bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability assessment of the definition of ultrasound enthesitis in SpA: results of a large, multicentre, international, web-based study
Authors: Di Matteo Andrea , Cipolletta Edoardo , Destro Castaniti Giulia Maria , Smerilli Gianluca , Airoldi Carla , Aydin Sibel Zehra , Becciolini Andrea , Bonfiglioli Karina , Bruns Alessandra , Carrara Greta , Cazenave Tomas , Ciapetti Alessandro , Cosatti Micaela Ana , de Agustín Juan José , Di Carlo Marco , Di Donato Eleonora , Di Geso Luca , Duran Emine , Elliott Ashley , Estrach Cristina , Farisogulları Bayram , Fiorenza Alessia , Fodor Daniela , Gabba Alessandra , Hernández-Díaz Cristina , Huang Feng , Hurnakova Jana , Li Ling , Jesus Diogo , Karadag Omer , Martire Maria Victoria , Massarotti Marco , Michelena Xabier , Musca Alice Andreea , Nair Jagdish , Okano Tadashi , Papalopoulos Ioannis , Rosemffet Marcos , Rovisco João , Rozza Davide , Salaffi Fausto , Satulu Iulia , Scioscia Crescenzio , Scirè Carlo Alberto , Sun Fei , Tamas Maria-Magdalena , Tanimura Shun , Ventura-Rios Lucio , Voulgari Paraksevi V , Vreju Florentin Ananu , Vukatana Gentiana , Wong Ernest , Yang Jinshui , Zacariaz Hereter Johana , Zanetti Anna , Grassi Walter , Filippucci Emilio 
Published: March 2022

AbstractObjectivesTo investigate the reliability of the OMERACT US Task Force definition of US enthesitis in SpA.MethodsIn this web exercise, based on the evaluation of 101 images and 39 clips of the main entheses of the lower limbs, the elementary components included in the OMERACT definition of US enthesitis in SpA (hypoechoic areas, entheseal thickening, power Doppler signal at the enthesis, enthesophytes/calcifications, bone erosions) were assessed by 47 rheumatologists from 37 rheumatology centres in 15 countries. Inter- and intra-observer reliability of the US components of enthesitis was calculated using Light’s kappa, Cohen’s kappa, Prevalence And Bias Adjusted Kappa (PABAK) and their 95% CIs.ResultsBone erosions and power Doppler signal at the enthesis showed the highest overall inter-reliability [Light’s kappa: 0.77 (0.76–0.78), 0.72 (0.71–0.73), respectively; PABAK: 0.86 (0.86–0.87), 0.73 (0.73–0.74), respectively], followed by enthesophytes/calcifications [Light’s kappa: 0.65 (0.64–0.65), PABAK: 0.67 (0.67–0.68)]. This was moderate for entheseal thickening [Light’s kappa: 0.41 (0.41–0.42), PABAK: 0.41 (0.40–0.42)], and fair for hypoechoic areas [Light’s kappa: 0.37 (0.36–0.38); PABAK: 0.37 (0.37–0.38)]. A similar trend was observed in the intra-reliability exercise, although this was characterized by an overall higher degree of reliability for all US elementary components compared with the inter-observer evaluation.ConclusionsThe results of this multicentre, international, web-based study show a good reliability of the OMERACT US definition of bone erosions, power Doppler signal at the enthesis and enthesophytes/calcifications. The low reliability of entheseal thickening and hypoechoic areas raises questions about the opportunity to revise the definition of these two major components for the US diagnosis of enthesitis.
Infection is associated with increased risk of MPO- but not PR3-ANCA-associated vasculitis
Authors: Rathmann Jens , Stamatis Pavlos , Jönsson Göran , Englund Martin , Segelmark Mårten , Jayne David , Mohammad Aladdin J 
Published: March 2022

Abstract

Objectives
To determine whether development of ANCA-associated vasculitis (AAV) shows a relationship with a prior infection and if prior infection affects disease characteristics and outcome.

Methods
All incident cases of AAV diagnosed in a defined region of Sweden from 2000 through 2016 were identified. For each case, 10 individuals from the general population, matched for age, sex and area of residence, were selected. Infections occurring in AAV patients and controls prior to the date of AAV diagnosis (index date for respective controls) were identified using an administrative database. Conditional logistic regression models were used to calculate odds ratios (OR) of developing AAV. Occurrence, clinical characteristics and outcome of AAV were analysed with respect to prior infection.

Results
Two-hundred and seventy patients with AAV (48% female) and 2687 controls were included. Prior to diagnosis/index date, 146 (54%) AAV patients had been diagnosed with infection vs 1282 (48%) controls, with OR for AAV 1.57 (95% CI 1.18, 2.19) in those with infections of the upper respiratory tract and 1.68 (1.02, 2.77) in those with pneumonia. Difference from controls was significant in patients with MPO-ANCA 1.99 (95% CI 1.25, 3.1) but not in those with PR3-ANCA 1.0 (0.61, 1.52). Patients with prior infection showed higher disease activity at AAV diagnosis. No differences in disease characteristics, comorbidities or outcome in those with and without prior infections were observed.

Conclusions
Respiratory tract infections are positively associated with development of MPO- but not PR3-ANCA vasculitis. Prior infection is associated with higher disease activity at AAV diagnosis.
Syrian Refugees’ Homemaking in Gaziantep: Uncertainty, Legality and Temporality
Authors: Sengul Irem 
Published: March 2022

ABSTRACT
Temporary protection has long been formulated and debated in policy circles as a practical interim response for large-scale refugee movements, awaiting durable solutions. This article critically engages with the top-down formulations of temporary protection by focusing on one of its latest and most comprehensive application in Turkey for Syrian refugees since 2011. The conceptual framework adopts a bottom-up approach in questioning how Syrian refugees interpret, conceive, and shape the category of temporary protection. By building upon empirical work conducted in the city of Gaziantep, which has become one of the important sites of refuge for Syrian refugees, and a hub for protection activities since the beginning of the Syrian displacement, this article uncovers Syrian refugees’ urges and attempts of “homemaking” in Turkey as a crucial aspect of understanding the dynamics of temporary protection. The article unpacks the interplay between the inherent uncertainties of the Turkish temporary protection regime, the legality of its Syrian beneficiaries, and homemaking practices of Syrian refugees during their protracted displacement. It concludes that it is only through a bottom-up understanding of the many dimensions of temporary protection—and its impacts on the refugees—that a truly workable framework will emerge, that focuses on protection rather than temporality.
Exogenous application of acetic acid enhances drought tolerance by influencing the MAPK signaling pathway induced by ABA and JA in apple plants
Authors: Sun Tingting , Zhang Junke , Zhang Qiang , Li Xingliang , Li Minji , Yang Yuzhang , Zhou Jia , Wei Qinping , Zhou Beibei 
Published: March 2022

Abstract
The external application of acetic acid (AA) has been shown to improve drought survival in plants, such as Arabidopsis, rice, maize, wheat, rapeseed and cassava, and the application of AA also increased drought tolerance in perennial woody apple (Malus domestica) plants. An understanding of AA-induced drought tolerance in apple plants at the molecular level will contribute to the development of technology that can be used to enhance drought tolerance. In this study, the morphological, physiological and transcriptomic responses to drought stress were analyzed in apple plants after watering without AA (CK), watering with AA (AA), drought treatment (D) and drought treatment with AA (DA). The results suggested that the AA-treated apple plants had a higher tolerance to drought than water-treated plants. Higher levels of chlorophyll and carotenoids were found under the DA conditions than under D stress. The levels of abscisic acid (ABA), jasmonic acid (JA) and methyl jasmonate were increased in AA-treated apple plants. Transcriptomic profiling indicated the key biological pathways involved in metabolic processes, mitogen-activated protein kinase (MAPK) signaling, plant hormone signal transduction and the biosynthesis of secondary metabolites in response to different drought conditions. The 9-cis-epoxycarotenoid dioxygenase, (9S,13S)-cis-oxophytodienoic acid reductase, allene oxide synthase, allene oxide cyclase and lipoxygenase genes participate in the synthase of ABA and JA under drought and AA treatments. Collectively, the results showed that external application of AA enhanced drought tolerance in apple plants by influencing the ABA- and JA-induced MAPK signaling pathways. These data indicated that the application of AA in plants is beneficial for enhancing drought tolerance and decreasing growth inhibition in agricultural fields.
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
Authors: Zhao Lele , Wymant Chris , Blanquart François , Golubchik Tanya , Gall Astrid , Bakker Margreet , Bezemer Daniela , Hall Matthew , Ong Swee Hoe , Albert Jan , Bannert Norbert , Fellay Jacques , Grabowski M Kate , Gunsenheimer-Bartmeyer Barbara , Günthard Huldrych F , Kivelä Pia , Kouyos Roger D , Laeyendecker Oliver , Meyer Laurence , Porter Kholoud , van Sighem Ard , van der Valk Marc , Berkhout Ben , Kellam Paul , Cornelissen Marion , Reiss Peter , Fraser Christophe , Ferretti Luca 
Published: March 2022

Abstract
Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.
Does early life phthalate exposure mediate racial disparities in children’s cognitive abilities?
Authors: Patti Marisa A. , Eliot Melissa , Li Nan , Yolton Kimberly , Lanphear Bruce P. , Chen Aimin , Braun Joseph M. 
Published: March 2022

Background:
Early life exposure to phthalates may be associated with reduced cognition. However, it is unknown if disproportionate exposure to phthalates contributes to racial disparities in children’s intellectual abilities.

Methods:
We used data from 253 mother-child pairs in Cincinnati, OH (the Health Outcomes and Measures of the Environment study, 2003–2006). We measured urinary concentrations of 11 phthalate metabolites twice during pregnancy and up to six times in childhood. We evaluated children’s cognitive abilities at ages 5 and 8 years. Using mediation models, we quantified covariate-adjusted direct and indirect effects of race on children’s Full-Scale Intelligence Quotient (IQ) scores for individual phthalate metabolite concentrations during gestation and childhood.

Results:
Average IQ scores among Black children (n = 90) were 7.0 points lower (95% confidence interval [CI] = −12, −1.8) than among White children (n = 145) after adjustment for socioeconomic factors. Urinary monobenzyl phthalate and monoethyl phthalate (MEP) concentrations during gestation and childhood were higher among Black than White children. We did not observe evidence that phthalate concentrations mediated the race-IQ association, with the exception of MEP. Childhood MEP concentrations partially mediated the race-IQ association. For instance, each 10-fold increase in MEP concentrations at age 2 years contributed to a 1.9-point disparity in IQ scores between Black and White children (95% CI = −4.7, 0.7). Other phthalate metabolite concentrations during pregnancy or childhood did not mediate the race-IQ association.

Conclusions:
Despite observing racial disparities in exposure to some phthalates and IQ, we found little evidence that phthalates contribute to IQ disparities.
Orbital Compartment Syndrome Following Incisional Biopsy of Orbital Natural Killer/T-Cell Lymphoma
Authors: Takahashi Yasuhiro , Vaidya Aric , Kakizaki Hirohiko 
Published: March 2022

Abstract:
A 73-year-old man presented with a swelling in the left upper eyelid and decreased vision for 3 weeks before referral to us. On the first examination, his left best-corrected visual acuity was 0.4. Magnetic resonance imaging demonstrated an orbital lesion on the left side. He consulted with us on 6 days post-incisional biopsy after noticing left eye vision loss at the postoperative 4 days. His left eye visual acuity was no light perception. Funduscopic and optical coherence tomographic examinations indicated left central retinal artery occlusion. Imaging studies demonstrated a left globe tenting with a posterior globe angle of 90°. Although steroid pulse therapy was started on the same day, the left eye vision loss did not recover. Four days later, the pathological result was obtained, which corresponded to natural killer/T-cell lymphoma. Chemotherapy using the CHOP regimen responded poorly, and the patient died 2 months after the biopsy.
Assessment of Skeletal Maturation in Male Children With Unilateral Cleft Lip and Palate
Authors: Yang Chenjie , Shi Jiajun , Chen Zhenqi , Yu Quan 
Published: March 2022

Objectives:
To assess the skeletal maturation in male children with unilateral cleft lip and palate (UCLP) in comparison to that of noncleft peers using the cervical vertebral maturation (CVM) method.

Methods:
A sample of 149 male UCLP patients aged from 8- to 16-year-old and 447 age-matched orthodontic individuals without clefts was retrospectively compiled. Cervical vertebral maturation was assessed based on the cephalometric radiographs.

Results:
The proportion of children in CVMSI and CVMSII was higher in the UCLP group compared to that in the noncleft group, but there was no significant difference in the CVM stage of the cleft patients compared to their noncleft peers. In the 12- to 14-year-old group, children with UCLP showed significantly delayed skeletal maturity in comparison with their noncleft peers. No significant difference was found in the other 3 age groups. There was a statistically significant correlation between the skeletal age and chronological age in both the UCLP group and the noncleft group. There was no significant difference in the mean age at CVMII and CVMIII between the cleft patients and noncleft peers.

Conclusions:
Males with UCLP aged 12- to 14-year-old have a statistically significant increased risk of delayed skeletal maturity in comparison with their noncleft peers. The chronological age is not an accurate indicator to assess the degree of skeletal maturation.
Predicted serotype distribution in invasive pneumococcal disease (IPD) among children less than five years prior to the introduction of the Pneumococcal Conjugate Vaccine (PCV) in Nigeria
Authors: Adamu Aishatu L , Ojal John. , Abubakar Isa S. , Bello Musa M. , Odeyemi Kofo , Okoromah Christy A.N. , Inem Victor , Karia Boniface , Karani Angela , Akech Donald. , Gallagher Katherine , Scott J. Anthony G , Adetifa Ifedayo M.O. 
Published: March 2022

ABSTRACTBackgroundThe 10-valent pneumococcal conjugate vaccine (PCV10) was introduced in Nigeria without any baseline data on serotype distribution in invasive pneumococcal disease (IPD). To estimate the proportion of IPD attributable to different serotypes, in children aged <5 years, we used statistical models based on the serotype-specific nasopharyngeal carriage prevalence and invasive capacity (IC).MethodsWe used the carriage data from one urban and one rural setting in Nigeria, collected within five months of PCV10 introduction (2016). For Model A, we used serotype-specific adult case-fatality ratios from Denmark as proxy for IC. In the second model, we used the ratio of IPD proportions to carriage prevalence (case-carrier ratios) from Kenya (Model B) and the ratio of IPD incidence to carriage acquisition (attack rates) from the UK (Model C) as measures of serotype IC.ResultsThe models predict that serotypes with high carriage prevalence (6A, 6B, 19F and 23F) will dominate IPD. Additionally, Models B and C predictions emphasize serotypes 1, 4, 5, and 14, which were not prevalent in carriage but had high IC estimates. Non-PCV10 serotypes,6A and 19A, also dominated IPD predictions across models and settings. The predicted proportion of IPD attributed to PCV10 serotypes varied between 56% and 74% by model and setting.ConclusionCarriage data can provide preliminary insights into IPD serotypes in settings that lack robust IPD data. The predicted PCV10-serotype coverage for IPD was moderately high. However, predictions for non-PCV10 serotypes indicate that higher-valency PCVs that cover serotypes 6A and 19A may have a larger impact on IPD reductions.
Broad Cross-reactive IgA and IgG Against Human Coronaviruses in Milk Induced by COVID-19 Vaccination and Infection
Authors: Wang Jiong , Young Bridget E. , Li Dongmei , Seppo Antti E. , Zhou Qian , Wiltse Alexander , Nowak-Wegrzyn Anna , Murphy Katherine , Widrick Kaili , Diaz Nicole , Cruz-Vasquez Joseline , Järvinen Kirsi M. , Zand Martin S. 
Published: March 2022

ABSTRACTIt is currently unclear if SARS-CoV-2 infection or mRNA vaccination can also induce IgG and IgA against common human coronaviruses (HCoVs) in lactating parents. Here we prospectively analyzed human milk (HM) and blood samples from lactating parents to measure the temporal patterns of anti-SARS-CoV-2 specific and anti-HCoV cross-reactive IgA and IgG responses. Two cohorts were analyzed: a vaccination cohort (n=30) who received mRNA-based vaccines for COVID-19 (mRNA-1273 or BNT162b2), and an infection cohort (n=45) with COVID-19 disease. Longitudinal HM and fingerstick blood samples were collected pre- and post-vaccination or, for infected subjects, at 5 time-points 14 - 28 days after confirmed diagnosis. The anti-spike(S) and antinucleocapsid(N) IgA and IgG antibody levels against SARS-CoV-2 and HCoVs were measured by multiplex immunoassay (mPlex-CoV). We found that vaccination significantly increased the anti-S IgA and IgG levels in HM. In contrast, while IgG levels increased after a second vaccine dose, blood and HM IgA started to decrease. Moreover, HM and blood anti-S IgG levels were significantly correlated, but anti-S IgA levels were not. SARS2 acute infection elicited anti-S IgG and IgA that showed much higher correlations between HM and blood compared to vaccination. Vaccination and infection were able to significantly increase the broadly cross-reactive IgG recognizing HCoVs in HM and blood than the IgA antibodies in HM and blood. In addition, the broader cross-reactivity of IgG in HM versus blood indicates that COVID-19 vaccination and infection might provide passive immunity through HM for the breastfed infants not only against SARS-CoV-2 but also against common cold coronaviruses.IMPORTANCEIt is unknown if COVID-19 mRNA vaccination and infection in lactating mothers results in cross-reactive antibodies against other common human coronaviruses. Our study demonstrates that mRNA vaccination and COVID-19 infection increase anti-spike SARS-CoV-2 IgA and IgG in both blood and milk. IgA and IgG antibody concentrations in milk were more tightly correlated with concentrations in blood after infection compared to mRNA vaccination. Notably, both infection and vaccination resulted in increased IgG against common seasonalβ-coronaviruses. This suggests that SARS-CoV-2 vaccination or infection in a lactating parent may result in passive immunity against SARS-CoV-2 and seasonal coronaviruses for the recipient infant.
A Genetic History of Continuity and Mobility in the Iron Age Central Mediterranean
Authors: Moots Hannah M. , Antonio Margaret , Sawyer Susanna , Spence Jeffrey P. , Oberreiter Victoria , Weiß Clemens L. , Lucci Michaela , Cherifi Yahia Mehdi Seddik , La Pastina Francesco , Genchi Francesco , Praxmeier Elisa , Zagorc Brina , Cheronot Olivia , Özdoğan Kadir T. , Demetz Lea , Amrani Selma , Candilio Francesca , De Angelis Daniela , Gasperetti Gabriella , Fernandes Daniel , Gao Ziyue , Fantar Mounir , Coppa Alfredo , Pritchard Jonathan K. , Pinhasi Ron 
Published: March 2022

AbstractThe Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. To investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia, and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbors together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.
Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods
Authors: Vijayan Abhishek , Fatima Shadma , Sowmya Arcot , Vafaee Fatemeh 
Published: March 2022

AbstractLiquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and the potential for novel biomarker discovery. However, the low concentration of relevant blood-based biosources and the heterogeneity of samples (i.e. the variability of relative abundance of molecules identified), pose major challenges to biomarker discovery. Moreover, the number of molecular measurements or features (e.g., transcript read counts) per sample could be in the order of several thousand, whereas the number of samples is often substantially lower, leading to the curse of dimensionality. These challenges, among others, elucidate the importance of a robust biomarker panel identification or feature extraction step wherein relevant molecular measurements are identified prior to classification for cancer detection. In this work, we performed a benchmarking study on eleven feature extraction methods using transcriptomic profiles derived from different blood-based biosources. The methods were assessed both in terms of their predictive performance and the robustness of the biomarker panels in diagnosing cancer or stratifying cancer subtypes. While performing the comparison, the feature extraction methods are categorised into feature subset selection methods and transformation methods. A transformation feature extraction method, namely PLS-DA, was found to perform consistently superior in terms of classification performance, while a feature subset selection method, namely Ranger, selected feature sets that were the most robust to sub-sampling in terms of consistently selecting the same features. As part of the benchmarking study, a generic pipeline has been created and made available as an R package to ensure reproducibility of the results and allow for easy extension of this study to other datasets.