bluuebunny/crossref_metadata_2025_split huggingface dataset:
EasyChain: an IoT-friendly blockchain for robust and energy-efficient authentication
Authors: Bapatla Anand K. , Puthal Deepak , Mohanty Saraju P. , Yanambaka Venkata P. , Kougianos Elias 
Published: August 2023

The Internet of Everything (IoE) is a bigger picture that tries to fit the Internet of Things (IoT) that is widely deployed in smart applications. IoE brings people, data, processes, and things to form a network that is more connected and increases overall system intelligence. A further investigation of the IoE can really mean creating a distributed network focusing on edge computing instead of relying on the cloud. Blockchain is one of the recently distributed network technologies which by structure and operations provide data integrity and security in trust-less P2P networks such as IoE. Blockchain can also remove the need for central entities which is the main hurdle for the wide adoption of IoT in large networks. IoT “things” are resource-constrained both in power and computation to adopt the conventional blockchain consensus algorithms that are power and compute-hungry. To solve that problem, this paper proposes EasyChain, a blockchain that is robust along with running on a lightweight authentication-based consensus protocol that is known as Proof-of-Authentication (PoAh). This blockchain based on the lightweight consensus protocol replaces the power-hungry transaction, blocks validation steps, and provides ease of usage in resource-constrained environments such as IoE. The proposed blockchain is designed using the Python language for an easy understanding of the functions and increased ease of integration into IoE applications. The designed blockchain system is also deployed on a single-board computer to analyze its feasibility and scalability. The latency observed in the simulated and experimental evaluations is 148.89 ms which is very fast compared to the existing algorithms.
In vitro cross-talk between metastasis-competent circulating tumor cells and platelets in colon cancer: a malicious association during the harsh journey in the blood
Authors: Eslami-S Zahra , Cortés-Hernández Luis Enrique , Glogovitis Ilias , Antunes-Ferreira Mafalda , D’Ambrosi Silvia , Kurma Keerthi , Garima Françoise , Cayrefourcq Laure , Best Myron G. , Koppers-Lalic Danijela , Wurdinger Thomas , Alix-Panabières Catherine 
Published: August 2023

Background: Platelets are active players in hemostasis, coagulation and also tumorigenesis. The cross-talk between platelets and circulating tumor cells (CTCs) may have various pro-cancer effects, including promoting tumor growth, epithelial-mesenchymal transition (EMT), metastatic cell survival, adhesion, arrest and also pre-metastatic niche and metastasis formation. Interaction with CTCs might alter the platelet transcriptome. However, as CTCs are rare events, the cross-talk between CTCs and platelets is poorly understood. Here, we used our established colon CTC lines to investigate the colon CTC-platelet cross-talk in vitro and its impact on the behavior/phenotype of both cell types.Methods: We exposed platelets isolated from healthy donors to thrombin (positive control) or to conditioned medium from three CTC lines from one patient with colon cancer and then we monitored the morphological and protein expression changes by microscopy and flow cytometry. We then analyzed the transcriptome by RNA-sequencing of platelets indirectly (presence of a Transwell insert) co-cultured with the three CTC lines. We also quantified by reverse transcription-quantitative PCR the expression of genes related to EMT and cancer development in CTCs after direct co-culture (no Transwell insert) with platelets.Results: We observed morphological and transcriptomic changes in platelets upon exposure to CTC conditioned medium and indirect co-culture (secretome). Moreover, the expression levels of genes involved in EMT (p &lt; 0.05) were decreased in CTCs co-cultured with platelets, but not of genes encoding mesenchymal markers (FN1 and SNAI2). The expression levels of genes involved in cancer invasiveness (MYC, VEGFB, IL33, PTGS2, and PTGER2) were increased.Conclusion: For the first time, we studied the CTC-platelet cross-talk using our unique colon CTC lines. Incubation with CTC conditioned medium led to platelet aggregation and activation, supporting the hypothesis that their interaction may contribute to preserve CTC integrity during their journey in the bloodstream. Moreover, co-culture with platelets influenced the expression of several genes involved in invasiveness and EMT maintenance in CTCs.
Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique
Authors: Nowling Ronald J. , Njoya Kimani , Peters John G. , Riehle Michelle M. 
Published: August 2023

IntroductionVarious sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion. Some of these techniques rely on indirect markers such as histone modifications (ChIP-seq with histone antibodies) or chromatin accessibility (ATAC-seq, DNase-seq, FAIRE-seq), while other techniques use direct measures such as episomal assays measuring the enhancer properties of DNA sequences (STARR-seq) and direct measurement of the binding of transcription factors (ChIP-seq with transcription factor-specific antibodies). The activities of cis-regulatory elements such as enhancers, promoters, and repressors are determined by their sequence and secondary processes such as chromatin accessibility, DNA methylation, and bound histone markers.MethodsHere, machine learning models are employed to evaluate the accuracy with which cis-regulatory elements identified by various commonly used sequencing techniques can be predicted by their underlying sequence alone to distinguish between cis-regulatory activity that is reflective of sequence content versus secondary processes.Results and discussionModels trained and evaluated on D. melanogaster sequences identified through DNase-seq and STARR-seq are significantly more accurate than models trained on sequences identified by H3K4me1, H3K4me3, and H3K27ac ChIP-seq, FAIRE-seq, and ATAC-seq. These results suggest that the activity detected by DNase-seq and STARR-seq can be largely explained by underlying DNA sequence, independent of secondary processes. Experimentally, a subset of DNase-seq and H3K4me1 ChIP-seq sequences were tested for enhancer activity using luciferase assays and compared with previous tests performed on STARR-seq sequences. The experimental data indicated that STARR-seq sequences are substantially enriched for enhancer-specific activity, while the DNase-seq and H3K4me1 ChIP-seq sequences are not. Taken together, these results indicate that the DNase-seq approach identifies a broad class of regulatory elements of which enhancers are a subset and the associated data are appropriate for training models for detecting regulatory activity from sequence alone, STARR-seq data are best for training enhancer-specific sequence models, and H3K4me1 ChIP-seq data are not well suited for training and evaluating sequence-based models for cis-regulatory element prediction.
COVID-19 alters human microbiomes: a meta-analysis
Authors: Reuben Rine Christopher , Beugnon Rémy , Jurburg Stephanie D. 
Published: August 2023

IntroductionSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world’s population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential.MethodsWe performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries.ResultsOur reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma.DiscussionOur findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.
Prognostic value of soluble ST2 in AL and TTR cardiac amyloidosis: a multicenter study
Authors: Nicol Martin , Vergaro Giuseppe , Damy Thibaud , Kharoubi Mounira , Baudet Mathilde , Canuti Elena Sofia , Aimo Alberto , Castiglione Vincenzo , Emdin Michele , Royer Bruno , Harel Stephanie , Cohen-Solal Alain , Arnulf Bertrand , Logeart Damien 
Published: August 2023

BackgroundBoth light-chain (AL) amyloidosis and transthyretin (ATTR) amyloidosis are types of cardiac amyloidosis (CA) that require accurate prognostic stratification to plan therapeutic strategies and follow-ups. Cardiac biomarkers, e.g., N-terminal pro-B-type natriuretic peptide (NT-proBNP) and high-sensitivity cardiac troponin T (Hs-cTnT), remain the cornerstone of the prognostic assessment. An increased level of soluble suppression of tumorigenesis-2 (sST2) is predictive of adverse events [all-cause death and heart failure (HF) hospitalizations] in patients with HF. This study aimed to evaluate the prognostic value of circulating sST2 levels in AL-CA and ATTR-CA.MethodsWe carried out a multicenter study including 133 patients with AL-CA and 152 patients with ATTR-CA. During an elective outpatient visit for the diagnosis of CA, Mayo Clinic staging [NT-proBNP, Hs-cTnT, differential of free light chains (DFLCs)] and sST2 were assessed for all AL patients. Gillmore staging [including estimated glomerular filtration rate (eGFR), NT-proBNP] and Grogan staging (including NT-proBNP and Hs-cTnT) were assessed for TTR-CA patients.ResultsThe median age was 73 years [interquartile range (IQR) 61–81], and 53% were men. The endpoint was the composite of all-cause death or first HF-related hospitalization. The median follow-up was 20 months (IQR 3–34) in AL amyloidosis and 33 months (6–45) in TTR amyloidosis. The primary outcome occurred in 70 (53%) and 99 (65%) of AL and TTR patients, respectively. sST2 levels were higher in patients with AL-CA than in patients with ATTR-CA: 39 ng/L (26–80) vs. 32 ng/L (21–46), p &lt; 0.001. In AL-CA, sST2 levels predicted the outcome regardless of the Mayo Clinic score (HR: 2.16, 95% CI: 1.17–3.99, p &lt; 0.001). In TTR-CA, sST2 was not predictive of the outcome in multivariate models, including Gillmore staging and Grogan staging (HR: 1.17, CI: 95% 0.77–1.89, p = 0.55).ConclusionsST2 level is a relevant predictor of death and HF hospitalization in AL cardiac amyloidosis and adds prognostic stratification on top of NT-proBNP, Hs cTnT, and DFLC.
When NIPT meets WES, prenatal diagnosticians face the dilemma: genetic etiological analysis of 2,328 cases of NT thickening and follow-up of pregnancy outcomes
Authors: Ji Xueqi , Li Qiongmei , Qi Yiming , Wang Xingwang , Ding Hongke , Lu Jian , Zhang Yan , Yin Aihua 
Published: August 2023

Objective: To assess the performance of diverse prenatal diagnostic approaches for nuchal translucency (NT) thickening and to investigate the optimal prenatal screening or diagnostic action with a NT thickening of 95th percentile-3.50 mm.Methods: A retrospective analysis of 2,328 pregnancies with NT ≥ 95th percentile through ultrasound-guided transabdominal chorionic villus sampling (CVS), amniocentesis, or cordocentesis obtained clinical samples (chorionic villi, amniotic fluid, and cord blood), and real-time quantitative fluorescent PCR (QF-PCR), chromosome karyotyping (CS), chromosome microarray analysis (CMA), or whole exome sequencing (WES) were provided to identify genetic etiologies.Results: In this study, the incidence of chromosomal defects increased with NT thickness. When NT ≥ 6.5 mm, 71.43% were attributed to genetic abnormalities. The 994 gravidas with fetal NT thickening underwent short tandem repeat (STR), CS, and CMA. In 804 fetuses with normal karyotypes, CMA detected 16 (1.99%) extra pathogenic or likely pathogenic copy number variations (CNVs). The incremental yield of CMA was only 1.16% (3/229) and 3.37% (10/297) in the group with NT 95th percentile-2.99 mm and NT 3.0–3.49 mm, separately. Among the 525 gravidas with fetal NT thickening who underwent STR, CMA, and WES, the incremental yield of WES was 4.09% (21/513). In the group of NT 95th percentile-2.99 mm, there were no additional single-nucleotide variations (SNVs) detected in WES, while in 143 cases with NT of 3.0–3.49 mm, the incremental yield of WES was 5.59% (8/143).Conclusion: In the group of NT 95th percentile-3.0 mm, since chromosomal aneuploidy and chromosomal copy number variation were the primary causes and the additional contribution of CMA and WES was not significant, we recommend NIPT-Plus for pregnant women with a NT thickening of 95th percentile-3.0 mm first. In addition, comprehensive prenatal genetic testing involving CMA and WES can benefit pregnancies with NT thickening of 3.0–3.49 mm.
Suppression of neutrophils by sodium exacerbates oxidative stress and arthritis
Authors: Zlatar Leticija , Mahajan Aparna , Muñoz-Becerra Marco , Weidner Daniela , Bila Galyna , Bilyy Rostyslav , Titze Jens , Hoffmann Markus H. , Schett Georg , Herrmann Martin , Steffen Ulrike , Muñoz Luis E. , Knopf Jasmin 
Published: August 2023

IntroductionTypical Western diet, rich in salt, contributes to autoimmune disease development. However, conflicting reports exist about the effect of salt on neutrophil effector functions, also in the context of arthritis.MethodsWe investigated the effect of sodium chloride (NaCl) on neutrophil viability and functions in vitro, and in vivo employing the murine K/BxN-serum transfer arthritis (STA) model.Results and discussionThe effects of NaCl and external reactive oxygen species (H2O2) were further examined on osteoclasts in vitro. Hypertonic sodium-rich media caused primary/secondary cell necrosis, altered the nuclear morphology, inhibited phagocytosis, degranulation, myeloperoxidase (MPO) peroxidation activity and neutrophil extracellular trap (NET) formation, while increasing total ROS production, mitochondrial ROS production, and neutrophil elastase (NE) activity. High salt diet (HSD) aggravated arthritis by increasing inflammation, bone erosion, and osteoclast differentiation, accompanied by increased NE expression and activity. Osteoclast differentiation was decreased with 25 mM NaCl or 100 nM H2O2 addition to isotonic media. In contrast to NaCl, external H2O2 had pro-resorptive effects in vitro. We postulate that in arthritis under HSD, increased bone erosion can be attributed to an enhanced oxidative milieu maintained by infiltrating neutrophils, rather than a direct effect of NaCl.
Risk factors and outcome of Chimeric Antigen Receptor T-Cell patients admitted to Pediatric Intensive Care Unit: CART-PICU study
Authors: Caballero-Bellón Marina , Alonso-Saladrigues Anna , Bobillo-Perez Sara , Faura Anna , Arqués Laura , Rivera Cristina , Català Albert , Dapena Jose Luis , Rives Susana , Jordan Iolanda 
Published: August 2023

IntroductionChimeric antigen receptor (CAR)T-cell CD19 therapy is an effective treatment for relapsed/refractory B-cell acute lymphoblastic leukemia. It can be associated with life-threatening toxicities which often require PICU admission. Purpose: to describe clinical characteristics, treatment and outcome of these patients.MethodsProspective observational cohort study conducted in a tertiary pediatric hospital from 2016-2021. Children who received CAR-T admitted to PICU were included. We collected epidemiological, clinical characteristics, cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS), treatment, length of stay and mortality.ResultsCAR T-cells (4-1BB constructs) were infused in 59 patients. Twenty-four (40.7%) required PICU admission, length of stay was 4 days (IQR 3-6). Median age was 8.3 years (range 4-24). Patients admitted to PICU presented higher disease burden before infusion: 24% blasts in bone marrow (IQR 5-72) vs. 0 (0-6.9), p&lt;0.001. No patients with &lt;5% blasts were admitted to PICU. Main reasons for admissions were CRS (n=20, 83.3%) and ICANS (n=3, 12.5%). Fourteen patients (58.3%) required inotropic support, 14(58.3%) respiratory. Sixteen patients (66.6%) received tocilizumab, 10(41.6%) steroids, 6(25.0%) anakinra, and 5(20.8%) siltuximab. Ten patients (41.6%) presented neurotoxicity, six of them severe (ICANS 3-4). Two patients died at PICU (8.3%) because of refractory CRS-hemophagocytic lymphohistyocitosis (carHLH) syndrome. There were no significant differences in relapse rate after CAR-T in patients requiring PICU, it was more frequently CD19 negative (p=0.344).DiscussionPICU admission after CAR-T therapy was mainly due to CRS. Supportive treatment allowed effective management and high survival. Some patients presenting with carHLH, can suffer a fulminant course.
Decision trees for early prediction of inadequate immune response to coronavirus infections: a pilot study on COVID-19
Authors: Pisano Fabio , Cannas Barbara , Fanni Alessandra , Pasella Manuela , Canetto Beatrice , Giglio Sabrina Rita , Mocci Stefano , Chessa Luchino , Perra Andrea , Littera Roberto 
Published: August 2023

IntroductionFew artificial intelligence models exist to predict severe forms of COVID-19. Most rely on post-infection laboratory data, hindering early treatment for high-risk individuals.MethodsThis study developed a machine learning model to predict inherent risk of severe symptoms after contracting SARS-CoV-2. Using a Decision Tree trained on 153 Alpha variant patients, demographic, clinical and immunogenetic markers were considered. Model performance was assessed on Alpha and Delta variant datasets. Key risk factors included age, gender, absence of KIR2DS2 gene (alone or with HLA-C C1 group alleles), presence of 14-bp polymorphism in HLA-G gene, presence of KIR2DS5 gene, and presence of KIR telomeric region A/A.ResultsThe model achieved 83.01% accuracy for Alpha variant and 78.57% for Delta variant, with True Positive Rates of 80.82 and 77.78%, and True Negative Rates of 85.00% and 79.17%, respectively. The model showed high sensitivity in identifying individuals at risk.DiscussionThe present study demonstrates the potential of AI algorithms, combined with demographic, epidemiologic, and immunogenetic data, in identifying individuals at high risk of severe COVID-19 and facilitating early treatment. Further studies are required for routine clinical integration.
Characteristics of headaches attributed to SARS-CoV-2 vaccination and factors associated with its frequency and prolongation: a cross-sectional cohort study
Authors: Jameie Melika , Togha Mansoureh , Azizmohammad Looha Mehdi , Jafari Elham , Yazdan Panah Mohammad , Hemmati Nima , Nasergivehchi Somayeh 
Published: August 2023

BackgroundHeadache is the most frequent neurological adverse event following SARS-CoV-2 vaccines. We investigated the frequency, characteristics, and factors associated with post-vaccination headaches, including their occurrence and prolongation (≥ 48 h).MethodsIn this observational cross-sectional cohort study, retrospective data collected between April 2021–March 2022 were analyzed. Univariate and multivariate logistic regressions were used to evaluate the effect of clinicodemographic factors on the odds of post-vaccination headache occurrence and prolongation.ResultsOf 2,500 people who were randomly sent the questionnaire, 1822 (mean age: 34.49 ± 11.09, female: 71.5%) were included. Headache prevalence following the first (V1), second (V2), and third (V3) dose was 36.5, 23.3, and 21.7%, respectively (p &lt; 0.001). Post-vaccination headaches were mainly tension-type (46.5%), followed by migraine-like (36.1%). Headaches were mainly bilateral (69.7%), pressing (54.3%), moderate (51.0%), and analgesic-responsive (63.0%). They mainly initiated 10 h [4.0, 24.0] after vaccination and lasted 24 h [4.0, 48.0]. After adjusting for age and sex, primary headaches (V1: aOR: 1.32 [95%CI: 1.08, 1.62], V2: 1.64 [1.15, 2.35]), post-COVID-19 headaches (V2: 2.02 [1.26, 3.31], V3: 2.83 [1.17, 7.47]), headaches following the previous dose (V1 for V2: 30.52 [19.29, 50.15], V1 for V3: 3.78 [1.80, 7.96], V2 for V3: 12.41 [4.73, 35.88]), vector vaccines (V1: 3.88 [3.07, 4.92], V2: 2.44 [1.70, 3.52], V3: 4.34 [1.78, 12.29]), and post-vaccination fever (V1: 4.72 [3.79, 5.90], V2: 6.85 [4.68, 10.10], V3: 9.74 [4.56, 22.10]) increased the odds of post-vaccination headaches. Furthermore, while primary headaches (V1: 0.63 [0.44, 0.90]) and post-COVID-19 headaches (V1: 0.01 [0.00, 0.05]) reduced the odds of prolonged post-vaccination headaches, psychiatric disorders (V1: 2.58 [1.05, 6.45]), headaches lasting ≥48 h following the previous dose (V1 for V2: 3.10 [1.08, 10.31]), and migraine-like headaches at the same dose (V3: 5.39 [1.15, 32.47]) increased this odds.ConclusionPatients with primary headaches, post-COVID-19 headaches, or headaches following the previous dose, as well as vector-vaccine receivers and those with post-vaccination fever, were at increased risk of post-SARS-CoV-2-vaccination headaches. Primary headaches and post-COVID-19 headaches reduced the odds of prolonged post-vaccination headaches. However, longer-lasting headaches following the previous dose, migraine-like headaches at the same dose, and psychiatric disorders increased this odd.