Miracle-dz/UniFAR-FTUs huggingface dataset:
Follicle-Stimulating Hormone and Its α and β Subunits in Rainbow Trout (Oncorhynchus mykiss): Purification, Characterization, Development of Specific Radioimmunoassays, and Their Seasonal Plasma and Pituitary Concentrations in Females1

Abstract Gonad development in fish, as in mammals, is regulated by two gonadotropins (GTHs), FSH and LH. The function of LH in fish has been clearly established; however, the function(s) of FSH is less certain. The lack of specific and sensitive assays to quantify FSH and its α and β subunits has hindered studies to assess physiological function. In this study, gel filtration chromatography, ion exchange chromatography, and HPLC were employed to purify FSH and its subunits from pituitary glands of rainbow trout (Oncorhynchus mykiss), and the identities of the isolates were confirmed by amino acid analysis. Polyclonal antibodies were raised against the free GTHα2 and free FSHβ subunits to develop specific RIAs. The sensitivities of the intact FSH, GTHα2, and FSHβ assays were 1 ng/ml, 0.2 ng/ml, and 0.1 ng/ml, respectively, and the cross-reaction of these molecules with each other and with intact LH in the heterologous assays was <10.4% throughout. Pituitary and plasma samples diluted in parallel with the standards in all three assays and spiked sample recoveries were >90% throughout. Measurement of plasma and pituitary concentrations of intact FSH in female rainbow trout confirmed the established seasonal profiles. Concentrations of free GTHα2 subunit were elevated both in the plasma and in the pituitary in females at ovulation (maximum concentrations: 34.93 ± 6.3 ng/ml in plasma; 37.63 ± 5.79 μg/pituitary). In both the plasma and the pituitary, free FSHβ subunit was present throughout the reproductive cycle but at very low concentrations when compared with both free GTHα2 and intact FSH. The presence of free GTHα2 subunit in the plasma similarly occurs in mammals, but its functional significance in fish has yet to be established.
Efficient Shuffle Arguments Research Seminar Project

Anonymous communication is useful in variety of online applications. Evoting, online chat software and data collection for surveying are some of the applications where anonymity is an important feature. One way to guarantee anonymous network communication is using a mix network (mix-net) protocol. A mix network is a protocol that contains several mix servers. A mix server collects user’s ciphertexts, cryptographically transforms and permutes them and then sends the ciphertexts to the destination or to another mix server. Shuffling guarantees that an adversary eavesdropping on the network cannot connect source of the ciphertext to the destination as long as at least one of the mix servers is honest. It is highly important that a mix server does the permutation correctly. For example in e-voting it would disastrous if a malicious mix server could change votes at will. At the same time revealing the permutation would defeat the purpose of a mix network. Solution is that the mix server must produce a zero-knowledge proof that the permutation was done correctly. Mix server must prove that the output ciphertexts are rerandomized and permuted input ciphertexts without revealing anything about the permutation. This report gives an overview of two efficient zero-knowledge arguments for shuffles. Section 1 gives a summary of mix-nets. Section 2 covers preliminaries needed for zero-knowledge arguments. In section 3 we look at interactive argument for shuffles introduced by Neff in article [1]. In section 4 we study a shuffle protocol by Groth from [3].
Impairment of conditioned freezing to tone, but not to context, in Fyn‐transgenic mice: relationship to NMDA receptor subunit 2B function

We previously demonstrated that transgenic mice overexpressing Fyn tyrosine kinase exhibit higher seizure susceptibility and enhanced tyrosine phosphorylation of several proteins, including the N‐methyl‐D‐aspartate (NMDA) receptor subunit 2B (NR2B). In the present study, we analysed behavioural phenotypes, especially conditioned fear responses, of Fyn‐transgenic (TG) mice to better understand the role of Fyn in learned emotional behaviour. Tone‐dependent conditioned freezing was significantly attenuated in Fyn‐TG mice, whereas context‐dependent freezing was unaffected. Neither massed nor spaced conditioning ameliorated the attenuation of tone‐dependent freezing. However, the selective NR2B antagonist ifenprodil, when administered before conditioning, restored tone‐dependent freezing in Fyn‐TG mice at a dose that did not affect freezing in wild‐type (WT) mice. These results suggest that impairment of tone‐dependent conditioned freezing in Fyn‐TG mice is caused by disruption of the NR2B‐containing NMDA receptor function. Tyrosine phosphorylation of brain proteins, including NR2B, was enhanced in Fyn‐TG mice compared with that in WT mice. We also found that ifenprodil significantly suppressed the enhanced tyrosine phosphorylation. Thus, our data support the notion that NMDA receptor activity is tightly correlated with protein tyrosine phosphorylation, and Fyn might be one key molecule that controls tone‐dependent conditioned freezing through the regulation of NMDA receptor function.
A Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location -- SALSA3D

To test the hypothesis that high quality 3D Earth models will produce seismic event locations which are more accurate and more precise, we are developing a global 3D P wave velocity model of the Earth's crust and mantle using seismic tomography. In this paper, we present the most recent version of our model, SALSA3D version 1.5, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth events. Our model is derived from the latest version of the Ground Truth (GT) catalog of P and Pn travel time picks assembled by Los Alamos National Laboratory. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays to produce representative rays. Reduction in the total number of ray paths is {approx}50%. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions. For our starting model, we use a simplified two layer crustal model derived from the Crust 2.0 model over a uniform AK135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changesmore » between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only around areas with significant velocity changes from the starting model. At each grid refinement level except the last one we limit the number of iterations to prevent convergence thereby preserving aspects of broad features resolved at coarser resolutions. Our approach produces a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. This scheme is computationally expensive, so we use a distributed computing framework based on the Java Parallel Processing Framework, providing us with {approx}400 processors. Resolution of our model is assessed using a variation of the standard checkerboard method. We compare the travel-time prediction and location capabilities of SALSA3D to standard 1D models via location tests on a global event set with GT of 5 km or better. These events generally possess hundreds of Pn and P picks from which we generate different realizations of station distributions, yielding a range of azimuthal coverage and ratios of teleseismic to regional arrivals, with which we test the robustness and quality of relocation. The SALSA3D model reduces mislocation over standard 1D ak135 regardless of Pn to P ratio, with the improvement being most pronounced at higher azimuthal gaps. « less
Issues Associated With the Use of Semantic Web Technology in Knowledge Acquisition for Clinical Decision Support Systems: Systematic Review of the Literature

Background Knowledge-based clinical decision support system (KB-CDSS) can be used to help practitioners make diagnostic decisions. KB-CDSS may use clinical knowledge obtained from a wide variety of sources to make decisions. However, knowledge acquisition is one of the well-known bottlenecks in KB-CDSSs, partly because of the enormous growth in health-related knowledge available and the difficulty in assessing the quality of this knowledge as well as identifying the “best” knowledge to use. This bottleneck not only means that lower-quality knowledge is being used, but also that KB-CDSSs are difficult to develop for areas where expert knowledge may be limited or unavailable. Recent methods have been developed by utilizing Semantic Web (SW) technologies in order to automatically discover relevant knowledge from knowledge sources. Objective The two main objectives of this study were to (1) identify and categorize knowledge acquisition issues that have been addressed through using SW technologies and (2) highlight the role of SW for acquiring knowledge used in the KB-CDSS. Methods We conducted a systematic review of the recent work related to knowledge acquisition MeM for clinical decision support systems published in scientific journals. In this regard, we used the keyword search technique to extract relevant papers. Results The retrieved papers were categorized based on two main issues: (1) format and data heterogeneity and (2) lack of semantic analysis. Most existing approaches will be discussed under these categories. A total of 27 papers were reviewed in this study. Conclusions The potential for using SW technology in KB-CDSS has only been considered to a minor extent so far despite its promise. This review identifies some questions and issues regarding use of SW technology for extracting relevant knowledge for a KB-CDSS.
Functional consequences of haemophilia in adults: the development of the Haemophilia Activities List

Summary. Several instruments can be used to evaluate the functional status of patients with haemophilia, but none of these instruments is specific for haemophilia. We developed a haemophilia‐specific self‐assessment questionnaire to evaluate and monitor a patient's perceived functional health status: the Haemophilia Activities List (HAL). In three separate but interlinked substudies, the questionnaire was constructed and tested for face, expert, and convergent validity, as well as internal consistency and patient‐evaluated relevance. Items for the questionnaire were collected by interviewing 162 patients, using the McMaster‐Toronto Arthritis Patient Preference Disability Questionnaire (MACTAR). The items were combined to generate the first version of the questionnaire [HAL(1)]. This version was evaluated and commented on by two focus groups (patients and caregivers), and then the questionnaire was adapted on the basis of these comments, forming the final version, HAL(2). This version was then validated in a pilot study with 50 consecutive patients using the Dutch Arthritis Impact Measurements Scales 2 (Dutch‐AIMS2) and the Impact on Participation and Autonomy (IPA) questionnaires. The HAL(2) showed good convergent validity (Pearson correlation 0.80–0.91; P < 0.01), and the internal consistency was good for six of the eight domains (Cronbach's α 0.83–0.95). Patients considered the content of the HAL to be more relevant to their situation than the content of the other questionnaires (P < 0.01). Three major factors (upper extremity function, lower extremity function, key activities/major problem activities) were identified by factor analysis. The questionnaire seems to be a useful tool to identify problematic activities as part of the functional health status of patients with haemophilia. The construct validity, test–retest reliability, and responsiveness of the HAL will be established in the future.
Characteristic Time of Diffusive Mixing in Cube with Reflecting Edges

V. V. Uchaikin suggested a mathematical model of an anomalous diffusion in a space. These model origins in an investigation of processes in complex systems with variable structure: glasses, liquid crystals, biopolymers, proteins and a turbulence in a plasma. Here a coordinate of diffusing particle has stable distribution and so its density satisfies diffusion equation with partial derivatives. In this paper, the anomalous diffusion with periodic initial conditions on an interval with reflecting edges, important for example in technical mechanics, is considered and analyzed.
Feature matching for underwater image via superpixel tracking

Feature matching is fundamental to many vision tasks. Due to the low visibility of images in underwater environments, traditional pixels-based matching methods suffer from miss-matching or error-matching. Recently, Superpixel based features have been applied to image feature analysis. However, most of existing methods dedicate to rectified stereo matching with images captured in the air. This paper presents a novel feature matching scheme aiming at underwater images. It targets the un-rectified image pair from the video sequence. The Superpixel matching process is fulfilled with multiclass labelling based on Markov Random Field (MRF). Experiments show that the proposed method produces competitive performance.
Evaluation of biologically relevant short alpha-helices stabilized by a main-chain hydrogen-bond surrogate.

We previously reported the design and synthesis of a new class of artificial alpha-helices in which an N-terminal main-chain hydrogen bond is replaced by a carbon-carbon bond derived from a ring-closing metathesis reaction [Chapman, R. N. ; Dimartino, G. ; Arora, P. S. J. Am. Chem. Soc. 2004, 126, 12252-12253]. Our initial study utilized an alanine-rich sequence; in the present manuscript we evaluate the potential of this method for the synthesis of very short (10 residues) alpha-helices representing two different biologically relevant alpha-helical domains. We extensively characterized these two sets of artificial helices by NMR and circular dichroism spectroscopies and find that the hydrogen-bond surrogate approach can afford well-defined short alpha-helical structures from sequences that do not spontaneously form alpha-helical conformations.
Sonido y sociabilidad: consistencia bioacústica en espacios públicos

Cual es el papel del sonido en la adaptacion al medio ambiente? En que medida ha influido la percepcion sonora y su modificacion en el peculiar devenir adaptativo de la especie humana? Mediante que mecanismos recodificamos la informacion auditiva que imprimimos en los espacios que hacemos sonar? Cual es el rol de la informacion sonora en la construccion del espacio publico? Preguntas a las que se intenta responder a traves de la extrapolacion de las teorias bioacusticas contemporaneas a los ambitos urbanos. Un analisis comparativo a raiz del conocimiento antropologico mediante herramientas conceptuales propias de la disciplina y de otras que, como la ecologia o la etologia, estudian campos limitrofes de fronteras difusas. Entre sonido, silencio y musica.
Application of data mining to medical risk management

This paper proposes an application of data mining to medical risk management, where data mining techniques were applied to detection, analysis and evaluation of risks potentially existing in clinical environments. We applied this technique to the following two medical domains: risk aversion of nurse incidents and infection control. The results show that data mining methods were effective to detection and aversion of risk factors.
Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L−1] and hypoxia (DO = 4□5 mg L−1) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.
Comptabilité sans frontières: intérêt d'une cartographie

Comme bien des domaines des sciences de gestion le champ de la comptabilite n'echappe pas aux metaphores. Parmi elles, l'expression " langage comptable " est sans doute la plus courante. Mais d'autres metaphores sont utilisees, comme celles de la photographie, des lentilles ou du jeu de societe Scrabble. Chacune met l'accent sur certaines des nombreuses caracteristiques de la comptabilite. Dans cet article nous proposons une nouvelle metaphore, celle de la carte, pour decrire, comprendre et expliquer un objet souvent percu comme complexe pour les non inities, et illisible par le grand public : les documents comptables. Cette metaphore permet, au-dela de son interet pedagogique, de vivifier la recherche comptable en deplacant l'attention de la fonction " communication " de la comptabilite vers celle de " representation ".
A 128 kb/s Hi-Fi Audio CODEC Based on Adaptive Transform Coding with Adaptive Block Size MDCT

A Hi-Fi audio codec with an improved adaptive transform coding (ATC) algorithm is presented using digital signal processors (DSPs). An audio signal with a 20 kHz bandwidth sampled at 48 kHz is coded at a rate of 128 kb/s. The algorithm utilizes adaptive block size selection, which is effective for preecho suppression. A modified discrete cosine transform (MDCT) with a simple window set is employed to reduce block boundary noise without decreasing the performance of transform coding. In addition, a fast MDCT calculation algorithm, based on a fast Fourier transform, is adopted. Weighted bit allocation is employed to quantize the transformed coefficients. The codec was realized by a multiprocessor system composed of newly developed DSP boards. Subjective tests with the codec show that the coding quality is comparable to that of compact disc signals. >
JINDY: A java library to support invokedynamic

Java 7 has included the new invokedynamic opcode in the Java virtual machine. This new instruction allows the user to define method linkage at runtime. Once the link is established, the virtual machine performs its common optimizations, providing better runtime performance than reflection. However, this feature has not been offered at the abstraction level of the Java programming language. Since the functionality of the new opcode is not provided as a library, the existing languages in the Java platform can only use it at the assembly level. For this reason, we have developed the JINDY library that offers invokedynamic to any programming language in the Java platform. JINDY supports three modes of use, establishing a trade-off between runtime performance and flexibility. A runtime performance and memory consumption evaluation is presented. We analyze the efficiency of JINDY compared to reflection, the MethodHandle class in Java 7 and the Dynalink library. The memory and performance costs compared to the invokedynamic opcode are also measured.
Molecular opacities for exoplanets

Spectroscopic observations of exoplanets are now possible by transit methods and direct emission. Spectroscopic requirements for exoplanets are reviewed based on existing measurements and model predictions for hot Jupiters and super-Earths. Molecular opacities needed to simulate astronomical observations can be obtained from laboratory measurements, ab initio calculations or a combination of the two approaches. This discussion article focuses mainly on laboratory measurements of hot molecules as needed for exoplanet spectroscopy.
HB-PLS: An algorithm for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression

Gene expression data features high dimensionality, multicollinearity, and the existence of outlier or non-Gaussian distribution noise, which make the identification of true regulatory genes controlling a biological process or pathway difficult. In this study, we embedded the Huber-Berhu (HB) regression into the partial least squares (PLS) framework and created a new method called HB-PLS for predicting biological process or pathway regulators through construction of regulatory networks. PLS is an alternative to ordinary least squares (OLS) for handling multicollinearity in high dimensional data. The Huber loss is more robust to outliers than square loss, and the Berhu penalty can obtain a better balance between the ℓ2 penalty and the ℓ1 penalty. HB-PLS therefore inherits the advantages of the Huber loss, the Berhu penalty, and PLS. To solve the Huber-Berhu regression, a fast proximal gradient descent method was developed; the HB regression runs much faster than CVX, a Matlab-based modeling system for convex optimization. Implementation of HB-PLS to real transcriptomic data from Arabidopsis and maize led to the identification of many pathway regulators that had previously been identified experimentally. In terms of its efficiency in identifying positive biological process or pathway regulators, HB-PLS is comparable to sparse partial least squares (SPLS), a very efficient method developed for variable selection and dimension reduction in handling multicollinearity in high dimensional genomic data. However, HB-PLS is able to identify some distinct regulators, and in one case identify more positive regulators at the top of output list, which can reduce the burden for experimental test of the identified candidate targets. Our study suggests that HB-PLS is instrumental for identifying biological process and pathway genes.