bluuebunny/crossref_metadata_2025 huggingface dataset:
An effective processing pipeline for harmonizing DNA methylation data from Illumina’s 450K and EPIC platforms for epidemiological studies
Authors: Vanderlinden Lauren A. , Johnson Randi K. , Carry Patrick M. , Dong Fran , DeMeo Dawn L. , Yang Ivana V. , Norris Jill M. , Kechris Katerina
Published: September 2021

Objective

Illumina BeadChip arrays are commonly used to generate DNA methylation data for large epidemiological studies. Updates in technology over time create challenges for data harmonization within and between studies, many of which obtained data from the older 450K and newer EPIC platforms. The pre-processing pipeline for DNA methylation is not trivial, and influences the downstream analyses. Incorporating different platforms adds a new level of technical variability that has not yet been taken into account by recommended pipelines. Our study evaluated the performance of various tools on different versions of platform data harmonization at each step of pre-processing pipeline, including quality control (QC), normalization, batch effect adjustment, and genomic inflation. We illustrate our novel approach using 450K and EPIC data from the Diabetes Autoimmunity Study in the Young (DAISY) prospective cohort.

Results

We found normalization and probe filtering had the biggest effect on data harmonization. Employing a meta-analysis was an effective and easily executable method for accounting for platform variability. Correcting for genomic inflation also helped with harmonization. We present guidelines for studies seeking to harmonize data from the 450K and EPIC platforms, which includes the use of technical replicates for evaluating numerous pre-processing steps, and employing a meta-analysis.
Toxic epidermal necrosis associated with phenobarbitone: a case report and brief review of the literatures
Authors: Ayele Biniyam A. , Ali Kemal , Mulatu Eliyas
Published: September 2021

Background

Toxic epidermal necrolysis (TEN)/Stevens–Johnson syndrome (SJS) is the spectrum of severe, acute, mucocutaneous, T-cell mediated delayed type IV hypersensitivity reaction and universally related to different drugs. Phenobarbitone is known to cause hypersensitivity reactions with benign pattern; ranging from a mild to moderate rashes but not life-threatening reactions such as TEN/SJS.

Case report

We report a 14-year-old asthmatic male patient admitted to a local hospital for an acute exacerbation of asthma, after he presented with shortness of breath, cough, and fever. He was treated with bronchodilator and antibiotics. On subsequent days, the patient developed new onset generalized tonic clonic seizure in the hospital for which he was started on phenobarbitone of 100 mg twice daily. Two weeks after initiation of phenobarbitone, the patient developed extensive blistering skin eruptions; which subsequently exfoliated unevenly. Associated with the hypersensitivity skin reaction, the patient reported low grade fever, sore throat, and dysphagia. The exfoliation also involved oral and conjunctival mucosa; with estimated 65% body surface area involvement. The laboratory investigations were relevant for mild leucocytosis, prolonged prothrombin time, and reduced albumin. Phenobarbitone was discontinued and replaced with clonazepam; and the patient was managed with fluids replacement, IV antibiotics, twice daily wound care, analgesics, and naso gastric tube feeding. On subsequent days the patients’ clinical condition started improving; the skin lesion also started to heal and exfoliate in most of the affected skin surface areas, and the patient was discharged improved after ten days of intensive care unit.

Conclusion

In summary, the present case describes, a 14-years-old young child with history of asthma and seizure disorder; and developed toxic epidermal necrosis following exposure to Phenobarbitone. This case also highlighted the better prognosis observed in pediatric population with TEN.
Shift of musical hallucinations to visual hallucinations after correction of the hearing deficit in a patient with Lewy body dementia: a case report
Authors: Montalvo Alexandre , Azevedo Eryco , de Mendonça Alexandre
Published: September 2021

Background

Musical hallucinations are a particular type of auditory hallucination in which the patient perceives instrumental music, musical sounds, or songs. Musical hallucinations are associated with acquired hearing loss, particularly within the elderly. Under conditions of reduced auditory sensory input, perception-bearing circuits are disinhibited and perceptual traces released, implying an interaction between peripheral sensory deficits and central factors related to brain dysfunction.

Case presentation

A 71-year-old Caucasian man with hearing loss complained of memory difficulties and resting tremor of the right upper limb in the previous 2 years. He already had difficulties in instrumental activities of daily life. Neurological examination showed Parkinsonian signs and hypoacusia. Neuropsychological examination identified deficits in executive functions and memory tests. Brain computerized tomography and nuclear magnetic resonance scans showed mild cortical and subcortical atrophy. The clinical diagnosis of possible dementia with Lewy bodies was established. Five years later, the patient began complaining of musical hallucinations. There had been no previous change in medication. An otorhinolaryngologist diagnosed age-related hearing loss and prescribed bilateral hearing aids. After using the hearing aids, the patient did not hear the songs any longer, only some tinnitus, described as a whistle. However, at the same time, the patient started experiencing visual hallucinations he never had before.

Discussion

To our knowledge, the immediate shift of hallucinations from one sensory modality to another sensory modality when perception is improved has not been previously described. This report emphasizes the interaction between brain pathology and sensory deficits for the genesis of hallucinations, and reinforces the theory that attention and control networks must couple properly to the default mode network, as well as integrate and select adequately peripheral signals to the somatosensory cortices, in order to keep a clear state of mind.

Conclusion

The clinician should bear in mind and let the patient know that improving one sensory modality to ameliorate hallucinations may sometimes paradoxically lead to hallucinations in a different sensory modality.
2D SIFt: a matrix of ligand-receptor interactions
Authors: Mordalski Stefan , Wojtuch Agnieszka , Podolak Igor , Kurczab Rafał , Bojarski Andrzej J.
Published: September 2021

Depicting a ligand-receptor complex via Interaction Fingerprints has been shown to be both a viable data visualization and an analysis tool. The spectrum of its applications ranges from simple visualization of the binding site through analysis of molecular dynamics runs, to the evaluation of the homology models and virtual screening. Here we present a novel tool derived from the Structural Interaction Fingerprints providing a detailed and unique insight into the interactions between receptor and specific regions of the ligand (grouped into pharmacophore features) in the form of a matrix, a 2D-SIFt descriptor. The provided implementation is easy to use and extends the python library, allowing the generation of interaction matrices and their manipulation (reading and writing as well as producing the average 2D-SIFt). The library for handling the interaction matrices is available via repository http://bitbucket.org/zchl/sift2d.
Loss of signal transducer and activator of transcription 3 impaired the osteogenesis of mesenchymal progenitor cells in vivo and in vitro
Authors: Huang Zijing , Feng Jingyi , Feng Xin , Chan Laiting , Lu Jiarui , Lei Lizhen , Huang Zhuwei , Zhang Xiaolei
Published: September 2021

Background

Signal transducer and activator of transcription 3 (Stat3) is a cytoplasmic transcription factor that participates in various biologic processes. Loss of Stat3 causes hyperimmunoglobulin E syndrome, presenting with skeletal disorders including osteoporosis, recurrent fractures, scoliosis, and craniosynostosis. The objective of this study is to explore the effect and mechanism of Stat3 on osteogenesis of mesenchymal progenitors.

Methods

Stat3 was conditionally knockout (CKO) in mesenchymal progenitors by crossing the pair-related homeobox gene 1-cre (Prx1-Cre) with Stat3-floxed strain mice. Whole-mount-skeletal staining, histology, and micro-CT were used to assess the differences between Stat3 CKO and control mice. Further, in vitro experiments were conducted to evaluate the osteogenesis potential of primary isolated bone marrow mesenchymal stem cells (BMSCs) from both control and Stat3 CKO mice. After osteogenic induction for 14d, alizarin red staining was used to show the calcium deposit, while the western blotting was applied to detect the expression of osteogenic markers.

Results

Compared with the control, Stat3 CKO mice were present with shortened limbs, multiple fractures of long bone, and open calvarial fontanels. The abnormal growth plate structure and reduced collagen fiber were found in Stat3 CKO limbs. According to micro-CT analysis, the reduced cortical bone thickness and bone volume were found on Stat3 CKO mice. The in vitro osteogenic differentiation of BMSCs was inhibited in Stat3 CKO samples. After osteogenic induction for 14d, the significantly diminished calcium deposits were found in Stat3 CKO BMSCs. The decreased expression of osteogenic markers (OPN and COL1A1) was observed in Stat3 CKO BMSCs, compared with the control.

Conclusions

Stat3 played a critical role in bone development and osteogenesis. Loss of Stat3 impaired the osteogenesis of mesenchymal progenitors in vivo and in vitro.
Protocol for a systematic review of outcomes from microsurgical free-tissue transfer performed on short-term collaborative surgical trips in low-income and middle-income countries
Authors: de Berker Henry T. , Čebron Urška , Bradley Daniel , Patel Vinod , Berhane Meklit , Almas Fernando , Walton Gary , Eshete Mekonen , McGurk Mark , Martin Dominique , Honeyman Calum
Published: September 2021

Background

In many units around the world, microsurgical free-tissue transfer represents the gold standard for reconstruction of significant soft tissue defects following cancer, trauma or infection. However, many reconstructive units in low-income and middle-income countries (LMICs) do not yet have access to the resources, infrastructure or training required to perform any microsurgical procedures. Long-term international collaborations have been formed with annual short-term reconstructive missions conducting microsurgery. In the first instance, these provide reconstructive surgery to those who need it. In the longer-term, they offer an opportunity for teaching and the development of sustainable local services.

Methods

A PRISMA-compliant systematic review and meta-analysis will be performed. A comprehensive, predetermined search strategy will be applied to the MEDLINE and Embase electronic databases from inception to August 2021. All clinical studies presenting sufficient data on free-tissue transfer performed on short-term collaborative surgical trips (STCSTs) in LMICs will be eligible for inclusion. The primary outcomes are rate of free flap failure, rate of emergency return to theatre for free flap salvage and successful salvage rate. The secondary outcomes include postoperative complications, cost effectiveness, impact on training, burden of disease, legacy and any functional or patient reported outcome measures. Screening of studies, data extraction and assessments of study quality and bias will be conducted by two authors. Individual study quality will be assessed according to the Oxford Evidence-based Medicine Scales of Evidence 2, and risk of bias using either the ‘Revised Cochrane risk of bias tool for randomized trials’ (Rob2), the ‘Risk of bias in non-randomized studies of interventions’ (ROBINS-I) tool, or the National Institute for Health Quality Assessment tool for Case Series. Overall strength of evidence will be assessed according to the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) approach.

Discussion

To-date the outcomes of microsurgical procedures performed on STCSTs to LMICs are largely unknown. Improved education, funding and allocation of resources are needed to support surgeons in LMICs to perform free-tissue transfer. STCSTs provide a vehicle for sustainable collaboration and training. Disseminating microsurgical skills could improve the care received by patients living with reconstructive pathology in LMICs, but this is poorly established. This study sets out a robust protocol for a systematic review designed to critically analyse outcomes.

Systematic review registration

PROSPERO 225613
Effect of the protection zone in a diffusive ratio-dependent predator–prey model with fear and Allee effect
Authors: Wang Huan , Xing Hui
Published: September 2021

In this paper, we study the influence of a protection zone for the prey on a diffusive predator–prey model with fear factor and Allee effect. The prior estimate, global existence, nonexistence of nonconstant positive solutions and bifurcation from semitrivial solutions are well discussed. We show the existence of a critical patch value $\lambda ^{D}_{1}(\Omega _{0})$

λ
1
D

(

Ω
0

)
of the protection zone, described by the principal eigenvalue of the Laplacian operator over $\Omega _{0}$

Ω
0

with Neumann boundary conditions. When the mortality rate of the predator $\mu \geq d_{2}\lambda ^{D}_{1}(\Omega _{0})$
μ
≥

d
2

λ
1
D

(

Ω
0

)
, we show that the semitrivial solutions $(1,0)$
(
1
,
0
)
and $(\theta,0)$
(
θ
,
0
)
are unstable and there is no bifurcation occurring along respective semitrivial branches.
Solving common nonmonotone equilibrium problems using an inertial parallel hybrid algorithm with Armijo line search with applications to image recovery
Authors: Suantai Suthep , Yambangwai Damrongsak , Cholamjiak Watcharaporn
Published: September 2021

In this work, we modify the inertial hybrid algorithm with Armijo line search using a parallel method to approximate a common solution of nonmonotone equilibrium problems in Hilbert spaces. A weak convergence theorem is proved under some continuity and convexity assumptions on the bifunction and the nonemptiness of the common solution set of Minty equilibrium problems. Furthermore, we demonstrate the quality of our inertial parallel hybrid algorithm by using image restoration, as well as its superior efficiency when compared with previously considered parallel algorithms.
The influence of window size on remote sensing-based prediction of forest structural variables
Authors: Ozkan Ulas Yunus , Demirel Tufan
Published: September 2021

Background

Determining the appropriate window size is a critical step in the estimation process of stand structural variables based on remote sensing data. Because the value of the reference laser and image metrics that affect the quality of the prediction model depends on window size. However, suitable window sizes are usually determined by trial and error. There are a limited number of published studies evaluating appropriate window sizes for different remote sensing data. This research investigated the effect of window size on predicting forest structural variables using airborne LiDAR data, digital aerial image and WorldView-3 satellite image.

Results

In the WorldView-3 and digital aerial image, significant differences were observed in the prediction accuracies of the structural variables according to different window sizes. For the estimation based on WorldView-3 in black pine stands, the optimal window sizes for stem number (N), volume (V), basal area (BA) and mean height (H) were determined as 1000 m2, 100 m2, 100 m2 and 600 m2, respectively. In oak stands, the R2 values of each moving window size were almost identical for N and BA. The optimal window size was 400 m2 for V and 600 m2 for H. For the estimation based on aerial image in black pine stands, the 800 m2 window size was optimal for N and H, the 600 m2 window size was optimal for V and the 1000 m2 window size was optimal for BA. In the oak stands, the optimal window sizes for N, V, BA and H were determined as 1000 m2, 100 m2, 100 m2 and 600 m2, respectively. The optimal window sizes may need to be scaled up or down to match the stand canopy components. In the LiDAR data, the R2 values of each window size were almost identical for all variables of the black pine and the oak stands.

Conclusion

This study illustrated that the window size has an effect on the prediction accuracy in estimating forest structural variables based on remote sensing data. Moreover, the results showed that the optimal window size for forest structural variables varies according to remote sensing data and tree species composition.
The epidemiology of bloodstream infections and antimicrobial susceptibility patterns in Thuringia, Germany: a five-year prospective, state-wide surveillance study (AlertsNet)
Authors: Schöneweck Franziska , Schmitz Roland P. H. , Rißner Florian , Scherag André , Löffler Bettina , Pletz Mathias W. , Weis Sebastian , Brunkhorst Frank M. , Hagel Stefan
Published: September 2021

Background

Monitoring pathogens of bloodstream infections (BSI) and their antibiotic susceptibility is important to guide empiric antibiotic treatment strategies and prevention programs.

This study assessed the epidemiology of BSI and antibiotic resistance patterns at the German Federal State of Thuringia longitudinally.

Methods

A surveillance network consisting of 26 hospitals was established to monitor BSIs from 01/2015 to 12/2019. All blood culture results, without restriction of age of patients, of the participating hospitals were reported by the respective microbiological laboratory. A single detection of obligate pathogens and a repeated detection of coagulase-negative staphylococci, Bacillus spp., Corynebacterium spp., Micrococcus spp. and Propionibacterium spp., within 96 h were regarded as a relevant positive blood culture. If one of the aforementioned non-obligate pathogens has been detected only once within 96 h, contamination has been assumed. Logistic regression models were applied to analyse the relationship between resistance, year of BSI and hospital size. Generalized estimating equations were used to address potential clustering.

Results

A total of 343,284 blood cultures (BC) of 82,527 patients were recorded. Overall, 2.8% (n = 9571) of all BCs were classified as contaminated. At least one relevant pathogen was identified in 13.2% (n = 45,346) of BCs. Escherichia coli (25.4%) was the most commonly detected pathogen, followed by Staphylococcus aureus (15.2%), Staphylococcus epidermidis (8.1%) and Klebsiella pneumoniae (4.6%). In S. aureus, we observed a decline of methicillin resistance (MRSA) from 10.4% in 2015 to 2.5% in 2019 (p < 0.001). The rate of vancomycin resistance in Enterococcus faecium (VRE) has increased from 16.7% in 2015 to 26.9% in 2019 (p < 0.001), with a peak in 2018 (42.5%). In addition, we observed an increase of Cefotaxime (3GC) resistance in E. coli from 10.7% in 2015 to 14.5% in 2019 (p = 0.007) whereas 3GC resistance in K. pneumoniae was stable (2015: 9.9%; 2019: 7.4%, p = 0.35). Carbapenem resistance was less than 1% for both pathogens. These patterns were robustly observed across sensitivity analyses.

Conclusions

We observed evidence for a decline in MRSA, an increase in VRE and a very low rate of carbapenem resistance in gram-negative bacteria. 3GC resistance in E. coli increased constantly over time.
Genetic parameters of drinking and feeding traits of wean-to-finish pigs under a polymicrobial natural disease challenge
Authors: Cheng Jian , Putz Austin M. , Harding John C. S. , Dyck Michael K. , Fortin Frederic , Plastow Graham S. , Canada Pig Gen , Dekkers Jack C. M.
Published: September 2021

Background

The pork industry faces unprecedented challenges from disease, which increases cost of production and use of antibiotics, and reduces production efficiency, carcass quality, and animal wellbeing. One solution is to improve the overall resilience of pigs to a broad array of common diseases through genetic selection. Behavioral changes in feeding and drinking are usually the very first clinical signs when animals are exposed to stressors such as disease. Changes in feeding and drinking behaviors in diseased pigs may reflect the way they cope with the challenge and, thus, could be used as indicator traits to select for disease resilience. The objectives of this study were to estimate genetic parameters of feeding and drinking traits for wean-to-finish pigs in a natural polymicrobial disease challenge model, to estimate genetic correlations of feeding and drinking traits with growth rate and clinical disease traits, and to develop indicator traits to select for disease resilience.

Results

In general, drinking traits had moderate to high estimates of heritability, especially average daily water dispensed, duration, and number of visits (0.44 to 0.58). Similar estimates were observed for corresponding feeding traits (0.35 to 0.51). Most genetic correlation estimates among drinking traits were moderate to high (0.30 to 0.92) and higher than among feeding traits (0 to 0.11). Compared to other drinking traits, water intake duration and number of visits had relatively stronger negative genetic correlation estimates with treatment rate and mortality, especially across the challenge nursery and finisher (− 0.39 and − 0.45 for treatment rate; − 0.20 and − 0.19 for mortality).

Conclusion

Most of the recorded drinking and feeding traits under a severe disease challenge had moderate to high estimates of heritability, especially for feed or water intake duration and number of visits. Phenotypic and genetic correlations among the recorded feeding traits under disease were generally low but drinking traits showed high correlations with each other. Water intake duration and number of visits are potential indicator traits to select for disease resilience because of their high heritability and had moderate genetic correlations with treatment and mortality rates under severe disease.
Problematic smartphone use and affective temperaments among Lebanese young adults: scale validation and mediating role of self-esteem
Authors: Zeidan Joanne , Hallit Souheil , Akel Marwan , Louragli Ismail , Obeid Sahar
Published: September 2021

Background

Adults all over the world face serious issues from problematic smartphone use (PSU). It influences them negatively on a cognitive, behavioral, and emotional level, as well as on their tendencies and well-being. In Lebanon, the prevalence of PSU was shown to be 20.2% within the adult population, specifically with young adults (18–34 years old). This study investigates the validity and reliability of the Smartphone Addiction Scale (SAS) Arabic version. In addition, this study evaluates the association between PSU and affective temperaments and the mediating role of self-esteem in this association.

Method

A cross-sectional study was carried out between August and September 2020, using a sample of community-dwelling participants aged 18 to 29 years. The Smartphone Addiction Scale—Short Version was used to evaluate smartphone addiction among adolescents and adults. The five different temperaments of the patients were assessed by using the Affective temperament Scale (TEMPS‐A). The Rosenberg Self-Esteem Scale was used to evaluate self-esteem.

Results

461 participants were included in this study. All items of the SAS were extracted and yielded a one-factor solution with Eigenvalues > 1 (variance explained = 49.96%; αCronbach = 0.886). The confirmatory analysis results consolidated those obtained from the factor analysis. Higher depressive temperament (B = 0.46) was significantly associated with more smartphone addiction, whereas higher self-esteem (B =  − 0.28) was significantly associated with less smartphone addiction. Self-esteem was found to mediate the association between depressive and hyperthymic temperaments with smartphone addiction.

Conclusion

This study added a better understanding of the high smartphone addiction rate among adults in Lebanon. It confirms the association between affective temperaments and PSU through the mediating effect of self-esteem on Lebanese adults.
A cross-sectional study of COVID-19-related bullying in a sample of Lebanese adults: scale validation, correlates, and mediating effect of fear and anxiety
Authors: Haddad Chadia , Sacre Hala , Bou Malhab Sandrella , Malaeb Diana , Saadeh Danielle , Abou Tayeh Christine , Salameh Pascale
Published: September 2021

Background

The COVID-19 pandemic has led to prolonged exposure to stress and anxiety, raising concerns about a large spectrum of psychological side effects. The primary objective of the study was to validate the COVID-19 Bullying Scale (CBS-11). The second objective was to explore factors associated with COVID-19-related bullying and evaluate the mediating effect of fear and anxiety between knowledge and COVID-19-related bullying.

Methods

A cross-sectional online survey conducted between December 20, 2020, and January 5, 2021, recruited 405 Lebanese adults using a snowball sampling technique. The CBS-11, an 11-item tool specifically created for this study, was used to measure bullying behaviors towards COVID-19 patients.

Results

All items of the CBS-11 converged over a 1-factor solution with an eigenvalue over 1, accounting for a variance of 75.16%. The scale has a high Cronbach’s alpha (.974), indicating excellent reliability. A positive correlation was found between the COVID-19 bullying scale and fear, anxiety, and stigma discrimination. The logistic regression showed that higher fear of COVID-19 (ORa = 1.04), a positive attitude toward COVID-19 preventive measures and hygiene recommendations (ORa = 1.18), higher stigma discrimination scores (ORa = 1.09), and having a health professional family member (ORa = 2.42) were significantly associated with bullying.

Conclusion

Our main findings showed that the CBS-11 could be an efficient tool to measure bullying behaviors toward COVID-19 patients. Stigma discrimination and fear from COVID-19 were associated with higher bullying attitudes. Future prospective studies are needed to understand better the factors related to bullying among adults during a pandemic, such as COVID-19.
Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors
Authors: Singh Omkar , Pratt Drew , Aldape Kenneth
Published: September 2021

It is recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of immune cell components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data in a large set of newly profiled samples (n = 741) as well as samples from external data sources (n = 3311) of methylation-defined glial and glioneuronal tumors. Using the cell-type proportion data as input, we used dimensionality reduction to visualize sample-wise patterns that emerge from the cell type proportion estimations. In IDH-wildtype glioblastomas (n = 2,072), we identified distinct tumor clusters based on immune cell proportion and demonstrated an association with oncogenic alterations such as EGFR amplification and CDKN2A/B homozygous deletion. We also investigated the immune cluster-specific distribution of four malignant cellular states (AC-like, OPC-like, MES-like and NPC-like) in the IDH-wildtype cohort. We identified two major immune-based subgroups of IDH-mutant gliomas, which largely aligned with 1p/19q co-deletion status. Non-codeleted gliomas showed distinct proportions of a key genomic aberration (CDKN2A/B loss) among immune cell-based groups. We also observed significant positive correlations between monocyte proportion and expression of PD-L1 and PD-L2 (R = 0.54 and 0.68, respectively). Overall, the findings highlight specific roles of the TME in biology and classification of CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic alterations.
A multi-scalar investigation of the colouring materials used in textile wrappings of Egyptian votive animal mummies
Authors: Tamburini Diego , Dyer Joanne , Vandenbeusch Marie , Borla Matilde , Angelici Debora , Aceto Maurizio , Oliva Cinzia , Facchetti Federica , Aicardi Sara , Davit Patrizia , Gulmini Monica
Published: September 2021

Commonly exhibited in museum galleries, animal mummies have been the focus of interest of both visitors and researchers alike. The study of these animal remains not only provides new insights into embalming techniques, but also brings a unique perspective on religious, social and economic practices. Twenty animal mummies are discussed in this study, including cats, ibises, crocodiles, calves and birds of prey from the collections of the British Museum (London, UK) and the Museo Egizio (Turin, Italy). The external textile wrappings encasing the mummified body of the animals were investigated with the main aim of identifying the colourants used. In fact, these are mostly patterned using undyed and coloured (mostly red, brown and black) linen strips. Broadband multispectral imaging (MSI) was initially carried out to obtain preliminary information at the macro-scale on the distribution and chemical nature of the colouring agents. Fibre optic reflectance spectroscopy (FORS) was then used to survey several coloured areas of the textile wrappings. Safflower (Carthamus tinctorius) and red ochre were identified non-invasively. Representative samples were then taken and observed using optical microscopy (OM) and scanning electron microscopy (SEM), in order to obtain information at the micro-scale on the distribution of the colouring agents on the fibres, as well as the presence of other materials, including those from environmental contamination. Energy dispersive X-ray spectrometry (EDX) revealed the elemental composition of particles and clear areas of the fibres, whereas high performance liquid chromatography tandem mass spectrometry (HPLC–MS/MS) provided the identification of the organic dyes at a molecular level. The use of hydrolysable and condensed tannins, in combination with iron as a mordant, was found to be used in the very dark shades, which generally corresponded to the textiles with the worst state of preservation. Nevertheless, other aspects, such as fibre processing and bleaching, fungal attack and presence of coating materials appeared to play a role in the evaluation of the conservation state of these textiles. The characterisation of the dyes and the additional inorganic materials contributed to elucidating the production technology of the colours used for animal mummification, and provided insights into ancient dyeing methods.
Prognosis of hemodialysis patients with progressive aortic stenosis: a prospective cohort study
Authors: Horiguchi Yoriko , Uemura Kaoru , Aoyama Naoyoshi , Nakajima Shinichi , Asai Tomoki , Motohashi Sachiko , Harada Manae , Ida Maoko , Yoshida Atsushi
Published: September 2021

Background

Whether progressive mild to moderate aortic stenosis in hemodialysis patients influences their prognosis has not been elucidated. This prospective cohort study explored whether progressive aortic stenosis predicted the rate of cardiac events and mortality in those patients.

Methods

A total of 283 consecutive hemodialysis patients (no aortic stenosis, 248; progressive aortic stenosis, 35) underwent echocardiography for assessment of aortic stenosis, with a median follow-up period of 4.1 years. Study endpoints were cardiac events, all-cause mortality, and cardiac death. Kaplan–Meier analysis and multivariate Cox proportional hazard analysis were performed to estimate cardiac events, all-cause mortality, and cardiac death.

Results

Cumulative cardiac event rate, all-cause mortality rate, and the rate of cardiac death at 3-year follow-up were 44.9%, 40.5%, and 26.4% in patients with progressive aortic stenosis and 22.1%, 19.0%, and 7.5% in those without aortic stenosis, respectively. Kaplan–Meier analysis demonstrated the cumulative rates of cardiac events and all-cause mortality. And cardiac death was significantly higher in patients with progressive aortic stenosis than in those without aortic stenosis. Multivariate Cox proportional hazard analysis revealed that progressive aortic stenosis was predictive of cardiac events (adjusted hazard ratio 2.47; 95% confidence interval 1.38–4.39) and cardiac death (adjusted hazard ratio 4.21; 95% confidence interval 2.10–8.46). Age, physical activity, C-reactive protein, and serum albumin levels—but not progressive aortic stenosis—predicted all-cause mortality.

Conclusions

The rates of cardiac events and cardiac death were higher in hemodialysis patients with progressive aortic stenosis than in those without aortic stenosis. Furthermore, progressive aortic stenosis predicted cardiac events and cardiac death. Compared with those without aortic stenosis, patients with progressive aortic stenosis had higher all-cause mortality, which was related to their comorbidities.

Trial registration This study was retrospectively registered with University Hospital Medical Information Network Clinical Trials Registry (registration number, UMIN 000024023) at September 12th, 2016.
Highlight selection of radiochemistry and radiopharmacy developments by editorial board
Authors: Alves Francisco , Antunes Inês F. , Cazzola Emiliano , Cleeren Frederik , Cornelissen Bart , Denkova Antonia , Engle Jonathan , Faivre-Chauvet Alain , Gillings Nic , Hendrikx Jeroen J. M. A. , Jalilian Amir R. , van der Meulen Nicholas P. , Mikolajczak Renata , Neels Oliver C. , Pillai Maroor R. A. , Reilly Raymond , Rubow Sietske , Seimbille Yann , Spreckelmeyer Sarah , Szymanski Wiktor , Taddei Carlotta
Published: September 2021

Background

The Editorial Board of EJNMMI Radiopharmacy and Chemistry releases a biyearly highlight commentary to update the readership on trends in the field of radiopharmaceutical development.

Results

This commentary of highlights has resulted in 21 different topics selected by each member of the Editorial Board addressing a variety of aspects ranging from novel radiochemistry to first in man application of novel radiopharmaceuticals. Also the first contribution in relation to MRI-agents is included.

Conclusions

Trends in (radio)chemistry and radiopharmacy are highlighted demonstrating the progress in the research field being the scope of EJNMMI Radiopharmacy and Chemistry.
Neurological sequelae of COVID-19: a review
Authors: Peterson Christopher J. , Sarangi Ashish , Bangash Fariha
Published: September 2021

Background

The COVID-19 pandemic has produced a myriad of challenges, including identifying and treating neurological sequelae.

Main body

COVID-19 can cause olfactory and respiratory dysfunction with average recovery within 1 month and a minority of patients experiencing symptoms at 8-month follow-up. Headaches are also very common (up to 93%) amongst patients with persistent COVID-19 symptoms. COVID-19 illness may also affect cognition, although results are mixed.

Conclusion

While many studies have focused on acute COVID-19 symptoms, more longitudinal studies will need to assess the neurological sequelae of the disease. Furthermore, care must be taken when attributing sequelae to COVID-19 illness and not an unrelated cause. Finally, there is concern that COVID-19 may be associated with secondary illnesses, such as Guillain–Barre, and may even contribute to the development of diseases, such as Alzheimer’s.
Narrative Inference with and without Statistics
Authors: Morgan Mary S.
Published: September 2021

This article investigates the role played by narrative in drawing inferences from statistics before the adoption of formal inference regimes in economics. Two well-known, and exemplary, cases of informal inference provide the materials. Nikolai Kondratiev’s struggles to make inferences about the existence of his “long waves” from heaps of statistics in the 1920s contrast sharply with Thomas Robert Malthus’s confident account of demographic-economic oscillations made on the basis of the limited numbers available in the late eighteenth century. Comparison of their inferential reasoning, using detailed textual analysis, casts attention on the important role of narrative. These cases prompt the notion of “narrative inference”: where informal statistical inference depends on narrative accounts—used to make sense of the numbers by Malthus or to add sense onto the numbers by Kondratiev.
“Everlasting Memorials”: Urban Improvement and the Shadow of Ruin in Mid-Eighteenth-Century London
Authors: O'Byrne Alison
Published: September 2021

This essay explores the relationship between plans for the improvement of London and other forms of writing about the city that imagine its inevitable decline and fall. Those lamenting the appearance of London in the eighteenth century frequently looked back to the Great Fire as a missed opportunity to rebuild the city in a grander, more magnificent manner. For these critics, London's built environment did little to stake the nation's claims to polite refinement and cultural prestige. Such concerns became especially pressing in the wake of Britain's victories in the Seven Years’ War, which made London the center of an extensive global empire. Through an examination of proposals for and accounts of urban improvements as well as works that look to a future moment when visitors survey London's faded glories, this essay considers how imagining London in ruins—a trope thus far explored in the context of the loss of the American colonies and Britain's role in the Revolutionary and Napoleonic Wars—served two competing purposes in mid-eighteenth-century Britain. While, on the one hand, improvers acknowledged the transience of imperial power by arguing that now was the time to build grand monuments to mark the achievements of the present, on the other, a range of writers invoked the trope of future ruin to indicate how the seeds of decline had already been sown. The manifold meanings of ruin to which these works gesture would continue to play out in the late eighteenth and early nineteenth centuries.
A Tale of Two Boycotts: Riot, Reform, and Sugar Consumption in Late Eighteenth-Century Britain and France
Authors: Van Dyk Garritt
Published: September 2021

Atlantic sugar production and European sugar consumption rose dramatically in the late eighteenth century. Despite this increase, there were two separate calls to refrain from consuming sugar in both Britain and France at the end of the eighteenth century. Demands for abstinence were directed toward women to stop household consumption of sugar. In Britain, abolitionists urged women to stop buying West Indian sugar because it was a slave good, produced on plantations where enslaved Africans were subject to cruelty and where mortality rates were high. In France, the call to forego sugar came during the early years of the Revolution of 1789, in response to rising sugar prices. The women of Paris were asked to refrain from buying sugar at high prices that were assumed to be a result of market manipulation by speculators and hoarders engaging in anti-revolutionary behavior. The increase in Parisian sugar prices was not driven primarily by profiteering, but by a global shortage caused by the slave revolt in the French colony of Saint-Domingue, now Haiti. Comparing these two sugar boycotts, one in Britain, the other in France, provides an opportunity outside of national historical narratives to consider how both events employed the same technique for very different aims. The call to renounce sugar in both cases used economic pressure to create political change. An exploration of these movements for abstinence will provide a better understanding of how they critiqued consumption, and translated discourses, both abolitionist and revolutionary, into practice.
Home Is Where the Heart Is: The Rise of Emotional Spaces in the German Late Enlightenment
Authors: Minsky Amir
Published: September 2021

The emergent political arena of the late eighteenth century, and the literary one that preceded it, were claimed to be based upon a functional dichotomy between a private sphere of emotive ties and associations, and a “public sphere” of rational criticism (Habermas, 1962). This categorical distinction, however, scantily registered the emergence of a corollary affective economy in this period, which redefined social, political, and physical spaces according to their emotional content, or lack thereof. This article focuses on the rise of emotional language, its spatial configurations, and its dissemination during the late German Enlightenment in three thematic contexts: the “popular Enlightenment” (Volksaufklärung) and its emphasis on the enhancement of literacy among the lower classes to achieve emotional refinement; the visual representation of domestic emotional scenarios in the context of the Franco-German cultural exchange surrounding the French Revolution; and the emergence of “homeland” (Heimat) as an increasingly ubiquitous emotion-bound metaphor in the nationalization of space toward the century's end. These contexts reveal major shifts in the cultural dynamics of space and emotion in this period: first, the reaffirmation of emotion as a culturally viable interpretive mode, set against earlier concerted attempts to suppress or control it; second, the osmosis between private and public that enabled emotional protocols to transgress supposedly natural boundaries of class, status, and gender across society, and establish new contacts between exclusive and excluded communities; and last, the article shows how the spatial imaginary that emerged in the second half of the eighteenth century—despite its reliance on older dispositions regarding space in German culture—deployed emotional vocabularies for engendering new forms of sociability, which went on to became central determinants of Germanness in the early nineteenth century.
Knock-in tagging in zebrafish facilitated by insertion into non-coding regions
Authors: Levic Daniel S. , Yamaguchi Naoya , Wang Siyao , Knaut Holger , Bagnat Michel
Published: September 2021

Zebrafish provide an excellent model for in vivo cell biology studies because of their amenability to live imaging. Protein visualization in zebrafish has traditionally relied on overexpression of fluorescently tagged proteins from heterologous promoters, making it difficult to recapitulate endogenous expression patterns and protein function. One way to circumvent this problem is to tag the proteins by modifying their endogenous genomic loci. Such an approach is not widely available to zebrafish researchers because of inefficient homologous recombination and the error-prone nature of targeted integration in zebrafish. Here, we report a simple approach for tagging proteins in zebrafish on their N or C termini with fluorescent proteins by inserting PCR-generated donor amplicons into non-coding regions of the corresponding genes. Using this approach, we generated endogenously tagged alleles for several genes that are crucial for epithelial biology and organ development, including the tight junction components ZO-1 and Cldn15la, the trafficking effector Rab11a, the apical polarity protein aPKC and the ECM receptor Integrin β1b. Our approach facilitates the generation of knock-in lines in zebrafish, opening the way for accurate quantitative imaging studies.
Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography
Authors: Panneels Valerie , Diaz Ana , Imsand Cornelia , Guizar-Sicairos Manuel , Müller Elisabeth , Bittermann Anne Greet , Ishikawa Takashi , Menzel Andreas , Kaech Andres , Holler Mirko , Grimm Christian , Schertler Gebhard
Published: September 2021

Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.
Rab7b regulates dendritic cell migration by linking lysosomes to the actomyosin cytoskeleton
Authors: Vestre Katharina , Persiconi Irene , Borg Distefano Marita , Mensali Nadia , Guadagno Noemi Antonella , Bretou Marine , Wälchli Sébastien , Arnold-Schrauf Catharina , Bakke Oddmund , Dalod Marc , Lennon-Dumenil Ana-Maria , Progida Cinzia
Published: September 2021

Lysosomal signaling facilitates the migration of immune cells by releasing Ca2+ to activate the actin-based motor myosin II at the cell rear. However, how the actomyosin cytoskeleton physically associates to lysosomes is unknown. We have previously identified myosin II as a direct interactor of Rab7b, a small GTPase that mediates the transport from late endosomes/lysosomes to the trans-Golgi network (TGN). Here, we show that Rab7b regulates the migration of dendritic cells (DCs) in one- and three-dimensional environments. DCs are immune sentinels that transport antigens from peripheral tissues to lymph nodes to activate T lymphocytes and initiate adaptive immune responses. We found that the lack of Rab7b reduces myosin II light chain phosphorylation and the activation of the transcription factor EB (TFEB), which controls lysosomal signaling and is required for fast DC migration. Furthermore, we demonstrate that Rab7b interacts with the lysosomal Ca2+ channel TRPML1 (also known as MCOLN1), enabling the local activation of myosin II at the cell rear. Taken together, our findings identify Rab7b as the missing physical link between lysosomes and the actomyosin cytoskeleton, allowing control of immune cell migration through lysosomal signaling.

This article has an associated First Person interview with the first author of the paper.