Miracle-dz/UniFAR-FTUs huggingface dataset:
Application d’une nouvelle technique d’IRM (Transfert d’Aimantation inhomogène - ihMT) à la sclérose en plaques

Introduction : la Sclerose en Plaques (SEP) est une pathologie inflammatoire, demyelinisante et chronique du systeme nerveux central. De nombreux mecanismes lesionnels sont impliques dans la physiopathogenicite de la SEP (inflammation, demyelinisation, perte axonale et gliose). Cependant l’atteinte de la myeline persiste au premier plan. Le developpement de nouvelles techniques d’IRM (Transfert d’aimantation (MT), myelin water fraction, DTI, tractographie, spectroscopie) a rendu possible une meilleure comprehension du processus lesionnel et une analyse plus fine de la substance blanche et grise d’apparence normale permettant de preciser l’atteinte focale et diffuse de la maladie. Cependant aucune de ces techniques d’IRM ne permet actuellement de visualiser specifiquement la myeline. Une nouvelle technique prometteuse, le « Transfert d’Aimantation Inhomogene (ihMT)», semble etre sensible et specifique a la myeline. L’objectif de notre etude etait d’evaluer la sensibilite de cette technique innovante « ihMT » a la SEP chez des patients atteints de SEP de type recurrente-remittente (RR). Methodes : 25 patients atteints de SEP de forme (RR) (20/5 femmes/hommes, âge moyen 42/41 ans) et 20 volontaires sains (14/6 femmes/hommes, âge moyen 42/39) ont participe a cette etude de recherche prospective sur l’IRM. Le protocole d’imagerie (IRM 1,5 Tesla), comprenait l’acquisition de sequences IRM ponderees en T1, T2, FLAIR et la sequence MT classique et ihMT (monocoupe 2D de 9mm). Une analyse par regions avec etude quantitative des ratios ihMT (ihMTR) et MT (MTR) a ete realisee dans les regions de substance blanche et grise d’apparence normale et dans les lesions des patients. Ces donnees ont ete comparees a celles obtenues chez les sujets temoins. Des correlations ont ete recherchees entre les variations de MTR/ihMTR et la severite clinique des patients (score EDSS). Resultats : une diminution des ratios MT/ihMT a ete observee chez les patients versus les temoins dans la substance blanche d’apparence normale frontale, occipitale, temporale et des thalami (p Discussions : cette premiere application clinique d’ihMT a permis de mettre en evidence une sensibilite de cette technique d’imagerie a la myeline et a la SEP. De plus, ihMT a rendu possible l’obtention d’informations complementaires a celles observees avec la technique MT classique. Ceci est illustre par des correlations plus fortes retrouvees entre les ratios ihMT et la severite clinique. Bien que nos resultats soient tres encourageants, de futurs travaux devront ete entrepris afin de confirmer et preciser sa specificite a la myeline. En conclusion,a la lumiere de notre etude preliminaire nous anticipons que la technique ihMT pourrait jouer un role important dans de futurs essais therapeutiques evaluant l’efficacite des molecules a visee remyelinisante en cours de developpement.
Combinatorial Auctions Do Need Modest Interaction

We study the necessity of interaction for obtaining efficient allocations in combinatorial auctions with subadditive bidders. This problem was originally introduced by Dobzinski, Nisan, and Oren (STOC’14) as the following simple market scenario: m items are to be allocated among n bidders in a distributed setting where bidders valuations are private and hence communication is needed to obtain an efficient allocation. The communication happens in rounds: In each round, each bidder, simultaneously with others, broadcasts a message to all parties involved. At the end, the central planner computes an allocation solely based on the communicated messages. Dobzinski et al. showed that (at least some) interaction is necessary for obtaining even an approximately efficient allocation: No non-interactive (1-round) protocol with polynomial communication (in the number of items and bidders) can achieve approximation ratio better than Ω(m1/4), while for any r ≥ 1, there exists r-round protocols that achieve Õ(r · m1/(r+1)) approximation with polynomial communication. This in particular implies that O(log m) rounds of interaction suffice to obtain an approximately efficient allocation—namely, a polylog(m)-approximation. A natural question at this point is to identify the "right" level of interaction (i.e., number of rounds) necessary to obtain approximately efficient allocations. In this article, we resolve this question by providing an almost tight round-approximation tradeoff for this problem: We show that for any r ≥ 1, any r-round protocol that uses poly(m, n) bits of communication can only approximate the social welfare up to a factor of Ω(1/r · m1/(2r+1)). This in particular implies that Ω(log m/log log m) rounds of interaction are necessary for obtaining any allocation with a reasonable welfare approximation—namely, a constant or even a polylog(m)-approximation. Our work builds on the multi-party round-elimination technique of Alon, Nisan, Raz, and Weinstein (FOCS’15)—used to prove similar-in-spirit lower bounds for round-approximation tradeoff in unit-demand markets—and settles an open question posed initially by Dobzinski et al. (STOC’14) and subsequently by Alon et al. (FOCS’15).
Purification of a glycoprotein elicitor of phytoalexin formation fromVerticillium dahliae

Abstract A glycoprotein, isolated from culture fluids of Verticillium dahliae was found to be a heat stable elicitor of phytoalexin biosynthesis in cotton cell suspension cultures. The elicitor was purified utilizing anion exchange, size exclusion, and Concanavalin-A (Con-A) chromatography in addition to electroelution from SDS-PAGE. The 65 kDa protein could be deglycosylated to a protein of molecular mass 53 kDa as determined by SDS-PAGE. Elicitor activity from the culture fluids as well as the Con-A chromatography purified elicitor was completely abolished by protease treatment, but not by periodate treatment or peptide N-glycosidase F (PNGase-F) digestion, indicating that only protein components are responsible for the elicitation of phytoalexins in cotton cells. The purified 65 kDa protein did not elicit H 2 O 2 formation in contrast to the crude elicitor, which elicited both phytoalexin accumulation and the oxidative burst. The 65 kDa species was found to aggregate to a high molecular weight protein which retained some of its phytoalexin-inducing activity. The glycoprotein elicitor should prove useful in identifying second messengers leading to induction of phytoalexin biosynthesis.
Water impacts of food patterns : sustainable diets and food waste water footprints

Global food demand is increasing and changing rapidly as a result of multiple drivers as population growth or urban dietary shifts. Managing food consumption (people’s eating habits) might deliver important co-benefits from a water perspective. Many recent studies have addressed the relationship between diet habits and associated water impacts. The goal of this study is to assess and compare the water footprint (WF) of two recommended diets (Mediterranean and American) in Spain and US. Moreover also focuses on assessing the WF of the food consumption and its associated food waste in Spanish households during one year. Our results show that the American diet has a 29% higher WF, regardless of products' origin. Food consumption and waste WFs in Spain are 3,302 and 131 litres/person day respectively. A shift back to a Mediterranean diet, in which fruits, fish and vegetables account for a larger share of the food intake, would deliver great water savings.
Upgrading Model Selection Criteria with Goodness of Fit Tests for Practical Applications

The Bayesian information criterion (BIC), the Akaike information criterion (AIC), and some other indicators derived from them are widely used for model selection. In their original form, they contain the likelihood of the data given the models. Unfortunately, in many applications, it is practically impossible to calculate the likelihood, and, therefore, the criteria have been reformulated in terms of descriptive statistics of the residual distribution: the variance and the mean-squared error of the residuals. These alternative versions are strictly valid only in the presence of additive noise of Gaussian distribution, not a completely satisfactory assumption in many applications in science and engineering. Moreover, the variance and the mean-squared error are quite crude statistics of the residual distributions. More sophisticated statistical indicators, capable of better quantifying how close the residual distribution is to the noise, can be profitably used. In particular, specific goodness of fit tests have been included in the expressions of the traditional criteria and have proved to be very effective in improving their discriminating capability. These improved performances have been demonstrated with a systematic series of simulations using synthetic data for various classes of functions and different noise statistics.
Obesity is associated with depot-specific alterations in adipocyte DNA methylation and gene expression

ABSTRACT The present study aimed to identify genes exhibiting concomitant obesity-dependent changes in DNA methylation and gene expression in adipose tissues in the mouse using diet-induced obese (DIO) C57BL/6J and genetically obese ob/ob mice as models. Mature adipocytes were isolated from epididymal and inguinal adipose tissues of ob/ob and DIO C57BL/6J mice. DNA methylation was analyzed by MeDIP-sequencing and gene expression by microarray analysis. The majority of differentially methylated regions (DMRs) were hypomethylated in obese mice. Global methylation of long interspersed elements indicated that hypomethylation did not reflect methyl donor deficiency. In both DIO and ob/ob mice, we observed more obesity-associated methylation changes in epididymal than in inguinal adipocytes. Assignment of DMRs to promoter, exon, intron and intergenic regions demonstrated that DIO-induced changes in DNA methylation in C57BL/6J mice occurred primarily in exons, whereas inguinal adipocytes of ob/ob mice exhibited a higher enrichment of DMRs in promoter regions than in other regions of the genome, suggesting an influence of leptin on DNA methylation in inguinal adipocytes. We observed altered methylation and expression of 9 genes in epididymal adipocytes, including the known obesity-associated genes, Ehd2 and Kctd15, and a novel candidate gene, Irf8, possibly involved in immune type 1/type2 balance. The use of 2 obesity models enabled us to dissociate changes associated with high fat feeding from those associated with obesity per se. This information will be of value in future studies on the mechanisms governing the development of obesity and changes in adipocyte function associated with obesity.
Resistance genes (R genes) in plants

The activation of plant defence to restrict pathogen invasion is often conferred by resistance (R) proteins. The most prevalent class of R proteins contain leucine-rich repeats (LRRs), a central nucleotide binding site and a variable amino terminal domain. Other classes possess an extracellular LRR domain, a transmembrane domain and sometimes an intracellular serine/threonine kinase domain. R proteins function in pathogen perception and/or the activation of conserved defence signalling networks. Upon infection, specific effectors produced by pathogens and presumed to promote growth in host tissue, are either directly recognized by different R proteins or are recognized by a targeted plant protein which is itself guarded by R proteins. Subsequently, various defence signalling networks are activated via R protein phosphorylation, oligomerization, degradation, conformational changes and by the shuttling of R proteins between the plant cell cytoplasm and the nucleus. The overall outcome is dramatic cellular reprogramming and the activation of coordinated defence responses both locally at the site of infection as well as systemically throughout the plant. Many R gene loci appear to be under positive genetic selection, which rapidly diversifies paralogous sequences. Some R genes are present in plant genomes at single loci as either a single sequence or an allelic series whilst others reside within tight or loose clusters of related R sequences. For a century, plant breeders have genetically characterized and used R genes to reduce the impact of pathogens on crop production. More recently, various transgenic approaches have been tested to provide broader spectrum control and improved durability. Keywords: biotic stress; defence; pathogen; disease resistance; disease control
Mass, Spacetime Symmetry, de Sitter Vacuum, and the Higgs Mechanism

We address the question of the intrinsic relation between mass, gravity, spacetime symmetry, and the Higgs mechanism implied by involvement of the de Sitter vacuum as its basic ingredient (a false vacuum). Incorporating the de Sitter vacuum, the Higgs mechanism implicitly incorporates the generic relation between mass, gravity, and spacetime symmetry revealed in the frame of General Relativity for all objects involving the de Sitter vacuum. We overview two observational cases which display and verify this relation, the case known as “negative mass square problem” for neutrino, and appearance of a minimal length scale in e + e − annihilation.
Maps between trees and cladistic analysis of historical associations among genes

The concept of a reconciled tree arose independently in molecular systematics, parasitology, and biogeography as a means of describing historical associations. Examples of historical associations include genes and organisms, host and parasitic organisms, and organisms and areas. A reconciled tree combines the tree for a host and its associate into a single summary of the historical association between the two entities under the assumption that no horizontal transmission of associates has occurred. In this paper, I define reconciled trees, describe an algorithm for their computation, and develop measures to quantify the degree of fit between host and associate trees. Examples are given of applying the method to gene trees and species trees, host-parasite cospeciation, and biogeography
The journey to clean cooking: Insights from Kenya and Zambia

A shift to advanced cookstoves can bring significant health and environmental benefits, but only with proper and consistent use. Yet empirical evidence of what drives households to adopt advanced cooking technologies is limited. We use case studies in peri-urban Kiambu County, Kenya, and urban Lusaka, Zambia, to examine what drives households to adopt clean stoves for most or all of their cooking needs, and to stick with those stoves for the long term. We use a service design methodology to build “user journeys” that illustrate the cook’s experience with the technology, from the point of hearing about it, to purchasing it, learning to use it, and making it part of daily routine. We find that the main motivating factors for buying a stove were the prospect of saving money and/or fuel, added convenience, and the aesthetic and aspirational appeal of the stove. However, those factors may not continue to motivate people as they begin to use the stove. At that point, what matters most is whether the stove works well and as expected. Most users also need to use the stove several times before realizing its full value. It is therefore crucial that users get the support they need to learn how to use the stove, so they do not abandon it in frustration. Key interventions that can support stove adoption include handson trials before purchase, to ensure that users know what to expect; high-quality user manuals; and building a trusting relationship between users and sales agents that continues after the purchase, to provide longer-term support. THE JOURNEY TO CLEAN COOKING: INSIGHTS FROM KENYA AND ZAMBIA SEI-WP-2016-13
Resistance to Wheat streak mosaic virus– a survey of resources and development of molecular markers

Wheat streak mosaic virus (WSMV) has been newly documented in Australia. The vulnerability of contemporary Australian elite wheat germplasm prompted a survey for effective resistance against an Australian isolate, WSMV-ACT. This study confirms the effectiveness of previously reported sources of resistance and shows that new sources of resistance also confer protection. The resistance derived from Thinopyrum intermedium (Wsm1) as a 4D translocation and a new 4A translocation, and two bread wheat resistances, Wsm2 and the new source c2652, were effective against WSMV-ACT in glasshouse experiments. Wsm1 was effective at lower temperatures but ineffective above 20°C, a temperature sensitivity shared with many of the derivatives of Wsm2 except for one new selection which was effective at 26°C. True wheats c2652 and Wsm2 selection CA745, and amphiploids Zhong1, Zhong2, Zhong4, Zhong5, TAF46, Summer1, Ot38 and OK7211542 were uniformly resistant at 20, 25 and 28°C. New sources of resistance were identified in a Th. scirpeum-wheat amphiploid, B84-994, and in chromosome addition lines Z2, Z6 and TAi27, derived from wheat-Th. intermedium partial amphiploids. Several new, tightly linked SSR, RAPD and EST-ILP PCR markers were developed for tracking the various Th. intermedium translocations associated with Wsm1, including the smaller translocations on wheat chromosome 4AS and 4DS. Three markers for the 4A-Wsm1 translocation were validated on a segregating breeding population.
MiR-23b/-27b Cluster Suppresses the Metastatic Phenotype of Aggressive Prostate Cancer Cells

of a dissertation at the University of Miami. Dissertation supervised by Professor Kerry L. Burnstein. No. of pages in text. (93) MicroRNAs (miRs) are small, endogenous, non-coding RNAs that regulate gene expressing by inhibiting the stability and/or translation of complementary mRNA targets. Expression of miR-23b/-27b, which are encoded in tandem as a cluster on chromosome 9, are specifically downregulated in metastatic prostate cancer tissue samples compared to benign prostate. MiR-23b/-27b levels are also lower in aggressive prostate cancer cell lines compared to more indolent cells. We show miR-23b/-27b suppress migration and invasion of two aggressive human prostate cancer cell lines. Furthermore, inhibition of miR-23b/-27b increases the migration and invasion potential of a less aggressive prostate cancer cell line. Interestingly, we found that the miR-23b/-27b cluster does not affect prostate cancer cell proliferation suggesting miR-23b/-27b are metastatic suppressors. We provide evidence that miR-23b/-27b suppress additional key tumorigenic processes. To understand the mechanism of miR-23b/-27b mediated suppression of metastatic cell processes, we examined the effects of miR-23b/-27b on Rac1, a Rho GTPase essential for the metastatic phenotype of prostate cancer cells. We show ectopic expression of miR-23b/-27b decrease Rac1 activity of aggressive prostate cancer cell lines while inhibition of these miRs increase Rac1 activity in a less aggressive prostate cancer cell line. In addition, we show that expression of miR-23b/-27b increase the cell adhesion protein E-cadherin, in two independent aggressive prostate cancer cell lines. Conversely inhibition of miR-23b/-27b in a less aggressive prostate cancer cell line decreases E-cadherin levels. These data establish an important role for miR-23b/-27b mediatedsuppression of invasion and migration of aggressive prostate cancer cells. Since miRs have great potential use as biomarkers and drug targets or mimics, elucidating the role and mechanism of miR-23b/-27b in prostate cancer is critical in the development of novel and effective therapies and prognostic indicators.
Effects of Monoclonal Antibodies to Specific Epitopes of Rat Interleukin‐1 Beta (IL‐Iβ) on IL‐1β‐Induced ACTH, Corticosterone and IL‐6 Responses in Rats

Recently, we developed a panel of monoclonal antibodies (MoAbs) to rat IL‐1β and found that MoAbs binding to the aminoacid sequences 66–85 and 123–143 of mature rIL‐1β inhibited the binding of rIL‐1β to murine EL4 cells. Here we study whether MoAbs to these and other domains of IL‐1 interfere with the biological effects of rIL‐1β in adult male rats in vivo. Administration of rIL‐1β (1 or 5 μg/kg i.v.) enhanced the plasma concentrations of ACTH, corticosterone (CORT) and of IL‐6 in a time‐ (0.5–4 h) and dose‐dependent manner. Because 2 h after 5μg/kg i.v. , all three parameters were consistently elevated, this dose and time interval was used for further studies. Prior to injection, rIL‐1β was incubated alone or in the presence of a MoAb (10 mg/kg) for 30 min at 37°C or at 4°C. Plasma ACTH, CORT and IL‐6 responses to these mixtures are compared to those obtained after preincubation of rIL‐1β with a non‐IL‐1 binding MoAb (PEN7). SILK 3, a MoAb that binds to the 66–85 domain of rIL‐1β, reduced the ACTH and IL‐6 responses by 48 and 45% respectively. In contrast, a MoAb to the 123–143 domain (SILK 5) and SILK 16, which binds to the 106–124 domain did not affect any of the IL‐1 induced responses, whereas a MoAb directed to domain 78–97 of rIL‐1β (SILK 20) enhanced the ACTH and CORT responses by 51 and 41% respectively, but not the IL‐6 response.
Microstructure Instance Segmentation from Aluminum Alloy Metallographic Image Using Different Loss Functions

Automatic segmentation of metallographic image is very important for the implementation of an automatic metallographic analysis system. In this paper, a novel instance segmentation framework of a metallographic image was implemented, which can assign each pixel to a physical instance of a microstructure. In this framework, we used the Mask R-CNN as the basic network to complete the learning and recognition of the latent feature of an aluminum alloy microstructure. Meanwhile, we implemented five different loss functions based on this framework and compared the influence of these loss functions on metallographic image segmentation performance. We carried out several experiments to verify the effectiveness of the proposed framework. In these experiments, we compared and analyzed six different evaluation metrics and provided constructive suggestions for the performance evaluation of metallographic image segmentation method. A large number of experimental results have shown that the proposed method can achieve the instance segmentation of an aluminum alloy metallographic image and the segmentation results are satisfactory.
Analysis of an Integrated Solar Combined Cycle with Recuperative Gas Turbine and Double Recuperative and Double Expansion Propane Cycle

The main objective of this paper is to present and analyze an innovative configuration of integrated solar combined cycle (ISCC). As novelties, the plant includes a recuperative gas turbine and the conventional bottoming Rankine cycle is replaced by a recently developed double recuperative double expansion (DRDE) cycle. The configuration results in a fuel saving in the combustion chamber at the expense of a decreased exhaust gas temperature, which is just adequate to feed the DRDE cycle that uses propane as the working fluid. The solar contribution comes from a solar field of parabolic trough collectors, with oil as the heat transfer fluid. The optimum integration point for the solar contribution is addressed. The performance of the proposed ISCC-R-DRDE design conditions and off-design operation was assessed (daily and yearly) at two different locations. All results were compared to those obtained under the same conditions by a conventional ISCC, as well as similar configurations without solar integration. The proposed configuration obtains a lower heat rate on a yearly basis in the studied locations and lower levelized cost of energy (LCOE) than that of the ISCC, which indicates that such a configuration could become a promising technology.