Miracle-dz/UniFAR-FTUs huggingface dataset:
Reducibility of automorphisms of Hurwitz surfaces and the η-invariant

In this paper, we discuss a relationship between the surface symmetry and the spectral asymmetry. More precisely we show that an automorphism of the Macbeath surface of genus 7, or one of the three Hurwitz surfaces of genus 14 is reducible if and only if the η-invariant of the corresponding mapping torus vanishes.
Preservation of mantle heterogeneities and serpentinization signature during antigorite dehydration: The example of the Bergell contact aureole

Major, minor, and trace element geochemistry as well as iron oxidation state and isotopes were investigated in serpentinites and olivine‐talc fels present along a metamorphic gradient in the Bergell contact aureole (Central European Alps) to evaluate element mobility during serpentine. This aureole is an ideal target to study dehydration of mantle rocks due to the increase in temperature from greenschist facies conditions (350°C) to amphibolite facies conditions (750°C) at low pressures of 0.4 GPa. Petrography and geochemistry document several events of fluid–rock interaction and metamorphism. Serpentinization of the mantle rocks started on the ocean floor. Subsequent Alpine regional metamorphism led to the formation of antigorite‐serpentinites containing olivine and diopside. These antigorite‐serpentinites were transformed into olivine‐talc fels in a large part of the contact‐aureole. Bulk‐rock major and trace element compositions maintain the geochemical signature of the precursor antigorite‐serpentinites. No apparent changes are indeed observed despite the fact that major dehydration reactions occurred. In addition, changes neither in Fe3+/Fetot ratio nor in δ56Fe values were observed. Local composition variations of antigorite‐serpentinites and olivine‐talc fels reflect chemical heterogeneities related to protolith composition and serpentinization processes on the ocean floor prior to contact metamorphism. Hence, prograde dehydration reactions occurring during contact metamorphism did not induce substantial element mobility, change in redox state, or isotopic fractionation in these contact metamorphic rocks.
A generic binding pocket for small molecule IKs activators at the extracellular inter-subunit interface of KCNQ1 and KCNE1 channel complexes

The cardiac IKs ion channel comprises KCNQ1, calmodulin, and KCNE1 in a dodecameric complex which provides a repolarizing current reserve at higher heart rates and protects from arrhythmia syndromes that cause fainting and sudden death. Pharmacological activators of IKs are therefore of interest both scientifically and therapeutically for treatment of IKs loss-of-function disorders. One group of chemical activators are only active in the presence of the accessory KCNE1 subunit and here we investigate this phenomenon using molecular modeling techniques and mutagenesis scanning in mammalian cells. A generalized activator binding pocket is formed extracellularly by KCNE1, the domain-swapped S1 helices of one KCNQ1 subunit and the pore/turret region made up of two other KCNQ1 subunits. A few residues, including K41, A44 and Y46 in KCNE1, W323 in the KCNQ1 pore, and Y148 in the KCNQ1 S1 domain, appear critical for the binding of structurally diverse molecules, but in addition, molecular modeling studies suggest that induced fit by structurally different molecules underlies the generalized nature of the binding pocket. Activation of IKs is enhanced by stabilization of the KCNQ1-S1/KCNE1/pore complex, which ultimately slows deactivation of the current, and promotes outward current summation at higher pulse rates. Our results provide a mechanistic explanation of enhanced IKscurrents by these activator compounds and provide a map for future design of more potent therapeutically useful molecules.
Molecular mechanisms of heavy metal adaptation of an extremophilic red alga Cyanidioschyzon merolae

The order of Cyanidiales comprise seven acido-thermophilic red microalgal species thriving in hot springs of volcanic origin characterized by extremely low pH, moderately high temperatures and the presence of elevated concentrations of sulphites and heavy metals that are prohibitive for most other organisms. Little is known about the molecular mechanisms of Cyanidiales long-term adaptation to such hostile environments, in particular to heavy metals, yet elucidation of these processes is important for understanding the evolution of the metabolic pathways underlying heavy metal detoxification for developing rational strategies for heavy metal bioremediation. Here, we investigated the long-term adaptive responses of Cyanidioschyzon merolae cells, a member of Cyanidiales, to extremely high nickel concentrations. Through complementary approaches based on physiological, microscopic and elemental analyses we dissect several molecular mechanisms underlying the long-term adaptation of this model extremophilic microalga to high Ni exposure. These include: (i) extrusion of Ni from the cells and lack of significant Ni accumulation inside the cells; (ii) maintenance of efficient photoprotective responses including non-photochemical quenching and state transitions; (iii) dynamic remodeling of the chloroplast ultrastructure such as formation of metabolically active prolamellar bodies and plastoglobuli together with loosening of the thylakoid membranes; (iv) activation of ROS amelioration metabolic pathways; and (v) preservation of the efficient respiratory chain functionality. All the dynamically regulated processes identified in this study underlie the remarkable adaptability of C. merolae to extremely high Ni levels that exceed by several orders of magnitude the levels of this heavy metal found in the natural environment of this extremophile.
Whole genome sequencing of Borrelia burgdorferi isolates reveals linked clusters of plasmid-borne accessory genome elements associated with virulence

Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting Borrelia burgdorferi spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of 299 patient-derived B. burgdorferi sensu stricto (Bbss) isolates from patients in the Eastern and Midwestern US and Central Europe. We develop a WGS-based classification of Bbss isolates, confirm and extend the findings of previous single- and multi-locus typing systems, define the plasmid profiles of human-infectious Bbss isolates, annotate the core and strain-variable surface lipoproteome, and identify loci associated with disseminated infection. A core genome consisting of ∼800 open reading frames and a core set of plasmids consisting of lp17, lp25, lp36, lp28-3, lp28-4, lp54, and cp26 are found in nearly all isolates. Strain-variable (accessory) plasmids and genes correlate strongly with phylogeny. Using genetic association study methods, we identify an accessory genome signature associated with dissemination and define the individual plasmids and genes that make up this signature. Strains within the RST1/WGS A subgroup, particularly a subset marked by the OspC type A genotype, are associated with increased rates of dissemination. OspC type A strains possess a unique constellation of strongly linked genetic changes including the presence of lp56 and lp28-1 plasmids and a cluster of genes that may contribute to their enhanced virulence compared to other genotypes. The patterns of OspC type A strains typify a broader paradigm across Bbss isolates, in which genetic structure is defined by correlated groups of strain-variable genes located predominantly on plasmids, particularly for expression of surface-exposed lipoproteins. These clusters of genes are inherited in blocks through strain-specific patterns of plasmid occupancy and are associated with the probability of invasive infection.
Patient-specific simulation of Retinal Hemangioblastoma provides new perspectives on the role of antiangiogenic therapy

Retinal Hemangioblastoma (RH) is the most frequent manifestation of the von Hippel-Lindau syndrome (VHL), a rare disease associated with the germline mutation of the von Hippel-Lindau protein (pVHL). An emblematic feature of RH is the high vascularity, which is easily explained by the overexpression of angiogenic factors (AFs) arising from the pVHL impairment. The introduction of Optical Coherence Tomography Angiography (OCTA) allowed observing this feature with exceptional detail. However, our understanding of RH is limited by the absence of an animal model fully recapitulating the tumor. Here, we exploit a cancer mathematical model as an alternative way to explore RH development and angiogenesis. We derived our model from the agreed pathology for this tumor and compared our results with patient-specific OCTA images. Our simulations closely resemble the medical images, proving the capability of our model to recapitulate RH pathology. Our results also suggest that angiogenesis in RH occurs suddenly when the tumor reaches a critical mass, with full capillary invasion in the order of days. These findings open a new perspective on the critical role of time in antiangiogenic therapy in RH, which has resulted ineffective. Indeed, it might be that when RH is diagnosed, angiogenesis is already too advanced to be effectively targeted with this mean.
Lifespan Changes in Brain Structure and Cognitive Performance Associated with Normal Aging in Mice

Institute of Medical Science, University of Toronto, Toronto, ON, Canada Centre for Addiction and Mental Health, Toronto, ON, Canada Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada. Departments of Pharmacology and Toxicology, University of Toronto, Toronto, Canada. Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Canada. Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, The University of Oxford, Oxford, UK Department of Medical Biophysics, The University of Toronto, Toronto, Canada Department of Psychiatry, University of Toronto, Toronto, Canada
Molecular abundances and low-mass star formation. 1: Si- and S-bearing species toward IRAS 16293-2422

Results from millimeter and submillimeter spectral line surveys of the protobinary source IRAS 16293-2422 are presented. Here we outline the abundances of silicon- and sulfur-containing species. A combination of rotation diagram and full statistical equilibrium/radiative transfer calculations is used to constrain the physical conditions toward IRAS 16293 and to construct its beam-averaged chemical composition over a 10-20" (1600-3200 AU) scale. The chemical complexity as judged by species such as SiO, OCS, and H_2S, is mtermedtate between that of dark molecular clouds such as Ll34N and hot molecular cloud cores such as Orion KL. From the richness of the spectra compared to other young stellar objects of similar luminosity, it is clear that molecular abundances do not scale simply with mass; rather, the chemistry is a strong function of evolutionary state, i.e., age.
Calorimetry for Lepton Collider Experiments – CALICE results and activities

The CALICE collaboration conducts calorimeter R&D for highly granular calorimeters, mainly for their application in detectors for a future lepton collider at the TeV scale. The activities ranges from generic R&D with small devices up to extensive beam tests with prototypes comprising up to several 100000 calorimeter cells. CALICE has validated the performance of particle flow algorithms with test beam data and delivers the proof of principle that highly granular calorimeters can be built, operated and understood. The successes achieved in the past years allows the step from prototypes to calorimeter systems for particle physics detectors to be addressed.
The effect of deep brain stimulation on cortico-subcortical networks in Parkinson’s disease patients with freezing of gait: Exhaustive exploration of a basic model

Current treatments of Parkinson’s disease (PD) have limited efficacy in alleviating freezing of gait (FoG). In this context, concomitant deep brain stimulation (DBS) of the subthalamic nucleus (STN) and the substantia nigra pars reticulata (SNr) has been suggested as a potential therapeutic approach. However, the mechanisms underlying this approach are unknown. While the current rationale relies on network-based hypotheses of intensified disinhibition of brainstem locomotor areas to facilitate the release of gait motor programs, it is still unclear how simultaneous high-frequency DBS in two interconnected basal ganglia nuclei affects large-scale cortico-subcortical network activity. Here, we use a basic model of neural excitation, the susceptible-excited-refractory (SER) model, to compare effects of different stimulation modes of the network underlying FoG. We develop a network-based computational framework to compare subcortical DBS targets through exhaustive analysis of the brain attractor dynamics in the healthy, PD and DBS states. We demonstrate the validity of the approach and the superior performance of combined STN+SNr DBS in the normalization of spike propagation flow in the FoG network. The framework aims to move towards a mechanistic understanding of the network effects of DBS and may be applicable to further perturbation-based therapies of brain disorders. AUTHOR SUMMARY Parkinson’s disease patients with Freezing of Gait (FoG) may be treated by deep brain stimulation, which produces effects mediated by brain networks. Currently, the approach of combined DBS of the subthalamic nucleus and the substantia nigra pars reticulata is investigated for being particularly beneficial for patients with axial symptoms, but the exact mechanisms of this effect are unknown. Here, we present a network-based computational framework using a basic excitable model that enables us to simulate the complete activity patterns of the brain network involved in FoG. These simulations reveal network mechanisms underlying STN+SNr DBS and its efficacy in alleviating FoG. The proposed framework can capture the influence of the DBS target sites on cortico-subcortical networks and help to identify suitable stimulation targets.
Performance of HIRLAM in a semiarid heterogeneous region: Evaluation of the land surface and boundary layer description using EFEDA observations

Observations from the European Field Experiment in a Desertification-threatened Area (EFEDA) are used to evaluate the performance of the radiation, land surface, and boundary layer description of the numerical weather prediction (NWP) system High-Resolution Limited Area Model (HIRLAM) in semiarid conditions. Model analysis and 6-h forecast data of the fully coupled three-dimensional model are compared with the comprehensive dataset of a case study representing a sample of 22 days of anticyclonic conditions. Distributed micrometeorological surface stations, radiosondes, flux aircraft, and airborne lidar provide a unique validation dataset of the diurnal cycle of surface and boundary layer processes. The model surface, soil, and boundary layer are found to be too moist and slightly too cold during most of the diurnal cycle. The model radiation and surface energy budgets are biased toward more humid conditions. Model shortcomings are identified essentially in four areas. These are the moisture data assimilation, the land-use and soil classification with its associated physiographic database, the aerosol parameterization in the radiation code, and the boundary layer vertical resolution and entrainment description. Practical steps for immediate improvement of the model performance are proposed. They focus on the use of a land-use and soil classification and physiographic database adapted to Mediterranean landscapes, in combination with the inclusion of aerosol parameters in the radiation scheme, that account for the typically higher aerosol load of arid and semiarid environments.
New measurement of exclusive decays of the χc0 and χc2 to two-meson final states

Using a sample of 2.59x10{sup 7} {psi}(2S) decays collected by the CLEO-c detector, we present results of a study of {chi}{sub c0} and {chi}{sub c2} decays into two-meson final states. We present the world's most precise measurements of the {chi}{sub cJ,(J=0,2)}{yields}{pi}{sup +}{pi}{sup -}, {pi}{sup 0}{pi}{sup 0}, K{sup +}K{sup -}, K{sub S}{sup 0}K{sub S}{sup 0}, {eta}{eta}, and {eta}{sup '}{eta}{sup '} branching fractions, and a search for {chi}{sub c} decays into {eta}{eta}{sup '}. These results shed light on the mechanism of charmonium decays into pseudoscalar mesons.
Optimization in scaling fiber-coupled laser-diode end-pumped lasers to higher power: influence of thermal effect

The optimum mode-to-pump ratio in scaling fiber-coupled laser-diode end-pumped lasers to higher power has been investigated by including the thermal effect into the space-dependent rate equation analysis. The optical path difference (OPD) distribution has been derived as a function of the pump-beam quality, focus position of pumping light, and pump radius at the focal plane under the assumption that the end faces of the crystal are thermally insulated. The diffraction losses arising from thermally induced spherical aberration have been estimated by the Strehl intensity ratio. The present results for the optimum mode-to-pump ratio are markedly different from previous analyses in which thermal effects are neglected. Here, the optimum mode-to-pump ratio is a decreasing function of input pump power, and is less than unity in the case of a slightly high pump power. The practical example of a Nd:YAG laser pumped by a 13-W fiber-coupled laser diode is considered to confirm our physical analysis.
Mass loss from evolved stars. III: Mass loss rates for fifty stars from CO J=1−0 observations

Observations de la raie CO J=1-0 a 2,6 mm de longueur d'onde dans les directions de 105 etoiles evoluees froides. On a detecte une emission pour 50 etoiles, dont la moitie sont des etoiles Mira de type M, deux sont des supergeantes, et le reste des etoiles S ou carbone
Combining Propensity Score Matching with Additional Adjustments for Prognostic Covariates

Abstract Propensity score matching refers to a class of multivariate methods used in comparative studies to construct treated and matched control samples that have similar distributions on many covariates. This matching is the observational study analog of randomization in ideal experiments, but is far less complete as it can only balance the distribution of observed covariates, whereas randomization balances the distribution of all covariates, both observed and unobserved. An important feature of propensity score matching is that it can be easily combined with model-based regression adjustments or with matching on a subset of special prognostic covariates or combinations of prognostic covariates that have been identified as being especially predictive of the outcome variables. We extend earlier results by developing approximations for the distributions of covariates in matched samples created with linear propensity score methods for the practically important situation where matching uses both the estimated linear propensity scores and a set of special prognostic covariates. Such matching on a subset of special prognostic covariates is an observational study analog of blocking in a randomized experiment. An example combining propensity score matching with Mahalanobis metric matching and regression adjustment is presented that demonstrates the flexibility of these methods for designing an observational study that effectively reduces both bias due to many observed covariates and bias and variability due to a more limited subset of covariates. Of particular importance, the general approach, which includes propensity score matching, was distinctly superior to methods that focus only on a subset of the prognostically most important covariates, even if those covariates account for most of the variation in the outcome variables. Also of importance, analyses based on matched samples were superior to those based on the full unmatched samples, even when regression adjustment was included.
Physics comparison and modelling of the JET and JT-60U core and edge: towards JT-60SA predictions

Extensive physics analysis and modelling has been undertaken for the typical operational regimes of the tokamak devices JET and JT-60U with the aim of extrapolating present day experiments to JT-60SA, which shares important characteristics with both tokamaks. A series of representative discharges of two operational scenarios, H-mode and hybrid, have been used for this purpose. Predictive simulations of core turbulence, particle transport, current diffusion and pedestal pressure have been carried out with different combinations of models. The ability of the models for reproducing the experimental data is analysed and scenario calculations for JT-60SA are performed following an optimum set of models.
A three-dimensional ultrasonic cage for characterization of individual cells

We demonstrate enrichment, controlled aggregation, and manipulation of microparticles and cells by an ultrasonic cage integrated in a microfluidic chip compatible with high-resolution optical microscopy. The cage is designed as a dual-frequency resonant filleted square box integrated in the fluid channel. Individual particles may be trapped three dimensionally, and the dimensionality of one-dimensional to three-dimensional aggregates can be controlled. We investigate the dependence of the shape and position of a microparticle aggregate on the actuation voltages and aggregate size, and demonstrate optical monitoring of individually trapped live cells with submicrometer resolution.
Questioning the Rules of Continuity Editing: An Empirical Study

We investigated phenomenal continuity across mid-action cuts in motion pictures. When a change of perspective is used in the midst of a dynamic event, film directors tend to agree that a straight-match cut is not advisable if the impression of smooth continuity is desired. Such a cut would embody an instantaneous transition from one camera angle or position to the next. Some film theorists recommend that some overlap of the action is desirable, surmising that the visual system needs time to digest the cut and to reorient. Others disagree and prefer a gap. We report two experiments that provide an empirical test of competing continuity hypotheses. We systematically varied the temporal parameters of a dynamic scene that continued across a camera jump. Computer-animated sequences had to be adjusted until they looked maximally smooth and temporally correct. Observers very consistently preferred gaps (ellipses). Implications for film editing and film theory are discussed.
Quantum Dotting the “i” of Inquiry: A Guided Inquiry Approach to Teaching Nanotechnology

When illuminating four “mystery” vials of nanoparticle solution with a 405‐nm light emitting diode (LED), four distinct colors related to the peak wavelength of fluorescent emission can be observed.1 This phenomenon perplexes high school physics students and leads to the subsequent exploratory question, “Why are the four vials emitting a different color light if they all contain the same material and are illuminated with the same light source? ” That question gives students the opportunity to collect and analyze data, which leads to the development of the inherent scientific concept that the color of the emitted light depends on the size of the material (quantum dot) suspended in solution.