Miracle-dz/UniFAR-FTUs huggingface dataset:
Palynomorphs from a lacustrine sequence provide evidence for palaeoenvironmental changes during the early Miocene in Central Anatolia, Turkey

Pollen samples belonging to 54 plant taxa from 32 intervals in a 59 m thick lacustrine sequence in the Harami open pit lignite mine in Konya Province, Turkey, were studied to evaluate early Miocene (Aquitanian) changes in vegetation, climate, and environments in Central Anatolia. The regional vegetation consisted of forests, whose composition changed through time. An abundance of sub-tropical and warm-temperate, mainly deciduous trees in the lower part of Harami section indicates a warm and humid climate in the region during the earliest Miocene. A trend towards cooler and drier conditions, driven by a combination of regional and local factors, is reflected by the sequential establishment of two kinds of coniferous forests: a cedar (Cedrus) dominated forest in the middle part of the section, followed by a mixed cedar and pine (Pinus) forest in the upper part of the section. The high percentages of Cedrus in the middle and upper portions of the Harami section suggest that high-elevation coniferous forests .
Basics, common errors and essentials of statistical tools and techniques in anesthesiology research

The statistical portion is a vital component of any research study. The research methodology and the application of statistical tools and techniques have evolved over the years and have significantly helped the research activities throughout the globe. The results and inferences are not accurately possible without proper validation with various statistical tools and tests. The evidencebased anesthesia research and practice has to incorporate statistical tools in the methodology right from the planning stage of the study itself. Though the medical fraternity is well acquainted with the significance of statistics in research, there is a lack of in-depth knowledge about the various statistical concepts and principles among majority of the researchers. The clinical impact and consequences can be serious as the incorrect analysis, conclusions, and false results may construct an artificial platform on which future research activities are replicated. The present tutorial is an attempt to make anesthesiologists aware of the various aspects of statistical methods used in evidence-based research and also to highlight the common areas where maximum number of statistical errors are committed so as to adopt better statistical practices.
The calcium paradox - What should we have to fear?

The calcium paradox was first mentioned in 1966 by Zimmerman et al. Thereafter gained great interest from the scientific community due to the fact of the absence of calcium ions in heart muscle cells produce damage similar to ischemia-reperfusion. Although not all known mechanisms involved in cellular injury in the calcium paradox intercellular connection maintained only by nexus seems to have a key role in cellular fragmentation. The addition of small concentrations of calcium, calcium channel blockers, and hyponatraemia hypothermia are important to prevent any cellular damage during reperfusion solutions with physiological concentration of calcium.
Minimizing CPU energy in real-time systems with discrete speed management

This article presents a general framework to analyze and design embedded systems minimizing the energy consumption without violating timing requirements. A set of realistic assumptions is considered in the model in order to apply the results in practical real-time applications. The processor is assumed to have as a set of discrete operating modes, each characterized by speed and power consumption. The energy overhead and the transition delay incurred during mode switches are considered. Task computation times are modeled with a part that scales with the speed and a part having a fixed duration, to take I/O operations into account. The proposed method allows to compute the optimal sequence of voltage/speed changes that approximates the minimum continuous speed, which guarantees the feasibility of a given set of real-time tasks, without violating the deadline constraints. The analysis is performed both under fixed and dynamic priority assignments.
Algorithms for routing and centralized scheduling to provide QoS in IEEE 802.16 mesh networks

We consider the problem of routing and centralized scheduling for IEEE 802.16 mesh networks. We first fix the routing, which reduces the network to a tree. We then present scheduling algorithms which provide per flow QoS (Quality of Service) guarantees to real and interactive data applications while utilizing the network resources efficiently. Our algorithms are also scalable: they do not require per flow processing and queueing and the computational requirements are minimal. We also discuss admission control policies which ensure that sufficient resources are available. We have verified our algorithms via extensive simulations.
This Reprint May Differ from the Original in Pagination and Typographic Detail. the Evolution, Diversity, and Host Associations of Rhabdoviruses

All material supplied via JYX is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user. Abstract Metagenomic studies are leading to the discovery of a hidden diversity of RNA viruses. These new viruses are poorly characterized and new approaches are needed predict the host species these viruses pose a risk to. The rhabdoviruses are a diverse family of RNA viruses that includes important pathogens of humans, animals, and plants. We have discovered thirty-two new rhabdoviruses through a combination of our own RNA sequencing of insects and searching public sequence databases. Combining these with previously known sequences we reconstructed the phylogeny of 195 rhabdovirus sequences, and produced the most in depth analysis of the family to date. In most cases we know nothing about the biology of the viruses beyond the host they were identified from, but our dataset provides a powerful phylogenetic approach to predict which are vector-borne viruses and which are specific to vertebrates or arthropods. By reconstructing ancestral and present host states we found that switches between major groups of hosts have occurred rarely during rhabdovirus evolution. This allowed us to propose seventy-six new likely vector-borne vertebrate viruses among viruses identified from vertebrates or biting insects. Based on currently available data, our analysis suggests it is likely there was a single origin of the known plant viruses and arthropod-borne vertebrate viruses, while vertebrate-and arthropod-specific viruses arose at least twice. There are also few transitions between aquatic and terrestrial ecosystems. Viruses also cluster together at a finer scale, with closely related viruses tending to be found in closely related hosts. Our data therefore suggest that throughout their evolution, rhabdoviruses have occasionally jumped between distantly related host species before spreading through related hosts in the same environment. This approach offers a way to predict the most probable biology and key traits of newly discovered viruses.
Hemoglobin and heme scavenging

Release of hemoglobin into plasma is a physiological phenomenon associated with intravascular hemolysis. In plasma, stable haptoglobin‐hemoglobin complexes are formed and these are subsequently delivered to the reticulo‐endothelial system by CD163 receptor‐mediated endocytosis. Heme arising from the degradation of hemoglobin, myoglobin, and of enzymes with heme prosthetic groups could be delivered in plasma. Albumin, haptoglobin, hemopexin, and high and low density lipoproteins cooperate to trap the plasma heme, thereby ensuring its complete clearance. Then hemopexin releases the heme into hepatic parenchymal cells only after internalization of the hemopexin‐heme complex by CD91 receptor‐mediated endocytosis. Moreover, α1‐microglobulin contributes to heme degradation by a still unknown mechanism, with the concomitant formation of heterogeneous yellow‐brown kynurenine‐derived chromophores which are very tightly bound to amino acid residues close to the rim of the lipocalin pocket. During hemoglobin synthesis, the erythroid α‐chain hemoglobin‐stabilizing protein specifically binds free α‐hemoglobin subunits limiting the free protein toxicity. Although highly toxic because capable of catalyzing free radical formation, heme is also a major and readily available source of iron for pathogenic organisms. Gram‐negative bacteria pick up the heme‐bound iron through the secretion of a hemophore that takes up either free heme or heme bound to heme‐proteins and transports it to a specific receptor, which, in turn, releases the heme and hence iron into the bacterium. Here, hemoglobin and heme trapping mechanisms are summarized. IUBMB Life, 57: 749‐759, 2005
Identification of subpopulations of prairie voles differentially susceptible to peer influence to decrease high alcohol intake

Peer influences are critical in the decrease of alcohol (ethanol) abuse and maintenance of abstinence. We previously developed an animal model of inhibitory peer influences on ethanol drinking using prairie voles and here sought to understand whether this influential behavior was due to specific changes in drinking patterns and to variation in a microsatellite sequence in the regulatory region of the vasopressin receptor 1a gene (avpr1a). Adult prairie voles’ drinking patterns were monitored in a lickometer apparatus that recorded each lick a subject exhibited during continuous access to water and 10% ethanol during periods of isolation, pair housing of high and low drinkers, and subsequent isolation. Analysis of fluid consumption confirmed previous results that high drinkers typically decrease ethanol intake when paired with low drinkers, but that a subset of voles do not decrease. Analysis of bout structure revealed differences in the number of ethanol drinking bouts in the subpopulations of high drinkers when paired with low drinkers. Lickometer drinking patterns analyzed by visual and by cross-correlation analyses demonstrated that pair housing did not increase the rate of subjects drinking in bouts occurring at the same time. The length of the avpr1a microsatellite did not predict susceptibility to peer influence or any other drinking behaviors. In summary, subpopulations of high drinkers were identified, by fluid intake and number of drinking bouts, which did or did not lower their ethanol intake when paired with a low drinking peer, and these subpopulations should be explored for testing the efficacy of treatments to decrease ethanol use in groups that are likely to be responsive to different types of therapy.
Little string theory from a double-scaled matrix model

Following Lin and Maldacena, we find exact supergravity solutions dual to a class of vacua of the plane wave matrix model by solving an electrostatics problem. These are asymptotically near-horizon D0-brane solutions with a throat associated with NS5-brane degrees of freedom. We determine the precise limit required to decouple the asymptotic geometry and leave an infinite throat solution found earlier by Lin and Maldacena, dual to Little String Theory on S5. By matching parameters with the gauge theory, we find that this corresponds to a double scaling limit of the plane wave matrix model in which N→∞ and the 't Hooft coupling λ scales as ln4(N), which we speculate allows all terms in the genus expansion to contribute even at infinite N. Thus, the double-scaled matrix quantum mechanics gives a Lagrangian description of Little String Theory on S5, or equivalently a ten-dimensional string theory with linear dilaton background.
Simple Shapes Elicit Different Emotional Responses in Children with Autism Spectrum Disorder and Neurotypical Children and Adults

According to the literature, simple shapes induce emotional responses. Current evaluations suggest that humans consider angular shapes as “bad” and curvilinear forms as “good,” but no behavioral data are available to support this hypothesis. Atypical development, such as autism spectrum disorder (ASD), could modify humans’ perception of visual stimuli and thereby their emotional effect. This study assessed the effects of simple stimuli (i.e., jagged edges shape, disk, star, spiral, eye-like shape, and head character) on the emotional responses of different groups of humans. First, we assessed the effects of a looming movement on neurotypical adults’ emotional responses. Second, we assessed the effects of atypical development on emotional responses by comparing the reactions of neurotypical children and of children with ASD. We used different methodological approaches: self-evaluation through questionnaires and direct observation of participants’ behavior. We found that (1) neurotypical adults tended to perceive looming stimuli negatively as they associated more negative feelings with them although few behavioral responses could be evidenced and (2) the emotional responses of neurotypical children and of children with ASD differed significantly. Neurotypical children perceived the spiral stimulus positively, i.e., a curvilinear shape, whereas children with ASD perceived the jagged edges stimulus positively, i.e., an angular shape. Although neurotypical children and children with ASD presented some behavioral responses in common, children with ASD smiled and vocalized more than did neurotypical children during stimuli presentations. We discuss our results in relation to the literature on humans’ perception of simple shapes and we stress the importance of studying behavioral components for visual cognition research.
Model-Based Analysis of Flow-Mediated Dilation and Intima-Media Thickness

We present an end-to-end system for the automatic measurement of flow-mediated dilation (FMD) and intima-media thickness (IMT) for the assessment of the arterial function. The video sequences are acquired from a B-mode echographic scanner. A spline model (deformable template) is fitted to the data to detect the artery boundaries and track them all along the video sequence. The a priori knowledge about the image features and its content is exploited. Preprocessing is performed to improve both the visual quality of video frames for visual inspection and the performance of the segmentation algorithm without affecting the accuracy of the measurements. The system allows real-time processing as well as a high level of interactivity with the user. This is obtained by a graphical user interface (GUI) enabling the cardiologist to supervise the whole process and to eventually reset the contour extraction at any point in time. The system was validated and the accuracy, reproducibility, and repeatability of the measurements were assessed with extensive in vivo experiments. Jointly with the user friendliness, low cost, and robustness, this makes the system suitable for both research and daily clinical use.
Design of 100Gbps double transverse coupled cavity VCSELs

We present a novel design of double-transverse-coupled-cavity VCSELs toward ultrahigh speed modulations of 100Gbps. In-plane lateral optical feedback in both cavities enables the large bandwidth enhancement of direct modulations. Clear eye opening can be observed up to 100Gbps and the frequency chirp is reduced by a factor more than two.
A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing

Copy number variations (CNVs), a common genomic mutation associated with various diseases, are important in research and clinical applications. Whole genome amplification (WGA) and massively parallel sequencing have been applied to single cell CNVs analysis, which provides new insight for the fields of biology and medicine. However, the WGA-induced bias significantly limits sensitivity and specificity for CNVs detection. Addressing these limitations, we developed a practical bioinformatic methodology for CNVs detection at the single cell level using low coverage massively parallel sequencing. This method consists of GC correction for WGA-induced bias removal, binary segmentation algorithm for locating CNVs breakpoints, and dynamic threshold determination for final signals filtering. Afterwards, we evaluated our method with seven test samples using low coverage sequencing (4∼9.5%). Four single-cell samples from peripheral blood, whose karyotypes were confirmed by whole genome sequencing analysis, were acquired. Three other test samples derived from blastocysts whose karyotypes were confirmed by SNP-array analysis were also recruited. The detection results for CNVs of larger than 1 Mb were highly consistent with confirmed results reaching 99.63% sensitivity and 97.71% specificity at base-pair level. Our study demonstrates the potential to overcome WGA-bias and to detect CNVs (>1 Mb) at the single cell level through low coverage massively parallel sequencing. It highlights the potential for CNVs research on single cells or limited DNA samples and may prove as a promising tool for research and clinical applications, such as pre-implantation genetic diagnosis/screening, fetal nucleated red blood cells research and cancer heterogeneity analysis.
Macroscopic cloud properties in the WRF NWP model: An assessment using sky camera and ceilometer data

The ability of six microphysical parameterizations included in the Weather Research and Forecasting (WRF) numerical weather prediction (NWP) model to represent various macroscopic cloud characteristics at multiple spatial and temporal resolutions is investigated. In particular, the model prediction skills of cloud occurrence, cloud base height, and cloud cover are assessed. When it is possible, the results are provided separately for low‐, middle‐, and high‐level clouds. The microphysical parameterizations assessed are WRF single‐moment six‐class, Thompson, Milbrandt‐Yau, Morrison, Stony Brook University, and National Severe Storms Laboratory double moment. The evaluated macroscopic cloud properties are determined based on the model cloud fractions. Two cloud fraction approaches, namely, a binary cloud fraction and a continuous cloud fraction, are investigated. Model cloud cover is determined by overlapping the vertically distributed cloud fractions following three different strategies. The evaluation is conducted based on observations gathered with a ceilometer and a sky camera located in Jaén (southern Spain). The results prove that the reliability of the WRF model mostly depends on the considered cloud parameter, cloud level, and spatiotemporal resolution. In our test bed, it is found that WRF model tends to (i) overpredict the occurrence of high‐level clouds irrespectively of the spatial resolution, (ii) underestimate the cloud base height, and (iii) overestimate the cloud cover. Overall, the best cloud estimates are found for finer spatial resolutions (1.3 and 4 km with slight differences between them) and coarser temporal resolutions. The roles of the parameterization choice of the microphysics scheme and the cloud overlapping strategy are, in general, less relevant.
An evolutionary approach to network-on-chip mapping problem

The paper addresses the problem of topological mapping of intellectual properties (IPs) on the tiles of a mesh-based network on chip (NoC) architecture. The aim is to obtain the Pareto mappings that maximize performance and minimize the amount of power consumption. As the problem is an NP-hard one, we propose a heuristic technique based on evolutionary computing to obtain an optimal approximation of the Pareto-optimal front in an efficient and accurate way. At the same time, two of the most widely-known approaches to mapping in mesh-based NoC architectures are extended in order to explore the mapping space in a multi-criteria mode. The approaches are then evaluated and compared, in terms of both accuracy and efficiency, on a platform based on an event-driven trace-based simulator which makes it possible to take account of important dynamic effects that have a great impact on mapping. The evaluation performed on real applications (an MPEG-4 codec) confirms the efficiency, accuracy and scalability of the proposed approach
Contribution of p 16 INK 4 a and p 21 CIP 1 pathways to induction of premature senescence of human endothelial cells : permissive role of p 53

Chen, Jun, Xuan Huang, Dorota Halicka, Sergey Brodsky, Ari Avram, Jonathan Eskander, Noah A. Bloomgarden, Zbigniew Darzynkiewicz, and Michael S. Goligorsky. Contribution of p16 and p21 pathways to induction of premature senescence of human endothelial cells: permissive role of p53. Am J Physiol Heart Circ Physiol 290: H1575–H1586, 2006. First published October 21, 2005; doi:10.1152/ajpheart.00364. 2005. —We have previously found that nonenzymatically glycated collagen I (GC), mimicking diabetic microenvironment, can induce senescent phenotype in early passage human umbilical vein endothelial cells (HUVECs). In the present study, we explored the functional involvement of cell cycle checkpoint pathways in initiating GC-induced premature endothelial cell senescence. When compared with native collagen, early passage HUVECs showed increased p53, p21 (p21), and p16 (p16) mRNA expression after exposure to GC. Twenty-four hours after transfection of p16, p21, and p53-enhanced green fluorescent protein (EGFP) recombinant plasmids, HUVECs entered G1-phase cell cycle arrest. By days 3 and 5, HUVECs transfected with p16-EGFP showed an increased proportion of senescent cells, and this increase was more prominent in the GFP-positive cell population, which exhibited 68% of senescent cells. Transfection of p21 also induced senescence but only by day 5. Cotransfection of p16 and p21 showed no additive effect. Transfection of p21 or p53 induced apoptosis in HUVECs. Next, we suppressed endogenous p53, p21, p16, or retinoblastoma (Rb) gene expression through small interference RNA strategy and investigated their influence in p16and p21-initiated endothelial cell senescence. Analysis indicated that suppression of p53 expression can abolish senescence induced by p16 overexpression. Paradoxically, this effect was not observed when p21 was suppressed. On the other hand, suppression of Rb eliminated senescence initiated by either p16 or p21 overexpression. In summary, the p53/p21 pathway is mainly responsible for GC-induced apoptosis, but the coordinated activation of the p53/p21 and p16 pathway is responsible for GC-induced endothelial cell senescence through a Rb-dependent mechanism.