CAMO: A molecular congruence analysis framework for evaluating model organisms

CAMO provides a rigorous and user-friendly solution for quantification and mechanistic exploration of omics congruence in model organisms and humans. It performs threshold-free differential analysis, quantitative concordance/discordance scoring, pathway-centric investigation, text-mining-based knowledge retrieval, and topological subnetwork detection. Instead of dichotomous claims of "poorly" or "greatly" mimicking, CAMO facilitates discovery and visualization of specific molecular mechanisms that are best or least mimicked, providing foundations for hypothesis generation and subsequent translational investigations.

Strategy for Connecting to the IHRF: Case Study for the Tide Gauge of Cananeia-SP

In July 2018, IBGE launched the new heights of the Brazilian Geodetic System (BGS), the normal height, which has associated gravity. These new heights are replacing the old normal-orthometric ones, in which there was only the non-parallelism correction. The IBGE informs that the values farther from the origin, have less accuracy. This lower accuracy may interfere in the future, the connection of the local tide gauges to IHRF (International Reference Frame Height). Thus, this paper proposes the integration of the local tide gauge of Cananeia-SP to the IHRF. In order to validate the methodology, the normal, Helmert, and rigorous orthometric heights using two distinct references: the Imbituba-SC tide gauge, as the origin of the BGS and the Cananeia-SP tide gauge, as a local tide gauge to be integrated into the IHRF. Calculating the three heights through these two origins, we analyzed the discrepancies in comparison to the heights calculated by IBGE. Numerical tests indicate that there was an improvement in terms of a mean and standard deviation when using the Cananeia gauge as origin in the calculation of normal, Helmert, and rigorous heights. In the congruence analysis, the calculations indicate that the highest standard deviation is presented when using IBGE normal heights. Thus, we have a new origin that is reliable and functional, can be integrated with the IHRF, where the Helmert and rigorous orthometric heights have the best statistical results.

Spatial Congruence Analysis (SCAN): A method for detecting biogeographical patterns based on species range congruences

Species with congruent geographical distributions, potentially caused by common historical and ecological spatial processes, constitute biogeographical units called chorotypes. Nevertheless, the degree of spatial range congruence characterizing these groups of species is rarely used as an explicit parameter. Methods conceived for the identification of patterns of shared ranges often suffer from scale bias associated with the use of grids, or the incapacity to describe the full complexity of patterns, from core areas of high spatial congruence, to long gradients of range distributions expanding from these core areas. Here, we propose a simple analytical method, Spatial Congruence Analysis (SCAN), which identifies chorotypes by mapping direct and indirect spatial relationships among species. Assessments are made under a referential value of congruence as an explicit numerical parameter. A one-layered network connects species (vertices) using pairwise spatial congruence estimates (edges). This network is then analyzed for each species, separately, by an algorithm which searches for spatial relationships to the reference species. The method was applied to two datasets: a simulated gradient of ranges and real distributions of birds. The simulated dataset showed that SCAN can describe gradients of distribution with a high level of detail. The bird dataset showed that only a small portion of range overlaps is biogeographically meaningful, and that there is a large variation in types of patterns that can be found with real distributions. Species analyzed separately may converge on similar or identical groups, may be nested in larger chorotypes, or may even generate overlapped patterns with no species in common. Chorotypes can vary from simple ones, composed by few highly congruent species, to complex, with numerous alternative component species and spatial configurations, which offer insights about possible processes driving these patterns in distinct degrees of spatial congruence. Metrics such as congruence, depth, richness, and ratio between common and total areas can be used to describe chorotypes in detail, allowing comparisons between patterns across regions and taxa.

Covariance

This chapter examines the covariance, which is either a comprehensive qualitative approach or the first step of a quantitative approach to the analysis of the relationship between two variables. On the one hand, in qualitative studies, and in particular in case study methods, covariation is an analytical approach used alongside causal process-tracing and congruence analysis. In the co-variational approach, causal inferences are drawn based on observed covariation between causal factors (independent variables) and causal effects (dependent variables). On the other hand, when the type of data allows a quantitative approach, looking at the covariance constitutes a first step in the statistical analysis. The covariance is then a measure of linear association between two variables.

Spatial Congruence Analysis (SCAN): An objective method for detecting biogeographical patterns based on species’ range congruences

Similar species ranges may represent outcomes of common biological processes and so form the basis for biogeographical concepts such as areas of endemism and ecoregions. Nevertheless, spatial range congruence is rarely quantified, much less incorporated in bioregionalization methods as an explicit parameter. Furthermore, most available methods suffer from limitations related to the loss, or the excess of range information, or scale bias associated with the use of grids, and the incapacity to recognize independent overlapped patterns or gradients of range distributions. Here, we propose an analytical method, Spatial Congruence Analysis (SCAN), to identify biogeographically meaningful groups of species, called biogeographic elements. Such elements are based on direct and indirect spatial relationships among species’ ranges and vary depending on an explicit measure of range congruence controlled as a numerical parameter in the analysis. A one-layered network connects species (vertices) using pairwise spatial congruence estimates (edges). This network is then analyzed for each species, separately, by an algorithm that accesses the entire web of spatial relationships to the reference species. The method was applied to two datasets: a simulated gradient of ranges and real distributions of birds. The gradient results showed that SCAN can describe gradients of distribution with a high level of detail, without confounding transition zones with true biogeographical units, a frequent pitfall of other methods. The bird dataset showed that only a small portion of range overlaps is biogeographically meaningful, and that there is a large variation in types of patterns that can be found with real distributions. Distinct reference species may converge on similar or identical groups of spatially related species, may lead to recognition of nested species groups, or may even generate similar spatial patterns with no species in common. The biological significance or causal processes of these patterns should be investigated a posteriori. Patterns can vary from simple ones, composed by few highly congruent species, to complex, with numerous alternative component species and spatial configurations, depending on particular parameter settings as determined by the investigator. This approach eliminates or reduces limitations of other methods and permits pattern description without hidden assumptions about processes, and so should make a valuable contribution to the biogeographer’s toolbox.“If there is any basic unit of biogeography, it is the geographic range of a species.” - Brown, Stevens & Kaufman [1].“[spatial] congruence […] should be optimized, while realizing that this criterion will most likely never be fully met” - HP Linder [2].

External Democracy Promotion in Time of Democratic Crisis: Linkage, Leverage, and Domestic Actors’ Diversionary Behaviours

Since the 1990s, the literature on External Democracy Promotion (EDP) expanded exponentially. Despite widely supported conclusions on EDP (in)effectiveness in fostering democratization and preventing democratic backsliding are still lacking, the literature has generated sophisticated explanations of these processes. Among them, Levitsky and Way’s (L&W’s) linkage and leverage theory stands out as one of the most influential. According to Tolstrup, however, their underestimation of domestic agency constitutes a crucial lacuna, which he proposes to fill through the concept of “Gatekeeping Elite” that underlines a significant impact of local actors on the linkage dimension and, consequently, on EDP (in)effectiveness. I believe that Tolstrup’s intuition can be further developed, expanding even more the explanatory power of L&W’s theory. I claim that domestic actors may exert a crucial influence also on the leverage dimension, thanks to “diversionary behaviours” that local elites may use to change external actors’ interests and preferences, persuading them to limit their democratizing pressures and thus reduce their own vulnerability to EDP processes. To assess the plausibility of this claim, I perform a congruence analysis on the recent and crucial case of autocratization in Serbia (EU candidate country), which is not fully explained by the aforementioned models.

Mitochondrial sequences of Rhipicephalus and Coxiella endosymbiont reveal evidence of lineages co-cladogenesis

ABSTRACT Rhipicephalus ticks are competent vectors of several pathogens, such as Spotted Fever Group Rickettsiae (SFGR) and many Babesia species. Within this genus, different R. sanguineus s.l. lineages show an unequal vector competence and resistance regarding some pathogenic strains. Current literature supports that tick endosymbionts may play an essential role in the transmission ability of a vector. Indeed, the microbial community of Rhipicephalus seems to be dominated by Coxiella-like endosymbionts (CLE). Still, their co-evolutionary associations with the complicated phylogeny of Rhipicephalus lineages and their transmissible pathogens remain unclear. We performed a phylogenetic congruence analysis to address whether divergent R. sanguineus s.l. lineages had a different symbiont composition. For that, we applied a PCR based approach to screen part of the microbial community present in 279 Rhipicephalus ticks from the Iberian Peninsula and Africa. Our analyses detected several qPCR-positive signals for both SFGR and Babesia species, of which we suggest R. sanguineus-tropical lineage as a natural vector of Babesia vogeli and R. sanguineus-temperate lineage of SFGR. The acquisition of 190 CLE sequences allowed to evaluate co-phylogenetic associations between the tick and the symbiont. With this data, we observed a strong but incomplete co-cladogenesis between CLE strains and their Rhipicephalus tick lineages hosts.

The Therapeutic Alliance Over 10 Sessions of Therapy for Borderline Personality Disorder: Agreement and Congruence Analysis and Relation to Outcome

The authors examined whether alliance dynamics are affected by tailoring the therapeutic relationship to the individual patient in brief psychotherapy of borderline personality disorder. Sixty patients were randomized to 10-session Good Psychiatric Management (GPM-BV) or GPM combined with Motive-Oriented Therapeutic Relationship techniques (MOTR+GPM-BV). Patient- and therapist-rated alliance was assessed weekly. Self-reported symptomatic distress was assessed pre-, mid-, and posttreatment. In MOTR+GPM-BV, stronger therapist-rated alliance predicted lower symptomatic distress in the same timepoint, but not in a lag, whereas symptomatic distress predicted therapist-rated alliance in a lag. Therapist-rated alliance was lower than patient-rated alliance in GPM-BV but not in MOTR+GPM-BV. In MOTR+GPM-BV, higher agreement on strong alliance tended to predict lower symptomatic distress. Patient- and therapist-rated alliances were temporally congruent, but congruence did not predict outcome. Addressing the relationship needs of patients may partly exert its salutary effect by increasing agreement between patients' and therapists' experience of the alliance.

The Devil is in the Detail

This chapter addresses the authority of the United Nations Security Council and its politicization by the BRICS. In particular, it explores the patterns of contestation for the reform of the United Nations Security Council and the Responsibility to Protect. How do the BRICS position themselves towards these two issues and how do they justify their demands? Do they build a challengers’ coalition? Using, first, a qualitative analysis of BRICS statements and, second, congruence analysis, this chapter maps and explains the positions of BRICS states on UNSC reform and R2P. We find that BRICS’ individual positions show a convergence on the basic contours of UNSC reform and R2P. The contestation pattern clearly indicates that this group favours the UNSC having strong international authority and also that they share concerns about the liberal content of the UNSC. While there is a strong tendency towards convergence on the one hand, BRICS strongly disagree on the details of the reform of the UNSC—as well as on the implementation of R2P on the other. These differences are so strong that they are unlikely to be resolved in the near future. Congruence analysis shows that power transition theory best explains their agreement ‘in principle’, but that none of the available theories explain their disagreement ‘in detail’. We conclude that, as things stand, the BRICS do not pose a challenge to the status quo in governance within the field of international security.