Miracle-dz/UniFAR-FTUs huggingface dataset:
The prediction of exons through an analysis of spliceable open reading frames

We have developed a computer program which predicts internal exons from naive genomic sequence data and which will run on any IBM-compatible 80286 (or higher) computer. The algorithm searches a sequence for 'spliceable open reading frames' (SORFs), which are open reading frames bracketed by suitable splice-recognition sequences, and then analyzes the region for codon usage. Potential exons are stratified according to the reliability of their prediction, from confidence levels 1 to 5. The program is designed to predict internal exons of length greater than 60 nucleotides. In an analysis of 116 genes of a training set, 384 out of 441 such exons (87.1%) are identified, with 280 (63.5%) of predictions matching the true exon exactly (at both 5' and 3' splice junctions and in the correct reading frame), and with 104 (23.6%) exons matching partially. In a similar analysis of 14 genes in a test set unrelated to the genes used to generate the parameters of the program, 70 out of 80 internal exons greater than 60 bp in length are identified (87.5%), with 47 completely and 23 partially matched. SORFs that partially match true internal exons share at least one splice junction with the exon, or share both splice junctions but are interpreted in an incorrect reading frame. Specificity (the percentage of SORFs that correspond to true exons) varies from 91% at confidence level 1 to 16% at confidence level 5, with an overall specificity of 35-40%. The output displays nucleotide position, confidence level, reading frame phase at the 5' and 3' ends, acceptor and donor sequences and scoring statistics and also gives an amino acid translation of the potential exon. SORFIND compares favourably with other programs currently used to predict protein-coding regions.
Singularity analysis of closed-loop kinematic chains

The different kinds of singularities encountered in closed-loop kinematics chains are analyzed. A general classification of these singularities in three main groups, which is based on the properties of the Jacobian matrices of the chain, is described. The identification of the singular configurations is particularly relevant for hard automation modules or robotic devices based on closed kinematic chains, such as linkages and parallel manipulators. Examples are given to illustrate the application of the method to these mechanical systems. >
A Reconfigurable 10-to-12-b 80-to-20-MS/s Bandwidth Scalable SAR ADC

An asynchronous successive approximation register analog-to-digital converter (ADC) for wideband multi-standard systems is presented. The ADC can be configured as an 80-MS/s 10-b, 40-MS/s 11-b, or 20-MS/s 12-b converter. Time-interleaved technique is applied to expand sampling bandwidth exponentially while resolution scales down. The channel mismatches are cancelled by the digital calibration technique. The bulk-biasing technique is used in the sampling switch to reduce the influence of the charge injection caused by the top-plate sampling. In addition, the configurable asynchronous processing is employed to extend the flexibility of speed and resolution tradeoff. Moreover, the two-step digital-to-analog converter (DAC) switching method is proposed to reduce the switching energy of the DAC. Prototyped in 180-nm CMOS process, the ADC achieves the 56.7-/61.2-/64.6-dB signal-to-noise and distortion ratio (SNDR) and 72.3-/74.8-/75.5-dB spurious-free dynamic range (SFDR) at 80-/40-/20-MHz sampling frequency with the power consumption of 2.61/2.05/1.77 mW.
An Empirical Study of Routing Bias in Variable-Degree Networks

Recent work on Internet measurement and topology characterization has revealed a feature sharply distinct from the early Erdős-Rényi random graph model: highly variable degree distributions which arguably follow power-laws. Such properties may significantly affect various network algorithms and protocols. This paper explores whether and how degree variability causes routing bias, a phenomenon that routing algorithms may strongly favor nodes with better connectivity. This paper demonstrates that in variable-degree networks, including both synthetic networks and measured Internet topologies, there is a super-linear preference for routing algorithms to choose high-degree nodes in routing decision; in addition, the level of such preference remarkably depends on the degree variability of the network. Empirical study shows that the probability of routing through a node with degree d is approximately proportional to d, where 1 < θ < 2 and its value is larger when degree variability is lower. These findings are important to various network practices, including traffic provisioning, routing algorithm design, and network measurement. In particular, this paper illustrates that in traceroute-based topology discovery, routing bias implies that links associated to less well-connected nodes are less likely to be discovered. Hence, routing bias can become an important contributor to the incompleteness of measured router-level topologies.
SDN-enabled Traffic Engineering and Advanced Blackholing at IXPs

While the clean slate approach proposed by Software Defined Networking (SDN) promises radical changes in the stagnant state of network management, SDN innovation has not gone beyond the intra-domain level. For the inter-domain ecosystem to benefit from the advantages of SDN, Internet Exchange Points (IXPs) are the ideal place: a central interconnection hub through which a large share of the Internet can be affected. In this demo, we showcase the ENDEAVOUR platform: a new software defined exchange approach readily deployable in commercial IXPs. We demonstrate here our implementations of traffic engineering and Distributed Denial of Service mitigation, as well as how member networks cash in on the advanced SDN-features of ENDEAVOUR, typically not available in legacy networks.
Spinal neurons specifically excited by noxious or thermal stimuli: marginal zone of the dorsal horn.

HIGH-THRESHOLD MECHANORECEPTORS and their centrally projecting myelinated fibers make up a functionally distinct group of cutaneous sensory units that have been suggested as part of the afferent apparatus for pain resulting from mechanical damage to the skin (3, 17). The argument for their relation to pain was based on two points: 1) the ability of such afferent elements, unique among those with medullated fibers, to provide signals differentiating noxious from innocuous mechanical events affecting the skin; and 2) the well-established correlation between pain and activity in thin myelinated afferent fibers
Hyperammonemia induced oxidative stress in cirrhotic rats without promoting differential protein expression in the brain cortex: A 2D-DIGE analysis

Oxidative stress induced by a high ammonia concentration could modify protein expression in the brain. This study was undertaken in order to investigate the impact of hyperammonemia, caused by thioacetmide (TAA) in rats, on brain cortex protein expression using 2D-DIGE, and analyzing its role in the pathogenesis of HE. Hyperammonemia was induced with TAA. Ammonia and active oxidants were measured by L-glutamate dehydrogenase and dichlorodihydrofluorescein diacetate methods, respectively. Lipid peroxidation and protein oxidation biomarkers were also studied. Differential protein expression in the cortex of TAA- and control-rats was studied by 2D-DIGE. Image analysis was performed using the DeCyder? Software. Ammonia concentration in plasma and brain tissue was higher in TAA-rats compared to control-rats, 3.12 and 2.43 fold higher, respectively. Active oxidants production in TAA-rats was increased by 2.7 fold compared to control-rats. Measurements of MDA, HNE and carbonyl groups, biomarkers of lipid peroxidation and protein oxidation respectively, were found to be statistically significantly increased in TAA-rats compared to control-rats (3.16-, 2.44- and 1.95-fold, respectively), reflecting the presence of oxidative stress in the brain of TAA-rats. 2D-DIGE analysis of brain cortex protein allowed the detection of 2896 spots, however, image analysis showed no statistically significant differential protein expression between the proteins expressed in TAA- and control-rats. No statistical significant differential protein expression in the cortex of TAA-rats was observed, although oxidative stress biomarkers for lipid and proteins were higher in the brain of TAA-rats than in control-rats. These results support the idea that oxidative post-translational modifications are implicated in HE physiopathology.
Index OCA - aplikace na země EU10

The purpose of this article is to identify, which of the new EU member countries is, in accordance with Optimum Currency Area (OCA) theory, appropriate candidate of the euro area membership. The author uses the OCA index to consider the suitability of monetary union membership. The OCA index is calculated for the EU10 countries and four selected traditional EU member states. The author concludes that, according to the OCA index, the Czech Republic is the best candidate for membership of the euro area. In the period 1999–2009, this amounted better value of the OCA index with the euro area than Austria and the Netherlands. Least suitable candidates are, according to the conclusions of the article, the Baltic countries.
Efficient Near-Duplicate Detection for Q&A Forum

This paper addresses the issue of redundant data in large-scale collections of Q&A forums. We propose and evaluate a novel algorithm for automatically detecting the near-duplicate Q&A threads. The main idea is to use the distributed index and Map-Reduce framework to calculate pair-wise similarity and identify redundant data fast and scalably. The proposed method was evaluated on a real-world data collection crawled from a popular Q&A forum. Experimental results show that our proposed method can eﬀectively and eﬃciently detect near-duplicate content in large web collections.
Improving Chronic Wound Healing

Wounds, especially chronic wounds, remain an agonizing dilemma in every country of the world, costing America alone more than $20 billion annually to treat. Diabetics are in even higher risk of suffering a chronic wound than non-diabetics, and have a 15% higher chance of amputation [1]. Therefore, cheaper and more effective treatments for wounds are continuously being sought after, but there is still plenty of room for improvement. Our goal was to improve on already-existent technologies to better chronic wound healing for normal as well as diabetic patients. To accomplish this, we tested the effects of stromal cell-derived factor-1 (SDF-1), a chemokine, on the migration of HL-60 cells, white blood cells (neutrophils), mouse cells, and diabetic mouse cells with and without Integra , a clinically-used skin substitute. HL-60 and the two types of mouse cells possess CRCX4, a receptor that binds with SDF-1, and should therefore migrate towards the chemokine. Neutrophils, however, do not possess the receptor and should move away from SDF-1. Tests were conducted using small transwells (membrane inserts used for cell cultures) with microscopic pores, which allowed cells to migrate across to different concentrations of SDF-1. We found that SDF-1 shows promise in the fight against chronic wounds. Without the presence of the skin substitute, a higher percentage of cells migrated to a solution of 200ng SDF-1/mL (16.500%) than to a solution without any SDF-1 (5.625%). With a skin substitute, more cells migrated to a 100ng SDF-1/mL solution (42.75%) than to a solution without SDF-1 (15.00%). SDF-1 concentrations had minimal effect on the migration of neutrophils, high concentrations of which could prevent wounds from closing correctly. SDF-1 attracted both normal and diabetic mouse cells, seeming to affect diabetic mouse cells (143.75%) more than normal mouse cells (93.13%) at a concentration of 200 ng/mL SDF-1. SDF-1 definitely stands as a possibility for bettering chronic wound healing in the future.
New plesiosaurs from the Upper Cretaceous of Antarctica

Abstract New plesiosaur remains from the Upper Cretaceous Lopez de Bertodano Formation (late Campanian-Maastrichtian) of Seymour Island, Antarctic Peninsula include Cryptoclididae and Elasmosauridae. The occurrence of Cryptoclididae is reported from the Antarctic region for the first time. The taxon represents a new genus and species, based on a skull and associated cervical vertebrae. The long, slender and delicate teeth may have formed a ‘trapping’ device that enabled cryptoclidids to feed on small fish and crustaceans that abound in the same deposits. The cryptoclidids had a restricted distribution, being known so far from the Middle and Late Jurassic of England, and the Late Cretaceous of Chile, Argentina, and Antarctica. Other specimens, represented by several postcranial skeletons, are taxonomically indeterminate, but they share some features with other contemporary elasmosaurid genera such as Hydrotherosaurus, Morenosaurus, Thalassomedon, and Mauisaurus. Unlike the cryptoclidids, the elasmosaurids had a cosmopolitan distribution during the Jurassic and Cretaceous periods. Trophic diversity within guilds of marine predators is examined in the Lopez de Bertodano palaeocommunities. Three predator guilds are recognized on the basis of tooth morphology and prey preference. The mosasaurs composed the ‘Cut guild’, and were the principal predators. The elasmosaurids constituted the ‘Pierce guild’, and the cryptoclidids formed the ‘Trap guild’. These marine reptiles exploited the various pelagic resources such as sharks, bony fish, soft cephalopods and crustaceans, and survived until the end of the Cretaceous. The plesiosaurs were excellent swimmers, and used their hyperphalangic paddles for subaqueous flight in the manner of modern sea lions.
Estimation of optical flow in a three-dimensional voting space for brightness change

There is a problem that precision of optical flow declines in situations such that brightness changes. In order to solve the problem, conventional methods have been proposed. Each conventional method has different effective properties for optical flow estimation in the situations of brightness change. We aim to propose the method which has all effective properties in conventional methods for optical flow estimation in the situations of brightness change.
Proceedings of the COLING-2000 Workshop on Using Toolsets and Architectures To Build NLP Systems

Many toolsets have been developed to support the implementation of single NLP components (taggers, parsers, generators, dictionaries) or complete Natural Language Processing applications (Information Extraction systems, Machine Translation systems). A source for available toolkits is the Natural Language Software Registry, an initiative of the Association for Computational Linguistics hosted by DFKI at http://registry.dfki. de. These tools aim at facilitating and lowering the cost of building NLP systems. Since the tools themselves are often complex pieces of software, they require a significant amount of effort to be developed and maintained in the first place. Is this effort worth the trouble? It is to be noted that NLP toolsets have often been originally developed for implementing a single component or application. In this case, why not build the NLP system using a general programming language such as Lisp or Prolog? There can be at least two answers. First, for pure efficiency issues (speed and space), it is often preferable to build a parameterized algorithm operating on a uniform data structure (e.g., a phrase-structure parser). Second, it is harder, and often impossible, to develop, debug and maintain a large NLP system directly written in a general programming language.
Impaired aerobic capacity in hypercholesterolemic mice : partial reversal by exercise training

JOSEF NIEBAUER,1,2 ANDREW J. MAXWELL,1,3 PATRICK S. LIN,1 PHILIP S. TSAO,1 JON KOSEK,4 DANIEL BERNSTEIN,3 AND JOHN P. COOKE1 1Section of Vascular Medicine, Division of Cardiovascular Medicine and 3Division of Pediatric Cardiology, Stanford University, and 4Department of Pathology, Veterans Administration Hospital, Stanford University, Stanford, California 94305; and 2Department of Cardiology, Heart Center, University of Leipzig, 04289 Leipzig, Germany
Moment-Based Methods for Real-Time Shadows and Fast Transient Imaging

We apply the theory of moments to develop computationally efficient methods for real-time rendering of shadows and reconstruction of transient images from few measurements. Given moments of an unknown probability distribution, i.e. the expectations of known, real random variables, the theory of moments strives to characterize all distributions that could have led to these moments. Earlier works in computer graphics only use the most basic results of this powerful theory. When filtering shadows based on shadow maps, the distribution of depth values within the filter region has to be estimated. Variance shadow mapping does this using two power moments. While this linear representation admits direct filtering, it leads to a very coarse reconstruction. We generalize this approach to use an arbitrary set of general moments and benchmark thousands of possible choices. Based on the results, we propose the use of moment shadow mapping which produces high-quality antialiased shadows efficiently by storing four power moments in 64 bits per shadow map texel. Techniques for shadow map filtering have been applied to a variety of problems. We combine these existing approaches with moment shadow mapping to render shadows of translucent occluders using alpha blending, soft shadows using summed-area tables and prefiltered single scattering using six power moments. All these techniques have a high overhead per texel of the moment shadow map but a low overhead per shaded pixel. Thus, they scale well to the increasingly high resolutions of modern displays. Transient images help to analyze light transport in scenes. Besides two spatial dimensions, they are resolved in time of flight. Earlier cost-efficient approaches reconstruct them from measurements of amplitude modulated continuous wave lidar systems but they typically take more than a minute of capture time. We pose this reconstruction problem as trigonometric moment problem. The maximum entropy spectral estimate and the Pisarenko estimate are known closed-form solutions to such problems which yield continuous and sparse reconstructions, respectively. By applying them, we reconstruct complex impulse responses with m distinct returns from measurements at as few as m non-zero frequencies. For m = 3 our experiments with measured data confirm this. Thus, our techniques are computationally efficient and simultaneously reduce capture times drastically. We successfully capture 18.6 transient images per second which leads to transient video. As an important byproduct, this fast and accurate reconstruction of impulse responses enables removal of multipath interference in range images.
Effects of oral and intravenous rehydration on ratings of perceived exertion and thirst.

The purpose of this investigation was to compare the effects of oral and intravenous saline rehydration on differentiated ratings of perceived exertion (RPE) and thirst. Eight men underwent three randomly assigned rehydration treatments following a 2- to 4-h exercise-induced dehydration bout to reduce body weight by 4%. Treatments included 0.45% saline infusion (i.v.), 0.45% saline oral ingestion (ORAL), and no fluid (NF). Following rehydration and rest (2 h total), subjects walked at 50% VO2max for 90 min at 36 degrees C (EX). Central RPE during ORAL was lower (P < 0.05) than i.v. and NF throughout EX. Local RPE during NF was higher (P < 0.05) than i.v. and ORAL at minutes 20 and 40 of EX and overall RPE during NF was higher (P < 0.05) than ORAL at minutes 20 and 40 of EX. Significant correlations were found between overall RPE and mean skin temperature for i.v. (r = 0.72) and NF (r = 0.75), and between overall RPE and thirst ratings for i.v. (r = 0.70). Thirst ratings were not different among trials at postdehydration. Following rehydration, thirst was higher (P < 0.05) during NF than i.v. and ORAL and lower (P < 0.05) during ORAL than i.v. at all subsequent time points. Results suggest that oral rehydration is likely to elicit lower RPE and thirst ratings compared with intravenous rehydration.
Antidiabetic, Lipid Normalizing, and Nephroprotective Actions of the Strawberry: A Potent Supplementary Fruit

The study was designed to assess the effect of different strawberry extracts on glucose levels, lipid profiles, and oxidative stress in nicotinamide-streptozotocin (NIC-STZ) induced diabetic rats. The associated changes were evaluated through biochemical, molecular, and histological assays. Diabetes was induced by intraperitoneal injection of STZ to albino Wistar rats after treatment with nicotinamide. Aqueous, hydroalcoholic, and alcoholic strawberry extracts were administrated orally to diabetic rats. Treatment of strawberry extracts improved lipid profile, liver function, and serum creatinine and led to a significant increase in antioxidant status in diabetic rats. Real-time PCR expression analysis of genes from the liver of animals treated with strawberry extracts exhibited downregulation of several fatty acid synthesis genes, transcription factors, such as Sterol regulatory Element Binding Transcription factor (SREBP) and Nuclear Factor-κβ (NF-κβ), and inflammatory markers, like Interleukin 6 (IL6) and Tumor Necrosis Factor-α (TNF-α). Strawberry extracts also upregulated liver Peroxisome Proliferator Activated Receptor-γ (PPAR-γ). Histological examination confirmed the nephroprotective and β-cell regeneration/protection effects of strawberry extracts. The present study demonstrates several beneficial effects of strawberry extracts along with its probable mechanism of action.
Interpreting shortwave albedo‐transmittance plots: True or apparent anomalous absorption?

The coefficients of linear regression lines fit to hourly observations of atmospheric transmittance and TOA albedo have been used previously to address the problem of anomalous cloud absorption (ACA). While these coefficients indicate, reasonably well, the impact of clouds on atmospheric absorptance for 1D model data, this is not necessarily the case for hourly data. This is because for nonuniform clouds, regression coefficients are reduced significantly relative to 1D model results due to the effects of horizontal transport of radiation and poor sampling of transmittance. These reductions are only illusions of ACA because domain‐averaged atmospheric absorptances are almost insensitive to cloud geometry. The ramifications of these effects can be seen in hourly data that were used in a previous study which claimed to support ACA. They are also demonstrated with a 3D Monte Carlo, broadband radiative transfer algorithm acting on data generated by a cloud‐resolving model.
Feature extraction with multiscale autoregression of multichannel time series for P300 speller BCI

P300 is one of the most studied components of event related potentials which reflects the responses of brain to events in the external environment. In this paper, we present a new method that utilizes multiresolution autoregression of multichannel time series (MAMTS) for feature extraction of P300 wave. First, it adopts multiresolution autoregression on dyadic tree to depict the characteristic of electroencephalogram (EEG) signal. Then the corresponding autoregression noise of multichannel time series is extracted as the feature. The experiment results verified the effectiveness of this new feature for P300 speller brain compute interface (BCI).