bluuebunny/crossref_metadata_2025 huggingface dataset:
Twisted moiré conductive thermal metasurface
Authors: Li Huagen , Wang Dong , Xu Guoqiang , Liu Kaipeng , Zhang Tan , Li Jiaxin , Tao Guangming , Yang Shuihua , Lu Yanghua , Hu Run , Lin Shisheng , Li Ying , Qiu Cheng-Wei
Published: March 2024

Extensive investigations on the moiré magic angle in twisted bilayer graphene have unlocked the emerging field—twistronics. Recently, its optics analogue, namely opto-twistronics, further expands the potential universal applicability of twistronics. However, since heat diffusion neither possesses the dispersion like photons nor carries the band structure as electrons, the real magic angle in electrons or photons is ill-defined for heat diffusion, making it elusive to understand or design any thermal analogue of magic angle. Here, we introduce and experimentally validate the twisted thermotics in a twisted diffusion system by judiciously tailoring thermal coupling, in which twisting an analog thermal magic angle would result in the function switching from cloaking to concentration. Our work provides insights for the tunable heat diffusion control, and opens up an unexpected branch for twistronics -- twisted thermotics, paving the way towards field manipulation in twisted configurations including but not limited to fluids.
Mi-2β promotes immune evasion in melanoma by activating EZH2 methylation
Authors: Li Cang , Wang Zhengyu , Yao Licheng , Lin Xingyu , Jian Yongping , Li Yujia , Zhang Jie , Shao Jingwei , Tran Phuc D. , Hagman James R. , Cao Meng , Cong Yusheng , Li Hong-yu , Goding Colin R. , Xu Zhi-Xiang , Liao Xuebin , Miao Xiao , Cui Rutao
Published: March 2024

Recent development of new immune checkpoint inhibitors has been particularly successfully in cancer treatment, but still the majority patients fail to benefit. Converting resistant tumors to immunotherapy sensitive will provide a significant improvement in patient outcome. Here we identify Mi-2β as a key melanoma-intrinsic effector regulating the adaptive anti-tumor immune response. Studies in genetically engineered mouse melanoma models indicate that loss of Mi-2β rescues the immune response to immunotherapy in vivo. Mechanistically, ATAC-seq analysis shows that Mi-2β controls the accessibility of IFN-γ-stimulated genes (ISGs). Mi-2β binds to EZH2 and promotes K510 methylation of EZH2, subsequently activating the trimethylation of H3K27 to inhibit the transcription of ISGs. Finally, we develop an Mi-2β-targeted inhibitor, Z36-MP5, which reduces Mi-2β ATPase activity and reactivates ISG transcription. Consequently, Z36-MP5 induces a response to immune checkpoint inhibitors in otherwise resistant melanoma models. Our work provides a potential therapeutic strategy to convert immunotherapy resistant melanomas to sensitive ones.
Dependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Authors: Campos-Pardos Elena , Uranga Santiago , Picó Ana , Gómez Ana Belén , Gonzalo-Asensio Jesús
Published: March 2024

Human and animal tuberculosis is caused by the Mycobacterium tuberculosis Complex (MTBC), which has evolved a genomic decay of cobalamin (vitamin B12) biosynthetic genes. Accordingly, and in sharp contrast to environmental, opportunistic and ancestor mycobacteria; we demonstrate that M. tuberculosis (Mtb), M. africanum, and animal-adapted lineages, lack endogenous production of cobalamin, yet they retain the capacity for exogenous uptake. A B12 anemic model in immunocompromised and immunocompetent mice, demonstrates improved survival, and lower bacteria in organs, in B12 anemic animals infected with Mtb relative to non-anemic controls. Conversely, no differences were observed between mice groups infected with M. canettii, an ancestor mycobacterium which retains cobalamin biosynthesis. Interrogation of the B12 transcriptome in three MTBC strains defined L-methionine synthesis by metE and metH genes as a key phenotype. Expression of metE is repressed by a cobalamin riboswitch, while MetH requires the cobalamin cofactor. Thus, deletion of metE predominantly attenuates Mtb in anemic mice; although inactivation of metH exclusively causes attenuation in non-anemic controls. Here, we show how sub-physiological levels of B12 in the host antagonizes Mtb virulence, and describe a yet unknown mechanism of host-pathogen cross-talk with implications for B12 anemic populations.
Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development
Authors: Kim Taehyeung , Martínez-Bonet Marta , Wang Qiang , Hackert Nicolaj , Sparks Jeffrey A. , Baglaenko Yuriy , Koh Byunghee , Darbousset Roxane , Laza-Briviesca Raquel , Chen Xiaoting , Aguiar Vitor R. C. , Chiu Darren J. , Westra Harm-Jan , Gutierrez-Arcelus Maria , Weirauch Matthew T. , Raychaudhuri Soumya , Rao Deepak A. , Nigrovic Peter A.
Published: March 2024

Fine-mapping and functional studies implicate rs117701653, a non-coding single nucleotide polymorphism in the CD28/CTLA4/ICOS locus, as a risk variant for rheumatoid arthritis and type 1 diabetes. Here, using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated risk allele is functional, reducing affinity for the inhibitory chromosomal regulator SMCHD1 to enhance expression of inducible T-cell costimulator (ICOS) in memory CD4+ T cells from healthy donors. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells and, in rheumatoid arthritis patients, of blood and joint fluid Tph cells as well as circulating plasmablasts. Correspondingly, ICOS ligation and carriage of the rs117701653 risk allele accelerate T cell differentiation into CXCR5-PD-1high Tph cells producing IL-21 and CXCL13. Thus, mechanistic dissection of a functional non-coding variant in human autoimmunity discloses a previously undefined pathway through which ICOS regulates Tph development and abundance.
Prefrontal control of superior colliculus modulates innate escape behavior following adversity
Authors: Ritter Ami , Habusha Shlomi , Givon Lior , Edut Shahaf , Klavir Oded
Published: March 2024

Innate defensive responses, though primarily instinctive, must also be highly adaptive to changes in risk assessment. However, adaptive changes can become maladaptive, following severe stress, as seen in posttraumatic stress disorder (PTSD). In a series of experiments, we observed long-term changes in innate escape behavior of male mice towards a previously non-threatening stimulus following an adverse shock experience manifested as a shift in the threshold of threat response. By recording neural activity in the superior colliculus (SC) while phototagging specific responses to afferents, we established the crucial influence of input arriving at the SC from the medial prefrontal cortex (mPFC), both directly and indirectly, on escape-related activity after adverse shock experience. Inactivating these specific projections during the shock effectively abolished the observed changes. Conversely, optogenetically activating them during encounters controlled escape responses. This establishes the necessity and sufficiency of those specific mPFC inputs into the SC for adverse experience related changes in innate escape behavior.
Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance
Authors: Xiang Xianke , He Yao , Zhang Zemin , Yang Xuerui
Published: March 2024

RNA splicing shapes the gene regulatory programs that underlie various physiological and disease processes. Here, we present the SCASL (single-cell clustering based on alternative splicing landscapes) method for interrogating the heterogeneity of RNA splicing with single-cell RNA-seq data. SCASL resolves the issue of biased and sparse data coverage on single-cell RNA splicing and provides a new scheme for classifications of cell identities. With previously published datasets as examples, SCASL identifies new cell clusters indicating potentially precancerous and early-tumor stages in triple-negative breast cancer, illustrates cell lineages of embryonic liver development, and provides fine clusters of highly heterogeneous tumor-associated CD4 and CD8 T cells with functional and physiological relevance. Most of these findings are not readily available via conventional cell clustering based on single-cell gene expression data. Our study shows the potential of SCASL in revealing the intrinsic RNA splicing heterogeneity and generating biological insights into the dynamic and functional cell landscapes in complex tissues.
AlphaPept: a modern and open framework for MS-based proteomics
Authors: Strauss Maximilian T. , Bludau Isabell , Zeng Wen-Feng , Voytik Eugenia , Ammar Constantin , Schessner Julia P. , Ilango Rajesh , Gill Michelle , Meier Florian , Willems Sander , Mann Matthias
Published: March 2024

In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making efficient analysis a principal challenge. A plethora of different computational tools can process the MS data to derive peptide and protein identification and quantification. However, during the last years there has been dramatic progress in computer science, including collaboration tools that have transformed research and industry. To leverage these advances, we develop AlphaPept, a Python-based open-source framework for efficient processing of large high-resolution MS data sets. Numba for just-in-time compilation on CPU and GPU achieves hundred-fold speed improvements. AlphaPept uses the Python scientific stack of highly optimized packages, reducing the code base to domain-specific tasks while accessing the latest advances. We provide an easy on-ramp for community contributions through the concept of literate programming, implemented in Jupyter Notebooks. Large datasets can rapidly be processed as shown by the analysis of hundreds of proteomes in minutes per file, many-fold faster than acquisition. AlphaPept can be used to build automated processing pipelines with web-serving functionality and compatibility with downstream analysis tools. It provides easy access via one-click installation, a modular Python library for advanced users, and via an open GitHub repository for developers.
Neural timescales reflect behavioral demands in freely moving rhesus macaques
Authors: Manea Ana M. G. , Maisson David J.-N. , Voloh Benjamin , Zilverstand Anna , Hayden Benjamin , Zimmermann Jan
Published: March 2024

Previous work demonstrated a highly reproducible cortical hierarchy of neural timescales at rest, with sensory areas displaying fast, and higher-order association areas displaying slower timescales. The question arises how such stable hierarchies give rise to adaptive behavior that requires flexible adjustment of temporal coding and integration demands. Potentially, this lack of variability in the hierarchical organization of neural timescales could reflect the structure of the laboratory contexts. We posit that unconstrained paradigms are ideal to test whether the dynamics of neural timescales reflect behavioral demands. Here we measured timescales of local field potential activity while male rhesus macaques foraged in an open space. We found a hierarchy of neural timescales that differs from previous work. Importantly, although the magnitude of neural timescales expanded with task engagement, the brain areas’ relative position in the hierarchy was stable. Next, we demonstrated that the change in neural timescales is dynamic and contains functionally-relevant information, differentiating between similar events in terms of motor demands and associated reward. Finally, we demonstrated that brain areas are differentially affected by these behavioral demands. These results demonstrate that while the space of neural timescales is anatomically constrained, the observed hierarchical organization and magnitude is dependent on behavioral demands.
Tuning polymer-backbone coplanarity and conformational order to achieve high-performance printed all-polymer solar cells
Authors: Wu Yilei , Yuan Yue , Sorbelli Diego , Cheng Christina , Michalek Lukas , Cheng Hao-Wen , Jindal Vishal , Zhang Song , LeCroy Garrett , Gomez Enrique D. , Milner Scott T. , Salleo Alberto , Galli Giulia , Asbury John B. , Toney Michael F. , Bao Zhenan
Published: March 2024

All-polymer solar cells (all-PSCs) offer improved morphological and mechanical stability compared with those containing small-molecule-acceptors (SMAs). They can be processed with a broader range of conditions, making them desirable for printing techniques. In this study, we report a high-performance polymer acceptor design based on bithiazole linker (PY-BTz) that are on par with SMAs. We demonstrate that bithiazole induces a more coplanar and ordered conformation compared to bithiophene due to the synergistic effect of non-covalent backbone planarization and reduced steric encumbrances. As a result, PY-BTz shows a significantly higher efficiency of 16.4% in comparison to the polymer acceptors based on commonly used thiophene-based linkers (i.e., PY-2T, 9.8%). Detailed analyses reveal that this improvement is associated with enhanced conjugation along the backbone and closer interchain π-stacking, resulting in higher charge mobilities, suppressed charge recombination, and reduced energetic disorder. Remarkably, an efficiency of 14.7% is realized for all-PSCs that are solution-sheared in ambient conditions, which is among the highest for devices prepared under conditions relevant to scalable printing techniques. This work uncovers a strategy for promoting backbone conjugation and planarization in emerging polymer acceptors that can lead to superior all-PSCs.
A Ce-CuZn catalyst with abundant Cu/Zn-OV-Ce active sites for CO2 hydrogenation to methanol
Authors: Ye Runping , Ma Lixuan , Mao Jianing , Wang Xinyao , Hong Xiaoling , Gallo Alessandro , Ma Yanfu , Luo Wenhao , Wang Baojun , Zhang Riguang , Duyar Melis Seher , Jiang Zheng , Liu Jian
Published: March 2024

CO2 hydrogenation to chemicals and fuels is a significant approach for achieving carbon neutrality. It is essential to rationally design the chemical structure and catalytic active sites towards the development of efficient catalysts. Here we show a Ce-CuZn catalyst with enriched Cu/Zn-OV-Ce active sites fabricated through the atomic-level substitution of Cu and Zn into Ce-MOF precursor. The Ce-CuZn catalyst exhibits a high methanol selectivity of 71.1% and a space-time yield of methanol up to 400.3 g·kgcat−1·h−1 with excellent stability for 170 h at 260 °C, comparable to that of the state-of-the-art CuZnAl catalysts. Controlled experiments and DFT calculations confirm that the incorporation of Cu and Zn into CeO2 with abundant oxygen vacancies can facilitate H2 dissociation energetically and thus improve CO2 hydrogenation over the Ce-CuZn catalyst via formate intermediates. This work offers an atomic-level design strategy for constructing efficient multi-metal catalysts for methanol synthesis through precise control of active sites.
Atlantic origin of the increasing Asian westerly jet interannual variability
Authors: Lin Lifei , Hu Chundi , Wang Bin , Wu Renguang , Wu Zeming , Yang Song , Cai Wenju , Li Peiliang , Xiong Xuejun , Chen Dake
Published: March 2024

The summer Eurasian westerly jet is reported to become weaker and wavier, thus promoting the frequent weather extremes. However, the primary driver of the changing jet stream remains in debate, mainly due to the regionality and seasonality of the Eurasian jet. Here we report a sharp increase, by approximately 140%, in the interannual variability of the summertime East Asian jet (EAJ) since the end of twentieth century. Such interdecadal change induces considerable changes in the large-scale circulation pattern across Eurasia, and consequently weather and climate extremes including heatwaves, droughts, and Asian monsoonal rainfall regime shifts. The trigger mainly emerges from preceding February North Atlantic seesaw called Scandinavian pattern (contributing to 81.1 ± 2.9% of the enhanced EAJ variability), which harnesses the “cross-seasonal-coupled oceanic-atmospheric bridge” to exert a delayed impact on EAJ and thus aids relevant predictions five months in advance. However, projections from state-of-the-art models with prescribed anthropogenic forcing exhibit no similar circulation changes. This sheds light on that, at the interannual timescale, a substantial portion of recently increasing variability in the East Asian sector of the Eurasian westerly jet arises from unforced natural variability.
Prediction of electrode microstructure evolutions with physically constrained unsupervised image-to-image translation networks
Authors: Sciazko Anna , Komatsu Yosuke , Shimura Takaaki , Shikazono Naoki
Published: March 2024

Microstructure of electrodes determines the performance of electrochemical devices such as fuel cells and batteries. The efficiency and economic feasibility of these technologies depend on the stability of the microstructures throughout their lifetime. Although modeling techniques were proposed for determining electrode performance from 2- or 3-dimensional microstructural data, it is still extremely challenging to predict long-term structural degradation by means of numerical simulations. One of the major challenges is to overcome the difficulties in obtaining experimental data of an identical sample through the degradation process. In this work, a machine learning-based framework for predicting microstructural evolutions with limited amount of un-paired training data is proposed. Physically-constrained unsupervised image-to-image translation (UNIT) network is incorporated to predict nickel oxide reduction process in solid oxide fuel cell anode. The proposed framework is firstly validated by simplified toy-problems. Secondly, the UNIT network is applied to real microstructures of solid oxide fuel cells, which results in excellent visual and statistical agreements between real and artificially reduced samples. The proposed network can predict evolutions in new microstructures, which have not been used during training. Furthermore, a conditional UNIT network (C-UNIT) was demonstrated, which can predict the microstructure evolutions based on process conditions as well as continuous time series of microstructural changes.
Highly reliable and stretchable OLEDs based on facile patterning method: toward stretchable organic optoelectronic devices
Authors: Nam Minwoo , Chang Jaehyeock , Kim Hagseon , Son Young Hyun , Jeon Yongmin , Kwon Jeong Hyun , Choi Kyung Cheol
Published: March 2024

Stretchable displays attract significant attention because of their potential applications in wearable electronics, smart textiles, and human-conformable devices. This paper introduces an electrically stable, mechanically ultra-robust, and water-resistant stretchable OLED display (SOLED) mounted on a stress-relief pillar platform. The SOLED is fabricated on a thin, transparent polyethylene terephthalate (PET) film using conventional vacuum evaporation, organic-inorganic hybrid thin film encapsulation (TFE), and a nonselective laser patterning process. This simple and efficient process yields an OLED display with exceptional stretchability, reaching up to 95% strain and outstanding durability, enduring 100,000 stretch-release cycles at 50% strain. Operational lifetime and water-resistant storage lifetime measurements confirm that the TFE provides effective protection even after the nonselective laser patterning process. A 3 × 3 array SOLED display module mounted on a stress-relief pillar platform is successfully implemented, marking the first case of water-resistant display array operation in the field of SOLEDs. This work aims to develop practical stretchable displays by offering a reliable fabrication method and device design for creating mechanically robust and adaptable displays, potentially paving the way for future advances in human-conformable electronics and other innovative applications.
Documentation of comorbidities, lifestyle factors, and asthma management during primary care scheduled asthma contacts
Authors: Takala Jaana , Vähätalo Iida , Tuomisto Leena E. , Niemelä Onni , Ilmarinen Pinja , Kankaanranta Hannu
Published: March 2024

Systematically assessing asthma during follow-up contacts is important to accomplish comprehensive treatment. No previous long-term studies exist on how comorbidities, lifestyle factors, and asthma management details are documented in scheduled asthma contacts in primary health care (PHC). We showed comorbidities and lifestyle factors were poorly documented in PHC in this real-life, 12-year, follow-up study. Documented information on rhinitis was found in 8.9% and BMI, overweight, or obesity in ≤1.5% of the 542 scheduled asthma contacts. Of the 145 patients with scheduled asthma contacts, 6.9% had undergone revision of their inhalation technique; 16.6% had documentation of their asthma action plan. Screening of respiratory symptoms was recorded in 79% but nasal symptoms in only 15.5% of contacts. Lifestyle guidance interventions were found in <1% of contacts. These results, based on documented patient data, indicate a need exists to further improve the assessment and guidance of asthma patients in PHC.
Two-dimensional phase diagram of the charge density wave in doped CsV3Sb5
Authors: Huai Linwei , Li Hongyu , Han Yulei , Luo Yang , Peng Shuting , Wei Zhiyuan , Shen Jianchang , Wang Bingqian , Miao Yu , Sun Xiupeng , Ou Zhipeng , Liu Bo , Yu Xiaoxiao , Xiang Ziji , Kuang Min-Quan , Qiao Zhenhua , Chen Xianhui , He Junfeng
Published: March 2024

Kagome superconductors AV3Sb5 (A = K, Rb and Cs) have attracted much recent attention due to the coexistence of multiple exotic orders. Among them, the charge density wave (CDW) order has been shown to host various unconventional behaviors. Here, we investigate the CDW order by a combination of both bulk and surface doping methods. While element substitutions in bulk doping change both carriers and the crystal lattice, the surface doping primarily tunes the carrier concentration. As such, our results reveal a two-dimensional phase diagram of the CDW in doped CsV3Sb5. In the lightly bulk doped regime, the existence of CDW order is reversible by tuning the carrier concentration. But excessive bulk doping permanently destroys the CDW, regardless of the carrier doping level. These results provide insights to the origin of the CDW from both electronic and structural degrees of freedom. They also open an avenue for manipulating the exotic CDW order in Kagome superconductors.
One-dimensional topological phase and tunable soliton states in atomic nanolines on Si(001) surface
Authors: Song Biyu , Zhi Guoxiang , Hua Chenqiang , Wu Meimei , Dou Wenzhen , Gao Wenjin , Li Tianzhao , Niu Tianchao , Zhou Miao
Published: March 2024

Formation of exotic topological states on technologically important semiconductor substrate is significant from the aspects of both fundamental research and practical implementation. Here, we demonstrate one-dimensional (1D) topological phase and tunable soliton states in atomic nanolines self-assembled on Si(001) surface. By first-principles calculations and tight-binding modeling, we reveal that Bi nanolines provide an ideal system to realize a multi-orbital Su–Schrieffer–Heeger (SSH) model, and the electronic properties can be modulated by substrate-orbital-filtering effect. The topological features are confirmed by nontrivial end states for a finite-length nanoline and (anti-)soliton states at the boundary of two topologically distinct phases. We demonstrate that solitons are highly mobile on the surface, and their formation could be controlled by surface B/N doping. As these nanolines can extend several micrometers long without kinks, and quantum transport simulations suggest clear signatures of topological states characterized by transmission resonance peaks, our work paves an avenue to achieve 1D topological phase compatible with semiconductor technology and to engineer the properties with high tunability and fidelity for quantum information processing.
Multivariate canonical correlation analysis identifies additional genetic variants for chronic kidney disease
Authors: Osborne Amy J. , Bierzynska Agnieszka , Colby Elizabeth , Andag Uwe , Kalra Philip A. , Radresa Olivier , Skroblin Philipp , Taal Maarten W. , Welsh Gavin I. , Saleem Moin A. , Campbell Colin
Published: March 2024

Chronic kidney diseases (CKD) have genetic associations with kidney function. Univariate genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN), two complementary kidney function markers. However, it is unknown whether additional SNPs for kidney function can be identified by multivariate statistical analysis. To address this, we applied canonical correlation analysis (CCA), a multivariate method, to two individual-level CKD genotype datasets, and metaCCA to two published GWAS summary statistics datasets. We identified SNPs previously associated with kidney function by published univariate GWASs with high replication rates, validating the metaCCA method. We then extended discovery and identified previously unreported lead SNPs for both kidney function markers, jointly. These showed expression quantitative trait loci (eQTL) colocalisation with genes having significant differential expression between CKD and healthy individuals. Several of these identified lead missense SNPs were predicted to have a functional impact, including in SLC14A2. We also identified previously unreported lead SNPs that showed significant correlation with both kidney function markers, jointly, in the European ancestry CKDGen, National Unified Renal Translational Research Enterprise (NURTuRE)-CKD and Salford Kidney Study (SKS) datasets. Of these, rs3094060 colocalised with FLOT1 gene expression and was significantly more common in CKD cases in both NURTURE-CKD and SKS, than in the general population. Overall, by using multivariate analysis by CCA, we identified additional SNPs and genes for both kidney function and CKD, that can be prioritised for further CKD analyses.
Antigen identification strategies and preclinical evaluation models for advancing tuberculosis vaccine development
Authors: Chugh Saurabh , Bahal Ritika Kar , Dhiman Rohan , Singh Ramandeep
Published: March 2024

In its myriad devastating forms, Tuberculosis (TB) has existed for centuries, and humanity is still affected by it. Mycobacterium tuberculosis (M. tuberculosis), the causative agent of TB, was the foremost killer among infectious agents until the COVID-19 pandemic. One of the key healthcare strategies available to reduce the risk of TB is immunization with bacilli Calmette-Guerin (BCG). Although BCG has been widely used to protect against TB, reports show that BCG confers highly variable efficacy (0-80%) against adult pulmonary TB. Unwavering efforts have been made over the past 20 years to develop and evaluate new TB vaccine candidates. The failure of conventional preclinical animal models to fully recapitulate human response to TB, as also seen for the failure of MVA85A in clinical trials, signifies the need to develop better preclinical models for TB vaccine evaluation. In the present review article, we outline various approaches used to identify protective mycobacterial antigens and recent advancements in preclinical models for assessing the efficacy of candidate TB vaccines.
De novo transcriptome for Chiloscyllium griseum, a long-tail carpet shark of the Indian waters
Authors: Harshan Pooja , Sukumaran Sandhya , Gopalakrishnan A.
Published: March 2024

Sharks have thrived in the oceans for 400 million years, experienced five extinctions and evolved into today’s apex predators. However, enormous genome size, poor karyotyping and limited tissue sampling options are the bottlenecks in shark research. Sharks of the family Orectolobiformes act as model species in transcriptome research with exceptionally high reproductive fecundity, catch prominence and oviparity. The present study illustrates a de novo transcriptome for an adult grey bamboo shark, Chiloscyllium griseum (Chondrichthyes; Hemiscyllidae) using paired-end RNA sequencing. Around 150 million short Illumina reads were obtained from five different tissues and assembled using the Trinity assembler. 70,647 hits on Uniprot by BLASTX was obtained after the transcriptome annotation. The data generated serve as a basis for transcriptome-based population genetic studies and open up new avenues in the field of comparative transcriptomics and conservation biology.
High resolution spatiotemporal modeling of long term anthropogenic nutrient discharge in China
Authors: Zhang Haoran , Sun Huihang , Zhao Ruikun , Tian Yu , Meng Yiming
Published: March 2024

High-resolution integration of large-scale and long-term anthropogenic nutrient discharge data is crucial for understanding the spatiotemporal evolution of pollution and identifying intervention points for pollution mitigation. Here, we establish the MEANS-ST1.0 dataset, which has a high spatiotemporal resolution and encompasses anthropogenic nutrient discharge data collected in China from 1980 to 2020. The dataset includes five components, namely, urban residential, rural residential, industrial, crop farming, and livestock farming, with a spatial resolution of 1 km and a temporal resolution of monthly. The data are available in three formats, namely, GeoTIFF, NetCDF and Excel, catering to GIS users, researchers and policymakers in various application scenarios, such as visualization and modelling. Additionally, rigorous quality control was performed on the dataset, and its reliability was confirmed through cross-scale validation and literature comparisons at the national and regional levels. These data offer valuable insights for further modelling the interactions between humans and the environment and the construction of a digital Earth.
A database of in situ water temperatures for large inland lakes across the coterminous United States
Authors: Sorensen Troy , Espey Eamon , Kelley John G. W. , Kessler James , Gronewold Andrew D.
Published: March 2024

Water temperature dynamics in large inland lakes are interrelated with internal lake physics, ecosystem function, and adjacent land surface meteorology and climatology. Models for simulating and forecasting lake temperatures often rely on remote sensing and in situ data for validation. In situ monitoring platforms have the benefit of providing relatively precise measurements at multiple lake depths, but are often sparser (temporally and spatially) than remote sensing data. Here, we address the challenge of synthesizing in situ lake temperature data by creating a standardized database of near-surface and subsurface measurements from 134 sites across 29 large North American lakes, with the primary goal of supporting an ongoing lake model validation study. We utilize data sources ranging from federal agency repositories to local monitoring group samples, with a collective historical record spanning January 1, 2000 through December 31, 2022. Our database has direct utility for validating simulations and forecasts from operational numerical weather prediction systems in large lakes whose extensive surface area may significantly influence nearby weather and climate patterns.
24-hour average PM2.5 concentration caused by aircraft in Chinese airports from Jan. 2006 to Dec. 2023
Authors: Cui Qiang , Jia Zike , Liu Yujie , Wang Yu , Li Ye
Published: March 2024

Since 2006, the rapid development of China’s aviation industry has been accompanied by a significant increase in one of its emissions, namely, PM2.5, which poses a substantial threat to human health. However, little data is describing the PM2.5 concentration caused by aircraft activities. This study addresses this gap by initially computing the monthly PM2.5 emissions of the landing-take-off (LTO) stage from Jan. 2006 to Dec. 2023 for 175 Chinese airports, employing the modified BFFM2-FOA-FPM method. Subsequently, the study uses the Gaussian diffusion model to measure the 24-hour average PM2.5 concentration resulting from flight activities at each airport. This study mainly draws the following conclusions: Between 2006 and 2023, the highest recorded PM2.5 concentration data at all airports was observed in 2018, reaching 5.7985 micrograms per cubic meter, while the lowest point was recorded in 2022, at 2.0574 micrograms per cubic meter. Moreover, airports with higher emissions are predominantly located in densely populated and economically vibrant regions such as Beijing, Shanghai, Guangzhou, Chengdu, and Shenzhen.
FishSNP: a high quality cross-species SNP database of fishes
Authors: Zhang Lei , Li Heng , Shi Mijuan , Ren Keyi , Zhang Wanting , Cheng Yingyin , Wang Yaping , Xia Xiao-Qin
Published: March 2024

The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP (http://bioinfo.ihb.ac.cn/fishsnp), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.
Fractional order memcapacitive neuromorphic elements reproduce and predict neuronal function
Authors: Vazquez-Guerrero Patricia , Tuladhar Rohisha , Psychalinos Costas , Elwakil Ahmed , Chacron Maurice J. , Santamaria Fidel
Published: March 2024

There is an increasing need to implement neuromorphic systems that are both energetically and computationally efficient. There is also great interest in using electric elements with memory, memelements, that can implement complex neuronal functions intrinsically. A feature not widely incorporated in neuromorphic systems is history-dependent action potential time adaptation which is widely seen in real cells. Previous theoretical work shows that power-law history dependent spike time adaptation, seen in several brain areas and species, can be modeled with fractional order differential equations. Here, we show that fractional order spiking neurons can be implemented using super-capacitors. The super-capacitors have fractional order derivative and memcapacitive properties. We implemented two circuits, a leaky integrate and fire and a Hodgkin–Huxley. Both circuits show power-law spiking time adaptation and optimal coding properties. The spiking dynamics reproduced previously published computer simulations. However, the fractional order Hodgkin–Huxley circuit showed novel dynamics consistent with criticality. We compared the responses of this circuit to recordings from neurons in the weakly-electric fish that have previously been shown to perform fractional order differentiation of their sensory input. The criticality seen in the circuit was confirmed in spontaneous recordings in the live fish. Furthermore, the circuit also predicted long-lasting stimulation that was also corroborated experimentally. Our work shows that fractional order memcapacitors provide intrinsic memory dependence that could allow implementation of computationally efficient neuromorphic devices. Memcapacitors are static elements that consume less energy than the most widely studied memristors, thus allowing the realization of energetically efficient neuromorphic devices.
A Koopman operator-based prediction algorithm and its application to COVID-19 pandemic and influenza cases
Authors: Mezić Igor , Drmač Zlatko , Črnjarić Nelida , Maćešić Senka , Fonoberova Maria , Mohr Ryan , Avila Allan M. , Manojlović Iva , Andrejčuk Aleksandr
Published: March 2024

Future state prediction for nonlinear dynamical systems is a challenging task. Classical prediction theory is based on a, typically long, sequence of prior observations and is rooted in assumptions on statistical stationarity of the underlying stochastic process. These algorithms have trouble predicting chaotic dynamics, “Black Swans” (events which have never previously been seen in the observed data), or systems where the underlying driving process fundamentally changes. In this paper we develop (1) a global and local prediction algorithm that can handle these types of systems, (2) a method of switching between local and global prediction, and (3) a retouching method that tracks what predictions would have been if the underlying dynamics had not changed and uses these predictions when the underlying process reverts back to the original dynamics. The methodology is rooted in Koopman operator theory from dynamical systems. An advantage is that it is model-free, purely data-driven and adapts organically to changes in the system. While we showcase the algorithms on predicting the number of infected cases for COVID-19 and influenza cases, we emphasize that this is a general prediction methodology that has applications far outside of epidemiology.
Mortality reduction and cumulative excess incidence (CEI) in the prostate-specific antigen (PSA) screening era
Authors: McLaughlin Patrick W. , Cousins Matthew M. , Tsodikov Alex , Soni Payal D. , Crook Juanita M.
Published: March 2024

The extent to which PSA screening is related to prostate cancer mortality reduction in the United States (US) is controversial. US Surveillance, Epidemiology, and End Results Program (SEER) data from 1980 to 2016 were examined to assess the relationship between prostate cancer mortality and cumulative excess incidence (CEI) in the PSA screening era and to clarify the impact of race on this relationship. CEI was considered as a surrogate for the intensity of prostate cancer screening with PSA testing and subsequent biopsy as appropriate. Data from 163,982,733 person-years diagnosed with 544,058 prostate cancers (9 registries, 9% of US population) were examined. Strong inverse linear relationships were noted between CEI and prostate cancer mortality, and 317,356 prostate cancer deaths were avoided. Eight regions of the US demonstrated prostate cancer mortality reduction of 46.0–63.7%. On a per population basis, the lives of more black men than white men were saved in three of four registries with sufficient black populations for comparison. Factor(s) independent of CEI (potential effects of treatment advances) explained 14.6% of the mortality benefit (p-value = 0.3357) while there was a significant main effect of CEI (effect = −0.0064; CI: [−0.0088, −0.0040]; p-value < 0.0001). Therefore, there is a strong relationship between CEI and prostate cancer mortality reduction that was not related to factors independent of screening utilization. Minority populations have experienced large mortality reductions in the context of PSA mass utilization.
Classical cannabinoid receptors as target in cancer-induced bone pain: a systematic review, meta-analysis and bioinformatics validation
Authors: Zeng Feier , Wade Abbie , Harbert Kade , Patel Shrina , Holley Joshua S. , Dehghanpuor Cornelia K. , Hopwood Thomas , Marino Silvia , Sophocleous Antonia , Idris Aymen I.
Published: March 2024

To test the hypothesis that genetic and pharmacological modulation of the classical cannabinoid type 1 (CB1) and 2 (CB2) receptors attenuate cancer-induced bone pain, we searched Medline, Web of Science and Scopus for relevant skeletal and non-skeletal cancer studies from inception to July 28, 2022. We identified 29 animal and 35 human studies. In mice, a meta-analysis of pooled studies showed that treatment of osteolysis-bearing males with the endocannabinoids AEA and 2-AG (mean difference [MD] − 24.83, 95% confidence interval [95%CI] − 34.89, − 14.76, p < 0.00001) or the synthetic cannabinoid (CB) agonists ACPA, WIN55,212-2, CP55,940 (CB1/2-non-selective) and AM1241 (CB2-selective) (MD − 28.73, 95%CI − 45.43, − 12.02, p = 0.0008) are associated with significant reduction in paw withdrawal frequency. Consistently, the synthetic agonists AM1241 and JWH015 (CB2-selective) increased paw withdrawal threshold (MD 0.89, 95%CI 0.79, 0.99, p < 0.00001), and ACEA (CB1-selective), AM1241 and JWH015 (CB2-selective) reduced spontaneous flinches (MD − 4.85, 95%CI − 6.74, − 2.96, p < 0. 00001) in osteolysis-bearing male mice. In rats, significant increase in paw withdrawal threshold is associated with the administration of ACEA and WIN55,212-2 (CB1/2-non-selective), JWH015 and AM1241 (CB2-selective) in osteolysis-bearing females (MD 8.18, 95%CI 6.14, 10.21, p < 0.00001), and treatment with AM1241 (CB2-selective) increased paw withdrawal thermal latency in males (mean difference [MD]: 3.94, 95%CI 2.13, 5.75, p < 0.0001), confirming the analgesic capabilities of CB1/2 ligands in rodents. In human, treatment of cancer patients with medical cannabis (standardized MD − 0.19, 95%CI − 0.35, − 0.02, p = 0.03) and the plant-derived delta-9-THC (20 mg) (MD 3.29, CI 2.24, 4.33, p < 0.00001) or its synthetic derivative NIB (4 mg) (MD 2.55, 95%CI 1.58, 3.51, p < 0.00001) are associated with reduction in pain intensity. Bioinformatics validation of KEGG, GO and MPO pathway, function and process enrichment analysis of mouse, rat and human data revealed that CB1 and CB2 receptors are enriched in a cocktail of nociceptive and sensory perception, inflammatory, immune-modulatory, and cancer pathways. Thus, we cautiously conclude that pharmacological modulators of CB1/2 receptors show promise in the treatment of cancer-induced bone pain, however further assessment of their effects on bone pain in genetically engineered animal models and cancer patients is warranted.
Hospitalizations for coronavirus disease 2019: an analysis of the occurrence waves
Authors: Garbin Juliana Rodrigues Tovar , Leite Franciéle Marabotti Costa , Dell’Antonio Cristiano Soares Silva , Dell’Antonio Larissa Soares , dos Santos Ana Paula Brioschi , Lopes-Júnior Luís Carlos
Published: March 2024

The pandemic has been characterized by several waves defined by viral strains responsible for the predominance of infections. We aimed to analyze the mean length of hospital stay for patients with COVID-19 during the first three waves of the pandemic and its distribution according to sociodemographic and clinical variables. This retrospective study used the notifications of patients hospitalized for COVID-19 in a Brazilian state during the period of the three waves of the disease as the data source. There were 13,910 hospitalizations for confirmed COVID-19 cases. The first wave was the longest, with 4101 (29.5%) hospitalizations, while the third, although shorter, had a higher number of hospitalized patients (N = 6960). The average length of stay in the hospital in all waves was associated with age groups up to 60 years old., elementary, high school and higher education, residents of the periurban area Regarding the presence of comorbidities, there was a statistically significant difference in the mean number of days of hospitalization among patients with chronic cardiovascular disease and obesity (P < 0.001). In conclusion, the COVID-19 pandemic has been distinctly revealed among the waves.
Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary
Authors: Papp Márton , Tóth Adrienn Gréta , Békési László , Farkas Róbert , Makrai László , Maróti Gergely , Solymosi Norbert
Published: March 2024

In Hungary, as part of a nationwide, climatically balanced survey for a next-generation sequencing-based study of the honey bee (Apis mellifera) gut microbiome, repeated sampling was carried out during the honey production season (March and May 2019). Among other findings, the presence of Apis mellifera filamentous virus (AmFV) was detected in all samples, some at very high levels. AmFV-derived reads were more abundant in the March samples than in the May samples. In March, a higher abundance of AmFV-originated reads was identified in samples collected from warmer areas compared to those collected from cooler areas. A lower proportion of AmFV-derived reads were identified in samples collected in March from the wetter areas than those collected from the drier areas. AmFV-read abundance in samples collected in May showed no significant differences between groups based on either environmental temperature or precipitation. The AmFV abundance correlated negatively with Bartonella apihabitans, Bartonella choladocola, and positively with Frischella perrara, Gilliamella apicola, Gilliamella sp. ESL0443, Lactobacillus apis, Lactobacillus kullabergensis, Lactobacillus sp. IBH004. De novo metagenome assembly of four samples resulted in almost the complete AmFV genome. According to phylogenetic analysis based on DNA polymerase, the Hungarian strains are closest to the strain CH-05 isolated in Switzerland.
Desert date seed extract-loaded chitosan nanoparticles ameliorate hyperglycemia and insulin deficiency through the reduction in oxidative stress and inflammation
Authors: Farid Alyaa , Ahmed Alaa , Alaa Olaya , Safwat Gehan
Published: March 2024

Plants represents a huge source of bioactive materials that have been used since the old times in the treatment of many diseases.Balanites aegyptiaca, known as desert date, has been used in treatment of fever, diabetes and bacterial infection. Desert dates contains a hard seed that resembles 50–60% of the fruit. The seed extract contains many fatty acids, amino acids and other bioactive materials that gives the extract its antioxidant and anti-inflammatory properties. The study aimed to useBalanitesseed extract-loaded chitosan nanoparticles (SeEx-C NPs) for the treatment of streptozotocin (STZ)-induced diabetes in male Sprague Dawley rats. Animals were divided into two main divisions (healthy and diabetic rats). Each division contained seven groups (5 rats/group): control untreated group I, SeEx treated group II and group III (10 and 20 mg/kg b.w., respectively), C NPs treated group IV and group V (10 and 20 mg/kg b.w., respectively) and SeEx-C NPs treated group VI and group VII (10 and 20 mg/kg b.w., respectively). The therapeutical effects of SeEx-C NPs were evaluated through biochemical and immunological assessments in rats’ pancreases. The results showed that SeEx-C NPs (10 and 20 mg/kg b.w.) reduced the oxidative stress and inflammation in rats’ pancreases allowing the islets neogenesis. The loading of SeEx on C NPs allowed the delivery of fatty acids (oleic, lauric and myristic acid), amino acids (lysine, leucine, phenylalanine and valine) and minerals to pancreatic beta-cells in a sustainable manner. SeEx-C NPs administration successfully increased insulin secretion, allowed pancreatic islets neogenesis and reduced oxidative stress and inflammation.