bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of Human Papillomavirus Immunization Programs on Rates of Anogenital Warts in British Columbia, Canada, 2000 to 2017
Authors: Lukac Christine D. , Donken Robine , Otterstatter Michael , Mazo Olga , Wong Stanley , Marra Fawziah , Smith Laurie , Naus Monika , Money Deborah , Krajden Mel , Grennan Troy , Gilbert Mark , Wong Jason , Ogilvie Gina S. 
Published: July 2020

Background
In 2008, British Columbia (BC) implemented a school-based quadrivalent human papillomavirus (HPV-4) immunization program for girls born in 1994 or later. In 2015, an expanded clinic-based program included men who report sex with men (MSM) born in 1989 or later. To evaluate the impacts of HPV-4 programs on anogenital warts (AGWs), diagnosis rates were measured among women who report sex with men (WSM), men who report sex with women (MSW), and MSM.

Methods
Diagnoses of AGW were ascertained from 16 sexually transmitted infection clinics. Rates were calculated as new AGW diagnoses over person-years (py) at risk and stratified by age group, calendar period, and birth cohort. Adjusted relative rates (aRR) were estimated using multivariable Poisson regression.

Results
There were 204,832 clinic visits by 85,158 individuals: 28,366 (33%) WSM, 35,688 (42%) MSW, and 14,534 (17%) MSM. After adjusting for age and period, AGW rates in the 1994–1996 birth cohort decreased by 56% overall (1.21 vs. 2.72 cases/100 py; aRR, 0.44; 95% confidence interval [CI], 0.34–0.59), 65% among WSM (0.97 vs. 2.77 cases/100 py; aRR, 0.35; 95% CI, 0.22–0.57), 58% among MSW (1.60 vs. 3.78 cases/100 py; aRR, 0.42; 95% CI, 0.28–0.65), and 41% among MSM (1.14 vs. 1.19 cases/100 py; aRR, 0.59; 95% CI, 0.38–0.91) versus the 1991–1993 birth cohort.

Conclusions
The HPV-4 programs had significant impacts on lowering AGW rates in BC. The greatest decrease was among WSM eligible for the school-based program, followed by birth cohorts of men who likely have sex with HPV-4 eligible women. The smallest decrease among MSM may reflect the later introduction of the clinic-based program.
Initial Results of the Use of a Standardized Diagnostic Criteria for Chest Computed Tomography Findings in Coronavirus Disease 2019
Authors: Miranda Magalhães Santos João Manoel , Paula Alves Fonseca Ana , Pinheiro Zarattini Anastacio Eduardo , Formagio Minenelli Fernanda , Furtado de Albuquerque Cavalcanti Conrado , Borges da Silva Teles Gustavo 
Published: July 2020

Objective
The objective of this study was to assess the initial results of chest computed tomography (CT) standardized diagnostic criteria proposed by the Radiological Society of North America in coronavirus disease 2019 (COVID-19) compared with reverse transcription–polymerase chain reaction (RT-PCR).

Methods
Seventy-one patients who underwent RT-PCR test for COVID-19 and chest CT within an interval of 4 days or less were included. Seventy-five CTs were reviewed and classified as typical, indeterminate, or atypical appearance or negative for pneumonia by 2 radiologists. With RT-PCR as reference standard, the performance of the CT diagnostic criteria in diagnosing COVID-19 was assessed.

Results
The prevalence of positive RT-PCR was 45.1%. It was obtained a sensitivity of 83% (95% confidence interval [CI], 78%–89%), a specificity of 97% (95% CI, 92%–99%), an accuracy of 91% (95% CI, 85%–96%), a positive predictive value of 97% (95% CI, 91%–99%), and a negative predictive value of 86% (95% CI, 80%–92%). The diagnostic performance was excellent, considering the area under the curve of 0.92 (95% CI, 0.84–0.99).

Conclusions
Chest CT standardized diagnostic criteria had high specificity and positive predictive value for the diagnosis of COVID-19 when presenting a typical appearance.
Failure to Cure in Patients Undergoing Surgery for Esophageal Carcinoma: Hospital of Surgery Influences Prospects for Cure
Authors: Voeten Daan M. , van der Werf Leonie R. , Wijnhoven Bas P. L. , van Hillegersberg Richard , van Berge Henegouwen Mark I. 
Published: July 2020

Objective:
This study aimed to describe failure to cure in terms of incidence, hospital variation, and as an outcome parameter for salvage esophagectomy.

Summary Background Data:

Failure to cure is a composite outcome measure that could be used for hospital comparison in esophageal carcinoma care.

Methods:
All patients registered in the Dutch Upper GI Cancer Audit who underwent potentially curative esophageal carcinoma surgery in 2011 to 2018, were included in this nationwide cohort study. Failure to cure was defined as: 1) no surgical resection due to intraoperative metastasis or locally irresectable tumor, 2) macroscopically or microscopically incomplete resection, or 3) 30-day/in-hospital mortality. Association of baseline characteristics with failure to cure was analyzed using multivariable logistic regression in the total population and in salvage patients.

Results:
Some 5894 patients from 22 hospitals were included, of whom 630 (10.7%) had failure to cure (hospital variation [5.5%–19.1%]). Higher age, preoperative weight loss, higher ASA-score, higher N-stage, neoadjuvant chemotherapy, or no neoadjuvant therapy (compared with neoadjuvant chemoradiotherapy), open surgery, and resection before 2014 were associated with failure to cure. After case-mix correction, 2 hospitals had statistically significant higher failure to cure percentages, whereas 2 had lower percentages. Of 151 salvage esophagectomy patients, 32.5% had failure to cure. The failure to cure rate after salvage surgery was 27.6% in high-volume hospitals and 47.6% in medium-volume hospitals.

Conclusions:
The incidence of failure to cure was 10.7%. Given the significant hospital variation in the percentage of failure to cure, improvement is needed. Since salvage procedures are more often successful in high-volume hospitals, further centralization of this procedure is warranted.
Multitasking and Time Pressure in the Operating Room
Authors: Modi Hemel N. , Singh Harsimrat , Darzi Ara , Leff Daniel R. 
Published: July 2020

Objective:
To assess the impact of multitasking and time pressure on surgeons’ brain function during laparoscopic suturing.

Summary Background Data:
Recent neuroimaging evidence suggests that deterioration in surgical performance under time pressure is associated with deactivation of the prefrontal cortex (PFC), an area important for executive functions. However, the effect of multitasking on operator brain function remains unknown.

Methods:
Twenty-nine surgical residents performed an intracorporeal suturing task under four conditions: 1) self-paced suturing, 2) time-pressured suturing, 3) self-paced suturing plus decision-making, and 4) time-pressured suturing plus decision-making. Subjective workload was quantified using the Surgical Task Load Index. Technical skill was objectively assessed using task progression scores, error scores, leak volumes, and knot tensile strengths. PFC activation was measured using optical neuroimaging.

Results:
Compared with self-paced suturing, subjective workload (au) was significantly greater in time-pressured suturing (146.0 vs 196.0, P < 0.001), suturing with decision-making (146.0 vs 182.0, P < 0.001), and time-pressured suturing with decision-making (146.0 vs 227.0, P < 0.001). Technical performance during combined suturing and decision-making tasks was inferior to suturing alone under time pressure or self-paced conditions (P < 0.001). Significant dorsolateral PFC (DLPFC) activations were observed during self-paced suturing, and ventrolateral PFC (VLPFC) deactivations were identified during time-pressured suturing. However, suturing in conjunction with decision-making resulted in significant deactivation across both the VLPFC and DLPFC (P < 0.05). Random effects regression analysis confirmed decision-making predicts VLPFC and DLPFC deactivation (z = −2.62, P < 0.05).

Conclusions:
Performance degradation during high workload conditions is associated with deactivation of prefrontal regions important for attentional control, working memory, and cognitive flexibility, particularly during tasks involving simultaneous motor and cognitive engagement.
Gastroesophageal resuscitative occlusion of the aorta: Physiologic tolerance in a swine model of hemorrhagic shock
Authors: Tiba Mohamad H. , McCracken Brendan M. , Colmenero Carmen I. , Plott Jeffery S. , Leander Danielle C. , Greer Nicholas L. , Wang Stewart C. , Shih Albert J. , Eliason Jonathan L. , Ward Kevin R. 
Published: July 2020

BACKGROUND
Resuscitative endovascular balloon occlusion of the aorta (REBOA) has been shown to be effective for management of noncompressible torso hemorrhage. However, this technique requires arterial cannulation, which can be time-consuming and not amendable to placement in austere environments. We present a novel, less invasive aortic occlusion device and technique designated gastroesophageal resuscitative occlusion of the aorta (GROA). In this study, we aimed to characterize the physiological tolerance and hemodynamic effects of a prototype GROA device in a model of severe hemorrhagic shock and resuscitation and compare with REBOA.

METHODS
Swine (N = 47) were surgically instrumented for data collection. A 35% controlled arterial hemorrhage was followed by randomizing animals to 30-minute, 60-minute, or 90-minute interventions of GROA, REBOA, or control. Following intervention, devices were deactivated, and animals received whole blood and crystalloid resuscitation. Animals were monitored for an additional 4 hours.

RESULTS
All animals except one GROA 90-minute application survived the duration of their intervention periods. Survival through resuscitation phase in GROA, REBOA, and control groups was similar in the 30-minute and 60-minute groups. The 90-minute occlusion groups exhibited deleterious effects upon device deactivation and reperfusion with two GROA animals surviving and no REBOA animals surviving. Mean (SD) arterial pressure in GROA and REBOA animals increased across all groups to 98 (31.50) mm Hg and 122 (24.79) mm Hg, respectively, following intervention. Lactate was elevated across all GROA and REBOA groups relative to controls during intervention but cleared by 4 hours in the 30-minute and 60-minute groups. Postmortem histological examination of the gastric mucosa revealed mild to moderate inflammation across all GROA groups.

CONCLUSION
In this study, the hemodynamic effects and physiological tolerance of GROA was similar to REBOA. The GROA device was capable of achieving high zone II full aortic occlusion and may be able to serve as an effective method of aortic impingement.
Downstream hospital system effects of a comprehensive trauma recovery services program
Authors: DeMario Belinda , Kalina Mark J. , Truong Evelyn , Hendrickson Sarah , Tseng Esther S. , Claridge Jeffrey A. , Vallier Heather , Ho Vanessa P. 
Published: July 2020

BACKGROUND
Trauma patients are often noted to have poor compliance but high recidivism and readmission rates. Participation in a trauma recovery services (TRS) program, which provides peer support and other psychosocial resources, may impact the trajectory of patient recovery by decreasing barriers to follow-up. We hypothesized that TRS participants would have greater downstream nonemergent use of our hospital system over the year following trauma, manifested by more positive encounters, fewer negative encounters, and lower emergency department (ED) charges.

METHODS
We studied trauma survivors (March 2017 to March 2018) offered TRS. Hospital encounters and charges 1 year from index admission were compared between patients who accepted and declined TRS. Positive encounters were defined as outpatient visits and planned admissions; negative encounters were defined as no shows, ED visits, and unplanned admissions. Charges were grouped as cumulative ED and non-ED charges (including outpatient and subsequent admission charges). Adjusted logistic and linear regression analyses were used to identify factors associated with positive/negative encounters and ED charges.

RESULTS
Of 511 identified patients (68% male; injury severity score, 14 [9–19]), 362 (71%) accepted TRS. Trauma recovery services patients were older, had higher injury severity, and longer index admission length of stay (all p < 0.05). After adjusting for confounders, TRS patients were more likely to have at least one positive encounter and were similarly likely to have negative encounters as patients who declined services. Total aggregate charges for this group was US $74 million, of which US $30 million occurred downstream of the index admission. Accepting TRS was associated with lower ED charges.

CONCLUSION
A comprehensive TRS program including education, peer mentors, and a support network may provide value to the patient and the health care system by reducing subsequent care provided by the ED in the year after a trauma without affecting nonemergent care.

LEVEL OF EVIDENCE
Therapeutic/care management, level IV.
Therapeutic strategies for Huntington's disease
Authors: Estevez-Fraga Carlos , Flower Michael D. , Tabrizi Sarah J. 
Published: July 2020

Purpose of reviewHuntington's disease is a fatal autosomal dominant neurodegenerative disorder caused by a trinucleotide expansion in theHTTgene, and current therapies focus on symptomatic treatment. This review explores therapeutic approaches that directly target the pathogenic mutation, disruptHTTmRNA or its translation.Recent findingsZinc-finger transcription repressors and CRISPR-Cas9 therapies targetHTTDNA, thereby preventing all downstream pathogenic mechanisms. These therapies, together with RNA interference (RNAi), require intraparenchymal delivery to the brain in viral vectors, with only a single delivery potentially required, though they may carry the risk of irreversible side-effects.Along with RNAi, antisense oligonucleotides (ASOs) target mRNA, but are delivered periodically and intrathecally. ASOs have safely decreased mutant huntingtin protein (mHTT) levels in the central nervous system of patients, and a phase 3 clinical trial is currently underway.Finally, orally available small molecules, acting on splicing or posttranslational modification, have recently been shown to decrease mHTT in animal models.SummaryHuntingtin-lowering approaches act upstream of pathogenic mechanisms and therefore have a higha priorilikelihood of modifying disease course. ASOs are already in late-stage clinical development, whereas other strategies are progressing rapidly toward human studies.
Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations
Authors: Moya Leire , Farashi Samaneh , Suravajhala Prashanth N , Janaththani Panchadsaram , Batra Jyotsna 
Published: July 2020

AbstractAimThe novel SARS-CoV-2 virus, which causes the COVID-19 disease, has infected more than 10 million people and caused 500K deaths worldwide. In Europe, over 2 million confirmed cases have been reported, while nearly 200K people have died from the disease. Despite strict containment measures in Spain and Italy after the first reported COVID-19 patient, these two countries have remained in the top five European nations with the highest mortality rate for over two months. We hypothesised that a genetic mechanism could partially explain the poor survival outcome observed in these two countries.MethodsAn extensive literature search to identify human candidate genes linked to SARS-CoV infection, host immune evasion and disease aggressiveness was carried out. Pathway analysis (IPA) was performed to select the most significantly associated canonical signalling pathways with the genes of interest. The genetic variants’ at these genes with ±1Mb flanking region was extracted (GRCh37/hg19 built). Over 80 million single nucleotide polymorphisms (SNPs) were analysed in genome-wide data of 2,504 individuals (1000 genomes, phase III,https://www.internationalgenome.org/). Principal component (PC) analysis was performed, ancestry by the whole genome was inferred and subsets of the regions of interest were extracted (PLINK v1.9b,http://pngu.mgh.harvard.edu/purcell/plink/). PC1 to PC20 values from five European ancestries, including the Spanish and Italian populations, were used for PC analysis. Gene function predictions were run with our genes of interest as a query to the GeneMANIA Cytoscape plugin (https://genemania.org/).ResultsA total of 437 candidate genes associated with SARS were identified, including 21 correlated with COVID-19 aggressiveness. The two most significant pathways associated with all 437 genes (Caveolar-mediated EndocytosisandMSP-RON Signalling) did not show any segregation at the population level. However, the most significant canonical pathway associated with genes linked to COVID-19 aggressiveness, theHepatic Fibrosis and Hepatic Stellate Cell Activation,showed population-specific segregation. Both the Spanish and Italian populations clustered together from the rest of Europe. This was also observed for the Finnish population but in the opposite direction. These results suggest some of the severe COVID-19 cases reported in Spain and Italy could be partially explained by a pre-existing liver condition (especially liver cancer) and/or may lead to further COVID-19 related liver complications.
Reduced phenotypic plasticity evolves in less predictable environments
Authors: Leung Christelle , Rescan Marie , Grulois Daphné , Chevin Luis-Miguel 
Published: July 2020

AbstractPhenotypic plasticity is a prominent mechanism for coping with variable environments, and a key determinant of extinction risk. Evolutionary theory predicts that phenotypic plasticity should evolve to lower levels in environments that fluctuate less predictably, because they induce mismatches between plastic responses and selective pressures. However this prediction is difficult to test in nature, where environmental predictability is not controlled. Here, we exposed 32 lines of the halotolerant microalgaDunaliella salinato ecologically realistic, randomly fluctuating salinity, with varying levels of predictability, for 500 generations. We found that morphological plasticity evolved to lower levels in lines that experienced less predictable environments. Evolution of plasticity mostly concerned phases with slow population growth, rather than the exponential phase where microbes are typically phenotyped. This study underlines that long-term experiments with complex patterns of environmental change are needed to test theories about population responses to altered environmental predictability, as currently observed under climate change.
CEREBRUM-7T: Fast and Fully-volumetric Brain Segmentation of 7 Tesla MR Volumes
Authors: Svanera Michele , Benini Sergio , Bontempi Dennis , Muckli Lars 
Published: July 2020

ABSTRACTUltra high-field MRI enables sub-millimetre resolution imaging of the human brain, allowing for the resolution of functional circuits at the meso-scale of cortical layers. An essential step in many functional and structural neuroimaging studies is segmentation, the operation of partitioning the MR brain images to delineate anatomical structures. Despite recent efforts in brain imaging analysis, the literature lacks of accurate and fast methods for segmenting 7 Tesla (7T) brain MRI. We here presentCEREBRUM-7T, an optimised end-to-end Convolutional Neural Network (CNN) architecture, that allows for the segmentation of a whole 7T T1wMRI brain volume at once, thus overcoming the drawbacks of partitioning the volume into 2D or 3D tiles. Training is performed in a weakly supervised fashion, exploiting labelling with errors obtained with automatic state-of-the-art methods. The trained model is able to produce accurate multi-structure segmentation masks on six different classes in only a few seconds. In the experimental part, a combination of objective numerical evaluations and subjective analysis carried out by experienced neuroimaging users, confirms that the proposed solution outperforms the training labels it was trained on in segmentation accuracy, and is suitable for neuroimaging studies, such as layer fMRI studies. Taking advantage of a fine-tuning operation on a reduced set of volumes, we also show how it is possible to efficiently and effectively applyCEREBRUM-7Tto data from different sites. Furthermore, to allow replicability and encourage extensions, we release the code, 7T data (142 volumes), and other materials, including the training labels and the Turing test.
DeepForest: A Python package for RGB deep learning tree crown delineation
Authors: Weinstein Ben. G. , Marconi Sergio , Aubry-Kientz Mélaine , Vincent Gregoire , Senyondo Henry , White Ethan 
Published: July 2020

AbstractRemote sensing of forested landscapes can transform the speed, scale, and cost of forest research. The delineation of individual trees in remote sensing images is an essential task in forest analysis. Here we introduce a new Python package, DeepForest, that detects individual trees in high resolution RGB imagery using deep learning.While deep learning has proven highly effective in a range of computer vision tasks, it requires large amounts of training data that are typically difficult to obtain in ecological studies. DeepForest overcomes this limitation by including a model pre-trained on over 30 million algorithmically generated crowns from 22 forests and fine-tuned using 10,000 hand-labeled crowns from 6 forests.The package supports the application of this general model to new data, fine tuning the model to new datasets with user labeled crowns, training new models, and evaluating model predictions. This simplifies the process of using and retraining deep learning models for a range of forests, sensors, and spatial resolutions.We illustrate the workflow of DeepForest using data from the National Ecological Observatory Network, a tropical forest in French Guiana, and street trees from Portland, Oregon.
ThermoFRET: A novel nanoscale G protein coupled receptor thermostability assay functional in crude solubilised membrane preparations
Authors: Tippett David N , Hoare Brad , Miljus Tamara , Sykes David A , Veprintsev Dmitry B. 
Published: July 2020

AbstractSensitive protein stability assays for membrane proteins are crucial for developing purification protocols, for structural and biophysical characterisation and drug discovery. Here, we describe a novel high-throughput 384-well FRET-based thermostability methodology, ThermoFRET, allowing for the ultrasensitive determination of G protein coupled receptor (GPCR) stability. This method measures FRET between a terbium-cryptate labelled GPCR and BODIPY-FL-Cystine, a thiolreactive dye that reacts with cysteine residues exposed upon protein unfolding in response to thermal denaturation. ThermoFRET is functional in crude solubilised membrane preparations, without protein purification and can detect receptor stabilising ligands, making it ideally suited for orphan receptor screening.