Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoreception and circadian clock system of the chicken pineal gland

Chicken pinealocytes contain three major components of the circadian clock system: 1) a self‐sustained oscillator, 2) a photic‐input pathway to the oscillator, and 3) an overt output represented by the rhythmic production of melatonin. Even under cultured conditions of isolated pineal gland or dissociated pinealocytes, the input‐oscillator‐output functions are well maintained. Because of these experimental advantages, chicken pineal gland has been one of the best models for the study of the circadian clock system. Since the finding of a pineal‐specific photoreceptive molecule, pinopsin, we have characterized the endogenous phototransduction pathway in the pinealocytes. On the other hand, despite the long history of chick pineal research, the molecular mechanism underlying the pineal clock oscillation has been largely unknown. Our recent characterization of the chick pineal clock genes strongly suggests that they constitute a transcription/translation‐based autoregulatory feedback loop, which is very similar to that generating circadian rhythmicity in mammalian SCN. Microsc. Res. Tech. 53:72–80, 2001. © 2001 Wiley‐Liss, Inc.
The promise and challenges of bioengineered recombinant clotting factors

Summary. The past 10 years of clinical experience have demonstrated the safety and efficacy of recombinant clotting factors. With the adoption of prophylactic strategies, there has been considerable progress in avoiding the complications of hemophilia. Now, insights from our understanding of clotting factor structure and function, mechanisms of hemophilia and inhibitors, gene therapy advances and a worldwide demand for clotting factor concentrates leave us on the brink of embracing targeted bioengineering strategies to further improve hemophilia therapeutics. The ability to bioengineer recombinant clotting factors with improved function holds promise to overcome some of the limitations in current treatment, the high costs of therapy and increase availability to a broader world hemophilia population. Most research has been directed at overcoming the inherent limitations of rFVIII expression and the inhibitor response. This includes techniques to improve rFVIII biosynthesis and secretion, functional activity, half‐life and antigenicity/immunogenicity. Some of these proteins have already reached commercialization and have been utilized in gene therapy strategies, while others are being evaluated in pre‐clinical studies. These novel proteins partnered with advances in gene transfer vector design and delivery may ultimately achieve persistent expression of FVIII leading to an effective long‐term treatment strategy for hemophilia A. In addition, these novel FVIII proteins could be partnered with new advances in alternative recombinant protein production in transgenic animals yielding an affordable, more abundant supply of rFVIII. Novel rFIX proteins are being considered for gene therapy strategies whereas novel rVIIa proteins are being evaluated to improve the potency and extend their plasma half‐life. This review will summarize the status of current recombinant clotting factors and the development and challenges of recombinant clotting factors bioengineered for improved function.
Current Strategies of Secondary Prevention After a Cerebrovascular Event: The Vienna Stroke Registry

Background and Purpose— Oral anticoagulation (OAC) and antiplatelet drugs are effective in the secondary prevention of ischemic cerebrovascular events. Only few data exist about the factors influencing the choice of a specific therapy for secondary prevention in patients with a recent stroke or transient ischemic attack (TIA). Methods— Within a cross-sectional study, nested in a cohort we identified 931 patients with a recent ischemic stroke or TIA who were discharged with OAC or with one of the antiplatelet medications aspirin, clopidogrel, or the combination of aspirin and extended-release dipyridamole. By means of multivariate logistic regression analysis, we determined the influence of several clinical variables on the decision between OAC and overall antiplatelet therapy as well as on the decision between different antiplatelet therapies. Results— A cardioembolic etiology of the index event and atrial fibrillation were independently associated with the use of OAC. Age was inversely associated with the use of OAC. Different estimations of contraindications to OAC were the main reason for the considerable variability among the participating centers. The most important factor promoting the use of clopidogrel was therapy with aspirin before the index event. Patients with large- or small-vessel disease received clopidogrel more often than those with an event of undetermined etiology. We found an extremely high interhospital variability for the use of the combination of aspirin with extended-release dipyridamole. Conclusions— Current recommendations are applied in clinical practice, but great variability between different centers remains. More clearly defined guidelines for indications for, as well as contraindications against, a specific therapy are necessary.
Code generation to support static and dynamic composition of software product lines

Software product lines (SPLs) are used to create tailor-made software products by managing and composing reusable assets. Generating a software product from the assets of an SPL is possible statically before runtime or dynamically at load-time or runtime. Both approaches have benefits and drawbacks with respect to composition flexibility, performance, and resource consumption. Which type of composition is preferable should be decided by taking the application scenario into account. Current tools and languages, however, force a programmer to decide between static and dynamic composition during development. In this paper, we present an approach that employs code generation to support static and dynamic composition of features of a single code base. We offer an implementation on top of FeatureC++, an extension of the C++ programming language that supports software composition based on features. To simplify dynamic composition and to avoid creation of invalid products we furthermore provide means to (1) validate the correctness of a composition at runtime, (2) automatically instantiate SPLs in case of stand-alone applications, and (3) automatically apply interaction code of crosscutting concerns.
Vax2 regulates retinoic acid distribution and cone opsin expression in the vertebrate eye

Vax2 is an eye-specific homeobox gene, the inactivation of which in mouse leads to alterations in the establishment of a proper dorsoventral eye axis during embryonic development. To dissect the molecular pathways in which Vax2 is involved, we performed a transcriptome analysis of Vax2–/– mice throughout the main stages of eye development. We found that some of the enzymes involved in retinoic acid (RA) metabolism in the eye show significant variations of their expression levels in mutant mice. In particular, we detected an expansion of the expression domains of the RA-catabolizing enzymes Cyp26a1 and Cyp26c1, and a downregulation of the RA-synthesizing enzyme Raldh3. These changes determine a significant expansion of the RA-free zone towards the ventral part of the eye. At postnatal stages of eye development, Vax2 inactivation led to alterations of the regional expression of the cone photoreceptor genes Opn1sw (S-Opsin) and Opn1mw (M-Opsin), which were significantly rescued after RA administration. We confirmed the above described alterations of gene expression in the Oryzias latipes (medaka fish) model system using both Vax2 gain- and loss-of-function assays. Finally, a detailed morphological and functional analysis of the adult retina in mutant mice revealed that Vax2 is necessary for intraretinal pathfinding of retinal ganglion cells in mammals. These data demonstrate for the first time that Vax2 is both necessary and sufficient for the control of intraretinal RA metabolism, which in turn contributes to the appropriate expression of cone opsins in the vertebrate eye.
The ramifications of sharing in data structures

Programs manipulating mutable data structures with intrinsic sharing present a challenge for modular verification. Deep aliasing inside data structures dramatically complicates reasoning in isolation over parts of these objects because changes to one part of the structure (say, the left child of a dag node) can affect other parts (the right child or some of its descendants) that may point into it. The result is that finding intuitive and compositional proofs of correctness is usually a struggle. We propose a compositional proof system that enables local reasoning in the presence of sharing. While the AI "frame problem" elegantly captures the reasoning required to verify programs without sharing, we contend that natural reasoning about programs with sharing instead requires an answer to a different and more challenging AI problem, the "ramification problem": reasoning about the indirect consequences of actions. Accordingly, we present a RAMIFY proof rule that attacks the ramification problem head-on and show how to reason with it. Our framework is valid in any separation logic and permits sound compositional and local reasoning in the context of both specified and unspecified sharing. We verify the correctness of a number of examples, including programs that manipulate dags, graphs, and overlaid data structures in nontrivial ways.
ViNO: SDN overlay to allow seamless migration across heterogeneous infrastructure

We propose ViNO (Virtual Network Overlay), an orchestration service that can be used to create arbitrary network topologies with OVS (Open vSwitch) switches and VMs. ViNO connects switches and VMs through an overlay network using VXLAN encapsulation. ViNO provisions VMs by making API calls to the underlying platform. Users specify the desired topology using an expressive Domain Specific Language that allows users to easily express commonly used network topologies while hiding the underlying complexity. An important use case for ViNO is enabling the seamless migration of Linux services across VMs in different regions with very little downtime.
End-user software engineering of cognitive robot applications using procedural parameters and complex event processing

Robots understand the world around them through sensing. To process the data produced by sensors we propose to use Procedural Parameters and Complex Event Processing (CEP). End-users model applications for robots as a CEP Graph, in which the end-users specify how input from the sensors of the robot is transformed to output for the actuators of the robot. Between input and output is a network of streams connected together by operators. By using Procedural Parameters a set of generic operators can be used within the CEP Graph. The CEP Graph can be executed on the robot or on a PC remotely controlling the robot.
Thermal and source bumps utilizing carbon nanotubes for flip-chip high power amplifiers

Carbon nanotubes (CNTs) have been successfully developed as thermal and source bumps for flip-chip high power amplifiers (HPAs). The newly developed 15 mum long CNT bumps exhibit thermal conductivity of 1400 W/m-K. A flip-chip AlGaN/GaN HEMT HPA with a gate width of 2.4 mm utilizing CNT bumps, operating voltage of 40 V, exhibits an output power of 39 dBm at, a frequency of 2.1 GHz without any degradation due to heat-up. To our knowledge, this is the first report about, a practical application of CNTs using their high thermal conductivity
Analytic comparison of two advanced C language-based parallel programming models

There are two main approaches for designing parallel language. The first approach states that parallel computing demands new programming concepts and radical intellectual changes regarding the way we think about programming, as compared to sequential computing. Therefore, the design of such a parallel language must present new constructs and new programming methodologies. The second approach states that there is no need to reinvent the wheel, and serial languages can be extended to support parallelism. The motivation behind this approach is to keep the language as friendly as possible for the programmer who is the main bridge toward wider acceptance of the new language. In this paper we present a qualitative evaluation of two contemporary parallel languages: OpenMP-C and Unified Parallel C (UPC). Both are explicit parallel programming languages based on the ANSI C standard. OpenMP-C was designed for shared-memory architectures and extends the base-language by using compiler directives that annotate the original source-code. On the other hand, UPC was designed for distribute-shared memory architectures and extends the base-language by new parallel constructs. We deconstruct each parallel language into its basic components, show examples, make a detailed analysis, compare them, and finally draw some conclusions.
Robust 3D-mapping with time-of-flight cameras

Time-of-flight cameras constitute a smart and fast technology for 3D perception but lack in measurement precision and robustness. The authors present a comprehensive approach for 3D environment mapping based on this technology. Imprecision of depth measurements are properly handled by calibration and application of several filters. Robust registration is performed by a novel extension to the Iterative Closest Point algorithm. Remaining registration errors are reduced by global relaxation after loop-closure and surface smoothing. A laboratory ground truth evaluation is provided as well as 3D mapping experiments in a larger indoor environment.
Combined Flocking and Distance-Based Shape Control of Multi-Agent Formations

Steepest descent control laws can be used for formation shape control based on specified inter-agent distances, assuming point agents with single integration of the control action to yield velocity. Separately, it is known how to achieve equal velocity for a collection of agents in a formation using consensus ideas, given appropriate properties for the graph describing information flows. This work shows how the two concepts of formation shape control and flocking behavior can be combined when one changes from an agent with single integration to one with double integration.
Preparation of BaTi2O5 single crystal by a floating zone method

Single crystalline BaTi 2 O 5 was prepared by a floating zone method. The single crystal was transparent having a (001) cleavage plane. The space group was C2, and the lattice parameters were a =1.6909(9)nm, b =0.3937(1)nm, c=0.9419(4)nm and β =103.12(6)°. The permittivity perpendicular to a (010) plane showed the maximum value of 20500 at 748 K. The permittivity perpendicular to (100) and (001) planes were about 140 and 70, respectively, independent of temperature.
Data pruning using confidence measures for concatenative synthesis system built using automatically transcribed audio

Today, we can record and store large amounts of single speaker audio data, and also download it from the web. Generally, these data are prosodically rich and can therefore act as excellent candidates for building concatenative text-to-speech (TTS) systems. But transcritpions for these audio data are often not available and automatic transcriptions are error prone. In addition, these audio data contain bad acoustic (poorly articulated, noisy, inaudible, unintelligible, clipped) regions. Both above reasons can damage the resulting synthesized voice. So, pruning bad data becomes necessary. In this paper, we describe the development of two concatenative TTS systems using a lecture speech downloaded from Coursera and an audiobook downloaded from Librivox. Confidence measures such as phone posterior probability and unit duration obtained from the ASR system are used to remove bad data. Voices built using automatic transcripts are compared with those built using reference transcripts, and the effect of data pruning is investigated in terms of intelligibility and naturalness with the help of perceptual evaluation on Blizzard 2013 test corpus.
Biventricular mechanical support devices – clinical perspectives

ABSTRACT Cardiac transplantation remains the optimal treatment for end stage heart failure in selected patients. However, the shortage of donor hearts, rigorous eligibility criteria and long waiting lists have increased the demand for alternative treatment strategies such as mechanical circulatory support. While many patients are adequately supported with left ventricular assist devices, frequently there is right heart failure or involvement of the right ventricle, requiring biventricular support. Pulsatile flow biventricular devices and total artificial hearts approved for temporary biventricular support have limitations including size, high rates of adverse events and restricted mobility which makes them unsuitable for long term support. A number of centres have reported dual continuous flow left ventricular assist devices as a means of supporting the left and right heart. This review will summarise the literature on the outcomes and complications from current biventricular support devices and assess the role of dual continuous flow VAD therapy, and the new continuous flow total heart replacement devices.
Pedestrian footpath level of service (FOOT-LOS) model for Johor Bahru

Pedestrian level of service (LOS) is an overall measure of walking conditions on a route, path, or facility. This is linked directly to factors that affect mobility, comfort and safety, reflecting pedestrian's perceptions of the degree to which the facility is pedestrian-friendly. A unique model called FOOT-LOS (short for pedestrian footpath level of service) was developed to facilitate the LOS measurement. The factors considered fall into three categories; physical, location and user attributes. Pedestrian conditions can be described through a grading system, i.e. from LOS A (ideal pedestrian condition) to LOS F (unsuitable pedestrian condition), based on an assessment of the factors affecting LOS. The assessment includes desktop and on-site assessment of LOS factors. The development of the model involved an iterative process that included testing and refinement. The research undertaken and the LOS model developed provide a sound basis for the measurement of LOS for pedestrian footpaths. The model not only provides a methodology for determining LOS, but also determines which factors predominantly contribute to the LOS of pedestrian footpaths. © Owned by the authors, published by EDP Sciences, 2016 Language: en
VIVA-uOttawa / CBSA at TRECVID 2012: Interactive Surveillance Event Detection

We present an interactive video event detection system for the TRECVID 2012 Surveillance Event Detection (SED) task (16). Inspired by previous TRECVID submissions, the underlying approach is built on combining automated de- tection of temporal regions of interest through the extrac- tion of binary spatio-temporal keypoint descriptors in ob- served video-sequences (Video Analytics module), and effi- cient manual filtering of false alarms through the use of a custom-designed graphical user interface (Visual Analytics module). We make the automated detection of temporal re- gions of interest feasible by using efficient binary feature de- scriptors. These descriptors allow for descriptor matching in the bag-of-words model to be orders of magnitude faster than traditional descriptors, such as SIFT and optical flow. The approach is evaluated on a single task, PersonRuns, as defined by the TRECVID 2012 guidelines. The combination of Visual Analytics and Video Analytics tools is shown to be essential for the success of a highly challenging task of de- tecting events of interest in unstructured environments using video surveillance cameras.
Political Evolution

We study a two dimensional opinion model on a predefined agent-agent network structure which defines the possible interactions between agents. When two agents interact they either come to a compromise or ignore each other according to some parameter dependent on distance in opinion space. If the two agents decide to ignore each other then with a given probability they decide to break their connection in the network and rewire this broken link to another agent uniformly across unconnected agents. We also introduce agents with static opinion whom we interpret as media outlets and these media outlets have a defined range over which they can influence agents and pull them towards their political outlook. Thus we have defined a tolerance for both media outlet and individual agent. As we vary this tolerance for both media and agent we see various different results such as the formation of clusters of agents with the same opinion or complete disagreement within society. The resulting degree distributions also vary with the tolerance parameters, rewiring rule and number of media sources. We often see a transition from the initially defined network structure, usually a network with a Poisson distribution for the degree sequence to that with other distributions.
"Once Upon a Place": Compute Your Meeting Location Privately

Popular services such as Doodle Mobile and Tymelie are extremely useful planning tools that enable mobile-phone users to determine common meeting time(s) for events. Similar planning tools for determining optimal meeting locations, based on the location preferences of the users, are highly desirable for event planning and management in popular mobile phone applications, such as taxi sharing, route planning and mobile participatory sensing. Yet, they have received very little attention by researchers. An important, and often overlooked, facet of such planning applications is the privacy of the participating users and their preferences; users want to agree on a meeting location without necessarily revealing their location preferences to the service provider or to the other users. In this paper, we address the problem of privacy-preserving optimal meeting-location computation, especially focusing on its applicability to current mobile devices and applications. We first define the notion of privacy in such computations. Second, we model the problem of optimal meeting-location computation as a privacy-preserving k-center problem and we design two solutions; both solutions take advantage of the homomorphic properties of well-known cryptosystems by Boneh-Goh-Nissim, ElGamal and Paillier in order to perform oblivious computations. Third, we implement the proposed solutions on a testbed of the latest generation Nokia mobile devices and study their performance. Finally, we assess the utility and expectations, in terms of privacy and usability, of the proposed solutions by means of a targeted survey and user-study of mobile-phone users.