Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving Captive Maintenance Techniques for New Zealand Native frogs (Leiopelma spp.)

The captive maintenance of healthy amphibian species requires an in depth knowledge of their dietary and environmental requirements. In New Zealand, only three of the four threatened native frog species within the genus Leiopelma are held in captivity. Each of these captive populations has suffered significant rates of disease and mortality, coupled with poor breeding success. To determine the suitability of current captive maintenance techniques used for Leiopelma, this thesis examined the differences between natural Leiopelma diets and environments and those provided to frogs in captivity. Chapter 2 completes the most thorough dietary analysis of wild L. hochstetteri to date, identifying 23 different prey groups in 73 faecal pellets. Potential prey items were sampled using pitfall traps and this showed monthly variation that was significantly different to the composition of the diet. Different age classes were found to eat similar prey groups in different frequencies. The results of the faecal pellet study were used to formulate a captive diet for juvenile L. hochstetteri. The diet analysis in Chapter 2 is followed by an investigation into the nutritional qualities of both invertebrates found in the natural diet of Leiopelma and those fed to this genus in captivity (Chapter 3). Importantly, the diet of wild frogs was found to contain invertebrates which were rich in calcium and had positive calcium to phosphorus ratios. These attributes were lacking in all but one of the invertebrate species fed to captive frogs, meaning that current diets are likely to hinder bone growth and development and require amendment. In order to inform dietary improvement, the efficacy of using the isopod Porcellio scaber to naturally increase calcium content in the diet of Leiopelma was assessed. This was made possible through a novel analysis of gut-retention time in L. archeyi, L. hochstetteri and L. pakeka. Calcium in P. scaber was found to be bioavailable to each Leiopelma species examined, with the highest calcium absorption occurring in L. archeyi and the lowest in L. pakeka. Porcellio scaber should thus be fed to all Leiopelma in captivity. Faecal analysis found that L. hochstetteri at Hamilton Zoo consume invertebrates which are self-introduced to their enclosures, indicating that their diet may be more nutritionally complete than previously
SemEval-2020 Task 4: Commonsense Validation and Explanation

In this paper, we present SemEval-2020 Task 4,CommonsenseValidation andExplanation(ComVE), which includes three subtasks, aiming to evaluate whether a system can distinguish anatural language statement thatmakes senseto humans from one that does not, and provide thereasons. Specifically, in our first subtask, the participating systems are required to choose from twonatural language statements of similar wording the one thatmakes senseand the one does not. Thesecond subtask additionally asks a system to select the key reason from three options why a givenstatement does not make sense. In the third subtask, a participating system needs to generate thereason automatically. 39 teams submitted their valid systems to at least one subtask. For SubtaskA and Subtask B, top-performing teams have achieved results closed to human performance.However, for Subtask C, there is still a considerable gap between system and human performance.The dataset used in our task can be found athttps://github.com/wangcunxiang/SemEval2020-Task4-Commonsense-Validation-and-Explanation.
COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation

To combat COVID-19, both clinicians and scientists need to digest the vast amount of relevant biomedical knowledge in literature to understand the disease mechanism and the related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence. All of the data, KGs, reports.
Interaction between Borrelia burgdorferi and Polymorphonuclear Leukocytes Phagocytosis and the Induction of the Respiratory Burst

The ability of polymorphonuclear leukocytes (PMN) to engulf and kill bacteria is of major importance in host defense against bacterial infection. An important microbicidal mechanism of phagocytic cells is the formation of toxic oxygen metabolites following the stimulation of the respiratory burst. The phagocytosis of Borrelia burgdorjeri by phagocytic cells has been described. ’” The ability of the spirochetes to induce the respiratory burst in PMN was also examined using a chemiluminescence assay. ’ Both of these studies described the phagocytosis of spirochetes in the presence and absence of immune serum, however little is known about the mechanism of uptake of these spirochetes in the absence of serum opsonins. In the present studies the early events in the phagocytosis of unopsonized Borrelia burgdorferi were examined ultrastructurally. In addition, the induction of the respiratory burst in PMN by opsonized and unopsonized spirochetes was compared using the nitroblue tetrazolium (NBT) reduction assay.3
Performance of Borel-Laplace integrator for the resolution of stiff and non-stiff problems

A stability analysis of the Borel-Laplace series summation technique, used as explicit time integrator, is carried out. Its numerical performance on stiff and non-stiff problems is analyzed. Applications to ordinary and partial differential equations are presented. The results are compared with those of many popular schemes designed for stiff and non-stiff equations.
Mechanism of the Initial Events in the Sorption of Marine Bacteria to Surfaces

Summary: The sorption of two marine bacteria to surfaces involved an instantaneous reversible phase, and a time-dependent irreversible phase. Reversible sorption of the non-motile Achromobacter strain R8 decreased to zero as the electrolyte concentration decreased, or as the thickness of the electrical double-layer increased. The electrolyte concentration at which all bacteria were repelled from the glass surface depended on the valency of the cation. The reversible phase is interpreted in terms of the balance between the electrical double-layer repulsion energies at different electrolyte concentrations and the van der Waals attractive energies. Even at the electrolyte concentration of seawater, the bacteria probably are held at a small distance from the glass surface by a repulsion barrier. Reversible sorption often led to rotational motion of the motile Pseudomonas sp. strain R3 at a liquid-glass interface. Pseudomonas R3 produced polymeric fibrils in artificial seawater; these may be concerned in the irreversible sorption of the bacteria to surfaces. Sorption and polymer production were stimulated by 7 mg. /l. glucose but higher levels inhibited irreversible sorption. Omission of Ca2+ and Mg2+ from the artificial seawater prevented growth, polymer production, and sorption to surfaces by Pseudomonas R3.
Early nutritional strategies

The embryonic and immediate post-hatch developmental period represents a significant phase in attaining quality broiler performance at marketing. An efficient transition period from late term embryo to a viable independent chick is necessary to achieve such results. Immediately, post-hatch birds must undergo a shift from egg and embryonic nutrients to exogenous feed. Under practical conditions, many birds have access to feed only 36 to 48 hours after hatching, and during this time body weight decreases, and intestine and muscle development are retarded. In order to overcome these limitations, a continuous feeding process can be established which would supply nutrients to the developing embryo, feed and water to the newly hatched chick within the hatchery, and a highly digestible pre-starter diet at placement. In ovo feeding stimulates intestinal development by enhancing villi, increasing intestinal capacity to digest and absorb nutrients and provides a basis for muscle growth. Immediate access to feed (1 hour after clearing the shell) initiates uptake and growth processes some 24 hours post-ingestion compared to poultry with delayed feed intake. The enhanced growth caused by early feeding improves nutritional maturity of the bird, stimulates yolk utilisation, increases intestinal development, and has long term metabolic effects. Providing highly digestible ingredients in the pre-starter diet increases body weight performance at day seven, and through to marketing. Together, these processes provide appropriate nutrition pre- and post-hatch which can accelerate gastrointestinal development, muscle growth and therefore result in increased performance. This paper will summarise studies dealing with the different approaches to early nutritional strategies in our modern, fast growing broiler.
Incorporating age and delay into models for biophysical systems

In many biological systems, chemical reactions or changes in a physical state are assumed to occur instantaneously. For describing the dynamics of those systems, Markov models that require exponentially distributed inter-event times have been used widely. However, some biophysical processes such as gene transcription and translation are known to have a significant gap between the initiation and the completion of the processes, which renders the usual assumption of exponential distribution untenable. In this paper, we consider relaxing this assumption by incorporating age-dependent random time delays (distributed according to a given probability distribution) into the system dynamics. We do so by constructing a measure-valued Markov process on a more abstract state space, which allows us to keep track of the ‘ages’ of molecules participating in a chemical reaction. We study the large-volume limit of such age-structured systems. We show that, when appropriately scaled, the stochastic system can be approximated by a system of partial differential equations (PDEs) in the large-volume limit, as opposed to ordinary differential equations (ODEs) in the classical theory. We show how the limiting PDE system can be used for the purpose of further model reductions and for devising efficient simulation algorithms. In order to describe the ideas, we use a simple transcription process as a running example. We, however, note that the methods developed in this paper apply to a wide class of biophysical systems.
Developed Waters for Wildlife: Science, Perception, Values, and Controversy

Abstract Human-made or -modified water sources (i.e., catchments) are widely used for wildlife management in the arid western United States, where thousands of such catchments have been built to enhance wildlife populations and mitigate for the loss of natural water sources. For decades, the need for and value of catchments to wildlife was unquestioned. Recently, however, the use of catchments has become controversial, particularly on public lands. Impacts to wildlife populations and wildlife habitats have been central to the debate, which has, in large part, been fueled by a paucity of scientific information. Value-based conflicts over management practices on public lands also have played a significant role.
Towards Better Understanding of Disentangled Representations via Mutual Information

Most existing works on disentangled representation learning are solely built upon an marginal independence assumption: all factors in disentangled representations should be statistically independent. This assumption is necessary but definitely not sufficient for the disentangled representations without additional inductive biases in the modeling process, which is shown theoretically in recent studies. We argue in this work that disentangled representations should be characterized by their relation with observable data. In particular, we formulate such a relation through the concept of mutual information: the mutual information between each factor of the disentangled representations and data should be invariant conditioned on values of the other factors. Together with the widely accepted independence assumption, we further bridge it with the conditional independence of factors in representations conditioned on data. Moreover, we note that conditional independence of latent variables has been imposed on most VAE-type models and InfoGAN due to the artificial choice of factorized approximate posterior $q(\rvz|\rvx)$ in the encoders. Such an arrangement of encoders introduces a crucial inductive bias for disentangled representations. To demonstrate the importance of our proposed assumption and the related inductive bias, we show in experiments that violating the assumption leads to decline of disentanglement among factors in the learned representations.
Fungus/Disease Analysis in Tomato Crop using Image Processing Techniques

The crop of tomato is very often infected by a disease that leaves spots of brown, gray or off-white colors on the plant's leafs in winter. Scientifically, this disease is known as cercospora leaf spot or cercospora cruciferarum. It's a kind of fungus that often kills young seedlings. The fungus spreads by air and can also infect tomato plants. Therefore, it is important to monitor the leaf at regular intervals so as to keep track on quality of growing tomato crop. In the presented paper, a novel machine vision system has been proposed that visual inspects the leafs coming out of the soil and based on spots on leaves, it determines the nature of fungus and its depth into the tomato steam. The size of the fungus, color depth and location and locus of the fungus on leaves give an accurate determination of crop quality under the soil. In the presented thesis work, the image of the crop leaves are taken by a good quality color camera and processed for getting a gray colored and segmented image depending upon the nature and size of the fungus. A criterion is set for acceptable and rejects crop quality based on the fungus level.
Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial

Antibody-dependent cellular cytotoxicity (ADCC) correlated with a reduced risk of infection from HIV-1 in the RV144 vaccine trial, the only HIV-1 vaccine trial to date to show any efficacy. Antibodies specific for CD4-induced envelope (Env) epitopes within constant region 1 and 2 (cluster A region) were induced in the RV144 trial and their ADCC activities were implicated in the vaccine efficacy. We present structural analyses of the antigen epitope targets of several RV144 antibodies specific for this region and C11, an antibody induced in natural infection, to show what the differences are in epitope specificities, mechanism of antigen recognition, and ADCC activities of antibodies induced by vaccination and during the course of HIV infection. Our data suggest that the truncated AIDSVAX gp120 variants used in the boost of the RV144 regimen may have shaped the vaccine response to this region, which could also have contributed to vaccine efficacy. ABSTRACT Antibodies (Abs) specific for CD4-induced envelope (Env) epitopes within constant region 1 and 2 (C1/C2) were induced in the RV144 vaccine trial, where antibody-dependent cellular cytotoxicity (ADCC) correlated with reduced risk of HIV-1 infection. We combined X-ray crystallography and fluorescence resonance energy transfer-fluorescence correlation spectroscopy to describe the molecular basis for epitopes of seven RV144 Abs and compared them to A32 and C11, C1/C2 Abs induced in HIV infection. Our data indicate that most vaccine Abs recognize the 7-stranded β-sandwich of gp120, a unique hybrid epitope bridging A32 and C11 binding sites. Although primarily directed at the 7-stranded β-sandwich, some accommodate the gp120 N terminus in C11-bound 8-stranded conformation and therefore recognize a broader range of CD4-triggered Env conformations. Our data also suggest that Abs of RV144 and RV305, the RV144 follow-up study, although likely initially induced by the ALVAC-HIV prime encoding full-length gp120, matured through boosting with truncated AIDSVAX gp120 variants. IMPORTANCE Antibody-dependent cellular cytotoxicity (ADCC) correlated with a reduced risk of infection from HIV-1 in the RV144 vaccine trial, the only HIV-1 vaccine trial to date to show any efficacy. Antibodies specific for CD4-induced envelope (Env) epitopes within constant region 1 and 2 (cluster A region) were induced in the RV144 trial and their ADCC activities were implicated in the vaccine efficacy. We present structural analyses of the antigen epitope targets of several RV144 antibodies specific for this region and C11, an antibody induced in natural infection, to show what the differences are in epitope specificities, mechanism of antigen recognition, and ADCC activities of antibodies induced by vaccination and during the course of HIV infection. Our data suggest that the truncated AIDSVAX gp120 variants used in the boost of the RV144 regimen may have shaped the vaccine response to this region, which could also have contributed to vaccine efficacy.
Free amino acids and water-soluble nitrogen as ripening indices in Montasio cheese*

Summary - Traditionally, in semi-hard and hard cheeses the development of proteolysis is followed by the increase of water-soluble nitrogen (SN) as a percentage of total nitrogen (TN), but the characterisation of proteolysis for each particular cheese must con sider ail the processes that lead to the formation of peptides, free amino acids and products of their catabolism. In Montasio cheese, a considerable variability in the SN values and the amino acid profiles of cheeses at the same stage of ripening was recorded. This variability was probably due to the different traditional technologies adopted. Therefore, no chemometric model could be set up to evaluate the typical nature of Montasio cheese. On the other han d, a relationship between the total free amino acid content and the SNrrN ratio was demonstrated and it was found that certain amino acids cou Id be used as an index for determining the level of proteolysis reached by the Montasio chee se. proteolysis / free amino acid / total nitrogen / water-soluble nitrogen / Montasio cheese
Multitask learning from clinical text and acute physiological conditions differentially improve the prediction of mortality and diagnosis at the ICU

The prediction of mortality of critically ill patients has stimulated the development of many severity scoring algorithms. The majority of the models use physiological measurements obtained during the first hours of admission (i.e., heart rate, arterial blood pressure, or respiratory rate). In this study, we propose to improve the performance of current scoring system by including free text from patient's medical history. Although the primary outcome was in-hospital mortality, we chose a model architecture to provide simultaneous assessment of ICD-9 codes and groupings. We hypothesized that including patients' medical history with a multitask learning approach would improve model performance. We compared the predictive performance obtained with our approach to the best models previously proposed in the literature (baseline models). We used the MIMIC publicly available database which includes > 60,000 ICU admissions between 2001 and 2012. The patients' condition at admission was accounted for by the preliminary diagnosis at admission and the medical history extracted from the discharge summaries notes. Unstructured data was processed through a Gated Recurrent Units layer with pre-trained word embeddings, and the hidden states were concatenated to the remaining structured-tabular data. Baseline models achieved similar results than in previously published work, but our artificial neural networks models showed significant improvement towards classification of mortality (AUC-ROC = 0.90). Including the medical history improved all tasks but relatively more the ICD-9 codes prediction than the mortality. The clinical prediction model presented here could be used to identify patients' risk groups, which would improve the quality of ICU care, and further help to efficiently allocate hospital resources.
User-based Adaptive Software Development for Gamified Systems

During the last few years many researchers have attempted to find a way to implement gamified systems that are adaptively personalized based on user types. Gamification, which is the use of game elements in a non-game context in a way that makes it like a game helps in increasing users' engagement. Thus, software engineers cannot follow the approach of "One size fit all" anymore as in the traditional software design. That is because different people are motivated with different ways and with different mechanics and dynamics based on their needs and personalities. This paper focuses on devising means to develop personalized gamified systems based on user types. We suggest achieving that by changing the gamification elements themselves and not to only adapt the game mechanics and dynamics values based on user types to get the most users' engagement, satisfaction and performance while using the developed software. We propose a method that provides a systematic process that guides the software engineers in designing adaptive gamified systems based on user types by mapping them to gamification elements. Moreover, to formalize the proposed method we develop an ontology that implements the mappings between game elements and user types by defining rules that govern their usage. The method also provides a systematic means to modify the system at runtime (i.e. while the system is in use) based on the users' preference and behavior by changing the existing elements based on the usage of each user.
Identification of Salt-induced Changes in Leaf and Root Proteomes of the Wild Tomato, Solanum chilense

This article reports salt-induced changes in leaf and root proteomes after wild tomato (Solanum chilense) plantswere treated with200mMNaCl.Inleaftissues, atotal of176proteinspotsshowed significantchanges(P <0.05), of which 104 spots were induced and 72 spots suppressed. Salt-induced proteins are associated with the following pathways: photosynthesis, carbohydrate metabolism, glyoxylate shunt, glycine cleavage system, branched-chain amino acid biosynthesis, protein folding, defense and cellular protection, signal transduction, ion transport, and antioxidant activities. Suppressed proteins belong to the following categories: oxidative phosphorylation pathway, photorespirationandproteintranslationalmachinery, oxidativestress,andATPases.Inroottissues,106proteinspots changed significantly (P < 0.05) after the salt treatment, 63 spots were induced, and 43 suppressed by salt treatment. Salt-induced proteins are associated with the following functional pathways: regeneration of S-adenosyl methionine, protein folding, selective ion transport, antioxidants and defense mechanism, signal transduction and gene expression regulation, and branched-chain amino acid synthesis. Salt-suppressed proteins are receptor kinase proteins, peroxidases and germin-like proteins, malate dehydrogenase, and glycine dehydrogenase. In this study, different members of proteins were identified from leaf and root tissues after plants were subjected to salt treatment. These proteins represent tissue-specific changes in salt-induced proteomes. When protein expression was compared in the context of metabolic pathways, the branched-chain amino acid biosynthesis, glucose catabolism toward reducing cellular glucose level, and the antioxidant, detoxification, and selective ion uptake and transport were induced in both root and leaf tissues. These changes appear to be associated with salt tolerance in the whole plant.