bluuebunny/crossref_metadata_2025_split huggingface dataset:
A latitudinal gradient in Darwin’s naturalization conundrum at the global scale for flowering plants
Authors: Fan Shu-ya , Yang Qiang , Li Shao-peng , Fristoe Trevor S. , Cadotte Marc W. , Essl Franz , Kreft Holger , Pergl Jan , Pyšek Petr , Weigelt Patrick , Kartesz John , Nishino Misako , Wieringa Jan J. , van Kleunen Mark 
Published: October 2023

AbstractDarwin’s naturalization conundrum describes two seemingly contradictory hypotheses regarding whether alien species closely or distantly related to native species should be more likely to naturalize in regional floras. Both expectations have accumulated empirical support, and whether such apparent inconsistency can be reconciled at the global scale is unclear. Here, using 219,520 native and 9,531 naturalized alien plant species across 487 globally distributed regions, we found a latitudinal gradient in Darwin’s naturalization conundrum. Naturalized alien plant species are more closely related to native species at higher latitudes than they are at lower latitudes, indicating a greater influence of preadaptation in harsher climates. Human landscape modification resulted in even steeper latitudinal clines by selecting aliens distantly related to natives in warmer and drier regions. Our results demonstrate that joint consideration of climatic and anthropogenic conditions is critical to reconciling Darwin’s naturalization conundrum.
ADRA2A and IRX1 are putative risk genes for Raynaud’s phenomenon
Authors: Hartmann Sylvia , Yasmeen Summaira , Jacobs Benjamin M. , Denaxas Spiros , Pirmohamed Munir , Gamazon Eric R. , Caulfield Mark J. ,   Genes & Health Research Team, Hemingway Harry , Pietzner Maik , Langenberg Claudia 
Published: October 2023

AbstractRaynaud’s phenomenon (RP) is a common vasospastic disorder that causes severe pain and ulcers, but despite its high reported heritability, no causal genes have been robustly identified. We conducted a genome-wide association study including 5,147 RP cases and 439,294 controls, based on diagnoses from electronic health records, and identified three unreported genomic regions associated with the risk of RP (p < 5 × 10−8). We prioritized ADRA2A (rs7090046, odds ratio (OR) per allele: 1.26; 95%-CI: 1.20-1.31; p < 9.6 × 10−27) and IRX1 (rs12653958, OR: 1.17; 95%-CI: 1.12–1.22, p < 4.8 × 10−13) as candidate causal genes through integration of gene expression in disease relevant tissues. We further identified a likely causal detrimental effect of low fasting glucose levels on RP risk (rG = −0.21; p-value = 2.3 × 10−3), and systematically highlighted drug repurposing opportunities, like the antidepressant mirtazapine. Our results provide the first robust evidence for a strong genetic contribution to RP and highlight a so far underrated role of α2A-adrenoreceptor signalling, encoded at ADRA2A, as a possible mechanism for hypersensitivity to catecholamine-induced vasospasms.
Deposition and water repelling of temperature-responsive nanopesticides on leaves
Authors: Tang Jie , Tong Xiaojing , Chen Yongjun , Wu Yue , Zheng Zhiyuan , Kayitmazer A. Basak , Ahmad Ayyaz , Ramzan Naveed , Yang Jintao , Huang Qingchun , Xu Yisheng 
Published: October 2023

AbstractPesticides are widely used to increase agricultural productivity, however, weak adhesion and deposition lead to low efficient utilization. Herein, we prepare a nanopesticide formulation (tebuconazole nanopesticides) which is leaf-adhesive, and water-dispersed via a rapid nanoparticle precipitation method, flash nanoprecipitation, using temperature-responsive copolymers poly-(2-(dimethylamino)ethylmethylacrylate)-b-poly(ε-caprolactone) as the carrier. Compared with commercial suspensions, the encapsulation by the polymer improves the deposition of TEB, and the contact angle on foliage is lowered by 40.0°. Due to the small size and strong van der Waals interactions, the anti-washing efficiency of TEB NPs is increased by 37% in contrast to commercial ones. Finally, the acute toxicity of TEB NPs to zebrafish shows a more than 25-fold reduction as compared to commercial formulation indicating good biocompatibility of the nanopesticides. This work is expected to enhance pesticide droplet deposition and adhesion, maximize the use of pesticides, tackling one of the application challenges of pesticides.
Large-scale recording of neuronal activity in freely-moving mice at cellular resolution
Authors: Das Aniruddha , Holden Sarah , Borovicka Julie , Icardi Jacob , O’Niel Abigail , Chaklai Ariel , Patel Davina , Patel Rushik , Kaech Petrie Stefanie , Raber Jacob , Dana Hod 
Published: October 2023

AbstractCurrent methods for recording large-scale neuronal activity from behaving mice at single-cell resolution require either fixing the mouse head under a microscope or attachment of a recording device to the animal’s skull. Both of these options significantly affect the animal behavior and hence also the recorded brain activity patterns. Here, we introduce a different method to acquire snapshots of single-cell cortical activity maps from freely-moving mice using a calcium sensor called CaMPARI. CaMPARI has a unique property of irreversibly changing its color from green to red inside active neurons when illuminated with 400 nm light. We capitalize on this property to demonstrate cortex-wide activity recording without any head fixation, tethering, or attachment of a miniaturized device to the mouse’s head. Multiple cortical regions were recorded while the mouse was performing a battery of behavioral and cognitive tests. We identified task-dependent activity patterns across motor and somatosensory cortices, with significant differences across sub-regions of the motor cortex and correlations across several activity patterns and task parameters. This CaMPARI-based recording method expands the capabilities of recording neuronal activity from freely-moving and behaving mice under minimally-restrictive experimental conditions and provides large-scale volumetric data that are currently not accessible otherwise.
HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation
Authors: Kuwayama Naohiro , Kujirai Tomoya , Kishi Yusuke , Hirano Rina , Echigoya Kenta , Fang Lingyan , Watanabe Sugiko , Nakao Mitsuyoshi , Suzuki Yutaka , Ishiguro Kei-ichiro , Kurumizaka Hitoshi , Gotoh Yukiko 
Published: October 2023

AbstractIdentification of factors that regulate chromatin condensation is important for understanding of gene regulation. High-mobility group AT-hook (HMGA) proteins 1 and 2 are abundant nonhistone chromatin proteins that play a role in many biological processes including tissue stem-progenitor cell regulation, but the nature of their protein function remains unclear. Here we show that HMGA2 mediates direct condensation of polynucleosomes and forms droplets with nucleosomes. Consistently, most endogenous HMGA2 localized to transposase 5– and DNase I–inaccessible chromatin regions, and its binding was mostly associated with gene repression, in mouse embryonic neocortical cells. The AT-hook 1 domain was necessary for chromatin condensation by HMGA2 in vitro and in cellulo, and an HMGA2 mutant lacking this domain was defective in the ability to maintain neuronal progenitors in vivo. Intrinsically disordered regions of other proteins could substitute for the AT-hook 1 domain in promoting this biological function of HMGA2. Taken together, HMGA2 may regulate neural cell fate by its chromatin condensation activity.
Oncogenic context shapes the fitness landscape of tumor suppression
Authors: Blair Lily M. , Juan Joseph M. , Sebastian Lafia , Tran Vy B. , Nie Wensheng , Wall Gregory D. , Gerceker Mehmet , Lai Ian K. , Apilado Edwin A. , Grenot Gabriel , Amar David , Foggetti Giorgia , Do Carmo Mariana , Ugur Zeynep , Deng Debbie , Chenchik Alex , Paz Zafra Maria , Dow Lukas E. , Politi Katerina , MacQuitty Jonathan J. , Petrov Dmitri A. , Winslow Monte M. , Rosen Michael J. , Winters Ian P. 
Published: October 2023

AbstractTumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the interactions between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged—the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context—and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.
ZSP1601, a novel pan-phosphodiesterase inhibitor for the treatment of NAFLD, A randomized, placebo-controlled phase Ib/IIa trial
Authors: Hu Yue , Li Haijun , Zhang Hong , Chen Xiaoxin , Chen Jinjun , Xu Zhongyuan , You Hong , Dong Ruihua , Peng Yun , Li Jing , Li Xiaojiao , Wu Dandan , Zhang Lei , Cao Di , Jin He , Qiu Dongdong , Yang Aruhan , Lou Jinfeng , Zhu Xiaoxue , Niu Junqi , Ding Yanhua 
Published: October 2023

AbstractNon-alcoholic fatty liver disease is a growing health burden with limited treatment options worldwide. Herein we report a randomized, double-blind, placebo-controlled, multiple-dose trial of a first-in-class pan-phosphodiesterase inhibitor ZSP1601 in 36 NAFLD patients (NCT04140123). There were three cohorts. Each cohort included twelve patients, nine of whom received ZSP1601 50 mg once daily, 50 mg twice daily, or 100 mg twice daily, and three of whom received matching placebos for 28 days. The primary outcomes were the safety and tolerability of ZSP1601. A total of 27 (27/36, 75%) patients experienced at least one treatment-emergent adverse event (TEAE). Most TEAEs were mild to moderate. There was no Serious Adverse Event. Diarrhea, transiently elevated creatinine and adaptive headache were frequently reported adverse drug reaction. We conclude that ZSP1601 is well-tolerated and safe, showing effective improvement in liver chemistries, liver fat content and fibrosis in patients with NAFLD.
Simplified equations for object trajectories in rotating space habitats and space juggling
Authors: Dipert R. Adam 
Published: October 2023

AbstractRotating space habitats provide artificial gravity as a physiological countermeasure for long-term space habitation, though the lived experience of a person in these habitats requires further investigation. Movement planning will require adaptation to the Coriolis and centrifugal forces. The multicultural arts of juggling may offer potential psycho-physiological countermeasures for some individuals and provide interesting insights into movement planning and arts in both microgravity and rotating habitats. Previously developed equations of motion for thrown objects in rotating habitats have not been centered within the lived rotating environment. Here, I show a set of simplified equations for object trajectories in rotating environments and their underlying mathematical framework. The full set of possible trajectories for objects thrown in rotating environments is provided and a simplified approach to the Coriolis and centrifugal force differential equation using complex algebra is demonstrated. Experimentation reported in this article was conducted on parabolic flights and an analog weightlessness and rotating apparatus. Near the surface of the Earth, thrown objects travel along parabolas. In rotating space environments, thrown objects will travel along a set of mathematical curves known as roulettes, created by a fixed circle and rolling line with generator point connected to the line. These roulette trajectories will be the everyday experience of every person living in a rotating space habitat, always.
Behavioral and brain responses to verbal stimuli reveal transient periods of cognitive integration of the external world during sleep
Authors: Türker Başak , Musat Esteban Munoz , Chabani Emma , Fonteix-Galet Alexandrine , Maranci Jean-Baptiste , Wattiez Nicolas , Pouget Pierre , Sitt Jacobo , Naccache Lionel , Arnulf Isabelle , Oudiette Delphine 
Published: October 2023

AbstractSleep has long been considered as a state of behavioral disconnection from the environment, without reactivity to external stimuli. Here we questioned this ‘sleep disconnection’ dogma by directly investigating behavioral responsiveness in 49 napping participants (27 with narcolepsy and 22 healthy volunteers) engaged in a lexical decision task. Participants were instructed to frown or smile depending on the stimulus type. We found accurate behavioral responses, visible via contractions of the corrugator or zygomatic muscles, in most sleep stages in both groups (except slow-wave sleep in healthy volunteers). Across sleep stages, responses occurred more frequently when stimuli were presented during high cognitive states than during low cognitive states, as indexed by prestimulus electroencephalography. Our findings suggest that transient windows of reactivity to external stimuli exist during bona fide sleep, even in healthy individuals. Such windows of reactivity could pave the way for real-time communication with sleepers to probe sleep-related mental and cognitive processes.
Activity in primate visual cortex is minimally driven by spontaneous movements
Authors: Talluri Bharath Chandra , Kang Incheol , Lazere Adam , Quinn Katrina R. , Kaliss Nicholas , Yates Jacob L. , Butts Daniel A. , Nienborg Hendrikje 
Published: October 2023

AbstractOrganisms process sensory information in the context of their own moving bodies, an idea referred to as embodiment. This idea is important for developmental neuroscience, robotics and systems neuroscience. The mechanisms supporting embodiment are unknown, but a manifestation could be the observation in mice of brain-wide neuromodulation, including in the primary visual cortex, driven by task-irrelevant spontaneous body movements. We tested this hypothesis in macaque monkeys (Macaca mulatta), a primate model for human vision, by simultaneously recording visual cortex activity and facial and body movements. We also sought a direct comparison using an analogous approach to those used in mouse studies. Here we found that activity in the primate visual cortex (V1, V2 and V3/V3A) was associated with the animals’ own movements, but this modulation was largely explained by the impact of the movements on the retinal image, that is, by changes in visual input. These results indicate that visual cortex in primates is minimally driven by spontaneous movements and may reflect species-specific sensorimotor strategies.
Shifted PAMs generate DNA overhangs and enhance SpCas9 post-catalytic complex dissociation
Authors: Wang Jinglong , Le Gall Julien , Frock Richard L. , Strick Terence R. 
Published: October 2023

AbstractUsing Sanger sequencing and high-throughput genome sequencing of DNA cleavage reactions, we find that the Streptococcus pyogenes SpCas9 complex responds to internal mechanical strain by robustly generating a distribution of overhanging, rather than blunt, DNA ends. Internal mechanical strain is generated by shifting (increasing or decreasing) the spacing between the RNA-DNA hybrid and the downstream canonical PAM. Up to 2-base 3′ overhangs can be robustly generated via a 2-base increase in the distance between hybrid and PAM. We also use single-molecule experiments to reconstruct the full course of the CRISPR–SpCas9 reaction in real-time, structurally and kinetically monitoring and quantifying R-loop formation, the first and second DNA-incision events, and dissociation of the post-catalytic complex. Complex dissociation and release of broken DNA ends is a rate-limiting step of the reaction, and shifted SpCas9 is sufficiently destabilized so as to rapidly dissociate after formation of broken DNA ends.
Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish
Authors: Xu Alan , Teefy Bryan B. , Lu Ryan J. , Nozownik Séverine , Tyers Alexandra M. , Valenzano Dario R. , Benayoun Bérénice A. 
Published: October 2023

AbstractThe African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging ‘omic’ studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.
Highly accelerated knee magnetic resonance imaging using deep neural network (DNN)–based reconstruction: prospective, multi-reader, multi-vendor study
Authors: Lee Joohee , Jung Min , Park Jiwoo , Kim Sungjun , Im Yunjin , Lee Nim , Song Ho-Taek , Lee Young Han 
Published: October 2023

AbstractIn this prospective, multi-reader, multi-vendor study, we evaluated the performance of a commercially available deep neural network (DNN)–based MR image reconstruction in enabling accelerated 2D fast spin-echo (FSE) knee imaging. Forty-five subjects were prospectively enrolled and randomly divided into three 3T MRIs. Conventional 2D FSE and accelerated 2D FSE sequences were acquired for each subject, and the accelerated FSE images were reconstructed and enhanced with DNN–based reconstruction software (FSE-DNN). Quantitative assessments and diagnostic performances were independently evaluated by three musculoskeletal radiologists. For statistical analyses, paired t-tests, and Pearson’s correlation were used for image quality comparison and inter-reader agreements. Accelerated FSE-DNN reduced scan times by 41.0% on average. FSE-DNN showed better SNR and CNR (p < 0.001). Overall image quality of FSE-DNN was comparable (p > 0.05), and diagnostic performances of FSE-DNN showed comparable lesion detection. Two of cartilage lesions were under-graded or over-graded (n = 2) while there was no significant difference in other image sets (n = 43). Overall inter-reader agreement between FSE-conventional and FSE-DNN showed good agreement (R2 = 0.76; p < 0.001). In conclusion, DNN-based reconstruction can be applied to accelerated knee imaging in multi-vendor MRI scanners, with reduced scan time and comparable image quality. This study suggests the potential for DNN-accelerated knee MRI in clinical practice.
Disentangling the origins of viticulture in the western Mediterranean
Authors: Breglia Francesco , Bouby Laurent , Wales Nathan , Ivorra Sarah , Fiorentino Girolamo 
Published: October 2023

AbstractWe present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450–1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.
MAxSIM: multi-angle-crossing structured illumination microscopy with height-controlled mirror for 3D topological mapping of live cells
Authors: Gardeazabal Rodriguez Pedro Felipe , Lilach Yigal , Ambegaonkar Abhijit , Vitali Teresa , Jafri Haani , Sohn Hae Won , Dalva Matthew , Pierce Susan , Chung Inhee 
Published: October 2023

AbstractMapping 3D plasma membrane topology in live cells can bring unprecedented insights into cell biology. Widefield-based super-resolution methods such as 3D-structured illumination microscopy (3D-SIM) can achieve twice the axial ( ~ 300 nm) and lateral ( ~ 100 nm) resolution of widefield microscopy in real time in live cells. However, twice-resolution enhancement cannot sufficiently visualize nanoscale fine structures of the plasma membrane. Axial interferometry methods including fluorescence light interference contrast microscopy and its derivatives (e.g., scanning angle interference microscopy) can determine nanoscale axial locations of proteins on and near the plasma membrane. Thus, by combining super-resolution lateral imaging of 2D-SIM with axial interferometry, we developed multi-angle-crossing structured illumination microscopy (MAxSIM) to generate multiple incident angles by fast, optoelectronic creation of diffraction patterns. Axial localization accuracy can be enhanced by placing cells on a bottom glass substrate, locating a custom height-controlled mirror (HCM) at a fixed axial position above the glass substrate, and optimizing the height reconstruction algorithm for noisy experimental data. The HCM also enables imaging of both the apical and basal surfaces of a cell. MAxSIM with HCM offers high-fidelity nanoscale 3D topological mapping of cell plasma membranes with near-real-time ( ~ 0.5 Hz) imaging of live cells and 3D single-molecule tracking.