bluuebunny/crossref_metadata_2025_split huggingface dataset:
Myelin Oligodendrocyte Glycoprotein Antibody Disease Optic Neuritis: A Structure–Function Paradox?
Authors: Ross Ruby , Kenney Rachel , Balcer Laura J. , Galetta Steven L. , Krupp Lauren , O'Neill Kimberly A. , Grossman Scott N. 
Published: March 2024

Background:
Myelin oligodendrocyte glycoprotein antibody disease (MOGAD) is a demyelinating disorder that most commonly presents with optic neuritis (ON) and affects children more often than adults. We report 8 pediatric patients with MOG-associated ON and characterize focal optical coherence tomography (OCT) abnormalities over time that help distinguish this condition from the trajectories of other demyelinating disorders. These OCT findings are examined in the context of longitudinal visual function testing.

Methods:
This is a retrospective case series of 8 pediatric patients with MOG-associated ON who were referred for neuro-ophthalmic evaluation. Longitudinal data for demographics, clinical history, physical examination, and OCT obtained in the course of clinical evaluations were collected through retrospective medical record review.

Results:
Patients demonstrated acute peripapillary retinal nerve fiber layer (RNFL) thickening in one or both eyes, consistent with optic disc swelling. This was followed by steady patterns of average RNFL thinning, with 9 of 16 eyes reaching significantly low RNFL thickness using OCT platform reference databases (P < 0.01), accompanied by paradoxical recovery of high-contrast visual acuity (HCVA) in every patient. There was no correlation between HCVA and any OCT measures, although contrast sensitivity (CS) was associated with global thickness, PMB thickness, and nasal/temporal (N/T) ratio, and color vision was associated with PMB thickness. There was a lower global and papillomacular bundle (PMB) thickness (P < 0.01) in clinically affected eyes compared with unaffected eyes. There was also a significantly higher N:T ratio in clinically affected eyes compared with unaffected eyes in the acute MOG-ON setting (P = 0.03), but not in the long-term setting.

Conclusions:
MOG shows a pattern of prominent retinal atrophy, as demonstrated by global RNFL thinning, with remarkable preservation of HCVA but remaining deficits in CS and color vision. These tests may be better clinical markers of vision changes secondary to MOG-ON. Of the OCT parameters measured, PMB thickness demonstrated the most consistent correlation between structural and functional measures. Thus, it may be a more sensitive marker of clinically significant retinal atrophy in MOG-ON. The N:T ratio in acute clinically affected MOG-ON eyes in our study was higher than the N:T ratio of neuromyelitis optica (NMO)-ON eyes and similar to the N:T ratio in multiple sclerosis (MS)-ON eyes as presented in the prior literature. Therefore, MOG may share a more similar pathophysiology to MS compared with NMO.
Hematologic and Serum Biochemical Values Associated With Different Stages of Hospital-Acquired Pressure Injuries in Patients
Authors: Chang Wen-Pei , Jen Hsiu-Ju , Chang Yu-Pei 
Published: March 2024

PURPOSE:
The primary purpose of this study was to determine whether hematologic and serum biochemical values used as indicators of nutritional status, anemia, and/or infection were associated with the risk of hospital-acquired pressure injuries (PIs) and stage of PIs in patients.

DESIGN:
A retrospective review of medical records.

SUBJECTS AND SETTING:
Data were collected from medical records including official PI records and PI incident reports of inpatients at a teaching hospital in Taiwan between January 2019 and October 2020.

METHODS:
We collected demographic variables of the inpatients and their hematologic and serum biochemical values within 1 day of PI occurrence (including the day of PI occurrence), 6 to 7 days before PI occurrence, and 13 to 14 days before PI occurrence.

RESULTS:
Among the 309 inpatients with official PI records, 105 (34.0%) had Stage 1 PIs, 131 (42.4%) had Stage 2 or 3 PIs, and 73 (23.6%) had unstageable or suspected deep tissue injuries. After controlling for the type of department where PIs occurred and length of hospital stay up to the day of PI occurrence, we found significant differences in levels of hemoglobin (odds ratio [OR] = 0.47, P = .009) within 1 day of PI occurrence and in albumin (OR = 0.30, P = .001) 13 to 14 days before PI occurrence.

CONCLUSIONS:
Study findings suggest that lower hemoglobin levels on the day of PI occurrence and lower albumin levels 2 weeks before PI occurrence resulted in a significantly higher risk of developing unstageable or suspected deep tissue injuries than of developing Stage 1 PIs.
High-energy particle observations from the Moon
Authors: Dandouras Iannis , Roussos Elias 
Published: March 2024

The Moon is a unique natural laboratory for the study of the deep space plasma and energetic particles environment. During more than 3/4 of its orbit around the Earth it is exposed to the solar wind. Being an unmagnetized body and lacking a substantial atmosphere, solar wind and solar energetic particles bombard the Moon's surface, interacting with the lunar regolith and the tenuous lunar exosphere. Energetic particles arriving at the Moon's surface can be absorbed, or scattered, or can remove another particle from the lunar regolith by sputtering or desorption. A similar phenomenon occurs also with the galactic cosmic rays, which have fluxes and energy spectra representative of interplanetary space. During the remaining part of its orbit the Moon crosses the tail of the terrestrial magnetosphere. It then provides the opportunity to study
in-situ
the terrestrial magnetotail plasma environment as well as atmospheric escape from the Earth's ionosphere, in the form of heavy ions accelerated and streaming downtail. The lunar environment is thus a unique natural laboratory for analysing the interaction of the solar wind, the cosmic rays and the Earth's magnetosphere with the surface, the immediate subsurface, and the surface-bounded exosphere of an unmagnetized planetary body.

This article is part of a discussion meeting issue ‘Astronomy from the Moon: the next decades (part 2)’.
Engineering Tumor Stroma Morphogenesis Using Dynamic Cell-Matrix Spheroid Assembly
Authors: Buckenmeyer Michael J. , Brooks Elizabeth A. , Taylor Madison S. , Yang Liping , Holewinski Ronald J. , Meyer Thomas J. , Galloux Mélissa , Garmendia-Cedillos Marcial , Pohida Thomas J. , Andresson Thorkell , St. Croix Brad , Wolf Matthew T. 
Published: March 2024

AbstractThe tumor microenvironment consists of resident tumor cells organized within a compositionally diverse, three-dimensional (3D) extracellular matrix (ECM) network that cannot be replicated in vitro using bottom-up synthesis. We report a new self-assembly system to engineer ECM-rich 3D MatriSpheres wherein tumor cells actively organize and concentrate microgram quantities of decellularized ECM dispersions which modulate cell phenotype. 3D colorectal cancer (CRC) MatriSpheres were created using decellularized small intestine submucosa (SIS) as an orthotopic ECM source that had greater proteomic homology to CRC tumor ECM than traditional ECM formulations such as Matrigel. SIS ECM was rapidly concentrated from its environment and assembled into ECM-rich 3D stroma-like regions by mouse and human CRC cell lines within 4-5 days via a mechanism that was rheologically distinct from bulk hydrogel formation. Both ECM organization and transcriptional regulation by 3D ECM cues affected programs of malignancy, lipid metabolism, and immunoregulation that corresponded with an in vivo MC38 tumor cell subpopulation identified via single cell RNA sequencing. This 3D modeling approach stimulates tumor specific tissue morphogenesis that incorporates the complexities of both cancer cell and ECM compartments in a scalable, spontaneous assembly process that may further facilitate precision medicine.
Effects of nano urea on growth and gene expression ofArabidopsis thalianain hydroponics
Authors: Jangir Neelam , Marik Debankona , Verma Devanshu , Dey Arpan , Shekhawat Rajveer Singh , Patel Deep , Yadav Pankaj , Sankhala Kirti , Sadhukhan Ayan 
Published: March 2024

AbstractIntroductionHydroponics enables precise control over nutrient delivery, optimized water requirements and growing conditions. The combination of nanotechnology and hydroponics paves the way towards sustainable agriculture with less environmental footprints. We investigated the effects of nano urea on the model plantArabidopsis thalianain hydroponics.MethodsA growth experiment in a nitrogen-free hydroponic medium compared the effects of a liquid nano urea formulation (NUF) marketed by Indian Farmers Fertilizer Cooperative (IFFCO) to an equimolar bulk urea. Transcriptome analysis identified the molecular mechanisms of growth enhancement. Dynamic light scattering and transmission electron microscopy confirmed NUF’s negative surface charge and sub-100 nm size, correlating its uptake and distribution in the plant.Results and discussionA two-week growth in the hydroponic medium with 70 μM NUF led to a 20% higher biomass and 16% higher chlorophyll content than a medium with 70 μM urea. Higher doses of NUF inhibited growth, whereas higher equivalent urea doses did not. NUF led to the differential expression of more genes than urea at 12 h to seven days of treatment. Nitrogen assimilation, growth, photosynthesis, and stress tolerance genes showed higher transcript levels in NUF than in urea. On the other hand, NUF led to greater suppression of many negative growth-regulating genes. After seven days of treatment, chlorophyll biosynthesis genes got up-regulated, while chlorophyll catabolism genes got down-regulated at higher levels by NUF than by urea, correlating with the higher chlorophyll content of NUF-treated seedlings. In conclusion, NUF outperformed equimolar urea for the growth promotion ofA. thalianaat a low concentration in hydroponics, leading to a greater regulation of genes for nitrogen metabolism and chlorophyll biosynthesis. Our results suggest a potential use of NUF as a nitrogen fertilizer for hydroponic agriculture.
Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data
Authors: Vo Duong H.T. , Thorne Thomas 
Published: March 2024

AbstractGene interaction networks are graphs in which nodes represent genes and edges represent functional interactions between them. These interactions can be at multiple levels, for instance, gene regulation, protein-protein interaction, or metabolic pathways. To analyse gene interaction networks at a large scale, gene co-expression network analysis is often applied on high-throughput gene expression data such as RNA sequencing data. With the advance in sequencing technology, expression of genes can be measured in individual cells. Single-cell RNA sequencing (scRNAseq) provides insights of cellular development, differentiation and characteristics at transcriptomic level. High sparsity and high-dimensional data structure pose challenges in scRNAseq data analysis. In this study, a sparse inverse covariance matrix estimation framework for scRNAseq data is developed to capture direct functional interactions between genes. Comparative analyses highlight high performance and fast computation of Stein-type shrinkage in high-dimensional data using simulated scRNAseq data. Data transformation approaches also show improvement in performance of shrinkage methods in non-Gaussian distributed data. Zero-inflated modelling of scRNAseq data based on a negative binomial distribution enhances shrinkage performance in zero-inflated data without interference on non zeroinflated count data. The optimal zero-inflated Stein-type shrinkage framework is applied on experimental scRNAseq data which demonstrates its potential to construct sparser gene interaction networks with higher precision.Availability and implementationhttps://github.com/calathea24/ZINBGraphicalModel
Development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography
Authors: Du Daniel X. , Bartnik Adam C. , Duncan Cameron J. R. , Choudhry Usama , Tabachnik Tanya , Sallah Chaim , Najafi Ebrahim , Yang Ding-Shyue , Maxson Jared M. , Fitzpatrick Anthony W. P. 
Published: March 2024

AbstractCryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy (cryo-EM) excels in determining protein structures purified from recombinant or endogenous sources, cryo-ET suffers from low contrast in crowded cellular milieux. A novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Further, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way towards exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexesin situ, thus advancing the field of cell biology.
Epidemiological, phylogenetic, and resistance heterogeneity amongAcinetobacter baumanniiin a major US Deep South healthcare center
Authors: Graffice Emma , Moates Derek B. , Leal Sixto M. , Amerson-Brown Megan , Calix Juan J. 
Published: March 2024

AbstractAcinetobacter baumannii(Ab) disease in the U.S. is commonly attributed to outbreaks of one or two monophyletic carbapenem resistance (CR)Ablineages that vary by region. However, there is limited knowledge regardingAbepidemiology and population structure in the U.S. Deep South, and few studies compare contemporary CR and carbapenem-susceptible (Cs)Ab, despite prevalence of the latter. We performed a 12-year time series analysis ofAbcases in a large hospital in Birmingham, AL, and 89 isolates from an ongoing surveillance project started in November 2021 were analyzed by whole genome sequencing and antibiotic susceptibility testing (AST). Cumulative CR rate among 2462 cases since 2011 was 19.4%, with increased rates during winter months resulting from seasonal changes in CsAbincidence. Sequenced CRAbbelonged to clonal complex (CC) 1, CC108, CC250, CC2, and CC499. Most CRAbCCs were comprised of isolates that clustered apart from U.S. counterparts in phylogenetic analysis, despite being identified in unrelated cases occurring ≥3 months apart. In contrast, 38/47 (81%) CsAbisolates each belonged to a distinct CC. CRAbisolates displayed lineage-distinct AST features, including unique carbapenem resistance genetic determinants and presumptive heteroresistance behaviors unique to CC108 and CC499 isolates. This first comprehensive analysis ofAbcases in the U.S. Deep South revealed epidemiological trends consistent with those in other regions and an unusually high degree of phylogenetic diversity among regional CRAbisolates. We also describe emergent U.S. CRAblineages whose unconventional antimicrobial resistance features must be integrated into ongoing diagnostic, treatment, and surveillance efforts.
Quantifying brain health in acute ischemic stroke through effective reserve
Authors: Schirmer Markus D. , Alhadid Kenda , Regenhardt Robert W. , Rost Natalia S. 
Published: March 2024

AbstractObjectiveTo quantify brain health using a measure of reserve that incorporates pre-existing pathology.MethodsWe analyzed two retrospective ischemic stroke cohorts (GASROS and SALVO) with neuroimaging and 90-day modified Rankin Scores (mRS) available. White matter hyperintensity (WMHv), brain, and intracranial volumes were automatically extracted, and brain parenchymal fraction (BPF) calculated. The latent variable effective reserve (eR) was modeled using age, WMHv, and BPF or brain volume in GASROS. Models were compared using Bayes Information Criterion (BIC). The best model’s eR estimates were categorized into quartiles and evaluated in SALVO.ResultsGASROS included 476 (median age: 65.8; 65.3% male) and SALVO included 43 (median age: 69.2; 62.8% male) patients. Inverse associations between eR and mRS was seen in both models, with brain volume outperforming BPF (path coefficients: -0.67, -0.48, respectively; p < 0.001; |ΔBIC| = 362). Quartile-based eR stratification in SALVO showed a similar inverse trend, with worse outcomes in the low reserve group (mRS≤2 - highest vs lowest quartile: 85/90% vs 59/45% for GASROS/SALVO).ConclusionsExpanding the concept of eR, highlights its clinical translational potential. The strong link between higher eR and better outcomes underscores its value as a protective brain health metric.
MultiSCRIPT-Cycle 1- A Pragmatic trial embedded within the Swiss Multiple Sclerosis Cohort (SMSC) on neurofilament light chain monitoring to inform personalized treatment decisions in Multiple Sclerosis: a study protocol for a randomized clinical trial
Authors: Janiaud Perrine , Zecca Chiara , Salmen Anke , Benkert Pascal , Schädelin Sabine , Orleth Annette , Demuth Lilian , Maceski Aleksandra Maleska , Granziera Cristina , Oechtering Johanna , Leppert David , Derfuss Tobias , Achtnichts Lutz , Findling Oliver , Roth Patrick , Lalive Patrice , Uginet Marjolaine , Müller Stefanie , Pot Caroline , Hoepner Robert , Disanto Giulio , Gobbi Claudio , Rooshenas Leila , Schwenkglenks Matthias , Lambiris Mark J , Kappos Ludwig , Kuhle Jens , Yaldizli Özgür , Hemkens Lars G 
Published: March 2024

AbstractBackgroundTreatment decisions for persons with relapsing-remitting multiple sclerosis (RRMS) rely on clinical and radiological disease activity, the benefit-harm profile of drug therapy, and preferences of patients and physicians. However, there is limited evidence to support evidence-based personalized decision-making on how to adapt disease modifying therapies treatments targeting no evidence of disease activity, while achieving better patient-relevant outcomes, fewer adverse events and improved care. Serum neurofilament light chain (sNfL) is a sensitive measure of disease activity that captures and prognosticates disease worsening in RRMS. sNfL might therefore be instrumental for a patient-tailored treatment adaptation. We aim to assess whether 6-monthly sNfL monitoring in addition to usual care improves patient-relevant outcomes compared to usual care alone.MethodsPragmatic multicenter, 1:1 randomized, platform trial embedded in the Swiss MS Cohort (SMSC). All patients with RRMS in the SMSC for ≥1 year are eligible. We plan to include 915 patients with RRMS, randomly allocated to two groups with different care strategies, one of them new (group A), one of them usual care (group B). In group A, 6-monthly monitoring of sNfL will together with information on relapses, disability and magnetic resonance imaging (MRI) inform personalized treatment decisions (e.g., escalation or de-escalation) supported by pre-specified algorithms. In group B, patients will receive usual care with their usual 6- or 12- monthly visits. Two primary outcomes will be used: 1) evidence of disease activity (EDA3: occurrence of relapses, disability worsening, or MRI activity) and 2) quality of life (MQoL-54) using 24-month follow-up. The new treatment strategy with sNfL will be considered superior to usual care if either more patients have no EDA3, or their health-related quality of life increases. Data collection will be embedded within the SMSC using established trial-level quality procedures.DiscussionMultiSCRIPT aims to be a platform where research and care are optimally combined to generate evidence to inform personalized decision-making in usual care. This approach aims to foster better personalized treatment and care strategies, at low cost and with rapid translation to clinical practice.Trial registrationNCT06095271
Phenotypic spectrum ofFAM47E-SHROOM3haplotype composition in a general population sample
Authors: Ghasemi-Semeskandeh Dariush , König Eva , Foco Luisa , Dordevic Nikola , Gögele Martin , Rainer Johannes , Ralser Markus , Acoba Dianne , Domingues Francisco S. , Peters Dorien J. M. , Pramstaller Peter P. , Pattaro Cristian 
Published: March 2024

AbstractGenome-wide association studies identified a locus on chromosome 4q21.1, spanning theFAM47E,STBD1,CCDC158, andSHROOM3genes, as associated with kidney function markers. Functional studies implicatedSHROOM3, encoding an actin-binding protein involved in cell shaping, into podocyte barrier damage. Despite the locus was also found associated with electrolytes, hematological and cardiovascular traits, systematic explorations of functional variants across all the genes in the locus are lacking.We reconstructed haplotypes covering the whole locus on 12,834 participants to the Cooperative Health Research in South Tyrol (CHRIS) study, using genotypes imputed on a whole-exome sequencing reference panel of a subsample of 3,422 participants. Haplotypes included 146 exonic and intronic variants over the four genes and were tested for association with 73 serum, urine and anthropometric traits, 172 serum metabolite and 148 plasma protein concentrations using linear regression models.We identified 11 haplotypes with 2% to 24% frequency. Compared to the most common haplotype, most haplotypes were associated with higher levels of the creatinine-based estimated glomerular filtration rate and lower serum magnesium levels. The second most common haplotype (12% frequency) was additionally associated with lower dodecanoyl-, hydroxyvaleryl- and tiglyl-carnitine serum concentrations. A haplotype of 4% frequency was also associated with lower red blood cell count, hemoglobin, and hematocrit levels. A haplotype of 2% frequency was associated with serum glutamine and putrescine concentrations. Cluster analysis revealed distinct groups of traits and of haplotypes.TheFAM47E-SHROOM3locus exhibits haplotype variability that corresponds to marked pleiotropic effects, implicating the existence of population subgroups with distinct biomarker profiles.