bluuebunny/crossref_metadata_2025 huggingface dataset:
Age and CRP Associated With Improved Tissue Pathogen Identification in Children With Blood Culture Negative Osteomyelitis: Results From the CORTICES Multicenter Database
Authors: Burns Jessica D. , Upasani Vidyadhar V. , Bastrom Tracey P. , Baldwin Keith D. , Schoenecker Jonathan G. , Shore Benjamin J. , Brighton Brian K. , Goldstein Rachel Y. , Heyworth Benton E. , Miller Mark L. , Sanders Julia S. , Truong Walter H. ,   Childrens ORthopedic Trauma and Infection Consortium for Evidence-Based Study
Published: June 2023

Background:

Acute hematogenous osteomyelitis (AHO) is a relatively common condition in children, and identifying the offending pathogen with blood or tissue cultures aids in diagnosis and medical management while reducing treatment failure. Recent 2021 AHO clinical practice guidelines from the Pediatric Infectious Disease Society recommend obtaining routine tissue cultures, particularly in cases with negative blood cultures. The purpose of this study was to identify variables associated with positive tissue cultures when blood cultures are negative.

Methods:

Children with AHO from 18 pediatric medical centers throughout the United States through the Children’s ORthopaedic Trauma and Infection Consortium for Evidence-based Study were evaluated for predictors of positive tissue cultures when blood cultures were negative. Cutoffs of predictors were determined with associated sensitivity and specificity.

Results:

One thousand three children with AHO were included, and in 688/1003 (68.6%) patients, both blood cultures and tissue cultures were obtained. In patients with negative blood cultures (n=385), tissue was positive in 267/385 (69.4%). In multivariate analysis, age (P<0.001) and C-reactive protein (CRP) (P=0.004) were independent predictors. With age >3.1 years and CRP >4.1 mg/dL as factors, the sensitivity of obtaining a positive tissue culture when blood cultures were negative was 87.3% (80.9–92.2%) compared with 7.1% (4.4–10.9%) if neither of these factors was present. There was a lower ratio of methicillin-resistant Staphylococcus aureus in blood culture-negative patients who had a positive tissue culture 48/188 (25.5%), compared with patients who had both positive blood and tissue cultures 108/220 (49.1%).

Conclusion:

AHO patients with CRP ≤ 4.1 mg/dL and age under 3.1 years are unlikely to have clinical value from tissue biopsy that exceeds the morbidity associated with this intervention. In patients with CRP > 4.1 mg/dL and age over 3.1 years, obtaining a tissue specimen may add value; however, it is important to note that effective empiric antibiotic coverage may limit the utility of positive tissue cultures in AHO.

Level of Evidence:

Level III—Retrospective comparative study.
Necrobiotic Xanthogranuloma With Associated Monoclonal Gammopathy Presenting as an Eyelid Nodule
Authors: Punyamurthy Nina T. , Tjahjono Leonardo A. , Harris Gerald J. , Wanat Karolyn A.
Published: June 2023

Necrobiotic xanthogranuloma (NXG) is a progressive non-Langerhans cell histiocytosis with a predilection for the periorbital area. NXG is most commonly associated with monoclonal gammopathy and ophthalmic complications. The authors present a 69-year-old man who was evaluated for a left upper eyelid nodule and plaques on the lower extremities, trunk, abdomen, and right upper extremity. Biopsy of the eyelid was supportive for NXG. Serum protein electrophoresis was positive for a monoclonal gammopathy, IgG light chain kappa. MRI showed preseptal involvement. The periocular nodules cleared with a high dose of prednisone; however, the other skin lesions persisted. Bone marrow biopsy showed kappa-restricted 6% plasma cells and he was treated with intravenous immunoglobulin. This case illustrates the importance of clinicopathologic correlations to render an NXG diagnosis.
Pediatric Trauma and Posttraumatic Symptom Screening at Well-child Visits
Authors: DiGiovanni Stephen S. , Hoffmann Frances Rebecca J. , Brown Rebecca S. , Wilkinson Barrett T. , Coates Gillian E. , Faherty Laura J. , Craig Alexa K. , Andrews Elizabeth R. , Gabrielson Sarah M. B.
Published: June 2023

Introduction:

Adverse childhood experiences (ACEs), including abuse or neglect, parental substance abuse, mental illness, or separation, are public health crises that require identification and response. We aimed to increase annual rates of trauma screening during well-child visits from 0% to 70%, post-traumatic stress disorder (PTSD) symptom screening for children with identified trauma from 0% to 30%, and connection to behavioral health for children with symptoms from 0% to 60%.

Methods:

Our interdisciplinary behavioral and medical health team implemented 3 plan-do-study-act cycles to improve screening and response to pediatric traumatic experiences. Automated reports and chart reviews measured progress toward goals as we changed screening methods and provider training.

Results:

During plan-do-study-act cycle 1, a chart review of patients with positive trauma screenings identified various trauma types. During cycle 2, a comparison of screening methods demonstrated that written screening identified trauma among more children than verbal screening (8.3% versus 1.7%). During cycle 3, practices completed trauma screenings at 25,287 (89.8%) well-child visits. Among screenings, 2,441 (9.7%) identified trauma. The abbreviated Post Traumatic Stress Disorder Reaction Index was conducted at 907 (37.2%) encounters and identified 520 children (57.3%) with PTSD symptoms. Among a sample of 250, 26.4% were referred to behavioral health, 43.2% were already connected, and 30.4% had no connection.

Conclusions:

It is feasible to screen and respond to trauma during well-child visits. Screening method and training implementation changes can improve screening and response to pediatric trauma and PTSD. Further work is needed to increase rates of PTSD symptomology screening and connection to behavioral health.
Eliminating Central Line Associated Bloodstream Infections in Pediatric Oncology Patients: A Quality Improvement Effort
Authors: Willis Daniel N. , Looper Karen , Malone Rema A. , Ricken Barbara , Slater Ashley , Fuller Amanda , McCaughey Meagan , Niesen Angela , Smith Joan R. , Brozanski Beverly
Published: June 2023

Introduction:

Central Line-Associated Bloodstream Infections (CLABSI) are the largest contributor to harm across the Children’s Hospital’s Solutions for Patient Safety network. Pediatric hematology/oncology (PHO) patients are at increased risk for CLABSI due to multiple factors. Consequently, traditional CLABSI prevention strategies are insufficient to eliminate CLABSI in this high-risk population.

Methods:

Our SMART aim was to reduce the CLABSI rate by 50% from a baseline of 1.89/1000 central line days to less than 0.9/1000 central line days by December 31, 2021. We created a multidisciplinary team being mindful to identify roles and responsibilities upfront. We developed a key driver diagram and designed and implemented interventions to influence our primary outcome.

Results:

We implemented interventions and conducted Plan-Do-Study-Act cycles concurrently. We found that performing audits by directly observing tasks rather than auditing documentation resulted in more accurate compliance assessments. As a result, our CLABSI rate improved from 1.89/1000 central line days in 2020 with 11 primary CLABSI to 0.73/1000 central line days in 2021 with four primary CLABSI. Average days between events improved from 30 days in 2020 to 73 days in 2021, and we achieved an unprecedented 542 days CLABSI-free, extending into 2022.

Conclusions:

Through a multimodal approach and utilizing characteristics of high-reliability organizations, we significantly reduced primary CLABSI, approaching zero in our PHO population and doubling the average days between events. Future efforts will focus on the sustained engagement of all stakeholders and improving our safety culture.
Quality Report: Postoperative Guideline Implementation Reduces Length of Stay after Fontan Procedure
Authors: Cox Virginia , Hart Stephen , Hersey Diane , Gauntt Jennifer , Carrillo Sergio , McConnell Patrick , Simsic Janet
Published: June 2023

Introduction:

Patients following the Fontan procedure have a physiology that results in prolonged pleural effusion, often delaying hospital discharge. The hospital length of stay (LOS) of patients following the Fontan procedure at our institution was significantly longer than the Society of Thoracic Surgery benchmark. This quality improvement project aimed to decrease hospital LOS in patients following the Fontan procedure from a baseline of 23 days to 7 days by January 1, 2021, and sustain indefinitely.

Methods:

We implemented standardized postoperative clinical practice guidelines in April 2020. We designed guidelines using previously published protocols. Key features included an ambulatory PleurX drain (BD, Franklin Lakes, N.J.), diuresis with fluid restriction, and pulmonary vasodilation with supplemental oxygen and sildenafil. All patients were discharged from the hospital with a PleurX drain in place. We compared clinical outcome variables before and after guideline implementation. As a balancing measure, we tracked 30-day readmissions.

Results:

One hundred seven patients underwent the Fontan procedure before guideline implementation from January 2015 to January 2020, with an average hospital LOS of 23 days. Postguideline implementation, 35 patients underwent the Fontan procedure from April 2020 to July 2022, with an average hospital LOS of 8 days in 2020, which further improved to an average hospital LOS of 7 days. There was no change in 30-day readmission after guideline implementation (24% pre versus 23% post; P = 0.86).

Conclusion:

Implementing clinical practice guidelines for patients following the Fontan procedure led to an over 50% reduction in hospital LOS without increasing 30-day readmission.
HYPERBILIRUBINEMIA AGGRAVATES RENAL ISCHEMIA REPERFUSION INJURY BY EXACERBATING PINK1-PARKIN–MEDIATED MITOPHAGY
Authors: Liao Pingping , Wang Xiaoyu , Dong He , Chai Dongyue , Yue Ziqi , Lyu Lin
Published: June 2023

Background: Hyperbilirubinemia is a common perioperative complication, which is associated with acute kidney injury. Bilirubin permeabilizes mitochondrial membranes leading to mitochondrial swelling and dysfunction. In this study, we aimed to determine the association between PINK1-PARKIN–mediated mitophagy and renal ischemia-reperfusion (IR) injury aggravated by hyperbilirubinemia. Methods: A C57BL/6 mouse hyperbilirubinemia model was induced via intraperitoneal injection of bilirubin solution. In addition, a hypoxia/reoxygenation (H/R) injury model of TCMK-1 cells was established. In these models, we determined the effects of hyperbilirubinemia on oxidative stress, apoptosis, mitochondrial damage, and fibrosis. Results:
In vitro, colocalization of GFP-LC3 puncta and Mito-Tracker Red showed that the number of mitophagosomes increased in TCMK-1 cells under H/R and bilirubin condition. Silencing of PINK1 or inhibition of autophagy alleviated mitochondrial damage, oxidative stress, and apoptosis in H/R injury aggravated by bilirubin and decreased cell death detected by methyl-thiazolyl-tetrazolium. In vivo, hyperbilirubinemia increased serum creatinine level in the renal IR injury mice model. Hyperbilirubinemia enhanced apoptosis induced by renal IR. In addition, hyperbilirubinemia increased mitophagosomes and autophagosomes and disrupted mitochondrial cristae in the IR kidney. Inhibition of PINK1 or autophagy reduced histological damages by alleviating apoptosis in renal IR injury, aggravated by hyperbilirubinemia. 3-MA or PINK1-shRNA-AAV9 treatment decreased the area of collagen and proteins related to fibrosis in renal IR injury, aggravated by hyperbilirubinemia. Conclusions: We have demonstrated that hyperbilirubinemia aggravated oxidative stress, apoptosis, mitochondrial damage, and fibrosis in renal IR injury by exacerbating PINK1-PARKIN–mediated mitophagy.
ABCB1 Gene Polymorphisms Are Closely Associated With Drug-Resistant Epilepsy: Evidence Based on 377 Subjects in Chinese Pediatric Patients
Authors: Zhao Ting , Li Hong-jian , Yu Jing , Zhang Hui-lan , Feng Jie , Wang Ting-ting , Yu Lu-hai , Sun Yan
Published: June 2023

Objective

P-glycoprotein plays a role in drug resistance of epileptic patients by limiting gastrointestinal absorption and brain access to antiseizure medications. This study aimed to evaluate the association between ABCB1 polymorphisms and drug resistance in epileptic pediatric patients.

Methods

Three hundred seventy-seven epileptic pediatric patients were treated with antiseizure medications and subsequently divided into the drug-responsive group (n = 256, 68%) and drug-resistant group (n = 121, 32%). The genomic DNA of patients in the different groups was extracted, followed by the determination of the ABCB1 gene polymorphisms using polymerase chain reaction–fluorescence staining in situ hybridization.

Results

Drug-resistant patients significantly exhibited a combined generalized and focal onset than drug-responsive patients (χ2 = 12.278, P < 0.001). The TT (χ2 = 5.776, P = 0.016) genotypes of G2677T and CT (χ2 = 6.165, P = 0.013) and TT (χ2 = 11.121, P = 0.001) genotypes of C3435T were significantly more frequent in drug-resistant patients than drug-responsive patients. Similarly, the GT-CT diplotype was significantly more frequent in drug-resistant patients than in drug-responsive patients.

Conclusion

Our study findings suggest that the ABCB1 G2677T and C3435T polymorphisms are significantly associated with drug resistance in epileptic patients.
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP
Authors: Yu Huijing , Zheng Zhenxian , Su Junhao , Lam Tak-Wah , Luo Ruibang
Published: June 2023

Background

With the continuous advances in third-generation sequencing technology and the increasing affordability of next-generation sequencing technology, sequencing data from different sequencing technology platforms is becoming more common. While numerous benchmarking studies have been conducted to compare variant-calling performance across different platforms and approaches, little attention has been paid to the potential of leveraging the strengths of different platforms to optimize overall performance, especially integrating Oxford Nanopore and Illumina sequencing data.

Results

We investigated the impact of multi-platform data on the performance of variant calling through carefully designed experiments with a deep learning-based variant caller named Clair3-MP (Multi-Platform). Through our research, we not only demonstrated the capability of ONT-Illumina data for improved variant calling, but also identified the optimal scenarios for utilizing ONT-Illumina data. In addition, we revealed that the improvement in variant calling using ONT-Illumina data comes from an improvement in difficult genomic regions, such as the large low-complexity regions and segmental and collapse duplication regions. Moreover, Clair3-MP can incorporate reference genome stratification information to achieve a small but measurable improvement in variant calling. Clair3-MP is accessible as an open-source project at:https://github.com/HKU-BAL/Clair3-MP.

Conclusions

These insights have important implications for researchers and practitioners alike, providing valuable guidance for improving the reliability and efficiency of genomic analysis in diverse applications.
Full-field strain distribution in hierarchical electrospun nanofibrous Poly-L(lactic) acid and Collagen based scaffolds for tendon and ligament tissue regeneration: a multiscale study
Authors: Sensini Alberto , Stamati Olga , Marchiori Gregorio , Sancisi Nicola , Gotti Carlo , Giavaresi Gianluca , Cristofolini Luca , Focarete Maria Letizia , Zucchelli Andrea , Tozzi Gianluca
Published: June 2023

Regeneration of injured tendons and ligaments (T/L) is a worldwide need. In this study electrospun hierarchical scaffolds made of a poly (L-lactic) acid and collagen blend were developed reproducing all the multiscale levels of aggregation of these tissues. Scanning electron microscopy, microCT and tensile mechanical tests were carried out, including a multiscale digital volume correlation analysis to measure the full-field strain distribution of electrospun structures. The principal tensile and compressive strains detected the pattern of strains caused by the nanofibers rearrangement, while the deviatoric strains revealed the related internal sliding of nanofibers and bundles. The results of this study confirmed the biomimicry of such electrospun hierarchical scaffolds, paving the way to further tissue engineering and clinical applications.

Graphical Abstract
A fungal RNA-dependent RNA polymerase is a novel player in plant infection and cross-kingdom RNA interference
Authors: Cheng An-Po , Lederer Bernhard , Oberkofler Lorenz , Huang Lihong , Platten Fabian , Dunker Florian , Tisserant Constance , Weiberg Arne
Published: June 2023

Small RNAs act as fungal pathogen effectors that silence host target genes to promote infection, a virulence mechanism termed cross-kingdom RNA interference (RNAi). The essential pathogen factors of cross-kingdom small RNA production are largely unknown. We here characterized the RNA-dependent RNA polymerase (RDR)1 in the fungal plant pathogenBotrytis cinereathat is required for pathogenicity and cross-kingdom RNAi.B. cinerea bcrdr1knockout (ko) mutants exhibited reduced pathogenicity and loss of cross-kingdom small RNAs. We developed a novel “switch-on” GFP reporter to study cross-kingdom RNAi in real-time within the living plant tissue which highlighted thatbcrdr1ko mutants were compromised in cross-kingdom RNAi. Moreover, blocking seven pathogen cross-kingdom small RNAs by expressing a short-tandem target mimic RNA in transgenicArabidopsis thalianaled to reduced infection levels of the fungal pathogenB. cinereaand the oomycete pathogenHyaloperonospora arabidopsidis. These results demonstrate that cross-kingdom RNAi is significant to promote host infection and making pathogen small RNAs an effective target for crop protection.
Haplotype-resolve genome assembly and resequencing provide insights into the origin and domestication of modern rose
Authors: Zhang Zhao , Liu Yang , Yang Tuo , Wu Shan , Sun Honghe , Wu Jie , Li Yonghong , Zheng Yi , Ren Haoran , Yang Yuyong , Shi Shaochuan , Wang Wenyan , Pan Qi , Lian Lijuan , Duan Shaowen , Zhu Yingxiong , Cai Youming , Zhou Hougao , Zhang Hao , Tang Kaixue , Cui Jiaopeng , Gao Dan , Chen Liyang , Jiang Yunhe , Sun Xiaoming , Zhou Xiaofeng , Fei Zhangjun , Ma Nan , Gao Junping
Published: June 2023

Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here, we report the haplotype-resolved chromosome-scale genome assembly of the tetraploidR. hybrida‘Samantha’ and a genome variation map of 233Rosaaccessions involving various wild species, and old and modern cultivars. The two subgenomes of ‘Samantha’ show no significant global bias in gene loss but substantial expression bias, and homoeologous exchanges are frequently observed between subgenomes. Population genomic and genomic composition analyses reveal the contributions of wildRosaspecies to modern roses, and highlight thatR. odorataand its derived cultivars contribute more to modern roses thanR. chinensis‘Old Blush’. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous flowering, floral organ identity, flower senescence, and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.
SNVstory: A dockerized algorithm for rapid and accurate inference of sub-continental ancestry
Authors: Bollas Audrey E. , Rajkovic Andrei , Ceyhan Defne , Gaither Jeffrey B. , Mardis Elaine R. , White Peter
Published: June 2023

Knowing a patient’s genetic ancestry is crucial in clinical settings, providing benefits such as tailored genetic testing, targeted health screening based on ancestral disease-predisposition rates, and personalized medication dosages. However, self-reported ancestry can be subjective, making it difficult to apply consistently. Moreover, existing approaches utilize genome sequencing data to infer ancestry at the continental level, creating the need for methods optimized for individual ancestry assignment. We present SNVstory, a method built upon three independent machine learning models for accurately inferring the sub-continental ancestry of individuals. SNVstory includes a feature-importance scheme, unique among open-source ancestral tools, which allows the user to track the ancestral signal broadcast by a given gene or locus. We apply SNVstory to a clinical dataset, comparing self-reported ethnicity and race to our inferred genetic ancestry. SNVstory represents a significant advance in methods to assign genetic ancestry, predicting ancestry across 36 different populations with high accuracy.
High-efficiency digitally scanned light-sheet fluorescence lifetime microscopy (DSLM-FLIM)
Authors: Nutt Kyle J. , Olesker Daniel , McGhee Ewan , Hungerford Graham , Leburn Christopher G. , Taylor Jonathan
Published: June 2023

Recently-developed kilopixel single-photon avalanche diode (SPAD) arrays with in-pixel timing hold great promise for fluorescence lifetime imaging microscopy of dynamic samples, thanks to their widefield single-photon time-of-arrival imaging capabilities. However digitally-scanned light-sheet microscope (DSLM) and two-photon microscope systems present significant technical barriers which have to date prevented full and efficient use of the capabilities of SPAD arrays. Because the 12.4 kHz frame-rate of our array camera is faster than achievable DSLM scan rates, most pixels would be sitting idle most of the time. We present a new optical design based around astigmatic imaging optics, enabling rapid and efficient acquisition of fluorescence lifetime imaging data. We demonstrate our system with both one- and two-photon excitation sources, validate performance with lifetime reference beads, and demonstrate separation of similar fluorescence emission spectra in biological samplesvialifetime contrast.
Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep
Authors: James Caelinn , Pemberton Josephine M. , Navarro Pau , Knott Sara
Published: June 2023

Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state genomic relatedness matrix (GRM) and an identity-by-descent GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms to investigate polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Each model was compared to an animal model with a single GRM based on all genotyped markers (the IBS GRM) using a log likelihood ratio test. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
“Isolation and characterization of a novel hormone receptor positive mammary adenocarcinoma MCa-P1362 with stromal drivers of tumor growth, metastasis, and drug resistance”
Authors: Jana Samir , Li Wende , Lei Pin-Ji , Wang Zixiong , Huang Peigen , Jones Dennis
Published: June 2023

Preclinical models that display spontaneous metastasis are necessary to improve therapeutic options for hormone receptor positive breast cancers. In this study, we conducted a detailed cellular and molecular characterization of MCa-P1362, a novel syngeneic Balb/c mouse model of metastatic breast cancer. MCa-P1362 cancer cells expressed estrogen receptors (ER), progesterone receptors (PR), and HER-2 receptors. MCa-P1362 cells proliferate in vitro and in vivo in response to estrogen, yet do not depend on steroid hormones for tumor progression. Further characterization of MCa-P1362 tumor explants shows that they contain a mixture of epithelial cancer cells and stromal cells. Based on transcriptomic and functional analyses of cancer and stromal cells, stem cells are present in both populations. Functional studies demonstrate that crosstalk between cancer and stromal cells promotes tumor growth, metastasis, and drug resistance. MCa-P1362 may serve as a useful preclinical model to investigate the cellular and molecular basis of hormone receptor positive tumor progression and therapeutic resistance.
Benchmarking DIA data analysis workflows
Authors: Staes An , Maia Teresa , Dufour Sara , Bouwmeester Robbin , Gabriels Ralf , Martens Lennart , Impens Francis , Devos Simon
Published: June 2023

Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still a lot of possibilities at the data analysis level. By benchmarking different DIA analysis workflows using a ground-truth sample, consisting of a differential spike-in of UPS2 in a constant yeast background, we provide a roadmap for DIA data analysis of shotgun samples based on whether sensitivity, precision or accuracy is of the essence. Three different commonly used DIA software tools (DIA-NN, EncyclopeDIA and SpectronautTM) were tested in both spectral library mode and spectral library-free mode. In spectral library mode we used the independent spectral library prediction tools PROSIT and MS2PIP together with DeepLC, next to the classical DDA-based spectral libraries. In total we benchmarked 12 DIA workflows. DIA-NN in library-free mode or usingin silicopredicted libraries, together with Spectronaut in library-free mode, shows the highest sensitivity maintaining a high reproducibility and accuracy. In general, DIA-NN shows the best reproducibility, while the accuracy is comparable for all DIA workflows.
Anti-NMDAR and non-anti-NMDAR antibodies promptly modulate NMDAR through p38 and flux-independent signaling: implications for anti-NMDAR encephalitis
Authors: Montes de Oca-B Pavel , Gómora-García Juan Carlos , Massieu Lourdes , Hernández-Cruz Arturo
Published: June 2023

Anti-N-methyl D-aspartic acid receptor (anti-NMDAR) encephalitis is caused by anti-NMDAR antibodies (Abs) that induce neurologic and psychiatric symptoms, explained mainly by NMDAR hypofunction. In the long-term, these Abs decrease surface NMDAR and NMDAR-mediated intracellular Ca2+([Ca2+]i) influx. However, there are contradictory findings regarding short-term mechanisms. We investigated NMDAR function in cultured neurons after 60 min treatment with three commercial, rabbit, anti-NMDAR Abs (anti-GluN1 extracellular (EC) domain; anti-GluN2B EC domain; and anti-GluN1 intracellular (IC) domain). The anti-GluN2B and anti-GluN1 IC Abs were previously reported to mimic patientś Ab effects in a rodentin vivomodel and decreased NMDAR-mediated [Ca2+]i entry after 24 h treatment in our cells. After 60 min incubation with anti-GluN2B or anti-GluN1 IC decreased the NMDAR-mediated [Ca2+]i rise, whereas anti-GluN1 EC slightly increased it. Interestingly, all Abs induced p38 phosphorylation (p-p38). However, surprisingly, it was also elicited by a rabbit Ab directed against a non-NMDAR intracellular epitope, which also reduced NMDAR-mediated [Ca2+]i entry. We further investigated the cellular mechanisms regulated by the anti-GluN2B Ab after 60 min. This Ab did not reduce surface NMDAR and p38 inhibition partially prevented its effect on NMDAR function. This Ab did not elicitper sean [Ca2+]i rise, whereas NMDAR inhibitors 7DCK and MK-801 did not prevent p-p38. Nonetheless, 7DCK prevented NMDAR-mediated [Ca2+]i reduction by the Ab, suggesting a role of GluN1 flux-independent signaling. These data indicate that anti-NMDAR and non-anti-NMDAR Ab modulate NMDAR function distinctly and p38 signaling in the short-term, and a role of a third-party mediator. Finally, our results suggest the involvement of NMDAR flux-independent signaling.
Potential involvement of protein phosphatase PP2CA on protein synthesis and cell cycle during SARS-CoV-2 infection. A meta analysis investigation
Authors: Otvos Luca P. , Garrito Giulia I.M. , Machado Luciana E.S.F.
Published: June 2023

Coronavirus disease 2019 is a multi-systemic syndrome that caused a pandemic. Proteomic studies demonstrate changes in protein expression and interaction involved in signaling pathways related to SARS-CoV-2 infections. Protein phosphatases are important for cell signaling regulation. Here we aimed to understand the involvement of protein phosphatases and the signaling pathways that may be involved during SARS-CoV-2 infection. Then, we carried out a metanalysis of protein phosphatase interaction directly or indirectly with viral proteins. Additionally, we analyzed the expression degree of protein phosphatases, and phosphorylation degree of intermediate proteins. Our analyses revealed that PP2CA and PTEN were the key protein involved in the cell cycle and apoptosis regulation, during SARS-CoV-2 infection. Showing it as potential target for COVID-19 control.
Rapid and sensitive detection of genome contamination at scale with FCS-GX
Authors: Astashyn Alexander , Tvedte Eric S. , Sweeney Deacon , Sapojnikov Victor , Bouk Nathan , Joukov Victor , Mozes Eyal , Strope Pooja K. , Sylla Pape M. , Wagner Lukas , Bidwell Shelby L. , Clark Karen , Davis Emily W. , Smith-White Brian , Hlavina Wratko , Pruitt Kim D. , Schneider Valerie A. , Murphy Terence D.
Published: June 2023

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 minutes. Testing FCS-GX on artificially fragmented genomes demonstrates sensitivity >95% for diverse contaminant species and specificity >99.93%. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination (0.16% of total bases), with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available athttps://github.com/ncbi/fcs/.
An exploratory study of gastrointestinal redox biomarkers in the presymptomatic and symptomatic Tg2576 mouse model of familial Alzheimer’s disease – phenotypic correlates and the effects of chronic oral D-galactose
Authors: Homolak Jan , Babic Perhoc Ana , Knezovic Ana , Osmanovic Barilar Jelena , Virag Davor , Salkovic-Petrisic Melita
Published: June 2023

The gut might play an important role in the etiopathogenesis of Alzheimer’s disease (AD) as gastrointestinal alterations often precede the development of neuropathological changes in the brain and correlate with disease progression in animal models. The gut has an immense capacity to generate free radicals whose role in the etiopathogenesis of AD is well known; however, it remains to be clarified whether gastrointestinal redox homeostasis is associated with the development of AD. The aim was to i) examine gastrointestinal redox homeostasis in the presymptomatic and symptomatic Tg2576 mouse model of AD; ii) investigate the effects of chronic oral D-galactose previously shown to alleviate cognitive deficits and metabolic changes in animal models of AD; iii) investigate the association between gastrointestinal redox biomarkers and behavioral alterations in Tg2576 mice. Presymptomatic Tg2576 have a heightened gastrointestinal electrophilic tone reflected in increased lipid peroxidation and activity of Mn/Fe-SOD. Chronic oral D-galactose treatment was associated with detrimental effects on redox homeostasis only in the wild-type controls. In the symptomatic stage, Tg2576 mice demonstrate compensated redox disbalance characterized by normalized lipid peroxidation and increased hydrogen peroxide dissociation capacity but diminished total antioxidant reserve alleviated with chronic oral D-galactose treatment. Conversely, D-galactose reduced antioxidant capacity and increased lipid peroxidation in the controls. Total antioxidant capacity was associated with greater spatial memory, while other biomarkers had a complex relationship with exploration, nesting, and grooming. Gut redox homeostasis might be involved in the development and progression of AD pathophysiology and should be further explored in this context.
Cryo-EM structures of the human G-protein coupled receptor 1 (GPR1) – Gi protein complexes bound to the full-length chemerin and to its C-terminal nonapeptide
Authors: Liu Aijun , Liu Yezhou , Chen Geng , Lyu Wenping , Ye Fang , Wang Junlin , Liao Qiwen , Zhu Lizhe , Du Yang , Ye Richard D.
Published: June 2023

Chemerin is an adipokine with chemotactic activity to a subset of leukocytes. Chemerin mainly acts through its C-terminal nonapeptide (YFPGQFAFS, C9) that bind to three G protein-coupled receptors including chemokine-like receptor 1 (CMKLR1), G-protein coupled receptor 1 (GPR1) and C-C chemokine receptor-like 2 (CCRL2). We examined C9 signaling through GPR1 and found this receptor capable of Gi signaling but very weak β-arrestin signaling. Here we report high-resolution cryo-EM structures of GPR1-Gi complexes bound to full-length chemerin and to C9, respectively. Unlike C9 that inserts directly into a transmembrane binding pocket, full-length chemerin uses its N-terminal globular core for extensive interaction with the N terminus of GPR1. Within the binding pocket, the C terminal loop containing the nonapeptide takes the same “S-shape” pose as synthetic C9 nonapeptide. These findings explain why the nonapeptide is a full agonist of GPR1, and demonstrate that chemerin uses a “two-site” model for interaction with GPR1. An analysis of the GPR1-Gi protein interface found high similarities to the CMKLR1-Gi complex, as confirmed by site-directed mutagenesis with functional verifications. Our structural analysis demonstrates shared features with chemokines in that chemerin acts as a “reverse chemokine” with switched functions of its N and C termini in the interaction with GPR1.
A Quantitative Analysis of Locomotor Patterns in DevelopingC. elegans
Authors: Hassinan Cera W. , Sterrett Scott C. , Summy Brennan , Khera Arnav , Wang Angie , Bai Jihong
Published: June 2023

Adult animals display robust locomotion, yet the timeline and mechanisms of how juvenile animals acquire coordinated movements and how these movements evolve during development are not well understood. Recent advances in quantitative behavioral analyses have paved the way for investigating complex natural behaviors like locomotion. In this study, we tracked the swimming and crawling behaviors of the nematodeCaenorhabditis elegansfrom postembryonic development through to adulthood. Our principal component analyses revealed that adultC. elegansswimming is low dimensional, suggesting that a small number of distinct postures, or eigenworms, account for most of the variance in the body shapes that constitute swimming behavior. Additionally, we found that crawling behavior in adultC. elegansis similarly low dimensional, corroborating previous studies. However, our analysis revealed that swimming and crawling are distinct gaits in adult animals, clearly distinguishable within the eigenworm space. Remarkably, young L1 larvae are capable of producing the postural shapes for swimming and crawling seen in adults, despite frequent instances of uncoordinated body movements. In contrast, late L1 larvae exhibit robust coordination of locomotion, while many neurons crucial for adult locomotion are still under development. In conclusion, this study establishes a comprehensive quantitative behavioral framework for understanding the neural basis of locomotor development, including distinct gaits such as swimming and crawling inC. elegans.
Contrasting responses to aridity by different-sized decomposers cause similar decomposition rates across a precipitation gradient
Authors: Torsekar Viraj R. , Sagi Nevo , Alfred Daniel J , Hawlena Yael , Gavish-Regev Efrat , Hawlena Dror
Published: June 2023

Litter decomposition is expected to be positively associated with precipitation despite evidence that decomposers of varying sizes have different moisture dependencies. We hypothesized that higher tolerance of macro-decomposers to aridity may counterbalance the effect of smaller decomposers, leading to similar decomposition rates across climatic gradients. We tested this hypothesis by placing plant litter baskets of different mesh sizes in seven sites along a sharp precipitation gradient, and by characterizing the macro-decomposer assemblages using pitfall trapping. We found that decomposers responded differently to precipitation levels based on their size. Microbial decomposition increased with precipitation in the winter while macro-decomposition peaked in arid sites during the summer. This led to similar overall decomposition rates across the gradient except in hyper-arid sites. Macro-decomposer richness, abundance and biomass peaked in arid environments. Our findings highlight the importance of macro-decomposition in arid-lands, possibly resolving the dryland decomposition conundrum, and emphasizing the need to contemplate decomposer size when investigating zoogeochemical processes.
Monocyte production of C1q potentiates CD8+T cell effector function following respiratory viral infection
Authors: Eddens Taylor , Parks Olivia B. , Lou Dequan , Fan Li , Sojati Jorna , Ramsey Manda Jo , Schmitt Lori , Salgado Claudia M. , Reyes-Mugica Miguel , Oury Tim D. , Byersdorfer Craig , Chen Kong , Williams John V.
Published: June 2023

Respiratory viral infections remain a leading cause of morbidity and mortality. Using a murine model of human metapneumovirus (HMPV), we identified recruitment of a C1q-producing inflammatory monocyte population concomitant with viral clearance by adaptive immune cells. Genetic ablation of C1q led to reduced CD8+T cell function. Production of C1q by a myeloid lineage was sufficient to enhance CD8+T cell function. Activated and dividing CD8+T cells expressed a putative C1q receptor, gC1qR. Perturbation of gC1qR signaling led to altered CD8+T cell IFN-γ production and metabolic capacity. Autopsy specimens from fatal respiratory viral infections in children demonstrated diffuse production of C1q by an interstitial population. Humans with severe COVID-19 infection also demonstrated upregulation of gC1qR on activated and rapidly dividing CD8+T cells. Collectively, these studies implicate C1q production from monocytes as a critical regulator of CD8+T cell function following respiratory viral infection.
Bifurcation in space: Emergence of function modularity in the neocortex
Authors: Wang Xiao-Jing , Jiang Junjie , Zeraati Roxana , Pereira-Obilinovic Ulises , Battista Aldo , Vezoli Julien , Kennedy Henry
Published: June 2023

How does functional modularity emerge in a cortex composed of repeats of a canonical local circuit? Focusing on distributed working memory, we show that a rigorous description of bifurcation in space describes the emergence of modularity. A connectome-based model of monkey cortex displays bifurcation in space during decision-making and working memory, demonstrating this new concept's generality. In a generative model and multi-regional cortex models of both macaque monkey and mouse, we found an inverted-V-shaped profile of neuronal timescales across the cortical hierarchy during working memory, providing an experimentally testable prediction of modularity. The cortex displays simultaneously many bifurcations in space, so that the corresponding modules could potentially subserve distinct internal mental processes. Therefore, a distributed process subserves the brain's functional specificity. We propose that bifurcation in space, resulting from connectivity and macroscopic gradients of neurobiological properties across the cortex, represents a fundamental principle for understanding the brain's modular organization.
Clustering temporal step-counting patterns for 24 hours with machine learning revealed potential heterogeneity in the categorization by a traditional tertile procedure
Authors: Nawrin Saida Salima , Inada Hitoshi , Momma Haruki , nagatomi Ryoichi
Published: June 2023

Objectives

Physical activity is a crucial aspect of health benefits in the public society. Although studies on the temporal physical activity patterns might lead to the protocol for efficient intervention/program, a standardized procedure to determine and analyze the temporal physical activity patterns remains to be developed. Here, we attempted to develop a procedure to cluster 24-hour patterns of physical activity as step counts measured with an accelerometer-based wearable sensor.

Methods

Data was collected from 42 healthy participants, comprising 35 males and 7 females, at the Sendai Oroshisho center in 2008. Using unsupervised machine learning, specifically the kernel k-means algorithm with the global alignment kernel was applied on a total of 815 days from 42 participants, and 6 activity patterns were identified. Further, the probability of each 24-hour step-counting pattern was calculated for every participant., and was used in MATLAB to apply spectral clustering, and 5 activity behaviors were identified.

Results

We could identify six 24-hour step-counting patterns and five daily step-behavioral clusters. When the amount of physical activity was categorized into tertile groups reflecting highly active, moderately active, and low active, each tertile group consisted of different proportions of six 24-hour step-counting patterns.

Conclusions

Our study introduces a novel approach using an unsupervised machine learning method to categorize daily hourly activity, revealing six distinct step counting patterns and five clusters representing daily step behaviors. Our procedure would be reliable for finding and clustering physical activity patterns/behaviors and reveal heterogeneity in the categorization by a traditional tertile procedure using total step amount.
DNA methylation signatures of early life adversity are exposure-dependent in wild baboons
Authors: Anderson Jordan A. , Lin Dana , Lea Amanda J. , Johnston Rachel A. , Voyles Tawni , Akinyi Mercy Y. , Archie Elizabeth A. , Alberts Susan C. , Tung Jenny
Published: June 2023

The early life environment can profoundly shape the trajectory of an animal’s life, even years or decades later. One mechanism proposed to contribute to these early life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early life effects on fitness-related traits.

Significance statement

The environment animals face when young can affect how they function throughout life. Long-lasting changes in DNA methylation—a chemical mark deposited on DNA that can affect gene activity—have been hypothesized to contribute to early life effects. But evidence for persistent, early environment-associated differences in DNA methylation is lacking in wild animals. Here, we show that early life adversity in wild baboons predicts DNA methylation levels in adulthood, especially for animals born in low resource environments and drought conditions. We also show that some of the changes we observe in DNA methylation have the capacity to influence gene activity levels. Together, our results support the idea that early experiences can become biologically embedded in the genomes of wild animals.
Biochemical characterization of mRNA capping enzyme from Faustovirus
Authors: Chan S. Hong , Molé Christa N. , Nye Dillon , Mitchell Lili , Dai Nan , Buss Jackson , Kneller Daniel W. , Whipple Joseph M. , Robb G. Brett
Published: June 2023

The mammalian mRNA 5’ cap structures play important roles in cellular processes such as nuclear export, efficient translation, and evading cellular innate immune surveillance and regulating 5’- mediated mRNA turnover. Hence, installation of the proper 5’ cap is crucial in therapeutic applications of synthetic mRNA. The core 5’ cap structure, Cap-0, is generated by three sequential enzymatic activities: RNA 5’ triphosphatase, RNA guanylyltransferase, and cap N7-guanine methyltransferase. Vaccinia virus RNA capping enzyme (VCE) is a heterodimeric enzyme that has been widely used in synthetic mRNA research and manufacturing. The large subunit of VCE D1R exhibits a modular structure where each of the three structural domains possesses one of the three enzyme activities, whereas the small subunit D12L is required to activate the N7-guanine methyltransferase activity. Here we report the characterization of a single-subunit RNA capping enzyme from an amoeba giant virus. Faustovirus RNA capping enzyme (FCE) exhibits a modular array of catalytic domains in common with VCE and is highly efficient in generating the Cap-0 structure without an activation subunit. Phylogenetic analysis suggests that FCE and VCE are descended from a common ancestral capping enzyme. We found that compared to VCE, FCE exhibits higher specific activity, higher activity towards RNA containing secondary structures, and broader temperature range, properties favorable for synthetic mRNA manufacturing workflows.