bluuebunny/crossref_metadata_2025_split huggingface dataset:
A network-based integrated framework for predicting virus–prokaryote interactions
Authors: Wang Weili , Ren Jie , Tang Kujin , Dart Emily , Ignacio-Espinoza Julio Cesar , Fuhrman Jed A , Braun Jonathan , Sun Fengzhu , Ahlgren Nathan A 
Published: June 2020

Abstract
Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures ($s_2^*$ and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n &gt; 27 000), greatly expanding the diversity of known virus–host interactions.
Selection of tree species for forests under climate change: is PSI functioning a better predictor for net photosynthesis and growth than PSII?
Authors: Pollastrini Martina , Salvatori Elisabetta , Fusaro Lina , Manes Fausto , Marzuoli Riccardo , Gerosa Giacomo , Brüggemann Wolfgang , Strasser Reto Jorg , Bussotti Filippo 
Published: June 2020

Abstract
A chlorophyll fluorescence (ChlF) assessment was carried out on oak seedlings (Quercus ilex L., Quercus pubescens Willd., Quercus frainetto Ten.) of Italian and Greek provenance, during the years 2017 and 2018, in a common garden in central Italy planted in 2017. This trial aimed to test the relative performances of the oak species in the perspective of assisted migration as part of the actions for the adaptation of forests to climate change. The assessment of the photosynthetic performance of the tree species included the analysis of the prompt chlorophyll fluorescence (PF) transient and the modulated reflection (MR) at 820 nm, leaf chlorophyll content, leaf gas exchange (net photosynthesis, stomatal conductance), plant growth (i.e., height) and mortality rate after 2 years from the beginning of the experiment. The assessment of the performance of the three oak species was carried out ‘in vivo’. Plants were generated from seeds and exposed to several environmental factors, including changing seasonal temperature, water availability, and soil biological and physical functionality. The results of PF indicate a stable functionality of the photosynthetic system PSII (expressed as FV/FM) across species and provenances and a decline in photochemistry functionality at the I–P phase (ΔVIP) in Q. frainetto, thus indicating a decline of the content of PSI in this species. This result was confirmed by the findings of MR analysis, with the speed of reduction and subsequent oxidation of PSI (VRED and VOX) strongly correlated to the amplitude of ΔVIP. The photosynthetic rates (net photosynthesis, PN) and growth were correlated with the parameters associated with PSI content and function, rather than those related to PSII. The low performance of Q. frainetto in the common garden seems to be related to early foliar senescence with the depletion of nitrogen, due to suboptimal climatic and edaphic conditions. Chlorophyll fluorescence allowed discrimination of populations of oak species and individuation of the less (or/and best) suitable species for future forest ecology and management purposes.
Shift of µ-opioid Receptor Signaling in the Dorsal Reticular Nucleus Is Implicated in Morphine-induced Hyperalgesia in Male Rats
Authors: Costa Ana Rita , Sousa Marília , Wilson Steven P. , Reguenga Carlos , Teixeira-Pinto Armando , Tavares Isaura , Martins Isabel 
Published: June 2020

Background
Increased descending pain facilitation accounts for opioid-induced hyperalgesia, but the underlying mechanisms remain elusive. Given the role of µ-opioid receptors in opioid-induced hyperalgesia in animals, the authors hypothesized that the dorsal reticular nucleus, a medullary pain facilitatory area, is involved in opioid-induced hyperalgesia through altered µ-opioid receptor signaling.

Methods
The authors used male Wistar rats (n = 5 to 8 per group), chronically infused with morphine, to evaluate in the dorsal reticular nucleus the expressions of the µ-opioid receptor and phosphorylated cAMP response element-binding, a downstream marker of excitatory µ-opioid receptor signaling. The authors used pharmacologic and gene-mediated approaches. Nociceptive behaviors were evaluated by the von Frey and hot-plates tests.

Results
Lidocaine fully reversed mechanical and thermal hypersensitivity induced by chronic morphine. Morphine-infusion increased µ-opioid receptor, without concomitant messenger RNA changes, and phosphorylated cAMP response element-binding levels at the dorsal reticular nucleus. µ-opioid receptor knockdown in morphine-infused animals attenuated the decrease of mechanical thresholds and heat-evoked withdrawal latencies compared with the control vector (von Frey [mean ± SD]: −17 ± 8% vs. −40 ± 9.0%; P < 0.001; hot-plate: −10 ± 5% vs. −32 ± 10%; P = 0.001). µ-opioid receptor knockdown in control animals induced the opposite (von Frey: −31 ± 8% vs. −17 ± 8%; P = 0.053; hotplate: −24 ± 6% vs. −3 ± 10%; P = 0.001). The µ-opioid receptor agonist (D-ALA2,N-ME-PHE4,GLY5-OL)-enkephalin acetate (DAMGO) decreased mechanical thresholds and did not affect heat-evoked withdrawal latencies in morphine-infused animals. In control animals, DAMGO increased both mechanical thresholds and heat-evoked withdrawal latencies. Ultra-low-dose naloxone, which prevents the excitatory signaling of the µ-opioid receptor, administered alone, attenuated mechanical and thermal hypersensitivities, and coadministered with DAMGO, restored DAMGO analgesic effects and decreased phosphorylated cAMP response element-binding levels.

Conclusions
Chronic morphine shifted µ-opioid receptor signaling from inhibitory to excitatory at the dorsal reticular nucleus, likely enhancing descending facilitation during opioid-induced hyperalgesia in the rat.

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Costs of Care for Low-Energy Extremity Gunshot Injuries are Reduced With Standardized Treatment
Authors: Nguyen Mai P. , Savakus Jonathan C. , Reich Michael S. , Golob Joseph F. , McDonald Amy A. , Como John J. , Vallier Heather A. 
Published: June 2020

Objectives:
(1) To determine the overall treatment costs associated with isolated low-energy gunshot wounds (GSWs) to the extremity and (2) to estimate cost savings associated with a single-dose IV antibiotic strategy administered in the emergency room for patients with simple GSWs.

Design:
Retrospective review.

Setting:
Level I trauma center.

Patients/Participants:
Patients (N = 380) with extremity-only GSW injuries from 2010 to 2015 were retrospectively reviewed. Treatment was recorded including type and duration of antibiotics, admission, and surgical intervention.

Main Outcome Measures:
Costs were calculated including facility services in the operating room and hospital.

Results:
There were 460 GSWs in 380 patients with a mean age of 30 years old. There were 309 admissions, 273 operations performed, and 1010 days of antibiotics prescribed. The total inpatient facility cost to treat all patients was $1,701,154. Among 179 patients who could be treated by the single-dose antibiotic care pathway for simple GSWs, 132 patients (73%) received additional treatment with 108 hospital admissions, 26 debridement surgeries, and 322 days of additional oral and/or IV antibiotics. The single-dose antibiotic care pathway would have saved an average of $1436 per patient with simple GSWs in actual facility expenses.

Conclusions:
The overall cost associated with isolated low-energy GSWs to the extremity is high. Limiting antibiotics to a single IV dose in the emergency room can reduce treatment expenses substantially for patients with simple GSWs.

Level of Evidence:
Economic Level IV. See instructions for authors for a complete description of levels of evidence.
Inflammation Profiling of Critically Ill Coronavirus Disease 2019 Patients
Authors: Fraser Douglas D. , Cepinskas Gediminas , Slessarev Marat , Martin Claudio , Daley Mark , Miller Michael R. , O’Gorman David B. , Gill Sean E. , Patterson Eric K. , dos Santos Claudia C. 
Published: June 2020

Objectives:
Coronavirus disease 2019 is caused by severe acute respiratory syndrome-coronavirus-2 infection to which there is no community immunity. Patients admitted to ICUs have high mortality, with only supportive therapies available. Our aim was to profile plasma inflammatory analytes to help understand the host response to coronavirus disease 2019.

Design:
Daily blood inflammation profiling with immunoassays.

Setting:
Tertiary care ICU and academic laboratory.

Subjects:
All patients admitted to the ICU suspected of being infected with severe acute respiratory syndrome-coronavirus-2, using standardized hospital screening methodologies, had daily blood samples collected until either testing was confirmed negative on ICU day 3 (coronavirus disease 2019 negative), or until ICU day 7 if the patient was positive (coronavirus disease 2019 positive).

Interventions:
None.

Measurements and Main Results:
Age- and sex-matched healthy controls and ICU patients that were either coronavirus disease 2019 positive or coronavirus disease 2019 negative were enrolled. Cohorts were well-balanced with the exception that coronavirus disease 2019 positive patients were more likely than coronavirus disease 2019 negative patients to suffer bilateral pneumonia. Mortality rate for coronavirus disease 2019 positive ICU patients was 40%. We measured 57 inflammatory analytes and then analyzed with both conventional statistics and machine learning. Twenty inflammatory analytes were different between coronavirus disease 2019 positive patients and healthy controls (p < 0.01). Compared with coronavirus disease 2019 negative patients, coronavirus disease 2019 positive patients had 17 elevated inflammatory analytes on one or more of their ICU days 1–3 (p < 0.01), with feature classification identifying the top six analytes between cohorts as tumor necrosis factor, granzyme B, heat shock protein 70, interleukin-18, interferon-gamma-inducible protein 10, and elastase 2. While tumor necrosis factor, granzyme B, heat shock protein 70, and interleukin-18 were elevated for all seven ICU days, interferon-gamma-inducible protein 10 transiently elevated on ICU days 2 and 3 and elastase 2 increased over ICU days 2–7. Inflammation profiling predicted coronavirus disease 2019 status with 98% accuracy, whereas elevated heat shock protein 70 was strongly associated with mortality.

Conclusions:
While many inflammatory analytes were elevated in coronavirus disease 2019 positive ICU patients, relative to healthy controls, the top six analytes distinguishing coronavirus disease 2019 positive ICU patients from coronavirus disease 2019 negative ICU patients were tumor necrosis factor, granzyme B, heat shock protein 70, interleukin-18, interferon-gamma-inducible protein 10, and elastase 2.
Lymphomatoid Papulosis With a Unique T Follicular Helper–Like Phenotype
Authors: Tran Jessica , Duvic Madeleine , Torres-Cabala Carlos A. 
Published: June 2020

Abstract:
Lymphomatoid papulosis (LyP) is a benign skin condition that typically presents with grouped or scattered lesions on the body that self-resolve within weeks or months of onset. LyP belongs to the group of CD30-positive lymphoproliferative disorders. Several histological variants of LyP exist, and the histological features of LyP can overlap with other lymphoproliferative disorders; therefore, both histological and clinical correlations are needed for a proper diagnosis of LyP. We report an unusual case of LyP displaying a T follicular helper cell–like phenotype and histopathologically resembling the primary cutaneous CD4-positive small-sized to medium-sized T-cell lymphoproliferative disorder.
Antihyperglycemic Therapies With Expansions of US Food and Drug Administration Indications to Reduce Cardiovascular Events: Prescribing Patterns Within an Academic Medical Center
Authors: Hamid Arsalan , Vaduganathan Muthiah , Oshunbade Adebamike A. , Ayyalasomayajula Krishna K. , Kalogeropoulos Andreas P. , Lien Lillian F. , Shafi Tariq , Hall Michael E. , Butler Javed 
Published: June 2020

Abstract:
Sodium-glucose cotransport protein-2 inhibitors (SGLT2is) and glucagon-like peptide-1 receptor agonists (GLP-1RAs) have been shown to reduce cardiovascular events in high-risk patients with type 2 diabetes mellitus (T2DM). We examined real-world use of these agents at a US academic medical center in the state of Mississippi. Prescriptions, provider specialty, and insurance status of users of SGLT2is and GLP-1RAs in patients with T2DM, and T2DM and cardiovascular disease (CVD) seen from 1st January 2013 to 30th June 2019 were obtained by electronic health records review. We identified 21,173 patients with T2DM and CVD. Overall, 306 (1.4%) and 349 (1.6%) patients received a SGLT2i and GLP-1RA, respectively. After the US Food and Drug Administration (FDA) expanded empagliflozin and liraglutide indications, a mean difference of 19.2 and 12.7 greater quarterly new prescriptions was noted, respectively, whereas no such rise in canagliflozin was observed. Primary care physicians accounted for 53.4% SGLT2i prescriptions, endocrinology for 30.3%, and cardiology for 6.0%. Primary care physicians accounted for 45.1% GLP-1RA prescriptions, endocrinology for 45.0%, and cardiology for 1.4%. Prescription patterns did not largely differ by patient insurance status. In conclusion, prescription of evidence-based therapies to improve CVD outcomes in high-risk patients with T2DM remains very low after several years of evidence generation. Low uptake was evident across insurance types. Modest increases in use were observed after regulatory expansions in labeling; however, cardiologists rarely engaged in prescription, underscoring the need for widespread implementation strategies across health care systems.
QUANTITATIVE TOPOGRAPHIC CURVATURE MAPS OF THE POSTERIOR EYE UTILIZING OPTICAL COHERENCE TOMOGRAPHY
Authors: McNabb Ryan P. , Liu Alice S. , Gospe Sidney M. , El-Dairi Mays , Meekins Landon C. , James Charlene , Vann Robin R. , Izatt Joseph A. , Kuo Anthony N. 
Published: June 2020

Purpose:
Deformations of the retina such as staphylomas in myopia or scleral flattening in high intracranial pressure can be challenging to quantify with en face imaging. We describe an optical coherence tomography-based method for the generation of quantitative posterior eye topography maps in normal and pathologic eyes.

Methods:
Using “whole eye” optical coherence tomography, we corrected for subjects' optical distortions to generate spatially accurate posterior eye optical coherence tomography volumes and created local curvature (K

M
, mm−1) topography maps for each consented subject. We imaged nine subjects, three normal, two with myopic degeneration, and four with papilledema including one that was imaged longitudinally.

Results:
Normal subjects mean temporal K

M
was 0.0923 mm−1, nasal K

M
was 0.0927 mm−1, and K

M
local variability was 0.0162 mm−1. In myopic degeneration, subjects K

M
local variability was higher at 0.0836 mm−1. In papilledema subjects nasal K

M
was flatter compared with temporal K

M
(0.0709 vs. 0.0885 mm−1). Mean intrasession K

M
repeatability for all subjects was 0.0036 mm−1.

Conclusion:
We have developed an optical coherence tomography based method for quantitative posterior eye topography that offers the ability to analyze local curvature with micron scale resolution and offers the potential to help clinicians and researchers characterize subtle, local retinal deformations earlier in patients and follow their development over time.
Aerosol generation through phacoemulsification
Authors: Lee Hanbin , Naveed Hasan , Ashena Zahra , Nanavaty Mayank A. 
Published: June 2020

Purpose:
To evaluate whether phacoemulsification is an aerosol-generating procedure in an ex vivo experimental model.

Setting:
Sussex Eye Hospital, Brighton, United Kingdom.

Design:
Experimental study.

Methods:
In this ex vivo study on 15 porcine eyes, an optical particle counter was used to measure particles of 10 µm and less using the cumulative mode based on the 6 in-built channel sizes. The 2 parts of the study were to: (1) assess the efficacy of the particle counter in the theater environment where there are dynamic changes in temperature and humidity; and (2) to measure aerosol generation with 3 phacoemulsification settings: (i) continuous power with 80% longitudinal (5 eyes); (ii) continuous power with 100% torsional (5 eyes); and (iii) continuous power with 80% longitudinal with application of hydroxypropyl methylcellulose (HPMC) on the ocular surface (5 eyes). Five measurements were taken prephacoemulsification and 5 during phacoemulsification per eye therefore totaling 75 measurements.

Results:
Maximum aerosols were captured when the counter faced the aerosol source. There was no significant difference in aerosol generation of all sizes during each phacoemulsification setting with torsional, longitudinal, and longitudinal with HPMC (P > .01). Combining data of all 3 phacoemulsification settings (150 measurements from 15 eyes), there was no significant difference comparing prephacoemulsification and during phacoemulsification for aerosols of 5 µm or less (1455 vs 1363.85, P = .60), more than 5 to 10 μm (1.5 vs 1.03, P = .43), and of 10 µm or less (1209 vs 1131.55, P = .60).

Conclusions:
Phacoemulsification did not generate aerosols of 10 μm or less with continuous power using 80% longitudinal, 100% torsional, and 80% longitudinal setting with HPMC on the surface.
Assessment of Gastric Emptying Times Between Pediatrics and Adults With Cyclic Vomiting Syndrome
Authors: Kamal Afrin , Sarvepalli Shashank , Selvakumar Praveen , Lopez Rocio , Radhakrishnan Kadakkal , Gabbard Scott 
Published: June 2020

Background & Aims:
Cyclic vomiting syndrome (CVS) is characterized by episodes of nausea and vomiting separated by symptom-free intervals. Rome IV guidelines have now distinguished CVS from other disorders such as cannabinoid hyperemesis. The pathogenesis of CVS, however, is poorly understood. Limited data exist on gastric emptying (GE) in patients with CVS. Therefore, the authors aim to measure the GE profile in pediatrics and adults with CVS.

Materials and Methods:
Patients with the diagnosis of CVS (per NASPGHAN and Rome IV) between December 1998 and March 2017 who underwent gastric emptying study (GES) and without documented cannabis use were included. Clinical features including demographics, medication use, and comorbidities were also recorded. Frequency of rapid, normal, and delayed emptying was reported, and multinomial univariate logistic regression was used to identify factors associated with each type of emptying.

Key Results:
Sixty-seven subjects were included (50.7% female individuals, pediatrics n=15, adults n=52). At 2-hour retention, 40% of pediatric patients met criteria for rapid, 33.3% for normal, and 26.7% for delayed GE. In adults, 50% met criteria for rapid, 46.2% for normal, and 3.8% for delayed GE. For every 5-year increase in age, odds of rapid emptying on GES increased.

Conclusions:
(1) GE is predominantly rapid at 2 hours in pediatrics and adults with CVS. (2) Rapid GE seems to increase with age. (3) Current guidelines do not recommend GE in the initial management, however, further studies may play a role to help differentiate CVS from other functional gastric disorders.
Dual tracer 68Ga-DOTATOC and 18F-FDG PET/computed tomography radiomics in pancreatic neuroendocrine neoplasms: an endearing tool for preoperative risk assessment
Authors: Mapelli Paola , Partelli Stefano , Salgarello Matteo , Doraku Joniada , Pasetto Stefano , Rancoita Paola M.V. , Muffatti Francesca , Bettinardi Valentino , Presotto Luca , Andreasi Valentina , Gianolli Luigi , Picchio Maria , Falconi Massimo 
Published: June 2020

Aim
To explore the potentiality of radiomics analysis, performed on 68Ga-DOTATOC and fluorine-18-fluorodeoxyglucose (18F-FDG) PET/computed tomography (CT) images, in predicting tumour aggressiveness and outcome in patients candidate to surgery for pancreatic neuroendocrine neoplasms (PanNENs).

Patients and methods
Retrospective study including 61 patients who underwent 68Ga-DOTATOC and 18F-FDG PET/CT before surgery for PanNEN. Semiquantitative variables [SUVmax and somatostatin receptor density (SRD) for 68Ga-DOTATOC PET; SUVmax and MTV for 18F-FDG PET] and texture features [intensity variability, size zone variability (SZV), zone percentage, entropy; homogeneity, dissimilarity and coefficient of variation (Co-V)] have been analysed to evaluate their possible role in predicting tumour characteristics. Principal component analysis (PCA) was firstly performed and then multiple regression analyses were performed by using the extracted principal components.

Results
Regarding 68Ga-DOTATOC PET, SZV, entropy, intensity variability and SRD were predictive for tumour dimension. Regarding 18F-FDG PET, intensity variability, SZV, homogeneity, SUVmax and MTV were predictive for tumour dimension. Four principal components were extracted from PCA: PC1 correlated with all 18F-FDG variables, while PC2, PC3 and PC4 with 68Ga-DOTATOC variables. PC1 was the only significantly predicting angioinvasion (P = 0.0222); PC4 was the only one significantly predicting lymph nodal involvement (P = 0.0151). All principal components except PC4 significantly predicted tumour dimension (P  <0.0001 for PC1, P = 0.0016 for PC2 and P < 0.0001 for PC3). Co-V from 68Ga-DOTATOC PET/CT was predictive of the outcome.

Conclusion
Specific texture features derived from preoperative 68Ga-DOTATOC and 18F-FDG PET/CT could noninvasively predict specific tumour characteristics and patients’ outcome, delineating the potential role of dual tracer technique and texture analysis in the risk assessment of patients with PanNENs.