bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrafine particle levels measured on board short-haul commercial passenger jet aircraft
Authors: Michaelis Susan , Loraine Tristan , Howard C. V. 
Published: August 2021

Abstract
Background
Airline crew members report adverse health effects during and after inhalation exposure to engine oil fumes sourced to the air supply system onboard commercial and military aircraft. Most investigations into the causal factors of their reported symptoms focus on specific chemical contaminants in the fumes. The adverse health effects reported in aircrew exposed to the aircraft air supply, bled unfiltered off the engine or Auxiliary Power Unit (APU) may be related to particulate exposures, which are widely known to effect health. While oil contaminates the aircraft air supply, some suggest that this will only occur when there is a bearing seal failure, others document that there is low level oil contamination of the air supply during normal engine operation. This brief pilot study explores whether particulate exposure may be associated with the normal engine/APU and air supply operation and to therefore increase the understanding that UFP exposures may have on crew and passengers.

Methods
An ultrafine particle counter was utilised by an experienced airline captain in the passenger cabin of four short-haul commercial passenger aircraft. All flights were under 90 min on aircraft from two different carriers ranging from 7 months to 14 years old.

Results
UFP concentrations showed maximum concentrations ranging from 31,300 to 97,800 particles/cm3 when APU was selected on as a source of air on the ground and with engine bleed air and the air conditioning packs selected on during the climb. In 2 of the 4 flights the peaks were associated with an engine oil smell. Increases in UFP particle concentrations occurred with changes in engine/APU power and air supply configuration changes.

Conclusions
This study identified increases in UFP concentrations associated with engine and APU power changes and changes in air supply configuration. These results correlated with times when engine and APU oil seals are known to be less effective, enabling oil leakage to occur. The concentrations reached in the passenger cabins exceeded those taken in other ground-based environments. UFP exposures in aircraft cabins during normal flight indicates there will be health consequences for long serving aircrew and some passengers.
Cells of the human respiratory tract support the replication of pathogenic Old World orthohantavirus Puumala
Authors: Hägele Stefan , Nusshag Christian , Müller Alexander , Baumann Alexandra , Zeier Martin , Krautkrämer Ellen 
Published: August 2021

Abstract
Background
Transmission of all known pathogenic orthohantaviruses (family Hantaviridae) usually occurs via inhalation of aerosols contaminated with viral particles derived from infected rodents and organ manifestation of infections is characterized by lung and kidney involvement. Orthohantaviruses found in Eurasia cause hemorrhagic fever with renal syndrome (HFRS) and New World orthohantaviruses cause hantavirus cardiopulmonary syndrome (HCPS). However, cases of infection with Old World orthohantaviruses with severe pulmonary manifestations have also been observed. Therefore, human airway cells may represent initial targets for orthohantavirus infection and may also play a role in the pathogenesis of infections with Eurasian orthohantaviruses.

Methods
We analyzed the permissiveness of primary endothelial cells of the human pulmonary microvasculature and of primary human epithelial cells derived from bronchi, bronchioles and alveoli for Old World orthohantavirus Puumala virus (PUUV) in vitro. In addition, we examined the expression of orthohantaviral receptors in these cell types. To minimize donor-specific effects, cells from two different donors were tested for each cell type.

Results
Productive infection with PUUV was observed for endothelial cells of the microvasculature and for the three tested epithelial cell types derived from different sites of the respiratory tract. Interestingly, infection and particle release were also detected in bronchial and bronchiolar epithelial cells although expression of the orthohantaviral receptor integrin β3 was not detectable in these cell types. In addition, replication kinetics and viral release demonstrate enormous donor-specific variations.

Conclusions
The human respiratory epithelium is among the first targets of orthohantaviral infection and may contribute to virus replication, dissemination and pathogenesis of HFRS-causing orthohantaviruses. Differences in initial pulmonary infection due to donor-specific factors may play a role in the observed broad variance of severity and symptoms of orthohantavirus disease in patients. The absence of detectable levels of integrin αVβ3 surface expression on bronchial and small airway epithelial cells indicates an alternate mode of orthohantaviral entry in these cells that is independent from integrin β3.
Quality of life of transplanted children and their parents: a cross-sectional study
Authors: Duvant Pauline , Fillat Magali , Garaix Florentine , Roquelaure Bertrand , Ovaert Caroline , Fouilloux Virginie , Tsimaratos Michel , Auquier Pascal , Fabre Alexandre , Baumstarck Karine 
Published: August 2021

AbstractBackgroundTransplantation is a saving therapeutic that has heavy consequences. The quality of life (QoL) of transplanted children and their parents has been little studied and should help physicians better manage these patients. The objectives of the study were to assess: (1) the QoL of transplanted children and parents and compare it with that of children with other chronic conditions associated with long-term consequences, and (2) potential variables modulating the QoL.MethodsThis cross-sectional study was performed in a multidisciplinary paediatric unit (Timone Hospital, Marseille, France). Children were less than 18 years old; had a liver, kidney or heart transplant; and had a time since transplantation of 1–10 years. Socio-demographics and clinical data were recorded from medical forms. The QoL was assessed using the VSP-A (Vécu et Santé Perçue de l’Adolescent et de l’Enfant) and the WhoQoL self-reported questionnaires.ResultsForty-five families were included (response rate: 76%). The transplanted organs were the liver for 20 children, the kidney for 15 children, and the heart for 10 children. The QoL of transplanted children reported by their parents was better than that of children with inborn errors of metabolism and similar to that of childhood leukaemia survivors. The QoL of parents of transplanted children was better than that of parents of children with inborn errors of metabolism and did not differ from French norms. The QoL did not differ according to the nature of the transplanted organ, sex or the main sociodemographic data. The main modulators decreasing QoL were residual treatment level, medications switch and the presence of another regular treatment.ConclusionTransplanted children and their families reported a fairly preserved QoL compared to children with other chronic health conditions. Special attention should be given to QoL modulators related to therapeutic management (medication switches, regular treatments) that might be amenable to improve the QoL.Trial registrationEthics committee of Aix-Marseille University, France (reference number: 2014-08-04-03, 24/4/2015;https://www.univ-amu.fr/fr/public/comite-dethique).
Identification of novel COX-2 / CYP19A1 axis involved in the mesothelioma pathogenesis opens new therapeutic opportunities
Authors: Nuvoli Barbara , Antoniani Barbara , Libener Roberta , Maconi Antonio , Sacconi Andrea , Carosi Mariantonia , Galati Rossella 
Published: August 2021

Abstract
Background
Based on previous studies highlighting that the induction of cyclooxygenase-2 (COX-2) and high prostaglandin E2 (PGE2) levels contribute to the pathogenesis of malignant pleural mesothelioma (MPM), and that aromatase (CYP19A1), an enzyme that plays a key role in estrogen biosynthesis, along with estradiol (E2) were expressed in MPM, this study aimed to investigate the possible interplay between COX-2 and CYP19A1 in the pathogenesis of mesothelioma, as well as the underlying mechanism.

Methods
The interaction between COX-2 and CYP19A1 was first investigated on different MPM lines upon PGE2, and COX-2 inhibitor (rofecoxib) treatment by western blot, RT-PCR. The key regulatory pathways involved in the COX-2 and CYP19A1 axis were further studied in MPM cells, after rofecoxib and exemestane (CYP19A1 inhibitor) treatment in monotherapy and in combination, by cell cycle distribution, western blot, and combination index analysis. To explore the role of COX-2/CYP19A1 axis in 3D preclinical models of MPM cells, we analyzed the effect of combination of COX-2 and CYP19A1 inhibitors in mesosphere formation. Immunohistochemical analysis of MPM mesosphere and specimens was utilized to evaluate the involvement of COX-2 on the CYP19A1 activity and the relationship between E2 and COX-2.

Results
PGE2 or rofecoxib treatment caused in MPM cells an increased or decreased, respectively, CYP19A1 expression at mRNA and protein levels. The effect of rofecoxib and exemestane combination in MPM cell proliferation was synergistic. Activation of caspase-3 and cleavage of PARP confirmed an apoptotic death for MPM cell lines. Increased expression levels of p53, p21, and p27, downregulation of cyclin D1 and inhibition of Akt activation (pAKT) were also found. The antagonistic effect of rofecoxib and exemestane combination found only in one cell line, was reverted by pretreatment with MK2206, a pAKT inhibitor, indicating pAKT as an actionable mediator in the COX-2-CYP19A1 axis. Reduction of size and sphere-forming efficiency in MPM spheres after treatment with both inhibitor and a decrease in COX-2 and E2 staining was found. Moreover, immunohistochemical analysis of 46 MPM samples showed a significant positive correlation between COX-2 and E2.

Conclusions
Collectively, the results highlighted a novel COX-2/CYP19A1 axis in the pathogenesis of MPM that can be pharmacologically targeted, consequently opening up new therapeutic options.
Machine learning identifies ICU outcome predictors in a multicenter COVID-19 cohort
Authors: Magunia Harry , Lederer Simone , Verbuecheln Raphael , Gilot Bryant Joseph , Koeppen Michael , Haeberle Helene A. , Mirakaj Valbona , Hofmann Pascal , Marx Gernot , Bickenbach Johannes , Nohe Boris , Lay Michael , Spies Claudia , Edel Andreas , Schiefenhövel Fridtjof , Rahmel Tim , Putensen Christian , Sellmann Timur , Koch Thea , Brandenburger Timo , Kindgen-Milles Detlef , Brenner Thorsten , Berger Marc , Zacharowski Kai , Adam Elisabeth , Posch Matthias , Moerer Onnen , Scheer Christian S. , Sedding Daniel , Weigand Markus A. , Fichtner Falk , Nau Carla , Prätsch Florian , Wiesmann Thomas , Koch Christian , Schneider Gerhard , Lahmer Tobias , Straub Andreas , Meiser Andreas , Weiss Manfred , Jungwirth Bettina , Wappler Frank , Meybohm Patrick , Herrmann Johannes , Malek Nisar , Kohlbacher Oliver , Biergans Stephanie , Rosenberger Peter 
Published: August 2021

AbstractBackgroundIntensive Care Resources are heavily utilized during the COVID-19 pandemic. However, risk stratification and prediction of SARS-CoV-2 patient clinical outcomes upon ICU admission remain inadequate. This study aimed to develop a machine learning model, based on retrospective & prospective clinical data, to stratify patient risk and predict ICU survival and outcomes.MethodsA Germany-wide electronic registry was established to pseudonymously collect admission, therapeutic and discharge information of SARS-CoV-2 ICU patients retrospectively and prospectively. Machine learning approaches were evaluated for the accuracy and interpretability of predictions. The Explainable Boosting Machine approach was selected as the most suitable method. Individual, non-linear shape functions for predictive parameters and parameter interactions are reported.Results1039 patients were included in the Explainable Boosting Machine model, 596 patients retrospectively collected, and 443 patients prospectively collected. The model for prediction of general ICU outcome was shown to be more reliable to predict “survival”. Age, inflammatory and thrombotic activity, and severity of ARDS at ICU admission were shown to be predictive of ICU survival. Patients’ age, pulmonary dysfunction and transfer from an external institution were predictors for ECMO therapy. The interaction of patient age with D-dimer levels on admission and creatinine levels with SOFA score without GCS were predictors for renal replacement therapy.ConclusionsUsing Explainable Boosting Machine analysis, we confirmed and weighed previously reported and identified novel predictors for outcome in critically ill COVID-19 patients. Using this strategy, predictive modeling of COVID-19 ICU patient outcomes can be performed overcoming the limitations of linear regression models.Trial registration“ClinicalTrials” (clinicaltrials.gov) under NCT04455451.
CoCoA-diff: counterfactual inference for single-cell gene expression analysis
Authors: Park Yongjin P. , Kellis Manolis 
Published: August 2021

AbstractFinding a causal gene is a fundamental problem in genomic medicine. We present a causal inference framework, CoCoA-diff, that prioritizes disease genes by adjusting confounders without prior knowledge of control variables in single-cell RNA-seq data. We demonstrate that our method substantially improves statistical power in simulations and real-world data analysis of 70k brain cells collected for dissecting Alzheimer’s disease. We identify 215 differentially regulated causal genes in various cell types, including highly relevant genes with a proper cell type context. Genes found in different types enrich distinctive pathways, implicating the importance of cell types in understanding multifaceted disease mechanisms.
Characterization and evaluation of a recombinant multiepitope peptide antigen MAG in the serological diagnosis of Toxoplasma gondii infection in pigs
Authors: Song Yongle , Zhao Yongjuan , Pan Ke , Shen Bang , Fang Rui , Hu Min , Zhao Junlong , Zhou Yanqin 
Published: August 2021

Abstract
Background
Toxoplasmosis caused by Toxoplasma gondii is a serious disease threatening human and animal health. People can be infected with T. gondii by ingesting raw pork contaminated with cysts or oocysts. Serological test is a sensitive and specific method usually used for large-scale diagnosis of T. gondii infection in humans and animals (such as pigs). Commercial pig Toxoplasma antibody ELISA diagnostic kits are expensive, which limits their use; moreover, the wide antigen composition used in these diagnostic kits is still unclear and difficult to standardize. The multiepitope peptide antigen is a novel diagnostic marker, and it has potential to be developed into more accurate and inexpensive diagnostic kits.

Methods
The synthetic multiepitope antigen (MAG) cDNA encoding a protein with epitopes from five T. gondii-dominant antigens (SAG1, GRA1, ROP2, GRA4, and MIC3) was designed, synthesized, and expressed in Escherichia coli BL21 (DE3) strain. The recombinant protein was detected through western blot with pig anti-T. gondii-positive and -negative serum, and then IgG enzyme-linked immunosorbent assay (ELISA) named MAG-ELISA was designed. The MAG-ELISA was evaluated in terms of specificity, sensitivity, and stability. The MAG-ELISA was also compared with a commercial PrioCHECK®Toxoplasma Ab porcine ELISA (PrioCHECK ELISA). Finally, the trend of pig anti-T. gondii IgG levels after artificial infection with RH tachyzoites was evaluated using MAG-ELISA and two other ELISA methods (rMIC3-ELISA and PrioCHECK ELISA).

Results
MAG antigen could be specifically recognized by pig anti-T. gondii-positive but not -negative serum. MAG-ELISA showed high diagnostic performance in terms of specificity (88.6%) and sensitivity (79.1%). MAG-ELISA could be used for detecting anti-T. gondii IgG in the early stage of T. gondii infection in pigs (at least 7 days after artificial infection).

Conclusions
Our results suggest that MAG antigen can be applied to specifically recognize anti-T. gondii IgG in pig, and MAG-ELISA has the potential for large-scale screening tests of T. gondii infection in pig farms and intensive industries.

Graphical abstract
Reliability of ultrasound versus digital vaginal examination in detecting cervical dilatation during labor: a diagnostic test accuracy systematic review
Authors: Mohaghegh Zaynab , Jahanfar Shayesteh , Abedi Parvin , El Aziz Mohamed A. Abd 
Published: August 2021

Abstract
Background
This systematic review aimed to investigate the reliability of ultrasound method compared with digital vaginal examinations in detecting cervical dilation.

Methods
We searched Cochrane (CENTRAL), MEDLINE, EMBASE, CINAHL, ISI Web of Science Core Collection, Trip Database, PubMed, DARE and NHS EED, HTA, and PROSPERO. Ten observational studies with a total sample size of 856 were included in the meta-analysis.

Results
The intraclass correlation coefficient (ICC) values ranged between 0.21 and 0.69. The fixed-effect models for the ultrasound test showed an average of ICC (r = 0.32 (95% CI 0.26–0.38). Correlation between two methods was poor (r = 0.359, 95% CI 0.26–0.44). In nulliparous and multigravida participants the correlation between ultrasound measurements and digital examinations was (r = 0.349, 95% CI 0.25–0.43) and ICC (r = 0.676, 95% CI 0.419–0.833), respectively.

Conclusion
Trans-perineal ultrasonography seems to be a reliable method for assessing labor progression in multigravida women, but its usage in nulliparous women needs further studies.
Probability of Alzheimer’s disease based on common and rare genetic variants
Authors: Escott-Price Valentina , Schmidt Karl Michael 
Published: August 2021

Abstract
Background
Alzheimer’s disease, among other neurodegenerative disorders, spans decades in individuals’ life and exhibits complex progression, symptoms and pathophysiology. Early diagnosis is essential for disease prevention and therapeutic intervention. Genetics may help identify individuals at high risk. As thousands of genetic variants may contribute to the genetic risk of Alzheimer’s disease, the polygenic risk score (PRS) approach has been shown to be useful for disease risk prediction. The APOE-ε4 allele is a known common variant associated with high risk to AD, but also associated with earlier onset. Rare variants usually have higher effect sizes than common ones; their impact may not be well captured by the PRS. Instead of standardised PRS, we propose to calculate the disease probability as a measure of disease risk that allows comparison between individuals.

Methods
We estimate AD risk as a probability based on PRS and separately accounting for APOE, AD rare variants and the disease prevalence in age groups. The mathematical framework makes use of genetic variants effect sizes from summary statistics and AD disease prevalence in age groups.

Results
The AD probability varies with respect to age, APOE status and presence of rare variants. In age group 65+, the probability of AD grows from 0.03 to 0.18 (without APOE) and 0.07 to 0.7 (APOE e4e4 carriers) as PRS increases. In 85+, these values are 0.08–0.6 and 0.3–0.85. Presence of rare mutations, e.g. in TREM2, may increase the probability (in 65+) from 0.02 at the negative tail of the PRS to 0.3.

Conclusions
Our approach accounts for the varying disease prevalence in different genotype and age groups when modelling the APOE and rare genetic variants risk in addition to PRS. This approach has potential for use in a clinical setting and can easily be updated for novel rare variants and for other populations or confounding factors when appropriate genome-wide association data become available.
The mutual patterning between the developing nephron and its covering tissues—valid reasons to rethink the search for traces left by impaired nephrogenesis
Authors: Minuth Will W. 
Published: August 2021

Abstract
Background
The impairment of nephrogenesis can cause the termination of nephron formation in preterm and low birth weight babies. This leads to oligonephropathy with severe health consequences in later life. Although many clinical parameters are known, surprisingly little information is available regarding the initial damage on the developing nephron. Equally astounding, the first morphological data regarding the specifics of nephron formation in the nephrogenic zone of the fetal human kidney during late gestation has only been published within the past few years. In this context, it was observed that each stage of nephron anlage is surrounded by a specific set of tissues. Although highly relevant for the normal progress of nephron formation, the mutual patterning has not been systematically described.

Results
To contribute, the different stages of nephron anlage in the nephrogenic zone of the fetal human kidney during late gestation were screened by the optical microscope and documented by images. Following this, magnifications (28 × 18 cm) were produced to trace the contours of the developing nephron and its covering tissues. The resulting sketches, almost true to scale, were scanned, edited, and processed by a design program. As a base, first the individual position, size, and shape of the nephrogenic niche, pretubular aggregate, renal vesicles, comma- and S-shaped bodies are presented. Secondly, their structural relations to the renal capsule, collecting duct ampulla, perforating radiate artery, and expanding interstitium are shown. Third of all, the focus is on less considered configurations, such as site-specific approximation, local distancing, punctual adhesion, integration, separation, delamination, formation of congruent and divergent surfaces, and folding and opening of interstitial clefts.

Conclusions
The present contribution illuminates the mutual patterning between the developing nephron and its covering tissues. It is indispensable to know about the microanatomical relations, in order to identify whether the noxae impairing nephrogenesis targets only the developing nephron or also its covering tissues as interacting and controlling instances.