Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards Online Detection of Neural Assemblies in Parallel Spike Trains

Neural assemblies are supposed to play an important role in the de- and encoding of information and stimuli in the brain. These groups of neurons are representing information by increased synchronous behavior. Spike trains are abstractions of recordings of the electrical potential emitted by individual neurons. We use a previously developed method to describe a single spike trains behavior and extend this method to distinguish between different neural assemblies. Our algorithm can be extended to work in an online fashion that will allow neurobiologists to verify the spike-time hypothesis and eventually observe neural assemblies in real-time.
Near-optimal Bayesian localization via incoherence and sparsity

This paper exploits recent developments in sparse approximation and compressive sensing to efficiently perform localization in a sensor network. We introduce a Bayesian framework for the localization problem and provide sparse approximations to its optimal solution. By exploiting the spatial sparsity of the posterior density, we demonstrate that the optimal solution can be computed using fast sparse approximation algorithms. We show that exploiting the signal sparsity can reduce the sensing and computational cost on the sensors, as well as the communication bandwidth. We further illustrate that the sparsity of the source locations can be exploited to decentralize the computation of the source locations and reduce the sensor communications even further. We also discuss how recent results in 1-bit compressive sensing can significantly reduce the amount of inter-sensor communications by transmitting only the intrinsic timing information. Finally, we develop a computationally efficient algorithm for bearing estimation using a network of sensors with provable guarantees.
Layering garments during rest and exercise in the cold (8°C): wearer responses and comparability with selected fabric properties

How garments contribute to performance of the clothing system during wear is of interest, as is understanding the value of using fabric properties to inform end-use characteristics. To investigate the influences of layering upper-body garments, four fabrics were used to construct two first-layer garments (wool and polyester) and two outer-layer garments (wool and membrane laminate). Over six sessions, 10 moderately trained males wore each first-layer garment as a single layer and in combination with each outer-layer garment while resting, running and walking in cold environmental conditions (8 ± 1°C, 81 ± 4% RH). Here, the type of garment arrangement worn (fabric type or number of layers) had little influence on heart rate, core body temperature and change in body mass. Weighted mean covered skin temperature was warmer and weighted mean next-to-skin vapour pressure was typically higher (following the onset of exercise) with two layers versus one. Differences among fabrics for individual properties were typically overstated compared to differences among corresponding garments for physiological and psychophysical variables under the conditions of this study. These findings inform the interpretation of particular fabric properties and highlight issues to be acknowledged during development/refinement of fabric test methods. Practitioner Summary: We examined the way in which selected fibre, fabric and garment (layering) characteristics contribute to performance of the clothing system during wear under cold conditions. Selected properties of the constituent fabrics were found to provide limited insight into how garments perform during wear under the conditions of this study.
Secure scan: a design-for-test architecture for crypto chips

Scan-based design-for-test (DFT) is a powerful testing scheme, but it can be used to retrieve the secrets stored in a crypto chip thus compromising its security. On one hand, sacrificing security for testability by using traditional scan-based DFT restricts its use in privacy sensitive applications. On the other hand, sacrificing testability for security by abandoning scan-based DFT hurts product quality. The security of a crypto chip comes from the small secret key stored in a few registers and the testability of a crypto chip comes from the data path and control path implementing the crypto algorithm. Based on this key observation, we propose a novel scan DFT architecture called secure scan that maintains the high test quality of traditional scan DFT without compromising the security. We used a hardware implementation of the advanced encryption standard (AES) to show that the traditional scan DFT scheme can compromise the secret key. We then showed that by using secure scan DFT, neither the secret key nor the testability of the AES implementation is compromised.
The Impact and Outreach of Soundscape Research

Soundscape has been growing steadily as a research field since its interdisciplinary concepts were first introduced about 50 years ago in music theory and acoustic ecology, and it currently affects a broad spectrum of disciplines ranging from social sciences to urban planning and noise control engineering. In spite of its strong research appeal, it is not clear what the actual impact and outreach of soundscape science is at a societal level; that is: how soundscape research is received by community. Using the Altmetric database, this review aims to map how and where soundscape research is “mentioned”, considering the number of mentions over time, their geographical spread and effectiveness of publication outlets. Results show that mentions are growing with time, they mostly originate in the United States and the United Kingdom, and they are generated by a limited number of research items.
Complete Modeling of Nonlinear Distortion in OFDM-Based Optical Wireless Communication

This paper presents a complete analytical framework for modeling memoryless nonlinear effects in an intensity modulation and direct detection optical wireless communication system based on orthogonal frequency division multiplexing. The theory employs the Bussgang theorem, which is widely accepted as a means to characterize the impact of nonlinear distortions on normally distributed signals. This paper proposes a new method to generalize this approach, and it describes how a closed-form analytical expression for the system bit error rate can be obtained for an arbitrary memoryless distortion. Major distortion effects at the transmitter stage such as quantization and nonlinearity from the light emitting diode are analyzed. Four known orthogonal-frequency-division-multiplexing-based modulation schemes for optical communication are considered in this paper: direct-current-biased optical OFDM, asymmetrically clipped optical OFDM, pulse-amplitude-modulated discrete multitone modulation, and unipolar orthogonal frequency division multiplexing.
Characterization of Saccharomyces cerevisiae genes encoding subunits of cyclic AMP-dependent protein kinase

Mutations in the SRA1 or SRA3 gene eliminate the requirement for either RAS gene (RAS1 or RAS2) in Saccharomyces cerevisiae. We cloned SRA1 and SRA3 and determined their DNA sequences. SRA1 encodes the regulatory subunit of the cyclic AMP (cAMP)-dependent protein kinase and therefore is identical to REG1 and BCY1. This gene is not essential, but its deletion confers many traits: reduction of glycogen accumulation, temperature sensitivity, reduced growth rate on maltose and sucrose, inability to grow on galactose and nonfermentable carbon sources, and nitrogen starvation intolerance. SRA3 is homologous to protein kinases that phosphorylate serine and threonine and likely encodes the catalytic subunit of the cAMP-dependent protein kinase. The wild-type SRA3 gene either triplicated in the chromosome or on episomal, low-copy plasmids behaves like spontaneous dominant SRA3 mutations by suppressing ras2-530 (RAS2::LEU2 disruption), cdc25, and cdc35 mutations. These findings indicate that the yeast RAS genes are dispensable if there is constitutive cAMP-dependent protein kinase activity.
Mining API patterns as partial orders from source code: from usage scenarios to specifications

A software system interacts with third-party libraries through various APIs. Using these library APIs often needs tofollow certain usage patterns. Furthermore, ordering rules (specifications) exist between APIs, and these rules govern the secure and robust operation of the system using these APIs. But these patterns and rules may not be well documented by the API developers. Previous approaches mine frequent association rules, itemsets, or subsequences that capture API call patterns shared by API client code. However, these frequent API patterns cannot completely capture some useful orderings shared by APIs, especially when multiple APIs are involved across different procedures. In this paper, we present a framework to automatically extract usage scenarios among user-specified APIs as partial orders, directly from the source code (API client code). We adapt a model checker to generate interprocedural control-flow-sensitive static traces related to the APIs of interest. Different API usage scenarios are extracted from the static traces by our scenario extraction algorithm and fed to a miner. The miner summarizes different usage scenarios as compact partial orders. Specifications are extracted from the frequent partial orders using our specification extraction algorithm. Our experience of applying the framework on 72 X11 clients with 200K LOC in total has shown that theextracted API partial orders are useful in assisting effective API reuse and checking.
2017 Valparaíso earthquake sequence and the megathrust patchwork of central Chile

In April 2017, a sequence of earthquakes offshore Valparaíso, Chile, raised concerns of a potential megathrust earthquake in the near future. The largest event in the 2017 sequence was a M6.9 on 24 April, seemingly colocated with the last great‐sized earthquake in the region—a M8.0 in March 1985. The history of large earthquakes in this region shows significant variation in rupture size and extent, typically highlighted by a juxtaposition of large ruptures interspersed with smaller magnitude sequences. We show that the 2017 sequence ruptured an area between the two main slip patches during the 1985 earthquake, rerupturing a patch that had previously slipped during the October 1973 M6.5 earthquake sequence. A significant gap in historic ruptures exists directly to the south of the 2017 sequence, with large enough moment deficit to host a great‐sized earthquake in the near future, if it is locked.
A reference model for workflow application development processes

The success of workflow projects to a large extent depends on how workflow application development processes are planned, organized, and conducted. Based on lessons learned from problems encountered during real-world workflow application development projects, this paper presents a reference model for workflow application development processes, which guides project managers and developers through the complex structure of these processes, with the aim of developing more adequate, usable, and reliable workflow applications.
Non-backtracking Spectrum of Random Graphs: Community Detection and Non-regular Ramanujan Graphs

A non-backtracking walk on a graph is a directed path such that no edge is the inverse of its preceding edge. The non-backtracking matrix of a graph is indexed by its directed edges and can be used to count on-backtracking walks of a given length. It has been used recently in the context of community detection and has appeared previously in connection with the Ihara zeta function and in some generalizations of Ramanujan graphs. In this work, we study the largest eigen valus of the non-backtracking matrix of the Erdos-Renyi random graph and of the Stochastic Block Model in the regime where the number of edges is proportional to the number of vertices. Our results confirm the "spectral redemption conjecture" that community detection can be made on the basis of the leading eigenvectors above the feasibility threshold.
Depletion Analysis of the Nigerian Research Reactor Fuel with 19.75% Enriched UO2 Material

The depletion analysis of the Nigerian research reactor fuel with 19.75% enriched UO2 have been performed using the VENTURE PC code. The matrix exponential method was selected in this work to perform the depletion analysis. The volume fraction of the materials in this mixture was calculated and multiplied by their respective atom densities to obtain the effective atom density of the nuclide in the water, Aluminium mix region of the fuel cell model. The plot of the variation of k infinity versus hydrogen to Uranium ratio was generated using Matlab programming language for processing of the computer code result. This shows that as the ratio of hydrogen to uranium in the core of the reactor is increased, the reactivity also increases by gradually increasing the fuel cell radii till it gets to the peak of 0.6193. Any further increment in the radius of the fuel cell radii, the reactivity of the reactor decreases as the hydrogen to uranium ratio increases.
Imaging of the Yellow Cameleon 3.6 Indicator Reveals That Elevations in Cytosolic Ca2+ Follow Oscillating Increases in Growth in Root Hairs of Arabidopsis1[W][OA]

In tip-growing cells, the tip-high Ca2+ gradient is thought to regulate the activity of components of the growth machinery, including the cytoskeleton, Ca2+-dependent regulatory proteins, and the secretory apparatus. In pollen tubes, both the Ca2+ gradient and cell elongation show oscillatory behavior, reinforcing the link between the two. We report that in growing root hairs of Arabidopsis (Arabidopsis thaliana), an oscillating tip-focused Ca2+ gradient can be resolved through imaging of a cytosolically expressed Yellow Cameleon 3.6 fluorescence resonance energy transfer-based Ca2+ sensor. Both elongation of the root hairs and the associated tip-focused Ca2+ gradient show a similar dynamic character, oscillating with a frequency of 2 to 4 min−1. Cross-correlation analysis indicates that the Ca2+ oscillations lag the growth oscillations by 5.3 ± 0.3 s. However, growth never completely stops, even during the slow cycle of an oscillation, and the concomitant tip Ca2+ level is always slightly elevated compared with the resting Ca2+ concentration along the distal shaft, behind the growing tip. Artificially increasing Ca2+ using the Ca2+ ionophore A23187 leads to immediate cessation of elongation and thickening of the apical cell wall. In contrast, dissipating the Ca2+ gradient using either the Ca2+ channel blocker La3+ or the Ca2+ chelator EGTA is accompanied by an increase in the rate of cell expansion and eventual bursting of the root hair tip. These observations are consistent with a model in which the maximal oscillatory increase in cytosolic Ca2+ is triggered by cell expansion associated with tip growth and plays a role in the subsequent restriction of growth.
Discovery of Contrapuntal Patterns

This paper develops and applies a new method for the discovery of polyphonic patterns. The method supports the representation of abstract relations that are formed between notes that overlap in time without being simultaneous. Such relations are central to understanding species counterpoint. The method consists of an application of the vertical viewpoint technique, which relies on a vertical slicing of the musical score. It is applied to two-voice contrapuntal textures extracted from the Bach chorale harmonizations. Results show that the new method is powerful enough to represent and discover distinctive modules of species counterpoint, including remarkably the suspension principle of fourth species counterpoint. In addition, by focusing on two voices in particular and setting them against all other possible voice pairs, the method can elicit patterns that illustrate well the unique treatment of the voices under investigation, e.g. the inner and outer voices. The results are promising and indicate that the method is suitable for computational musicology research.
Pivotal Evaluation of the Accuracy of a Biomarker Used for Classification or Prediction: Standards for Study Design

Research methods for biomarker evaluation lag behind those for evaluating therapeutic treatments. Although a phased approach to development of biomarkers exists and guidelines are available for reporting study results, a coherent and comprehensive set of guidelines for study design has not been delineated. We describe a nested case–control study design that involves prospective collection of specimens before outcome ascertainment from a study cohort that is relevant to the clinical application. The biomarker is assayed in a blinded fashion on specimens from randomly selected case patients and control subjects in the study cohort. We separately describe aspects of the design that relate to the clinical context, biomarker performance criteria, the biomarker test, and study size. The design can be applied to studies of biomarkers intended for use in disease diagnosis, screening, or prognosis. Common biases that pervade the biomarker research literature would be eliminated if these rigorous standards were followed.
Peroxiredoxin 6 Is Upregulated in Bovine Oocytes and Cumulus Cells During In Vitro Maturation: Role of Intercellular Communication1

Abstract Peroxiredoxins are peroxidases involved in antioxidant defense and intracellular signaling. Expression of transcripts coding for peroxiredoxin 6 (PRDX6) has been previously described to be upregulated in oocytes after in vitro maturation, a period during which general transcription decreases dramatically in oocytes. The aim of the present work was to evaluate PRDX6 regulation in bovine cumulus-oocyte complexes in relation to maturation and intercellular communication. PRDX6 expression was analyzed by reverse transcription-PCR and Western blotting in oocytes and cumulus cells before and after in vitro maturation. PRDX6 was found to be upregulated at the mRNA and protein levels in both cell types after maturation. The effect of paracrine and gap junctional communication on PRDX6 expression was then assessed by culturing cumulus clusters in the presence or absence of denuded oocytes. While PRDX6 upregulation in oocytes required intact cumulus-oocyte junctions, the presence of denuded oocytes was necessary but sufficient for the upregulation to occur in cumulus cells. Finally, the influence of recombinant mouse growth differentiation factor-9 (GDF-9) on PRDX6 expression in cumulus cells was studied. GDF-9 induced cumulus expansion and PRDX6 upregulation in bovine cumulus clusters. Altogether, our data suggest that PRDX6 upregulation in cumulus-oocyte complexes during in vitro maturation is mutually regulated by both cell types: PRDX6 upregulation in oocytes would require gap junctions with cumulus cells, while upregulation in cumulus would depend on secretion of oocyte paracrine factor(s) with GDF-9 being a likely candidate.
Diffusion Tensor Imaging: Exploring the Motor Networks and Clinical Applications

With the advances in diffusion magnetic resonance (MR) imaging techniques, diffusion tensor imaging (DTI) has been applied to a number of neurological conditions because DTI can demonstrate microstructures of the brain that are not assessable with conventional MR imaging. Tractography based on DTI offers gross visualization of the white matter fiber architecture in the human brain in vivo. Degradation of restrictive barriers and disruption of the cytoarchitecture result in changes in the diffusion of water molecules in various pathological conditions, and these conditions can also be assessed with DTI. Yet many factors may influence the ability to apply DTI clinically, so these techniques have to be used with a cautious hand.
Selective toxicity of persian gulf sea cucumber holothuria parva on human chronic lymphocytic leukemia b lymphocytes by direct mitochondrial targeting

Natural products isolated from marine environment are well known for their pharmacodynamic potential in diversity of disease treatments such as cancer or inflammatory conditions. Sea cucumbers are one of the marine animals of the phylum Echinoderm. Many studies have shown that the sea cucumber contains antioxidants and anti‐cancer compounds. Chronic lymphocytic leukemia (CLL) is a disease characterized by the relentless accumulation of CD5+ B lymphocytes. CLL is the most common leukemia in adults, about 25–30% of all leukemias. In this study B lymphocytes and their mitochondria (cancerous and non‐cancerous) were obtained from peripheral blood of human subjects and B lymphocyte cytotoxicity assay, and caspase 3 activation along with mitochondrial upstream events of apoptosis signaling including reactive oxygen species (ROS) production, collapse of mitochondrial membrane potential (MMP) and mitochondrial swelling were determined following the addition of Holothuria parva extract to both cancerous and non‐cancerous B lymphocytes and their mitochondria. Our in vitro finding showed that mitochondrial ROS formation, MMP collapse, and mitochondrial swelling and cytochrome c release were significantly (P < 0.05) increased after addition of different concentrations of H. parva only in cancerous BUT NOT normal non‐cancerous mitochondria. Consistently, different concentrations of H. parva significantly (P < 0.05) increased cytotoxicity and caspase 3 activation only in cancerous BUT NOT normal non‐cancerous B lymphocytes. These results showed that H. parva methanolic extract has a selective mitochondria mediated apoptotic effect on chronic lymphocytic leukemia B lymphocytes hence may be promising in the future anticancer drug development for treatment of CLL. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1158–1169, 2017.
Agents Secure Interaction in Data driven Languages

This paper discusses the security issues in data driven coordination languages. These languages rely on a data space shared by the agents and used to coordinate their activities. We extend these languages with a main distinguishing feature, which is the possibility to define fine-grained security conditions, associated with every datum in the shared space. Two main ideas makes it possible: the consideration of an abstraction of agents' states in the form of data at language level and the introduction of a richer interaction mechanism than state-of-the-art templates. This novel security mechanism allows both agents and system designers to prohibit undesirable interactions.