Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated DNA extraction for real-time PCR.

We evaluated the MagNA Pure LC System (Roche Applied Science) for automated DNA extraction for use in mutation detection and allele quantification. The system uses magnetic silica beads that bind DNA to a silica surface and transfer DNA through various steps of the extraction process. This system can be linked to LightCycler assays for further automation. The LightCycler is an enclosed thermocycler with continuous monitoring for PCR quantification and allele discrimination (1)(2)(3). Combined MagNA Pure/LightCycler automation of sample preparation, amplification, and detection has the potential to reduce human error in sample tracking and to standardize DNA extraction and inoculation into the PCR mixture. The MagNA Pure/LightCycler system has been evaluated for infectious disease applications, detecting PCR product by crossing point (4)(5). In this study we compared the MagNA Pure LC DNA extraction with the Qiagen 9604 BioRobot (Qiagen) for real-time mutation detection and allele quantification. We evaluated 280 samples with the MagNA Pure System and Qiagen 9604 BioRobot under an Internal Review Board-approved protocol for instrument validation. Genomic DNA was extracted from 200 μL of EDTA-anticoagulated whole blood by use of the MagNA Pure LC DNA Isolation Kit I (Roche Diagnostics), with its high-performance DNA protocol, and by the QIAamp 9604 DNA Blood BioRobot Kit (Qiagen) according to manufacturer’s instructions. Both methods initially use red blood cell lysis and a proteinase …
Mechanisms of CaMKII Activation in the Heart

Calcium/calmodulin (Ca2+/CaM) dependent protein kinase II (CaMKII) has emerged as a key nodal protein in the regulation of cardiac physiology and pathology. Due to the particularly elegant relationship between the structure and function of the kinase, CaMKII is able to translate a diverse set of signaling events into downstream physiological effects. While CaMKII is typically autoinhibited at basal conditions, prolonged rapid Ca2+ cycling can activate the kinase and allow post-translational modifications that depend critically on the biochemical environment of the heart. These modifications result in sustained, autonomous CaMKII activation and have been associated with pathological cardiac signaling. Indeed, improved understanding of CaMKII activation mechanisms could potentially lead to new clinical therapies for the treatment or prevention of cardiovascular disease. Here we review the known mechanisms of CaMKII activation and discuss some of the pathological signaling pathways in which they play a role.
Endocrine and neurophysiological examination of sleep disorders in Williams syndrome

Background: A high rate of sleep disturbances have been reported in individuals with Williams syndrome (WS), but the underlying aetiology has yet to be identified. Melatonin and cortisol levels are known to affect and regulate sleep/wake patterns. We investigated the changing levels of these hormones in order to explore any relationship with sleep disturbances in children with WS. Methods: Twenty seven children with WS and 27 typically developing (TD) children were recruited. Sleep was monitored using actigraphy and pulse oximetry. Parents completed Children’s Sleep Habit Questionnaire (CSHQ). Saliva and first void morning urine samples were collected from the children. Saliva was collected at three time points: 4-6pm, before bedtime and first thing after awakening. Levels of salivary melatonin and cortisol were analysed by enzyme linked immunoassays. For determination of melatonin, cortisol and their metabolites in urine samples, specific Ultra-High Performance Liquid Chromatography-Tandem Mass Spectrometry (UHPLC-MS/MS) method was developed. Results: CSHQ and actigraphy indicated that children with WS were significantly affected by several types of sleep disturbances, including: abnormally high sleep latency and excessive night waking. Children in WS group had shallower falls in salivary cortisol levels and less pronounced rises in salivary melatonin at bedtime compared to TD controls (p < 0.01 and p = 0.04 respectively). Furthermore, it was found that children with WS also had significantly higher levels of bedtime cortisol compared to TD controls (p = 0.03). Using UHPLC-MS/MS analysis it was shown that children with WS secrete less melatonin during the night compared to healthy controls (p < 0.01). Also, levels of cortisone, a metabolite of cortisol were significantly higher in the WS group (p = 0.05). Conclusions: We found that children with WS had significant sleep disturbances which may be associated with their increased bedtime cortisol and lower evening melatonin. Both hormones play a significant role in the circadian rhythm and sleep/wake cycle, therefore it was necessary to look closely at these endocrine markers in individuals suffering from sleep disorders. Sleep problems in children with WS may adversely affect daytime activity and the quality of life, as well as social, emotional, health and economic functioning of the entire family. Hence, finding their cause is of great importance for affected children and their families.
Expression, Purification, and Structural Characterization of CfrA, a Putative Iron Transporter from Campylobacter jejuni

ABSTRACT The gene for the Campylobacter ferric receptor (CfrA), a putative iron-siderophore transporter in the enteric food-borne pathogen Campylobacter jejuni, was cloned, and the membrane protein was expressed in Escherichia coli, affinity purified, and then reconstituted into model lipid membranes. Fourier transform infrared spectra recorded from the membrane-reconstituted CfrA are similar to spectra that have been recorded from other iron-siderophore transporters and are highly characteristic of a β-sheet protein (∼44% β-sheet and ∼10% α-helix). CfrA undergoes relatively extensive peptide hydrogen-deuterium exchange upon exposure to 2H2O and yet is resistant to thermal denaturation at temperatures up to 95°C. The secondary structure, relatively high aqueous solvent exposure, and high thermal stability are all consistent with a transmembrane β-barrel structure containing a plug domain. Sequence alignments indicate that CfrA contains many of the structural motifs conserved in other iron-siderophore transporters, including the Ton box, PGV, IRG, RP, and LIDG motifs of the plug domain. Surprisingly, a homology model reveals that regions of CfrA that are expected to play a role in enterobactin binding exhibit sequences that differ substantially from the sequences of the corresponding regions that play an essential role in binding/transport by the E. coli enterobactin transporter, FepA. The sequence variations suggest that there are differences in the mechanisms used by CfrA and FepA to interact with bacterial siderophores. It may be possible to exploit these structural differences to develop CfrA-specific therapeutics.
Obesity and U.S. military spouses: An examination of risk perception and health behavior

Obesity in the U.S. has become a national epidemic. The Military, in particular Military spouses are not exempt from the challenging issue of obesity. Understanding risk perception and health behavior is key to reducing the obesity epidemic, however insufficient research has been conducted among U.S. Military spouses to understand their perceived risk and health behaviors. This quantitative study was conducted among 291 Military spouses using the Extended Parallel Process Model and Social Cognitive Theory as the conceptual frameworks. The results indicated that perceived susceptibility of obesity and obesity related illness among overweight and obese Military spouses while reinforcing both response and self-efficacy is the focal area for communication. Key barriers to weight loss and health goals were identified and the setting of health goals is identified as important. The researcher provides a digital intervention recommendation to address the findings of this study.
Real-Time Detection of Eyes and FAces

Perceptual user interfaces will require the detection, tracking, and recognition of faces and other body and facial features. This paper introduces a robust, accurate, and low cost real-time solution for the eye and face detection problem. The method uses two infra-red illumination sources to generate bright and dark pupil images, which are combined to robustly detect pupils. Once the pupils are detected, the inter-ocular distance is used to determine the size and position of the bounding box around the face. The position of other facial features such as eye brows, nose, and mouth can be estimated once the face is detected. A real-time implementation of the system, which process 30 frames per second using interlaced images of resolution 640 480 pixels, is also presented.
Cognitive and gait decrements among non-demented older adults with Type 2 diabetes or hypertension: a systematic review

Abstract Objective: Older adults with Type 2 diabetes (DM2) and hypertension (HTN) often experience cognitive weaknesses. Growing evidence suggests that such weaknesses place patients at risk for gait disturbance and falls. The current systematic review evaluated (a) the impact of DM2 and HTN on cognition and gait and (b) the association between cognition and gait in the context of DM2 and HTN. Methods: PubMed was searched to identify studies published in English before 15 April 2017 that evaluated both cognition and gait among non-demented older adults either as a function of DM2 or HTN status or as a function of continuous variables that indicate disease severity and/or management (e.g. blood pressure, HbA1C). Risk of bias was assessed by examining the method of verifying HTN/DM2 and excluding dementia as well as included covariates. Results: In the majority of studies reviewed (n = 17), both DM2 and HTN status were associated with poorer cognitive and/or gait functioning (8 out of 10 studies). In addition, in 10 out of 11 studies cognition was reliably associated with gait. For continuous variables, higher systolic blood pressure (measured with ambulatory methods) was consistently related to poorer cognition and slower gait, but other continuous variables (e.g. HbA1C) were studied inconsistently with inconclusive results. Conclusions: Cognitive and gait decrements are not only common in the context of HTN and DM2, but also are related to each other. This suggests that clinical neuropsychologists should address cognitive contributions to gait disturbance and falls in their clinical work and research with these patient populations.
NOTE DE SYNTHÈSE - Interventions pédagogiques efficaces et réussite scolaire des élèves provenant de milieux défavorisés

Plusieurs etudes revelent que les eleves issus de milieux socio-economiquement faibles eprouvent plus de difficulte a l’ecole et accusent un retard scolaire plus marque que ceux provenant de milieux mieux nantis (Coleman, 1966 ; Forquin, 1982 ; Sevigny, 2003). Ces eleves risquent par consequent d’abandonner davantage l’ecole avant l’obtention de leur diplome d’etudes secondaires. De nombreuses recherches confirment en effet que ces eleves maintiennent un taux d’obtention de diplomes inferieur (Sevigny, 2003). C’est pourquoi cette clientele a fait l’objet d’une attention particuliere afin de contrer le decrochage scolaire qui la menace.
DXRAM: A Persistent In-Memory Storage for Billions of Small Objects

Large-scale interactive applications and real time data-processing are facing problems with traditional disk-based storage solutions. Because of the often irregular access patterns they must keep almost all data in RAM caches, which need to be manually synchronized with secondary storage and need a lot of time to be re-loaded in case of power outages. In this paper we propose a novel key-value storage keeping all data always in RAM by aggregating resources of potentially many nodes in a data center. We aim at supporting management of billions of small data objects (16-64 byte) like for example needed for storing graphs. A scalable low-overhead meta-data management is realized using a novel range-based ID approach combined with a super-overlay network. Furthermore, we provide persistence by a novel SSD-aware logging approach allowing to recover failed nodes very fast.
SDN and Optical Flow Steering for Network Function Virtualization

Introduction Middlebox traffic steering, the capability of routing traffic through different sequences of middleboxes, has been a popular application in software-define networks (SDN) [5]. In this work, we focus on network function virtualization (NFV) [2][3], especially on core virtualized network functions that process high-volume traffic, such as session border controllers (SBCs) and serving/gateway GPRS support node (SGSN/GGSN). While these core network functions (NFs) run in a virtualized environment in a data center/cloud instead of dedicated hardware, their locations are more dynamic and thus there is a strong need to steer traffic through them dynamically. Similar to [5], traffic will need to be routed across various intermediate NFs before reaching its destination, e.g. at the customer PE. This process is called traffic steering for NFV. Different from traditional middleboxes, the core NFs handle much higher volumes of traffic, and usually don't have the same fine-grained traffic steering requirements that normal middleboxes do. Thus, we argue that existing Layer2/Layer3 packet based traffic steering will have scalability issue for large traffic volume, and may also be associated with high energy cost.
Density Based Clustering algorithm for Vehicular Ad-Hoc Networks

In this paper we present a new multilevel clustering algorithm for Vehicular Ad-Hoc Networks (VANET), which we call the Density Based Clustering (DBC). Our solution is focused on the formation of stable, long living clusters. Cluster formation is based on a complex clustering metric which takes into account the density of the connection graph, the link quality and the road traffic conditions. The tests performed in the simulation environment composed of VanetMobiSim and Java in Simulation Time (JiST)/SWANS have shown that DBC performs better than the popular approach (the Lowest Id algorithm) – the clusters stability has been significantly increased.
CeBr$_{3}$ Scintillator Development for Possible Use in Space Missions

CeBr3 crystals have been studied to assess their utility as potential gamma ray spectrometers for future ESA planetary missions. Pulse height spectra, scintillation time profiles, X-ray excited emission spectra, and photoluminescence spectra have been recorded as a function of temperature between 78 and 600 K. In addition, the influence of exposing CeBr3 to various doses of gamma rays from a strong 60Co source on its scintillation performance has been investigated.
Endangered species and land use conflicts: a case study of the Virgin Islands boa (Epicrates granti).

—In situations where land is limited, such as on islands, wildlife conservation often takes a back seat to economic development. This is particularly the case in the Caribbean, where critical coastal resources are frequently converted into upscale developments. The United States Virgin Islands (USVI) has experienced intense and unmitigated development pressures in recent decades, presumably resulting in the loss of habitat for the endangered Virgin Islands Boa (Epicrates granti). This species is cryptic and difficult to locate, and thus it has been difficult to determine their full distribution and habitat needs. With ongoing development, there was an urgent need to identify locations where this species was likely to occur and to develop habitat conservation measures appropriate for developers. Using geographical information systems and opportunistic observations collected over 25 years, we created a habitat suitability model for E. granti that allowed for the prediction of presence in any particular area. We conducted microhabitat assessments to better understand habitat associations at a fine scale. Using this information, we developed a habitat delineation protocol for identifying appropriate habitat within a particular location. The habitat suitability model is being used by planning agencies to determine whether mitigation might be required for a given development project, and the habitat delineation protocols are being used by developers to identify areas within a proposed site that require additional protective measures. While the process is still in its infancy and not yet widely applied, there has been some success in scaling back development projects.
Detection of the time of failure of a hybrid system by particle filtering in a log-likelihood ratio approach

A particle filtering method is implemented within a log-likelihood ratio approach here specifically tailored to handle hybrid dynamic systems, i.e, systems characterized by transitions among discrete modes of operation and failure, each one giving rise to a specific continuous dynamics of evolution. An application to a case study of literature proves the capabilities of the newly devised algorithm.
Augmented online point to point trajectory planning, a new approach in catching a moving object by a manipulator

In a structured dynamic environment, due to the known variation of the environment, robot trajectory planning can be performed robots motion starts. Within an unstructured dynamic environment, environment variations are permanent, so that the surroundings information must be acquired in an online action. Likewise the data acquisition, robot trajectory planning must be executed online. In this paper a method for online trajectory planning based on adaptive prediction planning and execution (APPE) is proposed for robotic manipulators considering velocity and torque constraints. A vision-based data acquisition system is used to acquire object positions and velocities. To describe the end-effector trajectories in joint and Cartesian space a set of time polynomial function are used. Initially a primary trajectory is planned and it will be updated in definite time periods. This action will be frequently repeated until catching is occurred. Proposed method has been tested on an experimental setup and the experimental results are presented.
Factors Influencing Access to Urban General Practices and Primary Health Care by Aboriginal Australians—A Qualitative Study

This paper aims to explore the barriers and facilitators for Aboriginal and Torres Strait Islander Australians with chronic disease to access urban, mainstream general practice and primary health care. Six focus groups and five interviews were conducted with 40 participants that included Aboriginal people with diabetes, health service providers and policy makers. Using diabetes as the exemplar, participants were asked to relate their own experiences of diabetes management. Data was thematically analysed. Two overarching themes and seven other factors were identified as influencing Aboriginal people's access to health services. Cultural competence can be achieved within a health service when all nine factors are addressed in the context of the local community. Closing the health gap between Aboriginal and non-Aboriginal Australians requires a particular sensitivity and understanding of the facilitators and barriers for urban Aboriginal people accessing mainstream health services.
CRISPR-induced null alleles show that Frost protects Drosophila melanogaster reproduction after cold exposure

ABSTRACT The ability to survive and reproduce after cold exposure is important in all kingdoms of life. However, even in a sophisticated genetic model system like Drosophila melanogaster, few genes have been identified as functioning in cold tolerance. The accumulation of the Frost (Fst) gene transcript increases after cold exposure, making it a good candidate for a gene that has a role in cold tolerance. Despite extensive RNAi knockdown analysis, no role in cold tolerance has been assigned to Fst. CRISPR is an effective technique for completely knocking down genes, and is less likely to produce off-target effects than GAL4-UAS RNAi systems. We have used CRISPR-mediated homologous recombination to generate Fst-null alleles, and these Fst alleles uncovered a requirement for FST protein in maintaining female fecundity following cold exposure. However, FST does not have a direct role in survival following cold exposure. FST mRNA accumulates in the Malpighian tubules, and the FST protein is a highly disordered protein with a putative signal peptide for export from the cell. Future work is needed to determine whether FST is exported from the Malpighian tubules and directly interacts with female reproductive tissues post-cold exposure, or whether it is required for other repair/recovery functions that indirectly alter energy allocation to reproduction. Summary: The Drosophila gene Frost is expressed in response to cold exposure. Genome editing shows that its function is to protect post-cold reproduction rather than to improve tolerance during cold exposure.
Finding Fires with Twitter

This paper presents a notification system to identify in near-real-time Tweets describing fire events in Australia. The system identifies fire related ‘alert words’ published on Twitter which are further processed by a classifier to determine if they correspond to an actual fire event. We describe how the classifier has been established and report preliminary results. The original notification system did not include a classifier and could not discriminate between messages unrelated to ‘real’ fire events. In the first three months of operation, the system generated 42 ‘fire’ email notifications of which 20 related to actual fires and 12 of those contained Tweets that may have been of interest to fire fighting agencies. If the classifier had been used, 21 emails would have been issued: an improvement in accuracy from 48% to 78%. However, the recall score reduced from 1 to 0.8 which is not desirable for this particular task. We propose extensions to address this short coming.
Using support vector machine (SVM) for agriculture land use mapping with SAR data: Preliminary results from western Canada

Multi-temporal C-band RADARSAT-2 fine quad-pol data (5 scenes) and X-band TerraSAR-X stripmap data (8 scenes) were collected during the 2009 growing season from late May to late end of August. The study site was located in Carman, Manitoba in western Canada. A crop survey was conducted for 441 fields covering a wide range of annual and perennial crops (15 classes) including beans, canola, corn, fallow, field peas, flaxseed, hay/pasture, potato, soybean, sunflower, barley, oat, spring wheat and winter wheat. A supervised support vector machine method was used for image classification. Results revealed that the use of single-date single-frequency SAR data can only achieve marginal success in separating crop classes over regions with complex crop mixtures (15 classes). Better classification accuracies usually occur at the end of the growing season. The C-band SAR image data are generally superior to the X-band dataset. The overall classification accuracies using multi-temporal, single-frequency SAR data are within 50% for mid-season and 75% at the end of the growing season. The integration of RADARSAT-2 and TerraSAR-X data produced more favorable classification results.