Miracle-dz/UniFAR-FTUs huggingface dataset:
Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

ABSTRACT The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4 g dry weight soil−1 day−1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the 13C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis (type II; Alphaproteobacteria), Methylomonas, and Methylovulum (both, type I; Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas. Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum (type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
BioViz: An Interactive Visualization Engine for the Design of Digital Microfluidic Biochips

In order to shorten the required time for the analysis of medical substances, Digital Microfluidic Biochips (DMFBs) have been suggested. They allow for handling small amounts of samples and reagents on a circuit board and, thus, automatically execute medical experiments that are usually conducted manually in laboratories. However, there are various challenges in the design of DMFBs. Issues such as routing and layouting are complex and currently being investigated by various researchers and engineers. Although first automatic solutions assist them, the obtained results are usually provided in a complex and \mbox{non-intuitive} fashion. This makes the utilization and evaluation of existing approaches for DMFB design a tedious task. In this paper, we present a solution for this problem by proposing a visualization scheme for DMFBs that explicitly addresses these problems. To this end, a grammar is proposed which allows the description of resulting designs and their properties. The contributions of this work allow for a design methodology which is easy to use and provides a hassle-free environment for the involved researchers and engineers.
Tracking Objects Robot for Healthcare Environments

There are many elder who are affected from Alzheimer's disease. Memory problems, confusion and forgetting objects, recent conversations or places are example of Alzheimer symptoms. Nursing home needs medical devices or robot to provide service for patients. Tracking Objects Robot traces and locates objects for the Alzheimer's patients to find objects in environment. This paper uses frequency and recency technique in order to locate the location of objects in dynamic environment by associating semantic knowledge of object with instance in ontology.
Social foraging and individual consistency in following behaviour: testing the information centre hypothesis in free-ranging vultures

Uncertainties regarding food location and quality are among the greatest challenges faced by foragers and communal roosting may facilitate success through social foraging. The information centre hypothesis (ICH) suggests that uninformed individuals at shared roosts benefit from following informed individuals to previously visited resources. We tested several key prerequisites of the ICH in a social obligate scavenger, the Eurasian griffon vulture (Gyps fulvus), by tracking movements and behaviour of sympatric individuals over extended periods and across relatively large spatial scales, thereby precluding alternative explanations such as local enhancement. In agreement with the ICH, we found that ‘informed’ individuals returning to previously visited carcasses were followed by ‘uninformed’ vultures that consequently got access to these resources. When a dyad (two individuals that depart from the same roost within 2 min of each other) included an informed individual, they spent a higher proportion of the flight time close to each other at a shorter distance between them than otherwise. Although all individuals occasionally profited from following others, they differed in their tendencies to be informed or uninformed. This study provides evidence for ‘following behaviour’ in natural conditions and demonstrates differential roles and information states among foragers within a population. Moreover, demonstrating the possible reliance of vultures on following behaviour emphasizes that individuals in declining populations may suffer from reduced foraging efficiency.
Nanotechnology for Early Cancer Detection

Vast numbers of studies and developments in the nanotechnology area have been conducted and many nanomaterials have been utilized to detect cancers at early stages. Nanomaterials have unique physical, optical and electrical properties that have proven to be very useful in sensing. Quantum dots, gold nanoparticles, magnetic nanoparticles, carbon nanotubes, gold nanowires and many other materials have been developed over the years, alongside the discovery of a wide range of biomarkers to lower the detection limit of cancer biomarkers. Proteins, antibody fragments, DNA fragments, and RNA fragments are the base of cancer biomarkers and have been used as targets in cancer detection and monitoring. It is highly anticipated that in the near future, we might be able to detect cancer at a very early stage, providing a much higher chance of treatment.
Advanced shaping techniques in advanced ceramics

Improvements in powder processing and shaping technologies are methods for increasing the reliability of advanced ceramics while lowering their cost. Considerable effort has been put into the development of low cost technologies for high volumes of complex-shaped components that will have the ability to form complex-shaped thin-walled parts. Near-net-shaping of advanced ceramics are of particular interest. The following shaping processes are currently in the commercialisation or development stages: pressure slip casting, freeze casting, powder injection moulding, tape casting/lamination, rapid prototyping, and colloidal processing of powders. Especially the techniques based on colloidal processing, such as gel casting, electrophoretic casting, hydrolysis assisted solidification, direct coagulation casting, etc. are of great interest due to their ability to reduce critical defect size that originate during manufacturing. Specific manufacturing features, advantages, disadvantages and the limitations of these novel processes are described in detail in this paper.
Remyelination strategies in multiple sclerosis: a critical reflection

Remyelination is the natural repair mechanism of demyelination and can be a highly efficient process in multiple sclerosis. However, in the majority of lesions, this regenerative approach is incomplete or fails. It is believed that remyelination protects against progressive axonal damage and thus long-term disability in patients with multiple sclerosis. For this reason, therapeutic promotion of remyelination represents an attractive option for preventing disease progression. In this editorial we casts a critical eye over the most frequently used experimental settings which aim to uncover potential remyelination promoting drugs. This article reflects upon the personal opinion of the author who currently used animal models allow to assess the potency of pharmacological interventions to accelerate, but not to induce myelin repair. Furthermore, it is discussed how remyelination and neuroprotection might well be two separate entities. Thus, induction of remyelination does not necessarily prevent disease progression in multiple sclerosis patients.
Biological hierarchies and the nature of extinction

Hierarchy theory recognises that ecological and evolutionary units occur in a nested and interconnected hierarchical system, with cascading effects occurring between hierarchical levels. Different biological disciplines have routinely come into conflict over the primacy of different forcing mechanisms behind evolutionary and ecological change. These disconnects arise partly from differences in perspective (with some researchers favouring ecological forcing mechanisms while others favour developmental/historical mechanisms), as well as differences in the temporal framework in which workers operate. In particular, long‐term palaeontological data often show that large‐scale (macro) patterns of evolution are predominantly dictated by shifts in the abiotic environment, while short‐term (micro) modern biological studies stress the importance of biotic interactions. We propose that thinking about ecological and evolutionary interactions in a hierarchical framework is a fruitful way to resolve these conflicts. Hierarchy theory suggests that changes occurring at lower hierarchical levels can have unexpected, complex effects at higher scales due to emergent interactions between simple systems. In this way, patterns occurring on short‐ and long‐term time scales are equally valid, as changes that are driven from lower levels will manifest in different forms at higher levels. We propose that the dual hierarchy framework fits well with our current understanding of evolutionary and ecological theory. Furthermore, we describe how this framework can be used to understand major extinction events better. Multi‐generational attritional loss of reproductive fitness (MALF) has recently been proposed as the primary mechanism behind extinction events, whereby extinction is explainable solely through processes that result in extirpation of populations through a shutdown of reproduction. While not necessarily explicit, the push to explain extinction through solely population‐level dynamics could be used to suggest that environmentally mediated patterns of extinction or slowed speciation across geological time are largely artefacts of poor preservation or a coarse temporal scale. We demonstrate how MALF fits into a hierarchical framework, showing that MALF can be a primary forcing mechanism at lower scales that still results in differential survivorship patterns at the species and clade level which vary depending upon the initial environmental forcing mechanism. Thus, even if MALF is the primary mechanism of extinction across all mass extinction events, the primary environmental cause of these events will still affect the system and result in differential responses. Therefore, patterns at both temporal scales are relevant.
Adherence to antiretroviral therapy, stigma and behavioral risk factors in HIV-infected adolescents in Asia

ABSTRACT We studied behavioral risks among HIV-infected and uninfected adolescents using an audio computer-assisted self-interview. A prospective cohort study was initiated between 2013 and 2014 in Malaysia, Thailand, and Vietnam. HIV-infected adolescents were matched to uninfected adolescents (4:1) by sex and age group (12–14 and 15–18 years). We enrolled 250 HIV-infected (48% male; median age 14.5 years; 93% perinatally infected) and 59 uninfected (51% male; median age 14.1 years) adolescents. At enrollment, HIV-infected adolescents were on antiretroviral therapy (ART) for a median (IQR) of 7.5 (4.7–10.2) years, and 14% had HIV-RNA >1000 copies/mL; 19% reported adherence <80%. Eighty-four (34%) HIV-infected and 26 (44%) uninfected adolescents reported having ever smoked cigarettes or drunk alcohol (p = 0.13); 10% of HIV-infected and 17% of uninfected adolescents reported having initiated sexual activity; 6 of the HIV-infected adolescents had HIV-RNA >1000 copies/mL. Risk behaviors were common among adolescents, with few differences between those with and without HIV.
Obesity Accelerates Alzheimer-Related Pathology in APOE4 but not APOE3 Mice

Abstract Alzheimer’s disease (AD) risk is modified by both genetic and environmental risk factors, which are believed to interact to cooperatively modify pathogenesis. Although numerous genetic and environmental risk factors for AD have been identified, relatively little is known about potential gene-environment interactions in regulating disease risk. The strongest genetic risk factor for late-onset AD is the ε4 allele of apolipoprotein E (APOE4). An important modifiable risk factor for AD is obesity, which has been shown to increase AD risk in humans and accelerate development of AD-related pathology in rodent models. Potential interactions between APOE4 and obesity are suggested by the literature but have not been thoroughly investigated. In the current study, we evaluated this relationship by studying the effects of diet-induced obesity (DIO) in the EFAD mouse model, which combines familial AD transgenes with human APOE3 or APOE4. Male E3FAD and E4FAD mice were maintained for 12 weeks on either a control diet or a Western diet high in saturated fat and sugars. We observed that metabolic outcomes of DIO were similar in E3FAD and E4FAD mice. Importantly, our data showed a significant interaction between diet and APOE genotype on AD-related outcomes in which Western diet was associated with robust increases in amyloid deposits, β-amyloid burden, and glial activation in E4FAD but not in E3FAD mice. These findings demonstrate an important gene-environment interaction in an AD mouse model that suggests that AD risk associated with obesity is strongly influenced by APOE genotype.
LncRNA MALAT1 induces colon cancer development by regulating miR‐129‐5p/HMGB1 axis

Recent studies have exhibited significant roles of lncRNAs in various tumors' development, including colon cancer. Our study focused on the biological roles of lncRNA MALAT1 in colon cancer. In our study, it was demonstrated that MALAT1 was upregulated in human colon cancer cell lines including Lovo, HCT116, SW480, and HT29 cells compared to the normal human intestinal epithelial HIEC cells. Moreover, we observed that miR‐129‐5p was downregulated in colon cancer cells with a significant increase of HMGB1 expression. Inhibition of MALAT1 can inhibit the proliferation of colon cancer SW480 and HCT116 cells and next, bioinformatics analysis was used to predict the target microRNA of MALAT1. miR‐129‐5p was identified and confirmed as a direct regulator of MALAT1 and it was shown that miR‐129‐5p mimics were able to restrain the progression of colon cancer cells. In addition, high motility group box protein 1 (HMGB1), was predicted as a mRNA target of miR‐129‐5p. Furthermore, we found that MALAT1 exerted its biological functions through regulating HMGB1 by sponging miR‐129‐5p in vitro. Silencing MALAT1 greatly inhibited HMGB1 expression which can be reversed by miR‐129‐5p inhibitors. It was indicated in our investigation that MALAT1 may serve as a competing endogenous lncRNA (ceRNA) to mediate HMGB1 by sponging miR‐129‐5p in colon cancer. Taken together, our results indicated that MALAT1/miR‐129‐5p/HMGB1 axis could be provided as an important prognostic biomarker in colon cancer development.
Minimizing Cost in IaaS Clouds Via Scheduled Instance Reservation

Regular diurnal patterns are often seen in the workloads of cloud-based online applications. This kind of non-stationary workloads changes the processing demands over time. To run application services with minimum costs, the number of cloud instances can be dynamically adjusted according to the workload variations. Recently, a new type of scheduled instances has emerged in the Infrastructure-as-a-Service market to facilitate such configurations. Scheduled instances can be reserved based on a recurring schedule and they offer price discounts. Meanwhile, cloud vendors require minimum scheduled durations to avoid the overhead of frequently launching and terminating cloud instances. Coupled with traditional on-demand and reserved instances, it becomes more complicated for users to find the optimal combination of these three pricing options to minimize their monetary costs. For the new scheduled instances, not only the number of instances but also their start and stop times have to be decided. In this paper, we develop a fast and effective strategy to solve this problem. Based on the hourly workload distributions, we first compute the optimal number of instances to acquire for each pricing option. Then, we design a scheduling algorithm to arrange the scheduled instances in compliance with the restriction of their scheduled durations. Using the workloads of the LOL online game and the Wikipedia Mobile service as two case studies, the efficacy of our strategy is demonstrated.
Characterisation of Hidden Periodicity in Large-Scale Cloud Datacentre Environments

Given the energy consuming characteristics of the Cloud datacentres, reducing the associated energy implications of the datacentres has become a natural demand for the providers to promote eco-friendly datacentre execution. The characteristics of Cloud-based workloads are still not perfectly clear and the extensive level of heterogeneity found among both the Cloud workloads and the server resources impose various levels of intrinsic and extrinsic complexities in accurately characterising and modelling the workload behaviours in close correlation with the user activities. To this end, this paper conducts extensive analysis on the workload and user behaviours in a large-scale datacentre environment, with the motivation of exhibiting the periodic characteristics of Cloud Computing. Both the workloads and the users at the datacentre are analysed by subjecting their behaviours to various periodical effects. Important contributions of this research work is the characterisation of the workload and user behaviours at the datacentre in terms of the job arrival frequency, recurring trend of job submissions, session usage and job diversity. The inferences presented in this paper are believed to provide sufficient knowledge to the Cloud providers to achieve optimised scaling and allocation of server resources for promoting sustainable and eco-friendly datacentre execution in accordance with the workload and user behavioural trends.
Distributed Universal Constructions: a Guided Tour

The notion of a universal construction is central in computing science: the wheel has not to be reinvented for each new problem. In the context of n-process asynchronous distributed systems, a universal construction is an algorithm that is able to build any object defined by a sequential specification despite the occurrence of up to (n − 1) process crash failures. The aim of this paper is to present a guided tour of such universal constructions. Its spirit is not to be a catalog of the numerous constructions proposed so far, but a (as simple as possible) presentation of the basic concepts and mechanisms that constitute the basis these constructions rest on.
Are Hospital Workers Healthy?: A Study of Cardiometabolic, Behavioral, and Psychosocial Factors Associated With Obesity Among Hospital Workers

Objective: This study evaluated the cardiometabolic, behavioral, and psychosocial factors associated with weight status among hospital employees. Methods: A total of n = 924 employees across the six hospitals in Texas participated in this cross-sectional study, 2012 to 2013. Association between weight status and waist circumference, blood pressure, biomarkers, diet, physical activity, sedentary behaviors, and psychosocial factors was assessed. Results: About 78.1% of employees were overweight/obese. Obese participants (body mass index [BMI] ≥30.0 kg/m2) had higher consumption of potatoes, fats, sugary beverages, and spent more time watching television, playing computer games, and sitting than those having normal weight. Being obese was positively associated with blood pressure, blood glucose, low-density lipoprotein, and negatively associated with high-density lipoprotein. Finally, 78.8% of workers were dissatisfied with their worksite wellness with dissatisfaction being higher among obese employees. Being overweight (BMI 25.0 to 29.9 kg/m2) was positively associated with blood pressure, but not other variables. Conclusion: Understanding the risk profile of hospital workers is critical to developing effective interventions.
Discrimination of nitrogen fertilizer levels of tea plant (Camellia sinensis) based on hyperspectral imaging.

BACKGROUND Nitrogen (N) fertilizer plays an important role in tea plantation management, with significant impacts on the photosynthetic capacity, productivity and nutrition status of tea plants. The present study aimed to establish a method for the discrimination of N fertilizer levels using hyperspectral imaging technique. RESULTS Spectral data were extracted from the region of interest, followed by the first derivative to reduce background noise. Five optimal wavelengths were selected by principal component analysis. Texture features were extracted from the images at optimal wavelengths by gray-level gradient co-occurrence matrix. Support vector machine (SVM) and extreme learning machine were used to build classification models based on spectral data, optimal wavelengths, texture features and data fusion, respectively. The SVM model using fused data gave the best performance with highest correct classification rate of 100% for prediction set. CONCLUSION The overall results indicated that visible and near-infrared hyperspectral imaging combined with SVM were effective in discriminating N fertilizer levels of tea plants. © 2018 Society of Chemical Industry.
What We Know About Tuberculosis Transmission: An Overview

Abstract Tuberculosis remains a global health problem with an enormous burden of disease, estimated at 10.4 million new cases in 2015. To stop the tuberculosis epidemic, it is critical that we interrupt tuberculosis transmission. Further, the interventions required to interrupt tuberculosis transmission must be targeted to high-risk groups and settings. A simple cascade for tuberculosis transmission has been proposed in which (1) a source case of tuberculosis (2) generates infectious particles (3) that survive in the air and (4) are inhaled by a susceptible individual (5) who may become infected and (6) then has the potential to develop tuberculosis. Interventions that target these events will interrupt tuberculosis transmission and accelerate the decline in tuberculosis incidence and mortality. The purpose of this article is to provide a high-level overview of what is known about tuberculosis transmission, using the tuberculosis transmission cascade as a framework, and to set the scene for the articles in this series, which address specific aspects of tuberculosis transmission.
APPLICATION OF NATURAL ZEOLITES AS SORBENTS IN THE CLEAN-UP OF AQUEOUS STREAMS

Natural zeolites can be found in volcanogenic sediments as large, widespread, mineable, near-monomineralic deposits in tuffaceous rocks. Apart of their applications as building stone, as lightweight aggregate and pozzolans in cements and concretes, as filler in paper etc., their properties as low-cost natural materials mimicking those of many synthetic counterparts are exploited in environmental protection and cleanup. Natural zeolites found important uses in pollution control, the handling and storage of nuclear wastes, agriculture, and biotechnology. Considerable effort has made to find the most efficient ways to apply natural zeolites as an active counterpart in sorption, cation-exchange, dehydration–rehydration, and catalytic processes. The present paper analyses some aspects of the present status of research on application of natural zeolites in environmental protection. The overview provides a short appraisal of the recent discovery concerning the natural zeolites and their modified forms in the separation, binding and chemical stabilization of some inorganic and organic in aqueous systems.