bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parameters for one health genomic surveillance of Escherichia coli from Australia
Authors: Watt Anne E. , Cummins Max L. , Donato Celeste M. , Wirth Wytamma , Porter Ashleigh F. , Andersson Patiyan , Donner Erica ,   Australian Pathogen Genomics One Health Working Group, Sintchenko Vitali , Arnott Alicia , Zahedi Alireza , Bull Rowena , Webb Jessica R. , Ingle Danielle , Horan Kristy , Hoang Tuyet , Ferdinand Angeline , Zulfiqar Tehzeeb , Thompson Craig , Leong Lex E. X. , Hoye Bethany , Browning Glenn F. , Wille Michelle , Wright Rose , Donald Angela , Bartlett Zoe , Levy Avram , Bareja Christina , Gonzales Tatiana , Minney-Smith Cara , Flynn Erin , Phabmixay Aruna , Huynh Thy , Jennison Amy V. , Seemann Torsten , Djordjevic Steven P. , Howden Benjamin P. 
Published: January 2025

AbstractGenomics is a cornerstone of modern pathogen epidemiology yet demonstrating transmission in a One Health context is challenging, as strains circulate and evolve within and between diverse hosts and environments. To identify phylogenetic linkages and better define relevant measures of genomic relatedness in a One Health context, we collated 5471 Escherichia coli genome sequences from Australia originating from humans (n = 2996), wild animals (n = 870), livestock (n = 649), companion animals (n = 375), environmental sources (n = 292) and food (n = 289) spanning over 36 years. Of the 827 multi-locus sequence types (STs) identified, 10 STs were commonly associated with cross-source genomic clusters, including the highly clonal ST131, pandemic zoonotic lineages such as ST95, and emerging human ExPEC ST1193. Here, we show that assessing genomic relationships at ≤ 100 SNP threshold enabled detection of cross-source linkage otherwise obscured when applying typical outbreak-oriented relatedness thresholds ( ≤ 20 SNPs) and should be considered in interrogation of One Health genomic datasets.
Quantum-limited stochastic optical neural networks operating at a few quanta per activation
Authors: Ma Shi-Yuan , Wang Tianyu , Laydevant Jérémie , Wright Logan G. , McMahon Peter L. 
Published: January 2025

AbstractEnergy efficiency in computation is ultimately limited by noise, with quantum limits setting the fundamental noise floor. Analog physical neural networks hold promise for improved energy efficiency compared to digital electronic neural networks. However, they are typically operated in a relatively high-power regime so that the signal-to-noise ratio (SNR) is large (>10), and the noise can be treated as a perturbation. We study optical neural networks where all layers except the last are operated in the limit that each neuron can be activated by just a single photon, and as a result the noise on neuron activations is no longer merely perturbative. We show that by using a physics-based probabilistic model of the neuron activations in training, it is possible to perform accurate machine-learning inference in spite of the extremely high shot noise (SNR ~ 1). We experimentally demonstrated MNIST handwritten-digit classification with a test accuracy of 98% using an optical neural network with a hidden layer operating in the single-photon regime; the optical energy used to perform the classification corresponds to just 0.038 photons per multiply-accumulate (MAC) operation. Our physics-aware stochastic training approach might also prove useful with non-optical ultra-low-power hardware.
Heterodyne analysis of high-order partial waves in attosecond photoionization of helium
Authors: Jiang Wenyu , Roantree Luke , Han Lulu , Ji Jiabao , Xu Yidan , Zuo Zitan , Wörner Hans Jakob , Ueda Kiyoshi , Brown Andrew C. , van der Hart Hugo W. , Gong Xiaochun , Wu Jian 
Published: January 2025

AbstractPartial wave analysis is key to interpretation of the photoionization of atoms and molecules on the attosecond timescale. Here we propose a heterodyne analysis approach, based on the delay-resolved anisotropy parameters to reveal the role played by high-order partial waves during photoionization. This extends the Reconstruction of Attosecond Beating By Interference of Two-photon Transitions technique into the few-photon regime. We demonstrate that even for moderate ( ~ 1TW/cm2) intensities, near-infrared-assisted photoionization of helium through Rydberg states results in a tiny contribution from the g0 wave, which has a significant impact on the photoelectron angular distributions via interference with the s- and d0-waves. This modulation also causes a substantial deviation in the angular distribution of the recovered spectral phase shift. Our analysis provides an efficient method to resolve isolated partial wave contributions beyond the perturbative regime, and paves the way towards understanding resonance-enhancement of partial waves.
Probing SARS-CoV-2 membrane binding peptide via single-molecule AFM-based force spectroscopy
Authors: Zhang Qingrong , Rosa Raissa S. L. , Ray Ankita , Durlet Kimberley , Dorrazehi Gol Mohammad , Bernardi Rafael C. , Alsteens David 
Published: January 2025

AbstractThe SARS-CoV-2 spike protein’s membrane-binding domain bridges the viral and host cell membrane, a critical step in triggering membrane fusion. Here, we investigate how the SARS-CoV-2 spike protein interacts with host cell membranes, focusing on a membrane-binding peptide (MBP) located near the TMPRSS2 cleavage site. Through in vitro and computational studies, we examine both primed (TMPRSS2-cleaved) and unprimed versions of the MBP, as well as the influence of its conserved disulfide bridge on membrane binding. Our results show that the MBP preferentially associates with cholesterol-rich membranes, and we find that cholesterol depletion significantly reduces viral infectivity. Furthermore, we observe that the disulfide bridge stabilizes the MBP’s interaction with the membrane, suggesting a structural role in viral entry. Together, these findings highlight the importance of membrane composition and peptide structure in SARS-CoV-2 infectivity and suggest that targeting the disulfide bridge could provide a therapeutic strategy against infection.
Evidence for saddle point-driven charge density wave on the surface of heavily hole-doped iron arsenide superconductors
Authors: Hu Quanxin , Zheng Yu , Xu Hanxiang , Deng Junze , Liang Chenhao , Yang Fazhi , Wang Zhijun , Grinenko Vadim , Lv Baiqing , Ding Hong , Yim Chi Ming 
Published: January 2025

AbstractUnconventional superconductivity is known for its intertwining with other correlated states, making exploration of the intertwined orders important for understanding its pairing mechanism. In particular, spin and nematic orders are widely observed in iron-based superconductors; however, the presence of charge order is uncommon. Using scanning tunnelling microscopy, and through expanding the phase diagram of iron-arsenide superconductor Ba1−xKxFe2As2 to the hole-doping regime beyond KFe2As2 by surface doping, we demonstrate the formation of a charge density wave (CDW) on the arsenide surface of heavily hole-doped Ba1−xKxFe2As2. Its emergence suppresses superconductivity completely, indicating their direct competition. Notably, the CDW emerges when the saddle points approach the Fermi level, where its wavevector matches with those linking the saddle points, suggesting saddle-point nesting as its most probable formation mechanism. Our findings offer insights into superconductivity and intertwined orders, and a platform for studying them in iron-based superconductors close to the half-filled configuration.
Blobby is a synaptic active zone assembly protein required for memory in Drosophila
Authors: Lützkendorf J. , Matkovic-Rachid T. , Liu S. , Götz T. , Gao L. , Turrel O. , Maglione M. , Grieger M. , Putignano S. , Ramesh N. , Ghelani T. , Neumann A. , Gimber N. , Schmoranzer J. , Stawrakakis A. , Brence B. , Baum D. , Ludwig Kai , Heine M. , Mielke T. , Liu F. , Walter A. M. , Wahl M. C. , Sigrist S. J. 
Published: January 2025

AbstractAt presynaptic active zones (AZs), scaffold proteins are critical for coordinating synaptic vesicle release and forming essential nanoarchitectures. However, regulatory principles steering AZ scaffold assembly, function, and plasticity remain insufficiently understood. We here identify an additional Drosophila AZ protein, “Blobby”, essential for proper AZ nano-organization. Blobby biochemically associates with the ELKS family AZ scaffold protein Bruchpilot (BRP) and integrates into newly forming AZs. Loss of Blobby results in fewer AZs forming, ectopic AZ scaffold protein accumulations (“blobs”) and disrupts nanoscale architecture of the BRP-AZ scaffold. Functionally, blobby mutants show diminished evoked synaptic currents due to reduced synaptic vesicle release probability and fewer functional release sites. Blobby is also present in adult brain synapses, and post-developmental knockdown of Blobby in the mushroom body impairs olfactory aversive memory consolidation. Thus, our analysis identifies an additional layer of AZ regulation critical for developmental AZ assembly but also for AZ-mediated plasticity controlling behavior.
Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling
Authors: Kim David , Vanderbilt Chad M. , Yang Soo-Ryum , Nandakumar Subhiksha , Nafa Khedoudja , Feratovic Rusmir , Rekhtman Natasha , Rijo Ivelise , Casanova Jacklyn , Yun Anita , Brannon A. Rose , Berger Michael F. , Ladanyi Marc , Lin Oscar , Arcila Maria E. 
Published: January 2025

AbstractComprehensive molecular profiling by next-generation sequencing has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACTTM. Special emphasis is given to the use of residual supernatant cell-free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples are similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples have excellent performance overall, low-level cross-contamination is identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples have negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy, delivered successful results in 71% of cases where tumor tissue from CB was depleted.
Local correlations necessitate waterfalls as a connection between quasiparticle band and developing Hubbard bands
Authors: Krsnik Juraj , Held Karsten 
Published: January 2025

AbstractWaterfalls are anomalies in the angle-resolved photoemission spectrum where the energy-momentum dispersion is almost vertical, and the spectrum strongly smeared out. These anomalies are observed at relatively high energies, among others, in superconducting cuprates and nickelates. The prevalent understanding is that they originate from the coupling to some boson, with spin fluctuations and phonons being the usual suspects. Here, we show that waterfalls occur naturally in the process where a Hubbard band develops and splits off from the quasiparticle band. Our results for the Hubbard model with ab initio determined parameters well agree with waterfalls in cuprates and nickelates, providing a natural explanation for these spectral anomalies observed in correlated materials.
Reduced ATP turnover during hibernation in relaxed skeletal muscle
Authors: De Napoli Cosimo , Schmidt Luisa , Montesel Mauro , Cussonneau Laura , Sanniti Samuele , Marcucci Lorenzo , Germinario Elena , Kindberg Jonas , Evans Alina Lynn , Gauquelin-Koch Guillemette , Narici Marco , Bertile Fabrice , Lefai Etienne , Krüger Marcus , Nogara Leonardo , Blaauw Bert 
Published: January 2025

AbstractHibernating brown bears, due to a drastic reduction in metabolic rate, show only moderate muscle wasting. Here, we evaluate if ATPase activity of resting skeletal muscle myosin can contribute to this energy sparing. By analyzing single muscle fibers taken from the same bears, either during hibernation or in summer, we find that fibers from hibernating bears have a mild decline in force production and a significant reduction in ATPase activity. Single fiber proteomics, western blotting, and immunohistochemical analyses reveal major remodeling of the mitochondrial proteome during hibernation. Furthermore, using bioinformatical approaches and western blotting we find that phosphorylated myosin light chain, a known stimulator of basal myosin ATPase activity, is decreased in hibernating and disused muscles. These results suggest that skeletal muscle limits energy loss by reducing myosin ATPase activity, indicating a possible role for myosin ATPase activity modulation in multiple muscle wasting conditions.
Nucleus-translocated GCLM promotes chemoresistance in colorectal cancer through a moonlighting function
Authors: Lin Jin-Fei , Liu Ze-Xian , Chen Dong-Liang , Huang Ren-Ze , Cao Fen , Yu Kai , Li Ting , Mo Hai-Yu , Sheng Hui , Liang Zhi-Bing , Liao Kun , Han Yi , Li Shan-Shan , Zeng Zhao-Lei , Gao Song , Ju Huai-Qiang , Xu Rui-Hua 
Published: January 2025

AbstractMetabolic enzymes perform moonlighting functions during tumor progression, including the modulation of chemoresistance. However, the underlying mechanisms of these functions remain elusive. Here, utilizing a metabolic clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 knockout library screen, we observe that the loss of glutamate-cysteine ligase modifier subunit (GCLM), a rate-limiting enzyme in glutathione biosynthesis, noticeably increases the sensitivity of colorectal cancer (CRC) cells to platinum-based chemotherapy. Mechanistically, we unveil a noncanonical mechanism through which nuclear GCLM competitively interacts with NF-kappa-B (NF-κB)-repressing factor (NKRF), to promote NF-κB activity and facilitate chemoresistance. In response to platinum drug treatment, GCLM is phosphorylated by P38 MAPK at T17, resulting in its recognition by importin a5 and subsequent nuclear translocation. Furthermore, elevated expression of nuclear GCLM and phospho-GCLM correlate with an unfavorable prognosis and poor benefit from standard chemotherapy. Overall, our work highlights the essential nonmetabolic role and posttranslational regulatory mechanism of GCLM in enhancing NF-κB activity and subsequent chemoresistance.
Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice
Authors: Nishimura Akiyuki , Ogata Seiryo , Tang Xiaokang , Hengphasatporn Kowit , Umezawa Keitaro , Sanbo Makoto , Hirabayashi Masumi , Kato Yuri , Ibuki Yuko , Kumagai Yoshito , Kobayashi Kenta , Kanda Yasunari , Urano Yasuteru , Shigeta Yasuteru , Akaike Takaaki , Nishida Motohiro 
Published: January 2025

AbstractThe presence of redox-active molecules containing catenated sulfur atoms (supersulfides) in living organisms has led to a review of the concepts of redox biology and its translational strategy. Glutathione (GSH) is the body’s primary detoxifier and antioxidant, and its oxidized form (GSSG) has been considered as a marker of oxidative status. However, we report that GSSG, but not reduced GSH, prevents ischemic supersulfide catabolism-associated heart failure in male mice by electrophilic modification of dynamin-related protein (Drp1). In healthy exercised hearts, the redox-sensitive Cys644 of Drp1 is highly S-glutathionylated. Nearly 40% of Cys644 is normally polysulfidated, which is a preferential target for GSSG-mediated S-glutathionylation. Cys644 S-glutathionylation is resistant to Drp1 depolysulfidation-dependent mitochondrial hyperfission and myocardial dysfunction caused by hypoxic stress. MD simulation of Drp1 structure and site-directed mutagenetic analysis reveal a functional interaction between Cys644 and a critical phosphorylation site Ser637, through Glu640. Bulky modification at Cys644 via polysulfidation or S-glutathionylation reduces Drp1 activity by disrupting Ser637-Glu640-Cys644 interaction. Disruption of Cys644 S-glutathionylation nullifies the cardioprotective effect of GSSG against heart failure after myocardial infarction. Our findings suggest a therapeutic potential of supersulfide-based Cys bulking on Drp1 for ischemic heart disease.
PhpCNF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production
Authors: Srivastav Manjit Kumar , Folco H. Diego , Nathanailidou Patroula , Anil Anupa T , Vijayakumari Drisya , Jain Shweta , Dhakshnamoorthy Jothy , O’Neill Maura , Andresson Thorkell , Wheeler David , Grewal Shiv I. S. 
Published: January 2025

AbstractThe assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA-based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeats are transcribed has been unclear. Using fission yeast, we show that the conserved trimeric transcription factor (TF) PhpCNF-Y complex can infiltrate constitutive heterochromatin via its histone-fold domains to transcribe repeat elements. PhpCNF-Y collaborates with a Zn-finger containing TF to bind repeat promoter regions with CCAAT boxes. Mutating either the TFs or the CCAAT binding site disrupts the transcription of heterochromatic repeats. Although repeat elements are transcribed from both strands, PhpCNF-Y-dependent transcripts originate from only one strand. These TF-driven transcripts contain multiple cryptic introns which are required for the generation of small interfering RNAs (siRNAs) via a mechanism involving the spliceosome and RNAi machinery. Our analyses show that siRNA production by this TF-mediated transcription pathway is critical for heterochromatin nucleation at target repeat loci. This study reveals a mechanism by which heterochromatic repeats are transcribed, initiating their own silencing by triggering a primary cascade that produces siRNAs necessary for heterochromatin nucleation.
A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain
Authors: Gelabert Pere , Oberreiter Victoria , Straus Lawrence Guy , Morales Manuel Ramón González , Sawyer Susanna , Marín-Arroyo Ana B. , Geiling Jeanne Marie , Exler Florian , Brueck Florian , Franz Stefan , Cano Fernanda Tenorio , Szedlacsek Sophie , Zelger Evelyn , Hämmerle Michelle , Zagorc Brina , Llanos-Lizcano Alejandro , Cheronet Olivia , Tejero José-Miguel , Rattei Thomas , Kraemer Stephan M. , Pinhasi Ron 
Published: January 2025

Abstract
Caves are primary sites for studying human and animal subsistence patterns and genetic ancestry throughout the Palaeolithic. Iberia served as a critical human and animal refugium in Europe during the Last Glacial Maximum (LGM), 26.5 to 19 thousand years before the present (cal kya). Therefore, it is a key location for understanding human and animal population dynamics during this event. We recover and analyse sedimentary ancient DNA (sedaDNA) data from the lower archaeological stratigraphic sequence of El Mirón Cave (Cantabria, Spain), encompassing the (1) Late Mousterian period, associated with Neanderthals, and (2) the Gravettian (c. 31.5 cal kya), Solutrean (c. 24.5–22 cal kya), and Initial Magdalenian (d. 21–20.5 cal kya) periods, associated with anatomically modern humans. We identify 28 animal taxa including humans. Fifteen of these taxa had not been identified from the archaeozoological (i.e., faunal) record, including the presence of hyenas in the Magdalenian. Additionally, we provide phylogenetic analyses on 70 sedaDNA mtDNA genomes of fauna including the densest Iberian Pleistocene sampling of C. lupus. Finally, we recover three human mtDNA sequences from the Solutrean levels. These sequences, along with published data, suggest mtDNA haplogroup continuity in Iberia throughout the Solutrean/Last Glacial Maximum period.
Air pollution modifies colonisation factors in beneficial symbiont Snodgrassella and disrupts the bumblebee gut microbiome
Authors: Sampson Hannah R. , Allcock Natalie , Mallon Eamonn B. , Ketley Julian M. , Morrissey Julie A. 
Published: January 2025

AbstractParticulate air pollutants, a major air pollution component, are detrimental to human health and a significant risk to wildlife and ecosystems globally. Here we report the effects of particulate pollutant black carbon on the beneficial gut microbiome of important global insect pollinator, the buff-tailed bumblebee (Bombus terrestris). Our data shows that exposure to black carbon particulates alters biofilm structure, gene expression and initial adhesion of beneficial bee gut coloniser, Snodgrassella alvi. Exposure of adult Bombus terrestris to non-toxic black carbon particulates significantly increased viable bacteria on MRS agar and 16S absolute abundance of beneficial bacteria Bombilactobacillus in Post-treated bumblebees compared to Pre-treated, demonstrating disruption of the bumblebee gut microbiome. These findings show that black carbon exposure has direct, measurable effects on bees’ beneficial commensal bacteria and microbiome. Together these data highlight that black carbon, a single type of particulate pollution, is an underexplored risk to insect pollinator health.
Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment
Authors: Freitas Nancy L. , Walter Anthony Katey , Lenz Josefine , Porras Rachel C. , Torn Margaret S. 
Published: January 2025

Abstract
Thermokarst lakes cause abrupt and sustained permafrost degradation and have the potential to release large quantities of ancient carbon to the atmosphere. Despite concerns about how lakes will affect the permafrost carbon feedback, the magnitude of carbon dioxide and methane emissions from deep permafrost soils remains poorly understood. Here we incubated a very deep sediment core (20 m) to constrain the potential productivity of thawed Yedoma and underlying Quaternary sand and gravel deposits. Through radiocarbon dating, sediment incubations and sediment facies classifications, we show that extensive permafrost thaw can occur beneath lakes on timescales of decades to centuries. Although it has been assumed that shallow, aerobic carbon dioxide production will dominate the climate impact of permafrost thaw, we found that anaerobic carbon dioxide and methane production from deep sediments was commensurate with aerobic production on a per gram carbon basis, and had double the global warming potential at warmer temperatures. Carbon release from deep Arctic sediments may thus have a more substantial impact on a changing climate than currently anticipated. These environments are presently overlooked in estimates of the permafrost carbon feedback.