Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene‐centric analysis implicates nuclear encoded mitochondrial protein gene variants in migraine susceptibility

Migraine is a common neurological disorder which affects a large proportion of the population. The Norfolk Island population is a genetically isolated population and is an ideal discovery cohort for genetic variants involved in complex disease susceptibility given the reduced genetic and environmental heterogeneity. Given that the majority of proteins responsible for mitochondrial function are nuclear encoded, this study aimed to investigate the role of Nuclear Encoded Mitochondrial Protein (NEMP) genes in relation to migraine susceptibility.
Apolipoprotein D is the major protein component in cyst fluid from women with human breast gross cystic disease.

GCDFP(gross-cystic-disease-fluid protein)-24, a progesterone-binding protein present in large amounts in cyst fluid from human breast gross cystic disease, was purified in a one-step procedure by size-exclusion h.p.l.c. Peptide fragments obtained by trypsin digestion of the intact protein were purified by reverse-phase h.p.l.c. and analysed for their amino acid composition and subjected to automated Edman degradation. A search of the National Biomedical Research Foundation Data Bank revealed that all the sequenced tryptic peptides from protein GCDFP-24 matched perfectly with regions present in the amino acid sequence determined for human apolipoprotein D. Additional data on N-terminal sequence of the unblocked proteins, carbohydrate-attachment sites, amino acid composition and molecular-mass estimations supported the identity between both molecules. On the basis of this identity a possible role of apolipoprotein D in progesterone transport is proposed.
A decentralised, autonomous, and congestion-aware thermal monitoring infrastructure for photonic network-on-chip

Optical network-on-chips (oNoCs) are a promising candidate to replace electrical NoCs in many-core systems. Nanophotonic components provide high bandwidth and short transmission delay but they are very sensitive to the temperature. Temperature gradients are typically found on many-core systems. The precise reconstruction of the core's temperature and the prediction of its evolution are an inevitable requirement for an effective thermal management in oNoCs. In this work we present the first distributed and autonomous thermal monitoring infrastructure for oNoCs. It copes with the intrinsic temperature sensor's noise, provides accurate thermal predictions, and requires low communication overhead. Our approach combines Kalman filters, linear predictors, local data and global transmission to achieve an efficient implementation. The work reports a thorough analysis at the gate-level of the area overhead incurred by the communication and computation sub-modules. It shows the practicability of the approach. Further, experimental results for a 16-core SoC demonstrate that our prediction model is able to reduce by more than 92% the communication requirements of the monitoring infrastructure.
Building a high-quality sense inventory for improved abbreviation disambiguation

Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem. ac.uk/software/acromine/ and http://www.nactem. ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org
Selective Surface Smoothening of Polymer Microlenses by Depth Confined Softening

Polymeric refractive micro‐optical devices simultaneously demand striking smooth 3D topographies and precise shape accuracy for high performance and low stray light. Here, a surface selective smoothening of thermoplastic, polymeric material has been established while maintaining the high curvature corners required for a 50 µm tall, refractive, optical diffuser device. The 3D master structures are fabricated using direct write laser‐lithography with two‐photon absorption. Master structures are replicated into poly(methyl methacrylate) through a poly(dimethyl siloxane) intermediate copying step and subsequently smoothed out. Here, various high‐energy radiations have been considered to have a surface selective exposure and have been narrowed down to 172 nm ultraviolet exposure to be the ideal fit for this application. The 172 nm exposure provides selective modification of an up to 400 nm thick surface skin layer and negligible etching, which allows smoothening out up to 420 nm surface steps and reducing the RMS roughness from 22 nm down to below 10 nm by thermally driven material displacement, the so–called reflow, on a global pattern scale. Extreme ultraviolet exposure, as an alternative method, shows a higher modification efficiency than the 172 nm but has severe practical limitations.
The Effects on Microstructure and Hardness of 0.28% Vanadium and 0.87% Nickel Alloyed Ductile Iron after Boronizing Process

Boronizing/boriding is a thermo mechanical process which produced protective surface layers to enhance the performance of engineering components utilized in mechanical, wear and corrosion. The present study investigate the microstructure and the hardness of boride layers formed on 0.28% Vanadium and 0.87% Nickel alloyed ductile iron after boronizing process. Specimens were boronized at 950° C for 6, 8 and 10 hours holding time before being cooled in the furnace. The microstructure and boride layer formed on the surface of substrates were observed under Olympus BX60 Optical Microscope. Vickers Micro Hardness Tester was also performed to determine the hardness of boride layers. Boride layer was formed by diffusion of the boron into the metal lattice at the surface which composed double phase of FeB and Fe2B with saw-tooth morphology. The results of this study indicated that the thickness of boride layers increased from 109. 8μm at 6 hours to 195. 4μm at 8 hours holding time before they crack at 10 hours. The hardness of the material surface also increased from 1535 HV to 1623 HV at 6 and 8 hours respectively. In conclusion, the microstructure, borides thickness and hardness of borides layer were depending on boronizing time while temperature kept constant.
Epstein-Barr Virus Blocks the Autophagic Flux and Appropriates the Autophagic Machinery To Enhance Viral Replication

ABSTRACT Autophagy is a catabolic pathway that helps cells to survive under stressful conditions. Cells also use autophagy to clear microbiological infections, but microbes have learned how to manipulate the autophagic pathway for their own benefit. The experimental evidence obtained in this study suggests that the autophagic flux is blocked at the final steps during the reactivation of Epstein-Barr virus (EBV) from latency. This is indicated by the level of the lipidated form of LC3 that does not increase in the presence of bafilomycin and by the lack of colocalization of autophagosomes with lysosomes, which correlates with reduced Rab7 expression. Since the inhibition of the early phases of autophagy impaired EBV replication and viral particles were observed in autophagic vesicles in the cytoplasm of producing cells, we suggest that EBV exploits the autophagic machinery for its transportation in order to enhance viral production. The autophagic block was not mediated by ZEBRA, an immediate-early EBV lytic gene, whose transfection in Ramos, Akata, and 293 cells promoted a complete autophagic flux. The block occurred only when the complete set of EBV lytic genes was expressed. We suggest that the inhibition of the early autophagic steps or finding strategies to overcome the autophagic block, allowing viral degradation into the lysosomes, can be exploited to manipulate EBV replication. IMPORTANCE This study shows, for the first time, that autophagy is blocked at the final degradative steps during EBV replication in several cell types. Through this block, EBV hijacks the autophagic vesicles for its intracellular transportation and enhances viral production. A better understanding of virus-host interactions could help in the design of new therapeutic approaches against EBV-associated malignancies.
Incentive Mechanisms for Safe Driving: A Comparative Analysis with Dynamic Data

Abstract Road safety policies often use incentive mechanisms based on traffic violations to promote safe driving—for example, fines, experience rating, and point-record driver's licenses. We analyze the effectiveness of these mechanisms in promoting safe driving. We derive their theoretical properties with respect to contract time and accumulated demerit points. These properties are tested empirically with data from the Quebec public insurance plan. We find evidence of moral hazard, which means that drivers who accumulate demerit points become more careful because they are at risk of losing their license. An insurance rating scheme introduced in 1992 reduced the frequency of traffic violations by 15%. We use this result to derive monetary equivalents for traffic violations and license suspensions.
A test for paedomorphism in domestic pig cranial morphology

Domestic animals are often described as paedomorphic, meaning that they retain juvenile characteristics into adulthood. Through a three-dimensional landmark-based geometric morphometric analysis of cranial morphology at three growth stages, we demonstrate that wild boar (n = 138) and domestic pigs (n = 106) (Sus scrofa) follow distinct ontogenetic trajectories. With the exception of the size ratio between facial and neurocranial regions, paedomorphism does not appear to be the primary pattern describing the observed differences between wild and domestic pig cranial morphologies. The cranial phenotype of domestic pigs instead involves developmental innovation during domestication. This result questions the long-standing assumption that domestic animal phenotypes are paedomorphic forms of their wild counterparts.
Verification of Flow Matching Functionality in the Forwarding Plane of OpenFlow Networks

In OpenFlow, data and control plane are decoupled from switches or routers. While the data plane resides in the switches or routers, the control plane might be moved into one or more external servers (controllers). In this article, we propose verification mechanisms for the data plane functionality of switches. The latter consists of two parts: (1) Flow-Match Header part (to match a flow of incoming packets) and (2) action part (e.g., to forward incoming packets to an outgoing port). We propose a mechanism to verify the Flow-Match Header part of the data plane. The mechanism can be executed at the controller, or on an additional device or server (or virtual machines) attached to the network. Deploying a virtual machine (VM) or server for verification may decrease the load of the controller and/or consumed bandwidth between the controller and a switch. We propose a heuristic to place external verification devices or VMs in a network such that the verification time can be minimized. Verification time with respect to consumed resources are evaluated through emulation experiments. Results confirm that the verification time using the proposed heuristic is indeed shortened significantly, while requiring low bandwidth resources.
The Role of DNA Restriction-Modification Systems in the Biology of Bacillus anthracis

Restriction–modification (R–M) systems are widespread among prokaryotes and, depending on their type, may be viewed as selfish genetic elements that persist as toxin–antitoxin modules, or as cellular defense systems against phage infection that confer a selective advantage to the host bacterium. Studies in the last decade have made it amply clear that these two options do not exhaust the list of possible biological roles for R–M systems. Their presence in a cell may also have a bearing on other processes such as horizontal gene transfer and gene regulation. From genome sequencing and experimental data, we know that Bacillus anthracis encodes at least three methylation-dependent (typeIV) restriction endonucleases (RE), and an orphan DNA methyltransferase. In this article, we first present an outline of our current knowledge of R–M systems in B. anthracis. Based on available DNA sequence data, and on our current understanding of the functions of similar genes in other systems, we conclude with hypotheses on the possible roles of the three REs and the orphan DNA methyltransferase.
The SCADS Director: Scaling a Distributed Storage System Under Stringent Performance Requirements

Elasticity of cloud computing environments provides an economic incentive for automatic resource allocation of stateful systems running in the cloud. However, these systems have to meet strict performance Service-Level Objectives (SLOs) expressed using upper percentiles of request latency, such as the 99th. Such latency measurements are very noisy, which complicates the design of the dynamic resource allocation. We design and evaluate the SCADS Director, a control framework that reconfigures the storage system on-the-fly in response to workload changes using a performance model of the system. We demonstrate that such a framework can respond to both unexpected data hotspots and diurnal workload patterns without violating strict performance SLOs.
Investigation of Stress Corrosion Cracking in Magnesium Alloys by Quantitative Fractography Methods

The article shows that the use of quantitative fracture description may lead to significant progress in research on the phenomenon of stress corrosion cracking of the WE43 magnesium alloy. Tests were carried out on samples in air, and after hydrogenation in 0.1 M Na2SO4 with cathodic polarization. Fracture surfaces were analyzed after different variants of the Slow Strain Rate Test. It was demonstrated that the parameters for quantitative evaluation of fracture surface microcracks can be closely linked with the susceptibility of the WE43 magnesium alloy operating under complex state of the mechanical load in corrosive environments. The final result of the study was the determination of the quantitative relationship between Slow Strain Rate Test parameters, the mechanical properties, and the parameters of the quantitative evaluation of fracture surface (microcracks).
4 D SURFACE MATCHING FOR HIGH-SPEED STEREO SEQUENCES

In automotive industry, an increasing demand on 3D surface reconstruction from high-speed camera images can be observed, e.g. in car safety testing environments. The paper deals with the automatic photogrammetric measurement of free-form surfaces from synchronous stereo and multi-image sequences as they are required for dynamic area-based deformation analysis. Firstly, instrumental solutions for synchronous acquisition of multi-image sequences are discussed. For surface reconstruction different image-based matching methods are evaluated and compared with an object-based matching method based on the FAST Vision principle. For each step of the sequence, a three-dimensional surface model is generated, that can be enhanced to a 4D deformation model with time as fourth dimension. For visual analysis the photogrammetrically oriented image sequences can be resampled to sub-pixel accurate anaglyph movies. * Corresponding author.
Glitazones Induce Astroglioma Cell Death by Releasing Reactive Oxygen Species from Mitochondria: Modulation of Cytotoxicity by Nitric Oxide

The glitazones (or thiazolidinediones) are synthetic compounds used in type-2 diabetes, but they also have broad antiproliferative and anti-inflammatory properties still not well understood. We described previously the apoptotic effects of glitazones on astroglioma cells ( J Biol Chem279:8976-8985, 2004 ). At certain concentrations, we found a selective lethality on glioma cells versus astrocytes that was dependent on a rapid production of reactive oxygen species (ROS) and seemed unrelated to the receptor peroxisome proliferator activated receptor-γ. The present study was aimed at characterizing the oxygen derivatives induced by ciglitazone, rosiglitazone, and pioglitazone in C6 glioma cells and to investigate their intracellular source. We examined the interaction of ROS with nitric oxide (NO) and its consequences for glioma cell survival. Fluorescence microscopy and flow cytometry showed that glitazones induced superoxide anion, peroxynitrite, and hydrogen peroxide, with ciglitazone being the most active. ROS production was completely prevented by uncoupling of the electron transport chain and by removal of glucose as an energy substrate, whereas it was unaffected by inhibition of NADPH-oxidase and xanthine-oxidase. Moreover, glitazones inhibited state 3 respiration in permeabilized cells, and experiments with mitochondrial inhibitors suggested that complex I was the likely target of glitazones. Therefore, these results point to the mitochondrial electron transport chain as the source of glitazone-induced ROS in C6 cells. Glitazones also depolarized mitochondria and reduced mitochondrial pH. NO synthase inhibitors revealed that superoxide anion combines with NO to yield peroxynitrite and that the latter contributes to the cytotoxicity of glitazones in astroglioma cells. Future antitumoral strategies may take advantage of these findings.
Performance Evaluation of Vector Evaluated Gravitational Search Algorithm II

This paper presents a performance evaluation of a novel Vector Evaluated Gravitational Search Algorithm II (VEGSAII) for multi-objective optimization problems. The VEGSAII algorithm uses a number of populations of particles. In particular, a population of particles corresponds to one objective function to be minimized or maximized. Simultaneous minimization or maximization of every objective function is realized by exchanging a variable between populations. The results shows that the VEGSA is outperformed by other multi-objective optimization algorithms and further enhancements are needed before it can be employed in any application.
A Survey on Identity Management for the Future Network

The Internet as a platform for ubiquitous communication has quickly advanced in the last years. New services have emphasized the limits of the current Internet and motivated the development of the Future Internet. Future communication infrastructures intend to be more distributed and, ideally, more secure, resulting in high complexity. Further, as new technologies emerge, new requirements and security issues are highlighted. These issues reinforce the importance of Identity Management systems for the network infrastructure in the Future Internet, termed Future Network, to provide adequate dynamic services in relation to user's personal data and requirements. Hence, this survey presents the state of the art of Identity Management systems for the Future Network. It highlights the existing architectures, specific devices applied, challenges and future perspectives.
Monounsaturated Fatty Acids Prevent the Aversive Effects of Obesity on Locomotion, Brain Activity, and Sleep Behavior

Fat and physical inactivity are the most evident factors in the pathogenesis of obesity, and fat quality seems to play a crucial role for measures of glucose homeostasis. However, the impact of dietary fat quality on brain function, behavior, and sleep is basically unknown. In this study, mice were fed a diet supplemented with either monounsaturated fatty acids (MUFAs) or saturated fatty acids (SFAs) and their impact on glucose homeostasis, locomotion, brain activity, and sleep behavior was evaluated. MUFAs and SFAs led to a significant increase in fat mass but only feeding of SFAs was accompanied by glucose intolerance in mice. Radiotelemetry revealed a significant decrease in cortical activity in SFA-mice whereas MUFAs even improved activity. SFAs decreased wakefulness and increased non–rapid eye movement sleep. An intracerebroventricular application of insulin promoted locomotor activity in MUFA-fed mice, whereas SFA-mice were resistant. In humans, SFA-enriched diet led to a decrease in hippocampal and cortical activity determined by functional magnetic resonance imaging techniques. Together, dietary intake of MUFAs promoted insulin action in the brain with its beneficial effects for cortical activity, locomotion, and sleep, whereas a comparable intake of SFAs acted as a negative modulator of brain activity in mice and humans.
Diffusion Limited Reactions

Changes to the relative separation of molecules or other interacting species on account of diffusion accompany their associative or dissociative reaction. The molecules are symbolized, for two distinct types, $A,B$, by the relations $A+B \leftrightharpoons AB$, and, if $[A]$, $[B]$, and $[AB]$ denote the corresponding densities, the equation $\frac{d}{dt} [AB] = k_+ [A][B]$ specifies an associative process with forward rate constant $k_+$. An approximate version of the preceding takes the form of a linear differential equation, which can be employed to obtain significant estimates for both $k_+$ and the flux function $d [AB]/dt$. Such estimates are presented in different circumstances, including the localization of $A,B$ on a common planar surface or their distribution in space, and also when the domain of A is a half space whereas that of B is a bounding planar surface. It proves advantageous to reformulate the last, a mixed boundary value problem, in terms of a linear integral equation. Biological appli.
Design, synthesis, and biological evaluation of 3,4,5-trimethoxyphenyl acrylamides as antinarcotic agents

The synthesis and biological evaluation of 3,4,5-trimethoxyphenyl acrylamides 1a–f as novel antinarcotic agents are described. The molecules were prepared by the Wittig reaction, followed by a coupling reaction between 3,4,5-trimethoxycinnamic acid (9) and aliphatic amines, which resulted in good yields. When tested for biological activity, compounds 1d–f exhibited strong inhibitory effects on the morphine withdrawal syndrome in mice due to their high binding affinities with serotonergic 5-HT1A receptors.