Miracle-dz/UniFAR-FTUs huggingface dataset:
New Insights into the Evolutionary Rate of Hepatitis B Virus at Different Biological Scales

ABSTRACT The evolutionary rates of hepatitis B virus (HBV) estimated using contemporary sequences are 102 to 104 times higher than those derived from archaeological and genetic evidence. This discrepancy makes the origin of HBV and the time scale of its spread, both of which are critical for studying the burden of HBV pathogenicity, largely unresolved. To evaluate whether the dual demands (i.e., adaptation within hosts and colonization between hosts) of the viral life cycle affect this conundrum, the HBV quasispecies dynamics within and among hosts from a family consisting of a grandmother, her 5 children, and her 2 granddaughters, all of whom presumably acquired chronic HBV through mother-to-infant transmission, were examined by PCR cloning and next-generation sequencing methods. We found that the evolutionary rate of HBV between hosts was considerably lower than that within hosts. Moreover, the between-host substitution rates of HBV decreased as transmission numbers between individuals increased. Both observations were due primarily to changes at nonsynonymous rather than synonymous sites. There were significantly more multiple substitutions than expected for random mutation processes, and 97% of substitutions were changed from common to rare amino acid residues in the database. Continual switching between colonization and adaptation resulted in a rapid accumulation of mutations at a limited number of positions, which quickly became saturated, whereas substitutions at the remaining regions occurred at a much lower rate. Our study may help to explain the time-dependent HBV substitution rates reported in the literature and provide new insights into the origin of the virus. IMPORTANCE It is known that the estimated hepatitis B virus (HBV) substitution rate is time dependent, but the reason behind this observation is still elusive. We hypothesize that owing to the small genome size of HBV, transmission between hosts and adaptation within hosts must exhibit high levels of fitness trade-offs for the virus. By studying the HBV quasispecies dynamics for a chain of sequentially infected transmissions within a family, we found the HBV substitution rate between patients to be negatively correlated with the number of transmissions. Continual switching between hosts resulted in a rapid accumulation of mutations at a limited number of genomic sites, which quickly became saturated in the short term. Nevertheless, substitutions at the remaining regions occurred at a much lower rate. Therefore, the HBV substitution rate decreased as the divergence time increased.
Self-Organizing Map Based User Interface for Visual Surface Inspection

In visual surface inspection applications, a problem often faced is the collection and labelling of training material. The manual labelling of training samples requires much ef fort and is error prone since the defect classes may appear dif ficult to discriminate even for a human. Frequent changes in the inspected material or imaging conditions may lead to impractical often repeating training material collection c ycles. We propose a SOM (Self-Organizing Map) based classifier and user interf ace scheme for visual surface inspection problems. The approach combines the advantages of non-supervise d and supervised classification. The SOM based approach supports the labelling of training data, simplifies the retraining for changing material or imaging conditions, provides an intuitive user interface, and is computationally attractive for real-time applications.
TerraSAR-X Commissioning Phase Execution Summary

This paper provides an overview of the TerraSAR-X commissioning phase (CP). The overall CP planning and preparation is presented. The strategy for data-take (DT) command generation is discussed, and statistical reports summarize the acquired CP DTs. An overview summary on the main results in the different characterization and verification areas is provided together with synthetic aperture radar image examples.
Improving Security Using Extensible Lightweight Static Analysis

Most security attacks exploit instances of well-known classes of implementation flaws. Developers could detect and eliminate many of these flaws before deploying the software, yet these problems persist with disturbing frequency-not because the security community doesn't sufficiently understand them but because techniques for preventing them have not been integrated into the software development process. This article describes an extensible tool that uses lightweight static analysis to detect common security vulnerabilities (including buffer overflows and format string vulnerabilities).
Opposing Brain Differences in 16p11.2 Deletion and Duplication Carriers

Deletions and duplications of the recurrent ∼600 kb chromosomal BP4–BP5 region of 16p11.2 are associated with a broad variety of neurodevelopmental outcomes including autism spectrum disorder. A clue to the pathogenesis of the copy number variant (CNV)'s effect on the brain is that the deletion is associated with a head size increase, whereas the duplication is associated with a decrease. Here we analyzed brain structure in a clinically ascertained group of human deletion (N = 25) and duplication (N = 17) carriers from the Simons Variation in Individuals Project compared with age-matched controls (N = 29 and 33, respectively). Multiple brain measures showed increased size in deletion carriers and reduced size in duplication carriers. The effects spanned global measures of intracranial volume, brain size, compartmental measures of gray matter and white matter, subcortical structures, and the cerebellum. Quantitatively, the largest effect was on the thalamus, but the collective results suggest a pervasive rather than a selective effect on the brain. Detailed analysis of cortical gray matter revealed that cortical surface area displays a strong dose-dependent effect of CNV (deletion > control > duplication), whereas average cortical thickness is less affected. These results suggest that the CNV may exert its opposing influences through mechanisms that influence early stages of embryonic brain development.
Design Optimization and Fabrication of High-Sensitivity SOI Pressure Sensors with High Signal-to-Noise Ratios Based on Silicon Nanowire Piezoresistors

In order to meet the requirement of high sensitivity and signal-to-noise ratios (SNR), this study develops and optimizes a piezoresistive pressure sensor by using double silicon nanowire (SiNW) as the piezoresistive sensing element. First of all, ANSYS finite element method and voltage noise models are adopted to optimize the sensor size and the sensor output (such as sensitivity, voltage noise and SNR). As a result, the sensor of the released double SiNW has 1.2 times more sensitivity than that of single SiNW sensor, which is consistent with the experimental result. Our result also displays that both the sensitivity and SNR are closely related to the geometry parameters of SiNW and its doping concentration. To achieve high performance, a p-type implantation of 5 × 1018 cm−3 and geometry of 10 µm long SiNW piezoresistor of 1400 nm × 100 nm cross area and 6 µm thick diaphragm of 200 µm × 200 µm are required. Then, the proposed SiNW pressure sensor is fabricated by using the standard complementary metal-oxide-semiconductor (CMOS) lithography process as well as wet-etch release process. This SiNW pressure sensor produces a change in the voltage output when the external pressure is applied. The involved experimental results show that the pressure sensor has a high sensitivity of 495 mV/V·MPa in the range of 0–100 kPa. Nevertheless, the performance of the pressure sensor is influenced by the temperature drift. Finally, for the sake of obtaining accurate and complete information over wide temperature and pressure ranges, the data fusion technique is proposed based on the back-propagation (BP) neural network, which is improved by the particle swarm optimization (PSO) algorithm. The particle swarm optimization–back-propagation (PSO–BP) model is implemented in hardware using a 32-bit STMicroelectronics (STM32) microcontroller. The results of calibration and test experiments clearly prove that the PSO–BP neural network can be effectively applied to minimize sensor errors derived from temperature drift.
UvA-DARE ( Digital Academic Repository ) Inner accretion disk disapperance during a radio flare in GRS 1915 + 105

Simultaneous X–ray (BeppoSAX, 0.1–300 keV) and radio (Ryle Telescope, 15 GHz) observations of the superluminal galactic source GRS 1915+105 in high flux state were carried out starting October 1996. The source was in a phase of large X–ray intensity and spectral variability. Among the simultaneous observations, an isolated radio flare lasting ∼2000 s was detected accompanied by X–ray outbursting activity. Here we present the simultaneous radio/X–ray light curves of the flare event and the spectral and timing analysis of the relevant BeppoSAX data. The broad band (0.1–200 keV) energy spectrum of the source can be described in terms of the ‘standard’ spectral model for black hole candidates. We obtain evidence for a temporary disappearance and subsequent restoring of the inner portion of the accretion disk during the flare from the spectral analysis of the X–ray data. We find a variable power law photon index positively correlated to the variability of the exponential cut-off energy. In addition, frequency and intensity variations of a∼4–5 Hz quasi-periodic oscillation (QPO) are detected during the same time interval. The centroid frequency of the QPO is found to be correlated to the spectral power law photon index, and to the X–ray flux from the disk and the high energy flux from the power law. These observational results are discussed in the framework of the disk-instability model proposed for this source.
Enterprise Architecture: Enabling Integration, Agility And Change

Three core imperatives are essential for modern businesses and organizations: seamless integration of customer and operational processes, agility, and the ability to change. These imperatives are relevant in view of successfully executing strategic choices, but all too often not satisfied. Businesses and organizations are complex adaptive socio-technical systems and can be viewed from two fundamentally different perspectives: the functional (black-box) perspective and the constructional (white-box) perspective. Management and governance of businesses and organizations regard the functional, black-box perspective, which is inherently ill-suited for addressing the imperatives mentioned. It will be argued that establishing system integration, agility and change requires a focus on the system's design, hence necessitates the constructional perspective. The concept of architecture is considered fundamental for operationalizing the constructional perspective. Next to the more familiar notion of technology architecture, the concepts of business, organizational and information architecture are formally introduced and elucidated. Various domains within these architectures will be highlighted, whereby the importance of coherence and consistency is stressed, especially in view of the ability to change. Collectively, the four architectures are labeled Enterprise Architecture. Finally, enterprise architecture will be positioned as a crucial means for linking strategy development and execution.
Assessing Post-TAVR Cardiac Conduction Abnormalities Risk Using a Digital Twin of a Beating Heart

Transcatheter aortic valve replacement (TAVR) has rapidly displaced surgical aortic valve replacement (SAVR). However, certain post-TAVR complications persist, with cardiac conduction abnormalities (CCA) being one of the major ones. The elevated pressure exerted by the TAVR stent onto the conduction fibers situated between the aortic annulus and the His bundle, in proximity to the atrioventricular (AV) node, may disrupt the cardiac conduction leading to the emergence of CCA. In his study, an in-silico framework was developed to assess the CCA risk, incorporating the effect of a dynamic beating heart and pre-procedural parameters such as implantation depth and preexisting cardiac asynchrony in the new onset of post-TAVR CCA. A self-expandable TAVR device deployment was simulated inside an electro-mechanically coupled beating heart model in five patient scenarios, including three implantation depths, and two preexisting cardiac asynchronies: (i) a right bundle branch block (RBBB) and (ii) a left bundle branch block (LBBB). Subsequently, several biomechanical parameters were analyzed to assess the post-TAVR CCA risk. The results manifested a lower cumulative contact pressure on the conduction fibers following TAVR for aortic deployment (0.018 MPa) compared to baseline (0.29 MPa) and ventricular deployment (0.52 MPa). Notably, the preexisting RBBB demonstrated a higher cumulative contact pressure (0.34 MPa) compared to the baseline and preexisting LBBB (0.25 MPa). Deeper implantation and preexisting RBBB cause higher stresses and contact pressure on the conduction fibers leading to an increased risk of post-TAVR CCA. Conversely, implantation above the MS landmark and preexisting LBBB reduces the risk.
Optimizing Contingency Management with Reinforcement Learning

Contingency Management (CM) is a psychological treatment that aims to change behavior with financial incentives. In substance use disorders (SUDs), deployment of CM has been enriched by longstanding discussions around the cost-effectiveness of prized-based and voucher-based approaches. In prize-based CM, participants earn draws to win prizes, including small incentives to reduce costs, and the number of draws escalates depending on the duration of maintenance of abstinence. In voucher-based CM, participants receive a predetermined voucher amount based on specific substance test results. While both types have enhanced treatment outcomes, there is room for improvement in their cost-effectiveness: the voucher-based system requires enduring financial investment; the prize-based system might sacrifice efficacy. Previous work in computational psychiatry of SUDs typically employs frameworks wherein participants make decisions to maximize their expected compensation. In contrast, we developed new frameworks that clinical decision-makers choose actions, CM structures, to reinforce the substance abstinence behavior of participants. We consider the choice of the voucher or prize to be a sequential decision, where there are two pivotal parameters: the prize probability for each draw and the escalation rule determining the number of draws. Recent advancements in Reinforcement Learning, more specifically, in off-policy evaluation, afforded techniques to estimate outcomes for different CM decision scenarios from observed clinical trial data. We searched CM schemas that maximized treatment outcomes with budget constraints. Using this framework, we analyzed data from the Clinical Trials Network to construct unbiased estimators on the effects of new CM schemas. Our results indicated that the optimal CM schema would be to strengthen reinforcement rapidly in the middle of the treatment course. Our estimated optimal CM policy improved treatment outcomes by 32% while maintaining costs. Our methods and results have broad applications in future clinical trial planning and translational investigations on the neurobiological basis of SUDs.
Motion planning for robotic manipulation of deformable linear objects

Research on robotic manipulation has mainly focused on manipulating rigid objects so far. However, many important application domains require manipulating deformable objects, especially deformable linear objects (DLOs), such as ropes, cables, and sutures. Such objects are far more challenging to handle, as they can exhibit a much greater diversity of behaviors. This paper describes a new motion planner for manipulating DLOs and tying knots (self-knots and knots around simple static objects) using cooperating robot arms. The planner constructs a topologically-biased probabilistic roadmap in the DLO's configuration space. Unlike in traditional motion planning problems, the goal is a topological state of the world, rather than a geometric one. The implemented planner was tested in simulation to achieve various knots like bowline, neck-tie, bow (shoe-lace), and stun-sail
Development of a single-mode interstitial rotary probe for In Vivo deep brain fluorescence imaging

Ce memoire rend compte de l’expertise developpee par l’auteur au Centre de recherchede l’Institut universitaire en sante mentale de Quebec (CRIUSMQ) en endoscopie fibree. Il decrit la construction d’un nouveau type de microscope optique, le MicroscopeInterstitiel Panoramique (PIM). Par la juxtaposition d’un court morceau de fibre a gradientd’indice et d’un prisme a l’extremite d’une fibre monomode, la lumiere laser estfocalisee sur le cote de la sonde. Pour former une image, cette derniere est rapidementtournee autour de son axe pendant qu’elle est tiree verticalement par un actuateurpiezo-electrique. Ce design de systeme rotatif d’imagerie interstitielle peu invasif est uneffort pour limiter les degâts causes par la sonde tout en imageant la plus grande regionpossible en imagerie optique cerebrale profonde. %%%%This thesis documents the expertise developed by the author at the Centre de recherchede l’Institut universitaire en sante mentale de Quebec (CRIUSMQ) in fibered endoscopy,particularly the design and construction of a new kind of optical microscope: ThePanoramic Interstitial Microscope (PIM). Through the juxtaposition of a short piece ofGraded-Index fibre and a prism at the end of a single-mode fibre, laser light is focussedon the side of the probe. To form an image, the latter is quickly spun around its axiswhile it is being pulled vertically by a piezoelectric actuator. This minimally invasivefluorescence rotary interstitial imaging system is an endeavor to limit the damage causedby the probe while imaging enough tissue to provide good context to the user in deep brain optical imaging.
A new centralized access control for mmWave D2D communications

With the increment in users' data demand and the emergence of applications with stringent Quality of Service requirements, important improvements in cellular network architecture need to be made. In this paper we explore the symbiosis of three key communication technologies in 5G: Device-to-Device communications, 60 GHz unlicensed band transmissions and adaptive beamforming techniques. It provides notable energy saving, improvement in the system spectral efficiency, high achievable data rate and strong interference reduction. Despite these benefits, there are some issues to be analyzed: a limited communication range due to the high path loss, and the interferences among D2D communications, especially if users' density is high. To manage these problems, on the basis of a mmWave network architecture for high UE density indoor environments, we propose a new centralized control for radio access and an efficient multi-criteria scheduling algorithm using greedy graph vertex-coloring techniques. We aim to enhance transmission efficiency, exploiting concurrent transmissions, maximize throughput and minimize end-to-end delay, while taking into account to keep the computational load low.
Visual Pattern Extraction Using Energy-Efficient “2-PCM Synapse” Neuromorphic Architecture

We introduce a novel energy-efficient methodology “2-PCM Synapse” to use phase-change memory (PCM) as synapses in large-scale neuromorphic systems. Our spiking neural network architecture exploits the gradual crystallization behavior of PCM devices for emulating both synaptic potentiation and synaptic depression. Unlike earlier attempts to implement a biological-like spike-timing-dependent plasticity learning rule with PCM, we use a simplified rule where long-term potentiation and long-term depression can both be produced with a single invariant crystallizing pulse. Our architecture is simulated on a special purpose event-based simulator, using a behavioral model for the PCM devices validated with electrical characterization. The system, comprising about 2 million synapses, directly learns from event-based dynamic vision sensors. When tested with real-life data, it is able to extract complex and overlapping temporally correlated features such as car trajectories on a freeway. Complete trajectories can be learned with a detection rate above 90 %. The synaptic programming power consumption of the system during learning is estimated and could be as low as 100 nW for scaled down PCM technology. Robustness to device variability is also evidenced.
Evolving AIDS- and non-AIDS Mortality and Predictors in the PISCIS Cohort of People Living With HIV in Catalonia and the Balearic Islands (Spain), 1998–2020

Abstract Background Effective antiretroviral therapy (ART) has substantially reduced acquired immunodeficiency syndrome (AIDS)-related deaths, shifting the focus to non-AIDS conditions in people living with human immunodeficiency virus (HIV) (PLWH). We examined mortality trends and predictors of AIDS- and non-AIDS mortality in the Population HIV Cohort from Catalonia and Balearic Islands (PISCIS) cohort of PLWH from 1998 to 2020. Methods We used a modified Coding Causes of Death in HIV protocol, which has been widely adopted by various HIV cohorts to classify mortality causes. We applied standardized mortality rates (SMR) to compare with the general population and used competing risks models to determine AIDS-related and non-AIDS-related mortality predictors. Results Among 30 394 PLWH (81.5% male, median age at death 47.3), crude mortality was 14.2 per 1000 person-years. All-cause standardized mortality rates dropped from 9.6 (95% confidence interval [CI], 8.45–10.90) in 1998 through 2003 to 3.33 (95% CI, 3.14–3.53) in 2015 through 2020, P for trend = . 0001. Major causes were AIDS, non-AIDS cancers, cardiovascular disease, AIDS-defining cancers, viral hepatitis, and nonhepatitis liver disease. Predictors for AIDS-related mortality included being aged ≥40 years, not being a man who have sex with men, history of AIDS-defining illnesses, CD4 < 200 cells/µL, ≥2 comorbidities, and nonreceipt of ART. Non-AIDS mortality increased with age, injection drug use, heterosexual men, socioeconomic deprivation, CD4 200 to 349 cells/µL, nonreceipt of ART, and comorbidities, but migrants had lower risk (adjusted hazard risk, 0.69 [95% CI, .57–.83]). Conclusions Mortality rates among PLWH have significantly decreased over the past 2 decades, with a notable shift toward non–AIDS-related causes. Continuous monitoring and effective management of these non-AIDS conditions are essential to enhance overall health outcomes.