Miracle-dz/UniFAR-FTUs huggingface dataset:
Upper Airways Microbiota in Antibiotic-Naïve Wheezing and Healthy Infants from the Tropics of Rural Ecuador

Background Observations that the airway microbiome is disturbed in asthma may be confounded by the widespread use of antibiotics and inhaled steroids. We have therefore examined the oropharyngeal microbiome in early onset wheezing infants from a rural area of tropical Ecuador where antibiotic usage is minimal and glucocorticoid usage is absent. Materials and Methods We performed pyrosequencing of amplicons of the polymorphic bacterial 16S rRNA gene from oropharyngeal samples from 24 infants with non-infectious early onset wheezing and 24 healthy controls (average age 10.2 months). We analyzed microbial community structure and differences between cases and controls by QIIME software. Results We obtained 76,627 high quality sequences classified into 182 operational taxonomic units (OTUs). Firmicutes was the most common and diverse phylum (71.22% of sequences) with Streptococcus being the most common genus (49.72%). Known pathogens were found significantly more often in cases of infantile wheeze compared to controls, exemplified by Haemophilus spp. (OR = 2.12, 95% Confidence Interval (CI) 1.82–2.47; P = 5.46×10−23) and Staphylococcus spp. (OR = 124.1, 95%CI 59.0–261.2; P = 1.87×10−241). Other OTUs were less common in cases than controls, notably Veillonella spp. (OR = 0.59, 95%CI = 0.56–0.62; P = 8.06×10−86). Discussion The airway microbiota appeared to contain many more Streptococci than found in Western Europe and the USA. Comparisons between healthy and wheezing infants revealed a significant difference in several bacterial phylotypes that were not confounded by antibiotics or use of inhaled steroids. The increased prevalence of pathogens such as Haemophilus and Staphylococcus spp. in cases may contribute to wheezing illnesses in this age group.
STABLE SELF TUNING GENETIC FUZZY TEMPERATURE CONTROLLER FOR PLASTIC EXTRUSION SYSTEM

In this paper Genetic Algorithm based Fuzzy Logic Controller for temperature control in a plastic extrusion is developed and tested through a simulation study. A novel GA based FLC method is implemented to design a practicable advanced controller. Manifest feature of the proposed method is smoothing of undesired control signal of mamdani type FLC controller. Plastic extrusion system is generally nonlinear and the temperature of the plastic extrusion system may vary over a wide range subjected to various disturbances. The system is designed with two different control techniques to control temperature at different set point changes and as well as to control sudden input disturbances. The first technique is mamdani type FLC controller and the proposed method is GA based FLC. In order to use a controller it must first be tuned to the system. This tuning synchronizes the controller with the controlled variable, thus allowing the process to keep at its desired operating condition. The simulation study shows that the proposed controller has good set point tracking and disturbances rejection properties. Also it is robust against changes in the system parameters and superior to the Fuzzy controller
Declarative Programming Techniques for Many-Core Architectures

Future manycore architectures are likely to have heterogeneous computing resources which will include conventional CPUs as FPGAs. Many of the techniques that the reconfigurable computing community has championed will find new applications in mainstream applications. One challenge posed by such manycore architectures is the requirement to target multiple parallel computing resources from a single description (or code). This paper proposes a design methodology for the specification and implementation of data parallel computations that can be mapped to either circuits on FPGAs or pixel-shader code on GPUs from exactly the same description. These descriptions exploit higher order combinators and polymorphism to provide powerful glue for composing data parallel descriptions in a generic way. We present two implementations of these combinations: one in F# which is a variant of the ML functional language and the other in the C# language which uses generics and C# delegates to achieve the effect of higher order combinators. We present the results of implementations that execute on Virtex FPGAs and ATI graphics cards.
Efficient Consequence Finding

We present an extensive experimental study of consequence-finding algorithms based on kernel resolution, using both a trie-based and a novel ZBDD-based implementation, which uses ZeroSuppressed Binary Decision Diagrams to concisely store and process very large clause sets. Our study considers both the full prime implicate task and applications of consequence-finding for restricted target languages in abduction, model-based and faulttree diagnosis, and polynomially-bounded knowledge compilation. We show that the ZBDD implementation can push consequence-finding to a new limit, solving problems which generate over 1070 clauses.
Compression Artifacts in Modern Video Coding and State-of-the-Art Means of Compensation

This chapter describes and explains common as well as less common distortions in modern video coding, ranging from artifacts appearing in MPEG-2 Video, MPEG-4 Part 2, H.264 and VC-1 to scalable and multi-view video coding based distortions, including the proposals for next generation video coding (NVC). In addition to a discussion about avoiding these artifacts through encoder-side measures, a stateof-the-art overview of their compensation at the decoder side is given. Finally, artifacts emerging from new sophisticated coding tools in current and upcoming video coding standards are discussed.
Cooling Conditions Influence on Cortical Bovine Bones Derived Hydroxyapatite

The aim of the study is to highlight the influence of the cooling conditions on cortical bovine bones derived hydroxyapatite. Bone samples with thicknes of 50 mm were cut from the central part of the bovine femur with a jigsaw. Then, they were processed in order to remove all the proteins and collagen traces by boiling for 4 hours and heating and holding them at 450°C for 2 hours. They were heat treated at temperatures ranging from 1000° to 1300°C, being held for 3 hours and then rapidly cooled in air atmosphere or ice-water. A natural fracture of the samples appeared after the applied heat treatments, which allowed us to analyse the fragments without a further preparation. The morphological changes that occurred during the sample processing were highlighted using the scanning electron microscopy (SEM) techniques. The morphological changes occurred not only between the heat treated samples at different temperature, but also in samples cooled in different environments. Also, it was noticed that crystals sizes proportionaly increased with temperature, while the porosity considerably decreased and also a condensation of the porous matrix/structure appeared.
Logical Constants Across Varying Types

We investigate the notion of «logicality» for arbitrary categories of linguistic expression, viewed as a phenomenon which they can all possess to a greater or lesser degree. Various semantic aspects of logicality are analyzed in technical detail: in particular, invariance for permutations of individual objects, and respect for Boolean structure. We show how such properties are systematically related across different categories, using the apparatus of the typed lambda calculus
Structural determinants crucial to the RNA chaperone activity of glycine-rich RNA-binding proteins 4 and 7 in Arabidopsis thaliana during the cold adaptation process

Although glycine-rich RNA-binding proteins (GRPs) have been determined to function as RNA chaperones during the cold adaptation process, the structural features relevant to this RNA chaperone activity remain largely unknown. To uncover which structural determinants are necessary for RNA chaperone activity of GRPs, the importance of the N-terminal RNA recognition motif (RRM) and the C-terminal glycine-rich domains of two Arabidopsis thaliana GRPs (AtGRP4 harbouring no RNA chaperone activity and AtGRP7 harbouring RNA chaperone activity) was assessed via domain swapping and mutation analyses. The results of domain swapping and deletion experiments showed that the domain sequences encompassing the N-terminal RRM of GRPs were found to be crucial to the ability to complement cold-sensitive Escherichia coli mutant cells under cold stress, RNA melting ability, and freezing tolerance ability in the grp7 loss-of-function Arabidopsis mutant. In particular, the N-terminal 24 amino acid extension of AtGRP4 impedes the RNA chaperone activity. Collectively, these results reveal that domain sequences and overall folding of GRPs governed by a specific modular arrangement of RRM and glycine-rich sequences are critical to the RNA chaperone activity of GRPs during the cold adaptation process in cells.
An Hinf LPV design for sampling varying controllers : experimentation with a T inverted pendulum

—This paper deals with the adaptation of a real-time controller’s sampling period to account for the available computing resource variations. The design of such controllers requires a parameter-dependent discrete-time model of the plant, where the parameter is the sampling period. A polytopic approach for LPV (Linear Parameter Varying) systems is then developed to get an H ∞ sampling period dependent controller. A reduction of the polytope size is here performed which drastically reduces the conservatism of the approach and makes easier the controller implementation. Some experimental results on a T inverted pendulum are provided to show the efﬁciency of the approach.
Chaperones in Polyglutamine Aggregation: Beyond the Q-Stretch

Expanded polyglutamine (polyQ) stretches in at least nine unrelated proteins lead to inherited neuronal dysfunction and degeneration. The expansion size in all diseases correlates with age at onset (AO) of disease and with polyQ protein aggregation, indicating that the expanded polyQ stretch is the main driving force for the disease onset. Interestingly, there is marked interpatient variability in expansion thresholds for a given disease. Between different polyQ diseases the repeat length vs. AO also indicates the existence of modulatory effects on aggregation of the upstream and downstream amino acid sequences flanking the Q expansion. This can be either due to intrinsic modulation of aggregation by the flanking regions, or due to differential interaction with other proteins, such as the components of the cellular protein quality control network. Indeed, several lines of evidence suggest that molecular chaperones have impact on the handling of different polyQ proteins. Here, we review factors differentially influencing polyQ aggregation: the Q-stretch itself, modulatory flanking sequences, interaction partners, cleavage of polyQ-containing proteins, and post-translational modifications, with a special focus on the role of molecular chaperones. By discussing typical examples of how these factors influence aggregation, we provide more insight on the variability of AO between different diseases as well as within the same polyQ disorder, on the molecular level.
Unique Bisphenol A Transcriptome in Prostate Cancer: Novel Effects on ERβ Expression That Correspond to Androgen Receptor Mutation Status

Background Prostatic adenocarcinomas are dependent on androgen receptor (AR) activity for growth and progression, and therapy for disseminated disease depends on ablation of AR activity. Recurrent tumors ultimately arise wherein AR has been re-activated. One mechanism of AR restoration is via somatic mutation, wherein cells containing mutant receptors become susceptible to activation by alternative ligands, including bisphenol A (BPA). In tumors with specific AR mutations, BPA promotes therapeutic bypass, suggesting significant negative impact to the clinical management of prostate cancer. Objective Our goal was to determine the mechanism of BPA action in cancer cells carrying BPA-responsive AR mutants. Methods The molecular signature of BPA activity in prostate cancer cells harboring mutant AR was delineated via genetic microarray analysis. Specificity of BPA action was assessed by comparison with the molecular signature elicited by dihydrotestosterone (DHT). Results BPA and DHT elicited distinct transcriptional signatures in prostate cancer cells expressing the BPA-responsive mutant AR-T877A. BPA dramatically attenuated estrogen receptor beta (ERβ) expression; this finding was specific to prostate tumor cells in which BPA induces cellular proliferation. Conclusions BPA induces a distinct gene expression signature in prostate cancer cells expressing somatic AR mutation, and a major molecular consequence of BPA action is down-regulation of ERβ. Since ERβ functions to antagonize AR function and AR-dependent proliferation, these findings reveal a novel mechanism by which BPA likely regulates cellular proliferation. Future investigation directed at dissecting the importance of ERβ in the proliferative response to BPA will establish the contribution of this event to adverse effects associated with human exposure.
Comparing Single Molecule Tracking and correlative approaches : an application to the datasets recently presented in Nature Methods by Chenuard et al

approaches: an application to the datasets recently presented in Nature Methods by Chenuard et al. Carmine di Rienzo and Paolo Annibale 1 NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy (carmine.dirienzo@sns.it) 2 Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy 3 Department of Pharmacology, University of Wuerzburg, Wuerzburg, Germany (paolo.annibale@alumni.epfl.ch). Recent efforts to survey the numerous softwares available to perform single molecule tracking (SMT) highlighted a significant dependence of the outcomes on the specific method used, and the limitation encountered by most techniques to capture fast movements in a crowded environment [1]. Other approaches to identify the mode and rapidity of motion of fluorescently labeled biomolecules, that do not relay on the localization and linking of the images of isolated single molecules are, however, available [2, 3]. In particular, the molecular Mean Square Displacement (MSD) can be easily measured without identifying individual molecules positions by quantifying the enlargement in time of the Spatio-Temporal Image Correlation Function (STICS), the so called iMSD approach [2]. Alternatively, the iMSD can be applied to the spatio-temporal correlation of localization datasets, building on the improved spatial resolution obtained by the molecular localization process [3, 4]. We set to apply each of these methods to the benchmark dataset introduced by Chenouard et al. [1]. We chose the scenario where a "receptor" molecule undergoes diffusion in between intervals of directed motion, associated to "transport" along the cytoskeleton. Three exemplary levels of signal-to-noise (SNR) and particle concentrations were investigated as shown in Fig. 1. The conventional SMT analysis fails to quantitate accurately the presence of a directed motion (Fig. 1 a-d-g), due to the difficulty of correctly relinking the localizations of the fast moving molecules. This results in a sizable underestimation of the MSD, particularly at longer delays as shown by Chenuard et al. [1]. On the other hand, the iMSD (see supplementary information for further details) allows an accurate recovery of the expected MSD (Fig. 1 b-e-h). When this approach is applied to the localization datasets,
Publication Records of Faculty Promoted to Professor: Evidence from the UK Accounting and Finance Academic Community

This study investigates the publication profiles of 140 accounting and finance faculty promoted to the senior rank of professor at UK and Irish universities during the period 1992 to 2007. On average, approximately 9 papers in Association of Business Schools (ABS) (2008)-listed journals, with 5 at the highest 3*/4* quality levels in a portfolio of 20 outputs are required for promotion to professor. Multivariate analysis provides evidence that publication requirements in terms of ABS ranked journal papers have increased over time, an effect attributed to the government research assessment exercise. There is no evidence that requirements differ for: internal versus external promotion, male versus female candidates; accounting versus finance professors, research intensity of institution peer group; or government research ranking of unit. There is also no evidence of a substitution effect in relation to increased recent publication history, quantity of non-ABS outputs or sole-authorship, all of which show a significant complementary effect. It is noted that there is very limited overlap in the UK and US publication journal sets, suggesting underlying geographically-based paradigm differences. The benchmarks provided in this study are informative in a range of decision settings: recruitment; those considering making an application for promotion to a chair and those involved in promotion panels; cross-disciplinary comparisons; and resource allocation. The evidence presented also contributes to the emerging policy debates concerning the aging demographic profile of accounting faculty, the management of academic labour and the Research Excellence Framework.
Quasi-Polynomial Local Search for Restricted Max-Min Fair Allocation

The restricted max-min fair allocation problem (also known as the restricted Santa Claus problem) is one of few problems that enjoys the intriguing status of having a better estimation algorithm than approximation algorithm. Indeed, Asadpour et al. [2012] proved that a certain configuration LP can be used to estimate the optimal value within a factor of 1/(4 + ε), for any ε > 0, but at the same time it is not known how to efficiently find a solution with a comparable performance guarantee. A natural question that arises from their work is if the difference between these guarantees is inherent or results from a lack of suitable techniques. We address this problem by giving a quasi-polynomial approximation algorithm with the mentioned performance guarantee. More specifically, we modify the local search of Asadpour et al. [2012] and provide a novel analysis that lets us significantly improve the bound on its running time: from 2O(n) to nO(log n). Our techniques also have the interesting property that although we use the rather complex configuration LP in the analysis, we never actually solve it and therefore the resulting algorithm is purely combinatorial.
Genetic Polymorphisms of Stromal Interaction Molecule 1 Associated with the Erythrocyte Sedimentation Rate and C-Reactive Protein in HLA-B27 Positive Ankylosing Spondylitis Patients

Ankylosing spondylitis (AS) is a chronic inflammation of the sacroiliac joints, spine and peripheral joints. The development of ankylosing spondylitis is still unclear. Genetics factors such as human leukocyte antigen HLA-B27 and ERAP1 have been widely reported to associate to AS susceptibility. In this study, we enrolled 361 AS patients and selected four tagging single nucleotides polymorphisms (tSNPs) at STIM1 gene. The correlation between STIM1 genetic polymorphisms and AS activity index (BASDAI, BASFI, BAS-G) as well as laboratory parameters of inflammation (erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP)) were tested. Our results indicated that HLA-B27 positive AS patients who are carrying the minor allele homozygous G/G genotype of SNP rs3750996 significantly associated with a higher level of ESR in serum. Furthermore, rs3750996/rs3750994 pairwise allele analysis indicated that G-C haplotypes also significantly correlated with higher level of ESR as well as CRP. These findings provide a better understanding of STIM1 genetic contribution to the pathogenesis of AS.
Automatic extraction of bilingual word pairs from parallel corpora with various languages using learning for adjacent information

This paper presents a learning method using adjacent information as the method to extract bilingual word pairs efficiently from parallel corpora with various languages for which language resources are insufficient. In our method, information about correspondence between source language words and target language words is acquired automatically using the word strings that adjoin bilingual word pairs. That acquired information is used to solve the ambiguity problem of correspondence between source language words and target language words in various bilingual sentence pairs. First, the system using our method automatically acquires templates as information that indicates correspondence between source language words and target language words. The templates are based on word strings that adjoin the bilingual word pairs. Moreover, the system using our method efficiently extracts bilingual word pairs from bilingual sentence pairs using the acquired templates. Evaluation experiments showed that the system using our method extracted bilingual word pairs from parallel corpora with five kinds of languages. Results show that the total extraction rate was 60.1%. The total extraction rate was better by 8.0 percentage points compared to that obtained using a system based only on the Dice coefficient without our method. Those results confirm the effectiveness of our method. © 2006 Wiley Periodicals, Inc. Syst Comp Jpn, 37(13): 40–53, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ scj.20534
Determination of P phase arrival in low-amplitude seismic signals from coal-mines with wavelets

The aim of this article is to present an application of wavelet transform for P phase arrival detection in seismic signals from Polish coal-mines. The main idea is to use this methods to low amplitude, therefor noisy seismic signals. We can use the fact that the beginning of P wave of the seismic signal can appear in the wavelet coefficients across several scales. In this article the method is presented that locates these arrivals in one-component seismic signals.
Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB

RegulonDB is a database storing the biological information behind the transcriptional regulatory network (TRN) of the bacterium Escherichia coli. It is one of the key bioinformatics resources for Systems Biology investigations of bacterial gene regulation. Like most biological databases, the content drifts with time, both due to the accumulation of new information and due to refinements in the underlying biological concepts. Conclusions based on previous database versions may no longer hold. Here, we study the change of some topological properties of the TRN of E. coli, as provided by RegulonDB across 16 versions, as well as a simple index, digital control strength, quantifying the match between gene expression profiles and the transcriptional regulatory networks. While many of network characteristics change dramatically across the different versions, the digital control strength remains rather robust and in tune with previous results for this index. Our study shows that: (i) results derived from network topology should, when possible, be studied across a range of database versions, before detailed biological conclusions are derived, and (ii) resorting to simple indices, when interpreting high-throughput data from a network perspective, may help achieving a robustness of the findings against variation of the underlying biological information. Database URL: www.regulondb. ccg.unam. mx