Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Single-Pulse Observations of Radio Pulsars: V. On the Broadband Nature of The Pulse Nulling Phenomenon in PSR B1133+16

Aims. In this paper we revisit the well-known phenomenon of pulse nulling using high-quality single-pulse data of PSR B1133+16 from simultaneous multifrequency observations. Methods. Observations were made at 325, 610, 1400 and 4850 MHz as part of a joint program between the European Pulsar Network (EPN) and the Giant Metrewave Radio Telescope (GMRT). The pulse energy time series are analysed to derive improved statistics of nulling pulses as well as to investigate the frequency dependence of the phenomenon. Results. The pulsar is observed to be in null state for approximately 15% of the time; however, we find that nulling does not always occur simultaneously at all four frequencies of observation. We characterise the statistics of such “selective nulling” as a function of frequency, separation in frequency, and combination of frequencies. The most remarkable case of such selective nulling seen in our data is a significantly large number of nulls (≈6%) at lower frequencies, that are marked by the presence of a fairly narrow emission feature at the highest frequency of 4850 MHz. We refer to these as “low frequency (LF) nulls”. We characterise the properties of high frequency (HF) emission at the occurrence of LF nulls, and compare and contrast them with that of “normal emission” at 4850 MHz. Our analysis shows that this high frequency emission tends to occur preferentially over a narrow range in longitude and with pulse widths typically of the order of a few milliseconds. We discuss the implications of our results for the pulsar emission mechanism in general and for the broadbandness of nulling phenomenon in particular. Our results signify the presence of an additional process of emission which does not turn off when the pulsar nulls at low frequencies, and becomes more prominent at higher frequencies. Our analysis also hints at a possible outer gap origin for this new population of pulses, and thus a likely connection to some high-energy emission processes that occur in the outer parts of the pulsar magnetosphere.
Insights in 17β-HSD1 Enzyme Kinetics and Ligand Binding by Dynamic Motion Investigation

Background Bisubstrate enzymes, such as 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1), exist in solution as an ensemble of conformations. 17β-HSD1 catalyzes the last step of the biosynthesis of estradiol and, thus, it is a potentially attractive target for breast cancer treatment. Methodology/Principal Findings To elucidate the conformational transitions of its catalytic cycle, a structural analysis of all available crystal structures was performed and representative conformations were assigned to each step of the putative kinetic mechanism. To cover most of the conformational space, all-atom molecular dynamic simulations were performed using the four crystallographic structures best describing apoform, opened, occluded and closed state of 17β-HSD1 as starting structures. With three of them, binary and ternary complexes were built with NADPH and NADPH-estrone, respectively, while two were investigated as apoform. Free energy calculations were performed in order to judge more accurately which of the MD complexes describes a specific kinetic step. Conclusions/Significance Remarkably, the analysis of the eight long range trajectories resulting from this multi-trajectory/-complex approach revealed an essential role played by the backbone and side chain motions, especially of the βFαG′-loop, in cofactor and substrate binding. Thus, a selected-fit mechanism is suggested for 17β-HSD1, where ligand-binding induced concerted motions of the FG-segment and the C-terminal part guide the enzyme along its preferred catalytic pathway. Overall, we could assign different enzyme conformations to the five steps of the random bi-bi kinetic cycle of 17β-HSD1 and we could postulate a preferred pathway for it. This study lays the basis for more-targeted biochemical studies on 17β-HSD1, as well as for the design of specific inhibitors of this enzyme. Moreover, it provides a useful guideline for other enzymes, also characterized by a rigid core and a flexible region directing their catalysis.
MATCHING AND MERGING ANONYMOUS TERMS FROM WEB SOURCES

This paper describes a workflow of simplifying and matching special language terms in RDF generated from trawling term candidates from Web terminology sites with TermFactory, a Semantic Web framework for professional terminology. Term candidates from such sources need to be matched and eventually merged with resources already in TermFactory. While merging anonymous data, it is important not to lose track of provenance. For coding provenance in RDF, TF uses a minor but apparently novel variant of RDF reification. In addition, TF implements a toolkit of methods for dealing with graphs containing anonymous (blank) nodes.
FACT: fast communication trace collection for parallel applications through program slicing

A proper understanding of communication patterns of parallel applications is important to optimize application performance and design better communication subsystems. Communication patterns can be obtained by analyzing communication traces. However, existing approaches to generate communication traces need to execute the entire parallel applications on full-scale systems that are time-consuming and expensive. In this paper, we propose a novel technique, called Fact, which can perform FAst Communication Trace collection for large-scale parallel applications on small-scale systems. Our idea is to reduce the original program to obtain a program slice through static analysis, and to execute the program slice to acquire the communication traces. The program slice preserves all the variables and statements in the original program relevant to spatial and volume communication attributes. Our idea is based on an observation that most computation and message contents in message-passing parallel applications are independent of these attributes, and therefore can be removed from the programs for the purpose of communication trace collection. We have implemented Fact and evaluated it with NPB programs and Sweep3D. The results show that Fact can preserve the spatial and volume communication attributes of original programs and reduce resource consumptions by two orders of magnitude in most cases. For example, Fact collects the communication traces of the Sweep3D for 512 processes on a 4-node (32 cores) platform in just 6.79 seconds, consuming 1.25 GB memory, while the original program takes 256.63 seconds and consumes 213.83 GB memory on a 32-node (512 cores) platform. Finally, we present an application of Fact.
Hypertension After Preeclampsia Is Preceded by Changes in Cardiac Structure and Function

Preeclampsia is associated with a 4-fold higher risk for developing remote chronic hypertension. Preeclampsia is accompanied by left ventricular hypertrophy and decreased diastolic function, which may or may not resolve postpartum. We tested the hypothesis that increased measures of cardiac geometry and decreased cardiac function persisting for ≥6 months postpartum in normotensive women with a history of preeclampsia precede the development of later chronic hypertension. Formerly preeclamptic women (n=652) underwent echocardiography at 9 months (range, 6–19) postpartum. We excluded women with preexisting hypertension (n=42), hypertension at the postpartum screening (n=133), and those that did not return any checklist (n=128). Eventually, 349 women were included. Remote health was evaluated by a biennially checklist. We used Cox regression for analysis. Twenty-seven (8%) normotensive women had developed chronic hypertension during a medium follow-up period of 6 years. At screening they differed from their counterparts who remained normotensive by hazard ratio for left ventricular mass index (1.11; 95% confidence interval [CI], 1.03–1.18), diastolic blood pressure (1.13; 95% CI, 1.06–1.20), systolic blood pressure (1.07; 95% CI, 1.02–1.11), mean arterial pressure (1.11; 95% CI, 1.05–1.18), heart rate (1.05; 95% CI, 1.01–1.10), and E/A ratio (0.22; 95% CI, 0.06–0.85). Backward stepwise analysis showed independent hazard ratio for left ventricular mass index and diastolic blood pressure 1.08 (95% CI, 1.01–1.16) and 1.13 (95% CI, 1.06–1.21), respectively. In conclusion, the development of later chronic hypertension in initially normotensive formerly preeclamptic women is preceded by increased left ventricular mass index and diastolic blood pressure at postpartum screening.
Performance of AI algorithms for mining meaningful roles

Role-based access control (RBAC) is being today's dominant access control model due to its potential to mitigate the complexity and cost of access control administration. However, the migration from the access control lists (ACL) to RBAC for a large administration system may consume significant efforts, which challenges the adoption of RBAC. Role mining algorithms can significantly reduce the migration cost by providing a partially automatic construction of an RBAC policy. This paper explores Artificial Intelligence (AI) techniques in designing role mining algorithms, which can optimize policy quality in terms of policy size, user-attribute-based interpretability of the roles, and the combination of size and interpretability. We propose two algorithms, genetic algorithm (GA)-based and ant colony optimization (ACO)-based. GA-based algorithm works by starting with a set of all candidate roles and repeatedly removing roles. ACO-based algorithm works by starting with an empty policy and repeatedly adding candidate roles. We carry out extensive experiments with publicly available access control policies. The simulation results indicate that ®the proposed algorithms achieves better performance than the corresponding existing algorithms. (2) GA-based approach produces better results than ACO-based approach. □
Modernizing WAAS

The Wide Area Augmentation System (WAAS) became operational on July 10, 2003. Currently this system provides en-route through non-precision approach guidance. Further, the signals are capable of providing vertical guidance to bring an aircraft within 250 feet of the ground. WAAS offers significant benefit to both aviation and non-aviation users. However, the vertical guidance availability is vulnerable to disturbances in the ionosphere and to GPS satellite outages. Fortunately, solutions to these limitations are well underway in the form of GPS modernization and Galileo. GPS modernization will provide two civil frequencies that enable users to directly estimate and remove ionospheric effects. Galileo will provide many additional ranging sources that will make the user more robust to the loss of an individual one. Naturally, WAAS should also be modernized to take advantage of these new signals. We investigate different methods to incorporate the signals and model their improvement to the aviation user. The best performance comes to a fully modernized user who can incorporate both civil frequencies and both constellations (GPS and Galileo). However, there is still significant benefit to legacy users who can only receive single frequency GPS signals. By upgrading the WAAS Reference Station (WRS) receivers to measure Galileo signals we can double our sampling of the ionosphere. The increased sampling translates into smaller broadcast confidence values on the single frequency ionospheric corrections. These lower values lead to higher availability. Similarly, the L5 signal has better noise properties and can be acquired at a lower elevation angle. This leads less uncertainty in the ionospheric measurements and to smaller confidence values. Before the modernized GPS and the Galileo constellations are complete, we can take advantage of the first new satellites. Users who can recognize the signals can begin to take advantage of them if proper correction information is broadcast. Legacy users will begin to see confidences improve as the new signals are mixed in with the old. The airborne noise and multipath confidence factor will grow in importance. Currently, it is the smallest term in the protection level calculation. For a dual frequency user it may become the largest. Efforts are underway to better characterize this airborne environment. The level of service offered by the end state system will depend on the final curve used to bound the error.
HDL Interfere with the Binding of T Cell Microparticles to Human Monocytes to Inhibit Pro-Inflammatory Cytokine Production

Background Direct cellular contact with stimulated T cells is a potent mechanism that induces cytokine production in human monocytes in the absence of an infectious agent. This mechanism is likely to be relevant to T cell-mediated inflammatory diseases such as rheumatoid arthritis and multiple sclerosis. Microparticles (MP) generated by stimulated T cells (MPT) display similar monocyte activating ability to whole T cells, isolated T cell membranes, or solubilized T cell membranes. We previously demonstrated that high-density lipoproteins (HDL) inhibited T cell contact- and MPT-induced production of IL-1β but not of its natural inhibitor, the secreted form of IL-1 receptor antagonist (sIL-1Ra). Methodology/Principal Findings Labeled MPT were used to assess their interaction with monocytes and T lymphocytes by flow cytometry. Similarly, interactions of labeled HDL with monocytes and MPT were assessed by flow cytometry. In parallel, the MPT-induction of IL-1β and sIL-1Ra production in human monocytes and the effect of HDL were assessed in cell cultures. The results show that MPT, but not MP generated by activated endothelial cells, bond monocytes to trigger cytokine production. MPT did not bind T cells. The inhibition of IL-1β production by HDL correlated with the inhibition of MPT binding to monocytes. HDL interacted with MPT rather than with monocytes suggesting that they bound the activating factor(s) of T cell surface. Furthermore, prototypical pro-inflammatory cytokines and chemokines such as TNF, IL-6, IL-8, CCL3 and CCL4 displayed a pattern of production induced by MPT and inhibition by HDL similar to IL-1β, whereas the production of CCL2, like that of sIL-1Ra, was not inhibited by HDL. Conclusions/Significance HDL inhibit both MPT binding to monocytes and the MPT-induced production of some but not all cytokines, shedding new light on the mechanism by which HDL display their anti-inflammatory functions.
Base-delta-immediate compression: Practical data compression for on-chip caches

Cache compression is a promising technique to increase on-chip cache capacity and to decrease on-chip and off-chip bandwidth usage. Unfortunately, directly applying well-known compression algorithms (usually implemented in software) leads to high hardware complexity and unacceptable decompression/compression latencies, which in turn can negatively affect performance. Hence, there is a need for a simple yet efficient compression technique that can effectively compress common in-cache data patterns, and has minimal effect on cache access latency.
Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis

MOTIVATION Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by sufficiently detailed experiment descriptions. However, in many databases a substantial number of these annotations is in free-text format and not readily accessible to computer-aided analysis. RESULTS The Multi-Conditional Hybridization Intensity Processing System (M-CHIPS), a data warehousing concept, focuses on providing both structure and algorithms suitable for statistical analysis of a microarray database's entire contents including the experiment annotations. It addresses the rapid growth of the amount of hybridization data, more detailed experimental descriptions, and new kinds of experiments in the future. We have developed a storage concept, a particular instance of which is an organism-specific database. Although these databases may contain different ontologies of experiment annotations, they share the same structure and therefore can be accessed by the very same statistical algorithms. Experiment ontologies have not yet reached their final shape, and standards are reduced to minimal conventions that do not yet warrant extensive description. An ontology-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure. AVAILABILITY AND SUPPLEMENTARY INFORMATION http://www.dkfz. de/tbi/services/mchips
Tbx2 Directly Represses the Expression of the p21WAF1 Cyclin-Dependent Kinase Inhibitor

T-box factors play a crucial role in the development of many tissues, and mutations in T-box factor genes have been implicated in multiple human disorders. Some T-box factors have been implicated in cancer; for example, Tbx2 and Tbx3 can suppress replicative senescence, whereas Tbx3 can cooperate with Myc and Ras in cellular transformation. The p21WAF1 cyclin-dependent kinase inhibitor plays a key role in senescence and in cell cycle arrest after DNA damage. Here, using a combination of in vitro DNA-binding, transfection, and chromatin immunoprecipitation assays, we show that Tbx2 can bind and repress the p21 promoter in vitro and in vivo. Moreover, small interfering RNA-mediated down-regulation of Tbx2 expression results in a robust activation of p21 expression. Taken together, these results implicate Tbx2 as a novel direct regulator of p21 expression and have implications for our understanding of the role of T-box factors in the regulation of senescence and oncogenesis, as well as in development.
2 . 2 Stage 2 : Routing-Bottlenecks Computation

We make a case for packet-replay suppression at the network layer, a concept that has been generally neglected. Our contribution is twofold. First, we demonstrate a new attack, the router-reflection attack, that can be launched using compromised routers. In this attack, a compromised router degrades the connectivity of a remote Internet region just by replaying packets. The attack is feasible even if all packets are attributed to their sources, i.e., source authentication is in place, and our evaluation shows that the threat is pervasive—candidate routers for compromise are in the order of hundreds or thousands. Second, we design an in-network mechanism for replay suppression. We start by showing that designing such a mechanism poses unsolved challenges and simple adaptations of end-to-end solutions are not sufficient. Then, we devise, analyze, and implement a highly efficient protocol that suppresses replayed traffic at the network layer without global time synchronization. Our softwarerouter prototype can saturate a 10 Gbps link using only two CPU cores for packet processing.
Combined use of a novel dried cross-linked amniotic membrane and tissue adhesive to conjunctival defect following multiple trabeculectomy

A 74-year-old woman underwent trabeculectomy with mitomycin C in the left eye. A large conjunctival defect with aqueous leakage suddenly developed 2 days postoperatively. The patient had undergone extracapsular cataract extraction and five previous trabeculectomy procedures in the left eye. Amniotic membrane dried by a new method (Hyper-dry), then cross-linked by glutaraldehyde was inserted underneath the conjunctival bleb through the conjunctival defect site and 2-octyl cyanoacrylate adhesive was applied to the surrounding area inside the conjunctival defect edge to secure the amniotic membrane to the conjunctiva. The bare surface of the transplanted amniotic membrane was gradually covered with conjunctival epithelia and the defect was completely sealed14days later. The dried, cross-linked amniotic membrane did not dissolve during the 24-month follow-up period. This procedure may become a superior method of treating conjunctival defect following trabeculectomy and the novel dried cross-linked amniotic membrane appears to be a useful therapeutic material for glaucoma surgery.
DNA damage bypass operates in the S and G2 phases of the cell cycle and exhibits differential mutagenicity

Translesion DNA synthesis (TLS) employs low-fidelity DNA polymerases to bypass replication-blocking lesions, and being associated with chromosomal replication was presumed to occur in the S phase of the cell cycle. Using immunostaining with anti-replication protein A antibodies, we show that in UV-irradiated mammalian cells, chromosomal single-stranded gaps formed in S phase during replication persist into the G2 phase of the cell cycle, where their repair is completed depending on DNA polymerase ζ and Rev1. Analysis of TLS using a high-resolution gapped-plasmid assay system in cell populations enriched by centrifugal elutriation for specific cell cycle phases showed that TLS operates both in S and G2. Moreover, the mutagenic specificity of TLS in G2 was different from S, and in some cases overall mutation frequency was higher. These results suggest that TLS repair of single-stranded gaps caused by DNA lesions can lag behind chromosomal replication, is separable from it, and occurs both in the S and G2 phases of the cell cycle. Such a mechanism may function to maintain efficient replication, which can progress despite the presence of DNA lesions, with TLS lagging behind and patching regions of discontinuity.
Robustness of Local Binary Patterns in Brain MR Image Analysis

The aging population in developed countries has shifted considerable research attention to diseases related to age. Because age is one of the highest risk factors for neurodegenerative diseases, the need for automated brain image analysis has significantly increased. Magnetic resonance imaging (MRI) is a commonly used modality to image brain. MRI provides high tissue contrast; hence, the existing brain image analysis methods have often preferred the intensity information to others, such as texture. Recently, an easy-to- compute texture descriptor, local binary pattern (LBP), has shown promise in various applications outside the medical field. In this paper, after extensive experiments, we show that rotation-invariant LBP is invariant to some common MRI artifacts that makes it possible to use it in various high-level brain MR image analysis applications.
INVERTING WEAK DIHOMOTOPY EQUIVALENCE USING HOMOTOPY CONTINUOUS FLOW

A flow is homotopy continuous if it is indefinitely divisible up to S-homo- topy. The full subcategory of cofibrant homotopy continuous flows has nice features. Not only it is big enough to contain all dihomotopy types, but also a morphism between them is a weak dihomotopy equivalence if and only if it is invertible up to dihomotopy. Thus, the category of cofibrant homotopy continuous flows provides an implementation of Whitehead's theorem for the full dihomotopy relation, and not only for S-homotopy as in previous works of the author. This fact is not the consequence of the existence of a model structure on the category of flows because it is known that there does not exist any model structure on it whose weak equivalences are exactly the weak dihomotopy equivalences. This fact is an application of a general result for the localization of a model category with respect to a weak factorization system.