bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pattern and repeatability of ascarid-specific antigen excretion through chicken faeces, and the diagnostic accuracy of coproantigen measurements as compared with McMaster egg counts and plasma and egg yolk antibody measurements in laying hens
Authors: Oladosu Oyekunle John , Hennies Mark , Stehr Manuel , Metges Cornelia C. , Gauly Matthias , Daş Gürbüz 
Published: June 2023

Abstract
Background
A coproantigen enzyme-linked immunosorbent assay (ELISA) has recently been proposed for detecting ascarid infections in chickens. The excretion pattern of ascarid antigens through chicken faeces and the consistency of measurements over the course of infections are currently unknown. This study evaluates the pattern and repeatability of worm antigen per gram of faeces (APG) and compares the diagnostic performance of the coproantigen ELISA with a plasma and egg yolk antibody ELISA and McMaster faecal egg counts (M-FEC) at different weeks post-infection (wpi).

Methods
Faecal, blood and egg yolk samples were collected from laying hens that were orally infected with a mix of Ascaridia galli and Heterakis gallinarum eggs (N = 108) or kept as uninfected controls (N = 71). Measurements including (a) APG using a coproantigen ELISA, (b) eggs per gram of faeces (EPG) using the McMaster technique and (c) ascarid-specific IgY in plasma and in egg yolks using an ascarid-specific antibody ELISA) were performed between wpi 2 and 18.

Results
Time-dependent significant differences in APG between infected and non-infected laying hens were quantified. At wpi 2 (t(164) = 0.66, P = 1.00) and 4 (t(164) = −3.09, P = 0.094) no significant differences were observed between the groups, whereas infected hens had significantly higher levels of APG than controls by wpi 6 (t(164) =  −6.74, P < 0.001). As indicated by a high overall repeatability estimate of 0.91 (CI = 0.89–0.93), APG could be measured consistently from the same individual. Compared to McMaster and antibody ELISA, coproantigen ELISA showed the highest overall diagnostic performance (area under curve, AUC = 0.93), although the differences were time-dependent. From wpi 6 to 18 coproantigen ELISA had an AUC > 0.95, while plasma IgY ELISA showed the highest diagnostic performance in wpi 2 (AUC = 0.95). M-FEC had the highest correlation with total worm burden, while APG had highest correlations with weights and lengths of A. galli.

Conclusion
Ascarid antigen excretion through chicken faeces can be measured with high accuracy and repeatability using a coproantigen ELISA. The antigen excretion increases over time, and is associated with worm maturation, particularly with the size of A. galli. Our results suggest the necessity of complementary use of different diagnostic tools for a more accurate diagnosis of infections.

Graphical Abstract
Identification of the immune-related biomarkers in Behcet’s disease by plasma proteomic analysis
Authors: Liu Huan , Zhang Panpan , Li Fuzhen , Xiao Xiao , Zhang Yinan , Li Na , Du Liping , Yang Peizeng 
Published: June 2023

Abstract
Background
This study aimed to investigate the expression profile of immune response-related proteins of Behcet’s disease (BD) patients and identify potential biomarkers for this disease.

Methods
Plasma was collected from BD patients and healthy controls (HC). Immune response-related proteins were measured using the Olink Immune Response Panel. Differentially expressed proteins (DEPs) were used to construct prediction models via five machine learning algorithms: naive Bayes, support vector machine, extreme gradient boosting, random forest, and neural network. The prediction performance of the five models was assessed using the area under the curve (AUC) value, recall (sensitivity), specificity, precision, accuracy, F1 score, and residual distribution. Subtype analysis of BD was performed using the consensus clustering method.

Results
Proteomics results showed 43 DEPs between BD patients and HC (P < 0.05). These DEPs were mainly involved in the Toll-like receptor 9 and NF-κB signaling pathways. Five models were constructed using DEPs [interleukin 10 (IL10), Fc receptor like 3 (FCRL3), Mannan-binding lectin serine peptidase 1 (MASP1), NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor (NF2), FAM3 metabolism regulating signaling molecule B (FAM3B), and O-6-methylguanine-DNA methyltransferase (MGMT)]. Among these models, the neural network model showed the best performance (AUC = 0.856, recall: 0.692, specificity: 0.857, precision: 0.900, accuracy: 0.750, F1 score: 0.783). BD patients were divided into two subtypes according to the consensus clustering method: one with high disease activity in association with higher expression of tripartite motif-containing 5 (TRIM5), SH2 domain-containing 1A (SH2D1A), phosphoinositide-3-kinase adaptor protein 1 (PIK3AP1), hematopoietic cell-specific Lyn substrate 1 (HCLS1), and DNA fragmentation factor subunit alpha (DFFA) and the other with low disease activity in association with higher expression of C–C motif chemokine ligand 11 (CCL11).

Conclusions
Our study not only revealed a distinctive immune response-related protein profile for BD but also showed that IL10, FCRL3, MASP1, NF2, FAM3B, and MGMT could serve as potential immune biomarkers for this disease. Additionally, a novel molecular disease classification model was constructed to identify subsets of BD.
An early prediction model for gestational diabetes mellitus based on metabolomic biomarkers
Authors: Razo-Azamar Melissa , Nambo-Venegas Rafael , Meraz-Cruz Noemí , Guevara-Cruz Martha , Ibarra-González Isabel , Vela-Amieva Marcela , Delgadillo-Velázquez Jaime , Santiago Xanic Caraza , Escobar Rafael Figueroa , Vadillo-Ortega Felipe , Palacios-González Berenice 
Published: June 2023

Abstract
Background
Gestational diabetes mellitus (GDM) represents the main metabolic alteration during pregnancy. The available methods for diagnosing GDM identify women when the disease is established, and pancreatic beta-cell insufficiency has occurred.The present study aimed to generate an early prediction model (under 18 weeks of gestation) to identify those women who will later be diagnosed with GDM.

Methods
A cohort of 75 pregnant women was followed during gestation, of which 62 underwent normal term pregnancy and 13 were diagnosed with GDM. Targeted metabolomics was used to select serum biomarkers with predictive power to identify women who will later be diagnosed with GDM.

Results
Candidate metabolites were selected to generate an early identification model employing a criterion used when performing Random Forest decision tree analysis. A model composed of two short-chain acylcarnitines was generated: isovalerylcarnitine (C5) and tiglylcarnitine (C5:1). An analysis by ROC curves was performed to determine the classification performance of the acylcarnitines identified in the study, obtaining an area under the curve (AUC) of 0.934 (0.873–0.995, 95% CI). The model correctly classified all cases with GDM, while it misclassified ten controls as in the GDM group. An analysis was also carried out to establish the concentrations of the acylcarnitines for the identification of the GDM group, obtaining concentrations of C5 in a range of 0.015–0.25 μmol/L and of C5:1 with a range of 0.015–0.19 μmol/L.

Conclusion
Early pregnancy maternal metabolites can be used to screen and identify pregnant women who will later develop GDM. Regardless of their gestational body mass index, lipid metabolism is impaired even in the early stages of pregnancy in women who develop GDM.
SETD5 haploinsufficiency affects mitochondrial compartment in neural cells
Authors: Zaghi Mattia , Longo Fabiana , Massimino Luca , Rubio Alicia , Bido Simone , Mazzara Pietro Giuseppe , Bellini Edoardo , Banfi Federica , Podini Paola , Maltecca Francesca , Zippo Alessio , Broccoli Vania , Sessa Alessandro 
Published: June 2023

AbstractBackgroundNeurodevelopmental disorders (NDDs) are heterogeneous conditions due to alterations of a variety of molecular mechanisms and cell dysfunctions.SETD5haploinsufficiency leads to NDDs due to chromatin defects. Epigenetic basis of NDDs has been reported in an increasing number of cases while mitochondrial dysfunctions are more common within NDD patients than in the general population.MethodsWe investigated in vitro neural stem cells as well as the brain of theSetd5haploinsufficiency mouse model interrogating its transcriptome, analyzing mitochondrial structure, biochemical composition, and dynamics, as well as mitochondrial functionality.ResultsMitochondrial impairment is facilitated by transcriptional aberrations originated by the decrease of the SETD5 enzyme. Low levels of SETD5 resulted in fragmented mitochondria, reduced mitochondrial membrane potential, and ATP production both in neural precursors and neurons. Mitochondria were also mislocalized in mutant neurons, with reduced organelles within neurites and synapses.LimitationsWe found several defects in the mitochondrial compartment; however, we can only speculate about their position in the hierarchy of the pathological mechanisms at the basis of the disease.ConclusionsOur study explores the interplay between chromatin regulation and mitochondria functions as a possible important aspect ofSETD5-associated NDD pathophysiology. Our data, if confirmed in patient context, suggest that the mitochondrial activity and dynamics may represent new therapeutic targets for disorders associated with the loss of SETD5.
Features of a FAIR vocabulary
Authors: Xu Fuqi , Juty Nick , Goble Carole , Jupp Simon , Parkinson Helen , Courtot Mélanie 
Published: June 2023

AbstractBackgroundThe Findable, Accessible, Interoperable and Reusable(FAIR) Principles explicitly require the use of FAIR vocabularies, but what precisely constitutes a FAIR vocabulary remains unclear. Being able to define FAIR vocabularies, identify features of FAIR vocabularies, and provide assessment approaches against the features can guide the development of vocabularies.ResultsWe differentiate data, data resources and vocabularies used for FAIR, examine the application of the FAIR Principles to vocabularies, align their requirements with the Open Biomedical Ontologies principles, and propose FAIR Vocabulary Features. We also design assessment approaches for FAIR vocabularies by mapping the FVFs with existing FAIR assessment indicators. Finally, we demonstrate how they can be used for evaluating and improving vocabularies using exemplary biomedical vocabularies.ConclusionsOur work proposes features of FAIR vocabularies and corresponding indicators for assessing the FAIR levels of different types of vocabularies, identifies use cases for vocabulary engineers, and guides the evolution of vocabularies.
Inter-rater and intra-rater agreement of [99mTc]-labelled NM-01, a single-domain programmed death-ligand 1 (PD-L1) antibody, using quantitative SPECT/CT in non-small cell lung cancer
Authors: Hughes Daniel Johnathan , Chand Gitasha , Johnson Jessica , Bailey Damion , Adamson Kathryn , Goh Vicky , Cook Gary J. R. 
Published: May 2023

Abstract
Background
Immune checkpoint inhibitors, including those against programmed cell death protein-1 (PD-1) or its ligand (PD-L1), are routinely used to treat non-small cell lung cancer (NSCLC). PD-L1 is a validated prognostic and predictive immunohistochemical biomarker of anti-PD-1/PD-L1 therapy but displays temporospatial heterogeneity of expression. Non-invasive radiopharmaceutical techniques, including technetium-99m [99mTc]-labelled anti-PD-L1 single-domain antibody (NM-01) SPECT/CT, have the potential to improve the predictive value of PD-L1 assessment. This study aims to determine the inter- and intra-rater agreement of the quantitative measurement of [99mTc]NM-01 SPECT/CT in NSCLC.

Methods
Participants (n = 14) with untreated advanced NSCLC underwent [99mTc]NM-01 SPECT/CT at baseline (n = 3) or at baseline plus 9-week follow-up (n = 11). [99mTc]NM-01 uptake (of primary lung, lymph node, thoracic and distant metastases, and healthy reference tissues) was measured using SUVmax and malignant lesion-to-blood pool ratios with Siemens xSPECT Broad Quantification software by three independent raters. Intraclass correlation coefficients (ICC) were calculated and Bland–Altman plot analysis performed to determine inter- and intra-rater agreement.

Results
There was excellent inter-rater agreement of manual freehand SUVmax scores of primary lung tumour (T; n = 25; ICC 1.00; 95% CI 0.99–1.00), individual lymph node metastases (LN; n = 56; ICC 0.97; 95% CI 0.95–0.98), thoracic metastases (ThMet; n = 9; ICC 0.94; 95% CI 0.83–0.99) and distant metastases (DisMet; n = 21; ICC 0.91; 95% CI 0.83–0.96). The inter-rater ICCs of tumour-to-blood pool (T:BP), LN:BP, ThMet:BP and DisMet:BP measures of [99mTc]NM-01 uptake also demonstrated good or excellent agreement. Manual freehand scoring of T, LN, ThMet, DisMet and their ratios using [99mTc]NM-01 SPECT/CT following a 28-day interval was consistent for all raters with good or excellent intra-rater agreement demonstrated (ICCs range 0.86–1.00).

Conclusion
Quantitative assessment of [99mTc]NM-01 SPECT/CT in NSCLC, using SUVmax of malignant primary or metastatic lesions and their ratios with healthy reference tissues, demonstrated good or excellent inter- and intra-rater agreement in this study. Further validation with ongoing and future larger cohort studies is now warranted.

Clinical trial registration
ClinicalTrials.gov identifier no. NCT04436406 (registered 18th June 2020; available at https://clinicaltrials.gov/ct2/show/NCT04436406) and NCT04992715 (registered 5th August 2021; available at https://clinicaltrials.gov/ct2/show/NCT04992715).
Examination of sulfate resistance of nano-alumina added ordinary Portland cement paste, focusing on the two different crystallinity of nano-aluminas
Authors: Yu Juan , Sim Sungwon , Song Haemin , Kim Dohoon , Jang Kyungcheol , Jeon Dongho , Cho Seung , Oh Jae Eun 
Published: June 2023

AbstractThis study examined the influence of the crystallinity of added nano-alumina on the sulfate resistance of ordinary Portland cement (OPC) paste. Two crystalline types of nano-aluminas (α-and γ-phase) were incorporated in cement pastes, which were exposed to sulfate solution. In the results, both paste samples having α- and γ-phase aluminas had accelerated compressive strength loss and increased length expansion compared to the sample without alumina addition. In particular, the rapidly decreased dynamic elastic modulus of the nano-alumina added samples postulates the greatly increased internal stress likely by the increased formation of volume expansive reaction products, such as ettringite, which was supported by the XRD and TG results. The greater ettringite formation in the nano-alumina added samples was likely due to reactive AH3 (=Al(OH)3) gel formation as the higher consumption degree of portlandite in the alumina added samples indirectly indicates the active AH3 gel formation, resulting in additional ettringite formation from the reaction of AH3 with Na2SO4 solution. A further degree of sulfate attack was observed in the γ-alumina added sample for the long-term Na2SO4 exposure (180 days) mainly due to the greater degree of gypsum formation inducing more internal expansive stress compared to the α-alumina added sample.
Better richer than environmentally friendly? Describing preferences toward and factors affecting precision agriculture adoption in Italy
Authors: Troiano Stefania , Carzedda Matteo , Marangon Francesco 
Published: May 2023

AbstractPrecision agriculture is expected to support and strengthen the sustainability of food production. In spite of the demonstrated benefits of the application of Information Technology to improve agricultural practices, such as yield increase and input reduction, in Italy its adoption still lags behind. In order to understand limits of and perspectives on the adoption of such technologies, we conducted an explorative study. A survey with a choice experiment was carried out in Italy among 471 farmers and people interested in agricultural machinery and technologies. The results highlight how specific factors, such as excessive costs and lack of incentive policies, may limit the spread of precision agriculture. Conversely, the provision of adequate technical support would likely favor its adoption. Furthermore, latent class modeling was used to identify three segments of potential buyers: sustainability seekers; precision agriculture best features supporters; low emissions fans. Potential policy and market implications of this explorative study are discussed in the conclusion.
Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities
Authors: Liu Yuan , Daniel Scott G. , Kim Hye-Eun , Koo Hyun , Korostoff Jonathan , Teles Flavia , Bittinger Kyle , Hwang Geelsu 
Published: June 2023

Abstract
Background
Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by the synergistic polymicrobial interaction between the cariogenic bacterium, Streptococcus mutans, and an opportunistic fungal pathogen, Candida albicans. Although cross-sectional studies reveal their important roles in caries development, these exhibit limitations in determining the significance of these microbial interactions in the pathogenesis of the disease. Thus, it remains unclear the mechanism(s) through which the cross-kingdom interaction modulates the composition of the plaque microbiome. Here, we employed a novel ex vivo saliva-derived microcosm biofilm model to assess how exogenous pathogens could impact the structural and functional characteristics of the indigenous native oral microbiota.

Results
Through shotgun whole metagenome sequencing, we observed that saliva-derived biofilm has decreased richness and diversity but increased sugar-related metabolism relative to the planktonic phase. Addition of S. mutans and/or C. albicans to the native microbiome drove significant changes in its bacterial composition. In addition, the effect of the exogenous pathogens on microbiome diversity and taxonomic abundances varied depending on the sugar type. While the addition of S. mutans induced a broader effect on Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog abundances with glucose/fructose, S. mutans-C. albicans combination under sucrose conditions triggered unique and specific changes in microbiota composition/diversity as well as specific effects on KEGG pathways. Finally, we observed the presence of human epithelial cells within the biofilms via confocal microscopy imaging.

Conclusions
Our data revealed that the presence of S. mutans and C. albicans, alone or in combination, as well as the addition of different sugars, induced unique alterations in both the composition and functional attributes of the biofilms. In particular, the combination of S. mutans and C. albicans seemed to drive the development (and perhaps the severity) of a dysbiotic/cariogenic oral microbiome. Our work provides a unique and pragmatic biofilm model for investigating the functional microbiome in health and disease as well as developing strategies to modulate the microbiome.
Teaching computing for complex problems in civil engineering and geosciences using big data and machine learning: synergizing four different computing paradigms and four different management domains
Authors: Babović Zoran , Bajat Branislav , Barac Dusan , Bengin Vesna , Đokić Vladan , Đorđević Filip , Drašković Dražen , Filipović Nenad , French Stephan , Furht Borko , Ilić Marija , Irfanoglu Ayhan , Kartelj Aleksandar , Kilibarda Milan , Klimeck Gerhard , Korolija Nenad , Kotlar Miloš , Kovačević Miloš , Kuzmanović Vladan , Lehn Jean-Marie , Madić Dejan , Marinković Marko , Mateljević Miodrag , Mendelson Avi , Mesinger Fedor , Milovanović Gradimir , Milutinović Veljko , Mitić Nenad , Nešković Aleksandar , Nešković Nataša , Nikolić Boško , Novoselov Konstantin , Prakash Arun , Protić Jelica , Ratković Ivan , Rios Diego , Shechtman Dan , Stojadinović Zoran , Ustyuzhanin Andrey , Zak Stan 
Published: May 2023

AbstractThis article describes a teaching strategy that synergizes computing and management, aimed at the running of complex projects in industry and academia, in the areas of civil engineering, physics, geosciences, and a number of other related fields. The course derived from this strategy includes four parts: (a) Computing with a selected set of modern paradigms—the stress is on Control Flow and Data Flow computing paradigms, but paradigms conditionally referred to as Energy Flow and Diffusion Flow are also covered; (b) Project management that is holistic—the stress is on the wide plethora of issues spanning from the preparation of project proposals, all the way to incorporation activities to follow after the completion of a successful project; (c) Examples from past research and development experiences—the stress is on experiences of leading experts from academia and industry; (d) Student projects that stimulate creativity—the stress is on methods that educators could use to induce and accelerate the creativity of students in general. Finally, the article ends with selected pearls of wisdom that could be treated as suggestions for further elaboration.
Slight pelvic obliquity is normal in a healthy population: a cross‐sectional study
Authors: Moharrami Alireza , Mirghaderi Peyman , Hoseini Zare Nima , Moazen‐Jamshidi Mir Mansour , Ebrahimian Mazaher , Mortazavi Seyed Mohammad Javad 
Published: May 2023

AbstractPurposePelvic obliquity (PO) has not been extensively investigated, and there is no gold standard for measurement. The PO is essential for surgeons in planning hip arthroplasty, which includes the restoration of leg length discrepancy (LLD). We aimed to establish a normative range of PO angles by measuring healthy individuals without musculoskeletal disorders.MethodsOur study included 134 consecutive cases (70 females) referred to our institution between April 2020 and September 2021 for non‐orthopedic problems. Patients were screened for normal gait and posture using the visual observation method (VOM) and the Modified Gait Abnormality Rating Scale (GARS‐M). In standing standard radiographs, the PO angle was measured as the angle between the horizontal plane and the inter‐teardrop line.ResultsPatients' mean age and Body Mass Index (BMI) were 39.7 ± 16.8 and 22.3 ± 3.1, respectively. PO angles did not follow a normal distribution, with a median (IQR) of 2.0° (0.9°—3.1°). According to the Wilcoxon one‐sample test, the median PO angle differed significantly from zero (P < 0.001). The PO angle did not differ significantly between males and females (2° vs. 2°, P = 0.46), nor did it correlate significantly with age (P = 0.24). Considering the 95% percentile of PO angles was 5.6°, this range (0°—5.6°) was regarded as a normative value.ConclusionNormative values for PO in the normal healthy population range from 0° to 5.6°, with a median value of 2.0°. The PO angle was independent of age and sex and differed significantly from 0°. Slight pelvic obliquity may be normal, and physicians should not always assume that it is caused by pain, scoliosis, or weakness of the abductors.Level of evidenceIII.