Miracle-dz/UniFAR-FTUs huggingface dataset:
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity

MOTIVATION Protein structure alignment is key for transferring information from well-studied proteins to less studied ones. Structural alignment identifies the most precise mapping of equivalent residues, as structures are more conserved during evolution than sequences. Among the methods for aligning protein structures, maximum Contact Map Overlap (CMO) has received sustained attention during the past decade. Yet, known algorithms exhibit modest performance and are not applicable for large-scale comparison. RESULTS Graphlets are small induced subgraphs that are used to design sensitive topological similarity measures between nodes and networks. By generalizing graphlets to ordered graphs, we introduce GR-Align, a CMO heuristic that is suited for database searches. On the Proteus_300 set (44 850 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art CMO solvers Apurva, MSVNS and AlEigen7, and its similarity score is in better agreement with the structural classification of proteins. On a large-scale experiment on the Gold-standard benchmark dataset (3 207 270 protein domain pairs), GR-Align is several orders of magnitude faster than the state-of-the-art protein structure comparison tools TM-Align, DaliLite, MATT and Yakusa, while achieving similar classification performances. Finally, we illustrate the difference between GR-Align's flexible alignments and the traditional ones by querying a flexible protein in the Astral-40 database (11 154 protein domains). In this experiment, GR-Align's top scoring alignments are not only in better agreement with structural classification of proteins, but also that they allow transferring more information across proteins.
LEILA: Learning to Extract Information by Linguistic Analysis

One of the challenging tasks in the context of the Semantic Web is to automatically extract instances of binary relations from Web documents ‐ for example all pairs of a person and the corresponding birthdate. In this paper, we present L EILA, a system that can extract instances of arbitrary given binary relations from natural language Web documents ‐ without human interaction. Different from previous approaches, LEILA uses a deep syntactic analysis. This results in consistent improvements over comparable systems (such as e.g. Snowball or TextToOnto).
Towards the Automated Analysis and Database Development of Defibrillator Data from Cardiac Arrest

Background. During resuscitation of cardiac arrest victims a variety of information in electronic format is recorded as part of the documentation of the patient care contact and in order to be provided for case review for quality improvement. Such review requires considerable effort and resources. There is also the problem of interobserver effects. Objective. We show that it is possible to efficiently analyze resuscitation episodes automatically using a minimal set of the available information. Methods and Results. A minimal set of variables is defined which describe therapeutic events (compression sequences and defibrillations) and corresponding patient response events (annotated rhythm transitions). From this a state sequence representation of the resuscitation episode is constructed and an algorithm is developed for reasoning with this representation and extract review variables automatically. As a case study, the method is applied to the data abstraction process used in the King County EMS. The automatically generated variables are compared to the original ones with accuracies ≥90% for 18 variables and ≥85% for the remaining four variables. Conclusions. It is possible to use the information present in the CPR process data recorded by the AED along with rhythm and chest compression annotations to automate the episode review.
Effect of complex cardiac rehabilitation on physical activity and quality of life during long-term follow-up after surgical correction of congenital heart disease.

BACKGROUND Comprehensive cardiac rehabilitation (CCR) is an important element of the comprehensive management of grown-up congenital heart disease (GUCH) patients after surgical correction of congenital heart disease (CHD) but access to this treatment is still limited. We still lack Polish guidelines on CCR, including controlled training in young adults several years after surgical correction of CHD. AIM To assess the effect of a CCR program on physical capacity, exercise tolerance, quality of life, and severity of depressive symptoms in GUCH patients long-term after surgical correction of CHD. METHODS We studied 57 CHD patients (30 females, 27 males, mean age 23 ± 3.4 years) at least 12 months after surgical correction of a ventricular septal defect (VSD) or ostium secundum atrial septal defect (ASD II). All patients were offered a CCR program, and 31 of them participated (rehabilitation group [Reh]) and 26 refused (non-rehabilitated group [NReh]). All patients underwent baseline cardiopulmonary exercise testing (CPET) using a cycloergometer and a ramp protocol with an initial load of 20 W followed by 10 W load increments per minute. Psychological evaluation included the Beck Depression Inventory (BDI) and the Euro QoL 5D questionnaire to evaluate quality of life. Patients were reassessed 30 days after the initial evaluation using the same investigations. RESULTS During CPET, all patients reached peak exercise intensity at the level of 15-17 in the Borg scale without complications. Resting HR was lower in the Reh group (74 ± 8 bpm) compared to the NReh group (81 ± 14 bpm). During CPET, patients in the Reh group reached significantly higher peak HR and percent maximum HR. Workload increased nonsignificantly (144 W vs. 124 W, p = 0.121), while duration of exercise and peak oxygen consumption was significantly longer in the Reh group compared to the NReh group (14 min vs. 11 min, p = 0.001; and 27.5 mL/kg/min vs. 23 mL/kg/min, p = 0.003, respectively). Patients in the NReh group showed non significantly higher severity of depressive symptoms compared to the Reh group, as evaluated using BDI at 30 days (mean score 4.8 vs. 2.2, respectively, p = 0.59). In contrast, subjectively and objectively rated quality of life was significantly higher in the Reh group compared to the NReh (score 89 vs. 74.4, p < 0.01; and 94 vs. 83, p < 0.01, respectively). CONCLUSIONS Implementation of a CCR program improves physical capacity, exercise tolerance, and quality of life and reduces depressive symptoms in patients late after surgical correction of CHD. Introduction of such programs seems reasonable as a supplement to the holistic care for GUCH patients.
Estimation of an optimal external beam radiotherapy utilization rate for head and neck carcinoma

Radiotherapy is used commonly in the treatment of patients with head and neck carcinoma. The benchmark radiotherapy utilization rates for head and neck carcinoma largely are unknown. The objective of the current study was to determine the optimal radiotherapy utilization rate for patients with head and neck carcinoma and to compare this optimal rate with actual utilization rates where actual utilization data were available.
Using CCG categories to improve Hindi dependency parsing

We show that informative lexical categories from a strongly lexicalised formalism such as Combinatory Categorial Grammar (CCG) can improve dependency parsing of Hindi, a free word order language. We first describe a novel way to obtain a CCG lexicon and treebank from an existing dependency treebank, using a CCG parser. We use the output of a supertagger trained on the CCGbank as a feature for a state-of-the-art Hindi dependency parser (Malt). Our results show that using CCG categories improves the accuracy of Malt on long distance dependencies, for which it is known to have weak rates of recovery.
Global transcriptomic analysis of murine embryonic stem cell‐derived brachyury+ (T) cells

Brachyury+ mesodermal cell population with purity over 79% was obtained from differentiating brachyury embryonic stem cells (ESC) generated with brachyury promoter driven enhanced green fluorescent protein and puromycin‐N‐acetyltransferase. A comprehensive transcriptomic analysis of brachyury+ cells enriched with puromycin application from 6‐day‐old embryoid bodies (EBs), 6‐day‐old control EBs and undifferentiated ESCs led to identification of 1573 uniquely up‐regulated and 1549 uniquely down‐regulated transcripts in brachyury+ cells. Furthermore, transcripts up‐regulated in brachyury+ cells have overrepresented the Gene Ontology annotations (cell differentiation, blood vessel morphogenesis, striated muscle development, placenta development and cell motility) and Kyoto Encyclopedia of Genes and Genomes pathway annotations (mitogen‐activated protein kinase signaling and transforming growth factor beta signaling). Transcripts representing Larp2 and Ankrd34b are notably up‐regulated in brachyury+ cells. Knockdown of Larp2 resulted in a significantly down‐regulation BMP‐2 expression, and knockdown of Ankrd34b resulted in alteration of NF‐H, PPARγ and PECAM1 expression. The elucidation of transcriptomic signatures of ESCs‐derived brachyury+ cells will contribute toward defining the genetic and cellular identities of presumptive mesodermal cells. Furthermore, there is a possible involvement of Larp2 in the regulation of the late mesodermal marker BMP‐2. Ankrd34b might be a positive regulator of neurogenesis and a negative regulator of adipogenesis.
Thermal stress reduced maximum power point tracking for two stages photovoltaic converters

Several maximum power point tracking (MPPT) methods have been proposed to optimize the energy harvesting of photovoltaic systems. However, the optimization of the energy harvesting can produce extremely variable loading of the power semiconductors resulting in a decrease of the system lifetime. This work proposes a multi-objective MPPT for two-stage photovoltaic converters, where the semiconductor thermal stress is taken into account while searching for the maximum power point. A perturb and observe based algorithm which limits the positive temperature gradient and the maximum junction temperature of the power semiconductors of the boost converter is introduced and fully validated in the laboratory with a mission profile emulating variable irradiance conditions. The achievable lifetime improvement is evaluated against the reduction in the energy harvesting.
Instanton corrections to the universal hypermultiplet and automorphic forms on {$SU(2,1)$}

Abstract: The hypermultiplet moduli space in Type IIA string theory compactified on a rigid Calabi-Yau threefold X , corresponding to the “universal hypermultiplet”, is described at tree-level by the symmetric space SU(2,1)/(SU(2)×U(1)). To determine the quantum corrections to this metric, we posit that a discrete subgroup of the continuous tree-level isometry group SU(2,1), namely the Picard modular group SU(2,1;Z[i]), must remain un- broken in the exact metric – including all perturbative and non-perturbative quantum cor- rections. This assumption is expected to be valid when X admits complex multiplication by Z[i]. Based on this hypothesis, we construct an SU(2,1;Z[i])-invariant, non-holomorphic Eisenstein series, and tentatively propose that this Eisenstein series provides the exact contact potential on the twistor space over the universal hypermultiplet moduli space. We analyze its non-Abelian Fourier expansion, and show that the Abelian and non-Abelian Fourier coefficients take the required form for instanton corrections due to Euclidean D2- branes wrapping special Lagrangian submanifolds, and to Euclidean NS5-branes wrapping the entire Calabi-Yau threefold, respectively. While this tentative proposal fails to repro- duce the correct one-loop correction, the consistency of the Fourier expansion with physics expectations provides strong support for the usefulness of the Picard modular group in constraining the quantum moduli space.
THERAPEUTIC IMPLICATIONS OF COMPUTER MODELS OF BRAIN ACTIVITY FOR ALZHEIMER DISEASE

Neural models of large-scale brain processes help to explain many features of neuropsychological syndromes and psychiatric disease. Two associative memory models useful to understand some aspects of cognitive impairments in Alzheimer disease are discussed. The first model is based on the synaptic deletion and compensation while the second on the synaptic runaway phenomenon. The models seem to be complementary, explaining different types of Alzheimer disease. They allow to draw several therapeutic suggestions that may help to slow down the development of the disease in its early stages.
Learning Continuous Attractors in Recurrent Networks

One approach to invariant object recognition employs a recurrent neural network as an associative memory. In the standard depiction of the network's state space, memories of objects are stored as attractive fixed points of the dynamics. I argue for a modification of this picture: if an object has a continuous family of instantiations, it should be represented by a continuous attractor. This idea is illustrated with a network that learns to complete patterns. To perform the task of filling in missing information, the network develops a continuous attractor that models the manifold from which the patterns are drawn. From a statistical view-point, the pattern completion task allows a formulation of unsupervised learning in terms of regression rather than density estimation.
Error Analysis and Detection Procedures for a Hardware Implementation of the Advanced Encryption Standard

The goal of the Advanced Encryption Standard (AES) is to achieve secure communication. The use of AES does not, however, guarantee reliable communication. Prior work has shown that even a single transient error occurring during the AES encryption (or decryption) process will very likely result in a large number of errors in the encrypted/decrypted data. Such faults must be detected before sending to avoid the transmission and use of erroneous data. Concurrent fault detection is important not only to protect the encryption/decryption process from random faults. It will also protect the encryption/decryption circuitry from an attacker who may maliciously inject faults in order to find the encryption secret key. In this paper, we first describe some studies of the effects that faults may have on a hardware implementation of AES by analyzing the propagation of such faults to the outputs. We then present two fault detection schemes: The first is a redundancy-based scheme while the second uses an error detecting code. The latter is a novel scheme which leads to very efficient and high coverage fault detection. Finally, the hardware costs and detection latencies of both schemes are estimated.
Geometry-Adapted Hexahedral Meshes Improve Accuracy of Finite-Element-Method-Based EEG Source Analysis

Mesh generation in finite-element- (FE) method-based electroencephalography (EEG) source analysis generally influences greatly the accuracy of the results. It is thus important to determine a meshing strategy well adopted to achieve both acceptable accuracy for potential distributions and reasonable computation times and memory usage. In this paper, we propose to achieve this goal by smoothing regular hexahedral finite elements at material interfaces using a node-shift approach. We first present the underlying theory for two different techniques for modeling a current dipole in FE volume conductors, a subtraction and a direct potential method. We then evaluate regular and smoothed elements in a four-layer sphere model for both potential approaches and compare their accuracy. We finally compute and visualize potential distributions for a tangentially and a radially oriented source in the somatosensory cortex in regular and geometry-adapted three-compartment hexahedra FE volume conductor models of the human head using both the subtraction and the direct potential method. On the average, node-shifting reduces both topography and magnitude errors by more than a factor of 2 for tangential and 1.5 for radial sources for both potential approaches. Nevertheless, node-shifting has to be carried out with caution for sources located within or close to irregular hexahedra, because especially for the subtraction method extreme deformations might lead to larger overall errors. With regard to realistic volume conductor modeling, node-shifted hexahedra should thus be used for the skin and skull compartments while we would not recommend deforming elements at the grey and white matter surfaces.
Resistance of Foxp3+ Regulatory T Cells to Nur77-Induced Apoptosis Promotes Allograft Survival

The NR4A nuclear receptor family member Nur77 (NR4A1) promotes thymocyte apoptosis during negative selection of autoreactive thymocytes, but may also function in mature extrathymic T cells. We studied the effects of over-expression of Nur77 on the apoptosis of murine peripheral T cells, including thymic-derived Foxp3+ regulatory (Treg) cells. Overexpression of Nur77 in the T cell lineage decreased numbers of peripheral CD4 and CD8 T cells by ∼80% compared to wild-type (WT) mice. However, the proportions of Treg cells were markedly increased in the thymus (61% of CD4+Foxp3+ singly positive thymocytes vs. 8% in WT) and secondary lymphoid organs (40–50% of CD4+Foxp3+ T cells vs. 7–8% in WT) of Nur77 transgenic (Nur77Tg) mice, and immunoprecipitation studies showed Nur77 was associated with a recently identified HDAC7/Foxp3 transcriptional complex. Upon activation through the T cell receptor in vitro or in vivo, Nur77Tg T cells showed only marginally decreased proliferation but significantly increased apoptosis. Fully allogeneic cardiac grafts transplanted to Nur77Tg mice survived long-term with well-preserved structure, and recipient splenocytes showed markedly enhanced apoptosis and greatly reduced anti-donor recall responses. Allografts in Nur77Tg recipients had significantly increased expression of multiple Treg-associated genes, including Foxp3, Foxp1, Tip60 and HDAC9. Allograft rejection was restored by CD25 monoclonal antibody therapy, indicating that allograft acceptance was dependent upon Treg function in Nur77Tg recipients. These data show that compared to conventional CD4 and CD8 T cells, Foxp3+ Tregs are relatively resistant to Nur77-mediated apoptosis, and that tipping the balance between the numbers of Tregs and responder T cells in the early period post-transplantation can determine the fate of the allograft. Hence, induced expression of Nur77 might be a novel means to achieve long-term allograft survival.
VR is on the Edge: How to Deliver 360° Videos in Mobile Networks

VR/AR is rapidly progressing towards enterprise and end customers with the promise of bringing immersive experience to numerous applications. Soon it will target smartphones from the cloud and 360° video delivery will need unprecedented requirements for ultra-low latency and ultra-high throughput to mobile networks. Latest developments in NFV and Mobile Edge Computing reveal already the potential to enable VR streaming in cellular networks and to pave the way towards 5G and next stages in VR technology. In this paper we present a Field Of View (FOV) rendering solution at the edge of a mobile network, designed to optimize the bandwidth and latency required by VR 360° video streaming. Preliminary test results show the immediate benefits in bandwidth saving this approach can provide and generate new directions for VR/AR network research.
Inflammation in epilepsy: Clinical observations

Over the past decade, an increasing number of observations indicate that activation of inflammatory processes occurs in variety of focal epilepsies. Understanding the feature and consequences of neuroinflammation, including the contribution to development and perpetuation of seizures, as well as to mood or cognitive dysfunction, is a major requisite for delineating its role in epilepsy. The present article discusses the most recent observations supporting the involvement of the inflammatory response in human focal epilepsy. It also evaluates emerging evidence concerning the possibility to identify epilepsy‐associated inflammatory biomarkers in cerebrospinal fluid and serum, as well as the potential application of neuroimaging approaches to study the inflammatory reactions in chronic epilepsy patients in vivo, aiming to improve the recognition of appropriate patient populations who might benefit from antiinflammatory or immunomodulatory therapies.
Increased rectal mucosal enteroendocrine cells, T lymphocytes, and increased gut permeability following acuteCampylobacter enteritis and in post-dysenteric irritable bowel syndrome

BACKGROUND AND AIMS Post-dysenteric irritable bowel syndrome (PD-IBS) develops in up to 25% of patients followingCampylobacter enteritis. Our aim was to define the pathological basis of this subgroup of IBS. METHODS Twenty one patients (group 1) underwent serial rectal biopsy and gut permeability testing following acute Campylobacterenteritis as did 10 PD-IBS patients (group 2) and 12 asymptomatic controls. RESULTS In group 1, enteroendocrine cell (EC) numbers were markedly increased initially and at six and 12 weeks (p<0.001) compared with controls. Gut permeability, as assessed by the lactulose/mannitol ratio, was significantly elevated, initially and at 12 weeks (p<0.005). CD3, CD4, and CD8 lymphocyte counts in the lamina propria and intraepithelial lymphocytes (IEL) were significantly increased initially compared with controls. At visit 1, EC numbers were positively correlated with CD3 counts (r=0.6, p=0.01). At one year, seven subjects (five with persistent loose stools) had rectal biopsies which showed significantly elevated EC, CD3, and IEL counts. In group 2, EC and IEL counts were significantly increased compared with controls (p<0.001), as was gut permeability (p<0.01). CONCLUSION Increased EC, T lymphocytes, and gut permeability are acute changes followingCampylobacter enteritis which can persist for more than a year and may contribute to PD-IBS.
The Internal Sequence of the Peptide-Substrate Determines Its N-Terminus Trimming by ERAP1

Background Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims N-terminally extended antigenic peptide precursors down to mature antigenic peptides for presentation by major histocompatibility complex (MHC) class I molecules. ERAP1 has unique properties for an aminopeptidase being able to trim peptides in vitro based on their length and the nature of their C-termini. Methodology/Principal Findings In an effort to better understand the molecular mechanism that ERAP1 uses to trim peptides, we systematically analyzed the enzyme's substrate preferences using collections of peptide substrates. We discovered strong internal sequence preferences of peptide N-terminus trimming by ERAP1. Preferences were only found for positively charged or hydrophobic residues resulting to trimming rate changes by up to 100 fold for single residue substitutions and more than 40,000 fold for multiple residue substitutions for peptides with identical N-termini. Molecular modelling of ERAP1 revealed a large internal cavity that carries a strong negative electrostatic potential and is large enough to accommodate peptides adjacent to the enzyme's active site. This model can readily account for the strong preference for positively charged side chains. Conclusions/Significance To our knowledge no other aminopeptidase has been described to have such strong preferences for internal residues so distal to the N-terminus. Overall, our findings indicate that the internal sequence of the peptide can affect its trimming by ERAP1 as much as the peptide's length and C-terminus. We therefore propose that ERAP1 recognizes the full length of its peptide-substrate and not just the N- and C- termini. It is possible that ERAP1 trimming preferences influence the rate of generation and the composition of antigenic peptides in vivo.