bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross‐Orogen Granite Migration as an Indicator of Slab Rollback Along Eastern Gondwana
Authors: Zhang Qing , Buckman Solomon , Mitchell Ross N. , Nutman Allen P. , Li Xian‐Hua , Bennett Vickie C. , Beer Courtney 
Published: June 2023

AbstractSlab rollback during subduction plays a key role in controlling continental growth at convergent plate boundaries. The dynamics of currently subducting slabs can be precisely constrained using geophysical techniques. In contrast, ancient episodes of slab rollback can be difficult to constrain, yet are critical to unlocking the tectonic evolution of long‐lived orogens such as the Phanerozoic Australian Tasmanides of eastern Gondwana. Recognition of ancient slab rollback relies on the identification of the progressive migration of magmatic arcs. Here, we investigate the timing and isotopic variation of ∼90 km of the trans‐orogen migration of the Carboniferous Bathurst Batholith as a potential indicator of slab rollback. U–Pb–Hf isotopes, combined with a regional zircon Hf isotope data set, suggest that the eastward migration of the batholith over ∼18 Myr, from 340.1 to 322.4 Ma, records a maximum slab steepening rate of ∼0.6–1.2° Myr−1 in a relatively stable trench setting. These results provide a magmatic record of Carboniferous slab rollback and establish a missing link between the long‐lived Lachlan and New England orogens of the eastern Gondwanan Tasmanides.
Geochemical Constraints on the Origin of Primitive Potassic Lavas in the Eastern Virunga Volcanic Province
Authors: Pitcavage E. , Furman T. , Nelson W. R. , Graham D. W. , Shirey S. , Kulyanyingi P. K. , Barifaijo E. 
Published: June 2023

AbstractYoung mafic lavas from the East African Western Rift record melting of subcontinental lithospheric mantle that was metasomatically modified by multiple tectonic events. We report new isotope data from monogenetic cinder cones near Bufumbira, Uganda, in the Virunga Volcanic Field: 87Sr/86Sr = 0.7059–0.7079, εNd = −6.5 to −1.3, εHf = −6.3 to +0.9, 208Pb/204Pb = 40.1–40.7, 207Pb/204Pb = 15.68–15.75, and 206Pb/204Pb = 19.27–19.45. Olivine phenocrysts from the Bufumbira lavas have 3He/4He = 6.0–7.4 RA. The isotopic data, in conjunction with major and trace element systematics, indicate that primitive Bufumbira magmas are derived from two different metasomatized lithospheric source domains. Melts generated by lower degrees of melting record greater contributions from ∼1 to 2 Ga isotopically enriched garnet‐amphibole‐phlogopite pyroxenite veins within the lithosphere. As melting progresses, these vein melts become increasingly diluted by melts that originate near the lithosphere/asthenosphere boundary, shifting the isotopic compositions toward the common lithospheric mantle (CLM) proposed by Furman and Graham (1999, https://doi.org/10.1016/s0024-4937(99)00031-6). This ∼450–500 Ma source domain appears to underlie all Western Rift volcanic provinces and is characterized by 87Sr/86Sr ∼ 0.705, εNd ∼ 0, εHf ∼ +1 to +3, 206Pb/204Pb ∼ 19.0–19.2, 208Pb/204Pb ∼ 39.7, and 3He/4He ∼ 7 RA. Basal portions of the dense subcontinental lithospheric mantle may become gravitationally unstable and founder into underlying warmer asthenosphere, exposing surfaces where melting of locally heterogeneous veins produces small‐volume, alkaline mafic melts. Mafic lavas from all Western Rift volcanic provinces record mixing between the CLM and locally variable metasomatized source domains, suggesting this style of melt generation is fundamental to the development of magma‐poor rifts.
Deficits in integrative NMDA receptors caused by Grin1 disruption can be rescued in adulthood
Authors: Venkatesan Sridevi , Binko Mary A. , Mielnik Catharine A. , Ramsey Amy J. , Lambe Evelyn K. 
Published: June 2023

AbstractGlutamatergic NMDA receptors (NMDAR) are critical for cognitive function, and their reduced expression leads to intellectual disability. Since subpopulations of NMDARs exist in distinct subcellular environments, their functioning may be unevenly vulnerable to genetic disruption. Here, we investigate synaptic and extrasynaptic NMDARs on the major output neurons of the prefrontal cortex in mice deficient for the obligate NMDAR subunit encoded by Grin1 and wild-type littermates. With whole-cell recording in brain slices, we find that single, low-intensity stimuli elicit surprisingly-similar glutamatergic synaptic currents in both genotypes. By contrast, clear genotype differences emerge with manipulations that recruit extrasynaptic NMDARs, including stronger, repetitive, or pharmacological stimulation. These results reveal a disproportionate functional deficit of extrasynaptic NMDARs compared to their synaptic counterparts. To probe the repercussions of this deficit, we examine an NMDAR-dependent phenomenon considered a building block of cognitive integration, basal dendrite plateau potentials. Since we find this phenomenon is readily evoked in wild-type but not in Grin1-deficient mice, we ask whether plateau potentials can be restored by an adult intervention to increase Grin1 expression. This genetic manipulation, previously shown to restore cognitive performance in adulthood, successfully rescues electrically-evoked basal dendrite plateau potentials after a lifetime of NMDAR compromise. Taken together, our work demonstrates NMDAR subpopulations are not uniformly vulnerable to the genetic disruption of their obligate subunit. Furthermore, the window for functional rescue of the more-sensitive integrative NMDARs remains open into adulthood.
Ethambutol and visual assessment in England: current practice and recommendations
Authors: MacVinish Sally , McMaster David , Moledina Tanya , Tamne Surinder K. , Ashworth Jane , Anderson Sarah R. 
Published: June 2023

Abstract
Background
Standard treatment for tuberculosis (TB) in children and adults includes an initial two-month course of ethambutol, a drug that in rare cases can cause optic neuropathy and irreversible vision loss. There is a lack of clear guidance on what vision assessments are needed before and during treatment with ethambutol, with the Royal College of Ophthalmologists, National Institute for Health and Care Excellence, British National Formulary and British Thoracic Society offering different guidance. We aimed to assess how vision is routinely tested in patients treated with ethambutol in TB services across England.

Methods
An online survey developed by Public Health England was sent to all TB services in England in 2018 to assess current practice and inform the development of best practice recommendations for visual assessment of patients treated with ethambutol for TB.

Results
Sixty-six TB professionals from across England responded, a response rate of 54%. The results showed variations in practice, including when to omit ethambutol from treatment, the timing and frequency of visual assessment, the type of visual assessment, referral processes and management of visual changes.

Conclusion
This national survey highlights the need for clear guidelines on the testing of vision for patients taking ethambutol at recommended doses, before and during treatment. We suggest a pragmatic approach to visual assessment to reduce variation in practice, proposing a stepwise pathway for patients on standard TB treatment for local adaptation.
Mycobacterium abscessus VapC5 toxin potentiates evasion of antibiotic killing by ribosome overproduction and activation of multiple resistance pathways
Authors: Troian Eduardo A. , Maldonado Heather M. , Chauhan Unnati , Barth Valdir C. , Woychik Nancy A. 
Published: June 2023

AbstractMycobacterium abscessus (Mab) infections are inexplicably intractable to clearing after aggressive and lengthy treatment regimens. Here we discovered that acquisition of a single toxin-antitoxin system enables Mab to activate a phenotypic switch that enhances survival upon treatment with current first-line antibiotics. This switch is tripped when the VapC5 toxin inactivates tRNASerCGA by cleavage at only one site within its anticodon, leading to growth arrest. Concomitant tRNASerCGA depletion then reprograms the transcriptome to favor synthesis of proteins naturally low in the cognate Ser UCG codon including the transcription factor WhiB7 and members of its regulon as well as the ribosomal protein family. This programmed stockpiling of ribosomes is predicted to override the efficacy of ribosome-targeting antibiotics while the growth arrest phenotype attenuates antibiotics targeting cell wall synthesis. In agreement, VapC5 increases Mab persister formation upon exposure to amikacin and the next-generation oxazolidinone tedizolid (both target ribosomes) or cefoxitin (inhibits cell wall synthesis). These findings expand the repertoire of genetic adaptations harnessed by Mab to survive assaults intended to eradicate it, as well as provide a much-needed framework for selection of shorter and more efficacious alternate treatment options for Mab infections using currently available antimicrobials whose targets are not confounded by VapC5.
A magnetic hydrogel for the efficient retrieval of kidney stone fragments during ureteroscopy
Authors: Ge T. Jessie , Roquero Daniel Massana , Holton Grace H. , Mach Kathleen E. , Prado Kris , Lau Hubert , Jensen Kristin , Chang Timothy C. , Conti Simon , Sheth Kunj , Wang Shan X. , Liao Joseph C. 
Published: June 2023

AbstractOnly 60-75% of conventional kidney stone surgeries achieve complete stone-free status. Up to 30% of patients with residual fragments <2 mm in size experience subsequent stone-related complications. Here we demonstrate a stone retrieval technology in which fragments are rendered magnetizable with a magnetic hydrogel so that they can be easily retrieved with a simple magnetic tool. The magnetic hydrogel facilitates robust in vitro capture of stone fragments of clinically relevant sizes and compositions. The hydrogel components exhibit no cytotoxicity in cell culture and only superficial effects on ex vivo human urothelium and in vivo mouse bladders. Furthermore, the hydrogel demonstrates antimicrobial activity against common uropathogens on par with that of common antibiotics. By enabling the efficient retrieval of kidney stone fragments, our method can lead to improved stone-free rates and patient outcomes.
Oncogenic structural aberration landscape in gastric cancer genomes
Authors: Saito-Adachi Mihoko , Hama Natsuko , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Hosoda Fumie , Rokutan Hirofumi , Yachida Shinichi , Kato Mamoru , Fukagawa Akihiko , Shibata Tatsuhiro 
Published: June 2023

AbstractStructural variants (SVs) are responsible for driver events in gastric cancer (GC); however, their patterns and processes remain poorly understood. Here, we examine 170 GC whole genomes to unravel the oncogenic structural aberration landscape in GC genomes and identify six rearrangement signatures (RSs). Non-random combinations of RSs elucidate distinctive GC subtypes comprising one or a few dominant RS that are associated with specific driver events (BRCA1/2 defects, mismatch repair deficiency, and TP53 mutation) and epidemiological backgrounds. Twenty-seven SV hotspots are identified as GC driver candidates. SV hotspots frequently constitute complexly clustered SVs involved in driver gene amplification, such as ERBB2, CCNE1, and FGFR2. Further deconstruction of the locally clustered SVs uncovers amplicon-generating profiles characterized by super-large SVs and intensive segmental amplifications, contributing to the extensive amplification of GC oncogenes. Comprehensive analyses using adjusted SV allele frequencies indicate the significant involvement of extra-chromosomal DNA in processes linked to specific RSs.
Thermally trainable dual network hydrogels
Authors: Hu Shanming , Fang Yuhuang , Liang Chen , Turunen Matti , Ikkala Olli , Zhang Hang 
Published: June 2023

AbstractInspired by biological systems, trainable responsive materials have received burgeoning research interests for future adaptive and intelligent material systems. However, the trainable materials to date typically cannot perform active work, and the training allows only one direction of functionality change. Here, we demonstrate thermally trainable hydrogel systems consisting of two thermoresponsive polymers, where the volumetric response of the system upon phase transitions enhances or decreases through a training process above certain threshold temperature. Positive or negative training of the thermally induced deformations can be achieved, depending on the network design. Importantly, softening, stiffening, or toughening of the hydrogel can be achieved by the training process. We demonstrate trainable hydrogel actuators capable of performing increased active work or implementing an initially impossible task. The reported dual network hydrogels provide a new training strategy that can be leveraged for bio-inspired soft systems such as adaptive artificial muscles or soft robotics.
Increase in Cape Verde hurricanes during Atlantic Niño
Authors: Kim Dongmin , Lee Sang-Ki , Lopez Hosmay , Foltz Gregory R. , Wen Caihong , West Robert , Dunion Jason 
Published: June 2023

AbstractAt seasonal-to-interannual timescales, Atlantic hurricane activity is greatly modulated by El Niño–Southern Oscillation and the Atlantic Meridional Mode. However, those climate modes develop predominantly in boreal winter or spring and are weaker during the Atlantic hurricane season (June–November). The leading mode of tropical Atlantic sea surface temperature (SST) variability during the Atlantic hurricane season is Atlantic Niño/Niña, which is characterized by warm/cold SST anomalies in the eastern equatorial Atlantic. However, the linkage between Atlantic Niño/Niña and hurricane activity has not been examined. Here, we use observations to show that Atlantic Niño, by strengthening the Atlantic inter-tropical convergence zone rainband, enhances African easterly wave activity and low-level cyclonic vorticity across the deep tropical eastern North Atlantic. We show that such conditions increase the likelihood of powerful hurricanes developing in the deep tropics near the Cape Verde islands, elevating the risk of major hurricanes impacting the Caribbean islands and the U.S.
The integrated metallicity profile of the Milky Way
Authors: Lian Jianhui , Bergemann Maria , Pillepich Annalisa , Zasowski Gail , Lane Richard R. 
Published: June 2023

AbstractThe heavy element abundance profiles of galaxies place stringent constraints on galaxy growth and assembly history. As the Milky Way is currently the only spiral galaxy in which we can measure temporally resolved chemical abundances, it enables insights into the origin of metallicity gradients and their correlation with the growth history of galaxies. However, until now, these abundance profiles have not been translated into the integrated-light measurements that are needed to compare the Milky Way with the general galaxy population. Here we report the measurement of the light-weighted, integrated stellar metallicity profile of our Galaxy. We find that the integrated stellar metallicity profile of the Milky Way has a ∧-like broken shape, with a mildly positive gradient inside a Galactocentric radius of 7 kpc and a steep negative gradient outside. This broken integrated metallicity profile of the Milky Way is not unique but is not common among Milky Way-mass star-forming galaxies observed in the MaNGA survey and simulated in the TNG50 cosmological simulation. Our results suggest that the Milky Way might not have a typical metallicity distribution for a galaxy of its mass, and thus offers valuable insight into the rich variety of galaxy enrichment processes.
Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning
Authors: Liu Tairan , Li Yuzhu , Koydemir Hatice Ceylan , Zhang Yijie , Yang Ethan , Eryilmaz Merve , Wang Hongda , Li Jingxi , Bai Bijie , Ma Guangdong , Ozcan Aydogan 
Published: June 2023

AbstractA plaque assay—the gold-standard method for measuring the concentration of replication-competent lytic virions—requires staining and usually more than 48 h of runtime. Here we show that lens-free holographic imaging and deep learning can be combined to expedite and automate the assay. The compact imaging device captures phase information label-free at a rate of approximately 0.32 gigapixels per hour per well, covers an area of about 30 × 30 mm2 and a 10-fold larger dynamic range of virus concentration than standard assays, and quantifies the infected area and the number of plaque-forming units. For the vesicular stomatitis virus, the automated plaque assay detected the first cell-lysing events caused by viral replication as early as 5 h after incubation, and in less than 20 h it detected plaque-forming units at rates higher than 90% at 100% specificity. Furthermore, it reduced the incubation time of the herpes simplex virus type 1 by about 48 h and that of the encephalomyocarditis virus by about 20 h. The stain-free assay should be amenable for use in virology research, vaccine development and clinical diagnosis.
Coulomb-correlated electron number states in a transmission electron microscope beam
Authors: Haindl Rudolf , Feist Armin , Domröse Till , Möller Marcel , Gaida John H. , Yalunin Sergey V. , Ropers Claus 
Published: June 2023

AbstractWhile correlated electrons are at the heart of many phenomena in condensed matter, as well as atomic and molecular physics, Coulomb interactions in free-electron beams are generally considered detrimental. Here, we demonstrate the generation of Coulomb-correlated pair, triple and quadruple states of free electrons by femtosecond photoemission from a nanoscale field emitter inside a transmission electron microscope. Event-based electron spectroscopy allows the spatial and spectral characterization of the electron ensemble emitted by each laser pulse. We identify distinctive energy and momentum correlations arising from acceleration-enhanced interparticle energy exchange, revealing strong few-body Coulomb interactions at an energy scale of 2 eV. State-sorted beam caustics show a discrete increase in virtual source size and longitudinal source shift for few-electron states, associated with transverse momentum correlations. We observe field-controllable electron antibunching, attributed primarily to transverse Coulomb deflection. The pronounced spatial and spectral characteristics of these electron number states allow filtering schemes that control the statistical distribution of the pulse charge. In this way, the fraction of specific few-electron states can be actively suppressed or enhanced, facilitating the preparation of highly non-Poissonian electron beams for microscopy and lithography, including future heralding schemes and correlated multi-electron probing.
Single-cell m6A mapping in vivo using picoMeRIP–seq
Authors: Li Yanjiao , Wang Yunhao , Vera-Rodriguez Maria , Lindeman Leif Christopher , Skuggen Linda Ellevog , Rasmussen Erik M. K. , Jermstad Ingunn , Khan Shaista , Fosslie Madeleine , Skuland Trine , Indahl Marie , Khodeer Sherif , Klemsdal Eva Kristine , Jin Kang-Xuan , Dalen Knut Tomas , Fedorcsak Peter , Greggains Gareth D. , Lerdrup Mads , Klungland Arne , Au Kin Fai , Dahl John Arne 
Published: June 2023

AbstractCurrent N6-methyladenosine (m6A) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale m6A RNA immunoprecipitation and sequencing (picoMeRIP–seq) for studying m6A in vivo in single cells and scarce cell types using standard laboratory equipment. We benchmark m6A mapping on titrations of poly(A) RNA and embryonic stem cells and in single zebrafish zygotes, mouse oocytes and embryos.
Coswara: A respiratory sounds and symptoms dataset for remote screening of SARS-CoV-2 infection
Authors: Bhattacharya Debarpan , Sharma Neeraj Kumar , Dutta Debottam , Chetupalli Srikanth Raj , Mote Pravin , Ganapathy Sriram , Chandrakiran C. , Nori Sahiti , Suhail K. K. , Gonuguntla Sadhana , Alagesan Murali 
Published: June 2023

AbstractThis paper presents the Coswara dataset, a dataset containing diverse set of respiratory sounds and rich meta-data, recorded between April-2020 and February-2022 from 2635 individuals (1819 SARS-CoV-2 negative, 674 positive, and 142 recovered subjects). The respiratory sounds contained nine sound categories associated with variants of breathing, cough and speech. The rich metadata contained demographic information associated with age, gender and geographic location, as well as the health information relating to the symptoms, pre-existing respiratory ailments, comorbidity and SARS-CoV-2 test status. Our study is the first of its kind to manually annotate the audio quality of the entire dataset (amounting to 65 hours) through manual listening. The paper summarizes the data collection procedure, demographic, symptoms and audio data information. A COVID-19 classifier based on bi-directional long short-term (BLSTM) architecture, is trained and evaluated on the different population sub-groups contained in the dataset to understand the bias/fairness of the model. This enabled the analysis of the impact of gender, geographic location, date of recording, and language proficiency on the COVID-19 detection performance.
Human viral nucleic acids concentrations in wastewater solids from Central and Coastal California USA
Authors: Boehm Alexandria B. , Wolfe Marlene K. , Wigginton Krista R. , Bidwell Amanda , White Bradley J. , Hughes Bridgette , Duong Dorothea , Chan-Herur Vikram , Bischel Heather N. , Naughton Colleen C. 
Published: June 2023

AbstractWe measured concentrations of SARS-CoV-2, influenza A and B virus, respiratory syncytial virus (RSV), mpox virus, human metapneumovirus, norovirus GII, and pepper mild mottle virus nucleic acids in wastewater solids at twelve wastewater treatment plants in Central California, USA. Measurements were made daily for up to two years, depending on the wastewater treatment plant. Measurements were made using digital droplet (reverse-transcription–) polymerase chain reaction (RT-PCR) following best practices for making environmental molecular biology measurements. These data can be used to better understand disease occurrence in communities contributing to the wastewater.
Durable recovery from amblyopia with donepezil
Authors: Wu Carolyn , Gaier Eric D. , Nihalani Bharti R. , Whitecross Sarah , Hensch Takao K. , Hunter David G. 
Published: June 2023

AbstractAn elevated threshold for neuroplasticity limits visual gains with treatment of residual amblyopia in older children and adults. Acetylcholinesterase inhibitors (AChEI) can enable visual neuroplasticity and promote recovery from amblyopia in adult mice. Motivated by these promising findings, we sought to determine whether donepezil, a commercially available AChEI, can enable recovery in older children and adults with residual amblyopia. In this open-label pilot efficacy study, 16 participants (mean age 16 years; range 9–37 years) with residual anisometropic and/or strabismic amblyopia were treated with daily oral donepezil for 12 weeks. Donepezil dosage was started at 2.5 or 5.0 mg based on age and increased by 2.5 mg if the amblyopic eye visual acuity did not improve by 1 line from the visit 4 weeks prior for a maximum dosage of 7.5 or 10 mg. Participants < 18 years of age further patched the dominant eye. The primary outcome was visual acuity in the amblyopic eye at 22 weeks, 10 weeks after treatment was discontinued. Mean amblyopic eye visual acuity improved 1.2 lines (range 0.0–3.0), and 4/16 (25%) improved by ≥ 2 lines after 12 weeks of treatment. Gains were maintained 10 weeks after cessation of donepezil and were similar for children and adults. Adverse events were mild and self-limited. Residual amblyopia improves in older children and adults treated with donepezil, supporting the concept that the critical window of visual cortical plasticity can be pharmacologically manipulated to treat amblyopia. Placebo-controlled studies are needed.