Miracle-dz/UniFAR-FTUs huggingface dataset:
Topology-aware resource management for HPC applications

The Resource and Job Management System (RJMS) is a crucial system software part of the HPC stack. It is responsible for efficiently delivering computing power to applications in supercomputing environments. Its main intelligence relies on resource selection techniques to find the most adapted resources to schedule the users' jobs. Improper resource selection operations may lead to poor performance executions and global system utilization along with an increase of the system fragmentation and jobs starvation. These phenomena play a role in the increase of the platforms' total cost of ownership and should be minimized. This paper introduces a new method that takes into account the topology of the machine and the application characteristics to determine the best choice among the available nodes of the platform based upon their position within the network and taking into account the applications communication pattern. To validate our approach, we integrate this algorithm as a plugin for Slurm, a popular and widespread HPC resource and job management system (RJMS). We assess our plugin with different optimization schemes by comparing with the default topology-aware Slurm algorithm using both emulation and simulation of a large-scale platform, and by carrying out experiments in a real cluster. We show that transparently taking into account the job communication pattern and the topology allows for relevant performance gains.
Discrete states in light-like linear dilaton background

We study the spectrum of bosonic strings in the light-like linear dilaton background and find discrete states. These are physical states which exist only at specific values of momentum. All discrete states except one generate spacetime symmetries. The exceptional discrete state corresponds to constraints which are deformations of conservation laws. The constraints resemble those arising from symmetries, and are equally powerful, suggesting that our notion of symmetry should be generalized.
Exploiting Sample Diversity in Distributed Machine Learning Systems

With the increase of machine learning scalability, there is a growing need for distributed systems which can execute machine learning algorithms on large clusters. Currently, most distributed machine learning systems are developed based on iterative optimization algorithm and parameter server framework. However, most systems compute on all samples in every iteration and this method consumes too much computing resources since the amount of samples is always too large. In this paper, we study on the sample diversity and find that most samples ontribute little to model updating during most iterations. Based on these findings, we propose a new iterative optimization algorithm to reduce the computation load by reusing the iterative computing results. The experiment demonstrates that, compared to the current methods, the algorithm proposed in this paper can reduce about 23% of the whole computation load without increasing of communications.
Variation-Tolerant Quick-Start-Up CMOS Crystal Oscillator With Chirp Injection and Negative Resistance Booster

This paper presents a variation-tolerant quick-startup 39.25 MHz crystal oscillator and a theoretical analysis of a proposed chirp injector (CI) and negative resistance booster (NRB) for the quick start up. A new analysis of the theoretical minimum start-up time provides a new criterion for evaluating the start-up time in crystal oscillators. The calculated theoretical minimum start-up time at 39.25 MHz is 11.1 μs. Anew analysis of the proposed CI and NRB clarifies the validity of the universal optimum control method. It explains the reason why the proposed CI and NRB reduce the start-up time and its variation. The proposed crystal oscillator with the proposed CI and NRB exhibits a startup time of 158 μs at 39.25 MHz. The variation of the start-up time variations is ±13% over the supply voltage range of 1.2-1.8 V and ±7% over the temperature range of -30 to 125 °C. The power consumption of the crystal oscillator in the steady state is 181 μW with a phase noise of -147 dBc/Hz at 1 kHz offset frequency, which corresponds to a figure of merit (FoM) of 276 dB.
Touch in Human Space Exploration: Towards the Design of a Morphing Haptic Glove – ExoSkin

The spacesuit, particularly the spacesuit glove, creates a barrier between astronauts and their environment. Motivated by the vision of facilitating full-body immersion for effortless space exploration, it is necessary to understand the sensory needs of astronauts during extra-vehicular activities (EVAs). In this paper, we present the outcomes from a two-week field study performed at the Mars Desert Research Station, a facility where crews carry out Marssimulated missions. We used a combination of methods (a haptic logbook, technology probes, and interviews) to investigate user needs for haptic feedback in EVAs in order to inform the design of a haptic glove. Our results contradict the common belief that a haptic technology should always convey as much information as possible, but should rather offer a controllable transfer. Based on these findings, we identified two main design requirements to enhance haptic feedback through the glove: (i) transfer of the shape and pressure features of haptic information and (ii) control of the amount of haptic information. We present the implementation of these design requirements in the form of the concept and first prototype of ExoSkin. ExoSkin is a morphing haptic feedback layer that augments spacesuit gloves by controlling the transfer of haptic information from the outside world onto the astronauts’ skin.
Relationship between Sleep Quality and Quality of Life in Patients with Multiple Sclerosis

Background: Impaired quality of life (QOL) is an issue considered in patients with multiple sclerosis (MS). There are limited studies evaluated poor sleep and impaired QOL in these cases. The aim of this study was to evaluate quality of sleep and poor sleep in Iranian patients with MS and the relationship between Pittsburgh Sleep Quality Index (PSQI) score and QOL subscales. Methods: One-hundred and fourteen cases with definite MS due to MC Donald criteria enrolled who referred to MS clinic of Sina and Imam Hospitals were enrolled. Patients asked to fill valid and reliable Persian versions of PSQI and MSQOL-54 questionnaires. Demographic data (sex, age), duration of the disease, education level and marital status were extracted from patients medical files. After neurological examination, Kurtzke Expanded Disability Status Scale (EDSS) was assessed. Results: Ninety-one (79.8%) patients were female and 23 (20.2%) were male. Mean age and EDSS was 34.7 ± 9.6 years and 2.3 (median: 1.5). Mean PSQI score and overall QOL score were 4.5 and 57. Sixty-seven cases were good sleepers (PSQI ≤ 5) and 47 were poor sleepers (PSQI > 5). Except five subscales, all others were significantly different between good and poor sleepers. There was significant positive correlation between PSQI score and EDSS (r = 0.24, P < 0.001) and negative correlation between EDSS and physical and mental health (r = −0.48, P < 0.001, r = −0.43, P < 0.001). EDSS and total PSQI score were independent predictors of physical and mental health composites. Conclusions: Sleep quality as a factor which affecting QOL should be considered and evaluated properly in MS patients.
High-Throughput Sparsity-Based Inversion Scheme for Optoacoustic Tomography

The concept of sparsity is extensively exploited in the fields of data acquisition and image processing, contributing to better signal-to-noise and spatio-temporal performance of the various imaging methods. In the field of optoacoustic tomography, the image reconstruction problem is often characterized by computationally extensive inversion of very large datasets, for instance when acquiring volumetric multispectral data with high temporal resolution. In this article we seek to accelerate accurate model-based optoacoustic inversions by identifying various sources of sparsity in the forward and inverse models as well as in the single- and multi-frame representation of the projection data. These sources of sparsity are revealed through appropriate transformations in the signal, model and image domains and are subsequently exploited for expediting image reconstruction. The sparsity-based inversion scheme was tested with experimental data, offering reconstruction speed enhancement by a factor of 40 to 700 times as compared with the conventional iterative model-based inversions while preserving similar image quality. The demonstrated results pave the way for achieving real-time performance of model-based reconstruction in multi-dimensional optoacoustic imaging.
Frequency-of-occurrence of myoelectric patterns to evaluate gait motor control strategies after hip replacement surgery

Gait alterations are observed even years after hip replacement surgery. Such long-lasting alterations may arise from a global change of the motor control strategies. The aim of this work is to investigate the changes in gait motor control strategies of patients after hip replacement surgery by analyzing the frequency of occurrence (OF) of myoelectric activation patterns. We studied five lower limb muscles during gait, in hip prosthesis patients and controls. We found that patients adopt a motor control strategy that tends to prefer “simplified” myoelectric patterns, showing a smaller number of activations within the gait cycle. This altered motor control was present both on the prosthesis and the sound side, and did not improve during the 12-month follow-up. The reduced number of activations is even more evident in lateral hamstrings and gluteus medius, which are the muscles more affected by hip replacement surgery. Furthermore, this study demonstrated that the OF is a sensitive parameter able to discover subtle changes in motor control strategies. Its use can be extended to other studies involving motor coordination, motor learning and motor control adaptations.
Answer Set Programming and Bounded Model Checking Keijo Heljanko and Ilkka Niemelä

In this paper bounded model checking of asynchronous concurrent systems is introduced as a promising application area for answer set programming. This is an extension of earlier work where bounded model checking has been used for verification of sequential digital circuits. As the model of asynchronous systems a generalization of communicating automata, 1-safe Petri nets, are used. A mapping from bounded reachability and deadlock detection problems of 1-safe Petri nets to stable model computation is devised. Some experimental results on solving deadlock detection problems using the mapping and the Smodels system are presented. They indicate that the approach is quite competitive when searching for short executions of the system leading to deadlock.
Instruction level power analysis and optimization of software

The increasing popularity of power constrained mobile computers and embedded computing applications drives the need for analyzing and optimizing power in all the components of a system. Software constitutes a major component of today's systems, and its role is projected to grow even further. Thus, an ever increasing portion of the functionality of today's systems is in the form of instructions, as opposed to gates. This motivates the need for analyzing power consumption from the point of view of instructions—something that traditional circuit and gate level power analysis tools are inadequate for. This paper describes an alternative, measurement based instruction level power analysis approach that provides an accurate and practical way of quantifying the power cost of soft-ware. This technique has been applied to three commercial, architecturally different processors. The salient results of these analyses are summarized. Instruction level analysis of a processor helps in the development of models for power consumption of software executing on that processor. The power models for the subject processors are described and interesting observations resulting from the comparison of these models are highlighted. The ability to evaluate software in terms of power consumption makes it feasible to seach fow low power implementations of given programs. In addition, it can guide the development of general tools and techniques for low power software. Several ideas in this regard as motivated by the power analysis of the subject processors are also described.
Exercise hyperaemia: is anything obligatory but the hyperaemia?

Exercise can increase skeletal muscle blood flow by 100‐fold over values observed at rest. As this value was 3 to 4 times higher than so‐called ‘textbook’ values at the time it raised a number of issues about cardiovascular control. However, there is a continuing inability to identify the factor or combination of factors that explain this substantial increase in muscle blood flow. Moreover, these governing mechanism(s) must also explain the precise matching of muscle blood flow to metabolic demand and oxygen use or need. The difficulties identifying the mechanisms for exercise hyperaemia are especially disappointing due to the essentially concurrent discovery in the 1980s that the vascular endothelium was a key site of vasomotor control and that nitric oxide (NO) potentially released from nerves, endothelial cells, directly from tissues such as skeletal muscle, or perhaps released from red blood cells, might participate in vascular control in a way that would permit blood flow and metabolism to be closely matched.
Tracking menus

We describe a new type of graphical user interface widget, known as a "tracking menu. " A tracking menu consists of a cluster of graphical buttons, and as with traditional menus, the cursor can be moved within the menu to select and interact with items. However, unlike traditional menus, when the cursor hits the edge of the menu, the menu moves to continue tracking the cursor. Thus, the menu always stays under the cursor and close at hand.In this paper we define the behavior of tracking menus, show unique affordances of the widget, present a variety of examples, and discuss design characteristics. We examine one tracking menu design in detail, reporting on usability studies and our experience integrating the technique into a commercial application for the Tablet PC. While user interface issues on the Tablet PC, such as preventing round trips to tool palettes with the pen, inspired tracking menus, the design also works well with a standard mouse and keyboard configuration.
Oligomers of the cytoplasmic domain of the p62/E2 membrane protein of Semliki Forest virus bind to the nucleocapsid in vitro

We analyzed the interaction between the nucleocapsid and synthetic peptides corresponding to the complete or truncated cytoplasmic protein domain of the Semliki Forest virus p62/E2 glycoprotein. We found that the peptide corresponding to the full-length domain efficiently bound nucleocapsids when coupled to a solid matrix via specific antibodies, whereas the shorter one did not. In solution, a substantial fraction of the full-length peptide associated into oligomers. Binding studies showed that it was mostly these oligomers, rather than the monomeric form of the peptide, which were able to interact with the nucleocapsid. Thus, our findings demonstrate a direct interaction between the spike proteins and the viral nucleocapsid. Furthermore, they suggest that this interaction is directed through formation of complexes containing several p62 or E2 subunits.
Resistance to quinolones and tetracycline and its molecular background among Campylobacter strains isolated in Poland

The aim of this study was to investigate the resist ance to quinolones and tetracycline of 200 C. jejuni and C. coli strains isolated from poultry and poultry meat. Among the s trains tested, a high-level of resistance, ranging from 78% to 82% for nalidixid acid and ciprofloxacin, as well as from 44%-56% for tetracycline was observed. Moreover, all Campylobacter strains were examined for the molecular background of the appearing resis tance. Almost all resistant strains tested by MAMA- PCR carried the Thr-86-to-Ile mutation in the gyrA gene. This mutation was not found in the sensitive strains. These results were confirmed by DNA sequencing performed on a group of selected strains. Moreover, all tetracycline-resistant, but none of the sensit ive Campylobacter strains possessed the tet(O) gene. These data revealed that the antibiotic resi stance of Campylobacter strains represent a considerable risk for the consumption of poultry meat and should be monitored in the poultry production chain.
Secessionist Automobility: Racism, Anti-Urbanism, and the Politics of Automobility in Atlanta, Georgia

Automobility — the centering of society and everyday life around automobiles and their spaces — is one of the most contentious aspects of contemporary urban growth debates at the local, national, and global scale. The politics of automobility is a spatial struggle over how the city should be organized and for whom. Yet there is little research on how this struggle is unfolding, and how that politics is shaping urban space. Part of this stems from the essentialization of automobility in policy and academic discourses on cities. Moving beyond essentialization, this article will explore how contentious political struggles reveal nuanced and diverse discourses and ideologies surrounding automobility and space. Focusing on what I call ‘secessionist automobility’— using an automobile as an instrument of spatial secession — I examine Atlanta, Georgia’s contentious automobility debate. Secessionist automobility is bound with the blunt politics of race-based secession from urban space, but also more subtle forms of spatial secession rooted in anti-urban ideologies. Implications for local, national, and global contestation of automobility will be provided.
DNA Methylation: A Timeline of Methods and Applications

DNA methylation is a biochemical process where a DNA base, usually cytosine, is enzymatically methylated at the 5-carbon position. An epigenetic modification associated with gene regulation, DNA methylation is of paramount importance to biological health and disease. Recently, the quest to unravel the Human Epigenome commenced, calling for a modernization of previous DNA methylation profiling techniques. Here, we describe the major developments in the methodologies used over the past three decades to examine the elusive epigenome (or methylome). The earliest techniques were based on the separation of methylated and unmethylated cytosines via chromatography. The following years would see molecular techniques being employed to indirectly examine DNA methylation levels at both a genome-wide and locus-specific context, notably immunoprecipitation via anti-5′methylcytosine and selective digestion with methylation-sensitive restriction endonucleases. With the advent of sodium bisulfite treatment of DNA, a deamination reaction that converts cytosine to uracil only when unmethylated, the epigenetic modification can now be identified in the same manner as a DNA base-pair change. More recently, these three techniques have been applied to more technically advanced systems such as DNA microarrays and next-generation sequencing platforms, bringing us closer to unveiling a complete human epigenetic profile.
Remote Sensing Methods in the Identification of Oil Contaminations / Možnosti Využití Vybraných Metod Dpz Pro Identifikaci Ropných Kontaminací (Starých Ekologických Zátěží)

Abstract The article deals with the possibilities of using remote sensing methods for analysis, observation and identification of old ecological hazards caused by petroleum contaminations from insufficiently plugged and abandoned oil wells in the area of Hodonín. It is focused on the description and determination of areas of interests, remote sensing approaches to the problems of petroleum substance detection and establishing the methodology of an acquired data analysis. Moreover, proper methods, algorithms and satellite digital data parameters for this aim are discussed. The article also describes in-situ measurements, technical instruments and further research advancements. Finally, the proposals of the results evaluation, interpretation and complex comparisons with the results of past and future researches in the area of Nesyt - Hodonín are specified. Abstrakt V príspevku autori informujú o možnostiach využitia vybraných metód diaľkového prieskumu Zeme (DPZ) pre sledovanie, analýzy a identifikovanie starých ekologických záťaží spôsobených ropnými kontamináciami z nedostatočne zlikvidovaných ropných vrtov a sond na Hodonínsku. Zaoberajú sa popisom a vymedzením sledovaných lokalít, prístupmi DPZ k problematike detekcie ropných látok a navrhovanou metodikou vyhodnotenia zozbieraných vstupných dát. Ďalej sú diskutované metódy vhodné pre tento účel a taktiež parametre družicových dát. Opisované sú terénne experimenty, využitá technika a ďalšie smerovanie aktivít výskumu. Na záver sú spomenuté návrhy na využitie a komplexnejšie porovnanie výsledkov s už prebehnutými resp. plánovanými výskumami v oblastiach Nesytu - Hodonína.
Islands of failure: employing word accent information for pronunciation quality assessment of English L2 learners

So far, applied research aiming at computer-assisted pronunciation training has normally concentrated on segmental aspects. Here, we present a database with realizations of nonnative English speakers with German, French, Spanish, and Italian as native language. We concentrate on the acoustic-prosodic modelling of word accent position and use a large prosodic feature vector to automatically recognize erroneous word accent positions produced by non-native English speakers.
Molecular classification of urothelial carcinoma: global mRNA classification versus tumour‐cell phenotype classification

Global mRNA expression analysis is efficient for phenotypic profiling of tumours, and has been used to define molecular subtypes for almost every major tumour type. A key limitation is that most tumours are communities of both tumour and non‐tumour cells. This problem is particularly pertinent for analysis of advanced invasive tumours, which are known to induce major changes and responses in both the tumour and the surrounding tissue. To identify bladder cancer tumour‐cell phenotypes and compare classification by tumour‐cell phenotype with classification by global gene expression analysis, we analysed 307 advanced bladder cancers (cystectomized) both by genome gene expression analysis and by immunohistochemistry with antibodies for 28 proteins. According to systematic analysis of gene and protein expression data, focusing on key molecular processes, we describe five tumour‐cell phenotypes of advanced urothelial carcinoma: urothelial‐like, genomically unstable, basal/SCC‐like, mesenchymal‐like, and small‐cell/neuroendocrine‐like. We provide molecular pathological definitions for each subtype. Tumours expressing urothelial differentiation factors show inconsistent and abnormal protein expression of terminal differentiation markers, suggesting pseudo‐differentiation. Cancers with different tumour‐cell phenotypes may co‐cluster (converge), and cases with identical tumour‐cell phenotypes may cluster apart (diverge), in global mRNA analyses. This divergence/convergence suggests that broad global commonalities related to the invasive process may exist between muscle‐invasive tumours regardless of specific tumour‐cell phenotype. Hence, there is a systematic disagreement in subtype classification determined by global mRNA profiling and by immunohistochemical profiling at the tumour‐cell level. We suggest that a combination of molecular pathology (tumour‐cell phenotype) and global mRNA profiling (context) is required for adequate subtype classification of muscle‐invasive bladder cancer. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.