bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gonorrhea and Chlamydia Specimen Positivity Rate by Polymerase Chain Reaction at a Regional Veteran Affairs Medical Center
Authors: Petersen Jeffrey M , Patel Sahil , Dalal Sharvari , Jhala Darshana 
Published: June 2020

Abstract

Objective
Sexually transmitted infections because of Neisseria gonorrhoeae (NG) and/or Chlamydia trachomatis (CT) remain a major public health problem. Although the literature describes the population-based epidemiology of CT/NG, it does not appear to contain reference points for the statistical analyses of specimen positivity rates by nucleic acid testing (NAT) with polymerase chain reaction (PCR) that would be collected by a laboratory following best laboratory and regulatory practice. For facilities that diagnose NG and CT by a real-time PCR assay, an understanding of the expected specimen positivity rate of gonorrhea and chlamydia would be helpful for monitoring the assay for quality assurance. Therefore, on behalf of the Michael J. Crescenz Veteran Affairs Medical Center (VAMC), we present this novel quality assurance study on its CT/NG specimen positivity rates conducted by NAT with PCR.

Methods
Quality assurance/improvement quarterly data from April 1, 2012 to September 30, 2019 were reviewed to obtain both the test volume of PCR for CT/NG and the number of positive test results at the VAMC to collate and perform statistical analyses. Testing had been performed using the Abbott m2000 RealTime System (Abbott Park, IL).

Results
A total of 22,709 PCR tests for CT/NG had been performed on the veteran population; of these, 502 tests were positive for NG and 744 were positive for CT. Quarterly percentage rates ranged from 1.67% to 5.30% for CT and from 1.00% to 3.25% for NG, with average rates of 3.35% and 2.22% for CT and NG, respectively.

Conclusion
The establishment of an expected rate of specimen positivity of CT/NG by NAT with PCR at the VAMC is a significant novel reference point in the quality assurance (QA) literature and provides a benchmark that aids tremendously in QA for the microbiology/molecular laboratory.
EDGE: from quiescent to gas-rich to star-forming low-mass dwarf galaxies
Authors: Rey Martin P , Pontzen Andrew , Agertz Oscar , Orkney Matthew D A , Read Justin I , Rosdahl Joakim 
Published: June 2020

ABSTRACT
We study how star formation is regulated in low-mass field dwarf galaxies ($10^5 \le M_{\star } \le 10^6 \, \mbox{M}_\mathrm{\odot }$), using cosmological high-resolution ($3 \, \mathrm{pc}$) hydrodynamical simulations. Cosmic reionization quenches star formation in all our simulated dwarfs, but three galaxies with final dynamical masses of $3 \times 10^{9} \, \mbox{M}_\mathrm{\odot }$ are subsequently able to replenish their interstellar medium by slowly accreting gas. Two of these galaxies reignite and sustain star formation until the present day at an average rate of $10^{-5} \, \mbox{M}_\mathrm{\odot } \, \text{yr}^{-1}$, highly reminiscent of observed low-mass star-forming dwarf irregulars such as Leo T. The resumption of star formation is delayed by several billion years due to residual feedback from stellar winds and Type Ia supernovae; even at z = 0, the third galaxy remains in a temporary equilibrium with a large gas content but without any ongoing star formation. Using the ‘genetic modification’ approach, we create an alternative mass growth history for this gas-rich quiescent dwarf and show how a small $(0.2\, \mathrm{dex})$ increase in dynamical mass can overcome residual stellar feedback, reigniting star formation. The interaction between feedback and mass build-up produces a diversity in the stellar ages and gas content of low-mass dwarfs, which will be probed by combining next-generation H i and imaging surveys.
Binary-induced spiral arms inside the disc cavity of AB Aurigae
Authors: Poblete Pedro P , Calcino Josh , Cuello Nicolás , Macías Enrique , Ribas Álvaro , Price Daniel J , Cuadra Jorge , Pinte Christophe 
Published: June 2020

ABSTRACT
In this work we demonstrate that the inner spiral structure observed in AB Aurigae can be created by a binary star orbiting inside the dust cavity. We find that a companion with a mass-ratio of 0.25, semimajor axis of 40 au, eccentricity of 0.5, and inclination of 90° produces gaseous spirals closely matching the ones observed in 12CO (2-1) line emission. Based on dust dynamics in circumbinary discs (Poblete, Cuello & Cuadra 2019), we constrain the inclination of the binary with respect to the circumbinary disc to range between 60° and 90°. We predict that the stellar companion is located roughly 0.18 arcsec from the central star towards the east-southeast, above the plane of the disc. Should this companion be detected in the near future, our model indicates that it should be moving away from the primary star at a rate of 6 mas yr−1 on the plane of the sky. Since our companion is inclined, we also predict that the spiral structure will appear to change with time, and not simply corotate with the companion.
Radio constraints on dark matter annihilation in Canes Venatici I with LOFAR†
Authors: Vollmann Martin , Heesen Volker , W. Shimwell Timothy , Hardcastle Martin J , Brüggen Marcus , Sigl Günter , J. A. Röttgering Huub 
Published: June 2020

ABSTRACT
Dwarf galaxies are dark matter (DM) dominated and therefore promising targets for the search for weakly interacting massive particles (WIMPs), which are well-known candidates for DM. The annihilation of WIMPs produces ultrarelativistic cosmic ray electrons and positrons that emit synchrotron radiation in the presence of magnetic fields. For typical magnetic field strengths (few μG) and $\mathcal {O}$(GeV–TeV) WIMP masses, this emission peaks at hundreds of MHz. Here, we use the non-detection of 150-MHz radio continuum emission from the dwarf spheroidal galaxy Canes Venatici I with the Low-Frequency Array to derive constraints on the annihilation cross-section of WIMPs into primary electron–positron and other fundamental particle–antiparticle pairs. Our main underlying assumption is that the transport of the cosmic rays can be described by the diffusion approximation, thus requiring a non-zero magnetic field strength with small-scale structure. In particular, by adopting magnetic field strengths of $\mathcal {O}(1\, \mu$G) and diffusion coefficients $\sim \!10^{27}~\rm cm^2\, s^{-1}$, we obtain limits that are comparable with those set by the Fermi Large Area Telescope using gamma-ray observations of this particular galaxy. Assuming s-wave annihilation and WIMPs making up 100 per cent of the DM density, our benchmark limits exclude several thermal WIMP realizations in the [2, 20]-GeV mass range. We caution, however, that our limits for the cross-section are subject to enormous uncertainties that we also quantitatively assess. In particular, variations on the propagation parameters or on the DM halo can shift our limits up by several orders of magnitude (in the pessimistic scenario).
The imprint of arms and bars on rotation curves: in-plane and off-plane
Authors: Martinez-Medina Luis A , Pichardo Barbara , Peimbert Antonio 
Published: June 2020

ABSTRACT
Within rotation curves (RCs) is encoded the kinematical state of the stellar disc as well as information about the dynamical mechanisms driving the secular evolution of galaxies. To explain the characteristic features of RCs which arise by the influence of spiral patterns and bar, we study the kinematics of the stellar disc in a set of spiral galaxy models specifically tailored for this purpose. We find that, for our models, the induced non-circular motions are more prominent for spirals with larger pitch angle, the ones typical in late-type galaxies. Moreover, inside corotation, stars rotate slower along the spiral arms than along the interarm, which translates into a local minima or maxima in the RC, respectively. We also see, from off-plane RC, that the rotation is faster for stars that at observed closer to the plane, and diminishes as one looks farther off plane; this trend is more noticeable in our Sa galaxy model than our Sc galaxy model. Additionally, in a previous work we found that the diagonal ridges in the Vϕ–R plane, revealed through the GaiaDR2, have a resonant origin due to the spiral arms and bar and that these ridges project themselves as wiggles in the RC; here, we further notice that the development of these ridges, and the development of high orbital eccentricities in the stellar disc are the same. Hence, we conclude that, the following explanations of bumps and wiggles in RCs are equivalent: they are manifestations of diagonal ridges in the Vϕ–R plane, or of the rearrangement of the orbital eccentricities in the stellar disc.
The genotoxic effects in the leukocytes of workers handling nanocomposite materials
Authors: Novotna Bozena , Pelclova Daniela , Rossnerova Andrea , Zdimal Vladimir , Ondracek Jakub , Lischkova Lucie , Vlckova Stepanka , Fenclova Zdenka , Klusackova Pavlina , Zavodna Tana , Topinka Jan , Komarc Martin , Dvorackova Stepanka , Rossner Pavel 
Published: June 2020

Abstract
The extensive development of nanotechnologies and nanomaterials poses a number of questions to toxicologists about the potential health risks of exposure to nanoparticles (NP). In this study, we analysed DNA damage in the leukocytes of 20 workers who were long-term exposed (18 ± 10 years) to NP in their working environment. Blood samples were collected in September 2016, before and after a shift, to assess (i) the chronic effects of NP on DNA (pre-shift samples) and (ii) the acute effects of exposure during the shift (the difference between pre- and post-shift samples). The samples from matched controls were taken in parallel with workers before the shift. Leukocytes were isolated from heparinised blood on a Ficoll gradient. The enzyme-modified comet assay (DNA formamido-pyrimidine-glycosylase and endonuclease III) demonstrated a considerable increase of both single- and double-strand breaks in DNA (DNA-SB) and oxidised bases when compared with the controls (2.4× and 2×, respectively). Acute exposure induced a further increase of DNA-SB. The welding and smelting of nanocomposites represented a higher genotoxic risk than milling and grinding of nanocomposite surfaces. Obesity appeared to be a factor contributing to an increased risk of oxidative damage to DNA. The data also indicated a higher susceptibility of males vs. females to NP exposure. The study was repeated in September 2017. The results exhibited similar trend, but the levels of DNA damage in the exposed subjects were lower compared to previous year. This was probably associated with lower exposure to NP in consequence of changes in nanomaterial composition and working operations. The further study involving also monitoring of personal exposures to NP is necessary to identify (i) the main aerosol components responsible for genotoxic effects in workers handling nanocomposites and (ii) the primary cause of gender differences in response to NP action.
Oligonucleotides DNA containing 8-trifluoromethyl-2′-deoxyguanosine for observing Z-DNA structure
Authors: Bao Hong-Liang , Masuzawa Tatsuki , Oyoshi Takanori , Xu Yan 
Published: June 2020

AbstractZ-DNA is known to be a left-handed alternative form of DNA and has important biological roles as well as being related to cancer and other genetic diseases. It is therefore important to investigate Z-DNA structure and related biological events in living cells. However, the development of molecular probes for the observation of Z-DNA structures inside living cells has not yet been realized. Here, we have succeeded in developing site-specific trifluoromethyl oligonucleotide DNA by incorporation of 8-trifluoromethyl-2′-deoxyguanosine (FG). 2D NMR strongly suggested that FG adopted a syn conformation. Trifluoromethyl oligonucleotides dramatically stabilized Z-DNA, even under physiological salt concentrations. Furthermore, the trifluoromethyl DNA can be used to directly observe Z-form DNA structure and interaction of DNA with proteins in vitro, as well as in living human cells by19F NMR spectroscopy for the first time. These results provide valuable information to allow understanding of the structure and function of Z-DNA.
DeepCLIP: predicting the effect of mutations on protein–RNA binding with deep learning
Authors: Grønning Alexander Gulliver Bjørnholt , Doktor Thomas Koed , Larsen Simon Jonas , Petersen Ulrika Simone Spangsberg , Holm Lise Lolle , Bruun Gitte Hoffmann , Hansen Michael Birkerod , Hartung Anne-Mette , Baumbach Jan , Andresen Brage Storstein 
Published: June 2020

AbstractNucleotide variants can cause functional changes by altering protein–RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling of protein–RNA binding is critical when predicting the effects of sequence variations. Many RNA-binding proteins recognize a diverse set of motifs and binding is typically also dependent on the genomic context, making this task particularly challenging. Here, we present DeepCLIP, the first method for context-aware modeling and predicting protein binding to RNA nucleic acids using exclusively sequence data as input. We show that DeepCLIP outperforms existing methods for modeling RNA-protein binding. Importantly, we demonstrate that DeepCLIP predictions correlate with the functional outcomes of nucleotide variants in independent wet lab experiments. Furthermore, we show how DeepCLIP binding profiles can be used in the design of therapeutically relevant antisense oligonucleotides, and to uncover possible position-dependent regulation in a tissue-specific manner. DeepCLIP is freely available as a stand-alone application and as a webtool at http://deepclip.compbio.sdu.dk.
Impact of 3-Dimensional Versus 2-Dimensional Image Distortion Correction on Stereotactic Neurosurgical Navigation Image Fusion Reliability for Images Acquired With Intraoperative Magnetic Resonance Imaging
Authors: Yahanda Alexander T , Goble Timothy J , Sylvester Peter T , Lessman Gretchen , Goddard Stanley , McCollough Bridget , Shah Amar , Andrews Trevor , Benzinger Tammie L S , Chicoine Michael R 
Published: June 2020

Abstract

BACKGROUND
Fusion of preoperative and intraoperative magnetic resonance imaging (iMRI) studies during stereotactic navigation may be very useful for procedures such as tumor resections but can be subject to error because of image distortion.

OBJECTIVE
To assess the impact of 3-dimensional (3D) vs 2-dimensional (2D) image distortion correction on the accuracy of auto-merge image fusion for stereotactic neurosurgical images acquired with iMRI using a head phantom in different surgical positions.

METHODS
T1-weighted intraoperative images of the head phantom were obtained using 1.5T iMRI. Images were postprocessed with 2D and 3D image distortion correction. These studies were fused to T1-weighted preoperative MRI studies performed on a 1.5T diagnostic MRI. The reliability of the auto-merge fusion of these images for 2D and 3D correction techniques was assessed both manually using the stereotactic navigation system and via image analysis software.

RESULTS
Eight surgical positions of the head phantom were imaged with iMRI. Greater image distortion occurred with increased distance from isocenter in all 3 axes, reducing accuracy of image fusion to preoperative images. Visually reliable image fusions were accomplished in 2/8 surgical positions using 2D distortion correction and 5/8 using 3D correction. Three-dimensional correction yielded superior image registration quality as defined by higher maximum mutual information values, with improvements ranging between 2.3% and 14.3% over 2D correction.

CONCLUSION
Using 3D distortion correction enhanced the reliability of surgical navigation auto-merge fusion of phantom images acquired with iMRI across a wider range of head positions and may improve the accuracy of stereotactic navigation using iMRI images.
Two Novel PLS-Class Pentatricopeptide Repeat Proteins Are Involved in the Group II Intron Splicing of Mitochondrial Transcripts in the Moss Physcomitrella patens
Authors: Ichinose Mizuho , Ishimaru Airi , Sugita Chieko , Nakajima Kensaku , Kawaguchi Yasuhiro , Sugita Mamoru 
Published: June 2020

Abstract
Pentatricopeptide repeat (PPR) proteins are RNA-binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5′ region of nad5 exon 4 and the bulged A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that a certain set of PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns.
Extended Perineural Analgesia After Hip and Knee Replacement When Buprenorphine-Clonidine-Dexamethasone Is Added to Bupivacaine: Preliminary Report from a Randomized Clinical Trial
Authors: Williams Brian A , Ibinson James W , Ritter Marsha E , Ezaru Catalin S , Rakesh Hulimangala R , Paiste Henry J , Gilbert Karen L , Mikolic Joseph M , Muluk Visala S , Piva Sara R 
Published: June 2020

Abstract

Objective
We tested the hypothesis that buprenorphine-clonidine-dexamethasone (BCD) extends perineural analgesia compared with plain bupivacaine (BPV) nerve blocks used for hip and knee replacement surgery.

Design
Prospective, parallel-arms, randomized, double-blind trial.

Setting
A single veterans’ hospital.

Subjects
Seventy-eight veterans scheduled for total hip or knee replacement with plans for spinal as the primary anesthetic.

Methods
Participants underwent nerve/plexus blocks at L2–L4 and L4–S3 in advance of hip or knee joint replacement surgery. Patients were randomized to receive BPV-BCD or plain BPV in a 4:1 allocation ratio. Patients answered four block duration questions (listed below). Time differences between treatments were analyzed using the t test.

Results
Significant (P &lt; 0.001) prolongation of the time parameters was reported by patients after the BPV-BCD blocks (N = 62) vs plain BPV (N = 16). The time until start of postoperative pain was 26 vs 11 hours (mean difference = 15 hours, 95% CI = 8 to 21). The time until no pain relief from the blocks was 32 vs 15 hours (mean difference = 17 hours, 95% CI = 10 to 24). The time until the numbness wore off was 37 vs 21 hours (mean difference = 16 hours, 95% CI = 8 to 23). The time until the worst postoperative pain was 39 vs 20 hours (mean difference = 19 hours, 95% CI = 11 to 27).

Conclusions
BPV-BCD provided 26–39 hours of perineural analgesia in the L2–L4 and L4–S3 nerve distributions after hip/knee replacement surgery, compared with 11–21 hours for plain BPV.
Instruments for Measuring Satisfaction With Physical Therapy Care: A Systematic Review
Authors: Gutiérrez-Sánchez Daniel , Pérez-Cruzado David , Cuesta-Vargas Antonio I 
Published: June 2020

Abstract

Objective
Several instruments to measure patient satisfaction have been developed to assess satisfaction with physical therapy care. The selection of the most appropriate instrument is very important. The purpose of this study was to identify instruments for assessing satisfaction with physical therapy care and their psychometric properties and to evaluate the methodological quality of studies on psychometric properties.

Methods
A systematic search was conducted in ProQuest Medline, SciELO, ProQuest PsycINFO, Theseus, Cochrane Library, and Google Scholar. Articles published from 1990 to 2019, in English and Spanish, were used as limits. This systematic review followed the Consensus-based Standards for the Selection of Health Measurement Instruments and Preferred Reporting Items for Systematic Reviews and Meta-Analyses standards. The articles were evaluated by 2 independent reviewers using the Consensus-based Standards for the Selection of Health Measurement Instruments 4-point checklist. Eighteen studies were included.

Results
Nine instruments were found to be specifically designed to assess satisfaction with physical therapy care. The methodological quality of the studies was “fair” for most of the psychometric characteristics analyzed (43 items), with 24 properties scored as “poor,” 5 as “good,” and 3 as “excellent.”

Conclusions
Different instrument characteristics—such as the scope and population with which the instrument will be used, its dimensions, the number of items, and the evidence shown in the evaluation of each psychometric property—should be considered by clinicians and researchers to decide which instrument is the best to measure the construct of patient satisfaction with physical therapy.

Impact
Evaluating patient satisfaction is very useful in clinical practice at the hospital, community, and primary care levels. Physical therapist clinicians and researchers can use this systematic review to select instruments whose characteristics will best measure their patients’ satisfaction with physical therapy care.
Gender Regime Change in Decentralized States: The Case of Spain
Authors: Lombardo Emanuela , Alonso Alba 
Published: June 2020

AbstractThis article applies Walby’s systemic theory of gender regime to Spain’s decentralized state, to capture changes in the gender regime. Locating the “hegemon” at different levels of government for each domain (economy, polity, violence, and civil society) and considering interactions between governmental levels provided a clear understanding of changes in the gender regime. The relationship between governmental level acting as hegemon in specific domains and variations in political majorities across governmental levels explained changes toward a neoliberal–conservative type in the economy domain. Shifts toward a neoliberal gender regime in violence and polity, and toward a conservative type in civil society, were contested.
The Origins and Transformations of Conservative Gender Regimes in Germany and Japan
Authors: Shire Karen A , Nemoto Kumiko 
Published: June 2020

AbstractIn this article, we extend Walby’s analysis of gender transformations to theorize gender relations in conservative modernizations. We draw insights from a historical comparison of gender inequalities in Germany and Japan, to draw a distinction between conservative authoritarian and conservative democratic gender regimes, and their transformations. Conservative gender regimes, we argue, constitute the domestic as a public sphere and transform through social and family policies, which reinforce a gendered division of labor. The concept of conservative gender regimes, we argue, is relevant for analyzing transformations in other European and non-European world regions.