Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Expression and evolution of members of the Trypanosoma cruzi trypomastigote surface antigen multigene family Permalink

The trypomastigote specific surface antigens of Trvpanosoma cruzi are encoded by a supergene family which includes the TSA family. The TSA family is characterized by the presence of a 27-bp tandem repeat array in the coding region. Here, we report the characterization and analysis of the three TSA family members in the Esmeraldo strain of the parasite. In this strain 2 distinct telomeric members are expressed abundantly as 3.7-kb mRNAs, while the remaining member is located at an internal chromosomal site and is expressed at less than 2% of the level seen for the telomeric members. Based on hybridization to DNA separated by PFGE, 3 chromosomes of sizes 1.8 Mb, 0.98 Mb, and 0.90 Mb each contain one of the telomeric members. In addition, the two smaller chromosomes also contain the single internal member. Since both chromosomes contain similar TSA family members, and vary only slightly in size, we suggest that they are homologues. Comparisons of the nucleotide sequences of the different members of the family show that the internal gene differs from the telomeric genes primarily in sequences found 3' of the repeat array. These comparisons also reveal that the three genes are analogous, supporting the hypothesis that short segments between the family members are exchanged by gene conversion events. We propose that similar conversion events between members of different gene families may generate some of the diversity found within the supergene family.
Blind symbol detection and channel acquisition in fast-fading wireless systems with space diversity

In this paper we tackle the joint source symbol detection and multi-channel acquisition problem in the context of wireless digital flat-fading links with space diversity. We propose a simple parametric statistical channel model which decouples the time dynamics of the channel vector in amplitude and direction. We implement the corresponding maximum a posteriori (MAP) joint estimator for the amplitude and direction of the channel vector and the source information symbols. We derive a computationally attractive iterative scheme to solve the optimization problem associated with the MAP estimator. This scheme is based on differential-geometric concepts and fully exploits the curvature of the surface constraint. Preliminary computer simulations assessing the good performance of our proposed solutions are included.
Social status and personality: stability in social state can promote consistency of behavioural responses

Stability of ‘state’ has been suggested as an underlying factor explaining behavioural stability and animal personality (i.e. variation among, and consistency within individuals in behavioural responses), but the possibility that stable social relationships represent such states remains unexplored. Here, we investigated the influence of social status on the expression and consistency of behaviours by experimentally changing social status between repeated personality assays. We used male domestic fowl (Gallus gallus domesticus), a social species that forms relatively stable dominance hierarchies, and showed that behavioural responses were strongly affected by social status, but also by individual characteristics. The level of vigilance, activity and exploration changed with social status, whereas boldness appeared as a stable individual property, independent of status. Furthermore, variation in vocalization predicted future social status, indicating that individual behaviours can both be a predictor and a consequence of social status, depending on the aspect in focus. Our results illustrate that social states contribute to both variation and stability in behavioural responses, and should therefore be taken into account when investigating and interpreting variation in personality.
On-line Dialogue Policy Learning with Companion Teaching

On-line dialogue policy learning is the key for building evolvable conversational agent in real world scenarios. Poor initial policy can easily lead to bad user experience and consequently fail to attract sufficient users for policy training. A novel framework, companion teaching, is proposed to include a human teacher in the dialogue policy training loop to address the cold start problem. Here, dialogue policy is trained using not only user’s reward, but also teacher’s example action as well as estimated immediate reward at turn level. Simulation experiments showed that, with small number of human teaching dialogues, the proposed approach can effectively improve user experience at the beginning and smoothly lead to good performance with more user interaction data.
Analysis of Logic Circuits with Faults Using Input Signal Probabilities

A probabilistic treatment of general combinational networks has been developed. Using the notions of the probability of a signal and signal independence, algorithms have been presented to calculate the probability of the output of a logic circuit being 1. Simplifications to the algorithm result when sets of input probabilities are given the same value, and this process called bundling is described in the paper. Finally, a series of examples illustrate the application of the probabilistic approach to the analysis of faulty logic circuits.
The Facilitators and Barriers in Coping with Clinical Stress: The Experiences of Nursing Students in Iran

Introduction and purpose: Nursing students are faced with great stress in clinical settings. The knowledge of the facilitators and barriers in coping with such stresses is necessary for performing any kind of intervention. The present qualitative content analysis was conducted to determine the facilitators and barriers in coping with clinical stresses in nursing students. Materials and methods: This qualitative study was conducted in Jiroft city in 2017. Participants were 19 undergraduate nursing students and two nursing instructors selected through purposive sampling. Data were collected through semistructured interactive interviews and were then analyzed according to Graneheim and Lundman’s qualitative content analysis. Data were analyzed using the MAXQDA software. Findings: The analysis of the data led to the emergence of three main themes, including personal facilitators, professional facilitators and the uneven clinical path. Discussion and conclusion: By identifying the facilitators and barriers in coping with clinical stress in nursing students, the results of this study can lead to the efficient management of these factors by the students themselves as well as by their instructors, the education authorities and the nursing personnel.
The prevalence of BRCA1 mutations in Chinese patients with early onset breast cancer and affected relatives

The purpose of this study was to determine the prevalence of BRCA1 mutations in Chinese breast cancer patients in Singapore. BRCA1 analysis was conducted in consecutive patients with breast cancer before the age of 40 years (76 women), or whose relatives had breast or ovarian cancer (16 women). Ten patients had both early onset breast cancer and affected relatives. Genomic DNA from peripheral mononuclear blood cells was studied by using the protein transcription–translation assay (exon 11) and single-strand conformational polymorphism, with subsequent DNA sequencing. All six disease-causing mutations occurred in women under 40 years (8.6%) with three occurring in patients under 35 years (three out of 22 patients, 13.6%). Mis-sense mutations of unknown significance were found in three patients. Two of the ten women with affected relatives under 40 years had BRCA1 mutations. The prevalence of BRCA1 mutations in Chinese patients with early onset breast cancer is similar to that observed in Caucasian women. Most Chinese patients with affected relatives were not carriers of BRCA1 mutations. © 2000 Cancer Research Campaign
Identification of non-peptidic neuromedin U receptor modulators by a robust homogeneous screening assay

AbstractAim:To develop a homogeneous binding assay for high-throughput screening (HTS) of hit compounds at human neuromedin U receptor (hNMU-R) 1 and to identify non-peptidic small molecule hNMU-R modulators through functional assessments and structure-activity relationship (SAR) analyses.Methods:Membrane preparations of Chinese hamster ovary cells (CHO-K1) stably expressing hNMU-R1, [125I]hNMU-25, and wheat germ agglutinin-coupled microbeads were used to develop an HTS assay based on scintillation proximity assay (SPA) technology. This method was applied to a large-scale screening campaign against a diverse library of 36 000 synthetic compounds or natural products and subsequent confirmation studies. CHO-K1 cells stably expressing full-length hNMU-R1 or hNMU-R2 and a calcium-sensitive dye were employed to functionally measure intracellular calcium mobilization upon ligand stimulation. Preliminary SAR was determined based on limited structural modifications.Results:The Ki value (0.7 nmol/L) of hNMU-25 (the natural ligand) at hNMU-R1 measured by the SPA method was consistent with that reported in the literature, and the Z' factor for this HTS assay was 0.81. A total of 100 hits, showing more than 30% competitive inhibition on [125I]hNMU-25 binding to hNMU-R1, were identified initially, 3 of which were confirmed thereafter to have reasonable hNMU-R1-binding affinities and similar chemical structures. Based on their common molecular skeleton, 203 analogs were synthesized and tested. Among the 16 analogs that retained variable hNMU-R1-binding abilities, 2 elicited calcium influx in both hNMU-R1 and hNMU-R2-expressing cells, but none displayed antagonist activity.Conclusion:The homogeneous hNMU-R1 binding assay is an efficient and robust tool for screening potential hNMU-R modulators. Two non-selective hNMU-R agonists discovered are of low molecular weight nature with novel chemical structures. The preliminary SAR investigation suggests that both the triphenyl and guanidinol groups are crucial to the bioactivities observed.
New and Emerging Viruses of Blueberry and Cranberry

Blueberry and cranberry are fruit crops native to North America and they are well known for containing bioactive compounds that can benefit human health. Cultivation is expanding within North America and other parts of the world raising concern regarding distribution of existing viruses as well as the appearance of new viruses. Many of the known viruses of these crops are latent or asymptomatic in at least some cultivars. Diagnosis and detection procedures are often non-existent or unreliable. Whereas new viruses can move into cultivated fields from the wild, there is also the threat that devastating viruses can move into native stands of Vaccinium spp. or other native plants from cultivated fields. The aim of this paper is to highlight the importance of blueberry and cranberry viruses, focusing not only on those that are new but also those that are emerging as serious threats for production in North America and around the world.
Binary Relational Algebra Applied to Software Architecture

The architecture of a piece of software refers to its structure as given by its components and their interconnections. An architectural style is a set of commonalities among the structures of a number of software systems. We are concerned with architectures that are characterized by directed graphs. The graphs we are interested in contain edges that are "typed" or "colored", which means that there are a finite number of different kinds of edges. The nodes in the graphs represent entities such as procedures, modules and subsystems. The edges in the graphs represent relations among these entities, such as "calls", "accesses", "imports", "includes", and "uses". This paper shows how binary relational algebra, as defined by Tarski and refined by Schmidt and others, can be used to formalize this type of architectural style. We show how this algebraic approach can be used to give constraints among the relations in an architecture. For example, we can use a relational inequality to formalize the rule that: items within a object can be used from outside the object only if they have been exported from the object. We have developed a prototype "relational calculator", which reads data bases that represent sets of relations, and which allows us to compute new relations and sets. We have used this calculator in a reverse engineering project to determine the clients of a given subsystem, based on relations for containment and usage. We formalize the concept of an architectural style in terms of rules that limit the use of relations. We propose a form for rules in which each rule is written as a relational inequality. We show that such rules are monotonic, which implies that adding new edges can allow more edges, but cannot disallow previously allowed edges.
The World's First Competitive Business Model (Hint: it was Divine)

Lemma: The wealth of King Solomon is well documented and testified in many documents-not ‘just’ Hebrew documents, but also those of other nations. From where did this exemplary wealth derive? The land of Israel is not extraordinarily fertile, nor large, nor blessed with any ‘outstanding’, resource. Solomon did not have obvious mining operations (despite Rider Haggard’s “King Solomon’s Mines” and other such fictional works). All nations at that time were agricultural. If Israel was ‘simply’ an agricultural economy, like all others, particularly with the limited rainfall common to the land then there could not be wealth accrual. Israel is dependent upon local rains and does not have extensive water sources flowing in, such as the Nile Valley or Mesopotamia. In a bad rain-year, there would be hunger, not wealth! Farms were like everyone and everywhere. The source of wealth is not obvious; nor can accrual be accounted for in any usual manner. This question is the basis for this article. The answer was in a unique national business model and implementation mechanism: the Levites were central to it all. It should be stated that this article is a “shortened” form of a much longer piece, discussing the tribe of Levi in general, currently in process of being published as a book.
Context tracker: Exploring supporters and distracters in unconstrained environments

Visual tracking in unconstrained environments is very challenging due to the existence of several sources of varieties such as changes in appearance, varying lighting conditions, cluttered background, and frame-cuts. A major factor causing tracking failure is the emergence of regions having similar appearance as the target. It is even more challenging when the target leaves the field of view (FoV) leading the tracker to follow another similar object, and not reacquire the right target when it reappears. This paper presents a method to address this problem by exploiting the context on-the-fly in two terms: Distracters and Supporters. Both of them are automatically explored using a sequential randomized forest, an online template-based appearance model, and local features. Distracters are regions which have similar appearance as the target and consistently co-occur with high confidence score. The tracker must keep tracking these distracters to avoid drifting. Supporters, on the other hand, are local key-points around the target with consistent co-occurrence and motion correlation in a short time span. They play an important role in verifying the genuine target. Extensive experiments on challenging real-world video sequences show the tracking improvement when using this context information. Comparisons with several state-of-the-art approaches are also provided.
Enabling Solar Energy to Fuel Conversion on Silicon-based Nanomaterial Catalysts

This thesis presents the development of Silicon-based nanomaterials for use as the functional component in solar water splitting cells. Silicon satisfies the materials sustainability requirements being an earth abundant, inexpensive and the most widely-studied semiconductor. This research investigates the design and stability of cathode ensembles, by incorporating functional diamond stabilising coatings and hydrogen catalysts onto planar and nanostructured silicon interfaces. Various experimental techniques were implemented to better understand the optical and morphological attributes of the interface and especially test its performance for solar to hydrogen conversion. This thesis also investigates the durability of these materials for prospective solar hydrogen devices.
Stroop performance in drug users classified by HIV and hepatitis C virus serostatus

Hepatitis C virus (HCV) can be detected in the brain (Radkowski et al., 2002) and investigators speculate that HCV has neuroinvasive properties (Forton et al., 2003) with direct effects on cerebral function. MRS studies show that the basal ganglia and white matter of individuals with HCV have abnormal choline/creatine ratios, indicating CNS inflammation or infection (Forton et al., 2003). Patients with HCV show defects in working memory and information processing speed (Forton et al., 2003; Hilsabeck et al., 2002), similar to patients with basal ganglia disorders and HIV (e.g., Heaton et al., 1995).
The automatic generation of mutation operators for genetic algorithms

We automatically generate mutation operators for Genetic Algorithms (GA) and tune them to problem instances drawn from a given problem class. By so doing, we perform metalearning in which the base-level contains GAs (which learn about problem instances), and the meta-level contains GAmutation operators (which learn about problem classes). We use Register Machines to explore a constrained design space for mutation operators. We show how two commonly used mutation operators (viz. one-point and uniform mutation) can be expressed in this framework. Iterated local search is used to search the space of mutation operators, and on a test-bed of 7 problem classes we identify machine-designed mutation operators which outperform their human counterparts.
COSMO-SkyMed® for crops monitoring

The COSMO-SkyMed® X-band SAR satellites constellation, due to its capability to acquire dense temporal data series at very high to high ground resolution and in co and cross-polarizations, is a promising system for crops monitoring and management. Its use, in combination with other SAR and optical systems in a virtual constellation, can result in a very effective tool for agricultural practice monitoring, management and control. This work intends to show a preliminary analysis of a dataset of COSMO-SkyMed® products acquired at HH, VV and VH polarizations over the Marchfeld agricultural area in Austria. The analysis has been carried out at a regional scale by taking into consideration the temporal behavior of two different clusters of vegetation macro-classes distinct for their different Normalized Differential Vegetation Index (NDVI) temporal signatures. Preliminary results show a significant correlation of the NDVI values with the COSMO-SkyMed® HH backscattering coefficients for both the clusters of classes as well as a significant one with VV backscattering coefficients for NDVI values lower than 0.7.
Cigarette Smoke Extract-induced Reduction in Migration and Contraction in Normal Human Bronchial Smooth Muscle Cells

The proliferation, migration, cytokine release, and contraction of airway smooth muscle cells are key events in the airway remodeling process that occur in lung disease such as asthma, chronic obstruction pulmonary disease, and cancer. These events can be modulated by a number of factors, including cigarette smoke extract (CSE). CSE-induced alterations in the viability, migration, and contractile abilities of normal human airway cells remain unclear. This study investigated the effect of CSE on cell viability, migration, tumor necrosis factor (TNF)-α secretion, and contraction in normal human bronchial smooth muscle cells (HBSMCs). Treatment of HBSMCs with 10% CSE induced cell death, and the death was accompanied by the generation of reactive oxygen species (ROS). CSE-induced cell death was reduced by N-acetyl-l-cysteine (NAC), an ROS scavenger. In addition, CSE reduced the migration ability of HBSMCs by 75%. The combination of NAC with CSE blocked the CSE-induced reduction of cell migration. However, CSE had no effect on TNF-α secretion and NF-κB activation. CSE induced an increase in intracellular Ca2+ concentration in 64% of HBSMCs. CSE reduced the contractile ability of HBSMCs, and the ability was enhanced by NAC treatment. These results demonstrate that CSE treatment induces cell death and reduces migration and contraction by increasing ROS generation in normal HBSMCs. These results suggest that CSE may induce airway change through cell death and reduction in migration and contraction of normal HBSMCs.
Perceived Object Continuity and Spontaneous Retrieval of Features from an Inhibited Object

Abstract Previous research has shown that attention to an object can trigger the retrieval of features of a preceding object. The present study investigates whether such retrieval would occur to a recently inhibited object. In three experiments, participants saw two successively presented stimuli (S1 and S2) that varied in color and orientation. The task was to respond to the color or orientation of S2 in accordance with a task cue at the beginning of each trial. In separate experiments, we manipulated the number of the trials on which the task relevant features of S1 and S2 were matched versus mismatched, and the perceived object continuation between the two stimuli. Evidence for spontaneous feature retrieval was found when S1 and S2 could be seen as different instantiations of the same object but not when they were likely to be perceived as different types of objects. These results suggest that the features of a previously inhibited object can be retrieved spontaneously. However, such retrieval and its effect on a subsequent stimulus depend on the perceived object continuity between the two successive stimuli.
Adapting Data Mining for German Named Entity Recognition

In the latest decades, machine learning approaches have been intensively exper-imented for natural language processing. Most of the time, systems rely on using statistics within the system, by analyzing texts at the token level and, for labelling tasks, categorizing each among possible classes. One may notice that previous sym-bolic approaches (e.g. transducers) where designed to delimit pieces of text. Our re-search team developped mXS, a system that aims at combining both approaches. It lo-cates boundaries of entities by using se-quential pattern mining and machine learn-ing. This system, intially developped for French, has been adapted to German.
Sparse Estimation by Exponential Weighting

Consider a regression model with fixed design and Gaussian noise where the regression function can potentially be well approximated by a function that admits a sparse representation in a given dictionary. This paper resorts to exponential weights to exploit this underlying sparsity by implementing the principle of sparsity pattern aggregation. This model selection take on sparse estimation allows us to derive sparsity oracle in- equalities in several popular frameworks including ordinary sparsity, fused sparsity and group sparsity. One striking aspect of these theoretical re- sults is that they hold under no condition on the dictionary. Moreover, we describe an efficient implementation of the sparsity pattern aggregation principle that compares favorably to state-of-the-art procedures on some basic numerical examples.