Miracle-dz/UniFAR-FTUs huggingface dataset:
Thelopsis challenges the generic circumscription in the Gyalectaceae and brings new insights to the taxonomy of Ramonia

Abstract The genus Thelopsis was classified in the family Stictidaceae but its systematic position has never been investigated by molecular methods. In order to determine its family placement and to test its monophyly, fungal DNA of recent collections of Thelopsis specimens was sequenced. Phylogenetic analyses using nuLSU, RPB2 and mtSSU sequences reveal that members of Thelopsis form a monophyletic group within the genus Gyalecta as currently accepted. The placement of Thelopsis, including the generic type T. rubella, within the genus Gyalecta challenges the generic circumscription of this group because Thelopsis is well recognized by the combination of morphological characters: perithecioid ascomata, well-developed periphysoids, polysporous asci and small, few-septate ellipsoid-oblong ascospores. The sterile sorediate Opegrapha corticola is also placed in the Gyalectaceae as sister species to Thelopsis byssoidea + T. rubella. Ascomata of O. corticola are illustrated for the first time and support its placement in the genus Thelopsis. The hypothesis that O. corticola might represent the sorediate fertile morph of T. rubella is not confirmed because the species is phylogenetically and morphologically distinct. Thelopsis is recovered as polyphyletic, with T. melathelia being placed as sister species to Ramonia. The new combinations Thelopsis corticola (Coppins & P. James) Sanderson & Ertz comb. nov. and Ramonia melathelia (Nyl.) Ertz comb. nov. are introduced and a new species of Gyalecta, G. amsterdamensis Ertz, is described from Amsterdam and Saint-Paul Islands, characterized by a sterile thallus with discrete soralia. Petractis luetkemuelleri and P. nodispora are accommodated in the new genus Neopetractis, differing from the generic type (P. clausa) by having a different phylogenetic position and a different photobiont. Francisrosea bicolor Ertz & Sanderson gen. & sp. nov. is described for a sterile sorediate lichen somewhat similar to Opegrapha corticola but having an isolated phylogenetic position as sister to a clade including Gyalidea praetermissa and the genera Neopetractis and Ramonia. Gyalecta farlowii, G. nidarosiensis and G. carneola are placed in a molecular phylogeny for the first time. The taxonomic significance of morphological characters in Gyalectaceae is discussed.
Rapid determination of technetium-99 by automatic solid phase extraction and inductively coupled plasma mass spectrometry

Technetium-99 (99Tc) is a key nuclide, produced by the fission of uranium-235 (235U) and plutonium-239 (239Pu), through a cascade decay process, and is one kind of target element in environmental analysis due to its long half-life (t1/2 = 2.1 × 105 years). This study developed a 99Tc analytical technique using automatic solid phase extraction (SPE) with TEVA resin and inductively coupled plasma mass spectrometry (ICP-MS). The chemical recovery of 99Tc was 94.15 ± 3.14% and the minimum detectable activity (MDA) for cement solidified samples spiked with 99Tc was 1.5 mBq g−1 (2.4 pg mL−1). In this study, standard reference material (SRM), an environmental sample was measured by this analytical method. The proposed method is more convenient than traditional radiochemical methods in terms of reducing the time required for analysis, the consumption of reagents, and radiation exposure of operators.
Characterization of cardiac autonomic function in COVID-19 using heart rate variability: a hospital based preliminary observational study

Abstract Objectives The novel corona virus disease, which was initially reported in China in late 2019, has become a global pandemic affecting 330 million cases. COVID-19 affects predominantly the respiratory system, in addition to other organ systems, mainly the cardiovascular system. One of the hypotheses is that virus entering the target cells by binding to angiotensin converting enzyme 2 affecting hypothalamic pituitary axis could lead to dysautonomia which is measured by heart rate variability (HRV). HRV is a non-invasive measure of autonomic function that facilitates identification of COVID-19 patients at the risk of developing cardiovascular complications. So, we aimed to assess HRV in COVID patients and compare between COVID patients and normal controls. Methods In a case control design, we compared 63 COVID-19 infected patients with 43 healthy controls matched for age and gender. Along with clinical characterization, heart rate variability was evaluated using ambulatory 5 min ECG in lead II and expressed in frequency and time domain measures. Statistical analysis was performed using SPSS 17.0. Results Mean age of the study population was 49.1 ± 14.2 years and 71 (66.9%) were males. Frequency domain measures high (HF) and low (LF) frequency powers were significantly decreased in COVID-19 patients compared to controls. HF/LF and LF/HF ratios were not different between groups. Time domain measures rMSSD (root mean square of successive RR interval differences) and SDNN (standard deviation of NN intervals) were significantly increased among COVID-19 subjects. COVID-19 infection was associated with increased parasympathetic activity as defined by rMSSD>40 {adjusted odds ratio 7.609 (95% CI 1.61–35.94); p=0.01} and SDNN>60 {adjusted odds ratio 2.620 (95% CI 1.070–6.44); p=0.035} after adjusting for age, gender and comorbidities. Conclusions Our study results showed increased parasympathetic tone in COVID patients. Early diagnosis of autonomic imbalance in COVID patients is needed to plan management and limit progression of disease.
Artificial intelligence in prediction of non‐alcoholic fatty liver disease and fibrosis

Artificial intelligence (AI) has become increasingly widespread in our daily lives, including healthcare applications. AI has brought many new insights into better ways we care for our patients with chronic liver disease, including non‐alcoholic fatty liver disease and liver fibrosis. There are multiple ways to apply the AI technology on top of the conventional invasive (liver biopsy) and noninvasive (transient elastography, serum biomarkers, or clinical prediction models) approaches. In this review article, we discuss the principles of applying AI on electronic health records, liver biopsy, and liver images. A few common AI approaches include logistic regression, decision tree, random forest, and XGBoost for data at a single time stamp, recurrent neural networks for sequential data, and deep neural networks for histology and images.
A novel Rab11-Rab3a cascade required for lysosome exocytosis

Lysosomes are dynamic organelles, capable of undergoing exocytosis. This process is crucial for several cellular functions, namely plasma membrane repair. Nevertheless, the molecular machinery involved in this process is poorly understood. Here, we identify Rab11a and Rab11b as regulators of calcium-induced lysosome exocytosis. Interestingly, Rab11-positive vesicles transiently interact with lysosomes at the cell periphery, indicating that this interaction is required for the last steps of lysosome exocytosis. Additionally, we found that the silencing of the exocyst subunit Sec15, a Rab11 effector, impairs lysosome exocytosis independently of the exocyst complex, suggesting that Sec15 acts together with Rab11 in the regulation of lysosome exocytosis. Furthermore, we show that Rab11 binds the guanine nucleotide exchange factor for Rab3a (GRAB) and also Rab3a, which we described previously as a regulator of the positioning and exocytosis of lysosomes. Thus, our studies suggest that Rab11-positive vesicles transport GRAB to activate Rab3a on lysosomes, establishing a Rab11-Rab3 cascade that is essential for lysosome exocytosis.
Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

Structural variants (SVs) are an important source of human genome diversity but their functional effects are not well understood. We mapped 61,668 SVs in 613 individuals with deep genome sequencing data from the GTEx project and measured their effects on gene expression. We estimate that common SVs are causal at 2.66% of eQTLs, which is a 10.5-fold enrichment relative to their abundance in the genome and consistent with prior work using smaller sample sizes. Duplications and deletions were the most impactful variant types, whereas the contribution of mobile element insertions was surprisingly small (0.12% of eQTLs, 1.9-fold enriched). Multi-tissue analysis of expression effects revealed that gene-altering SVs show significantly more constitutive effects than other variant types, with 62.09% of coding SV-eQTLs active in all tissues with known eQTL activity compared to 23.08% of coding SNV- and indel-eQTLs, whereas noncoding SVs, SNVs and indels show broadly similar patterns. We also identified 539 rare SVs associated with nearby gene expression outliers. Of these, 62.34% are noncoding SVs that show strong effects on gene expression yet modest enrichment at known regulatory elements, demonstrating that rare noncoding SVs are a major source of gene expression differences but remain difficult to predict from current annotations. Remarkably, both common and rare noncoding SVs often show strong regional effects on the expression of multiple genes: SV-eQTLs affect an average of 1.82 nearby genes compared to 1.09 genes affected by SNV- and indel-eQTLs, and 21.34% of rare expression-altering SVs show strong effects on 2-9 different genes. We also observe significant effects on gene expression extending 1 Mb from the SV. This provides a mechanism by which individual noncoding SVs may have strong and/or pleiotropic effects on phenotypic variation and disease.
The human FLT1 regulatory element directs vascular expression and modulates angiogenesis pathways in vitro and in vivo

There is growing evidence that mutations in non-coding cis-regulatory elements (CREs) disrupt proper development. However, little is known about human CREs that are crucial for cardiovascular development. To address this, we bioinformatically identified cardiovascular CREs based on the occupancy of the CRE by the homeodomain protein NKX2-5 and cardiac chromatin histone modifications. This search defined a highly conserved CRE within the FLT1 locus termed enFLT1. We show that the human enFLT1 is an enhancer capable of driving reporter transgene expression in vivo throughout the developing cardiovascular system of medaka. Deletion of the human enFLT1 enhancer (ΔenFLT1) triggered molecular perturbations in extracellular matrix organisation and blood vessel morphogenesis in vitro in endothelial cells derived from human embryonic stem cells and vascular defects in vivo in medaka. These findings highlight the crucial role of the human FLT1 enhancer and its function as a regulator and buffer of transcriptional regulation in cardiovascular development.
Active enterohepatic cycling is not required for the choleretic actions of 24-norUrsodeoxycholic acid in mice

The superior ability of norursodeoxycholic acid (norUDCA) to induce a bicarbonate-rich hypercholeresis has been attributed to its ability to undergo cholehepatic shunting and norUDCA is currently being evaluated as a therapeutic for forms of liver disease. The goal of this study was to use mouse models to investigate contributions of bile acid transporters to the choleretic actions of norUDCA. Here, we show that the apical sodium-dependent bile acid transporter (ASBT) and Organic solute transporter-alpha (OSTα) are dispensable for norUDCA-stimulation of bile flow and biliary bicarbonate secretion in mice. Analysis of the liver transcriptome revealed that norUDCA induced hepatic expression of a limited number of transporter genes, particularly organic anion transporting polypeptide 1a4 (Oatp1a4). However, norUDCA potently stimulated a bicarbonate-rich hypercholeresis in Oatp1a/1b-deficient mice. Blocking intestinal bile acid reabsorption by co-administration of an ASBT inhibitor or bile acid sequestrant did not impact the ability of norUDCA to induce bile flow in wildtype mice. The results support the concept that these major bile acid transporters are not directly involved in the absorption, cholehepatic shunting, or choleretic actions of norUDCA. Additionally, the findings support further investigation of the therapeutic synergy between norUDCA and ASBT inhibitors or bile acid sequestrants for cholestatic liver disease.
Novel regulators of growth identified in the evolution of fin proportion in flying fish

Identifying the genetic foundations of trait variation and evolution is challenging as it is often difficult to parse meaningful signals from confounding signatures such as drift and epistasis. However, identification of the genetic loci underlying morphological and physiological traits can be honed through the use of comparative and complementary genetic approaches, whereby shared sets of genes that are repeatedly implicated across large evolutionary time periods as under selection can illuminate important pathways and epistatic relationships that function as novel regulators of trait development. Here we intersect comparative genomic analyses with unbiased mutagenesis screens in distantly related species to define the control of proportional growth, as changes in the size and relative proportions of tissues underlie a large degree of the variant forms seen in nature. Through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors, key innovations for flying fishes and flying halfbeaks. To refine our analysis, we intersected convergent phylogenomic signatures with mutants identified in distantly related zebrafish with altered fin size. Through these paired approaches, we identify a surprising role for an L-type amino acid transporter, lat4a, and the potassium channel, kcnh2a, in the regulation of fin proportion. We show that specific epistatic interaction between these genetic loci in zebrafish closely phenocopies the observed fin proportions of flying fishes. The congruence of experimental and phylogenomic findings point to a conserved, non-canonical signaling interaction that integrates bioelectric cues and amino acid transport in the establishment of relative size in development and evolution.
Trp53 ablation fails to prevent microcephaly in mouse pallium with impaired minor intron splicing

Mutations in minor spliceosome component RNU4ATAC, a small nuclear RNA (snRNA), are linked to primary microcephaly. We have reported that in the conditional knockout (cKO) mice for Rnu11, another minor spliceosome snRNA, minor intron splicing defect in minor intron-containing genes (MIGs) regulating cell cycle resulted in cell cycle defects, with a concomitant increase in γH2aX+ cells and p53-mediated apoptosis. Trp53 ablation in the Rnu11 cKO mice did not prevent microcephaly. However, RNAseq analysis of the double knockout (dKO) pallium reflected transcriptomic shift towards the control from the Rnu11 cKO. We found elevated minor intron retention and alternative splicing across minor introns in the dKO. Disruption of these MIGs resulted in cell cycle defects that were more severe and detected earlier in the dKO, but with delayed detection of γH2aX+ DNA damage. Thus, p53 might also play a role in causing DNA damage in the developing pallium. In all, our findings further refine our understanding of the role of the minor spliceosome in cortical development and identify MIGs underpinning microcephaly in minor spliceosome-related diseases.
Unfamiliar face matching, within-person variability, and multiple-image arrays

ABSTRACT Human unfamiliar face matching is error-prone, but some research suggests matching to multiple-image arrays instead of single images may yield improvements. Here, high or low variability arrays containing one, two, and three images, and a target image from the high and low variability image sets were displayed. Arrays were presented simultaneously or sequentially, and the target image was presented simultaneously with arrays or sequentially after arrays, in three experiments. Benefits from exposure to multiple images of the same person required simultaneous viewing of images and improvements were observed in match trials only. Only sequential viewing of a multiple-image array followed by a high variability target image enhanced overall accuracy across trial types, particularly for high variability arrays. Accuracy was highest when the target image and array items were visually similar. Results show the importance of image similarity, and suggest variability is most helpful when array and target are presented sequentially.
Determinants of Trade Openness in Sub-Saharan Africa: Do Institutions Matter?

ABSTRACT This paper aims to analyse the determinants of trade openness in Sub-Saharan Africa (SSA) countries focusing on the role play by domestic institutions. To achieve this, the Generalized Methods of Moments (GMM) is carried out on 36 SSA countries over the period 1996-2017. The results of our estimation reveal that domestic institutions as a composite index determines trade openness as a composite share of Squalli and Wilson (2011). In addition, government effectiveness, Regulatory quality and rule of law were all enhancing on trade openness. Moreover, access to sea, foreign direct investment, and trade openness lagged by one period all significantly determine trade openness in our estimations, with all these effects positive. When trade share was considered as a robustness check, inflation and population growth were further found to be significantly determine trade openness, whereas GDP per capital was significantly trade enhancing. This result was robust to alternative institutional measures and sensitive to the choices of countries and sample periods considered. The policy implications of study engaged the different states of SSA to focus on improving the quality of their domestic institutions in elaborating their international trade policies.
Human capital and income inequality revisited

ABSTRACT This paper revisits the relationship between human capital and income inequality, using an updated data set on human capital inequality and a novel database on earnings inequality. We find an inverted U-shaped relationship between these two inequality indicators, but with significant differences across countries regarding the turning point. Skill-biased technological change is found to be an additional force that may blur the relationship between human capital and earnings inequality. Over and above the effect exerted through earnings inequality, the paper shows that human capital inequality has a direct positive effect on income inequality.
External borders and internal freedoms: how the refugee crisis shaped the bordering preferences of European citizens

ABSTRACT The idea that internal inclusion requires external exclusion features prominently in many theoretical accounts of modern statehood and citizenship. In a similar vein, it has been argued that internal freedom of movement in the European Union requires strict immigration control at its external borders. This article sheds light on the relationship between internal de-bordering and external re-bordering, making two main contributions. First, we theorise the idea of an integration-demarcation conditionality based on the European Union's symbolic legitimacy and functional needs. Second, we test the common belief that public support for free movement within Europe depends on a restrictive border regime for non-European immigration. For this purpose, we assess how the external shock of the 2015 refugee crisis shaped the bordering preferences of European citizens. We find that the crisis primarily increased citizens’ support for external re-bordering, and did not substantially undermine their support for internal free movement. Thus, the large-scale arrival of refugees has not led to a general backlash against open borders and immigration but has, rather, increased public support for the European model of combining internal freedoms with external controls.
Behind the scenes: About hidden support to reach one’s audience

I have always been fascinated by glimpses into the inner workings of things, especially of organisations and processes of development. A recent experience of this was when I watched the documentary film “Backstage Vienna State Opera” by Stephanus Domanig (2019) which showcases the daily work of the people behind, next to, and underneath the stage of one of the largest opera houses in the world. Largely invisible to audiences, it is them and the interplay of their creativity, craftsmanship and collaborations that keep the complex clockwork of daily performances in a normally full house going. Sometimes, the complexity of operations needed to publish an academic journal like the Nordic Journal of Music Therapy (NJMT) reminds me of the challenges involved in staging an opera. Not only the passion and dedication of those working towards operatic performances might be similar to that felt by many in the music therapy field. It is also crucial in both realms that talents, resources and interactions are professionally and skilfully intertwined while paying due attention to timing and appropriate flexibility – and it is true that large amounts of the work involved is hidden. An indispensable group of people without whom this journal – and any other scientific journal relying on peer review – would not exist is those colleagues in music therapy and other relevant fields who generously provide their time and expertise to review manuscripts. If it wasn’t for the countless hours they spend to read, critically evaluate, and constructively comment on submissions, our journal would simply fall apart. As the NJMT is using the double-blind peer review model to allow for impartial evaluation and dialogue between reviewers and authors, they are mostly invisible to the journal’s audiences. Now, the time has come again to call them before the proverbial curtain in this issue: You will find a list of all those who acted as peer reviewers for the NJMT in 2019 and 2020 as online supplement to this issue (https://doi.org/10.1080/ 08098131.2021.1889149) We would like to take this opportunity to express our sincere thanks to these reviewers. Although some of them may be eligible to earn credits in continuing professional development schemes for manuscript review activities as part of their “service to the profession” accomplishments, or have their work recognised in commercial platforms tracking peer review and editorial contributions to academic journals, their reviewing is still a voluntary and a very time-consuming task. We often receive feedback from authors mentioning how valuable the reviewers’ feedback and suggestions were, and how they contributed to considerably improving their manuscripts. This is also in line with experiences by authors in other fields, as found in an international survey in which 90% of participating authors stated that peer review had improved the last paper they published (Mulligan et al., 2013). In general, the system of NORDIC JOURNAL OF MUSIC THERAPY 2021, VOL. 30, NO. 2, 103–105 https://doi.org/10.1080/08098131.2021. 1877390