Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualization of Graph based on the Three-dimensional Spring Model

A three-dimensional (3D) spring modeling algorithm is given for the 3D visualization of graph, which have been implemented in OpenGL. It avoids edge crossings more effectively, and strengthens the sense of tridimensionality and aesthetics of graph while laying out the graph in three dimensions. By the use of interactive computer visualization, we can observe the distributing character of undirected graph from multi-angles.
Factors contributing to high-cost hospital care for patients with COPD

Chronic obstructive pulmonary disease (COPD) is a leading cause of hospital admission, the fifth leading cause of death in North America, and is estimated to cost $49 billion annually in North America by 2020. The majority of COPD care costs are attributed to hospitalizations; yet, there are limited data to understand the drivers of high costs among hospitalized patients with COPD. In this study, we aimed to determine the patient and hospital-level factors associated with high-cost hospital care, in order to identify potential targets for the reorganization and planning of health services. We conducted a retrospective cohort study at a Canadian academic hospital between September 2010 and 2014, including adult patients with a first-time admission for COPD exacerbation. We calculated total costs, ranked patients by cost quintiles, and collected data on patient characteristics and health service utilization. We used multivariable regression to determine factors associated with highest hospital costs. Among 1,894 patients included in the study, the mean age was 73±12.6 years, median length of stay was 5 (interquartile range 3–9) days, mortality rate was 7.8% (n=147), and 9% (n=170) required intensive care. Hospital spending totaled $19.8 million, with 63% ($12.5 million) spent on 20% of patients. Factors associated with highest costs for COPD care included intensive care unit admission (odds ratio [OR] 32.4; 95% confidence interval [CI] 20.3, 51.7), death in hospital (OR 2.6; 95% CI 1.3, 5.2), discharge to long-term care facility (OR 5.7; 95% CI 3.5, 9.2), and use of the alternate level of care designation during hospitalization (OR 23.5; 95% CI 14.1, 39.2). High hospital costs are driven by two distinct groups: patients who require acute medical treatment for severe illness and patients with functional limitation who require assisted living facilities upon discharge. Improving quality of care and reducing cost in this high-needs population require a strong focus on early recognition and management of functional impairment for patients living with chronic disease.
Limit cycle running based on flat-footed passive dynamic walking with mechanical impedance at ankles

To realize energy-efficient running of flat-footed biped robots, we propose novel running based on flat-footed passive dynamic walking with mechanical impedance at ankles. In recent years, ZMP-based running is popular as one of the running of humanoid robots. However, ZMP-based locomotion of the biped robots are not energy-efficient, and they require complicated trajectory planning and feedback control. Flat-footed passive dynamic walkers with mechanical impedance at ankles have been proposed as a biped robot achieving energy-efficient walking. Since they achieve energy-efficient walking without any control, we are interested in locomotion based on this passive walking. Therefore, we expect that flat-footed biped robots achieve energy-efficient running by taking advantage of the dynamics of the passive dynamic walker. In this paper, we show that the proposed method for a flat-footed biped robot achieves energy-efficient and high-speed limit cycle running.
1 Real-time observation of replicative helicase assembly onto single-stranded DNA

Replicative helicases load onto DNA at the start of replication, and play a vital role by driving the replication fork forward. These helicases assemble into closed multimeric rings that need to encircle single-stranded (ss)DNA to be activated. Though helicase loading on substrates with accessible free ends has been well characterized for the T7 gp4 helicase, a model system for superfamily IV replicative helicases, the physiologically more relevant loading onto exposed ssDNA without free ends remains less well understood. Here, using a label-free assay that exploits changes in the DNA hairpin hopping dynamics to detect gp4 binding and activity, we characterize loading and activation of gp4 on exposed ssDNA without free ends, and find clear evidence of stepwise assembly of the helicase at the fork at physiologically relevant concentrations. The gradual loading onto ssDNA, rather than pre-forming in solution followed by spontaneous ring opening which appears favored at higher concentrations, suggests a new paradigm of stepwise assembly for the helicases in superfamily IV that do not require a separate loading enzyme.
Live imaging reveals the progenitors and cell dynamics of limb regeneration

Regeneration is a complex and dynamic process, mobilizing diverse cell types and remodelling tissues over long time periods. Tracking cell fate and behaviour during regeneration in active adult animals is especially challenging. Here, we establish continuous live imaging of leg regeneration at single-cell resolution in the crustacean Parhyale hawaiensis. By live recordings encompassing the first 4-5 days after amputation, we capture the cellular events that contribute to wound closure and morphogenesis of regenerating legs with unprecedented resolution and temporal detail. Using these recordings we are able to track cell lineages, to generate fate maps of the blastema and to identify the progenitors of regenerated epidermis. We find that there are no specialized stem cells for the epidermis. Most epidermal cells in the distal part of the leg stump proliferate, acquire new positional values and contribute to new segments in the regenerating leg. DOI: http://dx.doi. org/10.7554/eLife.19766. 001
Throughput analysis of AQM schemes under low-rate Denial of service attacks

Active Queue Management (AQM) scheme aims to achieve low loss rate and high throughput as well as high link utilization. We have tried to study the throughput for AQM schemes under denial-of-service (DoS) attacks. DoS is a very serious threat which degrade the TCP throughput in the Internet. DoS attacks consume resources such as network bandwidth, server CPU cycles, and server interrupt processing capacity. In this paper, we have presented a comparative performance analysis of existing AQM schemes under DoS attacks. We find RED achieved good performance even DoS attacks is permitted.
Serotonin receptors in human coronary arteries.

Serotonin (5-hydroxytryptamine, 5-HT) was first identified in serum in 1949 by M. Rapport. ' At k that time, the importance of 5-HT was quite modest: The serum vasoconstrictor that appeared when blood was allowed to clot was an important source of artifactual vasoconstriction in investigations aimed at discovering substances possibly causing hypertension. Since then, however, a great interest has been endowed to 5-HT research, as indicated by the remarkable number of full publications in this area of research. In mammals, about 90% of 5-HT present in the body is stored in the gastrointestinal tract, mainly in enterochromaffin cells. Of the remaining 5-HT, most is present in cells of the central nervous system and circulating platelets. Part of the 5-HT that is released by enterochromaffin cells overflows to the capillary blood and reaches the liver through the portal circulation. In the liver, most of it is degraded enzymatically. Of the remaining fraction, little escapes the uptake by the pulmonary endothelium that inactivates it by means of monoamine oxidase and catechol-O-methyltransferase. The final fraction of5-HT present in the plasma is taken up avidly by platelets, which store it in their dense granules. As a consequence, as long as platelets do not aggregate, peripheral arterial blood contains little or no free 5 -HT. However, whenever platelet aggregation is initiated and dense granules release their contents, 5-HT is liberated in the blood and can exert its pathophysiological effects through activation of specific membrane receptors.
Quantifying intrinsic parallelism via eigen-decomposition of dataflow graphs for algorithm/architecture co-exploration

Algorithmic complexity analysis and dataflow models play significant roles in the concurrent optimization of both algorithms and architectures, which is now a new design paradigm referred to as Algorithm/Architecture Co-exploration. One of the essential complexity metrics is the parallelism revealing the number of operations that can be concurrently executed. Inspired by the principle component analysis (PCA) capable of transforming random variables into uncorrelated ones and hence dependency analysis, this paper presents a systematic methodology for identifying independent operations in algorithms and hence quantifying the intrinsic degree of parallelism based on the dataflow modeling and subsequent eigen-decomposition of the dataflow graphs. Our quantified degree of parallelism is platform-independent and is capable of providing insight into architectural characteristics in early design stages. Starting from different dataflows derived from signal flow graphs in basic signal processing algorithms, the case study on DCT shows that our proposed method is capable of quantitatively characterizing the algorithmic parallelisms making possible the potentially facilitation of the design space exploration in early system design stages especially for parallel processing platforms.
Effect of NPK Fertilizer on Chemical Composition of Pumpkin (Cucurbita pepo Linn.) Seeds

An investigation of the proximate composition and antioxidant profile of pumpkin seeds obtained from different levels of NPK 15 : 15 : 15 compound fertilizer application at the Obafemi Awolowo University, Ile-Ife, Nigeria was carried out. Pumpkin seeds were grown in 2010 for two cropping seasons (May to August and August to November), and the following fertilizer rates were applied: 0, 50, 100, 150, 200, and 250 kg/ha. Standard analytical methods were used to determine protein, crude fibre, ash, fat, carbohydrate, antioxidant activities, phenol, flavonoid, proanthocyanidin, and anthocyanin. The highest concentrations of the proximate and antioxidants analysed were found from the seeds of control and those treated with lower NPK rates. The mean protein, ash, crude fibre, and carbohydrate values of pumpkin seeds at zero to 100 kg NPK/ha were 27%, 1.56%, 0.56%, and 11.7% respectively. At these same levels of fertilizer, pumpkin seed oil yield was 59%. Antioxidant activities ranged from 89.9 to 90.4% while total phenol was 47 mg/100 g. Except for carbohydrate, the % concentration of nutrients and antioxidants in pumpkin seeds was significantly (P = 0.05) depressed with fertilizer rates above 100 g/ha.
Dimension reducing of LSF parameters based on radial basis function neural network

In this paper, we investigate a novel method for transforming line spectral frequency (LSF) parameters to lower dimensional coefficients. Radial basis function neutral network (RBF NN) based transforming model is used to fit LSF vectors. In the training process, two criterions, including mean squared error and weighted mean squared error, are involved to measure distance between original vector and approximate vector. Besides, features of LSF parameters are taken into account to supervise the training process. As a result, LSF vectors are represented by the coefficient vectors of transforming model. The experimental results reveal that 24-order LSF vector can be transformed to 15-dimension coefficient vector with an average spectral distortion of approximately 1dB. Subjective evaluation manifests that the transforming method in this paper will not lead to significant voice quality decreasing.
Genome-Wide Assessments Reveal Extremely High Levels of Polymorphism of Two Active Families of Mouse Endogenous Retroviral Elements

Endogenous retroviral elements (ERVs) in mice are significant genomic mutagens, causing ∼10% of all reported spontaneous germ line mutations in laboratory strains. The majority of these mutations are due to insertions of two high copy ERV families, the IAP and ETn/MusD elements. This significant level of ongoing retrotranspositional activity suggests that inbred mice are highly variable in content of these two ERV groups. However, no comprehensive genome-wide studies have been performed to assess their level of polymorphism. Here we compared three test strains, for which sufficient genomic sequence is available, to each other and to the reference C57BL/6J genome and detected very high levels of insertional polymorphism for both ERV families, with an estimated false discovery rate of only 0.4%. Specifically, we found that at least 60% of IAP and 25% of ETn/MusD elements detected in any strain are absent in one or more of the other three strains. The polymorphic nature of a set of 40 ETn/MusD elements found within gene introns was confirmed using genomic PCR on DNA from a panel of mouse strains. For some cases, we detected gene-splicing abnormalities involving the ERV and obtained additional evidence for decreased gene expression in strains carrying the insertion. In total, we identified nearly 700 polymorphic IAP or ETn/MusD ERVs or solitary LTRs that reside in gene introns, providing potential candidates that may contribute to gene expression differences among strains. These extreme levels of polymorphism suggest that ERV insertions play a significant role in genetic drift of mouse lines.
Novel Method for SAR Image Segmentation with Application to Bridge Detection

A new method for SAR image segmentation is proposed in this paper. Region segmentation can be achieved by contour tracking, and we use the general Bayesian tracking framework to solve this problem. Due to the non-linearity of the tracking problem and the non-Gaussian noise of SAR image, Monte Carlo based particle filtering algorithm is adopted to obtain the Bayesian optimal solution. Based on the tracking framework, a particle filter based contour tracking method is proposed for region segmentation in SAR images. In this method, each particle is assigned to a linear segment with specific location and direction. The response of the local edge detector is used to calculate the particle weight while the global contextual knowledge, such as the smoothness of the region boundary, is guaranteed by the propagation of particles. The proposed method is employed for river boundary extraction on the SAR image. Furthermore, bridges over a river are detected
Atypical Protein Kinase C Regulates Primary Dendrite Specification of Cerebellar Purkinje Cells by Localizing Golgi Apparatus

Neurons have highly polarized structures that determine what parts of the soma elaborate the axon and dendrites. However, little is known about the mechanisms that establish neuronal polarity in vivo. Cerebellar Purkinje cells extend a single primary dendrite from the soma that ramifies into a highly branched dendritic arbor. We used the zebrafish cerebellum to investigate the mechanisms by which Purkinje cells acquire these characteristics. To examine dendritic morphogenesis in individual Purkinje cells, we marked the cell membrane using a Purkinje cell-specific promoter to drive membrane-targeted fluorescent proteins. We found that zebrafish Purkinje cells initially extend multiple neurites from the soma and subsequently retract all but one, which becomes the primary dendrite. In addition, the Golgi apparatus specifically locates to the root of the primary dendrite, and its localization is already established in immature Purkinje cells that have multiple neurites. Inhibiting secretory trafficking through the Golgi apparatus reduces dendritic growth, suggesting that the Golgi apparatus is involved in the dendritic morphogenesis. We also demonstrated that in a mutant of an atypical protein kinase C (aPKC), Prkci, Purkinje cells retain multiple primary dendrites and show disrupted localization of the Golgi apparatus. Furthermore, a mosaic inhibition of Prkci in Purkinje cells recapitulates the aPKC mutant phenotype. These results suggest that the aPKC cell autonomously controls the Golgi localization and thereby regulates the specification of the primary dendrite of Purkinje cells.
How compensation breaks down in Parkinson's disease: Insights from modeling of denervated striatum

The bradykinesia and other motor signs of Parkinson's disease (PD) are linked to progressive loss of substantia nigra dopamine (DA) neurons innervating the striatum. However, the emergence of idiopathic PD is likely preceded by a prolonged subclinical phase, which may be masked by a variety of pre‐ and postsynaptic compensatory mechanisms. It is often considered self‐evident that the signs of PD manifest only when nigrostriatal degeneration has proceeded to such an extent that putative compensatory mechanisms fail to accommodate the depletion of striatal DA levels. However, the precise nature of the compensatory mechanisms, and the reason for their ultimate failure, has been elusive. In a recent computational study we modeled the effects of progressive denervation, including changes in the dynamics of interstitial DA and also adaptive or compensatory changes in postsynaptic responsiveness to DA signaling in the course of progressive nigrostriatal degeneration. In particular, we found that failure of DA signaling can occur by different mechanisms at different disease stages. We review these results and discuss their relevance for clinical and translational research, and we draw a number of predictions from our model that might be tested in preclinical experiments. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Theoretical Implications of Periacetabular Osteotomy in Various Dysplastic Acetabular Cartilage Defects as Determined by Finite Element Analysis

Background Different extents and locations of acetabular cartilage defect have been supposed to be a major cause of undesirable outcomes of periacetabular osteotomy (PAO) in patients with developmental dysplasia of the hip (DDH). This study aimed to verify whether different locations of cartilage deficiency affect the biomechanical environment in a three-dimensional model utilizing finite element analysis (FEA). Material/Methods We developed 3 DDH models – DDH-1 (normal shape), DDH-2 (superior defect), and DDH-3 (anterosuperior defect) – by deforming from a normal hip model. We also developed 3 PAO models – PAO-1, PAO-2, and PAO-3 – through rotating osteotomized fragments. Results The maximum von Mises stress in the normal hip was 13.06 MPa. In the DDH-1 model, the maximum value on the load-bearing area decreased from 15.49 MPa pre-PAO to 14.28 MPa post-PAO, while stresses in the DDH-2 and DDH-3 models were higher than in the DDH-1 model, both pre-PAO and post-PAO (30.46 MPa to 26.04 MPa for DDH-2; 33.89 MPa to 27.48 MPa for DDH-3). Conclusions This study shows that, both pre- and post-PAO, different types of cartilage deficiency affect the biomechanical environment. Furthermore, in dysplastic hips, obtaining accurate three-dimensional information about the acetabular cartilage can contribute substantially to PAO decision making.
Logical Conditional Preference Theories

CP-nets represent the dominant existing framework for expressing qualitative conditional preferences between alternatives, and are used in a variety of areas including constraint solving. Over the last fifteen years, a significant literature has developed exploring semantics, algorithms, implementation and use of CP-nets. This paper introduces a comprehensive new framework for conditional preferences: logical conditional preference theories (LCP theories). To express preferences, the user specifies arbitrary (constraint) Datalog programs over a binary ordering relation on outcomes. We show how LCP theories unify and generalize existing conditional preference proposals, and leverage the rich semantic, algorithmic and implementation frameworks of Datalog.
Shoal: Smart Allocation and Replication of Memory For Parallel Programs

Modern NUMA multi-core machines exhibit complex latency and throughput characteristics, making it hard to allocate memory optimally for a given program's access patterns. However, sub-optimal allocation can significantly impact performance of parallel programs. We present an array abstraction that allows data placement to be automatically inferred from program analysis, and implement the abstraction in Shoal, a runtime library for parallel programs on NUMA machines. In Shoal, arrays can be automatically replicated, distributed, or partitioned across NUMA domains based on annotating memory allocation statements to indicate access patterns. We further show how such annotations can be automatically provided by compilers for high-level domainspecific languages (for example, the Green-Marl graph language). Finally, we show how Shoal can exploit additional hardware such as programmable DMA copy engines to further improve parallel program performance. We demonstrate significant performance benefits from automatically selecting a good array implementation based on memory access patterns and machine characteristics. We present two case-studies: (i) Green-Marl, a graph analytics workload using automatically annotated code based on information extracted from the high-level program and (ii) a manually-annotated version of the PARSEC Streamcluster benchmark.
Association between levels of vitamin D and inflammatory markers in healthy women

Background No one can deny that the biological importance of vitamin D is much beyond its classical role in bone metabolism. Several recent publications have highlighted its potential role in the functioning of the immune system. The overall objective of this study was to look into possible correlations between levels of vitamin D and inflammatory markers in sera of healthy adult women. These markers included proinflammatory cytokines (interleukin [IL]-1β, IL-6, IL-8, IL-17, interferon [IFN]-γ, and tumor necrosis factor [TNF]-α), anti-inflammatory cytokines (IL-4, IL-10, and IL-13), as well as C-reactive protein (CRP) as a general indicator of inflammation. Methods Venous blood samples were collected from 118 healthy adult women and serum levels of vitamin D, CRP, proinflammatory cytokines (IL-1β, IL-6, IL-8, IL-17, IFN-γ, and TNF-α), and anti-inflammatory cytokines (IL-4, IL-10, and IL-13) were measured. Results There were no significant direct correlations between serum levels of vitamin D and any of the inflammatory markers measured. However, subjects with deficient levels of vitamin D and high CRP produced significantly higher levels of the proinflammatory cytokines (TNF-α and IL-8) as compared to subjects with low CRP levels with nondeficient and deficient levels of vitamin D. Further, the anti-inflammatory/proinflammatory ratios suggest a role of vitamin D in maintaining an anti-inflammatory environment at low levels of CRP, an association that is weaker at high CRP levels in subjects with subclinical inflammatory situations. Conclusion These data point to a possible role of vitamin D as a contributing factor in balancing cytokines toward an anti-inflammatory role in inflammatory situations.