bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Microbial Succession in the Anchialine Ecosystem
Authors: Sterling James J , Sakihara Troy S , Brannock Pamela M , Pearson Zoe G , Maclaine Kendra D , Santos Scott R , Havird Justin C 
Published: June 2022

Synopsis
When new land is created, initial microbial colonization lays the foundation for further ecological succession of plant and animal communities. Primary microbial succession of new aquatic habitats formed during volcanic activity has received little attention. The anchialine ecosystem, which includes coastal ponds in young lava flows, offers an opportunity to examine this process. Here, we characterized microbial communities of anchialine habitats in Hawaii that were created during volcanic eruptions in 2018. Benthic samples from three habitats were collected ∼2 years after their formation and at later time points spanning ∼1 year. Sequence profiling (16S and 18S) of prokaryotic and eukaryotic communities was used to test whether communities were similar to those from older, established anchialine habitats, and if community structure changed over time. Results show that microbial communities from the new habitats were unlike any from established anchialine microbial communities, having higher proportions of Planctomycetota and Chloroflexi but lower proportions of green algae. Each new habitat also harbored its own unique community relative to other habitats. While community composition in each habitat underwent statistically significant changes over time, they remained distinctive from established anchialine habitats. New habitats also had highly elevated temperatures compared to other habitats. These results suggest that idiosyncratic microbial consortia form during early succession of Hawaiian anchialine habitats. Future monitoring will reveal whether the early communities described here remain stable after temperatures decline and macro-organisms become more abundant, or if microbial communities will continue to change and eventually resemble those of established habitats. This work is a key first step in examining primary volcanic succession in aquatic habitats and suggests young anchialine habitats may warrant special conservation status.
Delirium prediction in the ICU: designing a screening tool for preventive interventions
Authors: Bhattacharyya Anirban , Sheikhalishahi Seyedmostafa , Torbic Heather , Yeung Wesley , Wang Tiffany , Birst Jennifer , Duggal Abhijit , Celi Leo Anthony , Osmani Venet 
Published: June 2022

Abstract

Introduction
Delirium occurrence is common and preventive strategies are resource intensive. Screening tools can prioritize patients at risk. Using machine learning, we can capture time and treatment effects that pose a challenge to delirium prediction. We aim to develop a delirium prediction model that can be used as a screening tool.

Methods
From the eICU Collaborative Research Database (eICU-CRD) and the Medical Information Mart for Intensive Care version III (MIMIC-III) database, patients with one or more Confusion Assessment Method-Intensive Care Unit (CAM-ICU) values and intensive care unit (ICU) length of stay greater than 24 h were included in our study. We validated our model using 21 quantitative clinical parameters and assessed performance across a range of observation and prediction windows, using different thresholds and applied interpretation techniques. We evaluate our models based on stratified repeated cross-validation using 3 algorithms, namely Logistic Regression, Random Forest, and Bidirectional Long Short-Term Memory (BiLSTM). BiLSTM represents an evolution from recurrent neural network-based Long Short-Term Memory, and with a backward input, preserves information from both past and future. Model performance is measured using Area Under Receiver Operating Characteristic, Area Under Precision Recall Curve, Recall, Precision (Positive Predictive Value), and Negative Predictive Value metrics.

Results
We evaluated our results on 16 546 patients (47% female) and 6294 patients (44% female) from eICU-CRD and MIMIC-III databases, respectively. Performance was best in BiLSTM models where, precision and recall changed from 37.52% (95% confidence interval [CI], 36.00%–39.05%) to 17.45 (95% CI, 15.83%–19.08%) and 86.1% (95% CI, 82.49%–89.71%) to 75.58% (95% CI, 68.33%–82.83%), respectively as prediction window increased from 12 to 96 h. After optimizing for higher recall, precision and recall changed from 26.96% (95% CI, 24.99%–28.94%) to 11.34% (95% CI, 10.71%–11.98%) and 93.73% (95% CI, 93.1%–94.37%) to 92.57% (95% CI, 88.19%–96.95%), respectively. Comparable results were obtained in the MIMIC-III cohort.

Conclusions
Our model performed comparably to contemporary models using fewer variables. Using techniques like sliding windows, modification of threshold to augment recall and feature ranking for interpretability, we addressed shortcomings of current models.
Complications and surgical treatment after pathological fracture associated to HIV secondary disease. A case report
Authors: Fuentes-Sánchez Jorge , Gómez-Barrena Enrique 
Published: June 2022

Abstract
Due to advances in retroviral treatment, human immunodeficiency virus (HIV)-related disease may become chronic and the patient survival has substantially increased. Osteoarticular disease in those patients include multifocal osteonecrosis and its complications. Pain and functional limitation may be due to these complications, frequently underdiagnosed, including pathological fractures. Its prompt management may require a different approach than osteosynthesis. We present a long-term chronic HIV patient with severe pain and limitation. A tibial plateau pathological fracture associated to multifocal osteonecrosis was identified and treated with osteonecrosis debridement and total knee arthroplasty (TKA). Acute periprosthetic joint infection developed and required debridement, antibiotic and implant retention. The contralateral knee, also with multiple osteonecrosis foci, was managed with early TKA. We highlight the importance of timely surgical reconstruction to avoid serious limitation and complications.
Stellar graveyards: clustering of compact objects in globular clusters NGC 3201 and NGC 6397
Authors: Vitral Eduardo , Kremer Kyle , Libralato Mattia , Mamon Gary A , Bellini Andrea 
Published: June 2022

ABSTRACT
We analyse Gaia EDR3 and re-calibrated HST proper motion data from the core-collapsed and non-core-collapsed globular clusters NGC 6397 and NGC 3201, respectively, with the Bayesian mass-orbit modelling code MAMPOSSt-PM. We use Bayesian evidence and realistic mock data sets constructed with Agama to select between different mass models. In both clusters, the velocities are consistent with isotropy within the extent of our data. We robustly detect a dark central mass (DCM) of roughly $1000\, \rm M_\odot$ in both clusters. Our MAMPOSSt-PM fits strongly prefer an extended DCM in NGC 6397, while only presenting a mild preference for it in NGC 3201, with respective sizes of a roughly one and a few per cent of the cluster effective radius. We explore the astrophysics behind our results with the CMC Monte Carlo N-body code, whose snapshots best matching the phase space observations lead to similar values for the mass and size of the DCM. The internal kinematics are thus consistent with a population of hundreds of massive white dwarfs in NGC 6397, and roughly 100 segregated stellar-mass black holes in NGC 3201, as previously found with CMC. Such analyses confirm the accuracy of both mass-orbit modelling and Monte Carlo N-body techniques, which together provide more robust predictions on the DCM of globular clusters (core-collapsed or not). This opens possibilities to understand a vast range of interesting astrophysical phenomena in clusters, such as fast radio bursts, compact object mergers, and gravitational waves.
Mapping the aliphatic hydrocarbon content of interstellar dust in the Galactic plane
Authors: Günay B , Burton M G , Afşar M , Schmidt T W 
Published: June 2022

ABSTRACT
We implement a new observational method for mapping the aliphatic hydrocarbon content in the solid phase in our Galaxy, based on spectrophotometric imaging of the 3.4 $\mu$m absorption feature from interstellar dust. We previously demonstrated this method in a field including the Galactic Centre cluster. We applied the method to a new field in the Galactic Centre where the 3.4 $\mu$m absorption feature has not been previously measured and we extended the measurements to a field in the Galactic plane to sample the diffuse local interstellar medium, where the 3.4 $\mu$m absorption feature has been previously measured. We have analysed 3.4 $\mu$m optical depth and aliphatic hydrocarbon column density maps for these fields. Optical depths are found to be reasonably uniform in each field, without large source-to-source variations. There is, however, a weak trend towards increasing optical depth in a direction towards b = 0° in the Galactic Centre. The mean value of column densities and abundances for aliphatic hydrocarbon were found to be about several $\rm \times 10^{18} \, cm^{-2}$ and several tens × 10−6, respectively for the new sightlines in the Galactic plane. We conclude that at least 10–20 per cent of the carbon in the Galactic plane lies in aliphatic form.
Observational signatures of black hole accretion: rotating versus spherical flows with tilted magnetic fields
Authors: Jia(贾 赫) He , White Christopher J , Quataert Eliot , Ressler Sean M 
Published: June 2022

ABSTRACT
We study the observational signatures of magnetically arrested black hole accretion with non-rotating inflow on to a rotating black hole; we consider a range of angles between the black hole spin and the initial magnetic field orientation. We compare the results of our general relativistic magneto-hydrodynamic simulations to more commonly used rotating initial conditions and to the Event Horizon Telescope (EHT) observations of M87. We find that the mm intensity images, polarization images, and synchrotron emission spectra are very similar among the different simulations when post-processed with the same electron temperature model; observational differences due to different electron temperature models are significantly larger than those due to the different realizations of magnetically arrested accretion. The orientation of the mm synchrotron polarization is particularly insensitive to the initial magnetic field orientation, the electron temperature model, and the rotation of the inflowing plasma. The largest difference among the simulations with different initial rotation and magnetic tilt is in the strength and stability of the jet; spherical inflow leads to kink-unstable jets. We discuss the implications of our results for current and future EHT observations and for theoretical models of event-horizon-scale black hole accretion.
Relic jet activity in ‘Hanny’s Voorwerp’ revealed by the LOFAR two metre sky survey
Authors: Smith D J B , Krause M G , Hardcastle M J , Drake A B 
Published: June 2022

ABSTRACT
We report new observations of ‘Hanny’s Voorwerp’ (hereafter HV) taken from the second data release of the LOFAR Two-metre Sky Survey (LoTSS). HV is a highly-ionized region in the environs of the galaxy IC2497, first discovered by the Galaxy Zoo project. The new 150 MHz observations are considered in the context of existing multi frequency radio data and archival narrow-band imaging from the Hubble Space Telescope, centred on the [O iii] emission line. The combined sensitivity and spatial resolution of the LoTSS data – which far exceed what was previously available at radio frequencies – reveal clear evidence for large-scale extended emission emanating from the nucleus of IC2497. The radio jet appears to have punched a hole in the neutral gas halo, in a region co-located with HV. The new 150 MHz data, alongside newly-processed archival 1.64 GHz eVLA data, reveal that the extended emission has a steep spectrum, implying an age &gt;108 yr. The jet supplying the extended 150 MHz structure must have ‘turned off’ long before the change in X-ray luminosity reported in recent works. In this picture, a combination of jet activity and the influence of the radiatively efficient active galactic nucleus are responsible for the unusual appearance of HV.
The musca molecular cloud: The perfect ‘filament’ is still a sheet
Authors: Tritsis A , Bouzelou F , Skalidis R , Tassis K , Enßlin T , Edenhofer G 
Published: June 2022

ABSTRACT
The true three-dimensional (3D) morphology of the Musca molecular cloud is a topic that has received significant attention lately. Given that Musca does not exhibit intense star-formation activity, unveiling its shape has the potential to also reveal crucial information regarding the physics that dictates the formation of the first generation of stars within molecular clouds. Here, we revisit the shape of Musca and we present a comprehensive array of evidence pointing towards a shape that is extended along the line-of-sight dimension: (a) 3D maps of differential extinction; (b) new non-local thermodynamic equilibrium radiative transfer simulations of CO rotational transitions from a sheet-like, magnetically dominated simulated cloud; (c) an effective/critical density analysis of available CO observations; and (d) indirect consequences that a filamentary structure would have had, from a theoretical star-formation perspective. We conclude that the full collection of observational evidence strongly suggests that Musca has a sheet-like geometry.
Receipt of Baseline Laboratory Testing Recommended by the HIV Medicine Association for People Initiating HIV Care, United States, 2015–2019
Authors: Weiser John , Tie Yunfeng , Lu Jen-Feng , Colasanti Jonathan A , Fanfair Robyn Neblett , Beer Linda 
Published: June 2022

AbstractBackgroundThe HIV Medicine Association of the Infectious Disease Society of America publishes Primary Care Guidance for Persons with Human Immunodeficiency Virus. We assessed receipt of recommended baseline tests among newly diagnosed patients initiating HIV care.MethodsThe Medical Monitoring Project is a Centers for Disease Control and Prevention survey designed to produce nationally representative estimates of behavioral and clinical characteristics of adults with diagnosed HIV in the United States. We analyzed data for 725 participants in the 2015–2019 data collection cycles who received an HIV diagnosis within the past 2 years and had ≥1 HIV provider visit. We estimated the prevalence of having recommended tests after the first HIV provider visit and between 3 months before and 3/6 months after the first HIV provider visit and estimated prevalence differences of having 4 combinations of tests by sociodemographic and clinical characteristics.ResultsWithin 6 months of care initiation, HIV monitoring tests were performed for 91.3% (95% CI, 88.7%–93.8%) of patients; coinfection blood tests, 27.5% (95% CI, 22.5%–32.4%); site-based STI tests, 59.7% (95% CI, 55.4%–63.9%); and blood chemistry and hematology tests, 50.8% (95% CI, 45.8%–55.8%). Patients who were younger, gay, or bisexual were more likely to receive site-based STI tests, and patients receiving care at Ryan White HIV/AIDS Program (RWHAP)–funded facilities were more likely than patients at non-RWHAP-funded facilities to receive all test combinations.ConclusionsReceipt of recommended baseline tests among patients initiating HIV care was suboptimal but was more likely among patients at RWHAP-funded facilities. Embedding clinical decision support in HIV provider workflow could increase recommended baseline testing.
Outcomes of Cytomegalovirus Viremia Treatment in Critically Ill Patients With COVID-19 Infection
Authors: Schoninger Scott , Dubrovskaya Yanina , Marsh Kassandra , Altshuler Diana , Prasad Prithiv , Louie Eddie , Weisenberg Scott , Hochman Sarah , Fridman David , Trachuk Polina 
Published: June 2022

Abstract

Background
Patients with coronavirus disease 2019 (COVID-19) admitted to the intensive care unit (ICU) have poor outcomes and frequently develop comorbid conditions, including cytomegalovirus (CMV) reactivation. The implications of CMV reactivation in this setting are unknown. We aimed to investigate if treatment of CMV viremia improved in-hospital mortality in ICU patients with COVID-19.

Methods
In this single-center retrospective study, we analyzed clinical outcomes in patients diagnosed with COVID-19 pneumonia and CMV viremia admitted to an ICU from March 1, 2020, to April 30, 2021, who either received treatment (ganciclovir and/or valganciclovir) or received no treatment. The primary outcome was all-cause in-hospital mortality. Secondary outcomes were total hospital length of stay (LOS), ICU LOS, requirement for extracorporeal membrane oxygenation (ECMO) support, duration of mechanical ventilation (MV), and predictors of in-hospital mortality.

Results
A total of 80 patients were included, 43 patients in the treatment group and 37 in the control group. Baseline characteristics were similar in both groups. CMV-treated patients were more likely to test positive for CMV earlier in their course, more likely to be on ECMO, and received higher total steroid doses on average. In-hospital mortality was similar between the 2 groups (37.2% vs 43.2.0%; P = .749). There was no significant difference in hospital LOS, though CMV-treated patients had a longer ICU LOS.

Conclusions
Treatment of CMV viremia did not decrease in-hospital mortality in ICU patients with COVID-19, but the sample size was limited. CMV viremia was significantly associated with total steroid dose received and longer ICU stay.
Are Patients and Their Providers Talking About Long-Acting Injectable Antiretroviral Therapy? Penetration into Clinical Encounters at Three U.S. Care Sites
Authors: Christopoulos Katerina A , Colasanti Jonathan , Johnson Mallory O , Diaz Tsuzuki Manami , Erguera Xavier A , Flores Rey , Kerman Jared , Dance Kaylin , Sauceda John A , Neilands Torsten B , Dilworth Samantha E , Koester Kimberly A , Gutierrez Jose , Schneider John A , Montgomery Elizabeth , McNulty Moira C 
Published: June 2022

Abstract
Use of long-acting injectable antiretroviral therapy depends on patient awareness, provider discussion, and patient willingness to use. We conducted a postvisit survey with patients at 3 HIV clinics in San Francisco, Chicago, and Atlanta in May 2021 to assess for inequities in these early implementation phases.
Habitat edges influence the distribution of nest predators for Seaside Sparrows, but not nest placement or success
Authors: Newsome Corina D , Hunter Elizabeth A 
Published: June 2022

Abstract
Nest failure for coastal marsh bird species is primarily caused by predation and nest flooding. As sea level rise makes nest flooding more likely, the threat of nest predation will constrain the potential adaptive responses of marsh nesting species. Thus, understanding the predictors of nest predation is important for the conservation of salt marsh-dwelling bird species, such as the Seaside Sparrow (Ammospiza maritima). Predator activity may be influenced by landscape features (particularly habitat edges), potentially making nest predation predictable. We aimed to understand the predictability of Seaside Sparrow nest predation relative to two major landscape features: roads and tidal rivers, as both of these edges may be entryways or attractants for predators in marshes. In coastal Georgia, USA, we assessed mammalian predator activity relative to the two features of interest, and hypothesized that mammalian predator activity would be greater close to roads and tidal rivers. We also recorded Seaside Sparrow nest locations and nest predation events and hypothesized that nest predation events would increase with increasing predator activity. Consistent with our first hypothesis, mammalian predator activity increased close to roads and tidal rivers, but mammalian predator distribution did not explain the spatial variation in Seaside Sparrow nest predation thus not supporting our second hypothesis. Seaside Sparrows also placed their nests in locations with high mammalian predator activity, indicating that the ability to avoid nesting in high-risk areas may be constrained by habitat or resource limitations. Additionally, mammals may not be the primary nest predators, as we found that one bird species—Marsh Wren (Cistothorus palustris)—contributed substantially to nest predation rates. Understanding the predictability of mammalian predator distribution can allow for focused predator management efforts, such as exclusion, to habitat edges where we found the highest mammalian predator activity, which could relax the constraint of nest predation on Seaside Sparrow’s ability to respond to the intensifying threat of sea level rise.
Defining resistance and tolerance traits in Covid-19: towards a stratified medicine approach
Authors: Russell C D , Clohisey Hendry S 
Published: June 2022

Abstract
Successful host defence against infectious disease involves resistance (reduce pathogen load) and tolerance (reduce tissue damage associated with pathogen presence). Integration of clinical, immunologic, genetic and therapeutic discoveries has identified defects in both of these responses in the progression from SARS-CoV-2 infection to life-threatening coronavirus disease 2019 (Covid-19) lung injury. Early after infection with SARS-CoV-2, resistance can be compromised by a failed type 1 interferon (IFN-I) response, due to direct viral antagonism of induction and signalling, deleterious host genetic variants (IFNAR2, IFNA10, TYK2 and PLSCR1), and neutralizing auto-antibodies directed against IFN-I (predominantly IFN-α). Later in the disease, after pathogen sensing has activated a pro-inflammatory response, a failure to appropriately regulate this response compromises tolerance resulting in virus-independent immunopathology involving the lung and reticuloendothelial system. Monocytes are activated in the periphery (involving M-CSF, GM-CSF, IL-6, NLRP1 inflammasomes, TYK2 and afucosylated anti-spike IgG) then recruited to the lung (involving CCR2::MCP-3/MCP-1 and C5a::C5aR1 axes) as pro-inflammatory monocyte-derived macrophages, resulting in inflammatory lung injury. Phenotypic and genotypic heterogeneity is apparent in all these responses, identifying ‘treatable traits’ (therapeutically relevant components of inter-individual variation) which could be exploited to achieve a stratified medicine approach to Covid-19. Overall, Covid-19 pathogenesis re-affirms the importance of resistance in surviving an infectious disease and highlights that tolerance is also a central pillar of host defence in humans and can be beneficially modified using host-directed therapies.