from around the world spanning multiple scientific fields, who shared their expert opinions on DPGs and their thoughts about challenges related to their practical implementation in supporting the SDGs. Based on the survey results, the paper presents core principles in a proposed strategy, including establishment of international standards, adherence to open science and open data principles, and scalability in monitoring SDG indicators. A community-driven strategy to develop DPGs is proposed to accelerate DPG production in service of the SDGs while adhering to the core principles identified in the survey.
The UCLA Cosmochemistry Database
Authors: Zhang Bidong , Lehnert Kerstin A. , Rubin Alan E. , McKeegan Kevin D. , Warren Paul H. , Mays Jennifer L. , Profeta Lucia R. , Johansson Annika K. , Ni Peng , Young Edward D. , Kyte Frank T. , Liu Ming-Chang , Dunham Emilie T. , Tang Haolan , Ji Peng , Figueroa-Salazar Juan D. 
Published: December 2023

AbstractThe UCLA Cosmochemistry Database was initiated as part of a data-rescue and -storage project aimed at archiving a variety of cosmochemical data acquired at University of California, Los Angeles (UCLA). The data collection includes elemental compositions of extraterrestrial materials analyzed by UCLA cosmochemists over the last five decades. The analytical techniques include atomic absorption spectrometry (AAS) and neutron activation analysis (NAA) at UCLA. The data collection is stored on the Astromaterials Data System (Astromat). We provide both interactive tables and downloadable datasheets for users to access all data. The UCLA Cosmochemistry Database archives cosmochemical data that are essential tools for increasing our understanding of the nature and origin of extraterrestrial materials. Future studies can reference the data collection in the examination, analysis, and classification of newly acquired extraterrestrial samples.
Assessing household lifestyle exposures from consumer purchases, the My Purchases cohort
Authors: Møller Frederik T. , Junker Thor Grønborg , Kold Sørensen Kathrine , Eves Caroline , Wohlfahrt Jan , Dillner Joakim , Torp-Pedersen Christian , Wilkowski Bartlomiej , Chong Steven , Pers Tune H. , Yakimov Victor , Müller Heimo , Ethelberg Steen , Melbye Mads 
Published: December 2023

AbstractConsumer purchase data (CPD) is a promising instrument to assess the impact of purchases on health, but is limited by the need for manual scanning, a lack of access to data from multiple retailers, and limited information on product data and health outcomes. Here we describe the My Purchases cohort, a web-app enabled, prospective collection of CPD, covering several large retail chains in Denmark, that enables linkage to health outcomes. The cohort included 459 participants as of July 03, 2023. Up to eight years of CPD have been collected, with 2,225,010 products purchased, comprising 223,440 unique products. We matched 88.5% of all products by product name or item number to one generic food database and three product databases. Combined, the databases enable analysis of key exposures such as nutrients, ingredients, or additives. We found that increasing the number of retailers that provide CPD for each consumer improved the stability of individual CPD profiles and when we compared kilojoule information from generic and specific product matches, we found a median modified relative difference of 0.23. Combined with extensive product databases and health outcomes, CPD could provide the basis for extensive investigations of how what we buy affects our health.
Infection of wild-caught wood mice (Apodemus sylvaticus) and yellow-necked mice (A. flavicollis) with tick-borne encephalitis virus
Authors: Bakker Julian W. , Pascoe Emily L. , van de Water Sandra , van Keulen Lucien , de Vries Ankje , Woudstra Lianne C. , Esser Helen J. , Pijlman Gorben P. , de Boer Willem F. , Sprong Hein , Kortekaas Jeroen , Wichgers Schreur Paul J. , Koenraadt Constantianus J. M. 
Published: December 2023

AbstractThe distribution of tick-borne encephalitis virus (TBEV) is expanding to Western European countries, including the Netherlands, but the contribution of different rodent species to the transmission of TBEV is poorly understood. We investigated whether two species of wild rodents native to the Netherlands, the wood mouse Apodemus sylvaticus and the yellow-necked mouse Apodemus flavicollis, differ in their relative susceptibility to experimental infection with TBEV. Wild-caught individuals were inoculated subcutaneously with the classical European subtype of TBEV (Neudoerfl) or with TBEV-NL, a genetically divergent TBEV strain from the Netherlands. Mice were euthanised and necropsied between 3 and 21 days post-inoculation. None of the mice showed clinical signs or died during the experimental period. Nevertheless, TBEV RNA was detected up to 21 days in the blood of both mouse species and TBEV was also isolated from the brain of some mice. Moreover, no differences in infection rates between virus strains and mouse species were found in blood, spleen, or liver samples. Our results suggest that the wood mouse and the yellow-necked mouse may equally contribute to the transmission cycle of TBEV in the Netherlands. Future experimental infection studies that include feeding ticks will help elucidate the relative importance of viraemic transmission in the epidemiology of TBEV.
Comprehensive proteomic analysis reveals omega-3 fatty acids to counteract endotoxin-stimulated metabolic dysregulation in porcine enterocytes
Authors: Sundaram Tamil Selvi , Addis Maria Filippa , Giromini Carlotta , Rebucci Raffaella , Pisanu Salvatore , Pagnozzi Daniela , Baldi Antonella 
Published: December 2023

AbstractOmega-3 polyunsaturated fatty acids (n-3 PUFA), such as the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are reported to beneficially affect the intestinal immunity. The biological pathways modulated by n-3 PUFA during an infection, at the level of intestinal epithelial barrier remain elusive. To address this gap, we investigated the proteomic changes induced by n-3 PUFA in porcine enterocyte cell line (IPEC-J2), in the presence and absence of lipopolysaccharide (LPS) stress conditions using shotgun proteomics analysis integrated with RNA-sequencing technology. A total of 33, 85, and 88 differentially abundant proteins (DAPs) were identified in cells exposed to n-3 PUFA (DHA:EPA), LPS, and n-3 PUFA treatment followed by LPS stimulation, respectively. Functional annotation and pathway analysis of DAPs revealed the modulation of central carbon metabolism, including the glycolysis/gluconeogenesis, pentose phosphate pathway, and oxidative phosphorylation processes. Specifically, LPS caused metabolic dysregulation in enterocytes, which was abated upon prior treatment with n-3 PUFA. Besides, n-3 PUFA supplementation facilitated enterocyte development and lipid homeostasis. Altogether, this work for the first time comprehensively described the biological pathways regulated by n-3 PUFA in enterocytes, particularly during endotoxin-stimulated metabolic dysregulation. Additionally, this study may provide nutritional biomarkers in monitoring the intestinal health of human and animals on n-3 PUFA-based diets.
Pattern recognition of forced oscillation technique measurement results using deep learning can identify asthmatic patients more accurately than setting reference ranges
Authors: Funaita Chiune , Furuie Wakaba , Koike Fumika , Oyama Saki , Endo Junji , Otani Yoshio , Ichikawa Yuri , Ito Minako , Nakamura Yoichi , Komatuzaki Keiko , Hirata Akira , Miyazaki Yasunari , Sumi Yuki 
Published: December 2023

AbstractNo official clinical reference values have been established for MostGraph, which measures total respiratory resistance and reactance using the forced oscillation technique, complicating result interpretation. This study aimed to establish a reference range for MostGraph measurements and examine its usefulness in discriminating participants with asthma from controls (participants without any respiratory diseases). The study also aimed to investigate the effectiveness of deep learning in discriminating between the two aforementioned groups. To establish reference ranges, the MostGraph measurements of healthy controls (n = 215) were power-transformed to distribute the data more normally. After inverse transformation, the mean ± standard deviation × 2 of the transformed values were used to establish the reference ranges. The number of measured items outside the reference ranges was evaluated to discriminate patients with asthma (n = 941) from controls. Additionally, MostGraph measurements were evaluated using deep learning. Although reference ranges were established, patients with asthma could not be discriminated from controls. However, with deep learning, we could discriminate between the two groups with 78% accuracy. Therefore, deep learning, which considers multiple measurements as a whole, was more effective in interpreting MostGraph measurement results than use of reference ranges, which considers each result individually.