Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON

Abstract Large multiscale neuronal network simulations are of increasing value as more big data are gathered about brain wiring and organization under the auspices of a current major research initiative, such as Brain Research through Advancing Innovative Neurotechnologies. The development of these models requires new simulation technologies. We describe here the current use of the NEURON simulator with message passing interface (MPI) for simulation in the domain of moderately large networks on commonly available high-performance computers (HPCs). We discuss the basic layout of such simulations, including the methods of simulation setup, the run-time spike-passing paradigm, and postsimulation data storage and data management approaches. Using the Neuroscience Gateway, a portal for computational neuroscience that provides access to large HPCs, we benchmark simulations of neuronal networks of different sizes (500–100,000 cells), and using different numbers of nodes (1–256). We compare three types of networks, composed of either Izhikevich integrate-and-fire neurons (I&F), single-compartment Hodgkin-Huxley (HH) cells, or a hybrid network with half of each. Results show simulation run time increased approximately linearly with network size and decreased almost linearly with the number of nodes. Networks with I&F neurons were faster than HH networks, although differences were small since all tested cells were point neurons with a single compartment.
Snafu: Function-as-a-Service (FaaS) Runtime Design and Implementation

Snafu, or Snake Functions, is a modular system to host, execute and manage language-level functions offered as stateless (micro-)services to diverse external triggers. The system interfaces resemble those of commercial FaaS providers but its implementation provides distinct features which make it overall useful to research on FaaS and prototyping of FaaS-based applications. This paper argues about the system motivation in the presence of already existing alternatives, its design and architecture, the open source implementation and collected metrics which characterise the system.
Cannabidiol as a Potential Treatment for Febrile Infection-Related Epilepsy Syndrome (FIRES) in the Acute and Chronic Phases

Febrile infection-related epilepsy syndrome (FIRES) is a devastating epilepsy affecting normal children after a febrile illness. FIRES presents with an acute phase with super-refractory status epilepticus and all patients progress to a chronic phase with persistent refractory epilepsy. The typical outcome is severe encephalopathy or death. The authors present 7 children from 5 centers with FIRES who had not responded to antiepileptic drugs or other therapies who were given cannabadiol (Epidiolex, GW Pharma) on emergency or expanded investigational protocols in either the acute or chronic phase of illness. After starting cannabidiol, 6 of 7 patients’ seizures improved in frequency and duration. One patient died due to multiorgan failure secondary to isoflourane. An average of 4 antiepileptic drugs were weaned. Currently 5 subjects are ambulatory, 1 walks with assistance, and 4 are verbal. While this is an open-label case series, the authors add cannabidiol as a possible treatment for FIRES.
FRACTURE MECHANICS APPROACH TO EVALUATION OF FLEXURAL STRENGTH OF CONCRETE

Size effects and shape effects on the flexural strength of concrete were examined through experiments and numerical analysis with fracture mechanics concepts. Based on the numerical results, the authors proposed an equation for estimating the flexural strength of concrete beams with square or circular cross sections. The beam depth, tensile strength, and the characteristic length of concrete beams are the parameters in the proposed equation. The estimated values of flexural strength given by the equation are in good agreement with the experimental results, especially for square beams. The equation gives moderate values for the flexural strengths of various kinds of concrete, including normal concrete, high-strength concrete, lightweight concrete, mortar, and polyester resin concrete.
Characterization of the striatal M2 muscarinic receptor mediating inhibition of cyclic AMP using selective antagonists: a comparison with the brainstem M2 receptor.

Pharmacological profiles of the striatal and brainstem M2 receptors were developed with a group of selective muscarinic antagonists. The striatal M2 muscarinic receptor was identified by its inhibition of [3H]cyclic AMP levels, whereas the brainstem M2 receptor was characterized using competition with [3H]quinuclidinyl benzilate binding. The potency of pirenzepine does not differentiate clearly between the striatal M2 receptor (Ki approximately 300 nM) and the brainstem M2 receptor (Ki = 219 nM) or peripheral M2 receptors. In the present study, we used 4-diphenylacetoxy-N-methylpiperidine methbromide, hexahydrosiladifenidol, AF-DX 116 and methoctramine to characterize the striatal and brainstem M2 receptors in more pharmacological detail. For comparison, the potencies of these antagonists were also measured at cortical M2 receptors (using competition with [3H]pirenzepine binding). The potencies of 4-diphenylacetoxy-N-methylpiperidine methbromide (KB = 0.19 nM) and hexahydrosiladifenidol (KB = 14 nM) in blocking the striatal M2 receptor suggested similarity to those M2 receptors localized in certain smooth muscles or in glands. However, AF-DX 116 (KB = 155 nM) and methoctramine (KB = 47 nM) were considerably more potent in blocking the striatal M2 receptor than as reported in functional studies in smooth muscle or glands. Thus, the profile of the striatal M2 receptor obtained with these antagonists did not match in all respects with either glandular (probable M4 gene product) or cardiac (probable M2 gene product) muscarinic receptors. In contrast, our data with the brainstem M2 receptor was highly correlated (r = 0.93) with literature data regarding the cardiac muscarinic system. (ABSTRACT TRUNCATED AT 250 WORDS)
Optical Flow Motion Estimation for Approximate Motion Compensation in Cone-Beam CT

Image quality of volumetric image reconstructions is often degraded by residual patient motion when using slowly rotating Carm systems or radiotherapy linear accelerators. If the patient does not manage to hold his or her movements during data acquisition, the image resolution is impaired by strong motion blur artifacts. This work proposes a method to detect and to estimate arbitrary patient motion. The motion information is used within a motion-compensated variant of the FDK algorithm to improve the image quality. Results of two related experiments are shown. First, the motion is estimated in projection space by optical flow-based elastic image registration, using reference projections of a known static image. The motion-compensated FDK reconstruction from a simulated free breathing acquisition shows very good agreement with the objective image. Second, the motion is estimated from approximate reference projections that are computed by the SART method, using solely the acquired data.
CRISPRi Induced Suppression of Fimbriae Gene (fimH) of a Uropathogenic Escherichia coli: An Approach to Inhibit Microbial Biofilms

Urinary tract infection (UTI) is one the common infections caused by the recalcitrant nature of biofilms, developed after the pathogen has adhered to the inner lining of the urinary tract. Although significant research has been made in recent years to control these types of infection, but as of yet, no approach has sufficiently been able to reduce the prevalence of UTIs. The main objective of this study was to prevent UTIs through targeting the fimH gene, which is the major virulent factor responsible for biofilm formation. The novelty of this work lies in the use of CRISPRi, a gene specific editing tool to control such types of infections. Accordingly, the system was designed to target fimH gene, responsible for bacterial adherence and this approach was successfully validated by performing microscopic, biofilm and adherence assays.
Fatigue Strength of Heat‐treatable Steel Under Static Multiaxial Compression Stresses

Known conceptions of calculation for consideration of the influence of mean stresses on the fatigue strength are discussed. While previously known models do not consider the changed fracture behaviour due to acting compressive mean stresses or otherwise accept compressive mean stresses only for the same direction of action with the cyclic load, the presented new conception allows the strength assessment of arbitrary multiaxial loads.
Disruption-Tolerant Networking: A Comprehensive Survey on Recent Developments and Persisting Challenges

Nowadays, wireless networks are witnessing several deployments in various extreme environments where they suffer from different levels of link disruptions depending on the severity of the operating conditions. In all cases, their operation requirements are differently altered and their performance is negatively affected rendering them heterogeneous by nature. In the open literature, these networks are known as Intermittently Connected Networks (ICNs). The existing Internet protocols fail to operate properly in the context of ICNs, thus raising a variety of new challenging problems that are attracting the attention of the networking research community. Delay-/Disruption-Tolerant Networking emerged as a highly active area of research where networking experts compete in addressing the various ICN problems. Over time, unicast routing, one of the architectural key components common to all ICNs, became an almost independent field of research in which significant efforts continue to be invested. In contrast, network architectural designs, scheduling and forwarding issues dating from the early days of Inter-Planetary Networks (IPNs) have received relatively little attention and accumulate numerous pending challenges. Moreover, the gap caused by the lack of accurate ICN mathematical models is still large irrespective of some of the appreciated seminal works in this direction. This paper sheds the light over the latest advancements in each of the above-mentioned research sectors and highlight pending open issues in each of them.
Propriétés mécaniques de touffes ciliaires actives

The inner ear is one of the most important sensitive organs of all vertebrates. It shows an extraordinary performance, with a large dynamic range, high sensitivity and an exquisite frequency selectivity. The inner ear is not simply a passive detector, but a nonlinear active amplifier. The most striking manifestation of this activity is the fact that the ear does not only detect sound, but it can also emit one to several tones: the so-called spontaneous oto-acoustic emissions. The auditory sense is based on the transformation of mechanical stimuli into electrical signals, which is done by the sensory cells of the inner ear, the haircells. The mechanosensitive organelle of the haircell is the hair-bundle. Hair-bundles are active structures, they are namely displaying spontaneous oscillations. These spontaneous oscillations are a natural candidate for the active process underlying the activity of the inner ear. This work is a theoretical study of the mechanical properties of the hair-bundle. We discuss the physical principles underlying detection based on critical oscillations as well as specific mechanisms that can lead to oscillations and active behavior by hair-bundles. We present a simple description of active hair-bundle mechanics. We calculate the state diagram and show that fluctuations fundamentally change the mechanical response functions. We discuss different sources of fluctuations and estimate their influence on the hair-bundle’s mechanical properties. Furthermore, the linear and nonlinear response functions calculated numerically account for the observed properties of active hair-bundles.
Incidence of Infection in Prnp ARR/ARR Sheep following Experimental Inoculation with or Natural Exposure to Classical Scrapie

The prion protein gene (Prnp) is highly influential in determining risk and susceptibility of sheep exposed to classical scrapie. Sheep homozygous for alanine at codon 136 and arginine at codons 154 and 171 (ARR/ARR) of the Prnp gene are historically considered to be highly resistant to classical scrapie, although they form a significant fraction of cases of atypical scrapie. To date, experimental transmission of prions to ARR/ARR sheep has only been achieved with the BSE agent and mostly by the intracerebral route. We summarise here the results of six separate studies, in which 95 sheep of the ARR/ARR genotype were naturally exposed to (n = 18) or experimentally challenged with (n = 77) natural or experimental sources of classical scrapie by the oral, intra-intestinal, subcutaneous or intracerebral routes and allowed to survive for periods of up to 94 months post-infection. Only the intracerebral route resulted in disease and/or amplification of disease associated PrP (PrPd), and only in two of 19 sheep that survived for longer than 36 months. Discriminatory immunohistochemistry and Western blot confirmed the scrapie, non-BSE signature of PrPd in those two sheep. However, the neuropathological phenotype was different from any other scrapie (classical or atypical) or BSE source previously reported in sheep of any Prnp genotype. These studies confirm the widely held view that ARR/ARR sheep are highly resistant to classical scrapie infection, at least within their commercial lifespan. Moreover, within the constraints of the present studies (only two infected sheep), these results do not support the suggestion that atypical scrapie or BSE are generated by adaptation or mutation of classical scrapie in sheep of resistant ARR/ARR genotype.
Fast Huygens' sweeping methods for multiarrival Green's functions of Helmholtz equations in the high-frequency regime

ABSTRACTMultiarrival Green’s functions are essential in seismic modeling, migration, and inversion. Huygens-Kirchhoff (HK) integrals provide a bridge to integrate locally valid first-arrival Green’s functions into a globally valid multiarrival Green’s function. We have designed robust and accurate finite-difference methods to compute first-arrival traveltimes and amplitudes, so that first-arrival Green’s functions can be constructed rapidly. We adapted a fast butterfly algorithm to evaluate discretized HK integrals. The resulting fast Huygens’ sweeping method has the following unique features: (1) it precomputes a set of local traveltime and amplitude tables, (2) it automatically takes care of caustics, (3) it constructs Green’s functions of the Helmholtz equation for arbitrary frequencies and for many point sources, and (4) for a fixed number of points per wavelength, it constructs each Green’s function in nearly optimal complexity O(N log N) in terms of the total number of mesh points N, where the prefa.
Network Traffic Simulator 2.0: Simulating the internet traffic

The Internet consists of a global network that provides us an impressive accessibility to various services such as Word Wide Web, email and file sharing. Understanding how the Internet is built and how data are propagated between communication networks, and more precisely between each couple of two remote computers represent an interesting challenge. In this paper we present an open-source module implemented on top of Scilab that aims to provide a complete and efficient network simulator to academic and research communities. Network Traffic Simulator 2.0 referenced as NTS has been designed in order to simulate random traffic on a network topology according to the latest accurate data propagation models. The Internet topology is generated according to a dedicated toolbox named Network Topology Generator 2.0 (NTG). Conventional graphs are used to describe the connectivity between network nodes. Scilab has been selected as the core environment of our network simulator. This open source scientific software package for numerical computations provides a powerful open computing environment for engineering and scientific applications. Its METANET module is dedicated to graph and network. As the traffic dynamic directly depends on the manner how data packets are propagated on a network, we need to generate accurate graphs that reproduce several actual Internet topology parameters coming from real measurements. NTG aims to achieve this task. Afterwards NTS allows studying the transmission protocols effectiveness of any data connection on the generated topologies. As a matter of course, its analysis relies on the network structure where data are routed, the transmission protocols used by connections, the routing algorithms and the user demand effects.
Interaction of Helicobacter pylori with C-Type Lectin Dendritic Cell-Specific ICAM Grabbing Nonintegrin

In this study we asked whether Helicobacter pylori whole cells and lipopolysaccharide (LPS) utilize sugar moieties of Lewis (Le) antigenic determinants to interact with DC-SIGN (dendritic cell specific ICAM grabbing nonintegrin) receptor on dendritic cells (DCs). For this purpose the soluble DC-SIGN/Fc adhesion assay and the THP-1 leukemia cells with induced expression of DC-SIGN were used. We showed that the binding specificity of DC-SIGN with H. pylori LeX/Y positive whole cells and H. pylori LPS of LeX/Y type was fucose dependent, whereas in LeXY negative H. pylori strains and LPS preparations without Lewis determinants, this binding was galactose dependent. The binding of soluble synthetic LeX and LeY to the DC-SIGN-like receptor on THP-1 cells was also observed. In conclusion, the LeXY dependent as well as independent binding of H. pylori whole cells and H. pylori LPS to DC-SIGN was described. Moreover, we demonstrated that THP-1 cells may serve as an in vitro model for the assessment of H. pylori-DC-SIGN interactions mediated by LeX and LeY determinants.
Elevating High-Density Lipoprotein Cholesterol in Apolipoprotein E—Deficient Mice Remodels Advanced Atherosclerotic Lesions by Decreasing Macrophage and Increasing Smooth Muscle Cell Content

BackgroundHDL cholesterol levels are inversely correlated with coronary heart disease risk in humans, and in animal studies, HDL elevation decreases formation and progression of foam-cell lesions. The potential for HDL to affect preexisting advanced atherosclerotic lesions is not known. To approach this issue, we used a novel mouse aortic transplantation model. Methods and Results—ApoE-deficient (EKO) mice were fed a Western-type diet for 6 months, and thoracic aortic segments containing advanced lesions replaced segments of the abdominal aorta of 4-month-old EKO syngeneic mice not expressing (plasma HDL cholesterol ≈26 mg/dL) or expressing (HDL ≈64 mg/dL) a human apoAI (hAI) transgene. Both types of recipients had comparable non-HDL cholesterol levels. Five months after transplantation, mice were killed and grafts analyzed. Compared with lesion area in pretransplant mice (0.14±0.04 mm2, mean±SEM), there was progression in the EKO recipients (0.39±0.06 mm2, P <0.01). Compared with EKO recipients, hAI/EKO recipients had retarded progression (0.24±0.04 mm2, P <0.05). Immunostaining for CD68 and other macrophage-associated proteins, monocyte chemoattractant protein-1, acyl coenzyme A:cholesterol acyltransferase, and tissue factor, in lesions of pretransplant and EKO recipient mice showed abundant macrophages. In contrast, compared with any other group, lesional macrophage area in hAI/EKO mice decreased >80% (P <0.003), and smooth muscle cell content (&agr;-actin staining) increased >300% (P <0.006). The decrease in macrophages and increase in smooth muscle cells was primarily in the superficial subendothelial layer. Conclusions—Increasing HDL cholesterol levels in EKO mice retards progression of advanced atherosclerotic lesions and remodels them to a more stable-appearing phenotype.
802.11a transmitter: a case study in microarchitectural exploration

Hand-held devices have rigid constraints regarding power dissipation and energy consumption. Whether a new functionality can be supported often depends upon its power requirements. Concerns about the area (or cost) are generally addressed after a design can meet the performance and power requirements. Different micro-architectures have very different area, timing and power characteristics, and these need RTL-level models to be evaluated. In this paper we discuss the microarchitectural exploration of an 802.11a transmitter via synthesizable and highly-parameterized descriptions written in Bluespec SystemVerilog (BSV). We also briefly discuss why such architectural exploration would be practically infeasible without appropriate linguistic facilities. No knowledge of 802.11a or BSV is needed to read this paper
Microsomal prostaglandin E synthase‐1 and 5‐lipoxygenase: potential drug targets in cancer

Abstract. Rådmark O, Samuelsson B (Karolinska Institutet, Stockholm, Sweden). Microsomal prostaglandin Esynthase‐1 and 5‐lipoxygenase: potential drug targets in cancer (Review). J Intern Med 2010; 268:5–14.
Alcohol-attributable mortality and potential years of life lost in Canada 2001: implications for prevention and policy.

BACKGROUND Alcohol is one of the most important risk factors for burden of disease. OBJECTIVE To estimate the number of deaths and the years of life lost attributable to alcohol for Canada 2001 using different ways to measure alcohol exposure. METHODS Distribution of exposure was taken from a major national survey of Canada, the Canadian Addiction Survey, and corrected for per capita consumption from production and sales. For chronic disease, risk relations were taken from the published literature and combined with exposure to calculate age- and sex-specific alcohol-attributable fractions (AAFs). For injury, AAFs were taken directly from available statistics. Information on mortality, with cause of death coded according to the International Classification of Diseases version 10 (ICD-10) was obtained from Statistics Canada. RESULTS For Canada in 2001, 4,010 of all deaths in the group below 70 years of age were attributable to alcohol, 3,132 in men and 877 in women. This constituted 6.0% of all deaths in Canada in this age group, 7.6% for men, and 3.5% for women. The 4,010 deaths are a net figure, already taking into account the deaths prevented by moderate consumption of alcohol. Main causes of alcohol-attributable death were unintentional injuries, malignant neoplasms and digestive diseases. Ischaemic heart disease (IHD) was the biggest cause of death prevented by alcohol, with 78.7% of all alcohol-attributable prevented deaths in the age groups of 70 years and above. A total of 144,143 years of life were lost prematurely in Canada in that year, 113,079 years in men and 31,063 years in women. DISCUSSION Regardless of the assumptions made, alcohol is a major contributor to mortality in Canada. The impact of alcohol on social life is not confined to mortality, as other studies indicated that alcohol is linked even more strongly to disability and social harm. Alcohol-attributable harm could be substantially reduced, however, if known effective policies were introduced.
Design patterns applied for networked first person shooting game programming

We studied issues in FPS game development such as expressive play, game and character states management, rending scene, maps in game world, online and team communication, weapon management in game, and multi-enemy rendering. In order to increase reusability, maintainability, and quality of game development to adapt to evolutionary game development process, we explored on how to apply design patterns to handle issues with FPS game development. Although some design patterns are discussed, other design patterns might suitable as well because game programming are so complicated to separate each pattern independently.