Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of excreted-secreted antigens of filarial nematodes to develop diagnostic methods

The identification of excreted-secreted (ES) proteins of filarial nematodes as potential diagnostic reagents is an important requirement for the development of methods to determine level of infection in the host, especially for human filariae. Dirofilaria immitis, the canine heartworm, is a widespread and important veterinary pathogen and is a useful model for filarial parasites of humans. An analysis of proteins released from adult D. immitis (the secretome) in culture is available. We sought to identify D. immitis ES proteins found in vivo to validate the in vitro secretome and to investigate them as potential diagnostic reagents. Cultures of D. immitis adults obtained from infected dogs were maintained for 72 hr with daily changes of media. Proteins were concentrated from spent media by standard methods and were passed through Protein-A columns containing purified IgG antibodies from heartworm-infected dogs. Following extensive washing, heartworm proteins recognized by the antibodies were eluted from these columns and submitted for analysis by tandem mass-spectrometry (MS/MS). As a comparison, somatic proteins from adult D. immitis female parasites and microfilariae were also processed and analyzed by the same protocol. Six, nine and twelve proteins were identified by MS/MS in the ES, adult female, and microfilariae samples, respectively. The identification of the most abundantly secreted parasite proteins present in the serum of infected hosts offers a rational approach to the development of new diagnostic assays that may be applicable across the Filarioidea. %%%%L'identification des proteines excretees-secretees (ES) des nematodes filaires comme de potentiels reactifs a des fins diagnostiques est un prerequis important pour le developpement de methodes visant a determiner le niveau d'infection chez l'hote, particulierement dans le cas de filaires humains. Dirofilaria immitis, le ver du cœur canin, est un important pathogene veterinaire repandu et est un modele utile pour etudier les filaires parasitaires chez les humains. Une analyse des proteines secretees par des D. immitis adultes (le secretome) en culture in vitro est disponible. Nous cherchions a identifier des proteines ES de D. imitis presentes in vivo pour valider le secretome in vitro et pour les considerer comme de potentiels reactifs a des fins diagnostiques. Des cultures de D. immitis adultes obtenues de chiens infectes furent maintenues pendant 72 heures en changeant le milieu de culture quotidiennement. Les proteines contenues dans le milieu use furent concentrees par des methodes conventionnelles et furent passees a travers des colonnes Protein-A contenant des anticorps IgG purifies de chiens infectes avec des vers du cœur. Suivant un rincage rigoureux, les proteines des vers reconnues par les anticorps furent eluees et soumises a une analyse par spectrometrie de masse en tandem (MS/MS). A titre comparatif, les proteines somatiques de parasites D. immitis adultes femelles et microfilaires furent soumises au meme processus et…
Optimizing the Sensor Placement for Foot Plantar Center of Pressure without Prior Knowledge Using Deep Reinforcement Learning

We study the foot plantar sensor placement by a deep reinforcement learning algorithm without using any prior knowledge of the foot anatomical area. To apply a reinforcement learning algorithm, we propose a sensor placement environment and reward system that aims to optimize fitting the center of pressure (COP) trajectory during the self-selected speed running task. In this environment, the agent considers placing eight sensors within a 7 × 20 grid coordinate system, and then the final pattern becomes the result of sensor placement. Our results show that this method (1) can generate a sensor placement, which has a low mean square error in fitting ground truth COP trajectory, and (2) robustly discovers the optimal sensor placement in a large number of combinations, which is more than 116 quadrillion. This method is also feasible for solving different tasks, regardless of the self-selected speed running task.
Association of genetic variability in CD209 gene with bovine paratuberculosis disease: a case–control study in the Indian cattle population

Abstract This study aimed to explore the association of single nucleotide polymorphisms (SNPs) in CD209 gene with the occurrence of bovine paratuberculosis (PTB) disease caused by Mycobacterium avium subspecies paratuberculosis (MAP) in Indian cattle. A total of 213 animals were preliminarily selected on the basis of physical body condition score, which was then screened by a panel of diagnostic tests viz. Johnin, ELISA, fecal microscopy, and fecal culture, for the establishment of a case–control resource population. A total of four SNPs viz. rs208222804, rs211654540, rs208814257, and rs210748127 in CD209 gene were genotyped by PCR-RFLP. All SNPs, except rs210748127, were polymorphic in our population. Genotypic–phenotypic associations were assessed by the PROCLOGISTIC procedure of SAS 9.3. The SNP rs208814257 yielded three genotypes viz. CC, CG, and GG, which were significantly (p < 0.05) different in case as compared to the control population. The odds of CC and CG in comparison to GG genotype were 1.21 and 0.40, respectively. The CG genotype was significantly higher in control population, indicating that this genotype may provide resistance against PTB in our resource population. Upon validation in an independent, larger test population and following biological characterization, SNP rs208814257 can be incorporated in marker panel for selection of animals with greater resistance to MAP infection.
Engineered TALE Repeats for Enhanced Imaging‐Based Analysis of Cellular 5‐Methylcytosine

Transcription‐activator‐like effectors (TALEs) are repeat‐based, programmable DNA‐binding proteins that can be engineered to recognize sequences of canonical and epigenetically modified nucleobases. Fluorescent TALEs can be used for the imaging‐based analysis of cellular 5‐methylcytosine (5 mC) in repetitive DNA sequences. This is based on recording fluorescence ratios from cell co‐stains with two TALEs: an analytical TALE targeting the cytosine (C) position of interest through a C‐selective repeat that is blocked by 5 mC, and a control TALE targeting the position with a universal repeat that binds both C and 5 mC. To enhance this approach, we report herein the development of novel 5 mC‐selective repeats and their integration into TALEs that can replace universal TALEs in imaging‐based 5 mC analysis, resulting in a methylation‐dependent response of both TALEs. We screened a library of size‐reduced repeats and identified several 5 mC binders. Compared to the 5 mC‐binding repeat of natural TALEs and to the universal repeat, two repeats containing aromatic residues showed enhancement of 5 mC binding and selectivity in cellular transcription activation and electromobility shift assays, respectively. In co‐stains of cellular SATIII DNA with a corresponding C‐selective TALE, this selectivity results in a positive methylation response of the new TALE, offering perspectives for studying 5 mC functions in chromatin regulation by in situ imaging with increased dynamic range.
Experimental and Numerical Study on Withdrawal Strength of Different Types of Auxetic Dowels for Furniture Joints

Studies on the application of auxetic metamaterials and structures in furniture joints are very limited. However, they have huge potential for use in ready-to-assemble furniture. This study aimed to design and produce different types of auxetic dowels in 3D printing technology, and experimentally and numerically analyze the withdrawal strength of these dowels. In the scope of the study, 24 auxetic dowels with different types and size of inclusions, different diameter of holes, and a non-auxetic reference dowel were designed and produced with appropriate muffs. Dowels were 3D printed from polyamide (PA12). Poisson’s ratios, withdrawal strength, contact pressures, and friction coefficients of dowels were determined theoretically by means of numerical analyses and real static compression tests. After the pre-production of dowels, the dowels with triangular inclusions have not been found to have sufficient strength and stiffness. Withdrawal strength of dowels decreased as the size of inclusions is decreased, or dowel hole diameter is increased. Furthermore, contact pressures and stresses in auxetic dowels were considerably lower than non-auxetic dowels under the withdrawal force.
Transcriptomic Insights into the Effect of Melatonin in Saccharomyces cerevisiae in the Presence and Absence of Oxidative Stress

Melatonin is a ubiquitous indolamine that plays important roles in various aspects of biological processes in mammals. In Saccharomyces cerevisiae, melatonin has been reported to exhibit antioxidant properties and to modulate the expression of some genes involved in endogenous defense systems. The aim of this study was to elucidate the role of supplemented melatonin at the transcriptional level in S. cerevisiae in the presence and absence of oxidative stress. This was achieved by exposing yeast cells pretreated with different melatonin concentrations to hydrogen peroxide and assessing the entry of melatonin into the cell and the yeast response at the transcriptional level (by microarray and qPCR analyses) and the physiological level (by analyzing changes in the lipid composition and mitochondrial activity). We found that exogenous melatonin crossed cellular membranes at nanomolar concentrations and modulated the expression of many genes, mainly downregulating the expression of mitochondrial genes in the absence of oxidative stress, triggering a hypoxia-like response, and upregulating them under stress, mainly the cytochrome complex and electron transport chain. Other categories that were enriched by the effect of melatonin were related to transport, antioxidant activity, signaling, and carbohydrate and lipid metabolism. The overall results suggest that melatonin is able to reprogram the cellular machinery to achieve tolerance to oxidative stress.
A Retrospective, Matched Case-Control Study on the Risk Factors of Falls and Varying Severities of Fall-Related Injuries in Inpatients

Objective This study was to investigate the factors that influence falls and the severity of fall-related injuries in inpatients. Methods We adopted a retrospective, matched case-control design and conducted this study at a teaching hospital in Taiwan. Our study period ran from January 2016 to December 2019. We searched for inpatients with official fall records and obtained data from 823 patients, and then established a control group comprising 331 matching patients based on age, sex, length of hospital stay at time of fall incident, and ward type, thereby resulting in 1154 patients in all. A cumulative logistic regression model was applied to the data collected from medical records and fall incident reports to identify the factors that influence falls and the severity of fall-related injuries in inpatients. Results The results indicated that the use of sedatives (B = 0.49, P < 0.001), impaired consciousness (B = 0.64, P < 0.001), normal weight versus obese (B = −0.59, P = 0.008), low hemoglobin levels (B = −0.08, P = 0.003), an unsteady gait versus a normal gait (B = 1.82, P < 0.001), and history of falling within the past year (B = 0.56, P < 0.001) were correlated with the falls and the severity of fall-related injuries. Conclusions Our results indicate that the use of sedatives, impaired consciousness, obesity, low hemoglobin levels, poor gait function, and history of falling within the past year are all independent factors that influence falls and the severity of fall-related injuries. This study can provide medical personnel with a reference for the identification of patients with a high risk of falling and implementation of fall prevention measures.
Genomic loss in environmental and isogenic morphotype isolates of Burkholderia pseudomallei is associated with intracellular survival and plaque-forming efficiency

Background Burkholderia pseudomallei is an environmental bacterium that causes melioidosis. A facultative intracellular pathogen, B. pseudomallei can induce multinucleated giant cells (MNGCs) leading to plaque formation in vitro. B. pseudomallei can switch colony morphotypes under stress conditions. In addition, different isolates have been reported to have varying virulence in vivo, but genomic evolution and the relationship with plaque formation is poorly understood. Methodology/Principle findings To gain insights into genetic underpinnings of virulence of B. pseudomallei, we screened plaque formation of 52 clinical isolates and 11 environmental isolates as well as 4 isogenic morphotype isolates of B. pseudomallei strains K96243 (types II and III) and 153 (types II and III) from Thailand in A549 and HeLa cells. All isolates except one environmental strain (A4) and K96243 morphotype II were able to induce plaque formation in both cell lines. Intracellular growth assay and confocal microscopy analyses demonstrated that the two plaque-forming-defective isolates were also impaired in intracellular replication, actin polymerization and MNGC formation in infected cells. Whole genome sequencing analysis and PCR revealed that both isolates had a large genomic loss on the same region in chromosome 2, which included Bim cluster, T3SS-3 and T6SS-5 genes. Conclusions/Significance Our plaque screening and genomic studies revealed evidence of impairment in plaque formation in environmental isolates of B. pseudomallei that is associated with large genomic loss of genes important for intracellular multiplication and MNGC formation. These findings suggest that the genomic and phenotypic differences of environmental isolates may be associated with clinical infection.
CONTRASTING MODES OF EVOLUTION IN TWO GROUPS OF PEREZIA(MUTISIEAE; COMPOSITAE) OF SOUTHERN SOUTH AMERICA

Summary Two species groups of the closely knit South American section of the genus Perezia occur in the Andes of southern America but differ conspicuously in the number of species they contain, and the habitat and amount of morphological specialization of their constituent species. These differences reflect the contrasting evolutionary histories of the two species groups. The evolutionary mode most significant in forming each group has been, in turn, determined by the age, geographical extent and vicissitudes of the habitat in which each group occurs. In one case, the habitat is old, covers a large continuous geographical area and has remained relatively stable since the arrival of the ancestral stock well before the Pleistocene. In the second case, the habitat is young, of discontinuous and often limited extent and has undergone numerous rapid alterations since its inception at the end of the Pliocene. In the first case the Pereziae have followed a course of phyletic evolution; in the second, a mode of true speciation.
Increased arterial stiffness in males with abdominal aortic aneurysm

Abdominal aortic aneurysm (AAA), a localized dilatation of the abdominal aorta, has a prevalence of about 1.5%–3% among 65‐ to 70‐year‐old males in Europe. AAA confers an increased risk of developing major cardiovascular events in addition to the risk of aneurysm rupture. The aim of this study was to evaluate whether the arterial wall distensibility is altered in subjects with AAA.
Rapid multilayer microfabrication for modeling organotropic metastasis in breast cancer

Triple-negative breast cancer (TNBC) is one of the most insidious forms of breast cancer with high rates of metastasis, resulting in major mortalities in breast cancer patients. To better understand and treat TNBC metastasis, investigation of TNBC interactions with blood vasculatures is crucial. Among multiple metastatic processes, a step of TNBC exit from the blood vessels (‘extravasation’) in the pre-metastatic organs determines the final site of the metastasis. Here, we present a rapid multilayer microfabrication method of transferring a three-dimensional (3D) overhang pattern to a substrate with a sacrificial layer to reconstitute a 3D blood vessel surrounded by the extracellular matrix containing organ-specific parenchymal cells. Bones and lungs are the most common sites of breast cancer metastasis. We modeled organotropic bone and lung metastasis in TNBC by introducing subpopulations of TNBC metastases into a vessel lumen surrounded by osteoblasts, bone marrow derived mesenchymal stem cells, and lung fibroblasts. We found that bone-like microenviroment with osteoblasts and mesenchymal stem cells promoted extravasation of the bone-tropic TNBC cells, whereas the lung-like microenviroment promoted extravasation of the lung-tropic TNBC cells. Given that these organ-specific parenchymal cells do not impact vascular permeability, our results suggest that the parenchymal cells dictate selective extravasation of the bone-tropic or lung-tropic TNBC cells in our system.
An Organelle‐Specific Nanozyme for Diabetes Care in Genetically or Diet‐Induced Models

The development of nanozymes has made active impact in diagnosis and therapeutics. However, understanding of the full effects of these nanozymes on biochemical pathways and metabolic homeostasis remains elusive. Here, it is found that iron oxide nanoparticles (Fe3O4 NPs), a type of well‐established nanozyme, can locally regulate the energy sensor adenosine 5′‐monophosphate‐activated protein kinase (AMPK) via their peroxidase‐like activity in the acidic lysosomal compartment, thereby promoting glucose metabolism and insulin response. Fe3O4 NPs induce AMPK activation and enhance glucose uptake in a variety of metabolically active cells as well as in insulin resistant cell models. Dietary Fe3O4 NPs display therapeutic effects on hyperglycemia and hyperinsulinemia in Drosophila models of diabetes induced by genetic manipulation or high‐sugar diet. More importantly, intraperitoneal administration of Fe3O4 NPs stimulates AMPK activities in metabolic tissues, reduces blood glucose levels, and improves glucose tolerance and insulin sensitivity in diabetic ob/ob mice. The study reveals intrinsic organelle‐specific properties of Fe3O4 NPs in AMPK activation, glycemic control, and insulin‐resistance improvement, suggesting their potential efficacy in diabetes care.
Thermophilic anaerobic treatment to industrial wastewater: number of micro-organisms and biomass

This paper describes the determination of the microbial population, in terms of the number, biomass and composition, of single and two phase, laboratory-scale thermophilic (55”C) anaerobic reactors, under steady-state conditions. Epifluorescence microscopy with DAPI (4’,6-diamidine-2 -phenylindole) as fluorochrome was used to determine the total number of microorganisms in the reactors, and autofluorescence microscopy for the number of the total methanogenic populations. The results obtained by the direct count methods were compared to the quantity of biomass contained in the system, determined by volatile suspended solids (VSS). The concentration of acidogenic bacteria was estimated by subtraction of the autofluorescence results from those of the DAPI epifluorescence microscopy.
Notes on the Evolution of the Mammal-like Reptiles

The following investigation arose as the natural outgrowth of the description of Moschoides romeri, one of the herbivorous dinocephalians from the Karroo of South Africa (see Trans. Kan. Acad. Sci., 40:221-231, 1937). Only the postcranial skeleton was sufficiently well preserved to allow a complete description. Consequently especial care was exercised in reviewing the literature on the therapsids to accumulate the available information on postcranial structures. The material so gathered serves as the basis for this investigation. Comparative studies of the therapsids have been based largely on cranial structures. As a result, the current concepts of therapsid phylogeny give only meager recognition to the evidence presented by the postcranial skeleton. The reasons for such a tendency are valid, first, because unified skulls are more common as fossils than unified postcranial skeletons, second, because exact. preferably metric, descriptions of the postcranial skeleton have been attempted by very few authors, and third, because of the opinion that the characters of the skull serve as a better index of evolutionary advance than do postcranial features.
Identification of tannic cell walls at the outer surface of the endosperm upon Arabidopsis seed coat rupture

SUMMARY The seed coat is specialized dead tissue protecting the plant embryo from mechanical and oxidative damage. Tannins, a type of flavonoids, are antioxidants known to accumulate in the Arabidopsis seed coat and transparent testa mutant seeds, deficient in flavonoid synthesis, exhibit low viability. However, their precise contribution to seed coat architecture and biophysics remains evasive. A seed coat cuticle, covering the endosperm outer surface and arising from the seed coat inner integument 1 cell layer was, intriguingly, previously shown to be more permeable in transparent testa mutants deficient not in cuticular component synthesis, but rather in flavonoid synthesis. Investigating the role of flavonoids in cuticle permeability led us to identify periclinal inner integument 1 tannic cell walls being attached, together with the cuticle, to the endosperm surface upon seed coat rupture. Hence, inner integument 1 tannic cell walls and the cuticle form two fused layers present at the surface of the exposed endosperm upon seed coat rupture, regulating its permeability. Their potential physiological role during seed germination is discussed.
Mini-Project 1: Bag Models for Crop Yield Prediction

The central goal of crop yield predictions is to provide high-resolution mappings in order to alleviate the costs for agricultural producers to manually collect regional yield statistics and forecast future production. While recent breakthroughs in data processing of satellite imagery have provided modellers with the ability to look at the vegetation index of each individual crop ﬁeld, crop production data is often only collected at lower regional resolutions, such as provincial or county-wide. Recent work on kernel methods and aggregate output Gaussian processes ﬁt naturally into this framework. In this project, we compare different techniques that can be applied to the task of crop yield predictions and conduct experiments with a simulated Gaussian process and actual yield data in Germany, with the MODIS satellite and ECWMF weather datasets as features.
High concordance between chart review adjudication and electronic medical record data to identify prevalent and incident diabetes mellitus among persons with and without HIV

Electronic medical records (EMR) represent a rich source of data, but the value of EMR for health research relies on accurate ascertainment of clinical diagnoses. Identifying diabetes in EMR is complicated by the variety of accepted diagnostic criteria, some of which can be confounded by conditions such as HIV infection. We compared EMR‐based criteria for estimating diabetes prevalence and incidence in the Veterans Health Administration (VHA), overall and by HIV status, against physician chart review and adjudication.