Miracle-dz/UniFAR-FTUs huggingface dataset:
Photodynamic Therapy for Metastatic Melanoma Treatment: A Review

This review article is based on specifically targeted nanoparticles that have been used in the treatment of melanoma. According to the Skin Cancer Foundation, within 2017 an estimated 9730 people will die due to invasive melanoma. Conventional treatments for nonmalignant melanoma include surgery, chemotherapy, and radiation. For the treatment of metastatic melanoma, 3 therapeutic agents have been approved by the Food and Drug Administration: dacarbazine, recombinant interferon α-2b, and high-dose interleukin 2. Photodynamic therapy is an alternative therapy that activates a photosensitizer at a specific wavelength forming reactive oxygen species which in turn induces cell death; it is noninvasive with far less side effects when compared to conventional treatments. Nanoparticles are generally conjugated to photosynthetic drugs, since they are biocompatible, stabile, and durable, as well as have a high loading capacity, which improve either passive or active photosensitizer drug delivery to targeted cells. Therefore, various photosynthetic drugs and nanoparticle drug delivery systems specifically targeted for melanoma were analyzed in this review article in relation to either their passive or their active cellular uptake mechanisms in order to deduce the efficacy of photodynamic therapy treatment for metastatic melanoma which currently remains ongoing. The overall findings from this review concluded that no current photodynamic therapy studies have been performed in relation to active nanoparticle platform photosensitizer drug carrier systems for the treatment of metastatic melanoma, and so this type of research requires further investigation into developing a more efficient active nano-photosensitizer carrier smart drug that can be conjugated to specific cell surface receptors and combinative monoclonal antibodies so that a further enhanced and more efficient form of targeted photodynamic therapy for the treatment of metastatic melanoma can be established.
Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.
Hydroxyl radical‐induced early stage oxidation improves the foaming and emulsifying properties of ovalbumin

ABSTRACT As the most abundant protein in chicken eggs, ovalbumin plays an important role in the processing of high value‐added poultry products. The present study investigated the effects of hydroxyl radical‐induced early stage oxidation on the physicochemical and interfacial properties of chicken egg white ovalbumin. Protein carbonyl content of ovalbumin increased (from 0.78 to 1.13 nmol/mg) with the oxidation time (0‐5 h), while free sulfhydryl content (from 0.43 to 0.09 nmol/mg) and free amino group content (from 0.49 to 0.43 nmol/mg) decreased. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis showed that the exposure of ovalbumin to hydroxyl radicals caused self‐cross‐linking and resulted in the formation of dimers and trimers. Accompanied by these changes, the surface hydrophobicity of ovalbumin was enhanced about 1.5‐fold with the deepening of oxidation, and the value of zeta potential became more negative (from ‐7.15 to ‐20.51 mv). About 2 h of moderate oxidation improved the foaming and emulsifying properties of ovalbumin (1.2‐fold to 1.8‐fold), while excessive oxidation (3 h) decreased these interface properties. Hydroxyl radical‐induced oxidation changed the surface chemical groups and structures of ovalbumin, thereby affecting the surface properties. The foaming and emulsifying properties of ovalbumin could be improved by oxidation, increasing the application possibilities of ovalbumin in the food interface system.
MARS: Memory Aware Reordered Source

Memory bandwidth is critical in today's high performance computing systems. The bandwidth is particularly paramount for GPU workloads such as 3D Gaming, Imaging and Perceptual Computing, GPGPU due to their data-intensive nature. As the number of threads and data streams in the GPUs increases with each generation, along with a high available memory bandwidth, memory efficiency is also crucial in order to achieve desired performance. In presence of multiple concurrent data streams, the inherent locality in a single data stream is often lost as these streams are interleaved while moving through multiple levels of memory system. In DRAM based main memory, the poor request locality reduces row-buffer reuse resulting in underutilized and inefficient memory bandwidth. In this paper we propose Memory-Aware Reordered Source (\textit{MARS}) architecture to address memory inefficiency arising from highly interleaved data streams. The key idea of \textit{MARS} is that with a sufficiently large lookahead before the main memory, data streams can be reordered based on their row-buffer address to regain the lost locality and improve memory efficiency. We show that \textit{MARS} improves achieved memory bandwidth by 11\% for a set of synthetic microbenchmarks. Moreover, MARS does so without any specific knowledge of the memory configuration.
Differences in the Associations between Memory Complaints and Depressive Symptoms among Black and White Older Adults.

Objective To test whether race (specifically Black or White) moderates the relationship between memory complaints and depressive symptoms in cognitively normal older adults, and if these relationships vary by memory complaint characteristics. Methods Data from Black (n = 551) and White (n = 1158) cognitively intact participants (Mage = 77.1, SD = 7.5; 76.6% female) in the Minority Aging Research Study and the Rush Memory and Aging Project were used. Participants completed annual clinical evaluations, including the Center for Epidemiologic Studies Depression scale and two memory complaint questions, over periods of up to 18 years. Ordinal mixed effects models were used to examine within-person relationships between memory complaints and depressive symptoms over time, as well as whether race moderated these associations. Results Reports of greater memory change over time were associated with more depressive symptoms for both Black and White older adults. However, reports of greater frequency of memory problems were related to depressive symptoms for Black older adults only. Conclusion Findings suggest differential associations between memory complaints and depressive symptoms in cognitively normal Black and White older adults and call for future research to examine the influence of race and related factors on memory complaints and depressive symptoms.
ECG signal classification for the detection of cardiac arrhythmias using a convolutional recurrent neural network

Objective: The electrocardiogram (ECG) provides an effective, non-invasive approach for clinical diagnosis in patients with cardiac diseases such as atrial fibrillation (AF). AF is the most common cardiac rhythm disturbance and affects ~2% of the general population in industrialized countries. Automatic AF detection in clinics remains a challenging task due to the high inter-patient variability of ECGs, and unsatisfactory existing approaches for AF diagnosis (e.g. atrial or ventricular activity-based analyses). Approach: We have developed RhythmNet, a 21-layer 1D convolutional recurrent neural network, trained using 8528 single-lead ECG recordings from the 2017 PhysioNet/Computing in Cardiology (CinC) Challenge, to classify ECGs of different rhythms including AF automatically. Our RhythmNet architecture contained 16 convolutions to extract features directly from raw ECG waveforms, followed by three recurrent layers to process ECGs of varying lengths and to detect arrhythmia events in long recordings. Large 15 × 1 convolutional filters were used to effectively learn the detailed variations of the signal within small time-frames such as the P-waves and QRS complexes. We employed residual connections throughout RhythmNet, along with batch-normalization and rectified linear activation units to improve convergence during training. Main results: We evaluated our algorithm on 3658 testing data and obtained an F1 accuracy of 82% for classifying sinus rhythm, AF, and other arrhythmias. RhythmNet was also ranked 5th in the 2017 CinC Challenge. Significance: Potentially, our approach could aid AF diagnosis in clinics and be used for patient self-monitoring to improve the early detection and effective treatment of AF.
Weakly Supervised Learning of Indoor Geometry by Dual Warping

A major element of depth perception and 3D understanding is the ability to predict the 3D layout of a scene and its contained objects for a novel pose. Indoor environments are particularly suitable for novel view prediction, since the set of objects in such environments is relatively restricted. In this work we address the task of 3D prediction especially for indoor scenes by leveraging only weak supervision. In the literature 3D scene prediction is usually solved via a 3D voxel grid. However, such methods are limited to estimating rather coarse 3D voxel grids, since predicting entire voxel spaces has large computational costs. Hence, our method operates in image-space rather than in voxel space, and the task of 3D estimation essentially becomes a depth image completion problem. We propose a novel approach to easily generate training data containing depth maps with realistic occlusions, and subsequently train a network for completing those occluded regions. Using multiple publicly available datasets we benchmark our method against existing approaches and are able to obtain superior performance. We further demonstrate the flexibility of our method by presenting results for new view synthesis of RGB-D images.
Three‐dimensional printing with nano‐enabled filaments releases polymer particles containing carbon nanotubes into air

Fused deposition modeling (FDM™) 3-dimensional printing uses polymer filament to build objects. Some polymer filaments are formulated with additives, though it is unknown if they are released during printing. Three commercially available filaments that contained carbon nanotubes (CNTs) were printed with a desktop FDM™ 3-D printer in a chamber while monitoring total particle number concentration and size distribution. Airborne particles were collected on filters and analyzed using electron microscopy. Carbonyl compounds were identified by mass spectrometry. The elemental carbon content of the bulk CNT-containing filaments was 1.5 to 5.2 wt%. CNT-containing filaments released up to 1010 ultrafine (d < 100 nm) particles/g printed and 106 to 108 respirable (d ~0.5 to 2 μm) particles/g printed. From microscopy, 1% of the emitted respirable polymer particles contained visible CNTs. Carbonyl emissions were observed above the limit of detection (LOD) but were below the limit of quantitation (LOQ). Modeling indicated that, for all filaments, the average proportional lung deposition of CNT-containing polymer particles was 6.5%, 5.7%, and 7.2% for the head airways, tracheobronchiolar, and pulmonary regions, respectively. If CNT-containing polymer particles are hazardous, it would be prudent to control emissions during use of these filaments.
Head elevation beyond sniffing position – An aid to airway management

Direct laryngoscopy and tracheal intubation is one of the basic and the most important skills in anesthetic practice. This requires proper positioning of head and neck to adequately visualize the glottis and easily negotiate the tracheal tube through the glottic opening. The position traditionally recommended and taught to all learners of airway management is the “sniffing position” (SP). This involves neck flexion (head elevation) by putting a pillow under the head and then extending the head at atlanto‐occipital joint. The SP is thought to help by allowing the line of vision to fall straight on the laryngeal inlet by aligning oral, pharyngeal, and laryngeal axes. This is the three‐axes alignment theory (TAAT) that describes alignment of pharyngeal and laryngeal axes by flexion of neck and alignment of oral axis with the other two axes by extension of the head. [1]
Effects of self‐regulatory skill usage on weight management behaviours: Mediating effects of induced self‐efficacy changes in non‐obese through morbidly obese women

OBJECTIVES Self-regulation is thought to play a role in overcoming barriers to weight management behaviour changes. This research assessed the extent that relationship is manifested through associated changes in self-efficacy, and effects based on degree of obesity. DESIGN Data sets from three previous studies of the present research group were utilized. After assessment of change scores using repeated-measures ANOVA, mediation and moderation analyses assessed effects of changes in self-regulatory skill usage on changes in physical activity and fruit/vegetable intake through self-efficacy changes. Moderating effects of BMI were then assessed. METHODS Women with body compositions ranging from non-obese (BMI < 30 kg/m2 ) to those with morbid obesity (BMI ≥ 40 kg/m2 ) were administered similar cognitive-behavioural treatments, and assessed on theory-based psychosocial and behavioural measures over 6 months. RESULTS From baseline to Month 6, changes in self-regulation for physical activity and eating, physical activity behaviours, fruit/vegetable intake, and self-efficacy for controlled eating were significant in non-obese women (n = 48) and women with Class 1 (n = 43), Class 2 (n = 70), and Class 3 (n = 48) obesity. Positive effects were smaller in exercise self-efficacy. For each of the BMI-based groups, changes in self-efficacy significantly mediated the prediction of physical activity and fruit/vegetable intake by changes in self-regulation. In aggregated data, BMI significantly moderated the prediction of change in physical activity (higher BMI associated with a stronger association), but not fruit/vegetable intake, within those models. CONCLUSION Increasing self-regulatory skills to overcome lifestyle barriers was found to be important for fostering improved weight loss behaviours, especially in the treatment of higher degrees of obesity in women. Statement of contribution What is already known on this subject? Self-efficacy is a malleable factor that predicts behaviour change within multiple theories. Learned self-regulatory skills may effectively deal with lifestyle barriers associated with improvements in weight management behaviours. Increased physical activity and fruit/vegetable consumption predicts success with weight loss. What does this study add? Much of self-regulation's effect on physical activity and eating behaviours is through its impact on self-efficacy. Weight management treatments should emphasize self-regulatory skills development over simply health education. Effects of interrelations of self-regulation and self-efficacy are more effective as female weight increases.
CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type

Abstract Single-cell RNA sequencing (scRNA-seq) is a powerful tool to study heterogeneity and dynamic changes in cell populations. Clustering scRNA-seq is essential in identifying new cell types and studying their characteristics. We develop CellBIC (single Cell BImodal Clustering) to cluster scRNA-seq data based on modality in the gene expression distribution. Compared with classical bottom-up approaches that rely on a distance metric, CellBIC performs hierarchical clustering in a top-down manner. CellBIC outperformed the bottom-up hierarchical clustering approach and other recently developed clustering algorithms while maintaining the hierarchical structure of cells. Importantly, CellBIC identifies type 2 diabetes and age specific β cell signatures characterized by SIX3 and CDH2, respectively.
Loss of S100A1 expression leads to Ca2+ release potentiation in mutant mice with disrupted CaM and S100A1 binding to CaMBD2 of RyR1

Calmodulin (CaM) and S100A1 fine‐tune skeletal muscle Ca2+ release via opposite modulation of the ryanodine receptor type 1 (RyR1). Binding to and modulation of RyR1 by CaM and S100A1 occurs predominantly at the region ranging from amino acid residue 3614‐3640 of RyR1 (here referred to as CaMBD2). Using synthetic peptides, it has been shown that CaM binds to two additional regions within the RyR1, specifically residues 1975‐1999 and 4295‐4325 (CaMBD1 and CaMBD3, respectively). Because S100A1 typically binds to similar motifs as CaM, we hypothesized that S100A1 could also bind to CaMBD1 and CaMBD3. Our goals were: (1) to establish whether S100A1 binds to synthetic peptides containing CaMBD1 and CaMBD3 using isothermal calorimetry (ITC), and (2) to identify whether S100A1 and CaM modulate RyR1 Ca2+ release activation via sites other than CaMBD2 in RyR1 in its native cellular context. We developed the mouse model (RyR1D‐S100A1KO), which expresses point mutation RyR1‐L3625D (RyR1D) that disrupts the modulation of RyR1 by CaM and S100A1 at CaMBD2 and also lacks S100A1 (S100A1KO). ITC assays revealed that S100A1 binds with different affinities to CaMBD1 and CaMBD3. Using high‐speed Ca2+ imaging and a model for Ca2+ binding and transport, we show that the RyR1D‐S100A1KO muscle fibers exhibit a modest but significant increase in myoplasmic Ca2+ transients and enhanced Ca2+ release flux following field stimulation when compared to fibers from RyR1D mice, which were used as controls to eliminate any effect of binding at CaMBD2, but with preserved S100A1 expression. Our results suggest that S100A1, similar to CaM, binds to CaMBD1 and CaMBD3 within the RyR1, but that CaMBD2 appears to be the primary site of RyR1 regulation by CaM and S100A1.
Analysis of alternative splicing in chicken embryo fibroblasts in response to reticuloendotheliosis virus infection

ABSTRACT Alternative splicing (AS) plays a significant role in regulation of genomic expression at the transcriptional level and is involved in many important biological functions of cells, thus a gene can be spliced into distinct transcript variants then translated to many different kinds of protein. Reticuloendotheliosis virus (REV) is a kind of retrovirus that can infect multiple avian species, leading to runting syndrome, immunosuppression and oncogenesis. In this present study, we analyzed AS in REV-infected chicken embryo fibroblasts (CEFs) which were inoculated with the second generation of REV (group VB) and compared with normal CEFs (group C) by high-throughput RNA sequencing technology. A total of 6,939 genes which were alternatively spliced were detected, among them, skipped exon (SE) was the most common pattern. Moreover, 5,607 AS genes were detected as differentially expressed; compared with group C, group VB has 2,825 genes upregulated significantly and 2,782 genes downregulated significantly. These 5,607 differentially expressed AS genes are involved in many important biological processes. Many of them are involved in apoptosis and tumourigenesis. We also proved, by agarose gel electrophoresis, that AS events predicted by our study are authentic and AS is closely related with apoptosis and tumourigenesis in REV-infected CEFs. Our study provides the best analysis to date of the potential link between AS and CEFs in response to REV infection. Research highlights Transcriptomics analysis of REV-infected CEFs using high-throughput sequencing. Potential link between alternative splicing and CEFs in response to REV infection. Skipped exon is the most common spliced pattern in REV-infected CEFs. Differentially expressed genes mainly involved in apoptosis and tumourigenesis.
Ethanol Extract of Lycopus lucidus Turcz. ex Benth Inhibits Metastasis by Downregulation of Runx-2 in Mouse Colon Cancer Cells

Lycopus lucidus Turcz. ex Benth (LT) has been broadly used as a traditional medicinal herb in Asia including Korea, China, and Japan due to its noted ability to promote blood circulation and remove blood stasis. However, its anticancer mechanism is not understood. This study aims to elucidate the effects of ethanol extracts of LT (ELT) relative to the role of Runt-related transcription factor- (Runx-) 2 in the invasive and metastatic potentials of mouse colon cancer to determine the underlying mechanisms involved. ELT was evaluated for the antimetastasis activity using CT-26 colon cancer using wound healing, transwell matrigel, and western blot analysis. We used Runx-2-specific siRNA to further determine the relationship between Runx-2 and matrix metalloprotease- (MMP-) 9 in the migration and invasion of CT-26 cells. Runx-2 was first demonstrated to be a transcription factor that plays a remarkable role in diverse biological processes of chondrocytes and osteoblasts, but recently, Runx-2 has been reported to be associated with the progression of certain human cancers. ELT was not altered in its effects on growth inhibition. However, ELT significantly inhibited wound closure and cell invasion in a dose-dependent manner. ELT decreased the metastasis by regulating the activity of MMP-9 and Runx-2 at the translational levels. Our results demonstrate that ELT decreases metastasis by inhibiting the Runx-2–MMP-9 axis. We suggest that it can be used as a novel agent in therapeutic strategies for combating colon cancer.