Miracle-dz/UniFAR-FTUs huggingface dataset:
Stress response or beneficial temperature acclimation: transcriptomic signatures in Antarctic fish (Pachycara brachycephalum)

Research on the thermal biology of Antarctic marine organisms has increased awareness of their vulnerability to climate change, as a flipside of their adaptation to life in the permanent cold and their limited capacity to acclimate to variable temperatures. Here, we employed a species‐specific microarray of the Antarctic eelpout, Pachycara brachycephalum, to identify long‐term shifts in gene expression after 2 months of acclimation to six temperatures between −1 and 9 °C. Changes in cellular processes comprised signalling, post‐translational modification, cytoskeleton remodelling, metabolic shifts and alterations in the transcription as well as translation machinery. The magnitude of transcriptomic responses paralleled the change in whole animal performance. Optimal growth at 3 °C occurred at a minimum in gene expression changes indicative of a balanced steady state. The up‐regulation of ribosomal transcripts at 5 °C and above was accompanied by the transcriptomic activation of differential protein degradation pathways, from proteasome‐based degradation in the cold towards lysosomal protein degradation in the warmth. From 7 °C upwards, increasing transcript levels representing heat‐shock proteins and an acute inflammatory response indicate cellular stress. Such patterns may contribute to a warm‐induced energy deficit and a strong weight loss at temperatures above 6 °C. Together, cold or warm acclimation led to specific cellular rearrangements and the progressive development of functional imbalances beyond the optimum temperature. The observed temperature‐specific expression profiles reveal the molecular basis of thermal plasticity and refine present understanding of the shape and positioning of the thermal performance curve of ectotherms on the temperature scale.
Peripheral blood mononuclear cells produce normal amounts of defective Vif- human immunodeficiency virus type 1 particles which are restricted for the preretrotranscription steps

Previous studies have demonstrated the absence of viral replication of Vif- mutants in stimulated primary blood mononuclear cells (PBMC). Human immunodeficiency virus type 1 strain NDK Vif- mutants were propagated on the semipermissive CEM cell line, and the viral stock obtained was compared with the wild-type virus during a single cycle in PBMC. The Vif- virus was able to enter PBMC with the same efficiency as the wild type, as demonstrated by quantification of the strong-stop cDNA, and retrotranscription was observed for both viruses within 4 h postinfection. Using a PCR assay with an Alu-long terminal repeat pair of primers, we detected integration for both the wild-type and Vif- viruses. We then used qualitative and quantitative reverse transcription-mediated PCR techniques to study the steady-state level of intracellular and extracellular viral RNAs. All mRNA species were detected in PBMC infected with the wild-type virus or with the Vif- virus 36 h postinfection. Furthermore, quantification of viral RNA released from infected cells demonstrated similar levels of virus produced after a unique cycle of replication. However, the Vif- virus obtained after one replication cycle in PBMC was unable to initiate retrotranscription in permissive target cells. These data strongly suggest that the failure to infect target cells is due to a defect in the formation of the viral particle in PBMC.
GA-Based Affine PPM Using Matrix Polar Decomposition

Point pattern matching (PPM) arises in areas such as pattern recognition, digital video processing and computer vision. In this study, a novel Genetic Algorithm (GA) based method for matching affine-related point sets is described. Most common techniques for solving the PPM problem, consist in determining the correspondence between points localized spatially within two sets and then find the proper transformation parameters, using a set of equations. In this paper, we use this fact that the correspondence and transformation matrices are two unitary polar factors of Grammian matrices. We estimate one of these factors by the GA's population and then evaluate this estimation by computing an error function using another factor. This approach is an easily implemented one and because of using the GA in it, its computational complexity is lower than other known methods. Simulation results on synthetic and real point patterns with varying amount of noise, confirm that the algorithm is very effective.
Using cognates to align sentences in bilingual corpora

In a recent paper, Gale and Church describe an inexpensive method for aligning bitext, based exclusively on sentence lengths [3]. While this method produces surprisingly good results (a success rate around 96%), even better results are required to perform such tasks as the computer-assisted revision of translations. In this paper, we examine some of the weaknesses of Gale and Church's program, and explain how just a small amount of linguistic knowledge would help to overcome these weaknesses. We discuss how cognates provide for a cheap and reasonably reliable source of linguistic knowledge. To illustrate this, we describe a modification to the program in which the criterion is cognates rather than sentence lengths. Finally, we show how better and more efficient results may be obtained by combining the two criteria length and "cogneteness". Our method can be generalized to accommodate other sources of linguistic knowledge, and experimentation shows that it produces better results than alignments based on length alone, at a minimal cost.
A Robust Built-Up Area Presence Index by Anisotropic Rotation-Invariant Textural Measure

A procedure for the calculation of a texture-derived built-up presence index (PanTex) from textural characteristics of panchromatic satellite data is presented. The index is based on fuzzy rule-based composition of anisotropic textural co-occurrence measures derived from the satellite data by the gray-level co-occurrence matrix (GLCM). Examples are produced how the PanTex index reduces the edge effects of the nonbuilt-up linear features and improves capacity to discriminate between built-up and nonbuilt-up areas. The accuracy and robustness of the PanTex measure against seasonal changes, multisensor, multiscene, and data degradation by wavelet-based compression and histogram stretching is discussed with some examples.
Synthesis of frequency generator via spiking neurons network: A genetic algorithm approach

Inspired by the Theory of Neuronal Group Selection (TNGS), we have carried out synthesis of frequency generator via spiking neurons network through genetic algorithm. The TNGS sets that a neuronal group is the most basic unit in the cortical area and are generated by synapses of localized neural cells in the cortical area of the brain firing and oscillating in synchrony at a predefined frequency. Each one of these clusters (Neuronal Groups) is a set of localized, tightly coupled neurons developed in the embryo. According to this proposal, this paper describes a method of tuning the parameters of the Izhikevich spiking neuron model. Computational experiments consisting of a network with all neurons of the same type and a network with different neurons were conducted. A genetic algorithm was used to tune the parameters in these two different cases. The results were compared in order to find the best way to create a frequency generator of spiking neurons network.
Black men in the margins:Space tradersand the interpositional strategy against B(l)acklash

In this essay, the televisual narrative of Home Box Office's Space Traders is used to help theorize communicative performance from a marginal perspective as part of a broader effort to fight backlash. The notion of interpositionality is offered as an alternative to classical marginality theory, and a reading of Space Traders helps illustrate the interpositional strategy of creating dynamic identities. The authors suggest that the tensions of hegemonic space offer progressive strategies for resisting domination by expanding the margins of subjectivity in pursuit of both anti‐essentialist and non‐stereotypical identities.
Structured terminology for capsule endoscopy: results of retrospective testing and validation in 766 small-bowel investigations.

BACKGROUND AND STUDY AIMS Capsule endoscopy (CE) is an effective means of investigating the small bowel in patients with gastrointestinal diseases. Computerized reports are frequently used in endoscopy, and the Minimal Standard Terminology (MST) has been promoted by endoscopy societies as the official vocabulary for endoscopy. The aims of this study were to design a lexicon for CE reports based on the principles of the MST and to validate lists of terms for describing findings and reasons for performing a CE by cross-matching them with the results of CE procedures collected during ongoing clinical studies. MATERIALS AND METHODS A consensus-based Capsule Endoscopy Structured Terminology (CEST) was developed by experts involved in CE studies. Lists of terms suitable for CE were designed for the various sections of an endoscopic report. They were then correlated with the corresponding MST lists for duodenal and intestinal endoscopy. The results of 766 CE procedures, collected in an electronic case record form (eCRF), were analyzed to provide lists of reasons for performing the procedures and of the findings. The eCRF provided only a limited number of items for each data field, along with free-text facilities. Only descriptions pertaining to the small bowel were analyzed. Lists of terms were then reviewed by two experts to group obvious synonyms. The accuracy of the CEST was defined beforehand as the capability to describe 90 % of entries. RESULTS A total of 766 CE procedures were analyzed. The eCRF included 824 entries as reasons for the examination in 655 CEs (1.3 per procedure). These represented 122 different expressions. After grouping of synonyms, 28 expressions remained. Among them, 10 were matched with terms from the list of reasons for performing CE offered in the CEST. These were the most frequently used, accounting for 768 entries in this field (93.2 %). All eCRFs contained at least one description of findings. A total of 109 CE procedures were classified as normal (14.3 %). A total of 2624 entries for abnormal findings were recorded for 657 procedures (4.0 per procedure). In all, 213 different expressions were used to describe abnormal findings. After grouping of synonyms, 52 expressions remained. Among these, 27 were matched with terms from the list of findings in the CEST, covering 2403 entries (91.6 %). CONCLUSIONS In this study, CEST terms were capable of describing more than 90 % of the reasons for performance and of the findings in an unselected set of CE procedures. CEST is therefore suitable for use as the standard lexicon for CE reports. Adopted as a standard, it could significantly improve the quality of the data collected and reported in CE studies.
SPATIO-TEXTUAL SIMILARITY JOIN

Data mining is the process of discovering interesting patterns and knowledge from large amounts of data. Spatial databases store large space related data, such as maps, preprocessed remote sensing or medical imaging data. Modern mobile phones and mobile devices are equipped with GPS devices; this is the reason for the Location based services to gain significant attention. These Location based services generate large amounts of spatiotextual data which contain both spatial location and textual description. The spatiotextual objects have different representations because of deviations in GPS or due to different user descriptions. This calls for the need of efficient methods to integrate spatio-textual data. Spatio-textual similarity join meets this need. Spatio-textual similarity join: Given two sets of spatio-textual data, it finds all the similar pairs. Filter and refine framework will be developed to device the algorithms. The prefix filter technique will be extended to generate spatial and textual signatures and inverted indexes will be built on top of these signatures. Candidate pairs will be found using these indexes. Finally the candidate pairs will be refined to get the result. MBR-prefix based signature will be used to prune dissimilar objects. Hybrid signature will be used to support spatial and textual pruning simultaneously.
The Effects of Depressive Symptomology on Women’s Childbearing Considerations

Empirical literature dedicated to pursuing knowledge of the relationship between women who suffer from depression and their considerations of childbearing is lacking. Therefore, the primary purpose of this study was to determine the types of relationships that exist between depressive symptomology in women and their childbearing considerations. Secondary data analysis was the chosen form of research analysis, and the National Survey of Families and Households (Wave 1) was the data set employed. There were a total of four independent variables (depressive symptomology, global life satisfaction, global optimism, and self-esteem) and two dependent variables (10 constraint items and 4 motivational factor items) used to determine the relationships, with hierarchical regression analysis being the chosen analysis procedure. Results from the analysis revealed that there was a positive relationship between a woman’s level of depressive symptomology and several of the constraint and motivational factor items, namely, economic well-being, relationship issues, and the stress associated with caring for a child. Additionally, the self-esteem items were found to be negatively correlated with some items, but positively correlated with others. The items were most often negatively correlated with motivational factors (i.e., having someone to love , needing something to do , giving my parents grandchildren , and having someone to care for me when I am old ), and most often positively correlated with constraints regarding issues of time (e.g., worry that I will have time for my career). Finally, both the global optimism and global life satisfaction variables were dropped from the analysis because they proved to be poor measures. The findings of the study provide evidence that women who suffer from depression do appear to consider certain constraints and motivational factors when making decisions about their future status as mothers. The study concluded with recommendations for theory, future research, and family life education practice, as well as a description of limitations of the project.
Extracellular deposition of matrilin-2 controls the timing of the myogenic program during muscle regeneration

ABSTRACT Here, we identify a role for the matrilin-2 (Matn2) extracellular matrix protein in controlling the early stages of myogenic differentiation. We observed Matn2 deposition around proliferating, differentiating and fusing myoblasts in culture and during muscle regeneration in vivo. Silencing of Matn2 delayed the expression of the Cdk inhibitor p21 and of the myogenic genes Nfix, MyoD and Myog, explaining the retarded cell cycle exit and myoblast differentiation. Rescue of Matn2 expression restored differentiation and the expression of p21 and of the myogenic genes. TGF-&bgr;1 inhibited myogenic differentiation at least in part by repressing Matn2 expression, which inhibited the onset of a positive-feedback loop whereby Matn2 and Nfix activate the expression of one another and activate myoblast differentiation. In vivo, myoblast cell cycle arrest and muscle regeneration was delayed in Matn2−/− relative to wild-type mice. The expression levels of Trf3 and myogenic genes were robustly reduced in Matn2−/− fetal limbs and in differentiating primary myoblast cultures, establishing Matn2 as a key modulator of the regulatory cascade that initiates terminal myogenic differentiation. Our data thus identify Matn2 as a crucial component of a genetic switch that modulates the onset of tissue repair.
ATH1 and KNAT2 proteins act together in regulation of plant inflorescence architecture

The inflorescence of flowering plants is a highly organized structure, not only contributing to plant reproductive processes, but also constituting an important part of the entire plant morphology. Previous studies have revealed that the class-I KNOTTED1-like homeobox (KNOX) genes BREVIPEDICELLUS (BP or KNAT1), KNAT2, and KNAT6 play essential roles in inflorescence architecture. Pedicel morphology is known to contribute greatly to inflorescence architecture, and BP negatively regulates KNAT2 and KNAT6 to ensure that pedicels have a normal upward-pointing orientation. These findings indicate that a genetic network exists in controlling pedicel orientation, but how this network functions in the developmental process remains elusive. Here it is reported that the ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) gene, which belongs to the BELL1-like homeodomain gene family, is a new member participating in regulating pedicel orientation in the class-I KNOX network. In a genetic screening for suppressors of isoginchaku-2D, a gain-of-function ASYMMETRIC LEAVES2 mutant that displays downward-pointing pedicels, a suppressor mutant was obtained. Characterization of this mutant revealed that the mutation corresponds to ATH1. Genetic analysis indicated that ATH1 acts mainly in the KNAT2 pathway. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that ATH1 physically interacts with KNAT2. The data indicate that the ATH1–KNAT2 complex acts redundantly with KNAT6, both of which are negatively regulated by BP during pedicel development.
Agricultural Vegetation Parameter Estimation using Pol-SAR: Retrieval of Soil Moisture

In this paper the focus is given to the soil moisture retrieval under a vegetation cover, exemplarily for two crop types winter wheat and rape. For this Pol-SAR data over a whole vegetation period were used acquired in the frame of the AGRISAR campaign in 2006 at L-band. The potentials and limitations over time are investigated by modifications of the model based Freeman decomposition in order to decompose the scattering contributions and to invert the surface and dihedral scattering component for soil moisture estimation. The applied decomposition approaches for agricultural land surfaces are suitable, but exhibit deficiencies in modeling the volume component, even though some improvements due to the modifications could be presented. In the end the soil moisture estimation does not perform constantly well over the whole acquisition period due to the complexity of the crop vegetation.
Bi-criteria Genetic Selection of Bagging Fuzzy Rule-based Multiclassification Systems

Previously we proposed a scheme to generate fuzzy rule-based multiclassification systems by means of bagging, mutual information-based feature selection, and a multicriteria genetic al- gorithm (GA) for static component classifier selection guided by the ensemble training error. In the current contribution we extend the latter component by the use of two bi-criteria fitness functions, com- bining the latter error measure with the selected ensemble likelihood. A study on four popular UCI datasets with different dimensionalities is conducted in order to analyze the accuracy-complexity trade-off obtained by the two GAs, the initial fuzzy ensemble and a single fuzzy classifier.
Optimal data selection for unit selection synthesis

In this work, we address the issue of creating a set of utterances with optimal coverage for reliable, high quality concatenative synthesis, whether for general synthesis or domain synthesis. We present an automatic method that takes into account the acoustic distinctions made by a particular speaker and selects prompts from large databases of typical utterances. A general unit selection text-to-speech system created by this process can synthesize any input text, but the output is best for content intended to be similar to that in the database in terms of style, delivery, and coverage.
Detecting Concurrency Errors in Client-Side Java Script Web Applications

As web technologies have evolved, the complexity of dynamic web applications has increased significantly and web applications suffer concurrency errors due to unexpected orders of interactions among web browsers, users, the network, and so forth. In this paper, we present WAVE (Web Applications Virtual Environment), a testing framework to detect concurrency errors in client-side web applications written in JavaScript. WAVE generates various sequences of operations as test cases for a web application and executes a sequence of operations by dynamically controlling interactions of a target web application with the execution environment. We demonstrate that WAVE is effective and efficient for detecting concurrency errors through experiments on eight examples and five non-trivial real-world web applications.
Are There Qualitative Differences in the Representation of Abstract and Concrete Words? Within-Language and Cross-Language Evidence from the Semantic Priming Paradigm

The different organizational frameworks theory proposes that there is a qualitative difference between the representation of concrete and abstract words in memory: Concrete concepts would be primarily organized in terms of semantic similarity whereas abstract concepts would be mainly organized by their association with other concepts. Evidence in support of this proposal has been mostly obtained with neuropsychological populations and, to a lesser extent, with healthy participants. In the present work, we tested the different organizational frameworks theory by using, for the first time, a semantic priming paradigm both within language and across languages. The results revealed that there was priming for both semantically similar and associative relations when words were concrete. However, with abstract words, priming was only observed when pairs and targets were associated. These results do not support the proposal of Crutch and coworkers, suggesting that the experimental paradigm as well as the type of relations tested may modulate the pattern of effects obtained with concrete and abstract words.
The stressed eyewitness: the interaction of thematic arousal and post-event stress in memory for central and peripheral event information

Both arousal during the encoding of stimuli and subsequent stress can affect memory, often by increasing memory for important or central information. We explored whether event-based (thematic) arousal and post-event stress interact to selectively enhance eyewitnesses' memory for the central aspects of an observed incident. Specifically, we argue that memory for stimuli should be enhanced when (1) the stimuli are encoded under arousal (vs. non-arousal), and (2) stress is experienced soon after the encoding episode. We designed an experiment that extended previous research by manipulating arousal without changing the stimulus material, distinguishing between central and peripheral event information, and using a dynamic, life-like event instead of static pictures. After watching a video depicting a burglary under high or low thematic arousal, psychosocial stress was induced or not induced by the Trier Social Stress Test (TSST). Salivary cortisol was measured at standard intervals. Consistent with our prediction, we found a significant post-event stress × thematic arousal × centrality interaction, indicating that the recognition advantage for central event items over peripheral event items was most pronounced under both high thematic arousal and post-event stress. Because stress was induced after encoding this interaction cannot be explained by possible differences at encoding, such as narrowed attention. The centrality effect of post-event stress under high thematic arousal was statistically mediated by the cortisol increase, which suggests a key role of the stress hormone. We discuss implications of our findings for psychological and neuroscientific theories of emotional memory formation.