bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the molecular nature associated with microsatellite status in colon cancer identifies clinical implications for immunotherapy
Authors: Bao Xuanwen , Zhang Hangyu , Wu Wei , Cheng Shaobing , Dai Xiaomeng , Zhu Xudong , Fu Qihan , Tong Zhou , Liu Lulu , Zheng Yi , Zhao Peng , Fang Weijia , Liu Fanglong 
Published: October 2020

BackgroundMicrosatellite instability in colon cancer implies favorable therapeutic outcomes after checkpoint blockade immunotherapy. However, the molecular nature of microsatellite instability is not well elucidated.MethodsWe examined the immune microenvironment of colon cancer using assessments of the bulk transcriptome and the single-cell transcriptome focusing on molecular nature of microsatellite stability (MSS) and microsatellite instability (MSI) in colorectal cancer from a public database. The association of the mutation pattern and microsatellite status was analyzed by a random forest algorithm in The Cancer Genome Atlas (TCGA) and validated by our in-house dataset (39 tumor mutational burden (TMB)-low MSS colon cancer, 10 TMB-high MSS colon cancer, 15 MSI colon cancer). A prognostic model was constructed to predict the survival potential and stratify microsatellite status by a neural network.ResultsDespite the hostile CD8+cytotoxic T lymphocyte (CTL)/Th1 microenvironment in MSI colon cancer, a high percentage of exhausted CD8+T cells and upregulated expression of immune checkpoints were identified in MSI colon cancer at the single-cell level, indicating the potential neutralizing effect of cytotoxic T-cell activity by exhausted T-cell status. A more homogeneous highly expressed pattern of PD1 was observed in CD8+T cells from MSI colon cancer; however, a small subgroup of CD8+T cells with high expression of checkpoint molecules was identified in MSS patients. A random forest algorithm predicted important mutations that were associated with MSI status in the TCGA colon cancer cohort, and our in-house cohort validated higher frequencies ofBRAF,ARID1A,RNF43, andKM2Bmutations in MSI colon cancer. A robust microsatellite status–related gene signature was built to predict the prognosis and differentiate between MSI and MSS tumors. A neural network using the expression profile of the microsatellite status–related gene signature was constructed. A receiver operating characteristic curve was used to evaluate the accuracy rate of neural network, reaching 100%.ConclusionOur analysis unraveled the difference in the molecular nature and genomic variance in MSI and MSS colon cancer. The microsatellite status–related gene signature is better at predicting the prognosis of patients with colon cancer and response to the combination of immune checkpoint inhibitor–based immunotherapy and anti-VEGF therapy.
Transition to virtual appointments for interventional neuroradiology due to the COVID-19 pandemic: a survey of satisfaction
Authors: Lun Ronda , Walker Gregory , Daham Zeinab , Ramsay Tim , Portela de Oliveira Eduardo , Kassab Mohammed , Fahed Robert , Quateen Aiman , Lesiuk Howard , P dos Santos Marlise , Drake Brian 
Published: October 2020

BackgroundThe COVID-19 pandemic has changed the way medicine is practiced, including the implementation of virtual care in many specialties. In the field of interventional neuroradiology (INR), virtual clinics are an uncommon practice with minimal literature to support its use. Our objective was to report prospective, single-centre data regarding patient and physician experience with virtual INR clinics for routine follow-up appointments.MethodsWe surveyed all patients that participated in a virtual INR clinic follow-up appointment at our hospital over a 3 month period. Information gathered included length of appointment delays (ie, wait times), length of appointment times, overall satisfaction, and perceived safety metrics. A survey was also sent out to all physicians who participated in virtual clinics with similar questions.Results118/122 patients and 6/6 physicians completed the survey. Wait times before previous in-person appointments were perceived to be much longer than virtual appointments, whereas in-person appointment times were longer. 112/118 (94.9%) patients and 4/6 (67%) physicians reported general satisfaction with their virtual clinic experience. There were 8/118 patients who felt their conditions could not be safely assessed virtually, compared with 1/6 (17%) physicians. Lastly, 72.2% of patients reported that they would prefer virtual or telephone visits in the future for non-urgent follow-up, and 5/6 (83%) of physicians reported the same.ConclusionVirtual INR clinics are more efficient and are preferred among patients and physicians for non-urgent follow-up appointments. Our study demonstrates the feasibility of a virtual platform for INR care, which could be sustainable for future practice.
COVID-19: Current understanding of its Pathophysiology, Clinical presentation and Treatment
Authors: Parasher Anant 
Published: October 2020

ABSTRACTBackgroundThe severe acute respiratory syndrome (SARS) coronavirus-2 is a novel coronavirus belonging to the family Coronaviridae and is now known to be responsible for the outbreak of a series of recent acute atypical respiratory infections originating in Wuhan, China. The disease caused by this virus, termed coronavirus disease 19 or simply COVID-19, has rapidly spread throughout the world at an alarming pace and has been declared a pandemic by the WHO on March 11, 2020. In this review, an update on the pathophysiology, clinical presentation and the most recent management strategies for COVID-19 has been described.Materials and MethodsA search was conducted for literature and various articles/case reports from 1997 to 2020 in PUBMED/MEDLINE for the keywords coronavirus, SARS, Middle East respiratory syndrome and mRNA virus.Results and ConclusionsCOVID-19 has now spread globally with increasing morbidity and mortality among all populations. In the absence of a proper and effective antibody test, the diagnosis is presently based on a reverse-transcription PCR of nasopharyngeal and oropharyngeal swab samples. The clinical spectrum of the disease presents in the form of a mild, moderate or severe illness. Most patients are either asymptomatic carriers who despite being without symptoms have the potential to be infectious to others coming in close contact, or have a mild influenza-like illness which cannot be differentiated from a simple upper respiratory tract infection. Moderate and severe cases require hospitalisation as well as intensive therapy which includes non-invasive as well as invasive ventilation, along with antipyretics, antivirals, antibiotics and steroids. Complicated cases may require treatment by immunomodulatory drugs and plasma exchange therapy. The search for an effective vaccine for COVID-19 is presently in full swing, with pharmaceutical corporations having started human trials in many countries.
Cherenkov-channeling radiation by relativistic muons in crystals
Authors: Korotchenko K. B. , Rozhkova E. I. , Dabagov S. B. 
Published: October 2020

AbstractIn this work we analyse Cherenkov radiation by relativistic muons, positive and negative, channeled in optically transparent diamond and silicon crystals in comparison with ordinary Cherenkov radiation. We have shown that the maxima in the spectral angular distributions for both types of radiation are revealed at the derivative extrema for the media refractive index, while, due to the difference in scattering of positively and negatively charged particles at crystal channeling, the number of Cherenkov photons emitted by channeled positive muons might be over the one for negative muons. We have demonstrated that Cherenkov radiation by quasi free projectiles is described as one limiting approximation of a general expression for Cherenkov radiation by channeled projectiles, which takes into account non-zero derivative of the refractive index. The last may result in essential increase of radiation intensity.
Risk Factors of Subsequent Central Nervous System Tumors after Childhood and Adolescent Cancers: Findings from the French Childhood Cancer Survivor Study
Authors: Journy Neige Marie Yvanne , Zrafi Wael Salem , Bolle Stéphanie , Fresneau Brice , Alapetite Claire , Allodji Rodrigue Setcheou , Berchery Delphine , Haddy Nadia , Kobayashi Isao , Labbé Martine , Pacquement Hélène , Pluchart Claire , Schwartz Boris , Souchard Vincent , Thomas-Teinturier Cécile , Veres Cristina , Vu-Bezin Giao , Diallo Ibrahima , de Vathaire Florent 
Published: October 2020

Abstract

Background:
Childhood or adolescent cancer survivors are at increased risks of subsequent primary neoplasms (SPN) of the central nervous system (CNS) after cranial irradiation. In a large multicentric cohort, we investigated clinical and therapeutic factors associated with the long-term risk of CNS SPN, and quantified the dose–response relationships.

Methods:
We selected all CNS SPN cases diagnosed up to 2016 among members of the French Childhood Cancer Survivor Study at least 5 years after first cancer diagnosis in 1946–2000. Four controls per case were randomly selected within the cohort and matched by sex, year of/age at first cancer diagnosis, and follow-up time. On the basis of medical and radiological reports, cumulative radiation doses received to the SPN or matched location were retrospectively estimated using mathematical phantoms. We computed conditional logistic regression models.

Results:
Meningioma risk significantly increased with higher radiation doses [excess OR per Gy (EOR/Gy) = 1.377; P &lt; 0.001; 86 cases; median latency time = 30 years], after adjustment for reported genetic syndromes and first CNS tumor. It was higher among youngest individuals at first cancer diagnosis, but did not vary with follow-up time. On the opposite, radiation-related glioma risk (EOR/Gy = 0.049; P = 0.11; 47 cases; median latency time = 17 years) decreased over time (P for time effect = 0.05). There was a significant association between meningioma risk and cumulative doses of alkylating agents, but no association with growth hormone therapy.

Conclusions:
The surveillance of patients with cranial irradiation should continue beyond 30 years after treatment.

Impact:
The identified risk factors may inform long-term surveillance strategies.
Myeloid-Derived TSP1 (Thrombospondin-1) Contributes to Abdominal Aortic Aneurysm Through Suppressing Tissue Inhibitor of Metalloproteinases-1
Authors: Yang Huan , Zhou Ting , Sorenson Christine M. , Sheibani Nader , Liu Bo 
Published: October 2020

Objective:
Abdominal aortic aneurysm is characterized by the progressive loss of aortic integrity and accumulation of inflammatory cells primarily macrophages. We previously reported that global deletion of matricellular protein TSP1 (thrombospondin-1) protects mice from aneurysm formation. The objective of the current study is to investigate the cellular and molecular mechanisms underlying TSP1’s action in aneurysm.

Approach and Results:

Using RNA fluorescent in situ hybridization, we identified macrophages being the major source of TSP1 in human and mouse aneurysmal tissues, accounting for over 70% of cells that actively expressed
Thbs1
mRNA. Lack of TSP1 in macrophages decreased solution-based gelatinase activities by elevating TIMP1 (tissue inhibitor of metalloproteinases-1) without affecting the major MMPs (matrix metalloproteinases). Knocking down
Timp1
restored the ability of
Thbs1
−

/−

macrophages to invade matrix. Finally, we generated
Thbs1
flox/flox
mice and crossed them with
Lyz2-cre
mice. In the CaCl
2
-induced model of abdominal aortic aneurysm, lacking TSP1 in myeloid cells was sufficient to protect mice from aneurysm by reducing macrophage accumulation and preserving aortic integrity.

Conclusions:
TSP1 contributes to aneurysm pathogenesis, at least in part, by suppressing TIMP1 expression, which subsequently enables inflammatory macrophages to infiltrate vascular tissues.
Seasonality of Influenza‐Like‐Illness and Acute Cardiovascular Events Are Related Regardless of Vaccine Effectiveness
Authors: Kulick Erin R. , Canning Michelle , Parikh Neal S. , Elkind Mitchell S. V. , Boehme Amelia K. 
Published: October 2020

Background
Influenza has been identified as a trigger for stroke and myocardial infarction (MI) with prior studies demonstrating that influenza vaccination may decrease risk of stroke and MI.

Methods and Results

We used data from the New York Department of Health Statewide Planning and Research Cooperative System to evaluate whether annual variability in influenza vaccination effectiveness (VE) would be associated with cardiovascular events. Daily and monthly counts of outpatient and inpatient visits for influenza‐like illness (ILI), stroke, and MI were identified using
International Classification of Diseases, Ninth Revision
(
ICD‐9
) codes; VE data for each year are publicly available. We identified pertinent lags between ILI, stroke, and MI using prewhitening cross‐correlation functions and applied them to autoregressive integrated moving average time series regression models. Time series forecasting systems assessed correlations among ILI, stroke, and MI, and the effect of VE on these relationships. Cross‐correlation functions indicated stroke events increased 1 month after increases in ILI rates; MIs increased immediately. Accounting for seasonality and lag, peaks in ILI rates were significantly related to peaks in stroke (
P
=0.04) and MI (
P
=0.01). Time forecasting analyses indicated no relationship between VE and cardiovascular events.

Conclusions
We identified that seasonality of cardiovascular events may be associated with seasonality in ILI, though VE did not modify this relationship.
Role of the Metabolic Profile in Mediating the Relationship Between Body Mass Index and Left Ventricular Mass in Adolescents: Analysis of a Prospective Cohort Study
Authors: Carter Alice R. , Santos Ferreira Diana L. , Taylor Amy E. , Lawlor Deborah A. , Davey Smith George , Sattar Naveed , Chaturvedi Nishi , Hughes Alun D. , Howe Laura D. 
Published: October 2020

Background
We aimed to quantify the role of the plasma metabolic profile in explaining the effect of adiposity on cardiac structure.

Methods and Results

Body mass index (BMI) was measured at age 11 in the Avon Longitudinal Study of Parents and Children. Left ventricular mass indexed to height
2.7
(LVMI) was assessed by echocardiography at age 17. The metabolic profile was quantified via
1
H‐nuclear magnetic resonance spectroscopy at age 15. Multivariable confounder (maternal age, parity, highest qualification, maternal smoking, prepregnancy BMI, prepregnancy height, household social class, adolescent birthweight, adolescent smoking, fruit and vegetable consumption, and physical activity)–adjusted linear regression estimated the association of BMI with LVMI and mediation by metabolic traits. We considered 156 metabolomic traits individually and jointly as principal components explaining 95% of the variance in the nuclear magnetic resonance platform and assessed whether the principal components for the metabolic traits added to the proportion of the association explained by putative cardiovascular risk factors (systolic and diastolic blood pressures, insulin, triglycerides, low‐density lipoprotein cholesterol, and glucose). A 1 kg/m
2
higher BMI was associated with a 0.70 g/m
2.7
(95% CI, 0.53–0.88 g/m
2.7
) and 0.66 g/m
2.7
(95% CI, 0.53–0.79 g/m
2.7
) higher LVMI in males (n=437) and females (n=536), respectively. Putative risk factors explained 3% (95% CI, 2%–5%) of this association in males, increasing to 10% (95% CI, 8%–13%) when including metabolic principal components. In females, the standard risk factors explained 3% (95% CI, 2%–5%) of the association and did not increase when including the metabolic principal components.

Conclusions
The addition of the nuclear magnetic resonance‐measured metabolic traits appears to mediate more of the association of BMI on LVMI than the putative risk factors alone in adolescent males, but not females.
Hospital Presentations in Long-Term Survivors of Stroke
Authors: Andrew Nadine E. , Kilkenny Monique F. , Sundararajan Vijaya , Kim Joosup , Faux Steven G. , Thrift Amanda G. , Johnston Trisha , Grimley Rohan , Gattellari Melina , Katzenellenbogen Judith M. , Dewey Helen M. , Lannin Natasha A. , Anderson Craig S. , Cadilhac Dominique A. ,   On behalf of the Stroke123 Investigators and the AuSCR Consortium
Published: October 2020

Background and Purpose:
A comprehensive understanding of the long-term impact of stroke assists in health care planning. We aimed to determine changes in rates, causes, and associated factors for hospital presentations among long-term survivors of stroke.

Methods:
Person-level data from the AuSCR (Australian Stroke Clinical Registry) during 2009 to 2013 were linked with state-based health department emergency department and hospital admission data. The study cohort included adults with first-ever stroke who survived the first 6 months after discharge from hospital. Annualized rates of hospital presentations (nonadmitted emergency department or admission)/person/year were calculated for 1 to 12 months prior, and 7 to 12 months (inclusive) after hospitalization. Multilevel, negative binomial regression was used to identify associated factors after adjustment for prestroke hospital presentations and stratification for perceived impairment status. Perceived impairments to health were defined according to the subscales and visual analog health status scores on the 5-Dimension European Quality of Life Scale.

Results:
There were 7183 adults with acute stroke, 7-month survivors (median age 72 years; 56% male; 81% ischemic, and 42% with impairment at 90–180 days) from 39 hospitals included in this landmark analysis. Annualized presentations/person increased from 0.88 (95% CI, 0.86–0.91) to 1.25 (95% CI, 1.22–1.29) between the prestroke and poststroke periods, with greater rate increases in those with than without perceived impairment (55% versus 26%). Higher presentation rates were most strongly associated with older age (≥85 versus 65 years, incidence rate ratio, 1.52 [95% CI, 1.27–1.82]) and greater comorbidity score (incidence rate ratio, 1.06 [95% CI, 1.02–1.10]), whereas reduced rates were associated with greater social advantage (incidence rate ratio, 0.71 [95% CI, 0.60–0.84]). Poststroke hospital presentations (7–12 months) were most frequently related to recurrent cardiovascular and cerebrovascular events and sequelae of stroke.

Conclusions:
A large increase in annualized hospital presentation rates after stroke indicates the potential for improved community management and support for this vulnerable patient group.
Data Gaps within Atmospheric Rivers over the Northeastern Pacific
Authors: Zheng Minghua , Delle Monache Luca , Wu Xingren , Ralph F. Martin , Cornuelle Bruce , Tallapragada Vijay , Haase Jennifer S. , Wilson Anna M. , Mazloff Matthew , Subramanian Aneesh , Cannon Forest 
Published: October 2020

AbstractConventional observations of atmospheric rivers (ARs) over the northeastern Pacific Ocean are sparse. Satellite radiances are affected by the presence of clouds and heavy precipitation, which impact their distribution in the lower atmosphere and in precipitating areas. The goal of this study is to document a data gap in existing observations of ARs in the northeastern Pacific, and to investigate how a targeted field campaign called AR Reconnaissance (AR Recon) can effectively fill this gap. When reconnaissance data are excluded, there is a gap in AR regions from near the surface to the middle troposphere (below 450 hPa), where most water vapor and its transport are concentrated. All-sky microwave radiances provide data within the AR object, but their quality is degraded near the AR core and its leading edge, due to the existence of thick clouds and precipitation. AR Recon samples ARs and surrounding areas to improve downstream precipitation forecasts over the western United States. This study demonstrates that despite the apparently extensive swaths of modern satellite radiances, which are critical to estimate large-scale flow, the data collected during 15 AR Recon cases in 2016, 2018, and 2019 supply about 99% of humidity, 78% of temperature, and 45% of wind observations in the critical maximum water vapor transport layer from the ocean surface to 700 hPa in ARs. The high-vertical-resolution dropsonde observations in the lower atmosphere over the northeastern Pacific Ocean can significantly improve the sampling of low-level jets transporting water vapor to high-impact precipitation events in the western United States.
Analysis of Extreme Wind Speed Estimates in the Northern South China Sea
Authors: Yan Zhiduo , Pang Liang , Dong Sheng 
Published: October 2020

AbstractAn increasing number of coastal and offshore structures have been built for coastal protection and marine development in recent years, and these marine structures need to be reasonably designed on the basis of wind speed. In this paper, extreme wind speed estimates are studied in detail by using the best-track datasets of northwestern Pacific Ocean tropical cyclones and ERA5 wind field data. The extreme wind speed fits by five distributions are compared using a blended sample of the wind fields from the ERA5 dataset and parametric wind data. The blend of wind fields improved the data accuracy and extreme value estimation reliability. In addition, the effects of the distribution model, data, threshold, and parameter estimation methods on the calculated results are discussed. The results show that the data had the greatest influences on probability prediction, followed by the distribution model and the parameter estimation method, with the threshold presenting the least influence. In this study, the reliability of the estimates was improved and the uncertainty of the results was analyzed, and the findings provide a wind speed design reference for the northern South China Sea.
The Impact of the Tertiary Survey in an Established Trauma Program
Authors: Mitchell Brendan P. , Stumpff Kelly , Berry Stepheny , Howard James , Bennett Ashley , Winfield Robert D. 
Published: October 2020

Introduction The trauma tertiary survey (TTS) was first described in 1990 and is recognized as an essential practice in trauma care. The TTS remains effective in detecting secondary injuries in the modern era. Methods Trauma patients discharged between August 1, 2016, and December 31, 2016, were identified in our trauma registry. Collected data include TTS completion rates, detection of injuries, type of provider, and timing. TTS documentation was qualitatively evaluated. Results Out of 407 patients, 264 patients (65%) received a TTS. Injury detection rate was 1.1.%. Average time to TTS was 41 hours. TTS were completed by resident physicians (46%) and advanced practice providers (APPs; 46%). TTS documentation was more complete for APPs than for resident physicians. Conclusion TTS remains an integral component of modern trauma care. Ongoing education on the significance of TTS and the importance of thorough documentation is essential. Provision of real-time feedback to providers is also critical for improving current practices.