Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved turbidity estimates in complex inland waters using combined NIR–SWIR atmospheric correction approach for Landsat 8 OLI data

ABSTRACT Turbidity is one of the important water quality parameters, essentially a proxy to assess eutrophication state in inland coastal systems. In this article, a method of combined near-infrared–shortwave infrared (NIR–SWIR) atmospheric correction for Landsat 8 (L8) Operational Land Imager data is proposed to improve the turbidity retrieval in optically complex waters. From the extremely turbid to moderately turbid waters, the relative ranges in water-leaving reflectance in band 3 () are found to be 19–92% and 31–79% in band 4 (). The SWIR reflectances in and are 57% and 66% higher than that of standard NIR correction in extremely turbid waters. However, this method has resulted in ~30% higher reflectances than the NIR method in relatively less turbid waters; the latter method is still good in moderately turbid waters. Using Rayleigh corrected reflectances, a turbidity index, , was computed to discriminate the productive and/or turbid waters. The SWIR method was applied for water having Tind > 1.5 threshold and the NIR method in the other regions. A new turbidity algorithm has been developed using L8 two band ratio () optimized with in situ turbidity data from four data buoys for 2014. The Landsat 8 band-weighted in situ reflectances for bands 3 and 4 are used to derive turbidity using the present algorithm and validated against in situ turbidity, providing a good coefficient of determination of R2 = 0.87. As compared to the NIR-based correction, the turbidity obtained from the combined (NIR + SWIR) correction in extremely turbid waters is around 80–90% (absolute percentage difference (APD)) different. Whereas in the moderately turbid waters, the APD between the two corrections was around 50–75%. There are no obvious data discontinuities in using the combined approach. Comparisons were made with available single-band turbidity algorithms and found that the present turbidity algorithm performed well in the optically complex lagoon environment.
The T cell receptor repertoire of CD4-8+ thymocytes is altered by overexpression of the BCL-2 protooncogene in the thymus

The bcl-2 gene encodes an intracellular, membrane-associated protein that protects immature cortical thymocytes from a wide variety of apoptotic stimuli, including glucocorticoids, radiation, and anti-CD3 treatment. Since cortical thymocytes are the primary target cells for thymic positive and negative selection processes, and since these processes are associated with cell death, we evaluated the role of bcl- 2 in T cell development in two ways. In the first approach, transgenic mice expressing high levels of Bcl-2 in cortical thymocytes were mated with H-Y T cell receptor (TCR) transgenic mice, the latter being a well- defined system for the study of positive and negative selection of T cells. We found that the bcl-2 transgene had a dramatic effect on positive selection. This was manifested by a greatly increased production of mature thymocytes that were highly skewed towards the CD4- 8+ lineage. The change involving CD4-8+ thymocytes occurred not only in bcl-2 transgenic mice, but was also observed in H-Y TCR/bcl-2 doubly transgenic mice, regardless of whether the H-Y TCR was expressed in the selecting (H-2b) or nonselecting (H-2d) environments. Furthermore, a large proportion of CD4-8+ thymocytes produced in H-2b H-Y TCR/bcl-2 doubly transgenic female mice expressed endogenous TCR alpha chains rather than the transgenic TCR alpha chain. These observations are consistent with the model that high expression of Bcl-2 in cortical thymocytes overrides the normal apoptotic pathway. This then allows the selection of CD4-8+ thymocytes expressing TCRs that are otherwise nonselectable. However, the bcl-2 transgene did not protect CD4+8+ thymocytes expressing the male-specific TCR from deletion in male doubly transgenic mice. In the second approach, we determined the level of bcl-2 mRNA expression in populations of thymocytes defined by their CD4/CD8 phenotypes using quantitative reversed transcriptase PCR techniques. Our results indicate that bcl-2 mRNA was expressed at a high level in immature CD4-8- thymocytes and in mature CD4+8- thymocytes. There is a dramatic downregulation of bcl-2 mRNA in CD4+8+ thymocytes, particularly those expressing a low level of TCR. CD4+8+ thymocytes that upregulated their TCR, likely as a result of receiving positive selection signals, also upregulated bcl-2 mRNA. This observation suggests that rescue of immature thymocytes from the programmed cell death pathway by positive selection signals is accompanied by the upregulation of bcl-2 mRNA.
Compilation of Heterogeneous Models: Motivations and Challenges

The widespread use of model driven engineering in the development of software-intensive systems, including highintegrity embedded systems, gave rise to a “Tower of Babel” of modeling languages. System architects may use languages such as OMG SysML and MARTE, SAE AADL or EAST-ADL; control and command engineers tend to use graphical tools such as MathWorks Simulink/Stateflow or Esterel Technologies SCADE, or textual languages such as MathWorks Embedded Matlab; software engineers usually rely on OMG UML; and, of course, many inhouse domain specific languages are equally used at any step of the development process. This heterogeneity of modeling formalisms raises several questions on the verification and code generation for systems described using heterogeneous models: How can we ensure consistency across multiple modeling views? How can we generate code, which is optimized with respect to multiple modeling views? How can we ensure model-level verification is consistent with the run-time behavior of the generated executable application? In this position paper we describe the motivations and challenges of analysis and code generation from heterogeneous models when intra-view consistency, optimization and safety are major concerns. We will then introduce Project P and Hi-MoCo respectively FUI and Eurostars -funded collaborative projects tackling the challenges above. This work continues and extends, in a wider context, the work carried out by the Gene-Auto project [1], [2]. Hereby we will present the key elements of Project P and Hi-MoCo, in particular: (i) the philosophy for the identification of safe and minimal practical subsets of input modeling languages; (ii) the overall architecture of the toolsets, the supported analysis techniques and the target languages for code generation; and finally, (iii) the approach to cross-domain qualification for an open-source, community-driven toolset.
Herpesviruses use bidirectional fast-axonal transport to spread in sensory neurons

Alpha herpesviruses infect the vertebrate nervous system resulting in either mild recurrent lesions in mucosal epithelia or fatal encephalitis. Movement of virions within the nervous system is a critical factor in the outcome of infection; however, the dynamics of individual virion transport have never been assessed. Here we visualized and tracked individual viral capsids as they moved in axons away from infected neuronal cell bodies in culture. The observed movement was compatible with fast axonal flow mediated by multiple microtubule motors. Capsids accumulated at axon terminals, suggesting that spread from infected neurons required cell contact.
Mechanisms Underlying the Impairment of Hippocampal Long-term Potentiation and Memory in Experimental Parkinson's Disease Materials and Methods Procedure for L-dopa Treatments Immunohistological Procedure Behavioural Procedure

Although patients with Parkinson's disease show impairments in cognitive performance even at the early stage of the disease, the synaptic mechanisms underlying cognitive impairment in this pathology are unknown. Hippocampal long-term potentiation represents the major experimental model for the synaptic changes underlying learning and memory and is controlled by endogenous dopamine. We found that hippocampal long-term potentiation is altered in both a neurotoxic and transgenic model of Parkinson's disease and this plastic alteration is associated with an impaired dopaminergic transmission and a decrease of NR2A/NR2B subunit ratio in synaptic N-methyl-D-aspartic acid receptors. Deficits in hippocampal-dependent learning were also found in hemiparkinsonian and mutant animals. Interestingly, the dopamine precursor L-DOPA was able to restore hippocampal synaptic potentiation via D1/D5 receptors and to ameliorate the cognitive deficit in parkinsonian animals suggesting that dopamine-dependent impairment of hippocampal long-term potentiation may contribute to cognitive deficits in patients with Parkinson's disease. Introduction Parkinson's disease causes impairments in cognitive performance resembling those seen in frontal lobe patients (Robbins and Arnsten, 2009), and progression of these deficits can lead to dementia (Cools et al., 2001; Goetz et al., 2008). While the motor abnormalities in Parkinson's disease result from nigros-triatal dopamine depletion, memory dysfunctions are induced by degeneration of the dopaminergic mesocorticolimbic projections originating from the ventral tegmental area (Calabresi et al., 2006). The hippocampus is implicated in memory deficits observed in Parkinson's disease (Shohamy et al., 2009) since both structural and functional abnormalities of this structure have been observed in patients suffering from sporadic (Summerfield et al., 2005; Joelving et al., 2006) and genetic forms of the disease (Helton et al., 2008). In addition, hippocampal abnormalities positively correlate with memory deficits (Bruck et al. The hippocampus is essential for encoding spatial and episodic memories (Ryan et al., 2010), and for novelty detection (Jenkins et al., 2004). Novelty detection involves the comparison of an existing memory with new sensory information. Indeed, CA1 pyr-amidal cells also receive direct sensory inputs from the cortex (Lisman and Otmakhova, 2001). The dopaminergic system is a strong candidate for modulating novelty acquisition and synaptic plasticity in the hippocampal CA1 area. The ventral tegmental area, the major brain source of dopaminergic inputs to the limbic system and hippocampus, is part of a functional loop detecting novelty (Lisman and Grace, 2005). Hippocampal long-term potentiation (LTP) gates behaviourally relevant information into long-term memory (Lisman and Grace, 2005). Dopamine is critically involved in this process since novel …
Circadian Clocks in the Immune System

The immune system is a complex set of physiological mechanisms whose general aim is to defend the organism against non-self-bodies, such as pathogens (bacteria, viruses, parasites), as well as cancer cells. Circadian rhythms are endogenous 24-h variations found in virtually all physiological processes. These circadian rhythms are generated by circadian clocks, located in most cell types, including cells of the immune system. This review presents an overview of the clocks in the immune system and of the circadian regulation of the function of immune cells. Most immune cells express circadian clock genes and present a wide array of genes expressed with a 24-h rhythm. This has profound impacts on cellular functions, including a daily rhythm in the synthesis and release of cytokines, chemokines and cytolytic factors, the daily gating of the response occurring through pattern recognition receptors, circadian rhythms of cellular functions such as phagocytosis, migration to inflamed or infected tissue, cytolytic activity, and proliferative response to antigens. Consequently, alterations of circadian rhythms (e.g., clock gene mutation in mice or environmental disruption similar to shift work) lead to disturbed immune responses. We discuss the implications of these data for human health and the areas that future research should aim to address.
Fossil charcoal quantification using manual and image analysis approaches

Charcoal particles are evidence of past fire events and macro-charcoal particles have been shown to represent local fire events. There are several methods for the preparation and quantification of macro-charcoal particles, none of which have been universally accepted as standard. Very few studies compare methodological differences and no studies to date compare quantification by mass with quantification by volume using image analysis. Using three cores taken from a peatland located in SE Norway, we compare these two established methods using a generalized linear mixed model (GLMM) and a split-plot ANOVA test. We show that charcoal volume (image analysis method) was a better predictor of charcoal mass than charcoal particle number and the same size classes of charcoal as size class distributions were not spatially and temporally correlated. Although there is still a need for a common and unifying method, our results show that quantification of charcoal particles by image analysis including size (e.g. height in mm) and area (mm2)/volume (mm3) measurements provides more significant results in cross-site or multiple-site studies than quantifications based on particle number. This has implications for the interpretation of charcoal data from regional studies that are used to model drivers of wildfire activity and environmental change in boreal–temperate landscapes during the Holocene.
Obesity Alters the Microbial Community Profile in Korean Adolescents

Obesity is an increasing public health concern worldwide. According to the latest Organization for Economic Co-operation and Development (OECD) report (2014), the incidence of child obesity in Korea has exceeded the OECD average. To better understand and control this condition, the present study examined the composition of the gut microbial community in normal and obese adolescents. Fecal samples were collected from 67 obese (body mass index [BMI] ≥ 30 kg/m2, or ≥ 99th BMI percentile) and 67 normal (BMI < 25 kg/m2 or < 85th BMI percentile) Korean adolescents aged 13–16 years and subjected to 16S rRNA gene sequencing. Analysis of bacterial composition according to taxonomic rank (genus, family, and phylum) revealed marked differences in the Bacteroides and Prevotella populations in normal and obese samples (p < 0.005) at the genus and family levels; however, there was no difference in the Firmicutes-to-Bacteroidetes (F/B) ratio between normal and obese adolescents samples at the phylum level (F/B normal = 0.50 ± 0.53; F/B obese = 0.56 ± 0.86; p = 0.384). Statistical analysis revealed a significant association between the compositions of several bacterial taxa and child obesity. Among these, Bacteroides and Prevotella showed the most significant association with BMI (p < 0.0001 and 0.0001, respectively). We also found that the composition of Bacteroides was negatively associated with triglycerides (TG), total cholesterol, and high-sensitive C-reactive protein (hs-crp) (p = 0.0049, 0.0023, and 0.0038, respectively) levels, whereas that of Prevotella was positively associated with TG and hs-crp levels (p = 0.0394 and 0.0150, respectively). We then applied the association rule mining algorithm to generate “rules” to identify the association between the populations of multiple bacterial taxa and obesity; these rules were able to discriminate obese from normal states. Therefore, the present study describes a systemic approach to identify the association between bacterial populations in the gut and childhood obesity.
TERC polymorphisms are associated both with susceptibility to colorectal cancer and with longer telomeres

Background and aims Shorter telomeres have been associated with increased risk of malignancy, including colorectal cancer (CRC). Telomere length is heritable and may be an intermediate phenotype linked to genetic susceptibility to CRC. Methods In a large sample, the study investigated whether candidate single nucleotide polymorphisms (SNP) in ‘telomere biology’ genes were associated with telomere length in leucocytes. SNP associated with an increased risk of CRC were searched for separately. Results Carriers of the common allele at SNP rs10936599, near the telomerase RNA component (TERC) locus, had significantly longer telomeres. It was independently found that the same rs10936599 allele was associated with increased risk of both CRC and colorectal adenomas. Neither telomere length nor CRC risk was associated with variation near telomerase reverse transcriptase or other telomere biology genes. In silico analysis showed that SNP rs2293607 was strongly correlated with rs10936599, mapped within TERC transcripts, had a predicted effect on messenger RNA folding and lay at a reported transcription factor binding site. TERC mRNA were expressed, differing only at the alleles of rs2293607, in CRC cell line HCT116. The long-telomere/CRC-risk allele was associated with higher levels of TERC mRNA and the formation of longer telomeres. Conclusions Common genetic variation at TERC is associated with both longer telomeres and an increased risk of CRC, a potential mechanism being reduced levels of cell senescence or death. This finding is somewhat paradoxical, given retrospective studies reporting that CRC cases have shorter telomeres than controls. One possibility is that that association actually results from poorer survival in patients with longer telomeres.
Calvin: A System for Automating Cosmogenic Isotope Dating ; CU-CS-1040-08

Scientific reasoning is a complex process, alternately requiring flashes of insight and tedious analysis. This dichotomy is evident in constructing a geologic timeline for a landform using cosmogenic isotope dating. Experts in this field frequently spend months on repetitive mathematical tasks, until they have gathered enough information to suddenly understand the data. The Calvin project 1 is aimed at understanding and automating this process, particularly the semi-mechanical analysis tasks that must be performed on every new problem instance. Having this analysis done quickly and automatically will free experts for the more difficult and creative tasks in the field. Furthermore, it is my hope that Calvin's architecture can eventually be applied to other fields with similar challenges. The aims of the project are challenging because the science of cosmogenic isotope dating is quite new. There is only a relatively small number of completed, detailed analyses from which one can draw knowledge. Therefore, it is necessary to build a knowledge base through interaction with experts. Unfortunately, as is often the case, it is difficult for these experts to clearly articulate how and why they come to specific conclusions. I have been working with experts in this field for more than two years, but the knowledge base I have so far developed is still very incomplete. Complicating the difficulty of acquiring the knowledge used by experts, few theories in the area are completely formed or fully understood. As a result, most expert analysis relies on vague heuristics that are frequently contradictory. Finally, as is common in most scientific fields, observed data is typically noisy, often sparse, and not completely trustworthy. Any system that automates the timeline construction process, then, must be able to handle contradiction, uncertain heuristics, and untrustworthy inputs gracefully. Argumentation is an elegant and intuitive framework for automating this quixotic type of reasoning. It is a symbolic logic, which has a number of advantages. In particular, rules acquired from experts can be input directly into the system in a format that closely mirrors their original form, and answers generated by the system can be justified using human-readable explanations. Presenting the system's reasoning to the user in a legible format facilitates engagement and helps to speed further knowledge engineering. In the argumentation architecture used by Calvin, conclusions can receive partial support (modeling uncertain 1.Named for the character in the Calvin & Hobbes comics, who often starts arguments just for the sake of …
Plasma haptoglobin and immunoglobulins as diagnostic indicators of deoxynivalenol intoxication

This study aimed to discover potential biomarkers for dioxynivalenol (DON) intoxication. B6C3F1 male mice were orally exposed to 0.83, 2.5 and 7.5 mg/kg body weight (bw) DON for 8 days and the differential protein expressions in their blood plasma were determined by SELDI - Time-of-Flight/Mass Spectrometry (TOF/MS) and the immunoglobulins (Igs) G, A, M and E in the serum were investigated. 11.7 kDa protein was significantly highly expressed according to DON administration and this protein was purified by employing a methyl ceramic HyperD F column with using optimization buffer for adsorption and desorption. The purified protein was identified as a haptoglobin precursor by peptide mapping with using LC/Q-TOF/MS and MALDI-TOF/MS and this was confirmed by western blotting and ELISA. IgG and IgM in serum were decreased in a dose-dependent manner and IgA was decreased at 7.5 mg/kg bw DON administration, but the IgE level was not changed. To compare the expressions of haptoglobin and the Igs patterns between aflatoxin B1 (AFB1), zearalenone (ZEA) and DON intoxications, rats were orally administered with AFB1 1.0, ZEA 240 and DON 7.5 mg/kg bw for 8 days. Haptoglobin was increased only at DON 7.5 mg/kg bw, while it was slightly decreased at ZEA 240 mg/kg bw and it was not detected at all at AFB1 1.0 mg/kg bw. IgG and IgA were decreased by DON, but IgG, IgA, IgM and IgE were all increased by AFB1. No changes were observed by ZEA administration. These results show that plasma haptoglobin could be a diagnostic biomarker for DON intoxication when this is combined with examining the serum Igs.
The Transcriptomics of Secondary Growth and Wood Formation in Conifers

In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality.