Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic analysis on the soil bacteria distributed in karst forest

Phylogenetic composition of bacterial community in soil of a karst forest was analyzed by culture-independent molecular approach. The bacterial 16S rRNA gene was amplified directly from soil DNA and cloned to generate a library. After screening the clone library by RFLP, 16S rRNA genes of representative clones were sequenced and the bacterial community was analyzed phylogenetically. The 16S rRNA gene inserts of 190 clones randomly selected were analyzed by RFLP and generated 126 different RFLP types. After sequencing, 126 non-chimeric sequences were obtained, generating 113 phylotypes. Phylogenetic analysis revealed that the bacteria distributed in soil of the karst forest included the members assigning into Proteobacteria, Acidobacteria, Planctomycetes, Chloroflexi (Green nonsulfur bacteria), Bacteroidetes, Verrucomicrobia, Nitrospirae, Actinobacteria (High G+C Gram-positive bacteria), Firmicutes (Low G+C Gram-positive bacteria) and candidate divisions (including the SPAM and GN08).
Health Disparities Beginning in Childhood: A Life-Course Perspective

In this article we argue for the utility of the life-course perspective as a tool for understanding and addressing health disparities across socioeconomic and racial or ethnic groups, particularly disparities that originate in childhood. Key concepts and terms used in life-course research are briefly defined; as resources, examples of existing literature and the outcomes covered are provided along with examples of longitudinal databases that have often been used for life-course research. The life-course perspective focuses on understanding how early-life experiences can shape health across an entire lifetime and potentially across generations; it systematically directs attention to the role of context, including social and physical context along with biological factors, over time. This approach is particularly relevant to understanding and addressing health disparities, because social and physical contextual factors underlie socioeconomic and racial/ethnic disparities in health. A major focus of life-course epidemiology has been to understand how early-life experiences (particularly experiences related to economic adversity and the social disadvantages that often accompany it) shape adult health, particularly adult chronic disease and its risk factors and consequences. The strong life-course influences on adult health could provide a powerful rationale for policies at all levels—federal, state, and local—to give more priority to investment in improving the living conditions of children as a strategy for improving health and reducing health disparities across the entire life course. Pediatrics 2009;124:S163–S175
Every poset has a good comparison

We show that any finite partially ordered set P contains a pair of elements x and y such that the proportion of linear extensions of P in which x lies below y is between 3/11 and 8/11. A consequence is that the information-theoretic lower bound for sorting under partial information is tight up to a multiplicative constant. Precisely: if X is a totally ordered set about which we are given some partial information, and if e(X) is the number of total orderings of X compatible with this partial information, then it is possible to sort X using no more than c log2e(X) comparisons (c@@@@2.17).
Can Banks Provide Liquidity in a Financial Crisis

In financial crises of the recent past, investors often withdrew from securities markets and placed their funds into safer assets, such as U.S. Treasuries and bank deposits. During such episodes, a wide range of businesses shut out of securities markets sought to fund their operations by drawing down credit lines established with banks during normal times. Awash with funds from depositors seeking a safe haven, banks had no difficulty meeting these increased credit demands. Thus, banks helped avoid financial disruptions and business liquidations that would have occurred in the absence of a liquidity backstop. ; In 2007-09, however, banks were at the center of the financial crisis. While significant risks were present in some other financial institutions, this crisis was special in that commercial banks were much more exposed to losses than in recent past crises. This key feature of the crisis casts doubt on the notion that banks are a natural source of liquidity during financial crises. Were bank deposits still viewed as a safe haven, and if not, how compromised was their ability to meet the demand for liquidity? ; Mora examines how commercial bank deposits and lending evolved during the recent crisis compared with past episodes of financial stress. She concludes that the bank-centered nature of the crisis made it harder than in the past for banks to attract deposits and provide liquidity to borrowers shut out of securities markets.
Adiponectin and resistin in PCOS: a clinical, biochemical and molecular genetic study.

BACKGROUND We conducted a cross-sectional case-control study to evaluate the possible involvement of adiponectin and resistin in the pathogenesis of polycystic ovary syndrome (PCOS). METHODS Seventy-six PCOS patients and 40 non-hyperandrogenic women matched for BMI and degree of obesity were included. Serum adiponectin and resistin levels, anthropometrical and hormonal variables, the 45 T-->G and 276 G-->T polymorphisms in the adiponectin gene, and the -420 C-->G variant in the resistin gene, were analysed. RESULTS Serum adiponectin concentrations were reduced in PCOS patients compared with controls (P = 0.038) irrespective of the degree of obesity, whereas serum resistin levels were increased in overweight and obese women compared with lean subjects (P = 0.016), irrespective of their PCOS or controls status. The adiponectin and resistin polymorphisms were not associated with PCOS and did not influence serum levels of adiponectin, resistin and other clinical and hormonal variables. In a multiple regression model, the waist-to-hip ratio, free testosterone levels and age, but not insulin resistance, were the major determinants of hypoadiponectinaemia. CONCLUSIONS PCOS patients present with hypoadiponectinaemia, in relation with abdominal adiposity and hyperandrogenism. Our present results suggest that hyperandrogenism and abdominal obesity, by reducing the serum levels of the insulin sensitizer adipokine adiponectin, might contribute to the insulin resistance of PCOS.
Statically Verified Type-Preserving Code Transformations in Haskell

The use of typed intermediate languages can significantly increase the reliability of a compiler. By type-checking the code produced at each transformation stage, one can identify bugs in the compiler that would otherwise be much harder to find. We propose to take the use of types in compilation a step further by verifying that the transformation itself is type correct, in the sense that it is impossible that it produces an ill typed term given a well typed term as input. We base our approach on higher-order abstract syntax (HOAS), a representation of programs where variables in the object language are represented by meta-variables. We use a representation that accounts for the object language’s type system using generalized algebraic data types (GADTs). In this way, the full binding and type structure of the object language is exposed to the host language’s type system. In this setting we encode a type preservation property of a CPS conversion in Haskell’s type system, using witnesses of a type correctness proof encoded as values in a GADT.
A Proteomics Study of Brassinosteroid Response in Arabidopsis*S

The plant steroid hormones brassinosteroids (BRs) play an important role in a wide range of developmental and physiological processes. How BR signaling regulates diverse processes remains unclear. To understand the molecular details of BR responses, we performed a proteomics study of BR-regulated proteins in Arabidopsis using two-dimensional DIGE coupled with LC-MS/MS. We identified 42 BR-regulated proteins, which are predicted to play potential roles in BR regulation of specific cellular processes, such as signaling, cytoskeleton rearrangement, vesicle trafficking, and biosynthesis of hormones and vitamins. Analyses of the BR-insensitive mutant bri1-116 and BR-hypersensitive mutant bzr1-1D identified five proteins (PATL1, PATL2, THI1, AtMDAR3, and NADP-ME2) affected both by BR treatment and in the mutants, suggesting their importance in BR action. Selected proteins were further studied using insertion knock-out mutants or immunoblotting. Interestingly about 80% of the BR-responsive proteins were not identified in previous microarray studies, and direct comparison between protein and RNA changes in BR mutants revealed a very weak correlation. RT-PCR analysis of selected genes revealed gene-specific kinetic relationships between RNA and protein responses. Furthermore BR-regulated posttranslational modification of BiP2 protein was detected as spot shifts in two-dimensional DIGE. This study provides novel insights into the molecular networks that link BR signaling to specific cellular and physiological responses.
Memory-color test forms in real-world applications

Many images are received for distribution and reproduction without the possibility of a comparison to the source image. Image quality is difficult to measure and quantify without such a source image. However, test photographs consisting of memory colors can be compared to a remembered image. Test forms consisting of photographs of the real world are the only source of memory colors. They are used to test a graphic-arts color workflow. Such tests: (1) Display the color quality of various output devices. (2) Describe color differences by comparing the difference between reproduction of a test photograph and the remembered colors. (3) Help achieve a preferred state of color reproduction. (4) Characterize reproduction gamut problems of an output device. (5) Remotely trouble-shoot a color workflow. The human visual system cannot provide a precise measurement of quality but does provide direction and goals for a correction process. The criteria for the selection of image content and the usefulness of test photographs are described.
Hidden Markov model state estimation with randomly delayed observations

This paper considers state estimation for a discrete-time hidden Markov model (HMM) when the observations are delayed by a random time. The delay process is itself modeled as a finite state Markov chain that allows an augmented state HMM to model the overall system. State estimation algorithms for the resulting HMM are then presented, and their performance is studied in simulations. The motivation for the model stems from the situation when distributed sensors transmit measurements over a connectionless packet switched communications network.
Chaperone-mediated folding and assembly of myosin in striated muscle

De novo folding and assembly of striated muscle myosin was analyzed by expressing a GFP-tagged embryonic myosin heavy chain (GFP-myosin) in post-mitotic C2C12 myocytes using replication defective adenoviruses. In the early stages of muscle differentiation, the GFP-myosin accumulates in bright globular foci and short filamentous structures that are later replaced by brightly fluorescent myofibrils. Time-lapse microscopy shows that the intermediates are dynamic and are present in elongating and fusing myocytes and in multinucleated myotubes. Immunostaining reveals the co-localization of the molecular chaperones Hsc70 and Hsp90 with the GFP-myosin in the intermediates, but not in the mature myofibrils. Uninfected cells have similar intermediates suggesting a common pathway for myosin maturation. Two conformation-sensitive antibodies that bind the unfolded motor domain and the coiled-coil conformation of the rod demonstrate that in the intermediates, the myosin rod is folded but the motor domain is not folded. Electron microscopy reveals that the intermediates contain loose filament bundles surrounded by a protein rich matrix. Geldanamycin, a specific inhibitor of Hsp90, reversibly blocks myofibril assembly and triggers accumulation of myosin folding intermediates. We conclude that multimeric complexes of nascent myosin filaments associated with Hsc70 and Hsp90 are intermediates in the folding and assembly pathway of muscle myosin.
ICM‐DISCO docking by global energy optimization with fully flexible side‐chains

The ICM‐DISCO (Docking and Interface Side‐Chain Optimization) protein–protein‐docking method is a direct stochastic global energy optimization from multiple starting positions of the ligand. The first step is performed by docking of a rigid all‐atom ligand molecule to a set of soft receptor potentials precalculated on a 0.5 Å grid from realistic solvent‐corrected force‐field energies. This step finds the correct solution as the lowest energy conformation in almost 100% of the cases in which interfaces do not change on binding. The second step is needed to deal with the induced changes and includes the global optimization of the interface side‐chains of up to 400 best solutions. The CAPRI predictions were performed fully automatically with this method. Available experimental information was included as a filtering step to favor expected docking surfaces. In three of the seven proposed targets, the ICM‐DISCO method found a good solution (>50% of correct contacts) within the five submitted models. The procedure is global and fully automated. We demonstrate that the algorithm handles the induced changes of surface side‐chains but is less successful if the backbone undergoes large‐scale rearrangements. Proteins 2003;52:113–117. © 2003 Wiley‐Liss, Inc.
Performance of window synchronisation in coherent optical ofdm system

In this paper we investigate the performances of a robust and efficient technique for frame/symbol timing synchronization in coherent optical OFDM. It uses a preamble consisting of only two training symbol with two identical parts to achieve reliable synchronization schemes. The performances of the timing offset estimator at correct and incorrect timing in coherent optical OFDM are compared in term of mean and variance of the timing offset, and finally, we study the influence of number of subcarriers and chromatic dispersion.
Design Space Exploration Problem Formulation for Dataflow Programs on Heterogeneous Architectures

The implementations of signal processing systems on the emerging many-core or multi-core processing platforms require to solve a very difficult problem: how to partition and schedule the processing tasks according to given optimization functions such as data throughput, memory usage, energy consumption. Implementations based on dataflow programming approaches are recognized to be particularly interesting for this challenge, because dataflow network components can be partitioned onto the processing units always yielding correct system behaviors. Moreover, the space of feasible configurations can be explored using heuristics and this is not the case for other implementation approaches for which, for each configuration, it is required to rewrite entire parts of the application programs. This paper investigates the features of the design space exploration problem by considering a new formal formulation of the partitioning, scheduling and buffer dimensioning problem for the case of dynamic dataflow programs. Furthermore, it demonstrates which heuristics, with the associated optimization functions relying on this formulation, can be identified for providing high quality solutions.
Members of the LBD Family of Transcription Factors Repress Anthocyanin Synthesis and Affect Additional Nitrogen Responses in Arabidopsis[W][OA]

Nitrogen (N) and nitrate (NO3−) per se regulate many aspects of plant metabolism, growth, and development. N/NO3− also suppresses parts of secondary metabolism, including anthocyanin synthesis. Molecular components for this repression are unknown. We report that three N/NO3−-induced members of the LATERAL ORGAN BOUNDARY DOMAIN (LBD) gene family of transcription factors (LBD37, LBD38, and LBD39) act as negative regulators of anthocyanin biosynthesis in Arabidopsis thaliana. Overexpression of each of the three genes in the absence of N/NO3− strongly suppresses the key regulators of anthocyanin synthesis PAP1 and PAP2, genes in the anthocyanin-specific part of flavonoid synthesis, as well as cyanidin- but not quercetin- or kaempferol-glycoside production. Conversely, lbd37, lbd38, or lbd39 mutants accumulate anthocyanins when grown in N/NO3−-sufficient conditions and show constitutive expression of anthocyanin biosynthetic genes. The LBD genes also repress many other known N-responsive genes, including key genes required for NO3− uptake and assimilation, resulting in altered NO3− content, nitrate reductase activity/activation, protein, amino acid, and starch levels, and N-related growth phenotypes. The results identify LBD37 and its two close homologs as novel repressors of anthocyanin biosynthesis and N availability signals in general. They also show that, besides being developmental regulators, LBD genes fulfill roles in metabolic regulation.
The use of auditory and visual context in speech perception by listeners with normal hearing and listeners with cochlear implants

There is a wide range of acoustic and visual variability across different talkers and different speaking contexts. Listeners with normal hearing (NH) accommodate that variability in ways that facilitate efficient perception, but it is not known whether listeners with cochlear implants (CIs) can do the same. In this study, listeners with NH and listeners with CIs were tested for accommodation to auditory and visual phonetic contexts created by gender-driven speech differences as well as vowel coarticulation and lip rounding in both consonants and vowels. Accommodation was measured as the shifting of perceptual boundaries between /s/ and /∫/ sounds in various contexts, as modeled by mixed-effects logistic regression. Owing to the spectral contrasts thought to underlie these context effects, CI listeners were predicted to perform poorly, but showed considerable success. Listeners with CIs not only showed sensitivity to auditory cues to gender, they were also able to use visual cues to gender (i.e., faces) as a supplement or proxy for information in the acoustic domain, in a pattern that was not observed for listeners with NH. Spectrally-degraded stimuli heard by listeners with NH generally did not elicit strong context effects, underscoring the limitations of noise vocoders and/or the importance of experience with electric hearing. Visual cues for consonant lip rounding and vowel lip rounding were perceived in a manner consistent with coarticulation and were generally used more heavily by listeners with CIs. Results suggest that listeners with CIs are able to accommodate various sources of acoustic variability either by attending to appropriate acoustic cues or by inferring them via the visual signal.
Youth Fusion's Urban Environment Project: Increasing Youth Participation in Urban Planning through Place-Based Environmental Education

Abstract:Communities and planners alike have come to understand the potential benefits of youth participation in the planning of urban spaces. School retention is also seen as a societal priority. This field report presents a classroom program developed and piloted at a public high school in Montreal to explore how place-based education can be used to facilitate youth participation and school perseverance. Following a review of this program, its objectives, and its implementation, we conclude with a discussion of challenges and opportunities associated with place-based education.
The 4 th International Conference on Ambient Systems, Networks and Technologies (ANT 2013) A Study of Wireless Sensor Networks for Urban Traffic Monitoring: Applications and Architectures

With the constant increasing of vehicular traffic around the world, especially in urban areas, existing traffic management solutions become inefficient. This can be clearly seen in our life through persistent traffic jam and rising number of accidents. Wireless sensor networks (WSN) based intelligent transportation systems (ITS) have emerged as a cost effective technology that bear a pivotal potential to overcome these difficulties. This technology enables a new broad range of smart city applications around urban sensing including traffic safety, traffic congestion control, road state monitoring, vehicular warning services, and parking management. This manuscript gives a comprehensive review on WSN based ITS solutions. The main contribution of this paper is to classify current WSNs based ITS projects from the application perspective, with discussions on the fulfillment of the application requirements. © 2011 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of [name organizer]
Simulation-based Estimation of Contingent-claims Prices 1

A new methodology is proposed to estimate theortical prices of financial contingent-claims whose values are dependent on some other underlying financial assets. In the literature the preferred choice of estimator is usually maximum likelihood (ML). ML has strong asymptotic justification but is not necessarily the best method in finite samples. The present paper proposes instead a simulation-based method that improves the finite sample performance of the ML estimator while maintaining its good asymptotic properties. The methods are implemented and evaluated here in the Black-Scholes option pricing model and in the Vasicek bond pricing model, but have wider applicability. Monte Carlo studies show that the proposed procedures achieve bias reductions over ML estimation in pricing contingent claims. The bias reductions are sometimes accompanied by reductions in variance, leading to significant overall gains in mean squared estimation error. Empirical applications to US treasury bills highlight the differences between the bond prices implied by the simulation-based approach and those delivered by ML. Some consequences for the statistical testing of contingent-claim pricing models are discussed.
Framework to quantify the metabolic rate in the heart using Monte Carlo simulation and compartmental modeling

The Nuclear Medicine imaging using PET modality allows evaluating the physiological condition of the heart (i.e. heart disease, perfusion, cardiac stress, physics disorders, etc.), by the use of small amounts of radioactive material. While the visual information provided by PET image is quite important and today is heavily used by the specialists, it is clear that having quantitative values of the metabolism would help to determine the real condition of the myocardium, to get a more accurate diagnosis and to apply a better treatment. Thus, we developed a framework using different tools to simulate a real PET exam focused in the heart in order to analyze the metabolic exchange in this organ. This research produced realistic PET exams by using GATE platform that performs Monte Carlo simulations, together with an anthropomorphic phantom of the whole body called MASH. This study consisted of the modeling of a commercial PET scanner with BGO detectors, where the MASH's thorax was imaged by the scanner. In order to enhance the realism of the simulation, clinical data was considered, like the quantity of radiotracer (FDG) injected, time of acquisition, and number of frames along the time, among others. Next, the projections were reconstructed using STIR's algorithms. With the aim of obtaining a better quality of the volumes and to select the specific ROI, filtering and segmentation algorithms were applied, respectively. Finally, the heart metabolic analysis was performed using a mathematical model that seeks to describe and to quantify the level of consumption and exchange of glucose in the heart through a model with three compartments. The metabolic parameters obtained were: K1=0.5690, k2=0.2266, k3=0.0718, and k4=0.0243. It was evidenced that the process of metabolic quantification using compartmental modeling is significantly relevant because of its flexibility, noninvasiveness and reliability. Hereafter, we will apply this framework under real PET images.