bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts and implications for the post-COVID city: the case of Toronto
Authors: Brail Shauna , Kleinman Mark 
Published: June 2022

Abstract
Since the onset of COVID-19, scholars have questioned whether the pandemic will alter the fundamentals propelling the growth of global cities. Using a case study of Toronto, the paper examines and analyses changes impacting the city because of the pandemic, with a focus on work, mobility and housing. In assessing pandemic-related disruption, it outlines the experiences of the early phases of recovery and expectations of continued uncertainty. Moving through and beyond COVID-19, Toronto appears unlikely to move up the rankings of global cities. The city’s status as a second-tier global city is an enduring competitive advantage, likely to persist post-COVID.
Relevance of pre-existing anaemia for patients admitted for acute coronary syndrome to an intensive care unit: a retrospective cohort analysis of 7418 patients
Authors: Wischmann Patricia , Bruno Raphael Romano , Wernly Bernhard , Wolff Georg , Afzal Shazia , Rezar Richard , Cramer Mareike , Heramvand Nadia , Kelm Malte , Jung Christian 
Published: June 2022

Abstract

Aims
Patients with acute coronary syndrome (ACS) frequently suffer from anaemia, but its role in patients admitted to an intensive care unit (ICU) is unclear. This analysis evaluates the prognostic relevance of different degrees of anaemia and their specific impact on disease severity and the outcome in critically ill ACS patients.

Methods and results
and results The multi-centre electronic Intensive Care Unit Collaborative Research Database was used, and all patients admitted with ACS were included in a retrospective analysis. Anaemia and its degrees were defined according to the criteria by the World Health Organization. A multi-level logistic regression analysis was used to fit three sequential regression models for the binary primary outcome of hospital mortality. A total of 7418 patients were included; 3437 patients (46%) had anaemia on admission. Patients with anaemia were significantly older [61 (53–70) vs. 70 (61–78) years, P &lt; 0.001], more often female (P &lt; 0.001), and required an increased rate of vasopressor use (P &lt; 0.001) and mechanical ventilation (P &lt; 0.001). With the higher Sequential organ failure assessment score (1 vs. 2; P &lt; 0.001) and Acute Physiology And Chronic Health Evaluation (35 vs. 47; P &lt; 0.001) scores, a higher degree of anaemia was associated with prolonged ICU stay (2 vs. 5 days, P &lt; 0.001). Even patients with mild anaemia needed significantly from more intensive treatment and suffered worse outcome. Intensive care unit and hospital mortality were inversely associated with haemoglobin levels.

Conclusion
Nearly half of critically ill patients with ACS suffer from anaemia, which is associated with increased illness severity, complex ICU procedures, and mortality—even in mild anaemia. Haemoglobin on admission is an independent factor for adverse outcome.
The use of antibiotics in acute oral health patients presenting at public dental clinics in the Western Sydney region
Authors: Nguyen Stephanie , Ahmed Lamis , Villarosa Amy , George Ajesh , Yaacoub Albert 
Published: June 2022

Abstract

Background
There is a limited need for antibiotics when treating oral health problems, yet they are often prescribed, increasing risk of antimicrobial resistance (AMR). With AMR a threat to public health, the objectives of this study were to assess the frequency, suitability, and factors associated with antibiotic prescriptions for acute dental problems across Greater Western Sydney public dental clinics.

Methods
Patients’ reason for attending, details of any antibiotics use, and the treating dental practitioner’s clinical examination and diagnosis were compared to current prescribing guidelines, and logistic regression was used to identify predictors of antibiotic prescription.

Results
In all, 1,071 patients participated in the study, and 15.9% reported to using antibiotics for their dental problem. Over three-quarters obtained the antibiotics from their general medical practitioner (GMP). A high prevalence of antibiotics were not indicated for the patient’s complaint (71.8%) including for those with a history of extraction, pain, or intraoral swelling, who had significantly higher odds of antibiotic prescription (OR &gt; 9). The antibiotic type prescribed was generally suitable.

Conclusions
In summary, the data suggest that the majority of antibiotics were inappropriately prescribed for the patient’s dental complaints and there is a need for interventions to improve compliance with antibiotic prescribing guidelines.
A Decade of GigaScience: GigaDB and the Open Data Movement
Authors: Armit Chris , Tuli Mary Ann , Hunter Christopher I 
Published: June 2022

Abstract
The increasingly multidisciplinary nature of scientific research necessitates a need for Open Data repositories that can archive data in support of publications in scientific journals. Recognising this need, even before GigaScience launched in 2012, GigaDB was already in place and taking data for a year before (making it 11 this year). Since GigaDB launched, there has been a consistent growth in this resource in terms of data volume, data discoverability and data re-use. In this commentary, we provide a retrospective of key changes over the last decade, and the role of Data Curation in enhancing the user experience. Furthermore we explore a much needed emphasis on enabling researchers to interact with and explore datasets prior to data download.
A decade of GigaScience: A perspective on conservation genetics
Authors: O'Brien Stephen J 
Published: June 2022

Abstract
Wide interest in species conservation is young. To many it began early in 1903 when Teddy Roosevelt and John Muir set up a camp under the Grizzly Giant in the Mariposa Grove of California's Yosemite Valley. Over three days they decided to broaden the US National Park footprint across the USA. Conservationists were inspired in the coming decades by the writings of wildlife conservation pioneers—Osa Johnson (I Married Adventure), Karen Blixen (Out of Africa) and Rachel Carson (The Silent Spring). Countless crusaders developed a passion for preserving dwindling species in those early days, yet none of these conservation advocates mentioned the word genetics, let alone genomics. The genome sequencing projects that have followed on from these have brought in an enormous amount of data, including whole genome sequences for thousands of non-human species, both individual and population wide. This huge resource has revolutionized conservation genetics, bringing in ways to assess the health of at-risk populations, devise genetic-driven breeding strategies, and other means to attempt to preserve the over 1 million species (and growing) under threat today.
A Serum Biomarker Panel Can Accurately Identify Mucosal Ulcers in Patients With Crohn’s Disease
Authors: Holmer Ariela K , Boland Brigid S , Singh Siddharth , Neill Jennifer , Le Helen , Miralles Ara , Collins Angelina E , Sandborn William J , Dulai Parambir S 
Published: June 2022

AbstractBackgroundThe Endoscopic Healing Index (EHI) is a serum biomarker panel that can predict endoscopic inflammation in Crohn’s disease (CD).MethodsPaired serum samples with endoscopies from adult patients participating in a prospective biobank (June 2014 to December 2018) were analyzed post hoc. Diagnostic performance for EHI was assessed against the individual parameters of the Simple Endoscopic Score for CD using previously identified cutoffs. Confounders for EHI performance were identified using logistic regression.ResultsA total of 205 CD patients were included (50% male, median age 37 years). An EHI of 20 points was sensitive for ruling out any ulcers (85%; 95% confidence interval [CI], 77%-91%) and large (5-20 mm) or very large (&gt;20 mm) ulcers (93%; 95% CI, 84%-97%). An EHI of 50 points was specific for ruling in any ulcers (86%; 95% CI, 76%-92%) and large or very large ulcers (87%; 95% CI, 79%-92%). After accounting for total extent of inflamed mucosa, strictures, and disease location, each 20-point increase in EHI was associated with a 1.7-fold increased probability for the presence of large or very large ulcers (adjusted odds ratio, 1.7; 95% CI, 1.1-2.6).ConclusionsThe EHI was independently associated with ulcer size and accurately identified large or very large ulcers. A cutoff of 50 points can reliably rule in mucosal ulcers and allow for treatment adjustment. A cutoff of 20 points can reliably rule out mucosal ulcers and signal completion of treatment adjustment algorithms.
Decomposable Product Systems Associated to Non-stationary Poisson Processes
Authors: Shanmugasundaram Sundar 
Published: June 2022

AbstractLet $P$ be a closed convex cone in $\mathbb {R}^{d}$, which we assume is pointed and spanning, i.e, $P \cap -P=\{0\}$ and $P-P=\mathbb {R}^{d}$. We demonstrate that, when $d \geq 2$, in contrast to the one-parameter situation, Poisson processes on $\mathbb {R}^{d}$, with intensity measure absolutely continuous with respect to the Lebesgue measure, restricted to $P$-invariant closed subsets, provide us with a source of examples of decomposable $E_0$-semigroups that are not always CCR flows.
The Frobenius Characteristic of the Orlik–Terao Algebra of Type A
Authors: Pagaria Roberto 
Published: June 2022

AbstractWe provide a new virtual description of the symmetric group action on the cohomology of ordered configuration space on $SU_2$ up to translations. We use this formula to prove the Moseley–Proudfoot–Young conjecture. As a consequence we obtain the graded Frobenius character of the Orlik–Terao algebra of type $A_n$.
Metaphors in Neo-Confucian Korean philosophy
Authors: Kim Hannah H 
Published: June 2022

Abstract
A metaphor is an effective way to show how something is to be conceived. In this article, I look at two Neo-Confucian Korean philosophical contexts—the Four-Seven debate and Book of the Imperial Pivot—and suggest that metaphors are philosophically expedient in two further contexts: when both intellect and emotion must be addressed; and when the aim of philosophizing is to produce behavioral change. Because Neo-Confucians had a conception of the mind that closely connected it to the heart (心 xin), metaphor’s empathy-inducing and perspective-giving capacities made it an especially helpful mode of philosophizing in the history of Korean philosophy.
Morphometrics of the Tropical Bed Bug (Hemiptera: Cimicidae) From Cape Coast, Ghana
Authors: Deku Godwin , Combey Rofela , Doggett Stephen L 
Published: June 2022

AbstractBed bugs, Cimex lectularius (L.) (Hemiptera: Cimicidae) and Cimex hemipterus (F.), have become established worldwide in recent years largely due to the development of insecticide resistance. However, limited attention has been given to ongoing morphological and macroevolutionary changes within the species and their populations, which could have implications for their control. Here, we evaluated whether bed bugs of the species C. hemipterus inhabiting different communities in Cape Coast, Ghana are undergoing segregation, which could lead to possible speciation. We also aimed to provide a morphometric description of all nymphal stages. Nine-bed bug populations of C. hemipterus were field-collected in Cape Coast and were subjected to geometric morphometric analysis. The multivariate parameters applied distinguished various populations from each of the locations, indicating the presence of morphologically distinct subpopulations of C. hemipterus. Shape-based segregation and shape changes associated with the insect pronotum (which is an important taxonomic character in the Cimicidae) were evident across the populations. Through this comparative study of C. hemipterus, we showed that possible subpopulations of this bed bug are being spread from Ghana. The nymphal stages (first–fifth) of C. hemipterus were distinguished by the length of the last three antennal segment and pronota width; such information contributes to the taxonomic knowledge of the species.
Targeted Next-Generation Sequencing Reveals Divergent Clonal Evolution in Components of Composite Pleomorphic Xanthoastrocytoma-Ganglioglioma
Authors: Lucas Calixto-Hope G , Davidson Christian J , Alashari Mouied , Putnam Angelica R , Whipple Nicholas S , Bruggers Carol S , Mendez Joe S , Cheshier Samuel H , Walker Jeffrey B , Ramani Biswarathan , Cadwell Cathryn R , Sullivan Daniel V , Lu Rufei , Mirchia Kanish , Van Ziffle Jessica , Devine Patrick , Goldschmidt Ezequiel , Hervey-Jumper Shawn L , Gupta Nalin , Oberheim Bush Nancy Ann , Raleigh David R , Bollen Andrew , Tihan Tarik , Pekmezci Melike , Solomon David A , Phillips Joanna J , Perry Arie 
Published: June 2022

Abstract
Composite pleomorphic xanthoastrocytoma-ganglioglioma (PXA-GG) is an extremely rare central nervous system neoplasm with 2 distinct but intermingled components. Whether this tumor represents a “collision tumor” of separate neoplasms or a monoclonal neoplasm with divergent evolution is poorly understood. Clinicopathologic studies and capture-based next generation sequencing were performed on extracted DNA from all available PXA-GG at 2 medical centers. Five PXA-GG were diagnosed in 1 male and 4 female patients ranging from 13 to 25 years in age. Four arose within the cerebral hemispheres; 1 presented in the cerebellar vermis. DNA was sufficient for analysis in 4 PXA components and 3 GG components. Four paired PXA and GG components harbored BRAF p.V600E hotspot mutations. The 4 sequenced PXA components demonstrated CDKN2A homozygous deletion by sequencing with loss of p16 (protein product of CDKN2A) expression by immunohistochemistry, which was intact in all assessed GG components. The PXA components also demonstrated more frequent copy number alterations relative to paired GG components. In one PXA-GG, shared chromosomal copy number alterations were identified in both components. Our findings support divergent evolution of the PXA and GG components from a common BRAF p.V600E-mutant precursor lesion, with additional acquisition of CDKN2A homozygous deletion in the PXA component as is typically seen in conventional PXA.
Insights into diet-associated oxidative pathomechanisms in inflammatory bowel disease and protective effects of functional amino acids
Authors: Ji Yun , Yang Ying , Sun Shiqiang , Dai Zhaolai , Ren Fazheng , Wu Zhenlong 
Published: June 2022

Abstract
There has been a substantial rise in the incidence and prevalence of clinical patients presenting with inflammatory bowel disease (IBD), which includes Crohn’s disease and ulcerative colitis. Accumulating evidence has corroborated the view that dietary factors (particularly diets with high levels of saturated fat or sugar) are involved in the development and progression of IBD, which is predominately associated with changes in the composition of the gut microbiota and an increase in the generation of reactive oxygen species. Notably, the ecological imbalance of the gut microbiome exacerbates oxidative stress and inflammatory responses, leading to perturbations of the intestinal redox balance and immunity, as well as mucosal integrity. Recent findings have revealed that functional amino acids, including L-glutamine, glycine, L-arginine, L-histidine, L-tryptophan, and hydroxyproline, are effectively implicated in the maintenance of intestinal redox and immune homeostasis. These amino acids and their metabolites have oxygen free-radical scavenging and inflammation-relieving properties, and they participate in modulation of the microbial community and the metabolites in the gut. The principal focus of this article is a review of recent advances in the oxidative pathomechanisms of IBD development and progression in relation to dietary factors, with a particular emphasis on the redox and signal transduction mechanisms of host cells in response to unbalanced diets and enterobacteria. In addition, an update on current understanding of the protective effects of functional amino acids against IBD, together with the underlying mechanisms for this protection, have been provided.
Disparities in Electronic Patient Health Portal Use During Pregnancy According to Race, Ethnicity, and Language [A311]
Authors: Grimaldi Carolina Gomez , Delaney Tessa , Garrison Etoi 
Published: June 2022

INTRODUCTION:
Use of electronic patient health portals (EMR-PHP) was stressed during the first year of the COVID-19 pandemic as an important vehicle for equitable access to healthcare information. Disparate use of the EMR-PHP according to race, age, ethnicity, and insurance status has been reported. Less is known about disparities associated with EMR-PHP use in pregnancy. Further, the effect of the COVID-19 pandemic on EMR-PHP utilization according to race/ethnicity is unclear.

METHODS:
Institutional review board approval was obtained through Vanderbilt University Medical Center. A retrospective cohort study of patients who delivered and received prenatal care between 2018 and October 2021 was performed. Demographic and EMR-PHP activation/use data were stratified by race, ethnicity, and language. Differences in EMR-PHP registration/use in 2019 and in 2020, during the first year of the COVID-19 pandemic, were determined according to race, ethnicity, and primary language.

RESULTS:
In 2019-2020, an average of 4,400 patients delivered and self-identified as: White (54%), Black (17%), Hispanic (17%), English language (EL) (80%), and Spanish language (SL) (20%). EMR-PHP registration/use increased in 2020 for all patients. EMR-PHP registration increased more in Hispanic (44% increase 2020 vs 2019) and SL (54% increase 2020 vs 2019) patients compared to White and EL patients (P<.05). Despite significant gains in 2020, Hispanic and SL patients were less likely to register/use the EMR-PHP compared to White and EL patients at the time of delivery (P<.01).

CONCLUSION:
Significant disparities in EMR-PHP registration and use were identified in pregnancy. The patient, provider, and digital health access factors underlying low rates of EMR-PHP use in underserved populations require further investigation.
Effect of Menopause on Genital Human Papillomavirus Infection and the Microbiota in a Hispanic Cohort [A320]
Authors: Reguero-Cadilla Laura , Dominicci-Maura Anelisse , Godoy-Vitorino Filipa , Romaguera Josefina 
Published: June 2022

INTRODUCTION:
Genital human papillomavirus (HPV) infections are very commonly diagnosed sexually transmitted infections. High-risk HPV types are strongly linked to cervical cancer. The composition of the cervicovaginal microbiota in menopausal and non-menopausal Hispanic people and its relation to HPV infection has not been thoroughly studied. Preliminary data from our group have shown that these changes are also observed in non-menopausal women who are HPV positive and those with high-grade lesion. The association of HPV with the microbiota in menopausal Hispanic women remains unknown. Hence, we hypothesize that menopause creates an environment favorable for HPV infection due to changes associated with the vaginal microbiota.

METHODS:
Cervical swabs were obtained from 330 women (75 menopausal and 255 non-menopausal women) who visited colposcopy clinics in San Juan, Puerto Rico, after patients' consent, as part of an institutional review board–approved study (#1050114). A questionnaire accompanied collection of samples. Genomic DNA was extracted from swabs for 16S rDNA amplification and HPV genotyping (PR Science Technology and Research Trust #2020-00112).

RESULTS:
Analysis revealed that non-menopausal women have higher HPV infection rates than menopausal women (77.25% vs. 60%, respectively), with similar rates of high-risk HPV (43.13% vs 40%, respectively). Menopausal women have higher alpha diversity and lower abundances of Lactobacillus.

CONCLUSION:
Preliminary data show that even though menopausal women have higher diversity, this does not seem to affect HPV infection rates. Nonetheless, it is important to further develop study models to better relate microbial communities and specific HPV infection types to prevent cervical disease.
Medication Management of Early Pregnancy Loss: The Impact of the U.S. Food and Drug Administration Risk Evaluation and Mitigation Strategy [A289]
Authors: Neill Sara , Goldberg Alisa , Janiak Elizabeth 
Published: June 2022

INTRODUCTION:
Early pregnancy loss (EPL) occurs in 1 million U.S. patients annually. Mifepristone pretreatment for medication management increases efficacy but requires compliance with the U.S. Food and Drug Administration Risk Evaluation and Mitigation Strategy (REMS) program. This study examined how REMS influences mifepristone use for EPL among obstetrician–gynecologists (ob-gyns) in Massachusetts.

METHODS:
This mixed methods study included in-depth qualitative interviews focused on EPL management analyzed under a thematic analysis framework using multiple coders and a consensus method. Qualitative data informed development of a survey fielded among all ob-gyns in Massachusetts identified through the American Medical Association Physician Masterfile. The Partners IRB deemed this study exempt.

RESULTS:
Nearly all interviewees (17 of 19, 89%) listed the REMS as a barrier to mifepristone use. Barriers included belief that the REMS indicated mifepristone was not available to general ob-gyns, lack of pharmacy dispensing, and concerns about signing the required prescriber agreement. The REMS sometimes gave hospital or pharmacy leadership the impression that mifepristone is dangerous, prolonging protocol development and implementation. A total of 197 physicians responded to a subsequent survey. Of those, 37% did not offer mifepristone for EPL, and 40% were not or only somewhat familiar with mifepristone's REMS program. Among those who reported on barriers to mifepristone use (n=57), the most common was uncertainty with how to comply with the REMS (53%); 73% reported that removing these regulations would help them use mifepristone for EPL.

CONCLUSION:
The FDA REMS program for mifepristone impedes evidence-based medication management of EPL. Removing the REMS would improve access to this best practice.