Miracle-dz/UniFAR-FTUs huggingface dataset:
Catalyzing Clinical Diagnostic Pipelines Through Volumetric Medical Image Segmentation Using Deep Neural Networks: Past, Present, & Future

—Deep learning has made a remarkable impact in the ﬁeld of natural image processing over the past decade. Consequently, there is a great deal of interest in replicating this success across unsolved tasks in related domains, such as medical image analysis. Core to medical image analysis is the task of semantic segmentation which enables various clinical workﬂows. Due to the challenges inherent in manual segmenta- tion, many decades of research have been devoted to discovering extensible, automated, expert-level segmentation techniques. Given the groundbreaking performance demonstrated by recent neural network-based techniques, deep learning seems poised to achieve what classic methods have historically been unable. This paper will brieﬂy overview some of the state-of-the-art (SoTA) neural network-based segmentation algorithms with a particular emphasis on the most recent architectures, compar- ing and contrasting the contributions and characteristics of each network topology. Using ultrasonography as a motivating example, it will also demonstrate important clinical implications of effective deep learning-based solutions, articulate challenges unique to the modality, and discuss novel approaches developed in response to those challenges, concluding with the proposal of future directions in the ﬁeld. Given the generally observed ephemerality of the best deep learning approaches (i.e., the extremely quick succession of the SoTA), the main contributions of the paper are its contextu- alization of modern deep learning architectures with historical background and the elucidation of the current trajectory of volumetric medical image segmentation research.
First principle study of structural, elastic, electronic and optical properties of Pb0.5Sn0.5TiO3 and Pb0.5Sn0.5Ti0.5(Zr0.5)O3

The structural, electronic, elastic and optical properties of tetragonal (P4mm) phase of Pb0.5Sn0. 5TiO3 (PSTO) and Pb0.5Sn0. 5Ti0.5(Zr0.5)O3 (PSTZO) are examined by first-principles calculations based on the density functional theory (DFT) using the pseudo-potential plane wave (PP-PW) scheme in the frame of generalized gradient approximation (GGA). We have calculated the ground state properties such as equlibrium lattice constants, volume, bulk modulus and its pressure derivative. From elastic constants, mechanical parameters such as anisotropy factor, elastic modulus and Poisson's ratio are obtained from the Voigt-Reuss-Hill average approximation. Rather than their averages, the directional dependence of elastic modulus, and Poisson's ratio are modelled and visualized in the light of the elastic properties of both systems. In addition, some novel results, such as Debye temperatures, and sound velocities are obtained. Moreover, we have presented the results of the electronic band structure, densities of states and charge densities. These results were in favourable agreement with the existing theoretical data. The optical dielectric function and energy loss spectrum of both systems are also computed. Born effective charge (BEC) of each atoms for both systems is computed from functional perturbation theory (DFPT). Finally, the spontaneous polarization is also determined from modern theory of polarization to be 0.8662 C/m2 (PSTO) and 1.0824 C/m2 (PSTZO).
Cleavage of the Perlecan-Semaphorin 3A-Plexin A1-Neuropilin-1 (PSPN) Complex by Matrix Metalloproteinase 7/Matrilysin Triggers Prostate Cancer Cell Dyscohesion and Migration

The Perlecan-Semaphorin 3A-Plexin A1-Neuropilin-1 (PSPN) Complex at the cell surface of prostate cancer (PCa) cells influences cell–cell cohesion and dyscohesion. We investigated matrix metalloproteinase-7/matrilysin (MMP-7)’s ability to digest components of the PSPN Complex in bone metastatic PCa cells using in silico analyses and in vitro experiments. Results demonstrated that in addition to the heparan sulfate proteoglycan, perlecan, all components of the PSPN Complex were degraded by MMP-7. To investigate the functional consequences of PSPN Complex cleavage, we developed a preformed microtumor model to examine initiation of cell dispersion after MMP-7 digestion. We found that while perlecan fully decorated with glycosaminoglycan limited dispersion of PCa microtumors, MMP-7 initiated rapid dyscohesion and migration even with perlecan present. Additionally, we found that a bioactive peptide (PLN4) found in perlecan domain IV in a region subject to digestion by MMP-7 further enhanced cell dispersion along with MMP-7. We found that digestion of the PSPN Complex with MMP-7 destabilized cell–cell junctions in microtumors evidenced by loss of co-registration of E-cadherin and F-actin. We conclude that MMP-7 plays a key functional role in PCa cell transition from a cohesive, indolent phenotype to a dyscohesive, migratory phenotype favoring production of circulating tumor cells and metastasis to bone.
Identification and Immunological Characterization of Somatic Proteins from Adults of Toxocara cati by Proteomics Technique

Background: Toxocara cati is considered as one of the main etiological agents of toxocariasis with global and regional importance. As there is no information on proteomics of T. cati, herein, we reported the results obtained by proteomic analysis of somatic proteins extract, using a mass spectrometry (LC–MS/MS) approach. Methods: Somatic extract fractions were separated by two-dimensional SDS-PAGE and were electro blotted on to PVDF membranes for immunoblot analysis, then collected the immunogenic spots which response of antibodies of the paratenic hosts (mice) to the antigens (Mashhad, 2017), and analyzed by LC–MS/MS. The LC-MS/MS data were analyzed by Mascot database, Taxonomy Toxocara, and common contaminants, in Omics Center, Biotechnology Medical University of Graz (Austria, 2018). Result: The protein spots were isolated between 15–140 kDa ranges using 3–10 non-linear IPG strips and Brilliant Blue Coomassie. Ten proteins were characterized as immunogenic proteins, seven of them were identified and three of them were unknown proteins. Conclusion: This study provided additional information about the somatic antigens of T. cati, which can lead to the development of new strategies for novel immuno-modulators, drug targets, subunit vaccines and immunodiagnostic kits for toxocariasis.
Differences in Family Involvement in the Bedside Care of Patients in the ICU Based on Self-Identified Race

Supplemental Digital Content is available in the text. Objectives: Being a caregiver for a patient in the ICU can place emotional burden on families and engaging families in caregiving can reduce psychological distress. Our goal was to observe support methods used by families in the ICU and identify differences between race/ethnicity. Design: A secondary analysis of a multicenter before-and-after clinical trial. Setting: Three hospitals in Chicago, Providence, and Florence, Italy. Participants: Family members of patients admitted to the ICU. Interventions: In the primary study, an intervention was designed to engage families in seven domains that were based on the five physical senses (taste, touch, sight, smell, and sound), personal care, and spiritual care of the patient. During the control phase, nursing staff observed and recorded if they witnessed families participating in support methods unprompted. MEASUREMENTS AND MAIN RESULTS: We compared the use of support methods among families from different races, categorized by race as either White, Black, or other using generalized estimating equation population-averaged logistic regression analysis. A total of 133 patients and 226 family members were enrolled in the control arm of the primary study, with patients being 71.2% White, 17% Black, and 11.8% other. Compared with Whites, families who identified their race Black or other may be more likely to participate in support methods that included personal care, touch, or spiritual care. Families who identified as Black may also be more likely to incorporate audio or sound. There were no differences in the categories of sight, smell, or taste. Conclusions: Our study identifies racial differences in the use of bedside support methods in the ICU. Guiding families in a culturally congruent and open-minded manner may have the potential to decrease family distress and improve the experience for families in the ICU.
Towards Precise Interpretation of Oil Transformers via Novel Combined Techniques Based on DGA and Partial Discharge Sensors

Power transformers are considered important and expensive items in electrical power networks. In this regard, the early discovery of potential faults in transformers considering datasets collected from diverse sensors can guarantee the continuous operation of electrical systems. Indeed, the discontinuity of these transformers is expensive and can lead to excessive economic losses for the power utilities. Dissolved gas analysis (DGA), as well as partial discharge (PD) tests considering different intelligent sensors for the measurement process, are used as diagnostic techniques for detecting the oil insulation level. This paper includes two parts; the first part is about the integration among the diagnosis results of recognized dissolved gas analysis techniques, in this part, the proposed techniques are classified into four techniques. The integration between the different DGA techniques not only improves the oil fault condition monitoring but also overcomes the individual weakness, and this positive feature is proved by using 532 samples from the Egyptian Electricity Transmission Company (EETC). The second part overview the experimental setup for (66/11.86 kV–40 MVA) power transformer which exists in the Egyptian Electricity Transmission Company (EETC), the first section in this part analyzes the dissolved gases concentricity for many samples, and the second section illustrates the measurement of PD particularly in this case study. The results demonstrate that precise interpretation of oil transformers can be provided to system operators, thanks to the combination of the most appropriate techniques.
Carnauba Wax/Halloysite Nanotube with Improved Anti-Wetting and Permeability of Hydrophobic PVDF Membrane via DCMD

The hydrophobic membranes have been widely explored to meet the membrane characteristics for the membrane distillation (MD) process. Inorganic metal oxide nanoparticles have been used to improve the membrane hydrophobicity, but limited studies have used nano clay particles. This study introduces halloysite nanotube (HNT) as an alternative material to synthesis a hydrophobic poly(vinylidene fluoride) (PVDF)-HNT membrane. The PVDF membranes were fabricated using functionalized HNTs (e.g., carnauba wax and 1H,1H,2H,2H-perfluorooctyl-trichlorosilane (FOTS)). The results were determined by Fourier transform infrared-attenuated total reflection, scanning electron microscope, goniometer and porometer to determine the desired hydrophobic membrane for direct contact membrane distillation (DCMD). The addition of FOTS-HNT (fs-HNT) and carnauba wax-HNT (fw-HNT) in the PVDF membrane enhanced the water contact angle (CA) to 127° and 137°, respectively. The presence of fw-HNT in the PVDF membrane exhibited higher liquid entry pressure (LEP) (2.64 bar) compared to fs-HNT in the membrane matrix (1.44 bar). The PVDF/fw-HNT membrane (Pfw-HNT) obtained the highest flux of 7.24 L/m2h with 99.9% salt removal. A stable permeability in the Pfw-HNT membrane was obtained throughout 16 h of DCMD. The incorporation of fw-HNT in the PVDF membrane had improved the anti-wetting properties and the membrane performance with the anti-fouling effect.
Salivary Biomarkers for Dental Caries Detection and Personalized Monitoring

This study investigated the potential of salivary bacterial and protein markers for evaluating the disease status in healthy individuals or patients with gingivitis or caries. Saliva samples from caries- and gingivitis-free individuals (n = 18), patients with gingivitis (n = 17), or patients with deep caries lesions (n = 38) were collected and analyzed for 44 candidate biomarkers (cytokines, chemokines, growth factors, matrix metalloproteinases, a metallopeptidase inhibitor, proteolytic enzymes, and selected oral bacteria). The resulting data were subjected to principal component analysis and used as a training set for random forest (RF) modeling. This computational analysis revealed four biomarkers (IL-4, IL-13, IL-2-RA, and eotaxin/CCL11) to be of high importance for the correct depiction of caries in 37 of 38 patients. The RF model was then used to classify 10 subjects (five caries-/gingivitis-free and five with caries), who were followed over a period of six months. The results were compared to the clinical assessments of dental specialists, revealing a high correlation between the RF prediction and the clinical classification. Due to the superior sensitivity of the RF model, there was a divergence in the prediction of two caries and four caries-/gingivitis-free subjects. These findings suggest IL-4, IL-13, IL-2-RA, and eotaxin/CCL11 as potential salivary biomarkers for identifying noninvasive caries. Furthermore, we suggest a potential association between JAK/STAT signaling and dental caries onset and progression.
Breast Milk: A Source of Functional Compounds with Potential Application in Nutrition and Therapy

Breast milk is an unbeatable food that covers all the nutritional requirements of an infant in its different stages of growth up to six months after birth. In addition, breastfeeding benefits both maternal and child health. Increasing knowledge has been acquired regarding the composition of breast milk. Epidemiological studies and epigenetics allow us to understand the possible lifelong effects of breastfeeding. In this review we have compiled some of the components with clear functional activity that are present in human milk and the processes through which they promote infant development and maturation as well as modulate immunity. Milk fat globule membrane, proteins, oligosaccharides, growth factors, milk exosomes, or microorganisms are functional components to use in infant formulas, any other food products, nutritional supplements, nutraceuticals, or even for the development of new clinical therapies. The clinical evaluation of these compounds and their commercial exploitation are limited by the difficulty of isolating and producing them on an adequate scale. In this work we focus on the compounds produced using milk components from other species such as bovine, transgenic cattle capable of expressing components of human breast milk or microbial culture engineering.
Nanoemulsions for Enhancement of Curcumin Bioavailability and Their Safety Evaluation: Effect of Emulsifier Type

This work aimed at evaluating the effects of different emulsifiers on curcumin-loaded nanoemulsions’ behavior during digestion, its safety and absorption, to develop nanoemulsions that provide safety and improved curcumin functionality. Nanoemulsions (NEs) were produced using two bio-based (lecithin (LEC) and rhamnolipids (RHAM)) and one synthetic (Tween®80 (TWE)) emulsifier at similar concentrations. Different NEs were subjected to in vitro digestion. The cytotoxicity and permeability tests were performed in Caco-2 cells. NE_TWE were stable during all phases of in vitro digestion, whereas NE_LEC and NE_RHAM were found to be unstable from the gastric phase. NE_TWE showed 100% of free fatty acids released, followed by NE_RHAM and NE_LEC. Curcumin’s bioaccessibility and stability increased in the following order: NE_LEC > NE_RHAM > NE_TWE. NE_LEC and NE_TWE did not show cytotoxic effects in any of the concentrations tested, while NE_RHAM presented high cytotoxicity in all concentrations tested. The apparent permeability coefficients were determined for NE_LEC and NE_TWE; however, the results were not statistically different. These results showed that the emulsifier used has a high impact on nanoemulsions’ behavior under the digestion process and on their cytotoxicity. This work contributed to the state-of-the-art’s progress on the development of safer curcumin delivery systems with improved functionality, particularly regarding the proper selection of ingredients to produce said systems.
The Role of Innate and Adaptive Immune Cells in Skeletal Muscle Regeneration

Skeletal muscle regeneration is highly dependent on the inflammatory response. A wide variety of innate and adaptive immune cells orchestrate the complex process of muscle repair. This review provides information about the various types of immune cells and biomolecules that have been shown to mediate muscle regeneration following injury and degenerative diseases. Recently developed cell and drug-based immunomodulatory strategies are highlighted. An improved understanding of the immune response to injured and diseased skeletal muscle will be essential for the development of therapeutic strategies.
Phosphoproteomic Analysis of Subcutaneous and Omental Adipose Tissue Reveals Increased Lipid Turnover in Dairy Cows Supplemented with Conjugated Linoleic Acid

Phosphoproteomics is a cutting-edge technique that can be utilized to explore adipose tissue (AT) metabolism by quantifying the repertoire of phospho-peptides (PP) in AT. Dairy cows were supplemented with conjugated linoleic acid (CLA, n = 5) or a control diet (CON, n = 5) from 63 d prepartum to 63 d postpartum; cows were slaughtered at 63 d postpartum and AT was collected. We performed a quantitative phosphoproteomics analysis of subcutaneous (SC) and omental (OM) AT using nanoUPLC-MS/MS and examined the effects of CLA supplementation on the change in the phosphoproteome. A total of 5919 PP were detected in AT, and the abundance of 854 (14.4%) were differential between CON and CLA AT (p ≤ 0.05 and fold change ± 1.5). The abundance of 470 PP (7.9%) differed between OM and SC AT, and the interaction treatment vs. AT depot was significant for 205 PP (3.5% of total PP). The integrated phosphoproteome demonstrated the up- and downregulation of PP from proteins related to lipolysis and lipogenesis, and phosphorylation events in multiple pathways, including the regulation of lipolysis in adipocytes, mTOR signaling, insulin signaling, AMPK signaling, and glycolysis. The differential regulation of phosphosite on a serine residue (S777) of fatty acid synthase (FASN) in AT of CLA-supplemented cows was related to lipogenesis and with more phosphorylation sites compared to acetyl-coenzyme A synthetase (ACSS2). Increased protein phosphorylation was seen in acetyl-CoA carboxylase 1 (ACACA;8 PP), FASN (9 PP), hormone sensitive lipase (LIPE;6 PP), perilipin (PLIN;3 PP), and diacylglycerol lipase alpha (DAGLA;1 PP) in CLA vs. CON AT. The relative gene expression in the SC and OM AT revealed an increase in LIPE and FASN in CLA compared to CON AT. In addition, the expression of DAGLA, which is a lipid metabolism enzyme related to the endocannabinoid system, was 1.6-fold higher in CLA vs. CON AT, and the expression of the cannabinoid receptor CNR1 was reduced in CLA vs. CON AT. Immunoblots of SC and OM AT showed an increased abundance of FASN and a lower abundance of CB1 in CLA vs. CON. This study presents a complete map of the SC and the OM AT phosphoproteome in dairy cows following CLA supplementation and discloses many unknown phosphorylation sites, suggestive of increased lipid turnover in AT, for further functional investigation.
Light Sheet Microscopy-Assisted 3D Analysis of SARS-CoV-2 Infection in the Respiratory Tract of the Ferret Model

The visualization of viral pathogens in infected tissues is an invaluable tool to understand spatial virus distribution, localization, and cell tropism in vivo. Commonly, virus-infected tissues are analyzed using conventional immunohistochemistry in paraffin-embedded thin sections. Here, we demonstrate the utility of volumetric three-dimensional (3D) immunofluorescence imaging using tissue optical clearing and light sheet microscopy to investigate host–pathogen interactions of pandemic SARS-CoV-2 in ferrets at a mesoscopic scale. The superior spatial context of large, intact samples (>150 mm3) allowed detailed quantification of interrelated parameters like focus-to-focus distance or SARS-CoV-2-infected area, facilitating an in-depth description of SARS-CoV-2 infection foci. Accordingly, we could confirm a preferential infection of the ferret upper respiratory tract by SARS-CoV-2 and suggest clustering of infection foci in close proximity. Conclusively, we present a proof-of-concept study for investigating critically important respiratory pathogens in their spatial tissue morphology and demonstrate the first specific 3D visualization of SARS-CoV-2 infection.
A Review of Ex Vivo X-ray Microfocus Computed Tomography-Based Characterization of the Cardiovascular System

Cardiovascular malformations and diseases are common but complex and often not yet fully understood. To better understand the effects of structural and microstructural changes of the heart and the vasculature on their proper functioning, a detailed characterization of the microstructure is crucial. In vivo imaging approaches are noninvasive and allow visualizing the heart and the vasculature in 3D. However, their spatial image resolution is often too limited for microstructural analyses, and hence, ex vivo imaging is preferred for this purpose. Ex vivo X-ray microfocus computed tomography (microCT) is a rapidly emerging high-resolution 3D structural imaging technique often used for the assessment of calcified tissues. Contrast-enhanced microCT (CE-CT) or phase-contrast microCT (PC-CT) improve this technique by additionally allowing the distinction of different low X-ray-absorbing soft tissues. In this review, we present the strengths of ex vivo microCT, CE-CT and PC-CT for quantitative 3D imaging of the structure and/or microstructure of the heart, the vasculature and their substructures in healthy and diseased state. We also discuss their current limitations, mainly with regard to the contrasting methods and the tissue preparation.
Impact of Rising Temperature in the Deposition Patterns of Bioactive Compounds in Field Grown Food Barley Grains

High temperatures at the end of the season are frequent under Mediterranean conditions, affecting final grain quality. This study determined the deposition patterns throughout grain filling of dry matter, dietary fiber, phenolic compounds and antioxidant capacity for four barley genotypes under two contrasting temperatures. Deposition pattern for dietary fiber followed that of grain weight. Genotypic differences for duration were more significant than for rate. Anthocyanins followed a second-degree polynomial pattern, reaching a maximum before grain maturation. Free and bound phenols decreased as grain developed, suggesting that they are synthesized in early stages. Rate of bound phenols deposition was more sensitive to genotypic changes. Overall, antioxidant capacity decreased over time; the decay being less steep under stress for all genotypes. Heat stress negatively affected grain weight. It did not alter the profile of β-glucans and arabinoxylans deposition but positively changed the accumulation of some phenolic compounds, increasing the antioxidant capacity differentially across genotypes. These results support the growing of food barley in high-temperature stress-prone areas, as some bioactive compound and antioxidant capacity will increase, regardless of the smaller grain size. Moreover, if a market develops for food-barley ingredients, early harvesting of non-mature grain to maximize antioxidant capacity should be considered.