bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of herbicide programs for the control of knotroot foxtail [Setaria parviflora (Poir.) Kerguélen] in bermudagrass pasture
Authors: Dyer Logan M. , Henry Gerald M. , McCullough Patrick E. , Belcher Jason , Basinger Nicholas T.
Published: January 2024

Knotroot foxtail has become more prevalent and problematic in pastures and hayfields in the southeastern United States. Gaps exist in our knowledge of which herbicide practices are best for managing this species in bermudagrass forage production. This study was conducted to determine the efficacy of various ways to control knotroot foxtail in bermudagrass with herbicide applications in autumn, postemergence (POST), with and without also applying a herbicide in preemergence (PRE), in spring. The study was a randomized complete block with a factorial arrangement of treatments and included a nontreated control for both fall and spring timings. Glyphosate at two rates (0.35 or 0.7 kg ae ha−1), nicosulfuron (0.07 kg ai ha−1) + metsulfuron (0.012 kg ai ha−1), and hexazinone (1.3 kg ai ha−1) were applied alone in the fall or followed by indaziflam (0.067 kg ai ha−1) or pendimethalin (4.46 kg ai ha−1) in the spring. Three harvests were conducted throughout the growing season to evaluate weed species (knotroot foxtail, large crabgrass, and horsenettle) and bermudagrass biomass as well as overall species composition. The combination of fall and spring treatments did not affect weed species or bermudagrass biomass. Therefore, treatment main effects were analyzed by fall or spring application timing. A spring application of either pendimethalin or indaziflam increased bermudagrass biomass compared with that of the nontreated control. However, neither PRE herbicide effectively reduced knotroot foxtail biomass compared with the nontreated control, although pendimethalin did reduce season-long knotroot foxtail composition. Spring PRE herbicides are an effective tool for forage producers, but further research is needed to identify effective herbicides and additional approaches for the control of knotroot foxtail.
Reply to Comment by Terence McCarthy and Marc Humphries on “Highly Contrasted Geochemical Pattern in Sediments of the Okavango Delta, Botswana Driven by Dust Supply, Hydrological Heritage and Biogeochemical Reactions”
Authors: Jolivet M. , Dauteuil O. , Dia A. , Davranche M. , Pierson‐Wickmann A.‐C. , Barrier L. , Murray‐Hudson M. , Mazrui N. , Marsac R. , Cheng Feng , Li Xiangzhong
Published: January 2024

In southern Africa, the Okavango Delta is a large alluvial fan sustaining a unique wetlands ecosystem in the heart of the Kalahari desert. The Delta is fed by an annual flood that brings water from the Angolan plateaus to the north, down to the Okavango region. The fan is characterized by vegetated, permanent or seasonal floodplains, dotted with thousands of sandy islands of various origin (inverted paleo‐channels, paleo‐dunes, meander bars, etc). On at least some of these islands, shallow groundwater is characterized by a high pH (>8) and a high concentration of metals and metalloids, making it naturally toxic. In the 1990s, McCarthy and co‐workers explain the chemistry of that water through an evapotranspiration model, the flood‐water being pumped by the vegetation toward the center of the islands and progressively enriched in elements by evapotranspiration. This model has been widely applied to all islands in the Okavango, not considering their individual specificities nor that of the surrounding floodplain. Our work, based on a multidisciplinary approach including sedimentology, mineralogy and geochemistry, and discussed by McCarthy and Humphries, questions the established model suggesting that the alkaline water cannot derive from simple concentration of the floodwater.
Eddy‐Induced Dispersion of Sea Ice Floes at the Marginal Ice Zone
Authors: Gupta Mukund , Gürcan Emma , Thompson Andrew F.
Published: January 2024

Ocean heat exchanges at the marginal ice zone (MIZ) play an important role in melting sea ice. Mixed‐layer eddies transport heat and ice floes across the MIZ, facilitating the pack's access to warm waters. This study explores these frontal dynamics using disk‐shaped floes coupled to an upper‐ocean model simulating the sea ice edge. Numerical experiments reveal that small floes respond more strongly to fine‐scale ocean currents, which favors higher dispersion rates and weakens sea ice drag onto the underlying ocean. Floes with radii smaller than resolved turbulent filaments (∼2–4 km) result in a wider and more energetic MIZ, by a factor of 70% each, compared to larger floes. We hypothesize that this floe size dependency may affect sea ice break‐up by controlling oceanic energy propagation into the MIZ and modulate the sea ice pack's melt rate by regulating lateral heat transport toward the sea ice cover.
Optimal Recovery of Rayleigh‐Wave Overtones by Multi‐Directional Acquisition
Authors: Lellouch A. , Shimony E. , Sinitsyn P.
Published: January 2024

Rayleigh waves are ubiquitously used for subsurface characterization through dispersion curve inversion, whose quality depends on the number of useable overtones. Traditional analysis is based on vertical receivers and, for active surveys, sources. However, for layered media, eigenfunction theory shows that optimal recovery of any given dispersion mode and frequency can be achieved by either vertical source‐vertical receiver or radial source‐radial receiver configurations, with source directivity being more dominant. Multi‐directional near‐surface wave‐equation modeling and field examples, including distributed acoustic sensing data, validate these predictions. Statistical analysis of compaction‐type near‐surface models shows that overtones are better recovered for radial‐radial surveys in large portions of the useable spectrum, extending beyond 60% for the second and above modes. We conclude that incorporating radial‐radial data acquisition is beneficial and should become standard procedure in active surveying, as well as analyzing the radial component in ambient noise and earthquake‐induced Rayleigh waves.
Observations of Relativistic Electron Enhancement and Butterfly Pitch Angle Distributions at Low L (<3)
Authors: O'Brien D. , Li X. , Khoo L. , Selesnick R. S. , Hogan B. , Zhao H. , Mei Y. , Hoxie V. , Baker D. N. , Kanekal S. G.
Published: January 2024

Electrons in Earth's outer radiation belt are highly dynamic, with fluxes changing by up to orders of magnitude. The penetration of electrons from the outer belt to the inner belt is one such change observed during geomagnetic storms and was previously observed in electrons up to 1 MeV for some strong storms observed by the Van Allen Probes. We analyze pulse height analysis data from the Relativistic Electric and Proton Telescope (REPT) on the Van Allen Probes to produce electron flux measurements with lower minimum energy and significantly improved resolution compared to the standard REPT data and show that electron penetrations into the inner belt (L ≤ 2) extend to at least 1.3 MeV and penetrations into the slot region (2 < L < 2.8) extend to at least 1.5 MeV during certain geomagnetic storms. We also demonstrate that these penetrations are associated with butterfly pitch angle distributions from 1 to 1.3 MeV.
An Observing System Simulation Experiment Analysis of How Well Geostationary Satellite Trace‐Gas Observations Constrain NOx Emissions in the US
Authors: Hsu Chia‐Hua , Henze Daven K. , Mizzi Arthur P. , González Abad Gonzalo , He Jian , Harkins Colin , Naeger Aaron R. , Lyu Congmeng , Liu Xiong , Chan Miller Christopher , Pierce R. Bradley , Johnson Matthew S. , McDonald Brian C.
Published: January 2024

We investigate the benefit of assimilating high spatial‐temporal resolution nitrogen dioxide (NO2) measurements from a geostationary (GEO) instrument such as Tropospheric Emissions: Monitoring of Pollution (TEMPO) versus a low‐earth orbit (LEO) platform like TROPOspheric Monitoring Instrument (TROPOMI) on the inverse modeling of nitrogen oxides (NOx) emissions. We generated synthetic TEMPO and TROPOMI NO2 measurements based on emissions from the COVID‐19 lockdown period. Starting with emissions levels prior to the lockdown, we use the Weather Research and Forecasting Model coupled with Chemistry/Data Assimilation Research Testbed (WRF‐Chem/DART) to assimilate these pseudo‐observations in Observing System Simulation Experiments to adjust NOx emissions and quantify how well the assimilation of TEMPO versus TROPOMI measurements recovers the lockdown‐induced emissions changes. We find that NOx emission biases can be ameliorated using half as many simulation days when assimilating GEO observations, and the estimated NOx emissions in 23 out of 29 major urban regions in the US are more accurate. The root mean square error and coefficient of determination of posterior NOx emissions are reduced by 12.5%–41.5% and 1.5%–17.1%, respectively, across different regions. We conduct sensitivity experiments that use different data assimilation (DA) configurations to assimilate synthetic GEO observations. Results demonstrate that the temporal width of the DA window introduces −10% to −20% biases in the emissions inversion and constraining both NOx concentrations and emissions simultaneously yields the most accurate NOx emissions estimates. Our work serves as a valuable reference on how to appropriately assimilate GEO observations for constraining NOx emissions in future studies.
Characterizing Volcanic Ash Density and Its Implications on Settling Dynamics
Authors: Lau Sing , Grainger Roy G. , Taylor Isabelle A.
Published: January 2024

Volcanic ash clouds are carefully monitored as they present a significant hazard to humans and aircraft. The primary tool for forecasting the transport of ash from a volcano is dispersion modeling. These models make a number of assumptions about the size, sphericity and density of the ash particles. Few studies have measured the density of ash particles or explored the impact that the assumption of ash density might have on the settling dynamics of ash particles. In this paper, the raw apparent density of 23 samples taken from 15 volcanoes are measured with gas pycnometry, and a negative linear relationship is found between the density and the silica content. For the basaltic ash samples, densities were measured for different particle sizes, showing that the density is approximately constant for particles smaller than 100 μm, beyond which it decreases with size. While this supports the current dispersion model used by the London Volcanic Ash Advisory Centre (VAAC), where the density is held at a constant (2.3 g cm−3), inputting the measured densities into a numerical simulation of settling velocity reveals a primary effect from the silica content changing this constant. The VAAC density overestimates ash removal times by up to 18%. These density variations, including those varying with size beyond 100 μm, also impact short‐range particle‐size distribution measurements and satellite retrievals of ash.
Evaluation of a Stochastic Mixing Scheme in the Deep Convective Gray Zone Using a Tropical Oceanic Deep Convection Case Study
Authors: Stanford McKenna W. , Varble Adam C. , Morrison Hugh
Published: January 2024

A stochastic horizontal subgrid‐scale mixing scheme is evaluated in ensemble simulations of a tropical oceanic deep convection case using a horizontal grid spacing (Δh) of 3 km. The stochastic scheme, which perturbs the horizontal mixing coefficient according to a prescribed spatiotemporal autocorrelation scale, is found to generally increase mesoscale organization and convective intensity relative to a non‐stochastic control simulation. Perturbations applied at relatively short autocorrelation scales induce differences relative to the control that are more systematic than those from perturbations applied at relatively long scales that yield more variable outcomes. A simulation with mixing enhanced by a constant factor of 4 significantly increases mesoscale organization and convective intensity, while turning off horizontal subgrid‐scale mixing decreases both. Total rainfall is modulated by a combination of mesoscale organization, areal coverage of convection, and convective intensity. The stochastic simulations tend to behave more similarly to the constant enhanced mixing simulation owing to greater impacts from enhanced mixing as compared to reduced mixing. The impacts of stochastic mixing are robust, ascertained by comparing the stochastic mixing ensembles with a non‐stochastic mixing ensemble that has grid‐scale noise added to the initial thermodynamic field. Compared to radar observations and a higher resolution Δh = 1 km simulation, stochastic mixing seemingly degrades the simulation performance. These results imply that stochastic mixing produces non‐negligible impacts on convective system properties and evolution but does not lead to an improved representation of convective cloud characteristics in the case studied here.
Brazil Margin Stable Isotope Profiles for the Last Glacial Cycle: Implications for Watermass Geometry and Oceanic Carbon Storage
Authors: Shub A. B. , Lund D. C. , Oppo D. W. , Garity M. L.
Published: January 2024

Vertical profiles of benthic foraminiferal oxygen and carbon isotopes (δ18O and δ13C) imply the volume of southern source water (SSW) in the Atlantic basin expanded during the Last Glacial Maximum. Shoaling of the boundary between SSW and northern source water (NSW) may reduce mixing between the two watermasses, thereby isolating SSW and enhancing its ability to store carbon during glacial intervals. Here we test this hypothesis using profiles of δ18O and δ13C from the Brazil Margin spanning the last glacial cycle (0–150 ka). Shoaling of the SSW‐NSW boundary occurred during Marine Isotope Stage (MIS) 2, 4, and 6, consistent with expansion of SSW and greater carbon sequestration in the abyss. But the watermass boundary also shoaled during MIS 5e, when atmospheric CO2 levels were comparable to MIS 1. Additionally, we find there was little change in watermass structure across the MIS 5e‐d transition, the first major decline in CO2 of the last glacial cycle. Thus, the overall pattern in glacial‐interglacial geometry is inconsistent with watermass mixing acting as a primary control on atmospheric pCO2. We also find that δ13C values for MIS 5e are systematically lower than MIS 1, with the largest difference (∼1‰) occurring in the upper water column. Low δ13C during MIS 5e was most likely due to a long‐term imbalance in weathering and deposition of calcium carbonate or input of 13C‐depleted carbon from a reservoir external to the ocean‐atmosphere system.
Linking Sediment and Water Column Phosphorus Dynamics to Oxygen, Temperature, and Aeration in Shallow Eutrophic Lakes
Authors: Kirol A. P. , Morales‐Williams A. M. , Braun D. C. , Marti C. L. , Pierson O. E. , Wagner K. J. , Schroth A. W.
Published: January 2024

Water quality improvements in shallow eutrophic lakes are commonly delayed due to loading from legacy phosphorus (P)‐enriched sediments, even with reduced external nutrient loads. It is critical to understand the drivers of internal P loading to suppress or remove this source of P and meet water quality goals. We contrast the drivers of internal P loading in two shallow eutrophic systems (Lake Carmi and Missisquoi Bay). Legacy P dynamics in the unmanipulated systems were compared to Lake Carmi during aeration. In‐situ high frequency water column monitoring along with water and sediment sampling was used to study P dynamics in response to changing lake conditions and aeration. Despite both systems exhibiting P mobility controlled by iron redox cycling, we observed distinct differences in the spatial extent and drivers of internal P loading. Legacy P loading was controlled by seasonal drivers in Lake Carmi, but by spatially variable and highly transient wind driven forcing of hydrodynamics in Missisquoi Bay. Aeration altered the mixing regime of Lake Carmi and shifted loading dynamics to frequent wind‐driven pulses of legacy P to surface waters akin to those of Missisquoi Bay. Mean hypolimnetic dissolved oxygen increased with aeration, but greater oxygen demand rates and periods of anoxia under transient stratification still resulted in internal P loading. Surface P concentrations were higher in summer months with aeration compared to previous years. This research illustrates the dynamic nature of legacy P behavior within and between shallow eutrophic lakes and the challenges in addressing this common water resources threat.
Accuracy Assessment of Numerical Morphological Models Based on Reduced Saint‐Venant Equations
Authors: Barneveld H. J. , Mosselman E. , Chavarrías V. , Hoitink A. J. F.
Published: January 2024

Sustainable river management often requires long‐term morphological simulations. As the future is unknown, uncertainty needs to be accounted for, which may require probabilistic simulations covering a large parameter domain. Even for one‐dimensional models, simulation times can be long. One of the acceleration strategies is simplification of models by neglecting terms in the governing hydrodynamic equations. Examples are the quasi‐steady model and the diffusive wave model, both widely used by scientists and practitioners. Here, we establish under which conditions these simplified models are accurate. Based on results of linear stability analyses of the St. Venant‐Exner equations, we assess migration celerities and damping of infinitesimal, but long riverbed perturbations. We did this for the full dynamic model, that is, no terms neglected, as well as for the simplified models. The accuracy of the simplified models was obtained from comparison between the characteristics of the riverbed perturbations for simplified models and the full dynamic model. We executed a spatial‐mode and a temporal‐mode linear analysis and compared the results with numerical modeling results for the full dynamic and simplified models, for very small and large bed waves. The numerical results match best with the temporal‐mode linear analysis. We show that the quasi‐steady model is highly accurate for Froude numbers up to 0.7, probably even for long river reaches with large flood wave damping. Although the diffusive wave model accurately predicts flood wave migration and damping, key morphological metrics deviate more than 5% (10%) from the full dynamic model when Froude numbers exceed 0.2 (0.3).
Spatiotemporal Variation of Groundwater Nitrate Concentration Controlled by Groundwater Flow in a Large Basin: Evidence From Multi‐Isotopes (15N, 11B, 18O, and 2H)
Authors: Mao Hairu , Wang Guangcai , Liao Fu , Shi Zheming , Rao Zhi , Zhang Hongyu , Qiao Zhiyuan , Bai Yunfei , Chen Xianglong , Yan Xin , Wang Chenyu , Yang Yang
Published: January 2024

Elevated and increasing concentration in groundwater affect groundwater supplies in China and elsewhere. However, how groundwater flow affects concentration in groundwater has yet to be fully understood. Herein, multi‐isotopes (15N, 11B, 18O, and 2H) and local indicators of spatial association (LISA) were used to elucidate the spatiotemporal variation, sources, and patterns of and its response to groundwater flow in Poyang Lake Basin where agriculture, industry and urban coexist. The location of hotspots identified by LISA tended to move from the middle to lower reaches of Ganfu Plain with groundwater flow, and hotspots area expanded in the upper reaches of Xin River Basin and northwest of the study area during the transition from dry season to wet season. Our results revealed that variations of regional concentration were controlled by groundwater recharge or flow mode (vertical or lateral), biogeochemical processes and sources (sewage and manure). In some areas with the single stratigraphic structure (unconfined aquifer), spatiotemporal variation of concentration was influenced by local pollution sources and vertical recharge of current precipitation (vertical flow). In some areas with binary structures (confined aquifer), groundwater was mainly recharged by lateral flow and concentration was mainly affected by mixing effect of upstream groundwater, reflecting human activities in the upper reaches rather than local human activities. In lakeside floodplain, groundwater was attenuated by the dissimilatory reduction to . This study provides a novel insight into groundwater flow controlling on spatiotemporal distribution of concentration in the regional scale.
Experimental measurement and numerical modeling of deformation behavior of breast cancer cells passing through constricted microfluidic channels
Authors: Keshavarz Motamed Pouyan , Abouali Hesam , Poudineh Mahla , Maftoon Nima
Published: January 2024

During the multistep process of metastasis, cancer cells encounter various mechanical forces which make them deform drastically. Developing accurate in-silico models, capable of simulating the interactions between the mechanical forces and highly deformable cancer cells, can pave the way for the development of novel diagnostic and predictive methods for metastatic progression. Spring-network models of cancer cell, empowered by our recently proposed identification approach, promises a versatile numerical tool for developing experimentally validated models that can simulate complex interactions at cellular scale. Using this numerical tool, we presented spring-network models of breast cancer cells that can accurately replicate the experimental data of deformation behavior of the cells flowing in a fluidic domain and passing narrow constrictions comparable to microcapillary. First, using high-speed imaging, we experimentally studied the deformability of breast cancer cell lines with varying metastatic potential (MCF-7 (less invasive), SKBR-3 (medium-high invasive), and MDA-MB-231 (highly invasive)) in terms of their entry time to a constricted microfluidic channel. We observed that MDA-MB-231, that has the highest metastatic potential, is the most deformable cell among the three. Then, by focusing on this cell line, experimental measurements were expanded to two more constricted microchannel dimensions. The experimental deformability data in three constricted microchannel sizes for various cell sizes, enabled accurate identification of the unknown parameters of the spring-network model of the breast cancer cell line (MDA-MB-231). Our results show that the identified parameters depend on the cell size, suggesting the need for a systematic procedure for identifying the size-dependent parameters of spring-network models of cells. As the numerical results show, the presented cell models can simulate the entry process of the cell into constricted channels with very good agreements with the measured experimental data.
IFI35 limits antitumor immunity in triple-negative breast cancer via CCL2 secretion
Authors: Xu Baojin , Sun Hefen , Liu Simeng , Liao Li , Song Xiaoqing , Wu Yi , Hou Yifeng , Jin Wei
Published: January 2024

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with poor prognosis due to the lack of therapeutic targets. Although immunotherapy brings survival benefits to patients diagnosed with TNBC, it remains limited and treatment resistance is widespread. Here we demonstrate that IFI35 is highly expressed in tumor tissues and can be induced by Interferon-γ in a time-dependent and concentration-dependent manner in breast cancer cells. In xenograft models, we reveal that IFI35 dramatically increases myeloid-derived suppressor cells infiltration in tumors, along with depletion and anergy of CD8+T cells. IFI35 ablation leads to prolonged survival of the mice. Mechanistically, RNA-sequencing reveals that IFI35 promotes CCL2 secretion, resulting in the remodeling of TNBC immune microenvironment. Ablation of IFI35 promotes the infiltration of effector CD8+T cells, and thereby sensitizes TNBC to anti-PD-1 immunotherapy. Our data suggest that IFI35 limits antitumor immunity and may be expected to become a new immunotherapy target in TNBC.
FBXO31 is upregulated by METTL3 to promote pancreatic cancer progression via regulating SIRT2 ubiquitination and degradation
Authors: Chen Kai , Wang Yue , Dai Xingna , Luo Jingjing , Hu Shangshang , Zhou Zhihui , Shi Jinglong , Pan Xueshan , Cao Tong , Xia Jun , Li Yuyun , Wang Zhiwei , Ma Jia
Published: January 2024

FBXO31, a member of F-box family to comprise of SCF complex, contributes to a pivotal role in cancer progression. However, the possible involvements of FBXO31 in PC are unelucidated. Here, we reported that FBXO31 was overexpressed in PC patients, which was negatively associated with survival in PC patients. Furthermore, FBXO31 significantly enhanced growth, migration and invasion of PC cells in vitro. Consistently, FBXO31 overexpression promoted tumor growth in nude mice. Mechanistically, SIRT2 was a target of FBXO31 and interacted with FBXO31. Protein half-life and ubiquitination analysis demonstrated that FBXO31 promoted proteasome-dependent degradation of SIRT2. In addition, FBXO31 binds to sirtuin-type domain of SIRT2. Moreover, SIRT2 is required for the oncogenic role of FBXO31 in PC progression. Impressively, METTL3 induced m6A modification of FBXO31 and up-regulated FBXO31 expression, subsequently leading to SIRT2 down-regulation in PC cells. The results showed that METTL3 enhanced FBXO31 mRNA translation in YTHDF1-dependent manner. Taken together, we suggest that METTL3–FBXO31–SIRT2 axis was involved in PC tumorigenesis, which could identify new targets for PC treatment.
Germline specific genes increase DNA double-strand break repair and radioresistance in lung adenocarcinoma cells
Authors: Liu Wenqing , Bruggeman Jan Willem , Lei Qijing , van Pelt Ans M. M. , Koster Jan , Hamer Geert
Published: January 2024

In principle, germline cells possess the capability to transmit a nearly unaltered set of genetic material to infinite future generations, whereas somatic cells are limited by strict growth constraints necessary to assure an organism’s physical structure and eventual mortality. As the potential to replicate indefinitely is a key feature of cancer, we hypothesized that the activation of a “germline program” in somatic cells can contribute to oncogenesis. Our group recently described over one thousand germline specific genes that can be ectopically expressed in cancer, yet how germline specific processes contribute to the malignant properties of cancer is poorly understood. We here show that the expression of germ cell/cancer (GC) genes correlates with malignancy in lung adenocarcinoma (LUAD). We found that LUAD cells expressing more GC genes can repair DNA double strand breaks more rapidly, show higher rates of proliferation and are more resistant to ionizing radiation, compared to LUAD cells that express fewer GC genes. In particular, we identified the HORMA domain protein regulator TRIP13 to be predominantly responsible for this malignant phenotype, and that TRIP13 inhibition or expression levels affect the response to ionizing radiation and subsequent DNA repair. Our results demonstrate that GC genes are viable targets in oncology, as they induce increased radiation resistance and increased propagation in cancer cells. Because their expression is normally restricted to germline cells, we anticipate that GC gene directed therapeutic options will effectively target cancer, with limited side effects besides (temporary) infertility.
Activated hepatic stellate cell-derived Bmp-1 induces liver fibrosis via mediating hepatocyte epithelial-mesenchymal transition
Authors: Wan Sizhe , Liu Xianzhi , Sun Ruonan , Liu Huiling , Jiang Jie , Wu Bin
Published: January 2024

Liver fibrosis is a reparative response to injury that arises from various etiologies, characterized by activation of hepatic stellate cells (HSCs). Periostin, a secreted matricellular protein, has been reported to participate in tissue development and regeneration. However, its involvement in liver fibrosis remains unknown. This study investigated the roles and mechanisms of Periostin in phenotypic transition of HSCs and relevant abnormal cellular crosstalk during liver fibrosis. The fate of hepatic stellate cells (HSCs) during liver fibrogenesis was investigated using single-cell and bulk RNA sequencing profiles, which revealed a significant proliferation of activated HSCs (aHSCs) in fibrotic livers of both humans and mice. αSMA-TK mice were used to demonstrate that depletion of proliferative aHSCs attenuates liver fibrosis induced by carbon tetrachloride and 3,5-diethoxycarbonyl-1,4-dihydrocollidine. Through integrating data from single-cell and bulk sequencing, Periostin was identified as a distinctive hallmark of proliferative aHSC subpopulation. Elevated levels of Periostin were detected in fibrotic livers of both humans and mice, primarily within aHSCs. However, hepatic Periostin levels were decreased along with depletion of proliferative aHSCs. Deficiency of Periostin led to reduced liver fibrosis and suppressed hepatocyte epithelial-mesenchymal transition (EMT). Periostin-overexpressing HSCs, exhibiting a proliferative aHSC phenotype, release bone morphogenetic protein-1 (Bmp-1), which activates EGFR signaling, inducing hepatocyte EMT and contributing to liver fibrosis. In conclusion, Periostin in aHSCs drives their acquisition of a proliferative phenotype and the release of Bmp-1. Proliferative aHSC subpopulation-derived Bmp-1 induces hepatocyte EMT via EGFR signaling, promoting liver fibrogenesis. Bmp-1 and Periostin should be potential therapeutic targets for liver fibrosis.
Extracellular vesicle-mediated ferroptosis, pyroptosis, and necroptosis: potential clinical applications in cancer therapy
Authors: Yang Yi-Chi , Jiang Qian , Yang Ke-Ping , Wang Lingzhi , Sethi Gautam , Ma Zhaowu
Published: January 2024

Extracellular vesicles (EVs) have gained increasing recognition as significant regulators of intercellular communication in various physiological and pathological processes. These vesicles play a pivotal role in cancer progression by facilitating the transfer of diverse cargoes, including lipids, proteins, and nucleic acids. Regulated cell death (RCD), the orderly and autonomous death of cells, is controlled by a variety of biomacromolecules and, in turn, influences various biological processes and cancer progression. Recent studies have demonstrated that EV cargoes regulate diverse oncogenes and tumor suppressors to mediate different nonapoptotic forms of RCD, notably ferroptosis, pyroptosis, and necroptosis. Nevertheless, comprehensive exploration of EV-mediated nonapoptotic RCD forms in the context of cancer has not been performed. This review summarizes the progress regarding the biological functions and underlying mechanisms of EVs in mediating nonapoptotic RCD by delivery of cargoes to regulate tumor progression. Additionally, the review delves into the potential clinical applications of EV-mediated cell death and its significance in the areas of cancer diagnosis and therapy.
Leveraging mechanochemistry for sustainable polymer degradation
Authors: Aydonat Simay , Hergesell Adrian H. , Seitzinger Claire L. , Lennarz Regina , Chang George , Sievers Carsten , Meisner Jan , Vollmer Ina , Göstl Robert
Published: January 2024

Over 8 billion tons of plastic have been produced to date, and a 100% reclamation recycling strategy is not foreseeable. This review summarizes how the mechanochemistry of polymers may contribute to a sustainable polymer future by controlling the degradation not only of de novo developed designer polymers but also of plastics in existing waste streams. The historical development of polymer mechanochemistry is presented while highlighting current examples of mechanochemically induced polymer degradation. Additionally, theoretical and computational frameworks are discussed that may lead to the discovery and better understanding of new mechanochemical reactions in the future. This review takes into account technical and engineering perspectives converging the fields of trituration and polymer mechanochemistry with a particular focus on the fate of commodity polymers and potential technologies to monitor mechanochemical reactions while they occur. Therefore, a unique perspective of multiple communities is presented, highlighting the need for future transdisciplinary research to tackle the high-leverage parameters governing an eventually successful mechanochemical degradation approach for a circular economy.
Mutant KRAS-activated circATXN7 fosters tumor immunoescape by sensitizing tumor-specific T cells to activation-induced cell death
Authors: Zhou Chi , Li Wenxin , Liang Zhenxing , Wu Xianrui , Cheng Sijing , Peng Jianhong , Zeng Kaixuan , Li Weihao , Lan Ping , Yang Xin , Xiong Li , Zeng Ziwei , Zheng Xiaobin , Huang Liang , Fan Wenhua , Liu Zhanzhen , Xing Yue , Kang Liang , Liu Huashan
Published: January 2024

Mutant KRAS (KRASMUT) is often exploited by cancers to shape tumor immunity, but the underlying mechanisms are not fully understood. Here we report that tumor-specific cytotoxic T lymphocytes (CTLs) from KRASMUT cancers are sensitive to activation-induced cell death (AICD). circATXN7, an NF-κB-interacting circular RNA, governs T cell sensitivity to AICD by inactivating NF-κB. Mechanistically, histone lactylation derived from KRASMUT tumor cell-produced lactic acid directly activates transcription of circATXN7, which binds to NF-κB p65 subunit and masks the p65 nuclear localization signal motif, thereby sequestering it in the cytoplasm. Clinically, circATXN7 upregulation in tumor-specific CTLs correlates with adverse clinical outcomes and immunotherapeutic resistance. Genetic ablation of circAtxn7 in CD8+ T cells leads to mutant-selective tumor inhibition, while also increases anti-PD1 efficacy in multiple tumor models in female mice. Furthermore, targeting circATXN7 in adoptively transferred tumor-reactive CTLs improves their antitumor activities. These findings provide insight into how lymphocyte-expressed circRNAs contribute to T-cell fate decisions and anticancer immunotherapies.
Plant macrofossil data for 48-0 ka in the USGS North American Packrat Midden Database, version 5.0
Authors: Strickland Laura E. , Thompson Robert S. , Shafer Sarah L. , Bartlein Patrick J. , Pelltier Richard T. , Anderson Katherine H. , Schumann R. Randall , McFadden Andrew K.
Published: January 2024

Plant macrofossils from packrat (Neotoma spp.) middens provide direct evidence of past vegetation changes in arid regions of North America. Here we describe the newest version (version 5.0) of the U.S. Geological Survey (USGS) North American Packrat Midden Database. The database contains published and contributed data from 3,331 midden samples collected in southwest Canada, the western United States, and northern Mexico, with samples ranging in age from 48 ka to the present. The database includes original midden-sample macrofossil counts and relative-abundance data along with a standardized relative-abundance scheme that makes it easier to compare macrofossil data across midden-sample sites. In addition to the midden-sample data, this version of the midden database includes calibrated radiocarbon (14C) ages for the midden samples and plant functional type (PFT) assignments for the midden taxa. We also provide World Wildlife Fund ecoregion assignments and climate and bioclimate data for each midden-sample site location. The data are provided in tabular (.xlsx), comma-separated values (.csv), and relational database (.mdb) files.
A bite force database of 654 insect species
Authors: Rühr Peter Thomas , Edel Carina , Frenzel Melina , Blanke Alexander
Published: January 2024

Bite force is a decisive performance trait in animals because it plays a role for numerous life history components such as food consumption, inter- and intraspecific interactions, and reproductive success. Bite force has been studied across a wide range of vertebrate species, but only for 32 species of insects, the most speciose animal lineage. Here we present the insect bite force database with bite force measurements for 654 insect species covering 476 genera, 111 families, and 13 orders with body lengths ranging from 3.76 to 180.12 mm. In total we recorded 1906 bite force series from 1290 specimens, and, in addition, present basal head, body, and wing metrics. As such, the database will facilitate a wide range of studies on the characteristics, predictors, and macroevolution of bite force in the largest clade of the animal kingdom and may serve as a basis to further our understanding of macroevolutionary processes in relation to bite force across all biting metazoans.
An electricity smart meter dataset of Spanish households: insights into consumption patterns
Authors: Quesada Carlos , Astigarraga Leire , Merveille Chris , Borges Cruz E.
Published: January 2024

Smart meters are devices that provide detailed information about the energy consumed by specific electricity supply points, such as homes, offices, and businesses. Data from smart meters are useful for modeling energy systems, predicting electricity consumption, and understanding human behavior. We present the first smart meter dataset from Spanish electricity supply points, expanding the geographic diversity of available data on energy consumption at the household level and reducing biases in existing data, which typically come from a limited number of countries. The dataset consists of 25,559 raw hourly time series with an average length of nearly three years, spanning from November 2014 to June 2022. It also includes three subsets obtained by segmenting and cleaning the raw time series data, each focusing on the periods before, during, and after the COVID-19 lockdowns in Spain. This dataset is a valuable resource for studying electricity consumption patterns and behaviors that emerge in response to different natural experiments, such as nationwide and regional lockdowns, nighttime curfews, and changes in electricity pricing.
Genomic resources for a historical collection of cultivated two-row European spring barley genotypes
Authors: Schreiber Miriam , Wonneberger Ronja , Haaning Allison M. , Coulter Max , Russell Joanne , Himmelbach Axel , Fiebig Anne , Muehlbauer Gary J. , Stein Nils , Waugh Robbie
Published: January 2024

Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.
Developing an advanced prediction model for new employee turnover intention utilizing machine learning techniques
Authors: Park Jungryeol , Feng Yituo , Jeong Seon-Phil
Published: January 2024

In recent years, the turnover phenomenon of new college graduates has been intensifying. The turnover of new employees creates many difficulties for businesses as it is difficult to recover the costs spent on their hiring and training. Therefore, it is necessary to promptly identify and effectively manage new employees who are inclined to change jobs. So far previous studies related to turnover intention have contributed to understanding the turnover phenomenon of new employees by identifying factors influencing turnover intention. However, with these factors, there is a limitation that it has not been able to present how much it is possible to predict employees who are actually willing to change jobs. Therefore, this study proposes a method of developing a machine learning-based turnover intention prediction model to overcome the limitations of previous studies. In this study, data from the Korea Employment Information Service's Job Movement Path Survey for college graduates were used, and OLS regression analysis was performed to confirm the influence of predictors. And model learning and classification were performed using a logistic regression (LR), k-nearest neighbor (KNN), and extreme gradient boosting (XGB) classifier. A novel finding of this research is the diminished or reversed influence of certain traditional factors, such as workload importance and the relevance of one's major field, on turnover intention. Instead, job security emerged as the most significant predictor. The model's accuracy rates, highest with XGB at 78.5%, demonstrate the efficacy of applying machine learning in turnover intention prediction, marking a significant advancement over traditional econometric models. This study breaks new ground by integrating advanced predictive analytics into turnover intention research, offering a more nuanced understanding of the factors influencing the turnover intentions of new college graduates. The insights gained could guide organizations in effectively managing and retaining new talent, highlighting the need for a focus on job security and organizational satisfaction, and the shifting relevance of traditional factors like job preference.
MedGAN: optimized generative adversarial network with graph convolutional networks for novel molecule design
Authors: Macedo Bruno , Ribeiro Vaz Inês , Taveira Gomes Tiago
Published: January 2024

Generative Artificial Intelligence can be an important asset in the drug discovery process to meet the demand for novel medicines. This work outlines the optimization and fine-tuning steps of MedGAN, a deep learning model based on Wasserstein Generative Adversarial Networks and Graph Convolutional Networks, developed to generate new quinoline-scaffold molecules from complex molecular graphs, including hyperparameter adjustments and evaluations of drug-likeness attributes such as pharmacokinetics, toxicity, and synthetic accessibility. The best model was capable of generating 25% valid molecules, 62% fully connected, from which 92% were quinolines, 93% were novel, and 95% unique, preserving chirality, atom charge, and favorable drug-like properties while generating 4831 novel quinolines. These results provide valuable insights into how activation functions, optimizers, learning rates, neuron units, molecule size and constitution, and scaffold structure affect the performance of generative models and their potential to create new molecular structures, enhancing deep learning applications in computational drug design.
The ultrastructure of nymphal dermal pores and the genitalia of adult male of Phenacoccus solenopsis (Hemiptera: Pseudococcidae)
Authors: Abd El-Ghany Nesreen M. , Abd El-Aziz Shadia E. , Faucheux Michel J.
Published: January 2024

The cotton mealybug, Phenacoccus solenopsis, has established itself as an invasive insect pest worldwide. It causes structural and physiological damage to various crops and can cause substantial financial losses in their production. The successful reproduction of this pest under a wide range of conditions is a key to its success. Despite this, the morphology of its genitalia, genital sensilla, and wax-producing dermal pores has received little attention, with little descriptions of their ultrastructure. By investigating those features with SEM, the present study revealed considerable new insights into the identification of the nymphal and adult stages of P. solenopsis. In addition, the description of the ultrastructural genital morphology of the immature stages of P. solenopsis has revealed characteristics that facilitate their discrimination. Trilocular pores were observed on both sides of the body, while the quinquelocular pores were distributed only on the ventral surface in both the first and second nymphal instars. The adult male is characterized by two pairs of waxy caudal filaments surrounded by clusters of 55 to 60 stellate pores, and each pregenital segment bears a pair of stellate pores composed of 4 or 5 peripheral loculi. Sensilla trichodea and numerous microtrichia are present on the pregenital segments. The penile sheath bears three subtypes of sensilla basiconica and also campaniformia, whereas the style bears three subtypes of sensilla campaniformia. The findings of this study could assist in the identification of the adult and nymphal stages of P. solenopsis, and also provide insights into the structures found on the genitalia of the adult male that possibly have an important role in mating events and copulatory behavior. Furthermore, these findings were able to contribute to better understanding the functional morphology of P. solenopsis.
Exogenous melatonin induces salt and drought stress tolerance in rice by promoting plant growth and defense system
Authors: Khan Zakirullah , Jan Rahmatullah , Asif Saleem , Farooq Muhammad , Jang Yoon-Hee , Kim Eun-Gyeong , Kim Nari , Kim Kyung-Min
Published: January 2024

Due to global climate change, crops are certainly confronted with a lot of abiotic and biotic stress factors during their growth that cause a serious threat to their development and overall productivity. Among different abiotic stresses, salt and drought are considered the most devastating stressors with serious impact on crop’s yield stability. Here, the current study aimed to elucidate how melatonin works in regulating plant biomass, oxidative stress, antioxidant defense system, as well as the expression of genes related to salt and drought stress in rice plants. Eight groups of rice plants (3 replicates, 5 plants each) underwent varied treatments: control, melatonin, salt, drought, salt + drought, salt + melatonin, drought + melatonin, and salt + drought + melatonin. Melatonin (100 µM) was alternately applied a week before stress exposure; salt stress received 100 mM NaCl every 3 days for 3 weeks, and drought stress involved 10% PEG. Young leaves were randomly sampled from each group. The results showed that melatonin treatment markedly reduces salt and drought stress damage by promoting root, shoot length, fresh and dry weight, increasing chlorophyll contents, and inhibiting excessive production of oxidative stress markers. Salt and drought stress significantly decreased the water balance, and damaged cell membrane by reducing relative water contents and increasing electrolyte leakage. However, melatonin treated rice plants showed high relative water contents and low electrolyte leakage. Under salt and drought stress conditions, exogenous application of melatonin boosted the expression level of salt and drought stress responsive genes like OsSOS, OsNHX, OsHSF and OsDREB in rice plants. Taken together, our results reveal that melatonin treatment significantly increases salt and drought tolerance of rice plants, by increasing plant biomass, suppressing ROS accumulation, elevating antioxidants defense efficiency, and up-regulating the expression of salt and drought stress responsive genes.