bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas
Authors: Gordon Wei E. , Baek Seungbyn , Nguyen Hai P. , Kuo Yien-Ming , Bradley Rachael , Fong Sarah L. , Kim Nayeon , Galazyuk Alex , Lee Insuk , Ingala Melissa R. , Simmons Nancy B. , Schountz Tony , Cooper Lisa Noelle , Georgakopoulos-Soares Ilias , Hemberg Martin , Ahituv Nadav 
Published: January 2024

AbstractFrugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq and scATAC-seq) on insectivorous (Eptesicus fuscus; big brown bat) and frugivorous (Artibeus jamaicensis; Jamaican fruit bat) bat kidneys and pancreases and identify key cell population, gene expression and regulatory differences associated with the Jamaican fruit bat that also relate to human disease, particularly diabetes. We find a decrease in loop of Henle and an increase in collecting duct cells, and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the Jamaican fruit bat kidney. The Jamaican fruit bat pancreas shows an increase in endocrine and a decrease in exocrine cells, and differences in genes and regulatory elements involved in insulin regulation. We also find that these frugivorous bats share several molecular characteristics with human diabetes. Combined, our work provides insights from a frugivorous mammal that could be leveraged for therapeutic purposes.
Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma
Authors: Hamel Andrew R. , Yan Wenjun , Rouhana John M. , Monovarfeshani Aboozar , Jiang Xinyi , Mehta Puja A. , Advani Jayshree , Luo Yuyang , Liang Qingnan , Rajasundaram Skanda , Shrivastava Arushi , Duchinski Katherine , Mantena Sreekar , Wang Jiali , van Zyl Tavé , Pasquale Louis R. , Swaroop Anand , Gharahkhani Puya , Khawaja Anthony P. , MacGregor Stuart ,   International Glaucoma Genetics Consortium (IGGC), Hewitt Alex W. , Schuster Alexander K. , Viswanathan Ananth C. , Lotery Andrew J. , Cree Angela J. , Pang Calvin P. , Brandl Caroline , Klaver Caroline C. W. , Hayward Caroline , Khor Chiea Chuen , Cheng Ching-Yu , Hammond Christopher J. , van Duijn Cornelia , Mackey David A. , Stefansson Einer , Vithana Eranga N. , Pasutto Francesca , Jonansson Fridbert , Thorleifsson Gudmar , Koh Jacyline , Wilson James F. , Craig Jamie E. , Vergroesen Joëlle E. , Fingert John H. , Jonas Jost B. , Stefánsson Kári , Burdon Kathryn P. , Chen Li Jia , Kass Michael , Jansonius Nomdo M. , Pfeiffer Norbert , Polašek Ozren , Foster Paul J. , Mitchell Paul , Hysi Pirro G. , Wojciechowski Robert , Driessen Sjoerd J. , Tompson Stuart W. J. , Young Terri L. , Wong Tien Y. , Aung Tin , Thorsteinsdottir Unnur , de Vries Victor A. , Ramdas Wishal D. , Wang Ya Xing , Chen Rui , Vitart Veronique , Sanes Joshua R. , Wiggs Janey L. , Segrè Ayellet V. 
Published: January 2024

AbstractPrimary open-angle glaucoma (POAG), characterized by retinal ganglion cell death, is a leading cause of irreversible blindness worldwide. However, its molecular and cellular causes are not well understood. Elevated intraocular pressure (IOP) is a major risk factor, but many patients have normal IOP. Colocalization and Mendelian randomization analysis of >240 POAG and IOP genome-wide association study (GWAS) loci and overlapping expression and splicing quantitative trait loci (e/sQTLs) in 49 GTEx tissues and retina prioritizes causal genes for 60% of loci. These genes are enriched in pathways implicated in extracellular matrix organization, cell adhesion, and vascular development. Analysis of single-nucleus RNA-seq of glaucoma-relevant eye tissues reveals that the POAG and IOP colocalizing genes and genome-wide associations are enriched in specific cell types in the aqueous outflow pathways, retina, optic nerve head, peripapillary sclera, and choroid. This study nominates IOP-dependent and independent regulatory mechanisms, genes, and cell types that may contribute to POAG pathogenesis.
Identifying immune signatures of sepsis to increase diagnostic accuracy in very preterm babies
Authors: Das A. , Ariyakumar G. , Gupta N. , Kamdar S. , Barugahare A. , Deveson-Lucas D. , Gee S. , Costeloe K. , Davey M. S. , Fleming P. , Gibbons D. L. 
Published: January 2024

AbstractBacterial infections are a major cause of mortality in preterm babies, yet our understanding of early-life disease-associated immune dysregulation remains limited. Here, we combine multi-parameter flow cytometry, single-cell RNA sequencing and plasma analysis to longitudinally profile blood from very preterm babies (<32 weeks gestation) across episodes of invasive bacterial infection (sepsis). We identify a dynamically changing blood immune signature of sepsis, including lymphopenia, reduced dendritic cell frequencies and myeloid cell HLA-DR expression, which characterizes sepsis even when the common clinical marker of inflammation, C-reactive protein, is not elevated. Furthermore, single-cell RNA sequencing identifies upregulation of amphiregulin in leukocyte populations during sepsis, which we validate as a plasma analyte that correlates with clinical signs of disease, even when C-reactive protein is normal. This study provides insights into immune pathways associated with early-life sepsis and identifies immune analytes as potential diagnostic adjuncts to standard tests to guide targeted antibiotic prescribing.
N-linked Fc glycosylation is not required for IgG-B-cell receptor function in a GC-derived B-cell line
Authors: Kissel Theresa , Derksen Veerle F. A. M. , Bentlage Arthur E. H. , Koeleman Carolien , Hafkenscheid Lise , van der Woude Diane , Wuhrer Manfred , Vidarsson Gestur , Toes René E. M. 
Published: January 2024

AbstractIgG secreted by B cells carry asparagine N(297)-linked glycans in the fragment crystallizable (Fc) region. Changes in Fc glycosylation are related to health or disease and are functionally relevant, as IgG without Fc glycans cannot bind to Fcɣ receptors or complement factors. However, it is currently unknown whether ɣ-heavy chain (ɣHC) glycans also influence the function of membrane-bound IgG-B-cell receptors (BCR) and thus the outcome of the B-cell immune response. Here, we show in a germinal center (GC)-derived human B-cell line that ɣHC glycans do not affect membrane expression of IgG-BCRs. Furthermore, antigen binding or other BCR-facilitated mechanisms appear unaffected, including BCR downmodulation or BCR-mediated signaling. As expected, secreted IgG lacking Fc glycosylation is unable to carry out effector functions. Together, these observations indicate that IgG-Fc glycosylation serves as a mechanism to control the effector functions of antibodies, but does not regulate the activation of IgG-switched B cells, as its absence had no apparent impact on BCR function.
Climate-driven invasion and incipient warnings of kelp ecosystem collapse
Authors: Ling Scott D. , Keane John P. 
Published: January 2024

AbstractClimate change is progressively redistributing species towards the Earth’s poles, indicating widespread potential for ecosystem collapse. Detecting early-warning-signals and enacting adaptation measures is therefore a key imperative for humanity. However, detecting early-warning signals has remained elusive and has focused on exceptionally high-frequency and/ or long-term time-series, which are generally unattainable for most ecosystems that are under-sampled and already impacted by warming. Here, we show that a catastrophic phase-shift in kelp ecosystems, caused by range-extension of an overgrazing sea urchin, also propagates poleward. Critically, we show that incipient spatial-pattern-formations of kelp overgrazing are detectable well-in-advance of collapse along temperate reefs in the ocean warming hotspot of south-eastern Australia. Demonstrating poleward progression of collapse over 15 years, these early-warning ‘incipient barrens’ are now widespread along 500 km of coast with projections indicating that half of all kelp beds within this range-extension region will collapse by ~2030. Overgrazing was positively associated with deep boulder-reefs, yet negatively associated with predatory lobsters and subordinate abalone competitors, which have both been intensively fished. Climate-driven collapse of ecosystems is occurring; however, by looking equatorward, space-for-time substitutions can enable practical detection of early-warning spatial-pattern-formations, allowing local climate adaptation measures to be enacted in advance.
Lateral hypothalamic glutamatergic inputs to VTA glutamatergic neurons mediate prioritization of innate defensive behavior over feeding
Authors: Barbano M. Flavia , Zhang Shiliang , Chen Emma , Espinoza Orlando , Mohammad Uzma , Alvarez-Bagnarol Yocasta , Liu Bing , Hahn Suyun , Morales Marisela 
Published: January 2024

AbstractThe lateral hypothalamus (LH) is involved in feeding behavior and defense responses by interacting with different brain structures, including the Ventral Tegmental Area (VTA). Emerging evidence indicates that LH-glutamatergic neurons infrequently synapse on VTA-dopamine neurons but preferentially establish multiple synapses on VTA-glutamatergic neurons. Here, we demonstrated that LH-glutamatergic inputs to VTA promoted active avoidance, long-term aversion, and escape attempts. By testing feeding in the presence of a predator, we observed that ongoing feeding was decreased, and that this predator-induced decrease in feeding was abolished by photoinhibition of the LH-glutamatergic inputs to VTA. By VTA specific neuronal ablation, we established that predator-induced decreases in feeding were mediated by VTA-glutamatergic neurons but not by dopamine or GABA neurons. Thus, we provided evidence for an unanticipated neuronal circuitry between LH-glutamatergic inputs to VTA-glutamatergic neurons that plays a role in prioritizing escape, and in the switch from feeding to escape in mice.
Non-Faradaic optoelectrodes for safe electrical neuromodulation
Authors: Chen Jian , Liu Yanyan , Chen Feixiang , Guo Mengnan , Zhou Jiajia , Fu Pengfei , Zhang Xin , Wang Xueli , Wang He , Hua Wei , Chen Jinquan , Hu Jin , Mao Ying , Jin Dayong , Bu Wenbo 
Published: January 2024

AbstractNanoscale optoelectrodes hold the potential to stimulate optically individual neurons and intracellular organelles, a challenge that demands both a high-density of photoelectron storage and significant charge injection. Here, we report that zinc porphyrin, commonly used in dye-sensitized solar cells, can be self-assembled into nanorods and then coated by TiO2. The J-aggregated zinc porphyrin array enables long-range exciton diffusion and allows for fast electron transfer into TiO2. The formation of TiO2(e−) attracts positive charges around the neuron membrane, contributing to the induction of action potentials. Far-field cranial irradiation of the motor cortex using a 670 nm laser or an 850 nm femtosecond laser can modulate local neuronal firing and trigger motor responses in the hind limb of mice. The pulsed photoelectrical stimulation of neurons in the subthalamic nucleus alleviates parkinsonian symptoms in mice, improving abnormal stepping and enhancing the activity of dopaminergic neurons. Our results suggest injectable nanoscopic optoelectrodes for optical neuromodulation with high efficiency and negligible side effects.
LFA-1 nanoclusters integrate TCR stimulation strength to tune T-cell cytotoxic activity
Authors: Lacouture Claire , Chaves Beatriz , Guipouy Delphine , Houmadi Raïssa , Duplan-Eche Valérie , Allart Sophie , Destainville Nicolas , Dupré Loïc 
Published: January 2024

AbstractT-cell cytotoxic function relies on the cooperation between the highly specific but poorly adhesive T-cell receptor (TCR) and the integrin LFA-1. How LFA-1-mediated adhesion may scale with TCR stimulation strength is ill-defined. Here, we show that LFA-1 conformation activation scales with TCR stimulation to calibrate human T-cell cytotoxicity. Super-resolution microscopy analysis reveals that >1000 LFA-1 nanoclusters provide a discretized platform at the immunological synapse to translate TCR engagement and density of the LFA-1 ligand ICAM-1 into graded adhesion. Indeed, the number of high-affinity conformation LFA-1 nanoclusters increases as a function of TCR triggering strength. Blockade of LFA-1 conformational activation impairs adhesion to target cells and killing. However, it occurs at a lower TCR stimulation threshold than lytic granule exocytosis implying that it licenses, rather than directly controls, the killing decision. We conclude that the organization of LFA-1 into nanoclusters provides a calibrated system to adjust T-cell killing to the antigen stimulation strength.
Bidirectionally promoting assembly order for ultrastiff and highly thermally conductive graphene fibres
Authors: Li Peng , Wang Ziqiu , Qi Yuxiang , Cai Gangfeng , Zhao Yingjie , Ming Xin , Lin Zizhen , Ma Weigang , Lin Jiahao , Li Hang , Shen Kai , Liu Yingjun , Xu Zhen , Xu Zhiping , Gao Chao 
Published: January 2024

AbstractMacroscopic fibres assembled from two-dimensional (2D) nanosheets are new and impressing type of fibre materials besides those from one-dimensional (1D) polymers, such as graphene fibres. However, the preparation and property-enhancing technologies of these fibres follow those from 1D polymers by improving the orientation along the fibre axis, leading to non-optimized microstructures and low integrated performances. Here, we show a concept of bidirectionally promoting the assembly order, making graphene fibres achieve synergistically improved mechanical and thermal properties. Concentric arrangement of graphene oxide sheets in the cross-section and alignment along fibre axis are realized by multiple shear-flow fields, which bidirectionally promotes the sheet-order of graphene sheets in solid fibres, generates densified and crystalline graphitic structures, and produces graphene fibres with ultrahigh modulus (901 GPa) and thermal conductivity (1660 W m−1 K−1). We believe that the concept would enhance both scientific and technological cognition of the assembly process of 2D nanosheets.
Multiple pathways for glucose phosphate transport and utilization support growth of Cryptosporidium parvum
Authors: Xu Rui , Beatty Wandy L. , Greigert Valentin , Witola William H. , Sibley L. David 
Published: January 2024

AbstractCryptosporidium parvum is an obligate intracellular parasite with a highly reduced mitochondrion that lacks the tricarboxylic acid cycle and the ability to generate ATP, making the parasite reliant on glycolysis. Genetic ablation experiments demonstrated that neither of the two putative glucose transporters CpGT1 and CpGT2 were essential for growth. Surprisingly, hexokinase was also dispensable for parasite growth while the downstream enzyme aldolase was required, suggesting the parasite has an alternative way of obtaining phosphorylated hexose. Complementation studies in E. coli support a role for direct transport of glucose-6-phosphate from the host cell by the parasite transporters CpGT1 and CpGT2, thus bypassing a requirement for hexokinase. Additionally, the parasite obtains phosphorylated glucose from amylopectin stores that are released by the action of the essential enzyme glycogen phosphorylase. Collectively, these findings reveal that C. parvum relies on multiple pathways to obtain phosphorylated glucose both for glycolysis and to restore carbohydrate reserves.
Electrochemical and chemical cycle for high-efficiency decoupled water splitting in a near-neutral electrolyte
Authors: Slobodkin Ilya , Davydova Elena , Sananis Matan , Breytus Anna , Rothschild Avner 
Published: January 2024

AbstractGreen hydrogen produced by water splitting using renewable electricity is essential to achieve net-zero carbon emissions. Present water electrolysis technologies are uncompetitive with low-cost grey hydrogen produced from fossil fuels, limiting their scale-up potential. Disruptive processes that decouple the hydrogen and oxygen evolution reactions and produce them in separate cells or different stages emerge as a prospective route to reduce system cost by enabling operation without expensive membranes and sealing components. Some of these processes divide the hydrogen or oxygen evolution reactions into electrochemical and chemical sub-reactions, enabling them to achieve high efficiency. However, high efficiency has been demonstrated only in a batch process with thermal swings that present operational challenges. This work introduces a breakthrough process that produces hydrogen and oxygen in separate cells and supports continuous operation in a membraneless system. We demonstrate high faradaic and electrolytic efficiency and high rate operation in a near-neutral electrolyte of NaBr in water, whereby bromide is electro-oxidized to bromate concurrent with hydrogen evolution in one cell, and bromate is chemically reduced to bromide in a catalytic reaction that evolves oxygen in another cell. This process may lead the way to high-efficiency membraneless water electrolysis that overcomes the limitations of century-old membrane electrolysis.
Design of simple nonovershooting controllers for linear high order systems with or without time delay
Authors: Du Huanchao , Feng Bobo , Shen Jieshi , Li Dan 
Published: January 2024

AbstractIn this paper, we mainly considered the problem of nonovershooting control of high order systems with or without time delay by simple controllers. As basic principles for nonovershooting control systems, three propositions are offered and proved. Under direction of these principles, a nonovershooting dominant pole control structure having three dominant poles, i.e., one real pole and a pair of complex conjugate poles on its left, is proposed. While its zeroes and nondominant poles are on the left side of these three dominant poles with sufficient distance. The controllers adopted are composed by first order filter and PD-PID controller. Dominance of the three dominant poles can be checked and ensured through the computational method we offered. Two illustrating examples are given to show the effectiveness of our method.
Evaluation of Chlorella vulgaris biosorption capacity for phosphate and nitrate removal from wastewater
Authors: Asaad Amany A. , Amer Amany S. 
Published: January 2024

AbstractHigh wastewater production rates during the past few decades are mostly attributable to anthropogenic activities. The main components leading to the nutrient enrichment of natural water bodies are such as nitrogen, phosphorus, and other minerals. The main focus of this research was to assess the ability of using Chlorella vulgaris algae, a potent and environmentally benign material, to eliminate phosphate and nitrate ions from wastewater. FTIR results showed that the biologically active molecules that facilitate the binding of phosphate and nitrate ions unto the C. vulgaris are C=C and N–H amid. The ideal equilibrium time for adsorption was 24 h with an optimum pH of 7 and the mass ratio of algae and different anions concentration was 80%. Freundlich isotherm model was the best-fitted isotherm. Moreover, the results of the experiment fit more closely with the pseudo-second-order kinetic model than other models. Elovich kinetic model data for both ions showed that the adsorption rate was much higher than the desorption rate. The growing popularity of biosorbents in treating wastewater has led to an improvement in their affordability and availability, and C. vulgaris may now represent an environmentally friendly choice from an environmental, and economic standpoint.
Thermal analysis and temperature evaluation on a magnetic‐geared dual‐rotor machine
Authors: Tong Minghao , Liu Xiaoqiang , Sun Le 
Published: January 2024

AbstractThe thermal performance of the magnetic‐geared dual‐rotor machine (MGDRM) is investigated. Because the effective component in the outer airgap magnetic field harmonics is low, the torque production of MGDRM cannot match the regular permanent magnetic synchronous machine (PMSM). Although the analysis shows that the torque generation of the MGDRM is weak, this conclusion is limited in the electromagnetic field. The MGDRM outer rotor should also be considered from the thermal aspect, and the effect on the torque generation should be valued in particular. The outer rotor thermal buffer effect blocks the heating flow from the winding to the inner rotor magnets. Thus, the MGDRM can withstand a heavy electrical load in a short period, producing higher torque. With this understanding, the torque production ability of the MGDRM can extend to a higher level, even close to the regular PMSM. To validate the analysis, a MGDRM machine is prototyped, and the dual‐rotor temperature information acquisition is realised by a wireless data collection. The rotor temperature estimation technology on the dual‐rotor is then investigated as an auxiliary function. The estimation error can be limited around 5°C, which is good for warning the thermal risk. And thus the MGDRM overheating can be safely adopted to extend the torque generation.
Artificial swim by undulating rigid flagellum with joint controllers
Authors: Yano Ryosuke , Kuroda Hisayasu 
Published: January 2024

Abstract
In this paper, we investigate the locomotion of artificial (robotic) swimmers by an undulating rigid flagellum, whose joints are controlled by actuators. The locomotion of a swimmer with an undulating rigid flagellum inside a two-dimensional channel sandwiched by two non-slip walls is numerically analyzed using the immersed boundary lattice Boltzmann method. Multi-relaxation-time scheme is applied to calculate the flow field under a high Reynolds number (Re). Our numerical results show that the optimal Re exists to maximize the locomotion distance, whereas the direction of locomotion can be reversed in the lower and higher Re limits.
Bioinspired Fano-like resonant transmission: frequency selective impedance matching
Authors: Esposito Gennaro Andrea , Tallarico Domenico , Sayed Ahmed Moustafa , Miniaci Marco , Shahab Shima , Bergamini Andrea 
Published: January 2024

Abstract
The study of the impedance mismatch between the device and its surroundings is crucial when building an acoustic device to obtain optimal performance. In reality, a high impedance mismatch would prohibit energy from being transmitted over the interface, limiting the amount of energy that the device could treat. In general, this is solved by using acoustic impedance matching layers, such as gradients, similar to what is done in optical coatings. The simplest form of such a gradient can be considered as an intermediate layer with certain qualities resting between the two media to impedance match, and requiring a minimum thickness of at least one quarter wavelength of the lowest frequency under consideration. The desired combination(s) of the (limited) available elastic characteristics and densities has traditionally determined material selection. Nature, which is likewise limited by the use of a limited number of materials in the construction of biological structures, demonstrates a distinct approach in which the design space is swept by modifying certain geometrical and/or material parameters. The middle ear of mammals and the lateral line of fishes are both instances of this method, with the latter already incorporating an architecture of distributed impedance matched underwater layers. In this paper, we develop a resonant mechanism whose properties can be modified to give impedance matching at different frequencies by adjusting a small set of geometrical parameters. The mechanism in question, like the lateral line organ, is intended to serve as the foundation for the creation of an impedance matching meta-surface. A computational study and parameter optimization show that it can match the impedance of water and air in a deeply sub-wavelength zone.