bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound-guided resection of cerebellar racemose neurocysticercosis: novel insights from a unique scenario
Authors: Rojas-Apaza Rolando V , Bocanegra-Becerra Jhon E , Ruiz-Garcia Henry , Rabanal-Palacios Jorge , Zambrano-Reyna Francisco 
Published: April 2024

Abstract
Racemose neurocysticercosis (RNC) is a malignant form of Taenia solium infection. It carries high mortality due to widespread intraparenchymal invasion, mass effect, and cyst rupture. Cerebellar RNC is unusual and constitutes a surgical challenge. Scarce applications of ultrasound (US) -guided resection have been reported for RNC of the posterior fossa. We report the case of a 66-year-old woman who presented with ataxia and dysmetria. Her past medical history was relevant for seizures and hydrocephalus secondary to neurocysticercosis. Because of the increasing cyst invasion and threatening mass effect in the posterior fossa, the patient underwent US-guided resection of lesions. Postoperative computed tomography (CT) demonstrated complete excision of cysts, and a 2-year follow-up magnetic resonance imaging (MRI) showed no recurrence. On neurological examination, the patient had persistent ataxia without new-onset neurological deficits. The present case study illustrates the feasibility and cost-effective approach of US-guided resection to provide enhanced operative visualization and achieve complete cyst resection.
Drug induced gingival enlargement - phenytoin: an overview and case report
Authors: Dhalla Nipun , Gopal Lipika , Palwankar Pooja 
Published: April 2024

Abstract
Gingival enlargement is a side effect of several different medication, including immunosuppressants, anticonvulsants, and calcium channel blockers. It is an inflammatory response that starts when plaque and calculus build up on the tooth surface. The most prevalent long-term neurological condition affecting people is epilepsy. In affluent nations, the prevalence of epilepsy is ~ 1%, whereas in less developed countries, it may &gt;2%. The preferred medication for the condition, phenytoin, has major side effects include gingival enlargement. In addition to being visually disfiguring, this enlargement frequently affects speech, chewing and eating. Furthermore, those with poor dental hygiene, causes disabilities with motor coordination and muscular limitations leading to mental disability and physical impairments are more prone to periodontal disease. This article enlightened the mechanism of drug induced gingival enlargement clinically, microbiologically, and surgically.
Disrupting cell wall integrity impacts endomembrane trafficking to promote secretion over endocytic trafficking
Authors: Hoffmann Natalie , Mohammad Eskandar , McFarlane Heather E 
Published: April 2024

Abstract
The plant cell wall provides a strong yet flexible barrier to protect cells from the external environment. Modifications of the cell wall, either during development or under stress conditions, can induce cell wall integrity responses and ultimately lead to alterations in gene expression, hormone production, and cell wall composition. These changes in cell wall composition presumably require remodelling of the secretory pathway to facilitate synthesis and secretion of cell wall components and cell wall synthesis/remodelling enzymes from the Golgi apparatus. Here, we used a combination of live-cell confocal imaging and transmission electron microscopy to examine the short-term and constitutive impact of isoxaben, which reduces cellulose biosynthesis, and Driselase, a cocktail of cell-wall-degrading fungal enzymes, on cellular processes during cell wall integrity responses in Arabidopsis. We show that both treatments altered organelle morphology and triggered rebalancing of the secretory pathway to promote secretion while reducing endocytic trafficking. The actin cytoskeleton was less dynamic following cell wall modification, and organelle movement was reduced. These results demonstrate active remodelling of the endomembrane system and actin cytoskeleton following changes to the cell wall.
Stellar populations with optical spectra: deep learning versus popular spectrum fitting codes
Authors: Woo Joanna , Walters Dan , Archinuk Finn , Faber S M , Ellison Sara L , Teimoorinia Hossen , Iyer Kartheik 
Published: April 2024

ABSTRACT
We compare the performance of several popular spectrum fitting codes (firefly, starlight, pypipe3d, and ppxf), and a deep-learning convolutional neural network (starnet), in recovering known stellar population properties (mean stellar age, stellar metallicity, stellar mass-to-light ratio M*/Lr and the internal E(B−V)) of simulated galaxy spectra in optical wavelengths. Our mock spectra are constructed from star-formation histories from the IllustrisTNG100-1 simulation. These spectra mimic the Sloan Digital Sky Survey (SDSS) through a novel method of including the noise, sky residuals, and emission lines taken directly from SDSS. We find that starnet vastly outperforms all conventional codes in both speed and recovery of stellar population properties (error scatter &lt;0.08 dex, average biases &lt;0.02 dex for all tested quantities), but it requires an appropriate training set. Of the non-machine-learning codes, ppxf was a factor of 3–4 times faster than the other codes, and was the best in recovering stellar population properties (error scatter of &lt;0.11 dex, average biases &lt;0.08 dex). However, the errors and biases are strongly dependent on both true and predicted values of stellar age and metallicity, and signal-to-noise ratio. The biases of all codes can approach 0.15 dex in stellar ages, metallicities and log M*/Lr, but remain ≲0.05 for E(B−V). Using unrealistic Gaussian noise in the construction of mock spectra will underestimate the errors in the metallicities by a factor of 2 or more, and mocks without emission lines will underestimate the errors in stellar age and M*/Lr by a factor of 2.
Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity
Authors: Vialetto Elena , Miele Solange , Goren Moran G , Yu Jiaqi , Yu Yanying , Collias Daphne , Beamud Beatriz , Osbelt Lisa , Lourenço Marta , Strowig Till , Brisse Sylvain , Barquist Lars , Qimron Udi , Bikard David , Beisel Chase L 
Published: April 2024

Abstract
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.
Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor
Authors: Hwang Hye-Yeon , Gim Dongmin , Yi Hwalin , Jung Hyewon , Lee Jaecheol , Kim Daesik 
Published: April 2024

AbstractNucleotide repeat expansion disorders, a group of genetic diseases characterized by the expansion of specific DNA sequences, pose significant challenges to treatment and therapy development. Here, we present a precise and programmable method called prime editor–mediated correction of nucleotide repeat expansion (PE-CORE) for correcting pathogenic nucleotide repeat expansion. PE-CORE leverages a prime editor and paired pegRNAs to achieve targeted correction of repeat sequences. We demonstrate the effectiveness of PE-CORE in HEK293T cells and patient-derived induced pluripotent stem cells (iPSCs). Specifically, we focus on spinal and bulbar muscular atrophy and spinocerebellar ataxia type, two diseases associated with nucleotide repeat expansion. Our results demonstrate the successful correction of pathogenic expansions in iPSCs and subsequent differentiation into motor neurons. Specifically, we detect distinct downshifts in the size of both the mRNA and protein, confirming the functional correction of the iPSC-derived motor neurons. These findings highlight PE-CORE as a precision tool for addressing the intricate challenges of nucleotide repeat expansion disorders, paving the way for targeted therapies and potential clinical applications.
Epigenetic control of adaptive or homeostatic splicing during interval-training activities
Authors: Liu Ling , Nguyen Hai , Das Urmi , Ogunsola Samuel , Yu Jiankun , Lei Lei , Kung Matthew , Pejhan Shervin , Rastegar Mojgan , Xie Jiuyong 
Published: April 2024

Abstract
Interval-training activities induce adaptive cellular changes without altering their fundamental identity, but the precise underlying molecular mechanisms are not fully understood. In this study, we demonstrate that interval-training depolarization (ITD) of pituitary cells triggers distinct adaptive or homeostatic splicing responses of alternative exons. This occurs while preserving the steady-state expression of the Prolactin and other hormone genes. The nature of these splicing responses depends on the exon's DNA methylation status, the methyl-C-binding protein MeCP2 and its associated CA-rich motif-binding hnRNP L. Interestingly, the steady expression of the Prolactin gene is also reliant on MeCP2, whose disruption leads to exacerbated multi-exon aberrant splicing and overexpression of the hormone gene transcripts upon ITD, similar to the observed hyperprolactinemia or activity-dependent aberrant splicing in Rett Syndrome. Therefore, epigenetic control is crucial for both adaptive and homeostatic splicing and particularly the steady expression of the Prolactin hormone gene during ITD. Disruption in this regulation may have significant implications for the development of progressive diseases.
Proposing candidate genes under telomeric control based on cross-species position data
Authors: Projahn Elias F , Fuellen Georg , Walter Michael , Möller Steffen 
Published: April 2024

Abstract
In this paper, we present a comprehensive computational framework aimed at suggesting genes whose transcriptional regulation is likely to be influenced by their chromosomal position. This framework provides a user-friendly web interface, enabling researchers to explore the positional properties of all human genes and their orthologs across species, with a focus on their relation to the telomeres. Our approach involves multiple scoring methods, each adjustable by users, representing different features of the genes' positional variation across species. The resulting rankings can be combined to identify candidate genes that may be subject to position effects. Furthermore, the ranking can be tailored to a specific set of reference genes. We evaluate the method within the context of TPE-OLD, a mechanism where telomeres can exert a direct influence on gene expression across considerable genomic distances, and empower researchers to delve deeper into genes of interest, analyzing their position across species and estimating their susceptibility to position effects like TPE-OLD. We also provide simple enrichment analyses of user-provided gene lists in relation to top-ranking candidate genes.
CWGCNA: an R package to perform causal inference from the WGCNA framework
Authors: Liu Yu 
Published: April 2024

Abstract
WGCNA (weighted gene co-expression network analysis) is a very useful tool for identifying co-expressed gene modules and detecting their correlations to phenotypic traits. Here, we explored more possibilities about it and developed the R package CWGCNA (causal WGCNA), which works from the traditional WGCNA pipeline but mines more information. It couples a mediation model with WGCNA, so the causal relationships among WGCNA modules, module features, and phenotypes can be found, demonstrating whether the module change causes the phenotype change or vice versa. After that, when annotating the module gene set functions, it uses a novel network-based method, considering the modules' topological structures and capturing their influence on the gene set functions. In addition to conducting these biological explorations, CWGCNA also contains a machine learning section to perform clustering and classification on multi-omics data, given the increasing popularity of this data type. Some basic functions, such as differential feature identification, are also available in our package. Its effectiveness is proved by the performance on three single or multi-omics datasets, showing better performance than existing methods. CWGCNA is available at: https://github.com/yuabrahamliu/CWGCNA.
Frequent Disengagement and Subsequent Mortality Among People With HIV and Hepatitis C in Canada: A Prospective Cohort Study
Authors: Saeed Sahar , Thomas Tyler , Dinh Duy A , Moodie Erica , Cox Joseph , Cooper Curtis , Gill John , Martel-Laferriere Valerie , Panagiotoglou Dimitra , Walmsley Sharon , Wong Alexander , Klein Marina B 
Published: April 2024

Abstract

Background
The cascade of care, commonly used to assess HIV and hepatitis C (HCV) health service delivery, has limitations in capturing the complexity of individuals’ engagement patterns. This study examines the dynamic nature of engagement and mortality trajectories among people with HIV and HCV.

Methods
We used data from the Canadian HIV-HCV Co-Infection Cohort, which prospectively follows 2098 participants from 18 centers biannually. Markov multistate models were used to evaluate sociodemographic and clinical factors associated with transitioning between the following states: (1) lost-to-follow-up (LTFU), defined as no visit for 18 months; (2) reengaged (reentry into cohort after being LTFU); (3) withdrawn from the study (ie, moved); (4) death; otherwise remained (5) engaged-in-care.

Results
A total of 1809 participants met the eligibility criteria and contributed 12 591 person-years from 2003 to 2022. LTFU was common, with 46% experiencing at least 1 episode, of whom only 57% reengaged. One in 5 (n = 383) participants died during the study. Participants who transitioned to LTFU were twice as likely to die as those who were consistently engaged. Factors associated with transitioning to LTFU included detectable HCV RNA (adjusted hazards ratio [aHR], 1.37; 95% confidence interval [CI], 1.13–1.67), evidence of HCV treatment but no sustained virologic response result (aHR, 1.99; 95% CI, 1.56–2.53), and recent incarceration (aHR, 1.94; 95% CI, 1.58–2.40). Being Indigenous was a significant predictor of death across all engagement trajectories.

Interpretation
Disengagement from clinical care was common and resulted in higher death rates. People LTFU were more likely to require HCV treatment highlighting a priority population for elimination strategies.
Application of machine learning and grey Taguchi technique for the development and optimization of a natural fiber hybrid reinforced polymer composite for aircraft body manufacture
Authors: Esangbedo Moses Olabhele , Samuel Bassey Okon 
Published: April 2024

Abstract
The rapid expansion of the air transport industry raises significant sustainability concerns due to its substantial carbon emissions and contribution to global climate change. These emissions are closely linked to fuel consumption, which in turn is influenced by the weight of materials used in aircraft systems. This study extensively applied machine learning tools for the optimization of natural fiber-reinforced composite material production parameters for aircraft body application. The Taguchi optimization technique was used to study the effect of sisal fibers, glass fibers, fiber length, and NaOH treatment concentration on the performance of the materials. Multi-objective optimization methods like the grey relational analysis and genetic algorithm (using the MATLAB programming interface) were employed to obtain the best combination of the studied factors for low fuel consumption (low carbon emission) and high-reliability structural applications of aircraft. The models developed from regressional analysis had high accuracy of prediction, with R-Square values all &gt;80%. Optimization of the grey relational analysis of the developed composite using the genetic algorithm showed the best process parameter to achieve low weight material for aircraft application to be 40% sisal, 5% glass fiber at 35 mm fiber length, and 5% NaOH concentration with grey relational analysis at the highest possible level, which is unity.
VND Genes Redundantly Regulate Cell Wall Thickening during Parasitic Nematode Infection
Authors: Gushino Saki , Tsai Allen Yi-Lun , Otani Misato , Demura Taku , Sawa Shinichiro 
Published: April 2024

Abstract
Plant parasitic root-knot nematodes are major agricultural pests worldwide, as they infect plant roots and cause substantial damages to crop plants. Root-knot nematodes induce specialized feeding cells known as giant cells (GCs) in the root vasculature, which serve as nutrient reservoirs for the infecting nematodes. Here, we show that the cell walls of GCs thicken to form pitted patterns that superficially resemble metaxylem cells. Interestingly, VASCULAR-RELATED NAC-DOMAIN1 (VND1) was found to be upregulated, while the xylem-type programmed cell death marker XYLEM CYSTEINE PEPTIDASE 1 was downregulated upon nematode infection. The vnd2 and vnd3 mutants showed reduced secondary cell wall pore size, while the vnd1 vnd2 vnd3 triple mutant produced significantly fewer nematode egg masses when compared with the wild type. These results suggest that the GC development pathway likely shares common signaling modules with the metaxylem differentiation pathway and VND1, VND2, and VND3 redundantly regulate plant–nematode interaction through secondary cell wall formation.
Cell type-specific adaptation of the SARS-CoV-2 spike
Authors: Carrascosa-Sàez Marc , Marqués María-Carmen , Geller Ron , Elena Santiago F , Rahmeh Amal , Dufloo Jérémy , Sanjuán Rafael 
Published: April 2024

Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can infect various human tissues and cell types, principally via interaction with its cognate receptor angiotensin-converting enzyme-2 (ACE2). However, how the virus evolves in different cellular environments is poorly understood. Here, we used experimental evolution to study the adaptation of the SARS-CoV-2 spike to four human cell lines expressing different levels of key entry factors. After twenty passages of a spike-expressing recombinant vesicular stomatitis virus (VSV), cell-type-specific phenotypic changes were observed and sequencing allowed the identification of sixteen adaptive spike mutations. We used VSV pseudotyping to measure the entry efficiency, ACE2 affinity, spike processing, TMPRSS2 usage, and entry pathway usage of all the mutants, alone or in combination. The fusogenicity of the mutant spikes was assessed with a cell–cell fusion assay. Finally, mutant recombinant VSVs were used to measure the fitness advantage associated with selected mutations. We found that the effects of these mutations varied across cell types, both in terms of viral entry and replicative fitness. Interestingly, two spike mutations (L48S and A372T) that emerged in cells expressing low ACE2 levels increased receptor affinity, syncytia induction, and entry efficiency under low-ACE2 conditions. Our results demonstrate specific adaptation of the SARS-CoV-2 spike to different cell types and have implications for understanding SARS-CoV-2 tissue tropism and evolution.
Within-host influenza viral diversity in the pediatric population as a function of age, vaccine, and health status
Authors: Sobel Leonard Ashley , Mendoza Lydia , McFarland Alexander G , Marques Andrew D , Everett John K , Moncla Louise , Bushman Frederic D , Odom John Audrey R , Hensley Scott E 
Published: April 2024

Abstract
Seasonal influenza virus predominantly evolves through antigenic drift, marked by the accumulation of mutations at antigenic sites. Because of antigenic drift, influenza vaccines are frequently updated, though their efficacy may still be limited due to strain mismatches. Despite the high levels of viral diversity observed across populations, most human studies reveal limited intrahost diversity, leaving the origin of population-level viral diversity unclear. Previous studies show host characteristics, such as immunity, might affect within-host viral evolution. Here we investigate influenza A viral diversity in children aged between 6 months and 18 years. Influenza virus evolution in children is less well characterized than in adults, yet may be associated with higher levels of viral diversity given the lower level of pre-existing immunity and longer durations of infection in children. We obtained influenza isolates from banked influenza A-positive nasopharyngeal swabs collected at the Children’s Hospital of Philadelphia during the 2017–18 influenza season. Using next-generation sequencing, we evaluated the population of influenza viruses present in each sample. We characterized within-host viral diversity using the number and frequency of intrahost single-nucleotide variants (iSNVs) detected in each sample. We related viral diversity to clinical metadata, including subjects’ age, vaccination status, and comorbid conditions, as well as sample metadata such as virus strain and cycle threshold. Consistent with previous studies, most samples contained low levels of diversity with no clear association between the subjects’ age, vaccine status, or health status. Further, there was no enrichment of iSNVs near known antigenic sites. Taken together, these findings are consistent with previous observations that the majority of intrahost influenza virus infection is characterized by low viral diversity without evidence of diversifying selection.