Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat Fragmentation, Variable Edge Effects, and the Landscape-Divergence Hypothesis

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This ‘landscape-divergence hypothesis’, if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.
Antigen-Specific Transfer of Functional Programmed Death Ligand 1 from Human APCs onto CD8+ T Cells via Trogocytosis

Upon specific interaction with APCs, T cells capture membrane fragments and surface molecules in a process termed trogocytosis. In this study, we demonstrate that human Ag-specific CD8+ T cells acquire the coinhibitory molecule programmed death ligand 1 (PD-L1) from mature dendritic cells (mDC) and tumor cells in an Ag-specific manner. Immature dendritic cells were less effective in transferring surface molecules onto CD8+ T cells than mDCs. Interestingly, trogocytosis of PD-L1 requires cell–cell contact and cannot be induced by uptake of soluble proteins obtained from mDC lysates. The transfer process is impaired by inhibition of vacuolar ATPases in T cells as well as by fixation of dendritic cells. Of importance, CD8+ T cells that acquired PD-L1 complexes were able to induce apoptosis of neighboring programmed death 1–expressing CD8+ T cells. In summary, our data demonstrate that human CD8+ T cells take up functionally active PD-L1 from APCs in an Ag-specific fashion, leading to fratricide of programmed death 1–expressing, neighboring T cells. The transfer of functionally active coinhibitory molecules from APCs onto human CD8+ T cells could have a regulatory role in immune responses.
A Bayesian Graphical Model for ChIP-Seq Data on Histone Modifications

Histone modifications (HMs) are an important post-translational feature. Different types of HMs are believed to co-exist and co-regulate biological processes such as gene expression and, therefore, are intrinsically dependent on each other. We develop inference for this complex biological network of HMs based on a graphical model using ChIP-Seq data. A critical computational hurdle in the inference for the proposed graphical model is the evaluation of a normalization constant in an autologistic model that builds on the graphical model. We tackle the problem by Monte Carlo evaluation of ratios of normalization constants. We carry out a set of simulations to validate the proposed approach and to compare it with a standard approach using Bayesian networks. We report inference on HM dependence in a case study with ChIP-Seq data from a next generation sequencing experiment. An important feature of our approach is that we can report coherent probabilities and estimates related to any event or parameter of interest, including honest uncertainties. Posterior inference is obtained from a joint probability model on latent indicators for the recorded HMs. We illustrate this in the motivating case study. An R package including an implementation of posterior simulation in C is available from Riten Mitra upon request.
Self-poisoning in Sri Lanka: Factors Determining the Choice of the Poisoning Agents

Sri Lanka is a developing agricultural country with a high fatality rate due to self-poisoning with very toxic agrochemicals as the main poisoning agents. A prospective study of 97 consecutive admissions following self-poisoning reveals that easy availability of the agrochemicals together with the lack of knowledge regarding their lethality were the main causative factors determining the choice of poisoning agents. Developing community awareness of the lethality of these substances, educating the farmers with regards to proper storage and disposal of agrochemicals together with stricter legislation regarding their sale and distribution may reduce the incidence of self-poisoning due to these agents with a consequent reduction in mortality due to self-poisoning.
A SMASH PRODUCT CONSTRUCTION OF NONLOCAL VERTEX ALGEBRAS

A notion of vertex bialgebra and a notion of nonlocal vertex module-algebra for a vertex bialgebra are studied and then a smash product construction of nonlocal vertex algebras is presented. For every nonlocal vertex algebra V satisfying a suitable condition, a canonical bialgebra B(V) is constructed such that primitive elements of B(V) are essentially pseudo-derivations and group-like elements are essentially pseudo-endomorphisms. As an application, vertex algebras associated with the Heisenberg Lie algebras as well as those associated with the nondegenerate even lattices are reconstructed through smash products, and furthermore, a different approach to the construction of modules for the lattice vertex algebras is given.
COMPUTATIONAL MODELING OF IMPROVISATION IN TURKISH FOLK MUSIC USING VARIABLE-LENGTH MARKOV MODELS

The paper describes a new database, which currently consists of 64 songs encompassing approximately 6600 notes, and a system, which uses Variable-Length Markov Models (VLMM) to predict the melodies in the uzun hava (long tune) form, a melodic structure in Turkish folk music. The work shows VLMMs are highly predictive. This suggests that variable-length Markov models (VLMMs) may be applied to makam-based and non-metered musical forms, in addition to Western musical traditions [20]. To the best of our knowledge, the work presents the first symbolic, machine readable database and the first application of expressive modeling in Turkish folk music.
Prevalence of intestinal parasites in breeding cattery cats in Japan

Objectives To address the lack of up-to-date published data, the present study assessed the prevalence of intestinal parasites in breeding catteries in Japan. Methods Fresh faecal samples were randomly collected from 342 cats (aged 1 month to 12 years) in seven breeding catteries in Japan, located in prefectures of Nagano (n = 2), Saitama (n = 1), Aichi (n = 2), Gifu (n = 1) and Miyagi (n = 1), on a single occasion. The samples were tested for the presence of Giardia species copro-antigen using a commercially available enzyme-linked immunosorbent assay kit. Other intestinal parasites were identified microscopically using the formalin–ethyl acetate sedimentation technique. Results The total prevalence of intestinal parasites was 20.8%; only two genera of protozoa (Giardia species: 18.7% and Cystoisospora species: 5.0%) were detected. Coinfections of both protozoans were recorded in 2.9% of cats. In contrast, no helminths were detected. The presence of total infection, Giardia species, Cystoisospora species and multiple infections in cats <1 year old were significantly more prevalent than in cats ⩾1 year old. There were no significant differences among faecal conditions with or without intestinal parasites. Giardia species infection was present in samples from all breeding catteries, except for one facility. Cystoisospora species and coinfections were shown in four and two breeding catteries, respectively. The prevalence of intestinal parasites was markedly variable among the breeding catteries. Conclusions and relevance The present study demonstrates the significance of Giardia species and Cystoisospora species infections in breeding cattery cats. Additionally, it is suggested that environmental contamination is the most important factor influencing the prevalence of protozoal infections in breeding catteries.
Audit of Initial Management of Congenital Hypothyroidism in the United Kingdom - Comparison of UK Practice with European and UK Guidelines

BACKGROUND Prompt and adequate management of newly diagnosed congenital hypothyroidism (CH) has been shown to optimise intellectual outcome. METHODS A questionnaire survey of the British Society for Paediatric Endocrinology and Diabetes (BSPED) membership was undertaken, examining current clinical practice in neonatal CH. Results were compared with published management guidelines from Europe and the UK. RESULTS The response rate was 86%. The majority were largely compliant with both guidelines. 43% review newly referred infants on the day of notification. However, 26% treat severe CH with < 10 microg/kg/day thyroxine and nearly 20% do not follow up until at least 14 days after initiating treatment, in contrast to both guidelines. Despite a new liquid T4 preparation being licensed, respondents preferred tablet T4. CONCLUSION Rapidity of assessment and adequate follow up of suspected CH is critical to outcome. Existing European and UK guidelines should be reviewed and expanded to incorporate new evidence, together with increased advice on preparation and administration of T4.
Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants.

In the present study the CotA laccase from Bacillus subtilis has been mutated at two hydrophobic residues in the vicinity of the type 1 copper site. The mutation of Leu(386) to an alanine residue appears to cause only very subtle alterations in the properties of the enzyme indicating minimal changes in the structure of the copper centres. However, the replacement of Ile(494) by an alanine residue leads to significant changes in the enzyme. Thus the major visible absorption band is upshifted by 16 nm to 625 nm and exhibits an increased intensity, whereas the intensity of the shoulder at approx. 330 nm is decreased by a factor of two. Simulation of the EPR spectrum of the I494A mutant reveals differences in the type 1 as well as in the type 2 copper centre reflecting modifications of the geometry of these centres. The intensity weighted frequencies , calculated from resonance Raman spectra are 410 cm(-1) for the wild-type enzyme and 396 cm(-1) for the I494A mutant, indicating an increase of the Cu-S bond length in the type 1 copper site of the mutant. Overall the data clearly indicate that the Ile(494) mutation causes a major alteration of the structure near the type 1 copper site and this has been confirmed by X-ray crystallography. The crystal structure shows the presence of a fifth ligand, a solvent molecule, at the type 1 copper site leading to an approximate trigonal bipyramidal geometry. The redox potentials of the L386A and I494A mutants are shifted downwards by approx. 60 and 100 mV respectively. These changes correlate well with decreased catalytic efficiency of both mutants compared with the wild-type.
Ethylene-induced differential gene expression during abscission of citrus leaves

The main objective of this work was to identify and classify genes involved in the process of leaf abscission in Clementina de Nules (Citrus clementina Hort. Ex Tan.). A 7 K unigene citrus cDNA microarray containing 12 K spots was used to characterize the transcriptome of the ethylene-induced abscission process in laminar abscission zone-enriched tissues and the petiole of debladed leaf explants. In these conditions, ethylene induced 100% leaf explant abscission in 72 h while, in air-treated samples, the abscission period started later and took 240 h. Gene expression monitored during the first 36 h of ethylene treatment showed that out of the 12 672 cDNA microarray probes, ethylene differentially induced 725 probes distributed as follows: 216 (29.8%) probes in the laminar abscission zone and 509 (70.2%) in the petiole. Functional MIPS classification and manual annotation of differentially expressed genes highlighted key processes regulating the activation and progress of the cell separation that brings about abscission. These included cell-wall modification, lipid transport, protein biosynthesis and degradation, and differential activation of signal transduction and transcription control pathways. Expression data associated with the petiole indicated the occurrence of a double defensive strategy mediated by the activation of a biochemical programme including scavenging ROS, defence and PR genes, and a physical response mostly based on lignin biosynthesis and deposition. This work identifies new genes probably involved in the onset and development of the leaf abscission process and suggests a different but co-ordinated and complementary role for the laminar abscission zone and the petiole during the process of abscission.
Preparation of PLLA/PMMA and PLLA/PS binary blend nanoparticles by incorporation of PLLA in methyl methacrylate or styrene miniemulsion homopolymerization

Miniemulsion homopolymerization reactions of methyl methacrylate (MMA) and styrene (STY) using poly(L-lactide) as co-stabilizer were carried out in order to prepare poly(L-lactide)/poly(methyl methacrylate) (PLLA/PMMA) and poly(L-lactide)/polystyrene (PLLA/PS) binary blend nanoparticles. The effect of PLLA concentration on methyl methacrylate (MMA) and styrene (STY) homopolymerization reactions was evaluated. It was found that the incorporation of PLLA resulted on acceleration of MMA and STY homopolymerization reactions and led to a molar mass increase of up to 70% for PS in PLLA/PS blend nanoparticles in relation to those prepared without PLLA, which can be attributed to an increase of reaction loci viscosity (gel effect). PLLA also acted as an efficient co-stabilizer, since it was able to retard diffusional degradation of droplets when no other kind of co-stabilizer was used. Two isolated T g s were found in both PLLA/PMMA and PLLA/PS blend nanoparticles which can be associated to blend immiscibility. TEM images corroborate these results, suggesting that immiscible PLLA/PMMA and PLLA/PS blend nanoparticles could be formed with two segregated phases and core-shell morphology.
A Comparative Analysis of Current Intrusion Detection Technologies

Intrusion detection is a significant focus of research in the security of computer systems and networks. This paper presents an analysis of the progress being made in the development of effective intrusion detection systems for computer systems and distributed computer networks. The technologies which are discussed are designed to detect instances of the access of computer systems by unauthorized individuals and the misuse of system resources by authorized system users. A review of the foundations of intrusion detection systems and the methodologies which are the focus of current development efforts are discussed. The results of an informal survey of security and network professionals is discussed to offer a real-world view of intrusion detection. Finally, a discussion of the future technologies and methodologies which promise to enhance the ability of computer systems to detect intrusions is provided.
Transcript-specific induction of stop codon readthrough using CRISPR-dCas13 system

Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using CRISPR-dCas13 system. Using specific guide RNAs, we targeted dCas13 to the downstream region of the canonical stop codons of mammalian AGO1 and VEGFA, which are known to exhibit natural SCR. Results of readthrough assays revealed the enhancement of SCR of these mRNAs (both exogenous and endogenous) caused by dCas13. This effect was associated with ribosomal pausing, which has been reported in several SCR events. Furthermore, our results show that CRISPR-dCas13 can induce SCR across premature termination codons (PTC) in the mRNAs of green fluorescent protein and TP53. Finally, we demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
High Frequency and Intensity of Drinking may Attenuate Increased Inflammatory Cytokine Levels of Major Depression in Alcohol‐use Disorders

As major depression (MD) is often comorbid with alcohol‐use disorders (AUD) and alcohol itself modulates the immune system, we examined serum levels of interleukin (IL)‐6, IL‐10, tumor necrosis factor (TNF), and interferon (IFN)‐γ in AUD patients with and without MD. Putative interactions between alcohol variables and MD on cytokine levels were also assessed.
Selection of scFv Antibody Fragments Binding to Human Blood versus Lymphatic Endothelial Surface Antigens by Direct Cell Phage Display

The identification of marker molecules specific for blood and lymphatic endothelium may provide new diagnostic tools and identify new targets for therapy of immune, microvascular and cancerous diseases. Here, we used a phage display library expressing human randomized single-chain Fv (scFv) antibodies for direct panning against live cultures of blood (BECs) and lymphatic (LECs) endothelial cells in solution. After six panning rounds, out of 944 sequenced antibody clones, we retrieved 166 unique/diverse scFv fragments, as indicated by the V-region sequences. Specificities of these phage clone antibodies for respective compartments were individually tested by direct cell ELISA, indicating that mainly pan-endothelial cell (EC) binders had been selected, but also revealing a subset of BEC-specific scFv antibodies. The specific staining pattern was recapitulated by twelve phage-independently expressed scFv antibodies. Binding capacity to BECs and LECs and differential staining of BEC versus LEC by a subset of eight scFv antibodies was confirmed by immunofluorescence staining. As one antigen, CD146 was identified by immunoprecipitation with phage-independent scFv fragment. This antibody, B6-11, specifically bound to recombinant CD146, and to native CD146 expressed by BECs, melanoma cells and blood vessels. Further, binding capacity of B6-11 to CD146 was fully retained after fusion to a mouse Fc portion, which enabled eukaryotic cell expression. Beyond visualization and diagnosis, this antibody might be used as a functional tool. Overall, our approach provided a method to select antibodies specific for endothelial surface determinants in their native configuration. We successfully selected antibodies that bind to antigens expressed on the human endothelial cell surfaces in situ, showing that BECs and LECs share a majority of surface antigens, which is complemented by cell-type specific, unique markers.
Color Image Compression Based On Wavelet Packet Best Tree

In Image Compression, the researchers’ aim is to reduce the number of bits required to represent an image by removing the spatial and spectral redundancies. Recently discrete wavelet transform and wavelet packet has emerged as popular techniques for image compression. The wavelet transform is one of the major processing components of image compression. The result of the compression changes as per the basis and tap of the wavelet used. It is proposed that proper selection of mother wavelet on the basis of nature of images, improve the quality as well as compression ratio remarkably. We suggest the novel technique, which is based on wavelet packet best tree based on Threshold Entropy with enhanced run-length encoding. This method reduces the time complexity of wavelet packets decomposition as complete tree is not decomposed. Our algorithm selects the sub-bands, which include significant information based on threshold entropy. The enhanced run length encoding technique is suggested provides better results than RLE. The result when compared with JPEG-2000 proves to be better.
Management of Plant Disease Epidemics with Irrigation Practices

Adequate water provision to roots is essential to warrant sustainable harvests of agri- cultural crops globally. However, water applied in excess or in deficit may result in the development of many fungal and bacterial plant diseases, which compromise produce yield and quality. Leaf wetness duration, soil water tension and related water variables impact several aspects of different plant disease cycles, such as the sporulation, sur - vival of pathogen propagules, their dispersal to new hosts, germination and infection. Irrigation is thus arguably the most important cultural practice in the management of plant diseases, especially in the context of the quest of a more sustainable, less chemi cally dependent agriculture. The technology of water application and method of irriga - tion have been profusely studied as to their direct relation to plant diseases. Irrigation management has a strong impact on the disease severity and epidemic progress rates of many plant pathosystems, ranging from leaf blights to vascular wilts. In addition, plant virus vector population levels and vector dispersal are also affected by the method of irrigation. This chapter reviews experimental data on the effect of different irrigation configurations and management systems on some representative plant diseases.
A Survey of Face Detection, Extraction and Recognition

The goal of this paper is to present a critical survey of existing lite- ratures on human face recognition over the last 4-5 years. Interest and research activities in face recognition have increased significantly over the past few years, especially after the American airliner tragedy on September 11 in 2001. While this growth largely is driven by growing application demands, such as static matching of controlled photographs as in mug shots matching, credit card verification to surveillance video images, identification for law enforcement and authentication for banking and security system access, advances in signal analysis techniques, such as wavelets and neural networks, are also important catalysts. As the number of proposed techniques increases, survey and evaluation becomes important.
Conditioning Prices on Purchase History

Many transactions are now computer mediated, making it possible for sellers to condition their pricing on the history of interactions with individual consumers. This paper investigates conditions under which price conditioning will or will not be used. Our simplest model involves rational consumers with constant valuations for the good being sold and a monopoly seller who can commit to a pricing policy. In this framework, the seller will not find it profitable to condition pricing on past behavior. We consider various generalizations of this model, such as allowing the seller to offer enhanced services to previous customers, making the seller unable to commit to a pricing policy, and allowing competition in the marketplace. All of these generalizations have equilibria with price conditioning.