bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel Network Analysis and Communities Detection (PANC) Pipeline for the Analysis and Visualization of COVID-19 Data
Authors: Agapito Giuseppe , Milano Marianna , Cannataro Mario 
Published: September 2021

A new coronavirus, causing a severe acute respiratory syndrome (COVID-19), was started at Wuhan, China, in December 2019. The epidemic has rapidly spread across the world becoming a pandemic that, as of today, has affected more than 70 million people causing over 2 million deaths. To better understand the evolution of spread of the COVID-19 pandemic, we developed PANC (Parallel Network Analysis and Communities Detection), a new parallel preprocessing methodology for network-based analysis and communities detection on Italian COVID-19 data. The goal of the methodology is to analyze set of homogeneous datasets (i.e. COVID-19 data in several regions) using a statistical test to find similar/dissimilar behaviours, mapping such similarity information on a graph and then using community detection algorithm to visualize and analyze the initial dataset. The methodology includes the following steps: (i) a parallel methodology to build similarity matrices that represent similar or dissimilar regions with respect to data; (ii) an effective workload balancing function to improve performance; (iii) the mapping of similarity matrices into networks where nodes represent Italian regions, and edges represent similarity relationships; (iv) the discovering and visualization of communities of regions that show similar behaviour. The methodology is general and can be applied to world-wide data about COVID-19, as well as to all types of data sets in tabular and matrix format. To estimate the scalability with increasing workloads, we analyzed three synthetic COVID-19 datasets with the size of 90.0[Formula: see text]MB, 180.0[Formula: see text]MB, and 360.0[Formula: see text]MB. Experiments was performed on showing the amount of data that can be analyzed in a given amount of time increases almost linearly with the number of computing resources available. Instead, to perform communities detection, we employed the real data set.
Understanding geo-archaeology in Trans-Himalaya: a case study based on lithic assemblages from Dzamathang, Spiti Valley, Himachal Pradesh, India
Authors: Singh Ekta , Patel Raman , Bhatt Rakesh Chandra 
Published: September 2021

Abstract
The Spiti Valley is located in the Trans-Himalayan terrain of India, from where non-geometrical microliths have been discovered. While the Siwalik Hills have been subjected to extensive prehistoric surveys, this is the first evidence of lithic tools discovered in the Trans-Himalayan region of Himachal Pradesh, India. Due to its topographical and intense climatic features, the Trans-Himalayan region has generally been regarded as a barrier since prehistoric times. However, Dzamathang cannot be considered as an isolated site in the Trans-Himalayas. In fact, in the adjoining areas of Ladakh, Tibet and Nepal, similar lithics have been reported from several sites and been assigned to the Middle and Upper Palaeolithic. The discovery of this site suggests that the Trans-Himalayan zone may have acted as a possible route rather than a barrier during human migration. Large numbers of lithics have been recovered in the Dzamathang area of the Spiti Valley. Based on the collection of the artefacts from the surface, this paper tries to understand the geological and geographical setting of the area, particularly concerning prehistoric settlements in the Trans-Himalayas. This assemblage consists of assorted artefacts, which include a unifacial chopper, microlithic cores, flakes, blades, bladelets, burin and a large amount of debitage fragments. The majority of artefacts are on quartzite or quartzarenite. Future surveys will be targeted at recovering primary context sites for excavations and absolute dating.
Detrital gold as an indicator mineral
Authors: Chapman Robert J. , Moles Norman R. , Bluemel Britt , Walshaw Richard D. 
Published: September 2021

Abstract
Detrital gold fulfils the criteria of chemical inertia and physical durability required by indicator minerals but it has not found wide application in this role because it may be formed in different deposit types. This problem is soluble, because the generic compositional features of hydrothermal gold differ according to mineralization environment. The wide distribution of gold as a minor component of mineralization where other commodities are the principal exploration target extends the potential of an indicator methodology based on detrital gold to beyond the search for gold itself. Here we highlight how distinctive gold compositional signatures derived from alloy composition and deposit- specific suites of mineral inclusions could contribute to exploration for Cu–Au porphyries, redox-controlled uranium mineralization and ultramafic-hosted PGE mineralization. Future refinement this approach will focus on establishing the spatial distribution of elements at trace levels within gold particle sections using ToF-LA-ICP-MS and application of Exploratory Data Analysis to the resulting datasets. This approach is in its infancy, but aims to develop a classification algorithm useful to researchers irrespective of their previous experience. A pilot study has shown that random forests provide the best approach to establishing gold particle origins.
Location Matters: Profiling Diffuse Type Gastric Cancer At the Single-Cell Level
Authors: Huang Huocong , Brekken Rolf A. 
Published: September 2021

Abstract
Spatial single-cell transcriptomics of primary patient diffuse type gastric cancer reveals distinct cancer and stromal cell differences based on location. Expression of CCL2 by stromal cells in deep tumor regions is highlighted as potentially driving the immunosuppressive microenvironment and enhancing (directly or indirectly) the invasive capacity of tumor cells.
See related article by Jeong et al., p. 6529
Monitoring Circulating Tumor DNA During Surgical Treatment in Patients with Gastrointestinal Stromal Tumors
Authors: Johansson Gustav , Berndsen Marta , Lindskog Stefan , Österlund Tobias , Fagman Henrik , Muth Andreas , Ståhlberg Anders 
Published: September 2021

Abstract
The majority of patients diagnosed with advanced gastrointestinal stromal tumors (GISTs) are successfully treated with a combination of surgery and tyrosine kinase inhibitors (TKIs). However, it remains challenging to monitor treatment efficacy and identify relapse early. Here, we utilized a sequencing strategy based on molecular barcodes and developed a GIST-specific panel to monitor tumor-specific and TKI resistance mutations in cell-free DNA and applied the approach to patients undergoing surgical treatment. Thirty-two patients with GISTs were included, and 161 blood plasma samples were collected and analyzed at routine visits before and after surgery and at the beginning, during, and after surgery. Patients were included regardless of their risk category. Our GIST-specific sequencing approach allowed detection of tumor-specific mutations and TKI resistance mutations with mutant allele frequency &lt; 0.1%. Circulating tumor DNA (ctDNA) was detected in at least one timepoint in nine of 32 patients, ranging from 0.04% to 93% in mutant allele frequency. High-risk patients were more often ctDNA positive than other risk groups (P &lt; 0.05). Patients with detectable ctDNA also displayed higher tumor cell proliferation rates (P &lt; 0.01) and larger tumor sizes (P &lt; 0.01). All patients who were ctDNA positive during surgery became negative after surgery. Finally, in two patients who progressed on TKI treatment, we detected multiple resistance mutations. Our data show that ctDNA may become a clinically useful biomarker in monitoring treatment efficacy in patients with high-risk GISTs and can assist in treatment decision making.
Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer
Authors: El Ghamrasni Samah , Quevedo Rene , Hawley James , Mazrooei Parisa , Hanna Youstina , Cirlan Iulia , Zhu Helen , Bruce Jeff P. , Oldfield Leslie E. , Yang S.Y. Cindy , Guilhamon Paul , Reimand Jüri , Cescon Dave W. , Done Susan J. , Lupien Mathieu , Pugh Trevor J. 
Published: September 2021

Abstract

Whole-genome sequencing of primary breast tumors enabled the identification of cancer driver genes and noncoding cancer driver plexuses from somatic mutations. However, differentiating driver from passenger events among noncoding genetic variants remains a challenge. Herein, we reveal cancer-driver cis-regulatory elements linked to transcription factors previously shown to be involved in development of luminal breast cancers by defining a tumor-enriched catalogue of approximately 100,000 unique cis-regulatory elements from 26 primary luminal estrogen receptor (ER)+ progesterone receptor (PR)+ breast tumors. Integrating this catalog with somatic mutations from 350 publicly available breast tumor whole genomes, we uncovered cancer driver cistromes, defined as the sum of binding sites for a transcription factor, for ten transcription factors in luminal breast cancer such as FOXA1 and ER, nine of which are essential for growth in breast cancer with four exclusive to the luminal subtype. Collectively, we present a strategy to find cancer driver cistromes relying on quantifying the enrichment of noncoding mutations over cis-regulatory elements concatenated into a functional unit.

Implications:
Mapping the accessible chromatin of luminal breast cancer led to discovery of an accumulation of mutations within cistromes of transcription factors essential to luminal breast cancer. This demonstrates coopting of regulatory networks to drive cancer and provides a framework to derive insight into the noncoding space of cancer.
Intranasal Iloprost Prevents Tumors in a Murine Lung Carcinogenesis Model
Authors: Tennis Meredith A. , Smith Alex J. , Dwyer-Nield Lori D. , Keith Robert L. 
Published: September 2021

Abstract

Lung cancer chemoprevention with the prostacyclin analogue iloprost is the most promising approach to date for intercepting progression of premalignant lung lesions in former smokers. Previous preclinical studies of iloprost used oral delivery, but a study modeling delivery directly to the target organ was needed. In vivo and in vitro studies have identified gene expression changes following iloprost treatment, including increased e-cadherin and Ppargγ and decreased COX2 and vimentin. We used tumor counts and gene expression to demonstrate the effectiveness of intranasal delivery of iloprost in a murine model of premalignant adenomas. Intranasal delivery of iloprost reduced adenoma multiplicity 14 weeks after urethane exposure in FVB/N mice compared with untreated urethane controls. Intranasal iloprost reversed urethane-induced gene expression changes in tumors and whole lung. These results correspond to previous studies of oral iloprost and in vitro treatment of human bronchial epithelial cells. This study demonstrates that intranasal delivery of iloprost in a mouse model of lung premalignant lesions is effective chemoprevention. This will be an essential tool for exploring mechanisms and outcomes of iloprost chemoprevention, along with supporting ongoing clinical trials of inhaled iloprost chemoprevention.

Prevention Relevance:
Iloprost is a promising chemoprevention agent for lung cancer and this work describes a new delivery approach in vivo.
Loss of Pulmonary Vascular Volume as a Predictor of Right Ventricular Dysfunction and Mortality in Acute Pulmonary Embolism
Authors: Minhas Jasleen , Nardelli Pietro , Hassan Syed Moin , Al-Naamani Nadine , Harder Eileen , Ash Samuel , Sánchez-Ferrero Gonzalo Vegas , Mason Stefanie , Hunsaker Andetta R. , Piazza Gregory , Goldhaber Samuel Z. , Waxman Aaron B. , Kawut Steven M. , Estépar Raúl San José , Washko George R. , Rahaghi Farbod N. 
Published: September 2021

Background:
In acute pulmonary embolism, chest computed tomography angiography derived metrics, such as the right ventricle (RV): left ventricle ratio are routinely used for risk stratification. Paucity of intraparenchymal blood vessels has previously been described, but their association with clinical biomarkers and outcomes has not been studied. We sought to determine if small vascular volumes measured on computed tomography scans were associated with an abnormal RV on echocardiography and mortality. We hypothesized that decreased small venous volume would be associated with greater RV dysfunction and increased mortality.

Methods:
A retrospective cohort of patients with intermediate risk pulmonary embolism admitted to Brigham and Women’s Hospital between 2009 and 2017 was assembled, and clinical and radiographic data were obtained. We performed 3-dimensional reconstructions of vasculature to assess intraparenchymal vascular volumes. Statistical analyses were performed using multivariable regression and cox proportional hazards models, adjusting for age, sex, lung volume, and small arterial volume.

Results:

Seven hundred twenty-two subjects were identified of whom 573 had documented echocardiography. A 50% reduction in small venous volume was associated with an increased risk of RV dilation (relative risk: 1.38 [95% CI, 1.18–1.63],
P
<0.001), RV dysfunction (relative risk: 1.62 [95% CI, 1.36–1.95],
P
<0.001), and RV strain (relative risk: 1.67 [95% CI, 1.37–2.04],
P
<0.001); increased cardiac biomarkers, and higher 30-day and 90-day mortality (hazard ratio: 2.50 [95% CI, 1.33–4.67],
P
=0.004 and hazard ratio: 1.84 [95% CI, 1.11–3.04],
P
=0.019, respectively).

Conclusions:
Loss of small venous volume quantified from computed tomography angiography is associated with increased risk of abnormal RV on echocardiography, abnormal cardiac biomarkers, and higher risk of 30- and 90-day mortality. Small venous volume may be a useful marker for assessing disease severity in acute pulmonary embolism.
An Unknown Dutch Incunable Recovered
Authors: Kok Ina 
Published: September 2021

Abstract
This article discusses and reproduces a unique copy of a hitherto unknown Dutch incunable. It was recovered at a Belgian auction after 164 years and bought by the Athenaeum Library in Deventer, the Netherlands. Thus, the book returned to the city where it was printed by Jacobus de Breda, between 27 October 1495 and 16 April 1496.
Urban Diplomacy
Authors: Manfredi-Sánchez Juan Luis 
Published: September 2021

Abstract
By examining the great economic and political transformations of our time, it is revealed how cities and their hinterlands have become part of globalisation. The global city has joined the group of actors who develop diplomatic, political and communicative action in a manner that is de facto and lawful. Thus, the city is involved in the formulation of foreign policy at the same time that it proposes its own political agenda, which may or may not be aligned with its own country. The city thereby becomes a source of innovation in the field of diplomacy. The Covid-19 pandemic is accelerating the political and diplomatic role of cities, which have become epicentres of prevention and response in the face of this public health crisis.
Downward Trend in Resident Myringotomy and Tympanostomy Tube Experience
Authors: Dermody Sarah M. , Johng Stephanie Y. , Watkins Mariel O. , Malekzadeh Sonya , Ahn Jaeil , Harley Earl H. 
Published: September 2021

Introduction/Objective: Historically, myringotomy, and the insertion of tympanostomy tubes has served as one of the initial surgical training experiences for residents. Resident experience with this procedure since the introduction of pneumococcal conjugate vaccines has not been well described in the literature. The objective of this study was to identify trends in resident training experience with chronic otitis media-related surgeries, such as myringotomy and tympanostomy tube placement. While multiple factors influence resident experience, we hypothesize that resident experience has decreased since the introduction of the pneumococcal 13-valent conjugate vaccine (PCV13). Methods and Materials: In a retrospective review of Accreditation Council for Graduate Medical Education (ACGME) National Data Reports, mean number of myringotomy and tympanostomy tube cases logged in the Resident Case Log System from 2006 to 2019 were collated and plotted against years to identify monotonic trends. Mann-Whitney U test was used to compare pre-PCV13 era and post-PCV13 era data. Results: Since the introduction of PCV13, there is a national decreasing trend in the myringotomy and tympanostomy tube placement by otolaryngology residents ( P = .001). Conclusions: Otologic surgeries are an important part of resident education and historically have served as one of the initial surgical training experiences for residents. There has been a significant reduction in the number of myringotomy and tympanostomy procedures performed by otolaryngology residents in the past decade. While multiple factors influence resident experience, it is possible that introduction of PCV13 has impacted resident exposure to myringotomy and tympanostomy tube placement. Resident proficiency with this procedure has likely not been affected by introduction of PCV13. Data should be reassessed in 5 years to determine if an impact of the PCV13 vaccine on resident training is evident.
Will high school students ‘rethink their drink’? Findings from an impact evaluation of a healthy beverage curriculum
Authors: Strochlic Ron , Woodward-Lopez Gail , Plank Kaela , Hewawitharana Sridharshi , Richardson Jackie , Whetstone Lauren 
Published: September 2021

Objective: To promote healthy beverage consumption among 9–12 grade students (ages 14–18) by means of a 4-week curriculum promoting increased awareness of drinks containing added sugar and the association between sugar-sweetened beverage consumption and health risks. Design: Quasi-experimental pre–post design. Setting: High schools in Northern California with at least 50% of students eligible for free or reduced-price meals. Method: A 4-lesson version of the Rethink Your Drink high school curriculum was piloted in three high schools in two northern California counties. Two high schools in the same area served as comparison sites. A survey of beverage-related knowledge, behaviours, perceptions and self-efficacy was administered to intervention and comparison students before and after the intervention. Focus groups with students and an online survey and semi-structured interviews with teachers were conducted following the intervention. Results: Intervention students reported significantly greater frequency of reading Nutrition Facts labels and understanding of beverage choice influences and decreased consumption of diet soda than comparison students. A decrease of 0.26 times per day in consumption of sugar-sweetened beverages relative to the comparison group was not significant. Conclusion: The intervention resulted in some positive outcomes, but improvements in targeted beverage consumption were not significant. Students and teachers want shorter, more engaging and experiential curricula that build on previous learning. Findings point to actionable recommendations for improvement of high school healthy beverage curricula and suggest the need for reinforcement using a multi-level approach.
Family Disruption and Parenting During the COVID-19 Pandemic
Authors: Schmeer Kammi K. , Singletary Britt , Purtell Kelly M. , Justice Laura M. 
Published: September 2021

Using unique data from an economically and racially diverse sample of 448 caregivers with young children (ages 4–9 years) in Ohio, we assess multiple sources of family social and economic disruptions and their associations with parenting activities during the COVID-19 stay-at-home order. Caregivers reported extensive social and economic challenges during this time, while also increasing (on average) their time spent in play/learning activities. Time spent in discipline was less likely to increase during this period. We found significant associations among disadvantaged social conditions/experiences and parenting, and that some effects were moderated by 2019 household income status. Unexpectedly, changes in economic conditions, particularly caregiver job loss, were associated with higher odds of increases in reading/telling stories time across household income groups. Overall, findings indicate that social conditions associated with the stay-at-home period of COVID-19 might have been more disruptive to parenting for caregivers with young children than the short-term economic changes.
A pre-clinical animal study of a novel mechanical-only ablation device treatment for superficial venous disease
Authors: Kabnick Lowell S , Phelan Nigel , Cummins Seán , O Hynes Seán 
Published: September 2021

Objective Current minimally invasive techniques for ablation in superficial venous reflux are limited to thermal based systems requiring tumescent anesthesia, non-thermal chemical sclerosants and permanent glue implantation. The aim of this feasibility study was to determine the safety and efficacy of a novel mechanical-only ablation (MOA) device called EnVena, in a recognised large animal model with chronic follow up. Methods Venous ablation of six lateral saphenous veins in three sheep was performed using the EnVena device. Luminal patency and vein wall fibrosis were evaluated by histologic analysis at 51 and 89 days. Results All treated veins demonstrated fibrotic occlusion in contiguous segments at 51 and 89 days on histological analysis. From 45 consecutive segments spanning the treatment length across the six treated veins, 26 (57%) were fully occluded, 7 (16%) were impinged or partially occluded and 12 (27%) were open. There were no device related complications during the follow up period. Conclusions A purely mechanical approach to superficial venous ablation demonstrated safety and efficacy in a recognized large animal model based on histological findings.
Allograft Versus Autograft Osteochondral Transplant for Chondral Defects of the Talus: Systematic Review and Meta-analysis
Authors: Migliorini Filippo , Maffulli Nicola , Baroncini Alice , Eschweiler Jörg , Knobe Matthias , Tingart Markus , Schenker Hanno 
Published: September 2021

Background: It is unclear whether the results of osteochondral transplant using autografts or allografts for talar osteochondral defect are equivalent. Purpose: A systematic review of the literature was conducted to compare allografts and autografts in terms of patient-reported outcome measures (PROMs), MRI findings, and complications. Study Design: Systematic review; Level of evidence, 4. Methods: This study was conducted according to the PRISMA guidelines. The literature search was conducted in February 2021. All studies investigating the outcomes of allograft and/or autograft osteochondral transplant as management for osteochondral defects of the talus were accessed. The outcomes of interest were visual analog scale (VAS) score for pain, American Orthopaedic Foot and Ankle Society (AOFAS) score, and Magnetic Resonance Observation of Cartilage Repair Tissue (MOCART) score. Data concerning the rates of failure and revision surgery were also collected. Continuous data were analyzed using the mean difference (MD), whereas binary data were evaluated with the odds ratio (OR) effect measure. Results: Data from 40 studies (1174 procedures) with a mean follow-up of 46.5 ± 25 months were retrieved. There was comparability concerning the length of follow-up, male to female ratio, mean age, body mass index, defect size, VAS score, and AOFAS score ( P > .1) between the groups at baseline. At the last follow-up, the MOCART (MD, 10.5; P = .04) and AOFAS (MD, 4.8; P = .04) scores were better in the autograft group. The VAS score was similar between the 2 groups ( P = .4). At the last follow-up, autografts demonstrated lower rate of revision surgery (OR, 7.2; P < .0001) and failure (OR, 5.1; P < .0001). Conclusion: Based on the main findings of the present systematic review, talar osteochondral transplant using allografts was associated with higher rates of failure and revision compared with autografts at midterm follow-up.