Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial Rescue of Ocular Pigment Cells and Structure by Inducible Ectopic Expression of Mitf-M in MITF-Deficient Mice

Purpose Complete deficiency of microphthalmia transcription factor (MITF) in Mitfmi-vga9/mi-vga9 mice is associated with microphthalmia, retinal dysplasia, and albinism. We investigated the ability of dopachrome tautomerase (DCT) promoter-mediated inducible ectopic expression of Mitf-M to rescue these phenotypic abnormalities. Methods A new mouse line was created with doxycycline-inducible ectopic Mitf-M expression on an Mitf-deficient Mitfmi-vga9 background (DMV mouse). Adult DMV mice were phenotypically characterized and tissues were collected for histology, immunohistochemistry, and evaluation of Mitf, pigmentary genes, and retinal pigment epithelium (RPE) gene expression. Results Ectopic Mitf-M expression was specifically induced in the eyes, but was not detected in the skin of DMV mice. Inducible expression of Mitf-M partially rescued the microphthalmia, RPE structure, and pigmentation as well as a subset of the choroidal and iris melanocytes but not cutaneous melanocytes. RPE function and vision were not restored in the DMV mice. Conclusions Ectopic expression of Mitf-M during development of Mitf-deficient mice is capable of partially rescuing ocular and retinal structures and uveal melanocytes. These findings provide novel information about the roles of Mitf isoforms in the development of mouse eyes.
The effect of intrauterine growth restriction on Ca2+‐activated force and contractile protein expression in the mesenteric artery of adult (6‐month‐old) male and female Wistar‐Kyoto rats

Intrauterine growth restriction (IUGR) is known to alter vascular smooth muscle reactivity, but it is currently unknown whether these changes are driven by downstream events that lead to force development, specifically, Ca2+‐regulated activation of the contractile apparatus or a shift in contractile protein content. This study investigated the effects of IUGR on Ca2+‐activated force production, contractile protein expression, and a potential phenotypic switch in the resistance mesenteric artery of both male and female Wistar‐Kyoto (WKY) rats following two different growth restriction models. Pregnant female WKY rats were randomly assigned to either a control (C; N = 9) or food restriction diet (FR; 40% of control; N = 11) at gestational day‐15 or underwent a bilateral uterine vessel ligation surgery restriction (SR; N = 10) or a sham surgery control model (SC; N = 12) on day‐18 of gestation. At 6‐months of age, vascular responsiveness of intact mesenteric arteries was studied, before chemically permeabilization using 50 μmol/L β‐escin to investigate Ca2+‐activated force. Peak responsiveness to a K+‐induced depolarization was decreased (P ≤ 0.05) due to a reduction in maximum Ca2+‐activated force (P ≤ 0.05) in both male growth restricted experimental groups. Vascular responsiveness was unchanged between female experimental groups. Segments of mesenteric artery were analyzed using Western blotting revealed IUGR reduced the relative abundance of important receptor and contractile proteins in male growth restricted rats (P ≤ 0.05), suggesting a potential phenotypic switch, whilst no changes were observed in females. Results from this study suggest that IUGR alters the mesenteric artery reactivity due to a decrease in maximum Ca2+‐activated force, and likely contributed to by a reduction in contractile protein and receptor/channel content in 6‐month‐old male rats, while female WKY rats appear to be protected.
Reproducibility of Macular Vessel Density Calculations Via Imaging With Two Different Swept-Source Optical Coherence Tomography Angiography Systems

Purpose To evaluate the reproducibility of vessel density calculations using different binarization methods obtained via two commercially available swept-source optical coherence tomography angiography (SS-OCTA) systems. Methods Healthy volunteers were imaged using two swept-source optical coherence tomography angiography (SS-OCTA) devices, PLEXElite and Triton. SS-OCTA examinations were performed using a 3 × 3-mm volume scan pattern centered on the fovea. A total of six methods were used for binarization in ImageJ, two global thresholding and four local adaptive thresholding methods. Resultant vessel density values were compared between the instruments and binarization methods. Images for 60 eyes from 30 healthy subjects were assessed by two reviewers who were blinded to the scanning system used. Results Twenty-two eyes were excluded due to poor image quality (17 eyes from Triton, 4 eyes from PLEXElite, and 1 eye from both instruments, P = 0.003). A final 38 eyes from 23 subjects were eligible for analysis. Each binarization method and instrument led to different median values. The coefficients of variation for vessel density measurements ranged from 0.3% to 2.3% and 0.6% to 4.7% for the PLEXElite and Triton, respectively. Local adaptive thresholding methods revealed higher reproducibility than did global thresholding methods for both devices. Conclusions Macular scans with both SS-OCTA instruments showed good reproducibility for vessel density measurements. PLEXElite recorded fewer poor images and had higher reproducibility than did Triton. These findings will inform the selection of proper binarization methods for the clinical detection of vascular diseases affecting the central retina. Translational Relevance The reproducibility for macular vessel measurements with SS-OCTA instruments was good. PLEXElite recorded fewer poor images and had higher reproducibility than did Triton.
Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod

Abstract The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal waters. Here, we tested if a high‐graded SNP panel specifically designed to classify individual cod to population of origin may be unreliable because of natural selection acting on the SNPs or their linked background. Temporal samples of cod were collected from two fjords, starting at the earliest life stage (pelagic eggs) and carried on until late autumn (bottom‐settled juveniles), covering the period during summer of high natural mortality. Despite the potential for selective mortality during the study period, we found no evidence for selection, as both cod types occurred throughout the season, already in the earliest egg samples, and there was no evidence for a shift during the season in the proportions of one or the other type. We conclude that high‐graded marker panels under putative natural selection represent a valid and useful tool for identifying biological population structure in this highly fecund species and presumably in others.
Ecomorphological diversity of Australian tadpoles

Abstract Ecomorphology is the association between an organism's morphology and its ecology. Larval anuran amphibians (tadpoles) are classified into distinct ecomorphological guilds based upon morphological features and observations of their ecology. The extent to which guilds comprise distinct morphologies resulting from convergent evolution, the degree of morphological variability within each guild, and the degree of continuity in shape between guilds has not previously been examined in a phylogenetically informed statistical framework. Here, we examine tadpole ecomorphological guilds at a macroevolutionary scale by examining morphological diversity across the Australian continent. We use ecological data to classify species to guilds, and geometric morphometrics to quantify body shape in the tadpoles of 188 species, 77% of Australian frog diversity. We find that the ecomorphological guilds represented by Australian species are morphologically distinct, but there is substantial morphological variation associated with each guild, and all guilds together form a morphological continuum. However, in a phylogenetic comparative context, there is no significant difference in body shape among guilds. We also relate the morphological diversity of the Australian assemblage of tadpoles to a global sample and demonstrate that ecomorphological diversity of Australian tadpoles is limited with respect to worldwide species. Our results demonstrate that general patterns of ecomorphological variation are upheld in Australian tadpoles, but tadpole body shape is more variable and possibly generalist than generally appreciated.
Effects of AT1 receptor antagonism on interstitial and ultrastructural remodeling of heart in response to a hypercaloric diet

Palatable hypercaloric feeding has been associated with angiotensin‐II type 1 receptor (AT1R) stimulation and cardiac remodeling. This study analyzed whether AT1R antagonism attenuates cardiac remodeling in rats subjected to a palatable hypercaloric diet. Male Wistar‐Kyoto rats were subjected to a commercial standard rat chow (CD) or a palatable hypercaloric diet (HD) for 35 weeks and then allocated into four groups: CD, CL, HD, and HL; L groups received losartan in drinking water (30 mg/kg/day) for 5 weeks. Body weight, adiposity, and glycemia were evaluated. The cardiovascular study included echocardiography, and myocardial morphometric and ultrastructural evaluation. Myocardial collagen isoforms Type I and III were analyzed by Western blot. Both HD and HL had higher adiposity than their respective controls. Cardiomyocyte cross‐sectional‐area (CD 285 ± 49; HD 344 ± 91; CL 327 ± 49; HL 303 ± 49 μm2) and interstitial collagen fractional area were significantly higher in HD than CD and unchanged by losartan. HD showed marked ultrastructural alterations such as myofilament loss, and severe mitochondrial swelling. CL presented higher Type I collagen expression when compared to CD and HL groups. The ultrastructural changes and type I collagen expression were attenuated by losartan in HL. Losartan attenuates systolic dysfunction and ultrastructural abnormalities without changing myocardial interstitial remodeling in rats subjected to a palatable hypercaloric diet.
Biosynthesis of Metal Nanoparticles via Microbial Enzymes: A Mechanistic Approach

During the last decade, metal nanoparticles (MtNPs) have gained immense popularity due to their characteristic physicochemical properties, as well as containing antimicrobial, anti-cancer, catalyzing, optical, electronic and magnetic properties. Primarily, these MtNPs have been synthesized through different physical and chemical methods. However, these conventional methods have various drawbacks, such as high energy consumption, high cost and the involvement of toxic chemical substances. Microbial flora has provided an alternative platform for the biological synthesis of MtNPs in an eco-friendly and cost effective way. In this article we have focused on various microorganisms used for the synthesis of different MtNPs. We also have elaborated on the intracellular and extracellular mechanisms of MtNP synthesis in microorganisms, and have highlighted their advantages along with their challenges. Moreover, due to several advantages over chemically synthesized nanoparticles, the microbial MtNPs, with their exclusive and dynamic characteristics, can be used in different sectors like the agriculture, medicine, cosmetics and biotechnology industries in the near future.
A practical introduction to microbial molecular ecology through the use of isolation chips

Abstract In the context of antimicrobial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a 4 year undergraduate Masters Program, in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness/diversity indices as well as principal coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost‐effective manner.
Skewed Dendritic Cell Differentiation of MyD88-Deficient Donor Bone Marrow Cells, Instead of Massive Expansion as Myeloid-Derived Suppressor Cells, Aggravates GVHD

Graft-versus-host disease (GVHD), a life-threatening complication after bone marrow transplantation (BMT), is induced by activation of alloreactive donor T cells. Our previous study demonstrated that transplantation of myeloid differentiation factor 88 (MyD88)-deficient knockout (KO) bone marrow (BM) resulted in aggravation of GVHD. Here, to understand the cellular mechanism, we performed longitudinal in vivo imaging and flow cytometric analyses followed by transcriptome and functional examination of donor MyD88-KO BM progenies in GVHD hosts, using a major histocompatibility complex-matched but minor histocompatibility antigen-mismatched C57BL/6→BALB.B model. In GVHD hosts with MyD88-KO BMT, donor BM-derived CD11b+Gr-1+ cells were found to undergo cell death, a fate significantly different from the explosive expansion shown by the wild type (WT) counterparts, and also from the moderate expansion of the WT or MyD88-KO BM-derived cells in non-GVHD hosts. It was also revealed that MyD88-KO CD11b+Gr-1+ cells preferred differentiation into CD11c+ dendritic cells (DCs) to expansion as myeloid-derived suppressor cells in GVHD hosts or in high inflammatory in vitro conditions. These CD11c+ DCs comprised the majority of MyD88-KO CD11b+Gr-1+ apoptotic cells in GVHD hosts. Their ability to cross-present alloantigens of host origin contributed to the enhancement of T cell alloreactivity, causing GVHD aggravation and eventually death through the killing function of activated T cells. These results provide insights into the roles of MyD88 in myelopoiesis of donor BM and the protective effects in GVHD hosts, helpful information for development of a strategy to control GVHD.
The Relationship of Dry Eye Disease with Depression and Anxiety: A Naturalistic Observational Study

Purpose In recent years, the relationship between dry eye disease (DED) and psychiatric disorders has been gaining attention. The relationship between dry eye symptoms and psychiatric symptoms has been reported in multiple retrospective studies. However, in previous studies there have been limitations to these observations, such as a lack of close examination of either DED or mood symptoms. Methods In this study, we evaluated the psychological state and social functionality of DED patients by administering validated psychiatric tests as well as ophthalmologic examinations twice during the course of DED treatment. Forty subjects (61.3 ± 18.1-years old) received the primary psychiatric assessments and 26 received the secondary psychiatric assessments. Results In a cross-sectional examination, we found patients with depressive and/or anxiety symptoms had higher Dry Eye Related Quality of Life Score (DEQ) scores, whereas the objective symptoms of DED did not differ between groups. We also found a positive relationship between depression/anxiety scores and DED subjective symptoms. On the other hand, in longitudinal examination, we found psychiatric symptoms had no impact on subjective and objective DED symptoms throughout the course of DED symptoms. Conclusions We found depression and anxiety were related to the subjective symptoms of DED but not the objective symptoms. Translational Relevance It is important to pay attention to psychiatric symptoms in patients with DED and an investigation into appropriate treatment strategies for patients with DED in combination with psychiatric symptoms is needed in the future.
An in-place, subquadratic algorithm for permutation inversion

We assume the permutation $\pi$ is given by an $n$-element array in which the $i$-th element denotes the value $\pi(i)$. Constructing its inverse in-place (i.e. using $O(\log{n})$ bits of additional memory) can be achieved in linear time with a simple algorithm. Limiting the numbers that can be stored in our array to the range $[1.n]$ still allows a straightforward $O(n^2)$ time solution. The time complexity can be improved using randomization, but this only improves the expected, not the pessimistic running time. We present a deterministic algorithm that runs in $O(n^{3/2})$ time.
MultiDEC: Multi-Modal Clustering of Image-Caption Pairs

In this paper, we propose a method for clustering image-caption pairs by simultaneously learning image representations and text representations that are constrained to exhibit similar distributions. These image-caption pairs arise frequently in high-value applications where structured training data is expensive to produce but free-text descriptions are common. MultiDEC initializes parameters with stacked autoencoders, then iteratively minimizes the Kullback-Leibler divergence between the distribution of the images (and text) to that of a combined joint target distribution. We regularize by penalizing non-uniform distributions across clusters. The representations that minimize this objective produce clusters that outperform both single-view and multi-view techniques on large benchmark image-caption datasets.
A Unified Spatial Framework for UAV-Aided MmWave Networks

For unmanned aerial vehicle (UAV) aided millimeter wave (mmWave) networks, we propose a unified three-dimensional (3D) spatial framework in this paper to model a general case that uncovered users send messages to base stations via UAVs. More specifically, the locations of transceivers in downlink and uplink are modeled through the Poisson point processes and Poisson cluster processes (PCPs), respectively. For PCPs, Matern cluster and Thomas cluster processes, are analyzed. Furthermore, both 3D blockage processes and 3D antenna patterns are introduced for appraising the effect of altitudes. Based on this unified framework, several closed-form expressions for the coverage probability in the uplink and downlink, are derived. By investigating the entire communication process, which includes the two aforementioned phases and the cooperative transmission between them, tractable expressions of system coverage probabilities are derived. Next, three practical applications in UAV networks are provided as case studies of the proposed framework. The results reveal that the impact of thermal noise and non-line-of-sight mmWave transmissions is negligible. In the considered networks, mmWave outperforms sub-6 GHz in terms of the data rate, due to the sharp direction beamforming and large transmit bandwidth. Additionally, there exists an optimal altitude of UAVs, which maximizes the system coverage probability.
PyOD: A Python Toolbox for Scalable Outlier Detection

PyOD is an open-source Python toolbox for performing scalable outlier detection on multivariate data. Uniquely, it provides access to a wide range of outlier detection algorithms, including established outlier ensembles and more recent neural network-based approaches, under a single, well-documented API designed for use by both practitioners and researchers. With robustness and scalability in mind, best practices such as unit testing, continuous integration, code coverage, maintainability checks, interactive examples and parallelization are emphasized as core components in the toolbox's development. PyOD is compatible with both Python 2 and 3 and can be installed through Python Package Index (PyPI) or this https URL.
Text Mining Customer Reviews For Aspect-based Restaurant Rating

This study applies text mining to analyze customer reviews and automatically assign a collective restaurant star rating based on five predetermined aspects: ambiance, cost, food, hygiene, and service. The application provides a web and mobile crowd sourcing platform where users share dining experiences and get insights about the strengths and weaknesses of a restaurant through user contributed feedback. Text reviews are tokenized into sentences. Noun-adjective pairs are extracted from each sentence using Stanford Core NLP library and are associated to aspects based on the bag of associated words fed into the system. The sentiment weight of the adjectives is determined through AFINN library. An overall restaurant star rating is computed based on the individual aspect rating. Further, a word cloud is generated to provide visual display of the most frequently occurring terms in the reviews. The more feedbacks are added the more reflective the sentiment score to the restaurants’ performance.
Rethinking the Artificial Neural Networks: A Mesh of Subnets with a Central Mechanism for Storing and Predicting the Data

The Artificial Neural Networks (ANNs) have been originally designed to function like a biological neural network, but does an ANN really work in the same way as a biological neural network? As we know, the human brain holds information in its memory cells, so if the ANNs use the same model as our brains, they should store datasets in a similar manner. The most popular type of ANN architecture is based on a layered structure of neurons, whereas a human brain has trillions of complex interconnections of neurons continuously establishing new connections, updating existing ones, and removing the irrelevant connections across different parts of the brain. In this paper, we propose a novel approach to building ANNs which are truly inspired by the biological network containing a mesh of subnets controlled by a central mechanism. A subnet is a network of neurons that hold the dataset values. We attempt to address the following fundamental questions: (1) What is the architecture of the ANN model? Whether the layered architecture is the most appropriate choice? (2) Whether a neuron is a process or a memory cell? (3) What is the best way of interconnecting neurons and what weight-assignment mechanism should be used? (4) How to incorporate prior knowledge, bias, and generalizations for features extraction and prediction? Our proposed ANN architecture leverages the accuracy on textual data and our experimental findings confirm the effectiveness of our model. We also collaborate with the construction of the ANN model for storing and processing the images.