Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a selected reaction monitoring mass spectrometry-based assay to detect asparaginyl endopeptidase activity in biological fluids

Cancer Biomarkers have the capability to improve patient outcomes. They have potential applications in diagnosis, prognosis, monitoring of disease progression and measuring response to treatment. This type of information is particularly useful in the individualisation of treatment regimens. Biomarkers may take many forms but considerable effort has been made to identify and quantify proteins in biological fluids. However, a major challenge in measuring protein in biological fluids, such as plasma, is the sensitivity of the assay and the complex matrix of proteins present. Furthermore, determining the effect of proteases in disease requires measurement of their activity in biological fluids as quantification of the protein itself may not provide sufficient information. To date little progress has been made towards monitoring activity of proteases in plasma. The protease asparaginyl endopeptidase has been implicated in diseases such as breast cancer, leukaemia and dementia. Here we describe a new approach to sensitively and in a targeted fashion quantify asparaginyl endopeptidase activity in plasma using a synthetic substrate peptide protected from nonspecific hydrolysis using D-amino acids within the structure. Our selected reaction monitoring approach enabled asparaginyl endopeptidase activity to be measured in human plasma with both a high dynamic range and sensitivity. This manuscript describes a paradigm for future development of assays to measure protease activities in biological fluids as biomarkers of disease.
Fabrication of Piezoelectric Polyvinylidene Fluoride (PVDF) Polymer-Based Tactile Sensor Using Electrospinning Method

The polyvinylidene fluoride (PVDF) nanofiber has widely investigated as a sensor and transducer material, because of its high piezo and Ferro electric properties. The novel nano structure of PVDF has attracted considerable interest in the bio sensing and biomedical application. This paper deals with PVDF Tactile sensor. Basically The PVDF acts as piezoelectric effect which convert load into electrical signals. The tactile sensor has a main role for visual handicap and robotics. Any physical activities of robotic in all industrial the tactile sensor is a crucible role, whether it can left the object or handling glass parts pressure of object is main. The Sandwich type PVDF base tactile sensor has been fabricated using nanofiber. Using electro spinning method, the PVDF based nanofiber coated over coper the electrodes. In normal, the PVDF has α-phase and while applying electric pulse the PVDF polymer would be changed from α-phase into β-phase. Only in β-phase, the PVDF act as piezo electrics sensor and measure the piezoelectricity simultaneously measure pressure and temperature in real time. The pressure was monitored from the change in the electrical resistance via the piezo resistance of the material. The enhancement of PVDF properties has been carried by using SEM. The SEM image result showed that the size of nanofiber, the size of nanofiber is varied in the range of (180 nm-400 nm) with smooth surface. The X-Ray diffraction has shown that the PVDF was aggregated with the β-phase crystalline nature. Due to β-phase it was act as a piezo electric prosperity’s and its results are very high sensitivity.
Extended grasping behavior for autonomous human agents

Abstract In this paper we present an efficient technique allowing distantgrasp behaviors while preserving the static balance. This featuregreatly increases the autonomy of virtual humans. 1. Introduction Our goal is to provide an integrated reaching and graspingbehaviors for a virtual human agent. In most cases, grasping aclose object only involves the motion of one or both arms oftencomplemented with the independent motion of the head to looktowards the goal [RG91][MT94]. However the reach of distantobjects is a much more complex task as human beings can extendtheir field of action by various means. Let us imagine the processof grasping a relatively low object (Fig. 1a). To avoid a loss ofbalance the body posture is constrained so as to keep the verticalprojection of the center of mass inside the base of support (Fig.1b). However the object can be even more distant and additionalsupporting area has to be used. (Fig. 1c). In the case of Fig. 1c wecan reach the target with the left hand while leaning on the boxwith the right hand (Fig. 1d). The present approach solves thisclass of problems on a human body model with 95 degrees offreedom including the hands mobilbities [MT94]. a b cdFigure 1. Reaching a close object (a,b)and a distant target (c,d)
Improved privacy-preserving authentication scheme for roaming service in mobile networks

User authentication is an important security mechanism that allows mobile users to be granted access to roaming service offered by the foreign agent with assistance of the home agent in mobile networks. While security-related issues have been well studied, how to preserve user privacy in this type of protocols still remains an open problem. In this paper, we revisit the privacy-preserving two-factor authentication scheme presented by Li et al. at WCNC 2013. We show that, despite being armed with a formal security proof, this scheme actually cannot achieve the claimed feature of user anonymity and is insecure against offline password guessing attacks, and thus, it is not recommended for practical applications. Then, we figure out how to fix these identified drawbacks, and suggest an enhanced scheme with better security and reasonable efficiency. Further, we conjecture that under the non-tamper-resistant assumption of the smart cards, only symmetric-key techniques are intrinsically insufficient to attain user anonymity.
The Use of Polleverywhere in Engineering Technology Classes to Student Stimulate Critical Thinking and Motivation

Critical thinking is considered one of the most important aspects of the learning process at the college level, especially in the field of engineering technology. However, developing critical thinking can prove to be quite challenging. It takes a lot of instructional effort and support for undergraduate students enrolled in engineering technology programs to develop the ability to analyze, adequately synthesize conceptual knowledge, and then apply that knowledge to practical problem-solving situations. This ability is a critical component of any successful completion of job responsibilities for future engineers. In this study we examine the effectiveness of the web-based polling system Polleverywhere in promoting all stages of learning, with the emphasis on acquisition and generalization of new knowledge. The study also evaluates the effectiveness of the above-mentioned web-based system in promoting students’ motivation. Besides traditional face-to-face interaction in class (students asking questions and verbally responding to the instructor’s questions) students were engaged in class participation through the use of Polleverywhere software. A polling system increases the likelihood that all students in the class answer the questions presented. Furthermore, after polling, students can compare and discuss their answers across the entire group. This is a peer-review process important in the success of their learning. A survey was administrated towards the end of the class and data from this survey was used in the analysis. The evaluation in this study is based on a Circuits course in electrical engineering technology, for a relatively small-lecture classroom.
Nanoscale Tuning of VCAM-1 Determines VLA-4–Dependent Melanoma Cell Plasticity on RGD Motifs

The biophysical fine-tuning of cancer cell plasticity is crucial for tumor progression but remains largely enigmatic. Although vascular cell adhesion molecule-1 (VCAM-1/CD106) has been implicated in melanoma progression, here its presentation on endothelial cells was associated with diminished melanoma cell spreading. Using a specific nanoscale modulation of VCAM-1 (tunable from 70 to 670 ligands/μm²) next to integrin ligands (RGD motifs) in a bifunctional system, reciprocal regulation of integrin α4 (ITGA4/VLA-4/CD49d)-dependent adhesion and spreading of melanoma cells was found. As the VCAM-1/VLA-4 receptor pair facilitated adhesion, while at the same time antagonizing RGD-mediated spreading, melanoma cell morphogenesis on these bifunctional matrices was directly regulated by VCAM-1 in a dichotomic and density-dependent fashion. This was accompanied by concordant regulation of F-actin cytoskeleton remodeling, Rac1-expression, and paxillin-related adhesion formation. The novel function of VCAM-1 was corroborated in vivo using two murine models of pulmonary metastasis. The regulation of melanoma cell plasticity by VCAM-1 highlights the complex regulation of tumor–matrix interactions. Implications: Nanotechnology has revealed a novel dichotomic function of the VCAM-1/VLA-4 interaction on melanoma cell plasticity, as nanoscale tuning of this interaction reciprocally determines adhesion and spreading in a ligand density-dependent manner. Mol Cancer Res; 16(3); 528–42. ©2017 AACR.
Obstacle-avoiding robot with IR and PIR motion sensors

Obstacle avoiding robot was designed, constructed and programmed which may be potentially used for educational and research purposes. The developed robot will move in a particular direction once the infrared (IR) and the PIR passive infrared (PIR) sensors sense a signal while avoiding the obstacles in its path. The robot can also perform desired tasks in unstructured environments without continuous human guidance. The hardware was integrated in one application board as embedded system design. The software was developed using C++ and compiled by Arduino IDE 1.6. 5. The main objective of this project is to provide simple guidelines to the polytechnic students and beginners who are interested in this type of research. It is hoped that this robot could benefit students who wish to carry out research on IR and PIR sensors.
LncRNA ZFAS1 as a SERCA2a Inhibitor to Cause Intracellular Ca2+ Overload and Contractile Dysfunction in a Mouse Model of Myocardial Infarction

Rationale: Ca2+ homeostasis—a critical determinant of cardiac contractile function—is critically regulated by SERCA2a (sarcoplasmic reticulum Ca2+-ATPase 2a). Our previous study has identified ZFAS1 as a new lncRNA biomarker of acute myocardial infarction (MI). Objective: To evaluate the effects of ZFAS1 on SERCA2a and the associated Ca2+ homeostasis and cardiac contractile function in the setting of MI. Methods and Results: ZFAS1 expression was robustly increased in cytoplasm and sarcoplasmic reticulum in a mouse model of MI and a cellular model of hypoxia. Knockdown of endogenous ZFAS1 by virus-mediated silencing shRNA partially abrogated the ischemia-induced contractile dysfunction. Overexpression of ZFAS1 in otherwise normal mice created similar impairment of cardiac function as that observed in MI mice. Moreover, at the cellular level, ZFAS1 overexpression weakened the contractility of cardiac muscles. At the subcellular level, ZFAS1 deleteriously altered the Ca2+ transient leading to intracellular Ca2+ overload in cardiomyocytes. At the molecular level, ZFAS1 was found to directly bind SERCA2a protein and to limit its activity, as well as to repress its expression. The effects of ZFAS1 were readily reversible on knockdown of this lncRNA. Notably, a sequence domain of ZFAS1 gene that is conserved across species mimicked the effects of the full-length ZFAS1. Mutation of this domain or application of an antisense fragment to this conserved region efficiently canceled out the deleterious actions of ZFAS1. ZFAS1 had no significant effects on other Ca2+-handling regulatory proteins. Conclusions: ZFAS1 is an endogenous SERCA2a inhibitor, acting by binding to SERCA2a protein to limit its intracellular level and inhibit its activity, and a contributor to the impairment of cardiac contractile function in MI. Therefore, anti-ZFAS1 might be considered as a new therapeutic strategy for preserving SERCA2a activity and cardiac function under pathological conditions of the heart.
Trace semantics via determinization for probabilistic transition systems

A coalgebraic definition of finite and infinite trace semantics for probabilistic transition systems has recently been given using a certain Kleisli category. In this paper this semantics is developed using a coalgebraic method which is an instance of general determinization. Once applied to discrete systems, this point of view allows the exploitation of the determinized structure by up-to techniques. Thereby it becomes possible to algorithmically check the equivalence of two finite probabilistic transition systems.
Delft University of Technology On the “ Naturalness ” of Buggy Code

Real software, the kind working programmers produce by the kLOC to solve real-world problems, tends to be “natural”, like speech or natural language; it tends to be highly repetitive and predictable. Researchers have captured this naturalness of software through statistical models and used them to good effect in suggestion engines, porting tools, coding standards checkers, and idiom miners. This suggests that code that appears improbable, or surprising, to a good statistical language model is “unnatural” in some sense, and thus possibly suspicious. In this paper, we investigate this hypothesis. We consider a large corpus of bug fix commits (ca. 7,139), from 10 different Java projects, and focus on its language statistics, evaluating the naturalness of buggy code and the corresponding fixes. We find that code with bugs tends to be more entropic (i.e. unnatural), becoming less so as bugs are fixed. Ordering files for inspection by their average entropy yields cost-effectiveness scores comparable to popular defect prediction methods. At a finer granularity, focusing on highly entropic lines is similar in cost-effectiveness to some well-known static bug finders (PMD, FindBugs) and ordering warnings from these bug finders using an entropy measure improves the cost-effectiveness of inspecting code implicated in warnings. This suggests that entropy may be a valid, simple way to complement the effectiveness of PMD or FindBugs, and that search-based bug-fixing methods may benefit from using entropy both for fault-localization and searching for fixes.
Music Genre Classification using MFCC, SVM and BPNN

In the field of musical information retrieval, genre categorization is a complicated mission. MFCC is one of the feature extraction method use in classification of musical genre that is based on short speech signals. Searching and organizing are the main characteristics of the music genre classification system these days. This paper describes a new technique that uses support vector machines to classify songs based on features using MFCC, BPNN and SVM classifier does not classify songs based on the short signals. So these categories a number of acoustic features that include Melfrequency Cepstral coefficients are extracted to characterize the audio content. Support vector machines and BPNN classifies audio into their respective classes by learning from training data. The simulation is taken place in MATLAB by making experiments on different genres . The results obtained by this proposed technique are promising. General Terms Classification Algorithms, Pattern Recognition.
Stationary ergodic Jackson networks: results and counter-examples

This paper gives a survey of recent results on generalized Jackson networks, where classical exponential or i.i. d. assumptions on services and routings are replaced by stationary and ergodic assumptions. We first show that the most basic features of the network may exhibit unexpected behavior. Several probabilistic properties are then discussed, including a strong law of large numbers for the number of events in the stations, the existence, uniqueness and representation of stationary regimes for queue size and workload.
Evaluating Scoped Meaning Representations

Semantic parsing offers many opportunities to improve natural language understanding. We present a semantically annotated parallel corpus for English, German, Italian, and Dutch where sentences are aligned with scoped meaning representations in order to capture the semantics of negation, modals, quantification, and presupposition triggers. The semantic formalism is based on Discourse Representation Theory, but concepts are represented by WordNet synsets and thematic roles by VerbNet relations. Translating scoped meaning representations to sets of clauses enables us to compare them for the purpose of semantic parser evaluation and checking translations. This is done by computing precision and recall on matching clauses, in a similar way as is done for Abstract Meaning Representations. We show that our matching tool for evaluating scoped meaning representations is both accurate and efficient. Applying this matching tool to three baseline semantic parsers yields F-scores between 43% and 54%. A pilot study is performed to automatically find changes in meaning by comparing meaning representations of translations. This comparison turns out to be an additional way of (i) finding annotation mistakes and (ii) finding instances where our semantic analysis needs to be improved.
CurveUps

We present a computational approach for designing CurveUps, curvy shells that form from an initially flat state. They consist of small rigid tiles that are tightly held together by two pre-stretched elastic sheets attached to them. Our method allows the realization of smooth, doubly curved surfaces that can be fabricated as a flat piece. Once released, the restoring forces of the pre-stretched sheets support the object to take shape in 3D. CurveUps are structurally stable in their target configuration. The design process starts with a target surface. Our method generates a tile layout in 2D and optimizes the distribution, shape, and attachment areas of the tiles to obtain a configuration that is fabricable and in which the curved up state closely matches the target. Our approach is based on an efficient approximate model and a local optimization strategy for an otherwise intractable nonlinear optimization problem. We demonstrate the effectiveness of our approach for a wide range of shapes, all realized as physical prototypes.
The effect of epigallocatechin‐3‐gallate, a constituent of green tea, on transforming growth factor‐β1–stimulated wound contraction

Dermal fibrosis, or scarring, following surgical incisions, traumatic wounds and burns presents a major clinical burden. Transforming growth factor (TGF)‐β1 is a major factor known to stimulate fibroblast proliferation, collagen production, and the differentiation of fibroblast to myofibroblast promoting wound contraction. Furthermore, excessive or prolonged TGF‐β1 has been shown to be associated with scarring. Green tea contains high amounts of polyphenols with the major polyphenolic compound being epigallocatechin‐3‐gallate (EGCG). EGCG has been shown to be anti‐inflammatory, anti‐oxidant, and may improve wound healing and scarring, though its precise effect on TGF‐β1 remains unclear. This study aimed at determining the effect of EGCG on TGF‐β1 collagen contraction, gene expression and the differentiation of fibroblast to myofibroblast. EGCG appears to affect the role that TGF‐β1 plays in fibroblast populated collagen gel contraction and this seems to be through both myofibroblast differentiation and connective tissue growth factor gene expression and reduces the expression of collagen type I gene regulation.
A new approach to Particle Swarm Optimization for dynamic systems with multiple units

Maximum Power Point Trackers (MPPT) are widely used to track in real-time the optimal power output of dynamic systems. These systems are sometimes comprised of multiple units which are similar, but not necessarily identical in terms of power curve and dynamics. A good example of such a system would be a photovoltaic (PV) array, which consists of multiple PV cells. Hence, it can be more profitable to operate each unit to its own optimal operating point instead of operating the whole system to a common optimal operating point. This paper proposes to use Particle Swarm Optimization (PSO) as an MPPT where each particle is assigned to a unit of a system. Although the method is validated both through simulations of a PV model and experimentations using a test bench of PV cells, it can be applied to many different dynamic systems comprising multiple units. The method proved to improve the convergence rate of the system and its total power production.
High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres

Abstract Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG)n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. These features make the method a uniquely valuable new tool for improving the quality of genome assemblies in complex DNA regions. Based on single molecule mapping of telomere-terminal DNA fragments, we provide proof of principle for a novel method to estimate telomere lengths linked to distinguishable telomeric haplotypes; this single-telomere genotyping method may ultimately enable delineation of human cis elements involved in telomere length regulation.
Weibull verification of reduced pressure test as a tool for assessing Al melt quality

Abstract The credibility of reduced pressure test (RPT) as a substitute for Weibull analysis for benchmarking bifilm defects in Al alloys was confirmed by comparing the RPT parameters (2D and 3D porosity, and Bifilm Index) with the Weibull moduli for UTS values for pure Al and Al-0.05Sr alloys. The porosity of RPT samples was found to have an exponential decay relationship with Weibull modulus. A reasonable trend for Bifilm Index could not be found. 3D porosity of RPT samples was found to be more favourable than 2D porosity or Bifilm Index. Some evidence was also found of connections occurring between the sides of bifilm defects at the surfaces of the fractured tensile test bars of Al-0.05Sr alloy which had a relatively high UTS.
Contact area and size effects in discrete dislocation modeling of wedge indentation

Plane strain indentation of a single crystal by a rigid wedge is analyzed using discrete dislocation plasticity. We consider two wedge geometries having different sharpness, as specified by the half-angle of the indenter: α = 70° and 85°. The dislocations are all of edge character and modeled as line singularities in a linear elastic material. The crystal has initial sources and obstacles randomly distributed over three slip systems. The lattice resistance to dislocation motion, dislocation nucleation, dislocation interaction with obstacles, and dislocation annihilation are incorporated through a set of constitutive rules. Several definitions of the contact area (contact length in plane strain) are used to illustrate the sensitivity of the hardness value in the submicron indentation regime to the definition of contact area. The size dependence of the indentation hardness is found to be sensitive to the definition of contact area used and to depend on the wedge half-angle. For a relatively sharp indenter, with a half-angle of 70°, an indentation size effect is not obtained when the contact area is small and when the hardness is based on the actual contact length, while there does appear to be a size effect for some hardness values based on other measures of contact length.