Crossing the Rift valley: using complete mitogenomes to infer the diversification and biogeographic history of ethiopian highlands Ptychadena (anura: Ptychadenidae).

The Ethiopian Highlands are considered a biodiversity hotspot, harboring a high number of endemic species. Some of the endemic species probably diversified in situ; this is, for example, the case of a monophyletic clade containing 12 known species of grass frogs of the genus Ptychadena. The different species occur at elevations ranging from 1,500 to above 3,400 m and constitute excellent models to study the process of diversification in the highlands as well as adaptations to high elevations. In this study, we sampled 294 specimens across the distribution of this clade and used complete mitogenomes and genome-wide SNP data to better understand how landscape features influenced the population structure and dispersal of these grass frogs across time and space. Using phylogenetic inference, population structure analyses, and biogeographic reconstructions, we found that the species complex probably first diversified on the south-east side of the Great Rift Valley. Later on, species dispersed to the north-west side, where more recent diversification occurred. We further demonstrate that Ptychadena species have dispersed across the Great Rift Valley at different times. Our analyses allowed for a more complete understanding of the contribution of geological events, biogeographic barriers and climatic changes as drivers of species diversification and adaptation in this important biogeographic region.

A new species of the fish louse genus Dipteropeltis Calman, 1912 (Crustacea: Branchiura) from Peru.

Dipteropeltis is a poorly described genus of fish louse endemic to South America. In a small blackwater region within Loreto, Peru, 13 adult and juvenile specimens of an unidentified species of Dipteropeltis Calman, 1912, as well as one adult specimen of D. hirundo Calman, 1912, were observed and collected. Scanning electron and light micrographs were acquired to examine and measure key features of these specimens. Morphological differences from the two known species of Dipteropeltis, D. hirundo and D. campanaformis Neethling et al., 2014, indicate that the collected specimens represent a new species. Dipteropeltis longicaudatus sp. nov. is diagnosed by elongate abdominal lobes, a chevron-shaped carapace, and uniquely shaped maxillae. One specimen represents the longest branchiuran documented to date at 31.5 mm. Additionally, we provide the first sequence data for this genus using DNA barcoding, which corroborates our designation of a new species. Videos were also captured that document behaviors including host attachment, pulsating abdominal lobes, suction disc "walking", and swimming. Findings have implications for its teleost hosts, Triportheus albus Cope, 1872 and Brycon amazonicus Spix & Agassiz, 1829, the latter being a critical species for aquaculture and commercial fisheries in Amazonia.

Beyond Janzen's Hypothesis: How Amphibians That Climb Tropical Mountains Respond to Climate Variation.

Janzen's hypothesis (JH) posits that low thermal variation selects for narrow physiological tolerances, and thus small species distributional ranges and high species turnover along tropical elevational gradients. Although this hypothesis has been intensely revisited, it does not explain how many tropical species may exhibit broad distributions, encompassing altitudinal gradients. Moreover, the physiological responses of tropical species remain largely unknown, limiting our understanding on how they respond to climate variation. To fill these knowledge gaps, we tested a major component of JH, the climate variability hypothesis (CVH), which predicts broader thermal tolerance breadth (Tbr = CTmax - CTmin) with broader temperature variation. Specifically, we sampled populations of five amphibian species distributed in two mountain ranges in Brazil's Atlantic Forest to test how CTmin and CTmax vary along elevational gradients. Since both thermal and water balance traits are pivotal to the evolutionary history of amphibians, we also measured rates of dehydration and rehydration and their relations with thermal tolerances. We found that broader temperature variation with increasing altitude did not always lead to broader Tbr, since changes in CTmin and CTmax were species-specific. In addition, we found that water balance did not show consistent variation with altitude, also with low correlations between hydric and thermal traits. While we also found that highland populations are at lower risk of thermal stress than lowland counterparts, both are living far from their upper thermal limits. As a consequence of intraspecific variation in physiological traits and spatial variation in climate along altitude, responses to climate variation in tropical amphibian species were context-dependent and heterogeneous. Together with recent studies showing thermal tolerances of some tropical amphibians comparable to temperate taxa, our findings highlight that several responses to climate variation in tropical species may not conform to predictions made by either the CVH or other important hypotheses concerning physiological variation. This reinforces the need to overcome geographical bias in physiological data to improve predictions of climate change impacts on biodiversity. (Portuguese abstract) Resumo A Hipótese de Janzen (JH) postula que a baixa variação térmica seleciona tolerâncias fisiológicas estreitas e, portanto, amplitudes restritas de distribuição das espécies e alta substituição de espécies ao longo de gradientes altitudinais tropicais. Embora intensamente revisitada, essa hipótese não explica como espécies tropicais podem exibir amplas distribuições geográficas, abrangendo gradientes altitudinais. Além disso, as respostas fisiológicas das espécies tropicais permanecem amplamente desconhecidas, limitando nossa compreensão sobre como elas respondem à variação climática. Para preencher essas lacunas de conhecimento, testamos um componente importante da JH, a Hipótese de Variabilidade Climática (CVH), que prevê uma maior amplitude de tolerância térmica (Tbr = CTmax - CTmin) quando a variação da temperatura ambiental é mais ampla. Especificamente, amostramos populações de cinco espécies de anfíbios distribuídas em duas cadeias montanhosas na Mata Atlântica do Brasil para testar como CTmin e CTmax variam ao longo de gradientes de altitude. Dado que parâmetros térmicos e do balanço hídrico são fundamentais para a história evolutiva dos anfíbios, também medimos as taxas de desidratação e reidratação e suas relações com as tolerâncias térmicas. Encontramos que uma variação de temperatura ambiental mais ampla com o aumento da altitude nem sempre conduz a uma Tbr mais ampla, uma vez que as mudanças em CTmin e CTmax foram espécie-específicas. Além disso, encontramos que o balanço hídrico não apresentou variação consistente com a mudança de altitude, e que as correlações entre parâmetros hídricos e térmicos foram baixas. Embora populações das maiores altitudes apresentaram menor risco de estresse térmico do que populações da mesma espécie em altitudes menores, ambas estão vivendo longe de seus limites térmicos superiores. Em consequência da variação intraespecífica em parâmetros fisiológicos e variação espacial no clima ao longo da altitude, as respostas à variação climática em espécies de anfíbios tropicais foram contexto-dependentes e heterogêneas. Juntamente com estudos recentes indicando tolerâncias térmicas de alguns anfíbios tropicais comparáveis a de táxons temperados, nossas descobertas destacam que várias respostas à variação climática em espécies tropicais podem não estar de acordo com as previsões feitas pela CVH ou outras hipóteses importantes sobre a variação fisiológica. Isso reforça a necessidade de superar o viés geográfico em dados fisiológicos para aperfeiçoar previsões dos impactos das mudanças climáticas sobre a biodiversidade. (Spanish abstract) Resumen La hipótesis de Janzen (JH) postula que la baja variación térmica selecciona tolerancias fisiológicas estrechas y, por lo tanto, rangos de distribución de especies restringidos con alta rotación de especies a lo largo de gradientes de elevación tropicales. Aunque esta hipótesis ha sido intensamente discutida, no explica cómo várias especies tropicales pueden exhibir distribuciones amplias, abarcando gradientes altitudinales. Además, las respuestas fisiológicas de las especies tropicales siguen siendo bastante desconocidas, lo que limita la comprensión de cómo responden a la variación climática. Para llenar estos vacíos de conocimiento, examinamos un componente importante de JH, la Hipótesis de Variabilidad Climática (CVH), que predice mayor amplitud de tolerancia térmica (Tbr = CTmax - CTmin) cuando la variación de temperatura es más amplia. Específicamente, tomamos muestras de poblaciones de cinco especies de anfibios distribuidas en dos cadenas montañosas en el Bosque Atlántico de Brasil para verificar cómo CTmin y CTmax varían a lo largo de este gradiente de elevación. Dado que los rasgos de equilibrio térmico y hídrico son fundamentales para la historia evolutiva de los anfibios, también medimos las tasas de deshidratación y rehidratación y sus relaciones con las tolerancias térmicas. Encontramos que una variación de temperatura más amplia con el aumento de la altitud no siempre conduce a una Tbr más amplia, ya que los cambios en CTmin y CTmax son específicos de la especie. Además, encontramos que el balance hídrico no muestra variación consistente con la altitud, con bajas correlaciones también entre los rasgos hídricos y térmicos. Si bien las poblaciones de las tierras altas tienen un menor riesgo de estrés térmico que las contrapartes de las tierras bajas, ambas se encuentran lejos de sus límites térmicos superiores. Como consecuencia de la variación intraespecífica en los rasgos fisiológicos y la variación espacial en el clima a lo largo de la altitud, las respuestas a la variación climática en las especies de anfibios tropicales fueron dependientes del contexto y heterogéneas. Junto con estudios recientes que muestran tolerancias térmicas de algunos anfibios tropicales comparables a los taxones de zonas templadas, nuestros hallazgos resaltan que varias respuestas a la variación climática en especies tropicales pueden no ajustarse a las predicciones hechas por el CVH u otras hipótesis importantes sobre la variación fisiológica. Esto refuerza la necesidad de superar el sesgo geográfico en los datos fisiológicos para mejorar las predicciones de los impactos del cambio climático en la biodiversidad.

Formation of topological defects in nematic shells with a dumbbell-like shape.

The present study investigates dumbbell-shaped nematic liquid crystal shells. Using molecular dynamics (MD) simulations, we consider the effects of an external electric field on nematic ordering by computing the average molecular alignment's time evolution and equilibrium configuration. We show that the number and location of topological defects are strongly affected by the external field, with the orientational ordering's equilibrium configuration depending on field direction about the shell's long axis. For a transverse external field, it is verified that the defect rearrangement presents a non-linear dynamics, with a field independent characteristic time scale delimiting the short and long time regimes. Effects associated with varying the shell's Gaussian curvature are also analyzed.

Universal dynamical scaling laws in three-state quantum walks.

We perform a finite-time scaling analysis over the detrapping point of a three-state quantum walk on the line. The coin operator is parametrized by ρ that controls the wave packet spreading velocity. The input state prepared at the origin is set as a symmetric linear combination of two eigenstates of the coin operator with a characteristic mixing angle θ, one of them being the component that results in full spreading occurring at θ_{c}(ρ) for which no fraction of the wave packet remains trapped near the initial position. We show that relevant quantities, such as the survival probability and the participation ratio assume single parameter scaling forms at the vicinity of the detrapping angle θ_{c}. In particular, we show that the participation ratio grows linearly in time with a logarithmic correction, thus, shedding light on previous reports of sublinear behavior.

Asymmetric acoustic wave scattering by a nonreciprocal and position-dependent mass defect.

We investigate the asymmetric wave scattering in a phononic one-dimensional lattice with a nonreciprocal defect and position dependent masses coupled by the defect spring. The nonreciprocal interaction is characterized by a single parameter Δ while the nonlinear contribution due to position-dependent masses are controlled by a parameterχ. The transmission and reflection coefficients are analytically computed and the effects of the nonreciprocity and nonlinearity are detailed. We show that, in opposite with the linear case, the rectification factor has a frequency dependence, which leads to a more efficient diode-like action at large wavevectors. Further, the nonlinearity leads to an asymmetry of the reflected component, absent in the linear regime. We extend our analysis to a system with frictional forces which suppresses the multistability window promoted by the nonlinear mass contribution without compromising the rectification action.

Low-temperature pseudo-phase-transition in an extended Hubbard diamond chain.

We consider the extended Hubbard diamond chain with an arbitrary number of particles driven by chemical potential. The interaction between dimer diamond chain and nodal couplings is considered in the atomic limit (no hopping), whereas the dimer interaction includes the hopping term. We demonstrate that this model exhibits a pseudo-transition effect in the low-temperature regime. Here, we explore the pseudo-transition rigorously by analyzing several physical quantities. The internal energy and entropy depict sudden, although continuous, jumps which closely resembles discontinuous or first-order phase-transition. At the same time, the correlation length and specific heat exhibit astonishing strong sharp peaks quite similar to a second-order phase-transition. We associate the ascending and descending parts of the peak with power-law "pseudo-critical" exponents. We determine the pseudo-critical exponents in the temperature range where these peaks are developed, namely, ν=1 for the correlation length and α=3 for the specific heat. We also study the behavior of the electron density and isothermal compressibility around the pseudo-critical temperature.

Next-generation humanized patient-derived xenograft mouse model for pre-clinical antibody studies in neuroblastoma.

Faithful tumor mouse models are fundamental research tools to advance the field of immuno-oncology (IO). This is particularly relevant in diseases with low incidence, as in the case of pediatric malignancies, that rely on pre-clinical therapeutic development. However, conventional syngeneic and genetically engineered mouse models fail to recapitulate the tumor heterogeneity and microenvironmental complexity of human pathology that are essential determinants of cancer-directed immunity. Here, we characterize a novel mouse model that supports human natural killer (NK) cell development and engraftment of neuroblastoma orthotopic patient-derived xenograft (O-PDX) for pre-clinical antibody and cytokine testing. Using cytotoxicity assays, single-cell RNA-sequencing, and multi-color flow cytometry, we demonstrate that NK cells that develop in the humanized mice are fully licensed to execute NK cell cytotoxicity, permit human tumor engraftment, but can be therapeutically redirected to induce antibody-dependent cell-mediated cytotoxicity (ADCC). Although these cells share phenotypic and molecular features with healthy controls, we noted that they lacked an NK cell subset, termed activated NK cells, that is characterized by differentially expressed genes that are induced by cytokine activation. Because this subset of genes is also downregulated in patients with neuroblastoma compared to healthy controls, we hypothesize that this finding could be due to tumor-mediated suppressive effects. Thus, despite its technical complexity, this humanized patient-derived xenograft mouse model could serve as a faithful system for future testing of IO applications and studies of underlying immunologic processes.

Critical properties of the SIS model on the clustered homophilic network.

The spreading of epidemics in complex networks has been a subject of renewed interest of several scientific branches. In this regard, we have focused our attention on the study of the susceptible-infected-susceptible (SIS) model, within a Monte Carlo numerical simulation approach, representing the spreading of epidemics in a clustered homophilic network. The competition between infection and recovery that drives the system either to an absorbing or to an active phase is analyzed. We estimate the static critical exponents ß ∕ ν , 1 ∕ ν and γ ∕ ν , through finite-size scaling (FSS) analysis of the order parameter ρ and its fluctuations, showing that they differ from those associated with the contact process on a scale-free network, as well as those predicted by the heterogeneous mean-field theory.

Emerging extreme value and Fermi-Dirac distributions in the Lévy branching and annihilating process.

We study the dynamics of the branching and annihilating process with long-range interactions. Static particles generate an offspring and annihilate upon contact. The branching distance is supposed to follow a Lévy-like power-law distribution with P(r)∝1/r^{α}. We analyze the long term behavior of the mean particles number and its fluctuations as a function of the parameter α that controls the range of the branching process. We show that the dynamic exponent associated with the particle number fluctuations varies continuously for α<4 while the particle number exponent only changes for α<3. A crossover from extreme value Frechet (at α=3) and Gumbell (for 2<α<3) distributions is developed, similar to the one reported in recent experiments with cw-pumped random fiber lasers presenting underlying gain and Lévy processes. We report the dependence of the relevant dynamical power-law exponents on α showing that explosive growth takes place for α≤2. Further, the average occupation number distribution is shown to evolve from the standard Fermi-Dirac form to the generalized one within the context of nonextensive statistics.

Rectification of acoustic phonons in harmonic chains with nonreciprocal spring defects.

The scattering of acoustic phonons by nonreciprocal spring defects inserted in an harmonic chain is investigated. The degree of nonreciprocity of the forces mediated by the defect springs is parameterized by a single quantity Δ that effectively takes into account the interaction of the coupled masses with hidden degrees of freedom of an underlying nonequilibrium system. We demonstrate a pronounced rectification effect with transmission having a preferential direction. Nonreciprocity also allows energy exchange between the system and the medium. Further, we show a cooperative action between defects mediated by resonant cavity modes. The influence of damping forces is also explored and shown to promote the rectification of the reflected vibrational wave component.

ATRX In-Frame Fusion Neuroblastoma Is Sensitive to EZH2 Inhibition via Modulation of Neuronal Gene Signatures.

ATRX alterations occur at high frequency in neuroblastoma of adolescents and young adults. Particularly intriguing are the large N-terminal deletions of ATRX (Alpha Thalassemia/Mental Retardation, X-linked) that generate in-frame fusion (IFF) proteins devoid of key chromatin interaction domains, while retaining the SWI/SNF-like helicase region. We demonstrate that ATRX IFF proteins are redistributed from H3K9me3-enriched chromatin to promoters of active genes and identify REST as an ATRX IFF target whose activation promotes silencing of neuronal differentiation genes. We further show that ATRX IFF cells display sensitivity to EZH2 inhibitors, due to derepression of neurogenesis genes, including a subset of REST targets. Taken together, we demonstrate that ATRX structural alterations are not loss-of-function and put forward EZH2 inhibitors as a potential therapy for ATRX IFF neuroblastoma.

Localization-delocalization transition in discrete-time quantum walks with long-range correlated disorder.

We study the effects of spatially long-range correlated phase disorder on the Hadamard quantum walk on a line. The shift operator is built to exhibit an intrinsic disorder distribution featuring long-range correlations. To impose such, we resort to fractional Brownian motion with power-law spectrum 1/k^{2α} with α≥0 being the exponent that controls the degree of correlations. We discuss the scaling behavior of the walker's wave packet and report a localization-delocalization transition controlled by α. We unveil two intermediate dynamical regimes between exponential localization and full delocalization.

Enhanced nonreciprocal transmission through a saturable cubic-quintic nonlinear dimer defect.

The transmission properties through a saturable cubic-quintic nonlinear defect attached to lateral linear chains is investigated. Particular attention is directed to the possible non-reciprocal diode-like transmission when the parity-symmetry of the defect is broken. Distinct cases of parity breaking are considered including asymmetric linear and nonlinear responses. The spectrum of the transmission coefficient is analytically computed and the influence of the degree of saturation analyzed in detail. The transmission of Gaussian wave-packets is also numerically investigated. Our results unveil that spectral regions with high transmission and enhanced diode-like operation can be achieved.

Phylogeography of Atlantic Forest glassfrogs (Vitreorana): when geography, climate dynamics and rivers matter.

Recent advances in the field of landscape genetics provide ways to jointly analyze the role of present-day climate and landscape configuration in current biodiversity patterns. Expanding this framework into a phylogeographic study, we incorporate information on historical climatic shifts, tied to descriptions of the local topography and river configuration, to explore the processes that underlie genetic diversity patterns in the Atlantic Forest hotspot. We study two montane, stream-associated species of glassfrogs: Vitreorana eurygnatha and V. uranoscopa. By integrating species distribution modeling with geographic information systems and molecular data, we find that regional patterns of molecular diversity are jointly explained by geographic distance, historical (last 120 ky) climatic stability, and (in one species) river configuration. Mitochondrial DNA genealogies recover significant regional structure in both species, matching previous classifications of the northern and southern forests in the Atlantic Forest, and are consistent with patterns reported in other taxa. Yet, these spatial patterns of genetic diversity are only partially supported by nuclear data. Contrary to data from lowland taxa, historical climate projections suggest that these montane species were able to persist in the southern Atlantic Forest during glacial periods, particularly during the Last Glacial Maximum. These results support generally differential responses to climatic cycling by northern (lowland) and southern (montane) Atlantic Forest species, triggered by the joint impact of regional landscape configuration and climate change.

Phase diagram and re-entrant fermionic entanglement in a hybrid Ising-Hubbard ladder.

The degree of fermionic entanglement is examined in an exactly solvable Ising-Hubbard ladder, which involves interacting electrons on the ladder's rungs described by Hubbard dimers at half-filling on each rung, accounting for intrarung hopping and Coulomb terms. The coupling between neighboring Hubbard dimers is assumed to have an Ising-like nature. The ground-state phase diagram consists of four distinct regions corresponding to the saturated paramagnetic, the classical antiferromagnetic, the quantum antiferromagnetic, and the mixed classical-quantum phase. We have exactly computed the fermionic concurrence, which measures the degree of quantum entanglement between the pair of electrons on the ladder rungs. The effects of the hopping amplitude, the Coulomb term, temperature, and magnetic fields on the fermionic entanglement are explored in detail. It is shown that the fermionic concurrence displays a re-entrant behavior when quantum entanglement is being generated at moderate temperatures above the classical saturated paramagnetic ground state.

Unbalanced inflammatory reaction could increase tissue destruction and worsen skin infectious diseases - a comparative study of leishmaniasis and sporotrichosis.

The clinical presentations of skin diseases produced by different pathogens, as American tegumentary leishmaniasis (ATL) and sporotrichosis can be similar and possibly influenced by the skin immune system (SIS). The aim of the study was to understand the underlying mechanisms of skin inflammation produced by different pathogens. We used immunohistochemistry to analyze 96 patients: a- localized cutaneous leishmaniasis (LCL-ATL); b- sporotrichoid cutaneous leishmaniasis (SCL-ATL); c-lymphocutaneous (LC-SP); d- fixed (F-SP) sporotrichosis. LCL-ATL and SCL-ATL had a significantly higher percentage of CD8, FasL and NOS2 than sporotrichosis. In contrast, LC-SP had a substantially higher percentage of CD4, BCl2 and neutrophils than ATL lesions. These results indicated some differences in the profile of the in situ immune response suggesting that SIS is a complex, adaptable system capable of different responses to intracellular or extracellular pathogens. However, regardless of the etiological agents, the inflammatory reaction and clinical manifestations can be similar. SCL-ATL and LC-SP presented similarities in both clinical presentation and in situ inflammatory profile (CD3, CD22, neutrophils, macrophages). The clinical presentation of ATL and sporotrichosis could be explained by a combination of factors both of the host SIS and the etiological agent. The unbalanced host parasite relationship could result in atypical manifestations of skin disease.

More sex chromosomes than autosomes in the Amazonian frog Leptodactylus pentadactylus.

Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process.