bluuebunny/crossref_metadata_2025_split huggingface dataset:
NREM sleep oscillations and their relations with sleep-dependent memory consolidation in early course psychosis and first-degree relatives
Authors: Denis Dan , Baran Bengi , Mylonas Dimitrios , Spitzer Courtney , Raymond Nicolas , Talbot Christine , Kohnke Erin , Stickgold Robert , Keshavan Matcheri , Manoach Dara S. 
Published: November 2023

AbstractSleep spindles are believed to mediate sleep-dependent memory consolidation, particularly when coupled to neocortical slow oscillations. Schizophrenia is characterized by a deficit in sleep spindles that correlates with reduced overnight memory consolidation. Here, we examined sleep spindle activity, slow oscillation-spindle coupling, and both motor procedural and verbal declarative memory consolidation in early course, minimally medicated psychosis patients and non-psychotic first-degree relatives. Using a four-night experimental procedure, we observed significant deficits in spindle density and amplitude in patients relative to controls that were driven by individuals with schizophrenia. Schizophrenia patients also showed reduced sleep-dependent consolidation of motor procedural memory, which correlated with spindle density. Contrary to expectations, there were no group differences in the consolidation of declarative memory on a word pairs task. Nor did the relatives of patients differ in spindle activity or memory consolidation compared with controls, however increased consistency in the timing of SO-spindle coupling were seen in both patient and relatives. Our results extend prior work by demonstrating correlated deficits in sleep spindles and sleep-dependent motor procedural memory consolidation in early course, minimally medicated patients with schizophrenia, but not in first-degree relatives. This is consistent with other work in suggesting that impaired sleep-dependent memory consolidation has some specificity for schizophrenia and is a core feature rather than reflecting the effects of medication or chronicity.Statement of significanceWe investigated sleep neurophysiology and memory consolidation in minimally-medicated, early course psychosis patients and unaffected first-degree relatives of patients in a four-night study. Early-course schizophrenia patients had a sleep spindle deficit that correlated with reduced procedural memory consolidation. Although first-degree relatives did not show any deficit in spindles or memory consolidation, the spindles of both relatives and patients showed increased consistency of the temporal coupling of spindles with slow oscillations compared with controls. These results suggest that sleep spindle and memory consolidation deficits are a core feature of schizophrenia. Spindle deficits may be a biomarker of schizophrenia modifiable by treatment, and motivate the development of targeted novel interventions.
Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the mossPhyscomitrellopsis africana
Authors: Vuruputoor Vidya S. , Starovoitov Andrew , Cai Yuqing , Liu Yang , Rahmatpour Nasim , Hedderson Terry A. , Wilding Nicholas , Wegrzyn Jill L. , Goffinet Bernard 
Published: November 2023

AbstractThe first chromosome-scale reference genome of the rare narrow-endemic African mossPhyscomitrellopsis africanais presented here. Assembled from 73x nanopore long reads and 163x BGI-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes (BUSCO: C:94.8%[D:13.9%]). This genome holds two genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants and are thus interpreted as resulting from two unique horizontal gene transfers from microbes. Further,Physcomitrellopsis africanashares 176 of the 273 published HGT candidates identified inPhyscomitrium patens, but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired inP. patensin the last 40 million years following its divergence from its common ancestor withP. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses, during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extantPhyscomitrellopsis africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.Article SummaryThe first draft genome of the rare South African endemic mossPhyscomitrellopsis Africanais presented. The 414 Mb assembly contains 22,925 genes, including two uniquely horizontally transferred genes, but lacks 97 of the microbial genes previously identified in the closely related model,Physcomitrium patens- highlighting the dynamic role of HGT in the evolution of these moss genomes and loss. This study presents best practices for contamination detection and new insights into HGT identification.
Ipl1-controlled attachment maturation regulates Mps1 association with its kinetochore receptor
Authors: Pleuger Richard , Cozma Christian , Hohoff Simone , Denkhaus Christian , Dudziak Alexander , Kaschani Farnusch , Musacchio Andrea , Vetter Ingrid R. , Westermann Stefan 
Published: November 2023

AbstractFaithful chromosome segregation requires that sister chromatids establish bi-oriented kinetochore-microtubule attachments. The spindle assembly checkpoint (SAC) prevents premature anaphase onset with incomplete attachments. However, how microtubule attachment and checkpoint signaling are coordinated remains unclear. The conserved kinase Mps1 initiates SAC signaling by localizing transiently to kinetochores in prometaphase and is released upon bi-orientation. Using biochemistry, structure predictions, and cellular assays, we shed light on this dynamic behaviour inSaccharomyces cerevisiae. A conserved N-terminal segment of Mps1 binds the neck region of Ndc80:Nuf2, the main microtubule receptor of kinetochores. Mutational disruption of this interface, located at the backside of the paired CH-domains and opposite the microtubule-binding site, prevents Mps1 localization, eliminates SAC signalling, and impairs growth. The same interface of Ndc80:Nuf2 binds the microtubule-associated Dam1 complex. We demonstrate that the error correction kinase Ipl1/Aurora B controls the competition between Dam1 and Mps1 for the same binding site. Thus, binding of the Dam1 complex to Ndc80:Nuf2 may release Mps1 from the kinetochore to allow anaphase onset.
Conspicuous shell shape plasticity across lake-stream habitats in a freshwater mussel (Pyganodon grandis)
Authors: Keogh Sean M. , Minerich Ben J. , Ohlman Lindsay M. , Pletta Madeline E. , Scheunemann Anna E. , Schroeder Zoe K. , Secrist Zebulin A. , Franzen Alex J. , Sietman Bernard E. , Simons Andrew M. 
Published: November 2023

2.AbstractHydrodynamic forces and their absence appears to exert differential selection pressure between lake and stream populations, creating a tight fit between organismal phenotypes and their environments. Ecophenotypic variants may be the result from isolated genetic evolution or phenotypic plasticity, where a widespread genotype can produce multiple phenotypes dependent on the environment. Freshwater mussels possess a wide degree of morphological variation that frequently covaries with the environment, making them a good system to understand the mechanisms of ecophenotypic variation across hydrological conditions. We designed a two-year experiment where individuals from the samePyganodon grandismaternal brood (half-full siblings) were reared at a controlled site and four natural sites involving one lake and three streams. At the end of the experiment, shell shape was quantified for recaptured (N=70), wild (N=206), and zoo-reared (N=305) mussels. Analysis of covariance found significant differences in shell shape between rearing sites, particularly between stream and lake habitats, but no shape differences were detected across the three stream sites. At two of the four sites, shell shape of recaptured individuals matched the morphology of wild populations. Genomic sequencing and parentage analysis identified 27 different fathers among recaptured individuals. Yet, no genetic differences were present between stream and lake habitats and there was no effect of parentage on shell shape. Taken together, phenotypic plasticity, over genetic differentiation, is identified as the primary mechanism of shell shape ecophenotypy. Plasticity may be a key adaptation for freshwater mussels and possibly provide a buffer against their imperilment in degraded habitats.1.Summary statementStreamlined and obese freshwater mussel shell shapes in stream-lake environments are developed from the same maternal brood and may reflect adaptations to the presence and absence of streamflow.
Mining the neuroimaging literature
Authors: Dockès Jérôme , Oudyk Kendra , Torabi Mohammad , de la Vega Alejandro I , Poline Jean-Baptiste 
Published: November 2023

AbstractAutomated analysis of the biomedical literature (literature-mining) offers a rich source of insights. However, such analysis requires collecting a large number of articles and extracting and processing their content. This task is often prohibitively difficult and time-consuming. Here, we provide tools to easily collect, process and annotate the biomedical literature. In particular,pubgetis an efficient and reliable command-line tool for downloading articles in bulk from PubMed Central, extracting their contents and meta-data into convenient formats, and extracting and analyzing information such as stereotactic brain coordinates.Labelbuddyis a lightweight local application for annotating text, which facilitates the extraction of complex information or the creation of ground-truth labels to validate automated information extraction methods. Further, we describe repositories where researchers can share their analysis code and their manual annotations in a format that facilitates re-use. These resources can help streamline text-mining and meta-science projects and make text-mining of the biomedical literature more accessible, effective, and reproducible. We describe a typical workflow based on these tools and illustrate it with several example projects.
Behavioral Syndromes in Paper Wasps: links between social and non-social personality inPolistes fuscatus
Authors: Jomaa Fatima W. , Laub Emily C. , Tibbetts Elizabeth A. 
Published: November 2023

AbstractAlthough much work has focused on non-social personality traits such as activity, exploration, and neophobia, there is a growing appreciation that social personality traits play an important role in group dynamics, disease transmission, and fitness, and that social personality traits may be linked to non-social personality traits. These relationships are important because behavioral syndromes, defined here as correlated behavioral phenotypes, can constrain evolutionary responses. However, the strength and direction of relationships between social and non-social personality traits remain unclear. In this project, we examine social and non-social personality traits, and the relationships between them, in the paper waspPolistes fuscatus. With a novel assay we identify five personality traits, two non-social (exploration and activity) and three social (aggression, affiliation, and antennation) personality traits. We also find that social and non-social personality traits are phenotypically linked. We find a positive correlation between aggression and activity (rs =0.33) and a negative correlation between affiliation and activity (rs =- 0.35). We also find a positive correlation between exploration and activity. Our work is an important step in understanding how phenotypic linkage between social and non-social behaviors may influence behavioral evolution. As a burgeoning model system for the study of genetic and neurobiological mechanisms of social behavior,Polistes fuscatushas potential to add to this work through exploring the causes and consequences of individual behavioral variation.
Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues
Authors: Sanghvi Neel , Calvo-Alcañiz Camilo , Rajagopal Padma S. , Scalera Stefano , Canu Valeria , Sinha Sanju , Schischlik Fiorella , Wang Kun , Madan Sanna , Shulman Eldad , Papanicolau-Sengos Antonios , Blandino Giovanni , Ruppin Eytan , Nair Nishanth Ulhas 
Published: November 2023

SUMMARYMetastasis is a leading cause of cancer-related deaths, yet understanding how metastatic tumors adapt from their origin to target tissues is challenging. To address this, we assessed whether primary and metastatic tumors resemble their tissue of origin or target tissue in terms of gene expression. We analyzed gene expression profiles from various cancer types, including single-cell and bulk RNA-seq data, in both paired and unpaired primary and metastatic patient cohorts. We quantified the transcriptomic distances between tumor samples and their normal tissues, revealing that primary tumors are more similar to their tissue of origin, while metastases shift towards the target tissue. Pathway-level analysis highlighted critical transcriptomic changes during metastasis. Notably, primary cancers exhibited higher activity in cancer hallmarks, includingActivating Invasion and Metastasis, compared to metastatic cancers. This comprehensive landscape analysis provides insight into how cancer tumors adapt to their metastatic environments, providing a transcriptome-wide view of the processes involved.
Latitudinal trends in genetic diversity and distinctiveness ofQuercus roburrear edge forest remnants call for new conservation priorities
Authors: Avanzi Camilla , Bagnoli Francesca , Romiti Edoardo , Spanu Ilaria , Tsuda Yoshiaki , Vajana Elia , Vendramin Giovanni Giuseppe , Piotti Andrea 
Published: November 2023

AbstractKnowledge of the spatial distribution of intraspecific genetic variation is essential for planning conservation actions, designing networks of protected areas, and informing possible assisted migration strategies. Although the Italian peninsula harbours unique genetic variation as a legacy of Quaternary migrations, only sporadic genetic information is available for forest tree species.Here, we present the first geographically comprehensive genetic characterisation ofQuercus robur, an iconic broadleaved species of European floodplain forests, in an area which acted as a primary glacial refugium for the species. 745 individuals from 25 populations were sampled and genotyped with 16 microsatellite markers. Their genetic structure was assessed through various metrics of diversity and distinctiveness, as well as by Bayesian clustering and multivariate methods. The demographic history of inferred gene pools was evaluated through Approximate Bayesian Computation analysis.Genetic distinctiveness showed a decline with increasing latitude, while allelic richness reached its peak in central Italy. A south-to-north trend in the complexity of the genetic structure was observed, with peninsular Italy being characterised by intermingled gene pools in contrast to the relative homogeneity exhibited by northern populations. Demographic inference indicated that the southern gene pool has been genetically isolated since the penultimate interglacial, whereas populations from central Italy persisted locally in a mosaic of small refugia during the last glaciation.Our results brought out the complexity of the genetic structure of forest trees’ populations in southern Europe. At least threeQ. roburrefugia contributed to the genetic layout of extant populations after the last glacial period, but refugial areas were probably even more numerous in central Italy. Such a detailed characterization sheds new light on the priorities to be established for the conservation of highly fragmentedQ. roburpopulations in an area rich in diversified genetic lineages.
Developmental differences in canonical cortical networks: insights from microstructure-informed tractography
Authors: Genc Sila , Schiavi Simona , Chamberland Maxime , Tax Chantal , Raven Erika , Daducci Alessandro , Jones Derek K 
Published: November 2023

AbstractThere is a growing interest in incorporating white matter fibre-specific microstructural properties into structural connectomes to obtain a more quantitative assessment of brain connectivity. In a developmental sample aged 8-18 years, we studied age-related patterns of microstructure-informed network properties locally and globally. First, we computed the diffusion-weighted signal fraction associated with each tractography-reconstructed streamline. Then, we generated microstructure-informed connectomes from diffusion MRI data using the convex optimization modelling for microstructure-informed tractography (COMMIT) approach. Finally, we estimated network characteristics in eight functionally defined networks (visual, somatomotor, dorsal attention, ventral attention, limbic, frontoparietal, default mode and subcortical networks). Our findings reveal that throughout child and adolescent development, global efficiency increases in the visual, somatomotor, and default mode networks, and mean strength increases in the somatomotor and visual networks. Nodes belonging to the dorsal and ventral visual pathways demonstrate the largest age-dependence in local efficiency, supporting previous evidence of protracted maturation of dorsal and ventral visual pathways. Our results provide compelling evidence that there is a prolonged development of visual association cortices.
Left Ventricular Reverse Remodeling After Revascularization and Its Predictive Role for Survival
Authors: Wang Shaoping , Borah Bijan J. , Cheng Shujuan , Li Shiying , Liu Yanci , Gu Xiaoyan , Li Jinhua , Lyu Yi , Liu Jinghua 
Published: November 2023

AbstractAimsFor patients with ischemic heart failure who underwent revascularization, ejection fraction (EF) improvement is a major predictor of survival benefit. However, the association between left ventricular (LV) remodeling and outcomes has not been well-established. The aim of the study is to investigate the extent of LV remodeling after revascularization and its predictive role for long-term survival.MethodsPatients with reduced EF (≤40%), who underwent either coronary artery bypass grafting or percutaneous coronary intervention, and had echocardiography reassessment 3 months after revascularization were enrolled in a real-world cohort study (No. ChiCTR2100044378). Patients were categorized into 4 groups according to whether LV end-systolic dimension (LVESD) reduction was ≤7% or >7%, and absolute EF improvement ≤5% or >5%ResultsA total of 923 patients were identified. The percentage of LVESD reduction was 4.5±18.4%. The median follow-up time was 3.4 years, during which 123 patients died. Patients with greater percentage of LVESD reduction had lower risk of all-cause death (hazard ratio [HR] per 1% decrement in LVESD, 0.98; 95% CI, 0.97-0.99;P<.001). A reduction in LVESD of 7.2% was the optimal cutoff value to predict survival. Compared to patients with LVESD reduced and EF improved, 2.11-fold (95% CI, 1.04-4.29), 3.56-fold (95% CI, 1.60-7.91), and 7.54-fold (95% CI, 4.20-13.53) higher mortality were found in LVESD unreduced but EF improved, LVESD reduced but EF unimproved, and LVESD unreduced and EF unimproved group, respectively.ConclusionsAfter revascularization among patients with ischemic HF, a reduction in LVESD of 7% signifies clinically relevant revers remodeling. Combination of EF improvement and LVESD reduction might be more clinically precise approach of risk stratification in this population.Clinical Trial RegistrationThe name of the registry: Coronary Revascularization in Patients with Ischemic Heart Failure and Prevention of Sudden Cardiac Death.Registration number: ChiCTR2100044378 (http://www.chictr.org.cn).
Association between triglyceride glucose index and heart failure with preserved ejection fraction in patients with coronary heart disease — a RCSCD-TCM study in China
Authors: Li Zhu , Fan Xiang , Liu Yijia , Yu Lu , He Yuanyuan , Li Lin , Gao Shan , Chen Wei , Yang Rongrong , Yu Chunquan 
Published: November 2023

AbstractBackgroundThe triglyceride glucose (TyG) index serves as a surrogate indicator of insulin resistance. However, there is limited evidence on the association between the TyG index and heart failure with preserved ejection fraction (HFpEF) in patients with coronary heart disease (CHD).MethodsThe 62,794 CHD patients were included used to analyze the relationship between the TyG index and heart failure (HF) in CHD patients. Of these, 8,606 patients who underwent echocardiography were included to identify different types of HF, including HF with reduced ejection fraction (HFrEF), HF with intermediate-range ejection fraction (HFmrEF), and HFpEF. Logistic regression was used to analyze the relationship between the TyG index and HFpEF in CHD patients. The relationship between the TyG index and HFpEF according to sex, age, blood lipids and blood pressure states were also assessed.ResultsA baseline analysis of CHD patients divided into four groups according to the tertile level of the TyG index showed that there were significant differences in related parameters between the groups. In the multi-adjusted modles, the TyG index was significantly associated with the risk of HFpEF (OR: 1.56; 95% CI: 1.08–1.23). In addition, the TyG index of CHD patients was significantly associated with HFpEF in elderly (> 60 years old) patients (OR:1.19; 95% CI: 1.10-1.48), hypertension (OR:1.17; 95% CI: 1.10-1.25) and dyslipidemia (OR:1.16; 95% CI: 1.08-1.23). The association between the TyG index and HFpEF was not affected by sex. And the association between the TyG index of female and HFpEF was (OR:1.21; 95% CI: 1.10-1.34), which was higher than that of male (OR:1.11; 95% CI: 1.02-1.21).ConclusionsThis study demonstrated a significant association of the TyG index and HFpEF in CHD patients. In this study, the results show that the TyG index was independently associated with HFpEF in hypertension, dyslipidemia, and elder patients (> 60 years old). In addition, the association between the TyG index and HFpEF in CHD patients was higher in female.Graphical abstract
Desiccated cyanobacteria serve as efficient plasmid DNA carrier in space flight
Authors: Kakouridis Anne , Diamond Spencer , Eng Thomas , Mills Heath J. , Holzhaus Olivia Gámez , Summers Michael L. , Garcia-Pichel Ferran , Mukhopadhyay Aindrila 
Published: November 2023

AbstractEffective transport of biological systems as cargo during space travel is a critical requirement to use synthetic biology and biomanufacturing in outer space. Bioproduction using microbes will drive the extent to which many human needs can be met in environments with limited resources. Vast repositories of biological parts and strains are available to meet this need, but their on-site availability requires effective transport. Here, we explore an approach that allows DNA plasmids, a ubiquitous synthetic biology part, to be safely transported to the International Space Station and back to the Kennedy Space center, without low-temperature or cryogenic stowage. Our approach relied on the cyanobacteriumNostoc punctiformePC73102, that is naturally tolerant to prolonged desiccation. DesiccatedN. punctiformewas able to carry the non-native pSCR119 plasmid as intracellular cargo safely to space and back. Upon return to the laboratory, the extracted plasmid showed no DNA damage or additional mutations and could be used as intended to transform the model Synbio hostEscherichia colito bestow Kanamycin resistance. This proof-of-concept study provides the foundation for a ruggedized transport host for DNA to environments where there is a need to reduce equipment and infrastructure for biological parts stowage and storage.