bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets
Authors: Wang Xueqin , Xiong Tao , Wang Yiying , Zhang Xinru , Sun Miao
Published: January 2024

Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization target enrichment sequencing (Hyb-seq) is innovative and flexible, and then HTS strategy is widely adopted in phylogenomics. The universal Angiosperms353 probe sets (Angiosperms353) are instrumental in Hyb-seq and have been witnessed increased application in recent years. This review integrates numerous publications and empirical datasets to comprehensively assess the potential applications of Angiosperms353. Through evaluations using 18-taxa and 343-taxa genomic datasets, this review explores potential factors influencing Angiosperms353 gene capture. The RNA-seq strategy yielded the highest number of Angiosperms353 genes, followed by whole-genome sequencing and genome skimming. Increased sequencing depth enhanced gene capture yields, and no evident bias was observed across all tested angiosperm groups. In the genomics era with extensive HTS data, this review provides comprehensive guidelines for the practical application of Angiosperms353, promoting resource recycling and maximizing genomic data sharing and utilization.
Number Concepts
Authors: Samuels Richard , Snyder Eric
Published: January 2024

This Element, written for researchers and students in philosophy and the behavioral sciences, reviews and critically assesses extant work on number concepts in developmental psychology and cognitive science. It has four main aims. First, it characterizes the core commitments of mainstream number cognition research, including the commitment to representationalism, the hypothesis that there exist certain number-specific cognitive systems, and the key milestones in the development of number cognition. Second, it provides a taxonomy of influential views within mainstream number cognition research, along with the central challenges these views face. Third, it identifies and critically assesses a series of core philosophical assumptions often adopted by number cognition researchers. Finally, the Element articulates and defends a novel version of pluralism about number concepts.
Middle Ohio Valley Maize Histories: New Dates from the Crossroads of the Midcontinent
Authors: Comstock Aaron R. , Cook Robert A.
Published: January 2024

The transition to maize agriculture frames important cultural shifts in the Eastern Woodlands. However, the tempo and mode of this transition are unclear, particularly when analytical techniques are not standard across the region. In this article, we present evidence of directly dated maize macrobotanical fragments from the Turpin site in southwest Ohio that date between cal AD 552–649 and 684–994. These dates add to current dialogues on the spread of maize in the American Midcontinent and help further situate the Middle Ohio Valley as a cultural crossroads through which people and ideas flowed. We echo suggestions that, to refine our understanding of the introduction of maize into the region, we must develop pan-regional analytical standards and create multiple working hypotheses at a variety of scales.
THE PENTAGON AS A SUBSTRUCTURE LATTICE OF MODELS OF PEANO ARITHMETIC
Authors: SCHMERL JAMES H.
Published: January 2024

Wilkie proved in 1977 that every countable model

${\mathcal M}$

of Peano Arithmetic has an elementary end extension

${\mathcal N}$

such that the interstructure lattice

$\operatorname {\mathrm {Lt}}({\mathcal N} / {\mathcal M})$

is the pentagon lattice

${\mathbf N}_5$

. This theorem implies that every countable nonstandard

${\mathcal M}$

has an elementary cofinal extension

${\mathcal N}$

such that

$\operatorname {\mathrm {Lt}}({\mathcal N} / {\mathcal M}) \cong {\mathbf N}_5$

. It is proved here that whenever

${\mathcal M} \prec {\mathcal N} \models \mathsf {PA}$

and

$\operatorname {\mathrm {Lt}}({\mathcal N} / {\mathcal M}) \cong {\mathbf N}_5$

, then

${\mathcal N}$

must be either an end or a cofinal extension of

${\mathcal M}$

. In contrast, there are

${\mathcal M}^* \prec {\mathcal N}^* \models \mathsf {PA}^*$

such that

$\operatorname {\mathrm {Lt}}({\mathcal N}^* / {\mathcal M}^*) \cong {\mathbf N}_5$

and

${\mathcal N}^*$

is neither an end nor a cofinal extension of

${\mathcal M}^*$

.
Two Philosophical Issues Surrounding the Structure of Public-Policy Recommendations
Authors: Daoust Marc-Kevin , Babin Victor
Published: January 2024

One of the key responsibilities of public institutions in liberal democracies is to formulate recommendations for decision makers. However, public institutions realize that decision makers will often partly ignore their recommendations. This situation of “partial compliance” with recommendations raises a number of philosophical issues for institutions. Based on an analysis of 570 recommendations drawn from 40 Quebec public-sector documents and reports, we identify two issues surrounding the structure of public-policy recommendations.
The dynamical analysis of a nonlocal predator–prey model with cannibalism
Authors: Duan Daifeng , Niu Ben , Wei Junjie , Yuan Yuan
Published: January 2024

Cannibalism is often an extreme interaction in the animal species to quell competition for limited resources. To model this critical factor, we improve the predator–prey model with nonlocal competition effect by incorporating the cannibalism term, and different kernels for competition are considered in this model numerically. We give the critical conditions leading to the double Hopf bifurcation, in which the gestation time delay and the diffusion coefficient were selected as the bifurcation parameters. The innovation of the work lies near the double Hopf bifurcation point, and the stable homogeneous and inhomogeneous periodic solutions can coexist. The theoretical results of the extended centre manifold reduction and normal form method are in good agreement with the numerical simulation.
Rare cardiac tumour-nodular fasciitis
Authors: Ballal Natraj , Haryadi Neehar , Reyes Karl
Published: January 2024

Left ventricular tumour is a rare condition in children. The causes include vegetations, thrombus, and fibroma. 2-year-old asymptomatic female presented with an innocent heart murmur at 6 months of age. Subsequent follow-ups at 18 months of age showed left ventricular mass. Surgical pathology revealed “nodular fasciitis.” This type of tumour has never been described in the heart before.
Cross‐Shelf Carbon Transport in the East China Sea and Its Future Trend Under Global Warming
Authors: Hao Jiajia , Yuan Dongliang , He Lei , Yuan Huamao , Su Jian , Pohlmann Thomas , Ran Xiangbin
Published: January 2024

The cross‐shelf carbon transports across a section along the 100 m isobath from Taiwan to Cheju are estimated based on carbon concentration observations and ocean currents simulated by a regionally zoomed ocean‐atmosphere coupled model. Results show that the net cross‐shelf particulate organic carbon, dissolved organic carbon, and dissolved inorganic carbon transports are in the offshore direction at 1.81 ± 0.22, 51.8 ± 2.85, and 783 ± 58.9 TgC yr−1, respectively, which are high in spring and summer and low in winter and fall following the seasonality of the offshore volume transport. The carbon is transported into the East China Sea (ECS) mainly by the Taiwan Warm Current and the Yellow Sea Warm Current, whereas they are carried out of the ECS mainly by the East China Sea Current extension and the recirculation north of Taiwan. Assuming steady biological activity, future net total organic carbon transports are projected to increase by 5%∼19% offshore at the end of the 21st century, with the maximum increase in winter, in a high greenhouse gas emission scenario of RCP8.5. The increased carbon transports are due to the increased offshore volume transport, transferring more carbon‐rich coastal water away from the shelf in the warming future than at present. The results quantify cross‐shelf carbon burial in the ECS in the background of global warming.
Modification of Microphysical Parameterization Schemes and Their Application in the Simulation of an Extremely Heavy Rainfall Event in Zhengzhou
Authors: Yin Lei , Ping Fan , Cheng Rui , Mao Jiahua
Published: January 2024

In the present study, the Morrison and Thompson microphysics schemes in the Weather Research and Forecasting model were improved and used to simulate a record‐breaking heavy rainfall event occurred in Henan Province over central China during 19–21 July 2021. In the modified schemes, the terminal velocity of graupel and initial cloud droplet concentration were adjusted based on sensitivity tests. Results showed that the modified Morrison scheme (MORR_MOD) better captured the spatial distribution and temporal evolution of precipitation than the original scheme (MORR). Specifically, it produced a 40‐hr cumulative rainfall amount of 963 mm and an extreme hourly rainfall rate of 157.7 mm, which were closer to observations than MORR. Analysis of the dynamic and microphysical structures of the extreme‐rain‐producing convective clusters revealed that MORR_MOD predicted stronger updrafts, higher rain mass content and larger mean mass diameter of raindrops than MORR. By analyzing the tendencies of rain mass and number concentration, it was found that MORR_MOD predicted stronger accretion rates of cloud droplets by rain and weaker auto‐conversion rates of cloud droplets than MORR, which contributed to the high rain mixing ratio and low number concentration, respectively. In addition, MORR_MOD predicted stronger diabatic heating rates than MORR, which were primarily attributed to stronger condensation of water vapor, and may have been the reason why MORR_MOD simulated stronger updrafts.
Dune Geometry and the Associated Hydraulic Roughness in the Fluvial to Tidal Transition Zone of the Fraser River at Low River Flow
Authors: de Lange S. I. , Bradley R. , Schrijvershof R. A. , Murphy D. , Waldschläger K. , Kostaschuk R. , Venditti J. G. , Hoitink A. J. F.
Published: January 2024

In deltas and estuaries throughout the world, a fluvial‐to‐tidal transition zone (FTTZ) exists where both the river discharge and the tidal motion drive the flow. It is unclear how dune characteristics are impacted by changes in tidal flow strength, and how this is reflected in the hydraulic roughness. To understand dune geometry and variability in the FTTZ and possible impacts on hydraulic roughness, we assess dune variability from multibeam bathymetric surveys, and we use a calibrated 2D hydrodynamic model (Delft3D‐FM) of a sand‐bedded lowland river (Fraser River, Canada). We focus on a period of low river discharge during which tidal impact is strong. We find that the fluvial‐tidal to tidal regime change is not directly reflected in dune height, but local patterns of increasing and decreasing dune height are present. The fluvial‐to‐tidal regime change is reflected in dune shape, where dunes have lower leeside angles and are more symmetrical in the tidal regime. The calibrated model allows to estimate local patterns of dune heights using tidally averaged values of bed shear stress. However, the spatially variable dune morphology hampers local dune height estimation. Changes in dune shape do not significantly impact the reach‐scale roughness, and estimated dune roughness using dune height and length is similar to the dune roughness inferred from model calibration. Hydraulic model performance with a calibrated, constant roughness is not improved by implementing dune‐derived bed roughness. Instead, the data analysis revealed that large‐scale river morphology may explain differences in model roughness and corresponding estimates from dune predictors.
RUNX1/NPM1/H3K4me3 complex contributes to extracellular matrix remodeling via enhancing FOSL2 transcriptional activation in glioblastoma
Authors: Cui Xiaoteng , Huo Dawei , Wang Qixue , Wang Yunfei , Liu Xiaomin , Zhao Kai , You Yongping , Zhang Junxia , Kang Chunsheng
Published: January 2024

Extracellular matrix (ECM) remodeling has been implicated in the tumor malignant progression and immune escape in glioblastoma (GBM). Runt-related transcription factor 1 (RUNX1) is a vital transcriptional factor for promoting tumorigenesis and invasion in mesenchymal subtype of GBM. But the correlation between RUNX1 and ECM genes expression and regulatory mechanism of RUNX1 on ECM genes expression remain poorly understood to date. In this study, by using integral analysis of chromatin immunoprecipitation-sequencing and RNA sequencing, we reported that RUNX1 positively regulated the expression of various ECM-related genes, including Fibronectin 1 (FN1), Collagen type IV alpha 1 chain (COL4A1), and Lumican (LUM), in GBM. Mechanistically, we demonstrated that RUNX1 interacted with Nucleophosmin 1 (NPM1) to maintain the chromatin accessibility and facilitate FOS Like 2, AP-1 Transcription Factor Subunit (FOSL2)-mediated transcriptional activation of ECM-related genes, which was independent of RUNX1’s transcriptional function. ECM remodeling driven by RUNX1 promoted immunosuppressive microenvironment in GBM. In conclusion, this study provides a novel mechanism of RUNX1 binding to NPM1 in driving the ECM remodeling and GBM progression.
Id2 epigenetically controls CD8+ T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex
Authors: Li Yiming , Han Mingwei , Wei Haolin , Huang Wan , Chen Zhinan , Zhang Tianjiao , Qian Meirui , Jing Lin , Nan Gang , Sun Xiuxuan , Dai Shuhui , Wang Kun , Jiang Jianli , Zhu Ping , Chen Liang
Published: January 2024

CD8+ T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6+ progenitor exhausted (Texprog) and Tim-3+ terminally exhausted (Texterm) subpopulations. Inhibitor of DNA binding protein 2 (Id2) has been shown to play important roles in T-cell development and CD8+ T-cell immunity. However, the role of Id2 in CD8+ T-cell exhaustion is unclear. Here, we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm cells. Genetic deletion of Id2 dampens CD8+ T-cell-mediated immune responses and the maintenance of stem-like CD8+ T-cell subpopulations, suppresses PD-1 blockade and increases tumor susceptibility. Mechanistically, through its HLH domain, Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex, and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase LSD1. Therefore, Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter, modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+ Texprog cells. An LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing mice. Inhibition of LSD1 increases the abundance of Slamf6+Tim-3− Texprog cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+ T cells. This study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8+ T-cell exhaustion, and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.
IMA peptides regulate root nodulation and nitrogen homeostasis by providing iron according to internal nitrogen status
Authors: Ito Momoyo , Tajima Yuri , Ogawa-Ohnishi Mari , Nishida Hanna , Nosaki Shohei , Noda Momona , Sotta Naoyuki , Kawade Kensuke , Kamiya Takehiro , Fujiwara Toru , Matsubayashi Yoshikatsu , Suzaki Takuya
Published: January 2024

Legumes control root nodule symbiosis (RNS) in response to environmental nitrogen availability. Despite the recent understanding of the molecular basis of external nitrate-mediated control of RNS, it remains mostly elusive how plants regulate physiological processes depending on internal nitrogen status. In addition, iron (Fe) acts as an essential element that enables symbiotic nitrogen fixation; however, the mechanism of Fe accumulation in nodules is poorly understood. Here, we focus on the transcriptome in response to internal nitrogen status during RNS in Lotus japonicus and identify that IRON MAN (IMA) peptide genes are expressed during symbiotic nitrogen fixation. We show that LjIMA1 and LjIMA2 expressed in the shoot and root play systemic and local roles in concentrating internal Fe to the nodule. Furthermore, IMA peptides have conserved roles in regulating nitrogen homeostasis by adjusting nitrogen-Fe balance in L. japonicus and Arabidopsis thaliana. These findings indicate that IMA-mediated Fe provision plays an essential role in regulating nitrogen-related physiological processes.
Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction
Authors: Sun Haofan , Fu Bin , Qian Xiaohong , Xu Ping , Qin Weijie
Published: January 2024

The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies
Authors: Medina-Munoz Hugo C. , Kofman Eric , Jagannatha Pratibha , Boyle Evan A. , Yu Tao , Jones Krysten L. , Mueller Jasmine R. , Lykins Grace D. , Doudna Andrew T. , Park Samuel S. , Blue Steven M. , Ranzau Brodie L. , Kohli Rahul M. , Komor Alexis C. , Yeo Gene W.
Published: January 2024

RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
Strain-restricted transfer of ferromagnetic electrodes for constructing reproducibly superior-quality spintronic devices
Authors: Guo Lidan , Gu Xianrong , Hu Shunhua , Sun Wenchao , Zhang Rui , Qin Yang , Meng Ke , Lu Xiangqian , Liu Yayun , Wang Jiaxing , Ma Peijie , Zhang Cheng , Guo Ankang , Yang Tingting , Yang Xueli , Wang Guorui , Liu Yaling , Wang Kai , Mi Wenbo , Zhang Chuang , Jiang Lang , Liu Luqi , Zheng Kun , Qin Wei , Yan Wenjing , Sun Xiangnan
Published: January 2024

Spintronic device is the fundamental platform for spin-related academic and practical studies. However, conventional techniques with energetic deposition or boorish transfer of ferromagnetic metal inevitably introduce uncontrollable damage and undesired contamination in various spin-transport-channel materials, leading to partially attenuated and widely distributed spintronic device performances. These issues will eventually confuse the conclusions of academic studies and limit the practical applications of spintronics. Here we propose a polymer-assistant strain-restricted transfer technique that allows perfectly transferring the pre-patterned ferromagnetic electrodes onto channel materials without any damage and change on the properties of magnetism, interface, and channel. This technique is found productive for pursuing superior-quality spintronic devices with high controllability and reproducibility. It can also apply to various-kind (organic, inorganic, organic-inorganic hybrid, or carbon-based) and diverse-morphology (smooth, rough, even discontinuous) channel materials. This technique can be very useful for reliable device construction and will facilitate the technological transition of spintronic study.
Accurate additive manufacturing of lightweight and elastic carbons using plastic precursors
Authors: Smith Paul , Hu Jiayue , Griffin Anthony , Robertson Mark , Güillen Obando Alejandro , Bounds Ethan , Dunn Carmen B. , Ye Changhuai , Liu Ling , Qiang Zhe
Published: January 2024

Despite groundbreaking advances in the additive manufacturing of polymers, metals, and ceramics, scaled and accurate production of structured carbons remains largely underdeveloped. This work reports a simple method to produce complex carbon materials with very low dimensional shrinkage from printed to carbonized state (less than 4%), using commercially available polypropylene precursors and a fused filament fabrication-based process. The control of macrostructural retention is enabled by the inclusion of fiber fillers regardless of the crosslinking degree of the polypropylene matrix, providing a significant advantage to directly control the density, porosity, and mechanical properties of 3D printed carbons. Using the same printed plastic precursors, different mechanical responses of derived carbons can be obtained, notably from stiff to highly compressible. This report harnesses the power of additive manufacturing for producing carbons with accurately controlled structure and properties, while enabling great opportunities for various applications.
Defect passivation in methylammonium/bromine free inverted perovskite solar cells using charge-modulated molecular bonding
Authors: Khadka Dhruba B. , Shirai Yasuhiro , Yanagida Masatoshi , Ota Hitoshi , Lyalin Andrey , Taketsugu Tetsuya , Miyano Kenjiro
Published: January 2024

Molecular passivation is a prominent approach for improving the performance and operation stability of halide perovskite solar cells (HPSCs). Herein, we reveal discernible effects of diammonium molecules with either an aryl or alkyl core onto Methylammonium-free perovskites. Piperazine dihydriodide (PZDI), characterized by an alkyl core-electron cloud-rich-NH terminal, proves effective in mitigating surface and bulk defects and modifying surface chemistry or interfacial energy band, ultimately leading to improved carrier extraction. Benefiting from superior PZDI passivation, the device achieves an impressive efficiency of 23.17% (area ~1 cm2) (low open circuit voltage deficit ~0.327 V) along with superior operational stability. We achieve a certified efficiency of ~21.47% (area ~1.024 cm2) for inverted HPSC. PZDI strengthens adhesion to the perovskite via -NH2I and Mulliken charge distribution. Device analysis corroborates that stronger bonding interaction attenuates the defect densities and suppresses ion migration. This work underscores the crucial role of bifunctional molecules with stronger surface adsorption in defect mitigation, setting the stage for the design of charge-regulated molecular passivation to enhance the performance and stability of HPSC.
Nanoscale visualization and spectral fingerprints of the charge order in ScV6Sn6 distinct from other kagome metals
Authors: Cheng Siyu , Ren Zheng , Li Hong , Oh Ji Seop , Tan Hengxin , Pokharel Ganesh , DeStefano Jonathan M. , Rosenberg Elliott , Guo Yucheng , Zhang Yichen , Yue Ziqin , Lee Yongbin , Gorovikov Sergey , Zonno Marta , Hashimoto Makoto , Lu Donghui , Ke Liqin , Mazzola Federico , Kono Junichiro , Birgeneau R. J. , Chu Jiun-Haw , Wilson Stephen D. , Wang Ziqiang , Yan Binghai , Yi Ming , Zeljkovic Ilija
Published: January 2024

Charge density waves (CDWs) in kagome metals have been tied to many exotic phenomena. Here, using spectroscopic-imaging scanning tunneling microscopy and angle-resolved photoemission spectroscopy, we study the charge order in kagome metal ScV6Sn6. The similarity of electronic band structures of ScV6Sn6 and TbV6Sn6 (where charge ordering is absent) suggests that charge ordering in ScV6Sn6 is unlikely to be primarily driven by Fermi surface nesting of the Van Hove singularities. In contrast to the CDW state of cousin kagome metals, we find no evidence supporting rotation symmetry breaking. Differential conductance dI/dV spectra show a partial gap Δ1CO ≈ 20 meV at the Fermi level. Interestingly, dI/dV maps reveal that charge modulations exhibit an abrupt phase shift as a function of energy at energy much higher than Δ1CO, which we attribute to another spectral gap. Our experiments reveal a distinctive nature of the charge order in ScV6Sn6 with fundamental differences compared to other kagome metals.
An architecture for collaboration in systems biology at the age of the Metaverse
Authors: Jacopin Eliott , Sakamoto Yuki , Nishida Kozo , Kaizu Kazunari , Takahashi Koichi
Published: January 2024

As the current state of the Metaverse is largely driven by corporate interests, which may not align with scientific goals and values, academia should play a more active role in its development. Here, we present the challenges and solutions for building a Metaverse that supports systems biology research and collaboration. Our solution consists of two components: Kosmogora, a server ensuring biological data access, traceability, and integrity in the context of a highly collaborative environment such as a metaverse; and ECellDive, a virtual reality application to explore, interact, and build upon the data managed by Kosmogora. We illustrate the synergy between the two components by visualizing a metabolic network and its flux balance analysis. We also argue that the Metaverse of systems biology will foster closer communication and cooperation between experimentalists and modelers in the field.
Geographical location influence ‘Cabernet Franc’ fruit quality in Shandong province
Authors: Wang Chaoping , Chen Xueqin , Ren Yanhua , Xuan Xuxian , Pervaiz Tariq , Shangguan Lingfei , Fang Jinggui
Published: January 2024

Grape quality is a key factor in determining wine quality, and it depends not only on management skills, but also on the geographic location of the producing area. In China, Shandong is the province with the largest wine production, and ‘Cabernet Franc’ is widely planted. This study evaluated the ‘Cabernet Franc’ fruit quality in relation to geographical conditions in five ‘Cabernet Franc’ producing districts of Shandong province, China, including Dezhou Aodeman Winery (DZ), Tai’an Zhongqingsongshi Winery (TA), Penglai Longhu Winery (PL), Rushan Taiyihu Winery (RS), and Rizhao Taiyangcheng Winery (RZ). At the time of veraison and maturity, fruit was harvested from five areas, and compared for cosmetic and internal fruit quality. The soluble sugar content in the Rizhao area was rich, and the weight and volume of single fruit were relatively large. The titratable acid of the berries in Tai'an area was high. RNA-seq analysis showed that the number of genes in the véraison stage was 19,571–20,750, and the number of genes in the mature stage was 19,176–20,735. The analysis found that areas with multiple high-quality characteristics tended to have more DEGs (differential expressed genes). And the DEGs in different areas were mainly distributed on chromosome 7, and at least on chromosome 15. DEGs in 5 areas were enriched on 855 GO terms and 116 KEGG pathways during berries development. Among them, it was found that the up/down-regulation of DEGs was related to the formation of berry quality, which helps to explain the impact of environment on grape quality components. In summary, this study is helpful to understand the influence of cultivation location on the quality of 'Cabernet Franc' in different production areas in Shandong province, and further provide a reference for the production of high-quality wine grapes and winemaking.
Assessing perceptual chromatic equiluminance using a reflexive pupillary response
Authors: Liu Ye , Mahony Bridget W. , Wang Xiaochun , Daye Pierre M. , Wang Wei , Cavanagh Patrick , Pouget Pierre , Andolina Ian Max
Published: January 2024

Equiluminant stimuli help assess the integrity of colour perception and the relationship of colour to other visual features. As a result of individual variation, it is necessary to calibrate experimental visual stimuli to suit each individual’s unique equiluminant ratio. Most traditional methods rely on training observers to report their subjective equiluminance point. Such paradigms cannot easily be implemented on pre-verbal or non-verbal observers. Here, we present a novel Pupil Frequency-Tagging Method (PFTM) for detecting a participant’s unique equiluminance point without verbal instruction and with minimal training. PFTM analyses reflexive pupil oscillations induced by slow (< 2 Hz) temporal alternations between coloured stimuli. Two equiluminant stimuli will induce a similar pupil dilation response regardless of colour; therefore, an observer’s equiluminant point can be identified as the luminance ratio between two colours for which the oscillatory amplitude of the pupil at the tagged frequency is minimal. We compared pupillometry-based equiluminance ratios to those obtained with two established techniques in humans: minimum flicker and minimum motion. In addition, we estimated the equiluminance point in non-human primates, demonstrating that this new technique can be successfully employed in non-verbal subjects.
A cost-effective RNA extraction and RT-qPCR approach to detect California serogroup viruses from pooled mosquito samples
Authors: Avramov Marc , Gallo Vanessa , Gross Antonia , Lapen David R. , Ludwig Antoinette , Cullingham Catherine I.
Published: January 2024

Mosquito-borne diseases pose ongoing global health concerns, demanding more cost-efficient methods to detect pathogens to support enhanced surveillance efforts. This study introduces an adapted TRIzol-based high-throughput RNA extraction protocol, tailored for the detection of California serogroup viruses in pooled mosquito samples in a rapid and cost-effective manner. This approach provided consistent RNA yields and sensitive viral detection relative to two commercial extraction kits (QIAGEN RNeasy Mini Kit and MACHEREY–NAGEL NucleoSpin RNA Plus Kit). The incorporation of a user-friendly and non-spiking-based RT-qPCR internal control designed for the 18S rRNA gene in mosquitoes minimizes potential false positives/negatives, improving the fidelity of viral detection outcomes. Effective RNA yields, purity, and successful target amplification across 25 mosquito species and varied pool sizes (1–50 mosquitoes per tube) affirm the reliability of our approach. The extraction method is cost-effective, with an incurred cost of $0.58 CAD per sample, in contrast to the $5.25 CAD cost per sample of the two kits, rendering it promising for mosquito-borne disease surveillance initiatives.
Impact of pre-existing mental health diagnoses on development of post-COVID and related symptoms: a claims data-based cohort study
Authors: Greißel Anna , Schneider Antonius , Donnachie Ewan , Gerlach Roman , Tauscher Martin , Hapfelmeier Alexander
Published: January 2024

This study aimed to examine the association of prior mental health diagnoses with the onset of Post-COVID-19 condition (PCC). We conducted a retrospective comparative cohort study and secondary analysis of routinely collected claims data from participants in statutory health insurance in Bavaria, Germany, from January 2015 to June 2022. Study participants were 619,560 patients with confirmed COVID-19, 42,969 with other respiratory tract infection (ORI), and 438,023 controls. Using diagnoses coded according to the German modification of the ICD-10, the associations between prior mental health diagnoses and a PCC diagnosis (primary outcome) or associated symptoms (secondary outcomes) were estimated using multiple Cox proportional hazards regression models. Mental disorders (hazard ratio [HR] 1.36, 95% confidence interval [CI] 1.30–1.42), anxiety (HR 1.14, 95% CI 1.07–1.20), depression (HR 1.25, 95% CI 1.19–1.30) and somatoform disorders (HR 1.30, 95% CI 1.24–1.36) were associated with higher risks for PCC. Mental disorders were associated with the same or even greater risk for a diagnosis of malaise and fatigue in the control cohort (HR 1.71, 95% CI 1.52–1.93) and ORI cohort (HR 1.43, 95% CI 1.20–1.72), than in the COVID-19 cohort (HR 1.43, 95% CI 1.35–1.51). In summary, prior mental comorbidity was associated with an increased risk of PCC and its associated symptoms in all cohorts, not specifically in COVID-19 patients.
Efficient photocatalytic degradation of textile dye pollutants using thermally exfoliated graphitic carbon nitride (TE–g–C3N4)
Authors: Ganesan Selvaganapathy , Kokulnathan Thangavelu , Sumathi Shanmugam , Palaniappan Arunkumar
Published: January 2024

Graphitic carbon nitride (g–C3N4), an organic photocatalyst was reported to have beneficial properties to be used in wastewater treatment applications. However, g–C3N4, in its bulk form was found to have poor photocatalytic degradation efficiency due to its inherent limitations such as poor specific surface area and fast electron–hole pair recombination rate. In this study, we have tuned the physiochemical properties of bulk g–C3N4 by direct thermal exfoliation (TE–g–C3N4) and examined their photocatalytic degradation efficiency against abundant textile dyes such as methylene blue (MB), methyl orange (MO), and rhodamine B (RhB). The degradation efficiencies for MB, MO, and RhB dyes are 92 ± 0.18%, 93 ± 0.31%, and 95 ± 0.4% respectively in 60 min of UV light irradiation. The degradation efficiency increased with an increase in the exfoliation temperature. The prepared catalysts were characterized using FTIR, XRD, FE-SEM, EDAX, BET, and UV-DRS. In BET analysis, TE–g–C3N4 samples showed improved surface area (48.20 m2/g) when compared to the bulk g–C3N4 (5.03 m2/g). Further, the TE–g–C3N4 had 2.98 times higher adsorption efficiency than the bulk ones. The free radicals scavenging studies revealed that the superoxide radicals played an important role in the photodegradation for dyes, when compared to the hydroxyl radical (.OH) and the photo-induced holes (h+), Photoluminescence (PL) emission and electrochemical impedance spectroscopy (EIS) spectra of TE–g–C3N4 indicated a lowered electron–hole pairs’ recombination rate and an increased photo-induced charge transfer respectively. Further, the TE–g–C3N4 were found to have excellent stability for up to 5 cycles with only a minor decrease in the activity from 92% to 86.2%. These findings proved that TE–g–C3N4 was an excellent photocatalyst for the removal and degradation of textile dyes from wastewater.
Heparin enables the reliable detection of endotoxin in human serum samples using the Limulus amebocyte lysate assay
Authors: Harm Stephan , Schildböck Claudia , Cont Denisa , Weber Viktoria
Published: January 2024

The determination of lipopolysaccharide (endotoxin) in serum or plasma samples using Limulus amebocyte lysate (LAL)-based assays is currently not sufficiently reliable in clinical diagnostics due to numerous interfering factors that strongly reduce the recovery of LPS in clinical samples. The specific plasma components responsible for the endotoxin neutralizing capacity of human blood remain to be identified. There are indications that certain endotoxin-neutralizing proteins or peptides, which are part of the host defense peptides/proteins of the innate immune system may be responsible for this effect. Based on our finding that several antimicrobial peptides can be neutralized by the polyanion heparin, we developed a heparin-containing diluent for serum and plasma samples, which enables reliable quantification of LPS measurement in clinical samples using the LAL assay. In a preclinical study involving 40 donors, this improved protocol yielded an over eightfold increase in LPS recovery in serum samples, as compared to the standard protocol. This modified protocol of sample pretreatment could make LPS measurement a valuable tool in medical diagnostics.
Exploring the apoptotic effects of sericin on HCT116 cells through comprehensive nanostring transcriptomics and proteomics analysis
Authors: Ratanabunyong Siriluk , Siriwaseree Jeeraprapa , Wanaragthai Panatda , Krobthong Sucheewin , Yingchutrakul Yodying , Kuaprasert Buabarn , Choowongkomon Kiattawee , Aramwit Pornanong
Published: January 2024

Sericin, a silk protein from Bombyx mori (silkworms), has many applications, including cosmetics, anti-inflammation, and anti-cancer. Sericin complexes with nanoparticles have shown promise for breast cancer cell lines. Apoptosis, a programmed cell death mechanism, stops cancer cell growth. This study found that Sericin urea extract significantly affected HCT116 cell viability (IC50 = 42.00 ± 0.002 µg/mL) and caused apoptosis in over 80% of treated cells. S-FTIR analysis showed significant changes in Sericin-treated cells' macromolecule composition, particularly in the lipid and nucleic acid areas, indicating major cellular modifications. A transcriptomics study found upregulation of the apoptotic signaling genes FASLG, TNFSF10, CASP3, CASP7, CASP8, and CASP10. Early apoptotic proteins also showed that BAD, AKT, CASP9, p53, and CASP8 were significantly upregulated. A proteomics study illuminated Sericin-treated cells' altered protein patterns. Our results show that Sericin activated the extrinsic apoptosis pathway via the caspase cascade (CASP8/10 and CASP3/7) and the death receptor pathway, involving TNFSF10 or FASLG, in HCT116 cells. Upregulation of p53 increases CASP8, which activates CASP3 and causes HCT116 cell death. This multi-omics study illuminates the molecular mechanisms of Sericin-induced apoptosis, sheds light on its potential cancer treatment applications, and helps us understand the complex relationship between silk-derived proteins and cellular processes.
Multiplexed rectangular dielectric gratings with multiple narrow-band refractive index filtering and sensing
Authors: Abudula Aibibula , Maitiaximu Paiziliya , Abulaiti Abulizi , Mohamedsedik Melike , Rahmut Arzigul , Xu Feng , Tuersun Paerhatijiang
Published: January 2024

We propose a low-loss compound structure consisting of a multiplexed rectangular dielectric grating and a waveguide layer, which can function as multi-band optical filters and sensors in TE and TM polarization by utilizing the resonant mode of the waveguide (WG) and the hybrid SP, respectively. By manipulating the parameters and subsequently constraining the local density of multi-resonant modes to several distinct resonant wavelengths, we propose a novel category of highly sensitive refractive index sensing platforms. Spectral shifts ranging from 110 to 131 nm/RIU with FOM of (22, 26.2)/RIU under TE polarization and 80 to 114 nm/RIU with FOM of (5.7, 8.1)/RIU under TM polarization can be accurately discerned for multiple individual analytes across a broad spectral range. The proposed structures offer enhanced flexibility in the design of structures across a wide spectral range, catering to various potential applications in multi-band optical filters, sensors, and photodetectors.
Construction and optimization of representative actual driving cycles based on the improved autoencoder
Authors: Zhao Zhichao , Sun Xilei , Wang Xun , Wang Yi , Fu Jianqin , Liu Jingping
Published: January 2024

In this study, much work has been performed to accurately and efficiently develop representative actual driving cycles. Electric vehicle road tests were conducted and the associated data were gathered based on the manual driving method, and the Changsha Driving Cycle Construction (CS-DCC) method was proposed to achieve systematical construction of a representative driving cycle from the original data. The results show that the refined data exhibit greater stability and a smoother pattern in contrast to the original data after noise reduction by five-scale wavelet analysis. The Gaussian Kernel Principal Component Analysis (KPCA) algorithm is chosen to reduce the dimensionality of the characteristic matrix, and the number of principal components is selected as 5 with a cumulative contribution rate of 85.99%. The average error of the characteristic parameters between the optimized drive cycle and the total data is further reduced from 13.6 to 6.1%, with a reduction ratio of 55.1%. Meanwhile, the constructed driving cycle has prominent local characteristics compared with four standard driving cycles, demonstrating the necessity of constructing an actual driving cycle that reflects localized driving patterns. The findings present a powerful application of artificial intelligence in advancing engineering technologies.
Effects of workbook training using editorials and newspaper articles in adults with preclinical stage of dementia
Authors: Jin Sora , Yoon Ji Hye , Na Duk L.
Published: January 2024

Early detection and intervention in individuals in the pre-clinical stage of dementia are crucial. This study aimed to examine whether there are significant differences in (1) word retrieval, (2) subjective communication ability, (3) intervention satisfaction through the 'Fill-in-the-blanks in editorial and newspaper articles' training in patients with subjective cognitive decline and mild cognitive impairment corresponding to the pre-clinical stage of dementia. Ninety-nine patients (50 in the intervention group and 49 in the control group) aged 50–84 years were administered pre- and post-test after 6 weeks of intervention (30 sessions). Regarding word retrieval, there were significant intervention effects on confrontation naming, semantic fluency, and phonemic fluency. The majority of participants in the intervention group were highly satisfied with the training. In terms of intervention satisfaction, the majority of the participants in the intervention group showed high satisfaction with all the questions. This result confirmed the improvement of word retrieval ability through mass communication content-based 'Fill-in-the-blanks' training, and ultimately helps to provide a clinical basis for applying this intervention to prevent dementia.
Analysis of soil fertility and toxic metal characteristics in open-pit mining areas in northern Shaanxi
Authors: Wang Na , Liu Zhe , Sun Yingying , Lu Nan , Luo Yuhu
Published: January 2024

The study specifically focused on the Hongliulin mining area, where a total of 40 soil samples were meticulously collected and analyzed from within a 1000 m radius extending from the tailings dam. The findings revealed that soil pH within the 0–1000 m range generally leaned towards the alkaline side. In terms of soil nutrient content, encompassing factors such as soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali nitrogen (AK), available phosphorus (AP), and quick-acting potassium (AK), the variations fell within the following ranges: 2.23–13.58 g/kg, 0.12–0.73 g/kg, 0.18–1.15 g/kg, 9.54–35.82 g/kg, 2.89–6.76 mg/kg, 3.45–11.25 mg/kg, and 5.86–130.9 mg/kg. Collectively, these values indicate relatively low levels of soil nutrients. Within the 0–500 m range of soil samples, the average concentrations of Cd, Hg, Pb, and As were 0.778, 0.198, 24.87, and 17.92 mg/kg, respectively. These concentrations exceeded the established soil background values of Shaanxi Province and emerged as the primary pollutants in the study area. Within this same range, the mean values of eight toxic metals (Pi) were ranked in the following descending order: 1.726 (Hg), 1.400 (As), 1.129 (Cr), 1.109 (Pb), 0.623 (Zn), 0.536 (Cd), 0.309 (Cu), and 0.289 (Ni). With the exception of Hg, As, Cr, and Pb, which exhibited slight pollution, the other toxic metals were found to be within acceptable pollution limits for this sampling range, in line with the results obtained using the geo-accumulation index method. The average potential ecological risk index for the eight toxic metals in the study area stood at 185.0, indicating a moderate overall pollution level. When assessing individual elements, the proportions of ecological risk attributed to Hg, As, Pb, and Cd were 34.57%, 27.44%, 25.11%, and 23.11%, respectively. This suggests that the primary potential ecological risk elements in the study area are Hg and As, followed by Cd and Pb. Notably, toxic metals Hg and Pb, as well as As and Pb, exhibited significant positive correlations within the sampling area, suggesting a common source. An analysis of the relationship between soil physicochemical properties and toxic metals indicated that soil pH, SOM, TN, and TP were closely linked to toxic metal concentrations. The toxic metal elements in the research area's soil exhibit moderate variability (0.16 < CV < 0.36) to high variability (CV > 0.36). Within the range of 0–200 m, the CV values for Cd and Hg exceed 1, indicating a high level of variability. The coefficient of variation for SOM, TP, AP, AK and TK is relatively high with the of 2.93, 2.36, 2.36, 21.01, 7.54. The soil in the sampling area has undergone significant disturbances due to human activities, resulting in toxic metal pollution and nutrient deficiencies.
Exploring the genotype-environment interaction of bread wheat in ambient and high-temperature planting conditions: a rigorous investigation
Authors: Khare Vikrant , Shukla Rama Shankar , Pandey Suneeta , Singh Sanjay Kumar , Singh Charan
Published: January 2024

The current study is carried out to find out the stable wheat genotype in ambient and high temperature planting conditions. The objective was to estimate the genotype x environment interactions through various univariates and multivariate techniques. Twenty wheat genotypes were evaluated at Jabalpur, Narmadapuram, and Sagar districts of Madhya Pradesh, India, across cropping years 2019–20 and 2021–21, considering both timely and late planting conditions. The univariate and multivariate stability analysis were performed based on per-plant grain yield and grain filling rate. Our result revealed that environment, genotype, and GEI effects were significant (P < 0.001) across all the environments. The wheat genotypes JW3288, L8, and L13 have been discerned as top performers, exhibiting remarkable stability in grain yield per plant. Similarly, for grain filling rate, genotypes L11 and L13 have emerged as superior and consistently stable performers. Notably, the AMMI and GGE models demonstrated superior effectiveness and accuracy compared to the linear regression model. In conclusion, based on thorough univariate and multivariate stability analyses, L13 emerges as the most stable genotype across all environments under both planting conditions. Consequently, L13 holds promise for inclusion in future breeding programs. It's noteworthy that Jabalpur stands out as the most discriminating and representative environment among all the conditions assessed.