bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relationship between Lumbar Puncture Opening Pressure and Retinal Nerve Fiber Layer Thickness in the Diagnosis of Idiopathic Intracranial Hypertension
Authors: Kaya Tutar Nurhan , Kale Nilufer 
Published: October 2023

Objectives:
Idiopathic intracranial hypertension (IIH), is characterized by elevated intracranial pressure (ICP) without an identified cause. Today, lumbar puncture (LP) is the most common method used for diagnosis by measuring cerebrospinal fluid (CSF) pressure to reflect intracranial pressure. This invasive examination has significant disadvantages, such as complications and negative experiences for patients. Therefore, noninvasive methods for ICP measurement are desired. Optical coherence tomography (OCT) is widely used for the diagnosis and follow-up of IIH patients as it reflects papilledema. The aim of this study is to investigate the relationship between CSF pressure and OCT parameters and the ability of OCT in the diagnostic approach.

Methods:
In our study, patients who were followed up with a diagnosis of IIH with complete neuro-ophthalmological examinations, including visual acuity (VA), visual field, and OCT imaging within 24 hours before lumbar puncture, were retrospectively evaluated. CSF pressure, visual acuity LogMAR, mean deviation of visual fields, retinal nerve fiber layer (RNFL) thickness measured by OCT, and treatment protocols were obtained from our hospital data system.

Results:
A total of 42 eyes of 21 patients were enrolled in the study. A statistically significant positive and moderate correlation was found between CSF pressure values and average RNFL thickness (r=0.507; P=0.001). The same relationship was demonstrated in all 4 quadrants: inferior, superior, nasal, and temporal.

Conclusions:
Increased peripapillary RNFL thickness in optic nerve head OCT may be correlated with increased ICP in IIH patients. A larger number of patients are needed to better understand the correlation between OCT parameters and CSF pressure in patients with IIH.
Neurological Manifestations Induced by Nitrous Oxide Abuse
Authors: Pichon Maud , Majhadi Loubna , Menn Anne-Marie 
Published: October 2023

Introduction:
Nitrous oxide (NO) abuse is increasing among young people. This can result in severe neurological disorders such as myelopathy and/or peripheral neuropathy. We report the clinical presentations, biological, radiologic and electrophysiological findings of 5 patients hospitalized with neurological symptoms consecutive to NO abuse. In addition, a literature review was conducted to describe the neurological characteristics and to identify factors associated with a poor recovery.

Case report:
Among the 5 patients included, 2 had a myeloneuropathy, 2 had a sensorimotor neuropathy, and 1 had a normal spinal cord magnetic resonance imaging and electromyography despite neurological manifestations consistent with myeloneuropathy. After vitamin B12 supplementation, recovery was reported in 4 patients, and 1 was lost to follow-up.
From the literature review, 154 patients were included [94 males; median age 22 (19 to 26) y; NO exposure 9 (3 to 18) mo]. A myelopathy was identified in 116 patients (75%) and a peripheral neuropathy was documented in 89 patients (58%). Compared with patients who recovered, those with sequelae were more likely to have a motor deficit at presentation (P<0.001), to use NO regularly (P<0.001), to have a lower vitamin B12 level (P=0.04), and a higher concentration of homocysteine (P=0.04). A less extensive myelopathy was more frequently found in the group with favorable outcomes (P=0.002).

Conclusion:
Neurological disorders caused by NO may be challenging with severe clinical patterns. We identified several factors associated with a poor recovery, to make clinicians aware of NO-induced neurotoxicity.
Spinal Meningeal Mass Lesion
Authors: White Jessica D. , Clarke Michelle J. , Paludo Jonas , Feldman Andrew L. , Sener Ugur T. 
Published: October 2023

Introduction:The differential diagnosis of a spinal intradural extramedullary mass lesion is broad and includes meningioma, schwannoma, neurofibroma, leptomeningeal metastasis, and myxopapillary ependymoma. Though rare, lymphoma should be included in the differential diagnosis of a dural mass lesion.Case Report:A 38-year-old man presented with back pain that progressed over 1 month with associated focal tenderness over his mid to lower thoracic spine. He developed intermittent numbness of the bilateral lower extremities, nuchal rigidity, difficulty sleeping, and night sweats. A magnetic resonance imaging of the thoracic spine demonstrated a dorsal intradural extramedullary enhancing lesion from T7 to T10 extending outside the spinal canal. Dural thickening across the entire circumference of the spinal cord was noted. Computed tomography (CT)-guided biopsy of the thoracic lesion was performed, and pathology was consistent with follicular lymphoma. Fluorodeoxyglucose positron emission tomography:CT demonstrated no systemic disease. Bone marrow biopsy was negative for malignancy. Symptoms resolved with dexamethasone therapy. He was treated with bendamustine and rituximab with follow-up positron emission tomography:CT 2 months later demonstrating a complete response.Conclusions:Lymphoma can rarely present as an isolated dural lesion and should be considered in the differential diagnosis of intradural extramedullary spinal mass lesions. Prompt diagnosis and initiation of treatment can lead to complete response and resolution of symptoms.
Three-dimensional mandibular kinematics of mastication in the marsupialDidelphis virginiana
Authors: Stilson Kelsey T. , Luo Zhe-Xi , Li Peishu , Olson Selby , Ross Callum F. 
Published: October 2023

Didelphis virginiana(the Virginia opossum) is often used as an extant model for understanding feeding behaviour in Mesozoic mammaliaforms, primarily due to their morphological similarities, including an unfused mandibular symphysis and tribosphenic molars. However, the three-dimensional jaw kinematics of opossum chewing have not yet been fully quantified. We used biplanar videofluoroscopy and the X-Ray Reconstruction of Moving Morphology workflow to quantify mandibular kinematics in four wild-caught opossums feeding on hard (almonds) and soft (cheese cubes) foods. These data were used to test hypotheses regarding the importance of roll versus yaw in chewing by early mammals, and the impact of food material properties (FMPs) on jaw kinematics. The magnitude of roll exceeds that of yaw, but both are necessary for tooth-tooth or tooth-food-tooth contact between complex occlusal surfaces. We confirmed the utility of the four vertical kinematic gape cycle phases identified in tetrapods but we further defined two more in order to capture non-vertical kinematics. Statistical tests support the separation of chew cycle phases into two functional groups: occlusal and non-occlusal phases. The separation of slow close into two (occlusal) phases gives quantitative kinematic support for the long-hypothesized multifunctionality of the tribosphenic molar.This article is part of the theme issue ‘Food processing and nutritional assimilation in animals’.
Virologic outcomes on dolutegravir-, atazanavir-, or efavirenz-based ART in urban Zimbabwe: A longitudinal study
Authors: Shamu Tinei , Egger Matthias , Mudzviti Tinashe , Chimbetete Cleophas , Manasa Justen , Anderegg Nanina 
Published: October 2023

AbstractThere are few data from sub-Saharan Africa on the virological outcomes associated with second-line ART based on protease inhibitors or dolutegravir (DTG). We compared viral load (VL) suppression among people living with HIV (PLWH) on atazanavir (ATV/r)- or dolutegravir (DTG)-based second-line ART with PLWH on efavirenz (EFV)-based first-line ART. We analyzed data from the electronic medical records system of Newlands Clinic in Harare, Zimbabwe. We included patients aged ≥12 years when commencing first-line EFV-based ART or switching to second-line DTG- or ATV/r-based ART with ≥24 weeks follow-up after start or switch. We computed suppression rates (HIV VL <50 copies/mL) at weeks 12, 24, 48, 72, and 96 and estimated the probability of VL suppression by treatment regimen, time since start/switch of ART, sex, age, and CD4 cell count (at start/switch) using logistic regression in a Bayesian framework. We included 7013 VL measurements of 1049 PLWH (61% female) initiating first-line ART and 1114 patients (58% female) switching to second-line ART. Among those switching, 872 (78.3%) were switched to ATV/r and 242 (21.7%) to DTG. VL suppression was lower in second-line ART patients than first-line ART patients, except at week 12, when those on DTG showed higher suppression than those on EFV (aOR 2.10, 95%-credible interval [CrI] 1.48-3.00) and ATV/r-based regimens (aOR 1.87, 95%-CrI 1.32-2.71). In weeks ≥48, first-line patients had around 3 times the odds of VL suppression compared to second-line patients. There was no evidence of a difference between DTG and ATV/r for follow-up times ≥24 weeks in PLWH on second-line. Second-line ART patients had lower VL suppression rates than those receiving first-line ART, and there was no difference in suppression between DTG- and ATV/r-based second-line ART ≥6 months after switching. Virologic monitoring and adherence support remain essential to prevent second-line treatment failure in settings with limited treatment options.
Delineating yeast cleavage and polyadenylation signals using deep learning
Authors: Stroup Emily Kunce , Ji Zhe 
Published: October 2023

ABSTRACT3’-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared to well-defined regulatory elements in mammals. Especially, recent deep sequencing experiments showed extensive cleavage heterogeneity for some mRNAs inSaccharomyces cerevisiaeand uncovered the polyA motif differences betweenS. cerevisiaevs.Schizosaccharomyces pombe. The findings raised the fundamental question of how polyadenylation signals are formed in yeast. Here we addressed this question by developing deep learning models to deconvolute degeneratecis-regulatory elements and quantify their positional importance in mediating yeast polyA site formation, cleavage heterogeneity, and strength. InS. cerevisiae, cleavage heterogeneity is promoted by the depletion of U-rich elements around polyA sites as well as multiple occurrences of upstream UA-rich elements. Sites with high cleavage heterogeneity show overall lower strength. The site strength and tandem site distances modulate alternative polyadenylation (APA) under the diauxic stress. Finally, we developed a deep learning model to reveal the distinct motif configuration ofS. pombepolyA sites which show more precise cleavage thanS. cerevisiae. Altogether, our deep learning models provide unprecedented insights into polyA site formation across yeast species.
Monoallelicde novovariants inDDX17cause a novel neurodevelopmental disorder
Authors: Seaby Eleanor G. , Godwin Annie , Clerc Valentine , Meyer-Dilhet Géraldine , Grand Xavier , Fletcher Tia , Monteiro Laloe , Carelli Valerio , Palombo Flavia , Seri Marco , Olivucci Giulia , Grippa Mina , Ciaccio Claudia , D’Arrigo Stefano , Iascone Maria , Bermudez Marion , Fischer Jan , Donato Nataliya Di , Goesswein Sophie , Leung Marco L. , Koboldt Daniel C. , Myers Cortlandt , Bartholomew Dennis , Arnadottir Gudny Anna , Stefansson Kari , Sulem Patrick , Goldberg Ethan M. , Bruel Ange-Line , Tran Mau Them Frederic , Willems Marjolaine , Bjornsson Hans Tomas , Hognason Hakon Bjorn , Thorolfsdottir Eirny Tholl , Agolini Emanuele , Novelli Antonio , Zampino Giuseppe , Onesimo Roberta , Lachlan Katherine , Baralle Diana , Rehm Heidi L. , O’Donnell-Luria Anne , Courchet Julien , Guille Matt , Bourgeois Cyril F. , Ennis Sarah 
Published: October 2023

AbstractIntroductionDDX17 is an RNA helicase shown to be involved in critical processes during the early phases of neuronal differentiation. Globally, we identified 11 patients with neurodevelopmental phenotypes withde novomonoallelic variants inDDX17. All 11 patients had a neurodevelopmental phenotype, whereby intellectual disability, delayed speech and language, and motor delay predominated.Materials and methodsWe performedin uterocortical electroporation in the brain of developing mice, assessing axon complexity and outgrowth of electroporated neurons, comparing wild-type and Ddx17 knockdown. We then undertookex vivocortical electroporation on neuronal progenitors to quantitively assess axonal development at a single cell resolution. Homozygous and heterozygousddx17crispant knockouts inXenopus tropicaliswere generated for assessment of morphology, performed behavioural assays, and neuronal outgrowth measurements. We further undertook transcriptomic analysis of neuroblastoma SH-SY5Y cells, to identify differentially expressed genes in DDX17-KD cells compared to controls.ResultsKnockdown of Ddx17 in electroporated mouse neuronsin vivoshowed delayed neuronal migration as well as decreased cortical axon complexity. Mouse primary cortical neurons revealed reduced axon outgrowth upon knockdown ofDdx17 in vitro. The axon outgrowth phenotype was replicated in crispantddx17tadpoles, including in a heterozygous model. Crispant tadpoles had clear functional neural defects and showed an impaired neurobehavioral phenotype. Transcriptomic analysis identified a statistically significant number of differentially expressed genes involved in neurodevelopmental processes in DDX17-KD cells compared to control cells.DiscussionWe have identified a new gene,DDX17, representing a rare cause of neurodevelopmental delay. We provide evidence for the role of the gene and mechanistic basis of dysfunctional neurodevelopment in both mammalian and non-mammalian species.
Disruption of myelin structure and oligodendrocyte maturation in a pigtail macaque model of congenital Zika infection
Authors: Tisoncik-Go Jennifer , Stokes Caleb , Whitmore Leanne S. , Newhouse Daniel J. , Voss Kathleen , Gustin Andrew , Sung Cheng-Jung , Smith Elise , Stencel-Baerenwald Jennifer , Parker Edward , Snyder Jessica M. , Shaw Dennis W. , Rajagopal Lakshmi , Kapur Raj P. , Waldorf Kristina Adams , Gale Michael 
Published: October 2023

AbstractZika virus (ZikV) infection during pregnancy can cause congenital Zika syndrome (CZS) and neurodevelopmental delay in non-microcephalic infants, of which the pathogenesis remains poorly understood. We utilized an established pigtail macaque maternal-to-fetal ZikV infection/exposure model to study fetal brain pathophysiology of CZS manifesting from ZikV exposurein utero.We found prenatal ZikV exposure led to profound disruption of fetal myelin, with extensive downregulation in gene expression for key components of oligodendrocyte maturation and myelin production. Immunohistochemical analyses revealed marked decreases in myelin basic protein intensity and myelinated fiber density in ZikV-exposed animals. At the ultrastructural level, the myelin sheath in ZikV-exposed animals showed multi-focal decompaction consistent with perturbation or remodeling of previously formed myelin, occurring concomitant with dysregulation of oligodendrocyte gene expression and maturation. These findings define fetal neuropathological profiles of ZikV-linked brain injury underlying CZS resulting from ZikV exposurein utero. Because myelin is critical for cortical development, ZikV-related perturbations in oligodendrocyte function may have long-term consequences on childhood neurodevelopment, even in the absence of overt microcephaly.Graphical abstract
A distinct subpopulation of adipocytes in adult perirenal adipose tissue arises through brown-to-white conversion but reverts to a thermogenic phenotype upon cold exposure
Authors: Zhang Houyu , Li Yan , Ibáñez Carlos F. , Xie Meng 
Published: October 2023

AbstractPerirenal adipose tissue (PRAT) is a unique visceral depot that contains a mixture of brown and white adipocytes. The origin and plasticity of such cellular heterogeneity remains unknown. Here, we combine single-nucleus RNA sequencing with genetic lineage tracing to reveal the existence of a distinct subpopulation ofUcp1-/Cidea+adipocytes that arises from brown-to-white conversion during postnatal life in the peri-ureter region of mouse PRAT. Cold exposure restoresUcp1expression and a thermogenic phenotype in this subpopulation. These cells have a transcriptome that is distinct from subcutaneous beige adipocytes and may represent a unique type of cold-recruitable adipocytes. These results pave the way for studies of PRAT physiology and mechanisms controlling the plasticity of brown/white adipocyte phenotypes.
Alasemenia, the earliest ovule with three wings and without cupule
Authors: Wang Deming , Yang Jiangnan , Liu Le , Zhou Yi , Xu Peng , Qin Min , Huang Pu 
Published: October 2023

AbstractThe ovules or seeds (fertilized ovules) with wings are widespread and especially important for wind dispersal. However, the earliest ovules in the Famennian of the Late Devonian are rarely known about the dispersal syndrome and usually surrounded by a cupule. From Xinhang, Anhui, China, we now report a new taxon of Famennian ovules,Alasemenia triagen. et sp. nov. Each ovule of this taxon possesses three integumentary wings evidently extending outwards, folding inwards along abaxial side and enclosing most part of nucellus. The ovule is borne terminally on smooth dichotomous branches and lacks a cupule.Alasemeniasuggests that the integuments of the earliest ovules without a cupule evolved functions in probable photosynthetic nutrition and wind dispersal. It indicates that the seed wing originated earlier than other wind dispersal mechanisms such as seed plume and pappus, and that three- or four-winged seeds were followed by seeds with less wings. Mathematical analysis shows that three-winged seeds are more adapted to wind dispersal than seeds with one, two or four wings under the same condition.
Missing genomic resources for the next generation of environmental risk assessment
Authors: Roell Marc Sven , Ott Mark-Christoph , Mair Magdalena M. , Pamminger Tobias 
Published: October 2023

AbstractEnvironmental risk assessment traditionally relies on a wide range ofin vivotesting to assess the potential hazard of chemicals in the environment. These tests are often time-consuming, costly and can cause test organisms’ suffering. Recent developments of reliable low-cost alternatives, bothin vivo- andin silico-based, opened the door to reconsider current toxicity assessment. However, many of these new approach methodologies (NAMs) rely on high quality annotated genomes for surrogate species of the regulatory risk assessment. Currently, lacking genomic information slows the process of NAM development. Here, we present a phylogenetically resolved overview of missing genomic resources for surrogate species within regulatory ecotoxicological risk assessment. We call for an organized and systematic effort within the (regulatory) ecotoxicological community to provide these missing genomic resources. Further, we discuss the potential of a standardized genomic surrogate species landscape to enable a robust and non-animal reliant ecotoxicological risk assessment in the systems ecotoxicology era.Synopsis StatementWe identify missing genomic resources needed for the development and regulatory acceptance of new approach methodologies in environmental risk assessment.
An assembly of genomic dataset sequences of the sugar beet root maggotTetanops myopaeformis, TpSBRM_v1.0
Authors: Alkharouf Nadim W. , Chu Chenggen , Klink Vincent P. 
Published: October 2023

ABSTRACTThe sugar beet root maggot (SBRM),Tetanops myopaeformis(von Röder), is a devastating pathogen of sugar beet (SB),Beta vulgaris, ssp vulgaris (B. vulgaris), an important food crop, while also being one of only two plants globally from which sugar is widely produced, and accounting for 35% of global raw sugar with an annual farm value of $3 billion in the United States alone. SBRM is the most devastating pathogen of sugar beet in North America. The limited natural resistance ofB. vulgarisnecessitates an understanding of the SBRM genome to facilitate generating knowledge of its basic biology, including the interaction between the pathogen and its host(s). Presented is the de novo assembled draft genome sequence ofT. myopaeformisisolated from field-grownB. vulgarisin North Dakota, USA. The SBRM genome sequence will also be valuable for molecular genetic marker development to facilitate host resistance gene identification and knowledge, including SB polygalacturonase inhibiting protein (PGIP), and development of new control strategies for this pathogen.SPECIFICATIONSOrganism/cell line/tissue:Tetanops myopaeformisSequencer or array type: PacBio Revio flow cellData format: Raw and processedExperimental factors: DNA extracted from a wild-type strain, no treatmentExperimental features: Genome sequencingConsent n/aSample source location: Sugar beet field at Fargo, North Dakota, USADIRECT LINK TO DEPOSITED DATABioSample accession: SAMN37733483Temporary Submission ID: SUB13882507BioProject ID: PRJNA1026092Release date: 2024-09-09, or with the release of linked data, whichever is first
Place of Birth and Cognition among Older Americans: Findings from the Harmonized Cognitive Assessment Protocol
Authors: Lin Zhuoer , Chen Xi 
Published: October 2023

AbstractObjectivesGrowing evidence suggests that place of birth (PoB) and related circumstances may have long-lasting and multiplicative contributions to various later-life outcomes. However, the specific contributions to different domains of cognitive function in late life remain less understood. This study aimed to investigate the extent to which PoB contribute to a wide range of later-life cognitive outcomes.MethodsA nationally representative sample of Americans aged 65 and older (N=3,216) from the Health and Retirement Study (HRS) Harmonized Cognitive Assessment Protocol (HCAP) was utilized. Cognitive outcomes were assessed in HCAP and linked to HRS state-level PoB data to explore the contribution of birthplace to later-life cognitive disparities. Regression-based Shapley decompositions were employed to quantify this contribution.ResultsPoB significantly contributed to all assessed cognitive outcomes including memory, executive function, language and fluency, visuospatial function, orientation, global cognitive performance, cognitive impairment and dementia. Geographic disparities in cognitive outcomes were evident, with individuals born in US southern states and foreign-born individuals performing worse than those born in other states. PoB overall accounted for 2.4-13.9% of the total variance in cognition after adjusting for age and sex. This contribution reduced by half when adjusting for a rich set of sociodemographic and health factors over the life course, but PoB still independently explained 2.0-7.1% of the total variance in cognition.DiscussionPoB has lasting contributions to later-life cognitive health, with significant geographic disparities observed. Addressing these disparities requires promoting more equalized place-based policies, resources, and early-life environments to improve health equities over the life course.