Miracle-dz/UniFAR-FTUs huggingface dataset:
Approach of Complexity in Nature: Entropic Nonuniqueness

Boltzmann introduced in the 1870s a logarithmic measure for the connection between the thermodynamical entropy and the probabilities of the microscopic configurations of the system. His celebrated entropic functional for classical systems was then extended by Gibbs to the entire phase space of a many-body system and by von Neumann in order to cover quantum systems, as well. Finally, it was used by Shannon within the theory of information. The simplest expression of this functional corresponds to a discrete set of W microscopic possibilities and is given by S B G = − k ∑ i = 1 W p i ln p i (k is a positive universal constant; BG stands for Boltzmann–Gibbs). This relation enables the construction of BGstatistical mechanics, which, together with the Maxwell equations and classical, quantum and relativistic mechanics, constitutes one of the pillars of contemporary physics. The BG theory has provided uncountable important applications in physics, chemistry, computational sciences, economics, biology, networks and others. As argued in the textbooks, its application in physical systems is legitimate whenever the hypothesis of ergodicity is satisfied, i.e., when ensemble and time averages coincide. However, what can we do when ergodicity and similar simple hypotheses are violated, which indeed happens in very many natural, artificial and social complex systems. The possibility of generalizing BG statistical mechanics through a family of non-additive entropies was advanced in 1988, namely S q = k 1 − ∑ i = 1 W p i q q − 1 , which recovers the additive S B G entropy in the q→ 1 limit. The index q is to be determined from mechanical first principles, corresponding to complexity universality classes. Along three decades, this idea intensively evolved world-wide (see the Bibliography in http://tsallis.cat.cbpf.br/biblio.htm) and led to a plethora of predictions, verifications and applications in physical systems and elsewhere. As expected, whenever a paradigm shift is explored, some controversy naturally emerged, as well, in the community. The present status of the general picture is here described, starting from its dynamical and thermodynamical foundations and ending with its most recent physical applications.
Is information technology general education effective for non-engineering major students?: An exploratory study on ethnically Chinese classrooms

The role of computer and information literacy in the contemporary digital society is as important as language proficiency. This is widely exemplified in the graduate requirements in many tertiary institutions: students must pass the compulsory IT subject(s), often as a mandatory General Education (GE) course, before graduation irrespective of majors. Challenges arise to the computer science faculty as students are from different academic backgrounds with diversified level of IT background, and are often less motivated than taking a course in the major program. In this paper, we attempt to explore the reasons fostering students to devote efforts (i.e., persistence) in the GE IT course in tradition confucian examination-orientated educational settings. Student behavior and perceptions in two major groups of ethnically Chinese students (Mainland China and Hong Kong) are analyzed, revealing that mastery is the main reason leading to persistence in the mandatory IT course. Theoretically, we address the paucity on GE IT related research on ethnically Chinese students through validation and comparison of findings from the literature, leading to new directions of research. Practically, we generalize our experience from practitioner's view and propose different suggestions to effectively deliver GE IT courses under the confucian culture.
Modification of Lignin Polymers with COMT Anti-Sense Gene in the Jatropha curcas L. by Green Biotechnology Tools

Lignin, a complex aromatic polymer, is considered a part of the secondary cell wall. Also, it's called a "cell adhesive" based on provides strength and rigidity to plant tissues and fibers through strong cross-linking with cell wall components. Moreover, lignin acts as a line of defense for plants against biotic and abiotic stresses. In the field of plant biotechnology, particle bombardment remains the most important technique to directly transfer DNA from source to target organ and the most widely used method to generate transgenic plants for commercial purposes. Down-regulation of Jatropha curcas's lignin-producing caffeic acid 3-O-methyltransferase (COMT) gene production pathway led the transgenic plants to develop cell walls. The transgene COMT antisense is used as a selection marker pZMAS-COMT 10,907 bp plasmid (University of Illinois) to confer resistance to glufosinate herbicides under the 35S promoter. Irradiation of embryonic callus with bullet particles introduced the COMT antisense gene and reduced the amount of lignin. Transgenic green callus was used to extract DNA, RNA, and PCR & RT-PCR were performed to detect the presence of genes. A positive sharp band appeared in the green callus, indicating that the gene expression level was downregulated compared to the control. Transgenic shoots and green callus had lower lignin content compared to controls.
ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants

A webserver, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for ‘crystallization and preliminary X-ray analysis’ publications.
A Unified Formalization of Four Shared-Memory Models

The authors present a data-race-free-1, shared-memory model that unifies four earlier models: weak ordering, release consistency (with sequentially consistent special operations), the VAX memory model, and data-race-free-0. Data-race-free-1 unifies the models of weak ordering, release consistency, the VAX, and data-race-free-0 by formalizing the intuition that if programs synchronize explicitly and correctly, then sequential consistency can be guaranteed with high performance in a manner that retains the advantages of each of the four models. Data-race-free-1 expresses the programmer's interface more explicitly and formally than weak ordering and the VAX, and allows an implementation not allowed by weak ordering, release consistency, or data-race-free-0. The implementation proposal for data-race-free-1 differs from earlier implementations by permitting the execution of all synchronization operations of a processor even while previous data operations of the processor are in progress. To ensure sequential consistency, two sychronizing processors exchange information to delay later operations of the second processor that conflict with an incomplete data operation of the first processor. >
Methylmercury inhibits differentiation of rat neural stem cells via Notch signalling

The Notch receptor is essential for neural stem cell (NSC) characteristics. Relatively high concentrations (micromolar) of methylmercury (MeHg) activate Notch signalling in Drosophila cell lines; however, exposure of MeHg at such concentrations is rare, and the implications for mammalian cells are unclear. We have shown that MeHg at a nanomolar range inhibits neuronal differentiation of rodent embryonic NSCs. Here we show that low MeHg levels (2.5–10 nM) activated Notch signalling in NSCs, as assessed by the increased activity in a specific Notch-reporter assay and by the increased cleavage of the Notch intracellular domain. Importantly, pretreatment with Notch cleavage inhibitor reversed the MeHg-induced repression of neuronal differentiation, suggesting that Notch activation is involved in the inhibition of NSC differentiation by environmentally relevant levels of MeHg.
An Algorithm for Computing Extrinsic Camera Parameters for Accurate Stereo Photogrammetry of Clouds

In this paper, we present a technique for accurate stereo photogrammetry of clouds for observation and measurement of the formation of summer thunderstorms over elevated terrain. Two digital cameras are set on a ground baseline so that the straight-line distance between the two cameras and the highest terrain is about 16 km and the spacing between the center of cameras is about 0.6km. Stereo pair images are taken every 10 seconds and sent to a server via internet from the field. Due to large distances and other practical hurdles, we cannot accurately measure the location and orientation of the cameras. Further, the terrestrial landmarks chosen for calibration can not be precisely measured in the field. The discrepency between true and observed (measured or computed) photogrammetry parameters gives rise to the geometric error. The main contributions of this paper are twofold. One, we develop and present theoretical analysis of the geometric error and the necessity to find an accurate solution for location and its impact on determining accurate orientation parameters in a large scale scene. Second, we have developed a coarse to fine iterative algorithm that minimizes the geometric error to find the best parameters (location and orientation) for each camera given approximate values of these parameters. Validation of our algorithm is from experimental results which show that terrestrial position of clouds matches with the composite reflectivity from the WSR-88D radar and the calculated heights agree with the tropopause heights in the sounding data.
Video-microscopy observations of fast dynamic processes in the protozoon Giardia lamblia.

Video-microscopy in combination with digital image processing was used to analyze dynamic processes associated to the life cycle of Giardia lamblia trophozoites. These parasites swim and attach to the epithelial cells, producing the disease known as Giardiasis. Giardia is a multiflagellar cell, presenting 4 pairs of flagella. With the use of analogue and digital tools, we observed that in cells attached to glass slides only 2 of the 4 pairs present active beating (wave propagation). The frequency observed was 17-18 Hz to the anterior and 8-11 Hz to the ventral flagella. These data resulted from several hours of recording using both analogue video and high-speed digital camera. The caudal pair did not show active beating patterns and the same holds true for the posterior one. In this latter pair, oscillations were observed, but they were always associated to the transit of the wave produced by the ventral pair. The analysis performed with free moving cells showed that during its forward dislocation, Giardia lamblia presented either a lateral rocking or a complete rotational (tumbling) movement around its longitudinal axis. A dislocation of the caudal region of the cell both in the lateral and dorso-ventral direction was observed. This movement was completely independent from the flagellar beating and it is likely to be produced by a microtubular complex located in the caudal portion of the cell. The adhesion process of Giardia lamblia was also followed by video-microscopy and the data showed that the ventral disk had an active participation in this process.
That’s What She Said: Double Entendre Identification

Humor identification is a hard natural language understanding problem. We identify a subproblem --- the "that's what she said" problem --- with two distinguishing characteristics: (1) use of nouns that are euphemisms for sexually explicit nouns and (2) structure common in the erotic domain. We address this problem in a classification approach that includes features that model those two characteristics. Experiments on web data demonstrate that our approach improves precision by 12% over baseline techniques that use only word-based features.
Deep Episodic Memory: Encoding, Recalling, and Predicting Episodic Experiences for Robot Action Execution

We present a novel deep neural network architecture for representing robot experiences in an episodic-like memory that facilitates encoding, recalling, and predicting action experiences. Our proposed unsupervised deep episodic memory model as follows: First, encodes observed actions in a latent vector space and, based on this latent encoding, second, infers most similar episodes previously experienced, third, reconstructs original episodes, and finally, predicts future frames in an end-to-end fashion. Results show that conceptually similar actions are mapped into the same region of the latent vector space. Based on these results, we introduce an action matching and retrieval mechanism, benchmark its performance on two large-scale action datasets, 20BN-something-something and ActivityNet and evaluate its generalization capability in a real-world scenario on a humanoid robot.
Moderate Photoinhibition of Photosystem II Protects Photosystem I from Photodamage at Chilling Stress in Tobacco Leaves

It has been indicated that photosystem I (PSI) is susceptible to chilling-light stress in tobacco leaves, but the effect of growth light intensity on chilling-induced PSI photoinhibition in tobacco is unclear. We examined the effects of chilling temperature (4°C) associated with moderate light intensity (300 μmol photons m-2 s-1) on the activities of PSI and photosystem II (PSII) in leaves from sun- and shade-grown plants of tobacco (Nicotiana tabacum cv. k326). The sun leaves had a higher activity of alternative electron flow than the shade leaves. After 4 h chilling treatment, the sun leaves showed significantly a higher PSI photoinhibition than the shade leaves. At chilling temperature the sun leaves showed a greater electron flow from PSII to PSI, accompanying with a lower P700 oxidation ratio. When leaves were pre-treated with lincomycin, PSII activity decreased by 42% (sun leaves) and 47% (shade leaves) after 2 h exposure to the chilling-light stress, but PSI activity remained stable during the chilling-light treatment, because the electron flow from PSII to PSI was remarkably depressed. These results indicated that the stronger chilling-induced PSI photoinhibition in the sun leaves was resulted from a greater electron flow from PSII to PSI. Furthermore, moderate PSII photoinhibition depressed electron flow to PSI and then protected PSI activity against further photodamage in chilled tobacco leaves.
Redox Equilibrium in Mucosal T Cells Tunes the Intestinal TCR Signaling Threshold1

Mucosal immune tolerance in the healthy intestine is typified by lamina propria T cell (LPT) functional hyporesponsiveness after TCR engagement when compared with peripheral blood T cell (PBT). When LPT from an inflamed intestine are activated through TCR cross-linking, their responsiveness is stronger. LPT are thus capable of switching from a tolerant to a reactive state, toggling between high and low thresholds of activation. We demonstrate that in normal LPT global tyrosine phosphorylation upon TCR cross-linking or an increase in intracellular H2O2, an inhibitor of protein tyrosine phosphatases, is muted. Thus, we propose that LPT have a greater reducing capacity than PBT, shifting the balance between kinases and protein tyrosine phosphatases in favor of the latter. Surface γ-glutamyl transpeptidase, an indirect indicator of redox potential, and glutathione are significantly elevated in LPT compared with PBT, suggesting that elevated glutathione detoxifies TCR-induced reactive oxygen species. When glutathione is depleted, TCR-induced LPT tyrosine phosphorylation rises to PBT levels. Conversely, increasing glutathione in PBT attenuates tyrosine phosphorylation. In LPT isolated from inflamed mucosa, TCR cross-linking induces greater phosphorylation, and γ-glutamyl transpeptidase levels are reduced compared with those from autologous noninflamed tissue. We conclude that the high TCR signaling threshold of mucosal T cells is tuned by intracellular redox equilibrium, whose dysregulation may mediate intestinal inflammation.
The TRIM-NHL Protein LIN-41 and the OMA RNA-Binding Proteins Antagonistically Control the Prophase-to-Metaphase Transition and Growth of Caenorhabditis elegans Oocytes

In many animals, oocytes enter meiosis early in their development but arrest in meiotic prophase I. Oocyte growth, which occurs during this arrest period, enables the acquisition of meiotic competence and the capacity to produce healthy progeny. Meiotic resumption, or meiotic maturation, involves the transition to metaphase I (M phase) and is regulated by intercellular signaling and cyclin-dependent kinase activation. Premature meiotic maturation would be predicted to diminish fertility as the timing of this event, which normally occurs after oocyte growth is complete, is crucial. In the accompanying article in this issue, we identify the highly conserved TRIM-NHL protein LIN-41 as a translational repressor that copurifies with OMA-1 and OMA-2, RNA-binding proteins redundantly required for normal oocyte growth and meiotic maturation. In this article, we show that LIN-41 enables the production of high-quality oocytes and plays an essential role in controlling and coordinating oocyte growth and meiotic maturation. lin-41 null mutants display a striking defect that is specific to oogenesis: pachytene-stage cells cellularize prematurely and fail to progress to diplotene. Instead, these cells activate CDK-1, enter M phase, assemble spindles, and attempt to segregate chromosomes. Translational derepression of the CDK-1 activator CDC-25.3 appears to contribute to premature M-phase entry in lin-41 mutant oocytes. Genetic and phenotypic analyses indicate that LIN-41 and OMA-1/2 exhibit an antagonistic relationship, and we suggest that translational regulation by these proteins could be important for controlling and coordinating oocyte growth and meiotic maturation.
Chitosan coating to enhance the therapeutic efficacy of calcium sulfate-based antibiotic therapy in the treatment of chronic osteomyelitis

We demonstrate that coating calcium sulfate with deacetylated chitosan enhances the elution profile of daptomycin by prolonging the period during which high concentrations of antibiotic are released. Coatings reduced initial bolus release of daptomycin by a factor of 10 to approximately 1000 µg/ml, and levels remained above 100 µg/ml for up to 10 days. Chitosan-coated and uncoated calcium sulfate implants with and without 15% daptomycin were evaluated in an experimental model of staphylococcal osteomyelitis through bacteriology scores, radiology, histopathology, and Gram staining. Significant reduction in bacteriology scores was observed for implants containing daptomycin and coated with chitosan compared with all the other groups. We confirm that the use of chitosan-coated calcium sulfate beads for local antibiotic delivery can be correlated with an improved therapeutic outcome following surgical debridement in the treatment of chronic osteomyelitis.
Listen what I do: blind learners programming through audio

The development of programming skills is a motivating issue in computer science. Programming languages have been increasingly used to map end-users needs and mental models. The number of users who can program or learn how to program have been expanded. The majority of these languages are focused on sighted users. This study introduces APL, an Audio Programming Language for blind learners. APL is a programming language based on audio-based interfaces to assist blind learners to develop problem solving and algorithmic thinking skills. APL is also a way to help blind learners to construct meaning by making programs. APL is a programming language designed by and for blind learners. We tested APL with novice blind programmers during and after development. They tried, analyzed, and make improvements to APL. We exposed them to usability testing APL by solving problems with increasingly complexity and answering usability questionnaires. As a result, blind users understood APL, made programs, mapped the programming process and enjoyed the experience. Our preliminary results evidence that a programming language based on audio can be constructed to fit the needs and mental models of blind learners to help them to enter to the programming world and develop problem solving skills.
Heritability Estimates Identify a Substantial Genetic Contribution to Risk and Outcome of Intracerebral Hemorrhage

Background and Purpose— Previous studies suggest that genetic variation plays a substantial role in occurrence and evolution of intracerebral hemorrhage (ICH). Genetic contribution to disease can be determined by calculating heritability using family-based data, but such an approach is impractical for ICH because of lack of large pedigree-based studies. However, a novel analytic tool based on genome-wide data allows heritability estimation from unrelated subjects. We sought to apply this method to provide heritability estimates for ICH risk, severity, and outcome. Methods— We analyzed genome-wide genotype data for 791 ICH cases and 876 controls, and determined heritability as the proportion of variation in phenotype attributable to captured genetic variants. Contribution to heritability was separately estimated for the APOE (encoding apolipoprotein E) gene, an established genetic risk factor, and for the rest of the genome. Analyzed phenotypes included ICH risk, admission hematoma volume, and 90-day mortality. Results— ICH risk heritability was estimated at 29% (SE, 11%) for non-APOE loci and at 15% (SE, 10%) for APOE. Heritability for 90-day ICH mortality was 41% for non-APOE loci and 10% (SE, 9%) for APOE. Genetic influence on hematoma volume was also substantial: admission volume heritability was estimated at 60% (SE, 70%) for non-APOEloci and at 12% (SE, 4%) for APOE. Conclusions— Genetic variation plays a substantial role in ICH risk, outcome, and hematoma volume. Previously reported risk variants account for only a portion of inherited genetic influence on ICH pathophysiology, pointing to additional loci yet to be identified.
Iwssip 2010 -17th International Conference on Systems, Signals and Image Processing Color-ciratefi: a Color-based Rst-invariant Template Matching Algorithm

—Template matching is a technique widely used for finding patterns in digital images. An efficient template matching algorithm should be able to detect template instances that have undergone geometric transformations. Similarly, a color template matching should be able to deal with color constancy problem. Recently we have proposed a new grayscale template matching algorithm named Ciratefi, invariant to rotation , scale, translation, brightness and contrast. In this paper we introduce the Color-Ciratefi that takes into account the color information. We use a new similarity metric in the CIELAB space to obtain invariance to brightness and contrast changes. Experiments show that Color-Ciratefi is more accurate than C-color-SIFT, the well-known SIFT algorithm that uses a set of color in-variants. In conventional computers, Color-Ciratefi is slower than C-color-SIFT. However Color-Ciratefi is more suitable than C-color-SIFT to be implemented in highly parallel architectures like FPGA, because it repeats exactly the same set of operations for each pixel.