Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Throughput System for the Presentation of Secreted and Surface-Exposed Proteins from Gram-Positive Bacteria in Functional Metagenomics Studies

Complex microbial ecosystems are increasingly studied through the use of metagenomics approaches. Overwhelming amounts of DNA sequence data are generated to describe the ecosystems, and allow to search for correlations between gene occurrence and clinical (e.g. in studies of the gut microbiota), physico-chemical (e.g. in studies of soil or water environments), or other parameters. Observed correlations can then be used to formulate hypotheses concerning microbial gene functions in relation to the ecosystem studied. In this context, functional metagenomics studies aim to validate these hypotheses and to explore the mechanisms involved. One possible approach is to PCR amplify or chemically synthesize genes of interest and to express them in a suitable host in order to study their function. For bacterial genes, Escherichia coli is often used as the expression host but, depending on the origin and nature of the genes of interest and the test system used to evaluate their putative function, other expression systems may be preferable. In this study, we developed a system to evaluate the role of secreted and surface-exposed proteins from Gram-positive bacteria in the human gut microbiota in immune modulation. We chose to use a Gram-positive host bacterium, Bacillus subtilis, and modified it to provide an expression background that behaves neutral in a cell-based immune modulation assay, in vitro. We also adapted an E. coli – B. subtilis shuttle expression vector for use with the Gateway high-throughput cloning system. Finally, we demonstrate the functionality of this host-vector system through the cloning and expression of a flagellin-coding sequence, and show that the expression-clone elicits an inflammatory response in a human intestinal epithelial cell line. The expression host can easily be adapted to assure neutrality in other assay systems, allowing the use of the presented presentation system in functional metagenomics of the gut and other ecosystems.
On the Transfer of Painting Style to Photographic Images through Attention to Colour Contrast

This paper proposes a way to transfer the visual style of a painting as characterised by colour contrast to a photographic image by manipulating the visual attributes in terms of hue, saturation and lightness. We first extract the visual characteristics in hue, saturation and lightness from a painting. Then, these characteristics are transferred to a photographic image by histogram matching in saturation and lightness and dominant hue spread and relative position mapping along the RYB colour wheel. We evaluated the proposed transfer method on a number of paintings and photographs. The results are encouraging.
Overcoming the Cause Marketing Paradox

The current research examines whether and when cause marketing, whereby firms link product sales to the support of a charity or cause, can increase charitable giving and happiness. Previous research suggests that cause marketing might reduce charitable giving and happiness among consumers. However, the present research finds the opposite result by introducing nostalgia as a moderator; cause marketing can enhance consumers’ charity giving when their nostalgia is triggered. Moreover, results show that charitable giving increased by cause marketing improves feelings of happiness, suggesting that people view charitable behavior as a means of enhancing happiness. Interestingly, charitable giving and happiness are promoted by the situational priming of nostalgic events, but not by chronic individual differences such as nostalgia proneness.
Transmission Power Scheduling for Energy Harvesting Sensor in Remote State Estimation

We study remote estimation in a wireless sensor network. Instead of using a conventional battery-powered sensor, a sensor equipped with an energy harvester which can obtain energy from the external environment is utilized. We formulate this problem into an infinite time-horizon Markov decision process and provide the optimal sensor transmission power control strategy. In addition, a sub-optimal strategy which is easier to implement and requires less computation is presented. A numerical example is provided to illustrate the implementation of the sub-optimal policy and evaluation of its estimation performance.
Compilation of propositional weighted bases

In this paper, we investigate the extent to which knowledge compilation can be used to improve inference from propositional weighted bases. We present a general notion of compilation of a weighted base that is parametrized by any equivalence--preserving compilation function. Both negative and positive results are presented. On the one hand, complexity results are identified, showing that the inference problem from a compiled weighted base is as difficult as in the general case, when the prime implicates, Horn cover or renamable Horn cover classes are targeted. On the other hand, we show that the inference problem becomes tractable whenever DNNF-compilations are used and clausal queries are considered. Moreover, we show that the set of all preferred models of a DNNF-compilation of a weighted base can be computed in time polynomial in the output size. Finally, we sketch how our results can be used in model-based diagnosis in order to compute the most probable diagnoses of a system.
Accurate internal camera calibration using rotation, with analysis of sources of error

Describes a simple and accurate method for internal camera calibration based on tracking image features through a sequence of images while the camera undergoes pure rotation. A special calibration object is not required and the method can therefore be used both for laboratory calibration and for self calibration in autonomous robots. Experimental results with real images show that focal length and aspect ratio can be found to within 0.15 percent, and lens distortion error can be reduced to a fraction of a pixel. The location of the principal point and the location of the center of radial distortion can each be found to within a few pixels. We perform a simple analysis to show to what extent the various technical details affect the accuracy of the results. We show that having pure rotation is important if the features are derived from objects close to the camera. In the basic method accurate angle measurement is important. The need to accurately measure the angles can be eliminated by rotating the camera through a complete circle while taking an overlapping sequence of images and using the constraint that the sum of the angles must equal 960 degrees. <<ETX>>
Bayesian Inference in Treewidth-Bounded Graphical Models Without Indegree Constraints

We present new polynomial time algorithms for inference problems in Bayesian networks (BNs) when restricted to instances that satisfy the following two conditions: they have bounded treewidth and the conditional probability table (CPT) at each node is specified concisely using an r-symmetric function for some constant r. Our polynomial time algorithms work directly on the unmoralized graph. Our results significantly extend known results regarding inference problems on treewidth bounded BNs to a larger class of problem instances. We also show that relaxing either of the conditions used by our algorithms leads to computational intractability.
Topographic Variation in Aboveground Biomass in a Subtropical Evergreen Broad-Leaved Forest in China

The subtropical forest biome occupies about 25% of China, with species diversity only next to tropical forests. Despite the recognized importance of subtropical forest in regional carbon storage and cycling, uncertainties remain regarding the carbon storage of subtropical forests, and few studies have quantified within-site variation of biomass, making it difficult to evaluate the role of these forests in the global and regional carbon cycles. Using data for a 24-ha census plot in east China, we quantify aboveground biomass, characterize its spatial variation among different habitats, and analyse species relative contribution to the total aboveground biomass of different habitats. The average aboveground biomass was 223.0 Mg ha−1 (bootstrapped 95% confidence intervals [217.6, 228.5]) and varied substantially among four topographically defined habitats, from 180.6 Mg ha−1 (bootstrapped 95% CI [167.1, 195.0]) in the upper ridge to 245.9 Mg ha−1 (bootstrapped 95% CI [238.3, 253.8]) in the lower ridge, with upper and lower valley intermediate. In consistent with our expectation, individual species contributed differently to the total aboveground biomass of different habitats, reflecting significant species habitat associations. Different species show differently in habitat preference in terms of biomass contribution. These patterns may be the consequences of ecological strategies difference among different species. Results from this study enhance our ability to evaluate the role of subtropical forests in the regional carbon cycle and provide valuable information to guide the protection and management of subtropical broad-leaved forest for carbon sequestration and carbon storage.
Human Paraoxonase-1 Activity Is Related to the Number of CD4+ T-Cells and Is Restored by Antiretroviral Therapy in HIV-1-Infected Individuals

Background. Paraoxonase-1 (PON1) activity is suggested to be altered in individuals infected with human immunodeficiency virus type-1 (HIV-1). We investigated PON1 activity in individuals receiving different regimens of highly active antiretroviral therapy (HAART). Methods. PON1 activity was evaluated in 91 HIV-1 seronegative and 624 HIV-1 infected individuals (115 were not undergoing therapy (ART-naïve), and 509 were receiving HAART). HIV-1 infected individuals were treated with the following: efavirenz (EFV; n = 195) or nevirapine (NVP; n = 95) or lopinavir/ritonavir (LOP/r; n = 219). Serum levels of total cholesterol (TC), HDL, and low-density lipoprotein (LDL) fractions and the atherogenic indices (AI, TC : HDL, and LDL : HDL ratios) were determined. Results. PON1 activity (U/L) was lower in the ART-naïve group compared with the other groups. PON1 activity correlated with CD4+ T-cell number of ART-naïve group (r = 0,121; P = 0,014). The LOP/r group showed a reduction in HDL and an increase in AI (TC : HDL ratio) in comparison with other groups. Conclusion. PON1 activity was reduced in untreated individuals, but not in individuals receiving HAART. PON1 activity correlated with the number of CD4+ T-cells. The findings suggest that the activity of PON1 is associated with the immune status of HIV-1 infected individuals.
Exploring the challenges and potentialities of the database of religious history for cognitive historiography

This article explores the potential impact and contribution of the Database of Religious History (DRH) project within the field of Cognitive Historiography. The DRH aims to bring together, in a systematic and open-access format, data on religious groups from across the globe and throughout history. By utilizing robust, open-source technologies and best-practice software principles, the DRH constitutes a novel and innovative approach to historical and cultural studies. As a contribution to the scientific study of both religion and history, the DRH offers data amenable to statistical analyses, thus providing tools for assessing diachronic cultural innovation and adaptation, the testing of grand narrative theories of religious change, and for enriching and revitalizing traditional fields such as comparative religions, history of religion(s), and anthropology of religion. In this article we explore the methods employed in collecting and digitizing historical data, identify our unit of analysis, outline the challenges of recruiting historians of various fields, and highlight the DRH’s methodological potential for both Religious Studies and Cognitive Historiography.
Weak witnesses for Delaunay triangulations of submanifolds

The main result of this paper is an extension of de Silva's Weak Delaunay Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming a sufficiently fine sampling, we prove that i + 1 points in the sample span an i-simplex in the restricted Delaunay triangulation iff every subset of the i + 1 points has a weak witness.
TTSBOX: a MATLAB toolbox for teaching text-to-speech synthesis

This paper presents a new toolbox for teaching TTS synthesis. TTSBOX performs the synthesis of Genglish (for "generic English"), an imaginary language obtained by replacing English words by generic words. Genglish therefore has a rather limited lexicon, but its pronunciation maintains most of the problems encountered in natural languages. TTSBOX uses simple data-driven techniques (bigrams, CARTs, NUUs) while trying to keep the code minimal, so as to keep it readable for students with reasonable MATLAB practice. TTSBOX was designed with the hope that it can help to increase the personal involvement of undergraduate and graduate students in their TTS courses.
Halving Brazil ’ s Poverty , 1983 – 2006

With a population of 189 million and a per capita gross national income (GNI) of US$8,800.00 (at purchasing power parity [PPP] exchange rates) in 2006, Brazil is a large middle-income country that has long been accustomed to a high level of inequality. At its historical peak in 1989, the country’s Gini coefficient for per capita household income was 0.625. Although international comparisons of inequality statistics are fraught with problems, that figure meant that Brazil was the second most unequal country in the world, just after Sierra Leone. One key implication of such a high level of inequality is that Brazil’s poverty rate has been higher than that of most other countries with similar levels of per capita GNI at PPP. Using the international poverty line of two dollars a day,1 Brazil’s poverty rate was 21.2 percent in 2004. In contrast, the poverty rate of Belarus was less than 2 percent, Iran’s was 7.3 percent, Tunisia’s was 6.6 percent, and Turkey’s was 18.7 percent. Only Thailand had a slightly higher poverty rate, at 25.2 percent. Since the mid-1990s, however, Brazil has undergone something of a distributional reversal. Between 1993 and 2006, there was a substantial decline in inequality. While still anemic by emerging market standards, the country’s economic growth also improved: after growing at a paltry 0.8 percent per year from 1983 to 1993, Brazilian gross domestic product (GDP) per capita grew at an annual average rate of
Designing Parallel Algorithms for Clusters ∗

The use of the dependence transformation method has been pro posed to generate parallel algorithms suitable for cluster and gr id computing. In particular this method has been used to produce an efficient para llel algorithm for the problem of string alignment, an important problem in Bio inf rmatics. It obtains the alignment of two strings of lengths m andn in O(p) communication rounds andO(mn/p) local computing time, where p is the number of processors. The systolic approach, however, is vulnerable in a het erogeneous environment in which the performance varies from machine to machine . In this paper we discuss this problem, that can be solved with a redundant s ystolic solution. In an on-going research we show that the overhead incurred by redundancy is worth the performance improvement it provides. The experim ental results show that the overhead of the redundant approach is small compare d to the overall performance over the non-redundant solution.
From Toxoplasmosis to Schizophrenia via NMDA Dysfunction: Peptide Overlap between Toxoplasma gondii and N-Methyl-d-Aspartate Receptors As a Potential Mechanistic Link

The present work aims at investigating how Toxoplasma gondii (T. gondii) infection may be linked to N-methyl-d-aspartate receptor (NMDAR) dysfunction in schizophrenia and related disorders and puts forward the hypothesis that immune responses against T. gondii may involve NMDARs. Indeed, the analysis of the protozoan proteome and NMDAR subunits for peptide commonalities shows a massive peptide overlap and supports the possibility that anti-T. gondii immune responses raised during active protozoan infection may cross-react with host NMDARs, determining disruption of neural circuits and cognitive deficits. In particular, the NMDA 2D subunit, which is mainly expressed in parvalbumin-positive interneurons, appears to be a hotspot for potential T. gondii-induced cross-reactive immune attacks.
Stereoscopic image generation based on depth images for 3D TV

A depth-image-based rendering system for generating stereoscopic images is proposed. One important aspect of the proposed system is that the depth maps are pre-processed using an asymmetric filter to smoothen the sharp changes in depth at object boundaries. In addition to ameliorating the effects of blocky artifacts and other distortions contained in the depth maps, the smoothing reduces or completely removes newly exposed (disocclusion) areas where potential artifacts can arise from image warping which is needed to generate images from new viewpoints. The asymmetric nature of the filter reduces the amount of geometric distortion that might be perceived otherwise. We present some results to show that the proposed system provides an improvement in image quality of stereoscopic virtual views while maintaining reasonably good depth quality.
De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata

Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.
Induction of decision trees in numeric domains using set-valued attributes

Conventional algorithms for decision tree induction use an attribute-val ue representatio n scheme for instances. This paper explores the empirical consequences of using set-valued attributes. This simple representational extension, when used as a pre-processor for numeric data, is shown to yield significant gains in accuracy combined with attractive build times. It is also shown to improve the accuracy for the second best classification option, which has valuable ramifications for post-processing. To do so an intuitive and practical version of pre-pruning is employed. Moreover, the implementation of a simple pruning scheme serves as an example of pruning applicability over the resulted trees and also as an indication that the proposed discretization absorbs much of pruning potential. Finally, we construct several versions of the basic algorithm to examine the value of every component that comprises it.
Optimization of the normalization of fuzzy relational databases by using alternative methods of calculation for the Fuzzy Functional Dependency

Although, in comparison to standard databases, a tremendous benefit is often derived by using fuzzy databases, their distribution is very low. A reason for the relatively poor acceptance of fuzzy relational databases is to be seen in the difficulty to carry out an adequate normalization. The various procedures discussed in the literature possess miscellaneous weaknesses. In this work a normalization method is regarded whose most significant deficit lies in the fuzzy functional dependency (FFD) because thereby comprehensible results are not produced. Therefore, it is registered which alternatives for the determination of the degree of FFD exist. Furthermore, it is examined with which of these methods the just addressed disadvantage can be eliminated. For this purpose, the presented methods are applied to several examples in order to identify their characteristics.
Culturally sustaining pedagogy in higher education: teaching so that Black Lives Matter

Purpose The purpose of this paper is to show how the principles of Black Lives Matter can be used to enact a culturally sustaining pedagogy (CSP) in higher education settings, particularly in small colleges that serve significant populations of students who are underrepresented in higher education. Design/methodology/approach Drawing on examples from college courses in media and society, organizational communication, and interpersonal communication, the case study shows application of the principles of Black Lives Matter in the college classroom at two different institutions in the urban Northeast USA, where the majority of the students are young people of color and/or first-generation college students. Findings The paper shows how founding principles of Black Lives Matter, particularly diversity, intersectionality, loving engagement, and empathy, can be used to guide concrete pedagogical practices. It provides examples of how to use Black Lives Matter as a framework to enhance and improve college teaching to make it more diverse and inclusive. Research limitations/implications This case study is based on the author’s experiences teaching at two majority-minority colleges in Greater Boston, Massachusetts, USA. This paper is not the result of a systematic research study. Practical implications This paper has significant implications for how to enact CSP in higher education settings. This paper is valuable to those looking for specific strategies to include more diverse and inclusive teaching strategies. This research also shows both the utility and impact of Black Lives Matter when applied to higher education. Social implications This paper improves public understanding of Black Lives Matter as a social movement. Originality/value Since the Black Lives Matter movement is fairly new, there is limited academic research on it. Further, there has not been attention to how Black Lives Matter provides insight into pedagogy, particularly in higher education.
NEURAL NETWORK BASED SUPERVISED SELF

The word biometrics refers to the use of physiological or biological characteristics of human to recognize and verify the identity of an individual. Face is one of the human biometrics for passive identification with uniqueness and stability. In this manuscript we present a new face based biometric system based on neural networks supervised self organizing maps (SOM). We name our method named SOM-F. We show that the proposed SOM-F method improves the performance and robustness of recognition. We apply the proposed method to a variety of datasets and show the results.