bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaps and opportunities in modelling human influence on species distributions in the Anthropocene
Authors: Frans Veronica F. , Liu Jianguo 
Published: June 2024

AbstractUnderstanding species distributions is a global priority for mitigating environmental pressures from human activities. Ample studies have identified key environmental (climate and habitat) predictors and the spatial scales at which they influence species distributions. However, regarding human influence, such understandings are largely lacking. Here, to advance knowledge concerning human influence on species distributions, we systematically reviewed species distribution modelling (SDM) articles and assessed current modelling efforts. We searched 12,854 articles and found only 1,429 articles using human predictors within SDMs. Collectively, these studies of >58,000 species used 2,307 unique human predictors, suggesting that in contrast to environmental predictors, there is no ‘rule of thumb’ for human predictor selection in SDMs. The number of human predictors used across studies also varied (usually one to four per study). Moreover, nearly half the articles projecting to future climates held human predictors constant over time, risking false optimism about the effects of human activities compared with climate change. Advances in using human predictors in SDMs are paramount for accurately informing and advancing policy, conservation, management and ecology. We show considerable gaps in including human predictors to understand current and future species distributions in the Anthropocene, opening opportunities for new inquiries. We pose 15 questions to advance ecological theory, methods and real-world applications.
Ancient genomes reveal insights into ritual life at Chichén Itzá
Authors: Barquera Rodrigo , Del Castillo-Chávez Oana , Nägele Kathrin , Pérez-Ramallo Patxi , Hernández-Zaragoza Diana Iraíz , Szolek András , Rohrlach Adam Benjamin , Librado Pablo , Childebayeva Ainash , Bianco Raffaela Angelina , Penman Bridget S. , Acuña-Alonzo Victor , Lucas Mary , Lara-Riegos Julio César , Moo-Mezeta María Ermila , Torres-Romero Julio César , Roberts Patrick , Kohlbacher Oliver , Warinner Christina , Krause Johannes 
Published: June 2024

AbstractThe ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (ad 600–1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1–4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population’s genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around ad 500–900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
Inner core backtracking by seismic waveform change reversals
Authors: Wang Wei , Vidale John E. , Pang Guanning , Koper Keith D. , Wang Ruoyan 
Published: June 2024

AbstractThe solid inner core, suspended within the liquid outer core and anchored by gravity, has been inferred to rotate relative to the surface of Earth or change over years to decades based on changes in seismograms from repeating earthquakes and explosions1,2. It has a rich inner structure3–6 and influences the pattern of outer core convection and therefore Earth’s magnetic field. Here we compile 143 distinct pairs of repeating earthquakes, many within 16 multiplets, built from 121 earthquakes between 1991 and 2023 in the South Sandwich Islands. We analyse their inner-core-penetrating PKIKP waves recorded on the medium-aperture arrays in northern North America. We document that many multiplets exhibit waveforms that change and then revert at later times to match earlier events. The matching waveforms reveal times at which the inner core re-occupies the same position, relative to the mantle, as it did at some time in the past. The pattern of matches, together with previous studies, demonstrates that the inner core gradually super-rotated from 2003 to 2008, and then from 2008 to 2023 sub-rotated two to three times more slowly back through the same path. These matches enable precise and unambiguous tracking of inner core progression and regression. The resolved different rates of forward and backward motion suggest that new models will be necessary for the dynamics between the inner core, outer core and mantle.
Global variability in atmospheric new particle formation mechanisms
Authors: Zhao Bin , Donahue Neil M. , Zhang Kai , Mao Lizhuo , Shrivastava Manish , Ma Po-Lun , Shen Jiewen , Wang Shuxiao , Sun Jian , Gordon Hamish , Tang Shuaiqi , Fast Jerome , Wang Mingyi , Gao Yang , Yan Chao , Singh Balwinder , Li Zeqi , Huang Lyuyin , Lou Sijia , Lin Guangxing , Wang Hailong , Jiang Jingkun , Ding Aijun , Nie Wei , Qi Ximeng , Chi Xuguang , Wang Lin 
Published: June 2024

AbstractA key challenge in aerosol pollution studies and climate change assessment is to understand how atmospheric aerosol particles are initially formed1,2. Although new particle formation (NPF) mechanisms have been described at specific sites3–6, in most regions, such mechanisms remain uncertain to a large extent because of the limited ability of atmospheric models to simulate critical NPF processes1,7. Here we synthesize molecular-level experiments to develop comprehensive representations of 11 NPF mechanisms and the complex chemical transformation of precursor gases in a fully coupled global climate model. Combined simulations and observations show that the dominant NPF mechanisms are distinct worldwide and vary with region and altitude. Previously neglected or underrepresented mechanisms involving organics, amines, iodine oxoacids and HNO3 probably dominate NPF in most regions with high concentrations of aerosols or large aerosol radiative forcing; such regions include oceanic and human-polluted continental boundary layers, as well as the upper troposphere over rainforests and Asian monsoon regions. These underrepresented mechanisms also play notable roles in other areas, such as the upper troposphere of the Pacific and Atlantic oceans. Accordingly, NPF accounts for different fractions (10–80%) of the nuclei on which cloud forms at 0.5% supersaturation over various regions in the lower troposphere. The comprehensive simulation of global NPF mechanisms can help improve estimation and source attribution of the climate effects of aerosols.
Mental navigation in the primate entorhinal cortex
Authors: Neupane Sujaya , Fiete Ila , Jazayeri Mehrdad 
Published: June 2024

AbstractA cognitive map is a suitably structured representation that enables novel computations using previous experience; for example, planning a new route in a familiar space1. Work in mammals has found direct evidence for such representations in the presence of exogenous sensory inputs in both spatial2,3 and non-spatial domains4–10. Here we tested a foundational postulate of the original cognitive map theory1,11: that cognitive maps support endogenous computations without external input. We recorded from the entorhinal cortex of monkeys in a mental navigation task that required the monkeys to use a joystick to produce one-dimensional vectors between pairs of visual landmarks without seeing the intermediate landmarks. The ability of the monkeys to perform the task and generalize to new pairs indicated that they relied on a structured representation of the landmarks. Task-modulated neurons exhibited periodicity and ramping that matched the temporal structure of the landmarks and showed signatures of continuous attractor networks12,13. A continuous attractor network model of path integration14 augmented with a Hebbian-like learning mechanism provided an explanation of how the system could endogenously recall landmarks. The model also made an unexpected prediction that endogenous landmarks transiently slow path integration, reset the dynamics and thereby reduce variability. This prediction was borne out in a reanalysis of firing rate variability and behaviour. Our findings link the structured patterns of activity in the entorhinal cortex to the endogenous recruitment of a cognitive map during mental navigation.
Oligomerization-mediated autoinhibition and cofactor binding of a plant NLR
Authors: Ma Shoucai , An Chunpeng , Lawson Aaron W. , Cao Yu , Sun Yue , Tan Eddie Yong Jun , Pan Jinheng , Jirschitzka Jan , Kümmel Florian , Mukhi Nitika , Han Zhifu , Feng Shan , Wu Bin , Schulze-Lefert Paul , Chai Jijie 
Published: June 2024

AbstractNucleotide-binding leucine-rich repeat (NLR) proteins play a pivotal role in plant immunity by recognizing pathogen effectors1,2. Maintaining a balanced immune response is crucial, as excessive NLR expression can lead to unintended autoimmunity3,4. Unlike most NLRs, the plant NLR required for cell death 2 (NRC2) belongs to a small NLR group characterized by constitutively high expression without self-activation5. The mechanisms underlying NRC2 autoinhibition and activation are not yet understood. Here we show that Solanum lycopersicum (tomato) NRC2 (SlNRC2) forms dimers and tetramers and higher-order oligomers at elevated concentrations. Cryo-electron microscopy shows an inactive conformation of SlNRC2 in these oligomers. Dimerization and oligomerization not only stabilize the inactive state but also sequester SlNRC2 from assembling into an active form. Mutations at the dimeric or interdimeric interfaces enhance pathogen-induced cell death and immunity in Nicotianabenthamiana. The cryo-electron microscopy structures unexpectedly show inositol hexakisphosphate (IP6) or pentakisphosphate (IP5) bound to the inner surface of the C-terminal leucine-rich repeat domain of SlNRC2, as confirmed by mass spectrometry. Mutations at the inositol phosphate-binding site impair inositol phosphate binding of SlNRC2 and pathogen-induced SlNRC2-mediated cell death in N. benthamiana. Our study indicates a negative regulatory mechanism of NLR activation and suggests inositol phosphates as cofactors of NRCs.
Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression
Authors: Lobo Vivian , Shcherbinina Evgeniia , Westholm Jakub O. , Nowak Iwona , Huang Hsiang-Chi , Angeletti Davide , Anastasakis Dimitrios G. , Sarshad Aishe A. 
Published: June 2024

AbstractIn this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.
Microbial imbalance in Chinese children with diarrhea or constipation
Authors: Ren Jing , Ren Yi , Mu Yu , Zhang Lanying , Chen Binghan , Li Sisi , Fang Qinyi , Zhang Zhiming , Zhang Kejian , Li Sabrina , Liu Wei , Cui Yutao , Li Xu 
Published: June 2024

AbstractDiarrhea and constipation are common health concerns in children. Numerous studies have identified strong association between gut microbiota and digestive-related diseases. But little is known about the gut microbiota that simultaneously affects both diarrhea and constipation or their potential regulatory mechanisms. Stool samples from 618 children (66 diarrhea, 138 constipation, 414 healthy controls) aged 0–3 years were collected to investigate gut microbiota changes using 16S rRNA sequencing. Compared with healthy, children with diarrhea exhibited a significant decrease in microbial diversity, while those with constipation showed a marked increase (p < 0.05). Significantly, our results firstly Ruminococcus increased in constipation (p = 0.03) and decreased in diarrhea (p < 0.01) compared to healthy controls. Pathway analysis revealed that Ruminococcus highly involved in the regulation of five common pathways (membrane transport, nervous system, energy metabolism, signal transduction and endocrine system pathways) between diarrhea and constipation, suggesting a potential shared regulatory mechanism. Our finding firstly reveals one core microorganisms that may affect the steady balance of the gut in children with diarrhea or constipation, providing an important reference for potential diagnosis and treatment of constipation and diarrhea.
Solitonic solutions and stability analysis of Benjamin Bona Mahony Burger equation using two versatile techniques
Authors: Hussain Ejaz , Shah Syed Asif Ali , Bariq Abdul , Li Zhao , Ahmad Muhammad Riaz , Ragab Adham E. , Az-Zo’bi Emad A. 
Published: June 2024

AbstractThis study aims to explore the precise resolution of the nonlinear Benjamin Bona Mahony Burgers (BBMB) equation, which finds application in a variety of nonlinear scientific disciplines including fluid dynamics, shock generation, wave transmission, and soliton theory. Within this paper, we employ two versatile methodologies, specifically the extended $$\exp (-\Psi (\chi ))$$

exp
(
-
Ψ
(
χ
)
)

expansion technique and the novel Kudryashov method, to identify the exact soliton solutions of the nonlinear BBMB equation. The solutions we discovered involve trigonometric functions, hyperbolic functions, and rational functions. The uniqueness of this research lies in uncovering the bright soliton, kink wave solution, and periodic wave solution, and conducting stability analysis. Furthermore, the solutions’ graphical characteristics were explored through the utilization of the mathematical software Maple 2022 (https://maplesoft.com/downloads/selectplatform.aspx?hash=61ab59890f2313b2241fde3423fd975e). The system’s physical interpretation is defined through various types of graphs, including contour graphs, 3D-surface graphs, and line graphs, which use appropriate parameter values. These recommended techniques hold significant importance and are applicable in diverse nonlinear evolutionary equations found in the field of nonlinear sciences for illustrating nonlinear physical models.
Haliskia peterseni, a new anhanguerian pterosaur from the late Early Cretaceous of Australia
Authors: Pentland Adele H. , Poropat Stephen F. , Duncan Ruairidh J. , Kellner Alexander W. A. , Bantim Renan A. M. , Bevitt Joseph J. , Tait Alan M. , Grice Kliti 
Published: June 2024

AbstractPterosaur remains have been reported from every continent; however, pterosaur skeletons remain rare. A new pterosaur is presented here,Haliskia petersenigen. et sp. nov., constituting the most complete specimen from Australia from the upper Albian Toolebuc Formation of the Eromanga Basin (Queensland, Australia). A combination of features, including the presence of a premaxillary crest and curved teeth, and the morphology of the scapulocoracoid, support its referral to Anhangueria.Haliskiacan be distinguished from all other anhanguerian pterosaurs based on two dental characters: the 4th and 5th tooth pairs are smaller than the 3rd and 6th, and the 2nd and 5th alveoli are smaller than 3–4 and 6–8. Moreover, the hyoid is 70% the total length of the mandible. The phylogenetic analyses presented here placeHaliskiawithin Anhangueria. In one analysis,HaliskiaandFerrodracoare resolved as sister taxa, withTropeognathus mesembrinussister to that clade. The other resolvesHaliskia,MythungaandFerrodracoin a polytomy within Tropeognathinae. The new Australian pterosaur attests to the success of Anhangueria during the latest Early Cretaceous and suggests that the Australian forms were more taxonomically diverse and palaeobiogeographically complex than previously recognized.
MPXV DNA kinetics in bloodstream and other body fluids samples
Authors: Meschi Silvia , Colavita Francesca , Carletti Fabrizio , Mazzotta Valentina , Matusali Giulia , Specchiarello Eliana , Ascoli Bartoli Tommaso , Mondi Annalisa , Minosse Claudia , Giancola Maria Letizia , Pinnetti Carmela , Valli Maria Beatrice , Lapa Daniele , Mizzoni Klizia , Sullivan David J. , Ou Jiangda , Focosi Daniele , Girardi Enrico , Nicastri Emanuele , Antinori Andrea , Maggi Fabrizio 
Published: June 2024

AbstractSince spring 2022, the global epidemiology of the monkeypox virus (MPXV) has changed. The unprecedented increase of human clade II MPXV cases worldwide heightened concerns about this emerging zoonotic disease. We analysed the positivity rates, viral loads, infectiousness, and persistence of MPXV DNA for up to 4 months in several biological samples from 89 MPXV-confirmed cases. Our data showed that viral loads and positivity rates were higher during the first two weeks of symptoms for all sample types. Amongst no-skin-samples, respiratory specimens showed higher MPXV DNA levels and median time until viral clearance, suggesting their usefulness in supporting MPXV diagnosis, investigating asymptomatic patients, and monitoring viral shedding. Infectious virus was cultured from respiratory samples, semen, and stools, with high viral loads and collected within the first 10 days. Notably, only one saliva and one semen were found positive for viral DNA after 71 and 31 days from symptoms, respectively. The focus on bloodstream samples showed the best testing sensitivity in plasma, reporting the overall highest MPXV DNA detection rate and viral loads during the 3-week follow-up as compared to serum and whole-blood. The data here presented can be useful for MPXV diagnostics and a better understanding of the potential alternative routes of its onward transmission.
Inclusive study of peanut shells derived activated carbon as an adsorbent for removal of lead and methylene blue from water
Authors: Hashem Heba M. , El-Maghrabey Mahmoud , El-Shaheny Rania 
Published: June 2024

AbstractGreen and efficient agro-waste-based activated carbon has been prepared utilizing peanut shells for adsorptive elimination of an industrial dye, methylene blue, and lead from polluted water. The carbonaceous biomass obtained from peanut shells was chemically activated using either NaOH, ZnCl2, or steam and characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, and N2 adsorption and desorption studies. The adsorption process was optimal for methylene blue at alkaline pH, while pH 4.5 was optimal for Pb (II) adsorption. The adsorption takes place through pseudo-second-order kinetic, and the rate-governing step of the adsorption procedure are intraparticle diffusion and film diffusion. Furthermore, the thermodynamics of the adsorption process has been studied, and the obtained Gibbs free energy (ΔG°) values are negative (− 35.90 to − 43.59 kJ mol−1) indicating the spontaneous adsorption of the investigated pollutants on the prepared activated carbon. As per the correlation coefficient, the obtained results were best fit by the Langmuir isotherm with maximum adsorption capacity of 303.03 mg g−1 for methylene blue and 130.89 mg g−1 for Pb (II). The activated carbon successfully removed methylene blue and Pb (II) with %removal exceeding 95%. The mechanisms of interaction of Pb (II) with the activated carbon is a combination of electrostatic interaction and ion exchange, while methylene blue interacts with the activated carbon via π–π interaction, hydrogen bonds, and electrostatic interaction. Thus, the prepared activated carbon has been employed to decontaminate wastewater and groundwater samples. The developed agro-waste-based activated carbon is a promising, cost-efficient, green, and accessible tool for water remediation.
Unraveling the hepatic stellate cells mediated mechanisms in aging's influence on liver fibrosis
Authors: Wahid Reham M. , Hassan Nancy Husseiny , Samy Walaa , Abdelhadi Amina A. , Saadawy Sara F. , Elsayed Sherein F. , Seada Sara G. , Mohamed Sara Refaee Abdo 
Published: June 2024

AbstractAging enhances numerous processes that compromise homeostasis and pathophysiological processes. Among these, activated HSCs play a pivotal role in advancing liver fibrosis. This research delved into how aging impacts liver fibrosis mechanisms. The study involved 32 albino rats categorized into four groups: Group I (young controls), Group II (young with liver fibrosis), Group III (old controls), and Group IV (old with liver fibrosis). Various parameters including serum ALT, adiponectin, leptin, and cholesterol levels were evaluated. Histopathological analysis was performed, alongside assessments of TGF-β, FOXP3, and CD133 gene expressions. Markers of fibrosis and apoptosis were the highest in group IV. Adiponectin levels significantly decreased in Group IV compared to all other groups except Group II, while cholesterol levels were significantly higher in liver fibrosis groups than their respective control groups. Group III displayed high hepatic expression of desmin, α-SMA, GFAP and TGF- β and in contrast to Group I. Increased TGF-β and FOXP3 gene expressions were observed in Group IV relative to Group II, while CD133 gene expression decreased in Group IV compared to Group II. In conclusion, aging modulates immune responses, impairs regenerative capacities via HSC activation, and influences adipokine and cholesterol levels, elevating the susceptibility to liver fibrosis.