Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence, topography and protein coding potential of mouse int‐2: a putative oncogene activated by mouse mammary tumour virus.

A major proportion of carcinomas induced by mouse mammary tumour virus (MMTV) show evidence for proviral activation of a cellular gene, int‐2, on chromosome 7. The sequence of 7869 bp of DNA spanning the transcription unit of int‐2 was determined and compared with that of a series of int‐2‐specific cDNA clones derived from mammary tumour RNA. The predicted positions of intron‐exon boundaries, established by alignment of cDNA and chromosomal DNA sequences, indicate that the gene comprises at least three exons. An open reading frame capable of encoding a protein of 245 amino acids with an estimated mol. wt of 27 kd, is flanked by substantial non‐coding segments at both 5′ and 3′ ends. Comparison of the chromosomal DNA sequence and the predicted amino acid sequence with available data‐bases has revealed no homology to other known genes. These results are discussed in relation to the status of int‐2 as a candidate proto‐oncogene.
Planetary Period Modulation of Reconnection Bursts in Saturn's Magnetotail

We conduct a statistical analysis of 2,094 reconnection events in Saturn's near‐equatorial magnetotail previously identified in Cassini magnetometer data from intervals during 2006 and 2009/2010. These consist of tailward propagating plasmoids and planetward propagating dipolarizations, with approximately twice as many plasmoids as dipolarizations. We organize these by three related planetary period oscillation (PPO) phase systems, the northern and southern PPO phases relative to noon, the same phases retarded by a radial propagation delay, and the local retarded phases that take account of the azimuth (local time) of the observation. Clear PPO modulation is found for both plasmoid and dipolarization events, with local retarded phases best organizing the event data with the modulation in event frequency propagating across the tail as the PPO systems rotate. This indicates that the events are localized in azimuth, rather than simultaneously affecting much of the tail width. Overall, events occur preferentially by factors of ~3 at northern and southern phases where the tail current sheet is expected locally to be thinnest in the PPO cycle, with field lines contracting back from their maximum radial displacement, compared with the antiphase conditions. Separating the events into those representing the start of independent reconnection episodes, occurring at least 3 hr after the last, and events in subsequent clusters, shows that the above phases are predominantly characteristic of the majority cluster events. The phases at the start of independent reconnection episodes are typically ~60° earlier.
Higher plants n-alkane profiles as indicators of anthropogenic environmental

ABSTRACT The saturated biomarkers compositions of thirty angiosperms were analyzed by gas chromatography-mass spectrometry. The concentrations of the sum of 28 target n- alkanes (designated as∑28 n- alkanes) in the plants ranged from 1403 to 115405, 951 to 79441, 659 to 149855, 968 to 172191 and 2883 to 53284 ng/g in Uzere, Oginni, Olomoro, Irri and Calabar plants, respectively. M. sapientum showed high concentrations and strong bioaccumulation potential for n-alkanes among the studied plants. There is a marked distribution pattern among the n-alkanes in the plant; C27-C34 accounted for over 70% in most of the plants studied maximizing at C31 and C33. The mean Carbon preference index, pristane/phytane, pristane/C17, phytane/C18, odd-even predominance and natural n-alkane ratios ranged from 4.7 to 24.3, 0 to 2.8, 0.3+0.4, 0.6+0.9, 0.2 to 4.9 and -3.5 to 1.0 respectively. Applying these conventional n-alkane source diagnostic ratios, the n-alkane in the plants has strong fossil fuel combustion and petroleum inputs which further affirm the petrogenic pollution of soils, sediments and water bodies in the studied locations. The high concentrations of low molecular homologue members (C9 to C18) which hitherto has not been reported by previous workers in higher plants shows that they will serve as good markers to further establish anthropogenic contamination of an area. Key words : n-alkanes, pollution, diagnostics indices, petroleum, higher plants
A Study on Factors Affecting Combustion Characteristics of GCSC Injector

Factors affecting the combustion characteristics of gas-centered swirl coaxial (GCSC) injectors are investigated numerically and experimentally. The factors are fuel volume flow rate (Qf), momentum flux ratio (MFR) and oxidizer/fuel (O/F) ratio. Firstly, the flame pattern becomes asymmetric as the fuel volume flow rate increases with a fixed momentum flux ratio. Then, the suitable fuel volume flow rate is selected according to the results. Next, the momentum flux ratio is increased by increasing the oxidizer volume flow rate (Qo) with a fixed fuel volume flow rate. Results show that the spreading angle decreases as momentum flux ratio increases, which agrees with our previous results. Finally, in order to check effects of oxidizer/fuel ratio, the Qf, Qo, and MFR are kept the same but the O2 mole fraction of oxidizer is changed. From numerical and experimental results, it is found that flame pattern depends on oxidizer/fuel ratio and spreading angle increases as the O2 mole fraction decreases.
Read&Answer, A Tool to Capture on-Line Processing of Electronic Texts

This paper is aimed at presenting Read&Answer, a tool that records reading times, one of the main on-line methods employed in text processing research. Read&Answer allows the recording, analysis and interpretation of the learner processing in order to test specific hypotheses and explain final comprehension results. First, we will describe the tool, and then we will briefly explain some research studies using the tool. We will show how Read&Answer can be used in combination with another on-line method extensively employed in text processing research, i.e., verbal protocols, and we will also compare Read&Answer with eye movement tracking, a widely accepted on-line reading times technique.
Single phase power factor correction: a survey

New recommendations and future standards have increased the interest in power factor correction circuits. There are multiple solutions in which line current is sinusoidal. In addition, a great number of circuits have been proposed with nonsinusoidal line current. In this paper, a review of the most interesting solutions for single phase and low power applications is carried out. They are classified attending to the line current waveform, energy processing, number of switches, control loops, etc. The major advantages and disadvantages are highlighted and the field of application is found.
Synthetic and natural consensus design for engineering charge within an affibody targeting epidermal growth factor receptor

Protein ligand charge can impact physiological delivery with charge reduction often benefiting performance. Yet neutralizing mutations can be detrimental to protein function. Herein, three approaches are evaluated to introduce charged‐to‐neutral mutations of three cations and three anions within an affibody engineered to bind epidermal growth factor receptor. These approaches—combinatorial library sorting or consensus design, based on natural homologs or library‐sorted mutants—are used to identify mutations with favorable affinity, stability, and recombinant yield. Consensus design, based on 942 affibody homologs, yielded a mutant of modest function (Kd = 11 ±4 nM, Tm = 62°C, and yield = 4.0 ± 0.8 mg/L as compared to 5.3 ± 1.7 nM, 71°C, and 3.5 ± 0.3 mg/L for the parental affibody). Extension of consensus design to 10 additional mutants exhibited varied performance including a substantially improved mutant (Kd = 6.9 ± 1.4 nM, Tm = 71°C, and 12.7 ± 0.9 mg/L yield). Sorting a homolog‐based combinatorial library of 7 × 105 mutants generated a distribution of mutants with lower stability and yield, but did identify one strongly binding variant (Kd = 1.2 ± 0.3 nM, Tm = 69°C, and 6.0 ± 0.4 mg/L yield). Synthetic consensus design, based on the amino acid distribution in functional library mutants, yielded higher affinities (P = 0.05) with comparable stabilities and yields. The best of four analyzed clones had Kd = 1.7 ± 0.5 nM, Tm = 68°C, and 7.0 ± 0.5 mg/L yield. While all three approaches were effective in creating targeted affibodies with six charged‐to‐neutral mutations, synthetic consensus design proved to be the most robust. Synthetic consensus design provides a valuable tool for ligand engineering, particularly in the context of charge manipulation. Biotechnol. Bioeng. 2016;113: 1628–1638. © 2016 Wiley Periodicals, Inc.
A brief survey on corpus uses

Corpus opened up many new areas of research in the domain of linguistic, which would never been possible without it. Recently, corpus linguistic became a hot topic in the research community. However, entering this area for new computer researchers may take lots of effort and time. In this paper we provide new researchers in this domain with the basic terms, measures, and tools used in this area.
Segmentation-Based MAP Despeckling of SAR Images in the Undecimated Wavelet Domain

In this paper, a novel despeckling algorithm based on undecimated wavelet decomposition and maximum a posteriori estimation is proposed. Such a method represents an improvement with respect to the filter presented by the authors, and it is based on the same conjecture that the probability density functions (pdfs) of the wavelet coefficients follow a generalized Gaussian (GG) distribution. However, the approach introduced here presents two major novelties: 1) theoretically exact expressions for the estimation of the GG parameters are derived: such expressions do not require further assumptions other than the multiplicative model with uncorrelated speckle, and hold also in the case of a strongly correlated reflectivity; 2) a model for the classification of the wavelet coefficients according to their texture energy is introduced. This model allows us to classify the wavelet coefficients into classes having different degrees of heterogeneity, so that ad hoc estimation approaches can be devised for the different sets of coefficients. Three different implementations, characterized by different approaches for incorporating into the filtering procedure the information deriving from the segmentation of the wavelet coefficients, are proposed. Experimental results, carried out on both artificially speckled images and true synthetic aperture radar images, demonstrate that the proposed filtering approach outperforms the previous filters, irrespective of the features of the underlying reflectivity.
Facial Recognition in Hypothetically Schizotypic College Students: The Role of Generalized Poor Performance

This study investigated facial and facial affect recognition abilities among hypothetically schizotypic college men, defined by high scores on the perceptual aberration, magical ideation, and schizotypy scales. Groups were commensurate in age, handedness, and general intelligence. Multiple analyses of variance revealed that high-scoring subjects, relative to control subjects, made more errors on a facial affect recognition task (F = 5.32, p < .05) and on a facial recognition task (F = 8.5, p < .01). Additional multiple analyses of covariance using the face recognition scores as the covariant found no group differences. These results extend similar findings in schizophrenic individuals to hypothetically schizotypic college students, and suggest that both groups exhibit affect recognition deficits that reflect generalized attention and vigilance deficits rather than a specific emotion recognition deficit.
Generation of mice with a conditional allele for the p75NTR neurotrophin receptor gene

The p75NTR neurotrophin receptor has been implicated in multiple biological and pathological processes. While significant advances have recently been made in understanding the physiologic role of p75NTR, many details and aspects remain to be determined. This is in part because the two existing knockout mouse models (Exons 3 or 4 deleted, respectively), both display features that defy definitive conclusions. Here we describe the generation of mice that carry a conditional p75NTR (p75NTR‐FX) allele made by flanking Exons 4–6, which encode the transmembrane and all cytoplasmic domains, by loxP sites. To validate this novel conditional allele, both neural crest‐specific p75NTR/Wnt1‐Cre mutants and conventional p75NTR null mutants were generated. Both mutants displayed abnormal hind limb reflexes, implying that loss of p75NTR in neural crest‐derived cells causes a peripheral neuropathy similar to that seen in conventional p75NTR mutants. This novel conditional p75NTR allele will offer new opportunities to investigate the role of p75NTR in specific tissues and cells. genesis 49:862–869, 2011. © 2011 Wiley‐Periodicals, Inc.
Learning to Make Predictions In Partially Observable Environments Without a Generative Model

When faced with the problem of learning a model of a high-dimensional environment, a common approach is to limit the model to make only a restricted set of predictions, thereby simplifying the learning problem. These partial models may be directly useful for making decisions or may be combined together to form a more complete, structured model. However, in partially observable (non-Markov) environments, standard model-learning methods learn generative models, i.e. models that provide a probability distribution over all possible futures (such as POMDPs). It is not straightforward to restrict such models to make only certain predictions, and doing so does not always simplify the learning problem. In this paper we present prediction profile models: non-generative partial models for partially observable systems that make only a given set of predictions, and are therefore far simpler than generative models in some cases. We formalize the problem of learning a prediction profile model as a transformation of the original model-learning problem, and show empirically that one can learn prediction profile models that make a small set of important predictions even in systems that are too complex for standard generative models.
The life of regulatory T cells

Foxp3+ regulatory T (Treg) cells are essential for maintaining self‐tolerance and preventing autoimmune reactions. Treg cells arise as a consequence of self‐antigen recognition during the maturation of cells in the thymus, and also following self‐antigen recognition in the periphery. Both thymic and peripherally generated Treg cells respond to antigen recognition by expanding in number, increasing their suppressive activity, and accumulating in the tissue where the antigen is located. A fraction of these activated “effector” Treg cells survive even in the absence of antigen expression and continue to control inflammatory reaction in the tissues, thus functioning as a population of “memory” Treg cells. Antigen exposure and the presence of IL‐2 are key determinants in the generation of memory Treg cells. These results provide a foundation for studying the role of memory Treg cells in controlling and treating autoimmune disorders and for testing the hypothesis that defects in the generation and maintenance of these cells underlie chronic, relapsing inflammatory diseases.
First passage times of driven DNA hairpin unzipping

We model the dynamics of voltage-driven transport of DNA hairpins through transmembrane channels. A two-dimensional stochastic model of the DNA translocation process is fit to the measurements of Mathé, who pulled self-hybridized DNA hairpins through lipid-embedded α-hemolysin channels. As the channel was too narrow to accommodate hybridized DNA, dehybridization of the hairpin became the rate-limiting step of the transport process. We show that the mean first passage time versus voltage curve for the escape of the DNA from the transmembrane channel can be divided into two regions: (1) a low-voltage region where the DNA slides out of the pore in reverse and without undergoing significant dehybridization, and (2) a region where the DNA dehybridizes under the influence of the applied voltage and translocates across the membrane.
CBF 2 DREB 1 C is a negative regulator of CBF 1 DREB 1 B and CBF 3 DREB 1 A expression and plays a central role in stress tolerance in Arabidopsis

CBF DREB1 (C-repeat-binding factor dehydration responsive element-binding factor 1) genes encode a small family of transcriptional activators that have been described as playing an important role in freezing tolerance and cold acclimation in Arabidopsis. To specify this role, we used a reverse genetic approach and identified a mutant, cbf2, in which the CBF2 DREB1C gene was disrupted. Here, we show that cbf2 plants have higher capacity to tolerate freezing than WT ones before and after cold acclimation and are more tolerant to dehydration and salt stress. All these phenotypes correlate with a stronger and more sustained expression of CBF DREB1-regulated genes, which results from an increased expression of CBF1 DREB1B and CBF3 DREB1A in the mutant. In addition, we show that the expression of CBF1 DREB1B and CBF3 DREB1A in response to low temperature precedes that of CBF2 DREB1C. These results indicate that CBF2 DREB1C negatively regulates CBF1 DREB1B and CBF3 DREB1A, ensuring that their expression is transient and tightly controlled, which, in turn, guarantees the proper induction of downstream genes and the accurate development of Arabidopsis tolerance to freezing and related stresses.
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Evaluating a mobile spontaneous eye blink tracker for use in tele-presence HRI as a low bandwidth social communicative cue

Research suggests that the rate at which humans spontaneously blink their eyes over time is strongly related to their underlying cognitive state. The ability to present the real time blinking behaviour of a human teleoperator via a robot proxy therefore potentially offers observers a low bandwidth - yet salient - cue as to the cognitive state of the teleoperator.
BIOINFORMATICS APPLICATIONS

Motivation: Collecting millions of genetic variations is feasible with the advanced genotyping technology. With a huge amount of genetic variations data in hand, developing efﬁcient algorithms to carry out the gene–gene interaction analysis in a timely manner has become one of the key problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST), a recent work in GWAS, completes gene–gene interaction analysis in 2.5 days on a desktop computer. Compared with central processing units (CPUs), graphic processing units (GPUs) are highly parallel hardware and provide massive computing resources. We are, therefore, motivated to use GPUs to further speed up the analysis of gene–gene interactions. Results: We implement the BOOST method based on a GPU framework and name it GBOOST. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34h on a desktop computer equipped with Nvidia GeForce GTX 285 display card. Availability: GBOOST code is available at http://bioinformatics.ust . hk/BOOST.html#GBOOST.
Annotated raptor codes

In this paper, an extension of raptor codes is introduced which keeps all the desirable properties of raptor codes, including the linear complexity of encoding and decoding per information bit, unchanged. The new design, however, improves the performance in terms of the reception rate. Our simulations show a 10% reduction in the needed overhead at the benchmark block length of 64,520 bits and with the same complexity per information bit.
An evaluation of ring-based algorithms for the Eventually Perfect failure detector class

This paper presents an evaluation of two families of ring-based algorithms implementing the eventually perfect failure detector class (diamPscr). The evaluation is based on two kinds of performance parameters: communication efficiency, which refers to the number of links that carry messages forever, and quality of service, which includes the capability of the failure detector for providing right answers as well as reaction and initial stabilization times. The first family of algorithms includes several communication-efficient implementations of diamPscr introduced in a previous work. For the second family, introduced in this work, we start from the design of a non communication-efficient diamQscr algorithm, and then we apply a transformation to obtain a diamPscr algorithm, including some optimizations to improve the quality of service
User interface providing support for creating artistic patterns

As design work using computer spreads, usage environments are appearing which have operations involving aesthetic sensibilities via the GUIs in a variety of graphics software and have the representational capacity to represent three-dimensional images and images with the feel of oil paintings. However, their operation still relies on the user's sensibilities and knowledge. In this paper, we propose a user interface for a user support system for creating artistic patterns. Its features are summarized by the following three points. First, the system has knowledge about designs. The result of design analysis provided the following knowledge. (1) The elements producing a design are the colors, shapes, and composition. (2) To turn an image into a pattern, the image is conceived of as a specific scene, then the pattern can be drawn by extracting the colors, shapes, and composition based on the scene by combining these elements. This knowledge is held in the system. Second, there is a user interface to easily transmit the image to the system. The media to convey kansei (affective information) are considered to be both linguistic and nonlinguistic. And an interface was designed to enable direct manipulation by pen or mouse to select from a list box of a three-level kansei language and to select from a pattern candidate group. Another user interface was designed which accounts for the inability of a person to grasp the kansei from the start to completion and allows repeating the kansei specification by the user and the presentation of patterns by the system. Third, there is a mechanism that automatically creates the pattern in response to the user's kansei. We designed an algorithm to create a design by (1) using fuzzy logic to deduce the user's image and (2) creating the pattern by using the parameters needed to draw the pattern which were extracted from the deduced image. Furthermore, we developed a support system for creating artistic patterns that has the above functions, and had multiple testers test its operation to verify the system's effectiveness in application tests on real problems. © 2001 Scripta Technica, Syst Comp Jpn, 32(11): 20–37, 2001