bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondria-wide association study observed significant interactions of mitochondrial respiratory and the inflammatory in the development of anxiety and depression
Authors: Liu Li , Cheng Shiqiang , Qi Xin , Meng Peilin , Yang Xuena , Pan Chuyu , Chen Yujing , Zhang Huijie , Zhang Zhen , Zhang Jingxi , Li Chune , Wen Yan , Jia Yumeng , Cheng Bolun , Zhang Feng 
Published: June 2023

AbstractThe aim of this study was to investigate the possible interaction of mitochondrial dysfunction and inflammatory cytokines in the risk of anxiety and depression. We utilized the UK Biobank for the sample of this study. A mitochondria-wide association(MiWAS) and interaction analysis was performed to investigate the interaction effects of mitochondrial DNA (mtDNA)×C-reactive protein (CRP) on the risks of self-reported anxiety (N = 72,476), general anxiety disorder (GAD-7) scores (N = 80,853), self-reported depression (N = 80,778), Patient Health Questionnaire (PHQ-9) scores (N = 80,520) in total samples, females and males, respectively, adjusting for sex, age, Townsend deprivation index (TDI), education score, alcohol intake, smoking and 10 principal components. In all, 25 mtSNPs and 10 mtSNPs showed significant level of association with self-reported anxiety and GAD-7 score respectively. A total of seven significant mtDNA × CRP interactions were found for anxiety, such as m.3915G>A(MT-ND1) for self-reported anxiety in total subjects (P = 6.59 × 10−3), m.4561T>C(MT-ND2) (P = 3.04 × 10−3) for GAD-7 score in total subjects. For depression, MiWAS identified 17 significant mtSNPs for self-reported depression and 14 significant mtSNPs for PHQ-9 scores. 17 significant mtDNA associations (2 for self-reported depression and 15 for PHQ-9 score) was identified, such as m.14869G>A(MT-CYB; P = 2.22 × 10−3) associated with self-reported depression and m.4561T>C (MT-ND2; P value = 3.02 × 10−8) associated with PHQ-9 score in all subjects. In addition, 5 common mtDNA shared with anxiety and depression were found in MiWAS, and 4 common mtDNA variants were detected to interact with CRP for anxiety and depression, such as m.9899T>C(MT-CO3). Our study suggests the important interaction effects of mitochondrial function and CRP on the risks of anxiety and depression.
Mannosylated glycans impair normal T-cell development by reprogramming commitment and repertoire diversity
Authors: Vicente Manuel M. , Alves Inês , Fernandes Ângela , Dias Ana M. , Santos-Pereira Beatriz , Pérez-Anton Elena , Santos Sofia , Yang Tao , Correia Alexandra , Münster-Kühnel Anja , Almeida Afonso R. M. , Ravens Sarina , Rabinovich Gabriel A. , Vilanova Manuel , Sousa Ana E. , Pinho Salomé S. 
Published: June 2023

AbstractT-cell development ensures the formation of diverse repertoires of T-cell receptors (TCRs) that recognize a variety of antigens. Glycosylation is a major posttranslational modification present in virtually all cells, including T-lymphocytes, that regulates activity/functions. Although these structures are known to be involved in TCR-selection in DP thymocytes, it is unclear how glycans regulate other thymic development processes and how they influence susceptibility to disease. Here, we discovered stage-specific glycome compositions during T-cell development in human and murine thymocytes, as well as dynamic alterations. After restricting the N-glycosylation profile of thymocytes to high-mannose structures, using specific glycoengineered mice (Rag1CreMgat1fl/fl), we showed remarkable defects in key developmental checkpoints, including ß-selection, regulatory T-cell generation and γδT-cell development, associated with increased susceptibility to colon and kidney inflammation and infection. We further demonstrated that a single N-glycan antenna (modeled in Rag1CreMgat2fl/fl mice) is the sine-qua-non condition to ensure normal development. In conclusion, we revealed that mannosylated thymocytes lead to a dysregulation in T-cell development that is associated with inflammation susceptibility.
Imaging the field inside nanophotonic accelerators
Authors: Fishman Tal , Haeusler Urs , Dahan Raphael , Yannai Michael , Adiv Yuval , Abudi Tom Lenkiewicz , Shiloh Roy , Eyal Ori , Yousefi Peyman , Eisenstein Gadi , Hommelhoff Peter , Kaminer Ido 
Published: June 2023

AbstractControlling optical fields on the subwavelength scale is at the core of nanophotonics. Laser-driven nanophotonic particle accelerators promise a compact alternative to conventional radiofrequency-based accelerators. Efficient electron acceleration in nanophotonic devices critically depends on achieving nanometer control of the internal optical nearfield. However, these nearfields have so far been inaccessible due to the complexity of the devices and their geometrical constraints, hampering the design of future nanophotonic accelerators. Here we image the field distribution inside a nanophotonic accelerator, for which we developed a technique for frequency-tunable deep-subwavelength resolution of nearfields based on photon-induced nearfield electron-microscopy. Our experiments, complemented by 3D simulations, unveil surprising deviations in two leading nanophotonic accelerator designs, showing complex field distributions related to intricate 3D features in the device and its fabrication tolerances. We envision an extension of our method for full 3D field tomography, which is key for the future design of highly efficient nanophotonic devices.
Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
Authors: Devos Katrien M. , Qi Peng , Bahri Bochra A. , Gimode Davis M. , Jenike Katharine , Manthi Samuel J. , Lule Dagnachew , Lux Thomas , Martinez-Bello Liliam , Pendergast Thomas H. , Plott Chris , Saha Dipnarayan , Sidhu Gurjot S. , Sreedasyam Avinash , Wang Xuewen , Wang Hao , Wright Hallie , Zhao Jianxin , Deshpande Santosh , de Villiers Santie , Dida Mathews M. , Grimwood Jane , Jenkins Jerry , Lovell John , Mayer Klaus F. X. , Mneney Emmarold E. , Ojulong Henry F. , Schatz Michael C. , Schmutz Jeremy , Song Bo , Tesfaye Kassahun , Odeny Damaris A. 
Published: June 2023

AbstractFinger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis
Authors: Du Juan , Zhang Junlei , Wang Lin , Wang Xun , Zhao Yaxing , Lu Jiaoying , Fan Tingmin , Niu Meng , Zhang Jie , Cheng Fei , Li Jun , Zhu Qi , Zhang Daoqiang , Pei Hao , Li Guang , Liang Xingguang , Huang He , Cao Xiaocang , Liu Xinjuan , Shao Wei , Sheng Jianpeng 
Published: June 2023

AbstractUlcerative colitis is a chronic inflammatory bowel disorder with cellular heterogeneity. To understand the composition and spatial changes of the ulcerative colitis ecosystem, here we use imaging mass cytometry and single-cell RNA sequencing to depict the single-cell landscape of the human colon ecosystem. We find tissue topological changes featured with macrophage disappearance reaction in the ulcerative colitis region, occurring only for tissue-resident macrophages. Reactive oxygen species levels are higher in the ulcerative colitis region, but reactive oxygen species scavenging enzyme SOD2 is barely detected in resident macrophages, resulting in distinct reactive oxygen species vulnerability for inflammatory macrophages and resident macrophages. Inflammatory macrophages replace resident macrophages and cause a spatial shift of TNF production during ulcerative colitis via a cytokine production network formed with T and B cells. Our study suggests components of a mechanism for the observed macrophage disappearance reaction of resident macrophages, providing mechanistic hints for macrophage disappearance reaction in other inflammation or infection situations.
Artificial intelligence driven design of catalysts and materials for ring opening polymerization using a domain-specific language
Authors: Park Nathaniel H. , Manica Matteo , Born Jannis , Hedrick James L. , Erdmann Tim , Zubarev Dmitry Yu. , Adell-Mill Nil , Arrechea Pedro L. 
Published: June 2023

AbstractAdvances in machine learning (ML) and automated experimentation are poised to vastly accelerate research in polymer science. Data representation is a critical aspect for enabling ML integration in research workflows, yet many data models impose significant rigidity making it difficult to accommodate a broad array of experiment and data types found in polymer science. This inflexibility presents a significant barrier for researchers to leverage their historical data in ML development. Here we show that a domain specific language, termed Chemical Markdown Language (CMDL), provides flexible, extensible, and consistent representation of disparate experiment types and polymer structures. CMDL enables seamless use of historical experimental data to fine-tune regression transformer (RT) models for generative molecular design tasks. We demonstrate the utility of this approach through the generation and the experimental validation of catalysts and polymers in the context of ring-opening polymerization—although we provide examples of how CMDL can be more broadly applied to other polymer classes. Critically, we show how the CMDL tuned model preserves key functional groups within the polymer structure, allowing for experimental validation. These results reveal the versatility of CMDL and how it facilitates translation of historical data into meaningful predictive and generative models to produce experimentally actionable output.
Photo-produced aromatic compounds stimulate microbial degradation of dissolved organic carbon in thermokarst lakes
Authors: Hu Jie , Kang Luyao , Li Ziliang , Feng Xuehui , Liang Caifan , Wu Zan , Zhou Wei , Liu Xuning , Yang Yuanhe , Chen Leiyi 
Published: June 2023

AbstractPhotochemical and biological degradation of dissolved organic carbon (DOC) and their interactions jointly contribute to the carbon dioxide released from surface waters in permafrost regions. However, the mechanisms that govern the coupled photochemical and biological degradation of DOC are still poorly understood in thermokarst lakes. Here, by combining Fourier transform ion cyclotron resonance mass spectrometry and microbial high-throughput sequencing, we conducted a sunlight and microbial degradation experiment using water samples collected from 10 thermokarst lakes along a 1100-km permafrost transect. We demonstrate that the enhancement of sunlight on DOC biodegradation is not associated with the low molecular weight aliphatics produced by sunlight, but driven by the photo-produced aromatics. This aromatic compound-driven acceleration of biodegradation may be attributed to the potential high abilities of the microbes to decompose complex compounds in thermokarst lakes. These findings highlight the importance of aromatics in regulating the sunlight effects on DOC biodegradation in permafrost-affected lakes.
Gravitational effects on fibroblasts’ function in relation to wound healing
Authors: Radstake Wilhelmina E. , Gautam Kiran , Miranda Silvana , Van Rompay Cynthia , Vermeesen Randy , Tabury Kevin , Verslegers Mieke , Dowson Alan , Gorissen Jeffrey , van Loon Jack J. W. A. , Savage Nigel D. L. , Baatout Sarah , Baselet Bjorn 
Published: June 2023

AbstractThe spaceflight environment imposes risks for maintaining a healthy skin function as the observed delayed wound healing can contribute to increased risks of infection. To counteract delayed wound healing in space, a better understanding of the fibroblasts’ reaction to altered gravity levels is needed. In this paper, we describe experiments that were carried out at the Large Diameter Centrifuge located in ESA-ESTEC as part of the ESA Academy 2021 Spin Your Thesis! Campaign. We exposed dermal fibroblasts to a set of altered gravity levels, including transitions between simulated microgravity and hypergravity. The addition of the stress hormone cortisol to the cell culture medium was done to account for possible interaction effects of gravity and cortisol exposure. Results show a main impact of cortisol on the secretion of pro-inflammatory cytokines as well as extracellular matrix proteins. Altered gravity mostly induced a delay in cellular migration and changes in mechanosensitive cell structures. Furthermore, 20 × ghypergravity transitions induced changes in nuclear morphology. These findings provide insights into the effect of gravity transitions on the fibroblasts’ function related to wound healing, which may be useful for the development of countermeasures.
Proteomic analysis of the effect of hemin in breast cancer
Authors: Coló G. P. , Schweitzer K. , Oresti G. M. , Alonso E. G. , Chávez L. Fernández , Mascaró M. , Giorgi G. , Curino A. C. , Facchinetti M. M. 
Published: June 2023

AbstractHeme, an iron-containing prosthetic group found in many proteins, carries out diverse biological functions such as electron transfer, oxygen storage and enzymatic reactions. Hemin, the oxidised form of heme, is used to treat porphyria and also to activate heme-oxygenase (HO) which catalyses the rate-limiting step in heme degradation. Our group has previously demonstrated that hemin displays antitumor activity in breast cancer (BC). The aim of this work has been to study the effect of hemin on protein expression modifications in a BC cell line to gain insight into the molecular mechanisms of hemin antitumor activity. For this purpose, we carried out proteome analysis by Mass Spectrometry (MS) which showed that 1309 proteins were significantly increased in hemin-treated cells, including HO-1 and the proteases that regulate HO-1 function, and 921 proteins were significantly decreased. Furthermore, the MS-data analysis showed that hemin regulates the expression of heme- and iron-related proteins, adhesion and cytoskeletal proteins, cancer signal transduction proteins and enzymes involved in lipid metabolism. By biochemical and cellular studies, we further corroborated the most relevant in-silico results. Altogether, these results show the multiple physiological effects that hemin treatment displays in BC and demonstrate its potential as anticancer agent.
Explainable AI via learning to optimize
Authors: Heaton Howard , Fung Samy Wu 
Published: June 2023

AbstractIndecipherable black boxes are common in machine learning (ML), but applications increasingly require explainable artificial intelligence (XAI). The core of XAI is to establish transparent and interpretable data-driven algorithms. This work provides concrete tools for XAI in situations where prior knowledge must be encoded and untrustworthy inferences flagged. We use the “learn to optimize” (L2O) methodology wherein each inference solves a data-driven optimization problem. Our L2O models are straightforward to implement, directly encode prior knowledge, and yield theoretical guarantees (e.g. satisfaction of constraints). We also propose use of interpretable certificates to verify whether model inferences are trustworthy. Numerical examples are provided in the applications of dictionary-based signal recovery, CT imaging, and arbitrage trading of cryptoassets. Code and additional documentation can be found at https://xai-l2o.research.typal.academy.
Development of CuMnxOy (x = 2, and y = 4)-GO heterostructure for the synthesis of pyranoquinoline derivatives
Authors: Farajollahi Ayda , Noroozi Pesyan Nader , Poursattar Marjani Ahmad , Alamgholiloo Hassan 
Published: June 2023

AbstractThe pyranoquinoline derivatives are synthetically important due to their biological properties. In this research, these derivatives were produced through an environmentally friendly method. This method includes the use of CuMnxOy (x = 2, and y = 4)-GO as a nanocatalyst, which is easy to produce, has excellent performance, cost-effectiveness, and recyclability among its features, and also the use of water as a green solvent. Pyranoquinolines through the one-pot, the multi-component reaction between different derivatives of aryl glyoxal, ethyl cyanoacetate, and 4-hydroxyquinoline-2(1H)-one were synthesized using nanocatalyst, K2CO3, and H2O. Also, the structure of the CuMnxOy-GO nanocatalyst was evaluated and confirmed via different analyses. The distinguishing features of this work compared to previous works are easy workup, recyclability of nanocatalyst, facile synthesis process, and provide high yields of products.
Single-cell Raman microscopy with machine learning highlights distinct biochemical features of neutrophil extracellular traps and necrosis
Authors: Lelliott Patrick Michael , Hobro Alison Jane , Pavillon Nicolas , Nishide Masayuki , Okita Yasutaka , Mizuno Yumiko , Obata Sho , Nameki Shinichiro , Yoshimura Hanako , Kumanogoh Atsushi , Smith Nicholas Isaac 
Published: June 2023

AbstractThe defining biology that distinguishes neutrophil extracellular traps (NETs) from other forms of cell death is unresolved, and techniques which unambiguously identify NETs remain elusive. Raman scattering measurement provides a holistic overview of cell molecular composition based on characteristic bond vibrations in components such as lipids and proteins. We collected Raman spectra from NETs and freeze/thaw necrotic cells using a custom built high-throughput platform which is able to rapidly measure spectra from single cells. Principal component analysis of Raman spectra from NETs clearly distinguished them from necrotic cells despite their similar morphology, demonstrating their fundamental molecular differences. In contrast, classical techniques used for NET analysis, immunofluorescence microscopy, extracellular DNA, and ELISA, could not differentiate these cells. Additionally, machine learning analysis of Raman spectra indicated subtle differences in lipopolysaccharide (LPS)-induced as opposed to phorbol myristate acetate (PMA)-induced NETs, demonstrating the molecular composition of NETs varies depending on the stimulant used. This study demonstrates the benefits of Raman microscopy in discriminating NETs from other types of cell death and by their pathway of induction.
Foreign-born status and risk of gestational diabetes mellitus by years of residence in the United States
Authors: Noah Akaninyene I. , Perez-Patron Maria J. , Gongalla Megha , Hill Ashley V. , Taylor Brandie DePaoli 
Published: June 2023

AbstractTo explore the association between acculturation among foreign-born (FB) women, gestational diabetes (GDM) and GDM-associated adverse birth outcomes, we conducted a retrospective cohort study of 34,696 singleton pregnancies from Houston, TX, between 2011 and 2022. FB women (n = 18,472) were categorized based on years of residence in US (0–5, 6–10, and > 10 years), while US-born women (n = 16,224) were the reference group. A modified Poisson regression model determined the association between acculturative level and GDM within the entire cohort and stratified by race/ethnicity. Compared to US-born women, FB women with 0–5 years [adjusted relative risk (RRadj.) 1.27, 95% confidence interval [CI] 1.14–1.42)], 6–10 years (RRadj. 1.89, 95%CI 1.68–2.11) and > 10 years in the US (RRadj. 1.85, 95%CI 1.69–2.03) had higher risk of GDM. Results were consistent for all racial/ethnic groups, although associations were not significant at 0–5 years. FB women had lower risk of other adverse pregnancy outcomes, except for preeclampsia with severe features at higher levels of acculturation. Results were similar among those with and without GDM. In conclusion, FB status increases risk of GDM among all racial/ethnic groups but is elevated with higher acculturation levels.
HUBO and QUBO models for prime factorization
Authors: Jun Kyungtaek , Lee Hyunju 
Published: June 2023

AbstractThe security of the RSA cryptosystem is based on the difficulty of factoring a large number N into prime numbers $$p$$
p
and $$q$$
q
satisfying $$N=p\times q$$

N
=
p
×
q

. This paper presents a prime factorization method using a D-Wave quantum computer that could threaten the RSA cryptosystem in the future. The starting point for this method is very simple, representing two prime numbers as qubits. Then, we set the difference between the product of the two prime numbers expressed in qubits and N as a cost function, and we find the solution when the cost function is minimized. D-Wave's quantum annealer can find the minimum value of any quadratic problem. However, the cost function must be a higher-order unconstrained optimization (HUBO) model because it contains second- or higher-order terms. We used a hybrid solver accessible via Leap, D-Wave’s real-time quantum cloud service, and the dimod package provided by the D-Wave Ocean software development kit (SDK) to solve the HUBO problem. We also successfully factorized 102,454,763 with 26 logical qubits. In addition, we factorized 1,000,070,001,221 using the range-dependent Hamiltonian algorithm.
Green-adapted spectrophotometric determination of fostemsavir based on selective bromophenol blue extraction; reduction of hazardous consumption using computational calculations
Authors: Batubara Afnan S. , Ainousah Bayan E. , Gamal Mohammed , Almrasy Ahmed A. , Ramzy Sherif , Ghoneim Mohammed M. , Abdelazim Ahmed H. 
Published: June 2023

AbstractA computationally-assisted and green spectrophotometric method has been developed for the determination of fostemsavir, a recently FDA-approved drug used in combination with antiretroviral drugs to treat multidrug-resistant HIV-1 infection. The method was developed using computational studies and solvent selection based on green chemistry principles. The density functional theory method was employed to identify bromophenol blue as the preferred acid dye for efficient extraction of fostemsavir. The solvent selection process involved a careful evaluation of the green ranking of solvents, which led to the use of water as the solvent. The method involved the extraction of fostemsavir with bromophenol blue to form a yellow ion-pair complex, which exhibited maximally sharp peaks at 418 nm, enabling sensitive visible spectrophotometric determination of fostemsavir in bulk and pharmaceutical preparations. The extraction procedures were optimized, and the method was demonstrated to be sensitive over the concentration range of 2–12 μg/mL fostemsavir. Furthermore, the method was evaluated with respect to green chemistry principles using the analytical eco-scale, the green analytical method index, and analytical greenness metric approach, all of which confirmed that the data obtained by the proposed method were environmentally acceptable.