Miracle-dz/UniFAR-FTUs huggingface dataset:
Semantic version management based on formal certification

This paper describes a Semantic Version Management method that enables managing consistently digital resources throughout their life cycle. The core notion is that resources are described be means of logical specifications formally expressed using an extensible logical language. A new version is considered certified only if the resource owner is able to formally prove that it satisfies its logical specification. The method includes formal proofs for qualifying changes (occurring either on the resource content or on the corresponding specifications) and accordingly characterizing them via the definition of appropriate version labels. Based on the above method, a service-oriented solution is also described that enables managing changes consistently, in a sound manner, for both resource owners and users.
Secure Transmission in mmWave Wiretap Channels: On Sector Guard Zone and Blockages

Millimeter-wave (mmWave) communication is one of the key enabling technologies for fifth generation (5G) mobile networks. In this paper, we study the problem of secure communication in a mmWave wiretap network, where directional beamforming and link blockages are taken into account. For the secure transmission in the presence of spatially random eavesdroppers, an adaptive transmission scheme is adopted, for which sector secrecy guard zone and artificial noise (AN) are employed to enhance secrecy performance. When there exists no eavesdroppers within the sector secrecy guard zone, the transmitter only transmits information-bearing signal, and, conversely, AN along with information-bearing signal are transmitted. The closed-form expressions for secrecy outage probability (SOP), connection outage probability (COP) and secrecy throughput are derived under stochastic geometry. Then, we evaluate the effect of the sector secrecy guard zone and AN on the secrecy performance. Our results reveal that the application of the sector secrecy guard zone and AN can significantly improve the security of the system, and blockages also can be utilized to improve secrecy performance. An easy choice of transmit power and power allocation factor is provided for achieving higher secrecy throughput. Furthermore, increasing the density of eavesdroppers not always deteriorates the secrecy performance due to the use of the sector secrecy guard zone and AN.
Inducible SOS Response System of DNA Repair and Mutagenesis in Escherichia coli

Chromosomal DNA is exposed to continuous damage and repair. Cells contain a number of proteins and specific DNA repair systems that help maintain its correct structure. The SOS response was the first DNA repair system described in Escherichia coli induced upon treatment of bacteria with DNA damaging agents arrest DNA replication and cell division. Induction of the SOS response involves more than forty independent SOS genes, most of which encode proteins engaged in protection, repair, replication, mutagenesis and metabolism of DNA. Under normal growth conditions the SOS genes are expressed at a basal level, which increases distinctly upon induction of the SOS response. The SOS-response has been found in many bacterial species (e.g., Salmonella typhimurium, Caulobacter crescentus, Mycobacterium tuberculosis), but not in eukaryotic cells. However, species from all kingdoms contain some SOS-like proteins taking part in DNA repair that exhibit amino acid homology and enzymatic activities related to those found in E. coli. but are not organized in an SOS system. This paper presents a brief up-to-date review describing the discovery of the SOS system, the physiology of SOS induction, methods for its determination, and the role of some SOS-induced genes.
Recognizing the fold of a protein structure

This paper reports a graph-theoretic program, GRATH, that rapidly, and accurately, matches a novel structure against a library of domain structures to find the most similar ones. GRATH generates distributions of scores by comparing the novel domain against the different types of folds that have been classified previously in the CATH database of structural domains. GRATH uses a measure of similarity that details the geometric information, number of secondary structures and number of residues within secondary structures, that any two protein structures share. Although GRATH builds on well established approaches for secondary structure comparison, a novel scoring scheme has been introduced to allow ranking of any matches identified by the algorithm. More importantly, we have benchmarked the algorithm using a large dataset of 1702 non-redundant structures from the CATH database which have already been classified into fold groups, with manual validation. This has facilitated introduction of further constraints, optimization of parameters and identification of reliable thresholds for fold identification. Following these benchmarking trials, the correct fold can be identified with the top score with a frequency of 90%. It is identified within the ten most likely assignments with a frequency of 98%. GRATH has been implemented to use via a server (http://www.biochem.ucl.ac.uk/cgi-bin/cath/Grath.pl). GRATH's speed and accuracy means that it can be used as a reliable front-end filter for the more accurate, but computationally expensive, residue based structure comparison algorithm SSAP, currently used to classify domain structures in the CATH database. With an increasing number of structures being solved by the structural genomics initiatives, the GRATH server also provides an essential resource for determining whether newly determined structures are related to any known structures from which functional properties may be inferred.
Persuasive design and the web: How Cialdini principles are used in online successful companies.

III CONTENTS . IV 2 INTRODUCTION . 1 3 LITERATURE REVIEW . 3 3.1 DEFINING A PERSUASIVE WEB DESIGN. ¡ERROR! MARCADOR NO DEFINIDO. 3.2 HYGIENE FACTORS OF WEB DESIGN ON E-COMMERCE . 4 3.3 FUNCTIONALITY FACTORS . 6 3.3.1 Usability . 6 3.3.2 Interactivity . 7 3.4 PSYCHOLOGICAL ELEMENTS: ONLINE TRUST. 7 3.5 CONTENT ELEMENTS . 8 3.5. 1 Aesthetics . 8 3.5. 2 Marketing Mix . 9 3.5. 3 Stimuli factors for a persuasive web design . 10 3.5. 4 Reciprocation Principle. 10 3.5. 5 Commitment and Consistency Principle . 12 3.5. 6 Social Proof Principle . 13 3.5. 7 Liking Principle. 13 3.5. 8 Authority Principle . 14 3.5. 9 Scarcity Principle . 14 4 METHODOLOGY . 17 4.1 DATABASE . 17 4.1. 1 Procedure . 19 5 RESULTS . 21
Creating Visual Hull Models Using Only Two Mirrors and an Uncalibrated Perspective Camera

We present closed form solutions for the focal length and pose of a camera and two mirrors that are computed directly from the silhouette outlines that appear in a single image. In the noisy case, we show how these equations can be used to form an initial parameter estimate that can be reﬁned with a nonlinear iterative minimisation. This allows ﬁve-view visual hulls to be constructed from a single image. We show how these ﬁve-view visual hulls can be used to form initial estimates of the similarity transforms that relate multiple ﬁve-view silhouette sets of a rigid object in different poses. A nonlinear iterative minimisation is then used to reﬁne the solution so that all silhouettes are speci-ﬁed in a common reference frame, and visual hulls can be constructed from an arbitrary number of silhouettes. Experimental results demonstrating the reconstruction of a toy horse are presented.
Expression of T cell antigen receptor and immunoglobulin genes in lymphoid organs visualized by in situ hybridization.

In situ hybridization techniques were used to detect expression within lymphoid tissues of genes encoding T cell receptor (TCR) alpha, beta and gamma chains, as well as immunoglobulin kappa light chain. Transcripts of these genes were specifically detected in frozen sections of thymus, spleen and lymph node but not in non‐lymphoid tissues. Differences in the level of beta chain gene transcription were observed within and between the thymus cortex and medulla, with approximately 60% and 34% of cells in these areas labelled, respectively. Expression of the TCR alpha chain genes was more homogeneous, while amongst the cells transcribing the gamma chain gene, there was a subpopulation of 0.2% of heavily labelled cortical thymocytes. Labelling of T cell dependent areas of spleen and lymph nodes was observed with each of the TCR probes, but neither alpha nor beta gene expression was seen in lymphoid tissues of athymic nude mice. The gamma chain gene was, however, expressed in both spleen and lymph nodes of these mice. These results indicate that TCR gene expression is not limited to a small subpopulation of T cell precursors. They are discussed in relation to T cell differentiation within the thymus.
Cerebral Autoregulation Real-Time Monitoring

Cerebral autoregulation is a mechanism which maintains constant cerebral blood flow (CBF) despite changes in mean arterial pressure (MAP). Assessing whether this mechanism is intact or impaired and determining its boundaries is important in many clinical settings, where primary or secondary injuries to the brain may occur. Herein we describe the development of a new ultrasound tagged near infra red light monitor which tracks CBF trends, in parallel, it continuously measures blood pressure and correlates them to produce a real time autoregulation index. Its performance is validated in both in-vitro experiment and a pre-clinical case study. Results suggest that using such a tool, autoregulation boundaries as well as its impairment or functioning can be identified and assessed. It may therefore assist in individualized MAP management to ensure adequate organ perfusion and reduce the risk of postoperative complications, and might play an important role in patient care.
A novel deep learning scheme for morphology-based classification of mycobacterial infection in unstained macrophages

Objective Mycobacterium tuberculosis (Mtb) is an airborne, contagious bacterial pathogen that causes widespread infections in humans. Using Mycobacterium marinum (Mm), a surrogate model organism for Mtb research, the present study develops a deep learning-based scheme that can classify the Mm-infected and uninfected macrophages in tissue culture solely based on morphological changes. Methods A novel weak-and semi-supervised learning method is developed to detect and extract the cells, firstly. Then, transfer learning and fine-tuning from the CNN is built to classify the infected and uninfected cells. Results The performance is evaluated by accuracy (ACC), sensitivity (SENS) and specificity (SPEC) with 10-fold cross-validation. It demonstrates that the scheme can classify the infected cells accurately and efficiently at the early infection stage. At 2 hour post infection (hpi), we achieve the ACC of 0.923 ± 0.005, SENS of 0.938 ± 0.020, and SPEC of 0.905 ± 0.019, indicating that the scheme has detected significant morphological differences between the infected and uninfected macrophages, although these differences are hardly visible to naked eyes. Interestingly, the ACC at 12 and 24 hpi are 0.749 ± 0.010 and 0.824 ± 0.009, respectively, suggesting that the infection-induced morphological changes are dynamic throughout the infection. Finally, deconvolution with guided propagation maps the key morphological features contributing to the classification. Significance This proof-of-concept study provides a novel venue to investigate bacterial pathogenesis in a macroscopic level and has a great promise in diagnosis of bacterial infections.
Novel Mobile Variants of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus

ABSTRACT Staphylococcus aureus staphylococcal cassette chromosome mec type IV (SSCmec IV) is associated with virulent community-acquired methicillin-resistant Staphylococcus aureus (MRSA) and frequent horizontal transfer among staphylococci. To gain insight into the mechanism of transfer, we studied the ccrA/B type 2 recombinase-mediated excision of SCCmec IV (n = 5 strains) and SCCmec II (n = 2). In SCCmec IV- but not SCCmec II-containing strains, spontaneous excision of the cassette was observed. Introduction of ccrA/B type 2 recombinase genes under control of an S. aureus bacterial phage promoter in the different strains yielded excision of SCCmec II and multiple excision variants of SCCmec IV. Sequencing of the alternatively excised products in SCCmec IV strains identified a 100-bp shortened SCCmec′ variant and a 5,877-bp, conserved SCC-like element that lacks mecA and ccrA/B recombinases. Excision of the SCC-like element in wild-type S. aureus was dependent on the presence of SCCmec. The element could be excised separately or as part of a novel composite cassette together with SCCmec. The relative abundance of and variety in SCCmec IV excisions may contribute to the frequency of horizontal transfer and genetic plasticity in SCCmec IV MRSA strains.
A Streptococcal Adhesion System for Salivary Pellicle and Platelets

ABSTRACT A Streptococcus sanguis 133-79 adhesin identified by the monoclonal antibody 1.1 (MAb 1.1) binds both saliva-coated hydroxylapatite (sHA) and platelets. The complementary binding site(s) for the adhesin was identified by the anti-idiotypical MAb 2.1. To learn if this adhesion system, marked by the antiadhesin MAb 1.1 and anti-binding site MAb 2.1, is commonly used by strains within the sanguis group and other viridans group streptococci, 42 strains from seven species were tested. Strains that bind to both sHA and platelets use the same adhesin and binding site epitopes. Strains that do not adhere to platelets rely on other adhesin specificities to bind to sHA.
Colpocephaly

Colpocephaly is an anatomic finding in the brain manifested by occipital horns that are disproportionately enlarged in comparison with other parts of the lateral ventricles. It has been considered to result from localized outpocketing of the ventricular cavity due to failure of thickening of overlying brain. Four new cases are presented here, including a child of near-normal development who appears to be the first reported case of colpocephaly with an associated chromosomal anomaly. Our patients support the view that colpocephaly is a disorder of diverse causation that can arise from a variety of degenerative or encephaloclastic insults to the developing brain.
Transition state for protein–DNA recognition

We describe the formation of protein–DNA contacts in the two-state route for DNA sequence recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes in the transition state and constitutes the bottleneck of complex formation. Although a few nonspecific ionic interactions are formed at this early stage, they mainly play a stabilizing role in the final consolidated complex. The interface is fairly plastic in the transition state, likely because of a high level of hydration. The overall picture of this two-state route largely agrees with a smooth energy landscape for binding that speeds up DNA recognition. This “direct” two-state route differs from the parallel multistep pathway described for this system, which involves nonspecific contacts and at least two intermediate species that must involve substantial conformational rearrangement in either or both macromolecules.
Robust Blind Frequency and Transition Time Estimation for Frequency Hopping Systems

In frequency hopping spread spectrum (FHSS) systems, two major problems are timing synchronization and frequency estimation. A blind estimation scheme is presented for estimating frequency and transition time without using reference signals. The scheme is robust in the sense that it can avoid the unbalanced sampling block problem that occurs in existing maximum likelihood-based schemes, which causes large errors in one of the estimates of frequency. The proposed scheme has a lower computational cost than the maximum likelihood-based greedy search method. The estimated parameters are also used for the subsequent time and frequency tracking. The simulation results demonstrate the efficacy of the proposed approach.
What Took Them So Long? Explaining PhD Delays among Doctoral Candidates

A delay in PhD completion, while likely undesirable for PhD candidates, can also be detrimental to universities if and when PhD delay leads to attrition/termination. Termination of the PhD trajectory can lead to individual stress, a loss of valuable time and resources invested in the candidate and can also mean a loss of competitive advantage. Using data from two studies of doctoral candidates in the Netherlands, we take a closer look at PhD duration and delay in doctoral completion. Specifically, we address the question: Is it possible to predict which PhD candidates will experience delays in the completion of their doctorate degree? If so, it might be possible to take steps to shorten or even prevent delay, thereby helping to enhance university competitiveness. Moreover, we discuss practical do's and don'ts for universities and graduate schools to minimize delays.
Genetic Algorithm Control of Model Reduction Passive Quarter Car Suspension System

This paper portrays the demonstrating, and testing of passive suspension control techniques. The control execution of a two-degree of-opportunity quarter car passive suspension frameworks is explored utilizing Matlab/Simulink, display. A classical Proportional Integral and Derivative (PID), Linear Quadratic Control (LQR), and H2 controller design are proposed and compared with soft computing methods, such Fuzzy logic controller (FLC) and Genetic Algorithm (GA) controller. Simulation environment was used for all design methods, investigation of the effects of the control techniques in time-domain design specifications, their comparison and verification of the results obtained. The results are shows the effectiveness of the (GA) controller to satisfied design requirements compared with others methods.
AJEER: an aspectJ-enabled eclipse runtime

There are a number of technologies designed to improve modularity in software systems. The technique presented here combines two of them seamlessly to exploit their respective benefits: Eclipse plugins and AspectJ. The Eclipse runtime is based on the idea of plugins, enabling large systems to be built from smaller components. AspectJ is an AOP-enhanced version of the Java language that allows developers to modularize crosscutting concerns into aspects. While both technologies offer a number of interesting features, their seamless combination is not trivial. Several limitations make it impossible to exploit all the features of the combined technologies. AspectJ-Enabled Eclipse Runtime (AJEER) is designed to overcome these limitations. It integrates load-time weaving for AspectJ into the Eclipse runtime, thus allowing developers to implement aspects that modularize crosscutting concerns beyond the capability of individual plugins. In addition, the dynamic features of the OSGi-based Eclipse 3.0 runtime are preserved in this setting - making it possible to plug AspectJ aspects into and out of the running system dynamically.
Multiwavelength Observations of 1ES 1959+650, 1 Year after the Strong Outburst of 2002

In 2003 April-May, the blazar 1ES 1959+650 showed an increased level of X-ray activity. This prompted a multiwavelength observation campaign with the Whipple 10 m γ-ray telescope, the Rossi X-Ray Timing Explorer, the Bordeaux Optical Observatory, and the University of Michigan Radio Astronomy Observatory. We present the multiwavelength data taken from 2003 May 2 to June 7 and compare the source characteristics with those measured during observations taken during the years 2000 and 2002. The X-ray observations gave a data set with high signal-to-noise ratio light curves and energy spectra; however, the γ-ray observations did not reveal a major TeV γ-ray flare. Furthermore, we find that the radio and optical fluxes do not show statistically significant deviations from those measured during the 2002 flaring periods. While the X-ray flux and X-ray photon index appear correlated during subsequent observations, the apparent correlation evolved significantly among the years 2000, 2002, and 2003. We discuss the implications of this finding for the mechanism that causes the flaring activity.
Video Surveillance for Road Traffic Monitoring

This work proposes a framework for road traffic surveillance using computer vision techniques. After a foreground estimation, post processing techniques are applied to the detected vehicles in motion to generate blobs. Then, a tracking approach based on Kalman filters is used to extract instantaneous information throughout a video sequence, including speed and trajectory estimation and imprudent driving detection. The system has been developed in Python and can be launched in real-time using a standard CPU. The code is available at github: https://github.com/mcv-m6-video/mcv-m6-2018-team3.
Proceedings of the Workshop on Virtual Documents, Hypertext Functionality and the Web

This paper presents an implementation of the Navigational Context hypermedia design pattern. This pattern has been proposed by Rossi, Schwabe and Garrido, but implementation alternatives have not been fully explored specially regarding Web applications. The approach presented in this paper employs features of the HTML language to implements the features specified by the design pattern.
Fludarabine and Rituximab in Relapsed or Refractory Hairy Cell Leukmia Variant: A Case Report and Review of Literature

Hairy cell leukemia (HCL) is a relatively rare chronic B cell leukemia accounting for 2% of leukemia cases. It is characterized by the accumulation of small mature B cell lymphoid cells with an abundant cytoplasm and “hairy” projections found in the peripheral blood, bone marrow, and splenic red pulp. HCL variant (HCL-V) has similar clinical features of classic HCL but only infrequently includes reactivity for tartrate-resistant acid phosphatase (TRAP). The majority of patients do not require therapy immediately upon diagnosis. Treatment is reserved until symptomatic or threatening progression of HCL. In practice, treatment is initiated at the onset of neutropenia, thrombocytopenia, anemia resulting in increased risk of infection or bleeding, symptomatic anemia, or symptomatic splenomegaly. A number of treatment options are available for patients with symptomatic Kosin Medical Journal 2018;33:438-445. https://doi.org/10.7180/kmj.2018. 33.3. 438 KMJ Case Reports
A 4-component 2-D CFDFD method with equivalent SIBC for multilayer metal-coated coaxial waveguide

Equivalent surface impedance boundary condition is implemented in the compact 2-D finite difference frequency domain(2-D CFDFD) method to analyze the propagation characteristics of multilayer metal-coated coaxial waveguide. The advantages of the 2-D CFDFD are reserved by applying the equivalent surface impedance boundary condition(SIBC). Compared with the no-coating coaxial waveguide, the multilayer coating coaxial waveguide makes a better propagation performance.