Saliency-driven system models for cell analysis with deep learning.

Background and objectivesSaliency refers to the visual perception quality that makes objects in a scene to stand out from others and attract attention. While computational saliency models can simulate the expert's visual attention, there is little evidence about how these models perform when used to predict the cytopathologist's eye fixations. Saliency models may be the key to instrumenting fast object detection on large Pap smear slides under real noisy conditions, artifacts, and cell occlusions. This paper describes how our computational schemes retrieve regions of interest (ROI) of clinical relevance using visual attention models. We also compare the performance of different computed saliency models as part of cell screening tasks, aiming to design a computer-aided diagnosis systems that supports cytopathologists.MethodWe record eye fixation maps from cytopathologists at work, and compare with 13 different saliency prediction algorithms, including deep learning. We develop cell-specific convolutional neural networks (CNN) to investigate the impact of bottom-up and top-down factors on saliency prediction from real routine exams. By combining the eye tracking data from pathologists with computed saliency models, we assess algorithms reliability in identifying clinically relevant cells.ResultsThe proposed cell-specific CNN model outperforms all other saliency prediction methods, particularly regarding the number of false positives. Our algorithm also detects the most clinically relevant cells, which are among the three top salient regions, with accuracy above 98% for all diseases, except carcinoma (87%). Bottom-up methods performed satisfactorily, with saliency maps that enabled ROI detection above 75% for carcinoma and 86% for other pathologies.ConclusionsROIs extraction using our saliency prediction methods enabled ranking the most relevant clinical areas within the image, a viable data reduction strategy to guide automatic analyses of Pap smear slides. Top-down factors for saliency prediction on cell images increases the accuracy of the estimated maps while bottom-up algorithms proved to be useful for predicting the cytopathologist's eye fixations depending on parameters, such as the number of false positive and negative. Our contributions are: comparison among 13 state-of-the-art saliency models to cytopathologists' visual attention and deliver a method that the associate the most conspicuous regions to clinically relevant cells

Variabilidade da extremidade 3' do gene da polimerase de isolados de Grapevine leafroll-associated virus-3 do Submédio do Vale do São Francisco

Many viral diseases, including leafroll, which is of great economic importance, affect grapevines (Vitis spp.). A complex of eight viruses [Grapevine leafroll-associated virus (GLRaV) -1 to 8] is associated with this disease. The objective of this study was to compare the variability of the 3' terminal region of the polymerase gene of three isolates of GLRaV-3 (Grapevine leafroll-associated virus-3), from Submédio do Vale do Rio São Francisco (Petrolina-PE) with that of other isolates available at the GenBank, including an isolate from North America and another from Southern Brazil. The viral RNA was extracted from three infected ELISA reactive plants and a fragment of 340 bp was amplified, by RT-PCR, using primers that recognize that portion of the polymerase gene found between nucleotides 8267 and 8606. The three isolates from Vale do Rio São Francisco named Pet-1, Pet-2 and Pet-3, showed similarities ranging from 98% and 94%, respectively to the isolates from North America (AF037268) and Southern Brazilian (AF438411). Considering the whole genome, the main variation found was one amino acid change at position 2766 (F2766Y). These preliminary data indicate the existence of a natural variation among GLRaV-3 isolates from grapevines. This could be due to the vegetative propagation and long cycle of the plant, associated with the error-prone nature of RNA-dependent RNA polymerase.A videira (Vitis spp.) é afetada por diversas viroses, dentre essas, o enrolamento da folha se destaca pela importância econômica. A doença é causada por um complexo formado por até oito vírus [Grapevine leafroll-associated virus (GLRaV) -1 ao -8]. O objetivo desse trabalho foi comparar a variabilidade da extremidade 3' do gene da polimerase de isolados de GLRaV-3, provenientes do Submédio do Vale do Rio São Francisco (Petrolina, PE) com a de outros isolados disponíveis no GenBank, incluindo um isolado da América do Norte e um da região sul do Brasil. O RNA viral foi extraído de três amostras infetadas, reagentes em teste de ELISA, e um fragmento de 340 pb foi amplificado por RT-PCR, utilizando-se oligonucleotídeos para a região do gene da polimerase viral compreendida entre os nucleotídeos 8267 a 8606. Observou-se que os três isolados da região do São Francisco, denominados Pet-1, Pet-2 e Pet-3, apresentaram 98% e 94% de similaridade com o isolado norte-americano (AF037268) com aquele do sul do Brasil (AF438411), respectivamente. A principal variação observada foi uma troca de um aminoácido da posição 2766 (F2766Y), considerando-se o genoma completo. Esses dados preliminares indicam a existência de uma variabilidade natural entre isolados de GLRaV-3 em videiras. Isso pode ser explicado pela propagação vegetativa e pelo longo ciclo da planta associados à propensão ao erro da RNA polimerase dependente de RNA

Detection of tuberculosis drug resistance a comparison by Mycobacterium tuberculosis MLPA assay versus Genotype®MTBDRplus

BACKGROUND: To cope with the emergence of multidrug-resistant tuberculosis (MDR-TB), new molecular methods that can routinely be used to screen for a wide range of drug resistance related genetic markers in the Mycobacterium tuberculosis genome are urgently needed. OBJECTIVE: To evaluate the performance of multiplex ligaton-dependent probe amplification (MLPA) against Genotype® MTBDRplus to detect resistance to isoniazid (INHr) and rifampicin (RIFr). METHOD: 96 culture isolates characterised for identification, drug susceptibility testing (DST) and sequencing of rpoB, katG, and inhA genes were evaluated by the MLPA and Genotype®MTBDRplus assays. RESULTS: With sequencing as a reference standard, sensitivity (SE) to detect INHr was 92.8% and 85.7%, and specificity (SP) was 100% and 97.5%, for MLPA and Genotype®MTBDRplus, respectively. In relation to RIFr, SE was 87.5% and 100%, and SP was 100% and 98.8%, respectively. Kappa value was identical between Genotype®MTBDRplus and MLPA compared with the standard DST and sequencing for detection of INHr [0.83 (0.75-0.91)] and RIFr [0.93 (0.88-0.98)]. CONCLUSION: Compared to Genotype®MTBDRplus, MLPA showed similar sensitivity to detect INH and RIF resistance. The results obtained by the MLPA and Genotype®MTBDRplus assays indicate that both molecular tests can be used for the rapid detection of drug-resistant TB with high accuracy. MLPA has the added value of providing information on the circulating M. tuberculosis lineages.publishersversionpublishe

Blind Testing: DNA Barcoding Sheds Light Upon the Identity of Plant Fragments as a Subsidy for Cave Conservation

Plants living above and around caves represent an important, albeit poorly studied, resource within cave ecosystems. The presence of plant material (root-like structures or rhizothemes, saplings, seeds, and seedlings) correlates positively with the biodiversity of the cave dwelling animals as shown for iron-ore caves in Carajás, Pará, Brazil. Plant material collected in caves has proven to be difficult to identify by traditional botanical methods, thus this research aims to provide a qualitative insight into the taxonomy and morphology of rhizothemes and other plant fragments found in the caves. The identification process used a combination of different molecular markers (ITS2, rbcL, and trnH-psbA) followed by a comparison of the sequences obtained against publicly available databases. The rhizothemes were submitted to micromorphological analysis to ascertain their putative root or stem origin and to compare their anatomy with known patterns found in the plant families or genera recovered through molecular matches. All studied samples were Angiosperms, mostly belonging to subclass Rosideae, within four orders: Malpighiales (Euphorbiaceae, Hypericaceae), Sapindales (Anacardiaceae and Sapindaceae), Myrtales (Myrtaceae), Fabales (Fabaceae), and only two belonging to subclass Asteridae, order Gentianales (Apocynaceae). Some of the samples were matched to generic level, with ITS2 being the best marker to identify the fragments because it shows high degree of sequence variation even at specific level and result reliability. All rhizothemes turned out to be roots, and correspondence was found between the existing literature and the individual anatomical patterns for the families and genera retrieved. DNA barcode has proved to be a useful tool to identify plant fragments found in this challenging environment. However, the existence of well curated, authoritatively named collections with ample biological information has proven to be essential to achieve a reliable identification

Competition for endothelial cell polarity drives vascular morphogenesis in the mouse retina

© 2022 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Blood-vessel formation generates unique vascular patterns in each individual. The principles governing the apparent stochasticity of this process remain to be elucidated. Using mathematical methods, we find that the transition between two fundamental vascular morphogenetic programs-sprouting angiogenesis and vascular remodeling-is established by a shift of collective front-to-rear polarity of endothelial cells in the mouse retina. We demonstrate that the competition between biochemical (VEGFA) and mechanical (blood-flow-induced shear stress) cues controls this collective polarity shift. Shear stress increases tension at focal adhesions overriding VEGFA-driven collective polarization, which relies on tension at adherens junctions. We propose that vascular morphogenetic cues compete to regulate individual cell polarity and migration through tension shifts that translates into tissue-level emergent behaviors, ultimately leading to uniquely organized vascular patterns.Funding: European Research Council: C.A.F. (679368); X.T. (883739). European Commission: C.A.F. and M.O.B. (801423); X.T. and P.R.-C. (731957). H2020-MSCA-PF grants to M.G.-G. (797621) and M.O. (842498). Fondation LeDucq: C.A.F., A.E., and M.O.B. (17CVD03). EPSRC: M.O.B. (EP/T008806/1; EP/R029598/1). Fundação para a Ciência e Tecnologia: C.A.F. (PTDC/MED-PAT/31639/2017; PTDC/BIA-CEL/32180/2017; CEECIND/04251/2017). Spanish Ministry of Science and Innovation: P.R.-C. (PID2019-110298GB-I00); X.T. (PGC2018-099645-B-I00). Generalitat de Catalunya: X.T. and P.R.-C. (2017-SGR-1602). La Caixa Foundation: X.T. and P.R.-C. (LCF/PR/HR20/52400004). Fundació la Marató de TV3: X.T. (201903-30-31-32). EMBO: L.M.F. (ALTF 2-2018)info:eu-repo/semantics/publishedVersio

EM TEMPOS GLOBAIS, UM “NOVO” LOCAL: a Ford na Bahia

O artigo analisa a dinâmica da Região Metropolitana de Salvador (RMS) a partir da implantação da Ford, discutindo a perspectiva do ‘lugar’ (a periferia metropolitana), dentro de uma relação assimétrica com os negócios globais na era da flexibilidade. O texto caracteriza o complexo Ford de Camaçari a partir da reestruturação produtiva e das mudanças na organização e funcionamento dos territórios e, na segunda parte, seus impactos sobre a periferia metropolitana de Salvador. Na conclusão demonstra que as mesmas circunstâncias que permitiram a vinda da montadora para Camaçari constrangem as ambições originais de melhor equacionamento entre crescimento econômico e progresso social: a flexibilidade dos novos arranjos, que tornam os espaços periféricos estratégicos, compromete o “enraizamento” do investimento; a “produção enxuta”, exígua de emprego e diligente na sua precarização, inibe os benefícios sociais. PALAVRAS CHAVE: reestruturação produtiva, mercado de trabalho, indústria automobilística, periferia metropolitana, segregação socioespacial. IN GLOBAL TIMES, A “NEW” PLACE: Ford in Bahia Ângela Franco This paper makes an analysis of the dynamics of the Metropolitan Area of Salvador (in Portuguese, RMS) starting from the implantation of Ford, discussing the perspective of the ‘local’ (the metropolitan periphery), inside of an asymmetrical relationship with global businesses in the age of flexibility. The Ford Automotive Compound is caracterized in the first part of the paper from its productive reestructuring and changes in the organization and work of territories, and, in the second part, from its impact on the the metropolitan periphery from Salvador. In its conclusion it demonstrates that the same circumstances that allowed the arrival of the automotive maker in Camaçari constrain the original ambitions of better ratio between economical growth and social progress: the flexibility of the new automotive production methods, making peripheric spaces strategic, compromises on the permanence of the investments; and the “streamlined production”, easy on job production and hard on job flexibilization inhibit social benefits. KEYWORDS: productive restructuring, job market, automobile industry, metropolitan periphery, socioespatial segregation. EN PERIODE DE MONDIALISATION, UN “NOUVEAU” LOCAL: Ford à Bahia Ângela Franco Cet article traite de l’analyse de la dynamique de la Région Métropolitaine de Salvador (RMS), à partir de l’implantation de l’usine Ford. On y discute de la perspective du “lieu” (la périphérie métropolitaine), dans une relation asymétrique avec les affaires globales à une époque de flexibilité. On y caractérise le complexe Ford de Camaçari à partir de la restructuration productive et des changements dans l’organisation et le fonctionnement des territoires. Ses impacts sur la périphérie métropolitaine de Salvador sont présentés dans la deuxième partie. En conclusion, on y démontre que ce sont les mêmes circonstances qui ont permis l’arrivée de l’usine de montage à Camaçari qui représentent une contrainte pour les ambitions qui, à l’origine, voulaient atteindre une meilleure équation entre la croissance économique et le progrès social. La flexibilité de ces nouveaux arrangements, qui rendent les espaces périphériques stratégiques, compromet “l’enracinement” des investissements, la “production exiguë”, l’exiguïté des emplois et la diligence dans leur précarisation, elle inhibe les avantages sociaux. MOTS-CLÉS: restructuration productive, marché du travail, industrie automobile, périphérie métropolitaine, ségrégation sociale et spatiale. Publicação Online do Caderno CRH: http://www.cadernocrh.ufba.b

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio