bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycoplasma hominis Meningitis Diagnosed by Metagenomic Next-Generation Sequencing in a Preterm Newborn: a Case Report and Literature Review
Authors: Che Guanglu , Liu Fang , Chang Li , Lai Shuyu , Teng Jie , Yang Qiuxia 
Published: July 2022

Abstract
Mycoplasma hominis is mainly colonized in the genital tract and vertically transmitted to newborns; however, it rarely causes neonatal meningitis. We report a case of M. hominis meningitis in a premature infant. She was admitted to our hospital for treatment after 6 days of repeated fever. After admission, repeated cerebrospinal fluid (CSF) analysis showed that leukocytes and protein in CSF increased substantially and glucose decreased, but there was no growth in conventional CSF culture. The patient was diagnosed with M. hominis meningitis by metagenomic next-generation sequencing (mNGS). The antibiotic therapy used for the neonate was meropenem, vancomycin, and ampicillin against bacterial infection and azithromycin against mycoplasma infection. The child was subsequently considered cured and discharged from the hospital and followed up regularly in the neurology clinic. The mNGS may be a promising and effective diagnostic technique for identifying uncommon pathogens of meningitis in patients with meningitis symptoms and signs without microbial growth in routine CSF culture.
Atrophic autoimmune thyroiditis complicated with systemic lupus erythematosus
Authors: Wakatsuki Ryosuke , Shimizu Masaki , Shimbo Asami , Adachi Eriko , Kanamori Toru , Yamazaki Susumu , Udagawa Tomohiro , Takasawa Kei , Kashimada Kenichi , Morio Tomohiro , Mori Masaaki 
Published: July 2022

ABSTRACT
Atrophic autoimmune thyroiditis (AAT) is a type of autoimmune thyroiditis that causes hypothyroidism without thyroid enlargement. AAT is distinguished from Hashimoto’s disease (HD) by the absence of thyroid enlargement. AAT is rare in children and clinically characterised by severe primary hypothyroidism. Autoimmune thyroiditis, especially HD, is commonly complicated with systemic lupus erythematosus (SLE). Here, we reported the patient with AAT as the initial presentation of SLE complicated with generalised myxoedema, whose presentation was a diagnostic challenge. This patient illustrates the importance of the early recognition of an atypical presentation of SLE patients with autoimmune thyroiditis. It is possible that similar cases have existed in the past but have been overlooked as HD. A large-scale study is necessary to clarify the reality of AAT in SLE.
P-bodies directly regulate MARF1-mediated mRNA decay in human cells
Authors: Brothers William R , Fakim Hana , Kajjo Sam , Fabian Marc R 
Published: July 2022

AbstractProcessing bodies (P-bodies) are ribonucleoprotein granules that contain mRNAs, RNA-binding proteins and effectors of mRNA turnover. While P-bodies have been reported to contain translationally repressed mRNAs, a causative role for P-bodies in regulating mRNA decay has yet to be established. Enhancer of decapping protein 4 (EDC4) is a core P-body component that interacts with multiple mRNA decay factors, including the mRNA decapping (DCP2) and decay (XRN1) enzymes. EDC4 also associates with the RNA endonuclease MARF1, an interaction that antagonizes the decay of MARF1-targeted mRNAs. How EDC4 interacts with MARF1 and how it represses MARF1 activity is unclear. In this study, we show that human MARF1 and XRN1 interact with EDC4 using analogous conserved short linear motifs in a mutually exclusive manner. While the EDC4–MARF1 interaction is required for EDC4 to inhibit MARF1 activity, our data indicate that the interaction with EDC4 alone is not sufficient. Importantly, we show that P-body architecture plays a critical role in antagonizing MARF1-mediated mRNA decay. Taken together, our study suggests that P-bodies can directly regulate mRNA turnover by sequestering an mRNA decay enzyme and preventing it from interfacing with and degrading targeted mRNAs.
Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction
Authors: Banneville Anne-Sophie , Bouthier de la Tour Claire , De Bonis Salvatore , Hognon Cécilia , Colletier Jacques-Philippe , Teulon Jean-Marie , Le Roy Aline , Pellequer Jean-Luc , Monari Antonio , Dehez François , Confalonieri Fabrice , Servant Pascale , Timmins Joanna 
Published: July 2022

Abstract
Deinococcus radiodurans is a spherical bacterium well-known for its outstanding resistance to DNA-damaging agents. Exposure to such agents leads to drastic changes in the transcriptome of D. radiodurans. In particular, four Deinococcus-specific genes, known as DNA Damage Response genes, are strongly up-regulated and have been shown to contribute to the resistance phenotype of D. radiodurans. One of these, DdrC, is expressed shortly after exposure to γ-radiation and is rapidly recruited to the nucleoid. In vitro, DdrC has been shown to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at a resolution of 2.5 Å and further characterized its DNA binding and compaction properties. Notably, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and level of compaction of circular DNA. These findings suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damaging conditions.
Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides
Authors: Santorelli Angel , Gothelf Kurt V 
Published: July 2022

Abstract
Labelling of oligonucleotides with dyes, targeting ligands, and other moieties has become ever more essential in life-sciences. Conventionally, modifications are introduced to oligonucleotides during solid phase synthesis by special phosphoramidites functionalised with a chemical handle or the desired functional group. In this work, we present a facile and inexpensive method to introduce modifications to oligonucleotides without the need for special phosphoramidites. Sulfonyl azides are applied to react with one or more selected phosphite intermediates during solid phase synthesis. We have prepared 11 sulfonyl azides with different chemical handles such as amine, azide, alkyne, and thiol, and we have further introduced functionalities such as pyrene, other dyes, photo-switchable azobenzenes, and a steroid. The method is compatible with current phosphoramidite-based automated oligonucleotide synthesis and serves as a simple alternative to the unstable and expensive special phosphoramidites currently used for conjugation to oligonucleotides.
Small molecule-based detection of non-canonical RNA G-quadruplex structures that modulate protein translation
Authors: Katsuda Yousuke , Sato Shin-ichi , Inoue Maimi , Tsugawa Hisashi , Kamura Takuto , Kida Tomoki , Matsumoto Rio , Asamitsu Sefan , Shioda Norifumi , Shiroto Shuhei , Oosawatsu Yoshiki , Yatsuzuka Kenji , Kitamura Yusuke , Hagihara Masaki , Ihara Toshihiro , Uesugi Motonari 
Published: July 2022

Abstract
Tandem repeats of guanine-rich sequences in RNA often form thermodynamically stable four-stranded RNA structures. Such RNA G-quadruplexes have long been considered to be linked to essential biological processes, yet their physiological significance in cells remains unclear. Here, we report a approach that permits the detection of RNA G-quadruplex structures that modulate protein translation in mammalian cells. The approach combines antibody arrays and RGB-1, a small molecule that selectively stabilizes RNA G-quadruplex structures. Analysis of the protein and mRNA products of 84 cancer-related human genes identified Nectin-4 and CapG as G-quadruplex-controlled genes whose mRNAs harbor non-canonical G-quadruplex structures on their 5′UTR region. Further investigations revealed that the RNA G-quadruplex of CapG exhibits a structural polymorphism, suggesting a possible mechanism that ensures the translation repression in a KCl concentration range of 25–100 mM. The approach described in the present study sets the stage for further discoveries of RNA G-quadruplexes.
DBC1 is a key positive regulator of enhancer epigenomic writers KMT2D and p300
Authors: Kim Hwa Jin , Moon Sue Jin , Hong Sanghoon , Won Hong-Hee , Kim Jeong Hoon 
Published: July 2022

Abstract
Histone modification is a key epigenetic mechanism for regulation of chromatin dynamics and gene expression. Deleted in breast cancer 1 (DBC1) has been shown to act as a negative regulator of epigenetic modifiers and as a co-activator for nuclear receptors and other transcription factors. However, little is known about the role of DBC1 in the regulation of histone modifications and chromatin landscapes. Here, we analyzed genome-wide profiles of active enhancer and promoter marks in colorectal cancer cells and report DBC1 as a critical positive regulator of histone epigenetic writers KMT2D (H3K4 methyltransferase) and p300 (histone acetyltransferase). DBC1 is required for establishing the landscape of active enhancers, for genome-wide chromatin binding and enhancer recruitment of KMT2D and p300, and for gene activation involved in colorectal cancer progression. DBC1 interacts directly with KMT2D and p300, and enhances KMT2D-mediated histone H3K4 methylation (H3K4me1/2/3) and p300-mediated H3 acetylation. Importantly, DBC1 contributes to super-enhancer formation and function by facilitating the recruitment of KMT2D and p300 and by enhancing their functional interaction and cooperative cross-talk. Our results highlight the critical role of DBC1 as a key positive regulator of KMT2D and p300, and provide insights into regulatory mechanisms underlying the interplay between the enhancer epigenomic writers in enhancer activation.
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus
Authors: Aulicino Francesco , Pelosse Martin , Toelzer Christine , Capin Julien , Ilegems Erwin , Meysami Parisa , Rollarson Ruth , Berggren Per-Olof , Dillingham Mark Simon , Schaffitzel Christiane , Saleem Moin A , Welsh Gavin I , Berger Imre 
Published: July 2022

Abstract
CRISPR-based precise gene-editing requires simultaneous delivery of multiple components into living cells, rapidly exceeding the cargo capacity of traditional viral vector systems. This challenge represents a major roadblock to genome engineering applications. Here we exploit the unmatched heterologous DNA cargo capacity of baculovirus to resolve this bottleneck in human cells. By encoding Cas9, sgRNA and Donor DNAs on a single, rapidly assembled baculoviral vector, we achieve with up to 30% efficacy whole-exon replacement in the intronic β-actin (ACTB) locus, including site-specific docking of very large DNA payloads. We use our approach to rescue wild-type podocin expression in steroid-resistant nephrotic syndrome (SRNS) patient derived podocytes. We demonstrate single baculovirus vectored delivery of single and multiplexed prime-editing toolkits, achieving up to 100% cleavage-free DNA search-and-replace interventions without detectable indels. Taken together, we provide a versatile delivery platform for single base to multi-gene level genome interventions, addressing the currently unmet need for a powerful delivery system accommodating current and future CRISPR technologies without the burden of limited cargo capacity.
NAT10-mediated N4-acetylcytidine modification is required for meiosis entry and progression in male germ cells
Authors: Chen Lu , Wang Wen-Jing , Liu Qiang , Wu Yu-Ke , Wu Yun-Wen , Jiang Yu , Liao Xiu-Quan , Huang Fei , Li Yang , Shen Li , Yu Chao , Zhang Song-Ying , Yan Li-Ying , Qiao Jie , Sha Qian-Qian , Fan Heng-Yu 
Published: July 2022

Abstract
Post-transcriptional RNA modifications critically regulate various biological processes. N4-acetylcytidine (ac4C) is an epi-transcriptome, which is highly conserved in all species. However, the in vivo physiological functions and regulatory mechanisms of ac4C remain poorly understood, particularly in mammals. In this study, we demonstrate that the only known ac4C writer, N-acetyltransferase 10 (NAT10), plays an essential role in male reproduction. We identified the occurrence of ac4C in the mRNAs of mouse tissues and showed that ac4C undergoes dynamic changes during spermatogenesis. Germ cell-specific ablation of Nat10 severely inhibits meiotic entry and leads to defects in homologous chromosome synapsis, meiotic recombination and repair of DNA double-strand breaks during meiosis. Transcriptomic profiling revealed dysregulation of functional genes in meiotic prophase I after Nat10 deletion. These findings highlight the crucial physiological functions of ac4C modifications in male spermatogenesis and expand our understanding of its role in the regulation of specific physiological processes in vivo.
Brain radiotoxicity-related 15CAcBRT gene expression signature predicts survival prognosis of glioblastoma patients
Authors: Reyes-González Jesús , Barajas-Olmos Francisco , García-Ortiz Humberto , Magraner-Pardo Lorena , Pons Tirso , Moreno Sergio , Aguirre-Cruz Lucinda , Reyes-Abrahantes Andy , Martínez-Hernández Angélica , Contreras-Cubas Cecilia , Barrios-Payan Jorge , Ruiz-Garcia Henry , Hernandez-Pando Rogelio , Quiñones-Hinojosa Alfredo , Orozco Lorena , Abrahantes-Pérez María del Carmen 
Published: July 2022

Abstract

Background
Glioblastoma is the most common and devastating primary brain cancer. Radiotherapy is standard of care; however, it is associated with brain radiation toxicity (BRT). This study used a multi-omics approach to determine whether BRT-related genes (RGs) harbor survival prognostic value and whether their encoded proteins represent novel therapeutic targets for glioblastoma.

Methods
RGs were identified through analysis of single-nucleotide variants associated with BRT (R-SNVs). Functional relationships between RGs were established using Protein-Protein Interaction networks. The influence of RGs and their functional groups on glioblastoma prognosis was evaluated using clinical samples from the Glioblastoma Bio-Discovery Portal database and validated using the Chinese Glioma Genome Atlas dataset. The identification of clusters of radiotoxic and putative pathogenic variants in proteins encoded by RGs was achieved by computational 3D structural analysis.

Results
We identified the BRT-related 15CAcBRT molecular signature with prognostic value in glioblastoma, by analysis of the COMT and APOE protein functional groups. Its external validation confirmed clinical relevance independent of age, MGMT promoter methylation status, and IDH mutation status. Interestingly, the genes IL6, APOE, and MAOB documented significant gene expression levels alteration, useful for drug repositioning. Biological networks associated with 15CAcBRT signature involved pathways relevant to cancer and neurodegenerative diseases. Analysis of 3D clusters of radiotoxic and putative pathogenic variants in proteins coded by RGs unveiled potential novel therapeutic targets in neuro-oncology.

Conclusions
15CAcBRT is a BRT-related molecular signature with prognostic significance for glioblastoma patients and represents a hub for drug repositioning and development of novel therapies.
Disease-specific expansion of CD29+IL-17RA+ T effector cells possessing multiple signalling pathways in spondyloarthritis
Authors: Akiyama Mitsuhiro , Yoshimoto Keiko , Ishigaki Sho , Suzuki Katsuya , Takeuchi Tsutomu , Kaneko Yuko 
Published: July 2022

AbstractObjectivesT cells adhere to enthesis fibrocartilage via integrins and intrinsically require IL-17RA-mediated signals to maintain their effector function. We analysed CD29+IL-17RA+ T cells in inflamed lesions and peripheral blood in patients with SpA and investigated their association with disease activity and therapeutic response.MethodsTranscriptome analysis of synovial fluid T cells from PsA was performed using publicly available bulk cell RNA sequencing data. Blood samples were obtained from healthy controls (n = 37), RA (n = 12), IgG4-related disease (IgG4-RD; n = 12), large vessel vasculitis (LVV; n = 12) and SpA (n = 28) and were analysed by flow cytometry.ResultsT cells in the inflamed joints of PsA showed CD29 and IL-17RA expression. CD29+IL-17RA+ T cells showed enriched CXCR3+CD45RA+ effector cells and activation of spleen tyrosine kinase (Syk), nuclear factor κB (NF-κB) and Janus kinase–signal transducer and activator of transcription (JAK-STAT) pathways. The proportion of peripheral blood CD29+IL-17RA+ T cells was significantly increased in patients with SpA compared with patients with RA, IgG4-RD or LVV and in healthy controls. Based on the ASDAS-CRP scores, the proportion of CD29+IL-17RA+ T cells was positively correlated with disease activity in treatment-naïve patients with active SpA. Anti-IL-17 but not anti-TNF monoclonal antibodies reduced CD29+IL-17RA+ T cells.ConclusionsCD29+IL-17RA+ T effector cells with enhanced Syk, NF-κB and JAK-STAT pathways were specifically increased in SpA and were correlated with disease activity, implicating a role of this newly identified T cell population in the pathogenesis. Anti-IL-17 monoclonal antibodies may be effective for patients by reducing this pathogenic T cell population.
Neural processes of inhibitory control in American Indian peoples are associated with reduced mental health problems
Authors: White Evan J , Demuth Mara J , Nacke Mariah , Kirlic Namik , Kuplicki Rayus , Spechler Philip A , McDermott Timothy J , DeVille Danielle C , Stewart Jennifer L , Lowe John , Paulus Martin P , Aupperle Robin L 
Published: July 2022

AbstractAmerican Indians (AI) experience disproportionately high prevalence of suicide and substance use disorders (SUD). However, accounting for risk burden (e.g. historical trauma and discrimination), the likelihood of mental health disorders or SUD is similar or decreased compared with the broader population. Such findings have spurred psychological research examining the protective factors, but no studies have investigated its potential neural mechanisms. Inhibitory control is one of the potential neurobehavioral construct with demonstrated protective effects, but has not been examined in neuroimaging studies with AI populations specifically. We examined the incidence of suicidal thoughts and behaviors (STB) and SUD among AI (n = 76) and propensity matched (sex, age, income, IQ proxy and trauma exposure) non-Hispanic White (NHW) participants (n = 76). Among the AI sample, functional magnetic resonance imaging (fMRI) data recorded during the stop-signal task (SST) was examined in relation to STB and SUDs. AIs relative to NHW subjects displayed lower incidence of STB. AIs with no reported STBs showed greater activity in executive control regions during the SST compared with AI who endorsed STB. AI without SUD demonstrated lower activity relative to those individual reporting SUD. Results are consistent with a growing body of literature demonstrating the high level of risk burden driving disparate prevalence of mental health concerns in AI. Furthermore, differential activation during inhibitory control processing in AI individuals without STB may represent a neural mechanism of protective effects against mental health problems in AI. Future research is needed to elucidate sociocultural factors contributing protection against mental health outcomes in AIs and further delineate neural mechanisms with respect to specific concerns (e.g. SUD vs STB).
Dicey Rule 3(1) for the 21st Century—the revenue rule in a modern setting
Authors: McPherson George 
Published: July 2022

Abstract
This Article considers the conflict of laws principle, which precludes English courts having jurisdiction in respect of any action to enforce penal, revenue or other public laws of a foreign State (Dicey Rule 3(1)). It follows the Court of Appeal’s decision in the SKAT litigation in February 2022, which reinstated claims brought by the Danish tax authority against all but one of more than 100 defendants, to recover refunds of £1.44 billion of withholding tax, on the basis that Dicey Rule 3(1) did not render those claims inadmissible. The Article looks at (1) the rationale, scope and boundaries of the Rule; (2) how the Rule was applied in the SKAT case; and (3) what that case tells us about the likely future of the Rule.
Integration of allocentric and egocentric visual information in a convolutional/multilayer perceptron network model of goal-directed gaze shifts
Authors: Abedi Khoozani Parisa , Bharmauria Vishal , Schütz Adrian , Wildes Richard P , Crawford J Douglas 
Published: July 2022

Abstract
Allocentric (landmark-centered) and egocentric (eye-centered) visual codes are fundamental for spatial cognition, navigation, and goal-directed movement. Neuroimaging and neurophysiology suggest these codes are initially segregated, but then reintegrated in frontal cortex for movement control. We created and validated a theoretical framework for this process using physiologically constrained inputs and outputs. To implement a general framework, we integrated a convolutional neural network (CNN) of the visual system with a multilayer perceptron (MLP) model of the sensorimotor transformation. The network was trained on a task where a landmark shifted relative to the saccade target. These visual parameters were input to the CNN, the CNN output and initial gaze position to the MLP, and a decoder transformed MLP output into saccade vectors. Decoded saccade output replicated idealized training sets with various allocentric weightings and actual monkey data where the landmark shift had a partial influence (R2 = 0.8). Furthermore, MLP output units accurately simulated prefrontal response field shifts recorded from monkeys during the same paradigm. In summary, our model replicated both the general properties of the visuomotor transformations for gaze and specific experimental results obtained during allocentric–egocentric integration, suggesting it can provide a general framework for understanding these and other complex visuomotor behaviors.
Evaluation of the BEAT Meth Intervention for Emergency Department Patients with Methamphetamine Psychosis
Authors: Simpson Scott A. , Wolf Chelsea , Loh Ryan M. , Camfield Katherine , Rylander Melanie 
Published: July 2022

Objectives
Methamphetamine is the second leading cause of overdose death in America and a leading cause of emergency department (ED) visits. Methamphetamine-induced psychosis is a dangerous and difficult-to-treat consequence of methamphetamine use. We describe the pilot implementation and outcomes of a multimodal treatment intervention for ED patients with methamphetamine psychosis, Beginning Early and Assertive Treatment for Methamphetamine Psychosis (BEAT Meth).

Methods
BEAT Meth was implemented in an urban safety net health system. The protocol includes early identification and treatment of methamphetamine psychosis, a protocolized hospitalization, and support for transitioning patients to specialty addiction treatment. Patients receiving BEAT Meth were compared with ED patients with methamphetamine psychosis who were discharged. Implementation fidelity was measured to assess feasibility.

Results
BEAT Meth patients were nearly 3 times more likely to attend an outpatient specialty addiction appointment in the 30 days after discharge than comparison patients (32% vs 11%, P < 0.01). Subsequent ED utilization was common among all patients, and there was no significant difference in 30-day ED return rates between BEAT Meth and comparison patients (28% vs 37%, P = 0.10). Exploratory analyses suggested that increased attendance at outpatient treatment reduced ED utilization.

Conclusions
BEAT Meth is an intervention framework to support identification, management, and treatment engagement of ED patients with methamphetamine psychosis. Treatment strategies like BEAT Meth are necessary to manage the unique challenges of methamphetamine addiction. These findings will guide clinical care, program development, and research.