bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleeping Beauty
Transposition
Authors: Ivics Zoltán , Izsvák Zsuzsanna 
Published: May 2015

ABSTRACT

Sleeping Beauty
(
SB
) is a synthetic transposon that was constructed based on sequences of transpositionally inactive elements isolated from fish genomes.
SB
is a Tc1/
mariner
superfamily transposon following a cut-and-paste transpositional reaction, during which the element-encoded transposase interacts with its binding sites in the terminal inverted repeats of the transposon, promotes the assembly of a synaptic complex, catalyzes excision of the element out of its donor site, and integrates the excised transposon into a new location in target DNA.
SB
transposition is dependent on cellular host factors. Transcriptional control of transposase expression is regulated by the HMG2L1 transcription factor. Synaptic complex assembly is promoted by the HMGB1 protein and regulated by chromatin structure.
SB
transposition is highly dependent on the nonhomologous end joining (NHEJ) pathway of double-strand DNA break repair that generates a transposon footprint at the excision site. Through its association with the Miz-1 transcription factor, the
SB
transposase downregulates cyclin D1 expression that results in a slowdown of the cell-cycle in the G1 phase, where NHEJ is preferentially active. Transposon integration occurs at TA dinucleotides in the target DNA, which are duplicated at the flanks of the integrated transposon.
SB
shows a random genome-wide insertion profile in mammalian cells when launched from episomal vectors and “local hopping” when launched from chromosomal donor sites. Some of the excised transposons undergo a self-destructive autointegration reaction, which can partially explain why longer elements transpose less efficiently.
SB
became an important molecular tool for transgenesis, insertional mutagenesis, and gene therapy.
Ty3, a Position-specific Retrotransposon in Budding Yeast
Authors: Sandmeyer Suzanne , Patterson Kurt , Bilanchone Virginia 
Published: May 2015

ABSTRACTLong terminal repeat (LTR) retrotransposons constitute significant fractions of many eukaryotic genomes. Two ancient families are Ty1/Copia (Pseudoviridae) and Ty3/Gypsy (Metaviridae). The Ty3/Gypsy family probably gave rise to retroviruses based on the domain order, similarity of sequences, and the envelopes encoded by some members. The Ty3 element ofSaccharomyces cerevisiaeis one of the most completely characterized elements at the molecular level. Ty3 is induced in mating cells by pheromone stimulation of the mitogen-activated protein kinase pathway as cells accumulate in G1. The two Ty3 open reading frames are translated into Gag3 and Gag3–Pol3 polyprotein precursors. In haploid mating cells Gag3 and Gag3–Pol3 are assembled together with Ty3 genomic RNA into immature virus-like particles in cellular foci containing RNA processing body proteins. Virus-like particle Gag3 is then processed by Ty3 protease into capsid, spacer, and nucleocapsid, and Gag3–Pol3 into those proteins and additionally, protease, reverse transcriptase, and integrase. After haploid cells mate and become diploid, genomic RNA is reverse transcribed into cDNA. Ty3 integration complexes interact with components of the RNA polymerase III transcription complex resulting in Ty3 integration precisely at the transcription start site. Ty3 activation during mating enables proliferation of Ty3 between genomes and has intriguing parallels with metazoan retrotransposon activation in germ cell lineages. Identification of nuclear pore, DNA replication, transcription, and repair host factors that affect retrotransposition has provided insights into how hosts and retrotransposons interact to balance genome stability and plasticity.
An Unexplored Diversity of Reverse Transcriptases in Bacteria
Authors: Zimmerly Steven , Wu Li 
Published: May 2015

ABSTRACT
Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.
Topological Behavior of Plasmid DNA
Authors: Higgins N. Patrick , Vologodskii Alexander V. 
Published: May 2015

ABSTRACT

The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing
in vivo
and
in vitro
reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
Plasmid Detection, Characterization, and Ecology
Authors: Smalla Kornelia , Jechalke Sven , Top Eva M. 
Published: May 2015

ABSTRACT
Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
Risk factors for injury in sport climbing and bouldering: a systematic review of the literature
Authors: Woollings Kaikanani Y , McKay Carly D , Emery Carolyn A 
Published: May 2015

BackgroundRock climbing is an increasingly popular sport worldwide, as a recreational activity and a competitive sport. Several disciplines including sport climbing and bouldering have developed, each employing specific movements and techniques, leading to specific injuries.ObjectiveTo examine risk factors and prevention measures for injury in sport climbing and bouldering, and to assess the methodological quality of existing studies.Methods12 electronic databases and several other sources were searched systematically using predetermined inclusion and exclusion criteria. Eligible articles were peer-reviewed, based on primary research using original data; outcome measures included injury, morbidity or mortality in rock climbing, and included one or more potential risk factor or injury prevention strategy. Two independent reviewers assessed the methodology of research in each study using the Downs and Black Quality Index. The data extracted is summarised, and appraisals of the articles are presented with respect to the quality of evidence presented.Results19 studies met the inclusion criteria, and introduced 35 possible risk factors or injury prevention measures in climbing. Age, increasing years of climbing experience, highest climbing grade achieved (skill level), high climbing intensity score (CIS) and participating in lead climbing are potential risk factors. Results regarding injury prevention measures remain inconclusive.DiscussionThis field is relatively new and, as such, the data are not as robust as for more established sports with a larger research foundation. The key need is establishing modifiable risk factors using prospective studies and high quality methodology, such that injury prevention strategies can be developed. The CIS may be a useful measure in this field of research.
Extra Physiotherapy in Critical Care (EPICC) Trial Protocol: a randomised controlled trial of intensive versus standard physical rehabilitation therapy in the critically ill
Authors: Thomas Kirsty , Wright Stephen E , Watson Gillian , Baker Catherine , Stafford Victoria , Wade Clare , Chadwick Thomas J , Mansfield Leigh , Wilkinson Jennifer , Shen Jing , Deverill Mark , Bonner Stephen , Hugill Keith , Howard Philip , Henderson Andrea , Roy Alistair , Furneval Julie , Baudouin Simon V 
Published: May 2015

IntroductionPatients discharged from Critical Care suffer from excessive longer term morbidity and mortality. Physical and mental health measures of quality of life show a marked and immediate fall after admission to Critical Care with some recovery over time. However, physical function is still significantly reduced at 6 months. The National Institute for Health and Care Excellence clinical guideline on rehabilitation after critical illness, identified the need for high-quality randomised controlled trials to determine the most effective rehabilitation strategy for critically ill patients at risk of critical illness-associated physical morbidity. In response to this, we will conduct a randomised controlled trial, comparing physiotherapy aimed at early and intensive patient mobilisation with routine care. We hypothesise that this intervention will improve physical outcomes and the mental health and functional well-being of survivors of critical illness.Methods and analysis308 adult patients who have received more than 48 h of non-invasive or invasive ventilation in Critical Care will be recruited to a patient-randomised, parallel group, controlled trial, comparing two intensities of physiotherapy. Participants will be randomised to receive either standard or intensive physiotherapy for the duration of their Critical Care admission. Outcomes will be recorded on Critical Care discharge, at 3 and 6 months following initial recruitment to the study. The primary outcome measure is physical health at 6 months, as measured by the SF-36 Physical Component Summary. Secondary outcomes include assessment of mental health, activities of daily living, delirium and ventilator-free days. We will also include a health economic analysis.Ethics and disseminationThe trial has ethical approval from Newcastle and North Tyneside 2 Research Ethics Committee (11/NE/0206). There is a Trial Oversight Committee including an independent chair. The results of the study will be submitted for publication in peer-reviewed journals and presented at national and international scientific meetings.Trial registration numberISRCTN20436833.
Impact of Wind Direction, Wind Speed, and Particle Characteristics on the Collection Efficiency of the Double Fence Intercomparison Reference
Authors: Thériault Julie M. , Rasmussen Roy , Petro Eddy , Trépanier Jean-Yves , Colli Matteo , Lanza Luca G. 
Published: May 2015

AbstractThe accurate measurement of snowfall is important in various fields of study such as climate variability, transportation, and water resources. A major concern is that snowfall measurements are difficult and can result in significant errors. For example, collection efficiency of most gauge–shield configurations generally decreases with increasing wind speed. In addition, much scatter is observed for a given wind speed, which is thought to be caused by the type of snowflake. Furthermore, the collection efficiency depends strongly on the reference used to correct the data, which is often the Double Fence Intercomparison Reference (DFIR) recommended by the World Meteorological Organization. The goal of this study is to assess the impact of weather conditions on the collection efficiency of the DFIR. Note that the DFIR is defined as a manual gauge placed in a double fence. In this study, however, only the double fence is being investigated while still being called DFIR. To address this issue, a detailed analysis of the flow field in the vicinity of the DFIR is conducted using computational fluid dynamics. Particle trajectories are obtained to compute the collection efficiency associated with different precipitation types for varying wind speed. The results show that the precipitation reaching the center of the DFIR can exceed 100% of the actual precipitation, and it depends on the snowflake type, wind speed, and direction. Overall, this study contributes to a better understanding of the sources of uncertainty associated with the use of the DFIR as a reference gauge to measure snowfall.
The Formation of Moist Vortices and Tropical Cyclones in Idealized Simulations
Authors: Davis Christopher A. 
Published: May 2015

Abstract
The upscale aggregation of convection is used to understand the emergence of rotating, coherent midtropospheric structures and the subsequent process of tropical cyclone formation. The Cloud Model, version 1 (CM1), is integrated on an f plane with uniform sea surface temperature (SST) and prescribed uniform background flow. Deep convection is maintained by surface fluxes from an ocean with uniform surface temperature. Convection begins to organize simultaneously into moist and dry midtropospheric patches after 10 days. After 20 days, the patches begin to rotate on relatively small scales. Moist cyclonic vortices merge, eventually forming a single dominant vortex that subsequently forms a tropical cyclone on a realistic time scale of about 5 days. Radiation that interacts with clouds and water vapor aids in forming coherent rotating structures. Using the path to genesis provided by the aggregated solution, the relationship between thermodynamic changes within the vortex and changes in the character of convection prior to genesis is explored. Consistent with previous studies, the approach to saturation within the midtropospheric vortex accelerates the genesis process. A novel result is that, prior to genesis, downdrafts become widespread and somewhat stronger. The increased downdraft mass flux leads to stronger and larger surface cold pools. Shear–cold pool dynamics promote the organization of lower-tropospheric updrafts that spin up the surface vortex. It is inferred that the observed inconsistency between convective intensity and thermodynamic stabilization prior to genesis results from sampling limitations of the observations wherein the important cold pool gradients are unresolved.
Impact of the Depth-to-Width Ratio of Periodically Stratified Tidal Channels on the Estuarine Circulation
Authors: Schulz Elisabeth , Schuttelaars Henk M. , Gräwe Ulf , Burchard Hans 
Published: May 2015

AbstractThe dependency of the estuarine circulation on the depth-to-width ratio of a periodically, weakly stratified tidal estuary is systematically investigated here for the first time. Currents, salinity, and other properties are simulated by means of the General Estuarine Transport Model (GETM) in cross-sectional slice mode, applying a symmetric Gaussian-shaped depth profile. The width is varied over four orders of magnitude. The individual along-channel circulation contributions from tidal straining, gravitation, advection, etc., are calculated and the impact of the depth-to-width ratio on their intensity is presented and elucidated. It is found that the estuarine circulation exhibits a distinct maximum in medium-wide channels (intermediate depth-to-width ratio depending on various parameters), which is caused by a maximum of the tidal straining contribution. This maximum is related to a strong tidal asymmetry of eddy viscosity and shear created by secondary strain-induced periodic stratification (2SIPS): in medium channels, transverse circulation generated by lateral density gradients due to laterally differential longitudinal advection induces stable stratification at the end of the flood phase, which is further increased during ebb by longitudinal straining (SIPS). Thus, eddy viscosity is low and shear is strong in the entire ebb phase. During flood, SIPS decreases the stratification so that eddy viscosity is high and shear is weak. The circulation resulting from this viscosity–shear correlation, the tidal straining circulation, is oriented like the classical, gravitational circulation, with riverine outflow at the surface and oceanic inflow close to the bottom. In medium channels, it is about 5 times as strong as in wide (quasi one-dimensional) channels, in which 2SIPS is negligible.
Effect of Hematologic Parameters on Microvascular Reperfusion in Patients With ST-Segment Elevation Myocardial Infarction Treated With Primary Percutaneous Coronary Intervention
Authors: Karahan Zülküf , Uçaman Berzal , Uluğ Ali Veysel , Aydınalp Özlem , Uğurlu Murat , Çevik Kemal , Kaya İlyas , Öztürk Önder 
Published: May 2015

Objectives: Despite the significant role of certain hematologic parameters in reperfusion injury, their relationship with microvascular reperfusion remains not well understood. Therefore, our objective was to evaluate the relationship between hematologic parameters at admission and microvascular reperfusion in patients with ST-segment elevation myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (primary PCI). Methods: A total of 213patients (mean age: 57.5 ± 11 years) with STEMI were included. Blood samples were obtained from all patients prior to primary PCI. Electrocardiographic recordings were made for the evaluation of ST-segment resolution (STR) before and after primary PCI. Angiographic assessment in the infarct-related artery was performed using the myocardial blush grade (MBG) and thrombolysis in myocardial infarction (TIMI) flow. Patients were categorized into 2 groups as those with impaired microvascular reperfusion (STR <70%, TIMI: 0-1, and MBG: 0-1) and those with normal microvascular reperfusion (STR >70%, TIMI: 2-3, and MBG: 2-3). Results: Of the overall study group, 139, 105, and 69 patients had an STR of <70%, MBG of 0-1, and TIMI of 0-1, respectively. Demographic parameters in both groups are shown in the tables. Patients with impaired microvascular reperfusion were found to have higher white blood cell (WBC) count, neutrophil count, lymphocyte count, and mean platelet volume (MPV). Neutrophil–lymphocyte ratio and platelet count were similar between the 2 groups. Correlation analysis showed a negative correlation between lymphocyte count and STR ( r: −.195, P: .004), lymphocyte count and TIMI flow( r: −.09, P: .14), and lymphocyte count and MBG ( r: −.211, P: .002). Conclusion: Our results suggest that higher WBC count and MPV at admission are independent predictors of impaired microvascular perfusion in patients with STEMI. On the other hand, a negative correlation was found between lymphocyte count and impaired microvascular perfusion. Specifically, elevated lymphocyte count seemed to indicate the presence of impaired microvascular reperfusion in patients with STEMI.
Group Analysis in China—Challenges in a Changing Society
Authors: Beck Werner 
Published: May 2015

In 1988, a legendary conference took place in Kunming, China, introducing western psychotherapy to Chinese colleagues. It consisted of three branches: psychodynamic, behaviour therapy and systemic family therapy. This conference found an immense echo all over China and raised a strong desire for training in these therapies to be set up. Soon, curriculae were created and proffered. A real run on these trainings followed, most of them in individual therapies. A group of German psychoanalysts carried out the psychodynamic training in two-year long courses for Chinese psychologists and psychiatrists. In 2008, a two-year training course in psychodynamic group psychotherapy was added for those participants who had concluded their training as individual therapists. In the beginning this training was oriented towards the concept of the German psychoanalyst Hermann Argelander (close to Bion), but later on was influenced by the model of Foulkes, studying the standard book of Behr and Hearst, that was soon translated into Chinese. The participants were members of an experiential group and of a working and supervisory group as well. Group work was complemented by daily lectures. The two-year course consisted of four blocks of eight training days each, comprising 56 experiential sessions altogether. Towards the end of the course, the participants had to establish a group of their own, find a supervisor and conduct the group for a reasonable time. They then had to write a report about their group, which was discussed in the supervisory group. This led to the conclusion of the course. I joined this project from 2011 to 2013, conducted an experiential and a working group, and gave lectures on group analytic theory. During this period there were six such groups with German colleagues, who had regular meetings together with the Chinese staff and the interpreters. This article tries to sum up the process in the experiential group, to show the development of the group and its characteristic features in this very different society compared to our western cultures. Is there anything that is ‘typical Chinese’ in these 56 sessions? What could that be? Does the application of the group analytic approach in such a different culture with such a different foundation matrix make sense? There are many questions. I hope this clinical report answers at least some of them.