Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity and community structure of bacterioplankton in surface waters off the northern tip of the Antarctic Peninsula

Global climate change is significantly affecting marine life off the northern tip of the Antarctic Peninsula, but little is known about microbial ecology in this area. The main goal of this study was to investigate the bacterioplankton community structure in surface waters using pyrosequencing and to determine factors influencing this community. Pelagibacterales and Rhodobacterales (Alphaproteobacteria), Oceanospirillales and Alteromonadales (Gammaproteobacteria), and Flavobacteriales (Bacteroidetes) were the core taxa in our samples, and the five most relatively abundant genera were Pelagibacter, Polaribacter, Octadecabacter, group HTCC2207 and Sulfitobacter. Although nutrients and chlorophyll a (chl a) contributed more to bacterioplankton community structure than water masses or depth, only 30.39% of the variance could be explained by the investigated environmental factors, as revealed by RDA and pRDA. No significant difference with respect to nutrients and chl a was observed among water masses or depth, as indicated by ANOVA. Furthermore, significant correlations among the dominant bacterial genera were more common than correlations between dominant genera and environmental factors, as revealed by Spearman analysis. We conclude that nutrients and chl a become homogeneous and that interpopulation interactions may have a central role in influencing the bacterial community structure in surface waters off the northern tip of the Antarctic Peninsula during the summer.
Efficient discovery of Internet gateways in future vehicular communication systems

Future road communication scenarios are expected to deploy a radio ad hoc communication technology for the transmission of data between vehicles. Such ad hoc networks are able to support low latencies and cost efficiency, which is very important for, e.g., safety related applications. In addition to vehicle-to-vehicle communication, users also will be interested in accessing Internet services from within the vehicular network. Access can be gained by using roadside installed Internet Gateways, which are able to communicate with the vehicles. However, several difficulties must be addressed in such a scenario. Examples are the interoperability of communication protocol, mobility support, communication efficiency, the discovery of Internet gateways, and the handover of connections from one gateway to the next. In this paper, we are focusing on the aspect of discovering the Internet gateways. We therefore developed a service discovery protocol, which is highly optimized for the characteristics of future vehicular ad hoc networks. Besides the benefit of efficient service discovery, our protocol is able to choose the most suitable Internet gateway among others using fuzzy methods. Furthermore, evaluations show that we are able to decrease the overhead caused by the service discovery process significantly.
An Investigation of Cooley-Tukey Decompositions for the FFT

The goals of the research discussed in this report are to determine the impact of di erent Cooley Tukey decompositions on the performance of computer programs that compute the FFT evaluate di erent methods for nding the most e cient decompositions and deter mine the characteristics of the most e cient decompositions Experiments are conducted using three di erent FFT programs and three dynamic programming DP methods for searching for e cient decompositions The results show that even for FFTs of sizes under the runtime for the average decomposition may be up to three times the runtime for the optimal decomposition The results also show that a basic implementation of DP performs as well as an exhaustive search at nding fast decompositions for FFTs of sizes up to and that the simple DP performs as well as two more sophisticated versions of DP for FFT sizes up to Furthermore the results show that for an out of place implementation of the FFT right expanded decompositions are optimal because they require memory storage only for the input and output data arrays whereas other decompositions require additional temporary storage Moreover the results show that for an in place implementation of the FFT balanced decompositions are optimal if the algorithm is iterative and right expanded decompositions are optimal if the algorithm is recursive
Functional Data Analysis for Sparse Longitudinal Data

We propose a nonparametric method to perform functional principal components analysis for the case of sparse longitudinal data. The method aims at irregularly spaced longitudinal data, where the number of repeated measurements available per subject is small. In contrast, classical functional data analysis requires a large number of regularly spaced measurements per subject. We assume that the repeated measurements are located randomly with a random number of repetitions for each subject and are determined by an underlying smooth random (subject-specific) trajectory plus measurement errors. Basic elements of our approach are the parsimonious estimation of the covariance structure and mean function of the trajectories, and the estimation of the variance of the measurement errors. The eigenfunction basis is estimated from the data, and functional principal components score estimates are obtained by a conditioning step. This conditional estimation method is conceptually simple and straightforward to implement. A key step is the derivation of asymptotic consistency and distribution results under mild conditions, using tools from functional analysis. Functional data analysis for sparse longitudinal data enables prediction of individual smooth trajectories even if only one or few measurements are available for a subject. Asymptotic pointwise and simultaneous confidence bands are obtained for predicted individual trajectories, based on asymptotic distributions, for simultaneous bands under the assumption of a finite number of components. Model selection techniques, such as the Akaike information criterion, are used to choose the model dimension corresponding to the number of eigenfunctions in the model. The methods are illustrated with a simulation study, longitudinal CD4 data for a sample of AIDS patients, and time-course gene expression data for the yeast cell cycle.
A link between radio loudness and X-ray/optical properties of AGN

We have found empirically that the radio loudness of AGN can be understood as function of both the X-ray and optical luminosity. This way of considering the radio loudness was inspired by the hardness-intensity diagrams for X-ray binaries, in which objects follow a definite track with changes to their radio properties occurring in certain regions. We generalize the hardness-intensity diagram to a disk-fraction luminosity diagram, which can be used to classify the accretion states both of X-ray binaries and of AGN. Using a sample of nearly 5000 SDSS quasars with ROSAT matches, we show that an AGN is more likely to have a high radio:optical flux ratio when it has a high total luminosity or a large contribution from X-rays. Thus, it is necessary to take into account both the optical and the X-ray properties of quasars in order to understand their radio loudness. The success of categorizing quasars in the same way as X-ray binaries is further evidence for the unification of accretion onto stellar-mass and supermassive compact objects.
Genomic Stability of Murine Leukemia Viruses Containing Insertions at the Env-3′ Untranslated Region Boundary

ABSTRACT Retroviruses containing inserts of exogenous sequences frequently eliminate the inserted sequences upon spread in susceptible cells. We have constructed replication-competent murine leukemia virus (MLV) vectors containing internal ribosome entry site (IRES)-transgene cassettes at the env-3′ untranslated region boundary in order to examine the effects of insert sequence and size on the loss of inserts during viral replication. A virus containing an insertion of 1.6 kb replicated with greatly attenuated kinetics relative to wild-type virus and lost the inserted sequences in a single infection cycle. In contrast, MLVs containing inserts of 1.15 to 1.30 kb replicated with kinetics only slightly attenuated compared to wild-type MLV and exhibited much greater stability, maintaining their genomic integrity over multiple serial infection cycles. Eventually, multiple species of deletion mutants were detected simultaneously in later infection cycles; once detected, these variants rapidly dominated the population and thereafter appeared to be maintained at a relative equilibrium. Sequence analysis of these variants identified preferred sites of recombination in the parental viruses, including both short direct repeats and inverted repeats. One instance of insert deletion through recombination with an endogenous retrovirus was also observed. When specific sequences involved in these recombination events were eliminated, deletion variants still arose with the same kinetics upon virus passage and by apparently similar mechanisms, although at different locations in the vectors. Our results suggest that while lengthened, insert-containing genomes can be maintained over multiple replication cycles, preferential deletions resulting in loss of the inserted sequences confer a strong selective advantage.
Modeling and Evaluating Repeatability and Reproducibility of Ordinal Classifications

This paper argues that currently available methods for the assessment of the repeatability and reproducibility of ordinal classifications are not satisfactory. The paper aims to study whether we can modify a class of models from Item Response Theory, well established for the study of the reliability of categorical measurements in psychometrics and education, for use in business and industry, and whether the resulting approaches offer a satisfactory solution. The fitted models can be presented graphically, but also allow the calculation of probabilities of correct ordering and consistent classification. In addition, the model-based approach allows refined diagnostics, giving the user insight into the workings of a classification procedure, which is vital information for a user willing to improve a poor classification procedure. The approach is illustrated from a real-life example, and the proposed analysis is contrasted to two popular alternative analyses, based on Goodman and Kruskal’s gamma and Kendall’s.
The P2Y13 Met-158-Thr Polymorphism, Which Is in Linkage Disequilibrium with the P2Y12 Locus, Is Not Associated with Acute Myocardial Infarction

Background and Aims The aims of this study were to investigate (1) if P2Y12 polymorphisms defining the P2Y12 H2 allele are associated with any other SNPs that may explain the previously reported association with increased ADP induced platelet activation and association with peripheral arterial disease and coronary artery disease and (2) if such variants are associated with acute myocardial infarction (AMI) or classical risk factors for AMI. Methods and Results The P2Y13 Met-158-Thr polymorphism was found to be in linkage disequilibrium (LD) with the P2Y12 H2 haplotype (all examined SNPs: D′ = 1.0, r2 = 0.936–1.0), defining a novel P2Y12 H2/P2Y13 Thr-158 haplotype. Genotyping of an AMI case control population (n = 1244 cases, 2488 controls) revealed no association of the P2Y13 Thr-158 allele with AMI (OR = 0.96, 95% C.I. 0.82–1.12, P = 0.63). Also, no differences between the genotype frequencies of P2Y13 Met-158-Met and Met-158-Thr/Thr-158-Thr were seen in AMI case-control subpopulations (early onset AMI OR = 1.06, 95% C.I. 0.85–1.31, P = 0.62); family history of AMI (OR = 0.98, 95% C.I. 0.78–1.22, P = 0.83) nor in early onset AMIs with family history of AMI (OR = 1.0, 95% C.I. 0.74–1.36, P = 1.0). Genotyping of the P2Y13 Met-158-Thr polymorphism in a population based sample (n = 6055) revealed no association with cardiovascular risk factors. In addition, the P2Y13 Met-158-Thr polymorphism was genotyped in a diabetes case-control population, and associations were found neither with DM nor with any examined DM risk factors. Conclusion Genotyping The P2Y13 Met-158-Thr polymorphism is in tight LD with the P2Y12 locus but is not associated with AMI or classical cardiovascular risk factors.
Admission to the intensive care unit and well-being in patients with advanced chronic illness.

PURPOSE To describe the association of intensive care with trajectories of functional, emotional, social, and physical well-being in patients with 3 common advanced illnesses. METHODS Cross-sectional cohort study of 42 patients admitted to the intensive care unit selected from 210 patients with stage IV breast, prostate, or colon cancer or stage IIIb or IV lung cancer; New York Heart Association class III or IV congestive heart failure; and chronic obstructive pulmonary disease with hypercapnea (Pco2 > 46 mm Hg). Scores on subscales of the Functional Assessment of Chronic Illness Therapy-General survey were measured monthly for 6 months before and after admission to the intensive care unit and were analyzed by using the unit admission date as a point of discontinuous change to illustrate trajectories before and after the admission. RESULTS Overall, trajectories of well-being declined sharply after admission to the intensive care unit. Declines in physical, functional, and emotional well-being were statistically significant. During the 6 months after admission, physical, functional, and emotional well-being scores trended back up to baseline while social well-being scores continued to decline. CONCLUSIONS Well-being trajectories declined sharply after admission to the intensive care unit, with recovery in the subsequent 6 months, and may be characterized by common patterns. These results help to better describe intensive care as a marker for advancing illness in patients with advanced chronic illness.
T-Scan: a new tool for analyzing Dutch text

T-Scan is a new tool for analyzing Dutch text. It aims at extracting text features that are theoretically interesting, in that they relate to genre and text complexity, as well as practically interesting, in that they enable users and text producers to make text-specic diagnoses. T-Scan derives it features from tools such as Frog and Alpino, and resources such as SoNaR, SUBTLEX-NL and Referentie Bestand Nederlands. This paper oers a qualitative discussion of a number of T-Scan features, based on a minimal demonstration corpus of six texts, three of them scientic articles and three of them drawn from a women’s magazine. We discuss features concerning lexical complexity, sentence complexity, referential cohesion and lexical diversity, lexical semantics and personal style. For all these domains we examine the construct validity as well as the reliability of a number of important features. We conclude that T-Scan oers a number of promising lexical and syntactic features, while the interpretation of referential cohesion/ lexical diversity features and personal style features is less clear. Further developing the application and analyzing authentic text need to go hand in hand.
Statistical Resolution of Ambiguous HLA Typing Data

High-resolution HLA typing plays a central role in many areas of immunology, such as in identifying immunogenetic risk factors for disease, in studying how the genomes of pathogens evolve in response to immune selection pressures, and also in vaccine design, where identification of HLA-restricted epitopes may be used to guide the selection of vaccine immunogens. Perhaps one of the most immediate applications is in direct medical decisions concerning the matching of stem cell transplant donors to unrelated recipients. However, high-resolution HLA typing is frequently unavailable due to its high cost or the inability to re-type historical data. In this paper, we introduce and evaluate a method for statistical, in silico refinement of ambiguous and/or low-resolution HLA data. Our method, which requires an independent, high-resolution training data set drawn from the same population as the data to be refined, uses linkage disequilibrium in HLA haplotypes as well as four-digit allele frequency data to probabilistically refine HLA typings. Central to our approach is the use of haplotype inference. We introduce new methodology to this area, improving upon the Expectation-Maximization (EM)-based approaches currently used within the HLA community. Our improvements are achieved by using a parsimonious parameterization for haplotype distributions and by smoothing the maximum likelihood (ML) solution. These improvements make it possible to scale the refinement to a larger number of alleles and loci in a more computationally efficient and stable manner. We also show how to augment our method in order to incorporate ethnicity information (as HLA allele distributions vary widely according to race/ethnicity as well as geographic area), and demonstrate the potential utility of this experimentally. A tool based on our approach is freely available for research purposes at http://microsoft.com/science.
Spatial relationships between tree species and gap characteristics in broad-leaved deciduous woodland

Abstract Questions: 1. What are the spatial patterns of all trees, individual tree species, trees within particular height classes, all gaps and gaps with specific properties across the study site in broad-leaved deciduous forest at a range of scales? 2. Are patterns of the above features spatially associated? 3. Are these patterns indicative of gap creation mechanisms and phases of regeneration? Location: Frame Wood, New Forest, UK. Methods: Ripley's K-function analysis was applied to spatial information derived from airborne remotely sensed imagery to characterize the patterns of trees and gaps and to test for spatial interactions between these patterns. The patterns of trees and gaps with specific physical and spatial properties were analysed. Results: The pattern of all tree species combined was random for most scales; Quercus robur followed the same random pattern, while Fagus sylvatica and Betula pendula were clustered over most spatial scales. Large gaps (> 250 m2) and larger trees (> 17.5 m) were randomly distributed, while smaller gaps and smaller trees were clustered. Significant spatial relationships were demonstrated between the patterns of different tree species and between trees within different size classes, as well as between the patterns of trees and gaps with specific properties. Conclusions: Small gap patterns and field evidence indicated that progressive gap enlargement is the most likely creation mechanism for large gaps (> 250 m2). Clustered patterns of younger individuals were indicative of patches of past regeneration. As a complement to field-based data, data derived from remotely sensed imagery provides spatially comprehensive information with which to further investigate woodland stand/community processes and gap dynamics. Abbreviations: ATM = Airborne thematic mapper; CHM = Canopy height model; CSR = Complete spatial randomness; GHD = Gap height diversity; GSCI = Gap shape complexity index; LiDAR = Light detection and ranging.
A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback

Reward-modulated spike-timing-dependent plasticity (STDP) has recently emerged as a candidate for a learning rule that could explain how behaviorally relevant adaptive changes in complex networks of spiking neurons could be achieved in a self-organizing manner through local synaptic plasticity. However, the capabilities and limitations of this learning rule could so far only be tested through computer simulations. This article provides tools for an analytic treatment of reward-modulated STDP, which allows us to predict under which conditions reward-modulated STDP will achieve a desired learning effect. These analytical results imply that neurons can learn through reward-modulated STDP to classify not only spatial but also temporal firing patterns of presynaptic neurons. They also can learn to respond to specific presynaptic firing patterns with particular spike patterns. Finally, the resulting learning theory predicts that even difficult credit-assignment problems, where it is very hard to tell which synaptic weights should be modified in order to increase the global reward for the system, can be solved in a self-organizing manner through reward-modulated STDP. This yields an explanation for a fundamental experimental result on biofeedback in monkeys by Fetz and Baker. In this experiment monkeys were rewarded for increasing the firing rate of a particular neuron in the cortex and were able to solve this extremely difficult credit assignment problem. Our model for this experiment relies on a combination of reward-modulated STDP with variable spontaneous firing activity. Hence it also provides a possible functional explanation for trial-to-trial variability, which is characteristic for cortical networks of neurons but has no analogue in currently existing artificial computing systems. In addition our model demonstrates that reward-modulated STDP can be applied to all synapses in a large recurrent neural network without endangering the stability of the network dynamics.
Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes

Temperatures around hydrothermal vents are highly variable, ranging from near freezing up to 300°C. Nevertheless, animals thrive around vents, some of which live near the known limits of animal thermotolerance. Paralvinella sulfincola, an extremely thermotolerant vent polychaete, and Paralvinella palmiformis, a cooler-adapted congener, are found along the Juan de Fuca Ridge in the northwestern Pacific. We conducted shipboard high-pressure thermotolerance experiments on both species to characterize the physiological adaptations underlying P. sulfincola's pronounced thermotolerance. Quantitative proteomics, expressed sequence tag (EST) libraries and glutathione assays revealed that P. sulfincola (i) exhibited an upregulation in the synthesis and recycling of glutathione with increasing temperature, (ii) downregulated nicotinamide adenine dinucleotide (NADH) and succinate dehydrogenases (key enzymes in oxidative phosphorylation) with increasing temperature, and (iii) maintained elevated levels of heat shock proteins (HSPs) across all treatments. In contrast, P. palmiformis exhibited more typical responses to increasing temperatures (e.g. increasing HSPs at higher temperatures). These data reveal differences in how a mesotolerant and extremely thermotolerant eukaryote respond to thermal stress, and suggest that P. sulfincola's capacity to mitigate oxidative stress via increased synthesis of antioxidants and decreased flux through the mitochondrial electron transport chain enable pronounced thermotolerance. Ultimately, oxidative stress may be the key factor in limiting all metazoan thermotolerance.
SOBIE: A Novel Super-node P2P Overlay Based on Information Exchange

In order to guarantee both the efficiency and robustness in the Peer-to-Peer (P2P) network, the paper designs a novel Super-node Overlay Based on Information Exchange called SOBIE. Differing from current structured and unstructured, or meshed and tree-like P2P overlay, the SOBIE is a whole new structure to improve the efficiency of searching in the P2P network. The main contributions are 1) to select the super-nodes by considering the aggregation of not only the delay, distance, but also the information exchange frequency, exchange time and query similarity especially; 2) to set a score mechanism to identify and prevent the free-riders. Meanwhile, the SOBIE also guarantees the matching between the physical network and logical network and has small-world characteristic to improve the efficiency. Large number of experiment results show the advantages of the SOBIE including high efficiency and robustness by such different factors as the query success rate, the average query hops, the total number of query messages, the coverage rate and system connectivity.