bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three years of Sun-as-a-star radial-velocity observations on the approach to solar minimum
Authors: Collier Cameron A , Mortier A , Phillips D , Dumusque X , Haywood R D , Langellier N , Watson C A , Cegla H M , Costes J , Charbonneau D , Coffinet A , Latham D W , Lopez-Morales M , Malavolta L , Maldonado J , Micela G , Milbourne T , Molinari E , Saar S H , Thompson S , Buchschacher N , Cecconi M , Cosentino R , Ghedina A , Glenday A , Gonzalez M , Li C-H , Lodi M , Lovis C , Pepe F , Poretti E , Rice K , Sasselov D , Sozzetti A , Szentgyorgyi A , Udry S , Walsworth R 
Published: May 2019

Abstract
The time-variable velocity fields of solar-type stars limit the precision of radial-velocity determinations of their planets’ masses, obstructing detection of Earth twins. Since 2015 July, we have been monitoring disc-integrated sunlight in daytime using a purpose-built solar telescope and fibre feed to the HARPS-N stellar radial-velocity spectrometer. We present and analyse the solar radial-velocity measurements and cross-correlation function (CCF) parameters obtained in the first 3 yr of observation, interpreting them in the context of spatially resolved solar observations. We describe a Bayesian mixture-model approach to automated data-quality monitoring. We provide dynamical and daily differential-extinction corrections to place the radial velocities in the heliocentric reference frame, and the CCF shape parameters in the sidereal frame. We achieve a photon-noise-limited radial-velocity precision better than 0.43 m s−1 per 5-min observation. The day-to-day precision is limited by zero-point calibration uncertainty with an RMS scatter of about 0.4 m s−1. We find significant signals from granulation and solar activity. Within a day, granulation noise dominates, with an amplitude of about 0.4 m s−1 and an autocorrelation half-life of 15 min. On longer time-scales, activity dominates. Sunspot groups broaden the CCF as they cross the solar disc. Facular regions temporarily reduce the intrinsic asymmetry of the CCF. The radial-velocity increase that accompanies an active-region passage has a typical amplitude of 5 m s−1 and is correlated with the line asymmetry, but leads it by 3 d. Spectral line-shape variability thus shows promise as a proxy for recovering the true radial velocity.
Common envelope evolution on a moving mesh
Authors: Prust Logan J , Chang Philip 
Published: May 2019

AbstractWe outline the methodology of simulating common envelope evolution (CEE) with the moving-mesh code manga. We extend manga to include multiple time-steps. This provides substantial speedups for problems with large dynamic range. We describe the implementation of realistic equations of state relevant in stellar structure and the generation of suitable initial conditions. We then carry out two example simulations of a 2 M⊙ red giant with a 0.36 M⊙ core and a 1 M⊙ companion undergoing CEE for 240 days. In one simulation the red giant is set into corotation with the orbital motion and in the other it is non-rotating. We find that the separation between the companion and red giant core shrinks from 52 R⊙ to 3.6 R⊙ and 3.2 R⊙, respectively, ending with an eccentricity of 0.1. We also find that 66 and 63 per cent of the envelope mass is ejected. This is higher than in many previous works. Several reasons for this are discussed. These include our inclusion of recombination energy. Our simulations show that putting giants in corotation increases the fraction of mass ejected from the system and results in a larger final orbital separation. We conclude that the entire envelope of the red giant might be ejected during the plunge phase of CEE in this region of parameter space.
The tidal parameters of TRAPPIST-1b and c
Authors: Brasser R , Barr A C , Dobos V 
Published: May 2019

Abstract
The TRAPPIST-1 planetary system consists of seven planets within 0.05 au of each other, five of which are in a multiresonant chain. These resonances suggest the system formed via planet migration; subsequent tidal evolution has damped away most of the initial eccentricities. We used dynamical N-body simulations to estimate how long it takes for the multiresonant configuration that arises during planet formation to break. From there we use secular theory to pose limits on the tidal parameters of planets b and c. We calibrate our results against multilayered interior models constructed to fit the masses and radii of the planets, from which the tidal parameters are computed independently. The dynamical simulations show that the planets typically go unstable 30 Myr after their formation. Assuming synchronous rotation throughout, we compute $\frac{k_2}{Q} \gtrsim 2\times 10^{-4}$ for planet b and $\frac{k_2}{Q} \gtrsim 10^{-3}$ for planet c. Interior models yield (0.075–0.37) × 10−4 for TRAPPIST-1b and (0.4–2) × 10−4 for TRAPPIST-1c. The agreement between the dynamical and interior models is not too strong, but is still useful to constrain the dynamical history of the system. We suggest that this two-pronged approach could be of further use in other multiresonant systems if the planet’s orbital and interior parameters are sufficiently well known.
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
Authors: Li Shaojuan , Wan Changxin , Zheng Rongbin , Fan Jingyu , Dong Xin , Meyer Clifford A , Liu X Shirley 
Published: May 2019

AbstractCharacterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http://go.cistrome.org/.
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs
Authors: Liao Yuxing , Wang Jing , Jaehnig Eric J , Shi Zhiao , Zhang Bing 
Published: May 2019

AbstractWebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.
Can youth get the contraception they want? Results of a pilot study in the province of Quebec
Authors: Di Meglio Giuseppina , Yeates Jessica , Seidman Gillian 
Published: May 2019

Abstract

Objectives
Canadian contraceptive providers report many barriers to access to contraception, and perceive youth as particularly vulnerable to these barriers. This study explores Quebec youth’s experience of obtaining contraception.

Methods
A convenience sample of Quebec youth (aged 14 to 21 years) participated in an online anonymous survey of their experiences obtaining contraception. Data were collected between June 1, 2016 and December 31, 2016.

Results
One hundred and five youth were eligible to participate. Of these, 95 had used at least one form of contraception. Twelve (13%) reported not being able to obtain their preferred method of contraception, with cost being the most common barrier (N=10). Eleven participants (12%) stopped using their preferred contraceptive method: cost was a factor in four cases, and difficulty with access to the clinic/prescription in seven. Youth who required confidential access experienced more difficulty obtaining contraception (P&lt;0.01).

Conclusion
Despite benefitting from universal pharmacare and a network of youth sexual and reproductive health clinics, Quebec youth still experience barriers to obtaining and continuing their preferred contraceptive. Youth who desire confidential care are more likely to experience difficulty obtaining contraception.
Social Interactions of Clerks: The Role of Engagement, Imagination, and Alignment as Sources for Professional Identity Formation
Authors: Adema Marieke , Dolmans Diana H.J.M. , Raat Janet (A.N.) , Scheele Fedde , Jaarsma A. Debbie C. , Helmich Esther 
Published: May 2019

Purpose
Participating in clinical practice shapes students’ identities, but it is unclear how students build meaningful relationships while “dipping into” various social contexts. This study explored with whom students interacted, which social relationships they built, and how these relationships contributed to the formation of a professional identity.

Method
In this longitudinal study at University Medical Center Groningen, University of Groningen, the Netherlands, 9 undergraduate medical students recorded experiences of thinking about themselves as future professionals (September 2015 to March 2017). The authors conducted template analysis using both open coding and a priori themes derived from Wenger’s modes of belonging to communities of practice: engagement, imagination, and alignment.

Results
The authors received 205 recorded experiences. While rotating, students used engagement, imagination, and alignment to give meaning to clinical workplace social interactions. Participants considered relationships with doctors, patients, and peers as preconditions for engaging in meaningful experiences. Although imagination and alignment were less represented, discussing imagination with peers and physicians stimulated a deeper understanding of what it means to become a physician. Explicitly being invited “to the table” and awareness of the benefits of being a clerk were instances of alignment that stimulated the development of identities as future doctors.

Conclusions
To understand the nature of professional identity formation, Wenger’s modes of belonging must be considered. Where engagement is very prevalent, imagination and alignment are less spontaneously mentioned and therefore more difficult to foster. Looking for ways to support imagination and alignment is important for students’ sensemaking process of becoming a doctor.
Changes in Whole Brain Dynamics and Connectivity Patterns during Sevoflurane- and Propofol-induced Unconsciousness Identified by Functional Magnetic Resonance Imaging
Authors: Golkowski Daniel , Larroque Stephen Karl , Vanhaudenhuyse Audrey , Plenevaux Alain , Boly Melanie , Di Perri Carol , Ranft Andreas , Schneider Gerhard , Laureys Steven , Jordan Denis , Bonhomme Vincent , Ilg Rüdiger 
Published: May 2019

Abstract

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
A key feature of the human brain is its capability to adapt flexibly to changing external stimuli. This capability can be eliminated by general anesthesia, a state characterized by unresponsiveness, amnesia, and (most likely) unconsciousness. Previous studies demonstrated decreased connectivity within the thalamus, frontoparietal, and default mode networks during general anesthesia. We hypothesized that these alterations within specific brain networks lead to a change of communication between networks and their temporal dynamics.

Methods
We conducted a pooled spatial independent component analysis of resting-state functional magnetic resonance imaging data obtained from 16 volunteers during propofol and 14 volunteers during sevoflurane general anesthesia that have been previously published. Similar to previous studies, mean z-scores of the resulting spatial maps served as a measure of the activity within a network. Additionally, correlations of associated time courses served as a measure of the connectivity between networks. To analyze the temporal dynamics of between-network connectivity, we computed the correlation matrices during sliding windows of 1 min and applied k-means clustering to the matrices during both general anesthesia and wakefulness.

Results
Within-network activity was decreased in the default mode, attentional, and salience networks during general anesthesia (P < 0.001, range of median changes: –0.34, –0.13). Average between-network connectivity was reduced during general anesthesia (P < 0.001, median change: –0.031). Distinct between-network connectivity patterns for both wakefulness and general anesthesia were observed irrespective of the anesthetic agent (P < 0.001), and there were fewer transitions in between-network connectivity patterns during general anesthesia (P < 0.001, median number of transitions during wakefulness: 4 and during general anesthesia: 0).

Conclusions
These results suggest that (1) higher-order brain regions play a crucial role in the generation of specific between-network connectivity patterns and their dynamics, and (2) the capability to interact with external stimuli is represented by complex between-network connectivity patterns.
Toll-like Receptor 7 Contributes to Inflammation, Organ Injury, and Mortality in Murine Sepsis
Authors: Jian Wenling , Gu Lili , Williams Brittney , Feng Yan , Chao Wei , Zou Lin 
Published: May 2019

Abstract

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
Sepsis remains a critical illness with high mortality. The authors have recently reported that mouse plasma RNA concentrations are markedly increased during sepsis and closely associated with its severity. Toll-like receptor 7, originally identified as the sensor for single-stranded RNA virus, also mediates host extracellular RNA-induced innate immune responses in vitro and in vivo. Here, the authors hypothesize that innate immune signaling via Toll-like receptor 7 contributes to inflammatory response, organ injury, and mortality during polymicrobial sepsis.

Methods
Sepsis was created by (1) cecal ligation and puncture or (2) stool slurry peritoneal injection. Wild-type and Toll-like receptor 7 knockout mice, both in C57BL/6J background, were used. The following endpoints were measured: mortality, acute kidney injury biomarkers, plasma and peritoneal cytokines, blood bacterial loading, peritoneal leukocyte counts, and neutrophil phagocytic function.

Results
The 11-day overall mortality was 81% in wild-type mice and 48% in Toll-like receptor 7 knockout mice after cecal ligation and puncture (N = 27 per group, P = 0.0031). Compared with wild-type septic mice, Toll-like receptor 7 knockout septic mice also had lower sepsis severity, attenuated plasma cytokine storm (wild-type vs. Toll-like receptor 7 knockout, interleukin-6: 43.2 [24.5, 162.7] vs. 4.4 [3.1, 12.0] ng/ml, P = 0.003) and peritoneal inflammation, alleviated acute kidney injury (wild-type vs. Toll-like receptor 7 knockout, neutrophil gelatinase-associated lipocalin: 307 ± 184 vs.139 ± 41-fold, P = 0.0364; kidney injury molecule-1: 40 [16, 49] vs.13 [4, 223]-fold, P = 0.0704), lower bacterial loading, and enhanced leukocyte peritoneal recruitment and phagocytic activities at 24 h. Moreover, stool slurry from wild-type and Toll-like receptor 7 knockout mice resulted in similar level of sepsis severity, peritoneal cytokines, and leukocyte recruitment in wild-type animals after peritoneal injection.

Conclusions
Toll-like receptor 7 plays an important role in the pathogenesis of polymicrobial sepsis by mediating host innate immune responses and contributes to acute kidney injury and mortality.
Glucocorticoid-induced osteoporosis update
Authors: Adami Giovanni , Saag Kenneth G. 
Published: May 2019

Purpose of review
Steroid-induced osteoporosis or glucocorticoid-induced osteoporosis (GIOP) is a common form of secondary osteoporosis and is a cause of increased morbidity and mortality. The pathogenesis of GIOP includes decreased bone formation and increased bone resorption. Clinicians can rely on several effective medications for the treatment and prevention of GIOP, including antiresorptive drugs (i.e. bisphosphonates) and bone anabolic drugs (i.e. teriparatide).

Recent findings
Recent studies have further highlighted that GIOP is a major public health concern and have provided new insights on the pathogenesis of GIOP, in particular, the dose-dependent effects of glucocorticoids on bone. New evidence on the real-world effectiveness of established GIOP therapies have been recently published as well as the results of the 24-months denosumab randomized controlled trial in GIOP.

Summary
GIOP and fragility fractures are important adverse events related to the long-term use of glucocorticoids. Recent studies have provided additional data on the epidemiology and pathogenesis of GIOP and on the efficacy and effectiveness of GIOP therapies.
Harnessing the power of social media: how can it help in axial spondyloarthritis research?
Authors: Reuter Katja , Danve Abhijeet , Deodhar Atul 
Published: May 2019

Purpose of reviewAxial spondyloarthritis (axSpA) is a chronic inflammatory rheumatic disease that is relatively unknown among the general public. Most patients with axSpA are young or middle-aged adults and more likely to use some social media. This review highlights trends in the application of social media and different ways in which these tools do already or may benefit clinical research, delivery of care, and education in rheumatology, particularly in the field of axSpA.Recent findingsThis article discusses four areas in the biomedical field that social media has infused with novel ideas: (i) the use of patient-generated health data from social media to learn about their disease experience, (ii) delivering health education and interventions, (iii) recruiting study participants, and (iv) reform, transfer, and disseminate medical education. We conclude with promising studies in rheumatology that have incorporated social media and suggestions for future directions.SummaryRheumatologists now have the opportunity to use social media and innovate on many aspects of their practice. We propose further exploration of multiple ways in which social media might help with the identification, diagnosis, education, and research study enrollment of axSpA patients. However, standardization in study design, reporting, and managing ethical and regulatory aspects will be required to take full advantage of this opportunity.
Bilateral Facial Apocrine Fibrosing Hamartoma Mimicking Microcystic Adnexal Carcinoma
Authors: Llamas-Velasco Mar , Fraga Javier , Schaller Jörg , Requena Luis , Daudén Esteban , Rütten Arno 
Published: May 2019

Abstract:
An otherwise healthy 50-year-old woman was evaluated for the presence of 2 erythematous, and slightly pruritic plaques, involving both cheeks for 30 years. Left-side skin biopsy showed a diffuse proliferation of ductal structures horizontally arranged and involving the reticular dermis that resembled tubular adenoma embedded in a sclerotic stroma and surrounded by a peculiar periductal desmoplasia. Nuclear atypia or mitosis was not found. Contralateral biopsy showed identical findings. Differential diagnosis included microcystic adnexal carcinoma (MAC) and plaque-like syringoma and a peculiarly horizontally arranged tubular adenoma. We ruled out MAC as the lesions were long-standing, without infundibular cysts, solid strands, or perineural infiltration. Our case closely resembled those previously described as sweat duct proliferation associated with aggregates of elastic tissue and atrophoderma vermiculatum, although striking differences were observed, as our case did not present aggregates of elastic tissue, did not involve the papillary and superficial reticular dermis, and presented evidences of decapitation secretion as a sign of apocrine differentiation. We consider our case as a MAC simulator and we propose the descriptive name of bilateral facial apocrine fibrosing hamartoma.
Contact Lens–Associated Microbial Keratitis in a Tertiary Eye Care Center in Turkey
Authors: Karaca Irmak , Barut Selver Ozlem , Palamar Melis , Egrilmez Sait , Aydemir Sohret , Yagci Ayse 
Published: May 2019

Objectives:
To evaluate the risk factors, causative microorganisms, and presenting features of infection in patients with contact lens–associated microbial keratitis (CLAMK) admitted to a tertiary referral center in Turkey.

Methods:
A retrospective review of the medical records of 62 patients who were diagnosed as CLAMK in our clinic between 2012 and 2018 was conducted.

Results:
The mean age of the patients (22 men and 40 women) at the time of diagnosis was 24.5±8.3 years (range, 16–48). The mean best-corrected visual acuity (BCVA) was 0.7±0.9 log of minimal angle of resolution (logMAR) (0–3) before treatment and increased to 0.1±0.1 logMAR (0–0.4) at the end of the follow-up. All patients, except one using rigid gas-permeable CL, were frequent replacement soft CL users. Thirty-one (50%) patients declared overnight wear, and 37 (58.9%) patients declared showering or swimming in CLs regularly. Cultures of either corneal scrapings or CL materials were positive in 40 (64.5%) eyes, 12 (19.4%) of which had mixed infections. Thirteen strains of microorganisms were demonstrated, among which there were seven (53.8%) gram-negative bacteria, one (7.7%) gram-positive bacteria, four (30.7%) fungi, and Acanthamoeba (7.7%). The most common pathogen was Pseudomonas aeruginosa, followed by Serratia marcescens and Stenotrophomonas maltophilia. According to culture results, P. aeruginosa infections were associated with significantly worse BCVA. Keratitis foci were either centrally or paracentrally located in 39 (62.9%) eyes, and 16 eyes (25.8%) presented with hypopyon.

Conclusion:
Along with growing number of CL users, CLAMK constitutes an important problem with possibly worse visual outcomes. Thus, in addition to meticulous treatment, management of risk factors and behavioral modifications is crucial.
Toxic Keratitis After Application of Custard Apple Seed for Head Lice Infestation
Authors: Gandhi Preethika , Radhakrishnan Naveen , Khaitan Isha , Srinivasan Muthiah , Prajna Venkatesh N. 
Published: May 2019

Purpose:
To report the clinical features and outcomes of toxic keratitis after application of powdered custard apple seeds for hair washing for head lice infestation.

Methods:
Retrospective review of all patients with toxic keratitis after application of powdered custard apple seed for head lice infestation during the time period from January 2015 to December 2017. Demographic details, clinical features, and visual outcomes were documented.

Results:
Thirty-one eyes of 19 patients with toxic keratitis after application of crushed custard apple seeds for head lice infestation were included in the study. Eighteen females and 1 male with a median age of 14 years [interquartile range (IQR) 12–34 years] presented with severe epiphora, congestion, photophobia, and defective vision (median logMar visual acuity 0.4, IQR 0.2–0.8) after application of custard apple seed powder for hair washing. Ten eyes (32.2%) had an epithelial defect (median size 9 mm2, IQR 5–12 mm2), and 21 (67.7%) eyes had punctate epithelial erosions. All the patients were treated with topical antibiotics, and at 3 days follow-up, all of them had resolution of symptoms and signs with a median logarithm of the minimum angle of resolution (logMAR) visual acuity of 0 (IQR 0–0.2).

Conclusions:
Health education about the harmful effect of this traditional practice for head lice infestation will prevent further similar events.