Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS

Deformation and fracture processes in engineering materials often require simultaneous descriptions over a range of length and time scales, with each scale using a different computational technique. Here we present a high-performance parallel 3D computing framework for executing large multiscale studies that couple an atomic domain, modeled using molecular dynamics and a continuum domain, modeled using explicit finite elements. We use the robust Coupled Atomistic/Discrete-Dislocation (CADD) displacement-coupling method, but without the transfer of dislocations between atoms and continuum. The main purpose of the work is to provide a multiscale implementation within an existing large-scale parallel molecular dynamics code (LAMMPS) that enables use of all the tools associated with this popular open-source code, while extending CADD-type coupling to 3D. Validation of the implementation includes the demonstration of (i) stability in finite-temperature dynamics using Langevin dynamics, (ii) elimination of wave reflections due to large dynamic events occurring in the MD region and (iii) the absence of spurious forces acting on dislocations due to the MD/FE coupling, for dislocations further than 10 Å from the coupling boundary. A first non-trivial example application of dislocation glide and bowing around obstacles is shown, for dislocation lengths of ∼50 nm using fewer than 1 000 000 atoms but reproducing results of extremely large atomistic simulations at much lower computational cost.
Structure-Activity Studies and Therapeutic Potential of Host Defense Peptides of Human Thrombin

ABSTRACT Peptides of the C-terminal region of human thrombin are released upon proteolysis and identified in human wounds. In this study, we wanted to investigate minimal determinants, as well as structural features, governing the antimicrobial and immunomodulating activity of this peptide region. Sequential amino acid deletions of the peptide GKYGFYTHVFRLKKWIQKVIDQFGE (GKY25), as well as substitutions at strategic and structurally relevant positions, were followed by analyses of antimicrobial activity against the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, the Gram-positive bacterium Staphylococcus aureus, and the fungus Candida albicans. Furthermore, peptide effects on lipopolysaccharide (LPS)-, lipoteichoic acid-, or zymosan-induced macrophage activation were studied. The thrombin-derived peptides displayed length- and sequence-dependent antimicrobial as well as immunomodulating effects. A peptide length of at least 20 amino acids was required for effective anti-inflammatory effects in macrophage models, as well as optimal antimicrobial activity as judged by MIC assays. However, shorter (>12 amino acids) variants also displayed significant antimicrobial effects. A central K14 residue was important for optimal antimicrobial activity. Finally, one peptide variant, GKYGFYTHVFRLKKWIQKVI (GKY20) exhibiting improved selectivity, i.e., low toxicity and a preserved antimicrobial as well as anti-inflammatory effect, showed efficiency in mouse models of LPS shock and P. aeruginosa sepsis. The work defines structure-activity relationships of C-terminal host defense peptides of thrombin and delineates a strategy for selecting peptide epitopes of therapeutic interest.
Resuscitation of Asphyxic Newborn Infants with Room Air or 100% Oxygen

ABSTRACT: To test the hypothesis that room air is superior to 100% oxygen when asphyxiated newborns are resuscitated, 84 neonates (birth weight > 999 g) with heart rate <80 and/or apnea at birth were allocated to be resuscitated with either room air (n = 42) or 100% oxygen (n = 42). Serial, unblinded observations of heart rates at 1, 3, 5, and 10 min and Apgar scores at 1 min revealed no significant differences between the two groups. At 5 min, median (25th and 75th percentile) Apgar scores were higher in the room air than in the oxygen group [8 (7–9) versus 7 (6–8), p = 0.03]. After the initial resuscitation, arterial partial pressure of oxygen, pH, and base excess were comparable in the two groups. Assisted ventilation was necessary for 2.4 (1.5–3.4) min in the room air group and 3.0 (2.0–4.0) min in the oxygen group (p = 0.14). The median time to first breath was 1.5 (1.0–2.0) min in both the room air and oxygen groups (p = 0.59), and the time to first cry was 3.0 (2.0–4.0) min and 3.5 (2.5–5.5) min in the room air and oxygen groups, respectively (p = 0.19). Three neonates in the room air group and four in the oxygen group died in the neonatal period. At 28 d, 72 of the 77 surviving neonates were available for follow-up (36 in each group), and none had any neurologic sequelae. This preliminary study did not provide conclusive evidence that room air is superior to 100% oxygen in the resuscitation of asphyxiated newborns, although it indicated that room air is as effective as 100% oxygen. Additional trials with increased numbers of patients are necessary before deciding whether room air or oxygen should be used in clinical practice.
Boosting the Accuracy of Differentially-Private Queries Through Consistency

Recent differentially private query mechanisms offer strong privacy guarantees by adding noise to the query answer. For a single counting query, the technique is simple, accurate, and provides optimal utility. However, analysts typically wish to ask multiple queries. In this case, the optimal strategy is not apparent, and alternative query strategies can involve difficult trade-offs in accuracy, and may produce inconsistent answers. In this work we show that it is possible to significantly improve accuracy for a general class of histogram queries. Our approach carefully chooses a set of queries to evaluate, and then exploits consistency constraints that should hold over the noisy output. In a post-processing phase, we compute the consistent input most likely to have produced the noisy output. The final output is both private and consistent, but in addition, it is often much more accurate. We apply our techniques to real datasets and show they can be used for estimating the degree sequence of a graph very precisely, and for computing a histogram that can support arbitrary range queries accurately.
An application of information theory to intrusion detection

Zero-day attacks, new (anomalous) attacks exploiting previously unknown system vulnerabilities, are a serious threat. Defending against them is no easy task, however. Having identified "degree of system knowledge" as one difference between legitimate and illegitimate users, theorists have drawn on information theory as a basis for intrusion detection. In particular, Kolmogorov complexity (K) has been used successfully. In this work, we consider information distance (Observed_K - Expected_K) as a method of detecting system scans. Observed_K is computed directly, Expected_K is taken from compression tests shared herein. Results are encouraging. Observed scan traffic has an information distance at least an order of magnitude greater than the threshold value we determined for normal Internet traffic. With 320 KB packet blocks, separation between distributions appears to exceed 4sigma
Molecular Sequence Evidence for the Reclassification of Some Babesia Species

Abstract: Taxonomic characterization of organisms in the genera Theileria and Babesia was originally based on observations of morphology and certain general phenotypic characteristics, which enabled many parasites to be unequivocally assigned to a particular genus. However, application of molecular genetic techniques, such as the polymerase chain reaction (PCR) for gene amplification, and DNA sequencing, have revealed gross inconsistencies in the assignation of some parasite genetic variants, particularly those of the B. gibsoni and B. microti complexes, to the genus Babesia. These variants cannot be assigned, on the basis of sequence information and phylogenetic analysis, to either of the genera Theileria and Babesia. The gene for which most sequence information is available for phylogenetic analysis is the small subunit ribosomal RNA (srRNA) gene. This gene allows clear distinction of the genera Theileria and Babesia (sensu stricto) and reveals that many “Babesia” variants are phylogenetically distinct from both genera. This distinction is confirmed, for some of the variants, by β‐tubulin sequence data, suggesting that the organisms should be renamed and reclassified.
Screen-space silhouettes for visualizing ensembles of 3D isosurfaces

Visualizing sets of isosurfaces from 3D scalar ensemble fields is a difficult task due to inherent occlusion effects, yet it is often required to analyze the uncertainty represented by such an ensemble. In this paper, we present a novel visualization technique for ensembles of isosurfaces based on screen-space silhouettes. By using silhouettes, the displayed information is reduced to avoid occlusions, yet the major shape of the surfaces can be maintained. Our approach preserves spatial coherence and does not make any assumption about the underlying surface distribution. By providing additional mechanisms, i.e., picking, clustering, cutting and animation, we enable the user to explore an ensemble of surfaces interactively.
Supporting infobuttons with terminological knowledge

We have developed several prototype applications which integrate clinical systems with on-line information resources by using patient data to drive queries in response to user information needs. We refer to these collectively as infobuttons because they are evoked with a minimum of keyboard entry. We make use of knowledge in our terminology, the Medical Entities Dictionary (MED) to assist with the selection of appropriate queries and resources, as well as the translation of patient data to forms recognized by the resources. This paper describes the kinds of knowledge in the MED, including literal attributes, hierarchical links and other semantic links, and how this knowledge is used in system integration.
Dissecting popliteal cyst resulting from a fragmented, dislodged metal part of the patellar component after total knee arthroplasty.

Dissecting popliteal cyst is an uncommon complication after total knee arthroplasty, occurring mainly as a result of either rheumatoid arthritis or a malfunctioning knee prosthesis. Its association with a failed metal-backed patellar component has not been reported since the introduction of the resurfacing of the patella with this kind of design in 1980. We present a case of a late fracture-dislocation of the metal part of the patellar component that migrated to the posterior popliteal fossa, resulting in a cystic mass formation caused by a foreign body granuloma. The patient was treated successfully with a 2-stage operation: first, revision of the total knee arthroplasty and, second, excision of the cyst. The patient had a pain-free functional knee 7 years after surgery, with no recurrence of the symptoms or the popliteal cyst.
Pore diameter of more than 100 μm is not requisite for bone ingrowth in rabbits

The optimal pore size for bone ingrowth is claimed to be 100-400 microm. With the use of a highly standardized experimental model, the present study reevaluated whether a pore size of 100 microm is the threshold value for bone ingrowth into porous structures under non-load-bearing conditions. Titanium triangle-shaped plates 250 or 500 microm thick were perforated with the use of a laser in order to create standard-sized holes ( 50, 75, 100, and 125 microm) in multiple rows. The amount of bone ingrowth through the implant holes was studied in the cancellous bone of the distal rabbit femur. Twelve weeks after implantation, detailed analysis of bone ingrowth was performed with computerized image analysis of backscattered electron imaging techniques of scanning electron microscopy. The results showed that the amount of ingrown new bone was independent of the pore size and implant thickness. The median value for bone ingrowth varied between 64 and 78%. A striking feature was the formation of secondary osteonal structures even in the smallest holes. Based on these results, there is no threshold value for new bone ingrowth in pore sizes ranging from 50 to 125 microm under non-load-bearing conditions.
A Pseudo-Random Subchannel Selection scheme for downlink interference mitigation in two-tier cellular networks

Femtocell technology, which is adopted in broadband communication systems, has become an economical way to improve cellular coverage and system capacity. However, it is difficult to exploit the advantages of femtocells in two-tier OFDMA networks because of the interference among the macrocell and femtocells. In this paper, a Pseudo-Random Subchannel Selection (PRSS) scheme is proposed with hybrid frequency allocation for downlink transmission to mitigate the interference. Firstly, the PRSS scheme is performed to randomize the cross-tier interference by aggressor femtocells selecting subchannels pseudo-randomly. Then the proposed scheme utilizes Neighbor Relation Matrix, which could be simplified as the neighbor relationships of adjacent femtocells, to mitigate the co-tier interference. The simulation results showed that the PRSS scheme keeps interference lower while obtains better throughput compared to co-channel frequency allocation (CFA), dedicated frequency allocation (DFA), partial frequency allocation (PFA) and stochastic subchannel allocation (SSA).
Superficial layers of the medial entorhinal cortex replay independently of the hippocampus

Parallel computation in memory-making The hippocampus plays a central role in the encoding, consolidation, and recall of memories. Consolidation and recall are thought to be executed by the replay of previously acquired memory traces by hippocampal cell assemblies. The hippocampus is thus considered to be the initiator of memory redistribution processes. However, O'Neill et al. now report that the superficial layers of the medial entorhinal cortex show replay events that are independent of hippocampal activity (see the Perspective by Moser and Gardner). Computations in memory systems may thus be organized in a less hierarchical, more parallel way than previously thought. Science, this issue p. 184; see also p. 131 The medial entorhinal cortex can replay waking experiences independently of the hippocampus. The hippocampus is thought to initiate systems-wide mnemonic processes through the reactivation of previously acquired spatial and episodic memory traces, which can recruit the entorhinal cortex as a first stage of memory redistribution to other brain areas. Hippocampal reactivation occurs during sharp wave–ripples, in which synchronous network firing encodes sequences of places. We investigated the coordination of this replay by recording assembly activity simultaneously in the CA1 region of the hippocampus and superficial layers of the medial entorhinal cortex. We found that entorhinal cell assemblies can replay trajectories independently of the hippocampus and sharp wave–ripples. This suggests that the hippocampus is not the sole initiator of spatial and episodic memory trace reactivation. Memory systems involved in these processes may include nonhierarchical, parallel components.
A Proposed Three-Dimensional Constitutive Model for Shape Memory Alloys

The shape memory alloy (SMA) stress-strain response associated with martensitic twinning hysteresis and austenite-martensite/martensite-austenite superelasticity is modeled using constitutive equations. Compared to the modeling work done on viscoelastic and viscoplastic be havior, this has been an area of limited study. The equations which are presented here express the growth of inelastic strain in a rate-type formulation similar to viscoplastic laws. This constitutive model is obtained by extending a one-dimensional evolutionary model of SMA behavior to three dimensions. The resulting model is then reduced to meet the loading conditions of three special cases: uniaxial loading, shear loading, and non-proportional biaxial loading (combined axial- torsional loading). The model which is being considered, although nonlinear, is relatively simple in that only two evolutionary equations are required to model inelastic strain and a generalized back stress at a material point. Thus the model being presented uses only one internal variable, which is analogous to viscoplastic backstress. The consequences of variations of parameters in the equations of the model are also discussed.
Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments

Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most of the Archean, the ancient ocean evolved toward euxinic (anoxic and sulfide rich) conditions and, finally, much after the advent of oxygenic photosynthesis, to a predominantly oxic environment. Under these new conditions photoferrotrophs lost importance as primary producers, and now photoferrotrophy remains as a vestige of a formerly relevant photosynthetic process. Apart from the geological record and other biogeochemical markers, modern environments resembling the redox conditions of these ancient oceans can offer insights into the past significance of photoferrotrophy and help to explain how this metabolism operated as an important source of organic carbon for the early biosphere. Iron-rich meromictic (permanently stratified) lakes can be considered as modern analogs of the ancient Archean ocean, as they present anoxic ferruginous water columns where light can still be available at the chemocline, thus offering suitable niches for photoferrotrophs. A few bacterial strains of purple bacteria as well as of green sulfur bacteria have been shown to possess photoferrotrophic capacities, and hence, could thrive in these modern Archean ocean analogs. Studies addressing the occurrence and the biogeochemical significance of photoferrotrophy in ferruginous environments have been conducted so far in lakes Matano, Pavin, La Cruz, and the Kabuno Bay of Lake Kivu. To date, only in the latter two lakes a biogeochemical role of photoferrotrophs has been confirmed. In this review we critically summarize the current knowledge on iron-driven photosynthesis, as a remains of ancient Earth biogeochemistry.
Memory Profiling using Hardware Counters

Although memory performance is often a limiting factor in application performance, most tools only show performance data relating to the instructions in the program, not to its data. In this paper, we describe a technique for directly measuring the memory profile of an application. We describe the tools and their user model, and then discuss a particular code, the MCFbenchmark from SPEC CPU 2000. We show performance data for the data structures and elements, and discuss the use of the data to improve program performance. Finally, we discuss extensions to the work to provide feedback to the compiler for prefetching and to generate additional reports from the data.
BattTracker: Enabling energy awareness for smartphone using Li-ion battery characteristics

Energy awareness of mobile devices with limited battery capacity can be achieved by embedding battery drain rate monitoring capability into the devices. With Li-ion battery, battery drain rate varies with temperature and battery aging, since they affect battery characteristics such as capacity and internal resistance. We develop BattTracker, an algorithm to estimate battery drain rate without knowing the exact capacity and internal resistance by incorporating the concept of effective resistance. BattTracker tracks the instantaneous battery drain rate with up to 0.5 second time granularity. Extensive evaluation with smartphones demonstrates that BattTracker accurately estimates the battery drain rate with less than 5% estimation error, thus enabling energy-aware operation of smartphones with finegrained time granularity. To the best of our knowledge, this is the first effort to estimate the instantaneous battery drain rate by considering both temperature and aging effects on the battery characteristics.
Virtual engineering: challenges and solutions for intuitive offline programming for industrial robot

It¿s currently the market trend to make industrial robot easy to use. This paper analyzed the key areas and identified key bottlenecks that stop a robot simulation and offline programming tool to be intuitive and easy to use. The key areas are geometrical model handling, robot targets and paths handling, path configuration planning, etc. Based on the analysis, the solutions for each of the identified key areas were provided from easy of use perspective. The proposed solution has been implemented as a software product based on RobotStudio, ABB¿s simulation and offline programming tool.
Augmented Statistical Models for Speech Recognition

Recently there has been significant interest in developing new acoustic models for speech recognition. One such model, that allows complex dependencies to be represented, is the augmented statistical model. This incorporates additional dependencies by constructing a local exponential expansion of a standard HMM. Unfortunately, the resulting model often has an intractable normalisation term, rendering training difficult for all but binary classification tasks. In this paper, conditional augmented (C-Aug) models are proposed as an attractive alternative. Instead of modelling utterance likelihoods and inferring decision boundaries, C-Aug models directly model the posterior probability of class labels, conditioned on the utterance. The resulting model is easy to normalise and can be trained using conditional maximum likelihood estimation. In addition, as a convex model, the optimisation converges to a global maximum
I-MMSE relations in random linear estimation and a sub-extensive interpolation method

Consider random linear estimation with Gaussian measurement matrices and noise. One can compute infinitesimal variations of the mutual information under infinitesimal variations of the signal-to-noise ratio or of the measurement rate. We discuss how each variation is related to the minimum mean-square error and deduce that the two variations are directly connected through a very simple identity. The main technical ingredient is a new interpolation method called “sub-extensive interpolation method”. We use it to provide a new proof of an I-MMSE relation recently found by Reeves and Pfister [1] when the measurement rate is varied. Our proof makes it clear that this relation is intimately related to another I-MMSE relation also recently proved in [2]. One can directly verify that the identity relating the two types of variation of mutual information is indeed consistent with the one letter replica symmetric formula for the mutual information, first derived by Tanaka [3] for binary signals, and recently proved in more generality in [1,2,4,5] (by independent methods). However our proof is independent of any knowledge of Tanaka's formula.
High dose ascorbic acid does not reverse central sympathetic overactivity in chronic heart failure

What is known and Objective: The increased central sympathetic activity typically associated with chronic heart failure (CHF) is probably mediated by formation of reactive oxygen species (ROS) in the brain. Our objective was to undertake a trial to test our hypothesis that administration of the well‐known antioxidant and ROS scavenger ascorbic acid, would reverse or reduce the sympathetic overactivity in CHF patients.