Miracle-dz/UniFAR-FTUs huggingface dataset:
ARTS: alignment of RNA tertiary structures

MOTIVATION A fast growing number of non-coding RNAs have recently been discovered to play essential roles in many cellular processes. Similar to proteins, understanding the functions of these active RNAs requires methods for analyzing their tertiary structures. However, in contrast to the wide range of structure-based approaches available for proteins, there is still a lack of methods for studying RNA structures. RESULTS We present a new computational method named ARTS (alignment of RNA tertiary structures). The method compares two nucleic acid structures (RNAs or DNAs) and detects a-priori unknown common substructures. These substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs. To the best of our knowledge, this is the first method of this type. The method is highly-efficient and was used to conduct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank. AVAILABILITY The program, a web-server and supplementary information are available on http://bioinfo3d.cs. tau.ac. il/ARTS
On the Feasibility of a Cognitive Approach to the Study of Science / Zur Möglichkeit eines kognitiven Ansatzes in der Wissenschaftssoziologie

Zusammenfassung In diesem Aufsatz werden drei neuere Ansätze in der Wissenschaftsoziologie vorgestellt, die Alternativen zu dem bisher dominanten institutionellen Ansatz darstellen. Obwohl die Ansätze sich in ihren methodologischen und epistemologischen Voraussetzungen, wie auch in ihrer Zielsetzung, voneinander unterscheiden, weisen sie dennoch Gemeinsamkeiten auf, die es erlauben, sie als kognitiven Ansatz auszuweisen. Die Betonung liegt auf kognitiven Prozessen in der Erzeugung und im Wandel wissenschaftlicher Ideen statt auf der Untersuchung institutionalisierten Verhaltens und auf den informationsverarbeitenden Aspekten im Wissenschaftsbetrieb. Die konventionelle Ansicht von einer linearen Entwicklung der Wissenschaft wird abgelehnt. Daraus lassen sich für die Wissenschaftsoziologie eine Reihe von Konsequenzen ableiten, die zur Diskussion gestellt werden. Abstract In this paper three new approaches to the study of science are discussed that have emerged only recently and offer alternatives to the hitherto dominating institutional approach in the sociology of science. Although the three alternatives differ in many respects, they share certain features in common which qualifies to subsume them under the heading of a cognitive approach: the emphasis is on cognitive processes in the production and change of scientific ideas rather than on institutionalized behaviour, they disregard the conventional view of linear scientific development and focus in the production of scientific knowledge. The discussion is opened on several consequences of there alternatives.
Novel population‐based study finding higher than reported hepatocellular carcinoma incidence suggests an updated approach is needed

Hepatocellular carcinoma (HCC) incidence is rising rapidly in many developed countries. Primary epidemiological data have invariably been derived from cancer registries that are heterogeneous in data quality and registration methodology; many registries have not adopted current clinical diagnostic criteria for HCC and still rely on histology for classification. We performed the first population‐based study in Australia using current diagnostic criteria, hypothesizing that HCC incidence may be higher than reported. Incident cases of HCC (defined by American Association for the Study of Liver Diseases diagnostic criteria or histology) were prospectively identified over a 12‐month period (2012‐2013) from the population of Melbourne, Australia. Cases were captured from multiple sources: admissions to any of Melbourne's seven tertiary hospitals; attendances at outpatients; and radiology, pathology, and pharmacy services. Our cohort was compared to the Victorian Cancer Registry (VCR) cohort (mandatory notified cases) for the same population and period, and incidence rates were compared for both cohorts. There were 272 incident cases (79% male; median age: 65 years) identified. Cirrhosis was present in 83% of patients, with hepatitis C virus infection (41%), alcohol (39%), and hepatitis B virus infection (22%) the commonest etiologies present. Age‐standardized HCC incidence (per 100,000, Australian Standard Population) was 10.3 (95% confidence interval [CI]: 9.0‐11.7) for males and 2.3 (95% CI: 1.8 to 3.0) for females. The VCR reported significantly lower rates of HCC: 5.3 (95% CI: 4.4 to 6.4) and 1.0 (95% CI: 0.7 to 1.5) per 100,000 males and females respectively (P < 0.0001). Conclusions: HCC incidence in Melbourne is 2‐fold higher than reported by cancer registry data owing to under‐reporting of clinical diagnoses. Adoption of current diagnostic criteria and additional capture sources will improve registry completeness. Chronic viral hepatitis and alcohol remain leading causes of cirrhosis and HCC. (Hepatology 2016;63:1205–1212)
Community-based heuristic routing protocol for disrupted social network

Frequent change in the topology of a disrupted social network is a barrier in using traditional routing protocols. One way to deal with this problem is to collect mobility profiles of nodes and to utilize them for future routing decisions. The solution however lacks scalability since it is difficult for nodes to keep updated information of the whole network. The paper thus devises a scalable scheme that exploits the limited social circles of the mobile device owners; i.e. it breaks network into social communities and employs a fine-grained heuristic routing scheme for intra-community communication. Moreover the paper specifies a simple method for identification of bridging nodes to transfer message to destination lying outside the community. The idea paper is expected to bring a near to optimal routing solution for disrupted social networks.
The effect of content and language integrated learning on students' English and history competences – Killing two birds with one stone?

Abstract By failing to appropriately control for selection effects, most previous research has overestimated the effects of Content and Language Integrated Learning (CLIL) on the development of students' foreign language skills. Furthermore, the CLIL-effect on the content subject is still widely unknown. Therefore, the present study investigated skill development of 1806 German CLIL and non-CLIL eighth-graders in English and History controlling for a wide range of student, classroom and teacher characteristics. Results of multilevel modelling confirmed that CLIL-classrooms showed greater increases in English listening comprehension but not general English skills as measured by a C-test than non-CLIL-classrooms. In History, the increases in subject knowledge over one school year were comparable despite CLIL-students' larger amount of instruction (three instead of two hours per week). The results confirm previous, differential findings for English. For the content subject, they indicate that CLIL-classrooms need to invest substantially more time to achieve comparable learning outcomes.
Sperm-borne miRNAs and endo-siRNAs are important for fertilization and preimplantation embryonic development

Although it is believed that mammalian sperm carry small noncoding RNAs (sncRNAs) into oocytes during fertilization, it remains unknown whether these sperm-borne sncRNAs truly have any function during fertilization and preimplantation embryonic development. Germline-specific Dicer and Drosha conditional knockout (cKO) mice produce gametes (i.e. sperm and oocytes) partially deficient in miRNAs and/or endo-siRNAs, thus providing a unique opportunity for testing whether normal sperm (paternal) or oocyte (maternal) miRNA and endo-siRNA contents are required for fertilization and preimplantation development. Using the outcome of intracytoplasmic sperm injection (ICSI) as a readout, we found that sperm with altered miRNA and endo-siRNA profiles could fertilize wild-type (WT) eggs, but embryos derived from these partially sncRNA-deficient sperm displayed a significant reduction in developmental potential, which could be rescued by injecting WT sperm-derived total or small RNAs into ICSI embryos. Disrupted maternal transcript turnover and failure in early zygotic gene activation appeared to associate with the aberrant miRNA profiles in Dicer and Drosha cKO spermatozoa. Overall, our data support a crucial function of paternal miRNAs and/or endo-siRNAs in the control of the transcriptomic homeostasis in fertilized eggs, zygotes and two-cell embryos. Given that supplementation of sperm RNAs enhances both the developmental potential of preimplantation embryos and the live birth rate, it might represent a novel means to improve the success rate of assisted reproductive technologies in fertility clinics. Summary: The developmental potential of embryos fertilized with sperm from germline-specific Dicer or Drosha conditional knockout mice is impaired, highlighting key roles for paternal miRNAs/endo-siRNAs.
M-Cell Surface β1 Integrin Expression and Invasin-Mediated Targeting of Yersinia pseudotuberculosis to Mouse Peyer’s Patch M Cells

ABSTRACT Quantitative analysis of Yersinia pseudotuberculosisinfection of murine gut loops revealed that significantly more wild-type bacteria associated with Peyer’s patch M cells than with dome enterocytes or goblet cells. An invasin-deficient mutant was significantly attenuated for M-cell invasion, while β1 integrin expression was demonstrated in the apical membranes of M cells but not enterocytes. M-cell targeting by Yersinia pseudotuberculosis in vivo may, therefore, be mediated primarily by the interaction of invasin with cell surface β1 integrins.
Seasonal Adjustment and the Business Cycle in Unemployment

Several recent studies show that seasonal variation and cyclical variation in unemployment are correlated. A common finding is that seasonality tends to differ across the business cycle stages of recessions and expansions. Since seasonal adjustment methods assume that the two sources of variation can somehow be separated, the present study examines the impact of seasonal adjustment on the analysis of cyclical patterns. Seasonally adjusted quarterly unemployment data for five G-7 countries are modeled by a Smooth Transition Autoregression (STAR), whereas the corresponding unadjusted data are modeled by a so-called Seasonal STAR (SEASTAR). A comparison of the implied estimated peaks and troughs shows that there is substantial agreement on the business cycle chronologies, albeit that for seasonally adjusted data, recessionary periods tend to last longer.
Prediction of Reading Difficulty from Parental Preschool Report: A 3- Year Followup

The Minnesota Child Development Inventory (MCDI) was used to describe the developmental status of 59 children before the start of kindergarten. Three years later children were classified in one of four categories, based on the amount of supplemental reading instruction necessary during the three-year period. A number of variables from the MCDI were highly correlated with this continuum of difficulty in mastering reading, with parental report of the child's general development and knowledge of letters and numbers being most significant. Significant correlations with group achievement tests also were obtained. The findings should encourage the inclusion of parent reports by persons using or constructing preschool screening measures.
Isolation of a lipopolysaccharide-binding acute phase reactant from rabbit serum

This report describes the purification of an acute phase reactant from acute phase rabbit serum, which endows normal serum with the properties of acute phase serum, insofar as LPS is concerned. The acute phase reactant is referred to as LPS-binding protein, or LBP. LBP was purified approximately 2,000-fold by chromatography of acute phase serum on Bio-Rex 70 and Mono-Q resins. The resulting preparation consisted of two glycoproteins having molecular weights of 60,500 and 58,000; the two were obtained in a variable ratio, usually near 10:1, respectively. After separation by SDS-PAGE, the N-terminal 36 amino acid sequences of the two proteins were identical. From the N-terminal sequence, as well as other properties of LBP, LBP appears to be unrelated to any known acute phase reactants. The direct interaction of LPS and LBP was inferred from two types of evidence: first, immunoprecipitation of [3H]LPS from APRS by anti-LBP sera; and second, by the 125I-labeling of LBP when APRS-containing 125I-labeled 2-(p- azidosalicylamido)ethyl 1,3'-dithiopropionyl-LPS was photolysed. The data presented here support the concept that the 60-kD glycoprotein we have termed LBP is a newly recognized acute phase reactant that may modulate the biochemical and biologic properties of LPS in vivo.
Motivational Interviewing: Preparing People to Change Addictive Behavior

Since the initial publication of this classic text, motivational interviewing (MI) has been used by countless clinicians in diverse settings. Theory and methods have evolved apace, reflecting new knowledge on the process of behavior change, a growing body of outcome research, and the development of new applications within and beyond the addictions field. Including 25 nearly all-new chapters, this revised and expanded second edition now brings MI practitioners and trainees fully up to date. William R. Miller and Stephen Rollnick explain how to work through ambivalence to facilitate change, present detailed guidelines for using their approach with a variety of clinical populations, and reflect on the process of learning MI. Chapters contributed by other leading experts then address such special topics as MI and the stages-of-change model; using the approach with groups, couples, and adolescents; and applications to general medical care, health promotion, and criminal justice settings.
A Sinusoidal Model Approach to Acoustic Landmark Detection and Segmentation for Robust Segment-Based Speech Recognition

In this paper, we present a noise robust landmark detection and segmentation algorithm using a sinusoidal model representation of speech. We compare the performance of our approach under noisy conditions against two segmentation methods used in the SUMMIT segment-based speech recognizer, a full segmentation approach and an approach that detects segment boundaries based on spectral change. The word error rate of the spectral change segmentation method degrades rapidly in the presence of noise, while the sinusoidal and full segmentation models degrade more gracefully. However, the full segmentation method requires the largest computation time of the three approaches. We find that our new algorithm provides the best tradeoff between word accuracy and computation time of the three methods. Furthermore, we find that our model is robust when speech is contaminated by various noise types
From Plants to Landmarks: Time-invariant Plant Localization that uses Deep Pose Regression in Agricultural Fields

Agricultural robots are expected to increase yields in a sustainable way and automate precision tasks, such as weeding and plant monitoring. At the same time, they move in a continuously changing, semi-structured field environment, in which features can hardly be found and reproduced at a later time. Challenges for Lidar and visual detection systems stem from the fact that plants can be very small, overlapping and have a steadily changing appearance. Therefore, a popular way to localize vehicles with high accuracy is based on ex- pensive global navigation satellite systems and not on natural landmarks. The contribution of this work is a novel image- based plant localization technique that uses the time-invariant stem emerging point as a reference. Our approach is based on a fully convolutional neural network that learns landmark localization from RGB and NIR image input in an end-to-end manner. The network performs pose regression to generate a plant location likelihood map. Our approach allows us to cope with visual variances of plants both for different species and different growth stages. We achieve high localization accuracies as shown in detailed evaluations of a sugar beet cultivation phase. In experiments with our BoniRob we demonstrate that detections can be robustly reproduced with centimeter accuracy.
Review paper on denoising of ECG signal

All the real time signals are non-periodic and non-stationary, which gives more information for any signal processing techniques. Electrocardiogram (ECG) signal is an example of real time signal. ECG signal gives electrical activities that are useful information about the functioning of heart. ECG signals helps in diagnosing the complex cardiac diseases. ECG signals are low frequency signals and contain lot of clinical information. The important characteristic information called features are extracted from ECG signal and used for medical diagnosis. The denoising of signal becomes important stage in any signal processing technique and lot of scope involved in computer aided diagnosis of heart. Many research work focusing on denoising the signal for extracting important features like Extended Kalman Filter, Wavelet Transformation and Singular Value Decomposition (SVD). The denoising signal processing techniques evaluated using mean square error and signal to noise ratio. In addition, ECG signal is used for person authentication. The proposed paper focuses on the study of different techniques of denoising and an identification of person through an ECG signal.
O PROCESSO DE INTERNACIONALIZAÇÃO DAS EMPRESAS: O CASO BRASILEIRO

Neste artigo, analisa-se a internacionalizacao de empresas brasileiras e tipificam-se neste processo quatro grandes etapas: pre-envolvimento, envolvimento passivo, envolvimento ativo e envolvimento comprometido. As tres etapas iniciais estao voltadas ao entendimento do desenvolvimento incremental de exportacoes e a ultima ao envolvimento comprometido com ou sem investimento direto no exterior. As quatro grandes etapas sao divididas em estagios intermediarios. Descreve-se tambem o que leva uma empresa produtora exportadora a evoluir ou retroceder em seu processo de internacionalizacao. Constatou-se que as empresas produtoras exportadoras brasileiras, em sua maioria, sao exportadoras passivas, com o seu foco gerencial voltado para a area de producao em detrimento da comercializacao internacional de seus produtos. Por outro lado, as empresas produto-ras exportadoras brasileiras buscam formas mais comprometidas de atuacao, apos a obtencao de sucesso previo no processo incremental de exportacoes.
Practical Management: Community-Associated Methicillin-Resistant Staphylococcus Aureus (CA-MRSA): The Latest Sports Epidemic

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has gained international recognition as a superbug that causes serious infectious outbreaks in high-risk populations such as athletes. Clusters of cases in various athletic teams, particularly contact sports, have been reported since 1993 in the United States and more recently in Canada. CA-MRSA infections are not limited to North America, and all athletes are considered high risk. Skin-to-skin contact appears to be the primary mode of transmission. While typical infections are local skin and soft-tissue abscesses, CA-MRSA infections can spread systemically and lead to significant morbidity and mortality if not promptly identified and treated. The gold standard of treatment for all abscesses is incision and drainage with wound culture for bacterial identification and antibiotic sensitivity testing. A limited number of antibiotics are currently useful in the treatment of CA-MRSA and are reviewed. Geographical variation in patterns of antibiotic resistance further complicates the treatment. Meticulous, consistent use of infection prevention strategies is critical to control outbreaks in the athletic population. Good hygiene, prompt identification of infection, limited exposure to infected persons and contaminated objects, and proper treatment combined with close follow-up of infected athletes will help contain CA-MRSA outbreaks. Future research is needed to explore person-to-person and fomite transmission risks, to define the significance of nasal carriage and skin colonization in relation to CA-MRSA infections, and to further investigate antibiotic resistance patterns. Universal education is needed for all athletes and personnel who provide care in the athletic setting to help control this widespread epidemic.
Recommending materialized views and indexes with the IBM DB2 design advisor

Materialized views (MVs) and indexes both significantly speed query processing in database systems, but consume disk space and need to be maintained when updates occur. Choosing the best set of MVs and indexes to create depends upon the workload, the database, and many other factors, which makes the decision intractable for humans and computationally challenging for computer algorithms. Even heuristic-based algorithms can be impractical in real systems. In this paper, we present an advanced tool that uses the query optimizer itself to both suggest and evaluate candidate MVs and indexes, and a simple, practical, and effective algorithm for rapidly finding good solutions even for large workloads. The algorithm trades off the cost for updates and storing each MV or index against its benefit to queries in the workload. The tool autonomically captures the workload, database, and system information, optionally permits sampling of candidate MVs to better estimate their size, and exploits multi-query optimization to construct candidate MVs that will benefit many queries, over which their maintenance cost can then be amortized cost-effectively. We describe the design of the system and present initial experiments that confirm the quality of its results on a database and workload drawn from a real customer database.
Validation of a handoff assessment tool: the Handoff CEX.

AIMS AND OBJECTIVES Test the feasibility and validity of a handoff evaluation tool for nurses. BACKGROUND No validated tools exist to assess the quality of handoff communication during change of shift. DESIGN Prospective cohort study. METHODS A standardised tool, the Handoff CEX, was developed based on the mini-CEX. The tool consisted of seven domains scored on a 1-9 scale. Nurse educators observed shift-to-shift handoff reports among nurses and evaluated both the provider and recipient of the report. Nurses participating in the report simultaneously evaluated each other as part of their handoff. RESULTS Ninety-eight evaluations were obtained from 25 reports. Scores ranged from 3-9 in all domains except communication and setting (4-9). Experienced (>five years) nurses received significantly higher mean scores than inexperienced (≤ five years) nurses in all domains except setting and professionalism. Mean overall score for experienced nurses was 7·9 vs 6·9 for inexperienced nurses. External observers gave significantly lower scores than peer evaluators in all domains except setting. Mean overall score by external observers was 7·1 vs. 8·1 by peer evaluators. Participants were very satisfied with the evaluation (mean score 8·1). CONCLUSIONS A brief, structured handoff evaluation tool was designed that was well-received by participants, was felt to be easy to use without training, provided data about a wide range of communication competencies and discriminated well between experienced and inexperienced clinicians. Relevance to clinical practice. This tool may be useful for educators, supervisors and practicing nurses to provide training, ongoing assessment and feedback to improve the quality of handoff.