bluuebunny/crossref_metadata_2025 huggingface dataset:
Monocyte-to-lymphocyte ratio as a determinant of survival in patients with gastric cancer undergoing gastrectomy: A cohort study
Authors: An Soomin , Eo Wankyu , Lee Sookyung , Lee Yeong-Ju
Published: June 2023

The monocyte-to-lymphocyte ratio (MLR) is an important prognostic determinant of various malignancies. However, the prognostic role of MLR in patients with gastric cancer undergoing gastrectomy remains unclear. Patients with stage I to III gastric cancer who underwent curative-intent gastric resection were enrolled in this study. Cox regression analysis was used to determine the independent variables for overall survival (OS) and disease-free survival (DFS). The established models were validated internally. Inter-model comparisons were performed using the integrated area under the receiver operating characteristic curve and the concordance index. Multivariate Cox regression analysis revealed that age, tumor–node–metastasis (TNM) stage, perineural invasion, serum albumin level, and MLR were prognostic factors for OS and DFS and constituted the full model. The full model was internally validated using calibration curves and decision curve analysis. The integrated area under the curve and concordance index of the full model outperformed those of TNM stage. The full model was a significant determinant of OS and DFS. Additionally, the full model was suggested to outperform TNM stage in predicting patient survival outcomes.
Simultaneous use of plug-assisted and coil-assisted retrograde transvenous obliteration for treating refractory hepatic encephalopathy in a patient with two portosystemic shunts: A case report
Authors: Ju Seong Gyeong , Lee Jae Myeong , Shim Jongjoon
Published: June 2023

Rationale:

Plug-assisted retrograde transvenous obliteration (PARTO) or coil-assisted retrograde transvenous obliteration (CARTO) are alternative treatments for gastric variceal bleeding and hepatic encephalopathy. Both procedures have fewer complications related to balloon rupture or sclerosing agents and are shorter than balloon-occluded retrograde transvenous obliteration. Herein, we report a case of PARTO and CARTO was performed simultaneously to treat refractory hepatic encephalopathy in a patient with 2 portosystemic shunts.

Patient concerns:

A 59-year-old man with alcoholic liver cirrhosis presented to the emergency room with mental change. At presentation, the patient’s plasma ammonia level was 340 μg/dL.

Diagnoses:

A computed tomography scan revealed perisplenic collateral vessels and 2 splenorenal shunts.

Intervention:

PARTO and CARTO were performed to treat hepatic encephalopathy via the 2 splenorenal shunts.

Outcomes:

A follow-up computed tomography scan showed the splenorenal shunt was successfully embolized using a vascular plug and coil. After 3 weeks, the patient’s plasma ammonia level decreased to 80 μg/dL, and repeated hospitalizations due to hepatic encephalopathy ceased.

Lessons:

Depending on the patient’s anatomy, PARTO and CARTO can be performed simultaneously and, similar to balloon-occluded retrograde transvenous obliteration, are useful for treating hepatic encephalopathy.
Case report of laryngeal infection by Clinostomum complanatum 24 days after ingestion of raw fish
Authors: Kim Hyun-Gyu , Han Ji-Hee , Kwak Ji-Yoon , Jeon Han Kyu , Lee Sang-Soo , Kim Hyun Jin , Song Seul Ki , Na Byoung-Kuk , Cha Ra-Ri
Published: June 2023

Rationale:

Clinostomum complanatum is a laryngeal fluke whose hosts include birds and mammals.[1] In humans, infection occurs accidentally during the consumption of raw freshwater fish.[1,2]

Patient concerns:

A 59-year-old female presented to our hospital with throat pain and globus sensation. The patient had been prescribed Proton Pump Inibitor for 3 weeks at another hospital. The patient continued the medication, but the discomfort persisted, and she was admitted to our hospital for further examination. The patient had eaten raw fish 24 days before, and the symptoms occurred after eating the raw fish. Endoscopy under sedation showed a fluke, with an approximate length of 8.0 mm and width of 3.2 mm, on the interaryepiglottic fold, with active motility on the mucosa.

Diagnosis interventions:

It was extracted from the larynx using biopsy forceps and identified as C complanatum.

Outcomes:

After the fluke was removed, symptoms improved, and the patient was discharged. The globus symptoms completely resolved at the last follow-up visit.

Lessons:

To the best of our knowledge, this is an endoscopically diagnosed and treated case of human infection by C complanatum in Korea after the longest period of infection. This suggests that C complanatum can survive for up to 3 weeks or more in the gastrointestinal tract. Endoscopy is a useful tool for the diagnosis and treatment of patients with atypical extraesophageal symptoms who do not respond to Proton Pump Inibitors.
G-POEM for gastroparesis: past, present and future
Authors: Vohra Ishaan , Gopakumar Harishankar , Adler Douglas G.
Published: June 2023

Purpose of review

Gastroparesis is a chronic debilitating condition with rising incidence and healthcare burden. As abdominal surgeries, diabetes, viral infections and autoimmune diseases become more prevalent, gastroparesis will continue to upsurge. Conservative treatment options for gastroparesis are limited by their side effects and short-term efficacy. Gastric endoscopic pyloromyotomy (G-POEM) is a novel incisionless endosurgical technique with excellent long-term outcomes. This review is in time, as the demand for G-POEM will continue to escalate.

Recent findings

This review encompasses the conservative and nonconservative treatment options for gastroparesis. G-POEM is a nonconservative treatment option, and the aim of this review is to discuss the variations in technique of G-POEM, short-term and long-term clinical efficacy of G-POEM and adverse events associated with it.

G-POEM has high technical and clinical success with minimal adverse events. G-POEM outcomes are similar or superior when compared with other treatment options for refractory gastroparesis. G-POEM is being widely adopted and will become the preferred treatment choice in patients with refractory gastroparesis.
Prediction of MYCN Gene Amplification in Pediatric Neuroblastomas: Development of a Deep Learning–Based Tool for Automatic Tumor Segmentation and Comparative Analysis of Computed Tomography–Based Radiomics Features Harmonization
Authors: Yeow Ling Yun , Teh Yu Xuan , Lu Xinyu , Srinivasa Arvind Channarayapatna , Tan Eelin , Tan Timothy Shao Ern , Tang Phua Hwee , KN Bhanu Prakash
Published: June 2023

Objective

MYCN oncogene amplification is closely linked to high-grade neuroblastoma with poor prognosis. Accurate quantification is essential for risk assessment, which guides clinical decision making and disease management. This study proposes an end-to-end deep-learning framework for automatic tumor segmentation of pediatric neuroblastomas and radiomics features-based classification of MYCN gene amplification.

Methods

Data from pretreatment contrast-enhanced computed tomography scans and MYCN status from 47 cases of pediatric neuroblastomas treated at a tertiary children's hospital from 2009 to 2020 were reviewed. Automated tumor segmentation and grading pipeline includes (1) a modified U-Net for tumor segmentation; (2) extraction of radiomic textural features; (3) feature-based ComBat harmonization for removal of variabilities across scanners; (4) feature selection using 2 approaches, namely, (a) an ensemble approach and (b) stepwise forward-and-backward selection method using logistic regression classifier; and (5) radiomics features-based classification of MYCN gene amplification using machine learning classifiers.

Results

Median train/test Dice score for modified U-Net was 0.728/0.680. The top 3 features from the ensemble approach were neighborhood gray-tone difference matrix (NGTDM) busyness, NGTDM strength, and gray-level run-length matrix (GLRLM) low gray-level run emphasis, whereas those from the stepwise approach were GLRLM low gray-level run emphasis, GLRLM high gray-level run emphasis, and NGTDM coarseness. The top-performing tumor classification algorithm achieved a weighted F1 score of 97%, an area under the receiver operating characteristic curve of 96.9%, an accuracy of 96.97%, and a negative predictive value of 100%. Harmonization-based tumor classification improved the accuracy by 2% to 3% for all classifiers.

Conclusion

The proposed end-to-end framework achieved high accuracy for MYCN gene amplification status classification.
FFRCT and Static Computed Tomography Myocardial Perfusion Imaging for Therapeutic Decision-making and Prognosis in Patients With Coronary Artery Disease
Authors: Li Su Yu , Zhong Jian , Qiao Hong Yan , Schoepf U. Joseph , Emrich Tilman , Butler W. Nicholas , Zuo Rui , Xue Yi , Liu Ya , Dai Li Yan , Zhou Chang Sheng , Lu Guang Ming , Tang Chun Xiang , Zhang Long Jiang
Published: June 2023

Purpose:

The purpose of this study was to investigate the effect of integrated evaluation of resting static computed tomography perfusion (CTP) and coronary computed tomography angiography (CCTA)–derived fractional flow reserve (FFRCT) on therapeutic decision-making and predicting major adverse cardiovascular events (MACEs) in patients with suspected coronary artery disease.

Materials and Methods:

In this post hoc analysis of a prospective trial of CCTA in patients assigned to either CCTA or CCTA plus FFRCT arms, 500 patients in the CCTA plus FFRCT arm were analyzed. Both resting static CTP and FFRCT were evaluated by using the conventional CCTA. Perfusion defects in the myocardial segments with ≥50% degree of stenosis in the supplying vessels were defined as resting static CTP positive, and any vessel with an FFRCT value of ≤0.80 was considered positive. Patients were divided into 3 groups: (1) negative CTP-FFRCT match group (resting static CTP-negative and FFRCT-negative group); (2) mismatch CTP-FFRCT group (resting static CTP-positive and FFRCT-negative or resting static CTP-negative and FFRCT-positive group); and (3) positive CTP-FFRCT match group (resting static CTP-positive and FFRCT-positive group). We compared the revascularization-to-invasive coronary angiography ratio and the MACE rate among 3 subgroups at 1- and 3-year follow-ups. The adjusted Cox hazard proportional model was used to assess the prognostic value of FFRCT and resting static CTP to determine patients at risk of MACE.

Results:

Patients in the positive CTP-FFRCT match group were more likely to undergo revascularization at the time of invasive coronary angiography compared with those in the mismatch CTP-FFRCT group (81.4% vs 57.7%, P=0.033) and the negative CTP-FFRCT match group (81.4% vs 33.3%, P=0.001). At 1- and 3-year follow-ups, patients in the positive CTP-FFRCT match group were more likely to have MACE than those in the mismatch CTP-FFRCT group (10.5% vs 4.2%, P=0.046; 35.6% vs 9.4%, P<0.001) and the negative CTP-FFRCT match group (10.5% vs 0.9%, P<0.001; 35.6% vs 5.4%, P<0.001). A positive CTP-FFRCT match was strongly related to MACE at 1-year (hazard ratio=8.06, P=0.003) and 3-year (hazard ratio=6.23, P<0.001) follow-ups.

Conclusion:

In patients with suspected coronary artery disease, the combination of FFRCT with resting static CTP could guide therapeutic decisions and have a better prognosis with fewer MACE in a real-world scenario.
CLINICAL CHARACTERISTICS AND PREDICTORS OF MORTALITY DIFFER BETWEEN PULMONARY AND ABDOMINAL SEPSIS
Authors: Ren Enfeng , Xiao Hongli , Li Jiebin , Yu Han , Liu Bo , Wang Guoxing , Sun Xuelian , Duan Meili , Hang Chenchen , Zhang Guoqiang , Wu Caijun , Li Fengjie , Zhang Haiyan , Zhang Yun , Guo Wei , Qi Wenjie , Yin Qin , Zhao Yunzhou , Xie Miaorong , Li Chunsheng
Published: June 2023

Background: Pulmonary sepsis and abdominal sepsis have pathophysiologically distinct phenotypes. This study aimed to compare their clinical characteristics and predictors of mortality. Methods: In this multicenter retrospective trial, 1,359 adult patients who fulfilled the Sepsis-3 criteria were enrolled and classified into the pulmonary sepsis or abdominal sepsis groups. Plasma presepsin was measured, and the scores of Acute Physiology and Chronic Health Evaluation (APACHE) II, Mortality in Emergency Department Sepsis (MEDS), and Simplified Acute Physiology Score (SAPS) II were calculated at enrollment. Data on 28-day mortality were collected for all patients. Results: Compared with patients with abdominal sepsis (n = 464), patients with pulmonary sepsis (n = 895) had higher 28-day mortality rate, illness severity scores, incidence of shock and acute kidney injury, and hospitalization costs. Lactate level and APACHE II and MEDS scores were independently associated with 28-day mortality in both sepsis types. Independent predictors of 28-day mortality included Pao
2/Fio
2 ratio (hazard ratio [HR], 0.998; P < 0.001) and acute kidney injury (HR, 1.312; P = 0.039) in pulmonary sepsis, and SAPS II (HR, 1.037; P = 0.017) in abdominal sepsis. A model that combined APACHE II score, lactate, and MEDS score or SAPS II score had the best area under the receiver operating characteristic curve in predicting mortality in patients with pulmonary sepsis or abdominal sepsis, respectively. Interaction term analysis confirmed the association between 28-day mortality and lactate, APACHE II score, MEDS score, SAPS II score, and shock according to the sepsis subgroups. The mortality of patients with pulmonary sepsis was higher than that of patients with abdominal sepsis among patients without shock (32.9% vs. 8.8%; P < 0.001) but not among patients with shock (63.7 vs. 48.4%; P = 0.118). Conclusions: Patients with pulmonary sepsis had higher 28-day mortality than patients with abdominal sepsis. The study identified sepsis subgroup-specific mortality predictors. Shock had a larger effect on mortality in patients with abdominal sepsis than in those with pulmonary sepsis.
Development, Deployment, and Implementation of a Machine Learning Surgical Case Length Prediction Model and Prospective Evaluation
Authors: Zaribafzadeh Hamed , Webster Wendy L. , Vail Christopher J. , Daigle Thomas , Kirk Allan D. , Allen Peter J. , Henao Ricardo , Buckland Daniel M.
Published: June 2023

Objective:

Implement a machine learning model using only the restricted data available at case creation time to predict surgical case length for multiple services at different locations.

Background:

The Operating Room (OR) is one of the most expensive resources in a health system, estimated to cost $22-133 per minute and generate about 40% of the hospital revenue. Accurate prediction of surgical case length is necessary for efficient scheduling and cost-effective utilization of the OR and other resources.

Methods:

We introduced a similarity cascade to capture the complexity of cases and surgeon influence on the case length and incorporated that into a gradient boosting machine learning model. The model loss function was customized to improve the balance between over- and under-prediction of the case length. A production pipeline was created to seamlessly deploy and implement the model across our institution.

Results:

The prospective analysis showed that the model output was gradually adopted by the schedulers and outperformed the scheduler-predicted case length in Aug-Dec 2022. In 33,815 surgical cases across outpatient and inpatient platforms, the operational implementation predicted 11.2% fewer under-predicted cases and 5.9% more cases within 20% of the actual case length compared with the schedulers and only over-predicted 5.3% more. The model assisted schedulers to predict 3.4% more cases within 20% of the actual case length and 4.3% fewer under-predicted cases.

Conclusions:

We created a unique framework that is being leveraged every day to predict surgical case length more accurately at case posting time and could be potentially utilized to deploy future machine learning models.
minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping
Authors: Liyanage Kisaru , Samarakoon Hiruna , Parameswaran Sri , Gamaarachchi Hasindu
Published: June 2023

minimap2is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. Whileminimap2is relatively fast, further speedup is desirable, especially when processing a multitude of large datasets. In this work, we presentminimap2-fpga, a hardware-accelerated version ofminimap2that speeds up the mapping process by integrating an FPGA kernel optimised for chaining. We demonstrate speed-ups in end-to-end run-time for data from both Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio).minimap2-fpgais up to 79% and 53% faster thanminimap2for ∼ 30× ONT and ∼ 50× PacBio datasets respectively, when mapping without base-level alignment. When mapping with base-level alignment,minimap2-fpgais up to 62% and 10% faster thanminimap2for ∼ 30× ONT and ∼ 50× PacBio datasets respectively. The accuracy is near-identical to that of originalminimap2for both ONT and PacBio data, when mapping both with and without base-level alignment.minimap2-fpgais supported on Intel FPGA-based systems (evaluations performed on an on-premise system) and Xilinx FPGA-based systems (evaluations performed on a cloud system). We also provide a well-documented library for the FPGA-accelerated chaining kernel to be used by future researchers developing sequence alignment software with limited hardware background.
Stem cell memory EBV-specific T cells control post-transplant lymphoproliferative disease and persistin vivo
Authors: Palianina Darya , Mietz Juliane , Stühler Claudia , Arnold Brice , Bantug Glenn , Münz Christian , Chijioke Obinna , Khanna Nina
Published: June 2023

Adoptive T cell therapy (ACT), the therapeutic transfer of defined T cell immunity to patients, offers great potential in the fight against different human diseases including difficult-to-treat viral infections but response rates are still suboptimal. Very early differentiated stem cell memory T cells (TSCM) have superior self-renewal, engraftment, persistence, and anti-cancer efficacy, but their potential for anti-viral ACT remains unknown. Here, we developed a clinically-scalable protocol for expanding Epstein-Barr virus (EBV)-specific TSCM-enriched T cells with high proportions of CD4+T cells and broad EBV antigen coverage. These cells showed tumor control in a xenograft model of post-transplant lymphoproliferative disorder (PTLD) and were superior to previous ACT protocols in terms of tumor infiltration,in vivoproliferation, persistence, proportion of functional CD4+T cells, and diversity of EBV antigen specificity. Thus, our new protocol may pave the way for the next generation of potent unmodified antigen-specific cell therapies for EBV-associated diseases, including tumors, and other indications.
Secundary Structure of Physicochemical Clustered Proteins
Authors: Nelson Igor
Published: June 2023

Diverse methods have been proposed for protein secondary structure prediction. However, such task still presents a challenge in bioinformatics. In this article various of these methods are implemented and analysed. First, a baseline using Support Vector Machine. Then a convolutional neural network (CNN), a Long Short-Term Memory (LSTM) and a strategy of Ensembling both of these methods. Lastly, a novel technique Secundary Structure of Physicochemical Clustered Proteins (SSPCP) is proposed, which combines multiple CNNs trained accordingly to a protein feature clustering and combined using a neural network. The rationale behind SSPCP is that amino acids from proteins which have similar physicochemical characteristics should have the same secondary structure prediction for similar amino acids, but amino acids from differing proteins might have different structures. All of these methods use as features PSSM matrices extracted from PSIBLAST. For performance evaluation, 25pdb dataset was split into training and validation and the same subsets were used on all these methods achieving the Q3 score of CNN: 70.11%, LSTM: 69.25%, Ensemble: 70.71%, SSPCP: 70.91%.

The experimental results show that the features extracted from clustering of physicochemical properties of proteins seem to improve the accuracy of highly specific CNN models for accurate protein secondary structure prediction.
Computational Assessment on Catalytic Activity of PET Hydrolase
Authors: Nelson Igor , Ramos Rafael
Published: June 2023

Background

PET hydrolase fromIdeonella sakaiensismight provide a response for PET accumulation in the environment. In this project some previously studied mutations were implemented and their performance was evaluated via computational methods with tools such as Modeller, HADDOCK, PyMOL and Gromacs. One possible mutation that could lead to improved catalytic activity was proposed.

Results

PET hydrolase DM S209F W130H and I179 provide interesting binding results with studied ligands, however a solution that combines both mutations does not seem viable, since the binding cleft becomes occluded. Following the same rationale, the triple mutant S209F W130H I179Q is proposed but instead leaves space in the binding cleft for ligand to enter and might bond with the oxygen at the ester group. The experiments conducted with triple mutant S209F W130H I179Q failed to beat HADDOCK score for DM, however its experimental results could still increase PET degradation. Results from surface charge may indicate an increase in stability and binding affinity for the protein.

Conclusions

Among models implemented, DM S209F W130H seems the best model studied regarding BHET or PET binding. Despite Protein Engineering is a complex process, computational tools might provide a way of studying binding sites of hypothetical proteins.

Supplementary information

Supplementary data is available in annexes.
Epidermal Growth Factor potentiates EGFR(Y992/1173)-mediated therapeutic response of triple negative breast cancer cells to cold atmospheric plasma-activated medium
Authors: Wang Peiyu , Zhou Renwu , Zhou Rusen , Yu Lihui , Zhao Liqian , Li Wenshao , Lin Jinyong , Rajapakse Aleksandra , Lee Chia-Hwa , Furnari Frank B. , Burgess Antony W. , Gunter Jennifer H. , Liu Gang , Ostrikov Kostya (Ken) , Richard Derek J , Simpson Fiona , Dai Xiaofeng , Thompson Erik W.
Published: June 2023

Cold atmospheric plasma (CAP) holds promise as a cancer-specific treatment that selectively kills basal-like breast cancer cells. We used CAP-activated media (PAM) to capture the multi-modal chemical species of CAP. Specific antibodies, small molecule inhibitors and CRISPR/Cas9 gene-editing approaches showed an essential role for receptor tyrosine kinases, especially epidermal growth factor (EGF) receptor, in mediating triple negative breast cancer (TNBC) cell responses to PAM. EGF also dramatically enhanced the sensitivity and specificity of PAM against TNBC cells. Site-specific phospho-EGFR analysis, signal transduction inhibitors and reconstitution of EGFR-depleted cells with EGFR-mutants confirmed the role of phospho-tyrosines 992/1173 and phospholipase C gamma signaling in upregulating levels of reactive oxygen species above the apoptotic threshold. EGF-triggered EGFR activation enhanced the sensitivity and selectivity of PAM effects on TNBC cells, such that a strategy based on the synergism of CAP and EGF therapy may provide new opportunities to improve the clinical management of TNBC.
Genetic determinants of plasma protein levels in the Estonian population
Authors: Kalnapenkis Anette , Jõeloo Maarja , Lepik Kaido , Kukuškina Viktorija , Kals Mart , Alasoo Kaur ,   Estonian Biobank Research Team, Mägi Reedik , Esko Tõnu , Võsa Urmo
Published: June 2023

The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing the effects of common genetic variations on the proteome. Here, we assessed the impact of the common and rare genetic variations as well as the copy number variants (CNVs) on 326 plasma proteins measured in up to 500 individuals. We identified 184cisand 94transsignals for 157 protein traits, which were further fine-mapped to credible sets for 101cisand 87transsignals for 151 proteins. Rare genetic variation contributed to the levels of 7 proteins, with 5cisand 14transassociations. CNVs were associated with the levels of 11 proteins (7cisand 5trans), examples including a 3q12.1 deletion acting as a hub for multipletransassociations; and a CNV overlappingNAIP, a sensor component of the NAIP-NLRC4 inflammasome which is affecting pro-inflammatory cytokine interleukin 18 levels. In summary, this work presents a comprehensive resource of genetic variation affecting the plasma protein levels and provides the interpretation of identified effects.
Solvent based fractional biosynthesis, phytochemical analysis and biological activity of silver nanoparticles obtained from extract ofSalvia moorcroftiana
Authors: Khan Maham , Khan Tariq , Aasim Muhammad , Sherazi Tauqir A. , Wahab Shahid , Zahoor Muhammad
Published: June 2023

Multi-drug resistant bacteria sometimes known as “superbugs” developed through overuse and misuse of antibiotics are determined to be sensitive to small concentrations of silver nanoparticles. Various methods and sources are under investigation for the safe and efficient synthesis of silver nanoparticles having effective antibacterial activity even at low concentrations. We used a medicinal plant namedSalvia moorcroftianato extract phytochemicals with antibacterial, antioxidant, and reducing properties. Three types of solvents; from polar to nonpolar, i.e., water, dimethyl sulfoxide (DMSO), and hexane, were used to extract the plant as a whole and as well as in fractions. The biosynthesized silver nanoparticles in all extracts (except hexane-based extract) were spherical, smaller than 20 nm, polydispersed (PDI ranging between 0.2 and 0.5), and stable with repulsive force of action (average zeta value = −18.55±1.17). The tested bacterial strains i.e.,Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Enterococcus faecalis were found to be sensitive to even small concentrations of AgNPs, especiallyP. aeruginosa.The antibacterial effect of these AgNPs was associated with their ability to generate reactive oxygen species. DMSO (in fraction) could efficiently extract antibacterial phytochemicals and showed activity against MDR bacteria (inhibition zone = 11-12 mm). Thus, the antibacterial activity of fractionated DMSO extract was comparable to that of AgNPs because it contained phytochemicals having solid antibacterial potential. Furthermore, AgNPs synthesized from this extract owned superior antibacterial activity. However, whole aqueous extract based AgNPs MIC was least (7-32 µg/mL) as compared to others.
Separate Gut Plasma Cell Populations Produce Autoantibodies Against Transglutaminase 2 and Transglutaminase 3 in Dermatitis Herpetiformis
Authors: Das Saykat , Stamnaes Jorunn , Kemppainen Esko , Hervonen Kaisa , Lundin Knut E.A. , Parmar Naveen , Jahnsen Frode L. , Jahnsen Jørgen , Lindfors Katri , Salmi Teea , Iversen Rasmus , Sollid Ludvig M.
Published: June 2023

Dermatitis herpetiformis (DH) is an inflammatory skin disorder often considered as an extraintestinal manifestation of celiac disease (CeD). Hallmarks of CeD and DH are autoantibodies to transglutaminase 2 (TG2) and transglutaminase 3 (TG3), respectively. DH patients have autoantibodies reactive with both transglutaminase enzymes. We here report that in DH both gut plasma cells and serum autoantibodies are specific for either TG2 or TG3 with no TG2-TG3 cross-reactivity. By generating monoclonal antibodies from TG3-specific duodenal plasma cells of DH patients, we define three conformational epitope groups. Both TG2-specific and TG3-specific gut plasma cells have few immunoglobulin mutations, and the two transglutaminase-reactive populations show distinct selection of certain heavy and light chain V-genes. Mass spectrometry analysis of TG3-specific serum IgA corroborates preferential usage ofIGHV2-5in combination withIGKV4-1. Collectively, our results demonstrate parallel induction of anti-TG2 and anti-TG3 autoantibody responses involving separate B-cell populations in DH patients.
A Spatial Transcriptomics based Label-Free Method for Assessment of Human Stem Cell Distribution and Effects in a Mouse Model of Lung Fibrosis
Authors: Park Jeongbin , Lee Dongjoo , Lee Jae Eun , Lee Daeseung , Song In Ho , Park Hyun Soo , Choi Hongyoon , Im Hyung-Jun
Published: June 2023

Recently, cell therapy has emerged as a promising treatment option for various disorders. Given the intricate mechanisms of action (MOA) and heterogenous distribution in target tissues inherent to cell therapy, it is necessary to develop more sophisticated, unbiased approaches to evaluate the distribution of administered cells and the molecular changes at a microscopic level. In this study, we present a label-free approach for assessing the tissue distribution of administered human mesenchymal stem cells (hMSCs) and their MOA, leveraging spatially resolved transcriptomics (ST) analysis. We administered hMSCs to mouse model of lung fibrosis and utilized ST to visualize the spatial distribution of hMSCs within the tissue. This was achieved by capitalizing on interspecies transcript differences between human and mouse. Furthermore, we could examine molecular changes associated with the spatial distribution of hMSCs. We suggest that our method has the potential to serve as an effective tool for various cell-based therapeutic agents.
The pan-epigenome of the symbiotic nitrogen fixing bacteriumSinorhizobium melilotiunravels unexpected variability of DNA-methylation profiles in closely related strains
Authors: Passeri Iacopo , Cangioli Lisa , Fondi Marco , Mengoni Alessio , Fagorzi Camilla
Published: June 2023

In prokaryotes, DNA methylation has been found to be involved in several mechanisms, such as DNA repair, DNA–protein interactions, gene expression, cell cycle progression and self-DNA recognition (the Restriction-Modification systems). Studies on representatives from the same bacterial species have found that genome-wide DNA methylation patterns can be highly variable and may affect phenotypic variation and gene transfer among closely related strains. However, broader evolutionary studies on such epigenomic variation in bacteria are still scarce.

Here, we addressed this point by performing an epigenomic analysis on 21 strains of the facultative plant symbiotic nitrogen-fixing alphaproteobacteriumSinorhizobium meliloti. Strains of these species are characterized by a divided (multipartite) genome structure, including a chromosome, a chromid and a (more recently acquired) megaplasmid. Since these strains display extensive genomic and phenotypic variation, they are good models to test evolutionary hypotheses on the relationships among epigenomic signatures, genome structure evolution and phenotypic switches.

Results showed the presence of a wide pan-epigenome with 16 DNA methylated motifs, including both 4mC and 6mA palindromic and nonpalindromic motifs. While 9 motifs have been found methylated by all strains, the remaining had differential methylation betweenS. melilotistrains, constituting a dispensable epigenome. Differences in frequency of methylation were found among replicons, with the megaplasmid and the additional plasmids displaying several motifs with different methylation frequency with respect to the chromosome and the chromid. Moreover, differences between coding, upstream and intergenic regions, were found, suggesting that DNA methylation at specific motifs may play a role in gene regulation and consequently in phenotypic variability among strains.

Altogether, our data indicate the presence of a large epigenomic diversity inS. meliloti, with epigenome signatures differing between replicons, reflecting their timing of evolutionary acquisition inS. melilotigenomes and suggesting a role of DNA methylation in the variability of gene expression among strains.
Global patterns in gene content of soil microbiomes emerge from microbial interactions
Authors: Crocker Kyle , Lee Kiseok Keith , Chakraverti-Wuerthwein Milena , Li Zeqian , Tikhonov Mikhail , Mani Madhav , Gowda Karna , Kuehn Seppe
Published: June 2023

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH;nargene abundances increase whilenapabundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
Multiple E3 ligases control tankyrase stability and function
Authors: Perrard Jerome , Smith Susan
Published: June 2023

Tankyrase 1 and 2 are ADP-ribosyltransferases that use NAD+as a substrate to catalyze polyADP-Ribose (PAR) onto themselves and their protein binding partners. Tankyrases have diverse cellular functions, ranging from resolution of telomere cohesion to activation of the Wnt/β-catenin signaling pathway. Robust and specific small molecule tankyrase inhibitors have been developed and are being investigated for cancer therapies. Tankyrase is regulated by the PAR-binding E3 ligase RNF146, which promotes K48-linked polyubiquitylation and proteasomal degradation of PARylated tankyrases and their PARylated partners. We have identified a novel interaction between tankyrase and a distinct class of E3 ligases: the RING-UIM (Ubiquitin-Interacting Motif) family. We show that RING-UIM E3 ligases (specifically RNF114 and RNF166) bind and stabilize monoubiquitylated tankyrase and promote K11-linked diubiquitylation. This action competes with RNF146-mediated K48-linked polyubiquitylation and degradation, leading to stabilization of tankyrase and to a subset of its binding partners, including Angiomotin, a protein that functions in cancer signaling pathways. Moreover, we identify multiple PAR-binding E3 ligases (in addition to RNF146) that promote ubiquitylation of tankyrase and induce stabilization or degradation. Discovery of this novel K11 ubiquitylation of tankyrase that opposes K48-mediated degradation along with identification of multiple PAR-binding E3 ligases that ubiquitylate tankyrase, provide new insights into mechanisms of tankyrase regulation and may offer new uses for tankyrase inhibitors in cancer therapy.
NIRis: A low-cost, versatile imaging system for NIR fluorescence detection of phototrophic cell colonies used in science and education
Authors: Franz Ole , Häkkänen Heikki , Kovanen Salla , Heikkilä-Huhta Kati , Nissinen Riitta , Ihalainen Janne A.
Published: June 2023

A variety of costly research-grade imaging devices are available for the detection of spectroscopic features. Here we present an affordable, open-source and versatile device, suitable for a range of applications. We provide the files to print the imaging chamber with commonly available 3D printers and instructions to assemble it with easily available hardware. The imager is suitable for rapid sample screening in research, as well as for educational purposes. We provide details and results for an already proven set-up which suits the needs of a research group and students interested in UV-induced near-infrared fluorescence detection of microbial colonies grown on Petri dishes. The fluorescence signal confirms the presence of bacteriochlorophyllain aerobic anoxygenic phototrophic bacteria (AAPB). The imager allows for the rapid detection and subsequent isolation of AAPB colonies on Petri dishes with diverse environmental samples. To this date, 15 devices have been build and more than 7000 Petri dishes have been analyzed for AAPB, leading to over 1000 new AAPB isolates. Parts can be modified depending on needs and budget. The latest version with automated switches and double band pass filters costs around 350€ in materials and resolves bacterial colonies with diameters of 0.5 mm and larger. The low cost and modular build allow for the integration in high school classes to educate students on light properties, fluorescence and microbiology. Computer-aided design of 3D-printed parts and programming of the employed Raspberry Pi computer could be incorporated in computer sciences classes. Students have been also inspired to do agar art with microbes. The device is currently used in seven different high schools in Finland. Additionally, a science education network of Finnish universities has incorporated it in its program for high school students. Video guides have been produced to facilitate easy operation and accessibility of the device.

Abstract Figure
TERRA R-loops connect and protect sister telomeres in mitosis
Authors: Sze Samantha , Bhardwaj Amit , Fnu Priyanka , Azarm Kameron , Mund Rachel , Ring Katherine , Smith Susan
Published: June 2023

Resolution of cohesion between sister telomeres in human cells depends on TRF1-mediated recruitment of the polyADP-ribosyltransferase, tankyrase to telomeres. In cells where tankyrase is deleted or the tankyrase binding site in TRF1 is mutated, sister telomeres remain cohered in mitosis. Human aged cells and ALT cancer cells naturally exhibit persistent telomere cohesion due to shortened telomeres that do not recruit sufficient TRF1/tankyrase for resolution. Persistent cohesion plays a protective role, but the mechanism by which sister telomeres remain cohered is not well understood. Here we show that telomere repeat containing RNA (TERRA) holds sister telomeres together through RNA-DNA hybrid (R-loop) structures. We show that a tankyrase-interacting partner, the RNA-binding protein C19orf43 is required for resolution of telomere cohesion and for repression of TERRA R-loops. Depletion of C19orf43 led to persistent telomere cohesion and an increase in TERRA R-loops. Overexpression of RNaseH1 counteracted persistent cohesion in C19orf43-depleted cells, as well as in aged and ALT cells. In fact, treatment of cohered telomeres in mitotic cells with RNaseH1 in situ, was sufficient to resolve sister telomere cohesion, confirming that RNA-DNA hybrids hold sister telomeres together. Consistent with a protective role for persistent telomere cohesion, depletion of C19orf43 in aged cells reduced DNA damage and significantly delayed replicative senescence. We propose that the inherent inability of shortened telomeres to recruit R-loop repressing machinery permits a controlled onset of senescence.
How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot
Authors: Sahoo Bibekananda , Mou Zongjun , Liu Wei , Dubyak George , Dai Xinghong
Published: June 2023

NINJ1 is a recently identified active executioner of plasma membrane rupture (PMR), a process previously thought to be a passive osmotic lysis event in lytic cell death. NINJ2 is a close paralog of NINJ1 but it failed to mediate PMR. By cryoEM, we found that both NINJ1 and NINJ2 were able to assemble into linear filament that binds strongly to lipids on one side but is water-soluble on the other side. The more-or-less straight NINJ1 filament was able to wrap around a membrane bleb and solubilize it from the plasma membrane to induce PMR; however, the intrinsically curved NINJ2 filament failed to do so, explaining its incapability of mediating PMR. We further demonstrated that binding to cholesterol at the inner leaflet of the lipid bilayer was responsible for the curving of the NINJ2 filament, while strong lipid binding at the outer leaflet was contributing to NINJ1’s capability of mediating PMR.
Cross population comparison of complex migration strategies in a declining oceanic seabird
Authors: O'Hanlon Nina Jayne , van Bemmelen Rob S A , Snell Katherine R S , Conway Greg J , Thaxter Chris B , Aiton Helen , Aiton David , Balmer Dawn E , Hanssen Sveinn Are , Calladine John R , Hammer Sjurdur , Harris Sarah J , Moe Borge , Schekkerman Hans , Tulp Ingrid , Humphreys Elizabeth M
Published: June 2023

Human-driven change is impacting ecosystems globally, with consequential declines in biodiversity. Long-distance migrants are particularly susceptible as they depend on conditions over large geographical scales and are more likely to experience a greater range of pressures. One long-distance migrant that has experienced substantial declines across the North-East Atlantic is the Arctic Skua Stercorarius parasiticus however, little is known about their migratory behaviour or the routes they undertake. We used geolocators with salt-water switches to track Arctic Skuas from four breeding populations. To investigate migration strategies, we developed a Hidden Markov Model approach that used saltwater immersion data to classify stopovers and transit flights. We found that the skuas used several discrete staging areas during their south and northbound migrations with an area of apparent high marine productivity in the mid-North Atlantic being of high importance. Extensive overlap of individuals from different breeding populations occurred in staging areas, resulting in weak spatial connectivity between breeding and staging areas, further emphasizing their importance. At the population-level, variation in migration strategies was driven by individuals from Svalbard, which is declining less than the other populations tracked. Relative location of wintering areas also influenced migration strategies, with individuals migrating further spending a smaller proportion of their migration at stopovers compared to those wintering closer, and instead employed a fly-and-forage strategy. Identifying the complex non-breeding distribution, weak migratory connectivity and highly conserved migration strategies of Arctic Skuas is a vital step to link how conditions experienced during migration influences population dynamics and to prioritise future research and conservation actions.
SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes
Authors: Schmacke Niklas A. , Mädler Sophia C. , Wallmann Georg , Metousis Andreas , Bérouti Marleen , Harz Hartmann , Leonhardt Heinrich , Mann Matthias , Hornung Veit
Published: June 2023

Forward genetic screening associates phenotypes with genotypes by randomly inducing mutations and then identifying those that result in phenotypic changes of interest. Here we presentspatiallyresolvedCRISPRscreening (SPARCS), a platform for microscopy-based genetic screening for spatial cellular phenotypes. SPARCS uses automated high-speed laser microdissection to physically isolate phenotypic variantsin situfrom virtually unlimited library sizes. We demonstrate the potential of SPARCS in a genome-wide CRISPR-KO screen on autophagosome formation in 40 million cells. Coupled to deep learning image analysis, SPARCS recovered almost all known macroautophagy genes in a single experiment and discovered a role for the ER-resident protein EI24 in autophagosome biogenesis. Harnessing the full power of advanced imaging technologies, SPARCS enables genome-wide forward genetic screening for diverse spatial phenotypesin situ.
Microstructured silk-fiber scaffolds with enhanced stretchability
Authors: Viola Martina , Cedillo-Servin Gerardo , van Genderen Anne Metje , Imhof Isabelle , Vena Paula , Mihajlovic Marko , Piluso Susanna , Malda Jos , Vermonden Tina , Castilho Miguel
Published: June 2023

Despite extensive research, current methods for creating three-dimensional (3D) silk fibroin (SF) scaffolds lack control over molecular rearrangement, particularly in the formation of β-sheet nanocrystals, as well as hierarchical fiber organization at both micro- and macroscale. In this study, we introduce a fabrication process based on electrowriting of aqueous SF-based solutions followed by post-processing using an aqueous solution of sodium dihydrogen phosphate (NaH2PO4). This approach enables hierarchical assembly of SF chains via β-sheet and α-helix formation. Moreover, this process allows for precise control over micro- and macro-architectures in microfiber scaffolds, enabling the creation of 3D flat and tubular macrogeometries with square-based and crosshatch microarchitectures, featuring inter-fiber distances of 400 µm and approximately 97% open porosity. Remarkably, the printed structures demonstrated restored β-sheet and α-helix structures, which imparted an elastic response of up to 20% deformation and the ability to support cyclic loading without plastic deformation. Furthermore, the printed constructs supportedin vitroadherence and growth of human conditionally immortalized proximal tubular epithelial cells and glomerular endothelial cells, with cell viability above 95%. These cells formed uniform, aligned monolayers that deposited their own extracellular matrix. These findings represent a significant development in fabricating organized SF scaffolds with unique fiber structures, mechanical and biological properties, making them highly promising for regenerative medicine applications.
The actin cytoskeleton plays multiple roles in structural color formation in butterfly wing scales
Authors: Lloyd Victoria J. , Burg Stephanie L. , Harizanova Jana , Hill Olivia , Enciso-Romero Juan , Cooper Rory L. , Flenner Silja , Longo Elena , Greving Imke , Nadeau Nicola J. , Parnell Andrew J.
Published: June 2023

Vivid structural colors in butterflies are caused by photonic nanostructures scattering light. Structural colors evolved for numerous biological signaling functions and have technological applications. Optically, such structures are well understood, however their developmentin vivoremains obscure. We show that actin is intimately involved in structural color formation in the butterflyHeliconius sara. Using comparisons between iridescent (structurally colored) and non-iridescent scales in adult and developingH. sara, we show that iridescent scales have more densely packed actin bundles leading to an increased density of reflective ridges. Super-resolution microscopy revealed that actin is repeatedly re-arranged in later development, when optical nanostructures are forming. Furthermore, actin perturbation experiments at these later developmental stages resulted in near total loss of structural color. Overall, this shows that actin plays vital templating roles during structural color formation in butterfly scales, with mechanisms potentially universal across lepidoptera.

Teaser

The actin cytoskeleton is essential for templating the optical nanostructures responsible for structural color production in butterfly scales.

Actin templates the reflective ridges on butterfly scales and is directly involved in forming the color-producing nanostructures within these