Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Helix Cone Tree visualizations to dynamic call graph illustration

We describe a tool that enables users to record and visualise runtime behaviour of software applications developed in Java. The execution trace, stored in the form of an XML file is visualized using 3D call graphs that are an extension of the Cone Tree information visualisation technique. This tool gives the user the ability to create several call graph views from a program’s execution trace, providing additional representations of the program execution to both novice and expert programmers for the purposes of program execution analysis.
Comparison of Renal Allograft Outcomes in Combined Liver-Kidney Transplantation Versus Subsequent Kidney Transplantation in Liver Transplant Recipients: Analysis of UNOS Database

Background. There may be an allograft-enhancing effect by the liver on the renal allograft in the setting of simultaneous combined liver-kidney transplantation (CLKT) from the same donor. This study was performed to investigate whether an existing liver allograft could protect a kidney allograft from immunologic injury due to histoincompatibility in liver transplant recipients who received sequential kidney transplantation (KALT). Methods. Using the United Network for Organ Sharing database covering January 1996 to December 2003, outcomes of 352 KALT were compared to 1,136 CLKT. Incidence of acute and chronic rejection and rejection-free renal graft survival was compared between two groups. Results. Renal half-life of KALT allografts was shorter than CLKT group (6.6±0.9 vs. 11.7±1.3 years, P<0.001). Incidence of chronic rejection in KALT group was higher than CLKT group (4.6 vs. 1.2%, P<0.001). One and three-year rejection-free renal graft survival of KALT and CLKT groups were different (77% and 67% KALT vs. 85% and 78% CLKT, respectively; P<0.001). Among human leukocyte antigen mismatched and sensitized patients, rejection-free renal graft survival of KALT group was inferior to the CLKT group (75% at 1 year and 61% 3 years vs. 86% at 1 year and 79% 3 years, P<0.001). Conclusion. Liver allograft provided renal graft immunoprotection if both organs are transplanted simultaneously (immunogenetic identity), but not for kidneys transplanted subsequently.
Identification of Nicotinic Acetylcholine Receptor Recycling and Its Role in Maintaining Receptor Density at the Neuromuscular Junction In Vivo

In the CNS, receptor recycling is critical for synaptic plasticity; however, the recycling of receptors has never been observed at peripheral synapses. Using a novel imaging technique, we show here that nicotinic acetylcholine receptors (AChRs) recycle into the postsynaptic membrane of the neuromuscular junction. By sequentially labeling AChRs with biotin-bungarotoxin and streptavidin-fluorophore conjugates, we were able to distinguish recycled, preexisting, and new receptor pools at synapses in living mice. Time-lapse imaging revealed that recycled AChRs were incorporated into the synapse within hours of initial labeling, and their numbers increased with time. At fully functional synapses, AChR recycling was robust and comparable in magnitude with the insertion of newly synthesized receptors, whereas chronic synaptic activity blockade nearly abolished receptor recycling. Finally, using the same sequential labeling method, we found that acetylcholinesterase, another synaptic component, does not recycle. These results identify an activity-dependent AChR-recycling mechanism that enables the regulation of receptor density, which could lead to rapid alterations in synaptic efficacy.
Interactions between the nucleosome histone core and Arp8 in the INO80 chromatin remodeling complex

Actin-related protein Arp8 is a component of the INO80 chromatin remodeling complex. Yeast Arp8 (yArp8) comprises two domains: a 25-KDa N-terminal domain, found only in yeast, and a 75-KDa C-terminal domain (yArp8CTD) that contains the actin fold and is conserved across other species. The crystal structure shows that yArp8CTD contains three insertions within the actin core. Using a combination of biochemistry and EM, we show that Arp8 forms a complex with nucleosomes, and that the principal interactions are via the H3 and H4 histones, mediated through one of the yArp8 insertions. We show that recombinant yArp8 exists in monomeric and dimeric states, but the dimer is the biologically relevant form required for stable interactions with histones that exploits the twofold symmetry of the nucleosome core. Taken together, these data provide unique insight into the stoichiometry, architecture, and molecular interactions between components of the INO80 remodeling complex and nucleosomes, providing a first step toward building up the structure of the complex.
Segment-Based Classification of Damaged Building Roofs in Aerial Laser Scanning Data

Identifying damaged buildings after natural disasters such as earthquake is important for the planning of recovery actions. We present a segment-based approach to classifying damaged building roofs in aerial laser scanning data. A challenge in the supervised classification of point segments is the generation of training samples, which is difficult because of the complexity of interpreting point clouds. We evaluate the performance of three different classifiers trained with a small set of training samples and show that feature selection improves the training and the accuracy of the resulting classification. When trained with 50 training samples, a linear discriminant classifier using a subset of six features reaches a classification accuracy of 85%.
Database replication using generalized snapshot isolation

Generalized snapshot isolation extends snapshot isolation as used in Oracle and other databases in a manner suitable for replicated databases. While (conventional) snapshot isolation requires that transactions observe the "latest" snapshot of the database, generalized snapshot isolation allows the use of "older" snapshots, facilitating a replicated implementation. We show that many of the desirable properties of snapshot isolation remain. In particular, read-only transactions never block or abort and they do not cause update transactions to block or abort. Moreover, under certain assumptions on the transaction workload the execution is serializable. An implementation of generalized snapshot isolation can choose which past snapshot it uses. An interesting choice for a replicated database is prefix-consistent snapshot isolation, in which the snapshot contains at least all the writes of locally committed transactions. We present two implementations of prefix-consistent snapshot isolation. We conclude with an analytical performance model of one implementation, demonstrating the benefits, in particular reduced latency for read-only transactions, and showing that the potential downsides, in particular change in abort rate of update transactions, are limited.
Reduced Free Products of Unital AH Algebras and Blackadar and Kirchberg's MF Algebras

In the paper, we prove that reduced free products of unital AH algebras with respect to given faithful tracial states, in the sense of Voiculescu, are Blackadar and Kirhcberg's MF algebras. We also show that the reduced free products of unital AH algebras with respect to given faithful tracial states, under mild conditions, are not quasidiagonal. Therefore we conclude, for a large class of AH algebras, the Brown-Douglas-Fillmore extension semigroups of the reduced free products of these AH algebras with respect to given faithful tracial states are not groups. Our result is based on Haagerup and Thorbjorsen's work on the reduced C ∗ -algebras of free
Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): De Novo Assembly, Annotation and Marker Discovery

Background Giant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth. Methodology and Principal Findings A collection of 787,731 sequence reads (244.37 Mb) obtained from 454 pyrosequencing analysis of cDNA prepared from muscle, ovary and testis tissues taken from 18 adult prawns was assembled into 123,534 expressed sequence tags (ESTs). Of these, 46% of the 8,411 contigs and 19% of 115,123 singletons possessed high similarity to sequences in the GenBank non-redundant database, with most significant (E value < 1e–5) contig (80%) and singleton (84%) matches occurring with crustacean and insect sequences. KEGG analysis of the contig open reading frames identified putative members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light chain, tropomyosin and troponin with fundamental roles in muscle development and construction were abundant. Amongst the contigs, 834 single nucleotide polymorphisms, 1198 indels and 658 simple sequence repeats motifs were also identified. Conclusions The M. rosenbergii transcriptome data reported here should provide an invaluable resource for improving our understanding of this species' genome structure and biology. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs.
TRIPTYCH: An FPGA Architecture with Integrated Logic and Routing

We describe Triptych, a new FPGA architecture, that blends logic and routing resources to achieve efficient implementation of a wide range of circuits in both area and speed. The physical structure of Triptych attempts to match the structure of factored logic functions, thus providing an efficient substrate in which to implement these circuits. This approach both requires and takes advantage of an integrated approach to the mapping, placement and routing process. We first describe the Triptych architecture in detail. This is followed by the development of a new method for architectural comparison of FPGAs that is free of irrelevant implementation effects. Then the Triptych, Xilinx, Algotronix, and Concurrent Logic architectures are compared using this method to obtain normalized area and performance figures for a wide range of circuits, including both datapath elements and control logic. Our results indicate that Triptych is more area-efficient (Xilinx mappings average 3.5 times larger than Triptych mappings) and has at least comparable delay characteristics.
Scalability techniques in electronically processed CDMA for low cost and flexible optical access networks

Recently, the coding and decoding of code-division multiple-access (CDMA) signals using electronic transversal filters at a chip rate of 18 Gchips/s for use in passive optical access networks (PONs) was demonstrated. The system used 7-chip transversal filters giving a potential for 7 users, where each user had a data rate of 1.25 Gb/s. In this paper, we show two techniques to scale up the electronically processed CDMA (ECDMA) system, namely by increasing the number of chips in the code and doubling the capacity using I and Q modulation of two in-quadrature channels. For increasing the number of chips, we demonstrate an electronically processed Walsh Code with 16 chips at 18 Gchip/s. An auto-cross correlation ratio of 18.1 dB is achieved between two orthogonal codes after transmission over 10km of SMF. In addition, I-Q modulation of two electronic CDMA channels using the same electronic transversal filters is demonstrated. Here, two in-quadrature channels with chip rates of 18 Gchip/s show the potential of current technology for future 40 Gb/s throughput ECDMA PONs.
Commutativity in the Algorithmic Lovász Local Lemma

We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately.
Universität Augsburg Finding Disjoint Paths on Directed Acyclic Graphs

Given k + 1 pairs of vertices (s1, s2), (u1, v1), . , (uk, vk) of a directed acyclic graph, we show that a modified version of a data structure of Suurballe and Tarjan can output, for each pair (ul, vl) with 1 ≤ l ≤ k, a tuple (s1, t1, s2, t2) with {t1, t2} = {ul, vl} in constant time such that there are two disjoint paths p1, from s1 to t1, and p2, from s2 to t2, if such a tuple exists. Disjoint can mean vertexas well as edge-disjoint. As an application we show that the presented data structure can be used to improve the previous best known running time O(mn) for the so called 2-disjoint paths problem on directed acyclic graphs to O(m log2+m/n n + n log 3 n). In this problem, given four vertices s1, s2, t1, and t2, we want to construct two disjoint paths p1, from s1 to t1, and p2, from s2 to t2, if such paths exist.
How interview questions are placed in time influences caregiver description of social communication symptoms on the ADI-R.

BACKGROUND Caregiver report is crucial for the diagnosis of childhood onset psychiatric disorders, particularly autism. Three experiments were conducted to determine whether caregiver reports of past and current behaviors are affected by question timing and ordering. METHODS Using the Autism Diagnostic Interview - Revised (ADI-R), two studies systematically varied the order in which caregivers were asked about behaviors. In a third study, descriptions of children's current behaviors at age 5 were compared to retrospective descriptions of behaviors at age 5 collected at age 10. RESULTS Caregivers, who were first asked about a history of symptoms, described less severe past and present behavior than caregivers reporting current behaviors as well as caregivers reporting current and history of symptoms together. Caregivers retrospectively reported more severe behaviors for age 5 when their children were age 10 than they had when their children were age 5. CONCLUSIONS Caregivers describe past behaviors differently depending on whether they are asked about current symptoms first. Methods of caregiver reporting can influence interpretations of symptom severity with effects on diagnoses and research findings.
Vehicle motion intention reasoning using cooperative perception on urban road

As autonomous vehicles are venturing on the urban road, reasoning other vehicles' motion intention is always essential for anticipatory decision-making. This paper considers a new class of motion intention reasoning problem using cooperative perception. Specifically, thanks to the extended perception range contributed by cooperative perception, we can explicitly consider the behavior correlations among multiple vehicles, where each vehicle's motion intention can be inferred using both the temporal observations and the other vehicles' motion intention expectation. As such, a Simplified variant of Coupled Hidden Markov Model (S-CHMM) is proposed for motion intention inference. The experiment on an autonomous vehicle shows that the proposed algorithm can improve the motion intention accuracy and provide efficient overtaking triggering for autonomous driving on urban road.
Advances in MRI-based computational neuroanatomy: from morphometry to in-vivo histology.

PURPOSE OF REVIEW Current computational neuroanatomy based on MRI focuses on morphological measures of the brain. We present recent methodological developments in quantitative MRI (qMRI) that provide standardized measures of the brain, which go beyond morphology. We show how biophysical modelling of qMRI data can provide quantitative histological measures of brain tissue, leading to the emerging field of in-vivo histology using MRI (hMRI). RECENT FINDINGS qMRI has greatly improved the sensitivity and specificity of computational neuroanatomy studies. qMRI metrics can also be used as direct indicators of the mechanisms driving observed morphological findings. For hMRI, biophysical models of the MRI signal are being developed to directly access histological information such as cortical myelination, axonal diameters or axonal g-ratio in white matter. Emerging results indicate promising prospects for the combined study of brain microstructure and function. SUMMARY Non-invasive brain tissue characterization using qMRI or hMRI has significant implications for both research and clinics. Both approaches improve comparability across sites and time points, facilitating multicentre/longitudinal studies and standardized diagnostics. hMRI is expected to shed new light on the relationship between brain microstructure, function and behaviour, both in health and disease, and become an indispensable addition to computational neuroanatomy.
Identiication for Robust Control

Given measured data we propose a model consisting of a linear, time-invariant system aaected by perturbation. The kernel representations of the systems belonging to the resulting uncertain family form a convex set. Motivated by this representation, a robust control method is explored. It is based on results regarding the robust strict-positive realness property of a class of rational functions. This method allows the computation of a controller which maximizes the stability margin. Various lower and/or upper bounds of the optimal stability margin are obtained in terms of diierent measures of the uncertainty. These bounds describe the relation between the robust performance and the size of the uncertain family. The validation problem ensuing from this framework is also investigated.
Therapeutic management of complex anal fistulas by installing a nitinol closure clip: study protocol of a multicentric randomised controlled trial—FISCLOSE

Introduction Complex anal fistulas are responsible for pain, faecal incontinence and impaired quality of life. The rectal mucosa advancement flap (RMAF) procedure to cover the internal opening of the fistula remains a strategy of choice. However, a new procedure for closing anal fistulas is now available with the use of a nitinol closure clip (OTSC Proctology, OVESCO), which should ensure a better healing rate. This procedure is currently becoming more widespread, though without robust scientific validation, and it is therefore essential to carry out a prospective evaluation in order to determine the efficacy and safety of this new medical device for complex anal fistulas. Methods and analysis The FISCLOSE trial is aimed at evaluating the efficacy and safety of a nitinol closure clip compared to the RMAF procedure for the management of complex anal fistulas. This trial is a prospective, randomised, controlled, single-blind, bicentre and interventional study. Patients (n=46 per group) will be randomly assigned for management with either a closure clip or RMAF. The main objectives are to improve the healing rate of the anal fistula, lessen the postoperative pain and faecal incontinency, enhance the quality of life, and lower the number of reinterventions and therapeutic management costs. The primary outcome is the proportion of patients with a healed fistula at 3 months. The secondary outcomes are anal fistula healing (6 and 12 months), proctological pain (visual analogue scale), the faecal incontinence score (Jorge and Wexner questionnaire), digestive disorders and quality of life (Gastrointestinal Quality of Life Index and Euroqol EQ5D-3 L) up to 1 year. Ethics and dissemination The study was approved by an independent medical ethics committee 1 (IRB00008526, CPP Sud-Est 6, Clermont-Ferrand, France) and registered by the competent French authority (ANSM, Saint Denis, France). The results will be disseminated in a peer-reviewed journal and presented at international congresses. Trial registration number NCT02336867; pre-result.
The self-orientation of mammalian cells in optical tweezers—the importance of the nucleus

Here we present the first evidence showing that eukaryotic cells can be stably trapped in a single focused Gaussian beam with an orientation that is defined by the nucleus. A mammalian eukaryotic cell (in suspension) is trapped and is re-oriented in the focus of a linearly polarized Gaussian beam with a waist of dimension smaller than the radius of the nucleus. The cell reaches a position relative to the focus that is dictated by the nucleus and nuclear components. Our studies illustrate that the force exerted by the optical tweezers at locations within the cell can be predicted theoretically; the data obtained in this way is consistent with the experimental observations.
Distribute, store and retrieve management policies in wireless ad-hoc networks using the content delivery publish/subscribe paradigm

Policy management is a management paradigm that has been extensively studied for the case of fixed networks but limited work can be found for migrating it to mobile environments. It enables dynamic adaptation of the network behavior to current conditions based on high-level business and operational objectives. Publish/subscribe has become an important architectural style for designing distributed systems and especially for mobile environments due to the loose coupling of the components involved namely the publishers and the subscribers. In this paper, we present a policy-based management system for wireless ad-hoc networks using the publish/subscribe paradigm for distributing policies to the managed nodes ensuring this way that all nodes will receive the related defined policies, in an asynchronous and loosely coupled manner, achieving the desired network-wide behavior. Moreover, we enhance the publish/subscribe system with a novel request/response mechanism for tackling the problem of how newly joined nodes will retrieve previously introduced policies. Finally, we describe our initial design and implementation of the proposed mechanism, evaluate it through simulation and testbed experiments and give pointers to our future work.