Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimising the Decellularization Process of an Upper Limb Skeletal Muscle; Implications for Muscle Tissue Engineering.

Upper limb muscle reconstruction is required following cancer resection, trauma and congenital deformities. Current surgical reconstruction of the muscle involves local, regional and free flaps. However, muscle reconstruction is not always possible due to the size of the defect and functional donor site morbidity. These challenges could be addressed with the production of scaffolds composed of an extracellular matrix (ECM) derived from decellularized human skeletal muscle. This study aimed to find an optimal technique to decellularize a flexor digitorum superficialis muscle. The first two protocols were based on a detergent only (DOT) and a detergent-enzymatic protocol (DET). The third protocol avoided the use of detergents and proteolytic enzymes (NDNET). The decellularized scaffolds were characterized using qualitative techniques including histological and immunofluorescent staining and quantitative techniques assessing deoxyribonucleic acid (DNA), glycosaminoglycan (GAG) and collagen content. The DOT protocol consisting of 2% SDS for 4-hours was successful at decellularizing human FDS, as shown by DNA content assay and nuclei immunofluorescence staining. The DOT protocol maintained the microstructure of the scaffolds as shown by Massons Trichome staining and collagen and GAG content. DET and NDNET protocols maintained the ECM but were unsuccessful in removing all DNA content after 2-cycles of decellularization. Decellularization of skeletal muscle is a viable option for muscle reconstruction using a detergent only technique for upper limb defects. Further testing in vivo will assess the effectiveness of decellularized scaffolds for upper limb muscle skeletal tissue engineering.
ZFP281 Recruits MYC to Active Promoters in Regulating Transcriptional Initiation and Elongation

The roles of the MYC transcription factor in transcriptional regulation have been studied intensively. However, the general mechanism underlying the recruitment of MYC to chromatin is less clear. Here, we found that the Krüppel-like transcription factor ZFP281 plays important roles in recruiting MYC to active promoters in mouse embryonic stem cells. ABSTRACT The roles of the MYC transcription factor in transcriptional regulation have been studied intensively. However, the general mechanism underlying the recruitment of MYC to chromatin is less clear. Here, we found that the Krüppel-like transcription factor ZFP281 plays important roles in recruiting MYC to active promoters in mouse embryonic stem cells. At the genome scale, ZFP281 is broadly associated with MYC, and the depletion of ZFP281 significantly reduces the levels of MYC and RNA polymerase II at the ZFP281- and MYC-cobound genes. Specially, we found that recruitment is required for the regulation of the Lin28a oncogene and pri-let-7 transcription. Our results therefore suggest a major role of ZFP281 in recruiting MYC to chromatin and the integration of ZFP281 and the MYC/LIN28A/Let-7 loop into a multilevel circuit.
One-Pot Synthesis of Star Copolymers by the Combination of Metal-Free ATRP and ROP Processes

A completely metal-free strategy is demonstrated for the preparation of star copolymers by combining atom transfer radical polymerization (ATRP) and ring-opening polymerization (ROP) for the syntheses of block copolymers. These two different metal-free controlled/living polymerizations are simultaneously realized in one reaction medium in an orthogonal manner. For this purpose, a specific core with functional groups capable of initiating both polymerization types is synthesized. Next, vinyl and lactone monomers are simultaneously polymerized under visible light irradiation using specific catalysts. Spectral and chromatographic evidence demonstrates the success of the strategy as star copolymers are synthesized with controlled molecular weights and narrow distributions.
Cryptographic Considerations for Automation and SCADA Systems Using Trusted Platform Modules

The increased number of cyber threats against the Supervisory Control and Data Acquisition (SCADA) and automation systems in the Industrial-Internet-of-Things (IIoT) and Industry 4.0 era has raised concerns in respect to the importance of securing critical infrastructures and manufacturing plants. The evolution towards interconnection and interoperability has expanded the vulnerabilities of these systems, especially in the context of the widely spread legacy standard protocols, by exposing the data to the outside network. After gaining access to the system data by launching a variety of attacks, an intruder can cause severe damage to the industrial process in place. Hence, this paper attempts to respond to the security issue caused by legacy structures using insecure communication protocols (e.g., Modbus TCP, DNP3, S7), presenting a different perspective focused on the capabilities of a trusted platform module (TPM). Furthermore, the intent is to assure the authenticity of the data transmitted between two entities on the same (horizontal interoperation) or different (vertical interoperation) hierarchical levels communicating through Modbus TCP protocol based on functionalities obtained by integrating trusted platform modules. From the experimental results perspective, the paper aims to show the advantages of integrating TPMs in automation/SCADA systems in terms of security. Two methods are proposed in order to assure the authenticity of the messages which are transmitted, respectively the study presents the measurements related to the increased time latency introduced due to the proposed concept.
Human Cysteine Cathepsins Degrade Immunoglobulin G In Vitro in a Predictable Manner

Cysteine cathepsins are critical components of the adaptive immune system involved in the generation of epitopes for presentation on human leukocyte antigen (HLA) molecules and have been implicated in degradation of autoantigens. Immunoglobulin variable regions with somatic mutations and random complementarity region 3 amino acid composition are inherently immunogenic. T cell reactivity towards immunoglobulin variable regions has been investigated in relation to specific diseases, as well as reactivity to therapeutic monoclonal antibodies. Yet, how the immunoglobulins, or the B cell receptors, are processed in endolysosomal compartments of professional antigen presenting cells has not been described in detail. Here we present in silico and in vitro experimental evidence suggesting that cysteine cathepsins S, L and B may have important roles in generating peptides fitting HLA class II molecules, capable of being presented to T cells, from monoclonal antibodies as well as from central nervous system proteins including a well described autoantigen. By combining neural net models with in vitro proteomics experiments, we further suggest how such degradation can be predicted, how it fits with available cellular models, and that it is immunoglobulin heavy chain variable family dependent. These findings are relevant for biotherapeutic drug design as well as to understand disease development. We also suggest how these tools can be improved, including improved machine learning methodology.
Thermodynamic Properties of Stoichiometric Non-Superconducting Phase Y2BaCuO5

Y2BaCuO5 often occurs as an accompanying phase of the well-known high-temperature superconductor YBa2Cu3O7 (also known as YBCO). Y2BaCuO5, easily identifiable due to its characteristic green coloration, is often referred to as ‘green phase’ or ‘Y-211’. In this contribution, Y2BaCuO5 phase was studied in detail with a focus on its thermal and thermodynamic properties. Energy dispersive spectroscopy (EDS), X-ray diffraction (XRD), and scanning electron microscopy (SEM) were employed in the study of sample’s morphology and chemical composition. XRD data were further analyzed and lattice parameters refined by Rietveld analysis. Simultaneous thermal analysis was employed to study thermal stability. Particle size distribution was analyzed by laser diffraction. Finally, thermodynamic properties, namely heat capacity and relative enthalpy, were measured by drop calorimetry, differential scanning calorimetry (DSC), and physical properties measurement system (PPMS). Enthalpy of formation was assessed from ab-initio DFT calculations.
Identification of Citrus Trees from Unmanned Aerial Vehicle Imagery Using Convolutional Neural Networks

Remote sensing is important to precision agriculture and the spatial resolution provided by Unmanned Aerial Vehicles (UAVs) is revolutionizing precision agriculture workflows for measurement crop condition and yields over the growing season, for identifying and monitoring weeds and other applications. Monitoring of individual trees for growth, fruit production and pest and disease occurrence remains a high research priority and the delineation of each tree using automated means as an alternative to manual delineation would be useful for long-term farm management. In this paper, we detected citrus and other crop trees from UAV images using a simple convolutional neural network (CNN) algorithm, followed by a classification refinement using superpixels derived from a Simple Linear Iterative Clustering (SLIC) algorithm. The workflow performed well in a relatively complex agricultural environment (multiple targets, multiple size trees and ages, etc.) achieving high accuracy (overall accuracy = 96.24%, Precision (positive predictive value) = 94.59%, Recall (sensitivity) = 97.94%). To our knowledge, this is the first time a CNN has been used with UAV multi-spectral imagery to focus on citrus trees. More of these individual cases are needed to develop standard automated workflows to help agricultural managers better incorporate large volumes of high resolution UAV imagery into agricultural management operations.
The Role for Imaging in the Investigation of Isolated Objective Vestibular Weakness

Objective Unilateral vestibular weakness has considerable potential etiologies. One source is a vestibular schwannoma. This article evaluates, in the absence of other symptoms and signs, if unilateral vestibular weakness is an analogue to asymmetric sensorineural hearing loss and serves as an indication for lateral skull base imaging. Study Design Retrospective chart review. Setting Academic tertiary center. Subjects and Methods All patients undergoing caloric assessment between January 1, 2012, and June 30, 2018, were investigated. Patients with unilateral vestibular weakness (a left-right difference >25% on electronystagmography) were included in the study. A provincial encompassing image library was surveyed for potential adequate imaging (computed tomography internal auditory canal infused, magnetic resonance imaging [MRI] brain, MRI internal auditory canal) of the target population within the preceding 5 years. Presence/absence of vestibular schwannoma on imaging was determined. Results Of the 3531 electronystagmography reports reviewed during the period, 864 patients were identified with unilateral vestibular weakness. Of these, 542 had sufficient imaging, and 14 vestibular schwannomas were identified. Only 1 individual had a vestibular weakness in isolation, while the remaining 13 patients also suffered from documented sensorineural hearing loss that would have mandated MRI scanning. Conclusion The results of our study suggest that, in isolation, vestibular weakness is an insufficient indicator for lateral skull base imaging.
Greater Occipital Nerve Block for the Treatment of Chronic Migraine Headaches: A Systematic Review and Meta-Analysis.

BACKGROUND Few treatment options exist for chronic migraine headaches, with peripheral nerve blocks having long been used to reduce the frequency and severity of migraines. Although the therapeutic effects have been observed in clinical practice, the efficacy has never been fully studied. In the past decade, however, several randomized controlled clinical trials have been conducted to assess the efficacy of greater occipital nerve block in the treatment of chronic migraine headaches. METHODS A systematic review of the literature was performed in the citation databases PubMed, Embase, MEDLINE, and the Cochrane Library. The initial search of databases yielded 259 citations, of which 33 were selected as candidates for full-text review. Of these, nine studies were selected for inclusion in this meta-analysis. RESULTS Studies were analyzed that reported mean number of headache days per month in both intervention and control groups. A total of 417 patients were studied, with a pooled mean difference of -3.6 headache days (95 percent CI, -1.39 to -5.81 days). This demonstrates that greater occipital nerve block intervention significantly reduced the frequency of migraine headaches compared with controls (p < 0.00001). Pooled mean difference in pain scores of -2.2 (95 percent CI, -1.56 to -2.84) also demonstrated a significant decrease in headache severity compared with controls (p < 0.0121). CONCLUSIONS Greater occipital nerve blocking should be recommended for use in migraine patients, particularly those that may require future surgical intervention. The block may act as an important stepping stone for patients experiencing migraine headache because of its usefulness for potentially assessing surgical candidates for nerve decompression. CLINICAL QUESTION/LEVEL OF EVIDENCE Therapeutic, II.
A Robust Distance Measure for Similarity-Based Classification on the SPD Manifold

The symmetric positive definite (SPD) matrices, forming a Riemannian manifold, are commonly used as visual representations. The non-Euclidean geometry of the manifold often makes developing learning algorithms (e.g., classifiers) difficult and complicated. The concept of similarity-based learning has been shown to be effective to address various problems on SPD manifolds. This is mainly because the similarity-based algorithms are agnostic to the geometry and purely work based on the notion of similarities/distances. However, existing similarity-based models on SPD manifolds opt for holistic representations, ignoring characteristics of information captured by SPD matrices. To circumvent this limitation, we propose a novel SPD distance measure for the similarity-based algorithm. Specifically, we introduce the concept of point-to-set transformation, which enables us to learn multiple lower dimensional and discriminative SPD manifolds from a higher dimensional one. For lower dimensional SPD manifolds obtained by the point-to-set transformation, we propose a tailored set-to-set distance measure by making use of the family of alpha–beta divergences. We further propose to learn the point-to-set transformation and the set-to-set distance measure jointly, yielding a powerful similarity-based algorithm on SPD manifolds. Our thorough evaluations on several visual recognition tasks (e.g., action classification and face recognition) suggest that our algorithm comfortably outperforms various state-of-the-art algorithms.
Effect of Cuff Pressure on Blood Flow during Blood Flow-restricted Rest and Exercise.

PURPOSE This study investigated the relationship between blood flow restriction (BFR) cuff pressure and blood flow at rest and during exercise, with the aim of determining if lower cuff pressures will provide an ischemic stimulus comparable to higher pressures. METHODS The relationship between blood flow and cuff pressure at rest was determined by measuring blood flow (Doppler Ultrasound) through the superficial femoral artery (SFA) in 23 adults across a range of pressures (0-100% Arterial Occlusion Pressure at rest, rAOP). The interplay between cuff pressure, blood flow and exercise was assessed by determining AOP at rest and during plantar flexion exercise (eAOP) and subsequently measuring the blood flow response to plantar flexion exercise with BFR cuff pressure set to either 40% rAOP or 40% eAOP. RESULTS At rest, a non-linear relationship between cuff pressure and blood flow through the SFA exhibited a plateau at moderate pressures, with non-significant differences in blood flow (~9%, P = 1.0) appearing between pressures ranging from 40-80% rAOP. While eAOP was greater than rAOP (229±1.5 vs. 202±1.5 mmHg, P<0.01), blood flow during plantar flexion exercise did not significantly differ (P=0.49) when applying 40% rAOP or 40% eAOP. CONCLUSION Blood flow through the SFA exhibits a non-linear relationship with cuff pressure, such that cuff pressures in the range of 40-80% rAOP reduce blood flow to approximately the same degree. BFR interventions opting for lower (e.g. 40% AOP), more comfortable pressures will likely provide an ischemic stimulus comparable to that of higher (80% AOP), less-comfortable pressures.
Promoting School Engagement in Children with Cerebral Palsy: A Narrative Based Program

This study assessed the efficacy of an educational program focused on the promotion of school engagement in children with Cerebral Palsy. A 9 weeks, narrative-based intervention program, with a pre-post neuropsychological and self-report evaluation, was developed with a dual focus: a self-regulation theoretical model and executive function stimulation. Fifteen children with Cerebral Palsy participated in the study. Results showed a significant main effect of time (F(2.82) = 6.04, p = 0.0066, partial η2 = 0.30; F(2.82) = 9.91, p = 0.0006, partial η2 = 0.41; F(2.82) = 26.90, p < 0.0001, partial η2 = 0.66) in the three dimensions of school engagement. Findings indicate that the program to train self-regulated competences and executive function skills was efficacious in promoting school engagement in children with Cerebral Palsy. Educational implications were discussed.
Preventing physician distress: burnout syndrome, a sneaky disease.

The consequences of burnout are associated with a negative impact on patient care, and also an increase in medical errors and scarce patient care (West et al., 2006). The major causes associated with burnout are increased work hours, reduction in time on research and educational activities, and traumatic professional experiences. Also, younger age and/or fewer years of practice are also associated with a high risk of burnout (Murali and Banerjee, 2018).
Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding

Human endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1) has been suggested to regulate inflammatory responses in endothelial cells by controlling expression of proteins, interleukin-6 and vascular cell adhesion molecule-1, and by preventing apoptosis. To elucidate the structural basis of the EOLA1 function, we determined its crystal structure at 1.71 Å resolution and found that EOLA1 is structurally similar to an activating signal cointegrator-1 homology (ASCH) domain with a characteristic β-barrel fold surrounded by α-helices. Despite its low sequence identity with other ASCH domains, EOLA1 retains a conserved ‘GxKxxExR’ motif in its cavity structure. The cavity harbors aromatic and polar residues, which are speculated to accommodate nucleotide molecules as do YT521-B homology (YTH) proteins. Additionally, EOLA1 exhibits a positively charged cleft, similar to those observed in YTH proteins and the ASCH protein from Zymomonas mobilis that exerts ribonuclease activity. This implies that the positively charged cleft in EOLA1 could stabilize the binding of RNA molecules. Taken together, we suggest that EOLA1 controls protein expression through RNA binding to play protective roles against endothelial cell injuries resulting from lipopolysaccharide (LPS)-induced inflammation responses.
3D Bioprinting of the Sustained Drug Release Wound Dressing with Double-Crosslinked Hyaluronic-Acid-Based Hydrogels

Hyaluronic acid (HA)-based hydrogels are widely used in biomedical applications due to their excellent biocompatibility. HA can be Ultraviolet (UV)-crosslinked by modification with methacrylic anhydride (HA-MA) and crosslinked by modification with 3,3′-dithiobis(propionylhydrazide) (DTP) (HA-SH) via click reaction. In the study presented in this paper, a 3D-bioprinted, double-crosslinked, hyaluronic-acid-based hydrogel for wound dressing was proposed. The hydrogel was produced by mixing HA-MA and HA-SH at different weight ratios. The rheological test showed that the storage modulus (G’) of the HA-SH/HA-MA hydrogel increased with the increase in the HA-MA content. The hydrogel had a high swelling ratio and a high controlled degradation rate. The in vitro degradation test showed that the hydrogel at the HA-SH/HA-MA ratio of 9:1 (S9M1) degraded by 89.91% ± 2.26% at 11 days. The rheological performance, drug release profile and the cytocompatibility of HA-SH/HA-MA hydrogels with loaded Nafcillin, which is an antibacterial drug, were evaluated. The wound dressing function of this hydrogel was evaluated by Live/Dead staining and CCK-8 assays. The foregoing results imply that the proposed HA-SH/HA-MA hydrogel has promise in wound repair applications.
Overexpression of GmCAMTA12 Enhanced Drought Tolerance in Arabidopsis and Soybean

Fifteen transcription factors in the CAMTA (calmodulin binding transcription activator) family of soybean were reported to differentially regulate in multiple stresses; however, their functional analyses had not yet been attempted. To characterize their role in stresses, we first comprehensively analyzed the GmCAMTA family in silico and thereafter determined their expression pattern under drought. The bioinformatics analysis revealed multiple stress-related cis-regulatory elements including ABRE, SARE, G-box and W-box, 10 unique miRNA (microRNA) targets in GmCAMTA transcripts and 48 proteins in GmCAMTAs’ interaction network. We then cloned the 2769 bp CDS (coding sequence) of GmCAMTA12 in an expression vector and overexpressed in soybean and Arabidopsis through Agrobacterium-mediated transformation. The T3 (Transgenic generation 3) stably transformed homozygous lines of Arabidopsis exhibited enhanced tolerance to drought in soil as well as on MS (Murashige and Skoog) media containing mannitol. In their drought assay, the average survival rate of transgenic Arabidopsis lines OE5 and OE12 (Overexpression Line 5 and Line 12) was 83.66% and 87.87%, respectively, which was ~30% higher than that of wild type. In addition, the germination and root length assays as well as physiological indexes such as proline and malondialdehyde contents, catalase activity and leakage of electrolytes affirmed the better performance of OE lines. Similarly, GmCAMTA12 overexpression in soybean promoted drought-efficient hairy roots in OE chimeric plants as compare to that of VC (Vector control). In parallel, the improved growth performance of OE in Hoagland-PEG (polyethylene glycol) and on MS-mannitol was revealed by their phenotypic, physiological and molecular measures. Furthermore, with the overexpression of GmCAMTA12, the downstream genes including AtAnnexin5, AtCaMHSP, At2G433110 and AtWRKY14 were upregulated in Arabidopsis. Likewise, in soybean hairy roots, GmELO, GmNAB and GmPLA1-IId were significantly upregulated as a result of GmCAMTA12 overexpression and majority of these upregulated genes in both plants possess CAMTA binding CGCG/CGTG motif in their promoters. Taken together, we report that GmCAMTA12 plays substantial role in tolerance of soybean against drought stress and could prove to be a novel candidate for engineering soybean and other plants against drought stress. Some research gaps were also identified for future studies to extend our comprehension of Ca-CaM-CAMTA-mediated stress regulatory mechanisms.