bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid identification of Human Serum Albumin binding peptides from a phage display library：a back-of-the-envelope assessment of positive binders using titer-based criteria
Authors: Shi Yi-Feng , Li Min , Zhang Jia-Di , Bian Lei
Published: January 2018

Human serum albumin (HSA) is the most abundant protein in blood and has a 19-day in vivo half-life, the longest human blood protein. HSA has also been extensively studied as a drug carrier in a wide variety of clinical applications. HSA-binding, compared with HSA-fusion, is promising strategy for extending the plasma half-life of protein therapeutics. The construction of albumin-binding drugs requires assessment of a large enough quantity of HSA-binding peptide candidates for conjugation with therapeutic proteins. Here, we report a back-of-the-envelope assessment method to facilitate phage display selection of HSA-binding peptides. With an experimentally determined number of phage titers, we can calculate the specificity ratios and the recovery yields. The recovery yield is calculated using the titers of eluted phage divided by the titers of input phage. The specificity ratio is calculated using the titer of eluted phage from a target-coated plate divided by the titer of eluted phage from a blank-control plate. These parameters are defined as quantitative criteria for panning and characterization of binding phage clones. Consequently, this approach may enable more rapid and low-cost phage display screening of HSA-binding peptides, which could be used as candidates of HSA binders for conjugation with therapeutic proteins.
How do medical students utilize mobile handheld devices in learning?
Authors: Al-Moslih Ayad M , Driessen Erik
Published: January 2018

Introduction. The phenomenon of increased and ubiquitous use of mobile handheld devices by medical students triggered the interest to explore how these students utilize their devices while learning. Methods. This study was conducted at the Medical College of University of Sharjah in the United Arab Emirates during the period February to April 2012. A total of 463 students participated in the study. A mixed methodology was employed where an initial survey provided the necessary preliminary data and purposively sample the subjects, followed by two focus group discussions to explore this phenomenon in depth. Results. The survey results demonstrated that vast majority (95.9%) of students possess at least one type of mobile handheld device. Most of these students (90.1%) used their handheld device while learning. Students used these devices in different contexts, varying between Lectures, Problem-Based Learning (PBL) sessions, Hospitals and other contexts were identified (32.4%, 30.1%, 20% and 13% respectively). Majority of students (83.2%) use their handhelds when learning individually on their own time, whereas about half of them (48.3%) use it in learning with friends i.e. collaboratively. Focus group discussions revealed several aspects of how students utilized their mobile handheld devices while learning. Five themes were identified, which demonstrated the resources and accessed content, contexts of use, activities that involved learning, with whom students learned, and what made them learn or not learn while using these devices. Conclusion. Mobile handheld devices facilitated students learning “on-the-move” on and off-campus in different ways. Students utilized their devices mostly to complement and augment their learning in different contexts. Students believed that a huge gap exists between themselves and their teachers in terms of mobile learning.
Spectral characteristics of the mutant protein D-glucose/D-galactose-binding protein GGBP/H152C with an attached fluorescent dye BADAN: Influence of external conditions
Authors: Fonin Alexander V , Stepanenko Olga V , Povarov Olga I , Volova Catherine A , Filippova Elizaveta M , Bublikov Grigory S , Kuznetsova Irina M. , Demchenko Alexander P , Turoverov Konstantin K
Published: January 2018

The mutant form of the D-glucose/D-galactose-binding protein GGBP/H152C with the solvatochromic dye BADAN attached to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various factors on the physical-chemical properties of GGBP/H152C-BADAN and on its complexation with glicose . The high affinity (K d = 8.5 μM) and rapid binding of glucose ( even in solutions with a viscosity value of 4 cP, the formation time of the protein-glucose is not longer than three seconds ) allows for theuse of GGBP/H152C-BADAN to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that the changes in the ionic strength and pH within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system.
Impact of polybasic alcohols on biocompatibility and selectivity of Penicillin G Acylase for kinetically controlled synthesis
Authors: Shi Yi-Feng , Cao Zhu-An , Shen Zhong-Yao
Published: January 2018

The enzyme catalyzed synthesis of cephalexin (CEX) from 7-amino-3-deacetoxycephalosporanic acid (7-ADCA) and D-a-phenylglycine methyl ester (PGM) by Penicillin G acylase (PGA) is a model for kinetically controlled synthesis. The parallel hydrolysis of PGM, the activated acyl donor, is the principle competing pathway in this reaction, limiting the synthetic yield and reaction efficiency. To improve the performance of PGA catalyzed CEX synthesis, the biocompatibility and selectivity of various co-solvents were investigated. Polybasic alcohols such as ethylene glycol, glycerol and PEG400 did not cause deleterious changes to the enzyme, whereas monobasic alcohols, such as butyl alcohol, disrupted the PGA activity. Compared with the reaction in aqueous medium, the use of ethylene glycol as a co-solvent was found to have good selectivity in order to facilitate CEX synthesis and significantly minimize PGM hydrolysis. The pH of ethylene glycol medium was also optimized. The mechanism of the enhanced effect of polybasic alcohols as co-solvents on both biocompatibility and selectivity of enzymatic kinetically controlled synthesis is suggested.
Sedimentary facies and foraminiferal assemblages from Posidonia oceanica meadows of western Mediterranean Sea
Authors: Gaglianone Giovanni , Frezza Virgilio , Brandano Marco
Published: January 2018

Sedimentary facies and foraminiferal assemblages of sediments sampled into seven Posidonia oceanica meadows from Western Mediterranean Sea were investigated. Six sampling sites are localised in Italy (Maratea, Ponza Island, Santa Marinella, Giglio Island, Osalla and Alghero), and one in France (Argentella, Crovani Bay, Corsica). The role of P. oceanica meadows in the sedimentary processes was investigated in different contexts: sampled meadows are set up both on soft and hard substrates, often forming “mattes”, in geographical areas subject to different wind and sea conditions (waves and longshore currents) and characterised by various coastal landforms and terrigenous inputs derived from costal erosional processes and/or fluvial contributions. A sedimentological, compositional, micropaleontological and geochemical characterisation of 111 bottom sediment samples, collected by SCUBA diving between 0 and 35 mwd, was carried out and finally tested with a Q-mode cluster analysis. Five sedimentary facies have been recognised, from terrigenous to mixed siliciclastic-carbonate and carbonate. Facies (and subfacies) are distinguishable by sorting, gravel content, abundance and maturity of clastic sediments, and weighted average of carbonate content. In all facies, foraminifers and red algae dominate the bioclastic fraction, whereas other bioclastic components are very subordinate and show a variable distribution. In all the investigated sites, benthic foraminiferal assemblages are generally dominated by typical epiphytic species, such as Asterigerinata mamilla, Lobatula lobatula, Peneroplis pertusus, Planorbulina mediterranensis, Rosalina spp. and miliolids. Nevertheless, these assemblages show some differences in the different sites according to the presence or absence of terrigenous contributions and, consequently, to the water turbidity. This parameter influences symbiont-bearing foraminifer as P. pertusus. Moreover, the samples from Argentella (Crovany Bay) are characterised by a peculiar assemblage, in which Miniacina miniacea dominates with very high frequencies.
Assessment of carbon sequestrated within the matte of the Posidonia oceanica meadow at the NATURA 2000 site “Grand Herbier de la Plaine Orientale”
Authors: Pergent Gerard , Pergent-Martini Christine , De Florinier Marine , Bonacorsi Marina , Clabaut Philippe , Valette-Sansevin Audrey
Published: January 2018

The coastal vegetation, and in particular the seagrasses, plays a major role in the fixation of carbon. Posidonia oceanica, a species endemic to the Mediterranean, is of particular interest because of the constitution of a particular structure, the matte, which enables the sequestration of carbon over long periods of time. An initial assessment of the stocks of carbon sequestrated within the matte has been undertaken in two sectors of the NATURA 2000 site “Grand Herbier de la Plaine Orientale”, Biguglia in the north and Aléria in the south. The surface area of the meadow has been measured by means of the combined use of aerial remote sensing (shallow zone) and side-scan sonar (deep zone). The thickness of the matte has been assessed by means of seismic reflection using a 2.5 KHz sediment probe and a sparker. The calibration of the seismic data was performed by scuba diving at the level of intermatte cliffs, clearly visible on the seismic profiles. The seagrass meadow at the NATURA 2000 site extends from 3 to 41 m depth and covers an estimated total area of 22 667 ha, or 52.4% of the bottom between 0 and 50 m depth. The speed of propagation within the matte (celerity), estimated by comparison of the field data (intermatte) and the seismic profiles, ranges from 1 600 to 1 700 m.s-1. The thickness of the matte, estimated on the basis of the mean celerity, is on average 2.7 m for the Biguglia zone where it may locally exceed 8 m; it is on average 3.2 m for the Aléria zone where it may exceed 13 m, in particular off the mouth of the coastal river Tavignano. The presence of matte beneath the sediment should also be noted in patches of sand within the meadow and also beyond the lower limit. The quantity of carbon sequestered at this NATURA 2000 site may exceed 60 million tons. However, it would be necessary to carry out coring within the matte, in several representative sectors, in order to assess more accurately the amounts of carbon sequestered at this site.
Continuous mapping of the main habitats of the Corsican littoral
Authors: Valette-Sansevin Audrey , Alami Samy , Bonacorsi Marina , Damier Elodie , Pergent Gérard , Pergent-Martini Christine
Published: January 2018

The availability of maps of the main habitats and types of bottom constitutes a priority for managers of the marine environment. For several years, a number of studies have been undertaken in order to meet this requirement, but they generally only cover limited areas and the methods used, as well as their accuracy, vary widely from one site to another. An original approach has been initiated for this purpose along the coast of Corsica (1 000 km of coastline); it has involved (i) surveying all the available data (293 identified maps), (ii) selecting and extracting the most relevant data (date and method of acquisition, accuracy), (iii) updating the data on surface habitats (e.g. upper limits of the Posidonia oceanica meadows) by means of remote sensing of recent images, (iv) homogenizing all the available data (typology of benthic biocenoses in the Mediterranean), (v) assembling the full set of data within an easily incrementable Geographical Information System (GIS), and (v) proposing a scale of reliability making it possible to associate a degree of confidence to each point on the map. This approach has resulted in the production of a map covering the whole of the Corsican coastline down to 50 to 150 m depth (depending on the sector considered), including, where there is an overlap, only the data with the highest degree of reliability. The surface area mapped is estimated at more than 299 700 ha, which makes it one of the largest recent maps ever produced for the Mediterranean. The P. oceanica meadow covers a surface area of about 57 500 ha, or 45.3% of the seabed between 0 and 50 m depth. In relation to the earlier data collected in the 1990s (potential surface area of seagrass beds), the extension of P. oceanica has remained relatively stable, and the differences observed may be explained mainly by the accuracy of this new map which possesses a greater degree of reliability.
Error location in Python: where the mutants hide
Authors: Campbell Joshua C , Hindle Abram , Amaral José N
Published: January 2018

Dynamic scripting programming languages present a unique challenge to software engineering tools that depend on static analysis. Dynamic languages do not benefit from the full lexical and syntax analysis provided by compilers and static analysis tools. Prior work exploited a statically typed language (Java) and a simple \(n\)-gram language model to find syntax-error locations in programs. This work investigates whether \(n\)-gram-based error location on source code written in a dynamic language is effective without static analysis or compilation. UnnaturalCode.py is a syntax-error locator developed for the Python programming language. The UnnaturalCode.py approach is effective on Python code, but faces significantly more challenges than its Java counterpart did. UnnaturalCode.py generalizes the success of previous statically-typed approaches to a dynamically-typed language.
Reassembly and co-crystallization of a family 9 processive endoglucanase from its component parts: Structural and functional significance of the intermodular linker
Authors: Petkun Svetlana , Rozman Grinberg Inna , Lamed Raphael , Jindou Sadanari , Burstein Tal , Yaniv Oren , Shoham Yuval , Shimon Linda J.W. , Bayer Edward A , Frolow Felix
Published: January 2018

Non-cellulosomal processive endoglucanase 9I (Cel9I) from Clostridium thermocellum is a modular protein, consisting of a family-9 glycoside hydrolase (GH9) catalytic module and two family-3 carbohydrate-binding modules (CBM3c and CBM3b), separated by linker regions. GH9 does not show cellulase activity when expressed without CBM3c and CBM3b and the presence of the CBM3c was previously shown to be essential for endoglucanase activity. Physical reassociation of independently expressed GH9 and CBM3c modules (containing linker sequences) restored 60-70% of the intact Cel9I endocellulase activity. However, the mechanism responsible for recovery of activity remained unclear. In this work we independently expressed recombinant GH9 and CBM3c with and without their interconnecting linker in Escherichia coli. We crystallized and determined the molecular structure of the GH9/linker-CBM3c heterodimer at a resolution of 1.68 Å to understand the functional and structural importance of the mutual spatial orientation of the modules and the role of the interconnecting linker during their re-association. Enzyme activity assays and isothermal titration calorimetry were performed to study and compare the effect of the linker on the re-association. The results indicated that reassembly of the modules could also occur without the linker, albeit with only very low recovery of endoglucanase activity. We propose that the linker regions in the GH9/CBM3c endoglucanases are important for spatial organization and fixation of the modules into functional enzymes.
Is the Kidscreen-27 a valid measure of health-related quality of life in 10-year-old Norwegian children?
Authors: Andersen John Roger , Natvig Gerd Karin , Haraldstad Kristin , Skrede Turid , Aadland Eivind , Resaland Geir Kåre
Published: January 2018

The aim of this study was to investigate the reliability and validity of the Norwegian Kidscreen-27 questionnaire, a measure of generic health-related quality of life, in 10 year-old children. The Kidscreen-27 consists of five domains and was validated in a sample of 56 school children (29 boys). The children completed the questionnaire at three different time points during two consecutive school days. For convergent validity, the study was powered to detect a statistically significant correlation coefficient of 0.4. Cronbach's alpha values ranged from 0.73 to 0.83. Floor effects were all zero and ceiling effects ranged from 1.7% to 23.7%. Intraclass correlation values over time ranged from 0.71 to 0.81. However, some individual variability over time occurred and was illustrated by Bland Altman plots. The domains of physical well-being, psychological well-being and autonomy & parents improved over time (Ps < 0.05), while social support and school environment domains did not. We assessed convergent validity using general life satisfaction scores obtained by administering the Cantrils Ladder. All the Kidscreen-27 domains were significantly associated with general life satisfaction (Spearman rank correlations ranged from 0.29 to 0.59, Ps < 0.05). In conclusion, the Norwegian version of Kidscreen-27 has good reliability and validity.
Insight on the anatomy, systematic relationships, and age of the Early Cretaceous ankylopollexian dinosaur Dakotadon lakotaensis
Authors: Boyd Clint A , Pagnac Darrin C
Published: January 2018

Knowledge regarding the early evolution within the dinosaurian clade Ankylopollexia drastically increased over the past two decades, in part because of an increase in described taxa from the Early Cretaceous of North America. These advances motivated the recent completion of extensive preparation and conservation work on the holotype and only known specimen of Dakotadon lakotaensis, a basal ankylopollexian from the Lakota Formation of South Dakota. That specimen (SDSM 8656) preserves a partial skull, lower jaws, a single dorsal vertebra, and two caudal vertebrae. That new preparation work exposed several bones not included in the original description and revealed that other bones were previously misidentified. The presence of extensive deformation in areas of the skull is also noted that influenced inaccuracies in prior descriptions and reconstructions of this taxon. In addition to providing an extensive re-description of D. lakotaensis, this study reviews previously proposed diagnoses for this taxon, identifies two autapomorphies, and provides an extensive differential diagnosis. Dakotadon lakotaensis is distinct from the only other ankylopollexian taxon known from the Lakota Formation, Osmakasaurus depressus, in the presence of two prominent, anteroposteriorly oriented ridges on the ventral surfaces of the caudal vertebrae, the only overlapping material preserved between these taxa. The systematic relationships of D. lakotaensis are evaluated using both the parsimony and posterior probability optimality criteria, with both sets of analyses recovering D. lakotaensis as a non-hadrosauriform ankylopollexian that is more closely related to taxa from the Early Cretaceous (e.g., Iguanacolossus, Hippodraco, and Theiophytalia) than to more basally situated taxa from the Jurassic (e.g., Camptosaurus, Uteodon). This taxonomic work is supplemented by field work that relocated the type locality, confirming its provenance from unit L2 (lower Fuson Member equivalent) of the Lakota Formation. Those data, combined with recently revised ages for the members of the Lakota Formation based on charophyte and ostracod biostratigraphy, constrain the age of this taxon to the late Valanginian to early Barremian.
The charming code that error messages are talking about
Authors: Campbell Joshua C , Hindle Abram
Published: January 2018

The intent of high test coverage is to ensure that the dark nooks and crannies of code are exercised and tested. In a language like Python this is especially important as syntax errors can lurk in unevaluated blocks, only to be discovered once they are finally executed. Bugs that present themselves as error messages mentioning a line of code which is unrelated to the cause of the bug can be difficult and time-consuming to fix when a developer must first determine the actual location of the fault. A new code metric, charm, is presented. Charm can be used by developers, researchers, and automated tools to gain a deeper understanding of source code and become aware of potentially hidden faults, areas of code which are not sufficiently tested, and areas of code which may be more difficult to debug. Charm quantifies the property that error messges caused by a fault at one location don't always reference that location. In fact, error messages seem to prefer to reference some locations far more often than others. The quantity of charm can be estimated by averaging results from a random sample of similar programs to the one being measured by a procedure of random-mutation testing. Charm is estimated for release-quality Python software, requiring many thousands of similar Python programs to be executed. Charm has some correlation with a standard software metric, cyclomatic complexity. 21 code features which may have some relationship with charm and cyclomatic complexity are investigated, of which five are found to be significantly related with charm. These five features are then used to build a linear model which attempts to estimate charm cheaply.
Patch types in Posidonia oceanica meadows around Corsica: How can we use them in seascape ecology?
Authors: Abadie Arnaud , Bonacorsi Marina , Gobert Sylvie , Lejeune Pierre , Pergent Gérard , Pergent-Martini Christine
Published: January 2018

The meadows formed by the Mediterranean seagrass Posidonia oceanica are subjected to various natural (e.g., water movement, light availability, sedimentation) and anthropogenic (e.g., anchoring, trawling, fish farms, explosives) phenomena that erode them and create diverse types of patches. The assemblage of the P. oceanica matrix and these patches creates particular seascapes. On the basis of this assessment, we aimed to investigate the importance of the patch type in structuring P. oceanica seascapes and to offer new prospects in the large scale studies of seagrass meadows. Five sites encompassing large P. oceanica meadows ranging from 1.86 km² to 4.42 km² along the Corsican coast (France) were considered. Eleven patch types with different sizes, shapes and origins were identified using side scan sonar images (sonograms). Five were recognized as natural and five as anthropogenic. One can be of both origins. The resolution of the sonograms allowed to detect patches of various sizes ranging from 1 m² to 111 829 m². The relation between structural characteristics of patches and the whole seascape aspect was explored using seven landscape metrics relevant for the study of meadows patchiness (patch area, mean radius of gyration, area-weighted radius of gyration, coefficient of variation of the Euclidean nearest-neighbor distance, area-weighted perimeter-area ratio, landscape division index, number of patches). Only a small number of patch types appears to play the strongest role in the characterization of the P. oceanica seascapes. Furthermore, the use of seascape structures seems to be suitable for the development of new tools like indices for the assessment of human impacts on P. oceanica meadows. In this perspective we propose a new and simple index, the Patchiness Source Index (PaSI), to estimate the origin of the patchiness (natural or anthropogenic) for a given area. A landscape approach, as well as information on patch dynamic, should be integrated in the new indices that aim to assess the state of conservation of the whole P. oceanica ecosystem.
Designing patient education with distance learning
Authors: Franssen Bastiaan , Jafari Javad , Zary Nabil , Masiello Italo
Published: January 2018

Background: Self-management is crucial among patients with diabetes. Increasing the levels of self-management may prevent patients from developing further complications related to their disease. Tailoring education to the patient needs, and providing them with follow-up education on the various topics of diabetes could significantly improve patient understanding. The inclusion of distance learning, and especially Massive Open Online Courses (MOOC), in diabetes education has not been significant though. What topics should a distance-learning platform focus on when offering patient education to type 2 diabetics? How do patients perceive such a platform? And what education method should be used to better reach patient understanding, ultimately helping diabetics to reach better self-management? Objective: Describing the needs and requirements of type 2 diabetics for the development of an online learning platform. The study tried to analyse what topics patients need follow-up education on to reach better self-management and how. The study wants to get an answer where patients would use a knowledge-driven decision support method inside the patient centric learning model Methods: A qualitative approach for this study included 6 participants, aged 30 to 65 years old. They were diagnosed with type 2 diabetes not earlier than 6 months before the start of this study and had no further diabetes related complications. They participated in an interview on the several topics related to diabetes, which identified where the need and requirements for education in is at. To help identify which topics patients wanted to receive follow-up education on the Diabetes Self-Management education (DSME) was used. The interview contained structured and unstructured questions, and was performed with a high level of involvement to provide relevant information related to diabetes throughout the interview. Results: Participants welcomed the idea of receiving education via an online learning platform. The incorporation of multimedia was highly recommended, and the method of receiving education was recommended to change per subject, not per topic. Overall, patient-centric learning was a preferred method in all topics, but knowledge-driven decision support was welcomed as an addition to some of the subjects. Conclusion: The current education offered is limited to providing basic understanding of performing self-management. Participants felt the need for follow-up education, but could not be provided with this. The proposed platform, with possibilities to access information whenever the patients needed, was seen as a welcomed addition to the current education offered in the different setups. Using patient-centric learning, combined with the integration of knowledge-driven decision support, could provide education and information whenever needed and benefit in increasing self-management levels among diabetics.
Patient empowered education and research: Integration Study on how to integrate Patient Generated Health Data in Quality Registers
Authors: Fardis Michael , Zary Nabil
Published: January 2018

Background: Healthcare is transformed by the usage of new technologies, like Wearable Devices (WD). Patient generated health data (PGHD) from WDs could be found useful in the management and the research of a chronic disease, like Multiple Sclerosis (MS). Objective: The objective of the study was to propose a model for the import of PGHD from WDs to the MS Quality Register (MS QR), the main resource for research on MS in Sweden. The study focused both on the medical data that is needed and on the technical challenges that exist in such an implementation. Methods: Design Science was adopted as a methodology. The context of the study chosen was the MS QR. Participants were interviewed for the technical part and a questionnaire was delivered in order to find the most meaningful PGHD for MS QR. Based on the results, an artifact was created and evaluated from the perspective of the MS QR stakeholders. Results: The survey was answered by 35 healthcare professionals. The results revealed the factors that WDs can help track for the monitoring of a disease like MS. The interviews revealed several challenges and opportunities, like the legislative or organizational difficulties, but also the opportunities that appear with initiatives towards healthcare innovation. The evaluation triggered an optimization of the technical integration model, demonstrating that simple solutions could solve complex problems. Conclusion: The import of PGHD in MS QR, is technically possible. Applications should also be added together with WDs monitoring. The choice of model to use, is strongly related to how the data will be used within the organization.
The e-examination ecosystem in healthcare education: Information and process models
Authors: Alfredsson Jayne , Sejersen Ronny , Stathakarou Natalia , Zary Nabil
Published: January 2018

Background: High stake assessments are an important component in all stages of healthcare education that validate learners’ clinical performance but may also inform and promote the learning process. Informatics has been a driver to transform paper examinations to digital examinations (e-examinations) but knowledge about their efficient and effective application in the context of healthcare assessment is still limited. Objective: The aim of this study is therefore to investigate the main aspects of the examination process and information that may become more effective and efficient with the application of informatics. Method: With the use of a deductive approach, we wish to study four cases of e-assessment and develop a conceptual model to standardize the e-examination process. Results: Based on the four e-examination cases studied, we developed a common information model. To visualize the e-examination ecosystem we outlined different types of e-examination, the aspects composed in it, illustration of its processes, contextual components and stakeholders incorporated in it.
Best practices and processes for designing MOOC videos: a case study using edX courses
Authors: Sejersen Ronny , Stedt Peter , Zary Nabil
Published: January 2018

Background: MOOCs are “online courses designed for large numbers of participants, that can be accessed by anyone anywhere as long as they have an internet connection, are open to everyone without entry qualifications, and offer a full/complete course experience online for free”. Videos are usually a widely used resource in MOOCs and knowledge on different aspects that impacts the design and production of the videos is needed. Objective: To explore production aspects that can improve videos for MOOCs based on the video producers perspective Method: A qualitative case study was conducted, in Stockholm Sweden, among staff members in charge of the design and production of videos for MOOCs over a period of eighteen months. Data collection consisted in a series of field notes and journal conducted thought the development of three MOOCs (Explore statistics with R, Pragmatics randomized controlled trials in healthcare, Introduction to urology). Interpretive analysis aimed at revealing best practices and processed for designing MOOC videos. Results: The findings presented in this article consist of XX themes. (a) Time to establish a good relation between the faculty and video producers, (b) Storyboard driven production is preferred, (c) Technical affordances of the recording studio, (d) video length, source and faculty acting (e) Video editing process that allows faculty involvement Conclusions: Our findings provide an additional perspective to existing studies (Guo et al 2014, Alario-Hoyos et al 2014) with a focus on best practices and processes of benefits to video producers.
There and back again: Putting the vectorial movement planning hypothesis to a critical test
Authors: Kobak Eva-Maria , Cardoso de Oliveira Simone
Published: January 2018

Based on psychophysical evidence about how learning of visuomotor transformation generalizes, it has been suggested that movements are planned on the basis of movement direction and magnitude, i.e. the vector connecting movement origin and targets. This notion is also known under the term “vectorial planning hypothesis”. Previous psychophysical studies, however, have included separate areas of the workspace for training movements and testing the learning. This study eliminates this confounding factor by investigating the transfer of learning from forward to backward movements in a center-out-and-back task, in which the workspace for both movements is completely identical. Visual feedback allowed for learning only during movements towards the target (forward movements) and not while moving back to the origin (backward movements). When subjects learned the visuomotor rotation in forward movements, initial directional errors in backward movements also decreased to some degree. This learning effect in backward movements occurred predominantly when backward movements featured the same movement directions as the ones trained in forward movements (i.e., when opposite targets were presented). This suggests that learning was transferred in a direction specific way, supporting the notion that movement direction is the most prominent parameter used for motor planning.
Kinetic analysis of oil palm empty fruit bunch (OPEFB) pellets as feedstock for pyrolysis
Authors: Nyakuma Bemgba Bevan
Published: January 2018

The thermal behaviour and decomposition kinetics of pelletized oil palm empty fruit bunch (OPEFB) was investigated in this study using thermogravimetric analysis (TGA). The OPEFB pellets were heated from room temperature to 1000 ºC at different heating rates; 5, 10 and 20 °C min-1 under inert atmosphere. Thermal degradation occurred in three steps; drying, devolatization and char decomposition. Subsequently, the Popescu method was applied to the TG/DTG data to determine the kinetic parameters of the OPEFB pellets. The activation energy, E, for different degrees of conversion, α = 0.05 to 0.7 are 36.60 kJ/mol to 233.90 kJ/mol with high correlation R2 values. In addition, the drying and decomposition of lignin reactions displayed lower E values compared to the devolatization characterized by high E value of 233 kJ/mol at α = 0.2. This indicates that the devolatization process is slower and requires higher energy requirement to reach completion than the other stages of thermal decomposition of the fuel under inert atmosphere. Keywords: decomposition, kinetics, oil palm, empty fruit bunch, pyrolysis.
An approach to improve the efficiency of apriori algorithm
Authors: Aggarwal Sakshi , Sindhu Ritu
Published: January 2018

Association rule mining has a great importance in data mining. Apriori is the key algorithm in association rule mining. Many approaches are proposed in past to improve Apriori but the core concept of the algorithm is same i.e. support and confidence of item sets and previous studies finds that classical Apriori is inefficient due to many scans on database. In this paper, we are proposing a method to improve Apriori algorithm efficiency by reducing the database size as well as reducing the time wasted on scanning the transactions.
A Gauge model-based analysis of: Reduction(s) in osmolyte infusion interval and its effects on the aggregate measure of systemic failure for a unicellular system
Authors: Jeff-Eke Imadol V
Published: January 2018

This is a companion to A Gauge model for analysis of Biological systems. Here we reconcile the gauge model with a “real” system, which in this case is a unicellular system. We address effects of infusion of free osmolytes into an intracellular space of interest, and how changes to the frequency of infusion affects the aggregate measure of systemic failure. We also describe limitations to the functionality of the system that may stem from a limited availability of resources. We end by introducing a theoretical problem related to how well the system can tolerate random and extreme changes to the frequency of osmolytes presented via infusion.
Distribution, biomass and phenology of Zostera noltei meadows in the Northern lagoon of Tunis in the summer of 2014
Authors: Ben Souissi Imen , Shili Abdessalem
Published: January 2018

Seagrass meadows of Zostera noltei are widely distributed over the coasts of Tunisia and represent relatively dominant populations in the Northern lagoon of Tunis. This brackish environment was the subject of a plan of restoration and development implemented in the mid 1980’s to deal with problems of eutrophication. This work is a contribution to the characterization of seagrass meadows of Z. noltei in the Northern lagoon of Tunis, with (i) mapping meadows along 36 equally spaced and well distributed transects, (ii) measuring the biomass with its two components, above and below-ground, in representative stations of different types of seagrass meadows, and (iii) the observation of phenological characteristics of the plant. The results show that Z. noltei meadows grow over 40% of the total area of the lagoon. They spread gradually to the Southern part of the lagoon where they are able to survive and to thrive. The total biomass in the North lagoon of Tunis was about 2512 tons of DW in June of 2014. Most of this biomass comes from dense beds with cover of 50 to 90%. The phenological characteristic analysis shows that the mean density is about 1830 shoots/m², the average length and average width of the leaves are 26.6 cm (SD = 6.9) and 1.8 mm (SD = 0.2), respectively. Depending on the type of cover, the total length of rhizomes varies between 2.3 and 40.6 m/m² and the average number of leaves/shoot is between 3.1 and 4.5 (SD = 0.4). Flowering, which begins in April, continues until the end of August. The flowering rate varies between stations, ranging from 0 to 16% in June of 2014. The study should be extended to other seasons to better understand the characteristics and dynamics of Z. noltei meadows, which have a very important role in the restoration and the ecological balance of the Northern lagoon of Tunis.
The impact of Docker containers on the performance of genomic pipelines
Authors: Di Tommaso Paolo , Palumbo Emilio , Chatzou Maria , Prieto Pablo , Heuer Michael L , Notredame Cedric
Published: January 2018

Genomic pipelines consist of several pieces of third party software and, because their experimental nature, frequent changes and updates are commonly necessary thus raising serious distribution and reproducibility issues. Docker containers technology offers an ideal solution, as it allows the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.
Debriefing of virtual patient encounters: Systematic collection of nursing students clinical reasoning activities
Authors: Georg Carina , Welin Henriksson Elisabet , Jirwe Maria , Ulfvarson Johanna , Zary Nabil
Published: January 2018

Background. Studies have shown that nursing students have challenges in translating and applying their theoretical knowledge in a clinical context. Virtual patients (VPs) have been proposed as an adequate learning and assessment activity to improve clinical reasoning. Although feedback and debriefing are essential aspects to foster learning in medical simulation, few studies have explored systematic and theory anchored ways of supporting feed forward and debriefing based on student activity collected in a systematic manner. Objective. The aim of this study was to develop a systematic approach for collecting the nursing students’ clinical reasoning artifacts as they encounter virtual patients. Method. The Outcome-Present-State-Test (OPT) model for clinical reasoning was used as the starting point since it is an internationally common model used by faculty to plan for and design learning activities in nursing education (Pesut & Herman, 1999). Two virtual patients were developed using the virtual patient nursing design model vpNDM (Georg &Zary, 2014). Nighty-five participants from undergraduate nursing education encountered the VPs and the intervention was composed of the exploration of methods for tracking and collecting the participants’ clinical reasoning artifacts. Results. An instrument to collect the students’ clinical reasoning was developed. Artifacts are collected during the whole virtual patient encounter. The aspects collected are related to clinical judgment, nursing action, outcome and present states, cue logic and the client in context. The empirical demonstrated that the instrument was able to collect and expose quantitative and qualitative aspects of the students’ clinical reasoning. Conclusions. A method to systematically collect aspects of clinical reasoning during a virtual patient driven learning activity would allow purposeful feed forward and provide the necessary information for constructive debriefing sessions.
Age, growth and reproduction of the Galapagos sailfin grouper Mycteroperca olfax (Jenyns, 1840): an overdue and needed comprehensive baseline
Authors: Usseglio Paolo , Friedlander Alan M. , DeMartini Edward E. , Schuhbauer Anna , Salinas de Léon Pelayo
Published: January 2018

The Galapagos Sailfin grouper, Mycteroperca olfax, locally known as bacalao and listed as vulnerable by IUCN, is culturally, economically, and ecologically important to the Galapagos archipelago and its people. It is regionally endemic to the Eastern Tropical Pacific, and, while an important fishery resource that has shown substantial declines in recent years, to date no effective management regulations are in place to ensure the sustainability of its Galapagos fishery. Previous estimates of longevity and size of maturity for bacalao are inconsistent with estimates for congeners, which questions the accuracy of prior estimates. We set out to rigorously assess the age, growth, and reproductive biology of bacalao in order to provide more accurate life history information to inform more effective fisheries management for this species. The oldest fish in our sample was 24 years old, which is 2-3 times greater than previously reported estimates of longevity. Parameter estimates for the von Bertalanffy growth function (k= 0.07, L∞= 119.1 cm TL, and to= -2.33 years) show bacalao to grow much slower and obtain substantially larger asymptotic maximum length than previous studies. Mean size at maturity (as female) was estimated at 61.1 cm TL, corresponding to an age of 7.8 years. As a protogynous hermaphrodite, size at sex change (from adult female to adult male) occurred at 83.7 cm TL, corresponding to 15.2 years of age. We found that sex ratios were extremely female biased (0.015 M:1F), with a large majority of the individuals in our experimental catch being immature (73%). Our results show that bacalao grow slower, live longer, and mature at a much larger size and greater age than previously thought, with very few mature males in the population. These findings have key implications for the fishery of this valuable species and urge for a long-due species management plan to ensure its long-term sustainability.
The yeast telomerase RNA, TLC1, participates in two distinct modes of TLC1-TLC1 association processes in vivo
Authors: Matsuguchi Tet , Blackburn Elizabeth
Published: January 2018

Telomerase core enzyme minimally consists of the telomerase reverse transcriptase domain-containing protein (Est2 in budding yeast S. cerevisiae) and telomerase RNA, which contains the template specifying the telomeric repeat sequence synthesized. Here we report that in vivo, a fraction of S. cerevisiae telomerase RNA (TLC1) molecules form complexes containing at least two molecules of TLC1, via two separable modes: one requiring a sequence in the 3’ region of the immature TLC1 precursor and the other requiring Ku and Sir4. Such physical TLC1-TLC1 association peaked in G1 phase and did not require telomere silencing, telomere tethering to the nuclear periphery, telomerase holoenzyme assembly, or detectable Est2-Est2 protein association. These data indicate that TLC1-TLC1 associations reflect processes occurring during telomerase biogenesis; we propose that TLC1-TLC1 associations and subsequent reorganization may be regulatory steps in telomerase enzymatic activation.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks: Part 2
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

The characteristics of the culture vessel determine, to a large extent, the type of growth medium suitable for use. For example, most growth media for high cell density cultivation are designed for expensive bioreactors operating either in continuous or fed-batch mode, where provision of additional nutrients and/or removal of metabolic waste products from the basal medium (comprising salts, buffer components and small amount of carbon and nitrogen sources) help increase biomass yield by maintaining culture conditions within the range conducive for growth. The inexpensive and ubiquitous shake flask, in contrast, is usually operated in batch mode and contains, at the outset, a comprehensive medium with all necessary nutrients for conversion into biomass, and also serves as a repository for secreted metabolites - some of which are detrimental for cell growth. Thus, designing medium for high cell density cultivation in shake flask is an optimization process with the aim to increase biomass formation while reducing toxic metabolite secretion. This preprint reports improvements to a previously reported semi-defined medium for high cell density aerobic cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. Specifically, by reducing the concentrations of glucose (from 6.0 to 4.0 g/L) and ammonium chloride (from 1.5 to 1.0 g/L), the following improvements were obtained: a shorter diauxic lag phase (3 versus 5 hours); a higher maximum optical density (12.0 versus 11.0) in a shorter total culture period (27 versus 48 hours), and smaller pH variation during cultivation (6.0 to 7.6 versus 5.5 to 7.8). Similar to the earlier study, glucose and yeast extract served as principal carbon sources in separate growth phases for E. coli in the improved formulated medium (FMimproved). Specifically, an OD600nm of 6.6 was attained after 9 hours of growth on glucose at 37 oC. After a lag phase of 3 hours, growth resumed on yeast extract and the OD600nm reached 12.0 after 27 hours. The broth’s pH decreased from 7.1 to 6.0 during the first growth phase, whereupon it gradually rose to 7.6 at the end of culture. A smaller pH decrease along with higher biomass yield in the first growth phase suggested that the lower glucose concentration in FMimproved might have prevented overflow metabolism (and associated negative effects on growth); thus, resulting in a shorter diauxic lag phase and total culture period. Collectively, increase in cell yield, as well as decrease in total culture time and a shorter diauxic lag phase arise from a small reduction in glucose concentration - which suggested that an optimum exist, beyond which occurrence of overflow metabolism would reduce cell yield and biomass formation.