Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Supplement and Food Contaminations and Their Implications for Doping Controls

A narrative review with an overall aim of indicating the current state of knowledge and the relevance concerning food and supplement contamination and/or adulteration with doping agents and the respective implications for sports drug testing is presented. The identification of a doping agent (or its metabolite) in sports drug testing samples constitutes a violation of the anti-doping rules defined by the World Anti-Doping Agency. Reasons for such Adverse Analytical Findings (AAFs) include the intentional misuse of performance-enhancing/banned drugs; however, also the scenario of inadvertent administrations of doping agents was proven in the past, caused by, amongst others, the ingestion of contaminated dietary supplements, drugs, or food. Even though controversial positions concerning the effectiveness of dietary supplements in healthy subjects exist, they are frequently used by athletes, anticipating positive effects on health, recovery, and performance. However, most supplement users are unaware of the fact that the administration of such products can be associated with unforeseeable health risks and AAFs in sports. In particular anabolic androgenic steroids (AAS) and stimulants have been frequently found as undeclared ingredients of dietary supplements, either as a result of cross-contaminations due to substandard manufacturing practices and missing quality controls or an intentional admixture to increase the effectiveness of the preparations. Cross-contaminations were also found to affect therapeutic drug preparations. While the sensitivity of assays employed to test pharmaceuticals for impurities is in accordance with good manufacturing practice guidelines allowing to exclude any physiological effects, minute trace amounts of contaminating compounds can still result in positive doping tests. In addition, food was found to be a potential source of unintentional doping, the most prominent example being meat tainted with the anabolic agent clenbuterol. The athletes’ compliance with anti-doping rules is frequently tested by routine doping controls. Different measures including offers of topical information and education of the athletes as well as the maintenance of databases summarizing low- or high-risk supplements are important cornerstones in preventing unintentional anti-doping rule violations. Further, the collection of additional analytical data has been shown to allow for supporting result management processes.
Literature Review of BARD1 as a Cancer Predisposing Gene with a Focus on Breast and Ovarian Cancers

Soon after the discovery of BRCA1 and BRCA2 over 20 years ago, it became apparent that not all hereditary breast and/or ovarian cancer syndrome families were explained by germline variants in these cancer predisposing genes, suggesting that other such genes have yet to be discovered. BRCA1-associated ring domain (BARD1), a direct interacting partner of BRCA1, was one of the earliest candidates investigated. Sequencing analyses revealed that potentially pathogenic BARD1 variants likely conferred a low–moderate risk to hereditary breast cancer, but this association is inconsistent. Here, we review studies of BARD1 as a cancer predisposing gene and illustrate the challenge of discovering additional cancer risk genes for hereditary breast and/or ovarian cancer. We selected peer reviewed research articles that focused on three themes: (i) sequence analyses of BARD1 to identify potentially pathogenic germline variants in adult hereditary cancer syndromes; (ii) biological assays of BARD1 variants to assess their effect on protein function; and (iii) association studies of BARD1 variants in family-based and case-control study groups to assess cancer risk. In conclusion, BARD1 is likely to be a low–moderate penetrance breast cancer risk gene.
Development and Validation of the Recognizing Addictive Disorders Scale: A Transdiagnostic Measure of Substance-Related and Other Addictive Disorders

Abstract Objective Substance use disorders and behavioral addictions commonly co-occur. However, few available self-report measures reliably and validly assess the full range of addictive conditions. The development and initial validation of a new measure—Recognizing Addictive Disorders (RADs) scale addresses a significant gap in the literature. Method: After items were generated and evaluated in Study 1, Study 2 (N = 300), applied exploratory factor analysis to the item pool using an online-based community sample. In Study 3 (N = 427), the factor structure was validated using an independent online-based community sample and confirmatory factor analysis. Results: The scale demonstrated good internal consistency (a = .92) and construct validity, including replication of the factor structure (χ2 (553) = 760.83, p < . 001, CFI = . 997, TLI = . 997, RMSEA = . 030) and correlation with a related transdiagnostic measure of addiction (r = .72). Discussion: Overall, results support the preliminary validity of a brief transdiagnostic measure of addiction that considers a diverse range of behaviors. For patients presenting to substance abuse treatment, this tool may be useful in identifying symptoms of other types of non-substance problems, which could ultimately aid in treatment planning.
The multicomparative 2-n-way genome suite

To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the “2-n-way” software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, in which user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups. Thus, the 2-n-way software suite is ideal for performing multidirectional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose approximately 100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.
Circular RNA 000554 represses epithelial‐mesenchymal transition in breast cancer by regulating microRNA‐182/ZFP36 axis

Increasing evidence indicates that circular RNAs (circRNAs) play a crucial role in regulating microRNAs (miRs) and mRNAs during breast cancer (BC) progression. Based on the in silico analysis of circRNA/miR/mRNA in BC, we aim to define an important role of circRNA_000554 in BC in relation to miR‐182 and zinc finger protein 36 (ZFP36). Low expression of circRNA_000554 and ZFP36, and high miR‐182 expression were determined in the clinical BC tissues. CircRNA_000554 acted as a sponge of miR‐182, and miR‐182 directly targeted ZFP36. After that, in order to evaluate the effects of circRNA_000554, miR‐182, and ZFP36 on cellular process, we evaluated in vitro epithelial‐mesenchymal transition (EMT) and in vivo tumor growth after delivering a series of overexpression plasmids, mimic, inhibitor, or shRNAs into BC cells. Increasing circRNA_000554 suppressed EMT, cell invasion and migration during BC by depleting miR‐182 and increasing ZFP36. The inhibitory effect of circRNA_000554 on tumor growth was validated in vivo. Taken together, the present study confirms that circRNA_000554 functioned as an inhibitor of EMT in BC and suggests a molecular mechanism that circRNA_000554 bound to miR‐182 to upregulate ZFP36 in this process.
Genetic Diversity and Pathogenicity of Fusarium oxysporum f.sp. melonis Races from Different Areas of Italy

Fusarium wilt caused by Fusarium oxysporum f.sp. melonis (FOM) is a devastating disease of melon worldwide. Pathogenicity tests performed with F. oxysporum isolates obtained from Italian melon-growing areas allowed to identify thirty-four FOM isolates and the presence of all four races. The aims of this work were to examine genetic relatedness among FOM isolates by race determination and to perform phylogenetic analyses of identified FOM races including also other formae speciales of F. oxysporum of cucurbits. Results showed that FOM race 1,2 was the most numerous with a total of eighteen isolates, while six and nine isolates were identified as race 0 and 1, respectively, and just one isolate was assigned to race 2. Phylogenetic analysis was performed by random amplified polymorphic DNA (RAPD) profiling and by translation elongation factor-1α (TEF-1α) sequencing. The analysis of RAPD profiles separated FOM races into two distinct clades. Clade 1, which included races 0, 1 and 1,2, was further divided into ‘subclade a’ which grouped almost all race 1,2 isolates, and into ‘subclade b’ which included race 0 and 1 isolates. Clade 2 comprised only race 2 isolates. The phylogenetic analysis based on TEF-1α separated FOM from the other formae speciales of F. oxysporum. Also with TEF-1α analysis, FOM races 0, 1 and 1,2 isolates grouped in one single clade clearly separated from FOM race 2 isolates which grouped closer to F. oxysporum f.sp. cucumerinum. RAPD technique was more effective than TEF-1α in differentiating FOM race 1,2 isolates from those belonging to the closely related races 0 and 1. Both phylogenetic analyses supported the close relationship between the three different FOM races which might imply the derivation from one another and the different origin of FOM race 2.
Revision of total knee arthroplasty with the use of patient-specific instruments: an alternative surgical technique

ABSTRACT Introduction Accuracy in the placement of components in revision total knee arthroplasty (R-TKA) surgery is sometimes challenging. The applicability of patient‑specific instruments (PSI) in knee surgery has progressively expanded to types of surgery other than primary arthroplasty. Could this assistive technology be used to facilitate accurate R-TKA surgery? The aim of the current manuscript is to describe this new application of PSI for revision of TKA-to-TKA and to provide a step-by-step technical guideline for use. Areas covered We will describe the application and a detailed description of PSI technology to TKA revision surgery, step-by-step, from CT images acquisition for preoperative planning and PSI blocks production to the surgery. Expert commentary The system can facilitate the accomplishment of the bony cuts for optimal implant placement and that can be useful in minimally altering the femoral and the tibial joint line. It is obvious that technology alone will not replace surgical skill and that accuracy of the system will also depend on the quality of the CT images and the ability of the software to prevent metal artifacts. Despite that, our initial results are promising and prove that the concept of applying PSI technology to the R-TKA surgery is feasible.
Surveillance, Fire Detection and Protection System for Substations

- Fire detection is most important in substations, due to its dangerous nature. It is necessary to detect fire early with accuracy. There comes the need of an accurate system for fire detection. So with the help of Neural Network we can detect fire from a surveillance video. The older sensor based systems and image processing based methods are not accurate and they often give false alarms due to wrong detection in outdoor areas. They need high implementation cost and not easy to cover larger areas. The environmental changes can also affect them. They have low performance and cause false alarms while there are shadows, varying lights and fire coloured objects. Neural Network helps to improve the fire detection capability with increased accuracy. It can detect fire in multiple situations as like day and night. To provide a proper fire detection in substation yard, Neural network based fire detection is implemented. This system consists of a video camera which takes live footages of the area. The video is processed by the Neural Network on the basis of fire detection algorithm. The network is trained with different models and different settings to understand the nature of fire which is similar to the GoogLeNet. Various images of fire are given as input to train the network using ImageNet. In order to prevent false alarm fire like substances are taught to the network, which improves accuracy. As the no: of image sets used for training the network increases, the accuracy of the networks increases. Once the network is trained it will be able to detect fire and give alerts accurately. Compared to traditional fire detection methods neural networks provide accurate and fast response to fire in both indoor and outdoor conditions.
Specific Detection of Yersinia pestis Based on Receptor Binding Proteins of Phages

The highly pathogenic bacterium Yersinia pestis is the causative agent of plague, a notorious infectious zoonotic disease. When transmitted from person to person as pneumonic plague via droplets, Y. pestis is highly contagious and in most cases is fatal if left untreated. Thus, when plague is suspected, rapid diagnosis is crucial, as a serious course of the infection is only averted by early antibiotic therapy. The bacterium is easy to cultivate, accessible and has a high potential for nefarious use such as bioterrorism. Highly specific, rapid and easy-to-use confirmatory diagnostic methods are required to reliably identify the pathogen independently from PCR-based methods or F1 antigen-based immunological detection. Yersinia pestis specific phages such as L-413C and ΦA1122 are already used for detection of Y. pestis in bacterial plaque or biosensor assays. Here, we made use of the host specificities conferred by phage receptor binding (or tail fiber/spike) proteins (RBP) for developing a specific, fast and simple fluorescence-microscopy-based detection method for Y. pestis. Genes of putative RBP of phages L-413C (gpH) and ΦA1122 (gp17) were fused with those of fluorescent proteins and recombinant receptor-reporter fusion proteins were produced heterologously in Escherichia coli. When first tested on attenuated Y. pestis strain EV76, RBP-reporters bound to the bacterial cell surface. This assay could be completed within a few minutes using live or formaldehyde-inactivated cells. Specificity tests using cultures of closely related Yersinia species and several inactivated fully virulent Y. pestis strains exhibited high specificities of the RBP-reporters against Y. pestis. The L-413C RBP proved to be especially specific, as it only detected Y. pestis at all temperatures tested, whereas the RBP of ΦA1122 also bound to Y. pseudotuberculosis strains at 37 °C (but not at 28, 20 or 6 °C). Finally, the Y. pestis-specific capsule, produced when grown at 37 °C, significantly reduced binding of phage ΦA1122 RBP, whereas the capsule only slightly diminished binding of L-413C RBP.
AEMDA: inferring miRNA-disease associations based on deep autoencoder

MOTIVATION MicroRNAs (miRNAs) are a class of noncoding RNAs that play critical roles in various biological processes. Many studies have shown that miRNAs are closely related to the occurrence, development and diagnosis of human diseases. Traditional biological experiments are costly and time consuming. As a result, effective computational models have become increasingly popular for predicting associations between miRNAs and diseases, which could effectively boost human disease diagnosis and prevention. RESULTS We propose a novel computational framework, called AEMDA, to identify associations between miRNAs and diseases. AEMDA applies a learning-based method to extract dense and high-dimensional representations of diseases and miRNAs from integrated disease semantic similarity, miRNA functional similarity and heterogeneous related interaction data. In addition, AEMDA adopts a deep autoencoder that does not need negative samples to retrieve the underlying associations between miRNAs and diseases. Furthermore, the reconstruction error is used as a measurement to predict disease-associated miRNAs. Our experimental results indicate that AEMDA can effectively predict disease-related miRNAs and outperforms state-of-the-art methods. AVAILABILITY The source code and data are available at https://github.com/CunmeiJi/AEMDA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Vascular Protective Effects of Xanthotoxin and Its Action Mechanism in Rat Aorta and Human Vascular Endothelial Cells

Objective: Xanthotoxin (XAT) is a linear furanocoumarin mainly extracted from the plants Ammi majus L. XAT has been reported the apoptosis of tumor cells, anti-convulsant, neuroprotective effect, antioxidative activity, and vasorelaxant effects. This study aimed to investigate the vascular protective effects and underlying molecular mechanisms of XAT. Methods: XAT’s activity was studied in rat thoracic aortas, isolated with aortic rings, and human umbilical vein endothelial cells (HUVECs). Results: XAT induced endothelium-dependent vasodilation in a concentration-dependent manner in the isolated rat thoracic aortas. Removal of endothelium or pretreatment of aortic rings with L-NAME, 1H-[1,2,4]-oxadiazolo-[4,3-a]-quinoxalin-1-one, and wortmannin significantly inhibited XAT-induced relaxation. In addition, treatment with thapsigargin, 2-aminoethyl diphenylborinate, Gd3+, and 4-aminopyridine markedly attenuated the XAT-induced vasorelaxation. XAT increased nitric oxide production and Akt- endothelial NOS (eNOS) phosphorylation in HUVECs. Moreover, XAT attenuated the expression of TNF-α-induced cell adhesion molecules such as intercellular adhesion molecule, vascular cell adhesion molecule-1, and E-selectin. However, this effect was attenuated by the eNOS inhibitors L-NAME and asymmetric dimethylarginine. Conclusions: This study suggests that XAT induces vasorelaxation through the Akt-eNOS-cGMP pathway by activating the KV channel and inhibiting the L-type Ca2+ channel. Furthermore, XAT exerts an inhibitory effect on vascular inflammation, which is correlated with the observed vascular protective effects.
Graphene-Like Layers from Carbon Black: In Vivo Toxicity Assessment

Graphene-like (GL) layers, a new graphene-related material (GRM), possess peculiar chemical, colloidal, optical and transport properties. Considering the very recent promising application of GL layers in biomedical and bioelectronic fields, it is of utmost importance to investigate the toxicological profile of these nanomaterials. This study represents an important first report of a complete in vivo toxicity assessment of GL layers on embryonic zebrafish (Danio rerio). Our results show that GL layers do not lead to any perturbations in the different biological parameters evaluated, indicating their good biocompatibility on a vertebrate model. The new insight into the biosafety of GL layers will expand their applications in nanomedicine.
Behavior test for seven-week old puppies (Canis familiaris): Inter-rater reliability and factors associated with test performance

Behavioral development in domestic dogs has been investigated for predicting suitability for service dog work or for matching with the “right” families as well as for identifying predispositions to behavioral problems. Findings from the scientific literature seem to confirm that conducting behavioral tests at 7 weeks of age is too early to reliably predict the temperament and personality of a dog. However, this period for domestic dogs is sensitive for early life learning and conditions during this time could have important consequences in adulthood. The aims of this study were to evaluate inter-rater reliability of a simple standardized test and to investigate which factors influence the behavioral reaction of puppies. 105 seven-week old puppies were exposed to five subtests: social attraction, following, retrieving, sudden appearance, noise. During each task, the behaviour of each pup was scored on a 3–5 point scale that reflected the suitability of the pup’s reaction to the task. Scores were evaluated for a single subtest and for two aggregate indicators (i.e. response to a person: social attraction subtest and following subtest and response to object and noise: retrieving subtest, sudden appearance subtest and noise subtest). Three assessors independently scored the dogs’ reactions for each task. Inter-rater reliability of the three assessors were analyzed with Fleiss’ Kappa and Kendall’s coefficient, which showed a high inter-rater reliability in 4 of 5 tasks. The ordered logistic regression was carried out to obtain a proportional odds model that was used to model the relationship between sex, litter size, stimulating environment, parity of mother, adequate maternal behavior and high scores. Litter size and maternal parity were associated with test performance in response to a person. The variance of effect of litter was high in response to object and noise. Taken together, our results suggest that using this scoring system there is sufficient inter-rater reliability in the test and litter size and mother experience influences task performances related to dog-human interaction.
Suppression of GABAergic transmission in the spinal dorsal horn induces pain-related behavior in a chicken model of spina bifida

Spina bifida aperta (SBA), one of the most common congenital malformations, causes various neurological disorders. Pain is a common complaint of patients with SBA. However, little is known about the neuropathology of SBA-related pain. Because loss of γ-aminobutyric acid (GABA)ergic neurons in the spinal cord dorsal horn is associated with pain, we hypothesized the existence of cross-talk between SBA-related pain and alterations in GABAergic transmission in the spinal cord. Therefore, we investigated the kinetics of GABAergic transmission in the spinal cord dorsal horn in a chicken model of SBA. Neonatal chicks with SBA exhibited various pain-like behaviors, such as an increased number of vocalizations with elevated intensity (loudness) and frequency (pitch), reduced mobility, difficulty with locomotion, and escape reactions. Furthermore, the chicks with SBA did not respond to standard toe-pinching, indicating disruption of the spinal cord sensorimotor networks. These behavioral observations were concomitant with loss of GABAergic transmission in the spinal cord dorsal horn. We also found apoptosis of GABAergic neurons in the superficial dorsal horn in the early neonatal period, although cellular abnormalization and propagation of neurodegenerative signals were evident at middle to advanced gestational stages. In conclusion, ablation of GABAergic neurons induced alterations in spinal cord neuronal networks, providing novel insights into the pathophysiology of SBA-related pain-like complications.