Miracle-dz/UniFAR-FTUs huggingface dataset:
Exercise and prostate cancer: From basic science to clinical applications

Prostate cancer (PCa) is a disease of increasing medical significance worldwide. In developed countries, PCa is the most common non‐skin cancer in men, and one of the leading causes of cancer‐related deaths. Exercise is one of the environmental factors that have been shown to influence cancer risk. Moreover, systemic reviews and meta‐analysis have suggested that total physical activity is related to a decrease in the risk of developing PCa. In addition, epidemiological studies have shown that exercise, after diagnosis, has benefits regarding PCa development, and positive outcome in patients under treatment. The standard treatment for locally advanced or metastatic PCa is Androgen deprivation therapy (ADT). ADT produces diverse side effects, including loss of libido, changes in body composition (increase abdominal fat), and reduced muscle mass, and muscle tone. Analysis of numerous research publications showed that aerobic and/or resistance training improve patient's physical condition, such us, cardiorespiratory fitness, muscle strength, physical function, body composition, and fatigue. Therefore, exercise might counteract several ADT treatment‐induced side effects. In addition of the aforementioned benefits, epidemiological, and in vitro studies have shown that exercise might decrease PCa development. Thus, physical activity might attenuate the risk of PCa and supervised exercise intervention might improve deleterious effects of cancer treatment, such as ADT side effects. This review article provides evidence indicating that exercise could complement, and potentiate, the current standard treatments for advanced PCa, probably by creating an unfavorable microenvironment that can negatively affect tumor development, and progression.
High-precision three-dimensional laser measurement system by cooperative multiple mobile robots

This paper presents a high-precision three-dimensional laser measurement system of an architectural structure by cooperative multiple mobile robots. This system is composed of three mobile robots, that is, a parent robot and two child robots. The parent robot is equipped with a three-dimensional laser scanner, attitude sensor, total station, and auto-leveling device. On the other hand, the child robots are equipped with six corner mirrors. The parent robot moves and stops repeatedly, and measures a three-dimensional architectural shape using the equipped laser scanner at several positions. Meanwhile, the child robots also move and stop alternately, and act as mobile landmarks for the positioning of the parent robot. By replacing or newly installing several devices/mechanisms, the precision of the proposed system becomes incomparably higher than our previous system. We report the system achieves quite high accuracy of 0.03 0.05% of targets' size through indoor/outdoor experiments. We apply the proposed technique for the shape measurement system of tunnels under construction and verify that the accuracy of the developed system is as high as a conventional ground-fixed laser scanner.
A few good responses: which mechanical effects of IOP on the ONH to study?

PURPOSE The biomechanical effects of IOP on the optic nerve head (ONH) are believed to play a role in glaucomatous neuropathy. There is, however, no consensus on which effects of IOP should be prioritized for investigation. Our goal was to identify a small set of variables capturing the majority of the effects of acute IOP on the ONH. METHODS We produced 4646 finite element models of the human ONH representing a wide range of tissue anatomies and mechanical properties. The effects of IOP were quantified through a set of 25 responses including stress, strain, and geometric deformation of the lamina cribrosa (LC) and peripapillary sclera. The correlations between the responses were analyzed and principal component analysis (PCA) was used to identify uncorrelated variables capturing the largest possible variance in the responses. RESULTS The responses formed groups with strong correlations. The top five principal components (PCs) accounted for 72.8%, 13.0%, 7.1%, 3.1%, and 2.0% of the variance, respectively. CONCLUSIONS Few PCs capture the majority of the mechanical effects of acute changes in IOP on the ONH, which previously required 25 measures. The PCs represented four key effects of IOP: lateral deformation associated with canal expansion (PC1), anterior-posterior deformation of the LC and the forces through it determined by either the mechanical properties of the LC (PC2) or of the neural tissue (PC4), rotation of the peripapillary sclera (PC5), and forces through the peripapillary sclera (PC3). A small set of uncorrelated variables will simplify describing and understanding the effects of IOP on the ONH.
Bayesian Inference of Species Networks from Multilocus Sequence Data

Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network, and we assume a multispecies network coalescent (MSNC) prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. To quantify the power of our method, we reanalyze two large datasets of genes from spruces and yeasts. For the three closely related spruces, we verify the previously suggested homoploid hybridization event in this clade; for the yeast data, we find extensive hybridization events. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides an extensible framework for Bayesian inference of reticulate evolution.
Growth inhibitory effect of stevioside on ovarian cancer through Akt/ERK pathway

Phytochemicals play a prominent role as cancer preventive agents. Stevioside is a phytochemical which is isolated from Stevia rebaudiana and is known for its medicinal properties including prevention against cancer. Therefore, the present work intended to explore the antiproliferative activity of stevioside on ovarian cancer cell line, OVCAR-3. The results elucidated that stevioside treatment repressed the growth of OVCAR-3 cells and induced cytotoxicity, both dose dependently and time dependently. Furthermore, stevioside has been found to be associated with increased ROS production in the cell which suggests the initiation of apoptosis. Additionally, the decrease in mitochondrial membrane potential indicated the involvement of stevioside induced intrinsic apoptotic pathway in the cell. These results were further confirmed by increased level of caspase-3 and caspase-9 in OVCAR-3 cancer cells after stevioside treatment. Moreover, flow cytometric study established the apoptotic behavior of stevioside and showed cell cycle arrest in G2/M phase. Additionally, the inactivation of P13K/AKT signaling pathway was also revealed. Thus, the results may summarize the therapeutic potential of stevioside against ovarian cancer and its role as chemotherapeutic agent in future clinical applications.
A miR-200 c / 141-BMI 1 autoregulatory loop regulates oncogenic activity of BMI 1 in cancer cells

MicroRNAs (miRNAs) are known to function as oncomiRs or tumor suppressors and are important noncoding RNA regulators of oncogenesis. The miR-200c/141 locus on chromosome 12 encodes miR-200c and miR-141, two members of the miR-200 family, which have been shown to function as tumor suppressive miRNAs by targeting multiple oncogenic factors such as polycomb group protein BMI1. Here, we show that BMI1 reciprocally functions as a transcriptional repressor of the miR-200c/141 cluster and that BMI1 inhibitors upregulate expression of miR-200c and miR-141. Our data suggest that BMI1 binds to the miR-200c/141 promoter and regulates it through transcription factor binding motifs E-box 2 and Z-box 1 to repress expression of miR-200c/141 cluster. We also show that PTC-209, a small molecule inhibitor of BMI1 gene expression induces cellular senescence and transcriptionally upregulates expression of miR-200c/141 cluster in breast cancer cells. Furthermore, inhibition of expression of miR-200c or miR-141 overcomes tumor suppressive effects of PTC209 including induction of cellular senescence and downregulation of breast cancer stem cell phenotype. Therefore, our studies suggest a reciprocal regulation between BMI1 and miR-200c/141 cluster, and that BMI1 inhibitory drugs can further amplify their inhibitory effects on BMI1 via multiple mechanisms including posttranscriptional regulation by upregulating BMI1 targeting miRNAs.
Towards Geospatial Search for Honduras

Local Web search has become a major and popular means of gathering information with a geographic relation. Local search not only relies on powerful algorithms from Geographic Information Retrieval and other fields, but also on the broad availability of location-referenced data on the Web and in other sources. While available commercial systems work satisfactory in well-developed countries, other regions of the world pose challenges in all areas of geospatial search. This article examines the potential for local search for the country of Honduras. The challenges, among others, are the very sparse Web coverage, few reliable commercial or public databases, challenging informal address schemes, uncertain and only coarse location data as well as privacy and security issues. This article aims to discuss these challenges and provide solutions within ongoing work towards the development of a geospatial search engine for Honduras.
Enhanced Supercapacitor Performance with Pt Decorated Nanoporous-Gold/ MnO2 Hybrid Electrodes

Electrochemical supercapacitors (ECs) are at the frontier of the research effort as a versatile solution to a variety of emerging energy applications, because of their unique high-power performance associated with reasonably high energy density and long lifetime, which bridges the gap between these of batteries and conventional electrolytic capacitors[1]. The utilization of nanostructured metal oxide hybrid electrodes is considered to be a promising strategy to significantly enhance the electrochemical performance. Recently, current collectors fabricated in 3D nanoarchitectures are intensively studied to form hybrid electrodes[2]. Among them, the nanoporous gold(NPG) with a bicontinuous nanoporous structure is one of promising 3D scaffold, which contributes large surface area and enables great electrical/ionic conductivity [3-5] for MnO2-based hybrid electrodes.
The origin of mitochondria in light of a fluid prokaryotic chromosome model

Biologists agree that the ancestor of mitochondria was an α-proteobacterium. But there is no consensus as to what constitutes an α-proteobacterial gene. Is it a gene found in all or several α-proteobacteria, or in only one? Here, we examine the proportion of α-proteobacterial genes in α-proteobacterial genomes by means of sequence comparisons. We find that each α-proteobacterium harbours a particular collection of genes and that, depending upon the lineage examined, between 97 and 33% are α-proteobacterial by the nearest-neighbour criterion. Our findings bear upon attempts to reconstruct the mitochondrial ancestor and upon inferences concerning the collection of genes that the mitochondrial ancestor possessed at the time that it became an endosymbiont.
Phyllotactic regularity requires the Paf1 complex in Arabidopsis

In plants, aerial organs are initiated at stereotyped intervals, both spatially (every 137° in a pattern called phyllotaxis) and temporally (at prescribed time intervals called plastochrons). To investigate the molecular basis of such regularity, mutants with altered architecture have been isolated. However, most of them only exhibit plastochron defects and/or produce a new, albeit equally reproducible, phyllotactic pattern. This leaves open the question of a molecular control of phyllotaxis regularity. Here, we show that phyllotaxis regularity depends on the function of VIP proteins, components of the RNA polymerase II-associated factor 1 complex (Paf1c). Divergence angles between successive organs along the stem exhibited increased variance in vip3-1 and vip3-2 compared with the wild type, in two different growth conditions. Similar results were obtained with the weak vip3-6 allele and in vip6, a mutant for another Paf1c subunit. Mathematical analysis confirmed that these defects could not be explained solely by plastochron defects. Instead, increased variance in phyllotaxis in vip3 was observed at the meristem and related to defects in spatial patterns of auxin activity. Thus, the regularity of spatial, auxin-dependent, patterning at the meristem requires Paf1c. Summary: Analysis of divergence angles in VIP mutants reveals that the regularity of organ initiation at the shoot apical meristem requires Paf1c and is related to spatial patterns of auxin activity.
Calcium-Dependent Protein Kinase Family Genes Involved in Ethylene-Induced Natural Rubber Production in Different Hevea brasiliensis Cultivars

Natural rubber latex production can be improved by ethylene stimulation in the rubber tree (Hevea brasiliensis). However, the expression levels of most functional proteins for natural rubber biosynthesis are not induced after ethylene application, indicating that post-translational modifications, especially protein phosphorylation, may play important roles in ethylene signaling in Hevea. Here, we performed a comprehensive investigation on evolution, ethylene-induced expression and protein–protein interaction of calcium-dependent protein kinases (CPKs), an important serine/threonine protein kinase family, in Hevea. Nine duplication events were determined in the 30 identified HbCPK genes. Expression profiling of HbCPKs in three rubber tree cultivars with low, medium and high ethylene sensitivity showed that HbCPK6, 17, 20, 22, 24, 28 and 30 are induced by ethylene in at least one cultivar. Evolution rate analysis suggested accelerated evolution rates in two paralogue pairs, HbCPK9/18 and HbCPK19/20. Analysis of proteomic data for rubber latex after ethylene treatment showed that seven HbCPK proteins could be detected, including six ethylene-induced ones. Protein–protein interaction analysis of the 493 different abundant proteins revealed that protein kinases, especially calcium-dependent protein kinases, possess most key nodes of the interaction network, indicating that protein kinase and protein phosphorylation play important roles in ethylene signaling in latex of Hevea. In summary, our data revealed the expression patterns of HbCPK family members and functional divergence of two HbCPK paralogue pairs, as well as the potential important roles of HbCPKs in ethylene-induced rubber production improvement in Hevea.
Mitigating thermal beam damage with metallic coats in low voltage FEG-EPMA of geological materials

Field emission gun electronprobe microanalysis (FEG-EPMA) provides the analyst with the opportunity to characterize very small volumes of material. Using a low voltage source the irradiated volume is submicron. It is well known that some geological phases e.g. volcanic glass, carbonates, phosphates, hydrous silicates suffer beam damage under high beam current condition [e.g.1,2] and several authors suggest mechanisms either to mitigate beam damage (e.g. cryostage cooling, reduced beam currents, metallic coats etc. [2,3,4.5]) or to use the time dependent intensity to interpolate the count rate back to the original composition at zero time [5].
UGuide: User-Guided Discovery of FD-Detectable Errors

Error detection is the process of identifying problematic data cells that are different from their ground truth. Functional dependencies (FDs) have been widely studied in support of this process. Oftentimes, it is assumed that FDs are given by experts. Unfortunately, it is usually hard and expensive for the experts to define such FDs. In addition, automatic data profiling over dirty data in order to find correct FDs is known to be a hard problem. In this paper, we propose an end-to-end solution to detect FD-detectable errors from dirty data. The broad intuition is that given a dirty dataset, it is feasible to automatically find approximate FDs, as well as data that is possibly erroneous. Arguably, at this point, only experts can confirm true FDs or true errors. However, in practice, experts never have enough budget to find all errors. Hence, our problem is, given a limited budget of expert's time, which questions we should ask, either FDs, cells, or tuples, such that we can find as many data errors as possible. We present efficient algorithms to interact with the user. Extensive experiments demonstrate that our proposed framework is effective in detecting errors from dirty data.
Toward an Optimal Global Stem Cell Donor Recruitment Strategy

Population-specific matching probabilities (MP) are a key parameter to assess the benefits of unrelated stem cell donor registries and the need for further donor recruitment efforts. In this study, we describe a general framework for MP estimations of specific and mixed patient populations under consideration of international stem cell donor exchange. Calculations were based on population-specific 4-locus (HLA-A, -B, -C, -DRB1) high-resolution haplotype frequencies (HF) of up to 21 populations. In various scenarios, we calculated several quantities of high practical relevance, including the maximal MP that can be reached by recruiting a fixed number of donors, the corresponding optimal composition by population of new registrants, and the minimal number of donors who need to be recruited to reach a defined MP. Starting at current donor numbers, the largest MP increases due to n = 500,000 additional same-population donors were observed for patients from Bosnia-Herzegovina (+0.25), Greece (+0.21) and Romania (+0.20). Especially small MP increases occurred for European Americans (+0.004), Germans (+0.01) and Hispanic Americans (+0.01). Due to the large Chinese population, the optimal distribution of n = 5,000,000 new donors worldwide included 3.9 million Chinese donors. As a general result of our calculations, we observed a need for same-population donor recruitment in order to increase population-specific MP efficiently. This result was robust despite limitations of our input data, including the use of HF derived from relatively small samples ranging from n = 1028 (Bosnia-Herzegovina) to n = 33,083 (Turkey) individuals. National strategies that neglect domestic donor recruitment should therefore be critically re-assessed, especially if only few donors have been recruited so far.
Engineering of double recombinant vaccinia virus with enhanced oncolytic potential for solid tumor virotherapy

Vaccinia virus (VACV) oncolytic therapy has been successful in a number of tumor models. In this study our goal was to generate a double recombinant vaccinia virus (VV-GMCSF-Lact) with enhanced antitumor activity that expresses exogenous proteins: the antitumor protein lactaptin and human granulocyte-macrophage colony-stimulating factor (GM-CSF). Lactaptin has previously been demonstrated to act as a tumor suppressor in mouse hepatoma as well as MDA-MB-231 human adenocarcinoma cells grafted into SCID mice. VV-GMCSF-Lact was engineered from Lister strain (L-IVP) vaccinia virus and has deletions of the viral thymidine kinase and vaccinia growth factor genes. Cell culture experiments revealed that engineered VV-GMCSF-Lact induced the death of cultured cancer cells more efficiently than recombinant VACV coding only GM-CSF (VV-GMCSF-dGF). Normal human MCF-10A cells were resistant to both recombinants up to 10 PFU/cell. The selectivity index for breast cancer cells measured in pair cultures MCF-7/MCF-10A was 200 for recombinant VV-GMCSF-Lact coding lactaptin and 100 for VV-GMCSF-dGF. Using flow cytometry we demonstrated that both recombinants induced apoptosis in treated cells but that the rate in the cells with active caspase −3 and −7 was higher after treatment with VV-GMCSF-Lact than with VV-GMCSF-dGF. Tumor growth inhibition and survival outcomes after VV-GMCSF-Lact treatment were estimated using immunodeficient and immunocompetent mice models. We observed that VV-GMCSF-Lact efficiently delays the growth of sensitive and chemoresistant tumors. These results demonstrate that recombinant VACVs coding an apoptosis-inducing protein have good therapeutic potential against chemoresistant tumors. Our data will also stimulate further investigation of coding lactaptin double recombinant VACV in clinical settings.
The Doctrine of Original Antigenic Sin: Separating Good From Evil

Abstract The term “original antigenic sin” was coined approximately 60 years ago to describe the imprinting by the initial first influenza A virus infection on the antibody response to subsequent vaccination. These studies did not suggest a reduction in the response to current antigens but instead suggested anamnestic recall of antibody to earlier influenza virus strains. Then, approximately 40 years ago, it was observed that sequential influenza vaccination might lead to reduced vaccine effectiveness (VE). This conclusion was largely dismissed after an experimental study involving sequential administration of then-standard influenza vaccines. Recent observations have provided convincing evidence that reduced VE after sequential influenza vaccination is a real phenomenon. We propose that such reduction in VE be termed “negative antigenic interaction,” given that there is no age cohort effect. In contrast, the potentially positive protective effect of early influenza virus infection later in life continues to be observed. It is essential that we understand better the immunologic factors underlying both original antigenic sin and negative antigenic interaction, to support development of improved influenza vaccines and vaccination strategies.
Inhibitory Effects of Plumbagin on Retinal Pigment Epithelial Cell Epithelial-Mesenchymal Transition In Vitro and In Vivo

Background This study aimed to explore the effects of plumbagin (PLB) on epithelial-to-mesenchymal transition in retinal pigment epithelial (RPE) cells and in proliferative vitreoretinopathy (PVR) rabbit models. Material/Methods Rabbit RPE cells were exposed to various concentrations (0, 5, 15, and 25 μM) of PLB. Motility, migration, and invasion of PLB-treated cells were determined in vitro using Transwell chamber assays and scratch wound assays. The contractile ability was evaluated by cell contraction assay. Expression of matrix metalloproteinases (MMPs) and epithelial-mesenchymal transition (EMT) markers were assessed by western blotting. Furthermore, PLB was injected in rabbit eyes along with RPE cells after gas compression of the vitreous. The presence of PVR was determined by indirect ophthalmoscopy on days 1, 7, 14, and 21 after injection. Also, optical coherence tomography (OCT), ultrasound images, electroretinograms (ERG), and histopathology were used to assess efficacy and toxicity. Results PLB significantly inhibited the migration and invasion of RPE cells. The agent also markedly reduced cell contractive ability. Furthermore, PLB treatment resulted in the decreased expression of MMP-1, MMP2, α-SMA, and the protection of ZO-1. In addition, the PLB-treated eyes showed lower PVR grades than the untreated eyes in rabbit models. PLB exhibited a wide safety margin, indicating no evidence of causing retinal toxicity. Conclusions PLB effectively inhibited the EMT of rabbit RPE cells in vitro and in the experimental PVR models. The results open new avenues for the use of PLB in prevention and treatment of PVR.