Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the distribution of disease‐bearing rodents in human‐modified tropical landscapes

* We tested how habitat structure and fragmentation affect the spatial distribution of common murine rodents inhabiting human-dominated landscapes in South-East Asia. The spatial distribution patterns observed for each rodent species were then used to assess how changes in habitat structure may potentially affect the risk of several major rodent-borne diseases. * For this analysis, we used an extensive geo-referenced data base containing details of rodents trapped from seven sites in Thailand, Cambodia and Lao PDR. We also developed land-cover layers for each site. Results from published studies that screened for five major rodent-borne pathogens in rodents were used to estimate how these pathogens would likely be impacted by these alterations in habitat structure and composition. * Our results confirmed the specialist and/or synanthropic status of several rodent species, although the majority of species studied demonstrated some degree of low level of habitat specialization. * Habitat diversity and its alteration (decreasing forest cover, increasing fragmentation, increasing urbanization) were found to favour the presence of synanthropic rodent species such as Rattus tanezumi, known to damage crops and host important rodent-borne diseases. * Synthesis and applications. The five major rodent-borne pathogens were linked to ongoing changes in habitat structure. In particular, the presence of Bartonella spp. and hantaviruses seemed to be favoured in wooded landscapes affected by ongoing fragmentation and human encroachments. Rodents also pose significant problems for crop production in South-East Asia. Our results showed that the structure of the landscape affects the likely presence of rodent species considered as agricultural pests. The patchy structure of a landscape can either enhance, such as B. indica, or decrease, such as B. savilei, the presence of rodents that may cause serious damage to crops.
Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava

In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava’s full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.
Adenovirus RIDβ Subunit Contains a Tyrosine Residue That Is Critical for RID-Mediated Receptor Internalization and Inhibition of Fas- and TRAIL-Induced Apoptosis

ABSTRACT The adenovirus-encoded receptor internalization and degradation (RID) protein (previously named E3-10.4K/14.5K), which is composed of RIDα and RIDβ subunits, down-regulates a number of cell surface receptors in the tumor necrosis factor (TNF) receptor superfamily, namely Fas, TRAIL receptor 1, and TRAIL receptor 2. Down-regulation of these “death” receptors protects adenovirus-infected cells from apoptosis induced by the death receptor ligands Fas ligand and TRAIL. RID also down-regulates certain tyrosine kinase cell surface receptors, especially the epidermal growth factor receptor (EGFR). RID-mediated Fas and EGFR down-regulation occurs via endocytosis of the receptors into endosomes followed by transport to and degradation within lysosomes. However, the molecular interactions underlying this function of RID are unknown. To investigate the molecular determinants of RIDβ that are involved in receptor down-regulation, mutations within the cytoplasmic tail of RIDβ were constructed and the mutant proteins were analyzed for their capacity to internalize and degrade Fas and EGFR and to protect cells from death receptor ligand-induced apoptosis. The results demonstrated the critical nature of a tyrosine residue near the RIDβ C terminus; mutation of this residue to alanine abolished RID function. Mutating the tyrosine to phenylalanine did not abolish the function of RID, arguing that phosphorylation of the tyrosine is not required for function. These data suggest that this tyrosine residue forms part of a tyrosine-based sorting signal (Yxxφ). Additional mutations that target another potential sorting motif and several possible protein-protein interaction motifs had no discernible effect on RID function. It was also demonstrated that mutation of serine 116 to alanine eliminated phosphorylation of RIDβ but did not affect any of the functions of RID that were examined. These results suggest a model in which the tyrosine-based sorting signal in RID plays a role in RID's ability to down-regulate receptors.
How to assess Drosophila cold tolerance: chill coma temperature and lower lethal temperature are the best predictors of cold distribution limits

Summary 1. Thermal tolerance may limit and therefore predict ectotherm geographic distributions. However, which of the many metrics of thermal tolerance best predict distribution is often unclear, even for drosophilids, which constitute a popular and well-described animal model. 2. Five metrics of cold tolerance were measured for 14 Drosophila species to determine which metrics most strongly correlate with geographic distribution. The species represent tropical to temperate regions but all were reared under similar (common garden) conditions (20 °C). The traits measured were: chill coma temperature (CTmin), lethal temperature (LTe50), lethal time at low temperature (LTi50), chill coma recovery time (CCRT) and supercooling point (SCP). 3. Measures of CTmin, LTe50 and LTi50 proved to be the best predictors to describe the variation in realized latitudinal distributions (R 2 =0 699, R 2 =0 741 and 0550, respectively) and estimated environmental cold exposure (R 2 =0 633, R 2 =0 641 and 0511, respectively). Measures of CCRT also correlated significantly with estimated minimum temperature (R 2 =0 373), while the SCP did not. These results remained consistent after phylogenetically independent analysis or when applying nonlinear regression. Moreover, our findings were supported by a similar analysis based on existing data compiled from the Drosophila cold tolerance literature. 4. Trait correlations were strong between LTe50, LTi50 and CTmin, respectively (083 > R 2 >0 55). However, surprisingly, there was only a weak correlation between the entrance into coma (CTmin) and the recovery from chill coma (CCRT) (R 2 =0 256). 5. Considering the findings of the present study, data from previous studies and the logistical constraints of each measure of cold tolerance, we conclude that CTmin and LTe50 are superior measures when estimating the ecologically relevant cold tolerance of drosophilids. Of these two traits, CTmin requires less equipment, time and animals and thereby presents a relatively fast, simple and dynamic measure of cold tolerance.
Investigating leaf lifespans with interval-censored failure time analysis.

• Here leaf lifespans were investigated using interval-censored failure time analysis. The utility of this relatively novel approach is illustrated by comparing the leaf lifespan of winter-deciduous fuchsia (Fuchsia excorticata) and annual-evergreen wineberry (Aristotelia serrata). • Leaf emergence and mortality were first described using growth equations. Individual leaf lifespans were investigated using a parametric failure-time regression model that accounted for the interval-censored nature of leaf lifespan data. • Bud burst began 7 d earlier, the rate of leaf emergence was 0.06 leaves per shoot d-1 faster, and emergence ended 44 d earlier in fuchsia than in wineberry. The rate of leaf mortality was greatest in mid-summer in fuchsia, but nearly constant over the year for wineberry. There was a highly significant effect of the date of leaf emergence on leaf lifespan. Leaves emerging earlier in the growing season had shorter lifespans relative to later emerged leaves in fuchsia, whereas the reverse was true for wineberry. There was no significant effect of shoot height, branch order, or the number leaves of per shoot length on leaf lifespan. • These results highlight the utility of studying phenology at the individual leaf level using failure time analysis. Although growth equations precisely describe leaf emergence and mortality in wineberry and fuchsia, they obscured key differences between the species that were identified using failure time analysis.
Phytochemical screening and evaluation of antioxidant and cytotoxic activities of Halimeda opuntia.

Bioactive properties of seaweeds isolated from the Bay of Bengal of Bangladesh have hardly been studied. In the present study, Halimeda opuntia, a calcareous seaweed, which was collected from the St. Martin’s Island, was used to investigate its antioxidant and cytotoxicity profile along with the phytochemical constituents by using the ethanolic and methanolic extracts. Through phytochemical screening, we confirmed the presence of phenolic compounds and steroids in all extracts. Soaking samples in solvent with occasional shaking for 5-7 days may lead to extraction of higher quantities of compounds and thus higher bioactivities compared with 2-2.5 hours of shaking. Using the well-known 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay, we confirmed concentration-dependent DPPH scavenging activity. For cytotoxicity study, we used brine shrimp lethality assay and found considerable cytotoxicity highlighted by two ethanolic extracts that were highly toxic (LC50< 100 μg/mL) to brine shrimp Nauplii. So, H. opuntia can be a good source of novel and potent cytotoxic compounds possibly with anti-tumor properties, which should be further clarified. Thus, our study clearly suggested that due to the presence of considerable amounts of bioactive compounds, H. opuntia would be a valuable source of antioxidants with cytotoxic properties.
Of rowing boats, ocean liners and tests of the ANOVA homogeneity of variance assumption

One of the assumptions of analysis of variance (ANOVA) is that the variances of the groups being compared are approximately equal. This assumption is routinely checked before doing an analysis, although some workers consider ANOVA robust and do not bother and others avoid parametric procedures entirely. Two of the more commonly used heterogeneity tests are Bartlett's and Cochran's, although, as for most of these tests, they may well be more sensitive to violations of the ANOVA assumptions than is ANOVA itself. Simulations were used to examine how well these two tests protected ANOVA against the problems created by variance heterogeneity. Although Cochran's test performed a little better than Bartlett's, both tests performed poorly, frequently disallowing perfectly valid analyses. Recommendations are made about how to proceed, given these results.
Activities of enzymes involved in lignification during the postharvest storage of etiolated asparagus spears

The content of lignin and the activities of 5 enzymes involved in lignification were monitored along the length of etiolated spears of asparagus (Asparagus officinalis L., INRA Fl male hybrid n°156) stored for 22 h with their base in air (control), water or water containing the ethylene antagonist, silver thiosulfate (STS). At the time of harvest the lignin content increased basipetally, as did the activity of all the enzymes studied, viz., phenylalanine ammonia lyase (PAL; EC 4.3.1.5), hydroxycinnamate: CoA ligase (HCoAL; EC 6.2.1.12), cinnamoyl-CoA reductase (CCR: EC 1.2.1.44), cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195) and syringaldazine oxidase (SyrOx. a peroxidase [POD; EC 1.11.1.7] with syringaldazine as substrate). Neither the lignin content nor the activity of any enzyme changed in the spear apex during storage, regardless of treatment. In the spear base. all enzyme activities decrased during the first 2 to 4 h in every storage treatment. Subsequently. PAL and HCoAL activities remained constant. whereas the activities of CAD and SyrOx gradually increased. Lignification in the spear base was not affected by storage in air. However, storage in water increased lignin formation and SyrOx activity, whereas treatment with STS prevented both of these increases. The results indicate that postharvest lignification in etiolated asparagus spears is caused primarily by enhanced SyrOx activity, and that ethylene is involved in the control of this activity.
Systematic mutagenesis of the Helicobacter pylori cag pathogenicity island: essential genes for CagA translocation in host cells and induction of interleukin‐8

Helicobacter pylori (Hp) carries a type IV secretion system encoded by the cag pathogenicity island (cag‐PAI), which is used to: (i) translocate the bacterial effector protein CagA into different types of eukaryotic cells; and (ii) induce the synthesis and secretion of chemokines, such as interleukin‐8 (IL‐8). The cag‐PAI in Hp 26695 consists of 27 putative genes, six of which were identified as homologues to the basic type IV secretion system represented by the Agrobacterium tumefaciens virB operon. To define the role and contribution of each of the 27 genes, we applied a precise deletion/insertion mutagenesis procedure to knock out each individual gene without causing polar effects on the expression of downstream genes. Seventeen out of 27 genes were found to be absolutely essential for translocation of CagA into host cells and 14 out of 27 for the ability of Hp fully to induce transcription of IL‐8. The products of hp0524 (virD4 homologue), hp0526 and hp0540 are absolutely essential for the translocation of CagA, but not for the induction of IL‐8. In contrast, the products of hp0520, hp0521, hp0534, hp0535, hp0536 and hp0543 are not necessary for either translocation of CagA or for IL‐8 induction. Our data argue against a translocated IL‐8‐inducing effector protein encoded by the cag‐PAI. We isolated a variant of Hp 26695, which spontaneously switched off its capacity for IL‐8 induction and translocation of CagA, but retained the complete cag‐PAI. We identified a point mutation in gene hp0532, causing a premature translational stop in the corresponding polypeptide chain, providing a putative explanation for the defect in the type IV secretion system of the spontaneous mutant.
Trophic ecology of the whitemouth croaker, Micropogonias furnieri (Pisces: Sciaenidae), in south-western Atlantic waters

Ontogenetic and seasonal diet changes of the juveniles of the marine fish Micropogonias furnieri, a species inhabiting Bahía Blanca estuary (Argentina), were investigated. Two size-related dietary shifts, at 4·00 cm and 7·00 cm total length (LT), respectively, were found. Small juveniles (1·00–3·99 cm LT) ate mostly chaetognaths (Sagitta friderici); medium-sized juveniles (4·00–6·99 cm LT) fed intensively on mysid shrimps (mainly Neomysis americana) and polychaetes, whereas large juveniles (7·00–15·99 cm LT) fed almost exclusively on epibenthic crustaceans (primarily Peisos petrunkevitchi). Increased mouth gape was related to increased size spectrum and mean size of the most important prey items consumed by M. furnieri. Juveniles <510 cm LT ate prey items almost as large as their mouth opening, whereas juveniles >410 cm LT were capable of consuming larger prey items than those found in their stomachs, indicating that the maximum size of prey eaten was not constrained by mouth gape. Seasonal and selectivity dietary analyses showed that M. furnieri can be a highly opportunistic selective feeder. Juveniles relied on S. friderici and P. petrunkevitchi throughout the year, except in summer, when mysids abundance increased in the estuary. Electivity values also showed that prey size and prey relative abundance are important factors in prey selection mechanisms.
Relationships between diameter and height of trees in natural tropical forest in Tanzania

The relationship between tree height (h) and tree diameter at breast height (dbh) is an important element describing forest stands. In addition, h often is a required variable in volume and biomass models. Measurements of h are, however, more time consuming compared to those of dbh, and visual obstructions, rounded crown forms, leaning trees and terrain slopes represent additional error sources for h measurements. The aim of this study was therefore to develop h–dbh relationship models for natural tropical forest in Tanzania. Both general forest type specific models and models for tree species groups were developed. A comprehensive data set with 2 623 trees from 410 different tree species collected from a total of 1 191 plots and 38 sites covering the four main forest types of miombo woodland, acacia savanna, montane forest and lowland forests was applied. Tree species groups were constructed by using a k-means clustering procedure based on the h–dbh allometry, and a number of different non-linear model forms were tested. When considering the complexity of natural tropical forests in general and in particular variations of h–dbh relationships due to high species diversity in such forests, the model fit and performance were considered to be appropriate. Results also indicate that tree species group models perform better than forest type models. Despite the fact that the residual errors level associated with the models were relatively high, the models are still considered to be applicable for large parts of Tanzanian forests with an appropriate level of reliability.
Estudo da divergência genética entre linhagens de matrizes de frangos de corte por meio de análise multivariada

Genetic divergence among broiler lines (L1, L2, L3 and L4) was studied by multivariate analysis. Four economic important traits were evaluated in three periods (initial, medium and total): age at first egg, egg number, average egg weight and body weight. The study of the genetic divergence among lines included the following techniques:Multivariate analysis of variance, cluster analysis using Mahalanobis generalized distance and Tocher optimization method, and canonical variables analysis. Significant difference was obtained by the larget Roy eigenvalue test. The cluster analysis of traits in the initial (L1 and L2; L3 and L4) and medium (L2 and L4; L1 and L3) periods grouped the four genotypes in three groups, and in total period the genotypes were grouped in two groups (L2, L3, L4 and L1). Canonical variables analysis showed that the first two canonical variables accounted for more than 96% of the total variation in the three periods. This allowed to represent the performance of genotypes in a bidimensional dispersion graph. In the total period of production study the genetic divergence was lower.
Overcoming the transcatheter aortic valve replacement Achilles heel: conduction abnormalities-a systematic review.

Background Transcatheter aortic valve replacement (TAVR) has been shown to be a good alternative to surgery for treating severe symptomatic aortic stenosis (AS) across the whole range of surgical risk patients. Whereas most periprocedural TAVR complications have significantly decreased over time, conduction disturbances remain high. Approaches to decrease this shortcoming are under continuous investigation. Methods We conducted a systematic review focusing on modifiable factors impacting post-TAVR conduction disturbances, such as balloon aortic valvuloplasty (BAV), type of new-generation transcatheter valve and implantation depth (ID). Search strategies were based on the best available evidence from each study. Primary endpoints were post-TAVR need of permanent pacemaker implantation (PPI) and new onset left bundle branch block (NOLBBB). Results Data from 35 studies with a total of 29,982 patients were analyzed. BAV did not negatively impact PPI rates after TAVR. In propensity-matched and randomized trials, the Evolut R valve was associated with higher rates of PPI compared to the Sapien 3 valve (25% vs. 19.2% in propensity-matched studies; 22.9% vs. 19% in a randomized trial). The Acurate Neo valve was associated with the lowest PPI rate in observational studies (10.4%), but a PPI rate similar to Sapien 3 was reported in a randomized trial (10% vs. 9%). The Portico valve system was associated with a higher PPI risk (PPI rate of 21.9% and 27.7% in propensity-matched and randomized studies, respectively). ID and its relation with the membranous septum (MS) length predicted post-TAVR conduction disturbances, particularly with Evolut R and Sapien 3 valves. Conclusions Pre-TAVR BAV did not increase the risk of conduction disturbances post-TAVR. Among the new-generation transcatheter valve systems, Sapien 3 and Acurate Neo valves were associated with the lowest PPI rates followed by the Evolut and Portico valves. A deeper valve implantation and a shorter MS length determined an increased risk of conduction disturbances post-TAVR.
The Role of the Terminal and Subterminal Oxidation Pathways in Propane Metabolism by Bacteria

SUMMARY: Several strains of propane-utilizing bacteria were isolated from samples of pond and river water. They could be classified into three groups according to their ability to grow on acetone, and a representative strain from each group was selected for detailed study. All three strains belonged to the genus Arthrobacter. Strain B3aP could not grow on acetone and could not oxidize acetone after growth on propane. Strain PrIO3 grew slowly on acetone but could not oxidize acetone after growth on propane. Both strains excreted acetone during growth on propane. Simultaneous adaptation experiments demonstrated that, whilst propane was oxidized to both propan-1-ol and propan-2-ol, only propan-1-ol was metabolized completely suggesting that only the terminal oxidation pathway was involved in propane dissimilation. The third strain, B2, grew rapidly on acetone and was induced for acetone oxidation after growth on propane, suggesting that both propan-1-ol and propan-2-ol were produced and metabolized completely since no products of propane oxidation could be detected in culture supernatants. We compare these findings with previous reports concerning pathways of propane oxidation.