Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstruction and Clustering with Graph optimization and Priors on Gene networks and Images. (Reconstruction et classification à partir d'optimisation dans des graphes et a priori sur des réseaux de gènes et images)

The discovery of novel gene regulatory processes improves the understanding of cell phenotypic responses to external stimuli for many biological applications, such as medicine, environment or biotechnologies. To this purpose, transcriptomic data are generated and analyzed from DNA microarrays or more recently RNAseq experiments. They consist in genetic expression level sequences obtained for all genes of a studied organism placed in different living conditions. From these data, gene regulation mechanisms can be recovered by revealing topological links encoded in graphs. In regulatory graphs, nodes correspond to genes. A link between two nodes is identified if a regulation relationship exists between the two corresponding genes. Such networks are called Gene Regulatory Networks (GRNs). Their construction as well as their analysis remain challenging despite the large number of available inference methods. In this thesis, we propose to address this network inference problem with recently developed techniques pertaining to graph optimization. Given all the pairwise gene regulation information available, we propose to determine the presence of edges in the final GRN by adopting an energy optimization formulation integrating additional constraints. Either biological (information about gene interactions) or structural (information about node connectivity) a priori have been considered to restrict the space of possible solutions. Different priors lead to different properties of the global cost function, for which various optimization strategies, either discrete and continuous, can be applied. The post-processing network refinements we designed led to computational approaches named BRANE for "Biologically-Related A priori for Network Enhancement". For each of the proposed methods — BRANE Cut, BRANE Relax and BRANE Clust — our contributions are threefold: a priori-based formulation, design of the optimization strategy and validation (numerical and/or biological) on benchmark datasets from DREAM4 and DREAM5 challenges showing numerical improvement reaching 20%. In a ramification of this thesis, we slide from graph inference to more generic data processing such as inverse problems. We notably invest in HOGMep, a Bayesian-based approach using a Variational Bayesian Approximation framework for its resolution. This approach allows to jointly perform reconstruction and clustering/segmentation tasks on multi-component data (for instance signals or images). Its performance in a color image deconvolution context demonstrates both quality of reconstruction and segmentation. A preliminary study in a medical data classification context linking genotype and phenotype yields promising results for forthcoming bioinformatics adaptations.
An autopsied case of MM1-type sporadic Creutzfeldt-Jakob disease with pathology of Wernicke encephalopathy

ABSTRACT An 83-year-old Japanese man presented with gait disturbance followed by rapidly-progressive cognitive impairment. Magnetic resonance diffusion-weighted images showed extensive hyperintense regions in the cerebral cortex. Four weeks after symptom onset, myoclonus appeared, and the patient developed difficulty swallowing; intravenous peripheral continuous infusions without vitamin supplementation were administered during the last two months of the patient’s life. The patient reached the akinetic mutism state and died 12 weeks after symptom onset due to sepsis. The brain weighed 940 g and showed general cerebral atrophy. Extensive spongiform change were observed in the cerebral cortex, striatum, thalamus, and cerebellar cortex, but gliosis was generally mild. Numerous newly-developed hemorrhage foci were observed in the mammillary body, the areas adjacent to the third and fourth ventricles, and the periaqueduct of the midbrain; however, proliferation of capillaries and endothelium and collections of macrophages were relatively inconspicuous. These findings suggested comorbidity with the acute stage of Wernicke encephalopathy (WE). Immunostaining showed extensive diffuse synaptic-type prion protein deposition in the gray matter. According to the neuropathological, genetic, and molecular findings, the present case was finally diagnosed as MM1-type sporadic Creutzfeldt-Jakob disease (CJD) with WE. We should remain alert to the diagnosis of WE when CJD is suspected, and it is necessary to consider the complications of both diseases. This report emphasizes the importance of pathological investigations for the diagnosis of CJD, WE, and the coexistence of both.
Synaptic distributions of pS214‐tau in rhesus monkey prefrontal cortex are associated with spine density, but not with cognitive decline

Female rhesus monkeys and women are subject to age‐ and menopause‐related deficits in working memory, an executive function mediated by the dorsolateral prefrontal cortex (dlPFC). Long‐term cyclic administration of 17β‐estradiol improves working memory, and restores highly plastic axospinous synapses within layer III dlPFC of aged ovariectomized monkeys. In this study, we tested the hypothesis that synaptic distributions of tau protein phosphorylated at serine 214 (pS214‐tau) are altered with age or estradiol treatment, and couple to working memory performance. First, ovariectormized young and aged monkeys received vehicle or estradiol treatment, and were tested on the delayed response (DR) test of working memory. Serial section electron microscopic immunocytochemistry was then performed to quantitatively assess the subcellular synaptic distributions of pS214‐tau. Overall, the majority of synapses contained pS214‐tau immunogold particles, which were predominantly localized to the cytoplasm of axon terminals. pS214‐tau was also abundant within synaptic and cytoplasmic domains of dendritic spines. The density of pS214‐tau immunogold within the active zone, cytoplasmic, and plasmalemmal domains of axon terminals, and subjacent to the postsynaptic density within the subsynaptic domains of dendritic spines, were each reduced with age. None of the variables examined were directly linked to cognitive status, but a high density of pS214‐tau immunogold particles within presynaptic cytoplasmic and plasmalemmal domains, and within postsynaptic subsynaptic and plasmalemmal domains, accompanied high synapse density. Together, these data support a possible physiological, rather than pathological, role for pS214‐tau in the modulation of synaptic morphology in monkey dlPFC.
The optimal mating distance resulting from heterosis and genetic incompatibility

Offspring are fittest when parents are genetically neither too close nor too distant from each other. Theory predicts that the fitness of an individual is maximized when the genetic distance between its parents (i.e., mating distance) is neither too small nor too large. However, decades of research have generally failed to validate this prediction or identify the optimal mating distance (OMD). Respectively analyzing large numbers of crosses of fungal, plant, and animal model organisms, we indeed find the hybrid phenotypic value a humped quadratic polynomial function of the mating distance for the vast majority of fitness-related traits examined, with different traits of the same species exhibiting similar OMDs. OMDs are generally slightly greater than the nucleotide diversities of the species concerned but smaller than the observed maximal intraspecific genetic distances. Hence, the benefit of heterosis is at least partially offset by the harm of genetic incompatibility even within species. These results have multiple theoretical and practical implications for speciation, conservation, and agriculture.
Evaluation of relationship between nutritional status and oral health related quality of life in complete denture wearers

Introduction: The prevalence of malnutrition increases with old age, especially in developing countries like India, and it is the most common cause of morbidity and mortality, because of many factors out of which dentate status is one. Aim and Objective: The aim of this study is to evaluate and determine the effect of nutritional status and dietary intake on the oral health-related quality of life (OHRQOL) of elderly edentulous complete denture-wearing patients and to know whether elderly complete denture wearers have a higher risk of malnutrition. The objective was to assess the need to include dietary and nutritional counseling during prosthodontic rehabilitation of elderly edentulous patients. Materials and Methods: A cross-sectional study was conducted among 200 elderly denture-wearing patients above 60 years of age from Nagpur, Maharashtra. Mini-Nutritional Assessment (MNA) questionnaire was used to assess nutritional status, and Geriatric Oral Health Assessment Index (GOHAI) questionnaire was used to determine the OHRQOL of these patients. Descriptive statistics were used to analyze data using SPSS version 21 (SPSS Inc., Chicago, IL, USA). Results: Among the assessed participants, nearly 95% of them had total scores of GOHAI between 12 and 57 which require “needed dental care. ” As per MNA, 10.5% had adequate nutrition, 70% were at risk of malnutrition, and remaining 19.5% of participants were malnourished. There was a significant correlation between GOHAI and MNA scores. Conclusion: Low nutritional status was associated with the poor OHRQOL among the elderly. A strong association was found between mean GOHAI and MNA scores and thereby nutritional status and OHRQOL. The use of conventional dentures increases the risk of malnutrition in the elderly due to inability to eat and chew food properly. Dietary analysis and counseling should be strictly incorporated into geriatric treatment planning during prosthetic rehabilitation.
SYSTRAN Participation to the WMT2018 Shared Task on Parallel Corpus Filtering

This paper describes the participation of SYSTRAN to the shared task on parallel corpus filtering at the Third Conference on Machine Translation (WMT 2018). We participate for the first time using a neural sentence similarity classifier which aims at predicting the relatedness of sentence pairs in a multilingual context. The paper describes the main characteristics of our approach and discusses the results obtained on the data sets published for the shared task.
Trust and experience in online auctions

ABSTRACT This paper aims to shed light on the complexities and difficulties in predicting the effects of trust and the experience of online auction participants on bid levels in online auctions. To provide some insights into learning by bidders, a field study was conducted first, to examine auction and bidder characteristics from eBay auctions of rare coins. We proposed that such learning is partly because of institutional-based trust. Data were then gathered from 453 participants in an online experiment and survey, and a structural equation model was used to analyze the results. This paper reveals that experience has a nonmonotonic effect on the levels of online auction bids. Contrary to previous research on traditional auctions, as online auction bidders gain more experience, their level of institutional-based trust increases and leads to higher bid levels. Data also show that both a bidder’s selling and bidding experiences increase bid levels, with the selling experience having a somewhat stronger effect. This paper offers an in-depth study that examines the effects of experience and learning and bid levels in online auctions. We postulate this learning is because of institutional-based trust. Although personal trust in sellers has received a significant amount of research attention, this paper addresses an important gap in the literature by focusing on institutional-based trust.
Anaerobic biological treatment of industrial saline wastewater: fixed bed reactor performance and analysis of the microbial community structure and abundance

ABSTRACT The purpose of the present work is to treat saline Tuna fish wastewater, with the salt concentration of 43 g L−1 and total organic carbon (TOC) of 8.3 g L−1, using an anaerobic fixed bed reactor involving salt-tolerant bacteria from the natural hypersaline environment during 150 days. The highest volatile solids (VS) removal efficiency of 84.1% was recorded for the organic loading rate (OLR) of 1.04 g TOC L−1.d−1 and the lowest salinity of 14.6 g NaCl L−1. In addition, the maximum biogas production of 0.8 L−1.d−1 for a working volume of 4 L and an organic loading rate of 2.07 g TOC L−1.d−1 correlated with the decrease of Volatile fatty acids (VFA) content. The Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and the phylogenetic analysis of the bacterial community showed the action of hydrolytic, acidogenic, halotolerant sulfate-reducing and halophilic fermentative bacterium during the processing time. A stable archaeal and methanogenic community’s diversity including hydrogenotrophic methanogens was demonstrated with Quantitative-PCR (Q-PCR). The highest bacterial population abundance was detected for 1.45 g TOC L−1.d−1 and the important methanogenic community abundance for 2.07 g TOC L−1.d−1 may be related to the highest biogas production in this charge for an effluent salinity of 27.7 g NaCl L−1. GRAPHICAL ABSTRACT
Bromeliad Targeted Foliar Treatments with Aqualuer® 20-20 for Hot Spot Mitigation Using Three Hand Sprayers Against Aedes albopictus (Diptera: Culicidae)

ABSTRACT: Bromeliads serve as a key environmental resource for Aedes albopictus (Skuse) in some peridomestic landscapes and are not addressed through conventional source reduction. As an alternative, three handheld sprayers were evaluated in point-source applications of permethrin to bromeliads in Saint Augustine, FL. Each machine was screened for its utility in point-source harborage treatments, while we simultaneously evaluated bromeliad-focused treatments for reducing Ae. albopictus egg abundance in bromeliad plants. Semi-field tests against caged Ae. albopictus produced 100% mortality at 24 h with each sprayer. Three field sites were assigned to each machine and a control, and bromeliad residual applications of Aqualuer 20-20® were assessed through egg surveillance using ovitraps both within and beyond 30 m of the treated bromeliad harborage. The treatment decreased Ae. albopictus egg abundance across the field sites for three weeks post-treatment with no significant differences among the equipment. Functional differences among machines, such as automated pressure control or leak guards on the nozzle, depend on the accessories that offer the greatest logistical benefit to the user. The field results suggest bromeliads are a viable target for harborage treatments. Selective treatments to bromeliads could offer a possible solution to containers that homeowners refuse to eliminate.
A hierarchical stochastic modelling approach for reconstructing lung tumour geometry from 2D CT images

ABSTRACT Lung cancer is one of the deadliest cancers in both men and women. Nowadays, several methods are used to cure this cancer including surgery and radiotherapy. These methods require prior knowledge about the shape of tumours. This type of knowledge may also help physicians to determine the cancer type. In this paper we propose a novel approach for 3D reconstruction of tumour geometry from a sequence of 2D images. The proposed approach consists of two phases: tumour segmentation from computed tomography (CT) images and 3D shape reconstruction. Segmentation is conducted using snake optimisation and Gustafson–Kessel clustering. For 3D reconstruction, first, we propose a new approach to interpolate some intermediate slices between original slices. Then, the well-known marching cubes algorithm is used for surface reconstruction. Eventually, we smoothen the surface using an explicit fairing algorithm. Experiments show that our new approach can highly improve the quality and the accuracy of the reconstructed tumour shape.
Vesicle‐bound EBV‐BART13‐3p miRNA in circulation distinguishes nasopharyngeal from other head and neck cancer and asymptomatic EBV‐infections

Cell‐free microRNA (miRNA) in biofluids released by tumors in either protein or vesicle‐bound form, represent promising minimally‐invasive cancer biomarkers. However, a highly abundant non‐tumor background in human plasma and serum complicates the discovery and detection of tumor‐selective circulating miRNAs. We performed small RNA sequencing on serum and plasma RNA from Nasopharyngeal Carcinoma (NPC) patients. Collectively, Epstein Barr virus‐encoded miRNAs, more so than endogenous miRNAs, signify presence of NPC. However, RNAseq‐based EBV miRNA profiles differ between NPC patients, suggesting inter‐tumor heterogeneity or divergent secretory characteristics. We determined with sensitive qRT‐PCR assays that EBV miRNAs BART7‐3p, BART9‐3p and BART13‐3p are actively secreted by C666.1 NPC cells bound to extracellular vesicles (EVs) and soluble ribonucleoprotein complexes. Importantly, these miRNAs are expressed in all primary NPC tumor biopsies and readily detected in nasopharyngeal brushings from both early and late‐stage NPC patients. Increased levels of BART7‐3p, BART9‐3p and particularly BART13‐3p, distinguish NPC patient sera from healthy controls. Receiver operating characteristic curve analysis using sera from endemic NPC patients, other head and neck cancers and individuals with asymptomatic EBV‐infections reveals a superior diagnostic performance of EBV miRNAs over anti‐EBNA1 IgA serology and EBV‐DNA load (AUC 0.87–0.96 vs 0.86 and 0.66 respectively). The high specificity of circulating EBV‐BART13‐3p (97%) for NPC detection is in agreement with active secretion from NPC tumor cells. We conclude EV‐bound BART13‐3p in circulation is a promising, NPC‐selective, biomarker that should be considered as part of a screening strategy to identify NPC in endemic regions.
Privacy protection for health information research in New Zealand district health boards.

AIM To examine the practices used by New Zealand's 20 district health boards (DHBs) to protect patient privacy when patient information is used for research, and particularly practices for de-identifying information. METHOD An e-mailed questionnaire survey, using New Zealand's Official Information Act to request information on the policies and practices of each DHB. RESULTS 19/20 DHBs (95%) responded to the survey, one of which reported that it did not provide patient information for research. 18/18 (100%) of the DHBs that reported providing patient information for research required the project to have ethics approval. 18/18 (100%) of the DHBs that offered patient data for research also required individual patient consent and/or de-identification of the information before it was used for research. 14/18 DHBs (78%) deidentified data before releasing it for research, 8/18 DHBs (48%) sought individual patient consent before releasing data for research, and 5/18 (28%) used both methods. Other measures to protect privacy included confidentiality agreements, encryption and cybersecurity procedures. CONCLUSION Our findings show DHBs self-report that they have sufficient measures in place to protect privacy when patient information is used for research. However, these measures need to be continuously evaluated against rapidly evolving international practices and technological developments.
Pvlib Python: a Python Package for Modeling Solar Energy Systems

pvlib python is a community-supported open source tool that provides a set of functions and classes for simulating the performance of photovoltaic energy systems. pvlib python aims to provide reference implementations of models relevant to solar energy, including for example algorithms for solar position, clear sky irradiance, irradiance transposition, DC power, and DC-to-AC power conversion. pvlib python is an important component of a growing ecosystem of open source tools for solar energy (William F. Holmgren, Hansen, Stein, & Mikofski, 2018).
Bi-Directional Beamformer Training for Dynamic TDD Networks

In dynamic time-division-duplexing networks, the available resources per cell can be freely allocated to either uplink (UL) or downlink (DL) depending on the instantaneous traffic demand. Hence, complicated UL–DL and DL–UL interference scenarios arise due to simultaneous UL and DL data transmission in adjacent cells. In this paper, decentralized iterative beamformer designs are obtained for several traffic aware network optimization objectives such that only minimal information exchange is required among the coordinated base stations (BS) and user equipment (UE). Bi-directional forward–backward training via spatially precoded over-the-air pilot signaling is used to facilitate coordinated beamforming. This allows BSs and UEs to iteratively optimize their respective transmitters/receivers based on only locally measured reverse link pilot measurements. Novel bi-directional beamformer training strategies and methods for direct estimation (DE) of the stream specific beamformers are developed for each intermediate beamformer update in a limited and noisy pilot environment. The proposed signaling and DE schemes allow for non-orthogonal and overlapping pilots, which considerably reduces the resource coordination effort. Also, the decontamination ability of the proposed strategies are analyzed with limited pilot resources. The numerical examples illustrate the superior system performance of the proposed training and estimation framework in comparison to both the traditional stream-specific channel estimation method and an uncoordinated system.
A Dependency Graph-Based Keyphrase Extraction Method Using Anti-patterns

Keyphrase extraction is one of fundamental natural language processing (NLP) tools to improve many textmining applications such as document summarization and clustering. In this paper, we propose to use two novel techniques on the top of the state-of-the-art keyphrase extraction methods. First is the anti-patterns that aim to recognize non-keyphrase candidates. The state-of-the-art methods often used the rich feature set to identify keyphrases while those rich feature set cover only some of all keyphrases because keyphrases share very few similar patterns and stylistic features while non-keyphrase candidates often share many similar patterns and stylistic features. Second one is to use the dependency graph instead of the word co-occurrence graph that could not connect two words that are syntactically related and placed far from each other in a sentence while the dependency graph can do so. In experiments, we have compared the performances with different settings of the graphs (co-occurrence and dependency), and with the existing method results. Finally, we discovered that the combination method of dependency graph and anti-patterns outperform the state-of-the-art performances.