Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription

ABSTRACT DNA methylation can affect tissue-specific gene transcription in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). To elucidate the variety of associations between differentiation-related DNA hypermethylation and transcription, we used available epigenomic and transcriptomic profiles from 38 human cell/tissue types to focus on such relationships in 94 genes linked to hypermethylated DMRs in myoblasts (Mb). For 19 of the genes, promoter-region hypermethylation in Mb (and often a few heterologous cell types) was associated with gene repression but, importantly, DNA hypermethylation was absent in many other repressed samples. In another 24 genes, DNA hypermethylation overlapped cryptic enhancers or super-enhancers and correlated with down-modulated, but not silenced, gene expression. However, such methylation was absent, surprisingly, in both non-expressing samples and highly expressing samples. This suggests that some genes need DMR hypermethylation to help repress cryptic enhancer chromatin only when they are actively transcribed. For another 11 genes, we found an association between intergenic hypermethylated DMRs and positive expression of the gene in Mb. DNA hypermethylation/transcription correlations similar to those of Mb were evident sometimes in diverse tissues, such as aorta and brain. Our findings have implications for the possible involvement of methylated DNA in Duchenne's muscular dystrophy, congenital heart malformations, and cancer. This epigenomic analysis suggests that DNA methylation is not simply the inevitable consequence of changes in gene expression but, instead, is often an active agent for fine-tuning transcription in association with development.
Learning and Control Using Gaussian Processes

Building physics-based models of complex physical systems like buildings and chemical plants is extremely cost and time prohibitive for applications such as real-time optimal control, production planning and supply chain logistics. Machine learning algorithms can reduce this cost and time complexity, and are, consequently, more scalable for large-scale physical systems. However, there are many practical challenges that must be addressed before employing machine learning for closed-loop control. This paper proposes the use of Gaussian Processes (GP) for learning control-oriented models: (1) We develop methods for the optimal experiment design (OED) of functional tests to learn models of a physical system, subject to stringent operational constraints and limited availability of the system. Using a Bayesian approach with GP, our methods seek to select the most informative data for optimally updating an existing model. (2) We also show that black-box GP models can be used for receding horizon optimal control with probabilistic guarantees on constraint satisfaction through chance constraints. (3) We further propose an online method for continuously improving the GP model in closed-loop with a real-time controller. Our methods are demonstrated and validated in a case study of building energy control and Demand Response.
National Burn Repository 2005: A Ten-Year Review

In the early 1990s, the American Burn Association (ABA) started its first burn registry development initiatives. The impetus for the registry development software originated from several directions, including the following: (1) the recognition that national registries were widespread and of proven benefit; (2) growing demands from accrediting institutions, payers, and patient advocacy groups for objective and verifiable data regarding patient costs, treatments, and outcomes; and (3) the shift toward “evidence-based” medicine and the ongoing analysis of treatment effectiveness. The ABA has issued three calls for burn registry data for its National Burn Repository (NBR): 1994, 2002, and 2005. In 1994, 28 burn centers contributed data for more than 6,400 patients treated from 1991 to 1993. The ABA announced its second call for data in 2001 and distributed the published results of more than 54,000 acute burn admissions treated from 1974 to 2002 at the Association’s 2002 Annual Meeting. The third ABA call for data was issued in the Fall of 2005. The results are detailed in this report, which provides a summary of more than a quarter million acute burn admissions from 1995 to 2005, representing 70 hospitals from 30 states plus the District of Columbia. Statistics are presented in chart and table format to illustrate such key factors as patient age, burn size group, types of injuries, mortality rates, and average hospital charges by etiology and length of hospital stay. The data presented herein should help stimulate quality improvement programs in burn care, as burn centers compare their performance with the national data and as research is expanded using the NBR. The NBR will be published annually and, with continued refinements to the registry software, should become of increasing importance to clinicians, payers, researchers, and the public.
Chinese micro-blog sentiment analysis based on semantic features and PAD model

With the increasing impact of social networks, microblog becomes important carrier of information and social interaction for human beings, which contains emotional states that have important research significance. We try to analysis the microblog text with the methods of emotional vocabulary, combining domain knowledge of psychology and affective computing, continuous dimension of emotion psychology PAD model which is adopted as basis of sentiment analysis. Emotional state inherent in the text is analyzed to obtain a more accurate result and achieve purposes of emotional analysis. At the same time, to achieve emotional microblog text computability from the aspect of personal characteristics. Experimental results show that the method can improve the microblog text sentiment analysis accuracy and precision. The method is able to get a good application in the different themes and different emotional features.
Peritoneal dialysis in an extremely low-birth-weight infant with acute kidney injury

Critically ill neonates are at high risk for acute kidney injury (AKI). Renal supportive therapy (RST) can be an important tool for supporting critically ill neonates with AKI, particularly in cases of oliguria and fluid overload. There are few reports of RST for management of oligo-anuric AKI in the extremely low-birth-weight infant weighing <1000 g. We report successful provision of peritoneal dialysis (PD) to an 830-g neonate with oligo-anuric AKI through adaptation of a standard pediatric acute PD catheter.
Management of Congenital Bile Duct Cysts

Bile duct cysts (BDC) are rare congenital anomalies of the biliary tree that are characterized by cystic dilatation of the extrahepatic and/or intrahepatic bile ducts. Presence of an anomalous bilio-pancreatic junction allowing pancreatic juice to reflux into the biliary tree is the most widely aetiopathogenic concept currently accepted. BDC are associated with biliary stasis and lithiasis, and the whole biliary epithelium is considered at risk of malignant transformation. Magnetic resonance cholangio-pancreatography is currently the most accurate preoperative imaging study to assess cyst anatomy and classify the disease according to the standard Todani classification. Complete cyst excision with cholecystectomy followed by biliary reconstruction using a Roux-en-Y hepatico-jejunostomy is the treatment of choice for the extrahepatic component of the disease (type I and IV BDC), but cystic involvement up to the roof of the main biliary convergence represents a real surgical challenge to perform complete resection. The optimal treatment of intrahepatic bile duct dilatations remains controversial, especially for type IV-A BDC. In type V BDC (Caroli’s disease), extent of the liver resection is tailored to intrahepatic disease extent and takes into consideration the presence and severity of underlying chronic liver (congenital hepatic fibrosis) and kidney disease. Late postoperative cholangitis secondary to intrahepatic strictures and lithiasis, as well as the risk of metachronous cholangiocarcinoma that can occur throughout the whole biliary tree even after complete cyst excision, represent serious complications justifying careful long-term follow-up.
Multi-modal molecular diffuse optical tomography system for small animal imaging

A multi-modal optical imaging system for quantitative 3D bioluminescence and functional diffuse imaging is presented, which has no moving parts and uses mirrors to provide multi-view tomographic data for image reconstruction. It is demonstrated that through the use of trans-illuminated spectral near-infrared measurements and spectrally constrained tomographic reconstruction, recovered concentrations of absorbing agents can be used as prior knowledge for bioluminescence imaging within the visible spectrum. Additionally, the first use of a recently developed multi-view optical surface capture technique is shown and its application to model-based image reconstruction and free-space light modelling is demonstrated. The benefits of model-based tomographic image recovery as compared to two-dimensional (2D) planar imaging are highlighted in a number of scenarios where the internal luminescence source is not visible or is confounding in 2D images. The results presented show that the luminescence tomographic imaging method produces 3D reconstructions of individual light sources within a mouse-sized solid phantom that are accurately localized to within 1.5 mm for a range of target locations and depths, indicating sensitivity and accurate imaging throughout the phantom volume. Additionally the total reconstructed luminescence source intensity is consistent to within 15%, which is a dramatic improvement upon standard bioluminescence imaging. Finally, results from a heterogeneous phantom with an absorbing anomaly are presented, demonstrating the use and benefits of a multi-view, spectrally constrained coupled imaging system that provides accurate 3D luminescence images.
Environmental effects on Drosophila brain development and learning

ABSTRACT Brain development and behavior are sensitive to a variety of environmental influences including social interactions and physicochemical stressors. Sensory input in situ is a mosaic of both enrichment and stress, yet little is known about how multiple environmental factors interact to affect brain anatomical structures, circuits and cognitive function. In this study, we addressed these issues by testing the individual and combined effects of sub-adult thermal stress, larval density and early-adult living spatial enrichment on brain anatomy and olfactory associative learning in adult Drosophila melanogaster. In response to heat stress, the mushroom bodies (MBs) were the most volumetrically impaired among all of the brain structures, an effect highly correlated with reduced odor learning performance. However, MBs were not sensitive to either larval culture density or early-adult living conditions. Extreme larval crowding reduced the volume of the antennal lobes, optic lobes and central complex. Neither larval crowding nor early-adult spatial enrichment affected olfactory learning. These results illustrate that various brain structures react differently to environmental inputs, and that MB development and learning are highly sensitive to certain stressors (pre-adult hyperthermia) and resistant to others (larval crowding). Summary: Drosophila brain development is sensitive to environmental stimuli; the development of the mushroom bodies and associative learning are sensitive to heat stress but not larval density and adult living conditions.
Nonprehensile Dynamic Manipulation: A Survey

Nonprehensile dynamic manipulation can be reasonably considered as the most complex manipulation task. It might be argued that such a task is still rather far from being fully solved and applied in robotics. This survey tries to collect the results reached so far by the research community about planning and control in the nonprehensile dynamic manipulation domain. A discussion about current open issues is addressed as well.
Ischemic Stroke Risk in Patients With Atrial Fibrillation and CHA2DS2-VASc Score of 1: Systematic Review and Meta-Analysis.

BACKGROUND AND PURPOSE The CHA2DS2-VASc score aims to improve risk stratification of ischemic stroke among patients with atrial fibrillation to identify those who can safely forego oral anticoagulation. Oral anticoagulation treatment guidelines remain uncertain for CHA2DS2-VASc score of 1. We conducted a systematic review and meta-analysis of the risk of ischemic stroke for patients with atrial fibrillation and CHA2DS2-VASc score of 0, 1, or 2 not treated with oral anticoagulation. METHODS We searched MEDLINE, Embase, PubMed, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Web of Science from the start of the database up until April 15, 2015. We included studies that stratified the risk of ischemic stroke by CHA2DS2-VASc score for patients with nonvalvular atrial fibrillation. We estimated the summary annual rate of ischemic stroke using random effects meta-analyses and compared the estimated stroke rates with published net-benefit thresholds for initiating anticoagulants. RESULTS 1162 abstracts were retrieved, of which 10 met all inclusion criteria for the study. There was substantial heterogeneity among studies. The summary estimate for the annual risk of ischemic stroke was 1.61% (95% confidence interval 0%-3.23%) for CHA2DS2-VASc score of 1, meeting the theoretical threshold for using novel oral anticoagulants (0.9%), but below the threshold for warfarin (1.7%). The summary incident risk of ischemic stroke was 0.68% (95% confidence interval 0.12%-1.23%) for CHA2DS2-VASc score of 0 and 2.49% (95% confidence interval 1.16%-3.83%) for CHA2DS2-VASc score of 2. CONCLUSIONS Our meta-analysis of ischemic stroke risk in atrial fibrillation patients suggests that those with CHA2DS2-VASc score of 1 may be considered for a novel oral anticoagulant, but because of high heterogeneity, the decision should be based on individual patient characteristics.
Comparison of complementary feeding strategies to meet zinc requirements of older breastfed infants.

BACKGROUND The low zinc intake from human milk at ∼6 mo of age predicts the dependence on complementary foods (CF) to meet the zinc requirements of older breastfed-only infants. OBJECTIVE The objective of this study was to compare major variables of zinc homeostasis and zinc status in 9-mo-old breastfed infants who were randomly assigned to different complementary food regimens. DESIGN Forty-five exclusively breastfed 5-mo-old infants were randomly assigned to receive commercially available pureed meats, iron-and-zinc-fortified infant cereal (IZFC), or whole-grain, iron-only-fortified infant cereal (IFC) as the first and primary CF until completion of zinc metabolic studies between 9 and 10 mo of age. A zinc stable-isotope methodology was used to measure the fractional absorption of zinc (FAZ) in human milk and CF by dual-isotope ratios in urine. Calculated variables included the dietary intake from duplicate diets and 4-d test weighing, the total absorbed zinc (TAZ) from FAZ × diet zinc, and the exchangeable zinc pool size (EZP) from isotope enrichment in urine. RESULTS Mean daily zinc intakes were significantly greater for the meat and IZFC groups than for the IFC group (P < 0.001); only intakes in meat and IZFC groups met estimated average requirements. Mean (±SEM) TAZ amounts were 0.80 ± 0.08, 0.71 ± 0.09, and 0.52 ± 0.05 mg/d for the meat, IZFC, and IFC groups, respectively (P = 0.027). Zinc from human milk contributed <25% of TAZ for all groups. The EZP correlated with both zinc intake (r = 0.43, P < 0.01) and TAZ (r = 0.54, P < 0.001). CONCLUSION Zinc requirements for older breastfed-only infants are unlikely to be met without the regular consumption of either meats or zinc-fortified foods.
Intertumoral Heterogeneity within Medulloblastoma Subgroups

Florence M.G. Cavalli, Arthur and Sonia Labatt Brain Tumour Research Centre Marc Remke, University Hospital Dusseldorf Ladislav Rampasek, University of Toronto John Peacock, Arthur and Sonia Labatt Brain Tumour Research Centre David J.H. Shih, Arthur and Sonia Labatt Brain Tumour Research Centre Betty Luu, Arthur and Sonia Labatt Brain Tumour Research Centre Livia Garzia, Arthur and Sonia Labatt Brain Tumour Research Centre Jonathan Torchia, Arthur and Sonia Labatt Brain Tumour Research Centre Carolina Nor, Arthur and Sonia Labatt Brain Tumour Research Centre A. Sorana Morrissy, Arthur and Sonia Labatt Brain Tumour Research Centre
Miniaturized Monitors for Assessment of Exposure to Air Pollutants: A Review

Air quality has a huge impact on different aspects of life quality, and for this reason, air quality monitoring is required by national and international regulations. Technical and procedural limitations of traditional fixed-site stations for monitoring or sampling of air pollutants are also well-known. Recently, a different type of miniaturized monitors has been developed. These monitors, due to their characteristics (e.g., low cost, small size, high portability) are becoming increasingly important for individual exposure assessment, especially since this kind of instrument can provide measurements at high spatial and temporal resolution, which is a notable advantage when approaching assessment of exposure to environmental contaminants. The aim of this study is indeed to provide information regarding current knowledge regarding the use of miniaturized air pollutant sensors. A systematic review was performed to identify original articles: a literature search was carried out using an appropriate query for the search of papers across three different databases, and the papers were selected using inclusion/exclusion criteria. The reviewed articles showed that miniaturized sensors are particularly versatile and could be applied in studies with different experimental designs, helping to provide a significant enhancement to exposure assessment, even though studies regarding their performance are still sparse.
Research of image segmentation based on theory of morphological connectivity

Image segmentation is a common problem in image processing. Due to various image types and diversified applications, there is no widely accepted segmentation method. In this paper, the morphological connection theory is used to segment a color image into several irregularly shaped connected regions (i.e. equivalence class) based on their distributions of hue, intensity and texture, etc. As the pixels in a same connected region possesses the same or similar feature, the proposed method is provided with a good segmentation result for smooth and texture regions. The validity of proposed method is demonstrated through experiments.
Cooperative monitoring multiple humans using UAVs and fixed camera

The cooperative monitoring system using UAVs and fixed cameras is proposed for monitoring multiple humans in a particular area. In the proposed system, the UAVs pursue the humans who are not photographed by the fixed cameras to identify them. Fort the efficient pursuit, observation points of UAVs should be minimized. Based on the Image Information Added Map, the observation area for a person is determined. As for the necessary condition, one picture for each person should be taken. The optimization problem is solved by a set covering problem. The proposed algorithm is implemented on simulation and simulation results are shown.
Review of selective laser melting : materials and applications

Selective Laser Melting (SLM) is a particular rapid prototyping, 3D printing, or Additive Manufacturing (AM) technique designed to use high power-density laser to melt and fuse metallic powders. A component is built by selectively melting and fusing powders within and between layers. The SLM technique is also commonly known as direct selective laser sintering, LaserCusing, and direct metal laser sintering, and this technique has been proven to produce near net-shape parts up to 99.9% relative density. This enables the process to build near full density functional parts and has viable economic benefits. Recent developments of fibre optics and high-power laser have also enabled SLM to process different metallic materials, such as copper, aluminium, and tungsten. Similarly, this has also opened up research opportunities in SLM of ceramic and composite materials. The review presents the SLM process and some of the common physical phenomena associated with this AM technology. It then focuses on the following a.
Development of a tissue-simulating viscoelastic gel phantom for MR elastography

Poster: "ECR 2015 / C-0757 / Development of a tissue-simulating viscoelastic gel phantom for MR elastography" by: "M. Suga1, T. Mori1, R. Kishimoto1, T. Kurokawa2, T. Abe1, H. Tsuji1, T. Obata1; 1Chiba/JP, 2Sapporo/JP"
Characterization of MORE AXILLARY GROWTH Genes in Populus

Background Strigolactones are a new class of plant hormones that play a key role in regulating shoot branching. Studies of branching mutants in Arabidopsis, pea, rice and petunia have identified several key genes involved in strigolactone biosynthesis or signaling pathway. In the model plant Arabidopsis, MORE AXILLARY GROWTH1 (MAX1), MAX2, MAX3 and MAX4 are four founding members of strigolactone pathway genes. However, little is known about the strigolactone pathway genes in the woody perennial plants. Methodology/Principal Finding Here we report the identification of MAX homologues in the woody model plant Populus trichocarpa. We identified the sequence homologues for each MAX protein in P. trichocarpa. Gene expression analysis revealed that Populus MAX paralogous genes are differentially expressed across various tissues and organs. Furthermore, we showed that Populus MAX genes could complement or partially complement the shoot branching phenotypes of the corresponding Arabidopsis max mutants. Conclusion/Significance This study provides genetic evidence that strigolactone pathway genes are likely conserved in the woody perennial plants and lays a foundation for further characterization of strigolactone pathway and its functions in the woody perennial plants.
Meshless Local Petrov-Galerkin (MLPG) Formulation for Analysis of Thick Plates

An efficient meshless formulation based on the Local Petrov-Galerkin approach for the analysis of shear deformable thick plates is presented. Using the kinematics of a three-dimensional continuum, the local symmetric weak form of the equilibrium equations over the cylindrical shaped local sub-domain is derived. The linear test function in the plate thickness direction is assumed. Discretization in the in-plane directions is performed by means of the moving least squares approximation. The linear interpolation over the thickness is used for the in-plane displacements, while the hierarchical quadratic interpolation is adopted for the transversal displacement in order to avoid the thickness locking effect. The numerical efficiency of the proposed meshless formulation is illustrated by the numerical examples. keyword: meshless formulation, thick plates, threedimensional solid concept, moving least squares approximation.