Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive Coding for Dynamic Visual Processing: Development of Functional Hierarchy in a Multiple Spatiotemporal Scales RNN Model

This letter proposes a novel predictive coding type neural network model, the predictive multiple spatiotemporal scales recurrent neural network (P-MSTRNN). The P-MSTRNN learns to predict visually perceived human whole-body cyclic movement patterns by exploiting multiscale spatiotemporal constraints imposed on network dynamics by using differently sized receptive fields as well as different time constant values for each layer. After learning, the network can imitate target movement patterns by inferring or recognizing corresponding intentions by means of the regression of prediction error. Results show that the network can develop a functional hierarchy by developing a different type of dynamic structure at each layer. The letter examines how model performance during pattern generation, as well as predictive imitation, varies depending on the stage of learning. The number of limit cycle attractors corresponding to target movement patterns increases as learning proceeds. Transient dynamics developing early in the learning process successfully perform pattern generation and predictive imitation tasks. The letter concludes that exploitation of transient dynamics facilitates successful task performance during early learning periods.
Brush border enzyme activities in relation to histological lesion in pediatric celiac disease

Background and Aim: In celiac disease (CD), abnormalities of brush border enzyme activities have been detected in the course of the disease activity. There are conflicting results on intestinal mucosal enzyme activities and its correlation to mucosal injury in CD. The aim of the present study was to evaluate the brush border enzyme activities (disaccharidases and alkaline phosphatase) in the duodenal mucosa of North Indian children with CD and to examine their correlation to duodenal mucosal morphological alterations.
Recent results in mathematical modeling and performance evaluation of disks and disk array

In the seventies and eighties extensive work on mathematical modeling and performance evaluation of disks and disk arrays was carried out. The main tools were stochastic and combinatorial analysis. For the combinatorial approach led by C. K. Wong and his collaborators the reader is urged to consult [11]. for the stochastic approach led by E. G. Coffman and his collaborators one should consult [3]. Both references provide rather extensive bibliographies. In the late eighties and the nineties with the coming of the RAID "revolution", most of the work in the area has become rather heuristic in nature, see [5] for a survey, with a few notable exceptions.In this abstract we would like to report on two recent results which relate performance and modeling issues in disks and disk arrays to the theory of metric spaces and the theory of graph evolution and phase transition. We hope this will revive the spirit of the work done in the seventies and eighties (in other walks of life this may not be advisable). The results are taken from [2] and [4]
Disk schedulers for solid state drivers

In embedded systems and laptops, flash memory storage such as SSDs (Solid State Drive) have been gaining popularity due to its low energy consumption and durability. As SSDs are flash memory based devices, their performance behavior differs from those of magnetic disks. However, little attention has been paid on how to exploit SSDs from the disk scheduling algorithm view point. In this paper, we first describe behaviors of SSDs that inspires us to design a new disk scheduler for the Linux operating system. Specifically, read service time is almost constant in an SSD while write service time is not. Moreover, appropriate grouping of write requests eliminates any ordering-related restrictions and also maximizes write performance. From these observations, we propose two disk schedulers: IRBW-FIFO and IRBW-FIFO-RP. Both schedulers arrange write requests into bundles of an appropriate size while read requests are independently scheduled. Then, the IRBW-FIFO scheduler provides complete FIFO ordering to each bundle of write requests and each individual read requests while the IRBW-FIFO-RP scheduler gives higher priority to read requests than the bundles of write requests. We implement these schedulers in Linux 2.6. 23, and results of executing our set of benchmark programs shows that performance improvements of up to 17% compared to existing Linux disk schedulers are achieved.
MPlot—a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins

MPlot is a webserver that provides a quick and easy way for structural biologists to analyze, visualize and plot tertiary structure contacts of helical membrane proteins. As input, experimentally determined or computationally modeled protein structures in PDB format are required. The automatic analysis concatenates in house tools to calculate cut-off dependent van der Waals contacts or crossing angles of transmembrane helices with third party tools to compute main chain or side chain hydrogen bonds or membrane planes. Moreover, MPlot allows new features and tools to be added on a regular basis. For that purpose, MPlot was embedded in a framework that facilitates advanced users to compose new workflows from existing tools, or to substitute intermediate results with results from their (own) tools. The outputs can be viewed online in a Jmol based protein viewer, or via automatically generated scripts in PyMOL. For further illustration, the results can be downloaded as a 2D graph, representing the spatial arrangement of transmembrane helices true to scale. For analysis and statistics, all results can be downloaded as text files that may serve as inputs for or as standard data to validate the output of knowledge based tertiary structure prediction tools. URL: http://proteinformatics.charite. de/mplot/.
Focalization and phase models for classical extensions of non-associative Lambek calculus

Lambek's non-associative syntactic calculus (NL) excels in its resource consciousness: the usual structural rules for weakening, contraction, exchange and even associativity are all dropped. Recently, there have been proposals for conservative extensions dispensing with NL's intuitionistic bias towards sequents with single conclusions: De Groote and Lamarche's classical non-associative Lambek calculus (CNL) and the Lambek-Grishin calculus (LG) of Moortgat and associates. We demonstrate Andreoli's focalization property for said proposals: a normalization result for Cut-free sequent derivations identifying to a large extent those differing only by trivial rule permutations. In doing so, we proceed from a `uniform' sequent presentation, deriving CNL from LG through the addition of structural rules. The normalization proof proceeds by the construction of syntactic phase models wherein every `truth' has a focused proof, similar to work of Okada and of Herbelin and Lee.
Secure Sensor Design Against Undetected Infiltration: Minimum Impact-Minimum Damage

We propose a new defense mechanism against undetected infiltration into controllers in cyber-physical systems. To this end, we cautiously design the outputs of the sensors that monitor the state of the system. Different from the defense mechanisms that seek to detect infiltration, the proposed approach seeks to minimize the damage of possible attacks before they have been detected. Controller of a cyber-physical system could have been infiltrated into by an undetected attacker at any time of the operation. Disregarding such a possibility and disclosing system's state without caution benefits the attacker in his/her malicious objective. Therefore, secure sensor design can improve the security of cyber-physical systems further when incorporated along with other defense mechanisms. We, specifically, consider a controlled Gauss-Markov process, where the controller could have been infiltrated into at any time within the system's operation. In the sense of game-theoretic hierarchical equilibrium, we provide a semi-definite programming based algorithm to compute the optimal linear secure sensor outputs and analyze the performance for various scenarios numerically.
Tidal flows, sill dynamics, and mixing in the Canadian Arctic Archipelago

The transport of low-salinity waters through the Canadian Arctic Archipelago links the North Pacific, Arctic, and North Atlantic Oceans. This transport is influenced by many related small-scale processes including mixing, internal hydraulics, and internal tide generation. In this thesis, I quantify and elucidate the physics of such processes with aims of addressing discrepancies between observed and simulated fluxes through the Archipelago and advancing the skill of numerical models by identifying shortcomings and informing where and how progress can be achieved. To address the dearth of mixing rates across the network of channels, I first use a large-scale model to obtain baseline estimates of the spatial and seasonal variability of the vertical buoyancy flux. Much of the mixing occurs in the eastern half of the Archipelago and is attributed to the abundance of sills and narrow channels. Indeed, the so-called ’central sills area’ is shown to be a mixing hot spot. I investigate this region further using high-spatial-resolution observational transects to examine the role of tides, which are excluded from the large-scale model. The many shallow channels here accelerate tidal currents and thereby induce strong bottom boundary layer dissipation. This is the largest energy sink within an observationally constrained energy budget. The generation of internal tides is another primary sink of barotropic tidal energy. Because the study site lies poleward of the critical latitudes of the dominant tidal constituents, internal tides propagate as internal Kelvin waves. Idealized, process-oriented modelling demonstrates that the amplitudes of such waves, or similarly the energy extracted from the barotropic tide, is sensitive to channel width because waves generated at each side of the channel interfere. Given the multiple connecting channels of the Archipelago, it is difficult to make a priori estimates of internal tide generation for a given channel. Nevertheless, the phenomenology I describe will be detectable in, and a requisite to understanding, pan-Arctic or global three-dimensional tidal models, which are becoming more prevalent.
Coloring graphs with fixed genus and girth

It is well known that the maximum chromatic number of a graph on the orientable surface Sg is 0(g1/2). We prove that there are positive constants Cl, C2 such that every triangle-free graph on Sg has chromatic number less than c2(g/ log(g))1/3 and that some triangle-free graph on Sg has chromatic number at least cl l/g3) . We obtain similar results for graphs with restricted clique number or girth on Sg or Nk. As an application, we prove that an Sg-polytope has chromatic number at most 0(g3/7). For specific surfaces we prove that every graph on the double torus and of girth at least six is 3-colorable and we characterize completely those triangle-free projective graphs that are not 3-colorable.
Projection particle swarm optimizer

In this paper, a novel particle swarm optimizer is developed by introducing projection operators described by projection matrices into the algorithm. Under the projection operators, the particles will oscillate along the directions determined by the projection operators to enhance global explorations. At the same time, the particles explore locally the optimal solutions when they are close to the global best solution. Moreover, two oscillation factors are introduced into the standard particle swarm optimizer to depict the particles' oscillation amplitudes. Simulations on several benchmark functions and system approximation illustrate the significant and effective impact of the two projection parts on the particle swarm optimizer.
Joy’s Law, Anti-Hale classifications, and the evolution of emerging sunspot regions

This thesis aims to use analysis of the time dependence of sunspot locations and other physical characteristics to provide an improved empirical basis for understanding solar magnetic fields. Bipolar active regions in both hemispheres tend to be tilted with respect to the East–West Equator of the Sun in accordance with Joy’s law, which describes the average tilt angle as a function of latitude. We recommend a revision of Joy’s law towards a weaker dependence on latitude (slope of 0.13–0.26) and without forcing the tilt to zero at the Equator. We determine that the hemispheric mean tilt value of active regions varies with each solar cycle but mean tilt angles do not show a dependence on longitude for any hemisphere or cycle. We also explore the visual representation of magnetic tilt angles on a traditional butterfly diagram to show that the average latitude of anti-Hale regions does not differ from the average latitude of all regions in both hemispheres. The distribution of anti-Hale sunspot tilt angles is broadly distributed between 0 and 360° with a weak preference for east-west alignment 180° from their expected Joy’s law angle. Anti-Hale sunspots display a log-normal size distribution similar to that of all sunspots, indicating no preferred size for anti- Hale spots. In addition, we report that 8.4%±0.8% of all bipolar sunspot regions are misclassified as Hale in traditional catalogues. This percentage is slightly higher for groups within 5° of the Equator due to the misalignment of the magnetic and heliographic equators. We also investigate bipolar sunspot regions and how tilt angle and footpoint separation vary during emergence and decay, finding that within ±48 hours of the time of peak umbral area, large regions steadily increase in tilt angle, midsize regions are nearly constant, and small regions show evidence of negative tilt during emergence. A period of growth in footpoint separation occurs over a 72-hour period for all of the regions from roughly 40 to 70 Mm. The smallest bipoles are outliers in that they do not obey Joy’s law and have a much smaller footpoint separation. We confirm previous research that the sunspots appear to be two distinct populations, where the smallest spots are potentially supergranular precursors to the more familiar flux tube sunspots. In summary, this thesis has revealed increased complexity in sunspot behavior compared to previous studies and demonstrates that analysis of sunspot observations continues to provide an empirical basis for improved models of small-scale solar flux tubes and the underlying magnetic dynamo.
Dynamics of genome size evolution in birds and mammals

Significance Deciphering the forces and mechanisms modulating genome size is central to our understanding of molecular evolution, but the subject has been understudied in mammals and birds. We took advantage of the recent availability of genome sequences for a wide range of species to investigate the mechanism underlying genome size equilibrium over the past 100 million years. Our data provide evidence for an “accordion” model of genome size evolution in birds and mammals, whereby the amount of DNA gained by transposable element expansion, which greatly varies across lineages, was counteracted by DNA loss through large segmental deletions. Paradoxically, birds and bats have more compact genomes relative to their flightless relatives but exhibit more dynamic gain and loss of DNA. Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified “accordion” model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
Evidence for a ppGpp‐binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin‐binding domain

On amino acid starvation, Escherichia coli cells exhibit an adaptive facility termed the stringent response. This is characterized by the production of high levels of a regulatory nucleotide, ppGpp, and concomitant curtailment in rRNA synthesis. Various studies reported earlier indicated that RNA polymerase is the site of action of ppGpp although a direct demonstration of the interaction of ppGpp with E. coli RNA polymerase is still lacking. Here we report the labelling of PpGpp with a fluorescent probe, 1‐aminonapthalene‐5‐sulphonate (AmNS), at the terminal phosphates. AmNS‐ppGpp responded much like a ppGpp molecule in an in vitro total transcription assay at selective promoters. Fluorescence titration of the tryptophan emission of RNA polymerase by AmNS‐ppGpp indicated a unique binding site in the absence of template DNA. Competition experiments showed that unlabelled ppGpp binds to the enzyme at the same site. Sigma factor seems to have no effect on this binding. The titration profile is also characterized by a single slope in the Scatchard analysis. The presence of GTP or GDP does not influence the binding of AmNS‐ppGpp with RNA polymerase. Forster's distance measurement was carried out which placed AmNS‐ppGpp 27Å away from the rifampicin‐binding domain of RNA polymerase.
Distributed applications for collaborative augmented reality

This paper focuses on the distributed architecture of the collaborative augmented reality system Studierstube. The system allows multiple users to experience a shared 3D workspace populated by multiple applications using see-through head mounted displays or other presentation media such as projection systems. The system design is based on a distributed shared scene graph that alleviates the application programmer from explicitly considering distribution, and avoids a separation of graphical and application data. The idea of unifying all system data in the scene graph is taken to its logical consequence by implementing application instances as nodes in the scene graph. Through the distributed shared scene graph mechanism, consistency of scene graph replicas and the contained application nodes is assured. Multi-user 3D widgets allow concurrent interaction with minimal coordination effort from the application. Special interest is paid to migration of application nodes from host to host allowing dynamic workgroup management, such as load balancing, late joining and early exit of hosts, and some firms of ubiquitous computing.
Myths and Realities of Respondent Engagement in Online Surveys

This paper describes an experiment in which a single questionnaire was fielded in four different styles of presentation: Text Only, Decoratively Visual, Functionally Visual and Gamified. Respondents were randomly assigned to only one presentation version. To understand the effect of presentation style on survey experience and data quality, we compared response distributions, respondent behaviour (such as time to complete), and self-reports regarding the survey experience and level of engagement across the four experimental presentations. While the functionally visual and gamified treatments produced higher satisfaction scores from respondents, we found no real differences in respondent engagement measures. We also found few differences in response patterns.
Inducible nitric oxide synthase (iNOS) in sinonasal polyp pathogenesis.

OBJECTIVES We investigated the role of inducible nitric oxide synthase (iNOS) in the pathogenesis of sinonasal polyps. METHODS Adult patients (21 men, 3 women) with nasal polyposis underwent functional endoscopic sinus surgery. Nine adults without polyps (6 men) who underwent septoplasty and/or rhinoplasty served as controls. Polyp specimens came from three regions: the maxillary sinus (10), ethmoid sinus (14), and nasal cavity (10). Control group samples (9) came from the inferior turbinate. Specimens were evaluated in eight mucosal layers for count and distribution of inflammatory cells and iNOS expression. An iNOS positivity index (PI) was determined for the epithelium (E), subepithelial layer of the lamina propria (SE), and deep paraglandular layer of the mucosa (D). RESULTS Polymorphonuclear cell (PMNC) % values of the ethmoid and maxillary sinus and overall ethmoid sinus PI were significantly higher in the polyp group. Patients with longer polyp duration, D-perivascular (D-pv), and a higher Brinkmann index had decreased ethmoid sinus D PIs. However, in older patients and patients with longer polyp duration, perivascular PIs increased in maxillary sinus SE and D, respectively. Furthermore, as PMNC % and iNOS-PMNC PI increased, SE_glandular and epithelial_apical iNOS values decreased. In the ethmoid and maxillary sinuses, iNOS_D_. endothelial values increased but decreased in the nasal cavity. CONCLUSIONS iNOS may play a role in sinonasal polyp pathogenesis, especially in mucosal SE and D layers. Increased vascular permeability, stromal edema, inflammatory cell migration into the stroma of the mucosa, and increased mucosal gland secretion may result in polyp formation.
Group Sparse Reconstruction of Multi-Dimensional Spectroscopic Imaging in Human Brain in vivo

Four-dimensional (4D) Magnetic Resonance Spectroscopic Imaging (MRSI) data combining 2 spatial and 2 spectral dimensions provides valuable biochemical information in vivo; however, its 20–40 min acquisition time is too long to be used for a clinical protocol. Data acquisition can be accelerated by non-uniformly under-sampling (NUS) the ky− t1 plane, but this causes artifacts in the spatial-spectral domain that must be removed by non-linear, iterative reconstruction. Previous work has demonstrated the feasibility of accelerating 4D MRSI data acquisition through NUS and iterative reconstruction using Compressed Sensing (CS), Total Variation (TV), and Maximum Entropy (MaxEnt) reconstruction. Group Sparse (GS) reconstruction is a variant of CS that exploits the structural sparsity of transform coefficients to achieve higher acceleration factors than traditional CS. In this article, we derive a solution to the GS reconstruction problem within the Split Bregman iterative framework that uses arbitrary transform grouping patterns of overlapping or non-overlapping groups. The 4D Echo-Planar Correlated Spectroscopic Imaging (EP-COSI) gray matter brain phantom and in vivo brain data are retrospectively under-sampled 2×, 4×, 6×, 8×, and 10___ and reconstructed using CS, TV, MaxEnt, and GS with overlapping or non-overlapping groups. Results show that GS reconstruction with overlapping groups outperformed the other reconstruction methods at each NUS rate for both phantom and in vivo data. These results can potentially reduce the scan time of a 4D EP-COSI brain scan from 40 min to under 5 min in vivo.