Miracle-dz/UniFAR-FTUs huggingface dataset:
Current noninvasive tests for colorectal cancer screening: An overview of colorectal cancer screening tests

Colorectal cancer (CRC) has become the third most common cancer in the world. Screening has been shown to be an effective way to identify early CRC and precancerous lesions, and to reduce its morbidity and mortality. Several types of noninvasive tests have been developed for CRC screening, including the fecal occult blood test (FOBT), the fecal immunochemical test (FIT), the fecal-based DNA test and the blood-based DNA test (the SEPT9 assay). FIT has replaced FOBT and become the major screening test due to high sensitivity, specificity and low costs. The fecal DNA test exhibited higher sensitivity than FIT but its current cost is high for a screening assay. The SEPT9 assay showed good compliance while its performance in screening needs further improvements. These tests exhibited distinct sensitivity and specificity in screening for CRC and adenoma. This article will focus on the performance of the current noninvasive in vitro diagnostic tests that have been used for CRC screening. The merits and drawbacks for these screening methods will also be compared regarding the techniques, usage and costs. We hope this review can provide suggestions for both the public and clinicians in choosing the appropriate method for CRC screening.
Trisomy 21 consistently activates the interferon response

Although it is clear that trisomy 21 causes Down syndrome, the molecular events acting downstream of the trisomy remain ill defined. Using complementary genomics analyses, we identified the interferon pathway as the major signaling cascade consistently activated by trisomy 21 in human cells. Transcriptome analysis revealed that trisomy 21 activates the interferon transcriptional response in fibroblast and lymphoblastoid cell lines, as well as circulating monocytes and T cells. Trisomy 21 cells show increased induction of interferon-stimulated genes and decreased expression of ribosomal proteins and translation factors. An shRNA screen determined that the interferon-activated kinases JAK1 and TYK2 suppress proliferation of trisomy 21 fibroblasts, and this defect is rescued by pharmacological JAK inhibition. Therefore, we propose that interferon activation, likely via increased gene dosage of the four interferon receptors encoded on chromosome 21, contributes to many of the clinical impacts of trisomy 21, and that interferon antagonists could have therapeutic benefits. DOI: http://dx.doi. org/10.7554/eLife.16220. 001
A new discrete distribution arising in a model of DNA replication

During DNA replication, small fragments of DNA are formed. These have been observed experimentally and the mechanism of their formation modelled mathematically. Using the stochastic model of Cowan and Chiu (1992), (1994), we find the probability distribution of the number of fragments. A new discrete distribution arises. The work has interest as an application of the recent theory on quasirenewal equations in Piau (2000).
Improved technique for object detection using Similarity Based Region Merging

object segmentation is an important task in image processing and computer vision. We address a method to effectively discover a user’s concept when object of interest are involved in input image. In this paper our method corporate frameworks for object retrieval using semi-automatic method for object detection because fully automatic segmentation is very hard for natural images. To improve the effectiveness of region merging we propose a new similarity based object retrieval. The users only need to roughly indicate the after which steps desired objects closed contour is obtained during the automatic merging of similar regions. A similarity based region merging mechanism is proposed to guide the merging process with the help of initial segmentation technique. Any two or more regions are merged with its adjacent regions on the basis of similarity. The proposed method automatically merges the regions that are initially segmented through initial segmentation technique, and then effectively extracts the object contour by merging regions.
SPITZER SPECTROSCOPY OF MASS-LOSS AND DUST PRODUCTION BY EVOLVED STARS IN GLOBULAR CLUSTERS

We have observed a sample of 35 long-period variables (LPVs) and four Cepheid variables in the vicinity of 23 Galactic globular clusters using the Infrared Spectrograph on the Spitzer Space Telescope. The LPVs in the sample cover a range of metallicities from near solar to about 1/40th solar. The dust mass-loss rate (MLR) from the stars increases with pulsation period and bolometric luminosity. Higher MLRs are associated with greater contributions from silicate grains. The dust MLR also depends on metallicity. The dependence is most clear when segregating the sample by dust composition, less clear when segregating by bolometric magnitude, and absent when segregating by period. The spectra are rich in solid-state and molecular features. Emission from alumina dust is apparent across the range of metallicities. Spectra with a 13 μm dust emission feature, as well as an associated feature at 20 μm, also appear at most metallicities. Molecular features in the spectra include H2O bands at 6.4–6.8 μm, seen in both emission and absorption, SO2 absorption at 7.3–7.5 μm, and narrow emission bands from CO2 from 13.5 to 16.8 μm. The star Lyngå 7 V1 has an infrared spectrum revealing it to be a carbon star, adding to the small number of carbon stars associated with Galactic globular clusters.
Development of Affective Lexicon for Spanish with Mexican Slang Expressions

Nowadays exists a growing interest in the automatic extraction of subjective expressions (opinions, emotions and feelings) in texts. To identify the semantic orientation of a text, it is assumed that the occurrence of expressions that belong to some emotional category can be regarded as evidence that there is an affective state. Based on this assumption, we create an affective lexicon, consisting in the translation from English to Spanish of various lexical resources, including works based on psychological theories to identify words associated with emotions. The lexicon was manually enriched through semantic relationships as inclusion and synonymy using explanatory dictionaries. Expressions used in Mexican slang were also included in the lexicon. Every word in the lexicon was labeled with its semantic orientation; these are: “very positive”, “very negative”, “positive” or “negative”, for the translated words and “positive” or “negative” for the Mexican slang. The lexicon currently consists of 3550 words and 255 slang expressions.
Schema-summarization in linked-data-based feature selection for recommender systems

Recommender systems are emerging as an interesting application scenario for Linked Data (LD). In fact, by exploiting the knowledge encoded in LD datasets, a new generation of semantics-aware recommendation engines have been developed in the last years. As Linked Data is often very rich and contains many information that may result irrelevant and noisy for a recommendation task, an initial step of feature selection is always required in order to select the most meaningful portion of the original dataset. Many approaches have been proposed in the literature for feature selection that exploit different statistical dimensions of the original data. In this paper we investigate the role of the semantics encoded in an ontological hierarchy when exploited to select the most relevant properties for a recommendation task. In particular, we compare an approach based on schema summarization with a "classical" one, i.e., Information Gain. We evaluated the performance of the two methods in terms of accuracy and aggregate diversity by setting up an experimental testbed relying on the Movielens dataset.
Express bus fare optimization based on passenger choice behavior

A change in bus fare influences passenger choice behavior, resulting in a change of passenger flow and passengers’ total travel time. In this paper, a bi-level model was built to optimize the bus fare. The upper-level used the passenger flow and the travel time of passengers to optimize the bus fare. The lower-level is an agent-based simulation model that can simulate the passenger flow based on the passenger choice behavior. Then the tabu search algorithm was used to solve the bi-level model. Finally, the bi-level model is verified using two bus routes of Dalian, China. The result proves the bi-level model is reliable.
Dynamic Bandwidth Management in ATM Networks

This paper describes a system for dynamic bandwidth management of Virtual Path Connections in ATM networks. A two level hierarchical approach is taken consisting of network planning functions which take place on a longer time scale than the bandwidth distribution functions which attempt to track the usage of the VPCs in terms of the switched VCCs admitted onto them. The paper concentrates on approaches for the latter of these sets of functions and places them in the context of a larger system for network survivability and availability as studied by the ACTS REFORM project.
Strange evolution behavior of 7-bit binary string strategies in iterated prisoner's dilemma game

The prisoner's dilemma (PD) game is a well-known non-zero sum game. Its iterated version (IPD game) has been widely used to study the evolution of cooperative strategies. In this paper, we assume a noisy environment where a player chooses a different action from the suggested one by its own strategy with a pre-specified error probability. Generally, the noise in action selection makes the evolution of cooperation difficult because the player cannot distinguish between an intentional defection by the opponent's strategy and an unintentional defection by error. However, when a 7-bit binary string with a memory about opponent's two actions was used as a strategy of each player, we observed strange evolution behavior where the use of a small error probability increased the average payoff to the level close to the complete mutual cooperation. That is, the use of a small error probability seems to help the evolution of cooperation. Such a strange behavior was not clearly observed by other types of strategies (e.g., 3-bit binary string with a memory about opponent's single action, 15-bit binary strings with a memory about opponent's three actions). In this paper, we report our simulation results where our focus is placed on the strange evolution behavior of 7-bit binary string strategies. We also try to analyze their strange evolution behavior.
Inhibition of Mycobacterium tuberculosis RNA polymerase by 1 binding of a Gre factor homolog to secondary channel 2 3 4

4 Arnab China, Sonakshi Mishra, Priyanka Tare and Valakunja Nagaraja 2, * 5 6 7 Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 8 560012, India 9 Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India 10 To whom correspondence should be addressed. 11 E-mail: vraj@mcbl.iisc. ernet.in 12 Tel. No. +91-80-2360 0668 13 Fax No. +91-80-236
Measurement of the proton motive force in Rhizobium meliloti with the Escherichia coli lacY gene product

An Escherichia coli lac operon constitutive for lacY was subcloned into the EcoRI site of a wide-host-range plasmid of the Q incompatibility group, and the resulting recombinant plasmid was introduced into Tn5-generated Lac- mutants of Rhizobium meliloti. The R. meliloti transconjugants accumulated lactose about 1,000-fold, equivalent to a proton motive force of -170 to -180 mV, not significantly different from the values calculated from the distributions of weak acids and lipophilic cations.
Functionally-Impaired HIV-1 Nef Alleles from a Mother-Child Transmission Pair

Abstract: Unusual HIV-1 nef alleles were isolated from a woman and her vertically infected child. Both patients eventually progressed to develop AIDS. The child died at age 6.5 years, while the mother is currently alive, 13 years since her diagnosis with HIV-1. Predicted amino acid sequences of both mother and child Nefs diverged from the HIV-1 clade B consensus. In particular, they exhibited two separate 5-amino acid deletions bracketing a C-terminal dileucine regulatory motif and Trp-Gly mutations at the site for cleavage by the HIV-1 protease. The child’s Nef showed a modest ability to enhance HIV-1 infectivity in MAGI cells, whereas the mother’s Nef did not alter HIV-1 infectivity in the assay. Both Nefs were partially functional for CD4 down-regulation. The child’s Nef was fully functional for MHC-1 down-regulation, while the maternal Nef was non-functional. To our knowledge this study is the first to describe a functional divergence between Nef alleles in a case of mother-to-child HIV-1 transmission.
The complete nucleotide sequence of the chick a-actin gene and its evolutionary relationship to the actin gene family

The nucleotide sequence of the chick a-actin gene reveals that the gene is comprised of 7 exons separated by six very short intervening sequences (IVS). The first IVS interrupts the 73 nucleotide 5' untranslated segment between nucleotides 61 and 62. The remaining IVS interrupt the translated region at codons 41/42, 150, 204, 267, and 327/328. The 272 nucleotide 3' untranslated segment is not interrupted by IVS. The amino acid sequence derived from the nucleotide sequence is identical to the published sequence for chick a-actin except for the presence of a met-cys dipeptide at the amino-terminus. The IVS positions in the chick a-actin gene are identical to those of the rat a-actin gene. While there is partial coincidence of the IVS in the a-actin genes with the vertebrate b-actin genes and 2 sea urchin actin genes, there is no coincidence with actin genes from any other source except soybean where one IVS position is shared. This discordance in IVS positions makes the actin gene family unique among the eucaryotic genes analyzed to date.
Mapping students’ ideas to understand learning in a collaborative programming environment

Recent studies in learning programming have largely focused on high school and college students; less is known about how young children learn to program. From video data of 20 students using a graphical programming interface, we identified ideas that were shared and evolved through an elementary school classroom. In mapping these ideas and their resulting changes in programs and outputs, we were able to identify the contextual features which contributed to how ideas moved through the classroom as students learned. We suggest this process of idea mapping in visual programming environments as a viable method for understanding collaborative, constructivist learning as well as a context under which experiences can be developed to improve student learning.
Interplay of approximate planning strategies

Significance Many problems, particularly sequential planning problems, are computationally very demanding. How humans combine strategies to approximate and simplify these problems is not understood. Using modelling to unpick performance in a planning task, we find that humans are able to exploit the structure of the task to subdivide it and reduce processing requirements nearly optimally. Subtasks are combined in a simple, greedy manner, however, and within subtasks there is evidence of inhibitory reflexes in response to losses. Humans routinely formulate plans in domains so complex that even the most powerful computers are taxed. To do so, they seem to avail themselves of many strategies and heuristics that efficiently simplify, approximate, and hierarchically decompose hard tasks into simpler subtasks. Theoretical and cognitive research has revealed several such strategies; however, little is known about their establishment, interaction, and efficiency. Here, we use model-based behavioral analysis to provide a detailed examination of the performance of human subjects in a moderately deep planning task. We find that subjects exploit the structure of the domain to establish subgoals in a way that achieves a nearly maximal reduction in the cost of computing values of choices, but then combine partial searches with greedy local steps to solve subtasks, and maladaptively prune the decision trees of subtasks in a reflexive manner upon encountering salient losses. Subjects come idiosyncratically to favor particular sequences of actions to achieve subgoals, creating novel complex actions or “options. ”
SPATIAL METAPHORS FOR VISUALIZING INFORMATION SPACES

The growing volume and complexity of the World Wide Web creates a need for new forms of interaction with information. Spatial metaphors have been in the focus of interface research for a number of years. Recently, a related concept called spatialization has emerged as one possible strategy for dealing with modern information glut. However, the term remains ill-defined. We present a definition of spatialization that is based on the notion of information spaces that are non-spatial and high-dimensional. Through spatialization, they are projected into a low-dimensional form and made accessible for visual interpretation.
Modeling Indirect Effects of Paid Search Advertising: Which Keywords Lead to More Future Visits?

Many online shoppers initially acquired through paid search advertising later return to the same website directly. These so-called “direct type-in” visits can be an important indirect effect of paid search. Because visitors come to sites via different keywords and can vary in their propensity to make return visits, traffic at the keyword level is likely to be heterogeneous with respect to how much direct type-in visitation is generated. Estimating this indirect effect, especially at the keyword level, is difficult. First, standard paid search data are aggregated across consumers. Second, there are typically far more keywords than available observations. Third, data across keywords may be highly correlated. To address these issues, the authors propose a hierarchical Bayesian elastic net model that allows the textual attributes of keywords to be incorporated. The authors apply the model to a keyword-level data set from a major commercial website in the automotive industry. The results show a significant indirect effect of paid search that clearly differs across keywords. The estimated indirect effect is large enough that it could recover a substantial part of the cost of the paid search advertising. Results from textual attribute analysis suggest that branded and broader search terms are associated with higher levels of subsequent direct type-in visitation.
Construction of a tetR-Integrated Salmonella enterica Serovar Typhi CVD908 Strain That Tightly Controls Expression of the Major Merozoite Surface Protein of Plasmodium falciparum for Applications in Human Vaccine Production

ABSTRACT Attenuated Salmonella strains are an attractive live vector for delivery of a foreign antigen to the human immune system. However, the problem with this vector lies with plasmid segregation and the low level of expression of the foreign gene in vivo when constitutive expression is employed, leading to a diminished immune response. We have established inducible expressions of foreign genes in the Salmonella enterica serovar Typhi CVD908 vaccine strain using the tetracycline response regulatory promoter. To set up this system, a tetracycline repressor (tetR) was integrated into a defined ΔaroC locus of the chromosome via suicide plasmid pJG12/tetR-neo. To remove the neo gene conferring kanamycin resistance from the locus, a cre expression vector under the control of the tetracycline response promoter was transformed into the clone; expression of the Cre recombinase excised the neo gene and generated the end strain CVD908-tetR. Expression of the luciferase reporter gene in this strain is dependent on the presence of tetracycline in the medium and can be regulated up to 4,773-fold. Moreover, the tightly controlled expression of major merozoite surface protein 1 (MSP1) and parts of Plasmodium falciparum was achieved, and the product yield was increased when the inducible expression system was employed. Inoculation of bacteria harboring plasmid pZE11/MSP142 in mice produced the protein in liver and spleen controlled by the inducer. The persistence of the plasmid-carrying bacteria in mice was determined. Peak colonization of both liver and spleen was detected on the third day postinoculation and was followed by a decline in growth curves. After 14 days postinfection, the majority of the bacteria (>90%) recovered from the liver and spleen of the mice retained the plasmid when expression was induced; this clearly indicated that stability of the expression vector in vivo was improved by inducible expression. Establishment of the regulatory system in the vaccine strain may broaden the range of its use by enhancing plasmid stability and expression levels in vivo. Moreover, the availability of the vaccine strain inducibly expressing the entire MSP1 provides possibilities for examining its immunogenicity, particularly the cellular response in animal models.
3D local qupit quantum code without string logical operator

Recently Haah introduced a new quantum error correcting code embedded on a cubic lattice. One of the defining properties of this code is the absence of string logical operator. We present new codes with similar properties by relaxing the condition on the local particle dimension. The resulting code is well-defined when the local Hilbert space dimension is prime. These codes can be divided into two different classes: the local stabilizer generators are either symmetric or antisymmetric with respect to the inversion operation. These is a nontrivial correspondence between these two classes. For any symmetric code without string logical operator, there exists a complementary antisymmetric code with the same property and vice versa. We derive a sufficient condition for the absence of string logical operator in terms of the algebraic constraints on the defining parameters of the code. Minimal number of local particle dimension which satisfies the condition is 5. These codes have logarithmic energy barrier for any logical error.
An Optimal Global Method for Classification of Color Pixels

We propose in this article a color image segmentation technique based on an optimization of the Mean Shift method. It consists in classifying clusters of data points of a digital image, it does not require any preliminary designation of the number of classes and of their centers. The Mean Shift method applied to a digital color image creates a new image made up of aggregates of points belonging to a finished number of color classes. The complexity of this method based on a global approach of the image is in O(NxN), N being the number of pixels of the image. Our idea consists in applying a change of scale to the image to be segmented, to reduce the quantity of information and, in using a median filter to decrease the number of colors to minimize the complexity of the latter. The comparative study which we present shows that the optimization which we proposed gives better, reliable results than the classic use of the Mean Shift method.