Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases β and λ

A novel class of non-nucleoside triphosphate analogues, bearing hydrophobic groups sterically similar to nucleosides linked to the α-phosphate but lacking the chemical functional groups of nucleic acids, were tested against six different DNA polymerases (polymerases). Human polymerases α, β and λ, and Saccharomyces cerevisiae polymerase IV, were inhibited with different potencies by these analogues. On the contrary, Escherichia coli polymerase I and HIV-1 reverse transcriptase were not. Polymerase β incorporated these derivatives in a strictly Mn++-dependent manner. On the other hand, polymerase λ could incorporate some alkyltriphosphate derivatives with both Mg++ and Mn++, but only opposite to an abasic site on the template strand. The active site mutant polymerase λ Y505A showed an increased ability to incorporate the analogues. These results show for the first time that neither the base nor the sugar moieties of nucleotides are required for incorporation by family X DNA polymerases.
Single Ion Transport with a Single-Layer Graphene Nanopore

—Graphene material has found tremendous applications in water desalination, DNA sequencing and energy storage. Multiple nanopores are etched to create opening for water desalination and energy storage applications. The nanopores created are of the order of 3-5 nm allowing multiple ions to transport through the pore. In this paper, we present for the ﬁrst time, molecular dynamics study of single ion transport, where only one ion passes through the graphene nanopore. The diameter of the graphene nanopore is of the same order as the hydration layers formed around each ion. Analogous to single electron transport resulting from ionic transport is observed for the ﬁrst time. The current-voltage characteristics of such a device are similar to single electron transport in quantum dots. The current is blocked until a critical voltage, as the ions are trapped inside a hydration shell. The trapped ions have a high energy barrier compared to the applied input electrical voltage, preventing the ion to break free from the hydration shell. This region is called “Coulomb blockade region”. In this region, we observe zero transport of ions inside the nanopore. However, when the electrical voltage is beyond the critical voltage, the ion has sufﬁcient energy to break free from the energy barrier created by the hydration shell to enter into the pore. Thus, the input voltage can control the transport of the ion inside the nanopore. The device therefore acts as a binary storage unit, storing 0 when no ion passes through the pore and storing 1 when a single ion passes through the pore. We therefore postulate that the device can be used for ﬂuidic computing applications in chemistry and biology, mimicking a computer. Furthermore, the trapped ion stores a ﬁnite charge in the Coulomb blockade region; hence the device also acts a super capacitor.
Power Control in Non-uniform Wireless Sensor Networks Based on the Parallel Ant Colony Algorithm

Energy consumption is the most important problem in wireless sensor networks. Considering the non-uniform network, a new mechanism of power control based on the PACA (parallel ant colony algorithm) is presented for the energy consumption optimization. The mechanism can search the solution space and optimize the route of data transmission to homogenize the energy consumption of the nodes. In the simulation, three different network nodes distribution are adopted and the new mechanism is compared with the fixed power routing method. The results show that the new mechanism can homogenize the nodes' energy consumption and extend the whole network's life effectively.
Fault ride-through of doubly-fed induction generators

The aim of this paper is to explore the various dynamic controllers to enhance the fault ride-through (FRT) of doubly-fed induction generators (DFIGs). A wind farm of total capacity 9 MW is considered for the study. The flexible AC transmission system (FACTS) controllers like Static Synchronous Compensators (STATCOM) and Unified Power Flow Controllers (UPFC) are modelled and analysed to study their effect on the voltage at the point of common coupling (PCC) and FRT capability. This is then compared with the FRT capability of existing crow bar controller added to the converters of DFIG. The simulation is carried out using MATLAB/Simulink. A new Simulink model is developed for DFIG, to make it versatile for any FRT control strategy. The results presented show the effectiveness of the model.
Validating Game-based Measures of Implicit Science Learning

Building on prior work visualizing player behavior using interaction networks [1], we examined whether measures of implicit science learning collected during gameplay were significantly related to changes in external pre-post assessments of the same constructs. As part of a national implementation study, we collected data from 329 high school students playing an optics puzzle game, Quantum Spectre , and modeled their gameplay as an interaction network, examining errors hypothesized to be related to a lack of implicit understanding of the science concepts embedded in the game. Hierarchical linear modeling (HLM) showed a negative relationship between the science errors identified during gameplay and implicit science learning. These results suggest Quantum Spectre gameplay behaviors are valid assessments of implicit science learning. Implications for how gameplay data might inform classroom teaching in-game scaffolding is discussed.
Cognitive behaviour therapy for schizophrenia.

BACKGROUND Cognitive behavioural therapy (CBT) is now a recommended treatment for people with schizophrenia. This approach helps to link the person's feelings and patterns of thinking which underpin distress. OBJECTIVES To review the effects of CBT for people with schizophrenia when compared to standard care, specific medication, other therapies and no intervention. SEARCH STRATEGY This 2004 update built on past work by searching the Cochrane Schizophrenia Groups' Register of Trials (January 2004). We inspected all references of the selected articles for further relevant trials. SELECTION CRITERIA All relevant clinical randomised trials of cognitive behaviour therapy for people with schizophrenia-like illnesses. DATA COLLECTION AND ANALYSIS Studies were reliably selected and assessed for methodological quality. Two reviewers, working independently, extracted data. We analysed dichotomous data on an intention-to-treat basis and continuous data with 65% completion rate are presented. Where possible, for dichotomous outcomes, we estimated a relative risk (RR) with the 95% confidence interval (CI) along with the number needed to treat/harm (NNT/H). MAIN RESULTS 30 papers described 19 trials. CBT plus standard care did not reduce relapse and readmission compared with standard care (long term 4 RCTs, n=357, RR 0.8 CI 0.5 to 1.5), but did decrease the risk of staying in hospital (1 RCT, n=62, RR 0.5 CI 0.3 to 0.9, NNT 4 CI 3 to 15). CBT helped mental state over the medium term (2 RCTs, n=123, RR No meaningful improvement 0.7 CI 0.6 to 0.9, NNT 4 CI 3 to 9) but after one year the difference was gone (3 RCTs, n=211, RR 0.95 CI 0.6 to 1.5). Continuous measures of mental state (BDI, BPRS, CPRS, MADRS, PAS) do not demonstrate a consistent effect. When compared with supportive psychotherapy, CBT had no effect on relapse (1 RCT, n=59, RR medium term 0.6 CI 0.2 to 2; 2 RCTs, n=83, RR long term 1.1 CI 0.5 to 2.4). This also applies to the outcome of 'No clinically meaningful improvements in mental state' over the same time periods (1 RCT, n=59, RR medium term 0.8 CI 0.6 to 1.1; 2 RCT, n=100, RR long term 0.9 CI 0.8 to 1.1). When CBT was combined with a psychoeducational approach there was no significant reduction of readmission rates relative to standard care alone (1 RCT, n=91, RR 0.9 CI 0.6 to 1.4). REVIEWERS' CONCLUSIONS CBT is a promising but under evaluated intervention. Currently, trial-based data supporting the wide use of CBT for people with schizophrenia or other psychotic illnesses are far from conclusive. More trials are justified, especially in comparison with a lower grade supportive approach. These trials should be designed to be both clinically meaningful and widely applicable.
Two Models for Inferring Network Structure from Cascades

In many real-world scenarios, the underlying network over which the diffusions and propagations spread is unobserved, i.e. the edges of the network are invisible. In such cases, we can only infer the network structure from underlying observations. The goal of this paper is to find a model that generates realistic cascades with observed data, so that it can help us with link prediction and outlier detection. For this purpose, we investigate two cascade models. The first model is a naive two-class cascades that includes one class of positive (infected) nodes and one class of negative (uninfected) nodes. In this model, we use the sparse logistic regression method to infer network edges. In the second model, we discard all negative training nodes and treat the whole network as a single class. In this model, we use the one-class Support Vector Machines to predict underlying edges. Experiments show that even if we discarded all negative training instances, we can still infer network edges accurately.
Reflections on How a University Binge Drinking Prevention Initiative Supports Alcohol Screening, Brief Intervention, and Referral for Student Alcohol Use

What’s Your Cap: Know When to Put a Lid on Drinking (WYC) is a student-led and research-based binge-drinking prevention campaign at the University of Saskatchewan, Canada. It was formed to encourage a culture of alcohol moderation on the university campus through peer-to-peer engagement that emphasizes promotional items and activities of interest to students. Since its development in 2011, WYC has been guided by a logic model that promotes: 1) perceived and actual student drinking norms on campus; 2) benefits of a student-led initiative; and 3) merits of working with community partners. With the release of a clinical guide in Canada for alcohol screening, brief intervention, and referral (SBIR) in 2013, WYC was prompted to consider whether it is a form of population-based SBIR. SBIR is commonly undertaken in the substance use field by health care practitioners, and this paper shares the potential for a student-based SBIR modification on a university campus.
The MGED Ontology: a resource for semantics-based description of microarray experiments

MOTIVATION The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. RESULTS Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. AVAILABILITY The MGED Ontology version.1. 2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge. net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT Stoeckrt@pcbi.upenn. edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Factors that influence clinicians' assessment and management of family violence.

OBJECTIVES High rates of family violence and low rates of detection, report, and therapeutic intervention by health professionals are well documented. This study was undertaken to determine what factors influence clinicians' decision making about identifying abuse and intervening with victims. METHODS Survey data about clinicians' experiences with and attitudes toward family violence were gathered by mailed questionnaire from a random sample of practicing clinicians in six disciplines (n = 1521). RESULTS Data showed similarities within and wide differences among three groups of subjects: dentists/dental hygienists, nurses/physicians, and psychologists/social workers. Overall, a third of subjects reported having received no educational content on child, spouse, or elder abuse in their professional training programs. Subjects with education on the topic more commonly suspected abuse in their patients than those without; among all subjects, spouse abuse was suspected more often than child abuse while elder abuse was suspected infrequently. Significant numbers of subjects did not view themselves as responsible for dealing with problems of family violence. Subjects indicated low confidence in and low compliance with mandatory reporting laws. CONCLUSIONS There is a need for educators to expand curricula on family violence and for legislators to reexamine mandatory reporting laws.
Does heterochromatin protein 1 always follow code?

Heterochromatin protein 1 (HP1) is a conserved chromosomal protein that participates in chromatin packaging and gene silencing. A loss of HP1 leads to lethality in Drosophila and correlates with metastasis in human breast cancer cells. On Drosophila polytene chromosomes HP1 is localized to centric regions, telomeric regions, in a banded pattern along the fourth chromosome, and at many sites scattered throughout the euchromatic arms. Recently, one mechanism of HP1 chromosome association was revealed; the amino-terminal chromo domain of HP1 interacts with methylated lysine nine of histone H3, consistent with the histone code hypothesis. Compelling data support this mechanism of HP1 association at centric regions. Is this the only mechanism by which HP1 associates with chromosomes? Interest is now shifting toward the role of HP1 within euchromatic domains. Accumulating evidence in Drosophila and mammals suggests that HP1 associates with chromosomes through interactions with nonhistone chromosomal proteins at locations other than centric heterochromatin. Does HP1 play a similar role in chromatin packaging and gene regulation at these sites as it does in centric heterochromatin? Does HP1 associate with the same proteins at these sites as it does in centric heterochromatin? A first step toward answering these questions is the identification of sequences associated with HP1 within euchromatic domains. Such sequences are likely to include HP1 “target genes” whose discovery will aid in our understanding of HP1 lethality in Drosophila and metastasis of breast cancer cells.
Evaluating the Comprehension of Euler Diagrams

We describe an empirical investigation into layout criteria that can help with the comprehension of Euler diagrams. Euler diagrams are used to represent set inclusion in applications such as teaching set theory, database querying, software engineering, filing system organisation and bio-informatics. Research in automatically laying out Euler diagrams for use with these applications is at an early stage, and our work attempts to aid this research by informing layout designers about the importance of various Euler diagram aesthetic criteria. The three criteria under investigation were: contour jaggedness, zone area inequality and edge closeness. Subjects were asked to interpret diagrams with different combinations of levels for each of the criteria. Results for this investigation indicate that, within the parameters of the study, all three criteria are important for understanding Euler diagrams and we have a preliminary indication of the ordering of their importance.
Benefit of Conjugate Pneumococcal Vaccination in Preventing Influenza Hospitalization in Children: A Case-control Study

Background: The pneumococcal conjugate vaccine (PCV) might prevent hospitalizations in children because of the role of Streptococcus pneumoniae in the complications of influenza infection. We investigated the benefit of PCV vaccination in preventing influenza hospitalization in children <5 years of age during the 2009 to 2010 pandemic wave and the 2010 to 2011 influenza epidemic in Spain. Methods: A multicenter matched case-control study was undertaken in 27 hospitals from 7 Spanish regions between July 2009 and April 2011. A case was defined as a hospitalized patient between 6 months and 5 years of age with influenza virus infection confirmed by real-time reverse-transcription polymerase chain reaction. We selected 2 matched controls for each case from patients with unplanned hospital admission for reasons other than acute respiratory infection or influenza-like illness. Cases and controls were matched according to age, date of hospitalization and province of residence. Crude and adjusted odds ratios were calculated for associations between influenza hospitalization and PCV vaccination. Results: One hundred ninety-four cases and 342 controls were included in the study. In the 2009 to 2010 pandemic wave, the adjusted benefit in preventing hospitalization was 48% (95% confidence interval: 1 to 76) in fully vaccinated children compared with –79% (95% confidence interval: –341 to 27) in the 2010 to 2011 influenza season. Conclusions: The results obtained suggest that, in children <5 years of age, PCV vaccination reduced hospitalization during the 2009 to 2010 pandemic wave. By contrast, there was no observed benefit of vaccination in the 2010 to 2011 influenza season.
Cuffless Blood Pressure Estimation during Exercise Stress Test

 Abstract—Blood Pressure (BP) measurement without using a cuff is an interesting goal especially during Exercise Stress Test. Conventional methods like Cuff-based blood pressure measurement is not accurate enough due to high motion artifacts. High blood pressure during exercise test will cause pain and discomfort during inflation of cuff as well. Many researches have been conducted and shown Pulse Arrival Time (PAT), can be used in blood pressure estimation. This paper proposes a new calibration method for blood pressure estimation during exercise stress test that increases the quality of estimation. Besides PAT and heart rate, estimated blood pressure of previous stage is added as another input parameter. This technique increases the correlation coefficients between real and estimated blood pressures. We also show that by using ΔPAT, ΔHR instead of PAT and HR quality of estimation improves.
An insert in the covS gene distinguishes a pharyngeal and a blood isolate of Streptococcus pyogenes found in the same individual

Expression of the extensive arsenal of virulence factors by Streptococcus pyogenes is controlled by many regulators, of which CovRS is one of the best characterized and can influence ∼15 % of the genome. Animal models have established that mutants of covRS arise spontaneously in vivo resulting in highly invasive organisms. We analysed a pharyngeal and a blood isolate of S. pyogenes recovered from the same individual 13 days apart. The two isolates varied in many phenotypic properties including SpeB production, which were reflected in transcriptomic analyses. PFGE, multilocus sequence typing and partial sequencing of some key genes failed to show any differences except for an 11 bp insert in the covS gene in the blood isolate which caused a premature termination of transcription. Complementation of a fully functional covS gene into the blood isolate resulted in high expression of CovS and expression of speB. These results, showing a pharyngeal and a blood isolate from a single individual differing by a simple insertion, provide evidence for the model that regulatory gene mutations allow S. pyogenes to invade different niches in the body.
ResearchA systematic review of the impact of sedation practice in the ICU on resource use , costs and patient safety

Introduction: Patients in intensive care units (ICUs) often receive sedation for prolonged periods. In order to better understand the impact of sub-optimal sedation practice on outcomes, we performed a systematic review, including observational studies and controlled trials which were conducted in sedated patients in the ICU and which compared the impact of changes in or different protocols for sedation management on economic and patient safety outcomes. Methods: We searched Medline, Embase and CINAHL online literature databases from 1988 to 15th May 2008 and hand searched conferences. English-language studies set in the ICU, in sedated adult humans on mechanical ventilation, which reported the impact of sedation practice on cost and resource use and patient safety outcomes, were included. All abstracts were reviewed twice by two independent reviewers, with all conflicts resolved by a third reviewer, to check that they met the review inclusion criteria. Full-text papers of all included studies were retrieved and again reviewed twice against inclusion criteria. Data were doubly extracted from studies. Study aims, design, population, and outcomes including duration of mechanical ventilation, length of stay in ICU and hospital, costs and rates of mortality and adverse events were extracted. Due to heterogeneity between study designs and outcomes reported, no quantitative data synthesis such as meta-analysis was possible. Results: Included studies varied in design, patient population and aim, with the majority being before-after studies. Overall, studies showed that improvements in sedation practice, such as the introduction of guidelines and protocols, or daily interruption of sedation, were associated with improvements in outcomes including ICU and hospital length of stay, duration of mechanical ventilation, and costs. Mortality and the incidence of nosocomial infections were also
Scene-Based Geometry Synthesis

Digital artists have increasingly been required to design and create ever larger and more detailed virtual environments. The purpose of these environments ranges mostly between cinema and game development, but the challenges are the same in both; to create large amounts of detail in an unrealistically short timescale. Fractals are one instance of a tool being utilized to speed up production time, mostly for landscape generation. We present an alternative approach to generating unique and believable large-scale outdoor scenes. Through the utilization of texture synthesis and geometry synthesis techniques, it is possible to synthesize large natural environments based on a small predefined subregion. In this manner, an artist is only required to create a small portion of the product, and the algorithm will generate a full-scale scene with the same properties as the example. If built robustly enough, this system could dramatically improve production time of immersive movies and video games.
Nosocomial Outbreak of Pediatric Gastroenteritis Caused by CTX-M-14-Type Extended-Spectrum β-Lactamase-Producing Strains of Salmonella enterica Serovar London

ABSTRACT CTX-M-14-type extended-spectrum β-lactamase was first detected in Salmonella enterica serovar London strains which were isolated from three hospitalized pediatric patients with gastroenteritis. The isolates had pulsed-field gel electrophoresis patterns identical to those of the previously isolated antimicrobial-susceptible strains from community-acquired gastroenteritis, suggesting the susceptible clone acquired the resistance.