bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Prevalence and Trends Among Pregnant and Postpartum Individuals in Maine by Rurality and Pregnancy Conditions
Authors: Grantham Charlie O. , Ackerman-Banks Christina M. , Lipkind Heather S. , Palmsten Kristin , Ahrens Katherine A. 
Published: April 2023

ABSTRACTObjectiveTo estimate COVID-19 diagnosis prevalence and trends among pregnant and postpartum individuals in Maine by rurality and common pregnancy conditions.MethodsWe used the Maine Health Data Organization’s All Payer Claims Data to identify deliveries during 2020-2021. We identified COVID-19 during pregnancy (Apr 2020 to Dec 2021 deliveries) and during the first 6 months postpartum (Apr 2020 to Jun 2021 deliveries) using the ICD-10 diagnosis code U071 on medical claims. We used Joinpoint regression software to model trends. We stratified the analysis by rurality of residence (based on ZIP code) and by common pregnancy conditions: gestational diabetes (GDM), hypertensive disorders of pregnancy (HDP), and prenatal depression.ResultsWe included 13,457 deliveries in our pregnancy and 9,143 deliveries in our postpartum analysis. COVID-19 diagnosis prevalence among pregnant individuals increased from 0.5% in Apr 2020 to 10.5% in Dec 2021 (Oct 2020 was the start of slope [0.43 per month], p<.01). COVID-19 diagnosis prevalence postpartum increased from 0.9% in Apr 2020 to 3.2% in June 2021 deliveries (slope=0.12 per month, p<.01). Trends in prevalence of COVID-19 diagnosis among pregnant individuals living in urban areas were distinct from those living in rural areas (p=.02), with a steeper slope during the first months of the pandemic in urban areas, followed by a later increase among rural residents. Trends among postpartum individuals living in urban areas were distinct from those living in rural areas (p=.03), with a steeper slope for rural residents over the course of the pandemic. Trends in persons with prenatal depression showed a steeper increase in COVID-19 diagnosis prevalence in pregnancy after Dec 2020 (p<.01) and postpartum overall (p<.01) compared to those without prenatal depression. Individuals without GDM and individuals without HDP had steeper increases in COVID-19 diagnosis prevalence in postpartum compared to those without GDM (p<.01) and those without HDP (p=.03).ConclusionCOVID-19 diagnosis among pregnant and postpartum individuals in Maine showed distinct patterns by rurality of residence and select pregnancy conditions. This information can be used for assessing the impact of the COVID-19 pandemic on maternal and infant health.
CMR Reveals Myocardial Damage from Cardiotoxic Oncologic Therapies in Breast Cancer Patients
Authors: Kersten Johannes , Fink Visnja , Kersten Maria , May Lisa , Nunn Samuel , Tadic Marijana , Huober Jens , Bekes Inga , Radermacher Michael , Hombach Vinzenz , Rottbauer Wolfgang , Buckert Dominik 
Published: April 2023

AbstractBackgroundBreast cancer is a common and increasingly treatable disease. However, survivors have a significantly elevated risk of cardiac events afterwards. This study aimed to characterise cardiac changes during cardiotoxic cancer therapy using cardiovascular magnetic resonance (CMR) imaging.MethodsThis study involved 34 patients with histologically proven breast cancer and planned cardiotoxic therapy. All patients underwent CMR before starting therapy, and 6 and 12 months thereafter. The CMR protocol included volumetric and functional analyses, parametric mapping, and deformation analysis using feature tracking. As the control group, 10 healthy female volunteers were scanned using the same protocol.ResultsWith therapy, there was a significant reduction of left ventricular and right ventricular ejection fractions (both p < 0.05). Left ventricular radial (p = 0.008), circumferential (p = 0.010), and longitudinal strain (p = 0.036) were also reduced at follow-up. In the parametric mapping, there was a significant increase in native T1 time (1037 ± 41 ms vs. 1068 ± 51 ms vs. 1017 ± 57 ms, p < .001) and T2 time (55 ± 4 ms vs. 59 ± 3 ms vs. 57 ± 3 ms, p = 0.001), with unchanged extracellular volume and relative late gadolinium enhancement. Twelve months after cancer diagnosis, the breast cancer patients exhibited significant impairments in left ventricular global radial (p = 0.001), circumferential (p = 0.001), and longitudinal strain (p = 0.002) and T2 time (p = 0.008) compared to the healthy controls.DiscussionBreast cancer patients receiving cardiotoxic chemotherapy show persistent deterioration in left ventricular strain values. This is accompanied by inflammatory changes in non-invasive tissue characterisation. Larger studies with longer follow-up periods are needed to identify patients at risk and establish preventive and therapeutic approaches.
Mena and VASP are required for vascular smooth muscle relaxation
Authors: Ulrich Lea , Gliem Carla , Groneberg Dieter , Frömel Timo , Schuh Kai , Fleming Ingrid , Benz Peter M. 
Published: April 2023

AbstractEnabled/vasodilator stimulated phosphoproteins (Ena/VASP) proteins are important regulators of the cytoskeleton, linking kinase signaling pathways to actin assembly. In mammals, the Ena/VASP family of proteins consists of mammalian enabled (Mena), VASP, and Ena-VASP-like protein (EVL). The proteins are well known targets of cAMP- and cGMP-dependent protein kinases, PKA and PKG, respectively. Given the importance of cyclic nucleotide signaling in mediating vasodilation, we investigated the role of Ena/VASP protein in vascular smooth muscle relaxation. Whereas VASP and Mena were strongly expressed in vascular smooth muscle cells, EVL was undetectable in the arterial wall and EVL-deficiency had no impact on agonist-induced smooth muscle relaxation. VASP deletion impaired the acetylcholine (ACh)- and nitric oxide (NO)-induced relaxation murine mesenteric arteriesex vivo. Similarly, the ACh-induced and NO-dependent relaxation of aorta from 7-month-old but not 3- month-old VASP-/-mice was also reduced. Aortas from animals lacking VASP and expressing only minimal amounts of Mena displayed significantly impaired relaxations in response to NO, cAMP and cGMP stimulation. These results suggest that Mena and VASP play an important role in agonist induced smooth muscle relaxation and functionally compensate for each other.
Label-free Identification of Protein Aggregates Using Deep Learning
Authors: Ibrahim Khalid A. , Grußmayer Kristin S. , Riguet Nathan , Feletti Lely , Lashuel Hilal A. , Radenovic Aleksandra 
Published: April 2023

AbstractProtein misfolding and aggregation play central roles in the pathogenesis of various neurodegenerative diseases (NDDs), including Huntington’s disease, which is caused by a genetic mutation that leads to a polyglutamine repeat length > 35 in exon 1 of the Huntingtin protein (Httex1). Current research on protein aggregation often involves the use of fluorescent labels to visualize and monitor the dynamics of protein expression, which can alter the biophysical properties of proteins and the final ultrastructure, composition, and toxic properties of the formed aggregates. To overcome this limitation, we present a method for label-free identification of NDD-associated aggregates (LINA). Our approach utilizes deep learning to detect unlabeled and unaltered Httex1 aggregates in living cells from transmitted-light images, without the need for fluorescent labeling. We developed pixel-classification and pixel-regression models, which are robust across imaging conditions, and validated them on aggregates formed by different constructs of Httex1. Our results reveal that Httex1 proteins with shorter polyglutamine repeat lengths form aggregates with a higher average dry mass and area, highlighting the differences in their ultrastructure and aggregation mechanisms. LINA enables the dynamic identification of label-free aggregates and measurement of their dry mass and area changes during their growth process. Our highly-robust models offer high speed, specificity, and simplicity to analyze label-free protein aggregation dynamics and obtain high-fidelity information.
Topology-Aware Focal Loss for 3D Image Segmentation
Authors: Demir Andac , Massaad Elie , Kiziltan Bulent 
Published: April 2023

AbstractThe efficacy of segmentation algorithms is frequently compromised by topological errors like overlapping regions, disrupted connections, and voids. To tackle this problem, we introduce a novel loss function, namely Topology-Aware Focal Loss (TAFL), that incorporates the conventional Focal Loss with a topological constraint term based on the Wasserstein distance between the ground truth and predicted segmentation masks’ persistence diagrams. By enforcing identical topology as the ground truth, the topological constraint can effectively resolve topological errors, while Focal Loss tackles class imbalance. We begin by constructing persistence diagrams from filtered cubical complexes of the ground truth and predicted segmentation masks. We subsequently utilize the Sinkhorn-Knopp algorithm to determine the optimal transport plan between the two persistence diagrams. The resultant transport plan minimizes the cost of transporting mass from one distribution to the other and provides a mapping between the points in the two persistence diagrams. We then compute the Wasserstein distance based on this travel plan to measure the topological dissimilarity between the ground truth and predicted masks. We evaluate our approach by training a 3D U-Net with the MICCAI Brain Tumor Segmentation (BraTS) challenge validation dataset, which requires accurate segmentation of 3D MRI scans that integrate various modalities for the precise identification and tracking of malignant brain tumors. Then, we demonstrate that the quality of segmentation performance is enhanced by regularizing the focal loss through the addition of a topological constraint as a penalty term.
Massive expansion of the pig gut virome based on global metagenomic mining
Authors: Mi Jiandui , Jing Xiaoping , Ma Chouxian , Yang Yiwen , Li Yong , Zhang Yu , Long Ruijun , Zheng Haixue 
Published: April 2023

AbstractThe pig gut virome plays a crucial role in the gut microbial ecosystem of pigs, yet a comprehensive reference database is still lacking. To address this gap, we established the Pig Virome Database (PVD) of the gut that comprises 5,566,804 viral contig sequences from 4,650 publicly available gut metagenomic samples using a pipeline named “metav” developed in this study. The majority of viral operational taxonomic units (vOTUs) were identified asCaudoviricetes(65.36%). By clustering sequences, we identified 48,299 vOTU genomes, of which 92.83% were not found in existing major databases. The PVD database contains a total of 18,161,503 protein-coding genes that can be used to explore the functional potential of the pig gut virome. Our study showed that the PVD can improve the detection of viruses that carry antibiotic/metal resistance genes, mobile genetic elements, virulence factor genes, and quorum sensing systems. These findings highlight the extensive diversity of viruses in the pig gut and provide detailed insight into host‒virus interactions.
Molecular Coevolutionary Drive
Authors: Lynch Michael 
Published: April 2023

AbstractMost aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino-acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within lowNeenvironments can drive the rate of evolution of partner genes experiencing higherNe, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.Significance StatementA wide variety of features at the cellular level involve precise interactions between participating molecular partners, thereby requiring coordinated co-evolutionary changes within lineages. The same is true for ecological interactions between species. Although there has been much speculation on how such constraints might drive molecular evolutionary rates beyond the neutral expectation, there has been little formal evolutionary theory to evaluate the generality of such claims. Here, a general framework is developed for ascertaining how rates of sequence evolution depend on the population-genetic environments of both interacting partner molecules. Although the features of one site can indeed drive the evolution of the other, only under restrictive conditions does this process push rates beyond the neutral expectation.
The SToP (See, Treat, Prevent) Skin Sores and Scabies Trial - a stepped wedge cluster randomised trial for skin disease control in remote Western Australia: Statistical analysis plan
Authors: Jones Mark , Thomas Hannah , Snelling Thomas , Bowen Asha , Marsh Julie 
Published: April 2023

AbstractThe SToP trial is an (open-cohort) stepped-wedge cluster randomised trial (SWCRT) that aims to evaluate a skin health programme comprising three intervention components (1) seeing skin infections; (2) treating skin infections; and (3) preventing skin infections. Four community clusters in the remote Kimberley region of Western Australia will participate in the study. The primary outcome is the diagnosis of impetigo in children (5–9 years) observed during school-based surveillance visits. We provide a detailed, prospective statistical analysis plan (SAP). The plan was written by the trial statistician and details the study design as well as the statistical methods and reporting to be used. The SAP was produced prior to any of the authors viewing any of the trial data. Application of this SAP will minimise bias and supports transparent and reproducible research. SToP is registered under the Australian and New Zealand Clinical Trials Registry, ACTRN12618000520235.
Cortical Plasticity is associated with Blood-Brain-Barrier Modulation
Authors: Swissa Evyatar , Monsonego Uri , Yang Lynn T. , Schori Lior , Kamintsky Lyna , Mirloo Sheida , Burger Itamar , Uzzan Sarit , Patel Rishi , Sudmant Peter H , Prager Ofer , Kaufer Daniela , Friedman Alon 
Published: April 2023

SummaryBrain microvessels possess the unique properties of a blood-brain barrier (BBB), tightly regulating the passage of molecules from the blood to the brain neuropil and vice versa. In models of brain injury, BBB dysfunction and the associated leakage of serum albumin to the neuropil have been shown to induce pathological plasticity, neuronal hyper-excitability, and seizures. The effect of neuronal activity on BBB function and whether it plays a role in plasticity in the healthy brain remain unclear. Here we show that neuronal activity induces modulation of microvascular permeability in the healthy brain and that it has a role in local network reorganization. Combining simultaneous electrophysiological recording and vascular imaging with transcriptomic analysis in rats, and functional and BBB-mapping MRI in human subjects we show that prolonged stimulation of the limb induces a focal increase in BBB permeability in the corresponding somatosensory cortex that is associated with long-term synaptic plasticity. We further show that the increased microvascular permeability depends on neuronal activity and involves caveolae-mediated transcytosis and transforming growth factor beta signaling. Our results reveal a role of BBB modulation in cortical plasticity in the healthy brain, highlighting the importance of neurovascular interactions for sensory experience and learning.
NOCICEPTRA2.0 - a comprehensive ncRNA atlas of human native and iPSC-derived sensory neurons
Authors: Zeidler Maximilian , Tavares-Ferreira Diana , Brougher Jackson , Price Theodore J. , Kress Michaela 
Published: April 2023

AbstractNon-coding RNAs (ncRNAs) play a critical role in regulating gene expression during development and in the pathogenesis of diseases. In particular, microRNAs have been extensively studied in the context of neurogenesis, the differentiation of pain sensing nociceptive neurons and the pathogenesis of pain disorder, however, little is known about the developmental signatures of other ncRNA species throughout sensory neuron differentiation. Moreover, there is currently no information available about the general expression signatures of ncRNAs in human dorsal root ganglia (DRGs) harboring the cell bodies of primary afferent nociceptors.To bridge this knowledge gap, we developed a comprehensive atlas of small ncRNA species signatures during the differentiation of human induced pluripotent stem cell (iPSC)-derived nociceptive neurons. By employing a combination of iPSC-derived sensory neuron and human DRG long and short RNA co-sequencing, we identified specific signatures that describe the developmental processes and the signatures of all currently known small ncRNA species in detail.Our analysis revealed that different ncRNA species, including tRNAs, snoRNAs, lncRNAs, and piRNAs, are associated with different stages of sensory neuron differentiation and maturation. We retrieved pronounced similarities in ncRNA expression between human DRG and late-stage iPSC-derived sensory neurons, which further supports the use of iPSC-derived sensory neurons to uncover functional and regulatory changes in ncRNAs and their suitability as a as a human model system to bridge the translational gap between preclinical findings mostly from rodent models and our understanding of human disorders for the development of mechanism-based treatments.In summary, our findings provide important insights into the role of ncRNA species other than microRNAs in human nociceptors. The updated NOCICEPTRA2.0 Tool will be the first fully comprehensive searchable ncRNA database for human sensory neurons enabling researchers to investigate important hub ncRNA regulators in nociceptors in full detail.
Semantic feature production norms for manipulable objects
Authors: Valério Daniela , Hussain Akbar , Almeida Jorge 
Published: April 2023

AbstractFeature generation tasks and feature databases are important for understanding how knowledge is organized in semantic memory, as they reflect not only the kinds of information that individuals have about objects but also how objects are conceptually parse. Traditionally, semantic norms focus on a variety of object categories, and, as a result, have a small number of concepts per semantic category. Here, our main goal is to create a more finely-tuned feature database exclusively for one category of objects – manipulable objects. This database contributes to the understanding of within-category, content-specific processing. To achieve this, we asked 130 participants to freely generate features for 80 manipulable objects, and another group of 32 participants to generate action features for the same objects. We then compared our databases with other published semantic norms and found high structural similarity between them. In our databases, we calculated the similarity between visual, functional, encyclopedic, and action feature types. We discovered that objects were grouped in a distinctive and meaningful way according to feature type. Finally, we tested the validity of our databases by asking three groups of participants to perform a feature verification task while manipulating production frequency. Our results demonstrate that participants can recognize and associate the features of our databases with specific manipulable objects. Participants were faster to verify high-frequency features than low-frequency features. Overall, our data provide important insights into how we process manipulable objects and can be used to further inform cognitive and neural theories of object processing and identification.
Structural genomic variation and migratory behavior in wild songbirds
Authors: Delmore Kira E. , Van Doren Benjamin M. , Ullrich Kristian , Curk Teja , van der Jeugd Henk P. , Liedvogel Miriam 
Published: April 2023

AbstractStructural variants (SVs) are a major source of genetic variation, but accurate descriptions in natural populations and connections with phenotypic traits remain scarce. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (i) characterized the genome-wide distribution, frequency and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (ii) used these SVs to study the genetics of seasonal migration. We detected >15K SVs. Many SVs overlapped repetitive regions and exhibited evidence of purifying selection suggesting they have overall deleterious effects on fitness. We used estimates of genomic differentiation to identify SVs exhibiting evidence of selection in blackcaps with different migratory strategies. Insertions and deletions dominated these SVs and were associated with genes that are either directly (e.g., regulatory motifs that maintain circadian rhythms) or indirectly (e.g., through immune response) related to migration. We also broke migration down into individual traits (direction, distance and timing) using existing tracking data and tested if genetic variation at the SVs we identified could account for phenotypic variation at these traits. This was only the case for one trait – direction – and one specific SV (a deletion on chromosome 27) accounted for much of this variation. Our results highlight the evolutionary importance of SVs in natural populations and provide insight into the genetic basis of seasonal migration.
Outcomes of use of the quality outcome measure for individuals with dementia (QOMID) with people with Down’s syndrome and dementia
Authors: Ryan Aoife , Dodd Karen 
Published: April 2023

Purpose
This paper aims to describe the outcomes of the use of the Quality Outcome Measure for individuals with dementia (QOMID) within a dementia pathway for people with Down’s syndrome (DS). The QOMID is a tool for clinicians to use with 17 outcome domains, each with descriptors for early, mid and late stage dementia, rated on a four point scale from rarely achieved for the person (1) to consistently and completely achieved for the person (4).

Design/methodology/approach
Data from first time use of the QOMID with 49 people with DS and dementia was analysed to determine if specific outcome domains are more achievable than others, if this differs by stage of dementia and what recommendations are suggested.

Findings
Results suggest that there were significant differences in achievability across the domains but that achievability did not vary between early and mid-stages of dementia. The themes with most recommendations were: quality of paperwork and documentation; improving communication with the person with DS and dementia; and working together with health and social care professionals.

Practical implications
Results suggest that outcomes which fall outside of the typical learning disabilities skillset and are dementia specific are being achieved less often. Primarily, recommendations focused on practical solutions such as using visual timetables to communicate with the person and adapting their environment. Further work on integrating the QOMID and stage-related team training for care staff is underway.

Originality/value
To the best of the authors’ knowledge, this is the first detailed analysis of the use of the QOMID in clinical practice with people with DS and dementia.