bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endothelial cells regulate alveolar morphogenesis by constructing basement membranes acting as a scaffold for myofibroblasts
Authors: Watanabe-Takano Haruko , Kato Katsuhiro , Oguri-Nakamura Eri , Ishii Tomohiro , Kobayashi Koji , Murata Takahisa , Tsujikawa Koichiro , Miyata Takaki , Kubota Yoshiaki , Hanada Yasuyuki , Nishiyama Koichi , Watabe Tetsuro , Fässler Reinhard , Ishii Hirotaka , Mochizuki Naoki , Fukuhara Shigetomo 
Published: March 2024

AbstractAlveologenesis is a spatially coordinated morphogenetic event, during which alveolar myofibroblasts surround the terminal sacs constructed by epithelial cells and endothelial cells (ECs), then contract to form secondary septa to generate alveoli in the lungs. Recent studies have demonstrated the important role of alveolar ECs in this morphogenetic event. However, the mechanisms underlying EC-mediated alveologenesis remain unknown. Herein, we show that ECs regulate alveologenesis by constructing basement membranes (BMs) acting as a scaffold for myofibroblasts to induce septa formation through activating mechanical signaling. Rap1, a small GTPase of the Ras superfamily, is known to stimulate integrin-mediated cell adhesions. EC-specific Rap1-deficient (Rap1iECKO) mice exhibit impaired septa formation and hypo-alveolarization due to the decreased mechanical signaling in myofibroblasts. In Rap1iECKO mice, ECs fail to stimulate integrin β1 to recruit Collagen type IV (Col-4) into BMs required for myofibroblast-mediated septa formation. Consistently, EC-specific integrin β1-deficient mice show hypo-alveolarization, defective mechanical signaling in myofibroblasts, and disorganized BMs. These data demonstrate that alveolar ECs promote integrin β1-mediated Col-4 recruitment in a Rap1-dependent manner, thereby constructing BMs acting as a scaffold for myofibroblasts to induce mechanical signal-mediated alveologenesis. Thus, this study unveils a mechanism of organ morphogenesis mediated by ECs through intrinsic functions.
Genetic architecture of the structural connectome
Authors: Wainberg Michael , Forde Natalie J. , Mansour Salim , Kerrebijn Isabel , Medland Sarah E. , Hawco Colin , Tripathy Shreejoy J. 
Published: March 2024

AbstractMyelinated axons form long-range connections that enable rapid communication between distant brain regions, but how genetics governs the strength and organization of these connections remains unclear. We perform genome-wide association studies of 206 structural connectivity measures derived from diffusion magnetic resonance imaging tractography of 26,333 UK Biobank participants, each representing the density of myelinated connections within or between a pair of cortical networks, subcortical structures or cortical hemispheres. We identify 30 independent genome-wide significant variants after Bonferroni correction for the number of measures studied (126 variants at nominal genome-wide significance) implicating genes involved in myelination (SEMA3A), neurite elongation and guidance (NUAK1, STRN, DPYSL2, EPHA3, SEMA3A, HGF, SHTN1), neural cell proliferation and differentiation (GMNC, CELF4, HGF), neuronal migration (CCDC88C), cytoskeletal organization (CTTNBP2, MAPT, DAAM1, MYO16, PLEC), and brain metal transport (SLC39A8). These variants have four broad patterns of spatial association with structural connectivity: some have disproportionately strong associations with corticothalamic connectivity, interhemispheric connectivity, or both, while others are more spatially diffuse. Structural connectivity measures are highly polygenic, with a median of 9.1 percent of common variants estimated to have non-zero effects on each measure, and exhibited signatures of negative selection. Structural connectivity measures have significant genetic correlations with a variety of neuropsychiatric and cognitive traits, indicating that connectivity-altering variants tend to influence brain health and cognitive function. Heritability is enriched in regions with increased chromatin accessibility in adult oligodendrocytes (as well as microglia, inhibitory neurons and astrocytes) and multiple fetal cell types, suggesting that genetic control of structural connectivity is partially mediated by effects on myelination and early brain development. Our results indicate pervasive, pleiotropic, and spatially structured genetic control of white-matter structural connectivity via diverse neurodevelopmental pathways, and support the relevance of this genetic control to healthy brain function.
Notch2 controls developmental fate choices between germinal center and marginal zone B cells upon immunization
Authors: Babushku Tea , Lechner Markus , Ehrenberg Stefanie , Rambold Ursula , Schmidt-Supprian Marc , Yates Andrew J. , Rane Sanket , Zimber-Strobl Ursula , Strobl Lothar J. 
Published: March 2024

AbstractSustained Notch2 signals induce trans-differentiation of Follicular B (FoB) cells into Marginal Zone B (MZB) cells in mice, but the physiology underlying this differentiation pathway is still elusive. Here, we demonstrate that most B cells receive a basal Notch signal, which is intensified in pre-MZB and MZB cells. Ablation or constitutive activation of Notch2 upon T-cell-dependent immunization reveals an interplay between antigen-induced activation and Notch2 signaling, in which FoB cells that turn off Notch2 signaling enter germinal centers (GC), while high Notch2 signaling leads to generation of MZB cells or to initiation of plasmablast differentiation. Notch2 signaling is dispensable for GC dynamics but appears to be re-induced in some centrocytes to govern expansion of IgG1+ GCB cells. Mathematical modelling suggests that antigen-activated FoB cells make a Notch2 dependent binary fate-decision to differentiate into either GCB or MZB cells. This bifurcation might serve as a mechanism to archive antigen-specific clones into functionally and spatially diverse B cell states to generate robust antibody and memory responses.
Non-Hermitian non-equipartition theory for trapped particles
Authors: Li Xiao , Cao Yongyin , Ng Jack 
Published: March 2024

AbstractThe equipartition theorem is an elegant cornerstone theory of thermal and statistical physics. However, it fails to address some contemporary problems, such as those associated with optical and acoustic trapping, due to the non-Hermitian nature of the external wave-induced force. We use stochastic calculus to solve the Langevin equation and thereby analytically generalize the equipartition theorem to a theory that we denote the non-Hermitian non-equipartition theory. We use the non-Hermitian non-equipartition theory to calculate the relevant statistics, which reveal that the averaged kinetic and potential energies are no longer equal to kBT/2 and are not equipartitioned. As examples, we apply non-Hermitian non-equipartition theory to derive the connection between the non-Hermitian trapping force and particle statistics, whereby measurement of the latter can determine the former. Furthermore, we apply a non-Hermitian force to convert a saddle potential into a stable potential, leading to a different type of stable state.
QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration
Authors: Advani Jayshree , Mehta Puja A. , Hamel Andrew R. , Mehrotra Sudeep , Kiel Christina , Strunz Tobias , Corso-Díaz Ximena , Kwicklis Madeline , van Asten Freekje , Ratnapriya Rinki , Chew Emily Y. , Hernandez Dena G. , Montezuma Sandra R. , Ferrington Deborah A. , Weber Bernhard H. F. , Segrè Ayellet V. , Swaroop Anand 
Published: March 2024

Abstract
DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype–environment interaction in retina.
Limited impact of hydrogen co-firing on prolonging fossil-based power generation under low emissions scenarios
Authors: Oshiro Ken , Fujimori Shinichiro 
Published: March 2024

AbstractClimate change mitigation generally require rapid decarbonization in the power sector, including phase-out of fossil fuel-fired generators. Given recent technological developments, co-firing of hydrogen or ammonia, could help decarbonize fossil-based generators, but little is known about how its effects would play out globally. Here, we explore this topic using an energy system model. The results indicate that hydrogen co-firing occurs solely in stringent mitigation like 1.5 °C scenarios, where around half of existing coal and gas power capacity can be retrofitted for hydrogen co-firing, reducing stranded capacity, mainly in the Organization for Economic Co-operation and Development (OECD) countries and Asia. However, electricity supply from co-firing generators is limited to about 1% of total electricity generation, because hydrogen co-firing is mainly used as a backup option to balance the variable renewable energies. The incremental fuel cost of hydrogen results in lower capacity factor of hydrogen co-fired generators, whereas low-carbon hydrogen contributes to reducing emission cost associated with carbon pricing. While hydrogen co-firing may play a role in balancing intermittency of variable renewable energies, it will not seriously delay the phase-out of fossil-based generators.
A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme
Authors: Hutton Amy E. , Foster Jake , Crawshaw Rebecca , Hardy Florence J. , Johannissen Linus O. , Lister Thomas M. , Gérard Emilie F. , Birch-Price Zachary , Obexer Richard , Hay Sam , Green Anthony P. 
Published: March 2024

AbstractDirected evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.
Aqueous pyruvate partly dissociates under deep ultraviolet irradiation but is resilient to near ultraviolet excitation
Authors: Thøgersen Jan , Madzharova Fani , Weidner Tobias , Jensen Frank 
Published: March 2024

AbstractThe deep ultraviolet photochemistry of aqueous pyruvate is believed to have been essential to the origin of life, and near ultraviolet excitation of pyruvate in aqueous aerosols is assumed to contribute significantly to the photochemistry of the Earth’s atmosphere. However, the primary photochemistry of aqueous pyruvate is unknown. Here we study the susceptibility of aqueous pyruvate to photodissociation by deep ultraviolet and near ultraviolet irradiation with femtosecond spectroscopy supported by density functional theory calculations. The primary photo-dynamics of the aqueous pyruvate show that upon deep-UV excitation at 200 nm, about one in five excited pyruvate anions have dissociated by decarboxylation 100 ps after the excitation, while the rest of the pyruvate anions return to the ground state. Upon near-UV photoexcitation at a wavelength of 340 nm, the dissociation yield of aqueous pyruvate 200 ps after the excitation is insignificant and no products are observed. The experimental results are explained by our calculations, which show that aqueous pyruvate anions excited at 200 nm have sufficient excess energy for decarboxylation, whereas excitation at 340 nm provides the aqueous pyruvate anions with insufficient energy to overcome the decarboxylation barrier.
Filament formation drives catalysis by glutaminase enzymes important in cancer progression
Authors: Feng Shi , Aplin Cody , Nguyen Thuy-Tien T. , Milano Shawn K. , Cerione Richard A. 
Published: March 2024

AbstractThe glutaminase enzymes GAC and GLS2 catalyze the hydrolysis of glutamine to glutamate, satisfying the ‘glutamine addiction’ of cancer cells. They are the targets of anti-cancer drugs; however, their mechanisms of activation and catalytic activity have been unclear. Here we demonstrate that the ability of GAC and GLS2 to form filaments is directly coupled to their catalytic activity and present their cryo-EM structures which provide a view of the conformational states essential for catalysis. Filament formation guides an ‘activation loop’ to assume a specific conformation that works together with a ‘lid’ to close over the active site and position glutamine for nucleophilic attack by an essential serine. Our findings highlight how ankyrin repeats on GLS2 regulate enzymatic activity, while allosteric activators stabilize, and clinically relevant inhibitors block, filament formation that enables glutaminases to catalyze glutaminolysis and support cancer progression.
NDUFS4 regulates cristae remodeling in diabetic kidney disease
Authors: Mise Koki , Long Jianyin , Galvan Daniel L. , Ye Zengchun , Fan Guizhen , Sharma Rajesh , Serysheva Irina I. , Moore Travis I. , Jeter Collene R. , Anna Zal M. , Araki Motoo , Wada Jun , Schumacker Paul T. , Chang Benny H. , Danesh Farhad R. 
Published: March 2024

AbstractThe mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generate diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that conditional male mice with genetic overexpression of Ndufs4 exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping protein STOML2 in linking NDUFS4 with improved cristae morphology. Together, we provide the evidence on the central role of NDUFS4 as a regulator of cristae remodeling and mitochondrial function in kidney podocytes. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.
Molecular basis of TMPRSS2 recognition by Paeniclostridium sordellii hemorrhagic toxin
Authors: Zhou Ruoyu , He Liuqing , Zhang Jiahao , Zhang Xiaofeng , Li Yanyan , Zhan Xiechao , Tao Liang 
Published: March 2024

AbstractHemorrhagic toxin (TcsH) is a major virulence factor produced by Paeniclostridium sordellii, which is a non-negligible threat to women undergoing childbirth or abortions. Recently, Transmembrane Serine Protease 2 (TMPRSS2) was identified as a host receptor of TcsH. Here, we show the cryo-EM structures of the TcsH-TMPRSS2 complex and uncover that TcsH binds to the serine protease domain (SPD) of TMPRSS2 through the CROP unit-VI. This receptor binding mode is unique among LCTs. Five top surface loops of TMPRSS2SPD, which also determine the protease substrate specificity, constitute the structural determinants recognized by TcsH. The binding of TcsH inhibits the proteolytic activity of TMPRSS2, whereas its implication in disease manifestations remains unclear. We further show that mutations selectively disrupting TMPRSS2-binding reduce TcsH toxicity in the intestinal epithelium of the female mice. These findings together shed light on the distinct molecular basis of TcsH-TMPRSS2 interactions, which expands our knowledge of host recognition mechanisms employed by LCTs and provides novel targets for developing therapeutics against P. sordellii infections.
Adsorption of crystal violet dye from synthetic wastewater by ball-milled royal palm leaf sheath
Authors: Sen Neloy , Shefa Nawrin Rahman , Reza Kismot , Shawon Sk Md Ali Zaker , Rahman Md. Wasikur 
Published: March 2024

AbstractThe current study shows that using a batch approach to remove crystal violet dye from synthetic wastewater is feasible when using royal palm leaf sheath powder as an adsorbent. In order to investigate the effects of many parameters, including starting concentration, pH effect, dye concentration, adsorbent dose, contact time, and temperature, experiments were carried out under various operating conditions. Maximum removal was obtained at pH 6 and at a concentration of 100 ppm, which are considered as ideal values. The influence of pH and dye concentration was shown to be substantial. Langmuir, Freundlich, and Temkin isotherm models were fitted to equilibrium data. The Langmuir isotherm model, which showed a maximum monolayer adsorption capacity of 454.5455 mg/g, best described the equilibrium data. The Pseudo-second-order kinetic model was found to closely resemble rather than the first-order and intra-particle diffusion models. Standard enthalpy (∆H◦), entropy (∆S◦), and free energy (∆G◦) were evaluated as thermodynamic parameters. It was discovered that the adsorption contact was endothermic in nature. The outcomes highlight the applicability of the inexpensive, locally accessible adsorbent in the specialty area of wastewater treatment and can be used in commercial dye-enriched effluent.
Evidence for chronic headaches induced by pathological changes of myodural bridge complex
Authors: Song Xue , Yu Sheng-Bo , Yuan Xiao-Ying , Alam Shah M. Adeel , Li Chan , Chi Yan-Yan , Zheng Nan , Sui Hong-Jin 
Published: March 2024

AbstractClinical studies have shown that there may be a certain relationship between pathological changes of the myodural bridge complex (MDBC) and chronic headaches of unknown cause. But there is still a lack of experimental evidence to explain the possible mechanism. This study aims to further confirm this relationship between MDBC and chronic headaches and explore its potential occurrence mechanism in rats. Bleomycin (BLM) or phosphate-buffered saline (PBS) was injected into the myodural bridge fibers of rats to establish the hyperplastic model of MDBC. After 4 weeks, the occurrence of headaches in rats was evaluated through behavioral scores. The immunohistochemistry staining method was applied to observe the expression levels of headache-related neurotransmitters in the brain. Masson trichrome staining results showed that the number of collagen fibers of MDBC was increased in the BLM group compared to those of the other two groups. It revealed hyperplastic changes of MDBC. The behavioral scores of the BLM group were significantly higher than those of the PBS group and the blank control group. Meanwhile, expression levels of CGRP and 5-HT in the headache-related nuclei of the brain were increased in the BLM group. The current study further confirms the view that there is a relationship between pathological changes of MDBC and chronic headaches of unknown cause. This study may provide anatomical and physiological explanations for the pathogenesis of some chronic headaches of unknown cause.
A novel portable anechoic chamber using ultra-thin 2D microwave absorber for industrial 5.0
Authors: Baghel Amit Kumar , Bikrat Youssef , Tavares Joana , Chaves Henrique , Oliveira Vinicius Uchoa , Pinho Pedro , Carvalho Nuno Borges , Alves Helena 
Published: March 2024

AbstractIn this paper, the authors, for the first time, have shown the use of 2D conformal microwave absorbing material (MAM) in the design and fabrication of a portable Anechoic chamber (AC). The MAM is fabricated on the transparent and conductive metal oxide layer named indium-tin-oxide (ITO) with Polyethylene terephthalate as the substrate and the ground plane for zero transmission having overall thickness of 0.012$$\lambda$$
λ
where $$\lambda$$
λ
is calculated at 0.7 GHz. The MAM is characterized for 0.7 to 18 GHz for both TE- and TM-polarisation and oblique incidence. High sheet resistance, dipole-like resonance structure patterned on the ITO, and the air-spacing between the layers is optimized to achieve broadband absorption. The MAM is used to line the six sides of the rectangular anechoic chamber having inner dimensions of: (L × W × H: 850 × 650 × 720 mm3). The return loss (RL), gain, and radiation pattern of three antenna working at 1.56, 2.43, and 4.93 GHz are analyzed inside the AC. The measurement results for all frequencies very well match with the simulation studies, thus validating and opening the door for the future use of ultra-thin and planar MAM in the AC.
Radionuclides distribution and radiation hazards assessment of black sand separation plant’s minerals: a case study
Authors: Nabil Islam M. , El-Samrah Moamen G. , Sayed A. F. El , Shazly Ahmed , Omar Ahmed 
Published: March 2024

AbstractThis study assessed the radioactivity levels and associated risks in the black sand-separated products obtained from the black sand separation plant in Delta, Egypt. A total of sixteen samples were taken from hot spots during and after the separation process. These include water samples and other samples that represent monazite, rutile, zircon, granite, ilmenite, and silica products. The hot spots included the area where the ore was stored. The activity concentrations of $$^{232}Th$$

232

T
h

, $$^{226}Ra$$

226

R
a

, and $$^{40}K$$

40

K

were determined in these samples using a p-type HPGe detector. Based on gamma spectrometric analysis, samples of rutile, zircon, and monazite had the highest amounts of radioactivity because they contained the highest NORM’s activity concentrations. In addition, it indicated that the radiological hazard indices of the collected samples were higher than the average world limits for sand texture. These findings suggest that the black sand separation process reveals potential risks to human health and the environment, and therefore, appropriate measures need to be taken to mitigate these risks, especially for the safety of the workers on-site. Reducing the risk associated with those sites should be controlled by implementing the recommendations declared for the series of International Basic Safety Standards of the International Atomic Energy Agency (GSR) Part 3, as affirmed in Document No. 103 of 2007 by the International Commission on Radiological Protection (ICRP) as will be presented in the paper body.