Miracle-dz/UniFAR-FTUs huggingface dataset:
Haptic Sensing and Modeling of Nanomanipulation with an AFM

This paper describes a virtual reality and haptic interface between human and the atomic force microscope (AFM), which allows the operator to sense and touch the surface and nanoparticles during the manipulation with an AFM tip. The tip-sample interaction forces and intermolecular forces between the tip and surface are modeled based on Lennard-Jones potential and JKR theory, respectively. Our objective is to provide a 3D virtual reality interface capable of displaying topography of surface for the users and allow them to predict the results for the manipulation
Assortative model for social networks.

In this Brief Report we present a version of a network growth model, generalized in order to describe the behavior of social networks. The case of study considered is the preprint archive at cul.arxiv. org. Each node corresponds to a scientist, and a link is present whenever two authors wrote a paper together. This graph is a nice example of degree-assortative network, that is, to say a network where sites with similar degree are connected to each other. The model presented is one of the few able to reproduce such behavior, giving some insight on the microscopic dynamics at the basis of the graph structure.
Rollbacks in Time Warp - Analysis and Modelling

This paper presents a study of the interactions between the random number generator used and the run-time behaviour of the parallel Time Warp simulation kernel APSIS. A different rollback length distribution, with a far larger chance of long rollbacks taking place, is observed when the state of the random number generator is not preserved across the rollbacks. An explanation for this phenomenon is provided. An analytical model of the rollback behaviour in Time Warp is developed, for rollback length expressed in either the simulation time or the number of events to be rolled back. The hope is that, once the model is complete, it will be possible to determine under what circumstances it is profitable (not) to preserve the state of the random number generator.
Piezoelectrically driven silicon microgrippers integrated with sidewall piezoresistive sensor

This paper presents the design, fabrication, and application of an piezoelectrically driven microgripper integrated sidewall piezoresistive force sensor for measuring the gripping force. Surface and bulk micromachining technology is employed to fabricate end-effectors and sensor of the microgripper from a single crystal silicon wafer. Vertical sidewall surface piezoresistor etching technique is used to form the side direction sensors. The end-effectors of the gripper are four-bar structures. Two fixed cantilever beams integrated with piezoresistive sensor are designed to sense the gripping force, and a piezoelectrically driven microactuator is designed to provide the force to operate the other two movable bars. The piezoelectrically driver adhered with the silicon end-effectors generates a linear horizontal motion 9µm, which is amplified to 30µm at the bar tip of the microgripper. Then the range of the operation is 25µm-140µm. Testing results verify that the vertical sidewall surface piezoresistor etching technique is effective. The sensitivity of the piezoresistive sensors is better than 72V/N, and the resolution is better than 3µN.
Flexible reference-counting-based hardware acceleration for garbage collection

Languages featuring automatic memory management (garbage collection) are increasingly used to write all kinds of applications because they provide clear software engineering and security advantages. Unfortunately, garbage collection imposes a toll on performance and introduces pause times, making such languages less attractive for high-performance or real-time applications. Much progress has been made over the last five decades to reduce the overhead of garbage collection, but it remains significant. We propose a cooperative hardware-software technique to reduce the performance overhead of garbage collection. The key idea is to reduce the frequency of garbage collection by efficiently detecting and reusing dead memory space in hardware via hardware-implemented reference counting. Thus, even though software garbage collections are still eventually needed, they become much less frequent and have less impact on overall performance. Our technique is compatible with a variety of software garbage collection algorithms, does not break compatibility with existing software, and reduces garbage collection time by 31% on average on the Java DaCapo benchmarks running on the production build of the Jikes RVM, which uses a state-of-the-art generational garbage collector.
Hot Interstellar Gas and Stellar Energy Feedback in the Antennae Galaxies

We have analyzed Chandra archival observations of the Antennae galaxies to study the distribution and physical properties of its hot interstellar gas. Eleven distinct diffuse X-ray emission regions are selected according to their underlying interstellar structures and star formation activity. The X-ray spectra of these regions are used to determine their thermal energy content and cooling timescales. Young star clusters in these regions are also identified and their photometric measurements are compared to evolutionary stellar population synthesis models to assess their masses and ages. The cluster properties are then used to determine the stellar wind and supernova energies injected into the interstellar medium (ISM). Comparisons between the thermal energy in the hot ISM and the expected stellar energy input show that young star clusters are sufficient to power the X-ray-emitting gas in some, but not all, active star formation regions. Super star clusters, with masses ≥1 × 105 M☉, heat the ISM, but the yield of hot interstellar gas is not directly proportional to the cluster mass. Finally, there exist diffuse X-ray emission regions that do not show active star formation or massive young star clusters. These regions may be powered by field stars or low-mass clusters formed within the last ~100 Myr.
Advances in DNA Detection

DNA detection technologies have an increasing importance in our everyday lives, with applications ranging from microbial diagnostics to forensic analysis, food safety evaluation, and environmental monitoring. Currently, as the associated costs decrease, DNA diagnostic techniques are routinely used in research laboratories, in clinical and forensic practice. The first aim of this thesis is to unravel the potential of DNA detection on cellulose filter paper and further investigate the filter paper as a viable candidate for DNA array support. In Paper I, we studied the method of functionalizing the surface of filter paper and the possibility to detect DNA on the active paper using fluorescence. In Paper II, we addressed visual detection with magnetic beads and increased the detection throughput on the active filter paper, which required no instrumentation. Second, in pursuit of a rapid, sensitive and specific pathogen diagnosis in bloodstream infection (BSI), we explored the possibility of rare DNA detection in the presence of a high amount of background DNA by an enzymatic reaction, which can remove background DNA while enriching the rare DNA fraction. In order to overcome the challenge of the second objective, we developed a chemical fragmentation method to increase the efficiency of enzymatic digestion and hybridization. In addition, DNA library preparation for massively parallel sequencing may benefit from the chemical fragmentation. Paper III and Paper IV introduce this work. The findings in Paper I showed that XG-NH2 and PDITC can functionalize the cellulose filter paper and that the activated filter papers can covalently bind oligonucleotides modified with amino groups, while preserving the base pairing ability of the oligonucleotides. In Paper II, visual detection of DNA on active paper was achieved without instrumentation, based on the natural colour of magnetic beads. Furthermore, the possibility to increase the throughput of DNA detection on active paper was demonstrated by successful multiplex detection. In Paper III, the developed chemical fragmentation was verified to be suitable for DNA library preparation in massively parallel sequencing. The fragmentation technique is simple to perform, cost-effective and amenable to automation. In Paper IV, a limited amount of E.coli DNA was detected amid a much larger amount of human background DNA in a BSI model, which comprises of human and E.coli amplicons with an abundance ratio of 10. Human βactin amplicons were suppressed 10-fold, whereas the E.coli amplicons remained unaffected. The model system was applied to and improved with clinical plasma and blood samples from septic patients.
Local Similarities and Clustering of Biological Sequences: New Insights from N-local Decoding

The search for local similarities in sequences is a classical problem in biology, and several methods have been developed for this goal. We herein investigate the N-local decoding method due to Gilles Didier ([2]), in order to classify sequences according to the local similarity segments of a fixed length N that they share. The sites of our sequences are originally occupied by a nucleotide or an amino-acid, and, after the N-local decoding has been applied, these sites are occupied by new symbols (that we call GD-classes), which classify the sites according to the composition of their environment in words of length N. This method has already been successfully used to construct trees for the subtyping of HIV/SIV variants ([3]). After recalling the definitions and the original method of the N-local decoding, we will present new developments which aim, on the one hand to allow to exploit the information generated by the decoding, and on the other hand, to tackle the influence of the free parameter N.
Cisplatin promotes mesenchymal-like characteristics in osteosarcoma through Snail

More than 30% of patients with osteosarcoma succumb to pulmonary metastases. Epithelial-mesenchymal transition (EMT) is a biological process by which tumor cells gain an increased capacity for invasiveness and metastasis. A previous study confirmed the phenomenon of EMT in osteosarcoma, a mesenchymal-derived tumor. However, whether chemotherapy affects EMT remains to be elucidated. In the present study, the osteosarcoma cells were exposed to a sublethal dose of cisplatin, and any surviving cells were assumed to be more resistant to cisplatin. In addition, these cells exhibited a more mesenchymal phenotype. Immunofluorescence analysis revealed that the cisplatin treated cells had an increased long/short axis ratio and increased expression of N-cadherin compared with control cells. A panel of EMT-associated genes was subsequently assessed by quantitative PCR and western blot analysis, and they were observed to be significantly upregulated in the cisplatin treated cells. The in vitro wound healing and Transwell assay indicated that the cisplatin treated cells were more prone to migrate and invade. An in vivo assay showed that the cisplatin-treated xenograft had increased expression of EMT-associated genes, and exhibited increased pulmonary lesions compared with the control, which indicated an elevated capacity to metastasize. The expression of Snail was knocked down by specific small interfering RNA, and it was observed that Snail inhibition promoted cisplatin sensitivity, and cisplatin-induced EMT was significantly blocked. Taken together, the results of the present study supported that idea that Snail participates in cisplatin-induced EMT in osteosarcoma cells, and targeting EMT-transcription factors may offer promise for the therapeutics of osteosarcoma.
Dynamic Spirals Put to Test: An Agent-Based Model of Reinforcing Spirals Between Selective Exposure, Interpersonal Networks, and Attitude Polarization

Within the context of partisan selective exposure and attitude polarization, this study investigates a mutually reinforcing spiral model, aiming to clarify mechanisms and boundary conditions that affect spiral processes—interpersonal agreement and disagreement, and the ebb and flow of message receptions. Utilizing agent-based modeling (ABM) simulations, the study formally models endogenous dynamics of cumulative processes and its reciprocal effect of media choice behavior over extended periods of time. Our results suggest that interpersonal discussion networks, in conjunction with election contexts, condition the reciprocal effect of selective media exposure and its attitudinal consequences. Methodologically, results also highlight the analytical utility of computational social science approaches in overcoming the limitations of typical experimental and observations studies.
Computer control system and walking pattern control for a humanoid robot

A humanoid robot generally has more than thirty DOFs to be controlled in real-time and needs to deal with information of multiple sensors such as encoders, force and moment sensors, inertial attitude sensors and vision sensors. Therefore an effective control system is crucial for the humanoid robot. In this paper, we propose a distributed computer system consisting of the online planning sub-system and the real-time motion control sub-system based on CAN bus and Ethernet for humanoid robots. CAN bus is used for distributed real-time motion control and Ethernet is used for non-real-time and large data quantities communication between the online planning and motion control sub-systems. The Windows and RT-Linux are used as operating systems for the online planning and motion control sub-systems respectively. The walking pattern control modifies the planned walking pattern based on sensory information when there are unexpected sudden events. The effectiveness of our proposed computer system and walking pattern control method was confirmed by walking experiments on our newly-built humanoid robot.
SKen: A statistical test for removing outliers in optical flow a 3D reconstruction case

The 3D reconstruction can be employed in several areas such as markerless augmented reality, manipulation of interactive virtual objects and to deal with the occlusion of virtual objects by real ones. However, many improvements into the 3D reconstruction pipeline in order to increase its efficiency may still be done. In such context, this paper proposes a filter for optimizing a 3D reconstruction pipeline. It is presented the SKen technique, a statistical hypothesis test that classifies the features by checking the smoothness of its trajectory. Although it was not mathematically proven that inliers features performed smooth camera paths, this work shows some evidence of a relationship between smoothness and inliers. By removing features that did not present smooth paths, the quality of the 3D reconstruction was enhanced.
On Predicting Protein Secondary Structure from their Aminoacid Sequences using Inductive Logic Programming

We address the problem of predicting the stability of secondary structure motifs of proteins given their linear sequence of residues. Our study is restricted to the prediction of helix structures. We have applied an inductive logic programming (ILP) system to automatically synthesise the predictive rules. ILP systems are well known for being able to induce comprehensible models for data. Furthermore, the models components are definitions provided by a domain expert which makes the model more likely to be helpful in the understanding of the underlying process that produced the data. Our methodology has two stages. First, the system induces a model (set of rules) using just structural information and groupings of the residues to avoid biases by the domain expert. In the second stage, the residues properties are used to make the induced rules chemically/biologically appealing. We claim that this methodology is also valuable for general structure-activity relationship (SAR) problems
Policy implementation check in industrial networks

Security of industrial network is a hot topic that requires constant efforts. Access control models and related analysis are powerful tools for the design and verification of security policies. However, the methodologies developed in the standard ICT world are not always suitable for the application in industrial environments because of the well known limitations that these systems are constantly dealing with.We propose here an approach for the automatic verification of the implementation of security policies in industrial systems with a particular attention on the limited security mechanisms available in these environments. We leverage a formal class model suitable for the description of system device configurations and the related security policies.
Thoracic endovascular aortic repair of a severely angulated aorta using a double-wire technique

When endovascular treatment is performed, angulation of the access route for a device can make the operative procedure difficult. We encountered a case in which we successfully completed thoracic endovascular aortic repair (TEVAR) in a patient with severely angulated aorta by applying ‘double-wire technique’. The patient was an 80-year-old woman. An aneurysm with a 71-mm diameter was observed in the descending aorta. We performed TEVAR. Device delivery could not be achieved by a conventional procedure using one guide wire since the peripheral aorta was severely angulated. Therefore, in addition to a guide wire for main body, a stiff wire and a stiff sheath were introduced to straighten the angulation. The device was successfully introduced and TEVAR was completed. We used the Relay Plus® that facilitates tracking through the angulation. The device has a dual structure consisting of a hard sheath and a flexible sheath. We performed TEVAR successfully.
Modelling time-constrained software development

Commercial pressures on time-to-market often require the development of software in situations where deadlines are very tight and non-negotiable. This type of development can be termed ‘time-constrained software development. ’ The need to compress development timescales influences both the software process and the way it is managed. Conventional approaches to modelling tend to treat the development process as being linear, sequential and static. Whereas, the processes used to achieve timescale compression in industry are iterative, concurrent and dynamic. That is, they replace the notion of ‘right-first-time’ with one of ‘right-on-time. ’ In this paper we propose a new modelling technique, called Capacity-Based Scheduling (CBS), to control risk across a portfolio of time-constrained projects. We show how schedule constraints can be modelled in order to predict the consequences of alternative plans and control schedule risk across a portfolio of time-constrained projects.
Evaluating the requirements of communicating vehicles in collaborative automated driving

In this paper, we analyze mixed traffic environments consisting of fully autonomous vehicles, vehicles capable of communication only, and manually driven vehicles to determine what self-generated content should be shared among peer vehicles for increased traffic intelligence. For this purpose, we present information sharing utility-cost tables for a variety of communication strategies. These tables are used to determine communication requirements in terms of bandwidth, distance, packet delay and loss rate tolerance. We specifically evaluate vehicle lane change events due to their role as foundational building blocks in most other traffic scenarios. The presented work demonstrates requirements for the communication systems in mixed-traffic environments based on sharing and fusing necessary sensor information using occupancy grid mapping.
Role of Copper and Cholesterol Association in the Neurodegenerative Process

Age is one of the main factors involved in the development of neurological illnesses, in particular, Alzheimer, and it is widely held that the rapid aging of the world population is accompanied by a rise in the prevalence and incidence of Alzheimer disease. However, evidence from recent decades indicates that Cu and Cho overload are emerging causative factors in neurodegeneration, a hypothesis that has been partially investigated in experimental models. The link between these two variables and the onset of Alzheimer disease has opened up interesting new possibilities requiring more in-depth analysis. The aim of the present study was therefore to investigate the effect of the association of Cu + Cho (CuCho) as a possible synergistic factor in the development of an Alzheimer-like pathology in Wistar rats. We measured total- and nonceruloplasmin-bound Cu and Cho (free and sterified) contents in plasma and brain zones (cortex and hippocampus), markers of oxidative stress damage, inflammation, and programmed cell death (caspase-3 and calpain isoforms). The ratio beta-amyloid (1-42)/(1-40) was determined in plasma and brain as neurodegenerative biomarker. An evaluation of visuospatial memory (Barnes maze test) was also performed. The results demonstrate the establishment of a prooxidative and proinflammatory environment after CuCho treatment, hallmarked by increased TBARS, protein carbonyls, and nitrite plus nitrate levels in plasma and brain zones (cortex and hippocampus) with a consequent increase in the activity of calpains and no significant changes in caspase-3. A simultaneous increase in the plasma Aβ1-42/Aβ1-40 ratio was found. Furthermore, a slight but noticeable change in visuospatial memory was observed in rats treated with CuCho. We conclude that our model could reflect an initial stage of neurodegeneration in which Cu and Cho interact with one another to exacerbate neurological damage.
An Improved Phylogenetic Tree Comparison Method Table of Contents

Suneel Potiny An improved phylogenetic tree comparison method (Under the direction of Dr. Shawn Gomez) The comparison of phylogenetic trees is an evolving area of study. The need to analyze the similarities among trees found in phylogenetic databases is growing, and while several tree comparison methods exist, further work in this area can be beneficial. This research presents a novel, distance-based tree comparison method (MDS-Procrustes). Our approach begins with two trees and represents the patristic distances between nodes within each tree in separate distance matrices. Then we use classical multi-dimensional scaling to represent these distances as Euclidean structures in a high-dimensional space while maintaining the original distance information. Finally, Procrustes analysis is used to superimpose one Euclidean structure onto the other to generate a similarity score between the two trees. In this work, we compare the effectiveness of the proposed method to existing approaches found in the literature in terms of both similarity score distribution and computational performance.