Miracle-dz/UniFAR-FTUs huggingface dataset:
Short Interfering RNA Accumulation Correlates with Host Recovery in DNA Virus-Infected Hosts, and Gene Silencing Targets Specific Viral Sequences

ABSTRACT Viruses are both inducers and targets of posttranscriptional gene silencing (PTGS), a natural defense mechanism in plants. Here we report molecular evidence of the ability of single-stranded DNA (ssDNA) viruses to induce PTGS in infected plants irrespective of the severity of or recovery from the symptoms. Our results reveal that five distinct species of cassava-infecting geminiviruses were capable of triggering PTGS by producing two classes of virus-specific short interfering RNAs (siRNAs) of 21 to 26 nucleotides in two plant hosts, tobacco (Nicotiana benthamiana) and cassava (Manihot esculenta, Crantz). However, the efficacy of virus-induced PTGS varied depending on the intrinsic features of the virus and its interaction with the plant host. We found that symptom recovery over time in plants infected with the isolates of African cassava mosaic virus (ACMV-[CM]) or Sri Lankan cassava mosaic virus was associated with a much higher level of virus-derived siRNA accumulation compared to plants infected with viruses that do not show symptom recovery. Furthermore, we determined that the C terminus of AC1 that overlaps with the N terminus of AC2 early viral genes involved in virus replication were the primary targets for ACMV-[CM]-induced PTGS, whereas the C terminus of BC1 was targeted for the East African cassava mosaic Cameroon virus. In addition, our results reveal the possibility for double-stranded RNA formation during transcription in ssDNA viruses, which explains in part how these viruses can trigger PTGS in plants.
Cold Temperature Effects on Byssal Thread Production by the Native Mussel Geukensia demissa versus the Non-Native Mussel Mytella charruana

Mytella charruana is a Central/South American mussel that has been found as an introduced species along the southeastern Atlantic coast of the United States since 2004. Previous experiments have determined the lethal thermal minimum of M. charruana to be between 6-9° C. Continuous byssal thread production is essential for mussel survival as it is used for attachment to substrates in natural environments, but may decrease when environmental conditions deviate from their optimum. We sought to determine whether M. charruana exhibits a non-lethal, thermal response involving a reduction in byssal thread production. Mytella charruana and, for comparison, a native mussel species, Geukensia demissa, were collected for this study. Water temperature was manipulated with chillers to near lethal temperatures (10°, 13° C) and newly produced byssal threads of all mussels were counted and cut daily for seven days. Both mussel species had lower byssal thread production at the colder tested temperatures (10°, 13° C) than in the control (23° C). However, G. demissa produced some threads at 10° C while M. charruana produced none. Also, G. demissa showed no difference in mean byssal thread production between 13° and 23o C. Mytella charruana had significantly fewer byssal threads at 13° C than at 23° C. Our results suggest that G. demissa can withstand colder temperatures than M. charruana, owing to their increased ability to produce byssal threads at lower temperatures. These results have implications for the survival and future spread of non-native M. charruana.
FGFR4 Profile as a Prognostic Marker in Squamous Cell Carcinoma of the Mouth and Oropharynx

Background Fibroblast growth factor receptor 4 (FGFR4) is a member of a receptor tyrosine kinase family of enzymes involved in cell cycle control and proliferation. A common single nucleotide polymorphism (SNP) Gly388Arg variant has been associated with increased tumor cell motility and progression of breast cancer, head and neck cancer and soft tissue sarcomas. The present study evaluated the prognostic significance of FGFR4 in oral and oropharynx carcinomas, finding an association of FGFR4 expression and Gly388Arg genotype with tumor onset and prognosis. Patients and Methods DNA from peripheral blood of 122 patients with oral and oropharyngeal squamous cell carcinomas was used to determine FGFR4 genotype by PCR-RFLP. Protein expression was assessed by immunohistochemistry (IHC) on paraffin-embedded tissue microarrays. Results Presence of allele Arg388 was associated with lymphatic embolization and with disease related premature death. In addition, FGFR4 low expression was related with lymph node positivity and premature relapse of disease, as well as disease related death. Conclusion Our results propose FGFR4 profile, measured by the Gly388Arg genotype and expression, as a novel marker of prognosis in squamous cell carcinoma of the mouth and oropharynx.
Perspectives on: Cyclic nucleotide microdomains and signaling specificity: Mechanisms of cyclic AMP compartmentation revealed by computational models

Introduction Cyclic adenosine 3, 5-monophosphate (cAMP) is a widely used biochemical messenger, transducing extracellular stimuli into a myriad of cellular responses. In the late 1970s, data emerged showing that hormone receptors acting via cAMP have distinct effects on cardiac function. At hormone levels where -adrenergic and prostaglandin receptors induced similar changes in overall cAMP and PKA activity, only -adrenergic receptors were found to increase left ventricular contractility, glycogen metabolism, and troponin I phosphorylation (Brunton et al., 1979; Hayes et al., 1979). This indicated that cAMP does not indiscriminately activate its downstream targets, but rather it acts in a context-dependent manner. To explain the context-dependent specificity of cAMP, Brunton et al. (1981) proposed the compartmentation hypothesis, in which receptor-specific cAMP microdomains are distinctly coupled to cellular functions. Although this concept was initially quite controversial (Steinberg and Brunton, 2001), a variety of technologies has been developed over the past two decades that have enabled direct evidence of cAMP compartmentation. A key focus has become to understand the biochemical and biophysical mechanisms underlying cAMP compartmentation. Because of the limited ability to specifically perturb and measure all aspects of cAMP signaling experimentally, computational models have been developed to help understand how cAMP compartments are formed. Indeed, computational models are well suited for identifying biological mechanisms, predicting downstream consequences, and reducing the complexity of large datasets (Yang and Saucerman, 2011). As the experimental efforts to measure and manipulate cAMP compartmentation have been well reviewed elsewhere (Steinberg and Brunton, 2001; Saucerman and McCulloch, 2006; Willoughby and Cooper, 2007; Karpen, 2014; Rich et al, 2014), this Perspective will concentrate on the specific insights into cAMP compartmentation
Down-regulation of bcl-2 is a potential marker of the efficacy of progestin therapy in the treatment of endometrial hyperplasia.

OBJECTIVE The objective of this study was to evaluate the expression of bcl-2, a regulatory protein in programmed cell death, in endometrial hyperplasia before and after progestational therapy. METHODS Pre- and posttreatment paraffin-embedded endometrial tissue samples from 20 women with an initial diagnosis of endometrial hyperplasia were obtained from archived files. Cases were evaluated and classified as either complete resolution of hyperplasia or persistent hyperplasia in response to progestin treatment. Sections were examined for bcl-2, estrogen receptor, and progesterone receptor expression using immunohistochemistry and compared within the treatment response groups. RESULTS Among the 20 women studied, 13 had complete regression of their hyperplasia with progestin treatment and 7 had evidence of persistent disease after therapy. Bcl-2 expression was significantly decreased after treatment from a mean reactivity score of 2.08 to 0.31 (P = 0.0005) in the group of patients whose hyperplasia completely regressed with progestin administration. Among the women who had persistent hyperplasia after therapy, no significant change was observed between pre- and posttreatment bcl-2 expression, with a mean reactivity of 1.86 to 1. 29, respectively (P = 0.075). Progestational therapy significantly decreased the status of estrogen receptors from a mean score of 2.08 to 0.46 (P = 0.0005) in completely resolved cases of hyperplasia and from 2.00 to 0.43 (P = 0.0025) in persistent hyperplasias. Treatment also significantly decreased the status of progesterone receptors from a mean reactivity score of 1.92 to 0.31 (P = 0.0005) in cases of regressed hyperplasia and from a mean reactivity of 1.86 to 0.29 (P = 0.005) in persistent cases of hyperplasia. CONCLUSIONS Bcl-2 expression decreases following successful progestin treatment of endometrial hyperplasias, whereas it remains expressed in hyperplasias which persist despite progestational therapy. This suggests that bcl-2 expression may represent a component of the therapeutic effects exerted in the endometium during progestational therapy in the treatment of hyperplasia. The activity of the oncoprotein may be a potential measure of the progress of treatment.
Malaria hemozoin is immunologically inert but radically enhances innate responses by presenting malaria DNA to Toll-like receptor 9

Hemozoin (HZ) is an insoluble crystal formed in the food vacuole of malaria parasites. HZ has been reported to induce inflammation by directly engaging Toll-like receptor (TLR) 9, an endosomal receptor. “Synthetic” HZ (β-hematin), typically generated from partially purified extracts of bovine hemin, is structurally identical to natural HZ. When HPLC-purified hemin was used to synthesize the crystal, β-hematin had no inflammatory activity. In contrast, natural HZ from Plasmodium falciparum cultures was a potent TLR9 inducer. Natural HZ bound recombinant TLR9 ectodomain, but not TLR2. Both TLR9 stimulation and TLR9 binding of HZ were abolished by nuclease treatment. PCR analysis demonstrated that natural HZ is coated with malarial but not human DNA. Purified malarial DNA activated TLR9 but only when DNA was targeted directly to the endosome with a transfection reagent. Stimulatory quantities of natural HZ contain <1 μg of malarial DNA; its potency in activating immune responses was even greater than transfecting malarial DNA. Thus, although the malarial genome is extremely AT-rich, its DNA is highly proinflammatory, with the potential to induce cytokinemia and fever during disease. However, its activity depends on being bound to HZ, which we propose amplifies the biological responses to malaria DNA by targeting it to a TLR9+ intracellular compartment.
Experimental Transmission of Infectious Pancreatic Necrosis Virus from the Blue Mussel, Mytilus edulis, to Cohabitating Atlantic Salmon (Salmo salar) Smolts

ABSTRACT Integrated multitrophic aquaculture (IMTA) reduces the environmental impacts of commercial aquaculture systems by combining the cultivation of fed species with extractive species. Shellfish play a critical role in IMTA systems by filter-feeding particulate-bound organic nutrients. As bioaccumulating organisms, shellfish may also increase disease risk on farms by serving as reservoirs for important finfish pathogens such as infectious pancreatic necrosis virus (IPNV). The ability of the blue mussel (Mytilus edulis) to bioaccumulate and transmit IPNV to naive Atlantic salmon (Salmo salar) smolts was investigated. To determine the ability of mussels to filter and accumulate viable IPNV, mussels were held in water containing log 4.6 50% tissue culture infective dose(s) (TCID50) of the West Buxton strain of IPNV ml−1. Viable IPNV was detected in the digestive glands (DGs) of IPNV-exposed mussels as early as 2 h postexposure. The viral load in mussel DG tissue significantly increased with time and reached log 5.35 ± 0.25 TCID50 g of DG tissue−1 after 120 h of exposure. IPNV titers never reached levels that were significantly greater than that in the water. Viable IPNV was detected in mussel feces out to 7 days postdepuration, and the virus persisted in DG tissues for at least 18 days of depuration. To determine whether IPNV can be transmitted from mussels to Atlantic salmon, IPNV-exposed mussels were cohabitated with naive Atlantic salmon smolts. Transmission of IPNV did occur from mussels to smolts at a low frequency. The results demonstrate that a nonenveloped virus, such as IPNV, can accumulate in mussels and be transferred to naive fish.
Innovación tecnológica y externalización de procesos de conocimiento

La sinergia entre innovacion tecnologica y globalizacion de las TIC facilita la subcontratacion global de la interpretacion. La digitalizacion de imagenes y las comunicaciones globales reconfiguran los procesos de imagen medica. La digitalizacion de imagenes permite la exportacion via Internet a consultores externos globales flexibilizando los procesos de conocimiento y generando incertidumbre en los actores tradicionales. La tecnologia como imperativo de la racionalidad y eficiencia transforma los procesos y crea redes horizontales de organizaciones globales que flexibilizan el modelo organizativo tradicional.
Plasma phosphatidylcholine docosahexaenoic acid content and risk of dementia and Alzheimer disease: the Framingham Heart Study.

BACKGROUND Docosahexaenoic acid (DHA) is an abundant fatty acid in the brain. In the diet, DHA is found mostly in fatty fish. The content of DHA has been shown to be decreased in the brain and plasma of patients with dementia. OBJECTIVE To determine whether plasma phosphatidylcholine (PC) DHA content is associated with the risk of developing dementia. DESIGN, SETTING, AND PARTICIPANTS A prospective follow-up study in 899 men and women who were free of dementia at baseline, had a median age of 76.0 years, and were followed up for a mean of 9.1 years for the development of all-cause dementia and Alzheimer disease. MAIN OUTCOME MEASURES Plasma PC fatty acid levels were measured at baseline. Cox proportional regression analysis was used to assess relative risks of all-cause dementia and Alzheimer disease according to baseline plasma levels. RESULTS Ninety-nine new cases of dementia (including 71 of Alzheimer disease) occurred during the follow-up. After adjustment for age, sex, apolipoprotein E epsilon4 allele, plasma homocysteine concentration, and education level, subjects in the upper quartile of baseline plasma PC DHA levels, compared with subjects in the lower 3 quartiles, had a relative risk of 0.53 of developing all-cause dementia (95% confidence interval, 0.29-0.97; P=.04) and 0.61 of developing Alzheimer disease (95% confidence interval, 0.31-1.18; P=.14). Subjects in the upper quartile of plasma PC DHA levels had a mean DHA intake of 0.18 g/d and a mean fish intake of 3.0 servings per week (P<.001) in a subset of 488 participants. We found no other significant associations. CONCLUSION The top quartile of plasma PC DHA level was associated with a significant 47% reduction in the risk of developing all-cause dementia in the Framingham Heart Study.
The integrated routing algorithm for multi-satellites, multi-ground-stations and multi-processing-centers

The research of routing planning for satellites and ground stations always treats the whole process as two independent parts: transmission from satellites to ground stations and transmission in the ground networks. The separate research causes two problems that the two parts could not connect tightly and the delay is large. In order to solve these problems, the paper designs an integrated routing algorithm that treats the transmission as a whole. The algorithm considers the real-time link cost, calculates the normalization matrix, and searches the best real-time link for transmission. Simulation results show that comparing with the separate optimal solution, the integrated solution reduces the delay of the task sequences while keeping the sum of successful task priority and task success rate almost the same. The integrated routing algorithm improved the performance of routing planning for satellites and ground stations.
A Comparative Literature Review on RFID Security and Privacy

RFID provides the basis for the development of ubiquitous computing. This ever present computing environment creates new exploitable channels for adversaries. Therefore, numerous publications on RFID security appear every year, adding to the topic’s diversity. Nevertheless, there are only few state-of-the-art overviews that clarify common opinions on the topic. Hence, we examined the existing literature and present our observations on privacy and security in RFID.
Protein Interactions and Disease Phenotypes in the ABC Transporter Superfamily

ABC transporter proteins couple the energy of ATP binding and hydrolysis to substrate transport across a membrane. In humans, clinical studies have implicated mutations in 19 of the 48 known ABC transporters in diseases such as cystic fibrosis and adrenoleukodystrophy. Although divergent in sequence space, the overall topology of these proteins, consisting of two transmembrane domains and two ATP-binding cassettes, is likely to be conserved across diverse organisms. We examine known intra-transporter domain interfaces using crystallographic structures of isolated and complexed domains in ABC transporter proteins and find that the nucleotide binding domain interfaces are better conserved than interfaces at the transmembrane domains. We then apply this analysis to identify known disease-associated point and deletion mutants for which disruption of domain-domain interfaces might indicate the mechanism of disease. Finally, we suggest a possible interaction site based on conservation of sequence and disease-association of point mutants.
Incorporating Scenarios And Heuristics To Improve Flexibility In Real-Time Embedded Systems

Flexibility, the ability to adapt to change, is important for real-time systems. As in any type of system, changes arise from maintenance, enhancements and upgrades. These changes are only feasible if timing requirements imposed by the real-time nature of the system can still be met. A flexible design will allow tasks to be added without impinging on other tasks, causing them to miss deadlines. The design space for these systems consists of many configurations describing how tasks and messages are allocated to hardware and scheduled on a hardware platform. Heuristic search is a well recognised strategy for solving allocation and scheduling problems but most research is limited to finding any valid solution for a current set of requirements. The technique proposed here incorporates scenario based analysis into heuristic search strategies where the ability of a solution to meet a scenario is included as another heuristic for the changeability of a system. This allows future requirements to be taken into account when choosing a solution so that future changes can be accommodated with minimal alterations to the existing system.
Mobile Crowd Sensing and Computing

With the surging of smartphone sensing, wireless networking, and mobile social networking techniques, Mobile Crowd Sensing and Computing (MCSC) has become a promising paradigm for cross-space and large-scale sensing. MCSC extends the vision of participatory sensing by leveraging both participatory sensory data from mobile devices (offline) and user-contributed data from mobile social networking services (online). Further, it explores the complementary roles and presents the fusion/collaboration of machine and human intelligence in the crowd sensing and computing processes. This article characterizes the unique features and novel application areas of MCSC and proposes a reference framework for building human-in-the-loop MCSC systems. We further clarify the complementary nature of human and machine intelligence and envision the potential of deep-fused human--machine systems. We conclude by discussing the limitations, open issues, and research opportunities of MCSC.
THE ANALYSIS OF MULTISPECTRAL IMAGE DATA WITH SELF−ORGANIZING FEATURE MAPS

The analysis of multispectral sceneries is still a challenging task although many different algorithms for a mathematical analysis exist. Most classification algorithms work in a supervised mode only, i.e. they need to know the possible land usage classes prior to the calculation. In this step many simplifications and assumptions have to be done which directly influence the result. KOHONEN ́s self−organizing feature maps, which are based on a biological model, provide a powerful tool to describe the multispectral scenery under consideration with a limited number of reference vectors, the so−called codebook. The resulting code−book, generated with an unsupervised learning scheme, is a compressed description of the multi−dimensional data in terms of non−linear principal components which thus overcomes the problems of a linear principal component analysis. Using this code−book as a basis for a lateral fully interconnected network and introducing a non−linear activity flow between radial− basis functions located at the positions of the reference vectors results in an unsupervised clustering scheme. This method has been successfully adapted to multispectral sceneries recorded by casi (compact airborne spectrographic imager).
Two novel genes discovered in human mitochondrial DNA using PacBio full-length transcriptome data

In this study, we introduced a general framework to use PacBio full-length transcriptome sequencing for the investigation of the fundamental problems in mitochondrial biology, e.g. genome arrangement, heteroplasmy, RNA processing and the regulation of transcription or replication. As a result, we produced the first full-length human mitochondrial transcriptome from the MCF7 cell line based on the PacBio platform and characterized the human mitochondrial transcriptome with more comprehensive and accurate information. The most important finding is two novel genes hsa-MDL1 and hsa-MDL1AS, which are encoded by the mitochondrial D-loop regions. We propose hsa-MDL1 and hsa-MDL1AS, as the precursors of transcription initiation RNAs (tiRNAs), belong to a novel class of long non-coding RNAs (lnRNAs), which is named as long tiRNAs (ltiRNAs). Based on the mitochondrial RNA processing model, the primary tiRNAs, precursors and mature tiRNAs could be discovered to completely reveal tiRNAs from their origins to functions. The ltiRNA/tiRNA system and their regulation mechanisms could exist ubiquitously in eukaryotes and prokaryotes. These findings will enrich the basic concepts in the field of mitochondrial biology, lnRNA functions and regulation of gene expression.
Oligopeptidases of brush border membranes of rat small intestinal mucosal cells

1. The properties of peptidases located in the brush borders of rat small intestinal mucosal cells have been investigated using a new method for the assay of peptidase activity. In this method amino acids produced by hydrolysis of peptides are oxidized by ophidian L‐amino acid oxidase and the hydrogen peroxide produced during reoxidation of the reduced enzyme is estimated spectrophotometrically.
Towards a sociology for childhood : thinking from children's lives

Machine generated contents note: Chapter 1 Introduction 1 -- Chapter 2 Studying childhood 9 -- Chapter 3 Studying relational processes 27 -- Chapter 4 Relations with parents 42 -- Chapter 5 Childhood work 63 -- Chapter 6 The moral status of childhood 87 -- Chapter 7 Towards a child standpoint 112 -- Chapter 8 Comparing childhoods 140 -- Chapter 9 Generation and gender 159.