Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex- and Diet-Specific Changes of Imprinted Gene Expression and DNA Methylation in Mouse Placenta under a High-Fat Diet

Background Changes in imprinted gene dosage in the placenta may compromise the prenatal control of nutritional resources. Indeed monoallelic behaviour and sensitivity to changes in regional epigenetic state render imprinted genes both vulnerable and adaptable. Methods and Findings We investigated whether a high-fat diet (HFD) during pregnancy modified the expression of imprinted genes and local and global DNA methylation patterns in the placenta. Pregnant mice were fed a HFD or a control diet (CD) during the first 15 days of gestation. We compared gene expression patterns in total placenta homogenates, for male and female offspring, by the RT-qPCR analysis of 20 imprinted genes. Sexual dimorphism and sensitivity to diet were observed for nine genes from four clusters on chromosomes 6, 7, 12 and 17. As assessed by in situ hybridization, these changes were not due to variation in the proportions of the placental layers. Bisulphite-sequencing analysis of 30 CpGs within the differentially methylated region (DMR) of the chromosome 17 cluster revealed sex- and diet-specific differential methylation of individual CpGs in two conspicuous subregions. Bioinformatic analysis suggested that these differentially methylated CpGs might lie within recognition elements or binding sites for transcription factors or factors involved in chromatin remodelling. Placental global DNA methylation, as assessed by the LUMA technique, was also sexually dimorphic on the CD, with lower methylation levels in male than in female placentae. The HFD led to global DNA hypomethylation only in female placenta. Bisulphite pyrosequencing showed that neither B1 nor LINE repetitive elements could account for these differences in DNA methylation. Conclusions A HFD during gestation triggers sex-specific epigenetic alterations within CpG and throughout the genome, together with the deregulation of clusters of imprinted genes important in the control of many cellular, metabolic and physiological functions potentially involved in adaptation and/or evolution. These findings highlight the importance of studying both sexes in epidemiological protocols and dietary interventions.
MAGPIE: Simplifying access and execution of computational models in the life sciences

Over the past decades, quantitative methods linking theory and observation became increasingly important in many areas of life science. Subsequently, a large number of mathematical and computational models has been developed. The BioModels database alone lists more than 140,000 Systems Biology Markup Language (SBML) models. However, while the exchange within specific model classes has been supported by standardisation and database efforts, the generic application and especially the re-use of models is still limited by practical issues such as easy and straight forward model execution. MAGPIE, a Modeling and Analysis Generic Platform with Integrated Evaluation, closes this gap by providing a software platform for both, publishing and executing computational models without restrictions on the programming language, thereby combining a maximum on flexibility for programmers with easy handling for non-technical users. MAGPIE goes beyond classical SBML platforms by including all models, independent of the underlying programming language, ranging from simple script models to complex data integration and computations. We demonstrate the versatility of MAGPIE using four prototypic example cases. We also outline the potential of MAGPIE to improve transparency and reproducibility of computational models in life sciences. A demo server is available at magpie.imb. medizin.tu-dresden.de.
Object cosegmentation using deep Siamese network

Object cosegmentation addresses the problem of discovering similar objects from multiple images and segmenting them as foreground simultaneously. In this paper, we propose a novel end-to-end pipeline to segment the similar objects simultaneously from relevant set of images using supervised learning via deep-learning framework. We experiment with multiple set of object proposal generation techniques and perform extensive numerical evaluations by training the Siamese network with generated object proposals. Similar objects proposals for the test images are retrieved using the ANNOY (Approximate Nearest Neighbor) library and deep semantic segmentation is performed on them. Finally, we form a collage from the segmented similar objects based on the relative importance of the objects.
Paradoxical overexpression of MBNL2 in hepatocellular carcinoma inhibits tumor growth and invasion

Pre-mRNA alternative splicing is an essential step in the process of gene expression. It provides cells with the opportunity to create various protein isoforms. Disruptions of alternative splicing are associated with various diseases, including cancer. The muscleblind-like (MBNL) protein is a splicing regulatory protein. Overexpression of MBNL proteins in embryonic stem cells promotes differentiated cell-like alternative splicing patterns. We examined the expression level of MBNL2 in 143 resected HCCs using immunohistochemistry. MBNL2 was overexpressed in 51 (35.7%) HCCs. The overexpression of MBNL2 correlated with smaller tumor size (≤ 3 cm, P = 0.0108) and low tumor stage (Stage I, P = 0.0026), indicating that MBNL2 expression was lost in the late stage of HCC development. Furthermore, patients with MBNL2-positive HCCs had a borderline better 5-year overall survival (P = 0.0579). In non-cancerous liver parenchyma, MBNL2 was stained on the Canals of Hering and hepatocytes newly derived from hepatic progenitor cells. The overexpression of MBNL2 in Hep-J5 cells suppressed proliferation, tumorsphere formation, migration, and in vitro invasion, and also reduced in vivo tumor growth in NOD/SCID mice. In contrast, MBNL2 depletion with RNA interference in Huh7 cells increased in vitro migration and invasion, but did not enhance tumor growth. These results indicate that MBNL2 is a tumor suppressor in hepatocarcinogenesis.
13-0209 GNSS Satellite Orbit Validation Using Satellite Laser Ranging

With a total of four new regional and global navigation satellite systems that have launched first satellites or even started an operational service, the GNSS landscape has experienced major changes in recent years. As part of the Multi-GNSS Experiment (MGEX) of the International GNSS Service (IGS), a global network of multi-GNSS monitoring stations has been established and various analysis centers have started to determine orbits of selected GNSSs on a routine basis. As a key feature, all satellites of the new constellations (i.e. Galileo, BeiDou, QZSS and IRNSS) are equipped with laser ranging reflector arrays enabling high-precision two way ranging measurements. The paper illustrates the use of SLR observations collected by the ILRS for validation of precise and broadcast ephemerides of the new constellations. As an independent and unambiguous tracking system, SLR helps to gain a better understanding of the new satellites, which still lack a thorough characterization of their orbit and attitude dynamics. SLR tracking is thus considered an essential contribution for a future use of the new GNSSs in space geodesy. The paper also addresses operational aspects of SLR tracking of the new navigation satellites related to their specific orbits, regional distribution and continuously increasing number.
Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases

In Arabidopsis, root hair and non-hair cell fates are determined by a MYB-bHLH-WD40 transcriptional complex and are regulated by many internal and environmental cues. Brassinosteroids play important roles in regulating root hair specification by unknown mechanisms. Here, we systematically examined root hair phenotypes in brassinosteroid-related mutants, and found that brassinosteroid signaling inhibits root hair formation through GSK3-like kinases or upstream components. We found that with enhanced brassinosteroid signaling, GL2, a cell fate marker for non-hair cells, is ectopically expressed in hair cells, while its expression in non-hair cells is suppressed when brassinosteroid signaling is reduced. Genetic analysis demonstrated that brassinosteroid-regulated root epidermal cell patterning is dependent on the WER-GL3/EGL3-TTG1 transcriptional complex. One of the GSK3-like kinases, BIN2, interacted with and phosphorylated EGL3, and EGL3s mutated at phosphorylation sites were retained in hair cell nuclei. BIN2 phosphorylated TTG1 to inhibit the activity of the WER-GL3/EGL3-TTG1 complex. Thus, our study provides insights into the mechanism of brassinosteroid regulation of root hair patterning. DOI: http://dx.doi. org/10.7554/eLife.02525. 001
Studying Table-Top Manipulation Tasks: A Robust Framework for Object Tracking in Collaboration

Table-top object manipulation is a well-established test bed on which to study both basic foundations of general human-robot interaction and more specific collaborative tasks. A prerequisite, both for studies and for actual collaborative or assistive tasks, is the robust perception of any objects involved. This paper presents a real-time capable and ROS-integrated approach, bringing together state-of-the-art detection and tracking algorithms, integrating perceptual cues from multiple cameras and solving detection, sensor fusion and tracking in one framework. The highly scalable framework was tested in a HRI use-case scenario with 25 objects being reliably tracked under significant temporary occlusions. The use-case demonstrates the suitability of the approach when working with multiple objects in small table-top environments and highlights the versatility and range of analysis available with this framework.
Rapid direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples by MALDI-TOF MS analysis

Objectives Development of an automated MALDI-TOF MS-based method for the rapid, direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples within 90 min of sample reception. Methods A total of 3041 urine samples were processed by flow cytometry, and a cut-off value of ≥1.5 × 10 5 bacteria/mL was used to select samples for the study. Following these criteria, 608 samples were selected for direct bacterial identification. Detection of carbapenemase activity by MALDI-TOF MS analysis was only performed after reliable direct identification of Gram-negative bacilli. A novel protocol was developed for extracting bacteria from urine samples by using the Sepsityper Kit (Bruker Daltonik, Germany). Carbapenem resistance was detected with imipenem as an antibiotic marker and the results were automatically interpreted using the STAR-BL module of MALDI-TOF Biotyper Compass software (Bruker Daltonik, Germany). Results The MALDI-TOF MS-based assay yielded direct reliable identification of 91% (503/553) of the samples. The assay showed 100% sensitivity (30/30) and specificity (454/454) for detecting carbapenemase activity within 90 min of sample reception. Isolates included in the study were further characterized by PCR and sequencing, and bla OXA-48 was detected from all isolates that tested positive in the MALDI-TOF MS-based resistance assay. Conclusions The proposed protocol for the direct analysis of urine samples by MALDI-TOF MS is suitable for use in clinical laboratories to identify bacteria and detect carbapenemase activity, thus saving at least 24-48 h relative to current routine methods.
Pathogenesis, Diagnosis, and Treatment of Lumbar Zygapophysial (Facet) Joint Pain

Lumbar zygapophysial joint arthropathy is a challenging condition affecting up to 15% of patients with chronic low back pain. The onset of lumbar facet joint pain is usually insidious, with predisposing factors including spondylolisthesis, degenerative disc pathology, and old age. Despite previous reports of a “facet syndrome,” the existing literature does not support the use of historic or physical examination findings to diagnose lumbar zygapophysial joint pain. The most accepted method for diagnosing pain arising from the lumbar facet joints is with low-volume intraarticular or medial branch blocks, both of which are associated with high false-positive rates. Standard treatment modalities for lumbar zygapophysial joint pain include intraarticular steroid injections and radiofrequency denervation of the medial branches innervating the joints, but the evidence supporting both of these is conflicting. In this article, the authors provide a comprehensive review of the anatomy, biomechanics, and function of the lumbar zygapophysial joints, along with a systematic analysis of the diagnosis and treatment of facet joint pain.
Novel Bio-Logging Tool for Studying Fine-Scale Behaviors of Marine Turtles in Response to Sound

Increases in the spatial scale and intensity of activities that produce marine anthropogenic sound highlight the importance of understanding the impacts and effects of sound on threatened species such as marine turtles. Marine turtles detect and behaviorally respond to low-frequency sounds, however few studies have directly examined their behavioral responses to specific types or intensities of anthropogenic or natural sounds. Recent advances in the development of bio-logging tools, which combine acoustic and fine-scale movement measurements, have allowed for evaluations of animal responses to sound. Here, we describe these tools and present a case study demonstrating the potential application of a newly developed technology (ROTAG, Loggerhead Instruments, Inc.) to examine behavioral responses of freely swimming marine turtles to sound. The ROTAG incorporates a three-axis accelerometer, gyroscope, and magnetometer to record the turtle’s pitch, roll, and heading; a pressure sensor to record turtle depth; a hydrophone to record the turtle’s received underwater acoustic sound field; a temperature gauge; and two VHF radio telemetry transmitters and antennas for tag and turtle tracking. Tags can be programmed to automatically release via a timed corrodible link several hours or days after deployment. We describe an example of the data collected with these tags and present a case study of a successful ROTAG deployment on a juvenile green turtle (Chelonia mydas) in the Paranagua Estuary Complex, Brazil. The tag was deployed for 221 minutes, during which several vessels passed closely (<2km) by the turtle. The concurrent movement and acoustic data collected by the ROTAG were examined during these times to determine if the turtle responded to these anthropogenic sound sources. While fine-scale behavioral responses were not apparent (second-by-second), the turtle did appear to perform dives during which it remained still on or near the sea floor during several of the vessel passes. This case study provides proof of concept that ROTAGs can successfully be applied to free-ranging marine turtles to examine their behavioral response to sound. Finally, we discuss the broad applications that these tools have to study the fine-scale behaviors of marine turtles and highlight their use to aid in marine turtle conservation and management.
Performance analysis of series SPOs in a droop-controlled DC microgrid

In this paper, the performance of a photovoltaic system equipped with solar power optimizers, as one of the distributed generation units of a test microgrid has been investigated. The power sharing in the test DC microgrid is controlled through droop method. Since droop method leads to output voltage deviations in distributed generation units, there is a possibility that this voltage deviation eclipses the operation of solar power optimizers. To address this point of uncertainty, a simulated DC microgrid has been tested in MATLAB/Simulink environment, which confirms that solar power optimizers continue to operate properly.
Drying Schedule for 63 mm Thick Pinus massoniana Boards

The authors conducted an experiment to improve drying efficiency for 63 mm thick Pinus massoniana broads based on the currently used drying schedule.The results showed that the newly developed drying schedule greatly improved drying efficiency,thereby reducing the total drying time by 21% and increasing board quality,which met the 2nd level of national standard GB/T 6491-1999.The improved drying efficiency resulted in reduced manufacture costs.
The use of SHS-process slag for the preparation of foundry sand

The article presents the construction of a linear approximation of the response function (strength of molding sand on tensile strength and air permeability) in a given area by changing the investigated factors for which charge makeup of SHS-cast iron obtaining process and content of the slag product of this process in the molding mixture were used. The analysis of regression coefficients significance of the objective function was done to identify the most important input parameters.
Expression IRF/MUM1>25% Predictor to Three-year Survival of Diffuse Large B Cell Lymphoma in the Immunochemotherapy Era

Introduction: Non Hodgkin lymphoma-Diffuse large B cell lymphoma (DLBC) is composed of more varieties of one disease. Analysis and understanding of a wide range of characteristics of the disease, which include: clinical, immunohistochemical, cytogenetic and molecular characteristics may improve treatment results. Aim: achieving the estimated three-year survival and influence of IRF/MUM1 expression to three-year survival. Material and methods: A study was retrospective–prospective, patients were followed for seven years a period of dine. The study included 60 patients de novo DLBCL. Age was 18-72 years old, the average age 45 years, male 31 (51,7%) and female 29 (48.3%). Median follow-up was 47 months (3-91 months). To determine differentiation immunophenotype antibodies those were used anti-CD20, anti-CD10, anti-Bcl-6, IRF-4/MUM1, CD 138. Results: Included the GCB type was 65%. Impact prognostic index IPI>2 GBC vs non GBC p=0,038 X2. Statistically significant difference was confirmed compared to the IPI> 2 to 3 year OS p<0,0005 X2. Significantly longer three-year survival was provided in the group GCB 36 (92,3%) vs. non GCB 8 (38,1%) p=0,003 X2. Clinical and immunohistochemical factors showed a significant impact to three-year survival by univariate: LDH p=0,005, MUM1 p=0,003, while CD10 p=0,069 was confirmed on the level of borderline impact. Using multivariate analysis, expression MUM1 has the greatest impact p<0.0005 OR=0.083 (95% CI 0.23-0.303) on the disease outcome – three-year survival. Conclusion: expression MUM1 >25% has the greatest impact on the disease outcome – three-year survival.
APPLICATION OF COUPLED ELASTO-PLASTIC-DAMAGE MODEL WITH NON-LOCAL SOFTENING TO CONCRETE MATERIALS

The analysis of concrete elements is complex due to their stiffness degradation during cyclic loading caused by strain localization in the form of cracks and shear zones. The determination of the width and spacing of strain localization is crucial to evaluate the material strength at peak and in the post-peak regime. The aim of the present paper is to show the capability of two different coupled elastoplastic-damage continuum models to describe strain localization and stiffness degradation in concrete elements subject cyclic loading during bending, uniaxial compression and extension. First, a coupled elasto-plastic-damage model based on the idea by Pamin and de Borst. [1] was used [2]. Second, a coupled elasto-plastic-damage model using the formulation proposed by Carol et al.[3] and Hansen and Willam [4] was considered. To describe properly strain localization, to preserve the well-posedness of the boundary value problem, to obtain FE-results free from spurious discretization sensitivity and to capture a deterministic size effect, a integral-type non-local theory [5], [6] was used as a regularization technique in a softening regime [7]. It is achieved by weighted spatial averaging over a neighbourhood of each material point of a suitable state variable. Thus, stress at a certain material point depends not only on the state variable at that point but on the distribution of state variables in a finite neighbourhood of the point considered (the principle of a local action does not hold – the non-local interaction takes place between any two points). The first coupled model combines non-local damage with hardening plasticity and assumes that total strains are equal to strains in undamaged skeleton. Plastic flow can occur only in undamaged specimens, thus an elasto-plastic model is defined in terms of effective stresses. As a consequence, the damage degradation does not affect plasticity. In the second model, plasticity and damage are connected by two loading functions describing the behaviour of concrete in compression and tension. The model assumes that the damage approach can better simulate the behaviour of concrete under tension while plasticity is more suitable to describe the concrete behaviour under compression. According to this assumption, a failure envelope is created by combining a Drucker
Comparative study on improving high liquid limit clay as roadbed fillings in Chengdu area

Abstract In order to study the improvement of high liquid limit clay as roadbed fillings in Chengdu area, lime, fly ash, cement, lime and fly ash, sand and gravel were used in the comparative testing as the improvement reagents, respectively. The testing results indicate that the California bearing ratios of the high liquid limit clay after incorporating 4% and 5% lime are to increase 6·1, 6·3, 5·6 and 8·2, 7·3, 6·4 times, respectively; the improvement efficiency is not good after incorporating fly ash; the California bearing ratios of the high liquid limit clay after incorporating 3% and 4% cement are to increase 4·7, 3·9, 3·5 and 6·4, 5·5, 5·2 times, respectively; the value of California bearing ratios after incorporating lime and fly ash is to increase 3·2, 3·0, 3·0 and 6·5, 6·1, 5·4 times, respectively; and its value after incorporating sand and gravel is to increase 2·1, 1·9, 1·7 and 2·9, 2·6, 3·1 times, respectively. At the same time, they improve the anti-crack ability of the clay.
Word Sense Disambiguation for Lexicon-Based Sentiment Analysis

The total number of user generated data from several media such as social media, online forums, and micro blogs is increasing rapidly. This data contains people opinion and feeling about a product, service, or even an idea. Therefore, user generated data becomes important to serveral parties to see public response and make decision. Lexicon-based sentiment analysis is one of the techniques that can be used to analyze user generated data. Recent study found that ambiguous word is becoming the one issue on the lexicon-based sentiment analysis. This paper try to handle ambiguous issue by adding Word Sense Disambiguation process. We implement several methods of Path-based semantic relatedness to find the most appropriate sense. The result shows that word sense disambiguation process is able to improve the performance of sentiment analysis. When combined with word sense disambiguation, the classification f-score is better than sentiment analysis without word sense disambiguation.