bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the landscape of the intratumoral microbiota reveals that Streptococcus anginosus increases the risk of gastric cancer initiation and progression
Authors: Yuan Li , Pan Libin , Wang Yunzhe , Zhao Jing , Fang Luo , Zhou Ying , Xia Ruihong , Ma Yubo , Jiang Zhengchen , Xu Zhiyuan , Hu Can , Wang Yanan , Zhang Shengjie , Zhang Bo , Ding Haiying , Chen Mengxuan , Cheng Haibo , Goel Ajay , Zhang Zhao , Cheng Xiangdong 
Published: November 2024

AbstractAs a critical component of the tumour immune microenvironment (TIME), the resident microbiota promotes tumorigenesis across a variety of cancer types. Here, we integrated multiple types of omics data, including microbiome, transcriptome, and metabolome data, to investigate the functional role of intratumoral bacteria in gastric cancer (GC). The microbiome was used to categorize GC samples into six subtypes, and patients with a high abundance of Streptococcus or Pseudomonas had a markedly worse prognosis. Further assays revealed that Streptococcus anginosus (SA) promoted tumour cell proliferation and metastasis while suppressing the differentiation and infiltration of CD8+ T cells. However, antibiotic treatment significantly suppressed tumorigenesis in SA+ mice in vivo. We further demonstrated that the SA arginine pathway increased the abundance of ornithine, which may be a major contributor to reshaping of the TIME. Our findings demonstrated that SA, a novel risk factor, plays significant roles in the initiation and progression of GC, suggesting that SA might be a promising target for the diagnosis and treatment of GC.
Genotypes and phenotypes of neurofibromatosis type 1 patients in Japan: A Hereditary Tumor Cohort Study
Authors: Futagawa Mashu , Okazaki Tetsuya , Nakata Eiji , Fukano Chika , Osumi Risa , Kato Fumino , Urakawa Yusaku , Yamamoto Hideki , Ozaki Toshifumi , Hirasawa Akira 
Published: November 2024

Abstract
Neurofibromatosis type 1 (NF1) presents with a broad spectrum of clinical manifestations, including an increased risk of tumor development and hypertension. Comprehensive data on genotype‒phenotype correlations in patients with NF1 are limited. Therefore, in this study, we aimed to elucidate the detailed genetic and clinical characteristics of NF1 in a hereditary tumor cohort. We performed sequencing and copy number assays in a clinical laboratory and analyzed the clinical data of 44 patients with suspected NF1. Germline pathogenic variants were detected in 36 patients (81.8%), and 20.7% of the variants were novel. Notably, 40.0% of adult patients presented with malignancies; female breast cancer occurred in 20.0% of patients, which was a higher rate than that previously reported. Hypertension was observed in 30.6% of the adult patients, with one patient experiencing sudden death and another developing pheochromocytoma. Three patients with large deletions in NF1 exhibited prominent cutaneous, skeletal, and neurological manifestations. These results highlight the importance of regular surveillance, particularly for patients with malignancies and hypertension. Our findings provide valuable insights for genetic counseling and clinical management, highlighting the multiple health risks associated with NF1 and the need for comprehensive and multidisciplinary care.
Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels
Authors: Gangwar Shanti Pal , Yelshanskaya Maria V. , Aktolun Muhammed , Yen Laura Y. , Newton Thomas P. , Strømgaard Kristian , Kurnikova Maria G. , Sobolevsky Alexander I. 
Published: November 2024

AbstractKainate receptors (KARs) are a subtype of ionotropic glutamate receptor (iGluR) channels, a superfamily of ligand-gated ion channels which mediate the majority of excitatory neurotransmission in the central nervous system. KARs modulate neuronal circuits and plasticity during development and are implicated in neurological disorders, including epilepsy, depression, schizophrenia, anxiety, and autism. Calcium-permeable KARs undergo ion channel block, but the therapeutic potential of channel blockers remains underdeveloped, mainly due to limited structural knowledge. Here, we present closed-state structures of GluK2 KAR homotetramers in complex with ion channel blockers NpTx-8, PhTx-74, Kukoamine A, and spermine. We find that blockers reside inside the GluK2 ion channel pore, intracellular to the closed M3 helix bundle-crossing gate, with their hydrophobic heads filling the central cavity and positively charged polyamine tails spanning the selectivity filter. Molecular dynamics (MD) simulations of our structures illuminate interactions responsible for different affinity and binding poses of the blockers. Our structures elucidate the trapping mechanism of KAR channel block and provide a template for designing new blockers that can selectively target calcium-permeable KARs in neuropathologies.
Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instability
Authors: Smirnov Petr , Przybilla Moritz J. , Simovic-Lorenz Milena , Parra R. Gonzalo , Susak Hana , Ratnaparkhe Manasi , Wong John KL. , Körber Verena , Mallm Jan-Philipp , Philippos George , Sill Martin , Kolb Thorsten , Kumar Rithu , Casiraghi Nicola , Okonechnikov Konstantin , Ghasemi David R. , Maaß Kendra Korinna , Pajtler Kristian W. , Jauch Anna , Korshunov Andrey , Höfer Thomas , Zapatka Marc , Pfister Stefan M. , Huber Wolfgang , Stegle Oliver , Ernst Aurélie 
Published: November 2024

Abstract
Chromothripsis is a frequent form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or multiple chromosome(s). However, little is known about the heterogeneity of chromothripsis across different clones from the same tumour, as well as changes in response to treatment. Here we analyse single-cell genomic and transcriptomic alterations linked with chromothripsis in human p53-deficient medulloblastoma and neural stem cells (n = 9). We reconstruct the order of somatic events, identify early alterations likely linked to chromothripsis and depict the contribution of chromothripsis to malignancy. We characterise subclonal variation of chromothripsis and its effects on extrachromosomal circular DNA, cancer drivers and putatively druggable targets. Furthermore, we highlight the causative role and the fitness consequences of specific rearrangements in neural progenitors.
Can quantum computers do nothing?
Authors: Nico-Katz Alexander , Keenan Nathan , Goold John 
Published: November 2024

AbstractQuantum computing platforms are subject to contradictory engineering requirements: qubits must be protected from mutual interactions when idling (‘doing nothing’), and strongly interacting when in operation. If idling qubits are not sufficiently protected, information ‘leaks’ into neighbouring qubits, becoming ultimately inaccessible. Candidate solutions to this dilemma include many-body localization, dynamical decoupling, and active error correction. However, no protocol exists to quantify this effect in a similar way to e.g. SPAM errors. We develop a scalable, device non-specific, protocol for quantifying idle information loss by exploiting tools from quantum information theory. We implement this protocol in over 3500 experiments carried out across 4 months (Dec 2023–Mar 2024) on IBM’s entire Falcon 5.11 processor series. After accounting for other error sources, we detect information loss to high degrees of statistical significance. This work thus provides a firm quantitative foundation from which the protection-operation dilemma can be investigated and ultimately resolved.
A draft genome assembly of the reef-building coral Acropora hemprichii from the central Red Sea
Authors: Fiesinger Anna , Buitrago-López Carol , Sharaf Abdoallah , Cárdenas Anny , Voolstra Christian R. 
Published: November 2024

AbstractCoral reef ecosystems are under threat from climate change. Thus, active interventions to spur coral conservation/restoration are critical to support reef survival, greatly informed by a molecular understanding of resilience. The genus Acropora is a species-rich and globally prevalent reef builder that has experienced dramatic declines in the Caribbean. Here we generated a draft genome of the common coral Acropora hemprichii from the central Red Sea, one of the warmest water bodies in the world. We assembled the genome using 10x Chromium sequencing with subsequent scaffolding using a reference genome and Illumina short-read sequencing contigs. The A. hemprichii genome has an assembly size of 495.6 Mb confirmed using physical size estimation, of which 247.8 Mb (50%) are repeats. The scaffold N50 is 1.38 Mb with 99.6% of BUSCO genes identified (93.7% complete, 5.9% fragmented), providing a set of 26,865 protein-coding genes. The Red Sea A. hemprichii reference genome provides a valuable resource for studies aiming to decode the genomic architecture of resilience, e.g. through comparative analyses with other Acropora genomes.
A reference quality, fully annotated diploid genome from a Saudi individual
Authors: Kulmanov Maxat , Tawfiq Rund , Liu Yang , Al Ali Hatoon , Abdelhakim Marwa , Alarawi Mohammed , Aldakhil Hind , Alhattab Dana , Alsolme Ebtehal A. , Althagafi Azza , Angelov Angel , Bougouffa Salim , Driguez Patrick , Park Changsook , Putra Alexander , Reyes-Ramos Ana M. , Hauser Charlotte A. E. , Cheung Ming Sin , Abedalthagafi Malak S. , Hoehndorf Robert 
Published: November 2024

AbstractWe have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly. As a consequence, we provide a contiguous assembly of the complete genome of an individual from Saudi Arabia for all chromosomes except chromosome Y, and label this assembly . We transferred genome annotations from reference genomes to fully annotate , and we make all primary sequencing data, the assembly, and the genome annotations freely available in public databases using the FAIR data principles. is the first telomere-to-telomere-assembled genome from a Saudi individual that is freely available for any purpose.
Setting the standard for machine learning in phase field prediction: a benchmark dataset and baseline metrics
Authors: Rieger Laura Hannemose , Zelič Klemen , Mele Igor , Katrašnik Tomaž , Bhowmik Arghya 
Published: November 2024

AbstractPhase field models are an important mesoscale method that serves as a bridge between the atomic scale and the macroscale, used for modeling complex phenomena at the microstructure level. Machine learning can be employed to accelerate these simulations, enabling faster and more efficient analyses. However, the development of new machine learning algorithms depends on access to extensive datasets. This work introduces an accessible and well-documented dataset aimed at benchmarking new machine learning algorithms. We validate the dataset with a benchmark using U-Net regression, a widely used neural network architecture. Although direct comparisons are limited by the lack of existing benchmarks, our model’s error metrics are competitive with previous work and generalize across multiple domain sizes. This contribution provides a valuable resource for future efforts in machine learning model development for phase field simulations and demonstrates the potential of U-Net regression, highlighting the scope for novel method development in this area.
Expression and regulation of SETBP1 in the song system of male zebra finches (Taeniopygia guttata) during singing
Authors: Grönberg Dana Jenny , Pinto de Carvalho Sara Luisa , Dernerova Nikola , Norton Phillip , Wong Maggie Mei-Ki , Mendoza Ezequiel 
Published: November 2024

Abstract
Rare de novo heterozygous loss-of-function SETBP1 variants lead to a neurodevelopmental disorder characterized by speech deficits, indicating a potential involvement of SETBP1 in human speech. However, the expression pattern of SETBP1 in brain regions associated with vocal learning remains poorly understood, along with the underlying molecular mechanisms linking it to vocal production. In this study, we examined SETBP1 expression in the brain of male zebra finches, a well-established model for studying vocal production learning. We demonstrated that zebra finch SETBP1 exhibits a greater number of exons and isoforms compared to its human counterpart. We characterized a SETBP1 antibody and showed that SETBP1 colocalized with FoxP1, FoxP2, and Parvalbumin in key song nuclei. Moreover, SETBP1 expression in neurons in Area X is significantly higher in zebra finches singing alone, than those singing courtship song to a female, or non-singers. Importantly, we found a distinctive neuronal protein expression of SETBP1 and FoxP2 in Area X only in zebra finches singing alone, but not in the other conditions. We demonstrated SETBP1´s regulatory role on FoxP2 promoter activity in vitro. Taken together, these findings provide compelling evidence for SETBP1 expression in brain regions to be crucial for vocal learning and its modulation by singing behavior.
Simulation of a Rohksar–Kivelson ladder on a NISQ device
Authors: Gupta Sabhyata , Javanmard Younes , Osborne Tobias J. , Santos Luis 
Published: November 2024

AbstractWe present a quantum-classical algorithm to study the dynamics of the Rohksar–Kivelson plaquette ladder on NISQ devices. We show that complexity is largely reduced using gauge invariance, additional symmetries, and a crucial property associated to how plaquettes are blocked against ring-exchange in the ladder geometry. This allows for an efficient simulation of sizable plaquette ladders with a small number of qubits, well suited for the capabilities of present NISQ devices. We illustrate the procedure for ladders with simulation of up to 8 plaquettes in an IBM-Q machine, employing scaled quantum gates.
The influence of bio-based monomers on the structure and thermal properties of polyurethanes
Authors: Brzoska Joanna , Datta Janusz , Konefał Rafał , Pokorný Václav , Beneš Hynek 
Published: November 2024

AbstractMost polyurethanes (PU) are currently produced through the polyaddition reaction of polyisocyanates with polyols and chain extenders, using components of petrochemical origin. From an environmental and geopolitical point of view, and with regard to the problems of oil supply and processing, the replacement of petrochemical PU raw materials with renewable resources is highly desirable. It is also one of the principles of sustainable development and an important challenge for chemical companies and market competitiveness. Current research studies focus mainly on the use of bio-based polyols for PUs, while other PU components, in particular polyisocyanates, remain of petrochemical origin. In this work, a series of PUs have been synthesized by polyaddition reactions of different types of renewable polyols and bio-based polyisocyanates. The effects of the bio-derived components on the structure, thermal stability and phase transformations of the PU were studied using FTIR and NMR spectroscopy, SWAXS, TGA, DSC, DMTA and TGA-FTIR. A full conversion of the bio-based monomers was achieved in all cases, indicating good compatibility and reactivity of all bio-based components. It was observed that bio-based PU exhibited a lower degree of phase separation and slightly lower thermal stability compared to PUs from petrochemical monomers.
Severe toxicities in amazonian populations and the role of precision medicine in acute lymphoblastic leukemia treatment
Authors: Leitão Luciana Pereira Colares , Monte Natasha , Rodrigues Juliana Carla Gomes , de Freitas Lilian Marques , Ribeiro-dos-Santos André Maurício , Ribeiro-dos-Santos Ândrea , Santos Sidney , de Souza Sandro José , Fernandes Marianne Rodrigues , dos Santos Ney Pereira Carneiro 
Published: November 2024

AbstractCorticosteroids, such as prednisone or dexamethasone, constitute integral components of antineoplastic regimens for Acute Lymphoblastic Leukemia (ALL) therapy, albeit accompanied by significant adverse effects. The multifactorial nature of interindividual variability in drug response, encompassing genetic polymorphisms, underscores the complexity of pharmacotherapy outcomes. However, pharmacogenetic investigations hitherto have predominantly focused on cohorts of European and North American descent, thus limiting the generalizability of findings to populations with minimal representation. Indigenous populations in Brazil, particularly those inhabiting the Amazon region, exhibit a distinctive genetic heritage, predominantly characterized by Native American ancestry. These populations frequently manifest suboptimal therapeutic responses and elevated mortality rates following ALL treatment. Therefore, delineating the molecular signatures of genes implicated in the corticosteroid pathway within these indigenous cohorts assumes paramount importance. This study identified novel variants within genes associated with the glucocorticoid pathway in indigenous Amazonian populations and conducted comparative analyses of variant frequencies across diverse global populations. The findings underscore the genetic uniqueness of indigenous groups and highlight the potential impact of genetic factors on adverse responses to ALL treatment. Precision medicine approaches tailored to the genetic peculiarities of indigenous populations emerge as imperative strategies for optimizing therapeutic efficacy and mitigating treatment-related toxicities in these communities.
Porosity and cement controlling the response of artificially cemented tailings under hydrostatic loading to high pressures
Authors: Consoli Nilo Cesar , de Azambuja Carvalho João Vítor , Wagner Alexia Cindy , Carvalho Inácio , de Sousa Silva João Paulo 
Published: November 2024

AbstractCemented tailings find various applications in mining, such as open-pit and underground backfill, dam decommissioning and filtered tailings stacking. This research investigates the compression behaviour of iron ore tailings (IOT) mixed with distinct amounts of Portland cement and compacted in different conditions through isotropic compression, pulse velocity, and unconfined compression tests. The results show the adequacy of the porosity/cement index (η/Civ) in predicting elastic and plastic characteristics of compacted filtered IOT - Portland cement blends, an original correlation that has not been reported by previous work. This index is useful in selecting the cement content and target density for essential parameters required to design cemented IOT stacks. Besides, both cement addition and compaction have promoted the tailings isotropisation (conversion of an anisotropic system to an isotropic one). The evolution of the Post-Yield Compression Line (PYCL) with cementation is shown. Finally, it is demonstrated that distinct initial (after compaction) porosities of uncemented specimens reach a unique PYCL after isotropic pressures above 100 MPa, and cemented specimens do not reach a unique PYCL even at 120 MPa of isotropic pressures. The results underscore the requirement of rigorous compaction control in the field and offer a methodology for the dosage and technological control of artificially cemented tailings.
Modeling early phenotypes of Parkinson’s disease by age-induced midbrain-striatum assembloids
Authors: Barmpa Kyriaki , Saraiva Claudia , Lopez-Pigozzi Diego , Gomez-Giro Gemma , Gabassi Elisa , Spitz Sarah , Brandauer Konstanze , Rodriguez Gatica Juan E. , Antony Paul , Robertson Graham , Sabahi-Kaviani Rahman , Bellapianta Alessandro , Papastefanaki Florentia , Luttge Regina , Kubitscheck Ulrich , Salti Ahmad , Ertl Peter , Bortolozzi Mario , Matsas Rebecca , Edenhofer Frank , Schwamborn Jens C. 
Published: November 2024

AbstractParkinson’s disease, an aging-associated neurodegenerative disorder, is characterised by nigrostriatal pathway dysfunction caused by the gradual loss of dopaminergic neurons in the substantia nigra pars compacta of the midbrain. Human in vitro models are enabling the study of the dopaminergic neurons’ loss, but not the dysregulation within the dopaminergic network in the nigrostriatal pathway. Additionally, these models do not incorporate aging characteristics which potentially contribute to the development of Parkinson’s disease. Here we present a nigrostriatal pathway model based on midbrain-striatum assembloids with inducible aging. We show that these assembloids can develop characteristics of the nigrostriatal connectivity, with catecholamine release from the midbrain to the striatum and synapse formation between midbrain and striatal neurons. Moreover, Progerin-overexpressing assembloids acquire aging traits that lead to early neurodegenerative phenotypes. This model shall help to reveal the contribution of aging as well as nigrostriatal connectivity to the onset and progression of Parkinson’s disease.
Arctic plant-fungus interaction networks show major rewiring with environmental variation
Authors: Parisy Bastien , Schmidt Niels M. , Cirtwill Alyssa R. , Villa-Galaviz Edith , Tiusanen Mikko , Klütsch Cornelya F. C. , Aspholm Paul E. , Raundrup Katrine , Vesterinen Eero J. , Wirta Helena , Roslin Tomas 
Published: November 2024

AbstractGlobal environmental change may lead to changes in community structure and in species interactions, ultimately changing ecosystem functioning. Focusing on spatial variation in fungus–plant interactions across the rapidly changing Arctic, we quantified variation in the identity of interaction partners. We then related interaction turnover to variation in the bioclimatic environment by combining network analyses with general dissimilarity modelling. Overall, we found species associations to be highly plastic, with major rewiring among interaction partners across variable environmental conditions. Of this turnover, a major part was attributed to specific environmental properties which are likely to change with progressing climate change. Our findings suggest that the current structure of plant-root associated interactions may be severely altered by rapidly advancing global warming. Nonetheless, flexibility in partner choice may contribute to the resilience of the system.
Application of machine learning algorithms to identify serological predictors of COVID-19 severity and outcomes
Authors: Dhakal Santosh , Yin Anna , Escarra-Senmarti Marta , Demko Zoe O. , Pisanic Nora , Johnston Trevor S. , Trejo-Zambrano Maria Isabel , Kruczynski Kate , Lee John S. , Hardick Justin P. , Shea Patrick , Shapiro Janna R. , Park Han-Sol , Parish Maclaine A. , Caputo Christopher , Ganesan Abhinaya , Mullapudi Sarika K. , Gould Stephen J. , Betenbaugh Michael J. , Pekosz Andrew , Heaney Christopher D. , Antar Annukka A. R. , Manabe Yukari C. , Cox Andrea L. , Karaba Andrew H. , Andrade Felipe , Zeger Scott L. , Klein Sabra L. 
Published: November 2024

Abstract
Background
Critically ill hospitalized patients with COVID-19 have greater antibody titers than those with mild to moderate illness, but their association with recovery or death from COVID-19 has not been characterized.

Methods
In a cohort study of 178 COVID-19 patients, 73 non-hospitalized and 105 hospitalized patients, mucosal swabs and plasma samples were collected at hospital enrollment and up to 3 months post-enrollment (MPE) to measure virus RNA, cytokines/chemokines, binding antibodies, ACE2 binding inhibition, and Fc effector antibody responses against SARS-CoV-2. The association of demographic variables and more than 20 serological antibody measures with intubation or death due to COVID-19 was determined using machine learning algorithms.

Results
Predictive models reveal that IgG binding and ACE2 binding inhibition responses at 1 MPE are positively and anti-Spike antibody-mediated complement activation at enrollment is negatively associated with an increased probability of intubation or death from COVID-19 within 3 MPE.

Conclusions
At enrollment, serological antibody measures are more predictive than demographic variables of subsequent intubation or death among hospitalized COVID-19 patients.