Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic review of the evidence underlying the association between mineral metabolism disturbances and risk of all-cause mortality, cardiovascular mortality and cardiovascular events in chronic kidney disease.

BACKGROUND Chronic kidney disease (CKD) is a powerful risk factor for all-cause mortality and its most common aetiology, cardiovascular (CV) mortality. Mineral metabolism disturbances occur very early during the course of CKD but their control has been poor. A number of studies have assessed the relationship between all-cause mortality, CV mortality and events with mineral disturbances in CKD patients, but with considerable discrepancy and heterogeneity in results. Thus, a systematic review was conducted to assess methodological and clinical heterogeneity by comparing designs, analytical approaches and results of studies. METHODS Medline, EMBASE and Cochrane databases were systematically searched for articles published between January 1980 and December 2007. RESULTS Thirty-five studies were included in the review. All-cause mortality was the most commonly assessed outcome (n = 29). Data on CV mortality risk (n = 11) and CV events (congestive heart failure, stroke, myocardial infarction) (n = 4) are limited. The studies varied in populations scrutinized, exposure assessments, covariates adjusted and reference mineral levels used in risk estimation. A significant risk of mortality (all-cause, CV) and of CV events was observed with mineral disturbances. The data supported a greater mortality risk with phosphorus, followed by calcium and parathyroid hormone (PTH). The threshold associated with a significant all-cause mortality risk varied from 3.5-3.9 mg/dL (reference: 2.5-2.9) to 6.6-7.8 mg/dL (reference: 4.4-5.5) for high phosphorus, <3 mg/dL (reference: 5-7) to <5 mg/dL (reference: 5-6) for low phosphorus, 9.7-10.2 mg/dL (reference: < or =8.7) to >10.5 mg/dL (reference: 9-9.5) for high calcium, < or =8.8 mg/dL (reference: >8.8) to <9 mg/dL (reference: 9-9.5) for low calcium and >300 pg/mL (reference: 200-300) to >480 pg/mL (reference: < or =37) for PTH. Thresholds at which the CV mortality risk significantly increased were >5.5 (reference: 3.5-5.5) and >6.5 mg/dL (reference: <6.5) for phosphorus and >476.1 pg/mL (reference: <476.1) for PTH. CONCLUSIONS Serious limitations were observed in the quality and methodology across studies. In spite of enormous heterogeneity across studies, a significant mortality risk was observed with mineral disturbances in dialysis patients. Data on risk in pre-dialysis patients were less conclusive due to even more limited (numerically) evidence.
Delay Optimization in Bandwidth-Sharing Networks 1

Bandwidth-sharing networks as considered by Massoulié & Roberts provide a natural modeling framework for describing the dynamic flow-level interaction among elastic data transfers. Although valuable stability results have been obtained, crucial performance metrics such as flow-level delays and throughputs in these models have remained intractable in all but a few special cases. In particular, it is not well understood to what extent flow-level delays and throughputs achieved by standard bandwidth-sharing mechanisms such as -fair strategies leave potential room for improvement. In order to gain a better understanding of the latter issue, we set out to determine the scheduling policies that minimize the mean delay in some simple linear bandwidth-sharing networks. We compare the performance of the optimal policy with that of various -fair strategies so as to assess the efficacy of the latter and gauge the potential room for improvement. The results indicate that the optimal policy achieves only modest improvements, even when the value of is simply fixed, provided it is not too small.
Hierarchical Fingertip Space: A Unified Framework for Grasp Planning and In-Hand Grasp Adaptation

We present a unified framework for grasp planning and in-hand grasp adaptation using visual, tactile, and proprioceptive feedback. The main objective of the proposed framework is to enable fingertip grasping by addressing problems of changed weight of the object, slippage, and external disturbances. For this purpose we introduce the Hierarchical Fingertip Space as a representation enabling optimization for both efficient grasp synthesis and online finger gaiting. Grasp synthesis is followed by a grasp adaptation step that consists of both grasp force adaptation through impedance control and regrasping/finger gaiting when the former is not sufficient. Experimental evaluation is conducted on an Allegro hand mounted on a Kuka LWR arm.
Global registration of dynamic range scans for articulated model reconstruction

We present the articulated global registration algorithm to reconstruct articulated 3D models from dynamic range scan sequences. This new algorithm aligns multiple range scans simultaneously to reconstruct a full 3D model from the geometry of these scans. Unlike other methods, we express the surface motion in terms of a reduced deformable model and solve for joints and skinning weights. This allows a user to interactively manipulate the reconstructed 3D model to create new animations. We express the global registration as an optimization of both the alignment of the range scans and the articulated structure of the model. We employ a graph-based representation for the skinning weights that successfully handles difficult topological cases well. Joints between parts are estimated automatically and are used in the optimization to preserve the connectivity between parts. The algorithm also robustly handles difficult cases where parts suddenly disappear or reappear in the range scans. The global registration produces a more accurate registration compared to a sequential registration approach, because it estimates the articulated structure based on the motion observed in all input frames. We show that we can automatically reconstruct a variety of articulated models without the use of markers, user-placed correspondences, segmentation, or template model.
Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction

RAD51 DNA strand exchange protein catalyzes the central step in homologous recombination, a cellular process fundamentally important for accurate repair of damaged chromosomes, preservation of the genetic integrity, restart of collapsed replication forks and telomere maintenance. BRCA2 protein, a product of the breast cancer susceptibility gene, is a key recombination mediator that interacts with RAD51 and facilitates RAD51 nucleoprotein filament formation on single-stranded DNA generated at the sites of DNA damage. An accurate atomistic level description of this interaction, however, is limited to a partial crystal structure of the RAD51 core fused to BRC4 peptide. Here, by integrating homology modeling and molecular dynamics, we generated a structure of the full-length RAD51 in complex with BRC4 peptide. Our model predicted previously unknown hydrogen bonding patterns involving the N-terminal domain (NTD) of RAD51. These interactions guide positioning of the BRC4 peptide within a cavity between the core and the NTDs; the peptide binding separates the two domains and restricts internal dynamics of RAD51 protomers. The model’s depiction of the RAD51-BRC4 complex was validated by free energy calculations and in vitro functional analysis of rationally designed mutants. All generated mutants, RAD51E42A, RAD51E59A, RAD51E237A, RAD51E59A/E237A and RAD51E42A/E59A/E237A maintained basic biochemical activities of the wild-type RAD51, but displayed reduced affinities for the BRC4 peptide. Strong correlation between the calculated and experimental binding energies confirmed the predicted structure of the RAD51-BRC4 complex and highlighted the importance of RAD51 NTD in RAD51-BRCA2 interaction.
Data- and knowledge-based modeling of gene regulatory networks: an update

Gene regulatory network inference is a systems biology approach which predicts interactions between genes with the help of high-throughput data. In this review, we present current and updated network inference methods focusing on novel techniques for data acquisition, network inference assessment, network inference for interacting species and the integration of prior knowledge. After the advance of Next-Generation-Sequencing of cDNAs derived from RNA samples (RNA-Seq) we discuss in detail its application to network inference. Furthermore, we present progress for large-scale or even full-genomic network inference as well as for small-scale condensed network inference and review advances in the evaluation of network inference methods by crowdsourcing. Finally, we reflect the current availability of data and prior knowledge sources and give an outlook for the inference of gene regulatory networks that reflect interacting species, in particular pathogen-host interactions.
Efficient Memory Virtualization: Reducing Dimensionality of Nested Page Walks

Virtualization provides value for many workloads, but its cost rises for workloads with poor memory access locality. This overhead comes from translation look aside buffer (TLB) misses where the hardware performs a 2D page walk (up to 24 memory references on x86-64) rather than a native TLB miss (up to only 4 memory references). The first dimension translates guest virtual addresses to guest physical addresses, while the second translates guest physical addresses to host physical addresses. This paper proposes new hardware using direct segments with three new virtualized modes of operation that significantly speed-up virtualized address translation. Further, this paper proposes two novel techniques to address important limitations of original direct segments. First, self-ballooning reduces fragmentation in physical memory, and addresses the architectural input/output (I/O) gap in x86-64. Second, an escape filter provides alternate translations for exceptional pages within a direct segment (e.g., Physical pages with permanent hard faults). We emulate the proposed hardware and prototype the software in Linux with KVM on x86-64. One mode -- VMM Direct -- reduces address translation overhead to near-native without guest application or OS changes (2% slower than native on average), while a more aggressive mode -- Dual Direct -- on big-memory workloads performs better-than-native with near-zero translation overhead.
An industrial case study of the effectiveness of test generators

Automatic test generators pursue some type of systematic coverage of the program code or heuristic sampling of the program inputs. Test generators are effective after the assumption, often (enthusiastically) embraced by researchers, that the generated test cases produce informative data for domain experts, e.g., pinpoint important bugs. This paper investigates the validity of such assumption through a case study of using test generators on industrial software with nontrivial domain-specific peculiarities. Our results properly enhance the available body of knowledge on the strengths and weaknesses of test generators.
Outer edges of face-on spiral galaxies - Deep optical imaging of NGC 5923, UGC 9837 and NGC 5434

We present deep optical imaging of three face-on disk galaxies together with a detailed description of the reduction and calibration methods used, in order to measure the intrinsic shape of their outer stellar edges. Whereas it is now well accepted that disks of spiral galaxies are not infinite exponential beyond galactocentric distances of about 3-5 radial scalelengths, the genuine structure of the truncation region is not yet well known. Our data quantitatively establish a smooth truncation behaviour of the radial surface brightness profiles and is best described by a two-slope model, characterised by an inner and outer expo- nential scalelength separated at a relatively well defined break radius. This result disagrees with the frequently assumed sharply truncated nature of the radial surface brightness profiles and implies the presence of stars and even star-formation beyond the break radius. In addition, we do not find a strong influence of a nearby companion on the ratio of the break radius to the radial scalelength. Our results denote new observational constraints for the search of the physical explanation for these smooth disk truncations.
Cloud4IoT: A Heterogeneous, Distributed and Autonomic Cloud Platform for the IoT

We introduce Cloud4IoT, a platform offering automatic deployment, orchestration and dynamic configuration of IoT support software components and data-intensive applications for data processing and analytics, thus enabling plug-andplay integration of new sensor objects and dynamic workload scalability. Cloud4IoT enables the concept of Infrastructure as Code in the IoT context: it empowers IoT operations with the flexibility and elasticity of Cloud services. Furthermore it shifts traditionally centralized Cloud architectures towards a more distributed and decentralized computation paradigm, as required by IoT technologies, bridging the gap between Cloud Computing and IoT ecosystems. Thus, Cloud4IoT is playing a role similar to the one covered by solutions like Fog Computing, Cloudlets or Mobile Edge Cloud. The hierarchical architecture of Cloud4IoThosts a central Cloud platform and multiple remote edge Cloud modules supporting dedicated devices, namely the IoT Gateways, through which new sensor objects are made accessible to the platform. Overall, the platform is designed in order to support systems where IoT-based and data intensive applications may pose specific requirements for low latency, restricted available bandwidth, or data locality. Cloud4IoT is built on several Open Source technologies for containerisation and implementations of standards, protocols and services for the IoT. We present the implementation of the platform and demonstrate it in two different use cases.
Mitochondrial Probe Methyltriphenylphosphonium (TPMP) Inhibits the Krebs Cycle Enzyme 2-Oxoglutarate Dehydrogenase

Methyltriphenylphosphonium (TPMP) salts have been widely used to measure the mitochondrial membrane potential and the triphenylphosphonium (TPP+) moiety has been attached to many bioactive compounds including antioxidants to target them into mitochondria thanks to their high affinity to accumulate in the mitochondrial matrix. The adverse effects of these compounds on cellular metabolism have been insufficiently studied and are still poorly understood. Micromolar concentrations of TPMP cause a progressive inhibition of cellular respiration in adherent cells without a marked effect on mitochondrial coupling. In permeabilized cells the inhibition was limited to NADH-linked respiration. We found a mixed inhibition of the Krebs cycle enzyme 2-oxoglutarate dehydrogenase complex (OGDHC) with an estimated IC50 3.93 [3.70–4.17] mM, which is pharmacologically plausible since it corresponds to micromolar extracellular concentrations. Increasing the lipophilic character of the used TPP+ compound further potentiates the inhibition of OGDHC activity. This effect of TPMP on the Krebs cycle ought to be taken into account when interpreting observations on cells and mitochondria in the presence of TPP+ derivatives. Compounds based on or similar to TPP+ derivatives may also be used to alter OGDHC activity for experimental or therapeutic purposes.
Quantitative hydrodynamic investigation of fish caudal fin cupping motion using a bio-robotic model

The three-dimensional deformation of fish caudal fin during swimming was reported in several teleost bony fish species, e.g., bluegill sunfish (Lepomis macrochirus) and cichlid fish (Pseudotropheus greshakei). However, few study has addressed the effect of 3D locomotion on its thrust efficiency quantitatively. In this paper, we first performed biological observations on yellow perch (Perca flavescens) and confirmed the evidence of “cupping” motion for the steady swimming behaviors. The biological kinematics data was then extracted and appropriately programmed into to a robotic caudal fin model coupled with heave and pitch oscillatory motions. We then conducted systematic hydrodynamic experiments on this physical model by manipulating Strouhal numbers (St=0.16−0.50). Comparison between the cupping fin motion and the flat motion showed that the thrust force increased by 78% at the St of 0.32, and thrust efficiency increased 16% at the St of 0.28. DPIV experiments in the horizontal plane were conducted at representative experimental scenarios (St=0.22 and 0.5). We found that the cupping motion has a significant effect on the wake structure, which was distinct with the typically found wake structure, for example, reversed Karman vortex reported by many two-dimensional flapping foil studies. Quantitative analysis of wake flow further demonstrated that the caudal fin generated stronger vortex circulation with addition of cupping motion. We hypothesize that the fish may control the cupping motion to obtain better swimming efficiency under different swimming states.
Transmission Time and Throughput analysis of EEE LEACH , LEACH and Direct Transmission Protocol : A Simulation Based Approach

This paper gives a brief description about some routing protocols like EEE LEACH, LEACH and Direct Transmission protocol (DTx) in Wireless Sensor Network (WSN) and a comparison study of these protocols based on some performance matrices. Addition to this an attempt is done to calculate their transmission time and throughput. To calculate these, MATLAB environment is used. Finally, on the basis of the obtained results from the simulation, the above mentioned three protocols are compared. The comparison results show that, the EEE LEACH routing protocol has a greater transmission time than LEACH and DTx protocol and with smaller throughput.
Meta-heuristic Generation of Robust XPath Locators for Web Testing

Test scripts used for web testing rely on DOM locators, often expressed as XPaths, to identify the active web page elements and the web page data to be used in assertions. When the web application evolves, the major cost incurred for the evolution of the test scripts is due to broken locators, which fail to locate the target element in the new version of the software. We formulate the problem of automatically generating robust XPath locators as a graph exploration problem, for which we provide an optimal, greedy algorithm. Since such an algorithm has exponential time and space complexity, we present also a genetic algorithm.
Extracting local reliable text regions to segment complex handwritten textlines

Textline segmentation is an important preprocess before trying to recognize words. Handwritten texts include complex lines such as connected/overlapped, multi skewed, and curved textlines. In the proposed approach, to overcome these problems, local reliable text regions are locally extracted for each block of a handwritten text. Text image is first filtered by a set of directional 2D filters and filtered images are divided to a number of overlapping blocks. The filtered block with the highest contrast is selected to be used for text region detection. Experiments show that our proposed method accurately segments complex handwritten textlines.
On the Cost of Database Clusters Reconfiguration

Database clusters based on share-nothing replication techniques are currently widely accepted as a practical solution to scalability and availability of the data tier. A key issue when planning such systems is the ability to meet service level agreements when load spikes occur or cluster nodes fail. This translates into the ability to provision and deploy additional nodes. Many current research efforts focus on designing autonomic controllers to perform such reconfiguration, tuned to quickly react to system changes and spawn new replicas based on resource usage and performance measurements. In contrast, we are concerned about the inherent impact of deploying an additional node to an online cluster, considering both the time required to finish such an action as well as the impact on resource usage and performance of the cluster as a whole. If noticeable, such impact hinders the practicability of self-management techniques, since it adds an additional dimension that has to be accounted for. Our approach is to systematically benchmark a number of different reconfiguration scenarios to assess the cost of bringing a new replica online. We consider factors such as: workload characteristics, incremental and parallel recovery, flow control and outdatedness of the recovering replica. As a result, we show that research should be refocused from optimizing the capture and transmition of changes to applying them, which in a realistic setting dominates the cost of the recovery operation.
RNAStrAT : RNA Structure Analysis Toolkit

This poster presents RNAStrAT, a freely available web server that proposes several tools for the comparison of RNA secondary structures. The website interface is composed of 3 main sections: database, tools and information. The database section offers a web interface to browse RNA secondary structures, either by RNA family, species, ID (in our database) but also by structural properties. The tools section provides several options for comparing RNA secondary structures: comparing pairs of RNA secondary structures, searching a database for similar structures, computing a distance table for a set of RNA secondary structures, several rendering methods for single structures, simple alignments and consensus alignments. The information section provides documentation and help about the site, as well as examples and use cases.
From Statistical Detection to Decision Fusion: Detection of Underwater Mines in High Resolution SAS Images

Among all the applications proposed by sonar systems is underwater demining. Indeed, even if the problem is less exposed than the terrestrial equivalent, the presence of underwater mines in waters near the coast an d particularly the harbours provoke accidents and victims in fishing and trade activiti es, even a long time after conflicts. As for terrestrial demining (Milisavljeviþ et al., 2008), detection and classification of various types of underwater mines is cu rrently a crucial strategic task (U.S. Department of the Navy, 2000). Over the past decade, synthetic aperture sonar (SAS) has been increasingly used in seabed imaging, providing high-resolution images (Hayes & Gough, 1999). However, as with any active coherent imaging system, the speckle constructs images with a strong granular aspect that can seriously handicap the interpre tation of the data (Abbot & Thurstone, 1979). Many approaches have been proposed in underwater mine detection and classification using sonar images. Most of them use the charac teristics of the shadows cast by the objects on the seabed (Mignotte et al., 1997). These methods fail in case of buried objects, since no shadow is cast. That is why this last case has been less studied. In such cases, the echoes (high-intensity reflection of the wave on the objects) are the only hint suggesting the presence of the objects. Their small size, even in SAS imaging, and the similarity of their amplitude with the background make the detection more complex. Starting from a synthetic aperture image, a complete detection and classification process would be composed of three main parts as follows: 1. Pixel level: the decision consists in deciding whether a pixel belongs to an object or to the background. 2. Object level: the decision concerns the segmented object which is real or not: are these objects interesting (mines) or simple rocks, wastes? Shape parameters (size, ) and position information can be us ed to answer this question. 3. Classification of object: the decision concerns the type of object and its identification (type of mine). This chapter deals with the first step of this proc ess. The goal is to evaluate a confidence that a pixel belongs to a sought object or to the seabed. In the following, considering the object