bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the effects of SNPs on transcription factor binding affinity
Authors: Nishizaki Sierra S , Ng Natalie , Dong Shengcheng , Porter Robert S , Morterud Cody , Williams Colten , Asman Courtney , Switzenberg Jessica A , Boyle Alan P 
Published: August 2019

Abstract

Motivation
Genome-wide association studies have revealed that 88% of disease-associated single-nucleotide polymorphisms (SNPs) reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl).

Results
SEMpl estimates transcription factor-binding affinity by observing differences in chromatin immunoprecipitation followed by deep sequencing signal intensity for SNPs within functional transcription factor-binding sites (TFBSs) genome-wide. By cataloging the effects of every possible mutation within the TFBS motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci.

Availability and implementation
SEMpl is available from https://github.com/Boyle-Lab/SEM_CPP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Target enrichment from a DNA mixture by oligoribonucleotide interference-PCR (ORNi-PCR)
Authors: Fujita Toshitsugu , Motooka Daisuke , Fujii Hodaka 
Published: August 2019

Abstract
Oligoribonucleotide (ORN) interference-PCR (ORNi-PCR) is a method that suppresses PCR amplification of target DNA in an ORN-specific manner. In this study, we examined whether ORNi-PCR can be used to enrich desirable DNA sequences from a DNA mixture by suppressing undesirable DNA amplification. ORNi-PCR enriched edited DNA sequences from a mixture of genomic DNA subjected to genome editing. ORNi-PCR enabled more efficient analysis of the types of insertion/deletion mutations introduced by genome editing. In addition, ORNi-PCR reduced the detection of 16S ribosomal RNA (16S rRNA) genes in 16S rRNA gene-based microbiome profiling, which might permit a more detailed assessment of populations of other 16S rRNA genes. Enrichment of desirable DNA sequences by ORNi-PCR may be useful in molecular biology, medical diagnosis, and other fields.
Long-term Impact of Pneumococcal Conjugate Vaccines on Invasive Disease and Pneumonia Hospitalizations in Indigenous and Non-Indigenous Australians
Authors: Meder Kelley N , Jayasinghe Sanjay , Beard Frank , Dey Aditi , Kirk Martyn , Cook Heather , Strachan Janet , Sintchenko Vitali , Smith Helen , Giele Carolien , Howden Benjamin , Krause Vicki , Mcintyre Peter 
Published: August 2019

Abstract

Background
Universal pneumococcal conjugate vaccine (PCV) programs began in Indigenous Australian children in 2001 and all children in 2005, changing to 13-valent PCV (PCV13) in 2011. We used laboratory data for invasive pneumococcal disease (IPD) and coded hospitalizations for noninvasive pneumococcal community-acquired pneumonia (PnCAP) to evaluate long-term impact.

Methods
Annual incidence (per 100 000 population) was calculated for age-specific total IPD, PCV13 non–7-valent PCV (PCV7) serotypes, and PnCAP by Indigenous status. Incidence in the pre–universal PCV7 (2002–2004), early PCV7 (2005–2007), pre-PCV13 (2008 to mid-2011), and post-PCV13 (mid-2011 to 2016) periods was used to calculate incidence rate ratios (IRRs).

Results
In the total population, all-age incidence of IPD declined from 11.8 pre-PCV7 to 7.1 post-PCV13 (IRR, 0.61 [95% confidence interval {CI}, .59–.63]) but for PnCAP declined among ages &lt;1 year (IRR, 0.34 [95% CI, .25–.45]) and 1–4 years (IRR, 0.50 [95% CI, .43–.57]) but increased significantly among age ≥5 years (IRRs, 1.08–1.14). In Indigenous people, baseline PCV13 non-PCV7 IPD incidence was 3-fold higher, amplified by a serotype 1 epidemic in 2011. By 2015–2016, although incidence of IPD and PnCAP in children aged &lt;5 years decreased by 38%, neither decreased in people aged ≥5 years.

Conclusions
Fifteen years post-PCV and 5 years post-PCV13, direct and indirect impact on IPD and PnCAP differed by age and between Indigenous and non-Indigenous people, with potential implications for long-term PCV impact in comparable settings.
Fifteen years after pneumococcal conjugate vaccine (PCV) introduction and 5 years post-PCV13, direct and indirect impact on invasive pneumococcal disease and pneumococcal community-acquired pneumonia differed by age and between Indigenous and non-Indigenous people, with potential implications for long-term PCV impact in comparable settings.
Safety and Immunogenicity of a Second Dose of an Investigational Maternal Trivalent Group B Streptococcus Vaccine in Nonpregnant Women 4–6 Years After a First Dose: Results From a Phase 2 Trial
Authors: Leroux-Roels Geert , Bebia Zourab , Maes Cathy , Aerssens Annelies , De Boever Fien , Grassano Luca , Buffi Giada , Margarit Immaculada , Karsten Annette , Cho Stephen , Slobod Karen , Corsaro Bartholomew , Henry Ouzama 
Published: August 2019

AbstractBackgroundMaternal immunization against group B streptococcus (GBS) could protect infants from invasive GBS disease. Additional doses in subsequent pregnancies may be needed. We evaluated the safety and immunogenicity of a second dose of an investigational trivalent CRM197-glycoconjugate GBS vaccine (targeting serotypes Ia/Ib/III), administered to nonpregnant women 4–6 years postdose 1.MethodsHealthy women either previously vaccinated with 1 dose of trivalent GBS vaccine 4–6 years before enrollment (n = 53) or never GBS vaccinated (n = 27) received a single trivalent GBS vaccine injection. Adverse events (AEs) were recorded. Serotype-specific (Ia/Ib/III) anti-GBS antibodies were measured by multiplex immunoassay prevaccination and 30/60 days postvaccination.ResultsAEs were reported with similar rates after a first or second dose; none were serious. Of previously GBS-vaccinated women, 92%–98% had anti-GBS concentrations that exceeded an arbitrary threshold (8 µg/mL) for each serotype 60 days postdose 2 vs 36%–56% postdose 1 in previously non–GBS-vaccinated women. Of previously GBS-vaccinated women with undetectable baseline (predose 1) anti-GBS levels, 90%–98% reached this threshold postdose 2. For each serotype, anti-GBS geometric mean concentrations (GMCs) 30/60 days postdose 2 in previously GBS-vaccinated women were ≥200-fold higher than baseline GMCs. Among women with undetectable baseline anti-GBS levels, postdose 2 GMCs in previously GBS-vaccinated women exceeded postdose 1 GMCs in previously non–GBS-vaccinated women (≥7-fold).ConclusionsA second trivalent GBS vaccine dose administered 4–6 years postdose 1 was immunogenic with a favorable safety profile. Women with undetectable preexisting anti-GBS concentrations may benefit from a sufficiently spaced second vaccine dose.Clinical Trials RegistrationNCT02690181
Serologic Markers of Previous Malaria Exposure and Functional Antibodies Inhibiting Parasite Growth Are Associated With Parasite Kinetics Following a Plasmodium falciparum Controlled Human Infection
Authors: Achan Jane , Reuling Isaie J , Yap Xi Zen , Dabira Edgard , Ahmad Abdullahi , Cox Momodou , Nwakanma Davis , Tetteh Kevin , Wu Lindsey , Bastiaens Guido J H , Abebe Yonas , Manoj Anita , Kaur Harparkash , Miura Kazutoyo , Long Carole , Billingsley Peter F , Sim B Kim Lee , Hoffman Stephen L , Drakeley Chris , Bousema Teun , D’Alessandro Umberto 
Published: August 2019

AbstractBackgroundWe assessed the impact of exposure to Plasmodium falciparum on parasite kinetics, clinical symptoms, and functional immunity after controlled human malaria infection (CHMI) in 2 cohorts with different levels of previous malarial exposure.MethodsNine adult males with high (sero-high) and 10 with low (sero-low) previous exposure received 3200 P. falciparum sporozoites (PfSPZ) of PfSPZ Challenge by direct venous inoculation and were followed for 35 days for parasitemia by thick blood smear (TBS) and quantitative polymerase chain reaction. Endpoints were time to parasitemia, adverse events, and immune responses.ResultsTen of 10 (100%) volunteers in the sero-low and 7 of 9 (77.8%) in the sero-high group developed parasitemia detected by TBS in the first 28 days (P = .125). The median time to parasitemia was significantly shorter in the sero-low group than the sero-high group (9 days [interquartile range {IQR} 7.5–11.0] vs 11.0 days [IQR 7.5–18.0], respectively; log-rank test, P = .005). Antibody recognition of sporozoites was significantly higher in the sero-high (median, 17.93 [IQR 12.95–24] arbitrary units [AU]) than the sero-low volunteers (median, 10.54 [IQR, 8.36–12.12] AU) (P = .006). Growth inhibitory activity was significantly higher in the sero-high (median, 21.8% [IQR, 8.15%–29.65%]) than in the sero-low group (median, 8.3% [IQR, 5.6%–10.23%]) (P = .025).ConclusionsCHMI was safe and well tolerated in this population. Individuals with serological evidence of higher malaria exposure were able to better control infection and had higher parasite growth inhibitory activity.Clinical Trials RegistrationNCT03496454.
Chronology of Gloomy Scale (Hemiptera: Diaspididae) Infestations on Urban Trees
Authors: Backe Kristi M , Frank Steven D 
Published: August 2019

AbstractPest abundance on urban trees often increases with surrounding impervious surface. Gloomy scale (Melanaspis tenebricosa Comstock; Hemiptera: Diaspididae), a pest of red maples (Acer rubrum L.; Sapindales: Sapindaceae) in the southeast United States, reaches injurious levels in cities and reduces tree condition. Here, we use a chronosequence field study in Raleigh, NC, to investigate patterns in gloomy scale densities over time from the nursery to 13 yr after tree planting, with a goal of informing more efficient management of gloomy scale on urban trees. We examine how impervious surfaces affect the progression of infestations and how infestations affect tree condition. We find that gloomy scale densities remain low on trees until at least seven seasons after tree planting, providing a key timepoint for starting scouting efforts. Scouting should focus on tree branches, not tree trunks. Scale density on tree branches increases with impervious surface across the entire studied tree age range and increases faster on individual trees that are planted in areas with high impervious surface cover. There is a lag between the onset of pest infestations and a decline in tree condition, indicating that gloomy scale management should begin prior to a visible decline in tree condition. Our results inform management of gloomy scale in cities.
Comparison of the conventional frozen elephant trunk implantation technique with a modified implantation technique in zone 1
Authors: Gottardi Roman , Voetsch Andreas , Krombholz-Reindl Philip , Winkler Andreas , Steindl Johannes , Dinges Christian , Kirnbauer Michael , Neuner Matthias , Berger Tim , Seitelberger Rainald 
Published: August 2019

Abstract

OBJECTIVES
The aim of the study was to compare the conventional frozen elephant trunk implantation technique with a modified implantation technique with an aortic anastomosis in zone 1 and extra-anatomic revascularization of the left subclavian artery during reperfusion.

METHODS
Between May 2014 and March 2018, 40 patients (26 male; mean age 60.2 ± 11.2 years) underwent complete aortic arch replacement with the Thoraflex Hybrid prosthesis™ (Vascutek, Inchinnan, Scotland) at our institution. Seventeen patients underwent conventional arch replacement (group 1) and 23 patients the modified procedure (group 2). Indication for arch replacement included all types of acute and chronic diseases.

RESULTS
Cardiopulmonary bypass time (213.1 ± 53.5 vs 243.8 ± 67.0 min, P = 0.13) and aortic cross-clamp time (114.4 ± 40.7 vs 117.3 ± 56.6 min, P = 0.86) did not differ significantly between group 1 and 2. There was a trend towards a shorter circulatory arrest time (50.72 ± 9.6 vs 44.7 ± 15.5 min; P = 0.20) in group 2. Perioperative mortality was 10% (5.9% vs 13%; P = 0.62). Stroke occurred in 10% (5.9% vs 13%; P = 0.62) of patients. Spinal cord injury occurred in 7.5% of patients (11.8% vs 4.3% P = 0.57). Due to the a proximal aortic anastomosis, there was a significantly shorter coverage of the descending aorta with the prosthesis ending at vertebral level Th7.5 (6.75–8) in group 1 versus Th6.0 (5.0–6.0) in group 2 (P-value = 0.004).

CONCLUSIONS
Implantation of the frozen elephant trunk prosthesis in zone 1 allows for a more proximal aortic anastomosis that could make the procedure more feasible especially in patients with difficult anatomies or in an acute setting.
Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic
Authors: Willis Ciara , Desai Dhwani , LaRoche Julie 
Published: August 2019

ABSTRACT
Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.
Quick determination of earthquake source parameters from GPS measurements: a study of suitability for Taiwan
Authors: Lin Jiun-Ting , Chang Wu-Lung , Melgar Diego , Thomas Amanda , Chiu Chi-Yu 
Published: August 2019

SUMMARYWe test the feasibility of GPS-based rapid centroid moment tensor (GPS CMT) methods for Taiwan, one of the most earthquake prone areas in the world. In recent years, Taiwan has become a leading developer of seismometer-based earthquake early warning systems, which have successfully been applied to several large events. The rapid determination of earthquake magnitude and focal mechanism, important for a number of rapid response applications, including tsunami warning, is still challenging because of the limitations of near-field inertial recordings. This instrumental issue can be solved by an entirely different observation system: a GPS network. Taiwan is well posed to take advantage of GPS because in the last decade it has developed a very dense network. Thus, in this research, we explore the suitability of the GPS CMT inversion for Taiwan. We retrospectively investigate six moderate to large (Mw6.0 ∼ 7.0) earthquakes and propose a resolution test for our model, we find that the minimum resolvable earthquake magnitude of this system is ∼Mw5.5 (at 5 km depth). Our tests also suggest that the finite fault complexity, often challenging for the near-field methodology, can be ignored under such good station coverage and thus, can provide a fast and robust solution for large earthquake directly from the near field. Our findings help to understand and quantify how the proposed methodology could be implemented in real time and what its contributions could be to the overall earthquake monitoring system.
Receiver function mapping of mantle transition zone discontinuities beneath Alaska using scaled 3-D velocity corrections
Authors: van Stiphout A M , Cottaar S , Deuss A 
Published: August 2019

SUMMARYThe mantle transition zone is the region between the globally observed major seismic velocity discontinuities around depths of 410 and 660 km and is important for determining the style of convection and mixing between the upper and the lower mantle. In this study, P-to-S converted waves, or receiver functions, are used to study these discontinuities beneath the Alaskan subduction zone, where the Pacific Plate subducts underneath the North American Plate. Previous tomographic models do not agree on the depth extent of the subducting slab, therefore improved imaging of the Earth structure underneath Alaska is required. We use 27 800 high quality radial receiver functions to make common conversion point stacks. Upper mantle velocity anomalies are accounted for by two recently published regional tomographic S-wave velocity models. Using these two tomographic models, we show that the discontinuity depths within our CCP stacks are highly dependent on the choice of velocity model, between which velocity anomaly magnitudes vary greatly. We design a quantitative test to show whether the anomalies in the velocity models are too strong or too weak, leading to over- or undercorrected discontinuity depths. We also show how this test can be used to rescale the 3-D velocity corrections in order to improve the discontinuity topography maps.After applying the appropriate corrections, we find a localized thicker mantle transition zone and an uplifted 410 discontinuity, which show that the slab has clearly penetrated into the mantle transition zone. Little topography is seen on the 660 discontinuity, indicating that the slab has probably not reached the lower mantle. In the southwest, P410s arrivals have very small amplitudes or no significant arrival at all. This could be caused by water or basalt in the subducting slab, reducing the strength at the 410, or by topography on the 410 discontinuity, preventing coherent stacking. In the southeast of Alaska, a thinner mantle transition zone is observed. This area corresponds to the location of a slab window, and thinning of the mantle transition zone may be caused by hot mantle upwellings.
Playing with Power: Mechanisms of Energy Flow in Organismal Movement
Authors: Rosario Michael V , Olberding Jeffrey P , Deban Stephen M 
Published: August 2019

AbstractAcross multiple evolutionary clades and size scales, organismal movement requires controlling the flow of energy through the body to enhance certain functions. Whether energy is released or absorbed by the organism, proper function hinges on the ability to manipulate both where and when energy is transferred. For example, both power amplification and power attenuation rely on the use of springs for the intermediate storage of energy between the body and the environment; but variation in function is the result of the path and timing of energy flow. In this symposium, we have invited speakers that demonstrate the diversity of mechanisms used to control the flow of energy through the body and into the environment. By bringing together researchers investigating movements in the context of power and energy flow, the major goal of this symposium is to facilitate fresh perspectives on the unifying mechanical themes of energy transfer in organismal movement.
Fault diagnosis of air-conditioning refrigeration system based on sparse autoencoder
Authors: Wang Zhiyi , Zhong Jiachen , Li Jingfan , Xia Cui 
Published: August 2019

Abstract
To overcome the drawbacks of using supervised learning to extract fault features for classification and low nonlinearity of the features in most of current fault diagnosis of air-conditioning refrigeration system, sparse autoencoder (SAE) is presented to extract fault features that are used as the input to the classifier and to achieve fault diagnosis for air-conditioning refrigeration system. The SAE structure is tuned by adjusting the number of hidden layers and nodes to build the optimal model, which is compared with the fault diagnosis model based on support vector machine. Results indicate that the indexes of the model combined with SAE, such as accuracy, precision and recall, are all improved, especially for the faults with high complexity. Besides, SAE shows high generalization ability with small-scale sample data and high efficiency with large-scale data. Obviously, the use of SAE can effectively optimize the diagnosis performance of the classifier.
Toward energy-efficient governmental buildings in Egypt: investigating the impact of nano aerogel glazing on energy performance
Authors: Hegazy Ibrahim Rizk 
Published: August 2019

AbstractThe application of advanced materials in energy conservation is mostly among the urgent issues worldwide. In this context, nanosilica aerogel has received growing attention in the last decade due to its remarkably lower thermal conductivity. Aerogel panels laminated to drywall boards initiated to be used in substantially the energy sufficient buildings. Nevertheless, the greatest and most promising application of silica aerogel appears to be in substantially insulating glazing systems. The present research has concentrated on evaluating the energy performance of the nano aerogel glazing if implemented to the El-Dakahliya governmental headquarters building located in Mansoura city in Egypt, compared with single-glazed windows (base case) and double-glazed windows. The modeling was carried out in Autodesk Revit, and the process of energy performance simulation was carried out by Autodesk Ecotect Analysis by adopting the weather data of Mansoura. The results show that the nano aerogel glazing system succeeds in conserving approximately 19% in the annual energy consumption for a set-point temperature band of 19–27°C. The paper attempts to present significant research especially in studied country. Selected category of buildings may add more originality in term of implementation scope.
Safety and Immunogenicity of a Respiratory Syncytial Virus Fusion (F) Protein Nanoparticle Vaccine in Healthy Third-Trimester Pregnant Women and Their Infants
Authors: Muňoz Flor M , Swamy Geeta K , Hickman Somia P , Agrawal Sapeckshita , Piedra Pedro A , Glenn Gregory M , Patel Nita , August Allison M , Cho Iksung , Fries Louis 
Published: August 2019

AbstractBackgroundRespiratory syncytial virus (RSV) is the leading cause of infant lower respiratory tract disease and hospitalization worldwide.MethodsSafety and immunogenicity of RSV fusion (F) protein nanoparticle vaccine or placebo were evaluated in 50 healthy third-trimester pregnant women. Assessments included vaccine tolerability and safety in women and infants, and RSV-specific antibody measures in women before and after vaccination, at delivery and post partum.ResultsThe vaccine was well tolerated; no meaningful differences in pregnancy or infant outcomes were observed between study groups. RSV-specific antibody levels increased significantly among vaccine recipients, including responses competitive with well-described monoclonal antibodies specific for multiple RSV neutralizing epitopes. No significant antibody increase was seen among placebo recipients, although a shallow upward trend across the RSV season was noted. Transplacental antibody transfer was 90%–120% across assays for infants of vaccinated women. Women with an interval of ≥30 days between vaccination and delivery demonstrated higher placental antibody transfer rates than women with an interval <30 days. Half-lives of RSV-specific antibodies in infants approximated 40 days. There was no evidence of severe RSV disease in infants of vaccinated mothers.ConclusionsData from this phase 2 study support a maternal immunization strategy to protect infants from RSV disease.Clinical Trials RegistrationNCT02247726.