Miracle-dz/UniFAR-FTUs huggingface dataset:
A unified view on weakly correlated recurrent networks

The diversity of neuron models used in contemporary theoretical neuroscience to investigate specific properties of covariances in the spiking activity raises the question how these models relate to each other. In particular it is hard to distinguish between generic properties of covariances and peculiarities due to the abstracted model. Here we present a unified view on pairwise covariances in recurrent networks in the irregular regime. We consider the binary neuron model, the leaky integrate-and-fire (LIF) model, and the Hawkes process. We show that linear approximation maps each of these models to either of two classes of linear rate models (LRM), including the Ornstein–Uhlenbeck process (OUP) as a special case. The distinction between both classes is the location of additive noise in the rate dynamics, which is located on the output side for spiking models and on the input side for the binary model. Both classes allow closed form solutions for the covariance. For output noise it separates into an echo term and a term due to correlated input. The unified framework enables us to transfer results between models. For example, we generalize the binary model and the Hawkes process to the situation with synaptic conduction delays and simplify derivations for established results. Our approach is applicable to general network structures and suitable for the calculation of population averages. The derived averages are exact for fixed out-degree network architectures and approximate for fixed in-degree. We demonstrate how taking into account fluctuations in the linearization procedure increases the accuracy of the effective theory and we explain the class dependent differences between covariances in the time and the frequency domain. Finally we show that the oscillatory instability emerging in networks of LIF models with delayed inhibitory feedback is a model-invariant feature: the same structure of poles in the complex frequency plane determines the population power spectra.
Cluster Analysis , Data-Mining , Multi-dimensional Visualization of Earthquakes over Space , Time and Feature Space

A novel technique based on cluster analysis of the multi-resolutional structure of earthquake patterns is developed and applied to observed and synthetic seismic catalogs. The observed data represent seismic activities situated around the Japanese islands in the 1997-2003 time interval. The synthetic data were generated by numerical simulations for various cases of a heterogeneous fault governed by 3-D elastic dislocation and power-law creep. At the highest resolution, we analyze the local cluster structure in the data space of seismic events for the two types of catalogs by using an agglomerative clustering algorithm. We demonstrate that small magnitude events produce local spatio-temporal patches corresponding to neighboring large events. Seismic events, quantized in space and time, generate the multi-dimensional feature space of the earthquake parameters. Using a non-hierarchical clustering algorithm and multidimensional scaling, we explore the multitudinous earthquakes by real-time 3-D visualization and inspection of multivariate clusters. At the resolutions characteristic of the earthquake parameters, all of the ongoing seismicity before and after largest events accumulate to a global structure consisting of a few separate clusters in the feature space. We show that by combining the clustering results from low and high resolution spaces, we can recognize precursory events more precisely and decode vital information that cannot be discerned at a single level of resolution.
Only centromeres can supply the partition system required for ARS function in the yeast Yarrowia lipolytica.

Autonomously replicating sequences (ARSs) in the yeast Yarrowia lipolytica require two components: an origin of replication (ORI) and centromere (CEN) DNA, both of which are necessary for extrachromosomal maintenance. To investigate this cooperation in more detail, we performed a screen for genomic sequences able to confer high frequency of transformation to a plasmid-borne ORI. Our results confirm a cooperation between ORI and CEN sequences to form an ARS, since all sequences identified in this screen displayed features of centromeric DNA and included the previously characterized CEN1-1, CEN3-1 and CEN5-1 fragments. Two new centromeric DNAs were identified as they are unique, map to different chromosomes (II and IV) and induce chromosome breakage after genomic integration. A third sequence, which is adjacent to, but distinct from the previously characterized CEN1-1 region was isolated from chromosome I. Although these CEN sequences do not share significant sequence similarities, they display a complex pattern of short repeats, including conserved blocks of 9 to 14 bp and regions of dyad symmetry. Consistent with their A+T-richness and strong negative roll angle, Y. lipolytica CEN-derived sequences, but not ORIs, were capable of binding isolated Drosophila nuclear scaffolds. However, a Drosophila scaffold attachment region that functions as an ARS in other yeasts was unable to confer autonomous replication to an ORI-containing plasmid. Deletion analysis of CEN1-1 showed that the sequences responsible for the induction of chromosome breakage could be eliminated without compromising extrachromosomal maintenance. We propose that, while Y. lipolytica CEN DNA is essential for plasmid maintenance, this function can be supplied by several sub-fragments which, together, form the active chromosomal centromere. This complex organization of Y. lipolytica centromeres is reminiscent of the regional structures described in the yeast Schizosaccharomyces pombe or in multicellular eukaryotes.
Visibility-based blending for real-time applications

There are many situations in which virtual objects are presented half-transparently on a background in real time applications. In such cases, we often want to show the object with constant visibility. However, using the conventional alpha blending, visibility of a blended object substantially varies depending on colors, textures, and structures of the background scene. To overcome this problem, we present a framework for blending images based on a subjective metric of visibility. In our method, a blending parameter is locally and adaptively optimized so that visibility of each location achieves the targeted level. To predict visibility of an object blended by an arbitrary parameter, we utilize one of the error visibility metrics that have been developed for image quality assessment. In this study, we demonstrated that the metric we used can linearly predict visibility of a blended pattern on various texture images, and showed that the proposed blending methods can work in practical situations assuming augmented reality.
Morphology and DNA barcoding reveal three cryptic species within the Xylophanes neoptolemus and loelia species-groups ( Lepidoptera : Sphingidae )

Two species complexes within the genus Xylophanes are addressed using a combination of morphological study and analysis of DNA barcode sequences. The existence of two and three cryptic species respectively within the X. loelia and X. neoptolemus complexes is revealed following consideration of both adult habitus and genital morphology, and the results of a phylogenetic analysis of partial COI sequences—DNA barcodes—for 38 specimens. The taxonomic status of the available names is discussed and to clarify and stabilize the confused nomenclature of this group, a neotype for Sphinx neoptolemus Cramer, 1780, and lectotypes for Choerocampa loelia Druce, 1878 and Chaerocampa trilineata Walker, [1865], are designated. We describe three new species: X. lolita n. sp. Vaglia and Haxaire; X. balcazari n. sp. Haxaire and Vaglia; and X. cthulhu n. sp. Haxaire and Vaglia. The first is endemic to southeastern Brazil and closely allied to X. loelia; the second two are relatives of X. neoptolemus, of which the first is known only from Guerrero and Michoacán states in Mexico while the second is widely distributed in lowland forests of Central America.
Diastolic Coronary Artery Pressure‐Flow Relations in the Dog

Conscious dogs were used to investigate the relations between aortic (Pa) pressure and coronary flow (F) during individual diastoles. When the dogs were in a semibasal state, coronary pressure-flow relations were described by a family of lines, and diastolic flow was a linear function of aortic pressure. For a given perfusion pressure, higher flows were associated with lines of progressively greater slope and lower zero flow pressure intercept (Pf-o). Zero flow pressure intercepts were estimated by extrapolation and found to vary between 20 and 50 mm Hg, depending on the magnitude of flow. The zero flow pressure may represent the height of a vascular waterfall caused by vasomotor tone with the resistance-controlling coronary flow being (P-Pf-o)*F−1. Interventions that decrease vasomotor tone increase coronary flow by both decreasing vascular resistance and increasing the perfusion pressure gradient. The gradient increases because the effective coronary back pressure is the height of the vascular waterfall and the latter is reduced when vasomotor tone falls. Passive changes in vessel dimensions, arterial recruitment, and autoregulation appear to be of little importance during individual diastoles.
Study on Smooth Blasting of Tunnel in Fault Formation

From the characteristics of rock damage, the mechanism of rock blasting into seam was discussed. Based on the joint mechanism of stress waves and explosive gases, the blasting method adopting slotted pipe charge structure in fault formation was studied, and the test results were used in Guanjiao tunnel of Qinghai-Tibet railway. The field tests show that the perimeter hole adopting slotted pipe charge structure improves the phenomenon of over-excavation in fault formation obviously.
A Platform to Analyze DDR3 DRAM’s Power and Retention Time

<italic>Editor’s note:</italic> The authors explore the intrinsic trade-off in a DRAM between the power consumption (due to refresh) and the reliability. Their unique platform allows tailoring to the design constraints depending on whether power consumption, performance or reliability has the highest design priority. <italic>—Jörg Henkel, Karlsruhe Institute of Technology</italic>
On a Schrödinger equation with periodic potential involving critical growth

The main purpose of this paper is to establish the existence of a solution of the semilinear Schrodinger equation −∆u + V (x)u = f(u), in R where V is a 1-periodic functions with respect to x, 0 lies in a gap of the spectrum of −∆ + V , and f(s) behaves like ± exp(αs) when s → ±∞.
Nuclear Pore Complex Structure and Dynamics Revealed by Cryoelectron Tomography

Nuclear pore complexes (NPCs) are gateways for nucleocytoplasmic exchange. To analyze their structure in a close-to-life state, we studied transport-active, intact nuclei from Dictyostelium discoideum by means of cryoelectron tomography. Subvolumes of the tomograms containing individual NPCs were extracted in silico and subjected to three-dimensional classification and averaging, whereby distinct structural states were observed. The central plug/transporter (CP/T) was variable in volume and could occupy different positions along the nucleocytoplasmic axis, which supports the notion that it essentially represents cargo in transit. Changes in the position of the CP/T were accompanied by structural rearrangements in the NPC scaffold.
Subscription indexes for web syndication systems

The explosion of published information on the Web leads to the emergence of a Web syndication paradigm, which transforms the passive reader into an active information collector. Information consumers subscribe to RSS/Atom feeds and are notified whenever a piece of news (item) is published. The success of this Web syndication now offered on Web sites, blogs, and social media, however raises scalability issues. There is a vital need for efficient real-time filtering methods across feeds, to allow users to follow effectively personally interesting information. We investigate in this paper three indexing techniques for users' subscriptions based on inverted lists or on an ordered trie. We present analytical models for memory requirements and matching time and we conduct a thorough experimental evaluation to exhibit the impact of critical workload parameters on these structures.
DNA extraction from formalin-fixed, paraffin-embedded tissue.

Formalin-fixed, paraffin-embedded (FFPE) tissue is one of the most widely practiced methods for clinical sample preservation and archiving. It is estimated that, worldwide, over a billion tissue samples, most of them FFPE, are being stored in numerous hospitals, tissue banks, and research laboratories. These archived samples could potentially provide a wealth of information in retrospective molecular studies of diseased tissues. While standard for histopathology and microscopic investigation (e.g., hematoxylin and eosin [H&E] staining, immunohistochemistry [IHC], and tissue microarray [TMA]), FFPE samples pose a major challenge for molecular pathologists, because nucleic acids are heavily modified and trapped by extensive protein-nucleic acid and protein-protein cross linking. Historically, FFPE samples were not considered to be a viable source for molecular analyses. Recently, however, it has been discovered that with appropriate protease digestion, it is possible to release microgram amounts of DNA and RNA from FFPE samples. The purified nucleic acids, although highly fragmented, are suitable for a variety of downstream genomic and gene expression analyses, such as polymerase chain reaction (PCR), quantitative reverse transcription PCR (qRT-PCR), microarray, array comparative genomic hybridization (CGH), microRNA, and methylation profiling. Several commercial kits are currently available for FFPE extraction. The protocol reported here is adapted from the Ambion RecoverAll Total Nucleic Acid Isolation Kit, but includes several modifications. Although our protocol focuses on DNA isolation, the RecoverAll Kit can also be utilized to recover RNA, including microRNA.
Analyzing graph databases by aggregate queries

An important step in data analysis is the exploration of data. For traditional relational databases one of the most powerful tools for performing such analysis is the relational database and the aggregates and rankings that they can compute: for instance, simple statistics such as the average number of links between two types of entities (relations) are easily computed using a query on a relational database and may already provide valuable information. However, for the exploration of graph data, relational databases may not be most practical and scalable. For instance, a statistic such as the shortest path between two given nodes cannot be computed by a relational database. Surprisingly, however, tools for querying graph and network databases are much less well developed than for relational data, and only recently an increasing number of studies are devoted to graph or network databases. Our position is that the development of such graph databases is important both to make basic graph mining easier and to prepare data for more complex types of analysis. An important component of such databases is the language that is used to enable aggregating queries, such as shortest path queries. In this paper, we propose an extension to a previously proposed query language. This extension allows for querying and analyzing databases by using aggregates and ranking. A notable feature of our language is that it also supports probabilistic graph queries by conceiving of such queries as aggregating queries. We demonstrate its value on a simple data analysis task.
Deciphering human motion to discriminate social interactions: a developmental neuroimaging study

Abstract Non-verbal communication plays a major role in social interaction understanding. Using functional magnetic resonance imaging, we explored the development of the neural networks involved in social interaction recognition based on human motion in children (8–11), adolescents (13–17), and adults (20–41). Participants watched point-light videos depicting two actors interacting or moving independently and were asked whether these agents were interacting or not. All groups successfully performed the discrimination task, but children had a lower performance and longer response times than the older groups. In all three groups, the posterior parts of the superior temporal sulci and middle temporal gyri, the inferior frontal gyri and the anterior temporal lobes showed greater activation when observing social interactions. In addition, adolescents and adults recruited the caudate nucleus and some frontal regions that are part of the mirror system. Adults showed greater activations in parietal and frontal regions (part of them belonging to the social brain) than adolescents. An increased number of regions that are part of the mirror system network or the social brain, as well as the caudate nucleus, were recruited with age. In conclusion, a shared set of brain regions enabling the discrimination of social interactions from neutral movements through human motion is already present in 8-year-old children. Developmental processes such as refinements in the social brain and mirror system would help grasping subtle cues in non-verbal aspects of social interactions.
Representation and Processing of Complex DNA Spatial Architecture and its Annotated Genomic Content

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.
Traffic Optimization in Multi-layered WANs Using SDN

Wide area networks (WAN) forward traffic through a mix of packet and optical data planes, composed by a variety of devices from different vendors. Multiple forwarding technologies and encapsulation methods are used for each data plane (e.g. IP, MPLS, ATM, SONET, Wavelength Switching). Despite standards defined, the control planes of these devices are usually not interoperable, and different technologies are used to manage each forwarding segment independently (e.g. Open Flow, TL-1, GMPLS). The result is lack of coordination between layers and inefficient resource usage. In this paper we discuss the design and implementation of a system that uses unmodified Open Flow to optimize network utilization across layers, enabling practical bandwidth virtualization. We discuss strategies for scalable traffic monitoring and to minimize losses on route updates across layers. A prototype of the system was built using a traditional circuit reservation application and an unmodified SDN controller, and its evaluation was performed on a multi-vendor test bed.
Habituation and Cross‐Sensitization of Stress‐Induced Hypothalamic‐Pituitary‐Adrenal Activity: Effect of Lesions in the Paraventricular Nucleus of the Thalamus or Bed Nuclei of the Stria Terminalis

Habituation of the hypothalamic‐pituitary‐adrenal (HPA) response to chronic intermittent restraint stress (30 min/day for 15 days) and the cross‐sensitization to a heterotypic stress [i.p. lipopolysaccharide (LPS)] were investigated in intact male Sprague Dawley rats, and in rats bearing quinolinic acid lesions to the medial anterior bed nuclei of the stria terminalis (BST) or anterior region of the paraventricular nucleus of the thalamus (PVT). In intact animals, a single period of restraint increased plasma corticosterone levels at 30 min and led to an increase in corticotropin‐releasing hormone (CRH) mRNA levels in the PVN at 3 h. LPS had a smaller effect on corticosterone and more variable effect on CRH mRNA. Chronic intermittent restraint stress caused a decrease in body weight and increase in adrenal weights, with concomitant increase in basal corticosterone levels. These animals also displayed marked habituation of the corticosterone and CRH mRNA responses to the homotypic stress of restraint, but no loss of the corticosterone response to the heterotypic stress of LPS and a cross‐sensitization of the CRH mRNA response. This pattern of stress responses in control and chronically stressed animals was not significantly affected by lesions to the PVT or BST, two areas which have been implicated in the coping response to stress. Thus, these data provide evidence for independent adaptive mechanisms regulating HPA responses to psychological and immune stressors, but suggest that neither the medial anterior BST nor the anterior PVT participate in the mechanisms of habituation or cross‐sensitization.
Building Blocks for Time-Resolved Laser Emission in Mid-Infrared Quantum Well Lasers

Abstract : The objective of this research is to improve the performance of mid-infrared semiconductor quantum-well lasers. Lasers operating in the mid-infrared are useful for many Air Force applications which include infrared (IR) countermeasures in particular. Countermeasure applications require lasers that are compact, and able to emit at high powers while operating at room temperature. Limits to power increases are seen in the transverse modal development of laser oscillation. These modes typically form in the waveguiding active region contributing to the laser output. However, competing modes outside of this region also develop when the confining structural layers have the right characteristics. These competing modes may draw power away from the main lasing mode, causing efficiency to drop. Therefore, theoretical models indicate that these "ghost" modes should be extinguished. The goal of this work is to incorporate antimony-based semiconductor laser devices into a time-resolved photoluminescence (TRPL) experiment to examine modal development immediately after excitation. TRPL utilizes a non-linear wave mixing technique known as frequency upconversion to resolve sub-picosecond luminescence occurrences after excitation. Modification to the experiment is performed to produce laser emission from five mid-IR semiconductor laser samples. Both spontaneous and stimulated emission spectra are recorded. Alignment of the experiment is also carried out to produce upconversion of the PL signal to prepare for the incorporation of laser emission.
Age‐related differences in brain network activation and co‐activation during multiple object tracking

Multiple object tracking (MOT) is a powerful paradigm for measuring sustained attention. Although previous fMRI studies have delineated the brain activation patterns associated with tracking and documented reduced tracking performance in aging, age‐related effects on brain activation during MOT have not been characterized. In particular, it is unclear if the task‐related activation of different brain networks is correlated, and also if this coordination between activations within brain networks shows differential effects of age.