Miracle-dz/UniFAR-FTUs huggingface dataset:
A formal performance modeling framework for bio-inspired ad hoc routing protocols

Bio-inspired ad hoc routing is an active area of research. The designers of these algorithms predominantly evaluate the performance of their protocols with the help of simulation studies. Such studies are mostly scenario and simulator specific and their results cannot be generalized to other scenarios and simulators. Therefore, we argue that mathematical tools should be utilized to develop a consistent, provable and compatible formal framework in order to provide an unbiased evaluation of Bio-inspired ad hoc routing protocols. Motivated by this requirement, in this paper, we develop a probabilistic performance evaluation framework that can be used to model the following key performance metrics of an ad hoc routing algorithm: (1) routing overhead, (2) route optimality, and (3) energy consumption. We utilize this framework to model a well known Bee-inspired routing protocol for ad hoc sensor networks, BeeSensor. We also show that the proposed framework is generic enough and can easily be adapted to even model a classical routing protocol, Ad Hoc on Demand Distance Vector (AODV). The modeled metrics of the two algorithms not only allow unbiased performance comparison but also provide interesting insights into the parameters governing the behavior of these routing protocols.
Telomere position effect is regulated by heterochromatin-associated proteins and NkuA in Aspergillus nidulans

Gene-silencing mechanisms are being shown to be associated with an increasing number of fungal developmental processes. Telomere position effect (TPE) is a eukaryotic phenomenon resulting in gene repression in areas immediately adjacent to telomere caps. Here, TPE is shown to regulate expression of transgenes on the left arm of chromosome III and the right arm of chromosome VI in Aspergillus nidulans. Phenotypes found to be associated with transgene repression included reduction in radial growth and the absence of sexual spores; however, these pleiotropic phenotypes were remedied when cultures were grown on media with appropriate supplementation. Simple radial growth and ascosporogenesis assays provided insights into the mechanism of TPE, including a means to determine its extent. These experiments revealed that the KU70 homologue (NkuA) and the heterochromatin-associated proteins HepA, ClrD and HdaA were partially required for transgene silencing. This study indicates that TPE extends at least 30 kb on chromosome III, suggesting that this phenomenon may be important for gene regulation in subtelomeric regions of A. nidulans.
Distributed data storage for opportunistic grids

Grid applications typically need to deal with large amounts of data. The traditional approach for data storage is to employ high-performance dedicated servers with data replication. However, a class of computational grids, called opportunistic grids, focus on the usage of idle resources from shared machines. These machines normally have large quantities of unused storage space that could be used when the machines are idle, allowing opportunistic grids to share not only computational cycles, but also storage space.In this work, we present the initial design of OppStore, a middleware that provides reliable storage using the free storage space from shared grid machines. The storage can be transparently accessed from any grid machine, allowing easy data sharing among grid users and applications. The system uses a two-level peer-to-peer organization to connect grid machines in a scalable and fault-tolerant way. To deal with resource heterogeneity, we developed the concept of virtual ids, which allows the creation of virtual spaces located on top of the peer-to-peer routing substrate. These virtual spaces enables the middleware to perform heterogeneity-aware, load-balancing selection of storage sites using multiple simultaneous metrics.
Blood pressure circadian pattern and physical exercise assessment by accelerometer and 7-day physical activity recall scale.

BACKGROUND The relationship between regular physical activity, measured objectively and by self-report, and the circadian pattern of 24-hour ambulatory arterial blood pressure (BP) has not been clarified. METHODS We performed a cross-sectional study in a cohort of healthy patients. We included 1,345 patients from the EVIDENT study (mean age 55 ± 14 years; 59.3% women). Physical activity was assessed using the 7-day physical activity recall (PAR) questionnaire (metabolic equivalents (MET)/hour/week) and the Actigraph GT3X accelerometer (counts/minute) for 7 days; ambulatory arterial BP was measured with a radial tonometer (B-pro device). RESULTS The dipper-pattern patients showed a higher level of activity than nondipper patients, as assessed by accelerometer and 7-day PAR. Physical activity measures correlated positively with the percent drop in systolic BP (SBP; ρ = 0.19 to 0.11; P < 0.01) and negatively with the systolic and diastolic sleep to wake ratios (ρ = -0.10 to -0.18; P < 0.01) and heart rate (ρ = -0.13; P < 0.01). In logistic regression, considering the circadian pattern (1, dipper; 0, nondipper) as the dependent variable, the odds ratio of the third tertile of counts/minute was 1.79 (95% confidence interval [CI], 1.35-2.38; P < 0.01) and of MET/hour/week was 1.33 (95% CI, 1.01-1.75; P = 0.04) after adjustment for confounding variables. CONCLUSIONS Physical activity, as evaluated by both the accelerometer and the 7-day PAR, was associated with a more marked nocturnal BP dip and, accordingly, a lower SBP and diastolic BP sleep to wake ratio. CLINICAL TRIAL REGISTRATION Clinical Trials.gov Identifier: NCT01083082.
Contrasting multi-synchronous MPSoC design styles for fine-grained clock domain partitioning: the full-HD video playback case study

Fine-grained (per-core) multi-synchronous systems calls for new clocking strategies and new architecture design techniques. This paper compares two fundamental multi-synchronous implementation variants based on the extensive use of dual-clock FIFOs vs mesochronous synchronizers respectively. The architecture-homogeneous experimental setting, the cost-effective merging of synchronizers with NoC switch buffers, the sharing of as many physical synthesis steps as possible between the two architectures and the requirements of a realistic full-HD video playback application are the key innovations of this study.
Influence of Repellent Finishing on the Surface Free Energy of Cellulosic Textile Substrates

The aim of this research is to investigate the influence of a fluorochemical repellent treatment with and without an added durable press finish on the surface free energy changes of a cellulosic textile substrate as well as the durability of the finishing agents. For this purpose, contact angles are measured based on the goniometric-sessile drop tech nique. Different theoretical models are chosen to calculate the solid surface free energy and its dispersive and polar components. A statistical evaluation of the results with ANOVA (P < 0.01 ) shows that the values of the surface free energy components of the finished textile substrate depend on a theoretical model as well as the chosen liquid combinations. Coating the textile substrate with fluoropolymer repellents alone and in combination with the durable press finish changes the highly hydrophilic polar cellulosic fabric into an almost apolar low energy solid. Laundering of the finished substrate in a surfactant aqueous solution decreases oil repellency, and a full rearrangement of the fluorocarbon polymer film on the textile surface is achieved after the heat treatment. What is also achieved is excellent durability of the fluoropolymer film on the textile substrate.
Introduction to constraint databases

This book is the first textbook on constraint databases. Its author, together with P. Kanellakis and G. Kuper, introduced constraint databases in 1990 as a powerful generalization of the relational database model. Constraints, such as linear or polynomial equalities and inequalities, are used to finitely represent possibly infinite sets of points. They provide an elegant way to combine classical relational data with, for instance, spatial or temporal data. Since the early 1990s, the topic of constraint databases has received considerable research interest, both theoretical and towards systems development, and has been present at most database conferences during the past decade. It turned out to be a rich area in which a combination of techniques from, e.g., logic, (finite) model theory, algebraic and computational geometry, topology, query languages and symbolic computation are applied. A comprehensive survey of the research results in this field appeared two years ago (Constraint databases, edited by G. Kuper, L. Libkin and J. Paredaens, Springer, 2000). Whereas this survey mainly addresses researchers, the present book aims at making the topic of constraint databases accessible to advanced undergraduate and beginning graduate students and mainly addresses constraint databases from a developer's point of view. This book will certainly contribute to the exposure of constraint databases to a wider audience and hopefully also to its proliferation in a broader database practice. Summary of the book This textbook presents the constraint database model as a powerful extension of the relational model that allows a user or programmer to work easily with infinite data. It covers a wide range of constraint formalisms and shows that the constraint model provides an elegant tool for data modeling and querying in application areas such as geographic information systems (GIS), spatiotemporal data management, bioinformatics, genome databases and computer vision. This book covers a substantial part of constraint-database theory, emphasizes several developer's issues, and presents a number of sample constraint database systems. The author starts by developing the constraint data model from the relational one. Next, he shows how familiar query languages, such as the relational algebra, SQL, and various forms of Datalog carry over to the constraint model. A third broad part of the book focuses on query evaluation and addresses theoretical topics such as quantifierelimination algorithms for several constraint languages and the complexity of query evaluation in these languages. Also more specific data models and query languages are addressed, e.g., for spatiotemporal database applications. Next, the book describes a sample linear constraint database system, a Boolean constraint database system, and a spatiotemporal database system. A last part of the book presents a number of sample applications.
Compositional analysis for the Multi-Resource Server

The Multi-Resource Server (MRS) technique has been proposed to enable predictable execution of memory intensive real-time applications on COTS multi-core platforms. It uses resource reservation approaches in the context of CPU-bandwidth and memory-bus bandwidth reservations to bound the interference between the applications running on the same core as well as between the applications running on different cores. In this paper we present a complete composable local and global schedulability analysis for the Multi-Resource Server technique. Based on the proposed analysis, we further provide an experimental study that investigates the behaviour of the MRS and identifies the factors that contribute mostly on the overall system performance.
Design strategies in mineralized biological materials

Organisms have been producing mineralized skeletons for the past 550 million years. They have evolved many different strategies for improving these materials at almost all hierarchical levels from Angstroms to millimetres. Key components of biological materials are the macromolecules, which are intimately involved in controlling nucleation, growth, shaping and adapting mechanical properties of the mineral phase to function. One interesting tendency that we have noted is that organisms have developed several strategies to produce materials that have more isotropic properties. Much can still be learned from studying the principles of structure–function relations of biological materials. Some of this information may also provide new ideas for improved design of synthetic materials.
A picture is worth a thousand keywords: image-based object search on a mobile platform

Finding information based on an object's visual appearance is useful when specific keywords for the object are not known. We have developed a mobile image-based search system that takes images of objects as queries and finds relevant web pages by matching them to similar images on the web. Image-based search works well when matching full scenes, such as images of buildings or landmarks, and for matching objects when the boundary of the object in the image is available. We demonstrate the effectiveness of a simple interactive paradigm for obtaining a segmented object boundary, and show how a shape-based image matching algorithm can use the object outline to find similar images on the web.
Investigation of the Microstructure of SiC-Zn Nanocomposites by Microscopic Methods: SEM, AFM and TEM

SiC-Zn nanocomposites with about 20% volume fraction of metal were fabricated by infiltration process under the pressure of 2-8 GPa and at the temperature of 400_1000oC. SiC nanopowders used in the experiments formed loosely agglomerated chains of single crystal nanoparticles. The dimension of the agglomerates was in the micrometer range, the mean grain size was up to tens of nanometers. Microstructural investigations of the nanocomposites were performed at a different resolution levels using scanning, transmission electron microscopy and atomic force microscopy techniques (SEM, TEM, AFM, respectively). SEM observations indicate a presence of nano-dispersed, uniform (on the micrometer scale) mixture of two phases. TEM observations show that distribution of SiC and Zn nanocrystallites is uniform on the nanometer scale. High-resolution TEM images demonstrate an existence of thin (on the order of tens of Angstroms) Zn layers separating SiC grains. AFM images of the mechanically polished samples show a smooth surface with the roughness on the order of the SiC grain size (10-30 nm). After ion etching of some samples the AFM topographs show surface irregularities: periodically spaced hillocks 50-100 nm in height. The size of the SiC grains remains equal to that of the initial powder crystallites. The size of the Zn grains varies in the range of 20-100 nm depending on the initial SiC grain size and the composite fabrication conditions.
MMI-MAP and MPE-MAP for acoustic model adaptation

This paper investigates the use of discriminative schemes based on themaximum mutual information (MMI) and minimum phone error (MPE) objective functions for both task and gender adaptation. A method for incorporating prior information into the discriminative training framework is described. If an appropriate form of prior distribution is used, then this may be implemented by simply altering the values of the counts used for parameter estimation. The prior distribution can be based around maximum likelihood parameter estimates, giving a technique known as I-smoothing, or for adaptation it can be based around a MAP estimate of the ML parameters, leading to MMI-MAP, or MPE-MAP.MMI-MAP isshown tobe effectivefor taskadaptation, where data from one task (Voicemail) is used to adapt a HMM set trained on another task (Switchboard). MPE-MAP is shown to be effective for generating gender-dependent models for Broadcast News transcription.
G Protein-coupled Receptor Kinase 6A Phosphorylates the Na+/H+ Exchanger Regulatory Factor via a PDZ Domain-mediated Interaction*

The Na+/H+exchanger regulatory factor (NHERF) is constitutively phosphorylated in cells, but the site(s) of this phosphorylation and the kinase(s) responsible for it have not been identified. We show here that the primary site of constitutive NHERF phosphorylation in human embryonic kidney 293 (HEK-293) cells is Ser289, and that the stoichiometry of phosphorylation is near 1 mol/mol. NHERF contains two PDZ domains that recognize the sequence S/T-X-L at the carboxyl terminus of target proteins, and thus we examined the possibility that kinases containing this motif might associate with and phosphorylate NHERF. Overlay experiments and co-immunoprecipitation studies revealed that NHERF binds with high affinity to a splice variant of the G protein-coupled receptor kinase 6, GRK6A, which terminates in the motif T-R-L. NHERF does not associate with GRK6B or GRK6C, alternatively spliced variants that differ from GRK6A at their extreme carboxyl termini. GRK6A phosphorylates NHERF efficiently on Ser289 in vitro, whereas GRK6B, GRK6C, and GRK2 do not. Furthermore, the endogenous “NHERF kinase” activity in HEK-293 cell lysates is sensitive to treatments that alter the activity of GRK6A. These data suggest that GRK6A phosphorylates NHERF via a PDZ domain-mediated interaction and that GRK6A is the kinase in HEK-293 cells responsible for the constitutive phosphorylation of NHERF.
Finite Phase-separation FRET II: Determination of domain size from simulated data

We have developed a new model to describe FRET efficiency (E FRET) between freely-diffusing membrane probes in phase-separated bilayers (Finite Phase-separation FRET, or FP-FRET), that in principle applies to any system where phase domain dimensions are larger than ~Ro . Here we use Monte Carlo techniques to simulate E FRET for a range of probe partitioning behaviors and domain sizes, and then fit the simulated data to the FP-FRET model to recover simulation parameters. We find that FP-FRET can determine domain size to within 5% of simulated values for domain diameters up to ~ 5Ro, and to within 15% for diameters up to ~ 20Ro . We also investigated the performance of the model in cases where specific model assumptions are not valid.
Detecting rare gene transfer events in bacterial populations

Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.
Autologous transplantation of bone marrow cells improves damaged heart function.

BACKGROUND Autologous bone marrow cells (BMCs) transplanted into ventricular scar tissue may differentiate into cardiomyocytes and restore myocardial function. This study evaluated cardiomyogenic differentiation of BMCs, their survival in myocardial scar tissue, and the effect of the implanted cells on heart function. METHODS AND RESULTS IN VITRO STUDIES BMCs from adult rats were cultured in cell culture medium (control) and medium with 5-azacytidine (5-aza, 10 micromol/L), TGFbeta1 (10 ng/mL), or insulin (1 nmol/L) (n=6, each group). Only BMCs cultured with 5-aza formed myotubules which stained positively for troponin I and myosin heavy chain. In vivo studies: a cryoinjury-derived scar was formed in the left ventricular free wall. At 3 weeks after injury, fresh BMCs (n=9), cultured BMCs (n=9), 5-aza-induced BMCs (n=12), and medium (control, n=12) were autologously transplanted into the scar. Heart function was measured at 8 weeks after myocardial injury. Cardiac-like muscle cells which stained positively for myosin heavy chain and troponin I were observed in the scar tissue of the 3 groups of BMC transplanted hearts. Only the 5-aza-treated BMC transplanted hearts had systolic and developed pressures which were higher (P<0.05) than that of the control hearts. All transplanted BMCs induced angiogenesis in the scar. CONCLUSIONS Transplantation of BMCs induced angiogenesis. BMCs cultured with 5-aza differentiated into cardiac-like muscle cells in culture and in vivo in ventricular scar tissue and improved myocardial function.
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads

Motivation: Datasets from high-throughput sequencing technologies have yielded a vast amount of data about organisms in environmental samples. Yet, it is still a challenge to assess the exact organism content in these samples because the task of taxonomic classification is too computationally complex to annotate all reads in a dataset. An easy-to-use webserver is needed to process these reads. While many methods exist, only a few are publicly available on webservers, and out of those, most do not annotate all reads. Results: We introduce a webserver that implements the naïve Bayes classifier (NBC) to classify all metagenomic reads to their best taxonomic match. Results indicate that NBC can assign next-generation sequencing reads to their taxonomic classification and can find significant populations of genera that other classifiers may miss. Availability: Publicly available at: http://nbc.ece.drexel.edu. Contact: gailr@ece.drexel.edu
Parametric methods for spatial signal processing in the presence of unknown colored noise fields

Two methods for estimation of noise correlations along an array of sensors are presented. Both rely on a parametric (autoregressive moving average) noise model. The model has the advantage of describing the noise correlations by a small number of parameters and can be applied to a great variety of physical noises. The first method is related to the calculation of the likelihood of whitened observations, and the second is related to Pisarenko's method (1973) applied to whitened observations. Both methods are obtained by optimization of a criterion and are iterative. The noise estimates can be used for sensor-output whitening and it then provides a means to improve array processing performance. The two methods perform well, both on simulated and real data. However, the first method seems simpler and more robust than the second. >