Miracle-dz/UniFAR-FTUs huggingface dataset:
No evidence for the radiation time lag model after whole genome duplications in Teleostei

The short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the evolutionary success of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of key innovations, although the evolutionary success would not become apparent until a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed evolutionary success after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to evolutionary success in fishes.
Differentiating Mixed-Member Electoral Systems

The increasing use of mixed-member electoral systems has led to an explosion of research attempting to specify their effects. Yet there has been no work on the economic policy effects of such systems, even though this has been a significant subject of debate for scholars analyzing other electoral systems. An analysis of mixed-member system policy effects is problematic, given the wide variation in institutional rules among different systems. This article attempts to determine whether the institutional differences between mixed-member majoritarian (MMM) and mixed-member proportional (MMP) systems lead to differences in policy outputs. The political economy literature finds that government expenditures are positively correlated with electoral system proportionality. Our statistical analysis of government expenditures in 17 mixed-member systems between 1990 and 2000 shows that MMP systems, which are more proportional than MMM systems, are correlated with higher levels of government spending. Thus the MMM-MMP distinction produces significant policy differences.
Formation of gallium arsenide nanostructures in Pyrex glass

In this paper, we report on a simple, low-cost process to grow GaAs nanostructures of a few nm diameter and ∼50 nm height in Pyrex glass wafers. These nanostructures were grown by sequential plasma activation of GaAs and Pyrex glass surfaces using a low-temperature hybrid plasma bonding technology in air. Raman analyses of the activated surfaces show gallium oxide and arsenic oxide, as well as suppressed non-bridging oxygen with aluminate and boroxol chains in glass. The flow of alkaline ions toward the cathode and the replacement of alkaline ions by Ga and As ions in glass result in the growth of GaAs nanostructures in nanopores/nanoscratches in glass. These nanopores/nanoscratches are believed to be the origin of the growth of the nanostructures. It was found that the length of the GaAs nanostructures may be controlled by an electrostatic force. Cross-sectional observation of the bonded interface using high-resolution transmission electron microscopy confirms the existence of the nanostructures. A possible application of the nanostructures in glass is a filtration system for biomolecules.
Epidermal growth factor receptor tyrosine kinase inhibitors as potential cancer chemopreventives.

Among the most important targets for chemopreventive intervention and drug development are deregulated signal transduction pathways, and protein tyrosine kinases are key components of these pathways. Loss of tyrosine kinase regulatory mechanisms has been implicated in neoplastic growth; indeed, many oncogenes code for either receptor or cellular tyrosine kinases. Because of its deregulation in many cancers (bladder, breast, cervix, colon, esophagus, head and neck, lung, and prostate), the epidermal growth factor receptor (EGFR) has been selected as a potential target for chemoprevention. Because growth factor networks are redundant, selective inhibition of signaling pathways activated in precancerous and cancerous cells should be possible. Requirements for specific EGFR inhibitors include specificity for EGFR, high potency, activity in intact cells, and activity in vivo. Inhibition of autophosphorylation is preferred, because it should result in total blockade of the signaling pathway. Inhibitors that compete with substrate rather than at the ATP-binding site are also preferable, because they are not as likely to inhibit other ATP-using cellular enzymes. Several classes of specific EGFR inhibitors have been synthesized recently, including structures such as benzylidene malononitriles, dianilinophthalimides, quinazolines, pyrimidines, [(alkylamino)methyl]-acrylophenones, enollactones, dihydroxybenzylaminosalicylates, 2-thioindoles, aminoflavones, and tyrosine analogue-containing peptides. A possible testing strategy for the development of these and other EGFR inhibitors as chemopreventive agents includes the following steps: (a) determine EGFR tyrosine kinase inhibitory activity in vitro; (b) evaluate EGFR specificity and selectivity (relative to other tyrosine kinases and other protein kinases); (c) determine inhibition of EGFR-mediated effects in intact cells; (d) determine inhibition of EGFR-mediated effects in vivo (e.g., in nude mouse tumor xenografts); and (e) determine chemopreventive efficacy in vivo (e.g., in the hamster buccal pouch or mouse or rat bladder).
Computing TCP Throughput in a UMTS Network

We compute the throughput obtained by a TCP connection in a UMTS environment. For downloading data at a mobile terminal, the packets of each TCP connection are stored in separate queues at the base station (node B). Also due to fragmentation of the TCP packets into Protocol Data Units (PDU) and link layer retransmissions of PDUs there can be significant delays at the queue of the node B. In such a scenario the existing models of TCP may not be sufficient. Thus, we provide a new approximate TCP model and also obtain new closed-form expressions of mean window size. Using these we obtain the throughput of a TCP connection which matches with simulations quite well.
Unconditioned- and Conditioned- Stimuli Induce Differential Memory Reconsolidation and β-AR-Dependent CREB Activation

Consolidated long-term fear memories become labile and reconsolidated upon retrieval by the presentation of conditioned stimulus (CS) or unconditioned stimulus (US). Whether CS-retrieval or US-retrieval will trigger different memory reconsolidation processes is unknown. In this study, we introduced a sequential fear conditioning paradigm in which footshock (FS) was paired with two distinct sounds (CS-A and CS-B). The treatment with propranolol, a β-adrenergic receptor (β-AR) antagonist, after US (FS)-retrieval impaired freezing behavior evoked by either CS-A or CS-B. Betaxolol, a selective β1-AR antagonist, showed similar effects. However, propranolol treatment after retrieval by one CS (e.g., CS-A) only inhibited freezing behavior evoked by the same CS (i.e., CS-A), not the other CS (CS-B). These data suggest that β-AR is critically involved in reconsolidation of fear memory triggered by US- and CS-retrieval, whereas β-AR blockade after US-retrieval disrupts more CS-US associations than CS-retrieval does. Furthermore, significant CREB activation in almost the whole amygdala and hippocampus was observed after US-retrieval, but CS-retrieval only stimulated CREB activation in the lateral amygdala and the CA3 of hippocampus. In addition, propranolol treatment suppressed memory retrieval-induced CREB activation. These data indicate that US-retrieval activates more memory traces than CS-retrieval does, leading to memory reconsolidation of more CS-US associations.
Investigating Ductile Failure at the Microscale in Engineering Steels: A Micromechanical Finite Element Model

In this study, we present a microstructure-based micromechanical model to quantify failure mechanisms in engineering steels. Crystal plasticity at the microscale, governed by crystallographic slip, is explicitly taken into account in the frame-work of continuum mechanics. Furthermore, it is assumed that material damage at the microscale is controlled by the accumulated equivalent plastic strain, such that failure occurs once this strain exceeds a threshold. Both single- and poly-crystalline materials containing sufficient numbers of grains are investigated under a representative macroscopic loading. The calibration of the present model relies on uniaxial tensile test data. Both austenitic stainless steels (such as 316H) and martensitic steels (such as P91) are examined to illustrate the application of the method. The micromechanical modelling provides insights into understanding of the mechanical response at the microscale in engineering steels.Copyright © 2012 by ASME
Discovering Semantic Data of Interest from Un-mappable Memory with Confidence

Uncovering semantic data of interest in memory pages without memory mapping information is an important capability in computer forensics. Existing memory mappingguided techniques do not work in that scenario as pointers in the un-mappable memory cannot be resolved and navigated. To address this problem, we present a probabilistic inference-based approach called DIMSUM to enable the recognition of data structure instances from un-mappable memory. Given a set of memory pages and the specification of a target data structure, DIMSUM will identify instances of the data structure in those pages with quantifiable confidence. More specifically, it builds graphical models based on boolean constraints generated from the data structure and the memory page contents. Probabilistic inference is performed on the graphical models to generate results ranked with probabilities. Our experiments with realworld applications on both Linux and Android platforms show that DIMSUM achieves higher effectiveness than nonprobabilistic approaches without memory mapping information.
Readability of Bangla News Articles for Children

Many news papers publish articles for children. Journalists use their experience and intuition to write these. They might not aware of readability of articles they write. There is no evaluation tool or method available to determine how appropriate these articles are for the target readers. In this paper, we evaluate difficulty of Bangla news articles that are written for children.
Overall quality assessment of SKOS thesauri: An AHP-based approach

The article proposes a methodology for a thesauri quality assessment that supports decision-makers in selecting thesauri by exploiting an overall quality measure. This measure takes into account the subjective perceptions of the decision-maker according to the reuse of thesauri in a specific application context. The analytic hierarchy process methodology is adopted to capture both subjective and objective facets involved in the thesauri quality assessment, thus providing a ranking of the thesauri assessed. Our methodology is applied to a set of thesauri by using user-driven application contexts. A step-by-step explanation of how the approach supports the decision process in the creation, maintenance and exploitation of a framework of linked thesauri is provided.
Age and National Institutes of Health Stroke Scale Score Within 6 Hours After Onset Are Accurate Predictors of Outcome After Cerebral Ischemia: Development and External Validation of Prognostic Models

Background and Purpose— To date, no validated, comprehensive, and practicable model exists to predict functional recovery within the first hours of cerebral ischemic symptoms. The purpose of this study was to externally validate 2 prognostic models predicting functional outcome and survival at 100 days within the first 6 hours after onset of acute cerebral ischemia. Methods— On admission to a participating hospital, patients were registered prospectively and included according to defined criteria. Follow-up was performed 100 days after the event. With the use of prospectively collected data, 2 prognostic models were developed and internally calibrated in 1079 patients and externally validated in 1307 patients. By means of age and National Institutes of Health Stroke Scale (NIHSS) score as independent variables, model I predicts incomplete functional recovery (Barthel Index <95) versus complete functional recovery, and model II predicts mortality versus survival. Results— In the validation data set, model I correctly predicted 62.9% of the patients who were incompletely restituted or had died and 83.2% of the completely restituted patients, and model II correctly predicted 57.9% of the patients who had died and 91.5% of the surviving patients. Both models performed better than the treating physicians’ predictions made within 6 hours after admission. Conclusions— The resulting prognostic models are useful to correctly stratify treatment groups in clinical trials and should guide inclusion criteria in clinical trials, which in turn increases the power to detect clinically relevant differences.
Very Few RNA and DNA Sequence Differences in the Human Transcriptome

RNA editing is an important cellular process by which the nucleotides in a mature RNA transcript are altered to cause them to differ from the corresponding DNA sequence. While this process yields essential transcripts in humans and other organisms, it is believed to occur at a relatively small number of loci. The rarity of RNA editing has been challenged by a recent comparison of human RNA and DNA sequence data from 27 individuals, which revealed that over 10,000 human exonic sites appear to exhibit RNA-DNA differences (RDDs). Many of these differences could not have been caused by either of the two previously known human RNA editing mechanisms—ADAR-mediated A→G substitutions or APOBEC1-mediated C→U switches—suggesting that a previously unknown mechanism of RNA editing may be active in humans. Here, we reanalyze these data and demonstrate that genomic sequences exist in these same individuals or in the human genome that match the majority of RDDs. Our results suggest that the majority of these RDD events were observed due to accurate transcription of sequences paralogous to the apparently edited gene but differing at the edited site. In light of our results it seems prudent to conclude that if indeed an unknown mechanism is causing RDD events in humans, such events occur at a much lower frequency than originally proposed.
UWB sequential Monte Carlo positioning using virtual anchors

We present a novel UWB indoor localization concept that performs the position estimation with a set of virtual anchor nodes, generated from a single physical anchor and floor plan information. Using range estimates to the virtual anchors, we perform multilateration to estimate the position of an agent. Previous work has shown the general applicability of this concept. In this contribution, we use a moving agent to exploit the correlation in successive positions using state-space concepts. A motion model for the agent and the measurement likelihood function allow for the use of the powerful framework of Bayesian state estimation. With this concept, we can propagate prior information on the agent position from one time step to the next. The statistical model for the ranging to the virtual anchors accounts for several imperfections, which lead to multimodal and heavy-tailed measurement distributions. We show how modified versions of the Kalman filter as well as a particle filter can account for these imperfections and yield accurate and robust position estimates. In a typical indoor pedestrian motion scenario, we can achieve an accuracy of about 45 cm for 90% of the estimates.
Effects of emulsifiers, sorbitol, polydextrose, and crystalline cellulose on the texture of reduced-calorie cakes

The textural and sensory qualities of reduced-calorie cakes prepared from non-shortening batters in which sucrose was partly replaced with sorbitol or poly-dextrose (with the addition of carboxymethylcellulose or microcrystalline cellulose to the latter) was studied. The batters were treated with different types and concentrations of emulsifier (Tandem 22H, Atlas A and MD-SSL). At the 30% replacement of sucrose with 1.5% or 3.5% (on flour weight) of Tandem 22H or Atlas A, the cakes were of an acceptable quality. Higher levels of emulsifier treatment further enhanced the aeration capacity of the batters, but impaired the overall quality of the final product. The emulsifier MD-SSL was found to be less suitable under the given conditions of cake baking because of the excessive aeration of batters. With cakes of acceptable quality, the calorie value reduction was in a 15 to 23% range compared with a standard full-calorie cake.
Cooperation and coordination in virtual enterprises: The role of e-collaboration tools

Virtual Enterprises are an emerging model for the organization of innovative enterprises. They are characterized by brief relationships and geographical dispersion of members. E-collaboration tools play a critical role in the integration of such organizational systems. In particular these tools support both cooperation and coordination. Cooperation has been defined as the problem of aligning goals among the members of an organization. Coordination, instead, includes those processes through which actors which share a common goal align their actions. Traditional organizations typically face these problems through slow and complex processes based on face to face interactions. Virtual enterprises, instead, have to develop techniques to rapidly integrate members which interact mainly through electronic channels. This paper discusses how e-collaboration tools can support cooperation and coordination in a virtual enterprise. The evolution of their role during a virtual enterprise life is described. Special attention is paid to the interaction between technological and organizational factors. 1. Virtual Enterprises: definitions and criticalities A widespread, stereotyped image identifies a traditional organization with a physical place, where people work close to each other. In this ideal organization working time is standard, relationships have a long term orientation, decision rights belong to the owners and are delegated along a univocal and well defined hierarchy. Even culture is considered as largely shared among members. As globalization, technological innovation and market turbulence challenge traditional business logic, firms are experimenting with new organizational models: the network organization [MS86] [NE92], the flexible firm [Vo96], the shamrock organization [Ha95].
ACR: An Adaptive Cost-Aware Buffer Replacement Algorithm for Flash Storage Devices

Flash disks are being widely used as an important alternative to conventional magnetic disks, although accessed through the same interface by applications, their distinguished feature, i.e., different read and write cost in the aspects of time, makes it necessary to reconsider the design of existing replacement algorithms to leverage their performance potential. Different from existing flash-aware buffer replacement policies that focus on the asymmetry of read and write operations, we address the “discrepancy” of the asymmetry for different flash disks, which is the fact that exists for a long time, while has drawn little attention by researchers since most existing flash-aware buffer replacement polices are somewhat based on the assumption that the cost of read operation is neglectable compared with that of write operation. In fact, this is not true for current flash disks on the market. We propose an adaptive cost-aware replacement policy (ACR) that uses three cost-based heuristics to select the victim page, thus can fairly make trade off between clean pages (their content remain unchanged) and dirty pages (their content is modified), and hence, can work well for different type of flash disks of large discrepancy. Further, in ACR, buffer pages are divided into clean list and dirty list, the newly entered pages will not be inserted at the MRU position of either list, but at some position in the middle, thus the once-requested pages can be flushed out from the buffer quickly and the frequently-requested pages can stay in buffer for a longer time. Such mechanism makes ACR adaptive to workloads of different access patterns. The experimental results on different traces and flash disks show that ACR not only adaptively tunes itself to workloads of different access patterns, but also works well for different kind of flash disks compared with existing methods.
Range extension for the common dolphin (Delphinus sp.) to the Colombian Caribbean, with taxonomic implications from genetic barcoding and phylogenetic analyses

The nearest known population of common dolphins (Delphinus sp.) to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W) during two separate efforts: (a) a seismic vessel survey (December 2009—March 2010), and (b) three coastal surveys from small boats (May—July 2012, May 2013, and May 2014). Here we document ten sightings of common dolphins collected during these surveys, which extend the known range of the species by ~1000 km into the southwestern Caribbean. We also collected nine skin biopsies in 2013 and 2014. In order to determine the taxonomic identity of the specimens, we conducted genetic barcoding and phylogenetic analyses using two mitochondrial markers, the Control Region (mtDNA) and Cytochrome b (Cytb). Results indicate that these specimens are genetically closer to the short-beaked common dolphin (Delphinus delphis) even though morphologically they resemble a long-beaked form (Delphinus sp.). However, the specific taxonomic status of common dolphins in the Caribbean and in the Western Atlantic remains unresolved. It is also unclear whether the distribution of the species between northern Colombia and eastern Venezuela is continuous or disjoined, or whether they can be considered part of the same stock.
Software Metrics Based on Coding Standards Violations

Software metrics is one of promise technique to capture the size and quality of products, development process in order to assess a software development. Many software metrics based on various aspects of a product and/or a process have been proposed. There is some research which discuss the relation between software metrics and faults to use these metrics as the indicator of quality. Most of these software metrics are based on structural features of products or process information related to explicit fault. In this paper, we focus on latent faults detected by static analysis techniques. The coding checker is widely used to find coding standards violations which are strongly relating to latent faults. In this paper, we propose new software metrics based on coding standards violations to capture latent faults in a development. We analyze two open source projects by using proposed metrics and discuss the effectiveness.