bluuebunny/crossref_metadata_2025_split huggingface dataset:
Children Develop Adult-Like Visual Sensitivity to Image Memorability by the Age of Four
Authors: Guo Xiaohan (Hannah) , Bainbridge Wilma A. 
Published: December 2022

AbstractAdults have been shown to consistently remember and forget certain images despite large individual differences, suggesting a population-wide sensitivity to an image’s intrinsicmemorability—a measure of how successfully an image is remembered. While a decade of research has focused on image memorability among adults, the developmental trajectory of these consistencies in memory is understudied. Here, we investigate by what age children gain adultlike sensitivity to the image memorability effect. We utilized data from Saragosa-Harris et al. (2021), where 137 children aged between 3 and 5 years old encoded animal-scene image pairs and then after a 5-minute, 24-hour, or 1-week delay performed a cued recognition task for each scene target given its animal cue. We tested adults’ memory of the same scene images using ResMem (Needell & Bainbridge, 2022), a pre-trained deep neural network that predicts adult image memorability scores, and using an online behavioral continuous recognition task(N= 116). Results showed that ResMem predictions, as a proxy of adults’ memory, predicted scene memory of children by the age of 4 and were the most predictive of children’s memory across ages after a long, 1-week delay. Children at age 3 show non-adult-like consistent memory patterns, implying that the non-adult-like memory patterns were not due to poor memory performance. Instead, 3-year-olds may have consistently used certain visual memory strategies that become less optimal as they age. Our results suggest that adult-like sensitivity to image memorability emerges by the age of 4 through experience.Public Significance StatementThis study strongly suggests that children older than 4 years old tend to remember and forget the same images as adults. We recommend teachers and caregivers to utilize the ResMem DNN to select memorable images to be used in educational settings.
A pair of NLRs coordinately modulates NRC3-mediated ETI responses to facilitate age-dependent immunity
Authors: Dong Xiaohua , Zhang Xiaoyan , Yin Zhiyuan , Li Jialu , Xia Chuyan , Pan Weiye , Zhao Yaning , Jing Maofeng , Liu Jinding , Ai Gan , Dou Daolong 
Published: December 2022

AbstractTwo NLRs (Nucleotide-binding and Leucine-rich repeat Receptors) adjacent to each other on a locus, termed as paired NLRs, may act separately for effector recognition and subsequent signaling activation to mediate effector-triggered immunity (ETI) in many plants. However, it is largely unknown about their distribution and functions in Solanaceae species, in which NLR-Hs (Helpers NLR REQUIRED FOR CELL DEATHs) have been extensively studied. Here, we identified paired NLRs in Solanaceae species and found they harbor paired NLRs ranging from 6 to 100, which are significantly negatively correlated with the numbers of NLR-Hs.N. benthamianahas six paired NLRs, among which silencing ofNRCXexhibits phenotypes of dwarfism and accelerated senescence. Importantly,NRCX-silencing phenotypes could be restored by simultaneously silencing its head-to-head NLR pair, thus we named it asNRCY. NRCX/Y pair is specific in Solanaceae species. NRCY contains non-canonical walker B and MHD motifs, but could not induce autoactive cell death inN. benthamiana. Instead of that, silencingNRCYimpaired cell death triggered by Sw5b-Nsm and NRC3D480V, indicating NRCY is also an NLR modulator like NRCX. Furthermore, NRCX suppression of Sw5b-Nsm and NRC3-mediated cell death is dependent on NRCY. Remarkably, we found thatNRCXandNRCYexpressions were induced during plant senescence, whileNRCYwas induced more thanNRCX. Accordingly, the plant resistance was stronger during maturation, indicated NRCX/Y might be involved in age-dependent resistance. Our study reveals one of the paired NLRs coordinately regulates ETI to facilitate age-dependent immunity.
Metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments
Authors: Xiao Xi , Luo Min , Zhang Chuwen , Zhang Tingting , Yin Xiuran , Wu Xuemin , Zhao Jing , Tao Jun , Chen Zongheng , Liang Qianyong , Dong Xiyang 
Published: December 2022

AbstractAnaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Here, we combined geochemistry, muti-omics and numerical modeling to study metal-dependent AOM in methanic cold seep sediments in the northern continental slope of the South China Sea. Geochemical data based on methane concentrations, carbon stable isotope, solid-phase sediment analysis and pore water measurements indicate the occurrence of anaerobic methane oxidation coupled to metal oxides reduction in the methanic zone. The 16S rRNA gene amplicons and transcripts, along with metagenomic and metatranscriptomic data suggest that diverse ANME groups actively mediated methane oxidation in the methanic zone either independently or in syntrophy with e.g. ETH-SRB1 as potential metal reducers. Modeling results suggest that the estimated rates of methane consumption via Fe-AOM and Mn-AOM were both 0.3 μmol cm-2yr-1, which account for ∼3% of total CH4removal in sediments. Overall, our results highlight metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments.
STAT5 Gain-of-Function Variants Promote Precursor T-Cell Receptor Activation to Drive T-Cell Acute Lymphoblastic Leukemia
Authors: Suske Tobias , Sorger Helena , Ruge Frank , Prutsch Nicole , Zimmerman Mark W. , Eder Thomas , Maurer Barbara , Wagner Christina , Schönefeldt Susann , Spirk Katrin , Pichler Alexander , Pemovska Tea , Schweicker Carmen , Pölöske Daniel , Jungherz Dennis , Müller Tony Andreas , Aung Myint Myat Khine , Pham Ha Thi Thanh , Zimmel Kerstin , Krausgruber Thomas , Bock Christoph , Müller Mathias , Dahlhoff Maik , Boersma Auke , Rülicke Thomas , Fleck Roman , Gunning Patrick Thomas , Aittokallio Tero , Mustjoki Satu , Sanda Takaomi , Hartmann Sylvia , Grebien Florian , Hoermann Gregor , Haferlach Torsten , Staber Philipp Bernhard , Neubauer Heidi Anne , Look Alfred Thomas , Herling Marco , Moriggl Richard 
Published: December 2022

AbstractT-cell acute lymphoblastic leukemia (T-ALL) is an aggressive immature T-cell cancer. Hotspot mutations in JAK-STAT pathway membersIL7R,JAK1andJAK3were analyzed in depth. However, the role ofSTAT5AorSTAT5Bmutations promoting their hyperactivation is poorly understood in the context of T-cell cancer initiation and acute leukemia progression. Importantly, the driver mutationSTAT5BN642Hencodes the most frequent activating STAT5 variant in T-ALL associated with poor prognosis. Here, we show that hyperactive STAT5 promotes early T-cell progenitor (ETP)-ALL-like cancer in mice and upregulated genes involved in T-cell receptor signaling (TCR), even in absence of surface TCR promoting. Importantly, these genes were also overexpressed in human T-ALL and other STAT5-dependent T-cell cancers. Moreover, human T-ALL cells were sensitive to pharmacologic inhibition by dual STAT3/5 degraders or ZAP70 tyrosine kinase blockers. Thus, we define STAT5 target genes in T-ALL that promote pre-TCR signaling mimicry. We propose therapeutic targeting using selective ZAP70 or STAT3/5 inhibitors in a subgroup of T-ALL patients with prominent IL-7R-JAK1/3-STAT5 activity.SignificanceWe provide detailed functional characterizations of hyperactive STAT5A or STAT5B in thymic T-cell development and transformation. We found that hyperactive STAT5 transcribes T-cell-specific kinases or pre-TCR signaling hubs to promote T-ALL. Biomolecular and next-generation-sequencing methods, transgenesis and pharmacologic interference revealed that hyperactive STAT5 is a key oncogenic driver that can be targeted in T-ALL using STAT3/5 or SYK family member tyrosine kinase inhibitors.Conflict of interestThe authors declare no potential conflicts of interest.
Peripheral vs. Core Body Temperature as Hypocretin/Orexin Neurons Degenerate: Exercise Mitigates Increased Heat Loss
Authors: Sun Yu , Tisdale Ryan K. , Yamashita Akira , Kilduff Thomas S. 
Published: December 2022

AbstractHypocretins/Orexins (Hcrt/Ox) are hypothalamic neuropeptides implicated in diverse functions, including body temperature regulation through modulation of sympathetic vasoconstrictor tone. In the current study, we measured subcutaneous (Tsc) and core (Tb) body temperature as well as activity in a conditional transgenic mouse strain that allows the inducible ablation of Hcrt/Ox-containing neurons by removal of doxycycline (DOX) from their diet (orexin-DTAmice). Measurements were made during a baseline, when mice were being maintained on food containing DOX, and over 42 days while the mice were fed normal chow which resulted in Hcrt/Ox neuron degeneration. The home cages of theorexin-DTAmice were equipped with running wheels that were either locked or unlocked. In the presence of a locked running wheel, Tscprogressively decreased on days 28 and 42 in the DOX(-) condition, primarily during the dark phase (the major active period for rodents). This nocturnal reduction in Tscwas mitigated when mice had access to unlocked running wheels. In contrast to Tsc, Tbwas largely maintained until day 42 in the DOX(-) condition even when the running wheel was locked. Acute changes in both Tscand Tbwere observed preceding, during, and following cataplexy. Our results suggest that ablation of Hcrt/Ox-containing neurons results in elevated heat loss, likely through reduced sympathetic vasoconstrictor tone, and that exercise may have some therapeutic benefit to patients with narcolepsy, a disorder caused by Hcrt/Ox deficiency. Acute changes in body temperature may facilitate prediction of cataplexy onset and lead to interventions to mitigate its occurrence.HighlightsHypocretin/Orexin (Hcrt/Ox) neuron degeneration results in the sleep disorder Narcolepsy and reduced subcutaneous body temperature (Tsc) during the dark phase of the 24-h light/dark cycle.This reduction in dark phase Tscis mitigated by access to an exercise opportunity.In contrast to Tsc, core body temperature (Tb) is largely maintained as the Hcrt/Ox neurons degenerate.Reduced Tscwhile Tbis maintained suggests increased heat loss, possibly through modulation of sympathetic vasoconstrictor tone.Hcrt/Ox neuron loss in Narcolepsy results in cataplexy, whose occurrence is associated with acute changes in both Tscand Tb.Exercise may represent an effective intervention for mitigating heat loss resulting from Hcrt/Ox neuron loss in Narcolepsy.
Test-Retest Reliability of the Human Connectome: An OPM-MEG study
Authors: Rier Lukas , Michelmann Sebastian , Ritz Harrison , Shah Vishal , Hill Ryan M. , Osborne James , Doyle Cody , Holmes Niall , Bowtell Richard , Brookes Matthew J. , Norman Kenneth A. , Hasson Uri , Cohen Jonathan D. , Boto Elena 
Published: December 2022

ABSTRACTMagnetoencephalography with optically pumped magnetometers (OPM-MEG) offers a new way to record electrophysiological brain function, with significant advantages over conventional MEG including adaptability to head shape/size, free movement during scanning, better spatial resolution, increased signal, and no reliance on cryogenics. However, OPM-MEG remains in its infancy, with significant questions to be answered regarding optimal system design and robustness. Here, we present an open-source dataset acquired using a newly constructed OPM-MEG system with a triaxial sensor design averaging 168 channels. Using OPM-optimised magnetic shielding and active background-field control, we measure the test-retest reliability of the human connectome. We employ amplitude envelope correlation to measure whole-brain functional connectivity in 10 individuals whilst they watch a 600 s move clip. Our results show high repeatability between experimental runs at the group level, with a correlation coefficient of 0.81 in the theta, 0.93 in alpha and 0.94 in beta frequency ranges. At the individual subject level, we found marked differences between individuals, but high within-subject robustness (correlations of 0.56 ± 0.25, 0.72 ± 0.15 and 0.78 ± 0.13 in theta, alpha and beta respectively). These results compare well to previously reported findings using conventional MEG; they show that OPM-MEG is a viable way to characterise whole brain connectivity and add significant weight to a growing argument that OPMs can overtake cryogenic sensors as the fundamental building block of MEG systems.
DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence
Authors: Fang Yuqi , Ji Zhicheng , Zhou Weiqiang , Abante Jordi , Koldobskiy Michael A. , Ji Hongkai , Feinberg Andrew P. 
Published: December 2022

AbstractEpigenetic information defines tissue identity and is largely inherited in development through DNA methylation. While studied mostly for mean differences, methylation also encodes stochastic change, defined as entropy in information theory. Analyzing allelespecific methylation in 48 human tissue sample datasets, we find that methylation entropy is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Then applying information theory to 42 mouse embryo methylation datasets, we find that time- and tissue-specific patterns of development are more strongly correlated with methylation entropy than with mean, and methylation entropy is associated with sequence and chromatin features conserved with human. Moreover, methylation entropy is directly related to gene expression variability in development, suggesting a role for epigenetic entropy in developmental plasticity.
Glucosinolate catabolism maintains glucosinolate profiles and transport in sulfur-starvedArabidopsis
Authors: Zhang Liu , Kawaguchi Ryota , Enomoto Takuro , Nishida Sho , Burow Meike , Maruyama-Nakashita Akiko 
Published: December 2022

AbstractGlucosinolates (GSL) are sulfur (S)-rich specialized metabolites produced by plants of the Brassicales order. Our previous study found that in Arabidopsis seedlings, S deficiency (−S) promoted GSL catabolism by activating two ß-glucosidases (BGLU), BGLU28 and BGLU30. The induced GSL catabolism was a survival strategy for seedlings grown under −S, because S released from GSL was reincorporated into primary S metabolites which are essential for plant growth. However, as GSL profile in plants vary among growth stages and organs, we set out to test a potential contribution of BGLU28/30-dependent GSL catabolism at the reproductive growth stage. Thus, in this study, we assessed growth, metabolic, and transcriptional phenotypes of maturebglu28/30double mutants grown under different S conditions. Our results showed that compared to wild-type plants grown under −S, maturebglu28/30mutants displayed impaired growth and accumulated increased levels of GSL in their mature seeds, siliques, flowers, and rosette leaves of before bolting plants. In contrast, the levels of primary S-containing metabolites, glutathione and cysteine, were decreased in mature seeds. Furthermore, the transport of GSL from rosette leaves to the reproductive organs was stimulated in thebglu28/30mutants under −S. Transcriptome analysis revealed that genes related to other biological processes, such as phytohormone signaling and plant response to heat, responded differentially to −S in thebglu28/30mutants. Altogether, these findings broadened our understanding of the roles of BGLU28/30-dependent GSL catabolism in plant adaptation to nutrient stress.One-sentence summaryDisruption of glucosinolate catabolic genes,BGLU28andBGLU30, in sulfur-starved matureArabidopsisimpaired growth, affected glucosinolate distribution, and altered transcriptional profiles.
Immunomodulation of Neutrophil Granulocyte Functions by Bacterial Polyphosphates
Authors: Krenzlin Viola , Schöche Johannes , Walachowski Sarah , Reinhardt Christoph , Radsak Markus P. , Bosmann Markus 
Published: December 2022

AbstractPolyphosphates are highly conserved, linear polymers of monophosphates that reside in all living cells. Bacteria produce long chains containing hundreds to thousands of phosphate units, which can interfere with host defense to infection.Here, we report that intratracheal long-chain polyphosphate administration to C57BL/6J mice resulted in the release of proinflammatory cytokines and influx of Ly6G+polymorphonuclear neutrophils in the bronchoalveolar lavage fluid causing a disruption of the physiologic endothelial-epithelial small airway barrier and histologic signs of lung injury. Polyphosphate-induced effects were attenuated after neutrophil depletion in mice. In isolated murine neutrophils, long-chain polyphosphates modulated cytokine release induced by lipopolysaccharides (LPS) from gram-negative bacteria or lipoteichoic acid from gram-positive bacteria. In addition, long-chain polyphosphates induced immune evasive effects in human neutrophils. In detail, long-chain polyphosphates down-regulated CD11b and curtailed the phagocytosis ofE. coliparticles by neutrophils. Polyphosphates modulated the migration capacity by inducing CD62L shedding resulting in CD62Llowand CD11blowneutrophils. The release of IL-8 induced by LPS was also significantly reduced. Pharmacologic blockade of PI3K with wortmannin antagonized long-chain polyphosphate-induced effects on LPS-induced IL-8 release.In conclusion, polyphosphates govern immunomodulation in murine and human neutrophils suggesting polyphosphates as a therapeutic target for bacterial infections to restore innate immune defense.
Can hubs of the human connectome be identified consistently with diffusion MRI?
Authors: Gajwani Mehul , Oldham Stuart J. , Pang James C. , Arnatkevičiūtė Aurina , Tiego Jeggan , Bellgrove Mark A. , Fornito Alex 
Published: December 2022

AbstractRecent years have seen a surge in the use of diffusion MRI to map connectomes in humans, paralleled by a similar increase in processing and analysis choices. Yet these different steps and their effects are rarely compared systematically. Here, in a healthy young adult population (n=294), we characterized the impact of a range of analysis pipelines on one widely studied property of the human connectome; its degree distribution. We evaluated the effects of 40 pipelines (comparing common choices of parcellation, streamline seeding, tractography algorithm, and streamline propagation constraint) and 44 group-representative connectome reconstruction schemes on highly connected hub regions. We found that hub location is highly variable between pipelines. The choice of parcellation has a major influence on hub architecture, and hub connectivity is highly correlated with regional surface area in most of the assessed pipelines (ρ>0.70 in 69% of the pipelines), particularly when using weighted networks. Overall, our results demonstrate the need for prudent decision-making when processing diffusion MRI data, and for carefully considering how different processing choices can influence connectome organization.Author SummaryThe increasing use of diffusion MRI for mapping white matter connectivity has been matched by a similar increase in the number of ways to process the diffusion data. Here, we assess how diffusion processing affects hubs across 1760 pipeline variations. Many processing pipelines do not show a high concentration of connectivity within hubs. When present, hub location and distribution vary based on processing choices. The choice of probabilistic or deterministic tractography has a major impact on hub location and strength. Finally, node strength in weighted networks can correlate highly with node size. Overall, our results illustrate the need for prudent decision-making when processing and interpreting diffusion MRI data.Code and data availabilityAll the data used in this study is openly available on Figshare athttps://doi.org/10.26180/c.6352886.v1. Scripts to analyze these data are available on GitHub athttps://github.com/BMHLab/DegreeVariability.Competing InterestsThe authors declare that they have no competing interests.
Antibiotic-degrading resistance changes bacterial community structure via species-specific responses
Authors: Pathak Ayush , Angst Daniel C. , León-Sampedro Ricardo , Hall Alex R. 
Published: December 2022

AbstractSome bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to grow at degraded antibiotic concentrations.