bluuebunny/crossref_metadata_2025_split huggingface dataset:
1203Predictors of treatment and survival in hepatocellular carcinoma patients: A Bayesian parametric survival analysis
Authors: Taye Belaynew , Clark Paul , Hartel Gunter , Powell Elizabeth , Valery Patricia 
Published: September 2021

Abstract

Background
Culturally and linguistically diverse communities face several challenges to receiving screening and curative treatment of hepatocellular carcinoma (HCC). We reported the predictors of receipt of treatment and survival in a cohort of patients diagnosed with HCC in Southeast Queensland.

Methods
Data from 1651 HCC patients (147 migrants) followed between January 1, 2007, and December 31, 2016 were analyzed using chi-square statistic to test for the association between socio-economic variables and receipt of treatment. Bayesian Weibull Accelerated Failure Time regression was used to identify predictors of time to death, and we reported time ratios.

Results
Receipt of surgical resection for HCC was associated with non-metropolitan residence (P=0.02), non-English language (P&lt;0.001), country of origin (P&lt;0.001), and hepatitis B virus etiology (P&lt;0.001). The median survival time after HCC diagnosis was 9.0 months (interquartile range 2.0‒24.0). The strongest predictors of survival were undifferentiated tumor at presentation (time ratio (TR)=0.30, 95% credible interval (CrI) 0.23‒0.39), age ≥70 years (TR = 0.42, 95%CrI 0.34‒0.53), living in a remote area (TR = 0.67, 95%CrI 0.55‒0.80), and presence of ≥ 1 comorbidity (TR = 0.69 95%CrI 0.54‒0.90).

Conclusions
Improving access to HCC surveillance and uptake of timely curative treatment for persons living in remote areas and having socioeconomic disadvantage may help patients present to clinic with early stage tumor and provide better survival.

Key messages
Remoteness of residence is associated with late presentation, low rate of receipt of treatment and predicts survival of patients with HCC.
794Bisphosphonate use and risk of ovarian cancer, a nested case-control study using national health data
Authors: Tuesley Karen , Webb Penelope , Protani Melinda , Spilsbury Katrina , Pearson Sallie-Anne , Coory Michael D , Donovan Peter , Stewart Louise M , Pandeya Nirmala , Jordan Susan 
Published: September 2021

Abstract

Background
Epithelial ovarian cancer (EOC) is the eighth most common cancer in women, has a five-year survival of ∼45%, and very few established modifiable risk factors. Some evidence suggests that bisphosphonates could have chemopreventive benefits, but few epidemiological studies have investigated the association between bisphosphonate use and incidence of EOC.

Methods
We conducted a nested case-control study using linked administrative data. We identified 9,367 women over 50 years diagnosed with EOC (cases) from 2004 to 2013, and for each case identified five controls from the Australian Medicare Enrolment database matched by age, state, area of residence, and area-level socioeconomic disadvantage. We assessed the associations between bisphosphonate use using dispensed prescription data (ever use, duration and dose) and EOC (overall, by histotype), adjusting for comorbidities and MHT use. We conducted sensitivity analyses in women with complete ascertainment of dispensing claims and for residents of one Australian state that had linked with data linked to hospital procedures, including oophorectomy.

Results
Our analyses show an inverse association between bisphosphonate use and risk of EOC overall (OR = 0.81, 95%CI:0.75-0.88), and for endometrioid (OR = 0.51, 95%CI:0.33-0.79) and serous (OR = 0.84, 95%CI:0.75-0.93) histotypes. There was some evidence that higher dose and duration were associated with a greater reduction in risk. Results from sensitivity analyses were not appreciably different.

Conclusions
Bisphosphonate use was associated with lower risk of EOC, suggesting bisphosphonates may reduce risk of ovarian cancer development.

Key messages
Bisphosphonates may protect against development of serous and endometrioid ovarian cancers.
566Ear infection trajectories and academic, behavioural and quality of life outcomes: A population-based longitudinal study
Authors: Wang Jing , Quach Jon , Sung Valerie , Carew Peter , Wake Melissa 
Published: September 2021

Abstract

Background
Middle ear infection is a common disease in childhood. Outcomes might vary by its patterns and persistence over time. We aimed to investigate 1) typical trajectories of ear infections throughout childhood and 2) their associations with child outcomes.

Methods
Design & Participants: Two parallel cohorts assessed biennially from 2004 to 2014 spanning ages 0-1 to 10-11 years (B cohort, n = 3721) and ages 4-5 to 14-15 years (K cohort, n = 3489) in the Longitudinal Study of Australian Children. Ear infection: Parent-reported ongoing ear infections (B: waves 1-6; K: waves 1, 2, 4, 5). Outcomes (wave 6): National academic standardized test, teacher-reported learning, parent and teacher-reported behaviour and self-reported quality of life. Analysis: Latent class models identified ear infection trajectories. Linear regression quantified associations between trajectories and outcomes.

Results
Four probability trajectories of ear infection emerged in both cohorts: “consistently low” (B 86.2%, K 87.0%), “moderate to low” (5.5%, 9.7%), “low to moderate” (7.0%, 1.5%), and “consistently high” (1.4%, 1.8%). In K cohort, the “consistently high” group had the worst outcomes (effect sizes 0.2-0.8 SDs), with effect sizes largest for psychosocial and language outcomes. “Moderate to low” and “low to moderate” groups showed no to marginal academic associations, but behaviour and quality of life were 0.2-0.3 SDs poorer than the “consistently low” group. Similar but attenuated associations were seen in B cohort.

Conclusions
Sizable adverse outcomes followed the consistently high trajectory, suggesting cumulative rather than age-dependent burden. Additional information about comorbidities, predictors and objective presence of ear infections could inform causal relationships.

Key messages
Parent-reported ear infections follow four childhood trajectories (consistently low, moderate to low, low to moderate, consistently high). Sizable adverse outcomes follow the consistently high trajectory.
1230Should multiple imputation be stratified by exposure group when estimating causal effects via outcome regression?
Authors: Zhang Jiaxin , Ghazaleh Dashti S. , Carlin John B. , Lee Katherine J. , Moreno-Betancur Margarita 
Published: September 2021

Abstract

Background
Outcome regression remains widely applied for estimating causal effects in observational studies, in which causal inference is conceptualised as emulating a randomized controlled trial (RCT). Multiple imputation (MI) is a commonly used method for handling missing data, but while in RCTs it has been shown that MI should be conducted by treatment group to reduce bias, whether imputation should be conducted by exposure group in observational studies has not been studied.

Methods
We conducted a simulation study to evaluate the performance of seven methods for handling missing data: Complete-case analysis (CCA), MI of main effect, MI with interactions (between exposure and: outcome, a strong confounder, outcome and a strong confounder, all incomplete), and MI conducted by exposure group. We simulated data based on an example from the Victorian Adolescent Health Cohort Study. Three exposure prevalences and seven outcome generation models were considered, the latter ranging from no interaction to strong-positive or negative exposure-confounder interaction. Various missingness scenarios were examined: with incomplete outcome only or also incomplete confounders, and three levels of complexity regarding the missingness mechanism.

Results
For all scenarios, MI by exposure led to the least bias, followed by MI approaches that included exposure-confounder interactions.

Conclusions
If MI is adopted in outcome regression, we recommend conducting MI by exposure group and, when not feasible, including exposure-confounder interactions in the imputation model.

Key messages
Similar to RCTs, MI should be conducted by exposure group when estimating average causal effects using outcome regression in observational studies.
Moderately Discontinuous Homotopy
Authors: Fernández de Bobadilla Javier , Heinze Sonja , Pe Pereira Maria 
Published: August 2021

Abstract
We introduce a metric homotopy theory, which we call moderately discontinuous homotopy, designed to capture Lipschitz properties of metric singular subanalytic germs. It matches with the moderately discontinuous homology theory recently developed by the authors and E. Sampaio. The $k$-th MD homotopy group is a group $MDH^b_{\bullet }$ for any $b\in [1,\infty ]$ together with homomorphisms $MD\pi ^b\to MD\pi ^{b^{\prime}}$ for any $b\geq b^{\prime}$. We develop all its basic properties including finite presentation of the groups, long homotopy sequences of pairs, metric homotopy invariance, Seifert van Kampen Theorem, and the Hurewicz Isomorphism Theorem. We prove comparison theorems that allow to relate the metric homotopy groups with topological homotopy groups of associated spaces. For $b=1$, it recovers the homotopy groups of the tangent cone for the outer metric and of the Gromov tangent cone for the inner one. In general, for $b=\infty $, the $MD$-homotopy recovers the homotopy of the punctured germ. Hence, our invariant can be seen as an algebraic invariant interpolating the homotopy from the germ to its tangent cone. We end the paper with a full computation of our invariant for any normal surface singularity for the inner metric. We also provide a full computation of the MD-homology in the same case.
ProjectFlow: a configurable workflow management application for point of care research
Authors: Dhond Rupali , Elbers Danne , Majahalme Nilla , Dipietro Svitlana , Goryachev Sergey , Acher Ryan , Leatherman Sarah , Anglin-Foote Tori , Liu Qingzhu , Su Shaoyu , Seerapu Ramana , Hall Robert , Ferguson Ryan , Brophy Mary T , Ferraro Jeff , DuVall Scott L , Do Nhan V 
Published: September 2021

Abstract

Objective
To best meet our point-of-care research (POC-R) needs, we developed ProjectFlow, a configurable, clinical research workflow management application. In this article, we describe ProjectFlow and how it is used to manage study processes for the Diuretic Comparison Project (DCP) and the Research Precision Oncology Program (RePOP).

Materials and methods
The Veterans Health Administration (VHA) is the largest integrated health care system in the United States. ProjectFlow is a flexible web-based workflow management tool specifically created to facilitate conduct of our clinical research initiatives within the VHA. The application was developed using the Grails web framework and allows researchers to create custom workflows using Business Process Model and Notation.

Results
As of January 2021, ProjectFlow has facilitated management of study recruitment, enrollment, randomization, and drug orders for over 10 000 patients for the DCP clinical trial. It has also helped us evaluate over 3800 patients for recruitment and enroll over 370 of them into RePOP for use in data sharing partnerships and predictive analytics aimed at optimizing cancer treatment in the VHA.

Discussion
The POC-R study design embeds research processes within day-to-day clinical care and leverages longitudinal electronic health record (EHR) data for study recruitment, monitoring, and outcome reporting. Software that allows flexibility in study workflow creation and integrates with enterprise EHR systems is critical to the success of POC-R.

Conclusions
We developed a flexible web-based informatics solution called ProjectFlow that supports custom research workflow configuration and has ability to integrate data from existing VHA EHR systems.
Allocation strategies of carbon, nitrogen and phosphorus following a gradient of wildfire severities
Authors: Song Zhaopeng , Li Zhaolei , Luo Yiqi , Liu Yanhong 
Published: August 2021

AbstractWildfire is crucial in the regulation of nutrient allocation during the succession of boreal forests. However, the allocation strategies of carbon (C), nitrogen (N) and phosphorus (P) between leaves and fine roots in response to wildfire severities remain poorly studied. We aimed to explore the allocation strategies of C, N and P between leaves and fine roots among different fire severities. We selected four wildfire severities (unburned, low, moderate and high severity) after 10 years recovery in the Great Xing’an Mountains, northeast China, and compared C, N and P concentrations in leaves and fine roots of all species among fire severities using stoichiometry theory and allometric growth equations. Compared with unburned treatment, C concentrations in leaves and fine roots increased at low severity, and leaf N concentration was the greatest at high severity, but the lowest fine root N concentration occurred at high severity. Plant nutrient utilization tended to be P-limited at high fire severity according to the mean value of N:P ratio &gt; 16. More importantly, C, N and P allocation strategies between fine roots and leaves changed from allometry to isometry with increasing fire severities, which showed more elements allocated to leaves than to fine roots with increasing fire severities. These changes in patterns suggest that the allocation strategies of elements between leaves and fine roots are of imbalance with the wildfire severity. This study deepens our understanding of nutrient dynamics between plant and soil in ecosystem succession.
Giant abdominopelvic desmoid tumour herniated trough perineum: a case report
Authors: Tchangai Boyodi Katanga , Tchaou Mazamaesso , Alassani Fousseni , Amétitovi Joel Ekoué , Doh Kwamé , Darre Tchin , Dosseh David Ekoue 
Published: August 2021

Abstract
Desmoid tumours are deep aggressive fibromatoses that usually arise in the soft tissues of the limbs or the abdominal wall. Intra-abdominal localisation, rarely occurs and their treatment may be challenging. When necessary, surgery must be personalized to what is achievable in terms of margins while preserving functional outcomes. This condition is illustrated herein with the case of a 40-year-old female presenting an unusually large sporadic desmoid tumour with abdominal, pelvic and perineal involvement. Resection was performed without organ involvement through a combined perineal approach. Tumour resection was macroscopically completed except in the perineum, where the tumour was left (R2 resection) to preserve anal sphincter. Adjuvant treatment with tamoxifen was given to achieve local control. The hormonal treatment was well tolerated, and no recurrence was observed after 36 months of follow-up.
Playing Cute: Sensation Villainy and the Aesthetics of Small Things in The Woman in White and Lady Audley’s Secret
Authors: Eastlake Laura 
Published: September 2021

Abstract
In Our Aesthetic Categories (2012), Sianne Ngai defines ‘cute’ as an aesthetic ‘preoccupation with small, easy to handle things . . . an aesthetic that celebrates the diminutive and the vulnerable’. Although Ngai identifies the cute as a predominantly twentieth-century phenomenon, and one which is inextricably bound up with the mass-market commodification, even eroticization and fetishization of the cute object or person, it is difficult to imagine a literary character more enamoured with ‘small things’ – from tiny, sugary confections to his menagerie of pet mice – than Wilkie Collins’s Count Fosco, or a character who so perfectly conforms to the definition of the cute commodity itself as ‘appealing specifically . . . for protection and care’ than the ‘childish, helpless, babyfied’ Lucy Audley in Mary Elizabeth Braddon’s Lady Audley’s Secret (1862). This article reads Count Fosco and Lady Audley through the characteristics of cuteness to better understand the aesthetic and economic dynamics of their villainy, and to establish for the twentieth-century phenomenon of cuteness identified by Ngai a discernible genealogy in the specific conjunction of print culture, theatricality, commodification, and physical sensation that we now recognize as the sensation fiction of the 1860s.
Rapid recovery by fat- and muscle-depleted Blackpoll Warblers following trans-oceanic migration is driven by time-minimization
Authors: Bayly Nicholas J , Rosenberg Kenneth V , Norris D Ryan , Taylor Philip D , Hobson Keith A 
Published: September 2021

Abstract
Nonstop endurance flights are a defining characteristic of many long-distance migratory birds, but subsequent recovery phases are not typically distinguished from fueling phases (collectively “stopovers”), despite endurance flights inducing marked physiological changes including flight muscle atrophy and gastrointestinal tract reductions. Here, we hypothesize that recovery requires unique behavioral adaptations, leading to departures from the predictions of optimal migration theory for time-minimizing migrants. We predict that recovering birds will (1) select (moist) food-rich habitats on arrival; (2) have slow initial fueling rates due to decreased gastrointestinal capacity; (3) show a negative correlation between stopover duration and arrival condition instead of a negative correlation with fuel deposition rate (FDR); (4) stopover longer than required to store energy reserves for subsequent flights; and (5) show evidence of rebuilding flight muscles. To test these predictions, we studied Blackpoll Warblers (Setophaga striata) in northern Colombia following trans-oceanic flights &gt;2,250 km. Birds selected dry seasonal habitats, despite the proximity of moist forests, and among 1,227 captured individuals, 14–21% were emaciated and 88% had atrophied flight muscles. We recaptured 74 individuals, revealing net positive mass gains and, contrary to prediction (2), no evidence for slow initial recovery rates. Contrary to prediction (3), stopover duration was only weakly correlated with arrival condition and birds with high FDR (4.9% lean body mass day–1) had shorter durations (3 days) relative to birds with slower rates (7 days): both groups accumulated sufficient fuel to reach nonbreeding (over-wintering) grounds 500–1,000 km away. Mass increases were largely attributable to fat deposition but some birds improved flight muscle condition (31.9%), consistent with prediction (5). Together these results reveal a strong selection for time-minimization in the decisions made by Blackpoll Warblers following trans-oceanic flights, likely mediated through advantages to early arrival on nonbreeding grounds, contrary to our hypothesis of recovery imposing unique selection pressures.
Evaluation of inducible promoter–riboswitch constructs for heterologous protein expression in the cyanobacterial species Anabaena sp. PCC 7120
Authors: Svoboda Jessee , Cisneros Brenda , Philmus Benjamin 
Published: September 2021

Abstract
Cyanobacteria are promising chassis for synthetic biology applications due to the fact that they are photosynthetic organisms capable of growing in simple, inexpensive media. Given their slower growth rate than other model organisms such as Escherichia coli and Saccharomyces cerevisiae, there are fewer synthetic biology tools and promoters available for use in model cyanobacteria. Here, we compared a small library of promoter–riboswitch constructs for synthetic biology applications in Anabaena sp. PCC 7120, a model filamentous cyanobacterium. These constructs were designed from six cyanobacterial promoters of various strengths, each paired with one of two theophylline-responsive riboswitches. The promoter–riboswitch pairs were cloned upstream of a chloramphenicol acetyltransferase (cat) gene, and CAT activity was quantified using an in vitro assay. Addition of theophylline to cultures increased the CAT activity in almost all cases, allowing inducible protein production with natively constitutive promoters. We found that riboswitch F tended to have a lower induced and uninduced production compared to riboswitch E for the weak and medium promoters, although the difference was larger for the uninduced production, in accord with previous research. The strong promoters yielded a higher baseline CAT activity than medium strength and weak promoters. In addition, we observed no appreciable difference between CAT activity measured from strong promoters cultured in uninduced and induced conditions. The results of this study add to the genetic toolbox for cyanobacteria and allow future natural product and synthetic biology researchers to choose a construct that fits their needs.
Prevalence of Breast Cancer in Female Physicians Performing Procedures With Significant Fluoroscopy Exposure: Survey
Authors: Biglione Bianca , Nakhaei Masoud , Hamilton Barbara , Englander Meridith J. , Dua Anahita , Brook Olga R. 
Published: September 2021

Objective
The aim of this study was to assess self-reported breast cancer prevalence potentially associated with occupational radiation exposure from fluoroscopy-guided procedures in female physicians using current standard protection measures.

Methods
An institutional review board–approved survey was shared as a link to self-identified female physicians. We compared self-reported prevalence of breast cancer among women physicians with longer than 10 years of postfellowship practice in specialties with heavy fluoroscopy exposure versus specialties with low fluoroscopy exposure. We compared the distribution of breast cancer risk factors and personal radiation safety measures.

Results
A total of 303 women physicians participated in the survey. There were 8 (16%) of 49 from the first study group and 8 (18%) of 44 from the second study group who self-reported a diagnosis of breast cancer. There were no differences in the distribution of breast cancer risk factors between the 2 groups or prevalence of breast cancer (P = 0.81).

Conclusions
Self-reported breast cancer prevalence is similar between women physicians who are practicing fluoroscopically heavy and light medical specialties.