Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Daróczy-Tsallis capacities of discrete channels

In the past there has been an extensive work on generalized entropies and generalized channel capacities. One of the first was Daroczy, who introduced new parameterized generalization of Shannon entropy, which reduces to the Shannon case if the parameter is set to one. A variant of this entropy, with a different normalization constant, was later proposed by Tsallis, who set it up as a basis for non-extensive statistical mechanics. Based on the generalized entropy, Daroczy introduced generalized mutual information which shares several important properties with the Shannon case, such as symmetry with respect to input/output channel distributions, non-negativity (if the parameter is greater than one) and obeying the chain rule. Daroczy also introduced a generalized channel capacity as the maximum of the generalized mutual information and derived expressions for the capacities of symmetric channel and binary symmetric channel as a special case. In this paper we provide new expressions for Daroczy capacities of weakly symmetric channel, binary erasure channel and z-channel, extending the previous work by Daroczy. Similarly to the Shannon case, the capacity of weakly symmetric channel is expressed as the source entropy reduced by the entropy of the transition matrix row (scaled by appropriate constant), capacity of binary erasure channel is expressed as the q-average number of bits which can be recovered after transmission, while the capacity of z-channel is expressed in terms of q-logarithm and q-exponential of generalized binary entropy function. All the expressions are general and can be directly applied to Tsallis entropy, reducing to the Shannon capacity results in a limit case, when the parameter tends to one.
Optimal Capacity Sizing for a Completely Green Village With Programmable Appliances

Current trends show that renewable energy production costs continue to decrease with time, so that renewable energy sources (RES) are becoming more suitable as electricity sources. In addition to their environmental benefits, RES are especially appropriate for remote areas, where the expansion of existing power grid is impractical and fuel transportation for thermal generators is too expensive. In this regard, our work studies the optimal capacity sizing for a completely green village (CGV), which is an isolated residential microgrid (MG) whose power is entirely generated by RES. In particular, we consider a neighborhood composed of smart homes that contain programmable appliances, whose operations can be interrupted or automatically scheduled in time. Though there are many works in literature that investigate MG optimal capacity sizing, to our knowledge, our work is the first that utilizes the scheduling of programmable appliance to minimize MG investment costs. To establish the effectiveness of our method, we compare an optimal MG capacity sizing algorithm that utilizes appliances’ programmability (Opt-P) with an algorithm that places appliances into operation as soon as they are ready without shifting in time or preempting their operation (NoSchP). Our simulation results show that Opt-P reduces the investment cost by at least 42% compared to NoSch-P, when the ratio between the energy storage investment cost per kWh and the RES’ investment cost per kW is greater or equal to 10.
AMP peptide targets tight junctions to protect and heal barrier structure and function in models of IBD.

Background—A peptide derived from Antrum Mucosal Protein (AMP)-18 (gastrokine-1) reduces the extent of mucosal erosions and clinical severity in mice with dextran sulfate sodium (DSS)-induced colonic injury. The present study set out to determine if AMP peptide was also therapeutic for immuneand cytokine-mediated mouse models of intestinal injury and inflammatory bowel diseases (IBD) by enhancing and stabilizing tight junctions (TJs). Methods—Therapeutic effects of AMP peptide were examined in interleukin-10 deficient and a T cell adoptive transfer models of colitis in immunodeficient recombinase activating gene-1 knock-out (RAG-1−/−) mice. Mechanisms by which AMP peptide enhances barrier function and structure were studied ex vivo using intestine and colon from mice given lipopolysaccharide (LPS), and in AMP-18 deficient mice given DSS. Results—In interleukin-10 deficient mice given piroxicam, AMP peptide enhanced recovery after weight loss, protected against colon shortening and segmental dilation, and reduced the colitis activity score. In the T cell transfer model, treatment with the peptide protected against colon shortening. In mice given LPS in vivo to induce gut injury, AMP peptide prevented the onset of, and reversed established intestinal hyperpermeability by targeting TJ proteins and perijunctional actin. AMP-18-deficient mice challenged with DSS exhibited increased mortality, developed erosions in the colon, and had lower levels of ZO-1 in TJs than heterozygous littermates or wild-type mice. Conclusions—The results indicate that AMP-18/peptide may serve a protective role against injury along the GI mucosal barrier, and recommend further development of AMP peptide as a novel agent to treat patients with IBD. Correspondence authors: David L. Boone, Indiana University School of Medicine, 1234 N. Notre Dame Ave, RC122, South Bend, IN 46617, Telephone: 574-631-6040. , David.Boone. 16@nd.edu. F. Gary Toback, The University of Chicago, Department of Medicine, MC5100, 5841 South Maryland, Avenue, Chicago, IL 60637, Telephone: 773-702-1476, Fax: 773-702-5818. , gtoback@medicine.bsd. uchicago.edu. §Equal contribution. #Current address: Indiana University School of Medicine, South Bend, IN 46617 HHS Public Access Author manuscript Inflamm Bowel Dis. Author manuscript; available in PMC 2016 October 01. Published in final edited form as: Inflamm Bowel Dis. 2015 October ; 21(10): 2393–2402. doi:10.1097/MIB.0000000000000499. A uhor M anscript
THE EFFECT OF DIET SELENIUM SUPPLEMENT ON MEAT QUALITY

The health of farm animals depends on many factors and they all indicate that food plays an important role in preserving health, improving reproductive and productive characteristics and functioning of immune system. Besides numerous nutritional factors, antioxidants play a special role in the struggle for survival and good health state. An oxidative stress represents a condition induced by generating and reacting of reactive-oxygen species (ROS), and their toxic products, on different metabolic and physiological processes. The generating of ROS is induced by both endogenous and exogenous factors. In the case of the organism inability to expel the causative agents of oxidative stress they can damage cell lipids, proteins or DNA thus endangering the cell functions. Lipid peroxidation is a process which can lead to degradation of lipids and damage of cell membrane. Selenoenzyme glutathione peroxidase can protect organism from peroxidative damages, decrease the level of malondialdehyde protecting in this way a muscular tissue from oxidation. Recent research has shown that selenium has an effect of preserving sensory characteristics of meat and its texture, what is of great importance for consumers. Animal tissue incorporates supplemented selenium quickly thus it is possible to produce a selenium enriched meat and eggs. Selenium also shows positive effects on meat quality: it reduces water loss, influence the stability of colour, prolongs oxidative protection, and therefore the time of its shelf life.
nhanced cytocompatibility and reduced genotoxicity of olydimethylsiloxane modified by plasma immersion ion mplantation

Polydimethylsiloxane(PDMS) is a common industrial polymer with advantages such as ease of fabrication, tunable hardness, and other desirable properties, but the basic (-OSi(CH3)2-)n structure in PDMS is inherently hydrophobic thereby hampering application to biomedical engineering. In this study, plasma immersion ion implantation (PIII) is conducted on PDMS to improve the biological properties. PIII forms
Memory''s knowledge of its own knowledge: The accessibility account of the feeling of knowing

This chapter contrasts two theoretical approaches to the feeling of knowing. According to the commonly held trace-access approach, when people fail to recall a target from memory, they can nevertheless provide feeling-of-knowing (FOK) judgments by monitoring the presence of the target's trace in store. This approach assumes a twostage, monitoring-and-retrieval process, where people first ascertain the availability of the target in store before attempting to retrieve it. An alternative single-process account advocated in this chapter is that FOK is computed during the search and retrieval process itself, relying on the overall accessibility of partial information about the target. The implications of this approach for the analysis of the accuracy and inaccuracy of FOK are discussed, and some supportive experimental evidence is presented. This evidence suggests that people have no privileged access to information about the target's presence in store that is not already contained in the output of the retrieval attempt.
UvA-DARE ( Digital Academic Repository ) Textual Explanations for Self-Driving Vehicles

Deep neural perception and control networks have become key components of self-driving vehicles. User acceptance is likely to benefit from easyto-interpret textual explanations which allow end-users to understand what triggered a particular behavior. Explanations may be triggered by the neural controller, namely introspective explanations, or informed by the neural controller’s output, namely rationalizations. We propose a new approach to introspective explanations which consists of two parts. First, we use a visual (spatial) attention model to train a convolutional network end-to-end from images to the vehicle control commands, i.e., acceleration and change of course. The controller’s attention identifies image regions that potentially influence the network’s output. Second, we use an attention-based video-to-text model to produce textual explanations of model actions. The attention maps of controller and explanation model are aligned so that explanations are grounded in the parts of the scene that mattered to the controller. We explore two approaches to attention alignment, strongand weak-alignment. Finally, we explore a version of our model that generates rationalizations, and compare with introspective explanations on the same video segments. We evaluate these models on a novel driving dataset with ground-truth human explanations, the Berkeley DeepDrive eXplanation (BDDX) dataset. Code is available at https://github.com/JinkyuKimUCB/ explainable-deep-driving
Transcriptomic responses to heat stress and bleaching in the elkhorn coral Acropora palmata

The emergence of genomic tools for reef-building corals and symbiotic anemones comes at a time when alarming losses in coral cover are being observed worldwide. These tools hold great promise in elucidating novel and unforeseen cellular processes underlying the successful mutualism between corals and their dinoflagellate endosymbionts Symbiodinium spp. Since thermal stress trig- gers a breakdown in the symbiosis (coral bleaching), measuring the transcriptomic response to ther- mal stress-induced bleaching offers an extraordinary view of cellular processes that are specific to coral-algal symbioses. In the present study, we utilized a cDNA microarray containing 2059 genes of the threatened Caribbean elkhorn coral Acropora palmata to identify genes that are differentially expressed upon thermal stress. Fragments from replicate colonies were exposed to elevated temp- erature for 2 d, and samples were frozen for microarray analysis after 24 and 48 h. Totals of 204 and 104 genes were differentially expressed in samples that were collected 1 and 2 d after thermal stress, respectively. Analysis of the differentially expressed genes indicates a cellular stress response in A. palmata involving (1) growth arrest, (2) chaperone activity, (3) nucleic acid stabilization and repair, and (4) removal of damaged macromolecules. Other differentially expressed processes include sen- sory perception, metabolite transfer between host and endosymbiont, nitric oxide signaling, and modifications to the actin cytoskeleton and extracellular matrix. The results are compared with those from a previous coral microarray study of thermal stress in Montastraea faveolata, and point to an overall evolutionary conserved bleaching response in scleractinian corals.
Simple analytical model for short-channel MOS devices

A simple analytical model derived from a quasi-two-dimensional analysis with a nonvanishing E-field derivative at the pinchoff point and a continuous output conductance at the transition point for short-channel MOSFETs is presented. This model also covers mobility reduction, carrier velocity saturation, body, channel-length modulation, source-drain series resistance and short-channel effects for an accurate determination of the pinchoff point location without internal numerical iterations as compared to other models. This model can be used to describe the channel-length modulation effects more accurately in circuit simulation with short-channel MOSFETs.
Features and How to Find Them

The notion of features is commonly used to maintain, evolve, reuse, or re-engineer a software system. To this end, developers need to understand the features and their – potentially scattered – locations within the codebase of a system. Unfortunately, features are rarely documented, developers’ knowledge about the features fades quickly, and developers leave projects. In such cases, feature locations need to be recovered from the codebase – a costly, but still one of the most common tasks performed by developers. While automated feature-location techniques have been proposed, they typically require significant adjustments to the particular system and often fall short in their accuracy. To improve this situation, it is necessary to understand how developers perform feature location manually – a surprisingly neglected research area. In this chapter, we provide an overview on existing studies of manual feature location, focusing on the topics addressed in the studies and open issues. We find that the seven studies we identified analyze four topics of manual feature location in detail: Search tools, performance, influencing factors, and distinct phases. We observe that a focus of these studies is on understanding the process of manual feature location regarding the developers’ activities and actions. We also find that, still, little is known about the actual efforts of performing feature location, how different factors influence these efforts, how automated techniques are scoped to the identified phases, and which additional information sources help developers to locate features.
First Documentation of Cultural Transmission of Predator Recognition by Larval Amphibians

Predation is a pervasive selective agent shaping a prey's behaviour, morphology and life history. To survive, prey animals have to respond adaptively to predation threats and this can be achieved through learned predator recognition. Cultural transmission of predator recognition is likely a widespread means of learning in social animals, including mammals, birds and fishes. However, no studies have investigated the cultural transmission of predator recognition in amphibians. In our study, we examined whether naive woodfrog (Rana sylvatica) tadpoles can acquire the recognition of the odour of a predatory tiger salamander (Ambystoma tigrinum) from experienced conspecifics. After conditioning some tutors to recognize salamander odour, we paired naive observer tadpoles with either a salamander-naive or salamander-experienced tutor and exposed the pairs to either salamander odour or a water control. Observers were subsequently tested alone for a response to salamander odour. We found that when given salamander odour, observer tadpoles that were paired with a salamander-experienced tutor successfully learned to recognize the salamander odour as a threat, whereas the observers paired with salamander-naive tutors did not. Likewise, tadpoles exposed to the water control did not learn to recognize the salamander regardless of whether they were paired with a naive or experienced tutor. This is the first study demonstrating cultural transmission of predator recognition in an amphibian species.
UNC 93 B 1 Physically Associates with Human TLR 8 and Regulates TLR 8-Mediated Signaling

Toll-like receptors (TLRs) 3, 7, 8, and 9 are localized to intracellular compartments where they encounter foreign or self nucleic acids and activate innate and adaptive immune responses. The endoplasmic reticulum (ER)-resident membrane protein, UNC93B1, is essential for intracellular trafficking and endolysosomal targeting of TLR7 and TLR9. TLR8 is phylogenetically and structurally related to TLR7 and TLR9, but little is known about its localization or function. In this study, we demonstrate that TLR8 localized to the early endosome and the ER but not to the late endosome or lysosome in human monocytes and HeLa transfectants. UNC93B1 physically associated with human TLR8, similar to TLRs 3, 7, and 9, and played a critical role in TLR8-mediated signaling. Localization analyses of TLR8 tail-truncated mutants revealed that the transmembrane domain and the Toll/interleukin-1 receptor domain were required for proper targeting of TLR8 to the early endosome. Hence, although UNC93B1 participates in intracellular trafficking and signaling for all nucleotide-sensing TLRs, the mode of regulation of TLR localization differs for each TLR. Citation: Itoh H, Tatematsu M, Watanabe A, Iwano K, Funami K, et al. (2011) UNC93B1 Physically Associates with Human TLR8 and Regulates TLR8-Mediated Signaling. PLoS ONE 6(12): e28500. doi:10.1371/journal.pone. 0028500 Editor: Nick Gay, University of Cambridge, United Kingdom Received August 3, 2011; Accepted November 9, 2011; Published December 2, 2011 Copyright: 2011 Itoh et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported in part by Grants-in-Aid from the Ministry of Education, Science, and Culture, the Ministry of Health, Labor, and Welfare of Japan, and by the Akiyama Life Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: matumoto@pop.med.hokudai.ac. jp . These authors contributed equally to this work. ¤ Current address: Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
Atomistic Model for the Polyamide Formation from beta-Lactam Catalyzed by Candida antarctica Lipase B

Candida antarctica lipase B (CALB) is an established biocatalyst for a variety of transesterification, amidation, and polymerization reactions. In contrast to polyesters, polyamides are not yet generally accessible via enzymatic polymerization. In this regard, an enzyme-catalyzed ring-opening polymerization of β-lactam (2-azetidinone) using CALB is the first example of an enzymatic polyamide formation yielding unbranched poly(β-alanine), nylon 3. The performance of this polymerization, however, is poor, considering the maximum chain length of 18 monomer units with an average length of 8, and the molecular basis of the reaction so far is not understood. We have employed molecular modeling techniques using docking tools, molecular dynamics, and QM/MM procedures to gain insight into the mechanistic details of the various reaction steps involved. As a result, we propose a catalytic cycle for the oligomerization of β-lactam that rationalizes the activation of the monomer, the chain elongation by additional β-l.
Patterns of elevational beta diversity in micro‐ and macroorganisms

Aim While ecologists have long been interested in diversity in mountain regions, elevational patterns in beta diversity are still rarely studied across different life forms ranging from micro- to macroorganisms. Also, it is not known whether the patterns in turnover among organism groups are affected by the degree to which the environment is modified by human activities. Location Laojun Mountain, Yunnan Province, China. Methods The beta diversity patterns of benthic microorganisms (i.e.diatoms and bacteria) and macroorganisms (i.e. macroinvertebrates) in a stony stream were simultaneously investigated between elevations of 1820 and 4050 m. Data were analysed by using a distance-based approach and variation partitioning based on canonical redundancy analysis. Results Analyses of community dissimilarities between adjacent sampling sites showed comparable small-scale beta diversity along the elevational gradient for the organism groups. However, bacteria clearly showed the lowest elevational turnover when analyses were conducted simultaneously for all pairwise sites. Variation partitioning indicated that species turnover was mostly related to environmental heterogeneity and spatial gradients including horizontal distance and elevation, while purely human impacts were shown to be less important. Main conclusions The elevational beta diversity at large scales was lower for bacteria than for eukaryotic microorganisms or macroorganisms, perhaps indicative of high dispersal ability and good adaptability of bacteria to harsh environmental conditions.However,the small-scale beta diversity did not differ among the groups. Elevation was the major driver for the turnover of eukaryotic organisms, while the turnover of bacteria was correlated more with environmental variation.
Best Management Practice for Understanding Learning in Sustainable Water Resource Management (WRM) for Secondary Science Teachers in Thailand.

The aim of this study is to investigate the effects of training teachers to enhance their students’ achievements in water resource and disaster course and to compare the effects of using the curriculum framework between training teachers or using curriculum framework in the secondary schools in Khon Kaen Province of Thailand. It was found that the 28-science teachers were able to manage their learning units and lesson plans on WRD. Statistically significance was differentiated between participating teachers and non participating teachers at . 01 confidence levels (ρ < .01). Significant differences in students’ achievements between the controlled and experimental groups were found. Key words: practice, learning, water resource, management, science teacher.