Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycobacterial inactivation protein extraction protocol for matrix-assisted laser desorption ionization time-of-flight characterization of clinical isolates

Background: Rapid identification of mycobacteria has been made possible with matrix assisted laser desorption ionization time-of-flight (MALDI-TOF) in recent years. Working with high concentrations of mycobacteria in a PC-3 containment facility makes MALDI-TOF cumbersome and costly. Therefore removing the inactivated isolate's protein extract from the PC-3 facility is needed for efficient identification in a routine PC-2 laboratory. Methods: This work describes a novel chemical and mechanical disruption protein extraction method, which provides reliable MALDI-TOF results from solid and liquid media, while ensuring laboratory safety. Results: When compared to sequencing results, 93.9% of the clinical isolates were identified in LJ media and 89% of the clinical isolates were identified in MGIT media. Conclusion: The MIPE protocol produces a high quality protein extract with improved isolate identification without compromising result turn-around-times or laboratory safety.
Inter‐ and intra‐specific differences in muscarinic acetylcholine receptor expression in the neural pathways for vocal learning in songbirds

Acetylcholine receptors (AChRs) abound in the central nervous system of vertebrates. Muscarinic AChRs (mAChRs), a functional subclass of AChRs, mediate neuronal responses via intracellular signal transduction. They also play roles in sensorimotor coordination and motor skill learning by enhancing cortical plasticity. Learned birdsong is a complex motor skill acquired through sensorimotor coordination during a critical period. However, the functions of AChRs in the neural circuits for vocal learning and production remain largely unexplored. Here, we report the unique expression of mAChRs subunits (chrm2–5) in the song nuclei of zebra finches. The expression of excitatory subunits (chrm3 and chrm5) was downregulated in the song nuclei compared with the surrounding brain regions. In contrast, the expression of inhibitory mAChRs (chrm2 and chrm4) was upregulated in the premotor song nucleus HVC relative to the surrounding nidopallium. Chrm4 showed developmentally different expression in HVC during the critical period. Compared with chrm4, individual differences in chrm2 expression emerged in HVC early in the critical period. These individual differences in chrm2 expression persisted despite testosterone administration or auditory deprivation, which altered the timing of song stabilization. Instead, the variability in chrm2 expression in HVC correlated with parental genetics. In addition, chrm2 expression in HVC exhibited species differences and individual variability among songbird species. These results suggest that mAChRs play an underappreciated role in the development of species and individual differences in song patterns by modulating the excitability of HVC neurons, providing a potential insight into the gating of auditory responses in HVC neurons.
Ablation Index for Catheter Ablation of Atrial Fibrillation　- Clinical Applicability and Comparison With Force-Time Integral.

BACKGROUND Key determinants for lesion formation in catheter ablation are contact force, radiofrequency (RF) power and time. The aim of this study was to evaluate the clinical applicability of ablation index (AI), a novel non-linear formula based on these components, and to compare AI with the conventional linear force-time interval (FTI) in pulmonary vein isolation (PVI). Methods and Results: Target AI ranges were defined for anatomical segments of the ipsilateral pulmonary veins. The operator was blinded to AI during PVI for the initial 11 patients (group A), and was unblinded for the remaining 23 patients (group B). We assessed (1) the clinical value of AI to avoid excessively high and low values with an operator blinded vs. non-blinded to AI; and (2) the relation of AI and FTI in predefined ranges. In group A, 235/564 lesions (41.7%) were in the predefined target range as compared with 1,171/1,412 lesions (82.9%) in group B (P<0.001). A given AI may correspond to a wide range of FTI, as reflected by a quartile coefficient of dispersion for AI of 0.11 vs. a quartile coefficient of dispersion for FTI of 0.36. CONCLUSIONS Incorporating RF current power, the non-linear AI provides more comprehensive information during PVI compared with FTI. Given that the FTI for a given AI varies widely, the value of FTI in clinical practice is questionable.
Decreased Expression of ZWINT is Associated With Poor Prognosis in Patients With HCC After Surgery

Background: ZW10 interactor was recently reported to correlate with human cancers. However, the prognostic value of ZW10 interactor in hepatocellular carcinoma was not reported. Methods: The expression level of ZW10 interactor was evaluated by Western blot and immunohistochemistry using tissue microarray. In the present study, we used 5 pairs of hepatocellular carcinoma and peritumoral frozen tissues for Western blot, and 70 paired paraffin-embedded hepatocellular carcinoma and peritumoral tissues as expression pattern cohort (cohort 1), and 280 paraffin-embedded hepatocellular carcinoma tissues were used as prognostic cohort (cohort 2). The integral optic density representing the expression level of ZW10 interactor in each tissue sample, was calculated using Image-Pro Plus. The integral optic density was added to the X-tile software for calculating the outcome-based cut point. Kaplan-Meier and Cox regression were used to evaluate the prognostic values. Results: The expression level ZW10 interactor was decreased in hepatocellular carcinoma tissues in 85.7% (60/70) of the cases compared to the corresponding peritumoral tissues evaluated by immunohistochemistry. Similar result was obtained by Western blot analysis using frozen tissue. Expression of ZW10 interactor was closely correlated with age (P = .0001) and liver cirrhosis in cohort 1 and tumor node metastasis (P = .018), tumor size (P = .005), and vascular invasion (P = .022) in cohort 2 based on χ2 analyses. Survival analyses indicated that patients with hepatocellular carcinoma having low ZW10 interactor expression had a shorter overall survival time and time to recurrence compared to cases with high ZW10 interactor expression in the prognostic cohort (P < .0001 for both overall survival and time to recurrence ). Univariate and multivariate Cox analyses indicated that ZW10 interactor was an independent prognostic factor for overall survival (P = .033). Conclusions: The present study clearly showed that ZW10 interactor was frequently decreased in hepatocellular carcinoma compared to nontumoral liver tissues, and ZW10 interactor could serve as a potential prognostic marker in patients with hepatocellular carcinoma after surgery.
Removal of silver nanoparticles coated with different stabilizers from aqueous medium by electrocoagulation

ABSTRACT This study evaluated the removal of silver nanoparticles (AgNPs), coated with different stabilizers, from aqueous media using the electrocoagulation technique. The AgNPs dispersions were synthesized by chemical reduction with silver nitrate as precursor, sodium borohydride as reducing agent and sodium carboxymethylcellulose (CMC), polyvinyl alcohol (PVA) and polyvinylpyrrolidone (PVP) as stabilizers with initial concentrations of 1 and 3% (w/v). The dispersions were named AgNPs-CMC1, AgNPs-CMC3, AgNPs-PVA1, AgNPs-PVA3, AgNPs-PVP1, and AgNPs-PVP3. Electrocoagulation treatments of AgNPs-PVA1, AgNPs-PVP1 and AgNPs-PVP3 dispersions resulted in total silver removals above 99.90% in 10 min. For the AgNPs-PVP3 dispersion 99.98% of removal was obtained in 20 min. After 15 min of electrolysis, The AgNPs-CMC1 and AgNPs-CMC3 dispersions showed a reduction in total silver concentration of 71.72 and 52.15%, respectively. Therefore, these results showed that the removal of AgNPs from the aqueous medium by electrocoagulation is possible, but their efficiency and viability depends on the nature, the molecular structure and the concentration of stabilizers. Furthermore, the toxicity analysis using the Vibrio fischeri bacteria demonstrated that only the dispersions stabilized with PVP became suitable for disposal after the electrocoagulation treatment. GRAPHICAL ABSTRACT
edge2vec: Learning Node Representation Using Edge Semantics

Representation learning for networks provides a new way to mine graphs. Although current researches in this area are able to generate reliable results of node embeddings, they are still limited to homogeneous networks in which all nodes and edges are of the same type. While, increasingly, graphs are heterogeneous with multiple node- and edge- types in the real world. Existing heterogeneous embedding methods are mostly task-based or only able to deal with limited types of node&edge. To tackle this challenge, in this paper, an edge2vec model is proposed to represent nodes in ways that incorporate edge semantics represented as different edge-types in heterogeneous networks. An edge-type transition matrix is optimized from an Expectation-Maximization (EM) framework as an extra criterion of a biased node random walk on networks, and a biased skip-gram model is leveraged to learn node embeddings based on the random walks afterwards. edge2vec is validated and evaluated using three medical domain problems on an ensemble of complex medical networks (more than 10 node- \&edge- types): medical entity classification, compound-gene binding prediction, and medical information searching cost. Results show that by considering edge semantics, edge2vec significantly outperforms other state-of-art models on all three tasks.
Measuring Psychological Inflexibility in Children and Adolescents: Evaluating the Avoidance and Fusion Questionnaire for Youth

The Avoidance and Fusion Questionnaire for Youth (AFQ-Y8) was developed to measure psychological inflexibility. Although the questionnaire is a well-known tool in clinical practice, its psychometric properties have not been widely investigated in the target population of children and adolescents. The purpose of this study was to investigate the factor structure and validity of the AFQ-Y8 (N = 1,572, mean age 15.39 years, girls 51%) on a Hungarian sample. We also tested the invariance of the measurement model across two age groups (11-14 and 15-20 years old). Results confirmed the single-factor structure of the AFQ-Y8. Psychological inflexibility was also found to be positively related to emotional instability, externalizing, and internalizing problems. Furthermore, psychological inflexibility explained the variance of life satisfaction when personality dimensions, emotional, and behavioral problems were accounted for. Measurement invariance across age groups was partially supported. These results suggest that the AFQ-Y8 is a reliable and valid instrument for assessing psychological inflexibility in children and adolescents.
DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy

ABSTRACT Ionizing radiation (IR) causes DNA double-strand breaks (DSBs) and activates a versatile cellular response regulating DNA repair, cell-cycle progression, transcription, DNA replication and other processes. In recent years proteomics has emerged as a powerful tool deepening our understanding of this multifaceted response. In this study we use SILAC-based proteomics to specifically investigate dynamic changes in cytoplasmic protein abundance after ionizing radiation; we present in-depth bioinformatics analysis and show that levels of proteins involved in autophagy (cathepsins and other lysosomal proteins), proteasomal degradation (Ubiquitin-related proteins), energy metabolism (mitochondrial proteins) and particularly translation (ribosomal proteins and translation factors) are regulated after cellular exposure to ionizing radiation. Downregulation of no less than 68 ribosomal proteins shows rapid changes in the translation pattern after IR. Additionally, we provide evidence of compartmental cytosol-nuclear translocation of numerous DNA damage related proteins using protein correlation profiling. In conclusion, these results highlight unexpected cytoplasmic processes actively orchestrated after genotoxic insults and protein translocation from the cytoplasm to the nucleus as a fundamental regulatory mechanism employed to aid cell survival and preservation of genome integrity.
Extending set functors to generalised metric spaces

For a commutative quantale $\mathcal{V}$, the category $\mathcal{V}-cat$ can be perceived as a category of generalised metric spaces and non-expanding maps. We show that any type constructor $T$ (formalised as an endofunctor on sets) can be extended in a canonical way to a type constructor $T_{\mathcal{V}}$ on $\mathcal{V}-cat$. The proof yields methods of explicitly calculating the extension in concrete examples, which cover well-known notions such as the Pompeiu-Hausdorff metric as well as new ones. Conceptually, this allows us to to solve the same recursive domain equation $X\cong TX$ in different categories (such as sets and metric spaces) and we study how their solutions (that is, the final coalgebras) are related via change of base. Mathematically, the heart of the matter is to show that, for any commutative quantale $\mathcal{V}$, the `discrete' functor $D:\mathsf{Set}\to \mathcal{V}-cat$ from sets to categories enriched over $\mathcal{V}$ is $\mathcal{V}-cat$-dense and has a density presentation that allows us to compute left-Kan extensions along $D$.
Mapping mammalian replication domains using the ion torrent semiconductor sequencing platform

ABSTRACT Here, we show that semiconductor-based sequencing technology can be used to map mammalian replication domains, chromosomal units with similar DNA replication timing. Replicating DNA purified from mammalian cells was successfully sequenced by the Ion Torrent platform. The resultant replication domain map of mouse embryonic stem cells is comparable to those obtained by the conventional microarray-based method.
Demand for Imported Crude Oil in Pakistan: NARDL Framework

This research article analyzes the long run relationship between real GDP growth rate and demand for imported crude oil in Pakistan assuming asymmetries. Annual time series data for quantity of imported crude oil, real GDP growth rate and price of imported crude oil are used from 1970 to 2014. Using Nonlinear Autoregressive Distributed Lag (NARDL) Model, the variables are found to be cointegrated. As theory predicts, demand for imported crude oil is relatively in-elastic and negatively related to its price. There is no evidence of non-linear or asymmetrical relationship between real GDP growth rate and demand for imported crude oil in the long run. However, dis-aggregation shows that negative changes in real GDP growth rate lead to a rise in the demand for imported crude oil while positive changes have no significant effect. The results suggest that even though local crude oil production is increasing, there is still a growing dependence on imported crude oil and thus, it is important to invest in local and alternative energy resources to revive the crumbling energy sector in Pakistan.
Neutrophilic fixed drug eruption: a mimic of neutrophilic dermatoses

1 Aizawa N, Asahina A, Ishii N et al. The nose as a predilection site of pemphigus. Clin Exp Dermatol 2018; 43: 71–2. 2 Kishibe M, Kinouchi M, Ishida-Yamamoto A et al. Pemphigus foliaceous localised to the nose. Clin Exp Dermatol 2003; 28: 554–64. 3 Ioannides D, Hytiroglou P, Phelps RG, Bystryn JC. Regional variation in the expression of pemphigus foliaceous, pemphigus erythematosus and pemphigus vulgaris antigens in human skin. J Invest Dermatol 1991; 96: 159–61. 4 Sebaratnam D, Martin LK, Rubin AI et al. Reversible relapse of pemphigus foliaceus triggered by topical imiquimod suggests that Toll-like receptor 7 inhibitors may be useful treatments for pemphigus. Clin Exp Dermatol 2011; 36: 91–3. 5 Kano Y, Shimosegawa M, Mizukawa Y, Shiohara T. Pemphigus foliaceus induced by exposure to sunlight. Dermatology 2000; 201: 132–8.
Variational data assimilation for transient blood flow simulations: Cerebral aneurysms as an illustrative example

Several cardiovascular diseases are caused from localised abnormal blood flow such as in the case of stenosis or aneurysms. Prevailing theories propose that the development is caused by abnormal wall shear stress in focused areas. Computational fluid mechanics have arisen as a promising tool for a more precise and quantitative analysis, in particular because the anatomy is often readily available even by standard imaging techniques such as magnetic resonance and computed tomography angiography. However, computational fluid mechanics rely on accurate initial and boundary conditions, which are difficult to obtain. In this paper, we address the problem of recovering high‐resolution information from noisy and low‐resolution physical measurements of blood flow (for example, from phase‐contrast magnetic resonance imaging [PC‐MRI]) using variational data assimilation based on a transient Navier‐Stokes model. Numerical experiments are performed in both 3D (2D space and time) and 4D (3D space and time) and with pulsatile flow relevant for physiological flow in cerebral aneurysms. The results demonstrate that, with suitable regularisation, the model accurately reconstructs flow, even in the presence of significant noise.
Comparison of the Mitochondrial Genome Sequences of Six Annulohypoxylon stygium Isolates Suggests Short Fragment Insertions as a Potential Factor Leading to Larger Genomic Size

Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in the eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium (Lév.) were assembled from raw reads from PacBio and Illumina sequencing. The diversity of genomic structures, conserved genes, intergenic regions and introns were analyzed and compared. Genome sizes ranged from 132 to 147 kb and contained the same sets of conserved protein-coding, tRNA and rRNA genes and shared the same gene arrangements and orientation. In addition, most intergenic regions were homogeneous and had similar sizes except for the region between cytochrome b (cob) and cytochrome c oxidase I (cox1) genes which ranged from 2,998 to 8,039 bp among the six isolates. Sixty-five intron insertion sites and 99 different introns were detected in these genomes. Each genome contained 45 or more introns, which varied in distribution and content. Introns from homologous insertion sites also showed high diversity in size, type and content. Comparison of introns at the same loci showed some complex introns, such as twintrons and ORF-less introns. There were 44 short fragment insertions detected within introns, intergenic regions, or as introns, some of them located at conserved domain regions of homing endonuclease genes. Insertions of short fragments such as small inverted repeats might affect or hinder the movement of introns, and these allowed for intron accumulation in the mitochondrial genomes analyzed, and enlarged their size. This study showed that the evolution of fungal mitochondrial introns is complex, and the results suggest short fragment insertions as a potential factor leading to larger mitochondrial genomes in A. stygium.
Advancements in imaging technology for microvascular free tissue transfer

The use of preoperative imaging has become routine for many reconstructive microsurgeons to help localize perforators for planning of microvascular free flaps. However, with advancements in imaging technology, perforator mapping represents only one potential benefit as virtual planning and medical modeling, and flap tissue perfusion are also rapidly becoming commonplace and the standard of care for many surgeons who perform high‐volume free flap reconstruction for the breast, head and neck, torso, and the extremities.
Preservation of microbial DNA in marine sediments: insights from extracellular DNA pools

Marine sediments harbour extracellular DNA (exDNA) not associated with currently living organisms. Including this exDNA in genetic surveys may distort abundance and diversity estimates of living prokaryotic communities. We separately extract exDNA and intracellular DNA (inDNA) from 11 horizons in a 10-m deep sediment core from Aarhus Bay (Denmark) that spans > 9000 years of Holocene sedimentation. We compare depth profiles of bacterial and archaeal 16S rRNA gene compositions to those of macrofaunal activity (bioturbation), sulfate and methane concentrations, sediment age and lithology. Among these variables, bioturbation shows the strongest relationship with the two DNA pools. In bioturbated surface sediments, the majority of Operational Taxonomic Units (OTUs) present in exDNA is absent from inDNA, thus belonging to microorganisms that were not alive at the time of sampling. Below the bioturbation zone, the two DNA pools display a much higher phylogenetic similarity. At all depths, the majority of exDNA and inDNA sequences show highest sequence similarities to sediment microorganisms, a finding that is additionally supported by separate analyses on low- and high-molecular weight exDNA. Our results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.
Predicting lung nodule malignancies by combining deep convolutional neural network and handcrafted features

To predict lung nodule malignancy with a high sensitivity and specificity for low dose CT (LDCT) lung cancer screening, we propose a fusion algorithm that combines handcrafted features (HF) into the features learned at the output layer of a 3D deep convolutional neural network (CNN). First, we extracted twenty-nine HF, including nine intensity features, eight geometric features, and twelve texture features based on grey-level co-occurrence matrix (GLCM). We then trained 3D CNNs modified from three 2D CNN architectures (AlexNet, VGG-16 Net and Multi-crop Net) to extract the CNN features learned at the output layer. For each 3D CNN, the CNN features combined with the 29 HF were used as the input for the support vector machine (SVM) coupled with the sequential forward feature selection (SFS) method to select the optimal feature subset and construct the classifiers. The fusion algorithm takes full advantage of the HF and the highest level CNN features learned at the output layer. It can overcome the disadvantage of the HF that may not fully reflect the unique characteristics of a particular lesion by combining the intrinsic CNN features. Meanwhile, it also alleviates the requirement of a large scale annotated dataset for the CNNs based on the complementary of HF. The patient cohort includes 431 malignant nodules and 795 benign nodules extracted from the LIDC/IDRI database. For each investigated CNN architecture, the proposed fusion algorithm achieved the highest AUC, accuracy, sensitivity, and specificity scores among all competitive classification models.