bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uveitic glaucoma-like features in Yap conditional knockout mice
Authors: Bitard Juliette , Grellier Elodie-Kim , Lourdel Sophie , Filipe Helena Prior , Hamon Annaïg , Fenaille François , Castelli Florence Anne , Chu-Van Emeline , Roger Jérôme E. , Locker Morgane , Perron Muriel 
Published: January 2024

AbstractGlaucoma is a multifactorial neurodegenerative disease characterized by the progressive and irreversible degeneration of the optic nerve and retinal ganglion cells. Despite medical advances aiming at slowing degeneration, around 40% of treated glaucomatous patients will undergo vision loss. It is thus of utmost importance to have a better understanding of the disease and to investigate more deeply its early causes. The transcriptional coactivator YAP, an important regulator of eye homeostasis, has recently drawn attention in the glaucoma research field. Here we show that Yap conditional knockout mice (Yap cKO), in which the deletion of Yap is induced in both Müller glia (i.e. the only retinal YAP-expressing cells) and the non-pigmented epithelial cells of the ciliary body, exhibit a breakdown of the aqueous-blood barrier, accompanied by a progressive collapse of the ciliary body. A similar phenotype is observed in human samples that we obtained from patients presenting with uveitis. In addition, aged Yap cKO mice harbor glaucoma-like features, including deregulation of key homeostatic Müller-derived proteins, retinal vascular defects, optic nerve degeneration and retinal ganglion cell death. Finally, transcriptomic analysis of Yap cKO retinas pointed to early-deregulated genes involved in extracellular matrix organization potentially underlying the onset and/or progression of the observed phenotype. Together, our findings reveal the essential role of YAP in preserving the integrity of the ciliary body and retinal ganglion cells, thereby preventing the onset of uveitic glaucoma-like features.
Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer
Authors: Lykoskoufis Nikolaos M. R. , Planet Evarist , Ongen Halit , Trono Didier , Dermitzakis Emmanouil T. 
Published: January 2024

AbstractTransposable elements (TEs) are prevalent repeats in the human genome, play a significant role in the regulome, and their disruption can contribute to tumorigenesis. However, TE influence on gene expression in cancer remains unclear. Here, we analyze 275 normal colon and 276 colorectal cancer samples from the SYSCOL cohort, discovering 10,231 and 5,199 TE-expression quantitative trait loci (eQTLs) in normal and tumor tissues, respectively, of which 376 are colorectal cancer specific eQTLs, likely due to methylation changes. Tumor-specific TE-eQTLs show greater enrichment of transcription factors, compared to shared TE-eQTLs suggesting specific regulation of their expression in tumor. Bayesian networks reveal 1,766 TEs as mediators of genetic effects, altering the expression of 1,558 genes, including 55 known cancer driver genes and show that tumor-specific TE-eQTLs trigger the driver capability of TEs. These insights expand our knowledge of cancer drivers, deepening our understanding of tumorigenesis and presenting potential avenues for therapeutic interventions.
Noise learning of instruments for high-contrast, high-resolution and fast hyperspectral microscopy and nanoscopy
Authors: He Hao , Cao Maofeng , Gao Yun , Zheng Peng , Yan Sen , Zhong Jin-Hui , Wang Lei , Jin Dayong , Ren Bin 
Published: January 2024

AbstractThe low scattering efficiency of Raman scattering makes it challenging to simultaneously achieve good signal-to-noise ratio (SNR), high imaging speed, and adequate spatial and spectral resolutions. Here, we report a noise learning (NL) approach that estimates the intrinsic noise distribution of each instrument by statistically learning the noise in the pixel-spatial frequency domain. The estimated noise is then removed from the noisy spectra. This enhances the SNR by ca. 10 folds, and suppresses the mean-square error by almost 150 folds. NL allows us to improve the positioning accuracy and spatial resolution and largely eliminates the impact of thermal drift on tip-enhanced Raman spectroscopic nanoimaging. NL is also applicable to enhance SNR in fluorescence and photoluminescence imaging. Our method manages the ground truth spectra and the instrumental noise simultaneously within the training dataset, which bypasses the tedious labelling of huge dataset required in conventional deep learning, potentially shifting deep learning from sample-dependent to instrument-dependent.
Unraveling radiation damage and healing mechanisms in halide perovskites using energy-tuned dual irradiation dosing
Authors: Kirmani Ahmad R. , Byers Todd A. , Ni Zhenyi , VanSant Kaitlyn , Saini Darshpreet K. , Scheidt Rebecca , Zheng Xiaopeng , Kum Tatchen Buh , Sellers Ian R. , McMillon-Brown Lyndsey , Huang Jinsong , Rout Bibhudutta , Luther Joseph M. 
Published: January 2024

AbstractPerovskite photovoltaics have been shown to recover, or heal, after radiation damage. Here, we deconvolve the effects of radiation based on different energy loss mechanisms from incident protons which induce defects or can promote efficiency recovery. We design a dual dose experiment first exposing devices to low-energy protons efficient in creating atomic displacements. Devices are then irradiated with high-energy protons that interact differently. Correlated with modeling, high-energy protons (with increased ionizing energy loss component) effectively anneal the initial radiation damage, and recover the device efficiency, thus directly detailing the different interactions of irradiation. We relate these differences to the energy loss (ionization or non-ionization) using simulation. Dual dose experiments provide insight into understanding the radiation response of perovskite solar cells and highlight that radiation-matter interactions in soft lattice materials are distinct from conventional semiconductors. These results present electronic ionization as a unique handle to remedying defects and trap states in perovskites.
WNT-dependent interaction between inflammatory fibroblasts and FOLR2+ macrophages promotes fibrosis in chronic kidney disease
Authors: Cohen Camille , Mhaidly Rana , Croizer Hugo , Kieffer Yann , Leclere Renaud , Vincent-Salomon Anne , Robley Catherine , Anglicheau Dany , Rabant Marion , Sannier Aurélie , Timsit Marc-Olivier , Eddy Sean , Kretzler Matthias , Ju Wenjun , Mechta-Grigoriou Fatima 
Published: January 2024

AbstractChronic kidney disease (CKD) is a public health problem driven by myofibroblast accumulation, leading to interstitial fibrosis. Heterogeneity is a recently recognized characteristic in kidney fibroblasts in CKD, but the role of different populations is still unclear. Here, we characterize a proinflammatory fibroblast population (named CXCL-iFibro), which corresponds to an early state of myofibroblast differentiation in CKD. We demonstrate that CXCL-iFibro co-localize with macrophages in the kidney and participate in their attraction, accumulation, and switch into FOLR2+ macrophages from early CKD stages on. In vitro, macrophages promote the switch of CXCL-iFibro into ECM-secreting myofibroblasts through a WNT/β-catenin-dependent pathway, thereby suggesting a reciprocal crosstalk between these populations of fibroblasts and macrophages. Finally, the detection of CXCL-iFibro at early stages of CKD is predictive of poor patient prognosis, which shows that the CXCL-iFibro population is an early player in CKD progression and demonstrates the clinical relevance of our findings.
Structure and elasticity of CaC2O5 suggests carbonate contribution to the seismic anomalies of Earth’s mantle
Authors: Wang Hanyu , Liu Lei , Gao Zihan , Yang Longxing , Naren Gerile , Mao Shide 
Published: January 2024

AbstractKnowledge of carbonate compounds under high pressure inside Earth is key to understanding the internal structure of the Earth, the deep carbon cycle and major geological events. Here we use first-principles simulations to calculate the structure and elasticity of CaC2O5-minerals with different symmetries under high pressure. Our calculations show that CaC2O5-minerals represent a group of low-density low-seismic-wave velocity mantle minerals. Changes in seismic wave velocity caused by the phase transformation of CaC2O5-Cc to CaC2O5-I$$\bar{4}$$

4

¯

2d (CaC2O5-C2-l) agree with wave velocity discontinuity at a depth of 660 km in the mantle transition zone. Moreover, when CaC2O5-Fdd2 transforms into CaC2O5-C2 under 70 GPa, its shear wave velocity decreases by 7.4%, and its density increases by 5.8%, which is consistent with the characteristics of large low-shear-velocity provinces (LLSVPs). Furthermore, the shear wave velocity of CaC2O5-I$$\bar{4}$$

4

¯

2d is very similar to that of cubic Ca-perovskite, which is one of the main constituents of the previously detected LLSVPs. Therefore, we propose that CaC2O5 and its high-pressure polymorphs may be a main component of LLSVPs.
Revisiting the Plasmodium sporozoite inoculum and elucidating the efficiency with which malaria parasites progress through the mosquito
Authors: Kanatani Sachie , Stiffler Deborah , Bousema Teun , Yenokyan Gayane , Sinnis Photini 
Published: January 2024

AbstractMalaria is initiated when infected anopheline mosquitoes inoculate sporozoites as they probe for blood. It is thought that all infected mosquitoes are equivalent in terms of their infectious potential, with parasite burden having no role in transmission success. In this study, using mosquitoes harboring the entire range of salivary gland sporozoite loads observed in the field, we demonstrate a strong and highly significant correlation between mosquito parasite burden and inoculum size. We then link the inoculum data to oocyst counts, the most commonly-used metric to assess mosquito infection in the field, and determine the efficiency with which oocyst sporozoites enter mosquito salivary glands. Taken together our data support the conclusion that mosquitoes with higher parasite burdens are more likely to initiate infection and contribute to onward transmission. Overall these data may account for some of the unexplained heterogeneity in transmission and enable more precise benchmarks for transmission-blocking interventions.
Efficient, narrow-band, and stable electroluminescence from organoboron-nitrogen-carbonyl emitter
Authors: Cheng Ying-Chun , Tang Xun , Wang Kai , Xiong Xin , Fan Xiao-Chun , Luo Shulin , Walia Rajat , Xie Yue , Zhang Tao , Zhang Dandan , Yu Jia , Chen Xian-Kai , Adachi Chihaya , Zhang Xiao-Hong 
Published: January 2024

AbstractOrganic light-emitting diodes (OLEDs) exploiting simple binary emissive layers (EMLs) blending only emitters and hosts have natural advantages in low-cost commercialization. However, previously reported OLEDs based on binary EMLs hardly simultaneously achieved desired comprehensive performances, e.g., high efficiency, low efficiency roll-off, narrow emission bands, and high operation stability. Here, we report a molecular-design strategy. Such a strategy leads to a fast reverse intersystem crossing rate in our designed emitter h-BNCO-1 of 1.79×105 s−1. An OLED exploiting a binary EML with h-BNCO-1 achieves ultrapure emission, a maximum external quantum efficiency of over 40% and a mild roll-off of 14% at 1000 cd·m−2. Moreover, h-BNCO-1 also exhibits promising operational stability in an alternative OLED exploiting a compact binary EML (the lifetime reaching 95% of the initial luminance at 1000 cd m−2 is ~ 137 h). Here, our work has thus provided a molecular-design strategy for OLEDs with promising comprehensive performance.
A developmental increase of inhibition promotes the emergence of hippocampal ripples
Authors: Pochinok Irina , Stöber Tristan M. , Triesch Jochen , Chini Mattia , Hanganu-Opatz Ileana L. 
Published: January 2024

AbstractSharp wave-ripples (SPW-Rs) are a hippocampal network phenomenon critical for memory consolidation and planning. SPW-Rs have been extensively studied in the adult brain, yet their developmental trajectory is poorly understood. While SPWs have been recorded in rodents shortly after birth, the time point and mechanisms of ripple emergence are still unclear. Here, we combine in vivo electrophysiology with optogenetics and chemogenetics in 4 to 12-day-old mice to address this knowledge gap. We show that ripples are robustly detected and induced by light stimulation of channelrhodopsin-2-transfected CA1 pyramidal neurons only from postnatal day 10 onwards. Leveraging a spiking neural network model, we mechanistically link the maturation of inhibition and ripple emergence. We corroborate these findings by reducing ripple rate upon chemogenetic silencing of CA1 interneurons. Finally, we show that early SPW-Rs elicit a more robust prefrontal cortex response than SPWs lacking ripples. Thus, development of inhibition promotes ripples emergence.
2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein
Authors: Ghanim George E. , Sekne Zala , Balch Sebastian , van Roon Anne-Marie M. , Nguyen Thi Hoang Duong 
Published: January 2024

AbstractTelomerase is a ribonucleoprotein (RNP) enzyme that extends telomeric repeats at eukaryotic chromosome ends to counterbalance telomere loss caused by incomplete genome replication. Human telomerase is comprised of two distinct functional lobes tethered by telomerase RNA (hTR): a catalytic core, responsible for DNA extension; and a Hinge and ACA (H/ACA) box RNP, responsible for telomerase biogenesis. H/ACA RNPs also have a general role in pseudouridylation of spliceosomal and ribosomal RNAs, which is critical for the biogenesis of the spliceosome and ribosome. Much of our structural understanding of eukaryotic H/ACA RNPs comes from structures of the human telomerase H/ACA RNP. Here we report a 2.7 Å cryo-electron microscopy structure of the telomerase H/ACA RNP. The significant improvement in resolution over previous 3.3 Å to 8.2 Å structures allows us to uncover new molecular interactions within the H/ACA RNP. Many disease mutations are mapped to these interaction sites. The structure also reveals unprecedented insights into a region critical for pseudouridylation in canonical H/ACA RNPs. Together, our work advances understanding of telomerase-related disease mutations and the mechanism of pseudouridylation by eukaryotic H/ACA RNPs.
Engineering metal-carbide hydrogen traps in steels
Authors: Liu Pang-Yu , Zhang Boning , Niu Ranming , Lu Shao-Lun , Huang Chao , Wang Maoqiu , Tian Fuyang , Mao Yong , Li Tong , Burr Patrick A. , Lu Hongzhou , Guo Aimin , Yen Hung-Wei , Cairney Julie M. , Chen Hao , Chen Yi-Sheng 
Published: January 2024

AbstractHydrogen embrittlement reduces the durability of the structural steels required for the hydrogen economy. Understanding how hydrogen interacts with the materials plays a crucial role in managing the embrittlement problems. Theoretical models have indicated that carbon vacancies in metal carbide precipitates are effective hydrogen traps in steels. Increasing the number of carbon vacancies in individual metal carbides is important since the overall hydrogen trapping capacity can be leveraged by introducing abundant metal carbides in steels. To verify this concept, we compare a reference steel containing titanium carbides (TiCs), which lack carbon vacancies, with an experimental steel added with molybdenum (Mo), which form Ti-Mo carbides comprising more carbon vacancies than TiCs. We employ theoretical and experimental techniques to examine the hydrogen trapping behavior of the carbides, demonstrating adding Mo alters the hydrogen trapping mechanism, enabling hydrogen to access carbon vacancy traps within the carbides, leading to an increase in trapping capacity.
MHC-I upregulation safeguards neoplastic T cells in the skin against NK cell-mediated eradication in mycosis fungoides
Authors: Chang Yun-Tsan , Prompsy Pacôme , Kimeswenger Susanne , Tsai Yi-Chien , Ignatova Desislava , Pavlova Olesya , Iselin Christoph , French Lars E. , Levesque Mitchell P. , Kuonen François , Bobrowicz Malgorzata , Brunner Patrick M. , Pascolo Steve , Hoetzenecker Wolfram , Guenova Emmanuella 
Published: January 2024

AbstractCancer-associated immune dysfunction is a major challenge for effective therapies. The emergence of antibodies targeting tumor cell-surface antigens led to advancements in the treatment of hematopoietic malignancies, particularly blood cancers. Yet their impact is constrained against tumors of hematopoietic origin manifesting in the skin. In this study, we employ a clonality-supervised deep learning methodology to dissect key pathological features implicated in mycosis fungoides, the most common cutaneous T-cell lymphoma. Our investigations unveil the prominence of the IL-32β–major histocompatibility complex (MHC)-I axis as a critical determinant in tumor T-cell immune evasion within the skin microenvironment. In patients’ skin, we find MHC-I to detrimentally impact the functionality of natural killer (NK) cells, diminishing antibody-dependent cellular cytotoxicity and promoting resistance of tumor skin T-cells to cell-surface targeting therapies. Through murine experiments in female mice, we demonstrate that disruption of the MHC-I interaction with NK cell inhibitory Ly49 receptors restores NK cell anti-tumor activity and targeted T-cell lymphoma elimination in vivo. These findings underscore the significance of attenuating the MHC-I-dependent immunosuppressive networks within skin tumors. Overall, our study introduces a strategy to reinvigorate NK cell-mediated anti-tumor responses to overcome treatment resistance to existing cell-surface targeted therapies for skin lymphoma.
Chromosome-level genome assembly of Hippophae gyantsensis
Authors: Chen Mingyue , Yang Danni , Yang Shihai , Yang Xingyu , Chen Zhiyu , Yang Tianyu , Yang Yunqiang , Yang Yongping 
Published: January 2024

AbstractHippophae gyantsensis, which is a native tree species in China, is ideal for windbreak and sand-fixing forests. It is an economically and ecologically valuable tree species distributed exclusively in the Qinghai-Tibet Plateau in China. In our study, we assembled a chromosome-level genome of H. gyantsensis using Illumina sequencing, Nanopore sequencing and chromosome structure capture technique. The genome was 716.32 Mb in size with scaffold N50 length of 64.84 Mb. A total of 716.25 Mb genome data was anchored and orientated onto 12 chromosomes with a mounting rate of up to 99.99%. Additionally, the genome was found to comprise approximately 56.84% repeat sequences, of which long terminal repeats(LTRs) that accounted for 33.19% of the entire genome. Meanwhile, a total of 32,316 protein-coding genes were predicted, and 91.07% of these genes were functionally annotated. We also completed a series of comparative genomic analyses to provide researchers with useful reference material for future studies on seabuckthorn.
Learning prevalent patterns of co-morbidities in multichronic patients using population-based healthcare data
Authors: Seghieri Chiara , Tortù Costanza , Tricò Domenico , Leonetti Simone 
Published: January 2024

AbstractThe prevalence of longstanding chronic diseases has increased worldwide, along with the average age of the population. As a result, an increasing number of people is affected by two or more chronic conditions simultaneously, and healthcare systems are facing the challenge of treating multimorbid patients effectively. Current therapeutic strategies are suited to manage each chronic condition separately, without considering the whole clinical condition of the patient. This approach may lead to suboptimal clinical outcomes and system inefficiencies (e.g. redundant diagnostic tests and inadequate drug prescriptions). We develop a novel methodology based on the joint implementation of data reduction and clustering algorithms to identify patterns of chronic diseases that are likely to co-occur in multichronic patients. We analyse data from a large adult population of multichronic patients living in Tuscany (Italy) in 2019 which was stratified by sex and age classes. Results demonstrate that (i) cardio-metabolic, endocrine, and neuro-degenerative diseases represent a stable pattern of multimorbidity, and (ii) disease prevalence and clustering vary across ages and between women and men. Identifying the most common multichronic profiles can help tailor medical protocols to patients’ needs and reduce costs. Furthermore, analysing temporal patterns of disease can refine risk predictions for evolutive chronic conditions.
Functional neurogenomic responses to acoustic threats, including a heterospecific referential alarm call and its referent, in the auditory forebrain of red-winged blackbirds
Authors: Antonson N. D. , Enos J. K. , Lawson S. L. , Uy F. M. K. , Gill S. A. , Lynch K. S. , Hauber M. E. 
Published: January 2024

AbstractIn animal communication, functionally referential alarm calls elicit the same behavioral responses as their referents, despite their typically distinct bioacoustic traits. Yet the auditory forebrain in at least one songbird species, the black-capped chickadee Poecile atricapillus, responds similarly to threat calls and their referent predatory owl calls, as assessed by immediate early gene responses in the secondary auditory forebrain nuclei. Whether and where in the brain such perceptual and cognitive equivalence is processed remains to be understood in most other avian systems. Here, we studied the functional neurogenomic (non-) equivalence of acoustic threat stimuli perception by the red-winged blackbird Agelaius phoeniceus in response to the actual calls of the obligate brood parasitic brown-headed cowbird Molothrus ater and the referential anti-parasitic alarm calls of the yellow warbler Setophaga petechia, upon which the blackbird is known to eavesdrop. Using RNA-sequencing from neural tissue in the auditory lobule (primary and secondary auditory nuclei combined), in contrast to previous findings, we found significant differences in the gene expression profiles of both an immediate early gene, ZENK (egr-1), and other song-system relevant gene-products in blackbirds responding to cowbird vs. warbler calls. In turn, direct cues of threats (including conspecific intruder calls and nest-predator calls) elicited higher ZENK and other differential gene expression patterns compared to harmless heterospecific calls. These patterns are consistent with a perceptual non-equivalence in the auditory forebrain of adult male red-winged blackbirds in response to referential calls and the calls of their referents.