bluuebunny/crossref_metadata_2025_split huggingface dataset:
A minimal Fanconi Anemia complex in Early Diverging Fungi
Authors: Barua Drishtee , Plecha Magdalena , Muszewska Anna 
Published: January 2024

Abstract

Background:
Fanconi Anemia (FA) pathway resolves DNA interstrand cross links (ICL), the phenomenon preventing separation of DNA strands and blocking transcription and replication. A typical FA pathway in humans consists of six protein complexes working in an orchestrated manner. This pathway was initially recognized only in vertebrates, but later on was also confirmed in other animals and speculated in fungi. For instance, FANCM, FANCL and FANCJ proteins are present in Saccharomyces cerevisiae but at the same time, their mechanism of interaction to resolve ICL is still unclear. Unlike Dikarya, early diverging fungi possess more traits shared with animals. In this work, we trace the evolutionary history of FA pathway genes across Opisthokonta. We scanned complete proteomes for FA-related homologs to establish their taxonomic distribution and analyzed their phylogenetic trees to trace evolutionary events. We checked transcription profiles of FA genes to test if they respond to environmental conditions and their genomic localizations for potential co-localization.
Results:
We identified fungal homologs of the activation and ID complex, 6 out of 13 core proteins, all of the endonucleases, and deubiquitination proteins. All fungal taxa lack FANCC, FANCF and FANCG proteins responsible for post-replication repair and chromosome stability in animals. The observed taxonomic distribution of the FA components can be attributed to a gradual degradation of the pathway from early diverging fungi (EDF) to Dikarya. One of the key differences is that EDF have the ID complex responsible for recruiting endonucleases to the site of DNA damage. Moreover, 20 out of 26 identified FA genes are not only expressed but also upregulated in response to different growth conditions. We observed that several genes encoding FA proteins are co-localized in fungal genomes which also could facilitate co-expression.
Conclusions:
Our results indicate that EDF share another ancestral eukaryotic trait with their sister evolutionary group, animals. A minimal FA pathway might still be functional in Mucoromycota with a gradual loss of components in Dikarya ancestors.
Clinical accuracy of instrument-based SARS-CoV-2 antigen diagnostic tests: A systematic review and meta-analysis
Authors: Manten Katharina , Katzenschlager Stephan , Brümmer Lukas E. , Schmitz Stephani , Gaeddert Mary , Erdmann Christian , Grilli Maurizio , Pollock Nira R. , Macé Aurélien , Erkosar Berra , Carmona Sergio , Ongarello Stefano , Johnson Cheryl C. , Sacks Jilian A. , Faehling Verena , Bornemann Linus , Weigand Markus A. , Denkinger Claudia M. , Yerlikaya Seda 
Published: January 2024

Abstract

Background
During the COVID-19 pandemic, antigen diagnostic tests were frequently used for screening, triage, and diagnosis because they are faster and less expensive than molecular tests, despite being less sensitive terms of analytical and clinical performance. Novel instrument-based antigen tests (iAg tests) hold the promise of outperforming their instrument-free, visually-read counterparts. Here, we provide a systematic review and meta-analysis of the SARS-CoV-2 iAg tests’ clinical accuracy.
Methods
We systematically searched MEDLINE (via PubMed), Web of Science, medRxiv, and bioRxiv for articles published before November 7th, 2022, evaluating the accuracy of iAg tests for SARS-CoV-2 detection. We performed a random effects meta-analysis to estimate sensitivity and specificity and used the QUADAS-2 tool to assess study quality and risk of bias.
Results
We compiled the data from 117 studies involving 95,181 individuals and assessing the clinical accuracy of 24 commercial COVID-19 iAg tests. The studies varied in risk of bias but showed high applicability. Of 24 iAg tests from 99 studies assessed in the meta-analysis, the pooled sensitivity and specificity compared to molecular testing of a paired NP swab sample were 76.7% (95% CI 73.5 to 79.7) and 98.4% (95% CI 98.0 to 98.7), respectively. Out of the eight tests with sufficient data for test-specific meta-analysis, only LumiraDx satisfied the WHO's sensitivity and specificity standards. Higher sensitivity was noted in individuals with high viral load (99.6% [95% CI 96.8 to 100] at Ct-level ≤ 20) and within the first week of symptom onset (84.6% [95% CI 78.2 to 89.3]), but did not differ between tests conducted as per manufacturer’s instructions and those conducted differently, or between point-of-care and lab-based testing.
Conclusion
Our study reveals that iAg tests' pooled sensitivity increases with lower Ct-values, a proxy for viral load, or within the first week of symptom onset, enabling reliable identification of most COVID-19 cases. While these characteristics are similar to those of instrument-free antigen diagnostics, different types of iAg tests might allow standardized result interpretation to curb human error, automated reporting, upscaling test runs or additional test-specific functions, such as the indication of antigen levels. Depending on their setup, they can be used at the point of care or at a laboratory with high-throughput.
An interface of genetically engineered human forebrain assembloids and polymeric nanofiber scaffolds for multiscale profiling of interneuron migration disorders
Authors: Rauthan Riya , Bharti Vishal , Agashe Atharva , Singh Praveen , York Harrison M , Nain Amrinder S. , Arumugam Senthil , Chakraborty Debojyoti 
Published: January 2024

Abstract

Neuronal migration is a fundamental process during brain development in which different types of neurons migrate from their place of origin to the site where they reside and make networks crucial for the formation of proper brain architecture and its overall function. Interneuron migration anomalies due to genetic or environmental perturbations can lead to malfunctions in the neural circuitry and are observed in the case of multiple neuropsychiatric conditions. Variants in Erb-B2 Receptor Tyrosine Kinase 4 (ERBB4), a member of Tyr protein kinase family and the epidermal growth factor receptor subfamily that functions as a surface receptor in interneurons, have been associated with human neurodevelopment disorders such as schizophrenia, epilepsy, and intellectual disability. Animal studies elucidate the function of ERBB4 in neuronal migration, synaptogenesis, synaptic transmission, and plasticity. However, the exact mechanistic role of ERBB4 in the migration of GABAergic cortical interneurons in humans is unidentified. In this study, we employ CRISPR/Cas9 to knockout ERBB4 in human induced pluripotent stem cells and report its effect on the phenotype and global gene expression upon deriving dorsal and ventral human forebrain identity organoids. Additionally, fluorescent reporter knock-in using CRISPR/Cas9 at an interneuron-specific marker in the same hiPS cell line allowed distinct temporal fluorescence expression in the derived ventral forebrain organoids allowing the capture of tangential migration of labeled cortical interneurons in intact fused 3D assembloids, to pinpoint the role of ERBB4 in migration and function of these neurons. To capture the changes in migration dynamics of individual ERBB4−/− interneurons in high resolution, we recapitulated the migration behaviour. on nanofiber scaffolds that mimic the in vivo fibrous extracellular microenvironment. Our findings uncover the function of ERBB4 in the context of human interneuron migration.
Structural and functional connectivity associations with anterior cingulate sulcal variability
Authors: Harper Luke , Strandberg Olof , Spotorno Nicola , Nilsson Markus , Lindberg Olof , Hansson Oskar , Santillo Alexander F 
Published: January 2024

Abstract

Background:
Sulcation of the anterior cingulate may be defined by presence of a paracingulate sulcus, a tertiary sulcus developing during the third gestational trimester with implications on cognitive function and disease.
Methods:
In this retrospective analysis we examine task-free resting state functional connectivity and diffusion-weighted tract segmentation data from a cohort of healthy adults (< 60-year-old, n = 129), exploring the impact of ipsilateral paracingulate sulcal presence on structural and functional connectivity.
Results:
Presence of a left paracingulate sulcus was associated with reduced fractional anisotropy in the left cingulum (P = 0.02) bundle and the peri-genual (P = 0.002) and dorsal (P = 0.03) but not the temporal cingulum bundle segments. Left paracingulate sulcal presence was associated with increased left peri-genual radial diffusivity (P = 0.003) and tract volume (P = 0.012). A significant, predominantly intraregional frontal component of altered resting state functional connectivity was identified in individuals possessing a left PCS (P = 0.01). Seed-based functional connectivity in pre-defined networks was not associated with paracingulate sulcal presence.
Conclusion:
These results identify a novel association between neurodevelopmentally derived sulcation and altered structural connectivity in a healthy adult population with implications for conditions where this variation is of interest. Furthermore, they provide evidence of a link between the structural and functional connectivity of the brain in the presence of a paracingulate sulcus which may be mediated by a highly connected local functional network reliant on short association fibres.
Effect of Mn(Ⅱ) from cathode on silicon anode in lithium-ion batteries (LIBs)
Authors: Zeng Yingying , Chen Haihui , Wenming Liao , Yi Xiuguang , Liu Limin 
Published: January 2024

Abstract

It is still unknown how dissolved manganese ions affect the silicon anode's electrochemical performance in thelithium-ion batteries (LIBs). In this study, the damage mechanism of Mn2+ to silicon electrode in LIBs was studied by adding Mn2+ into electrolyte system to simulate the electrochemical environment. Through the comparison between full cell and half cell, the mechanism of the capacity fading of silicon electrode is revealed. In order to compare the amount of SEI growth on silicon anode during the cycling, the heat flux of SEi was analyzed by DSC. Experiments show that the Mn2+ could make SEI more fragile, more easily break, and then accelerate the SEI thickening. So Mn2+ could reduce the coulomb efficiency and electrochemical capacity of the silicon anode. Electrochemical capacity of negative electrode in full cell decays much faster than that in half-cell environment, whose coulomb efficiency of full cell is only 32%, while that of the half cell is higher than 97%. In addition to the damage of the Mn2+ to silicon anode, the depletion of active lithium ion source in full cell is also an important reason for the rapid decline of electrochemical capacity.
Interplay of miR-542, miR-126, miR-143 and miR-26b withPI3K-AKT is a diagnostic signal and putative regulatory target in HPV-Positive Cervical Cancer
Authors: Rahimi-Moghaddam Akram , Ghorbanmehr Nassim , Gharbi Sedigheh , Nili Fatemeh , Korsching Eberhard 
Published: January 2024

Abstract
Human papillomavirus accounts for 99.7% of all cervical cancer cases worldwide. The viral oncoproteins alter normal cell signaling and gene expression, resulting in loss of cell cycle control and cancer development. Also, microRNAs (miRNAs) have been reported to play a critical role in cervical carcinogenesis. Especially these are not only appropriate targets for therapeutic intervention in cervical cancer but also early diagnostic signals. The given study tries to improve the sparse knowledge on miRNAs and their role in this physiological context. Deregulated miRNAs were extracted by analyzing the raw data of the GSE20592 dataset including 16 tumor/normal pairs of human cervical tissue samples. The GSE20592 dataset was quantified by a conservative strategy based on HTSeq and SALMON, followed by target prediction via TargetScan and miRDB. The comprehensive pathway analysis of all factors was performed using DAVID. The theoretical results were subject of a stringent experimental validation in a well-characterized clinical cohort of 30 tumor/normal pairs of cervical samples. The top 31 miRNAs and their 140 primary target genes were involved in the PI3K-AKT signaling pathway. MiR-21-3p and miR-1-3p showed a prominent regulatory role while MiR-542, miR-126, miR-143, and miR-26b are directly targeting both PI3k and AKT. This study provides insights into the regulation of PI3K-AKT signaling as an important inducer of cervical cancer and identified miR-542, miR-126, miR-143, and miR-26b as promising inhibitors of the PI3k-AKT pathway.
Studying the High Loading of Lead-Rubber Nanocomposites as Gamma Radiations Shielding.
Authors: Habeeb Salih Abbas 
Published: January 2024

Abstract
This research aims to prepare a polymeric composite material from styrene butadiene rubber (SBR) reinforced with lead nanoparticles (Pb-NPs) to make protective shields from gamma rays to protect the healthy tissues of cancer patients while receiving treatment and to protect workers in nuclear reactors and malignant tumors centers. The basic principle is to attenuate the gamma-ray photons emitted by the Cesium source (Cs137) with an energy of 663 keV. The basis for studying the shielding properties after adding the 50,100,150,200, and 300 phr lead nanoparticles. The results showed increased mass density, linear attenuation, and mass attenuation coefficients by 743.712%, 390.47%, and 180.95% with increasing loading levels of Pb-NPs in SBR composites up to 300 p h r. At the same time, the half-value and tenth-value layers decrease by 64% compared with the control sample (without Pb-NPs). The field emission scanning electron microscope (FE-SEM) images show good dispersion and homogeneity of these particles in the rubber matrix, and few agglomerations occur with increasing lead loading. The swelling ratio decreased by 199%, increasing the volume fraction of rubber and cross-link densities by about 7.1% and 14%, respectively. the addition of lead nanoparticles leads to enhanced crystalline properties.
Distinct longitudinal changes in EEG measures reflecting functional network disruption in ALS cognitive phenotypes
Authors: Metzger Marjorie , Dukic Stefan , McMackin Roisin , Giglia Eileen , Mitchell Matthew , Bista Saroj , Costello Emmet , Peelo Colm , Tadjine Yasmine , Sirenko Vladyslav , McManus Lara , Buxo Teresa , Fasano Antonio , Chipika Rangariroyashe , Pinto-Grau Marta , Schuster Christina , Heverin Mark , Coffey Amina , Broderick Michael , Iyer Parameswaran M. , Mohr Kieran , Gavin Brighid , Pender Niall , Bede Peter , Muthuraman Muthuraman , Hardiman Orla , Nasseroleslami Bahman 
Published: January 2024

Abstract

Amyotrophic lateral sclerosis (ALS) is characterised primarily by motor system degeneration, with clinical evidence of cognitive and behavioural change in up to 50% of cases. We have shown previously that resting-state EEG captures the dysfunction in motor and cognitive networks in ALS. However, the longitudinal development of the network-level dysfunction patterns remains unclear, particularly in the networks related to cognitive-behavioural functions. We examined 124 ALS individuals with 128-channel resting-state EEG recordings, categorised by cognitive impairment (ALSci, n = 27), behavioural impairment (ALSbi, n = 58), or non-impaired (ALSncbi, n = 53). Using linear mixed-effects models, we characterised the general and phenotype-specific longitudinal changes in brain network, and their association with cognitive performance, fine motor symptoms, and survival. We observed significant decline in \(\theta\)-band spectral power over time in the temporal region along with increased \({\gamma }_{l}\)-band power in the fronto-temporal region in the ALS group. ALSncbi participants showed widespread β-band synchrony decrease, while ALSci participants exhibited increased co-modulation correlated with verbal fluency decline. Longitudinal network-level changes varied between ALS subgroups, correlating with motor, cognitive, and behavioural decline. Spectral EEG measures can longitudinally track abnormal network patterns, serving as a candidate stratification tool for clinical trials and personalized treatments in ALS.
An ecophysiological basis for the assembly of Australian rainforest tree communities
Authors: Radford_Smith Julian , Weeren Ella Cathcart-van , Lai Hao Ran , Dwyer John 
Published: January 2024

Abstract
Understanding how past climate has filtered different tree strategies into communities is crucial for predicting how future climates will impact species and communities, yet few studies have used physiologically interpretable traits to explain the assembly of entire tree communities across large, continuous climatic gradients. To address this gap, we systematically surveyed rainforest tree communities across the Australian subtropics (spanning 600 to 2,500 mm rainfall yr− 1) and measured functional traits on 285 (91%) of the recorded tree species, including detailed measurements of xylem anatomy to describe species’ hydraulic strategies. The direction and shape of species’ occurrence trends across the regional moisture gradient were strongly related to their hydraulic strategies. Evergreen species with efficient hydraulics were more prevalent in mesic locations, while those with safer hydraulics favoured drier climates. Despite having extremely efficient hydraulics, deciduous species declined along the moisture gradient. At the dry end of the gradient, lower soil fertility increased the prevalence of very safe evergreen strategies and decreased the prevalence of deciduous species, relative to high-fertility sites. Overall, we reveal how climate, soil and biogeography have jointly filtered tree strategies into communities across the Australian subtropics, providing a general foundation for prediction under ongoing climate change.
Early-onset gasrtric cancer (review)
Authors: Pugaev D. M. , Lyubchenko L. N. , Ryabov A. B. , Kaprin A. D. 
Published: January 2024

Objective. Early-onset gastric cancer (EOGC) constitutes a serious medical and social problem. Early-onset gastric cancer accounts for approximately 6% of all malignant epithelial neoplasms.Material and Methods. We reviewed retrospective and prospective randomized trials using Medline and Elibrary databases.Results. The applied significance of the molecular genetic classifications consist in the formation of groups for evaluating prognosis of the disease using multifactorial analysis. This classification indicates that EOGC diagnosed at a locally advanced stage and primary dissemination is most often caused by GS (TCGA) and MSS/EMT(ACRG) subtypes and is characterized by mutations in CDH1, RhoA, CLDN18-ARHGAP genes. These changes are accompanied by the prevalence of diffuse histological type of gastric cancer according to the Lauren classification and ulcerated or infiltrative type according to the Borrmann classification (type III and IV) with the presence of high-grade adenocarcinoma with a signet ring cell component.Conclusion. Considering the aggressiveness of gastric cancer in young patients, who more frequently present with locally advanced and metastatic disease at the time of diagnosis, there is a need for increased cancer alertness among physicians of other specialties, early endoscopic controls to detect cancer at early stages and benefit from both surgical and multimodal treatment.
Combined modality treatment of early breast cancer. Literature review
Authors: Akhmetzyanov F. Sh. , Akhmetzyanova R. F. , Ankhimova L. E. , Gorshkova E. S. , Karamanyan A. V. 
Published: January 2024

The object of the study was to conduct a systematic literature review on combined modality treatment for early-stage breast cancer using postoperative and intraoperative radiation therapy, and consider new treatment approaches for early breast cancer.Material and Methods. The search for sources relevant to the review topic was carried out in the Medline, Cochrane Library, and Elibrary systems. A total of 905 studies on combination treatments for early breast cancer were identified, of which 43 were included in the review.Results. Data analysis showed that the rate of local relapses in early breast cancer was lower in patients who underwent breast-conserving surgery in combination with adjuvant radiation therapy than in patients without adjuvant radiation therapy. Research is ongoing on radiotherapy deintensification using intraoperative radiation therapy for patients at low risk of recurrence. Ongoing clinical trials support the omission of radiotherapy after breast-conserving surgery for elderly women with hormone receptor-positive early-stage breast cancer, who receive adjuvant endocrine therapy. Understanding the characteristics of the tumor process will allow us to personalize the treatment of patients with early breast cancer, reduce the risk of local relapses, and avoid unnecessary treatment-related complications.Conclusion. To improve survival in breast cancer patients is only possible by maximizing the tumor control. The effectiveness of adjuvant radiation therapy, which is an integral component in the combined modality treatment of early breast cancer, has been proven. However, third-generation studies discuss the feasibility of identifying a low-risk group of patients with a favorable clinical prognosis, who receive adequate endocrine therapy, and additional radiation do not provide a significant survival benefit.
Prediction of pancreatic fstula after pancreatoduodenectomy using machine learning
Authors: Suvorov V. A. , Panin S. I. , Kovalenko N. V. , Zhavoronkova V. V. , Postolov M. P. , Tolstopyatov S. E. , Bublikov A. E. , Panova A. V. , Popova V. O. 
Published: January 2024

Objective: to analyze the results of pancreatoduodenectomy (PD) and identify predictive risk factors for postoperative pancreatic fistula (PF) using machine learning (ML) technology.Material and Methods. A nonrandomized study of treatment outcomes in 128 patients, who underwent PD for periampullary carcinoma between 2018 and 2023, was conducted. To predict PF, the ML models based on the multilayer perceptron and binary logistic regression (BLR) in SPSS Statistics v.26, were used. The Receiver Operator Characteristics (ROC) analysis was used to assess the accuracy of the models. To compare ROC curves, the DeLong test was used.Results. Clinically significant PF occurred in 19 (14.8 %) patients (grade B according to ISGPS 2016 – in 16 (12.5 %), grade C – in 3 (2.3 %)). The data of 90 (70.3 %) patients were used to train the neural network, and 38 (29.7 %) were used to test the predictive model. In multivariate analysis, the predictors of PF were a comorbidity level above 7 points on the age-adjusted Charlson scale, a diameter of the main pancreatic duct less than 3 mm, and a soft pancreatic consistency. The diagnostic accuracy of the ML model estimated using the area under the ROC curve was 0.939 ± 0.027 (95 % CI: 0.859–0.998, sensitivity: 84.2 %, specificity; 96.3 %). The predictive model, which was developed using BLR, demonstrated lower accuracy: 0.918±0.039 (95 % CI: 0.842–0.994, sensitivity: 78.9 %, specificity: 94.5 %) (p=0.02).Conclusion. The use of machine learning technologies makes it possible to increase the probability of a correct prediction of the occurrence of pancreatic fistula after pancreatoduodenectomy.