Miracle-dz/UniFAR-FTUs huggingface dataset:
VMS data analyses and modeling for the monitoring and surveillance of Indonesian fisheries. (Analyse et modélisation des données VMS pour le suivi et la surveillance des pêches indonésiennes)

Le suivi, le controle et la surveillance (MCS) des peches marines sont des problemes essentiels pour la gestion durable des ressources halieutiques. Dans cette these, nous etudions le suivi spatial des activites des navires de peche en utilisant les donnees de trajectoire du systeme de surveillance des navires (VMS) dans le cadre du projet INDESO (2013-2017). Notre objectif general est de developper une chaine de traitement des donnees VMS afin de: i) effectuer un suivi de l'effort de peche des flottilles de palangriers indonesiens, ii) detecter les activites de peche illegales et evaluer leur importance. L'approche proposee repose sur des modeles de melange gaussien (GMM) et les modeles de Markov caches (HMM), en vue d'identifier les comportements elementaires des navires de peche, tels que les voyages, la recherche et les activites de peche, dans un cadre non supervise. Nous considerons differentes parametrisations de ces modeles avec une etude particuliere des palangriers indonesiens, pour lesquels nous pouvons beneficier de donnees d'observateurs embarques afin de proceder a une evaluation quantitative des modeles proposes et testes.Nous exploitons ensuite ces modeles statistiques pour deux objectifs differents: a) la discrimination des differents flottilles de peche a partir des trajectoires des navires de peche et l'application a la detection et a l'evaluation des activites de peche illegale, b) l'evaluation d'un effort de peche spatialise a partir des donnees VMS. Nous obtenons de tres bons taux de reconnaissance (environ 97%) pour la premiere tâche et nos experiences soutiennent le potentiel d'une exploration operationnelle de l'approche proposee. En raison du nombre limite de donnees d'observateurs embarques, seules des analyses preliminaires on pu etre effectuees pour l'estimation de l'effort de peche a partir des donnees VMS. Au-dela des developpements methodologiques potentiels, cette these met l'accent sur l'importance de la qualite de donnees d'observation en mer representatives pour developper davantage l'exploitation des donnees VMS tant pour la recherche que pour les questions operationnelles.
Preserving Privacy and Quality of Service in Complex Event Processing through Event Reordering

The Internet of Things (IoT) envisions a huge number of networked sensors connected to the internet. These sensors collect large streams of data which serve as input to wide range of IoT applications and services such as e-health, e-commerce, and automotive services. Complex Event Processing (CEP) is a powerful tool that transforms streams of raw sensor data into meaningful information required by these IoT services. Often these streams of data collected by sensors carry privacy-sensitive information about the user. Thus, protecting privacy is of paramount importance in IoT services based on CEP. In this paper we present a novel pattern-level access control mechanism for CEP based services that conceals private information while minimizing the impact on useful non-sensitive information required by the services to provide a certain quality of service (QoS). The idea is to reorder events from the event stream to conceal privacy-sensitive event patterns while preserving non-privacy sensitive event patterns to maximize QoS. We propose two approaches, namely an ILP-based approach and a graph-based approach, calculating an optimal reordering of events. Our evaluation results show that these approaches are effective in concealing private patterns without significant loss of QoS.
Robust Chance Constrained Power Allocation Scheme for Multiple Target Localization in Colocated MIMO Radar System

Taking into account the probabilistic uncertainty on the target radar cross section (RCS) parameter, a robust chance constrained power allocation (RCC-PA) scheme is presented for multiple target localization in colocated multiple-input multiple-output radar system. Such a system adopts a multibeam working mode, in which multiple simultaneous transmit beams are synthesized to illuminate multiple targets independently. We formulate the RCC-PA problem into a chance constrained programming model, where the total power consumption of the multiple beams is minimized to meet a specified multitarget localization accuracy requirement with high probability. Various target RCS fluctuation models have been discussed with different forms of probability distributions. We analytically show that the chance constrained programming problem for each RCS fluctuation model can equivalently be formulated as a deterministic convex optimization problem. Then, by formulating the Karush-Kuhn-Tuckers conditions, we transform the convex optimization problem into a nonlinear equation solving problem, and then solve it by using the bisection method. Simulation results show that our RCC-PA scheme can enhance the power utilization efficiency, and is more robust than the existing deterministic PA schemes.
FPGA implementation of covariance lattice LPC method using burg algorithm

Aiming at the defects of classical lattice algorithm of speech signal linear prediction analysis, an improved algorithm for hardware implementation is proposed in this paper. The recursive form and symmetry characteristic is used to transform the formula of intermediate covariance and three mean square errors, which increase the speed of hardware calculation. The improved algorithm is implementation on Virtex5 XC5VLX110T FPGA, with the maximum frequency of 100.220MHz, while the latency is 9.54us and 17195 LUTs are utilized. The functional test shows that the normalized MSE between MATLAB and FPGA is 1.12% and the reflection factors are all smaller than 1, which means the system is stable.
Faithful chromosome segregation in Trypanosoma brucei requires a cohort of divergent spindle-associated proteins with distinct functions

Abstract Faithful chromosome segregation depends on correct spindle microtubule-kinetochore attachment and requires certain spindle-associated proteins (SAPs) involved in regulating spindle dynamics and chromosome segregation. Little is known about the spindle-associated proteome in the early divergent Trypanosoma brucei and its roles in chromosome segregation. Here we report the identification of a cohort of divergent SAPs through localization-based screening and proximity-dependent biotin identification. We identified seven new SAPs and seventeen new nucleolar proteins that associate with the spindle, and demonstrated that the kinetochore protein KKIP4 also associates with the spindle. These SAPs localize to distinct subdomains of the spindle during mitosis, and all but one localize to nucleus during interphase and post-mitotic phases. Functional analyses of three nucleus- and spindle-associated proteins (NuSAPs) revealed distinct functions in chromosome segregation. NuSAP1 is a kinetoplastid-specific protein required for equal chromosome segregation and for maintaining the stability of the kinetochore proteins KKIP1 and KKT1. NuSAP2 is a highly divergent ASE1/PRC1/MAP65 homolog playing an essential role in promoting the G2/M transition. NuSAP3 is a kinetoplastid-specific Kif13-1-binding protein maintaining Kif13-1 protein stability and regulating the G2/M transition. Together, our work suggests that chromosome segregation in T. brucei requires a cohort of kinetoplastid-specific and divergent SAPs with distinct functions.
Quantizing deep convolutional networks for efficient inference: A whitepaper

We present an overview of techniques for quantizing convolutional neural networks for inference with integer weights and activations. Per-channel quantization of weights and per-layer quantization of activations to 8-bits of precision post-training produces classification accuracies within 2% of floating point networks for a wide variety of CNN architectures. Model sizes can be reduced by a factor of 4 by quantizing weights to 8-bits, even when 8-bit arithmetic is not supported. This can be achieved with simple, post training quantization of weights.We benchmark latencies of quantized networks on CPUs and DSPs and observe a speedup of 2x-3x for quantized implementations compared to floating point on CPUs. Speedups of up to 10x are observed on specialized processors with fixed point SIMD capabilities, like the Qualcomm QDSPs with HVX. Quantization-aware training can provide further improvements, reducing the gap to floating point to 1% at 8-bit precision. Quantization-aware training also allows for reducing the precision of weights to four bits with accuracy losses ranging from 2% to 10%, with higher accuracy drop for smaller networks.We introduce tools in TensorFlow and TensorFlowLite for quantizing convolutional networks and review best practices for quantization-aware training to obtain high accuracy with quantized weights and activations. We recommend that per-channel quantization of weights and per-layer quantization of activations be the preferred quantization scheme for hardware acceleration and kernel optimization. We also propose that future processors and hardware accelerators for optimized inference support precisions of 4, 8 and 16 bits.
Designing miRNA-Based Synthetic Cell Classifier Circuits Using Answer Set Programming

Cell classifier circuits are synthetic biological circuits capable of distinguishing between different cell states depending on specific cellular markers and engendering a state-specific response. An example are classifiers for cancer cells that recognize whether a cell is healthy or diseased based on its miRNA fingerprint and trigger cell apoptosis in the latter case. Binarization of continuous miRNA expression levels allows to formalize a classifier as a Boolean function whose output codes for the cell condition. In this framework, the classifier design problem consists of finding a Boolean function capable of reproducing correct labelings of miRNA profiles. The specifications of such a function can then be used as a blueprint for constructing a corresponding circuit in the lab. To find an optimal classifier both in terms of performance and reliability, however, accuracy, design simplicity and constraints derived from availability of molcular building blocks for the classifiers all need to be taken into account. These complexities translate to computational difficulties, so currently available methods explore only part of the design space and consequently are only capable of calculating locally optimal designs. We present a computational approach for finding globally optimal classifier circuits based on binarized miRNA datasets using Answer Set Programming for efficient scanning of the entire search space. Additionally, the method is capable of computing all optimal solutions, allowing for comparison between optimal classifier designs and identification of key features. Several case studies illustrate the applicability of the approach and highlight the quality of results in comparison with a state of the art method. The method is fully implemented and a comprehensive performance analysis demonstrates its reliability and scalability.
AFM tips: how sharp are they?

From both simple estimates and a ‘blind’ reconstruction based on cryo‐AFM images of filamentous actin, we find that the radius of curvature at the apex of Si3N4 tips can be as small as 1 nm with a conical angle in the range 30~40°, revealing a relatively high aspect ratio that is much greater than previously anticipated. Our results show that commercially available cantilevers are often sharp enough for routine high resolution imaging of biological materials, and suggest that factors other than an inherent blunt tip are probably responsible for frequent occurrences of poor resolution.
Studies of Microbiota Dynamics Reveals Association of “Candidatus Liberibacter Asiaticus” Infection with Citrus (Citrus sinensis) Decline in South of Iran

Citrus Decline Disease was recently reported to affect several citrus species in Iran when grafted on a local rootstock variety, Bakraee. Preliminary studies found “Candidatus Phytoplasma aurantifoliae” and “Candidatus Liberibacter asiaticus” as putative etiological agents, but were not ultimately able to determine which one, or if an association of both, were causing the disease. The current study has the aim of characterizing the microbiota of citrus plants that are either asymptomatic, showing early symptoms, or showing late symptoms through amplification of the V1–V3 region of 16S rRNA gene using an Illumina sequencer in order to (i) clarify the etiology of the disease, and (ii) describe the microbiota associated to different symptom stages. Our results suggest that liberibacter may be the main pathogen causing Citrus Decline Disease, but cannot rule out the possibility of phytoplasma being involved as well. The characterization of microbiota shows that the leaves show only two kinds of communities, either symptomatic or asymptomatic, while roots show clear distinction between early and late symptoms. These results could lead to the identification of bacteria that are related to successful plant defense response and, therefore, to immunity to the Citrus Decline Disease.
Rapid Eye Movement Sleep, Sleep Continuity and Slow Wave Sleep as Predictors of Cognition, Mood, and Subjective Sleep Quality in Healthy Men and Women, Aged 20–84 Years

Sleep and its sub-states are assumed to be important for brain function across the lifespan but which aspects of sleep associate with various aspects of cognition, mood and self-reported sleep quality has not yet been established in detail. Sleep was quantified by polysomnography, quantitative Electroencephalogram (EEG) analysis and self-report in 206 healthy men and women, aged 20–84 years, without sleep complaints. Waking brain function was quantified by five assessments scheduled across the day covering objectively assessed performance across cognitive domains including sustained attention and arousal, decision and response time, motor and sequence control, working memory, and executive function as well as self-reports of alertness, mood and affect. Controlled for age and sex, self-reported sleep quality was negatively associated with number of awakenings and positively associated with the duration of Rapid Eye Movement (REM) sleep, but no significant associations with Slow Wave Sleep (SWS) measures were observed. Controlling only for age showed that associations between objective and subjective sleep quality were much stronger in women than in men. Analysis of 51 performance measures demonstrated that, after controlling for age and sex, fewer awakenings and more REM sleep were associated significantly with better performance on the Goal Neglect task, which is a test of executive function. Factor analysis of the individual performance measures identified four latent variables labeled Mood/Arousal, Response Time, Accuracy, and Visual Perceptual Sensitivity. Whereas Mood/Arousal improved with age, Response Times became slower, while Accuracy and Visual perceptual sensitivity showed little change with age. After controlling for sex and age, nominally significant association between sleep and factor scores were observed such that Response Times were faster with more SWS, and Accuracy was reduced where individuals woke more often or had less REM sleep. These data identify a positive contribution of SWS to processing speed and in particular highlight the importance of sleep continuity and REM sleep for subjective sleep quality and performance accuracy across the adult lifespan. These findings warrant further investigation of the contribution of sleep continuity and REM sleep to brain function.
The potential of four woody species for the revegetation of fly ash deposits from the 'Nikola Tesla - A' thermoelectric plant (Obrenovac, Serbia).

Four woody species, Tamarix tentandra Pallas, Populus alba L. and Robinia pseudoacacia L. (planted) and Amorpha fruticosa L. (naturally colonized) were studied at two fly ash deposit lagoons, weathered 3 (L1) and 11 years (L2). All species were assessed in terms of their invasive ability, photosynthetic efficiency, photosynthetic pigments and damage symptoms, while the characteristics of the habitat were assessed in terms of trace element content and the pH and EC of the ash. A reduced vitality of all populations growing on the ash was observed, except for the naturally colonized A. fruticosa. High vitality on all sites, except at L2, increased chlorophyll content and absence of damage symptoms indicates a tolerance in relation to the uptake of toxic elements from the ash. Therefore, the characteristics of naturally colonized species can be used for modeling future actions of biological restoration of fly ash deposits.
High-intensity Interval Training in Different Exercise Modes: Lessons from Time to Exhaustion

Abstract To provide information for high-intensity interval training (HIIT) load, we compared the temporal variables of VO2 response at, and after, a time sustained at the exercise intensity corresponding to VO2max (Tlim) in different exercise modes. Forty-five trained male swimmers (11), rowers (13), runners (10) and cyclists (11) completed an incremental protocol to determine the velocity (vVO2max) or power (wVO2max) at VO2max and a square wave exercise from rest to 100% of vVO2max/wVO2max. The temporal variables of VO2 response were examined using a breath-by-breath gas analyzer. VO2 responses were not different between exercise modes, except for the percentage of VO2max at 50% of Tlim, which was ~6% higher in rowing compared to cycling (97.70±2.90 vs 92.40±5.69%, p=0.013). During the recovery period, both swimmers and rowers evidenced higher percentages of VO2max compared to cyclists at 30 s (65.1±10.4 and 65.7±5.6 vs 52.7±5.6%) and 60 s (41.7±10.8 and 38.4±5.4 vs 30.4±1.8%) time periods, all for p<0.01. Furthermore, swimmers presented higher time values to reach 50% VO2max compared to runners and cyclists (51.1±15.6 vs 38.1±6.7 and 33.8±4.7%; p<0.001). When training at 100% of VO2max intensity, fixed intervals for HIIT could be set freely. However, recovery periods based on time or intensity are exercise-mode dependent.
Progress and Innovations in the Management of Adult Acute Lymphoblastic Leukemia

Importance Remarkable progress has occurred in understanding the pathophysiology and in developing improved personalized therapies in adult acute lymphoblastic leukemia (ALL). Observations We searched MEDLINE (1990-2018), the American Society of Clinical Oncology, and American Society of Hematology websites (2010-2018). We used the search terms “acute lymphoblastic or lymphocytic leukemia” or “ALL. ” We largely selected publications in the past 5 years but did not exclude commonly referenced and highly regarded older publications. Target therapies toward specific transcripts (eg, BCR-ABL1 tyrosine kinase oncoprotein by tyrosine kinase inhibitors) and specific leukemic cell surface antigens (eg, CD20, CD22, and CD19 monoclonal antibodies) are major breakthroughs. Current treatments produce long-term survival in 50% of patients with precursor B-cell ALL including 50% to 70% with Philadelphia chromosome (Ph)-positive ALL, 50% to 60% with T-cell ALL, and 80% with mature B-cell ALL. Next-generation sequencing and genomic profiling in ALL have identified new prognostic markers, targets, and ALL subtypes (eg, Ph-like ALL). Monoclonal antibodies, bispecific antibody constructs, and chimeric antigen receptor T cellular therapies developed in the past 5 to 7 years have revolutionized the treatment of ALL and resulted in US Food and Drug Administration approvals of blinatumomab in 2014, as well as inotuzumab and tisagenlecleucel in 2017 as ALL salvage strategies. Their use in combined modalities as salvage and frontline therapies is currently under investigation. Conclusions and Relevance Therapies targeting specific transcripts or leukemic cell surface antigens are major breakthroughs in the treatment of adults with ALL. The incorporation of new monoclonal antibodies and other targeted approaches into frontline regimens is showing promising results. If confirmed, such strategies may increase the cure rates in adults to levels achieved in pediatric ALL and reduce the need for intensive and prolonged chemotherapy.
The HER2 inhibitor lapatinib potentiates doxorubicin-induced cardiotoxicity through iNOS signaling

Rationale: Lapatinib (LAP) is a crucial alternative to trastuzumab upon the onset of drug resistance during treatment of metastatic human epidermal growth factor receptor 2-positive breast cancer. Like trastuzumab, LAP is commonly used alongside anthracyclines as a combination therapy, due to enhanced anti-cancer efficacy. However, this is notably associated with cardiotoxicity so it is imperative to understand the mechanisms driving this cardiotoxicity and develop cardioprotective strategies. To this end, here we utilize human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), which exhibit several characteristics representative of in vivo cardiomyocytes that make them breakthrough models to study drug toxicity. Methods: We investigated LAP- and doxorubicin (DOX)-induced toxicity in hPSC-CMs and evaluated the involvement of inducible nitric oxide (NO) synthase (iNOS). The significance of iNOS-mediated cardiotoxicity was furthermore evaluated in animal studies. Results: LAP synergistically increased DOX toxicity in hPSC-CMs in a dose- and time-dependent manner. At concentrations that were otherwise non-apoptotic when administered separately, LAP significantly potentiated DOX-induced hPSC-CM apoptosis. This was accompanied by increased iNOS expression and pronounced production of NO. iNOS inhibition significantly reduced hPSC-CM sensitivity to LAP and DOX co-treatment (LAP-plus-DOX), leading to reduced apoptosis. Consistent with our observations in vitro, delivery of an iNOS inhibitor in mice treated with LAP-plus-DOX attenuated myocardial apoptosis and systolic dysfunction. Moreover, inhibition of iNOS did not compromise the anti-cancer potency of LAP-plus-DOX in a murine breast cancer xenograft model. Conclusions: Our findings suggest that iNOS inhibition is a promising cardioprotective strategy to accompany HER2-inhibitor/anthracycline combination therapies. Furthermore, these results support the promise of hPSC-CMs as a platform for investigating cardiotoxicity and developing cardioprotectants as a whole.