bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of candidemia in Shiraz, southern Iran: A prospective multicenter study (2016–2018)
Authors: Arastehfar Amir , Yazdanpanah Samira , Bakhtiari Mina , Fang Wenjie , Pan Weihua , Mahmoudi Shahram , Pakshir Keyvan , Daneshnia Farnaz , Boekhout Teun , Ilkit Macit , Perlin David S , Zomorodian Kamiar , Zand Farid 
Published: July 2020

AbstractSystematic candidemia studies, especially in southern Iran, are scarce. In the current prospective study, we investigated candidemia in three major healthcare centers of Shiraz, the largest city in southern Iran. Yeast isolates from blood and other sterile body fluids were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and subjected to antifungal susceptibility testing (AFST) using the broth microdilution method. Clinical data were retrieved from patients’ medical records. In total, 113 yeast isolates were recovered from 109 patients, over 60% of whom received fluconazole. Antifungal drugs were prescribed without considering species identification or AFST. The all-cause mortality rate was 28%. Almost 30% of the patients were from intensive care units (ICUs). Candida albicans (56/113; 49.5%) was the most prevalent species followed by C. glabrata (26/113; 23%), C. parapsilosis (13/113; 11.5%), C. tropicalis (7/113; 6.2%), and C. dubliniensis (5/113; 4.4%). Only five isolates showed antifungal resistance or decreased susceptibility to fluconazole: one C. orthopsilosis isolate from an azole-naïve patient and two C. glabrata, one C. albicans, and one C. dubliniensis isolates from patients treated with azoles, who developed therapeutic failure against azoles later. Our results revealed a low level of antifungal resistance but a notable rate of azole therapeutic failure among patients with candidemia due to non-albicans Candida species, which threaten the efficacy of fluconazole, the most widely used antifungal in southern regions of Iran. Candidemia studies should not be confined to ICUs and treatment should be administered based on species identification and AFST results.
Successive line-locked C iv doublets in quasar SDSS J115122.14+020426.3
Authors: Lin Ying-Ru , Lu Wei-Jian 
Published: July 2020

ABSTRACT
Rodríguez Hidalgo et al. (2013, ApJ, 775, 14) have reported the transition of a C iv mini-broad absorption line (mini-BAL) into a BAL in quasar SDSS J115122.14+020426.3 (hereafter J1151+0204). Based on the two-epoch spectra obtained from the Sloan Digital Sky Survey, we further investigate the three BAL systems (systems A, B and C) in J1151+0204. First, we confirm that the absorption-line variability in J1151+0204 is most likely caused by the change in ionization in response to the continuum variation, according to at least the following observational factors: coordinated strengthening is detected between multiple absorption troughs, and the continuum shows obvious weakening. According to photoionization simulations, asynchronized variability between the continuum and absorption lines indicates that the mini-BAL (system A) of J1151+0204 actually represents the state of a higher ionization level and lower C iv column density of the outflow, while its BAL identifies the state of a lower ionization level and higher C iv column density. Second, we find a rare case of a quintuple, which is due to four successive line-locked C iv doublets, within system C. This indicates that these outflow clouds have achieved a high degree of clumpiness, and that the radiative forces play a significant role in the acceleration process of these clumpy outflow clouds.
X-ray spectroscopy of the γ-ray brightest nova V906 Car (ASASSN-18fv)
Authors: Sokolovsky Kirill V , Mukai Koji , Chomiuk Laura , Lopes de Oliveira Raimundo , Aydi Elias , Li Kwan-Lok , Steinberg Elad , Vurm Indrek , Metzger Brian D , Kawash Adam , Linford Justin D , Mioduszewski Amy J , Nelson Thomas , Ness Jan-Uwe , Page Kim L , Rupen Michael P , Sokoloski Jennifer L , Strader Jay 
Published: July 2020

ABSTRACT
Shocks in γ-ray emitting classical novae are expected to produce bright thermal and non-thermal X-rays. We test this prediction with simultaneous NuSTAR and Fermi/LAT observations of nova V906 Car, which exhibited the brightest GeV γ-ray emission to date. The nova is detected in hard X-rays while it is still γ-ray bright, but contrary to simple theoretical expectations, the detected 3.5–78 keV emission of V906 Car is much weaker than the simultaneously observed &gt;100 MeV emission. No non-thermal X-ray emission is detected, and our deep limits imply that the γ-rays are likely hadronic. After correcting for substantial absorption (NH ≈ 2 × 1023 cm−2), the thermal X-ray luminosity (from a 9 keV optically thin plasma) is just ∼2 per cent of the γ-ray luminosity. We consider possible explanations for the low thermal X-ray luminosity, including the X-rays being suppressed by corrugated, radiative shock fronts or the X-rays from the γ-ray producing shock are hidden behind an even larger absorbing column (NH &gt; 1025 cm−2). Adding XMM–Newton and Swift/XRT observations to our analysis, we find that the evolution of the intrinsic X-ray absorption requires the nova shell to be expelled 24 d after the outburst onset. The X-ray spectra show that the ejecta are enhanced in nitrogen and oxygen, and the nova occurred on the surface of a CO-type white dwarf. We see no indication of a distinct supersoft phase in the X-ray light curve, which, after considering the absorption effects, may point to a low mass of the white dwarf hosting the nova.
Nature of the DLA towards Q 0528−250: High pressure and strong UV field revealed by excitation of C i, H2, and Si ii
Authors: Balashev S A , Ledoux C , Noterdaeme P , Srianand R , Petitjean P , Gupta N 
Published: July 2020

ABSTRACT
We present the detection of excited fine-structure energy levels of singly ionized silicon and neutral carbon associated with the proximate damped Lyman-α system at zabs = 2.811 towards Q 0528−250. This absorber has an apparent relative velocity that is inconsistent with the Hubble flow indicating motion along the line-of-sight towards the quasar, i.e. zabs &gt; zem. We measure the metallicity of the system to be [Zn/H] = −0.68 ± 0.02. Using the relative populations of the fine-structure levels of Si ii and C i, as well as the populations of H2 rotational levels, we constrain the physical conditions of the gas. We derive hydrogen number densities of $n_{\rm H}=190^{+70}_{-50}$ cm−3 and $260^{+30}_{-20}$ cm−3 in two velocity components where both C i and H2 are detected. Taking into account the kinetic temperature in each component, ∼150 K, we infer high values of thermal pressure in the cold neutral medium probed by the observations. The strengths of the UV field in Draine’s unit are $I_{\rm UV} = 10^{+5}_{-3}$ and $14^{+3}_{-3}$ in each of these two components, respectively. Such enhanced UV fluxes and thermal pressure compared to intervening DLAs are likely due to the proximity of the quasar. The typical size of the absorber is ∼104 au. Assuming the UV flux is dominated by the quasar, we constrain the distance between the quasar and the absorber to be ∼150−200 kpc. This favours a scenario where the absorption occurs in a companion galaxy located in the group where the quasar-host galaxy resides. This is in line with studies in emission that revealed the presence of several galaxies around the quasar.
Determination of the relative inclination and the viewing angle of an interacting pair of galaxies using Convolutional Neural Networks
Authors: Prakash Prem , Banerjee Arunima , Perepu Pavan Kumar 
Published: July 2020

ABSTRACT
Constructing dynamical models for interacting galaxies constrained by their observed structure and kinematics crucially depends on the correct choice of the values of their relative inclination (i) and viewing angle (θ) (the angle between the line of sight and the normal to the plane of their orbital motion). We construct Deep Convolutional Neural Network (DCNN) models to determine the i and θ of interacting galaxy pairs, using N-body + smoothed particle hydrodynamics (SPH) simulation data from the GalMer data base for training. GalMer simulates only a discrete set of i values (0°, 45°, 75°, and 90°) and almost all possible values of θ values in the range, [−90°, 90°]. Therefore, we have used classification for i parameter and regression for θ. In order to classify galaxy pairs based on their i values only, we first construct DCNN models for (i) 2-class (i = 0 °, 45°) (ii) 3-class (i = 0°, 45°, 90°) classification, obtaining F1 scores of 99 per cent and 98 per cent respectively. Further, for a classification based on both i and θ values, we develop a DCNN model for a 9-class classification using different possible combinations of i and θ, and the F1 score was 97${{\ \rm per\ cent}}$. To estimate θ alone, we have used regression, and obtained a mean-squared error value of 0.12. Finally, we also tested our DCNN model on real data from Sloan Digital Sky Survey. Our DCNN models could be extended to determine additional dynamical parameters, currently determined by trial and error method.
An Evolutionarily Primitive and Distinct Auxin Metabolism in the Lycophyte Selaginella moellendorffii
Authors: Kaneko Shutaro , Cook Sam David , Aoi Yuki , Watanabe Akie , Hayashi Ken-Ichiro , Kasahara Hiroyuki 
Published: July 2020

Abstract
Auxin is a key regulator of plant growth and development. Indole-3-acetic acid (IAA), a plant auxin, is mainly produced from tryptophan via indole-3-pyruvate (IPA) in both bryophytes and angiosperms. Angiosperms have multiple, well-documented IAA inactivation pathways, involving conjugation to IAA-aspartate (IAA-Asp)/glutamate by the GH3 auxin-amido synthetases, and oxidation to 2-oxindole-3-acetic acid (oxIAA) by the DAO proteins. However, IAA biosynthesis and inactivation processes remain elusive in lycophytes, an early lineage of spore-producing vascular plants. In this article, we studied IAA biosynthesis and inactivation in the lycophyte Selaginella moellendorffii. We demonstrate that S. moellendorffii mainly produces IAA from the IPA pathway for the regulation of root growth and response to high temperature, similar to the angiosperm Arabidopsis. However, S. moellendorffii exhibits a unique IAA metabolite profile with high IAA-Asp and low oxIAA levels, distinct from Arabidopsis and the bryophyte Marchantia polymorpha, suggesting that the GH3 family is integral for IAA homeostasis in the lycophytes. The DAO homologs in S. moellendorffii share only limited similarity to the well-characterized rice and Arabidopsis DAO proteins. We therefore suggest that these enzymes may have a limited role in IAA homeostasis in S. moellendorffii compared to angiosperms. We provide new insights into the functional diversification of auxin metabolic genes in the evolution of land plants.
Perceptions of ICU Care Following Do-Not-Resuscitate Orders: A Military Perspective
Authors: Dishman Sydney E. , Driggers Kathryn E. , Johnson Laura S. , Olsen Cara H. , Ryan Andrea B. , McLawhorn Melissa M. , Chung Kevin K. 
Published: July 2020

Objectives:
Although do-not-resuscitate orders only prohibit cardiopulmonary resuscitation in the case of cardiac arrest, the common initiation of this code status in the context of end-of-life care may lead providers to draw premature conclusions about other goals of care. The aim of this study is to identify concerns regarding care quality in the setting of do-not-resuscitate orders within the Department of Defense and compare differences in perceptions between members of the critical care team.

Design:
A cross sectional observational study was conducted.

Setting:
This study took place in the setting of critical care within the Department of Defense.

Subjects:
All members of the Uniformed Services Section of the Society of Critical Care Medicine were invited to participate.

Interventions:
A validated 31-question survey exploring the perceptions of care quality in the setting of do-not-resuscitate status was distributed.

Measurements and Main Results:
Exploratory factor analysis was used to categorically group survey questions, and average factor scores were compared between respondent groups using t tests. Responses to individual questions were also analyzed between comparison groups using Fisher exact tests. Factor analysis revealed no significant differences between respondents of different training backgrounds; however, those with do-not-resuscitate training were more likely to agree that active treatment would be pursued (p = 0.024) and that trust and communication would be maintained (p = 0.005). Although 38% of all respondents worry that quality of care will decrease, 93% agree that life-prolonging treatments should be offered. About a third of providers wrongly believed that a do-not-resuscitate order must be reversed prior to an operation.

Conclusions:
Although providers across training backgrounds held similar concerns about decreased care quality in the ICU, there is wide belief that the routine and noninvasive interventions are offered as indicated. Those with do-not-resuscitate training were more likely to believe that standards of care continued to be met after code status change.
Broadly neutralizing antibodies combined with latency-reversing agents or immune modulators as strategy for HIV-1 remission
Authors: Gunst Jesper Damsgaard , Højen Jesper Falkesgaard , Søgaard Ole Schmeltz 
Published: July 2020

Purpose of review
Antiretroviral therapy (ART) is extremely effective in controlling HIV-1 infection; however, ART is not curative. Here, we review broadly neutralizing anti-HIV-1 antibodies (bNAbs) combined with latency-reversing agents (LRAs) or immune modulators as strategy for achieving long-term HIV-1 remission.

Recent findings
Clinical trials testing the effect of a single intervention such as a LRA ‘shock and kill’, immune modulator or bNAbs among HIV-1 infected individuals on long-term suppressive ART have not lead to long-term HIV-1 remission when ART is stopped. Novel combinations of interventions designed to eliminate infected cells and enhance immune-effector functions are being investigated. Findings in nonhuman primates (NHPs) of such combinations are very promising and clinical trials are now ongoing. These trials will provide the first indication of the efficacy of combinations of bNAbs and LRA or immune modulators for achieving durable HIV-1 remission.

Summary
bNAbs facilitate the elimination of HIV-1 infected cells and boost immune responses. Preclinical findings show that these effects can be harnessed by simultaneous administration of LRAs or immune modulators such as Toll-like receptor agonists. The clinical success of such combination strategies may be impacted by factors such as immune exhaustion, bNAbs sensitivity as well as the pharmacodynamics of the investigational compounds.
Visual Field Artifacts From Face Mask Use
Authors: Young Su Ling , Smith Margaret L. , Tatham Andrew J. 
Published: July 2020

Purpose:
The coronavirus (COVID-19) pandemic has had a profound impact on how glaucoma care is delivered, necessitating reduced clinic flow, social distancing, and use of face coverings by patients and staff. This case highlights the need to be aware of improperly fitted face masks as a cause of artifact on standard automated perimetry (SAP).

Clinical Presentation:
A 32-year-old female underwent SAP with the 24-2 SITA Fast test of the Humphrey Field Analyzer wearing an ear-loop surgical face mask. At the end of testing, it was noted that the mask had ridden up the patient’s face. Small amounts of condensate were noted on the perimeter lens.

Clinical Findings:
SAP demonstrated good reliability indices but in both eyes, there was a marked reduction in sensitivity inferiorly. The glaucoma hemifield test was outside normal limits. It was ensured the upper border of the mask was well sealed with the loops secured around the ears and nasal strip of the mask pinched down. Visual fields were repeated and were found to be normal.

Conclusions:
Poorly fitting face masks represent a new cause of visual field artifact which may mimic pathologic field defects. Without careful attention during testing, the cause of such artifacts may not be apparent, especially as reliability indices may be normal. Adjustments to the fit of face masks may help prevent fogging or mask slippage and increase test reliability.
A Predictive Model for Temporal Artery Biopsy in the Setting of Suspected Giant Cell Arteritis: A Validation Study
Authors: Weis Ezekiel , Waite Chris , Roelofs Kelsey A. 
Published: July 2020

Purpose:
A previously published predictive model based on threshold parameters for erythrocyte sedimentation rate, c-reactive protein, and platelet count demonstrated that 40% of patients who underwent biopsy may not have required it. The current study was performed to evaluate the model’s performance on an independent data set.

Methods:
This is a retrospective consecutive series of patients undergoing temporal artery biopsy (TAB) in a single health region in Canada. The model was applied to a multicenter cohort of patients undergoing TAB by a variety of surgical services. A centralized pathological database serving multiple institutions and surgical services was used to identify patients undergoing TAB.

Results:
Over a 7-year period, patients undergoing TAB were identified via a central pathological database. Those who had concurrent illnesses which would likely affect erythrocyte sedimentation rate, c-reactive protein, and platelet count, patients on steroids for >2 weeks by the time of biopsy, and those with missing serum markers were excluded. The previously developed model was applied to the 222 patients enrolled. The model correctly identified 29% of patients with a pretest probability of 0% for a positive biopsy and 9% with a pretest probability of 100%, suggesting that in total, 38% of patients could have avoided TAB.

Conclusion:
The results of this independent data set support the previously published predictive formula. Utilizing a simple, clinically applicable predictive model of the pretest probabilities, approximately 38% of TAB currently being performed may be avoided. The results suggest that evaluation with a prospective multicentre study would be appropriate.
Quantitative shadowgraphy of aerosol and droplet creation during oscillatory motion of the microkeratome amid COVID-19 and other infectious diseases
Authors: Khamar Pooja , Shetty Rohit , Balakrishnan Nikhil , Kabi Prasenjit , Roy Durbar , Basu Saptarshi , Sinha Roy Abhijit 
Published: July 2020

Purpose:
To quantify the atomization of liquid over the cornea during flap creation using microkeratome using high-speed shadowgraphy.

Setting:
Laboratory study.

Design:
Laboratory investigational study.

Method:
In an experimental setup, flap creation was performed on enucleated goat's eyes (n = 8) mounted on a stand using One Use-Plus SBK Moria microkeratome (Moria SA) to assess the spread of aerosols and droplets using high-speed shadowgraphy. Two conditions were computed. A constant airflow assumed uniform air velocity throughout the room. A decaying jet assumed that local air velocity at the site of measurements was smaller than the exit velocity from the air duct.

Results:
With the advancement of the microkeratome across the wet corneal surface, the atomization of a balanced salt solution was recorded on shadowgraphy. The minimum droplet size was ∼90 μm. The maximum distance traversed was ∼1.8 m and ∼1.3 m assuming a constant airflow (setting of refractive surgery theater) and decaying jet condition (setting of an operating theater with air-handling unit), respectively.

Conclusions:
The microkeratome-assisted LASIK flap creation seemed to cause spread of droplets. The droplet diameters and velocities did not permit the formation of aerosols. Therefore, the risk of transmission of the virus to the surgeon and surgical personnel due to the microkeratome procedure seemed to be low.
Expanding the Molecular Spectrum of Secretory Carcinoma of Salivary Glands With a Novel VIM-RET Fusion
Authors: Skálová Alena , Banečkova Martina , Thompson Lester D.R. , Ptáková Nikola , Stevens Todd M. , Brcic Luka , Hyrcza Martin , Michal Michael , Simpson Roderick H.W. , Santana Thalita , Michal Michal , Vaněček Tomas , Leivo Ilmo 
Published: July 2020

Background:
Secretory carcinoma (SC), originally described as mammary analogue SC, is a predominantly low-grade salivary gland neoplasm characterized by a recurrent t(12;15)(p13;q25) translocation, resulting in ETV6-NTRK3 gene fusion. Recently, alternative ETV6-RET, ETV6-MAML3, and ETV6-MET fusions have been found in a subset of SCs lacking the classic ETV6-NTRK3 fusion transcript, but still harboring ETV6 gene rearrangements.

Design:
Forty-nine cases of SC revealing typical histomorphology and immunoprofile were analyzed by next-generation sequencing using the FusionPlex Solid Tumor kit (ArcherDX). All 49 cases of SC were also tested for ETV6, RET, and NTRK3 break by fluorescence in situ hybridization and for the common ETV6-NTRK3 fusions using reverse transcription polymerase chain reaction.

Results:
Of the 49 cases studied, 37 (76%) occurred in the parotid gland, 7 (14%) in the submandibular gland, 2 (4%) in the minor salivary glands, and 1 (2%) each in the nasal mucosa, facial skin, and thyroid gland. SCs were diagnosed more frequently in males (27/49 cases; 55%). Patients’ age at diagnosis varied from 15 to 80 years, with a mean age of 49.9 years. By molecular analysis, 40 cases (82%) presented the classic ETV6-NTRK3 fusion, whereas 9 cases (18%) revealed an alternate fusion. Of the 9 cases negative for the ETV6-NTRK3 fusion, 8 cases presented with ETV6-RET fusion. In the 1 remaining case in the parotid gland, next-generation sequencing analysis identified a novel VIM-RET fusion transcript. In addition, the analysis indicated that 1 recurrent high-grade case in the submandibular gland was positive for both ETV6-NTRK3 and MYB-SMR3B fusion transcripts.

Conclusions:
A novel finding in our study was the discovery of a VIM-RET fusion in 1 patient with SC of the parotid gland who could possibly benefit from RET-targeted therapy. In addition, 1 recurrent high-grade case was shown to harbor 2 different fusions, namely, ETV6-NTRK3 and MYB-SMR3B. The expanded molecular spectrum provides a novel insight into SC oncogenesis and carries important implications for molecular diagnostics, as this is the first SC-associated translocation with a non-ETV6 5′ fusion partner. This finding further expands the definition of SC while carrying implications for selecting the appropriate targeted therapy.