bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D biofilms: in search of the polysaccharides holding together lichen symbioses
Authors: Spribille Toby , Tagirdzhanova Gulnara , Goyette Spencer , Tuovinen Veera , Case Rebecca , Zandberg Wesley F 
Published: February 2020

ABSTRACT
Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.
Estimating the relative probability of direct transmission between infectious disease patients
Authors: Leavitt Sarah V , Lee Robyn S , Sebastiani Paola , Horsburgh C Robert , Jenkins Helen E , White Laura F 
Published: February 2020

AbstractBackgroundEstimating infectious disease parameters such as the serial interval (time between symptom onset in primary and secondary cases) and reproductive number (average number of secondary cases produced by a primary case) are important in understanding infectious disease dynamics. Many estimation methods require linking cases by direct transmission, a difficult task for most diseases.MethodsUsing a subset of cases with detailed genetic and/or contact investigation data to develop a training set of probable transmission events, we build a model to estimate the relative transmission probability for all case-pairs from demographic, spatial and clinical data. Our method is based on naive Bayes, a machine learning classification algorithm which uses the observed frequencies in the training dataset to estimate the probability that a pair is linked given a set of covariates.ResultsIn simulations, we find that the probabilities estimated using genetic distance between cases to define training transmission events are able to distinguish between truly linked and unlinked pairs with high accuracy (area under the receiver operating curve value of 95%). Additionally, only a subset of the cases, 10–50% depending on sample size, need to have detailed genetic data for our method to perform well. We show how these probabilities can be used to estimate the average effective reproductive number and apply our method to a tuberculosis outbreak in Hamburg, Germany.ConclusionsOur method is a novel way to infer transmission dynamics in any dataset when only a subset of cases has rich contact investigation and/or genetic data.
Immunological and Inflammatory Biomarkers of Susceptibility and Severity in Adult Respiratory Syncytial Virus Infections
Authors: Wiseman Dexter J , Thwaites Ryan S , Drysdale Simon B , Janet Sophie , Donaldson Gavin C , Wedzicha Jadwiga A , Openshaw Peter J ,   RESCEU Investigators, Nair Harish , Campbell Harry , Shi Ting , Zhang Shanshan , Li You , Openshaw Peter , Wedzicha Jadwiga , Falsey Ann , Miller Mark , Beutels Philippe , Bont Louis , Pollard Andrew , Molero Eva , Martinon-Torres Federico , Heikkinen Terho , Meijer Adam , Kølsen Fischer Thea , van den Berge Maarten , Giaquinto Carlo , Mikolajczyk Rafael , Hackett Judy , Tafesse Eskinder , Cai Bing , Knirsch Charles , Gonzalez Lopez Antonio , Dieussaert Ilse , Dermateau Nadia , Stoszek Sonia , Gallichan Scott , Kieffer Alexia , Demont Clarisse , Cheret Arnaud , Gavart Sandra , Aerssens Jeroen , Wyffels Veronique , Cleenewerck Matthias , Fuentes Robert , Rosen Brian , Nair Harish , Campbell Harry , Shi Ting , Zhang Shanshan , Li You , Openshaw Peter , Wedzicha Jadwiga , Falsey Ann , Miller Mark , Beutels Philippe , Bont Louis , Pollard Andrew , Molero Eva , Martinon-Torres Federico , Heikkinen Terho , Meijer Adam , Kølsen Fischer Thea , van den Berge Maarten , Giaquinto Carlo , Mikolajczyk Rafael , Hackett Judy , Tafesse Eskinder , Cai Bing , Knirsch Charles , Gonzalez Lopez Antonio , Dieussaert Ilse , Dermateau Nadia , Stoszek Sonia , Gallichan Scott , Kieffer Alexia , Demont Clarisse , Cheret Arnaud , Gavart Sandra , Aerssens Jeroen , Wyffels Veronique , Cleenewerck Matthias , Fuentes Robert , Rosen Brian 
Published: February 2020

AbstractBackgroundRespiratory syncytial virus (RSV) is the most common cause of bronchiolitis in young infants. However, it is also a significant pathogen in older adults. Validated biomarkers of RSV disease severity would benefit diagnostics, treatment decisions, and prophylactic interventions. This review summarizes knowledge of biomarkers for RSV disease in adults.MethodsA literature review was performed using Ovid Medline, Embase, Global health, Scopus, and Web of Science for articles published 1946–October 2016. Nine articles were identified plus 9 from other sources.ResultsFrom observational studies of natural infection and challenge studies in volunteers, biomarkers of RSV susceptibility or disease severity in adults were: (1) lower anti-RSV neutralizing antibodies, where neutralizing antibody (and local IgA) may be a correlate of susceptibility/severity; (2) RSV-specific CD8+ T cells in bronchoalveolar lavage fluid preinfection (subjects with higher levels had less severe illness); and (3) elevated interleukin-6 (IL-6), IL-8, and myeloperoxidase levels in the airway are indicative of severe infection.ConclusionsFactors determining susceptibility to and severity of RSV disease in adults have not been well defined. Respiratory mucosal antibodies and CD8+ T cells appear to contribute to preventing infection and modulation of disease severity. Studies of RSV pathogenesis in at-risk populations are needed.
Characteristics and Outcomes of ERCP at a Canadian Tertiary Centre: Initial Results from a Prospective High-Fidelity Biliary Endoscopy Registry
Authors: Forbes Nauzer , Koury Hannah F , Bass Sydney , Cole Martin , Mohamed Rachid , Turbide Christian , Gonzalez-Moreno Emmanuel , Kayal Ahmed , Chau Millie , Lethebe B Cord , Hilsden Robert J , Heitman Steven J 
Published: February 2020

Abstract

Background
Endoscopic retrograde cholangiopancreatography (ERCP) is an essential procedure in the management of pancreatic and biliary disease. While its role is firmly established, further well-designed prospective ERCP research is required, as a large portion of previous work has employed retrospective or administrative methodologies, both prone to potential biases. The aim of the Calgary Registry for Advanced and Therapeutic Endoscopy (CReATE) is to be a high-fidelity prospective multicentre registry.

Methods
The study population consisted of consecutive adult ERCP patients from September 2018 to September 2019. Informed consent was acquired for each patient. All relevant preprocedural, procedural, peri-procedural and postprocedural data were captured in real time by a full-time third-party research assistant directly observing procedures. Outcomes were ascertained by comprehensive medical record review and patient phone interview 30 days after the index procedure.

Results
Five endoscopists performed 895 ERCP procedures, 90.1% of which were deemed successful. Suspected choledocholithiasis was the most common indication for ERCP, followed by suspected or confirmed stricture(s), at 61.0% and 29.5%, respectively. 61.0% of procedures were performed on ERCP-naive patients. Post-ERCP pancreatitis occurred following 4.9% of procedures, with clinically significant bleeding or perforation occurring following 1.8% and 0.1% of procedures, respectively.

Discussion
Through 12 months, CReATE captured 895 procedures prospectively, with each entry containing over 300 data fields. Active expansion to additional tertiary centres is underway, and this will enhance the existing data pool. CReATE has the potential to improve multiple facets of ERCP, including training, optimal procedural techniques, mitigation of adverse events and personalized patient care.
Systematic Review of Health Literacy in Childhood Cancer Patients, Survivors, and Their Caregivers
Authors: Lynn Courtney , Quast Lauren , Rogers Hannah , Effinger Karen , Gilleland-Marchak Jordan 
Published: February 2020

Abstract

Objective
This systematic review examined the literature regarding health literacy among pediatric cancer patients, survivors, and their caregivers. Specific aims were to identify and summarize measures used, levels of and demographic correlates of health literacy, effects of health literacy interventions, and associations between health literacy and health outcomes.

Methods
The search strategy was executed in the following databases: PubMed, EMBASE, PsycINFO, CINAHL, ERIC, and the Cochrane Library. Of the 842 unique studies retrieved, 9 met the inclusion criteria and were included in the systematic review.

Results
Studies used a variety of validated and study-specific measures with no measure emerging as the standard. Levels of health literacy were typically assessed subjectively and across studies the majority of those sampled self-reported adequate health literacy. Few studies examined demographic correlates of health literacy, precluding the identification of consistent predictors. Health literacy intervention research for this population is in its infancy and only pilot projects were identified; effects could not be evaluated. No studies assessed the impact of health literacy on health outcomes.

Conclusions
Very few studies assessed health literacy in pediatric oncology. As treatment for childhood cancer becomes increasingly complex, and patients and caregivers are expected to have adequate understanding of health information, health literacy is a critical construct that should not be overlooked.
A case of peeping testis moving from the inguinal position into the abdomen
Authors: Tatekawa Yukihiro 
Published: February 2020

Abstract
We report herein a 14-month-old boy with a left-sided peeping testis. At the age of 1 month, the left testis was palpated between the inguinal canal and the scrotum. When he was 6 months old, ultrasonography showed the left testis in the inguinal canal. At the age of 13 months, the left testis was not palpable. At the age of 14 months, he underwent surgery for a planned inguinal orchidopexy with a preoperative diagnosis of an undescended testis. When the inguinal canal was opened, a patent processus vaginalis was observed and the testis was found inside the abdominal cavity. The patent processus vaginalis was closed, a dartos pouch was created and the testis was guided into the pouch and fixed to its wall. We describe a case of a peeping testis moving from the inguinal position into the abdomen.
SN 2016gsd: an unusually luminous and linear Type II supernova with high velocities
Authors: Reynolds T M , Fraser M , Mattila S , Ergon M , Dessart L , Lundqvist P , Dong Subo , Elias-Rosa N , Galbany L , Gutiérrez C P , Kangas T , Kankare E , Kotak R , Kuncarayakti H , Pastorello A , Rodriguez O , Smartt S J , Stritzinger M , Tomasella L , Chen Ping , Harmanen J , Hosseinzadeh G , Howell D Andrew , Inserra C , Nicholl M , Nielsen M , Smith K , Somero A , Tronsgaard R , Young D R 
Published: February 2020

ABSTRACT
We present observations of the unusually luminous Type II supernova (SN) 2016gsd. With a peak absolute magnitude of V = −19.95 ± 0.08, this object is one of the brightest Type II SNe, and lies in the gap of magnitudes between the majority of Type II SNe and the superluminous SNe. Its light curve shows little evidence of the expected drop from the optically thick phase to the radioactively powered tail. The velocities derived from the absorption in H α are also unusually high with the blue edge tracing the fastest moving gas initially at 20 000 km s−1, and then declining approximately linearly to 15 000 km s−1 over ∼100 d. The dwarf host galaxy of the SN indicates a low-metallicity progenitor which may also contribute to the weakness of the metal lines in its spectra. We examine SN 2016gsd with reference to similarly luminous, linear Type II SNe such as SNe 1979C and 1998S, and discuss the interpretation of its observational characteristics. We compare the observations with a model produced by the jekyll code and find that a massive star with a depleted and inflated hydrogen envelope struggles to reproduce the high luminosity and extreme linearity of SN 2016gsd. Instead, we suggest that the influence of interaction between the SN ejecta and circumstellar material can explain the majority of the observed properties of the SN. The high velocities and strong H α absorption present throughout the evolution of the SN may imply a circumstellar medium configured in an asymmetric geometry.
Convection with misaligned gravity and rotation: simulations and rotating mixing length theory
Authors: Currie Laura K , Barker Adrian J , Lithwick Yoram , Browning Matthew K 
Published: February 2020

ABSTRACT
We present numerical simulations, using two complementary set-ups, of rotating Boussinesq thermal convection in a three-dimensional Cartesian geometry with misaligned gravity and rotation vectors. This model represents a small region at a non-polar latitude in the convection zone of a star or planet. We investigate the effects of rotation on the bulk properties of convection at different latitudes, focusing on determining the relation between the heat flux and temperature gradient. We show that our results may be interpreted using rotating mixing length theory (RMLT). The simplest version of RMLT (due to Stevenson) considers the single mode that transports the most heat. This works reasonably well in explaining our results, but there is a systematic departure from these predictions (up to approximately $30{{\ \rm per\ cent}}$ in the temperature gradient) at mid-latitudes. We develop a more detailed treatment of RMLT that includes the transport afforded by multiple modes, and we show that this accounts for most of the systematic differences. We also show that convectively generated zonal flows and meridional circulations are produced in our simulations, and that their properties depend strongly on the dimensions of the box. These flows also affect the heat transport, contributing to departures from RMLT at some latitudes. However, we find the theoretical predictions of the multi-mode theory for the mid-layer temperature gradient, the root-mean-square (rms) vertical velocity, the rms temperature fluctuation, and the spatial spectrum of the heat transport at different latitudes are all in reasonably good agreement with our numerical results when zonal flows are small.
The faint host galaxies of C IV absorbers at z &gt; 5
Authors: Finlator Kristian , Doughty Caitlin , Cai Zheng , Díaz Gonzalo 
Published: February 2020

ABSTRACT
We explore the expected galaxy environments of $\mathrm{C\, \small {IV}}$ absorbers at z &gt; 5 using the Technicolor Dawn simulations. These simulations reproduce the observed history of reionization, the z ∼ 6 galaxy stellar mass function, the Ly α forest transmission at z &gt; 5, and the $\mathrm{Si\, \small {IV}}$ column density distribution (CDD) at z ≈ 5.5. None the less, the $\mathrm{C\, \small {IV}}$ CDD remains underproduced. Comparison with observed $\mathrm{C\, \small {II}}/\mathrm{Si\, \small {II}}$ equivalent width ratios and the $\mathrm{C\, \small {II}}$ line incidence suggests that a low carbon yield accounts for some, but not all, of the $\mathrm{C\, \small {IV}}$ discrepancy. Alternatively, a density-bounded escape scenario could harden the metagalactic ionizing background more dramatically even than binary stellar evolution, boosting the $\mathrm{C\, \small {IV}}$ CDD into near agreement with observations. In this case, galaxies ionize more efficiently and fewer are required to host a given high-ionization absorber. Absorbers’ environments therefore constrain ionizing escape. Regardless of the escape scenario, galaxies correlate with $\mathrm{C\, \small {IV}}$ absorbers out to 300 proper kpc (pkpc). The correlation strengthens independently with galaxy luminosity and $\mathrm{C\, \small {IV}}$ column density. Around strong systems ($\log (N_\mathrm{C\, \small {IV}}/{\rm cm}^{-2})\gt 14)$), the overdensity of galaxies with MUV &lt; −18 or log (LLy α/erg s−1) &gt; 41.9 declines from 200–300 within 100 pkpc to 40–60 within 250 pkpc. The previously suggested association between strong $\mathrm{C\, \small {IV}}$ absorbers and Ly α emitters at z &gt; 5 is not expected. It may arise if both populations inhabit large-scale voids, but for different reasons. Although most neighbouring galaxies are too faint for HST, JWST will, with a single pointing, identify ∼10 neighbouring galaxies per strong $\mathrm{C\, \small {IV}}$ absorber at z &gt; 5. Ground-based tests of these predictions are possible via deep surveys for Ly α emission using integral field units.
Evolution of porous dust grains in protoplanetary discs – I. Growing grains
Authors: Garcia Anthony J L , Gonzalez Jean-François 
Published: February 2020

ABSTRACT
One of the main problems in planet formation, hampering the growth of small dust to planetesimals, is the so-called radial-drift barrier. Pebbles of cm to dm sizes are thought to drift radially across protoplanetary discs faster than they can grow to larger sizes, and thus to be lost to the star. To overcome this barrier, drift has to be slowed down or stopped, or growth needs to be sped up. In this paper, we investigate the role of porosity on both drift and growth. We have developed a model for porosity evolution during grain growth and applied it to numerical simulations of protoplanetary discs. We find that growth is faster for porous grains, enabling them to transition to the Stokes drag regime, decouple from the gas, and survive the radial-drift barrier. Direct formation of small planetesimals from porous dust is possible over large areas of the disc.
Classification of blazar candidates of uncertain type from the Fermi LAT 8-yr source catalogue with an artificial neural network
Authors: Kovačević M , Chiaro G , Cutini S , Tosti G 
Published: February 2020

ABSTRACTThe Fermi Large Area Telescope (LAT) has detected more than 5000 γ-ray sources in its first 8 yr of operation. More than 3000 of them are blazars. About 60 per cent of the Fermi-LAT blazars are classified as BL Lacertae objects (BL Lacs) or Flat Spectrum Radio Quasars (FSRQs), while the rest remain of uncertain type. The goal of this study was to classify those blazars of uncertain type, using a supervised machine learning method based on an artificial neural network, by comparing their properties to those of known γ-ray sources. Probabilities for each of 1329 uncertain blazars to be a BL Lac or FSRQ are obtained. Using 90 per cent precision metric, 801 can be classified as BL Lacs and 406 as FSRQs while 122 still remain unclassified. This approach is of interest because it gives a fast preliminary classification of uncertain blazars. We also explored how different selections of training and testing samples affect the classification and discuss the meaning of network outputs.
Clusterix 2.0: a virtual observatory tool to estimate cluster membership probability
Authors: Balaguer-Núñez L , López del Fresno M , Solano E , Galadí-Enríquez D , Jordi C , Jimenez-Esteban F , Masana E , Carbajo-Hijarrubia J , Paunzen E 
Published: February 2020

ABSTRACT
Clusterix 2.0 is a web-based, Virtual Observatory compliant, interactive tool for the determination of membership probabilities in stellar clusters based on proper-motion data using a fully non-parametric method. In an area occupied by a cluster, the frequency function is made up of two contributions: cluster and field stars. The tool performs an empirical determination of the frequency functions from the vector point diagram without relying on any previous assumption about their profiles. Clusterix 2.0 allows us to search the appropriate spatial areas in an interactive way until an optimal separation of the two populations is obtained. Several parameters can be adjusted to make the calculation computationally feasible without interfering with the quality of the results. The system offers the possibility to query different catalogues, such as Gaia, or upload a user’s own data. The results of the membership determination can be sent via Simple Application Messaging Protocol (SAMP) to Virtual Observatory (VO) tools such as Tool for OPerations on Catalogues And Tables (TOPCAT). We apply Clusterix 2.0 to several open clusters with different properties and environments to show the capabilities of the tool: an area of five degrees radius around NGC 2682 (M67), an old, well-known cluster; a young cluster NGC 2516 with a striking elongated structure extended up to four degrees; NGC 1750 and NGC 1758, a pair of partly overlapping clusters; the area of NGC 1817, where we confirm a little-known cluster, Juchert 23; and an area with many clusters, where we disentangle two overlapping clusters situated where only one was previously known: Ruprecht 26 and the new Clusterix 1.