Quantum Ripples in Strongly Correlated Metals

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)We study how well-known effects of the long-ranged Friedel oscillations are affected by strong electronic correlations. We first show that their range and amplitude are significantly suppressed in strongly renormalized Fermi liquids. We then investigate the interplay of elastic and inelastic scattering in the presence of these oscillations. In the singular case of two-dimensional systems, we show how the anomalous ballistic scattering rate is confined to a very restricted temperature range even for moderate correlations. In general, our analytical results indicate that a prominent role of Friedel oscillations is relegated to weakly interacting systems.10423Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)NSF [DMR-0542026]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [04/12098-6, 07/57630-5]CAPES [1455/07-9]CNPq [305227/2007-6]NSF [DMR-0542026

Alternative tissue fixation for combined histopathological and molecular analysis in a clinically representative setting

Formalin is the principal tissue fixative used worldwide for clinical and research purposes. Despite optimal preservation of morphology, its preservation of DNA and RNA is poor. As clinical diagnostics increasingly incorporates molecular-based analysis, the requirement for maintaining nucleic acid quality is of increasing importance. Here we assess an alternative non-formalin-based tissue fixation method, PAXgene Tissue system, with the aim of better preserving nucleic acids, while maintaining the quality of the tissue to be used for vital existing diagnostic techniques. In this study, these criteria are assessed in a clinically representative setting. In total, 203 paired PAXgene Tissue and formalin-fixed samples were obtained. Blind-scored haematoxylin and eosin (H&E) sections showed comparable and acceptable staining. Immunohistochemistry (IHC) staining was suboptimal using existing protocols but improved with minor method adjustment and optimisation. Quality of DNA and RNA was significantly improved by PAXgene tissue fixation [RIN 2.8 versus 3.8 (p < 0.01), DIN 5.68 versus 6.77 (p < 0.001)], which translated into improved performance on qPCR assay. These results demonstrate the potential of PAXgene Tissue to be used routinely in place of formalin, maintaining adequate histological staining and significantly improving the preservation of biological molecules in the genomic era

Using the Pneumatic method to estimate embolism resistance in species with long vessels: A commentary on the article “A comparison of five methods to assess embolism resistance in trees”

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordComparisons among methods are essential to validate plant traits measured across studies. However, a rigorous analysis is a complex task that needs to take into account not only the principle of the method and its correct use, but also inherent intraspecific trait variability, something we feel is not fully considered by Sergent et al. (2020). They compared the Bench dehydration, MicroCT, and Pneumatic methods using three long-vesseled species and found divergence among these methods. As a key finding, Sergent and colleagues reported unreliable estimates of Ψ50 for Olea europaea when using the Pneumatic method in a such long-vesseled species. Here, we tested this finding by measuring independently vulnerability curves for O. europaea. Our results reinforce the viability of the Pneumatic method to estimate embolism vulnerability in long-vesseled species, as already found by others. Briefly, we also discuss important procedures when using the Pneumatic method and encourage further experiments, as the only way to know better the limitations of available methods and improve our understanding about plant water relations.São Paulo Research Foundation (FAPESP)Royal SocietyNational Council for Scientific and Technological Development (CNPq, Brazil

Presence of Helicobacter pylori in betel chewers and non betel chewers with and without oral cancers

<p>Abstract</p> <p>Background</p> <p>Betel chewing has been shown to predispose to periodontal disease and oral cancer. Studies show that people with gum disease are more likely to test positive for <it>Helicobacter pylori (H. pylori)</it>. It is not known if the lesions produced by betel quid and the resulting, chemical changes predispose to colonization by <it>H. pylori</it>. Further the role of this organism in oral cancer is not known. Our objective was to determine the presence of <it>H. pylori </it>in oral lesions of thirty oral cancer patients and to determine the presence of IgG antibodies to <it>H. pylori </it>in oral cancer patients who are betel chewers and non betel chewers, healthy betel chewers and healthy non-betel chewers and to compare the presence of <it>H</it>. <it>pylori </it>in these four groups. This case control study was conducted at the Cancer Institute Maharagama and the Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura.</p> <p>Methods</p> <p>One hundred and seventy three subjects, of whom fifty three were patients presenting with oral cancer to the Cancer Institute Maharagama, sixty healthy betel chewers and sixty healthy non-betel chewers from the Religious and Welfare Service Centre Maharagama were tested for <it>H. pylori </it>by serology. Thirty oral biopsies from oral cancer patients were cultured under microaerophilic condition to isolate <it>H. pylori</it>. The statistic used was Chi-square test.</p> <p>Results</p> <p>Of the fifty-three oral cancer patients, forty-four were betel chewers. Among the 53 oral cancer patients examined, ten of forty-four (10/44 = 22.7%) patients who are betel chewers and four of nine (4/9 = 44.4%) patients who are non-betel chewers were detected positive for IgG antibody against <it>H. pylori</it>. In the healthy group (betel chewers and non betel chewers) ten (16.7%) of the healthy betel chewers tested positive for <it>H. pylori </it>by serology. None of the healthy non-betel chewers tested positive for <it>H. pylori</it></p> <p>Fourteen [26.4%] of oral cancer patients tested positive for <it>H. pylori </it>by serology, of which two were also culture positive (Only thirty samples were cultured). The presence of <it>H. pylori </it>in betel chewers (with or without cancer) compared to non-betel chewers was statistically significant. (Chi-square test p < 0.05) The use of tobacco and areca nut in betel chewers was significant with the presence of <it>H. pylori </it>(p < 0.05).</p> <p>Conclusion</p> <p>There is a significant higher proportion of <it>H. pylori </it>in betel chewers compared to non-betel chewers but not between oral cancer patients compared to patients without oral cancer. Hence Betel chewing may predispose to colonisation with <it>H. pylori </it>in the digestive tract through swallowing the quid or during betel chewing.</p

Restoration and conservation of priority areas of caatinga’s semi‐arid forest remnants can support connectivity within an agricultural landscape

Land-use and land-cover (LULC) changes are major drivers of biodiversity loss in semi-arid regions, such as the Caatinga biome located in the Northeast of Brazil. We investigated landscape dynamics and fragmentation in an area of the São Francisco Valley in the Brazilian Caatinga biome and measured the effect of these dynamics on ecological, functional and structural connectivity over a 33-year period (1985–2018). We calculated landscape connectivity indices based on graph theory to quantify the effect of further agricultural expansion on ecological connectivity at the landscape scale. We used a multicriteria decision analysis that integrates graph-based connectivity indices at the habitat patch scale, combined with an index of human disturbance to identify patches that, if conserved and restored, preserve the connectivity of the landscape most effectively. In the period studied, agriculture increased at a rate of 2104 ha/year, while native Caatinga vegetation decreased at a rate of 5203 ha/year. Both dense and open Caatinga became more fragmented, with the number of fragments increasing by 85.2% and 28.6%, respectively, whilst the average fragment size decreased by 84.8% and 6.1% for dense and open Caatinga, respectively. If agriculture patches were to expand by a 300 m buffer around each patch, the overall ecological connectivity could be reduced by 6–15%, depending on the species’ (small- to mid-size terrestrial vertebrates) mobility characteristics for which the connectivity indices were calculated. We provided explicit spatial connectivity and fragmentation information for the conservation and restoration of the Caatinga vegetation in the studied area. This information helps with conservation planning in this rapidly changing ecosystem.</jats:p

Structural Changes of the Paraflagellar Rod during Flagellar Beating in Trypanosoma cruzi

, the agent of Chagas disease, is a protozoan member of the Kinetoplastidae family characterized for the presence of specific and unique structures that are involved in different cell activities. One of them is the paraflagellar rod (PFR), a complex array of filaments connected to the flagellar axoneme. Although the function played by the PFR is not well established, it has been shown that silencing of the synthesis of its major proteins by either knockout of RNAi impairs and/or modifies the flagellar motility.Here, we present results obtained by atomic force microscopy (AFM) and transmission electron microscopy (TEM) of replicas of quick-frozen, freeze-fractured, deep-etched and rotary-replicated cells to obtain detailed information of the PFR structures in regions of the flagellum in straight and in bent state. The images obtained show that the PFR is not a fixed and static structure. The pattern of organization of the PFR filament network differs between regions of the flagellum in a straight state and those in a bent state. Measurements of the distances between the PFR filaments and the filaments that connect the PFR to the axoneme as well as of the angles between the intercrossed filaments supported this idea.Graphic computation based on the information obtained allowed the proposal of an animated model for the PFR structure during flagellar beating and provided a new way of observing PFR filaments during flagellar beating

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets