bluuebunny/crossref_metadata_2025 huggingface dataset:
Oral health status and associated factors among 12 to 15-year-old Chinese adolescents in Southeast China: A cross-sectional study
Authors: Su Shuwen , Zhang Jianming , Deng Ruibing , Wang Weiping , Cui Tianqiang , Su Yuwu , Li Xia
Published: February 2024

This study assessed oral health conditions and associated factors (including sociodemographic characteristics and self-reported oral health-related behaviors) among Chinese adolescents. This cross-sectional study enrolled 3840 adolescents aged 12 to 15 years from 12 middle schools in Foshan, Southeast China, in 2016, using multistage, stratified cluster sampling. Participants underwent a clinical oral examination and completed a questionnaire. The prevalence of dental caries, probe bleeding, and calculus was 37.6%, 46.2%, and 39.7%, respectively; the mean decayed/missed/filled teeth index was 0.86 ± 1.58. A mean of 2.09 ± 3.65 and 1.85 ± 3.52 teeth showed probe bleeding and calculus, respectively. Only 0.3% and 0.1% of adolescents aged 15 years had periodontal pockets (depth ≥ 4 mm) and attachment loss, respectively, which were most common in tooth positions 46 and 36 (Federation Dentaire International 2-digit system). Regarding oral health-related behavior, 49.1% of the participants failed to brush their teeth at least twice daily, 98.5% never or rarely used dental floss, and 58.7% reported middle–high frequency sugar consumption. Older age, female, administrative region, maternal education lower than university, brushing teeth less than twice daily, flossing less than once daily, and frequent sugar consumption were significant risk factors of caries. Older age, female, administrative region, brushing less than twice daily, and flossing less than once daily significantly increased periodontal risk. Despite the overall low prevalence of adverse dental conditions among adolescents in Foshan, their oral hygiene habits were undeveloped. Thus, their identified risk factors need close monitoring, and families, schools, communities, and the government should jointly promote adolescents’ oral health.
Percutaneous short segmental fixation combined with bone cement augmentation for stage III Kümmell’s disease without nerve deformity
Authors: Guo Xiang , Qiu Yujin , Liu Xiaowei , Teng Haijun , Hu Hongtao
Published: February 2024

The objective of this study was to evaluate the safety and efficacy of percutaneous pedicle screw fixation combined with bone cement augmentation in the management of stage III Kümmell disease without nerve deformity. A retrospective analysis was conducted on 17 patients diagnosed with stage III Kümmell disease without nerve deformity, who underwent treatment with percutaneous pedicle screw fixation combined with bone cement augmentation between April 2019 and 2022. Preoperative, postoperative, and final follow-up clinical outcome measures were collected, including Visual Analog Scale scores and Oswestry Disability Index scores. Additionally, lateral radiography was used to measure the Cobb angle and height of the anterior border of the affected vertebral body. Operative time, volume of injected bone cement, intraoperative cement leakage, and other complications were recorded. All patients underwent successful surgery, resulting in significant reductions in Visual Analog Scale scores, Oswestry Disability Index scores, and Cobb angle postoperatively; meanwhile there was a significant increase in height of the anterior border of the affected vertebral body. No major complications occurred during the follow-up period. In conclusion, percutaneous pedicle screw short-segment fixation combined with bone cement augmentation appears to be an effective surgical option for treating stage III Kümmell disease without nerve deformities.
Overview of invasive fungal infections in children in South America – the threat of resistant Candida species and the role of climate change in the new geographic distribution of endemic systemic mycosis
Authors: Fonseca Silvia Nunes Szente
Published: February 2024

Purpose of review

Invasive fungal infection (IFI) in children is a growing problem with crescent morbidity and mortality, well recognized in developed countries, affecting mainly immunocompromised children, including neonates and children in intensive care units. The burden of IFI in South American children is less well comprehended. In addition, the current epidemiology of endemic systemic mycoses in children may have changed over time.

Recent findings

Candida spp. infections are very prevalent in South America hospitalized children, especially in neonates, in a rate far superior compared to developed countries. C. auris, has already been responsible for outbreaks in neonates and children in Venezuela and Colombia. Sporotrichosis is well established as an urban zoonosis in impoverish families. Paracoccidioidomycosis and histoplasmosis are affecting new areas of Brazil, probably due to climate change, deforestation, and human migration.

This review aims to unveil the real dimension of these infections in South American children. Hopefully, the awareness brought by this review will help healthcare professionals to recognize IFI more easily and it will provide support for getting more resources for IFI treatment and prevention.
Clinical updates in inborn errors of immunity: a focus on the noninfectious clinical manifestations
Authors: Campbell Emily , Shaker Marcus S. , Williams Kelli W.
Published: February 2024

Purpose of review

In the last 5 years, several new inborn errors of immunity (IEI) have been described, especially in the areas of immune dysregulation and autoinflammation. As a result, the clinical presentation of IEIs has broadened. We review the heterogeneous presentation of IEIs and detail several of the recently described IEIs with a focus on the noninfectious manifestations commonly seen.

Recent findings

IEIs may present with early onset and/or multiple autoimmune manifestations, increased risk for malignancy, lymphoproliferation, severe atopy, autoinflammation and/or hyperinflammation. Because of this, patients can present to a wide array of providers ranging from primary care to various pediatric subspecialists. The International Union of Immunological Societies (IUIS) expert committee has created a phenotypic classification of IEIs in order to help clinicians narrow their evaluation based on the laboratory and clinical findings.

Both primary care pediatricians and pediatric subspecialists need to be aware of the common clinical features associated with IEI and recognize when to refer to allergy-immunology for further evaluation. Early diagnosis can lead to earlier treatment initiation and improve clinical outcomes for our patients.
Efficacy and Toxicity of Palliative Chemotherapy in Elderly Patients With Advanced Pancreatic Cancer
Authors: Jeong Han Taek , Kim Ho Gak , Han Jimin
Published: February 2024

Objectives

We aimed to compare the efficacy and toxicity of palliative chemotherapy in elderly patients with pancreatic ductal adenocarcinoma (PDAC) with those in younger patients.

Methods

A total of 60 patients with locally advanced or metastatic PDAC who received FOLFIRINOX or nab-paclitaxel plus gemcitabine at our institution from January 2014 to December 2021 were analyzed. Patients 70 years or older were classified into an elderly group.

Results

The elderly group included 16 patients (26.7%). In the elderly group, nab-paclitaxel plus gemcitabine was used more than FOLFIRINOX compared with the young group (75.0% and 25.0% vs 34.1% and 64.9%, respectively; P = 0.008). The overall survival was not significantly different between the 2 groups (15.6 vs 13.4 months, P = 0.259). However, the elderly group showed better progression-free survival (11.4 vs 7.4 months, P = 0.034). The incidence of adverse events including neutropenia (75.0% vs 81.8%, P = 0.716), thrombocytopenia (25.0% vs 31.3%, P = 0.743), and anemia (50.0% vs 43.2%, P = 0.771) was not different between the 2 groups. Peripheral neuropathy was more common in the elderly group (18.3% vs 2.3%, P = 0.054), though not statistically significant.

Conclusion

The efficacy and toxicity of chemotherapy in elderly patients with advanced PDAC were comparable with those in younger patients.
The Resurgence of Lymphogranuloma Venereum: Changing Presentation of Lymphogranuloma Venereum in the Era of HIV Preexposure Prophylaxis, 2004 to 2022
Authors: Gupta Amit K. , Lyons Brody , Hunter Ian , Arnold Barbra , Gilbert Mark , Hoang Linda , Malleson Sarah , Ryan Venessa , Romney Marc G. , Severini Alberto , Wong Jason , Grennan Troy
Published: February 2024

Background

Before the early 2000s, the sexually transmitted infection lymphogranuloma venereum (LGV) was rare in high-income countries. Initially, most cases in these countries were among symptomatic men who have sex with men (MSM) living with HIV. In the context of widespread HIV preexposure prophylaxis (PrEP), LGV's epidemiology may be changing. We aimed to characterize the epidemiology and clinical presentation of LGV in the PrEP era.

Methods

A retrospective chart review was performed on all LGV cases occurring between November 2004 to October 2022 in British Columbia (BC), Canada. Cases were stratified by having occurred before (2004–2017) or after widespread PrEP availability in BC (2018–2022). Annual rates and test positivity percentages were calculated. Bivariate logistic regression was performed to identify drivers of asymptomatic infection in the PrEP era.

Results

Among 545 cases identified, 205 (37.6%) occurred pre-PrEP and 340 (62.4%) occurred during the PrEP era. Most cases were among MSM (97.2%). The estimated rate of LGV has doubled from 2018 to 2022, reaching 1535.2 cases per 100,000 PrEP users. Most PrEP-era cases were among HIV-negative individuals (65.3%), particularly those on PrEP (72.6%). Cases in the PrEP era were often asymptomatic compared with pre-PrEP (38.6% vs. 19.3%;P< 0.001). Users of PrEP were more likely to experience asymptomatic infection compared with HIV-negative PrEP nonusers (odds ratio, 2.07; 95% confidence interval, 1.07–3.99).

Conclusions

In the context of increased asymptomatic testing, LGV may be increasing in BC. Most infections now occur among HIV-negative MSM. A high proportion of infections are asymptomatic.
Spread Through Air Spaces in Stage I to III Resected Lung Adenocarcinomas
Authors: Laville David , Désage Anne-Laure , Fournel Pierre , Bayle-Bleuez Sophie , Neifer Chaouki , Picot Tiphanie , Sulaiman Abdulrazzak , Tiffet Olivier , Forest Fabien
Published: February 2024

In recent years, the concept of spread through air spaces (STAS) has been discussed as an adverse prognostic factor for lung cancer. The aim of our study is to clarify the prognostic role of STAS in relation to the main recognized prognostic factors in a retrospective cohort of 330 European patients who underwent stages I to III lung adenocarcinoma resection. On univariate analysis, the presence of STAS was related to progression-free survival (PFS; hazard ratio [HR]: 1.48; 95% CI: 1.02-2.19; P = 0.038) and overall survival (OS; HR: 1.61; 95% CI: 1.03-2.52; P = 0.50). On multivariate analysis, STAS was related to PFS (HR: 1.51; 95% CI: 1.00-2.17; P = 0.050) and to OS (HR: 1.67; 95% CI: 1.00-2.81; P = 0.050). We showed that the presence of STAS was associated with lower PFS, equivalent to the next pathologic T stage, especially the median PFS of T3 stages without STAS was at 62.8 months while the median PFS of T3 stages with STAS was at 15.7 months, closer to the median PFS of 17.4 months in T4 stages. To conclude, STAS is an independent prognostic factor of PFS in this European cohort and is close to significance for OS. We suggest that the presence of STAS might lead to an upstaging of lung adenocarcinoma.
Criteria for classification, nomenclature, and reference sequence selection for HIV sub-subtypes of CRF01_AE and CRF07_BC strains in China
Authors: Wang Dong , Feng Yi , Ruan Yuhua , Liao Lingjie , Hao Jingjing , Song Chang , Hu Jing , Shao Yiming , Xing Hui
Published: February 2024

The available knowledge regarding classification, nomenclature, and reference sequence selection for the various sub-subtypes of circulating recombinant forms (CRFs) is inadequate to fulfill the growing demands of research focused on HIV prevention. We analyzed the spread of CRF01_AE and CRF07_BC strains, mainly in China, to complement and update the existing nomenclature and to propose a reference sequence selection criteria for sub-subtypes of CRFs.
Use of Banked Fibula for Improved Nasal Reconstruction Following Free Fibula Midface Reconstruction
Authors: Bernstein Jaime L. , Reeve Gwendolyn , Kutler David I. , Spector Jason A.
Published: February 2024

Objective:

Anterior maxillary deficiency caused by trauma or oncologic resection presents a complex reconstructive challenge. The authors present a technique for 2-stage midface reconstruction utilizing a vascularized free fibula flap for maxillary reconstruction, followed by nasal reconstruction at a second stage utilizing a banked fibula graft.

Methods:

This case series utilizes a 2-stage technique for midface reconstruction. In the first stage, a fibula-free flap was used to reconstruct the maxilla with the excess banked in the abdomen. In the second stage, this bone graft was used to restore the nasal dorsum.

Results:

Two patients were included in this series. Patient 1 was a 28-year-old man who presented after a remote gunshot wound to his face, resulting in complete loss of his anterior maxilla and nasal support with midface collapse. Patient 2 was a 65-year-old man who presented with squamous cell carcinoma of the hard palate with extension into the maxilla and nasal septum. In both cases, the flaps healed without complication, providing midface restoration. Placement of the banked fibula graft in a second stage resulted in restoration of dorsal nasal projection.

Conclusion:

The authors describe the use of “spare” fibula parts for nasal reconstruction after loss of the maxilla and cartilaginous septum. The use of the fibula bone as a graft to restore the nasal dorsum in a delayed manner allows for a better assessment of the esthetic needs after the massive swelling from the initial surgery has abated. Further, this approach eliminates the need for a second donor site for nasal reconstruction.
Prevalence of Craniofacial Injuries in the Elderly Population
Authors: Chepyala Pranav , Stead Thor S. , Mangal Rohan K. , Ganti Latha
Published: February 2024

Introduction:

Recognizing and understanding risk factors for craniofacial injury in the elderly is of paramount importance in prevention. This research aims to investigate the prevalence of craniofacial injuries in connection with extrinsic preventable factors, particularly identifying common household products that pose the greatest risk for such injuries.

Materials and Methods:

This study was done with the utilization of the 2013 to 2022 National Electronic Injury Surveillance System (NEISS). Data gathered included patient age, injury type, cause of injury, and year of incidence. “Elderly” was defined as an individual of 65 years of age or older.

Results:

There was a total of 9,703,688 estimated national cases of elderly craniofacial injury from 2013 to 2022. In all, 5,888,112 (60.68%) of these occurred in females. In descending order, the 5 most common items responsible for craniofacial injury in the elderly are floors/flooring Materials (3,741,706, 30.92%), beds/bed frames (1,250,396, 10.33%), stairs/steps (907,92, 7.50%), chairs (546,697, 4.52%), and tables (453,989, 3.75%). These top 5 account for roughly 57% of all cases. The 5 most common presenting diagnoses were internal injury (2,957,095, 40.21%), lacerations (1,435,926, 19.53%), ABR (1,191,008, 16.20%), fracture (568,842, 7.74%), and hematoma (355,871, 4.84%).

Conclusions:

Out of the roughly 10 million cases of craniofacial injury in the last decade, ~three-fifths have happened to women. The majority of injuries occur in a home setting. The overwhelming majority of cases were related to the product code 1807-floors or flooring materials, and the largest diagnosis was internal injury by a wide margin. Evidently, there is a large population of elderly patients who suffer from craniofacial injuries related to objects and items that permeate within their living residences. The elimination of excess elderly craniofacial injury can be achieved by reducing fall risk factors in the immediate vicinity of the elderly.
The Use and Outcomes of 3D Printing in Pediatric Craniofacial Surgery: A Systematic Review
Authors: Clegg Devin J. , Deek Andrew J. , Blackburn Caleb , Scott Christopher A. , Daggett Justin R.
Published: February 2024

Three-dimensional (3D) printing has demonstrated efficacy in multiple surgical specialties. As accessibility improves, its use in specific fields deserves further attention. We conducted a systematic review of the implementation and outcomes of 3D printing in pediatric craniofacial surgery, as none has been performed. A systematic review was conducted according to Cochrane and PRISMA guidelines. PubMed, Embase, Cochrane library, and Clinicaltrials.gov were queried with combinations of the terms: “3D printing,” “craniofacial,” “surgery,” and “pediatric.” Original human studies containing patients <18 years old implementing 3D printing to aid in craniofacial surgery were included. Study selection, grading, and data extraction were performed independently by multiple authors. After screening 120 articles, 7 (3 case series and 4 case reports) were included, published from 2017 to 2022. All studies addressed patients with different disease processes including craniosynostosis, cleft lip/palate, and mandibular hypoplasia. 3D printing was used to create mock surgical models in 2 studies, intraoperative cutting guides/molds (CGs) in 6 studies, and cranioplasty implants in 2 studies. Two case series determined the accuracy of the CGs was acceptable within historical comparison, while 4 articles included subjective statements on improved accuracy. Five studies noted reduced operating time, 2 noted reduced intraoperative blood loss, and 1 felt the use of 3D printed materials was responsible for shorter hospitalization duration. No adverse events were reported. Despite the limitations of the current literature, all studies concluded that the use of 3D printing in pediatric craniofacial surgery was beneficial. Definitive conclusions cannot be made until further controlled research is performed.
Effect of Therapeutic Radiation on Polycaprolactone/Hydroxyapatite Biomaterials in a Calvarial Model
Authors: Park Hojin , Jeong Woo Shik , Choi Jong Woo
Published: February 2024

Bone defects caused by cancer resection often require postoperative radiotherapy. Although various synthetic polymers have been introduced as graft materials, their biological behavior after radiation exposure remains unclear. Here, we investigated how polycaprolactone/hydroxyapatite (PCL/HA) implants respond to therapeutic radiation exposure (in terms of volume and bone regeneration). Four 8 mm diameter calvaria defects were surgically created on the parietal bone of 6 rabbits. PCL/HA implants made of porous, solid, and hybrid polymers were grafted by random placement in each defect. The fourth defect was left untreated. Four weeks after surgery, radiation exposure was conducted weekly for 6 weeks (total: 48 Gy). Micro-computed tomography and histologic analysis were performed at 3 and 6 months, and 6 months postradiation, respectively. The total augmented volumes of all implants showed no significant differences between 3- and 6-months postradiation computed tomography images. In histologic analysis, new bone areas were 0.45±0.11 mm2, 2.02±0.34 mm2, and 3.60±0.77 mm2 in solid, hybrid, and porous polymer grafts, respectively. Bone regeneration was limited to the periphery of the defect in the hybrid and porous polymer grafts, whereas new bone formed inside the porous implant. The total augmented volume of the defect was maintained without significant absorption even after radiation exposure. The PCL/HA implant maintained its structure despite radiation exposure. The porous PCL/HA implant demonstrated excellent bone regeneration, followed by the hybrid and solid implants. The PCL/HA implant is a promising candidate for bone defect reconstruction.
Prevalence of co-infection between high-risk human papillomavirus and common sexually transmitted infections in cervical specimens
Authors: Kostera Joshua , Tursunovic Almedina , Botts Paige , Galloway Regina , Davis April , Yang Tong
Published: February 2024

Objectives

Evidence suggests that co-infection with sexually transmitted infection (STI) pathogens may support HPV infection persistence and cervical disease progression and neoplasia. We examined the prevalence of HPV and co-infection with other common STI pathogens in liquid-based cytology (LBC) cervical specimens, and their association with cervical disease by cytology.

Methods

In this retrospective, cross-sectional study, 149 randomly selected remnant cervical specimens, collected in LBC as part of routine cervical cancer screening in a large urban academic healthcare system, were tested on the Alinity m HR HPV assay and Alinity m STI assay. All specimens were processed for cytology and graded as negative for intraepithelial lesions or malignancy (NILM), atypical squamous cells of undetermined significance (ASC-US) or having any atypical cytology beyond ASC-US (≥LSIL).

Results

62.4% (n=93/149) of specimens had abnormal (≥ASC-US) cytology and the remaining 37.6% (n=56/149) had NILM cytology. HR HPV was detected in 62.4% (93/149) of specimens and a single STI pathogen was detected in 11.4% (17/149) of specimens. Most specimens with a positive HPV result (73.1%; n=68/93) or positive STI result (94.1%; n=16/17) had ≥ASC-US cytology. Compared to HPV infection alone, co-infection with HPV and STI was associated with an increased prevalence of ASC-US (39.8% vs. 50.0%) and ≥LSIL cytology (33.3% vs. 41.7%). Having ≥LSIL cytology (OR= 4.1667; 95%CI: 1.6110;10.7763) or a positive STI result (OR= 1.5111; 95%CI: 0.5027;4.5420) were predictive of a positive Alinity m HR HPV assay result.

Conclusions

Our study confirmed an association between co-infection with HPV and STI pathogens and abnormal cytology in cervical specimens. HPV and STI co-testing may provide granular analyses of the risk of cervical disease associated with co-infections by specific HPV genotypes and STI pathogens.

KEY MESSAGES

What is already known on this topic

Recent studies have suggested a possible link between HPV and STI co-infection, HPV persistence in the reproductive tract, and cervical neoplasia.

What this study adds

Compared to cervical specimens positive for HPV infection alone, specimens with HPV/STI co-infection had a higher prevalence of abnormal cytology.

Having abnormal cytology or a positive Alinity m STI assay result were predictive of a positive Alinity m HR HPV assay result.

How this study might affect research, practice, or policy

Molecular testing for high-risk HPV and common STI pathogens may reveal additional insight for predictors of cervical disease.
De novo HDAC3variants leading to epigenetic machinery dysfunction are associated with a neurodevelopmental disorder
Authors: Yoon Jihoon G. , Lim Seong-Kyun , Seo Hoseok , Lee Seungbok , Cho Jaeso , Kim Soo Yeon , Koh Hyun Yong , Poduri Annapurna H. ,   Deciphering Developmental Disorders Study, Ko Jung Min , Han Dohyun , Chae Jong-Hee , Lee Chul-Hwan
Published: February 2024

Histone deacetylase 3 (HDAC3) is a crucial epigenetic modulator essential for brain development. Although its dysfunction is increasingly recognized in various neurodevelopmental disorders, there have been no reports of human diseases related to HDAC3 dysfunction in Online Mendelian Inheritance in Man (OMIM). This study establishes a novel link between heterozygousde novovariants inHDAC3and a distinct neurodevelopmental syndrome, characterized by intellectual disability, developmental delays, and other variable manifestations such as musculoskeletal anomalies and congenital heart defects. In a cohort of six individuals, we identifiedde novomissenseHDAC3variants (D93N, A110T, P201S, L266S, G267S, and R359C), all located in evolutionarily conserved sites. Using trio exome sequencing and extensive phenotypic analysis, we correlated these genetic alterations with the observed clinical spectrum. Our investigations using HDAC assays and western blot analyses identified reduced deacetylation activity in the L266S and G267S variants, positioned near the enzymatic pocket. Additionally, proteomic analysis employing co-immunoprecipitation revealed that disrupted interactions with key multi-protein complexes, particularly CoREST and NCoR in the A110T variant, suggesting a critical pathogenic mechanism. Moreover, immunofluorescence analysis revealed diminished fluorescence intensity (nuclear to cytoplasmic ratio) in the A110T, G267S, and R359C variants, indicating impaired nuclear localization. This study highlights thatde novo HDAC3variants are associated with a novel neurodevelopmental syndrome, emphasizing the importance of histone deacetylase activity, multi-protein complex interactions, and nuclear localization for normal cellular function of HDAC3. These insights open new possibilities for understanding the molecular mechanisms of this uncharacterized neurodevelopmental disorder and may inform future therapeutic approaches.

Graphical abstract

This study identifiesde novo HDAC3variants in patients with neurodevelopmental disorders, characterized by intellectual disability, developmental delays, and other variable manifestations. We demonstrate that these variants result in reduced HDAC activity, compromised interactions with multi-protein complexes, and improper nuclear localization of the HDAC3 protein. This provides a novel gene-disease association and offers insights into the molecular underpinnings of this disorder.
Effects of Maize Development and Phenology on the Field Infestation Dynamics of the European Corn Borer (Lepidoptera: Crambidae)
Authors: Revillon Sacha , Dillmann Christine , Galic Nathalie , Bauland Cyril , Palaffre Carine , Malvar Rosa Ana , Butron Ana , Rebaudo François , Legrand Judith
Published: February 2024

Phenological match/mismatch between cultivated plants and their pest could impact pest infestastion dynamics in the field. To explore how such match/mismatch of plant and pest phenologies may interact with plant defense dynamics, we studied the infestation dynamics of maize by one of its main pests in Europe, the European Corn Borer (Ostrinia nubilalis; Lepidoptera: Crambidae). A two-year field experiment was carried out on a collection of 23 maize inbred lines contrasted for their earliness. Each inbred line was sown at three different dates in order to expose different developmental stages of maize to natural European corn borer infestation. The effect of the sowing date depended on the inbred line, the pest generation and the year. In 2021, the final pest incidence ranged from 36% to 91% depending on inbred lines and sowing date. In 2022, it ranged from 2% to 77%. This variability in final pest incidence can be related to variations in plant development during plant exposure to pest infestation. However, this relationship was not straightforward. Indeed, the shape and intensity of the relationship depended on the timing of the onset of the pest infestation. When infestation occurred while plants were in a vegetative stage, a non-linear relationship between development and pest incidence was observed with the least and most developed plants being the most infested. When infestation occurred when all plants were in the mature phase, the most developed plants were the least infested. Our results highlight the effect of plant-pest phenological match/mismatch on pest infestation dynamics and underline the importance of taking plant-pest interactions into account to propose relevant control strategies.
Long G4-rich enhancer physically interacts with EXOC3 promoter via a G4:G4 DNA-based mechanism
Authors: DeMeis Jeffrey D , Roberts Justin T , Delcher Haley A , Godang Noel L , Coley Alexander B , Brown Cana L , Shaw Michael H , Naaz Sayema , Alsatari Enas S , Dahal Ayush , Alqudah Shahem Y , Nguyen Kevin N , Nguyen Anita D , Paudel Sunita S , Dang Hong , O’Neal Wanda K. , Knowles Michael R. , Houserova Dominika , Gillespie Mark N , Borchert Glen M
Published: February 2024

Enhancers are genomic sequences that function as regulatory elements capable of increasing the transcription of a given gene often located at a considerable distance. The broadly accepted model of enhancer activation involves bringing an enhancer-bound activator protein complex into close spatial proximity to its target promoter through chromatin looping. Equally relevant to the work described herein, roles for guanine (G) rich sequences in transcriptional regulation are now widely accepted. Non-coding G-rich sequences are commonly found in gene promoters and enhancers, and various studies have described specific instances where G-rich sequences regulate gene expression via their capacity to form G-quadruplex (G4) structures under physiological conditions. In light of this, our group previously performed a search for long human genomic stretches significantly enriched for minimal G4 motifs (referred to as LG4s herein) leading to the identification of 301 LG4 loci with a density of at least 80 GGG repeats / 1,000 basepairs (bp) and averaging 1,843 bp in length. Further, in agreement with previous reports indicating that minimal G4s are highly enriched in promoters and enhancers, we found 217/301 LG4 sequences overlap a GeneHancer annotated enhancer, and the gene promoters regulated by these LG4 enhancers were found to be similarly, markedly enriched with G4-capable sequences. Importantly, while the generally accepted model for enhancer:promoter specificity maintains that interactions are dictated by enhancer- and promoter-bound transcriptional activator proteins, the current study was designed to test an alternative hypothesis: that LG4 enhancers physically interact with their cognate promoters via a direct G4:G4 DNA-based mechanism. As such, this work employs a combination of informatic mining and locus-specific immunoprecipitation strategies to establish the spatial proximity of enhancer:promoter pairs within the nucleus then biochemically confirms the ability of individual LG4 ssDNAs to directly and specifically interact with DNA sequences found in their target promoters. In addition, we also identify four single nucleotide polymorphisms (SNPs), occurring within a LG4 enhancer on human chromosome 5, significantly associated with Cystic Fibrosis (CF) lung disease severity (avg. p value = 2.83E-9), presumably due to their effects on the expressions of CF-relevant genes directly regulated by this LG4 enhancer (e.g., EXOC3 and CEP72).

Graphical Abstract

In brief: LG4 enhancers physically interact with gene promoters by forming composite G4 structures where both the LG4 and cognate promoter contribute half of the necessary sequence for G4 formation.
The mitochondrial thiolase ACAT1 regulates monocyte/macrophage type I interferonviaepigenetic control
Authors: Wu Jing , Singh Komudi , Shing Vivian , Gupta Anand K. , Huffstutler Rebecca D. , Lee Duck-Yeon , Sack Michael N.
Published: February 2024

Lipid-derived acetyl-CoA is shown to be the major carbon source for histone acetylation. However, there is no direct evidence demonstrating lipid metabolic pathway contribututions to this process. Mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes the final step of ß-oxidation, the aerobic process catabolizing fatty acids (FA) into acetyl-CoA. To investigate this in the context of immunometabolism, we generated macrophage cell line lacking ACAT1.13C-carbon tracing combined with mass spectrometry confirmed incorporation of FA-derived carbons into histone H3 and this incorporation was reduced in ACAT1 KO macrophage cells. RNA-seq identified a subset of genes downregulated in ACAT1 KO cells including STAT1/2 and interferon stimulated genes (ISGs). CHIP analysis demonstrated reduced acetyl-H3 binding to STAT1 promoter/enhancer regions. Increasing histone acetylation rescued STAT1/2 expression in ACAT1 KO cells. Concomitantly, ligand triggered IFNβ release was blunted in ACAT1 KO cells and rescued by reconstitution of ACAT1. Furthermore, ACAT1 promotes FA-mediated histone acetylation in an acetylcarnitine shuttle-dependent manner. In patients with obesity, levels of ACAT1 and histone acetylation are abnormally elevated. Thus, our study identified a novel link between ACAT1 mediated FA metabolism and epigenetic modification on STAT1/2 that uncovers a regulatory role of lipid metabolism in innate immune signaling and opens novel avenues for interventions in human diseases such as obesity.
Recurrent drought increases grassland community seasonal synchrony
Authors: Müller Lena M. , Bahn Michael , Weidle Maximillian , Leitinger Georg , in ‘t Zandt Dina
Published: February 2024

1. Climate change increases the frequency and severity of drought events with strong repercussions on grassland ecosystems. While the effects of single drought events on ecosystem structure and functioning are well understood, it is largely unknown whether and how drought frequency modifies ecosystem responses to drought.

2. Here, we assessed how the increase in frequency of severe, annual summer drought impacted grassland communities. We examined these effects in a species-rich sub-alpine mountain meadow with a drought frequency of one, three, and 13 years, as well as ambient conditions.

3. We found that high drought frequency increased seasonal plant community synchrony through a reduction in species richness, a shift of plant functional groups, a loss of early-seasonal plant species, and the constrained establishment of seedlings throughout the growing season. These changes were associated with a decreased fraction of biomass as drought frequency increased.

4. Furthermore, we show that negative drought effects were enhanced with an increasing drought frequency, and that negative drought effects on plant communities outweighed the weak adaptive effects of species.

5. Synthesis. We conclude that single and low-frequency drought studies may not adequately predict longer-term changes in our rapidly shifting climate. With the ongoing increase in drought frequency due to climate change, we predict that grassland plant communities will increase in seasonal synchrony. We suggest that this increase in synchrony will leave ecosystems highly vulnerable to future disturbances, because asynchrony is a critical component of stability. Moreover, given the weak adaptive effects of plant species to long-term recurrent drought, we conclude that plant communities are unlikely to be able to adapt to the rapid increase in recurrent drought events.
More than a token photo: humanizing scientists enhances student engagement
Authors: Costello Robin A. , Driessen Emily P. , Kjelvik Melissa K. , Schultheis Elizabeth H. , Youngblood Rachel M. , Zemenick Ash T. , Weber Marjorie G. , Ballen Cissy J.
Published: February 2024

Highlighting scientists from historically excluded groups in educational materials increases student engagement in STEM. However, which specific elements of these educational materials maximize their impact remains untested, leaving educators guessing how to best highlight counter-stereotypical scientists in their classrooms. We tested the effects of including visual and humanizing descriptions of scientists featured in quantitative biology activities on over 3,700 students across 36 undergraduate institutions. We found that including humanizing information about counter-stereotypical scientists increased the extent to which students related to those scientists, which in turn translated to higher student engagement. Students who shared one or more excluded identity(s) with the featured scientists related most strongly. Our findings demonstrate the importance of humanizing counter-stereotypical scientists in classrooms, beyond simply adding a photo to increase representation.
iPAR: a new reporter for eukaryotic cytoplasmic protein aggregation
Authors: Lecinski Sarah , Howard Jamieson A.L. , MacDonald Chris , Leake Mark C.
Published: February 2024

Background

Cells employ myriad regulatory mechanisms to maintain protein homeostasis, termed proteostasis, to ensure correct cellular function. Dysregulation of proteostasis, which is often induced by physiological stress and ageing, often results in Protein Aggregation in cells. These aggregated structures can perturb normal physiological function, compromising cell integrity and viability, a prime example being early onset of several neurodegenerative diseases. Understanding aggregate dynamicsin vivois therefore of strong interest for biomedicine and pharmacology. However, factors involved in formation, distribution and clearance of intracellular aggregates are not fully understood.

Methods

Here, we report an improved methodology for production of fluorescent aggregates in model budding yeast which can be detected, tracked and quantified using fluorescence microscopy in live cells. This new openly-available technology, iPAR (inducible Protein Aggregation Reporter), involves monomeric fluorescent protein reporters fused to a ΔssCPY* aggregation biomarker, with expression controlled under the copper-regulatedCUP1promoter.

Results

Monomeric tags overcome challenges associated with non-physiological reporter aggregation, whilstCUP1provides more precise control of protein production. We show that iPAR and the associated bioimaging methodology enables quantitative study of cytoplasmic aggregate kinetics and inheritance featuresin vivo. We demonstrate that iPAR can be used with traditional epifluorescence and confocal microscopy as well as single-molecule precise Slimfield millisecond microscopy. Our results indicate that cytoplasmic aggregates are mobile and contain a broad range of number of iPAR molecules, from tens to several hundred per aggregate, whose mean value increases with extracellular hyperosmotic stress.

Discussion

Time lapse imaging shows that although larger iPAR aggregates associate with nuclear and vacuolar compartments, and for the first time we show directly that these proteotoxic accumulations are not inherited by daughter cells, unlike nuclei and vacuoles. If suitably adapted, iPAR offers new potential for studying diseases relating to protein oligomerization processes in other model cellular systems.
Comparing structure and dynamics of transition graphs by the symmetric difference metric over an edge-filtration
Authors: Pascual Belén García , Salbu Lars M. , Renz Jessica , Giannakis Konstantinos , Johnston Iain G.
Published: February 2024

Transition graphs or transition diagrams, describing the rates and probabilities with which a system changes between discrete states, are common throughout the sciences. In many cases, parameterisations of transition graphs are inferred from different datasets, for example in the context of Markov or hidden Markov models. An important task for followup analysis is to find efficient and effective ways to compare transition graphs with different parameterisations. Here, we introduce the Weight-Filtration Comparison Curve (WFCC), an approach by which the differences between two or more parameterisations of a transition graph can be quantified and compared. Borrowing from topological data analysis, the WFCC allows graphs learned from different datasets and/or null models to be systematically compared, and differences in both the fine- and coarse-grained structure and dynamics of transition graphs to be quantitatively assessed. We demonstrate WFCC with simple illustrative cases and real-world cases of transition graphs inferred from global data on the evolution of antimicrobial resistance in different countries, showing how different inferred dynamics, and different levels of uncertainty, are reported by structural aspects of these comparison curves.
Nonreciprocal synchronization in embryonic oscillator ensembles
Authors: Ho Christine , Jutras-Dubé Laurent , Zhao Michael , Mönke Gregor , Kiss István Z. , François Paul , Aulehla Alexander
Published: February 2024

Synchronization of coupled oscillators is a universal phenomenon encountered across different scales and contexts e.g., chemical wave patterns, superconductors and the unison applause we witness in concert halls. The existence of common underlying coupling rules define universality classes, revealing a fundamental sameness between seemingly distinct systems. Identifying rules of synchronization in any particular setting is hence of paramount relevance. Here, we address the coupling rules within an embryonic oscillator ensemble linked to vertebrate embryo body axis segmentation. In vertebrates, the periodic segmentation of the body axis involves synchronized signaling oscillations in cells within the presomitic mesoderm (PSM), from which somites, the pre-vertebrae, form. At the molecular level, it is known that intact Notch-signaling and cell-to-cell contact is required for synchronization between PSM cells. However, an understanding of the coupling rules is still lacking. To identify these, we develop a novel experimental assay that enables direct quantification of synchronization dynamics within mixtures of oscillating cell ensembles, for which the initial input frequency and phase distribution are known. Our results reveal a “winner-takes-it-all” synchronization outcome i.e., the emerging collective rhythm matches one of the input rhythms. Using a combination of theory and experimental validation, we develop a new coupling model, the “Rectified Kuramoto” (ReKu) model, characterized by a phase-dependent, non-reciprocal interaction in the coupling of oscillatory cells. Such non-reciprocal synchronization rules reveal fundamental similarities between embryonic oscillators and a class of collective behaviours seen in neurons and fireflies, where higher level computations are performed and linked to non-reciprocal synchronization.
StaVia: Spatially and temporally aware cartography with higher order random walks for cell atlases
Authors: Stassen Shobana V. , Kobashi Minato , Huang Yuanhua , Ho Joshua W. K. , Tsia Kevin K.
Published: February 2024

Single-cell atlases are critical for unraveling the cellular basis of health and disease, yet their sheer diversity and vast data landscape in time and space pose daunting computational challenges pertaining to the delineation of multiple simultaneously emerging lineages, the integration of spatial and temporal information, and the visualization of trajectories across large atlases with enough resolution to observe localized transitions. To tackle this intricacy, we introduce StaVia, a computational framework that synergizes multi-faceted single-cell data—spanning time-series data, spatial gene expression patterns, and directional trends from RNA velocity— with higher-order random walks that leverage the memory of cells’ past states. StaVia fuses this method with a cartographic “Atlas View” that offers intuitive graph visualization, simultaneously capturing the nuanced details of cellular development at single-cell resolution as well as the broader connectivity of cell lineages, avoiding common pitfalls of merged distinct trajectories or missed transitional states seen in existing methods which are all memoryless. Notably, we demonstrate that StaVia unlocks new insights into placode development, radial glia pluripotency during neurulation, and the transitions pivotal to these processes in a large-scale Zebrafish developmental atlas. StaVia also allows spatially aware cartography that captures relationships between cell populations based on their spatial location as well as their gene expressions in a MERFISH dataset - underscoring its potential to dissect complex biological landscapes in both spatial and temporal contexts.
Targeting PD-L1 in solid cancer with myeloid cells expressing a CAR-like immune receptor
Authors: Chen Kayla Myers , Grun Daniel , Gautier Brian , Venkatesha Shivaprasad , Maddox Michael , Zhang Ai-Hong , Andersen Peter
Published: February 2024

Myeloid cells are prevalent in solid cancers, but they frequently exhibit a pro-tumor phenotype, hindering cancer immunotherapy. Their abundance makes engineered myeloid cell therapy an intriguing approach to tackle challenges posed by solid cancers, such as tumor trafficking and infiltration along with tumor cell heterogenicity and immunosuppressive tumor microenvironment (TME). Solid cancers often upregulate the checkpoint molecule PD-L1 to evade immune responses. Thus, we devised an adoptive cell therapy strategy based on myeloid cells expressing a Chimeric Antigen Receptor (CAR)-like immune receptor (CARIR). The extracellular domain of CARIR is derived from the natural inhibitory receptor PD-1, while the intracellular domain(s) are derived from CD40 and/or CD3ξ. To assess the efficacy of CARIR-engineered myeloid cells, we conducted proof-of-principle experiments using co-culture and flow cytometry-based phagocytosis assaysin vitro. Additionally, we employed a fully immune-competent syngeneic tumor mouse model to evaluate the strategy’s effectivenessin vivo. Co-culturing CARIR-expressing human monocytic THP-1 cells with PD-L1+target cells lead to upregulation of the co-stimulatory molecule CD86 along with expression of proinflammatory cytokines TNF-1α and IL-1β. Moreover, CARIR expression significantly enhanced phagocytosis of multiple PD-L1+human solid tumor cell linesin vitro. Similar outcomes were observed with CARIR-expressing human primary macrophages. In experiments conducted on Balb/c mice bearing aggressive 4T1 mammary tumors, infusing murine myeloid cells expressing a murine version of CARIR significantly slowed tumor growth and prolonged survival. Taken together, our results demonstrate that adoptive transfer of PD-1 CARIR-engineered myeloid cells may be an effective strategy in treating PD-L1+solid tumors.

Graphic Abstract

In Brief

We described here an adoptive cell therapy approach employing PD-L1-specific CAR-like immune receptor (CARIR) modified myeloid cells as a potential immune cell therapy strategy for treating PD-L1+solid cancer.

CARIR expression directed human THP-1 macrophages to recognize PD-L1+target cells, which led to an upregulation of co-stimulatory molecule CD86 and production of proinflammatory cytokines TNF-α and IL-1β.

CARIR expression in human THP-1 macrophages had increased % phagocytosis and killing against PD-L1+tumor cellsin vitro.

Adoptive transfer of CARIR transduced myeloid cells in immunocompetent syngeneic mice with established aggressive 4T1 tumor significantly slowed tumor growth and prolonged survival.