bluuebunny/crossref_metadata_2025_split huggingface dataset:
HPV+ oropharyngeal squamous cell carcinomas from patients with two tumors display synchrony of viral genomes yet discordant mutational profiles and signatures
Authors: Faden Daniel L , Langenbucher Adam , Kuhs Krystle , Lewis James S , Mirabello Lisa , Yeager Meredith , Boland Joseph F , Bass Sara , Steinberg Mia , Cullen Michael , Lawrence Michael S , Ferris Robert L 
Published: October 2020

Abstract
Human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (HPV + OPSCC) is increasing in prevalence in the USA, as are cases of patients with multiple HPV + OPSCCs (mHPV + OPSCC). mHPV + OPSCCs present a unique opportunity to examine HPV + OPSCC mutation acquisition and evolution. We performed sequencing of the viral genome, somatic exome and somatic transcriptome from 8 patients each with 2 spatially distinct HPV + OPSCCs, and 37 ‘traditional’ HPV + OPSCCs to first address if paired tumors are caused by the same viral isolate and next, if acquired alterations, and the underlying processes driving mutagenesis, are shared within pairs. All tumor pairs contained viral genomes from the same HPV type 16 sublineage and differed by 0–2 clonal single nucleotide polymorphisms (SNPs), suggesting infection with the same viral isolate. Despite this, there was significant discordance in expression profiles, mutational burden and mutational profiles between tumors in a pair, with only two pairs sharing any overlapping mutations (3/3343 variants). Within tumor pairs there was a striking discrepancy of mutational signatures, exemplified by no paired tumors sharing high APOBEC mutational burden. Here, leveraging mHPV + OPSCCs as a model system to study mutation acquisition in virally mediated tumors, in which the germline, environmental exposures, immune surveillance and tissue/organ type were internally controlled, we demonstrate that despite infection by the same viral isolate, paired mHPV + OPSCCs develop drastically different somatic alterations and even more strikingly, appear to be driven by disparate underlying mutational processes. Thus, despite a common starting point, HPV + OPSCCs evolve through variable mutational processes with resultant stochastic mutational profiles.
Economic Evaluations of New Antibiotics: The High Potential Value of Reducing Healthcare Transmission Through Decolonization
Authors: Toth Damon J A , Samore Matthew H , Nelson Richard E 
Published: October 2020

AbstractBackgroundAntibiotics designed to decolonize carriers of drug-resistant organisms could offer substantial population health benefits, particularly if they can help avert outbreaks by interrupting person-to-person transmission chains. However, cost effectiveness of an antibiotic is typically evaluated only according to its benefits to recipients, which can be difficult to demonstrate for carriers of an organism that may not pose an immediate health threat to the carrier.MethodsWe developed a mathematical transmission model to quantify the effects of 2 hypothetical antibiotics targeting carbapenem-resistant Enterobacteriaceae (CRE) among long-term acute care hospital inpatients: one assumed to decrease the death rate of patients with CRE bloodstream infections (BSIs) and the other assumed to decolonize CRE carriers after clinical detection. We quantified the effect of each antibiotic on the number of BSIs and deaths among patients receiving the drug (direct effect) and among all patients (direct and indirect effect) compared to usual care. We applied these results to a cost-effectiveness analysis with effectiveness outcome of life-years gained and assumed costs for antibiotic doses and for CRE BSI.ResultsThe decolonizing antibiotic, once indirect effects were included, produced increased relative effectiveness and decreased relative costs compared to both usual care and the BSI treatment antibiotic. In fact, in most scenarios, the decolonizing drug was the dominant treatment strategy (ie, less costly and more effective).ConclusionsAntibiotics that decolonize carriers of drug-resistant organisms can be highly cost-effective when considering indirect benefits within populations vulnerable to outbreaks. Public health could benefit from finding ways to incentivize development of decolonizing antibiotics in the US, where drugs with unclear direct benefits to recipients would pose difficulties in achieving FDA approval and financial benefit to the developer.
Rural School-Based Mental Health Services: Parent Perceptions of Needs and Barriers
Authors: van Vulpen Kimberly Searcey , Habegar Amy , Simmons Teresa 
Published: October 2020

Abstract
The benefits of school-based mental health services have been supported in prior research and literature. Studies have shown that approximately one in five youths in schools today have diagnosable mental health disorders. However, research has identified that close to 70 percent of those youths do not receive the services they need. This gap in care has a significant impact on the academic, social, and emotional well-being of youths. Parent involvement is essential in bridging services. However, parents often face barriers in accessing mental health care for their child. The aim of this study was to explore parent perceptions of needs and barriers to school-based mental health services. This exploratory study included 607 parent and guardian respondents. Findings showed that parents were overwhelmingly in support of schools being involved in addressing the mental health needs of students. Anxiety, depression, and bullying were the top emotional and behavioral issues that parents recognized as the main challenge for their child. Lack of parent support, understanding that mental health issues even exist in youths, and lack of supportive school programs were identified as key factors that place youths at risk of not receiving the services they need.
Clinical Outcomes of Covid-19 in Patients With Inflammatory Bowel Disease: A Nationwide Cohort Study
Authors: Derikx Lauranne A A P , Lantinga Marten A , de Jong Dirk J , van Dop Willemijn A , Creemers Rob H , Römkens Tessa E H , Jansen Jeroen M , Mahmmod Nofel , West Rachel L , Tan Adriaan C I T L , Bodelier Alexander G L , Gorter Moniek H P , Boekema Paul J , Halet Eric R C , Horjus Carmen S , van Dijk Maarten A , Hirdes Meike M C , Epping Stippel Ludger S M , Jharap Bindia , Lutgens Maurice W M D , Russel Maurice G , Gilissen Lennard P L , Nauta Sjoukje , van Bodegraven Adriaan A , Hoentjen Frank 
Published: October 2020

Abstract

Background and Aims
The COVID-19 risk and disease course in inflammatory bowel disease [IBD] patients remains uncertain. Therefore, we aimed to assess the clinical presentation, disease course, and outcomes of COVID-19 in IBD patients. Second, we determined COVID-19 incidences in IBD patients and compared this with the general population.

Methods
We conducted a multicentre, nationwide IBD cohort study in The Netherlands and identified patients with COVID-19. First, we assessed the COVID-19 disease course and outcomes. Second, we compared COVID-19 incidences between our IBD study cohort and the general Dutch population.

Results
We established an IBD cohort of 34 763 patients. COVID-19 was diagnosed in 100/34 763 patients [0.29%]; 20/100 of these patients [20%] had severe COVID-19 defined as admission to the intensive care unit, mechanical ventilation, and/or death. Hospitalisation occurred in 59/100 [59.0%] patients and 13/100 [13.0%] died. All patients who died had comorbidities and all but one were ≥65 years old. In line, we identified ≥1 comorbidity as an independent risk factor for hospitalisation (odds ratio [OR] 4.20, 95% confidence interval [CI] 1.58–11.17,; p = 0.004). Incidences of COVID-19 between the IBD study cohort and the general population were comparable (287.6 [95% CI 236.6–349.7] versus 333.0 [95% CI 329.3–336.7] per 100000 patients, respectively; p = 0.15).

Conclusions
Of 100 cases with IBD and COVID-19, 20% developed severe COVID-19, 59% were hospitalised and 13% died. A comparable COVID-19 risk was found between the IBD cohort [100/34 763 = 0.29%] and the general Dutch population. The presence of ≥1 comorbidities was an independent risk factor for hospitalisation due to COVID-19.
Atrial fibrillation in heart failure with reduced ejection fraction: a case report of exercise training
Authors: Guimarães Guilherme Veiga , Roque Jean Marcelo , Machado Alexander D T , Fernandes-Silva Miguel Morita , Chizzola Paul Roberto , Bocchi Edimar Alcides 
Published: October 2020

Abstract

Background
Heart failure (HF) and atrial fibrillation (AF) are often concomitant and act in a vicious cycle. Atrial fibrillation is associated with greater functional limitations and increased morbidity and mortality in patients with HF. Moreover, AF associated with HF increases patients' physical inactivity, worsening their clinical condition, and prognosis. Exercise training is safe and has clear benefits in HF. However, these benefits have not been demonstrated when AF is associated with HF.

Case summary
We present the case of a 57-year-old man with permanent AF and HF with reduced ejection fraction, who underwent 12 weeks of exercise training that included cardiopulmonary exercise testing, neuromuscular sympathetic activity (NMSA), and muscle blood flow (MBF) before and after training.

Discussion
Exercise training was shown to have a potential benefit in reducing the activity of the sympathetic nerve and increasing muscle blood flow, as well as increasing VO2peak and decreasing the VE/VCO2 slope in a patient with AF associated with HF with reduced ejection fraction. These results may indicate favourable clinical implications in this group of patients.
The burden of cholesterol accumulation through the lifespan: why pharmacological intervention should start earlier to go further?
Authors: Zambon Alberto , Mello e Silva Alberto , Farnier Michel 
Published: October 2020

Abstract
Among the cardiovascular risk factors, cholesterol-rich atherogenic lipoproteins play a central role in the pathogenesis of atherosclerosis. In middle-aged adults, the size of the total atherosclerotic plaque burden is influenced by both the concentration of circulating atherogenic lipoproteins and the total duration of exposure to these lipoproteins. This review describes the evidence supporting a causal link between lifelong elevations in atherogenic lipoproteins and future risk of atherosclerosis; evidence strengthened by recent epidemiological, genetic, and clinical data. By consequence, adolescence and early adulthood are a crucial time for determining later cardiovascular disease risk. Arguments showing that early optimal lipid control leads to improved outcomes will be presented and suggestions put forward for how those most at risk should be identified and managed.
Ulcerative Colitis Narrative Global Survey Findings: Communication Gaps and Agreements Between Patients and Physicians
Authors: Rubin David T , Hart Ailsa , Panaccione Remo , Armuzzi Alessandro , Suvanto Ulla , Deuring J Jasper , Woolcott John , Cappelleri Joseph C , Steinberg Kathy , Wingate Laura , Schreiber Stefan 
Published: October 2020

Abstract

Background
The Ulcerative Colitis (UC) Narrative global surveys examined patient and physician perspectives on living with UC and tried to identify gaps in optimal care. Questions explored patient-physician interactions, UC management goals, and resources for improving communication.

Methods
Questionnaires were conducted across 10 countries, covering aspects of UC including diagnosis, treatment, and impact on patient quality of life, in addition to standard demographic information. Descriptive statistics were calculated.

Results
Globally, 2100 patients and 1254 physicians were surveyed (from August 2017 to February 2018). Results showed 85% of patients were satisfied with the communication they had with their physician, including discussions relating to symptoms (86%) and medication options (81%). However, 72% of patients wished for more information and support at initial diagnosis, and 48% did not feel comfortable talking to their physician about emotional concerns. Most patients (71%) set UC management goals with their physician. Both patients (63%) and physicians (79%) wished for longer appointments. Although 84% of physicians believed patient advocacy organizations to be important in UC management, more than half (54%) never discussed them with patients.

Conclusions
These survey results highlight overall patient satisfaction with patient-physician communication but emphasize areas for improvement, such as patient desire to have more information earlier in their disease course. There is an unmet need for better information, materials, and support. Physicians need to consider which of the available tools and resources can help patients talk more openly, and accurately, because informed patients are more likely to engage with physicians in a shared decision-making process.
Chern Class Inequalities on Polarized Manifolds and Nef Vector Bundles
Authors: Li Ping , Zheng Fangyang 
Published: October 2020

AbstractThis article is concerned with Chern class and Chern number inequalities on polarized manifolds and nef vector bundles. For a polarized pair $(M,L)$ with $L$ very ample, our 1st main result is a family of sharp Chern class inequalities. Among them the 1st one is a variant of a classical result and the equality case of the 2nd one is a characterization of hypersurfaces. The 2nd main result is a Chern number inequality on it, which includes a reverse Miyaoka–Yau-type inequality. The 3rd main result is that the Chern numbers of a nef vector bundle over a compact Kähler manifold are bounded below by the Euler number. As an application, we classify compact Kähler manifolds with nonnegative bisectional curvature whose Chern numbers are all positive. A conjecture related to the Euler number of compact Kähler manifolds with nonpositive bisectional curvature is proposed, which can be regarded as a complex analogue to the Hopf conjecture.
Utility of Point of Care and Rapid Diagnostics in Humanitarian Emergencies
Authors: Chadwick Stephen , Townes David A , Perrone Lucy A 
Published: October 2020

Abstract

Background
In 2019, there were 70.8 million forcibly displaced people worldwide. Among the top causes of morbidity and mortality were measles, diarrhea, respiratory illness, and malaria. Availability of accurate diagnostics that are of low complexity, affordable, and produce timely results on site without the need for expensive laboratory equipment, extensive training, or distant transport of samples, are essential tools in the response to humanitarian emergencies (HE). Early detection of infectious diseases with epidemic potential and coordinated outbreak response, can result in significant decrease in morbidity and mortality.

Content
This review explores the utility of point of care and rapid diagnostic tests (POCT/RDTs) in HE and presents a review and analysis of the low complexity, availability, and ease of use of these diagnostic modalities that make them helpful tools in these settings, despite the generally lower test performance metrics associated with them over conventional laboratory-based assays. We review the literature to understand how POCT/RDTs have been used in HE response to produce lifesaving information without the need for a robust system for transporting test samples to more sophisticated laboratories, as this is often prohibitive in areas affected by conflict or natural disasters.

Summary
We propose that POCT/RDTs be considered essential healthcare tools provided to countries following a HE and suggest that UN agencies and vulnerable countries include effective RDTs in their essential diagnostics as part of their national preparedness and response plans.
A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease
Authors: Karki Sujit Jung , Reilly Aisling , Zhou Binbin , Mascarello Maurizio , Burke James , Doohan Fiona , Douchkov Dimitar , Schweizer Patrick , Feechan Angela 
Published: October 2020

Abstract
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
Detailed Studies of IPHAS sources. II. Sab 19, a true planetary nebula and its mimic crossing the Perseus Arm.
Authors: Guerrero M A , Ortiz R , Sabin L , Ramos-Larios G , Alfaro E J 
Published: October 2020

Abstract
The INT Photometric Hα Survey (IPHAS) has provided us with a number of new-emission line sources, among which planetary nebulae (PNe) constitute an important fraction. Here we present a detailed analysis of the IPHAS nebula Sab 19 (IPHASX J055242.8+262116) based on radio, infrared, and optical images and intermediate- and high-dispersion longslit spectra. Sab 19 consists of a roundish 0.10 pc in radius double-shell nebula surrounded by a much larger 2.8 pc in radius external shell with a prominent H-shaped filament. We confirm the nature of the main nebula as a PN whose sub-solar N/O ratio abundances, low ionized mass, peculiar radial velocity, and low-mass central star allow us to catalog it as a type III PN. Apparently, the progenitor star of Sab 19 became a PN when crossing the Perseus Arm during a brief visit of a few Myr. The higher N/O ratio and velocity shift ≃40 km s−1 of the external shell with respect to the main nebula and its large ionized mass suggest that it is not truly associated with Sab 19, but it is rather dominated by a Strömgren zone in the interstellar medium ionized by the PN central star.
Multiwaveband quasi-periodic oscillation in the blazar 3C 454.3
Authors: Sarkar Arkadipta , Gupta Alok C , Chitnis Varsha R , Wiita Paul J 
Published: October 2020

ABSTRACT
We report the detection (&gt;4σ) of a quasi-periodic oscillation (QPO) in the gamma-ray light curve of 3C 454.3 along with a simultaneous marginal QPO detection (&gt;2.4σ) in the optical light curves. Periodic flux modulations were detected in both of these wavebands with a dominant period of ∼47 d. The gamma-ray QPO lasted for over 450 d (from MJD 56800 to 57250), resulting in over nine observed cycles which is among the highest number of periods ever detected in a blazar light curve. The optical light curve was not well sampled for almost half of the gamma-ray QPO span due to the daytime transit of the source, which could explain the lower significance of the optical QPO. Autoregressive Integrated Moving Average (ARIMA) modelling of the light curve revealed a significant, exponentially decaying, trend in the light curve during the QPO, along with the 47 d periodicity. We explore several physical models to explain the origin of this transient quasi-periodic modulation and the overall trend in the observed flux with a month-like period. These scenarios include a binary black hole system, a hotspot orbiting close to the innermost stable circular orbit of the supermassive black hole, and precessing jets. We conclude that the most likely scenario involves a region of enhanced emission moving helically inside a curved jet. The helical motion gives rise to the QPO and the curvature (∼0.05○ pc−1) of the jet is responsible for the observed trend in the light curve.
Cosmological consequences of intrinsic alignments supersample covariance
Authors: Ansarifard Saeed , Movahed S M S 
Published: October 2020

ABSTRACTWe examine cosmological constraints from high-precision weak-lensing surveys including supersample covariance (SSC) due to the finite survey volume. Specifically, we focus on the contribution of beat coupling in the intrinsic alignments as a part of full cosmic shear signal under flat-sky approximation. The SSC-effect grows by going to lower redshift bin and indicates considerable footprint on the intermediate and high multipoles for cumulative signal-to-noise ratio (SNR). The SNR is reduced by $\approx 10{{\ \rm per\ cent}}$ as a consequence of including the intrinsic alignment SSC, for the full cosmic shear signal, depending on the amplitude of intrinsic alignments, the ellipticity dispersion, and the survey redshift ranges, while the contribution of photometric redshift error can be ignored in the cumulative SNR. Using the Fisher-matrix formalism, we find that the impact of large modes beyond the volume of the surveys on the small modes alters the intrinsic alignments. However, corresponding impact on the cosmological parameters’ estimation is marginal compared to that of for gravitational weak lensing, particularly, when all available redshift bins are considered. Our results also demonstrate that including SSC-effect on the intrinsic alignments in the analytical covariance matrix of full cosmic shear leads to increase marginally the confidence interval for σ8 by $\approx 10{{\ \rm per\ cent}}$ for a sample with almost high intrinsic alignment amplitude.
Testing the star formation scaling relations in the clumps of the North American and Pelican nebulae cloud complex
Authors: Das Swagat R , Jose Jessy , Samal Manash R , Zhang Shaobo , Panwar Neelam 
Published: October 2020

ABSTRACT
The processes that regulate star formation within molecular clouds are still not well understood. Various star formation scaling relations have been proposed as an explanation, one of which is to formulate a relation between the star formation rate surface density $\rm \Sigma _{SFR}$ and the underlying gas surface density $\rm \Sigma _{gas}$. In this work, we test various star formation scaling relations, such as the Kennicutt–Schmidt relation, the volumetric star formation relation, the orbital time model, the crossing time model and the multi free-fall time-scale model, towards the North American Nebula and Pelican Nebula and in the cold clumps associated with them. Measuring stellar mass from young stellar objects and gaseous mass from CO measurements, we estimate the mean $\rm \Sigma _{SFR}$, the star formation rate per free-fall time and the star formation efficiency for clumps to be 1.5 $\rm M_{\odot}\, yr^{-1}\, kpc^{-2}$, 0.009 and 2.0 per cent, respectively, while for the whole region covered by both nebulae (which we call the ‘NAN’ complex) the values are 0.6 $\rm M_{\odot}\, yr^{-1}\, kpc^{-2}$, 0.0003 and 1.6 per cent, respectively. For the clumps, we notice that the observed properties are in line with the correlation obtained between $\rm \Sigma _{SFR}$ and $\rm \Sigma _{gas}$, and between $\rm \Sigma _{SFR}$ and $\rm \Sigma _{gas}$ per free-fall time and orbital time for Galactic clouds. At the same time, we do not observe any correlation with $\rm \Sigma _{gas}$ per crossing time and multi free-fall time. Even though we see correlations in the former cases, however, all models agree with each other within a factor of 0.5 dex. It is not possible to discriminate between these models because of the current uncertainties in the input observables. We also test the variation of $\rm \Sigma _{SFR}$ with the dense gas but, because of low statistics, a weak correlation is seen in our analysis.