julilili42/papers huggingface dataset:
Automation improves repeatability of retinal oximetry measurements
2021-12-16

Purpose Retinal oximetry is a technique based on spectrophotometry where images are analyzed with software capable of calculating vessel oxygen saturation and vessel diameter. In this study, the effect of automation of measurements of retinal vessel oxygen saturation and vessel diameter is explored. Methods Until now, operators have had to choose each vessel segment to be measured explicitly. A new, automatic version of the software automatically selects the vessels once the operator defines a measurement area. Five operators analyzed image pairs from the right eye of 23 healthy subjects with semiautomated retinal oximetry analysis software, Oxymap Analyzer (v2.5.1), and an automated version (v3.0). Inter- and intra-operator variability was investigated using the intraclass correlation coefficient (ICC) between oxygen saturation measurements of vessel segments in the same area of the retina. Results For semiautomated saturation measurements, the inter-rater ICC was 0.80 for arterioles and venules. For automated saturation measurements, the inter-rater ICC was 0.97 for arterioles and 0.96 for venules. For semiautomated diameter measurements, the inter-rater ICC was 0.71 for arterioles and venules. For automated diameter measurements the inter-rater ICC was 0.97 for arterioles and 0.95 for venules. The inter-rater ICCs were different ( p &lt; 0.01) between the semiautomated and automated version in all instances. Conclusion Automated measurements of retinal oximetry values are more repeatable compared to measurements where vessels are selected manually.
Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank
2021-12-16

Abstract Background The role of copy number variants (CNVs) in susceptibility to asthma is not well understood. This is, in part, due to the difficulty of accurately measuring CNVs in large enough sample sizes to detect associations. The recent availability of whole-exome sequencing (WES) in large biobank studies provides an unprecedented opportunity to study the role of CNVs in asthma. Methods We called common CNVs in 49,953 individuals in the first release of UK Biobank WES using ClinCNV software. CNVs were tested for association with asthma in a stage 1 analysis comprising 7,098 asthma cases and 36,578 controls from the first release of sequencing data. Nominally-associated CNVs were then meta-analysed in stage 2 with an additional 17,280 asthma cases and 115,562 controls from the second release of UK Biobank exome sequencing, followed by validation and fine-mapping. Results Five of 189 CNVs were associated with asthma in stage 2, including a deletion overlapping the HLA-DQA1 and HLA-DQB1 genes, a duplication of CHROMR/PRKRA , deletions within MUC22 and TAP2 , and a duplication in FBRSL1 . The HLA-DQA1, HLA-DQB1, MUC22 and TAP2 genes all reside within the human leukocyte antigen (HLA) region on chromosome 6. In silico analyses demonstrated that the deletion overlapping HLA-DQA1 and HLA-DQB1 is likely to be an artefact arising from under-mapping of reads from non-reference HLA haplotypes, and that the CHROMR/PRKRA and FBRSL1 duplications represent presence/absence of pseudogenes within the HLA region. Bayesian fine-mapping of the HLA region suggested that there are two independent asthma association signals. The variants with the largest posterior inclusion probability in the two credible sets were an amino acid change in HLA-DQB1 (glutamine to histidine at residue 253) and a multi-allelic amino acid change in HLA-DRB1 (presence/absence of serine, glycine or leucine at residue 11). Conclusions At least two independent loci characterised by amino acid changes in the HLA-DQA1, HLA-DQB1 and HLA-DRB1 genes are likely to account for association of SNPs and CNVs in this region with asthma. The high divergence of haplotypes in the HLA can give rise to spurious CNVs, providing an important, cautionary tale for future large-scale analyses of sequencing data.
Clinical Evaluation of an Abbreviated Contrast-Enhanced Whole-Body MRI for Oncologic Follow-Up Imaging
2021-12-16

Over the last decades, overall survival for most cancer types has increased due to earlier diagnosis and more effective treatments. Simultaneously, whole-body MRI-(WB-MRI) has gained importance as a radiation free staging alternative to computed tomography. The aim of this study was to evaluate the diagnostic confidence and reproducibility of a novel abbreviated 20-min WB-MRI for oncologic follow-up imaging in patients with melanoma. In total, 24 patients with melanoma were retrospectively included in this institutional review board-approved study. All patients underwent three consecutive staging examinations via WB-MRI in a clinical 3 T MR scanner with an abbreviated 20-min protocol. Three radiologists independently evaluated the images in a blinded, random order regarding image quality (overall image quality, organ-based image quality, sharpness, noise, and artifacts) and regarding its diagnostic confidence on a 5-point-Likert-Scale (5 = excellent). Inter-reader agreement and reproducibility were assessed. Overall image quality and diagnostic confidence were rated to be excellent (median 5, interquartile range [IQR] 5–5). The sharpness of anatomic structures, and the extent of noise and artifacts, as well as the assessment of lymph nodes, liver, bone, and the cutaneous system were rated to be excellent (median 5, IQR 4–5). The image quality of the lung was rated to be good (median 4, IQR 4–5). Therefore, our study demonstrated that the novel accelerated 20-min WB-MRI protocol is feasible, providing high image quality and diagnostic confidence with reliable reproducibility for oncologic follow-up imaging.
Is ‘Africa’ a racial slur and should the continent be renamed?
2021-12-16

In this paper, we will investigate whether or not the name ‘Africa’ can be seen as a slur. Since the name was given by European exploiters, slavers and colonists, it raises the question of whether such a name should continue to be accepted or abandoned. It may seem that just as the slavers renamed their victims and the colonists renamed the territories they conquered, the name Africa/ns similarly was an imposition on the continent and its peoples. It can also be argued that the naming of the continent by an external aggressor is a form of epistemic subordination that vitiates the dignity of the inhabitants. That is to say that European slavers took it upon themselves to give the inhabitants an identity that highlights climate and possibly skin colour because it was something they could not do for themselves. This presents the inhabitants as inferior to their namers and whose millennia-old civilisational achievements can comfortably be overlooked. We argue that the two preceding arguments constitute compelling reasons to abandon the name Africa as a compromised identity and offer an idea for the renaming of the continent.
Development of a sensitive trial-ready poly(GP) CSF biomarker assay for C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis
2021-12-16

Abstract A GGGGCC repeat expansion in the C9orf72 gene is the most common cause of genetic frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). As potential therapies targeting the repeat expansion are now entering clinical trials, sensitive biomarker assays of target engagement are urgently required. We utilised the single molecule array (Simoa) platform to develop an immunoassay for measuring poly(GP) dipeptide repeat proteins (DPRs) generated by the repeat expansion in CSF of people with C9orf72 -associated FTD/ALS. We show the assay to be highly sensitive and robust, passing extensive qualification criteria including low intra- and inter-plate variability, a high precision and accuracy in measuring both calibrators and samples, dilutional parallelism, tolerance to sample and standard freeze-thaw and no haemoglobin interference. We used this assay to measure poly(GP) DPRs in the CSF of samples collected through the Genetic FTD Initiative. We found it had 100% specificity and 100% sensitivity and a large window for detecting target engagement, as the C9orf72 CSF sample with the lowest poly(GP) signal had 8-fold higher signal than controls and on average values from C9orf72 samples were 38-fold higher than controls, which all fell below the lower limit of quantification of the assay. These data indicate that a Simoa-based poly(GP) DPR assay is suitable for use in clinical trials to determine target engagement of therapeutics aimed at reducing C9orf72 repeat-containing transcripts.
Bright Luminescence by Combining Chiral [2.2]Paracyclophane with a Boron–Nitrogen‐Doped Polyaromatic Hydrocarbon Building Block
2021-12-17

Abstract Novel BN‐doped compounds based on chiral, tetrasubstituted [2.2]paracyclophane and NBN‐benzo[ f , g ]tetracene were synthesized by Sonogashira–Hagihara coupling. Conjugated ethynyl linkers allow electronic communication between the π‐electron systems through‐bond, whereas through‐space interactions are provided by strong π–π overlap between the pairs of NBN‐building blocks. Excellent optical and chiroptical properties in racemic and enantiopure conditions were measured, with molar absorption coefficients up to ε =2.04×10 5 M −1 cm −1 , fluorescence quantum yields up to Φ PL =0.70, and intense, mirror‐image electronic circular dichroism and circularly polarized luminescence signals of the magnitude of 10 −3 for the absorption and luminescence dissymmetry factors. Computed g lum,calcd. values match the experimental ones. Electroanalytical data show both oxidation and reduction of the ethynyl‐linked tetra‐NBN‐substituted paracyclophane, with an overlap of two redox processes for oxidation leading to a diradical dication.
CXCR4 and CXCR7 Inhibition Ameliorates the Formation of Platelet–Neutrophil Complexes and Neutrophil Extracellular Traps through Adora2b Signaling
2021-12-17

Peritonitis and peritonitis-associated sepsis are characterized by an increased formation of platelet–neutrophil complexes (PNCs), which contribute to an excessive migration of polymorphonuclear neutrophils (PMN) into the inflamed tissue. An important neutrophilic mechanism to capture and kill invading pathogens is the formation of neutrophil extracellular traps (NETs). Formation of PNCs and NETs are essential to eliminate pathogens, but also lead to aggravated tissue damage. The chemokine receptors CXCR4 and CXCR7 on platelets and PMNs have been shown to play a pivotal role in inflammation. Thereby, CXCR4 and CXCR7 were linked with functional adenosine A2B receptor (Adora2b) signaling. We evaluated the effects of selective CXCR4 and CXCR7 inhibition on PNCs and NETs in zymosan- and fecal-induced sepsis. We determined the formation of PNCs in the blood and, in addition, their infiltration into various organs in wild-type and Adora2b−/− mice by flow cytometry and histological methods. Further, we evaluated NET formation in both mouse lines and the impact of Adora2b signaling on it. We hypothesized that the protective effects of CXCR4 and CXCR7 antagonism on PNC and NET formation are linked with Adora2b signaling. We observed an elevated CXCR4 and CXCR7 expression in circulating platelets and PMNs during acute inflammation. Specific CXCR4 and CXCR7 inhibition reduced PNC formation in the blood, respectively, in the peritoneal, lung, and liver tissue in wild-type mice, while no protective anti-inflammatory effects were observed in Adora2b−/− animals. In vitro, CXCR4 and CXCR7 antagonism dampened PNC and NET formation with human platelets and PMNs, confirming our in vivo data. In conclusion, our study reveals new protective aspects of the pharmacological modulation of CXCR4 and CXCR7 on PNC and NET formation during acute inflammation.
A reference induced pluripotent stem cell line for large-scale collaborative studies
2021-12-17

Abstract Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate iPSC lines and deeply characterised their genetic properties using whole genome sequencing, their genomic stability upon CRISPR/Cas9-based gene editing, and their phenotypic properties including differentiation to commonly-used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and hundreds of its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field. Summary The authors of this collaborative study deeply characterized human induced pluripotent stem cell (iPSC) lines to rationally select a clonally-derived cell line that performs well across multiple modalities. KOLF2.1J was identified as a candidate reference cell line based on single-cell analysis of its gene expression in the pluripotent state, whole genome sequencing, genomic stability after highly efficient CRISPR-mediated gene editing, integrity of the p53 pathway, and the efficiency with which it differentiated into multiple target cell populations. Since it is deeply characterized and can be readily acquired, KOLF2.1J is an attractive reference cell line for groups working with iPSCs. Graphical abstract
Muscle Fatigue Revisited – Insights From Optically Pumped Magnetometers
2021-12-17

So far, surface electromyography (sEMG) has been the method of choice to detect and evaluate muscle fatigue. However, recent advancements in non-cryogenic quantum sensors, such as optically pumped magnetometers (OPMs), enable interesting possibilities to flexibly record biomagnetic signals. Yet, a magnetomyographic investigation of muscular fatigue is still missing. Here, we simultaneously used sEMG (4 surface electrode) and OPM-based magnetomyography (OPM-MMG, 4 sensors) to detect muscle fatigue during a 3 × 1-min isometric contractions of the left rectus femoris muscle in 7 healthy participants. Both signals exhibited the characteristic spectral compression distinctive for muscle fatigue. OPM-MMG and sEMG slope values, used to quantify the spectral compression of the signals, were positively correlated, displaying similarity between the techniques. Additionally, the analysis of the different components of the magnetic field vector enabled speculations regarding the propagation of the muscle action potentials (MAPs). Altogether these results show the feasibility of the magnetomyographic approach with OPMs and propose a potential alternative to sEMG for the study of muscle fatigue.
Association of Cholinergic Basal Forebrain Volume and Functional Connectivity with Markers of Inflammatory Response in the Alzheimer’s Disease Spectrum
2021-12-17

Background: Inflammation has been described as a key pathogenic event in Alzheimer’s disease (AD), downstream of amyloid and tau pathology. Preclinical and clinical data suggest that the cholinergic basal forebrain may moderate inflammatory response to different pathologies. Objective: To study the association of cholinergic basal forebrain volume and functional connectivity with measures of neuroinflammation in people from the AD spectrum. Methods: We studied 261 cases from the DELCODE cohort, including people with subjective cognitive decline, mild cognitive impairment, AD dementia, first degree relatives, and healthy controls. Using Bayesian ANCOVA, we tested associations of MRI indices of cholinergic basal forebrain volume and functional connectivity with cerebrospinal fluid (CSF) levels of sTREM2 as a marker of microglia activation, and serum levels of complement C3. Using Bayesian elastic net regression, we determined associations between basal forebrain measures and a large inflammation marker panel from CSF and serum. Results: We found anecdotal to moderate evidence in favor of the absence of an effect of basal forebrain volume and functional connectivity on CSF sTREM2 and serum C3 levels both in Aβ42/ptau-positive and negative cases. Bayesian elastic net regression identified several CSF and serum markers of inflammation that were associated with basal forebrain volume and functional connectivity. The effect sizes were moderate to small. Conclusion: Our data-driven analyses generate the hypothesis that cholinergic basal forebrain may be involved in the neuroinflammation response to Aβ42 and phospho-tau pathology in people from the AD spectrum. This hypothesis needs to be tested in independent samples.
Biallelic Loss‐of‐Function NDUFA12 Variants Cause a Wide Phenotypic Spectrum from Leigh/Leigh‐Like Syndrome to Isolated Optic Atrophy
2021-12-17

Abstract Background Biallelic loss‐of‐function NDUFA12 variants have hitherto been linked to mitochondrial complex I deficiency presenting with heterogeneous clinical and radiological features in nine cases only. Objectives To fully characterize, both phenotypically and genotypically, NDUFA12 ‐related mitochondrial disease. Methods We collected data from cases identified by screening genetic databases of several laboratories worldwide and systematically reviewed the literature. Results Nine unreported NDUFA12 cases from six pedigrees were identified, with presentation ranging from movement disorder phenotypes (dystonia and/or spasticity) to isolated optic atrophy. MRI showed basal ganglia abnormalities ( n = 6), optic atrophy ( n = 2), or was unremarkable ( n = 1). All carried homozygous truncating NDUFA12 variants, three of which are novel. Conclusions Our case series expands phenotype–genotype correlations in NDUFA12 ‐associated mitochondrial disease, providing evidence of intra‐ and inter‐familial clinical heterogeneity for the same variant. It confirms NDUFA12 variants should be included in the diagnostic workup of Leigh/Leigh‐like syndromes – particularly with dystonia – as well as isolated optic atrophy.
The Narrative of the Rise of China and Authoritarianism in the Global South: The Case of Egypt
2021-12-17

Authoritarian regimes in the Global South diffuse compelling narratives of China, the Belt and Road Initiative (BRI) and its development success to reinforce authoritarian practices discursively. A case illustrative of this process is that of Egypt under President Abdul Fatah el-Sisi. An analysis drawing on strategic narrative theory highlights that the el-Sisi regime has been deploying a persuasive narrative on China, its development experience and the BRI to reinforce authoritarianism discursively under the pretext of preserving the state's sovereignty and achieving progress and the public good. Such a process is called Authoritarian Reinforcement (AR).
Technical Note: Novel Use of CytoSorb™ Haemadsorption to Provide Wound Healing Support in Case of Severe Burn Trauma via Reduction of Hyperbilirubinaemia
2021-12-17

Hyperbilirubinaemia has been shown to compromise wound healing in severely burned patients. The therapy options for patients with impairment of wound healing and subsequent severe liver dysfunction are limited. A novel extracorporeal treatment, CytoSorb ® (CytoSorbents Corp, USA), is a whole blood adsorber composed of highly biocompatible and porous polystyrene divinylbenzene copolymer beads covered in a polyvinylpyrrolidone coating. It is capable of extracting mainly hydrophobic middle-sized (up to 55 kDa) molecules from blood via size exclusion, including cytokines and bilirubin. We performed therapy with CytoSorb ® on a severely burned (48% Total Body Surface Area-TBSA) patient with secondary sclerosing cholangitis (SCC) to promote the wound healing process by reducing bilirubin concentrations and to bridge the time to spontaneous liver regeneration or eventually to liver transplantation after two skin transplantations had failed to provide wound closure. In the first 6 days the cartridge was changed on a daily basis and later after every 2–4 days. The therapy with six adsorbers decreased a total bilirubin concentration from 14.02 to 4.29 mg/dl. By maintaining a stable bilirubin concentration under 5 mg/dl, debridement of abdomen and upper extremities with autologous skin grafting and, 4 weeks later, autologous skin grafting of the back from scrotum and lower extremities were performed successfully. After wound healing had been achieved, the CytoSorb therapy was discontinued after 57 days and 27 adsorber changes. CytoSorb therapy can be a promising support of wound and skin graft healing in patients with severe burns and liver dysfunction due to a significant reduction of total bilirubin concentration.
Population coding and oscillatory subspace synchronization integrate context into actions
2021-12-17

Abstract Contextual cues and prior evidence guide human goal-directed behavior. To date, the neurophysiological mechanisms that implement contextual priors to guide subsequent actions remain unclear. Here we demonstrate that increasing behavioral uncertainty introduces a shift from an oscillatory to a continuous processing mode in human prefrontal cortex. At the population level, we found that oscillatory and continuous dynamics reflect dissociable signatures that support distinct aspects of encoding, transmission and execution of context-dependent action plans. We show that prefrontal population activity encodes predictive context and action plans in serially unfolding orthogonal subspaces, while prefrontal-motor theta oscillations synchronize action-encoding population subspaces to mediate the hand-off of action plans. Collectively, our results reveal how two key features of large-scale population activity, namely continuous population trajectories and oscillatory synchrony, operate in concert to guide context-dependent human behavior.
Thickness‐Dependent Energy‐Level Alignment at the Organic–Organic Interface Induced by Templated Gap States
2021-12-17

Abstract Planar organic heterostructures are widely explored and employed in photovoltaic cells, light‐emitting diodes, and bilayer field‐effect transistors. An important role for device performance plays the energy level alignment at the inorganic–organic and organic–organic interfaces. In this work, incremental ultraviolet photoelectron spectroscopy measurements and real‐time X‐ray scattering experiments are used to thoroughly investigate the thickness‐dependent electronic and structural properties of a perfluoropentacene (PFP)‐on‐[6]phenacene heterostructure. For both materials an incremental increase of the material work function (positive interface dipole) is found. For [6]phenacene, this can be assigned to a thickness‐dependent change of molecular arrangement evident from a change of the unit cell volume and a consequential alteration of the ionization energy. In the case of PFP the interface dipole stems from charge transfer from the substrate into unoccupied molecular orbitals resulting in an electrostatic potential on the surface. The magnitude of this potential can be correlated with an increased gap state density resulting from templated structural defects mediated by the bottom layer.