Miracle-dz/UniFAR-FTUs huggingface dataset:
A synonymous codon variant in two patients with autosomal recessive bestrophinopathy alters in vitro splicing of BEST1

Purpose Autosomal recessive bestrophinopathy (ARB) is a newly defined retinal dystrophy caused by biallelic mutations in bestrophin-1 (BEST1) and is hypothesized to represent the null bestrophin-1 phenotype in humans. The aim was to determine whether a synonymous BEST1 variant, c.102C>T, identified in two unrelated ARB patients, alters pre-mRNA splicing of the gene. Additionally a detailed phenotypic characterization of this distinctive condition is presented for both patients. Methods BEST1 was analyzed by direct sequencing. Patients underwent standard ophthalmic assessment. In silico and in vitro analysis using a minigene system was performed to assess whether a synonymous variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing of BEST1. Results Both ARB patients harbored either proven (patient 1; c.102C>T p.Gly34Gly and c.572T>C p.Leu191Pro) or presumed (patient 2; c.102C>T p.Gly34Gly and c.1470_1471delCA, p.His490GlnfsX24) biallelic mutations in BEST1 and were found to have phenotypes consistent with ARB. In vitro analysis of the synonymous variant, c.102C>T p.Gly34Gly, demonstrated it to introduce a cryptic splice donor site 52 nucleotides upstream of the actual splice donor site. Conclusions The novel BEST1 variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing in vitro and is potentially pathogenic. In vivo this splicing variant is predicted to lead to the production of an mRNA transcript with a premature termination codon (p.Glu35TrpfsX11) that is predicted to be degraded by NMD.
PET evaluation of lung cancer.

In the last hundred years, lung cancer has risen from a reportable disease to the most common cause of death from cancer in both men and women in developed countries (1). When descriptions of lung cancer were published in 1912, there were only 374 reported cases (2). In the 1950s, little more than the chest radiograph and sputum cytologic analysis were available for lung cancer screening. Since then, the mortality from lung cancer has decreased, but the 5-y cure rates have barely improved (1). The annual number of deaths from lung cancer is greater than the numbers of deaths from breast, colon, and prostate cancers combined. More than 150,000 patients died of lung cancer in 2004. The 5-y survival rates currently are 16% in the United States and 5% in the United Kingdom. The association of lung cancer with tobacco smoking was initially reported in the 1950s (3) and subsequently led to the determination by the U.S. Surgeon General that smoking is harmful to one’s health (4). Further investigation has led to the discovery that this association is related to the type and amount of tobacco product used, the age at initiation, and the duration of use. Lung cancer often presents as a solitary pulmonary nodule on chest radiographs. Chest radiographs usually are performed for patients as a preoperative or physical examination screening test, often in the absence of symptoms. Few signs and symptoms are present at an early stage, leading to more advanced disease when patients present to their physicians. One third of lung nodules in patients more than 35 y old are found to be malignant. Over 50% of the radiographically indeterminate nodules resected at thoracoscopy are benign (5). It is clear that there is a need for the accurate diagnosis of these lesions. The use of PET has much promise as an aid to the noninvasive evaluation of lung cancer. 18F-FDG PET currently is indicated for the characterization of lung lesions, staging of non–small cell lung carcinoma (NSCLC), detection of distant metastases, and diagnosis of recurrent disease. Furthermore, many institutions have found significant value in 18F-FDG PET for treatment monitoring (6–8).
Constructing Anisotropic Geometric Metrics using Octrees and Skeletons

A three-dimensional anisotropic metric for geometry-based mesh adaptation is constructed from a triangulated domain definition. First, a Cartesian background octree is refined according to not only boundary curvature but also a local separation criterion from digital topology theory. This octree is then used to extract the domain skeleton through a medial axis transform. Finally, an efficient anisotropic metric is computed on the octree using the curvature tensor estimated from the boundary triangulation and the local domain thickness information embedded in the skeleton. Applications to geometric adaptation of overlay meshes used in grid-based methods for unstructured hexahedral mesh generation are also presented.
A New Physical-Layer Network Coding Scheme with Eigen-Direction Alignment Precoding for MIMO Two-Way Relaying

We investigate efficient communication over multiple-input multiple-output (MIMO) two-way relay channels (TWRCs), where two multi-antenna users exchange information via a multi-antenna relay. We propose a new MIMO physical-layer network coding (PNC) scheme that includes novel eigen-direction alignment (EDA) precoding. The proposed EDA precoding efficiently aligns the two-user's eigen-modes into the same set of orthogonal directions, and multiple independent PNC streams are implemented over the aligned eigen-modes. We derive an achievable rate-pair of the proposed scheme, for given EDA precoding parameters, over a MIMO TWRC. To maximize the achievable rate-region, we formulate a design criterion for the EDA precoding parameters, and present solutions to the formulation. Closed-form bounds on the sum-rates of the designed EDA-PNC schemes are derived. Numerical results show that there is only a small gap between the achievable rate of the proposed scheme and the capacity upper bound of the MIMO TWRC. It is shown that the proposed scheme can significantly outperforms existing schemes in the literature.
Properties of Concrete made with Waste Clay Brick as Sand Incorporating Nano SiO 2

The present study aims to investigate the use of clay bricks in concrete preparation. In the first phase of the study, the clay bricks as waste materials from building remains were collected and ground by jaw mills and finally graded in the range of standard sand. The first experiments like XRF, water absorption, and unit weight were then carried out on the materials. After that, some samples with substitution percents of zero to one hundred from waste bricks as sand were made and the new concrete parameters such as compressive strength, water absorption and unit Weight were examined. In the second phase, nano SiO 2 in all mixes from the brick waste materials were replaced for the cement and then the experiments of compressive strength and water absorption were done on the samples that contained nano SiO 2 and waste clay bricks. The results clearly revealed that, in light of some positive effect such as a reduction in the concrete unit weight and recycling the waste materials and also the minimum reduction of compressive strength, using brick waste materials may be considered a suitable choice in concrete especially in areas close to brick furnaces. Furthermore, nano SiO 2 can improve the strength and durability of concrete. Conclusively, using waste bricks can be an effective measure in sustainable development.
Rubberlike Elasticity: A Molecular Primer

FUNDAMENTALS. Some Rubberlike Materials. Preparation Statistical Theory for Idealized Networks. Statistical Theory for Real Networks. Elastic Equations of State. Swelling of Networks. Force as a Function of Deformation. Force as a Function of Temperature. Force as a Function of Structure. ADDITIONAL TOPICS. Networks Prepared under Unusual Conditions. Strain--induced Crystallization and Ultimate Properties. Bimodal Networks and Non--Gaussian Behavior. Birefringence. Segmental Orientation. Rotational Isomerization. Osmotic Compressibility, Critical Phenomena, and Gel Collapse. Neutron Scattering from Networks. Bioelastomers. Filled Elastomers. Current Problems and New Directions. Appendixes. References. Bibliography. Index.
Does the Majority Always Know Best? Young Children's Flexible Trust in Majority Opinion

Copying the majority is generally an adaptive social learning strategy but the majority does not always know best. Previous work has demonstrated young children's selective uptake of information from a consensus over a lone dissenter. The current study examined children's flexibility in following the majority: do they overextend their reliance on this heuristic to situations where the dissenting individual has privileged knowledge and should be trusted instead? Four- to six- year-olds (N = 103) heard conflicting claims about the identity of hidden drawings from a majority and a dissenter in two between-subject conditions: in one, the dissenter had privileged knowledge over the majority (he drew the pictures); in the other he did not (they were drawn by an absent third party). Overall, children were less likely to trust the majority in the Privileged Dissenter condition. Moreover, 5- and 6- year-olds made majority-based inferences when the dissenter had no privileged knowledge but systematically endorsed the dissenter when he drew the pictures. The current findings suggest that by 5 years, children are able to make an epistemic-based judgment to decide whether or not to follow the majority rather than automatically following the most common view.
The spectrum of MHD flows about X points

A recently proposed method to calculate the spectrum of linear, incompressible, unbounded plasma flows is applied to magnetohydrodynamic flows about X points. The method transforms the two-dimensional spectral problem in physical space into a one-dimensional problem in Fourier space. The latter problem is far easier to solve. Application of this method to X-point plasma flows results in two kinds of essential spectra. One kind corresponds to stable perturbations and the other one to perturbations that become overstable whenever the square of the poloidal Alfvén Mach number becomes larger than 1. Apart from these two spectra, no other spectral values were found.
First simultaneous NIR/X-ray detection of a flare from Sgr A

We report on the first simultaneous near-infrared/X-ray detection of the Sgr A* counterpart associated with the massive 3-4 × 10 6 Mblack hole at the center of the Milky Way. The observations have been carried out using the NACO adaptive optics (AO) instrument at the European Southern Observatory's Very Large Telescopeand the ACIS-I instrument aboard the Chandra X-ray Observatory. We also report on quasi-simultaneous observations at a wavelength of 3.4 mm using the Berkeley-Illinois-Maryland Association (BIMA) array. A flare was detected in the X-domain with an excess 2-8 keV luminosity of about 6 × 10 33 erg/s. A fading flare of Sgr A* with >2 times the interim-quiescent flux was also detected at the beginning of the NIR observations, that overlapped with the fading part of the X-ray flare. Compared to 8-9 h before the NIR/X-ray flare we detected a marginally significant increase in the millimeter flux density of Sgr A* during measurements about 7-9 h afterwards. We find that the flaring state can be conveniently explained with a synchrotron self-Compton model involving up-scattered sub-millimeter photons from a compact source component, possibly with modest bulk relativistic motion. The size of that component is assumed to be of the order of a few times the Schwarzschild radius. The overall spectral indices αNIR/X−ray (S ν ∝ ν −α ) of both states are quite comparable with a value of ∼1.3. Since the interim-quiescent X-ray emission is spatially extended, the spectral index for the interim-quiescent state is probably only a lower limit for the compact source Sgr A*. A conservative estimate of the upper limit of the time lag between the ends of the NIR and X-ray flare is of the order of 15 min.
Efficient estimation of the total number of acini in adult rat lung

Pulmonary airways are subdivided into conducting and gas‐exchanging airways. An acinus is defined as the small tree of gas‐exchanging airways, which is fed by the most distal purely conducting airway. Until now a dissector of five consecutive sections or airway casts were used to count acini. We developed a faster method to estimate the number of acini in young adult rats. Right middle lung lobes were critical point dried or paraffin embedded after heavy metal staining and imaged by X‐ray micro‐CT or synchrotron radiation‐based X‐rays tomographic microscopy. The entrances of the acini were counted in three‐dimensional (3D) stacks of images by scrolling through them and using morphological criteria (airway wall thickness and appearance of alveoli). Segmentation stopper were placed at the acinar entrances for 3D visualizations of the conducting airways. We observed that acinar airways start at various generations and that one transitional bronchiole may serve more than one acinus. A mean of 5612 (±547) acini per lung and a mean airspace volume of 0.907 (±0.108) μL per acinus were estimated. In 60‐day‐old rats neither the number of acini nor the mean acinar volume did correlate with the body weight or the lung volume.
An Interface Agent for Attention Manipulation (Extended Abstract)

This paper describes the idea of an interface agent that is able to manipulate the visual attention of a human, in order to support naval crew in a tactical picture compilation task. The agent will consist of four submodels, including a model to reason about a subject’s attention. In a study (not presented here) a practical case study was formally analysed, and the results were verified using automated checking tools. These results show how a human subject’s attention is manipulated by adjusting luminance, based on comparative assessment involving a descriptive and a prescriptive model of the subject’s attention.
An Example-based Decoder for Spoken Language Machine Translation

In this paper, we propose an example-based decoder for a statistical machine translation (SMT) system, which is used for spoken language machine translation. In this way, it will help to solve the re-ordering problem and other problems for spoken language MT, such as lots of omissions, idioms etc. Through experiments, we show that this approach obtains improvements over the baseline on a Chinese-English spoken language translation task.
Peroxisome proliferator-activated receptors: nuclear control of metabolism.

I. Introduction II. Molecular Aspects A. PPAR isotypes: identity, genomic organization and chromosomal localization B. DNA binding properties C. PPAR ligand-binding properties D. Alternative pathways for PPAR activation E. PPAR-mediated transactivation properties III. Physiological Aspects A. Differential expression of PPAR mRNAs B. PPAR target genes and functions in fatty acid metabolism C. PPARs and control of inflammatory responses D. PPARs and atherosclerosis E. PPARs and the development of the fetal epidermal permeability barrier F. PPARs, carcinogenesis, and control of the cell cycle IV. Conclusions
Estimating the number of endmembers from hyperspectral image using noncentral chi-squared distribution model

In this paper, a statistical method of estimating the number of endmembers from hyperspectral images is proposed. A noncentra chi-squared distribution model is applied to calculate this number. Endmembers are important parameters in many hyperspectral detection algorithms based on Linear Mixture Model(LMM). The number of endmenbers is the only preset parameter and needed in some anomaly detectors. However, this number is hard to estimate because it has a relationship with the complexity of the scene of images. In this paper, we use a noncentral chi-squared distribution to approximate the projected image of subspace based on anomaly detectors, and estimate the number of endmembers by calculating the degrees of freedom. Firstly, the statistical model of the projected multivariate data is analysed, and a noncentral chi-squared distribution is deduced. Then, the parameter calculation and endmember number estimation are introduced respectively. At last, the aerial hyperspectral images are used to verify the effectiveness of the proposed method.
Spatial-Temporal Distribution of Manganese in Lake Baiyangdian, China

The concentrations of Mn in water and sediments of different functional areas in Lake Baiyangdian were monitored in representative months from 2009 to 2010. The results showed that the concentration of Mn had spatial-temporal distribution characteristics. Mn in the overlying water ranged from 0.05 to 2.39 mgL-1, and was higher in May and October than that in August and March. Sites in the fish-rearing zone had the highest Mn concentration, while natural site had the lowest Mn concentration. The concentration of Mn in the surface of sediments ranged from 144.95 to 1317.04 mgkg-1. The concentration of Mn was higher in March than in other months. Sites in the duck-rearing zone had the highest Mn concentration, while garbage dumping site had the lowest Mn concentration. Human activity such as aquaculture had an obvious effect on the concentration of Mn in Lake Baiyangdian.
Development of novel carbon nanotube reinforced magnesium nanocomposites using the powder metallurgy technique

Carbon nanotube (CNT) reinforced magnesium was synthesized using the powder metallurgy technique followed by hot extrusion. Up to 0.3 wt% of CNTs were added as reinforcements. The effects of the carbon nanotubes on the physical and mechanical properties of Mg were investigated. The thermo-mechanical property results show an increase in thermal stability with increasing amount of CNTs in the Mg nanocomposites. Mechanical property characterizations reveal an improvement of yield strength, ductility and work of fracture with higher weight percentages of CNTs incorporated. An attempt is made to correlate the physical and mechanical properties with the increasing weight fractions of carbon nanotubes in the pure Mg matrix.
Template Recognition Mechanisms by Replicase Proteins Differ between Bipartite Positive-Strand Genomic RNAs of a Plant Virus

ABSTRACT Recognition of RNA templates by viral replicase proteins is one of the key steps in the replication process of all RNA viruses. However, the mechanisms underlying this phenomenon, including primary RNA elements that are recognized by the viral replicase proteins, are not well understood. Here, we used aptamer pulldown assays with membrane fractionation and protein-RNA coimmunoprecipitation in a cell-free viral translation/replication system to investigate how viral replicase proteins recognize the bipartite genomic RNAs of the Red clover necrotic mosaic virus (RCNMV). RCNMV replicase proteins bound specifically to a Y-shaped RNA element (YRE) located in the 3′ untranslated region (UTR) of RNA2, which also interacted with the 480-kDa replicase complexes that contain viral and host proteins. The replicase-YRE interaction recruited RNA2 to the membrane fraction. Conversely, RNA1 fragments failed to interact with the replicase proteins supplied in trans. The results of protein-RNA coimmunoprecipitation assays suggest that RNA1 interacts with the replicase proteins coupled with their translation. Thus, the initial template recognition mechanisms employed by the replicase differ between RCNMV bipartite genomic RNAs and RNA elements are primary determinants of the differential replication mechanism.
PERFECT CODES ON SOME ORDERED SETS

Using the concept of codes on ordered sets introduced by Brualdi, Graves and Lawrence, we consider perfect codes on the ordinal sum of two ordered sets, the standard ordered sets and the disjoint sum of two chains. In the classical coding theory all perfect codes are completely described in terms of parameters (cf. [2, 3]). They are mathematically interesting structures. Brualdi et al. [1] recently introduced the notion of a code on an ordered set. In this paper we consider perfect codes on the ordinal sum of two ordered sets, the standard ordered sets and the disjoint sum of two chains. A chain is an ordered set in which every two elements are comparable and an antichain in which no two elements are comparable. Then we denote by n and n denote the chain and the antichain, respectively, on the set {1, 2, . , n}. Let P and Q be two disjoint ordered sets. The disjoint sum P + Q of P and Q is the ordered set on P ∪ Q such that x < y if and only if x, y ∈ P and x < y in P or x, y ∈ Q and x < y in Q, and the ordinal sum P ⊕ Q of P and Q is obtained from P + Q by adding the new relations x < y for all x ∈ P and y ∈ Q. Let Fq be a finite field with q = p (p a prime, d a positive integer). For u = (u1, . . . , un) ∈ Fq , the support of u and the Hamming weight of u are respectively given by Supp(u) = {i : 1 ≤ i ≤ n, ui 6= 0},
Smoothing of ultrasonically drilled holes in borosilicate glass by wet chemical etching

Besides silicon various types of glass play an important role in microsystem technology. One requirement of the glasses is that they have to be microstructurable. In many applications for microsensors and microstructures the glass must be suitable for anodic bonding. Usually borosilicate glass (e.g. Corning Pyrex code 7740 glass) is used, which has a thermal expansion coefficient that is almost equal to the thermal expansion coefficient of silicon and which has the necessary electrical conductivity at the temperature at which the bonding process occurs. For many applications, e.g., microfluidic systems, it is necessary to have fluids flown through ultrasonically drilled holes in the Pyrex glass to the silicon chip. The main objective of the investigation was to obtain smooth walls of ultrasonically drilled holes because every contamination influences the performance of the microsystem. In this paper the ultrasonic drilling method is compared with two other procedures for machining holes (sand blasting and laser machining). Other ways of structuring glass have been presented previously. A process was developed to smooth the walls of the drilled holes with different concentrations of hydrofluoric acid.
A fast asynchronous Huffman decoder for compressed-code embedded processors

This paper presents the architecture and design of a high-performance asynchronous Huffman decoder for compressed-code embedded processors. In such processors, embedded programs are stored in compressed form in instruction ROM then are decompressed on demand during instruction cache refill. The Huffman decoder is used as a code decompression engine. The circuit is non-pipelined, and is implemented as an iterative self-timed ring. It achieves a high-speed decode rate with very low area overhead. Simulations using Lsim show an average throughput of 32 bits/25 ns on the output side (or 163 MBytes/sec, or 1303 Mbit/sec), corresponding to about 889 Mbit/sec on the input side. The area of the design is extremely small: under 1 mm/sup 2/ in a 0.8 micron full-custom layout. The decoder is estimated to have higher throughput than any comparable synchronous Huffman decoder (after normalizing for feature size and voltage), yet is much smaller than synchronous designs. Its performance is also 83% faster than a recently published asynchronous Huffman decoder using the same technology.