bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanics of a plant in fluid flow
Authors: Gosselin Frédérick P 
Published: June 2019

AbstractPlants live in constantly moving fluid, whether air or water. In response to the loads associated with fluid motion, plants bend and twist, often with great amplitude. These large deformations are not found in traditional engineering application and thus necessitate new specialized scientific developments. Studying fluid–structure interaction (FSI) in botany, forestry, and agricultural science is crucial to the optimization of biomass production for food, energy, and construction materials. FSIs are also central in the study of the ecological adaptation of plants to their environment. This review paper surveys the mechanics of FSI on individual plants. I present a short refresher on fluid mechanics then dive into the statics and dynamics of plant–fluid interactions. For every phenomenon considered, I examine the appropriate dimensionless numbers to characterize the problem, discuss the implications of these phenomena on biological processes, and propose future research avenues. I cover the concept of reconfiguration while considering poroelasticity, torsion, chirality, buoyancy, and skin friction. I also assess the dynamical phenomena of wave action, flutter, and vortex-induced vibrations.
The binary millisecond pulsar PSR J1023+0038 – II. Optical spectroscopy
Authors: Shahbaz T , Linares M , Rodríguez-Gil P , Casares J 
Published: June 2019

ABSTRACT
We present time-resolved optical spectroscopy of the ‘redback’ binary millisecond pulsar system PSR J1023+0038 during both its radio pulsar (2009) and accretion disc states (2014 and 2016). We provide observational evidence for the companion star being heated during the disc state. We observe a spectral type change along the orbit, from ∼G5 to ∼F6 at the secondary star’s superior and inferior conjunction, respectively, and find that the corresponding irradiating luminosity can be powered by the high-energy accretion luminosity or the spin-down luminosity of the neutron star. We determine the secondary star’s radial velocity semi-amplitude from the metallic (primarily Fe and Ca) and Hα absorption lines during these different states. The metallic and Hα radial velocity semi-amplitude determined from the 2009 pulsar-state observations allows us to constrain the secondary star’s true radial velocity K2 = 276.3 ± 5.6  km s−1 and the binary mass ratio q = 0.137 ± 0.003. By comparing the observed metallic and Hα absorption-line radial velocity semi-amplitudes with model predictions, we can explain the observed semi-amplitude changes during the pulsar state and during the pulsar/disc-state transition as being due to different amounts of heating and the presence of an accretion disc, respectively.
Dynamics of magnetic flux tubes in accretion discs of T Tauri stars
Authors: Dudorov A E , Khaibrakhmanov S A , Sobolev A M 
Published: June 2019

Abstract
Dynamics of slender magnetic flux tubes (MFTs) in the accretion discs of T Tauri stars is investigated. We perform simulations taking into account buoyant, aerodynamic, and turbulent drag forces, radiative heat exchange between MFT and ambient gas, and magnetic field of the disc. The equations of MFT dynamics are solved using Runge–Kutta method of the fourth order. The simulations show that there are two regimes of MFT motion in absence of external magnetic field. In the region r < 0.2 au, the MFTs of radii $0.05 \le a_0 \le 0.16\, H$ (H is the scale height of the disc) with initial plasma beta of 1 experience thermal oscillations above the disc. The oscillations decay over some time, and MFTs continue upward motion afterwards. Thinner or thicker MFTs do not oscillate. MFT velocity increases with initial radius and magnetic field strength. MFTs rise periodically with velocities up to 5–15 km s−1 and periods of 0.5–10 yr determined by the toroidal magnetic field generation time. Approximately 20 per cent of disc mass and magnetic flux can escape to disc atmosphere via the magnetic buoyancy over characteristic time of disc evolution. MFTs dispersal forms expanding magnetized corona of the disc. External magnetic field causes MFT oscillations near the disc surface. These magnetic oscillations have periods from several days to 1–3 months at r < 0.6 au. The magnetic oscillations decay over few periods. We simulate MFT dynamics in accretion discs in the Chameleon I cluster. The simulations demonstrate that MFT oscillations can produce observed IR-variability of T Tauri stars.
Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate DNA
Authors: Solomon William C , Myint Wazo , Hou Shurong , Kanai Tapan , Tripathi Rashmi , Kurt Yilmaz Nese , Schiffer Celia A , Matsuo Hiroshi 
Published: June 2019

AbstractThe potent antiretroviral protein APOBEC3G (A3G) specifically targets and deaminates deoxycytidine nucleotides, generating deoxyuridine, in single stranded DNA (ssDNA) intermediates produced during HIV replication. A non-catalytic domain in A3G binds strongly to RNA, an interaction crucial for recruitment of A3G to the virion; yet, A3G displays no deamination activity for cytidines in viral RNA. Here, we report NMR and molecular dynamics (MD) simulation analysis for interactions between A3Gctd and multiple substrate or non-substrate DNA and RNA, in combination with deamination assays. NMR ssDNA-binding experiments revealed that the interaction with residues in helix1 and loop1 (T201-L220) distinguishes the binding mode of substrate ssDNA from non-substrate. Using 2′-deoxy-2′-fluorine substituted cytidines, we show that a 2′-endo sugar conformation of the target deoxycytidine is favored for substrate binding and deamination. Trajectories of the MD simulation indicate that a ribose 2′-hydroxyl group destabilizes the π-π stacking of the target cytosine and H257, resulting in dislocation of the target cytosine base from the catalytic position. Interestingly, APOBEC3A, which can deaminate ribocytidines, retains the ribocytidine in the catalytic position throughout the MD simulation. Our results indicate that A3Gctd catalytic selectivity against RNA is dictated by both the sugar conformation and 2′-hydroxyl group.
Transcriptome signature of cellular senescence
Authors: Casella Gabriel , Munk Rachel , Kim Kyoung Mi , Piao Yulan , De Supriyo , Abdelmohsen Kotb , Gorospe Myriam 
Published: June 2019

Abstract
Cellular senescence, an integral component of aging and cancer, arises in response to diverse triggers, including telomere attrition, macromolecular damage and signaling from activated oncogenes. At present, senescent cells are identified by the combined presence of multiple traits, such as senescence-associated protein expression and secretion, DNA damage and β-galactosidase activity; unfortunately, these traits are neither exclusively nor universally present in senescent cells. To identify robust shared markers of senescence, we have performed RNA-sequencing analysis across eight diverse models of senescence triggered in human diploid fibroblasts (WI-38, IMR-90) and endothelial cells (HUVEC, HAEC) by replicative exhaustion, exposure to ionizing radiation or doxorubicin, and expression of the oncogene HRASG12V. The intersection of the altered transcriptomes revealed 50 RNAs consistently elevated and 18 RNAs consistently reduced across all senescence models, including many protein-coding mRNAs and some non-coding RNAs. We propose that these shared transcriptome profiles will enable the identification of senescent cells in vivo, the investigation of their roles in aging and malignancy and the development of strategies to target senescent cells therapeutically.
Noise-reducing optogenetic negative-feedback gene circuits in human cells
Authors: Guinn Michael Tyler , Balázsi Gábor 
Published: June 2019

Abstract
Gene autorepression is widely present in nature and is also employed in synthetic biology, partly to reduce gene expression noise in cells. Optogenetic systems have recently been developed for controlling gene expression levels in mammalian cells, but most have utilized activator-based proteins, neglecting negative feedback except for in silico control. Here, we engineer optogenetic gene circuits into mammalian cells to achieve noise-reduction for precise gene expression control by genetic, in vitro negative feedback. We build a toolset of these noise-reducing Light-Inducible Tuner (LITer) gene circuits using the TetR repressor fused with a Tet-inhibiting peptide (TIP) or a degradation tag through the light-sensitive LOV2 protein domain. These LITers provide a range of nearly 4-fold gene expression control and up to 5-fold noise reduction from existing optogenetic systems. Moreover, we use the LITer gene circuit architecture to control gene expression of the cancer oncogene KRAS(G12V) and study its downstream effects through phospho-ERK levels and cellular proliferation. Overall, these novel LITer optogenetic platforms should enable precise spatiotemporal perturbations for studying multicellular phenotypes in developmental biology, oncology and other biomedical fields of research.
Quantitative assessment of renal structural and functional changes in chronic kidney disease using multi-parametric magnetic resonance imaging
Authors: Buchanan Charlotte E , Mahmoud Huda , Cox Eleanor F , McCulloch Thomas , Prestwich Benjamin L , Taal Maarten W , Selby Nicholas M , Francis Susan T 
Published: June 2019

Abstract

Background
Multi-parametric magnetic resonance imaging (MRI) provides the potential for a more comprehensive non-invasive assessment of organ structure and function than individual MRI measures, but has not previously been comprehensively evaluated in chronic kidney disease (CKD).

Methods
We performed multi-parametric renal MRI in persons with CKD (n = 22, 61 ± 24 years) who had a renal biopsy and measured glomerular filtration rate (mGFR), and matched healthy volunteers (HV) (n = 22, 61 ± 25 years). Longitudinal relaxation time (T1), diffusion-weighted imaging, renal blood flow (phase contrast MRI), cortical perfusion (arterial spin labelling) and blood-oxygen-level-dependent relaxation rate (R2*) were evaluated.

Results
MRI evidenced excellent reproducibility in CKD (coefficient of variation &lt;10%). Significant differences between CKD and HVs included cortical and corticomedullary difference (CMD) in T1, cortical and medullary apparent diffusion coefficient (ADC), renal artery blood flow and cortical perfusion. MRI measures correlated with kidney function in a combined CKD and HV analysis: estimated GFR correlated with cortical T1 (r = −0.68), T1 CMD (r = −0.62), cortical (r = 0.54) and medullary ADC (r = 0.49), renal artery flow (r = 0.78) and cortical perfusion (r = 0.81); log urine protein to creatinine ratio (UPCR) correlated with cortical T1 (r = 0.61), T1 CMD (r = 0.61), cortical (r = −0.45) and medullary ADC (r = −0.49), renal artery flow (r = −0.72) and cortical perfusion (r = −0.58). MRI measures (cortical T1 and ADC, T1 and ADC CMD, cortical perfusion) differed between low/high interstitial fibrosis groups at 30–40% fibrosis threshold.

Conclusion
Comprehensive multi-parametric MRI is reproducible and correlates well with available measures of renal function and pathology. Larger longitudinal studies are warranted to evaluate its potential to stratify prognosis and response to therapy in CKD.
Central venous catheter use increases ischemic stroke risk: a nationwide population-based study
Authors: Liao P -H , Lai C -Y , Wu C -H , Su Y -C , Wei C -W , Kao C -H 
Published: June 2019

Abstract

Background
Central venous catheter (CVC) placement is a common procedure used for the treatment of critically ill patients. However, ischemic stroke is a complication after CVC placement.

Aim
This study investigated the association between CVC placement and ischemic stroke risk in an Asian population.

Design
Population-based retrospective study.

Methods
We enrolled 37 623 patients who ever-received CVC placement over 2000–10 and propensity score-matched individuals without CVC placement as the comparison cohort from the Taiwan National Health Insurance Research Database. We determined the cumulative incidence rates and adjusted hazard ratios (aHRs) for ischemic stroke.

Results
We finally identified and enrolled 34 164 propensity score-matched pairs of individuals. Compared with the comparison group, CVC placement increased the average annual ischemic stroke incidence [19.5 vs. 11.6 per 10 000 person-years; crude HR=1.28, 95%, confidence interval (CI)=1.21–1.35; adjusted subhazard ratio (aSHR)=1.4, 95% CI = 1.33–1.47; P<0.001). In addition, compared with those aged >35 years, stroke risk was significantly higher in <35-year-old patients with CVC placement (aSHR=14.3, 95% CI=6.11–33.4; P<0.001). After <1-year follow-up, the ischemic stroke incidence rate in the CVC placement group was ∼3.25-fold higher than that in the comparison group (aHR=3.25, 95% CI=2.9–3.63; P<0.0001).

Conclusion
CVC placement increases ischemic stroke risk, particularly in those aged ≤35 years; this trend warrants further investigation.
Gender and Citizenship in Australia: Government Approaches to Paid Parental Leave Policy 1996–2017
Authors: Newsome Lucie 
Published: June 2019

AbstractIn Western welfare states women’s citizenship rights are increasingly conferred on the basis of labor force participation rather than maternalism. This article examines the policy positions and discourse associated with paid parental leave of successive Australian governments from 1996 to 2017 to examine the extent to which this has occurred in the Australian context. It reveals a slow movement away from maternalism that has been constrained by path dependencies associated with the male breadwinner model and is shaped by philosophies of liberalism and small government.
Evolutionary dynamics and molecular epidemiology of West Nile virus in New York State: 1999–2015
Authors: Bialosuknia Sean M , Tan Yi , Zink Steven D , Koetzner Cheri A , Maffei Joseph G , Halpin Rebecca A , Mueller Emmi A , Novotny Mark , Shilts Meghan , Fedorova Nadia B , Amedeo Paolo , Das Suman R , Pickett Brett , Kramer Laura D , Ciota Alexander T 
Published: June 2019

AbstractFollowing its introduction into New York State (NYS) in 1999, West Nile virus (WNV; Flavivirus, Flaviviridae) underwent a rapid expansion throughout the USA and into Canada and Latin America. WNV has been characterized as being evolutionarily stable, with weak geographic structure, a dominance of purifying selection and limited adaptive change. We analyzed all available full-genome WNV sequences, focusing on the 543 available sequences from NYS, which included 495 newly sequenced 2000–15 isolates. In addition, we analyzed deep-sequencing data from 317 of these isolates. While our data are generally in agreement with the limited pace of evolutionary change and broad geographic and temporal mixing identified in other studies, we have identified some important exceptions. Most notably, there are 14 codons which demonstrated evidence of positive selection as determined by multiple models, including some positions with evidence of selection in NYS exclusively. Coincident with increased WNV activity, genotypes possessing one or more of these mutations, designated NY01, NY07, and NY10, have increased in prevalence in recent years and displaced historic strains. In addition, we have found a geographical bias with many of these mutations, which suggests selective pressures and adaptations could be regional. Lastly, our deep-sequencing data suggest both increased overall diversity in avian tissue isolates relative to mosquito isolates and multiple non-synonymous minority variants that are both host-specific and retained over time and space. Together, these data provide novel insight into the evolutionary pressures on WNV and the need for continued genetic surveillance and characterization of emergent strains.
Sexual Assault in the Military and Increased Odds of Sexual Pain Among Female Veterans
Authors: Pulverman Carey S. , Creech Suzannah K. , Mengeling Michelle A. , Torner James C. , Syrop Craig H. , Sadler Anne G. 
Published: June 2019

OBJECTIVE:
To examine whether the relationship between childhood sexual abuse and sexual function in civilian women is also found among female veterans, and to consider the additional effects of sexual assault in the military.

METHODS:
Using a retrospective cohort design, participants (N=1,004) from two midwestern Department of Veterans Affairs medical centers and associated clinics completed a telephone-assisted interview on sexual assault, sexual pain, and mental health. Binary logistic regression was used to compare the rates of sexual pain between women with no sexual assault history, histories of childhood sexual abuse alone, histories of sexual assault in the military alone, and histories of childhood sexual abuse and sexual assault in the military.

RESULTS:
Female veterans with histories of childhood sexual abuse and sexual assault in the military reported the highest rates of sexual pain (χ2(3)=40.98, P<.001), posttraumatic stress disorder (PTSD, χ2(3)=88.18, P<.001), and depression (χ2(3)=56.07, P<.001), followed by women with sexual assault in the military histories alone, women with childhood sexual abuse histories alone, and women with no sexual assault. Female veterans with histories of childhood sexual abuse and sexual assault in the military were 4.33 times more likely to report sexual pain, 6.35 times more likely to report PTSD, and 3.91 times more likely to report depression than female veterans with no sexual assault.

CONCLUSION:
The relationship between sexual assault and sexual pain in female veterans is distinct from their civilian peers. For female veterans, sexual assault in the military is more detrimental to sexual function (specifically sexual pain) than childhood sexual abuse alone, and the combination of childhood sexual abuse and sexual assault in the military confers the greatest risk for sexual pain. Given this difference in sexual health, treatments for sexual dysfunction related to a history of childhood sexual abuse in civilian women may not be adequate for female veterans. Female veterans may require a targeted treatment approach that takes into account the particular nature and consequences of sexual assault in the military.
Chemotherapy, Radiation, or Combination Therapy for Stage III Uterine Cancer
Authors: Syeda Sbaa , Chen Ling , Hou June Y. , Tergas Ana I. , Khoury-Collado Fady , Melamed Alexander , St. Clair Caryn M. , Ananth Cande V. , Neugut Alfred I. , Hershman Dawn L. , Wright Jason D. 
Published: June 2019

OBJECTIVE:
To compare the outcomes of women with stage III uterine cancer treated with chemotherapy alone, external beam radiation alone, and combination chemotherapy and radiation.

METHODS:
The National Cancer Database was used to identify women with stage III endometrioid, serous, and clear cell uterine cancer treated with either chemotherapy (with or without vaginal brachytherapy) alone, external beam radiation (with or without brachytherapy), or combination chemotherapy and external beam radiation (with or without vaginal brachytherapy) from 2004 to 2015. Survival was estimated using Cox proportional hazards models and adjusted survival curves after propensity score analysis using inverse probability of treatment weighting to balance the clinical and demographic characteristics between the cohorts.

RESULTS:
Of the 20,873 patients identified, 9,456 (45.3%) received chemotherapy alone, 2,417 (11.6%) were treated with radiation alone, and 9,000 (43.1%) received chemotherapy in combination with external beam radiation. Use of combination therapy was 33.0% in 2004, and then rose to 50.5% in 2015. The mortality of the cohort was 33.1% and median survival was 115 months. Within the cohort, combination therapy was associated with a 23% reduction in mortality (hazard ratio [HR]=0.77; 95% CI 0.73–0.80) compared with chemotherapy alone. Similar findings of decreased mortality were noted in subgroup analyses for both stage IIIA (HR=0.81; 95% CI 0.68–0.98) and stage IIIC (HR=0.79; 95% CI 0.75–0.84) tumors. Similarly, when compared with radiation alone, combination therapy was accompanied by a 19% decrease in mortality (HR=0.81; 95% CI 0.73–0.89). Combination chemoradiation was associated with decreased mortality across all of the histologic subtypes.

CONCLUSION:
Among women with stage III uterine cancer, combination chemotherapy and external beam radiation is associated with decreased mortality compared with chemotherapy or radiation alone.
An Opportunity to Engage Obstetrics and Gynecology Patients Through Shared Visit Notes
Authors: Herlihy Mary , Harcourt Kendall , Fossa Alan , Folcarelli Patricia , Golen Toni , Bell Sigall K. 
Published: June 2019

OBJECTIVE:
To assess obstetrics and gynecology patients' interest in reading their ambulatory visit notes, identification of documentation errors, and perceptions of sensitive language through a quality improvement (QI) initiative.

METHODS:
Beginning April 2016, as part of a QI project all obstetrics and gynecology patients (except family planning) were invited to read their ambulatory visit notes and provide feedback using a patient reporting tool codeveloped with patients. Two physicians with safety expertise reviewed all patient-reported errors over the first 16 months.

RESULTS:
Among obstetrics and gynecology patients with an active portal account and an available note, 6,594 of 9,550 (69%) read at least one note. Two hundred twelve (3.2%) patients used the electronic reporting tool, submitting a total of 232 reports, in a “natural” environment with no advertisement, incentives, or clinician encouragement. In total, 94% felt they understood the notes, 95% understood the next steps in the care plan, and 92% felt the notes accurately described their visit. Of all reports, 27% of patients identified inaccuracies in the notes, including descriptions of symptoms (29%); family history (21%); medications (15%); health problems (15%); social history and physical examination, including elements that were reportedly documented but not performed (each 11%). Patients rated inaccuracies as important in 58% of reports, and, on clinician review, 75% of patient-reported mistakes had the potential to affect care. Among all reports, 7% of patients indicated bothersome words. More than half (56%) of patients included voluntary positive feedback such as appreciation for the health care provider, reassurance from notes, greater visit recall and care plan adherence, and positive effects on the patient–doctor relationship.

DISCUSSION:
Obstetrics and gynecology patients are interested in reading notes, which can promote engagement and safety. Few patients provided feedback, but those who did identified documentation inaccuracies in about one quarter of reports; the majority were relevant to care. Greater outreach and patient encouragement are needed to further engage patients in safety.
Postpartum Galactostasis of the Vulva in a Case of Bilateral Lactating Ectopic Breast Tissue
Authors: Mayer Richard B. , Enengl Sabine , Witzany Herbert , Trautner Philip , Shebl Omar , Oppelt Peter 
Published: June 2019

BACKGROUND:
In the general population, the incidence of accessory breast tissue, a congenital malformation, is 1–5%. The most common site is the lower axilla. Detecting such tissue may be problematic, and accessory breasts below the umbilicus are extremely rare.

CASE:
This report describes the case of a 5-day postpartum 29-year-old woman, G2P2, with painful vulvar swelling 6 cm in diameter. The patient was diagnosed with polymastia in the vulva, without polythelia, with galactostasis due to suturing of a birth laceration covering an excretory duct. The sutures were removed, and the pain decreased. Breastfeeding was continued.

CONCLUSION:
Ectopic breast tissue is rare but should be taken into consideration in the differential diagnosis of a vulvar mass, especially postpartum in lactating women.