Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid prediction of chlorophylls and carotenoids content in tea leaves under different levels of nitrogen application based on hyperspectral imaging.

BACKGROUND Photosynthetic pigments perform critical physiological functions in tea plants. Their content is an essential indicator of photosynthetic efficiency and nutritional status. The present study aimed to predict chlorophyll a (Chl a), chlorophyll b (Chl b), total chlorophyll (total Chl), and carotenoid (Car) content in tea leaves under different levels of nitrogen treatment using hyperspectral imaging (HSI) in combination with variable selection algorithms. RESULTS A total of 150 samples were collected and scanned using the HSI system. The mean spectrum in the region of interest (ROI) was extracted, and the pigment content was measured by traditional chemical methods. Five and seven optimal wavelengths (OWs) were selected using the regression coefficients (RCs) of partial least squares regression (PLSR) and the second-derivative (2-Der), respectively. The optimal 2-Der-PLSR models for Chl a, Chl b, total Chl, and Car performed remarkably well based on seven OWs with correlation coefficients of prediction (RP ) of 0.9337, 0.9322, 0.9333 and 0.9036, root mean square errors in prediction (RMSEP) of 0.1100, 0.0511, 0.1620, and 0.0300 mg g-1 , respectively. CONCLUSION The results of this study revealed that HSI combined with variable selection method can be employed as a rapid and accurate method for predicting the content of pigments in tea plants. © 2018 Society of Chemical Industry.
The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh

Background Visceral leishmaniasis (VL) is characterised by a high degree of spatial clustering at all scales, and this feature remains even with successful control measures. VL is targeted for elimination as a public health problem in the Indian subcontinent by 2020, and incidence has been falling rapidly since 2011. Current control is based on early diagnosis and treatment of clinical cases, and blanket indoor residual spraying of insecticide (IRS) in endemic villages to kill the sandfly vectors. Spatially targeting active case detection and/or IRS to higher risk areas would greatly reduce costs of control, but its effectiveness as a control strategy is unknown. The effectiveness depends on two key unknowns: how quickly transmission risk decreases with distance from a VL case and how much asymptomatically infected individuals contribute to transmission. Methodology/Principal findings To estimate these key parameters, a spatiotemporal transmission model for VL was developed and fitted to geo-located epidemiological data on 2494 individuals from a highly endemic village in Mymensingh, Bangladesh. A Bayesian inference framework that could account for the unknown infection times of the VL cases, and missing symptom onset and recovery times, was developed to perform the parameter estimation. The parameter estimates obtained suggest that, in a highly endemic setting, VL risk decreases relatively quickly with distance from a case—halving within 90m—and that VL cases contribute significantly more to transmission than asymptomatic individuals. Conclusions/Significance These results suggest that spatially-targeted interventions may be effective for limiting transmission. However, the extent to which spatial transmission patterns and the asymptomatic contribution vary with VL endemicity and over time is uncertain. In any event, interventions would need to be performed promptly and in a large radius (≥300m) around a new case to reduce transmission risk.
Protective Effect and Mechanism of Alprostadil in Acute Respiratory Distress Syndrome Induced by Oleic Acid in Rats

Background This study investigated the role and mechanism of alprostadil in acute respiratory distress syndrome (ARDS) induced by oleic acid (OA) in rats. Material/Methods Sprague-Dawley rats were randomly divided into control, OA model, and OA + Alprostadil (2.5, 5, and 10 μg/kg, respectively) groups. The ARDS model was induced by femoral vein injection of OA, and alprostadil was administrated immediately. Lung injury was evaluated by lung wet-dry weight ratio (W/D) and histological analyses. Expressions of ACE, inflammatory mediators, apoptotic-related proteins, and proteins in the MAPKs and NF-κB signaling pathways were determined by Western blot or immunohistochemical staining. Results Compared with the control group, the OA model group had significantly increased W/D, lung injury score, and collagen deposition at 3 h after OA injection. However, alprostadil (10 μg/kg) treatment significantly reduced OA-induced elevation of these indicators. Additionally, OA-induced expression of TNF-α and IL-1β were suppressed by alprostadil. The OA-induced activation of nuclear factor (NF) κB p65 was also reduced by alprostadil. Furthermore, we found that Alprostadil had an inhibitory effect on the phosphorylation of JNK, ERK1/2, and p38 MAPKs. Alprostadil inhibited Bax but increased Bcl-2, indicating a suppressive role in apoptosis. Remarkably increased expression of ACE in the OA model group was observed, which was decreased by alprostadil. Conclusions Alprostadil has a protective effect on ARDS induced by OA in rats, possibly through inhibiting apoptosis, suppressing the activation of MAPKs and NF-κB signaling pathways, and decreasing ACE protein expression. Therefore, the use of alprostadil in clinical ARDS treatment is promising.
A Model for Trans-Kingdom Pathogenicity in Fonsecaea Agents of Human Chromoblastomycosis

The fungal genus Fonsecaea comprises etiological agents of human chromoblastomycosis, a chronic implantation skin disease. The current hypothesis is that patients acquire the infection through an injury from plant material. The present study aimed to evaluate a model of infection in plant and animal hosts to understand the parameters of trans-kingdom pathogenicity. Clinical strains of causative agents of chromoblastomycosis (Fonsecaea pedrosoi and Fonsecaea monophora) were compared with a strain of Fonsecaea erecta isolated from a living plant. The clinical strains of F. monophora and F. pedrosoi remained concentrated near the epidermis, whereas F. erecta colonized deeper plant tissues, resembling an endophytic behavior. In an invertebrate infection model with larvae of a beetle, Tenebrio molitor, F. erecta exhibited the lowest survival rates. However, F. pedrosoi produced dark, spherical to ovoidal cells that resembled muriform cells, the invasive form of human chromoblastomycosis confirming the role of muriform cells as a pathogenic adaptation in animal tissues. An immunologic assay in BALB/c mice demonstrated the high virulence of saprobic species in animal models was subsequently controlled via host higher immune response.
Filipino Nurses' Use of Smartphones in Clinical Settings

While previous research has examined specific ways that nurses have used smartphones for work purposes in clinical settings, large-sample quantitative studies are limited, particularly in Asia. To address this research gap, this study provided a ranking on how nurses have used their smartphones for work purposes in clinical settings and identified differences based on demographic and organizational factors. In January to June 2017, a pen-and-paper survey was administered to 517 staff nurses employed in 19 tertiary-level general hospitals in Metro Manila, Philippines. Results show that nurses frequently used their smartphones to exchange voice calls and text messages with other nurses and doctors. Results also showed that specific items reflecting the use of smartphones for communication purposes differed according to gender, age, hospital ownership, nursing area, number of patients handled in last shift, and presence of a hospital-provided mobile phone. Next, some items for information-seeking purposes differed according to highest educational attainment and years of clinical experience. Moreover, some items for documentation purposes differed according to age, hospital ownership, and number of patients handled in last shift. Overall, the results of this study can be used to guide policies on the use of smartphones in clinical settings.
Deceptive nest defence in ground-nesting birds and the risk of intermediate strategies

Nest predation is an important determinant of reproductive success and ground-nesting birds exhibit a variety of nest defence strategies to mitigate the risk. Many small-bodied, ground nesting birds rely on deceptive behaviours such as injury-feigning to reduce nest predation: we call this behaviour active deception. However, active deception may entail risks to adults, and passive deceptive behaviour, where individuals effectively sneak away from the nest by flushing at long distances, may be an alternative means of avoiding nest predation. We provide a simple model to demonstrate that these tails of the flush distance distribution could minimize predation risk; an intermediate strategy of moderate flush distances means that birds flush more often than with short-distance flushes, and once flushed, the nest is more easily located than for long-distance flushes. We tested this model using two species of ground nesting shorebirds, the White-rumped Sandpiper (Calidris fuscicollis) and the Red Phalarope (Phalaropus fulicarius). We demonstrate that short-distance flushes are associated with active deception and intermediate-distance flushes are associated with an increased risk of nest predation. However, we found no evidence that this potential selective pressure against intermediate strategies has produced a bimodal distribution of nest defence traits. The heritability of defence behaviours, or the ability of individuals to learn, is unknown and other factors such as energetic constraints or risks to adults might also influence flush distances and defence behaviours.
In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability

The delivery of blood-borne therapeutic agents to solid tumours depends on a broad range of biophysical factors. We present a novel multiscale, multiphysics, in-silico modelling framework that encompasses dynamic tumour growth, angiogenesis and drug delivery, and use this model to simulate the intravenous delivery of cytotoxic drugs. The model accounts for chemo-, hapto- and mechanotactic vessel sprouting, extracellular matrix remodelling, mechano-sensitive vascular remodelling and collapse, intra- and extravascular drug transport, and tumour regression as an effect of a cytotoxic cancer drug. The modelling framework is flexible, allowing the drug properties to be specified, which provides realistic predictions of in-vivo vascular development and structure at different tumour stages. The model also enables the effects of neoadjuvant vascular normalisation to be implicitly tested by decreasing vessel wall pore size. We use the model to test the interplay between time of treatment, drug affinity rate and the size of the vessels’ endothelium pores on the delivery and subsequent tumour regression and vessel remodelling. Model predictions confirm that small-molecule drug delivery is dominated by diffusive transport and further predict that the time of treatment is important for low affinity but not high affinity cytotoxic drugs, the size of the vessel wall pores plays an important role in the effect of low affinity but not high affinity drugs, that high affinity cytotoxic drugs remodel the tumour vasculature providing a large window for the normalisation of the vascular architecture, and that the combination of large pores and high affinity enhances cytotoxic drug delivery efficiency. These results have implications for treatment planning and methods to enhance drug delivery, and highlight the importance of in-silico modelling in investigating the optimisation of cancer therapy on a personalised setting.
Likelihood of Neoplasia for Diagnoses Modified by Probability Terms in Canine and Feline Lymph Node Cytology: How Probable Is Probable?

Background: Descriptive probability modifiers are used often to convey the uncertainty of a pathology diagnosis, but they also contribute to ambiguity in communication between pathologists and clinicians. Objectives: Our goal was to determine the frequency and use of probability modifiers in canine and feline lymph node cytology diagnoses, and to determine the actual likelihood of neoplasia for diagnoses with and without modifiers, based on the histologic outcome. Methods: Canine and feline lymph node cytology and histology reports over an 11-year period (2001–2011; n = 367) were evaluated retrospectively. Diagnoses were categorized as neoplastic/malignant (lymphoma, metastatic) or non-neoplastic/benign. The frequency and type of modifier, and the sensitivity, specificity, and predictive values for neoplasia were determined for modified and unmodified diagnoses using histology as the gold standard. Results: Ninety-one of 367 (24.8%) cytology diagnoses were modified by probability terms, including 25/204 (12.2%) diagnoses of non-neoplastic lesions and 66/163 (40.5%) diagnoses of neoplasia. In addition, 26 unmodified diagnoses of neoplasia were followed by a probability phrase indicating specific tumor type. Based on the histologic outcome, modified diagnoses had higher sensitivity (87.3%, confidence interval [CI] 75.5, 94.7%) but lower specificity (50.0%, CI 32.9, 67.1%) for neoplasia than did unmodified diagnoses (60.6 and 100%, respectively; P < 0.0001, Chi square). Modified phrases indicating the probability of a specific tumor type were accurate in 22/26 (84.6%) cases. Positive predictive values for neoplasia were 100% (CI 96.2, 100%) for unmodified and 72.7% (CI 60.4, 83.0%) for modified diagnoses. Negative predictive values were 65.9% (CI 58.5, 72.8%) for unmodified and 72.0% (CI 60.4, 83.0%) for modified diagnoses. No significant difference was found in the likelihood of neoplasia for individual terms used to modify a cytologic diagnosis except for “cannot rule out” (P = 0.0368). Conclusions: Most modified diagnoses of cancer in canine and feline lymph node cytology have a 60–83% likelihood of neoplasia based on histologic outcome, compared with 96–100% for unmodified diagnoses. Non-neoplastic lesions, regardless of modifiers, have a 12–49% likelihood of neoplasia. A limited number of risk categories based on these likelihoods may be a more effective and accurate way to communicate the risk of malignancy in lymph node cytology.
Team based communication and the healthcare communication space.

PURPOSE While previous studies have described structural, process and social aspects of the healthcare communication space there is no overall model of it. Such a model is an essential first step to improving the operationalization and management of healthcare communication. The paper aims to discuss these issues. DESIGN/METHODOLOGY/APPROACH This paper used a case study approach to study team-based communication on a palliative care unit. Non-participant observation, interviews and documents were analyzed using qualitative content analysis. FINDINGS The analysis developed an overall model of the healthcare communication space that consists of five stages: purpose, practices and workflows, structures, implementation, and the development of common ground to support team-based communication. The authors' findings emphasized that implicit communication remains a predominant means of communication and workflow issues at the individual level are a frequent cause of unnecessary group communication tasks. ORIGINALITY/VALUE To improve team-based communication we first need to develop protocols that support team communication needs such as loop closing of group communication tasks in order to minimize unnecessary individual communication tasks. We also need to develop common ground at the protocol, document and terminology levels as part of supporting team-based communication.
Exploring Effects of Chitosan Oligosaccharides on Mice Gut Microbiota in in vitro Fermentation and Animal Model

Chitosan oligosaccharides (COS) have shown positive effects on host gut health and influence on intestinal microbial community. However, the bioactivity and mechanism of COS on gut microbiota is still poorly understood. Here, we presented systematic studies of COS on mice fecal/gut microbiota. During in vitro fermentation of COS by mice gut microbiota, total bacterial population significantly decreased after 8-h COS treatment but was returned to the normal level after extended incubation. Consumption of COS and production of SCFAs suggested that COS were utilized by the microbe, although the consumption of chitosan pentasaccharides was obviously slower than others. COS treatments on mice fecal samples caused the decrease of potential pathogenic genera Escherichia/Shigella and the increase of genus Parabacteroides. In vivo animal study indicated that COS reduced population of probiotic genera Lactobacillus, Bifidobacterium and harmful genus Desulfovibrio, and increased abundance of genus Akkermansia. Phylum Proteobacteria was significantly inhibited by COS both in the animal model and in vitro fermentation. Our findings suggested that COS could reform the community structure of gut microbiota. The relationship among COS, gut microbiota and host health deserve further study.
Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

Significance Evolutionary and comparative genomics, combined with reverse genetics, have the power to identify and characterize new biology. Here, we use these approaches in several nontraditional model species of budding yeasts to characterize a budding yeast secondary metabolite gene cluster, a set of genes responsible for production and reutilization of the siderophore pulcherrimin. We also use this information to assign roles in pulcherrimin utilization for two previously uncharacterized Saccharomyces cerevisiae genes. The evolution of this gene cluster in budding yeasts suggests an ecological role for pulcherrimin akin to other microbial public goods systems. Secondary metabolites are key in how organisms from all domains of life interact with their environment and each other. The iron-binding molecule pulcherrimin was described a century ago, but the genes responsible for its production in budding yeasts have remained uncharacterized. Here, we used phylogenomic footprinting on 90 genomes across the budding yeast subphylum Saccharomycotina to identify the gene cluster associated with pulcherrimin production. Using targeted gene replacements in Kluyveromyces lactis, we characterized the four genes that make up the cluster, which likely encode two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, a chelator that binds iron outside the cell for subsequent uptake. Surprisingly, we identified homologs of the putative transporter and transcription factor genes in multiple yeast genera that lacked the biosynthesis genes and could not make pulcherrimin, including the model yeast Saccharomyces cerevisiae. We deleted these previously uncharacterized genes and showed they are also required for pulcherrimin utilization in S. cerevisiae, raising the possibility that other genes of unknown function are linked to secondary metabolism. Phylogenetic analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms.
On Breiman's Dilemma in Neural Networks: Phase Transitions of Margin Dynamics

Margin enlargement over training data has been an important strategy since perceptrons in machine learning for the purpose of boosting the robustness of classifiers toward a good generalization ability. Yet Breiman shows a dilemma (Breiman, 1999) that a uniform improvement on margin distribution \emph{does not} necessarily reduces generalization errors. In this paper, we revisit Breiman's dilemma in deep neural networks with recently proposed spectrally normalized margins. A novel perspective is provided to explain Breiman's dilemma based on phase transitions in dynamics of normalized margin distributions, that reflects the trade-off between expressive power of models and complexity of data. When data complexity is comparable to the model expressiveness in the sense that both training and test data share similar phase transitions in normalized margin dynamics, two efficient ways are derived to predict the trend of generalization or test error via classic margin-based generalization bounds with restricted Rademacher complexities. On the other hand, over-expressive models that exhibit uniform improvements on training margins, as a distinct phase transition to test margin dynamics, may lose such a prediction power and fail to prevent the overfitting. Experiments are conducted to show the validity of the proposed method with some basic convolutional networks, AlexNet, VGG-16, and ResNet-18, on several datasets including Cifar10/100 and mini-ImageNet.
Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.