Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing Yeasts Phylogenies and Ancestors from Whole Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data Genome Data

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, and limited types of evolutionary events. Here, we provide an alternative way to resolve phylogenetic problems based on analyses of real genome data. We use phylogenetic signals from all types of genome level evolutionary events, and overcome the conflicting issues existing in traditional phylogenetic approaches. Further, we build an automated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolution real yeast genome datasets. Comparison results with recent studies and publications show that we reconstruct very accurate and robust phylogenies and ancestors. Finally, we identify and analyze the conserved syntenic blocks among reconstructed ancestral genomes and present yeast species. Phylogenetic studies used to be the domain of morphological area, and were based on outward appearances and internal structures 1 . Later, molecular characters and DNA sequencing technologies have augmented these studies in building robust phylogenies 2,3 , although they often yield conflicting results 4–8 . Because local and biased sequences may not be enough to represent the entire genome. These sequences may also evolve in distinct rates, and cause conflicting phylogenetic signals. Currently, the widely accepted phylogenetic approach to alleviate these conflicting issues is to analyze shared gene datasets, and concatenate/coalesce their results from multiple sequence alignments to obtain a final
Whole Body Tracking Interaction Evaluation

Sensors such as Kinect and leap motion have made whole body tracking a lot easier, and there has being an emergence and trend that the whole body tracking have interaction with computers. It is an interesting study to explore the ups and downs of this type of interaction. In addition, it cannot be denied that the ups and downs are related to the advantages and disadvantages of this type of interaction. However, how to assess the advantages and disadvantages is complicated because many factors need to be considered. We need to combine these factors and come up with a comprehensive function, at the same time, the method of assessment are supposed to be objective and accuracy. In this report, I will describe the literature review of seven articles related to whole body tracking interaction, and this file offers an integrated understanding of these related papers, especially focus on the analysis and evaluation of a whole body tracking interaction. Author
Effect of Baroclinicity on Double-Diffusive Interleaving

Although ocean fronts are often baroclinic, existing models of double-diffusive interleaving have ignored such baroclinic effects as velocity shear and horizontal density gradients. To determine the importance of these effects, the authors have formulated a linear instability analysis applicable to baroclinic fronts. Two limiting cases are considered: one for fronts with strong vertical and/or horizontal shear, the other for fronts with weak shear. In both limits, double-diffusive interleaving can be enhanced or suppressed by baroclinicity. Interleaving motion is enhanced if isopycnals rise toward the fresh side of the front. Conversely, interleaving is suppressed if isopycnals slope downward across the front. A significant result is that the salinity gradient along isopycnals is not a good indicator of interleaving strength. As an example, the model is applied to a Mediterranean salt lens. The effect of baroclinicity is significant: the predicted growth rates are increased by 35%‐90%. The large-scale velocity and hydrographic fields indicate that Meddy Sharon lies somewhere between the high- and low-shear limits. Nevertheless, the model predictions agree reasonably well with the observed interleaving characteristics.
METHODS AND MATERIAL 2 . 1 . Characterization of the Fluvial Marine Plains

Fluvial marine plains harbor environments with reduced declivity, but with different environmental attributes that may be relevant ecosystem services in their watersheds, which can be transformed into opportunities for the development of environmental services payments. This study digitally spatialized part of the ecosystem services related to water availability in the microbasins of the Guandu Basin Hydrographic Basin, the main source of water supply for the metropolitan region of Rio de Janeiro, based on geo-environmental factors and the effects of transposition of watersheds, in order to facilitate the formulation of public policies regarding environmental services. The excerpts with the highest potential for producing environmental services from subsurface water flows, Topographic Wetness Index-ITU (ITU > 11), flat formation and low altimetry (< 40 m), are close to the old silted thalwegs, which can be potentialized by the effects of transposition, notably in the APA Guandu conservation unit. These areas should be prioritized in public and private water systems’ preservation programs. The areas near the transposition canals feature environmental services that depend directly on the transposition, and may be subject to management, as found in Guandu conservation unit. Flat areas with (7<ITU< 11) have their ecosystem services transferred from subsurface water flows to surface water flows and are dependent more on meteorological phenomena and on ways to manage heavy rain showers through their use, especially as altimetry and slope increase.
Upper D region chemical kinetic modeling of LORE relaxation times

The recovery times of upper D region electron density elevations, caused by lightning‐induced electromagnetic pulses (EMP), are modeled. The work was motivated from the need to understand a recently identified narrowband VLF perturbation named LOREs, an acronym for LOng Recovery Early VLF events. LOREs associate with long‐living electron density perturbations in the upper D region ionosphere; they are generated by strong EMP radiated from large peak current intensities of ±CG (cloud to ground) lightning discharges, known also to be capable of producing elves. Relaxation model scenarios are considered first for a weak enhancement in electron density and then for a much stronger one caused by an intense lightning EMP acting as an impulsive ionization source. The full nonequilibrium kinetic modeling of the perturbed mesosphere in the 76 to 92 km range during LORE‐occurring conditions predicts that the electron density relaxation time is controlled by electron attachment at lower altitudes, whereas above 79 km attachment is balanced totally by associative electron detachment so that electron loss at these higher altitudes is controlled mainly by electron recombination with hydrated positive clusters H+(H2O)n and secondarily by dissociative recombination with NO+ ions, a process which gradually dominates at altitudes >88 km. The calculated recovery times agree fairly well with LORE observations. In addition, a simplified (quasi‐analytic) model build for the key charged species and chemical reactions is applied, which arrives at similar results with those of the full kinetic model. Finally, the modeled recovery estimates for lower altitudes, that is <79 km, are in good agreement with the observed short recovery times of typical early VLF events, which are known to be associated with sprites.
Neurophysiology of Tactile Perception : A Tribute to Steven Hsiao Genetically identified spinal interneurons integrating tactile afferents for motor control

Bui TV, Stifani N, Panek I, Farah C. Genetically identified spinal interneurons integrating tactile afferents for motor control. J Neurophysiol 114: 3050–3063, 2015. First published October 7, 2015; doi:10.1152/jn.00522. 2015. —Our movements are shaped by our perception of the world as communicated by our senses. Perception of sensory information has been largely attributed to cortical activity. However, a prior level of sensory processing occurs in the spinal cord. Indeed, sensory inputs directly project to many spinal circuits, some of which communicate with motor circuits within the spinal cord. Therefore, the processing of sensory information for the purpose of ensuring proper movements is distributed between spinal and supraspinal circuits. The mechanisms underlying the integration of sensory information for motor control at the level of the spinal cord have yet to be fully described. Recent research has led to the characterization of spinal neuron populations that share common molecular identities. Identification of molecular markers that define specific populations of spinal neurons is a prerequisite to the application of genetic techniques devised to both delineate the function of these spinal neurons and their connectivity. This strategy has been used in the study of spinal neurons that receive tactile inputs from sensory neurons innervating the skin. As a result, the circuits that include these spinal neurons have been revealed to play important roles in specific aspects of motor function. We describe these genetically identified spinal neurons that integrate tactile information and the contribution of these studies to our understanding of how tactile information shapes motor output. Furthermore, we describe future opportunities that these circuits present for shedding light on the neural mechanisms of tactile processing.
High-pressure/low-temperature metamorphism and the dynamics of an accretionary wedge

Summary The preservation and exhumation of high-pressure rocks is an important observation in understanding the geodynamics of orogenic processes. A numerical tool is developed to estimate quantitatively the effect of the complex interplay between the mechanical and thermodynamical behaviour, and to assess under which conditions the preservation of metastable denser phases is possible. A finite difference numerical method is used to solve the continuity, Navier–Stokes and thermal equations for a Newtonian compressible fluid medium. In the model we take into account a typical forcing induced by a subduction process in a collisional environment according to a corner flow model. We follow the evolution of different phases in the crust including a pressure–temperature-dependent phase transition in the numerical code. Although eclogite is formed at depth when the phase diagram is only prescribed from thermodynamics, it cannot reach the surface. The kinetic effects of thermally activated diffusion and of the nucleation processes are taken into account in the modelling of the phase transition. Our simplified model does not explicitly take into account the presence of water. It assumes that the rate of phase transformation can be computed from a knowledge of pressure, temperature and phase content. The parameters of the kinetic equations are empirically chosen to reproduce qualitatively the typical pressure–temperature–time paths recorded in the Alpine belt. To obtain significant concentrations of high-pressure phases at the surface, different activation energies for the prograde and retrograde reactions are needed. This difference may be related to changes in the water content of the crust between its burial and its exhumation.
Impact, scope of practice and competencies of Advanced Practice Nurses within APN-led models of care for young and middle-aged adult patients with multimorbidity and/or complex chronic conditions in hospital settings: a scoping review protocol

Introduction The increase of young and middle-aged adult patients with multimorbid and/or complex chronic conditions has created new challenges for healthcare systems and services. Advanced Practice Nurses (APNs) play an essential role in treating these patients because of their expertise and advanced nursing skills. Little is known about competencies, scope of practice and impact of APNs within APN-led care models for young and middle-aged adult patients with multimorbidity and/or complex chronic conditions in hospital settings. The objective of this scoping review is to describe the impact, scope of practice and competencies of APNs within APN-led care models for young and middle-aged adult patients in hospital settings. Methods and analysis This scoping review will be conducted using the methodological framework proffered by Arksey and O'Malley, incorporating the methodological enhancement of Levac et al. It will comply with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) for Scoping Reviews’ guidelines of Tricco et al. Systematic research will be conducted in the databases MEDLINE (PubMed), CINAHL (EBSCO), EMBASE (Ovid), CENTRAL and PsycINFO (Ovid) using all recognised keywords, index terms and search strings. Grey literature will be scanned. Bibliography of all selected studies will be hand searched. Studies will be selected based on defined inclusion and exclusion criteria, screened by title and abstracts. Data from full-text articles meeting the inclusion criteria will be extracted independently by two authors. Disagreements in evaluation will be discussed and resolved by consensus. Results will be reported in the form of descriptive tables. Narrative summery is used to present the results of the review in the context of the study’s objectives and questions. Ethics and dissemination This scoping review does not require ethics approval. The review will be handed in as part of a doctoral thesis and published in a peer-reviewed journal. Trial registration number OSF 4PM38.
Effects of biventricular shunt on pump characteristics in a maglev total artificial heart

Severe left ventricular failure can progress to right ventricular failure, necessitating alternatives to heart transplantation, such as total artificial heart (TAH) treatment. Conventional TAHs encounter challenges associated with miniaturization and hemocompatibility owing to their reliance on mechanical valves and bearings. A magnetically levitated TAH (IB-Heart) was developed, utilizing a magnetic bearing. The IB-Heart features a distinctive biventricular shunt channel situated between the flow paths of the left and right centrifugal blood pumps, simplifying and miniaturizing its control system. However, the impact of these shunt channels remains underexplored. This study aimed to investigate the effects of shunt flow on pump characteristics and assess the IB-Heart’s potential to regulate flow balance between systemic and pulmonary circulation. At a rotational speed of 2000 rpm and flow rate range of 0–10 L/min, shunt flow exhibited a minor impact, with a 1.4 mmHg (1.3%) effect on pump characteristics. Shunt flow variation of about 0.13 L/min correlated with a 10 mmHg pressure difference between the pumps’ afterload and preload conditions. This variance was linked to changes in the inlet flow rates of the left and right pumps, signifying the ventricular shunt structure’s capacity to mirror the function of an atrial shunt in alleviating pulmonary congestion. The IB-Heart’s ventricular shunt structure enables passive regulation of left-right flow balance. The findings establish a fundamental technical groundwork for the development of IB-Hearts and TAHs with similar shunt structures. The innovative coupling of centrifugal pumps and the resultant effects on flow dynamics contribute to the advancement of TAH technology.
Rayleigh-Wave Multipathing along the West Coast of North America

We have created a movie of surface ground motion for the 3 November 2002 Denali fault earthquake based on spectral-element simulations using crustal model CRUST2.0, mantle model S20RTS, topography and bathymetry model ETOPO5, and a finite-fault slip model. The movie features two anomalous wave packets that travel along the west coast of the North American plate following off- great-circle paths. These wave packets are Rayleigh waves with dominant periods around 20 sec, which are also found in seismograms recorded by the Southern Cali- fornia Seismic Network. One of these packets is the direct surface wave, whose group arrival time changes laterally as dictated by the shape of the Oregon coast. The other packet is a surface wave reflected by a lateral interface underneath the Rocky Moun- tains. A linear reflector parallel to the Canadian coast offsetting it by a few hundred kilometers can explain its arrival time, but the offsetting distance derived from the synthetic seismograms puts the reflector 350 km northeast of the result obtained from the data, indicating a need to update the crustal and mantle models in this area. Online material: Animation of normalized simulated vertical displacement for the 2002 Denali earthquake.
National debt management and business sustainability in Africa’s largest economy: A focus on the private sector

In many developing economies, high and increasing public debt profile constitutes an essential means of financial risk. An appropriate debt management is germane for survival of business and good international reputation though its effect on private sector credit mobilization had been seldomly investigated. This study seeks to know whether strategic debt management approach exacts a significant effect on the Nigerian private sector and Africa at large resulting to higher credit availability for sustainable enterprise establishment. The study used a time-series observation spanning from 1981–2021. The method of data analysis employed the unit root test for stationarity. Johansen cointegration and vector error correction approach. The result of the unit root test indicates the series were all stationary after first difference and thus were integrated of order1. The Johansen cointegration test support the existence of a cointegrating series between the private credit and its determinants. More empirical evidence from the study shows that proper debt management and increase revenue generation through net taxes on products accounted for 0.93 and 1.32% increase in private sector credit mobilization, while total external debt stock was responsible for a significant negative influence of 0.60% on private sector credit mobilization. The study recommends that the government should always be proactive in their strategic and innovative approach to debt management, revenue generation and sources of funds. This will help not only to avoid crowding out of the private sector but will enhance adequate credit mobilization for effective operations of the private sector.
Application of Contactless Conductivity Detection to Ice Core Analysis

Ice cores enclose a variety climate proxies that are extremely valuable for understanding the past climate of our planet. These proxies include trace gases, salts, dust, stable isotopes and acids. Salts, dust and acids can originate from many different sources, and each one of them indicates a certain atmospheric and environmental condition. Continuous Flow Analysis (CFA) is a method of measuring these chemical impurities by analyzing the meltwater that derives from melting a certain piece cut from the ice core. The CFA system includes a dust detector, for measuring the dust that is incorporated into the ice, the absorption and fluorescence detective methods that measure the concentration of certain ionic species and a conductivity meter that measures the conductivity of the meltwater, which is the bulk of its ionic constituents. In this project, the EDAQ C4D conductivity detector was tested for discrete and continuous measurements of conductivity standards in the range of the conductivity values typically found in the ice cores. The output of the instrument is voltage, which depends on the frequency of the input AC voltage. For discrete measurements the response of the instrument is dominated by a high peak matching with the 859kHz frequency and a broad maximum, whose location in the frequency range depends on the value of conductivity measured, and the type of tube used. The wide range maximum lies in the interval 8-48kHz and shifts towards the lower frequencies as the value of conductivity decreases. For continuous measurements the instrument is set to measure in the frequency, which gives a linear relation between the voltage output and the conductivity value of the standard. This is found to be f = 19219Hz for clear PFA tube of I.D. =0.03’’. Then the EDAQ C4D system was applied to analyze the conductivity of the shallow South Dome ice core from Greenland. The results are compared with the Model Series 380, a standard instrument for electrical conductivity detection, and with other detection methods of the CFA system as well. The comparison of the measurements of the two instruments, EDAQ C4D and Model 382 Series showed that there is a linear relation of high correlation, between them for the certain voltage interval of 0.1V to 0.5V. This upper limit is apparent in the discrete measurements too. Moreover the EDAQ C4D exhibits a faster response in conductivity changes. The dust and conductivity profiles obtained from the shallow South Dome ice core are compared to the dust and conductivity profiles of the upper part of the NEGIS shallow ice core. Conductivity and dust lie within a certain range respectively, however there are some notable differences that could be due attributed to the different precipitation rates of the geographical areas of origination for the two ice cores.