pinecone/core-2020-05-10-deduplication huggingface dataset:
Quantifying evolutionary development using non-model organisms: Integrating morphology, metrical frameworks, and gene expression

Keeping pace with the forward progression of evolutionary developmental studies and their trajectory toward ever-more integrative and broad-scale study presents a challenge for researchers from diverse disciplines. Increasing the capacity for discourse and opening opportunity to further interdisciplinary work is highly desirable, and one way that activities can be hindered is through a lack of communication between those developing new methods and those applying methods to new data sets. The goal of this special issue, which brings together contributions from a recent symposium at the 10th International Congress for Vertebrate Morphology (ICVM 10, Barcelona, July 2013) along with select additions, was to integrate methodological developments with molecular and morphological data to present a broad spectrum of avenues for investigating ontogeny in land vertebrates. A balance between methods-focused papers and papers presenting novel data and perspectives from molecular and morphological approaches in evo-devo was sought with the hope of promoting greater interchange between each side, and drawing attention to new opportunities for future research on non-model organisms
What to compare and how: Comparative transcriptomics for Evo-Devo.

Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372-382, 2015. © 2015 Wiley Periodicals, Inc
Recovery from a depressive episode during postgraduate residency training is associated with senior doctors\u27 support

BackgroundDepression among doctors in residency training can have significant impacts on the health of the residents and on patient safety. This study aimed to investigate factors associated with recovery from a depressive episode experienced during postgraduate residency training.MethodsA questionnaire was administered to 2935 first‐year residents at the beginning of residency training in 2011; follow‐up surveys were conducted after 3 months and at the end of the training in 2013. The questionnaire included the Center for Epidemiologic Studies Depression Scale and the Senior Doctor\u27s Support Scale (SDSS). Logistic regression was used to identify associations between factors that may have been related to recovery from depressive episodes.ResultsA total 182 residents experienced a depressive episode in the 3 months after starting residency training. When reassessed at the end of the 2‐year training, 102 (56%) residents had recovered from the episode and 80 (44%) had not. Increased odds of recovery were associated with a middle or high score on the SDSS (middle score odds ratios [OR] 4.45, 95% confidence interval [CI] 1.0‐18.0, P = .04; and high score OR 5.70, 95% CI 1.4‐23.4, P = .02).ConclusionsSupport from senior doctors should be enhanced to optimize recovery from depressive episodes experienced after the start of residency training
Adherence to blood pressure measurement guidelines in long-term care facilities: A cross sectional study

ObjectiveTo assess the extent to which long‐term care facilities in Japan adhere to blood pressure (BP) measurement guidelines.DesignCross‐sectional, observational survey.SettingJapan (nationwide).ParticipantsGeriatric health service facilities that responded to a questionnaire among 701 facilities that provide short‐time daycare rehabilitation services in Japan.MethodsA written questionnaire that asked about types of measurement devices, number of measurements used to obtain an average BP, resting time prior to measurement, and measurement methods when patients’ arms were covered with thin (eg, a light shirt) or thick sleeves (eg, a sweater) was administered.Main outcome measureProportion of geriatric health service facilities adherent to BP measurement guidelines.ResultsThe response rate was 63.2% (443/701). Appropriate upper‐arm BP measurement devices were used at 302 facilities (68.2%). The number of measurements was appropriate at 7 facilities (1.6%). Pre‐measurement resting time was appropriate (≥5 minutes) at 205 facilities (46.3%). Of the 302 facilities that used appropriate BP measurement devices, 4 (1.3%) measured BP on a bare arm if it was covered with a thin sleeve, while 266 (88.1%) measured BP over a thin sleeve. When arms were covered with thick sleeves, BP was measured on a bare arm at 127 facilities (42.1%) and over a sleeve at 78 facilities (25.8%).ConclusionsBP measurement guidelines were not necessarily followed by long‐term care service facilities in Japan. Modification of guidelines regarding removing thick sweaters and assessing BP on a visit‐to‐visit basis might be needed
Prevalence of obstructive sleep apnea in primary care patients with hypertension

BackgroundAs the number of patients with hypertension who have obstructive sleep apnea (OSA) might be underestimated, this study aimed to explore the prevalence of OSA and develop a diagnostic algorithm for moderate or severe OSA among primary care (PC) patients with hypertension.MethodsThis multicenter cross‐sectional study enrolled patients diagnosed with hypertension aged 18 years or older in Japan from October 2012 to September 2014.ResultsForty‐nine patients (64.5%) had 22 or more obstructive respiratory events during sleep.ConclusionsThe prevalence of OSA among PC patients with hypertension might be much higher than previously thought
Protective vaccination with hepatitis C virus NS3 but not core antigen in a novel mouse challenge model

BACKGROUND:
Efficient vaccines against hepatitis C virus (HCV) infection are urgently needed. Vaccine development has been hampered by the lack of suitable small animal models to reliably test the protective capacity of immmunization.
METHODS:
We used recombinant murine gammaherpesvirus 68 (MHV-68) as a novel challenge virus in mice and tested the efficacy of heterologous candidate human vaccines based on modified vaccinia virus Ankara or adenovirus, both delivering HCV non-structural NS3 or core proteins.
RESULTS:
Recombinant MHV-68 expressing NS3 (MHV-68-NS3) or core (MHV-68-core) were constructed and characterized in vitro and in vivo. Mice immunized with NS3-specific vector vaccines and challenged with MHV-68-NS3 were infected but showed significantly reduced viral loads in the acute and latent phase of infection. NS3-specific CD8+ T cells were amplified in immunized mice after challenge with MHV-68-NS3. By contrast, we did neither detect a reduction of viral load nor an induction of core-specific CD8+ T cells after core-specific immunization.
CONCLUSIONS:
Our data suggest that the challenge system using recombinant MHV-68 is a highly suitable model to test the immunogenicity and protective capacity of HCV candidate vaccine antigens. Using this system, we demonstrated the usefulness of NS3-specific immunization. By contrast, our analysis rather discarded core as a vaccine antigen
Investigating relationship between transfection and permeabilization by the electric field and/or the Pluronic® L64 in vitro and in vivo.

International audienceBACKGROUND: Electrotransfer can be obtained by the successive delivery of a high voltage short duration pulse (HV) inducing membrane destabilization and then a low voltage long duration pulse (LV), allowing DNA electrophoresis (HVLV mode). Pluronic® L64 (L64) (Fluka, Sigma-Aldrich, L'Isle-d'Abeau Chesnes, Saint-Quentin Fallavier, France) has permeabilizing properties and amplifies the expression of DNA. We aimed to determine whether L64 could have an adjuvant effect on transfection by electrotransfer and whether the sequence L64 injection and then application of a LV pulse could induce transfection comparable to that observed with the HVLV mode. METHODS: In vitro, we used fluorescence-activated cell sorting to evaluate Chinese hamster ovary (CHO) cell transfection by a plasmid coding green fluorescent protein, and permeabilization to propidium iodide. In vivo, the transfection efficiency of mice tibial cranial muscle was evaluated by optical imaging using a plasmid DNA encoding luciferase. For the same animals, permeabilization indices were evaluated by magnetic resonance imaging from the uptake of a T(1) contrast agent. RESULTS: Using the HVLV mode, transfection efficiency was low in vitro on CHO cells but high for muscles in vivo. Pre-treatment by L64 increased the transfection efficiency of electrotransfer for CHO cells but not for muscle. In mice muscles, the L64 amplified the expression of DNA. Nevertheless, neither transgene expression, nor permeability indices were further amplified by subsequent delivery of one LV pulse. CONCLUSIONS: A major finding of the present study is that the nature of the membrane modification induced by electric pulses is not comparable to that mediated by L64. The electrophoretic LV pulse does not induce additive effects to that of L64 for transfection improvement
Quantification of cytosolic plasmid DNA degradation using high‐throughput sequencing: implications for gene delivery

Background  Although cytosolic DNA degradation plays an important role in decreasing transgene expression, the plasmid degradation pattern remains largely unexplored.    Methods  Illumina dye sequencing was employed to provide degradation site information for S1 and cytosolic nucleases. S1 nuclease provided a positive control for a comparison between the agarose gel method and sequencing approaches.    Results  The poly(A) region between the β‐lactamase gene and the cytomegalovirus (CMV) promoter was identified as the most likely cut site for polyplex‐treated cytosol. The second most likely site, at the 5' end of the β‐lactamase gene, was identified by gel electrophoresis and sequencing. Additional sites were detected in the  OriC  region, the SV40/poly(A) region, the luciferase gene and the CMV promoter. Sequence analysis of plasmid treated with cytosol from control cells showed the greatest cut activity in the  OriC  region, the β‐lactamase gene and the poly(A) region following the luciferase gene. Additional regions of cut activity include the SV40 promoter and the β‐lactamase poly(A) termination sequence. Both cytosolic nucleases and the S1 nuclease showed substantial activity at the bacterial origin of replication ( OriC ).    Conclusions  High‐throughput plasmid sequencing revealed regions of the luciferase plasmid DNA sequence that are sensitive to cytosolic nuclease degradation. This provides new targets for improving plasmid and/or polymer design to optimize the likelihood of protein expression. Copyright © 2014 John Wiley & Sons, Ltd
Promoter Optimisation of Lentiviral Vectors for E fficient Insulin Gene Expression in Canine Mesenchymal Stromal Cells: Potential Surrogate Beta Cells

Background:
The lack of an ideal cell type that can be easily acquired, modified to produce insulin, and re-implanted has been a limitation for ex vivo insulin gene therapy. Canine diabetes is currently treated with human insulin and is a good model for human diabetes. Mesenchymal stromal cells (MSCs) are a promising candidate cell type for gene therapy. Here we optimised insulin production using lentiviral transduced canine MSCs aiming to evaluate their ability for use as surrogate beta cells.
Method:
Canine MSCs were derived from bone marrow and validated by measuring expression of MSC lineage specific markers. Lentivirus vectors encoding the proinsulin gene (with or without a Kozak sequence) under the control of SFFV, CMV, EF1α and SV40 promotors were generated and used to transduce primary cMSCs and a hepatocyte cell line. The insulin producing capacity of transduced primary canine MSCs was assessed by measuring the concentration of C-peptide produced.
Result:
Primary canine MSC could be readily expanded in culture and efficiently transduced using lentiviral vectors encoding proinsulin. Increasing the multiplicity of infection from 3 to 20, led to an increase in C-peptide secretion (1700 pmol/l to 4000 pmol/l). The SFFV promoter conferred the strongest transcriptional ability.
Conclusion:
Our results suggest that optimised lentiviral transduction of the insulin gene into primary canine MSCs renders these cells capable of secreting insulin both short- and long-term, in sufficient quantities in vitro to support their potential use in insulin gene therapy.The study was funded by the Lollipop Trust. Work in the laboratory is supported by the Biomedical Research Centre.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/jgm.290
Efficient and non-toxic gene delivery by anionic lipoplexes based on polyprenyl ammonium salts and their effects on cell physiology

Background\ud
One of the major challenges limiting development of gene therapy is absence of efficient and safe gene carriers. Among the non-viral gene delivery methods, lipofection is considered as one of the most promising. In this study a set of cationic polyprenyl derivatives (trimethylpolyprenylammonium iodides – PTAI) with different lengths of polyprenyl chains (from 7, 8 and 11 to 15 isoprene units) was suggested as a component of efficient DNA vehicles.\ud
Methods\ud
Optimization studies were conducted for PTAI in combination with co-lipid DOPE (dioleoylphosphatidylethanolamine) on DU145 human prostate cancer cells using: size and zeta potential measurements, confocal microscopy, fluorescein diacetate/ethidium bromide test, cell counting, time-lapse monitoring of cell movement, gap junctional intracellular coupling analysis, antimicrobial activity assay, red blood cell hemolysis test.\ud
Results\ud
The results show that the lipofecting activity of PTAI allows effective transfection of plasmid DNA complexes in negatively charged lipoplexes of 200 - 500 nm size into cells without significant side effects on cell physiology (viability, proliferation, morphology, migration and gap junctional intercellular coupling – GJIC). Moreover, PTAI-based vehicles exhibit a potent bactericidal activity against Staphylococcus aureus and Escherichia coli. The developed anionic lipoplexes are safe towards human red blood cell membranes which are not disrupted in their presence.\ud
Conclusions\ud
The developed carriers constitute a group of promising lipofecting agents of a new type and can be utilized as effective lipofecting agents in vitro and are a promising basis for in vivo applications
Upscaling of lentiviral vector production by tangential flow filtration

BACKGROUND: HIV-1-derived vectors are promising tools for gene transfer into the brain. Application of these vectors for gene therapy or for the creation of animal models for neurodegenerative diseases requires standardization and upscaling of lentiviral vector production methods. METHODS: In this study, serum-free HIV-1 vector production was efficiently upscaled by use of cell factories and the introduction of tangential flow filtration (TFF) prior to centrifugation. RESULTS: Vector titers (TU/ml) and p24 values (pg p24/ml) for a serum-free HIV-1 vector produced in cell factories and using TFF prior to centrifugation were comparable to those of small-scale productions. TFF allowed a 66-fold concentration of the vectors with complete vector recovery. Further concentration of the vector (30-fold) was achieved either by low-speed centrifugation or by ultracentrifugation. Combination of TFF and ultracentrifugation resulted in a vector recovery of 90-100% and titers that increased 1800-fold and 900-fold for transducing units and p24 concentration, respectively. CONCLUSIONS: With this new standardized method for lentiviral vector production and concentration, 1 ml of concentrated vector is routinely produced with titers of 10(9)-10(10) TU/ml starting from 2 l of cell-culture medium. Moreover, stereotactic injection of this vector in mouse striatum resulted in a large transduced brain volume in the absence of any immune response.status: publishe
Structure of Titan ’ s induced magnetosphere under varying background magnetic fi eld conditions: Survey of Cassini magnetometer data from fl ybys TA – T85

Cassini magnetic field observations between 2004 and 2012 suggest the ambient field conditions near Titan’s orbit to differ significantly from the frequently applied pre-Cassini picture (background magnetic field homogeneous and perpendicular to Titan’s orbital plane, stationary upstream conditions). In this study, we analyze the impact of these varying background field conditions on the structure of Titan’s induced magnetosphere by conducting a systematic survey of Cassini magnetic field observations in the interaction region during flybys TA–T85 (July 2004–July 2012). We introduce a set of criteria that allow to identify deviations in the structure of Titan’s induced magnetosphere—as seen by the Cassini magnetometer (MAG)—from the picture of steady-state field line draping. These disruptions are classified as “weak”, “moderate”, or “strong”. After applying this classification scheme to all available Titan encounters, we survey the data for a possible correlation between the disruptions of the draping pattern and the ambient magnetospheric field conditions, as characterized by Simon et al. [2010a]. Our major findings are: (1) When Cassini is embedded in the northern or southern lobe of Saturn’s magnetodisk within a ` 3 h interval around closest approach, Titan’s induced magnetosphere shows little or no deviations at all from the steady-state draping picture. (2) Even when Titan is embedded in perturbed current sheet fields during an encounter, the notion of draping the average background field around the moon’s ionosphere is still applicable to explain MAG observations from numerous Titan flybys. (3) Only when Titan is exposed to intense north- south oscillations of Saturn’s current sheet at the time of an encounter, the signatures of the moon’s induced magnetosphere may be completely obscured by the ambient field perturbations. (4) So far, T70 is the only flyby that fully meets the idealized pre-Cassini picture of the Titan interaction (steady background field perpendicular to Titan’s orbital plane, steady upstream flow, unperturbed induced magnetosphere).Fil: Simon, Sven. University of Cologne. Institute of Geophysics and Meteorology; Alemania;Fil: van Treeck, Shari C.. University of Cologne. Institute of Geophysics and Meteorology; Alemania;Fil: Wennmacher, Alexandre. University of Cologne. Institute of Geophysics and Meteorology; Alemania;Fil: Saur, Joachim. University of Cologne. Institute of Geophysics and Meteorology; Alemania;Fil: Neubauer, Fritz M.. University of Cologne. Institute of Geophysics and Meteorology; Alemania;Fil: Bertucci, Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio(i); Argentina;Fil: Dougherty, Michele K.. Imperial College Of Science And Technology. Space and Atmospheric Physics Group; Reino Unido
Advancing In Situ Modeling of ICMEs: New Techniques for New Observations

It is generally known that multi-spacecraft observations of interplanetary
coronal mass ejections (ICMEs) more clearly reveal their three-dimensional
structure than do observations made by a single spacecraft. The launch of the
STEREO twin observatories in October 2006 has greatly increased the number of
multipoint studies of ICMEs in the literature, but this field is still in its
infancy. To date, most studies continue to use on flux rope models that rely on
single track observations through a vast, multi-faceted structure, which
oversimplifies the problem and often hinders interpretation of the large-scale
geometry, especially for cases in which one spacecraft observes a flux rope,
while another does not. In order to tackle these complex problems, new modeling
techniques are required. We describe these new techniques and analyze two ICMEs
observed at the twin STEREO spacecraft on 22-23 May 2007, when the spacecraft
were separated by ~8 degrees. We find a combination of non-force-free flux rope
multi-spacecraft modeling, together with a new non-flux rope ICME plasma flow
deflection model, better constrains the large-scale structure of these ICMEs.
We also introduce a new spatial mapping technique that allows us to put
multispacecraft observations and the new ICME model results in context with the
convecting solar wind. What is distinctly different about this analysis is that
it reveals aspects of ICME geometry and dynamics in a far more visually
intuitive way than previously accomplished. In the case of the 22-23 May ICMEs,
the analysis facilitates a more physical understanding of ICME large-scale
structure, the location and geometry of flux rope sub-structures within these
ICMEs, and their dynamic interaction with the ambient solar wind
Production of very high potential differences by intracloud lightning discharges in connection with terrestrial gamma ray flashes

International audience[1] Terrestrial gamma-ray flashes (TGFs) have been correlated with an early development stage of high altitude positive intracloud (+IC) flashes in which the negative leader propagates up toward the upper positive charge region, while the positive leader propagates down toward the lower negative charge region. The resultant bidirectional leaders develop electrical potential differences in the vicinity of their heads with respect to the ambient potential distribution created by the thundercloud charges. These potential differences are believed to be of essential importance for the generation of TGFs. Using electrostatic calculations and a three-dimensional Cartesian fractal model, we quantify these potential differences produced in a developing +IC lightning discharge for given thunderstorm electric configurations. We present a case of a +IC lightning discharge in a realistic thunderstorm configuration that leads to a very high ($300 MV) potential difference and show how a delay in the development of the negative leader with respect to the positive one in a bidirectional leader system can facilitate a high potential difference in the negative leader head region. Citation: Mallios, S. A., S. Celestin, and V. P. Pasko (2013), Production of very high potential differences by intracloud lightning discharges in connection with terrestrial gamma ray flashes, J. Geophys. Res. Space Physics, 118, 912–918, doi:10.1002/jgra.50109