bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bespoke Instrumental Variable Approach to Correction for Exposure Measurement Error
Authors: Richardson David B , Keil Alexander P , Edwards Jessie K , Cole Stephen R , Tchetgen Tchetgen Eric J 
Published: August 2022

Abstract
A covariate-adjusted estimate of an exposure-outcome association may be biased if the exposure variable suffers measurement error. We propose an approach to correct for exposure measurement error in a covariate-adjusted estimate of the association between a continuous exposure variable and outcome of interest. Our proposed approach requires data for a reference population in which the exposure was a priori set to some known level (e.g., 0, and is therefore unexposed); however, our approach does not require an exposure validation study or replicate measures of exposure, which are typically needed when addressing bias due to exposure measurement error. A key condition for this method, which we refer to as “partial population exchangeability,” requires that the association between a measured covariate and outcome in the reference population equals the association between that covariate and outcome in the target population in the absence of exposure. We illustrate the approach using simulations and an example.
Cost-Efficient Multiply Matched Case-Control Study Designs
Authors: Sandoval Grecio J , Bebu Ionut , Lachin John M 
Published: August 2022

AbstractIn multiply matched case-control studies, a number of cases and controls may be included in each matched set. However, when per-participant costs between cases and controls differ, investigators should be aware of how the numbers of cases and controls per matched set affect the overall total study cost. Traditional statistical approaches to designing case-control studies do not account for study costs. Given an effect size, the power to detect differences is typically a function of the numbers of cases and controls within each matched set. Therefore, the same level of statistical power will be achieved based on various combinations of the numbers of cases and controls. Typical matched case-control studies match a case to a number of controls by levels of 1 or more known factors. Several authors have shown that for study designs with 1 case per matched set, the optimal number of controls within each matched set that minimizes the total study cost is the square root of the ratio of the cost of a case to the cost of a control. Herein, we extend this result to the setting of a multiply matched case-control study design, when 1 or more cases are matched to controls within each matched set. A Shiny web application implementation of the proposed methods is presented.
The Association of Serum High-Sensitivity C-Reactive Protein Level With the Risk of Site-Specific Cancer Mortality: The Health Examinees (HEXA) Study Cohort
Authors: Lee Sang-Ah , Kwon Sung-Ok , Song Minkyo , Choi Ji-Yeob , Shin Aesun , Shu Xiao-Ou , Zheng Wei , Lee Jong-Koo , Kang Daehee 
Published: August 2022

Abstract
Few studies have investigated the association between high-sensitivity C-reactive protein (hsCRP) level and site-specific cancer mortality. In this study, we aimed to examine the associations of hsCRP with overall and site-specific cancer mortality among South Koreans using data on the Health Examinees (HEXA) Study cohort (41,070 men and 81,011 women aged ≥40 years). We obtained mortality information from the National Statistical Office of Korea, which provided the dates and causes of all deaths occurring through December 31, 2015, by linking mortality data with each participant’s unique national identifier. Cox proportional hazards and restricted cubic spline models were used to assess the association between hsCRP and cancer mortality with adjustment for covariates. An analysis of site-specific cancer mortality was focused on 5 major cancers (lung, liver, gastric, colorectal, and breast/prostate). Median hsCRP levels were 0.77 mg/L and 0.59 mg/L for men and women, respectively. A dose-response association between hsCRP and overall cancer mortality was observed in men but disappeared in women after exclusion of deaths occurring in the first 1 or 2 years of follow-up. Elevated hsCRP levels increased the risks of lung, liver, and gastric cancer mortality in men, but the risks of colorectal and breast cancer mortality were not increased. The dose-response association between hsCRP and cancer mortality was observed differently depending on site-specific cancer mortality by sex.
Paraneoplastic syndromes: A focus on pathophysiology and supportive care
Authors: Chung Clement , Allen Emily , Umoru Godsfavour 
Published: August 2022

AbstractPurposeThis article aims to increase awareness of, outline pathophysiology for, and offer guidance on supportive care strategies for specific endocrine, neurological, and immunological syndromes associated with paraneoplastic syndromes (PNSs).SummaryPNS refers to remote effects that cannot be attributed to the direct or invasive effects of a malignancy. These syndromes are considered clinically important because they may provide early recognition, diagnosis, and management of the malignancy in a timely manner. Many of their presenting symptoms such as ectopic Cushing’s syndrome, hypercalcemia of malignancy (HCM), syndrome of inappropriate secretion of antidiuretic hormone (SIADH), neurological dysfunctions, and paraneoplastic autoimmune thrombocytopenia overlap with those of nonneoplastic disorders, yet their pathogenesis and responses to treatments differ. Management of ectopic Cushing’s syndrome due to a PNS consists of treatment of the underlying malignancy and its comorbidities. Drug therapies may include ketoconazole, mitotane, metyrapone, somatostatin analogs, and dopamine agonists. Hypercalcemia may be classified into cases with parathyroid hormone (PTH)–dependent causes or PTH-independent causes such as HCM, in which osteoclast inhibitors may be deployed. Treatments of PNS-mediated SIADH include treatment of the underlying malignancy and strategies to increase serum sodium levels. Amifampridine is now considered the first-line agent for paraneoplastic Lambert-Eaton myasthenic syndrome, whereas steroids, intravenous immune globulin, thrombopoietin receptor agonists (eg, romiplostim, eltrombopag, and avatrombopag), fostamatinib, and rituximab may find their niche in treatment of PNS-mediated autoimmune thrombocytopenia.ConclusionSupportive care for PNSs lends opportunities to pharmacists to add quality, value, and safety.
Computational models, databases and tools for antibiotic combinations
Authors: Lv Ji , Liu Guixia , Hao Junli , Ju Yuan , Sun Binwen , Sun Ying 
Published: August 2022

Abstract
Antibiotic combination is a promising strategy to extend the lifetime of antibiotics and thereby combat antimicrobial resistance. However, screening for new antibiotic combinations is both time-consuming and labor-intensive. In recent years, an increasing number of researchers have used computational models to predict effective antibiotic combinations. In this review, we summarized existing computational models for antibiotic combinations and discussed the limitations and challenges of these models in detail. In addition, we also collected and summarized available data resources and tools for antibiotic combinations. This study aims to help computational biologists design more accurate and interpretable computational models.
Nonunique UPGMA clusterings of microsatellite markers
Authors: Segura-Alabart Natàlia , Serratosa Francesc , Gómez Sergio , Fernández Alberto 
Published: August 2022

Abstract
Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology. In this work, we focus on a critical problem, the nonuniqueness of the clustering when there are tied distances, for which several solutions exist but are not implemented in most hierarchical clustering packages. We analyze the magnitude of this problem in one particular setting: the clustering of microsatellite markers using the Unweighted Pair-Group Method with Arithmetic Mean. To do so, we have calculated the fraction of publications at the Scopus database in which more than one hierarchical clustering is possible, showing that about 46% of the articles are affected. Additionally, to show the problem from a practical point of view, we selected two opposite examples of articles that have multiple solutions: one with two possible dendrograms, and the other with more than 2.5 million different possible hierarchical clusterings.
Letter on the results of the BASiNET method in the paper ‘A systematic evaluation of computational tools for lncRNA identification’
Authors: Martins Lopes Fabrício , Pimenta-Zanon Matheus H 
Published: August 2022

Abstract
This letter points out a conceptual error made by the authors of a published paper, which presents a review and evaluation of computational methods in lncRNA identification. The error was made in the execution of the BASiNET method when considering an example file (toy model) made available by the authors with the aim of showing how a classification model could be stored in a file for later use. In this letter, this error is contextualized, the correct use of the BASiNET method is pointed out and the results of its correct execution to one of the datasets used in the review article are presented. The results clearly show the misuse of the method and present its correct use so that it can be fairly compared with other methods in the literature and prevent its misuse from being replicated by new studies.
Population level variation in silk chemistry but not web architecture in a widely distributed orb web spider
Authors: Henneken Jessica , Blamires Sean J , Goodger Jason Q D , Jones Therésa M , Elgar Mark A 
Published: July 2022

Abstract
Spider webs are iconic examples of extended phenotypes that are remarkably plastic across different environments. Orb webs are not only effective traps for capturing prey, but can also provide information to potential mates and, in some cases, potential predators and prey through silk-based chemicals. As with regular phenotypic traits, variability in the properties of spider webs is thought to be mediated by a combination of genetic and environmental effects. Here, we examined variation in several key features of the webs of the orb-weaving spider Argiope keyserlingi across five geographically disparate populations. We documented variation in web architecture and chemical properties of webs collected directly from the field. We then probed the potential for the underlying environmental driver of local insect abundance to explain this variation, by analysing the properties of orb webs constructed by the spiders from these different populations, but under identical laboratory conditions. We found no evidence of variation across populations in the architecture of webs constructed in the laboratory, despite the large geographic distances. Nonetheless, we discovered between population variation in the composition of chemicals found on the surface of silk and in the taxonomic distribution of available prey. Furthermore, there was a positive correlation between the quantity of nitrogenous compounds in web silks and female body condition. When combined, these findings suggest that environmental mechanisms can drive variation in web traits across spider populations.
Enhancing the relevance of social work education in Nigeria
Authors: Amadasun Solomon , Gray Mel 
Published: August 2022

Abstract
Quality locally relevant social work education is essential in social workers’ professional development and, in Nigeria, in the profession’s struggle for legitimacy and connection with local families and communities. It is also pivotal to efficient and effective service delivery in the contemporary digitally connected world, where myriad social issues warrant the professional intervention of skilled practitioners in diverse fields. Social workers’ responsiveness and effectiveness depend crucially on the quality and relevance of the education and training they receive at the start of and throughout their professional careers. This article examines social work education, its relatively recent origins and issues in contemporary Nigerian society highlighting the ongoing need for socio-cultural relevance in the interests of professional recognition. It proposes that social work educators and administrators have a crucial role to play in enhancing the profession’s relevance and suggests a way forward.
Feminist accountability: deconstructing feminist praxes, solidarities and LGBTQI+ activisms in Ghana
Authors: Mohammed Wunpini Fatimata 
Published: July 2022

AbstractThis article examines how mainstream feminist organizations in Ghana worked to support LGBTQI+ communities when they were subjected to state and institutionalized violence in February 2021. Through an African feminist critical discourse analysis (FCDA) of the solidarity statements issued by feminist and gender advocacy organizations, I highlight the way that mainstream feminist groups relate to LGBTQI+ communities. I argue that although there is increasing visibility in activism and organizing around issues affecting queer and trans Ghanaians, feminist and gender advocacy groups which have dominated the organizing space in the country are actively working to undermine the work that radical activists are doing to create a better society for LGBTQI+ people. I contextualize the study within recent theory and praxis around queer and trans issues while drawing attention to the ways that feminist groups are falling short when it comes to LGBTQI+ organizing in the country and what they could do better.
Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations
Authors: Manggabarani Andi Madihah , Hashiguchi Takuyu , Hashiguchi Masatsugu , Hayashi Atsushi , Kikuchi Masataka , Mustamin Yusdar , Bamba Masaru , Kodama Kunihiro , Tanabata Takanari , Isobe Sachiko , Tanaka Hidenori , Akashi Ryo , Nakaya Akihiro , Sato Shusei 
Published: August 2022

AbstractAs soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (G×E). To achieve this goal, we conducted the field experiments for soybean core collections using multiple sowing times in multi-latitudinal fields. Sowing time shifts altered the flowering time (FT) and growth phenotypes, and resulted in increasing the combinations of genotypes and environments. Genome-wide association studies for the obtained phenotypes revealed the effects of field and sowing time to the significance of detected alleles, indicating the presence of G×E. By using accumulated phenotypic and environmental data in 2018 and 2019, we constructed multiple regression models for FT and growth pattern. Applicability of the constructed models was evaluated by the field experiments in 2020 including a novel field, and high correlation between the predicted and measured values was observed, suggesting the robustness of the models. The models presented here would allow us to predict the phenotype of the core collections in a given environment.
Outcomes of valve-sparing surgery in heritable aortic disorders: results from the AVIATOR registry
Authors: Chauvette Vincent , Kluin Jolanda , de Kerchove Laurent , El Khoury Gebrine , Schäfers Hans-Joachim , Lansac Emmanuel , El-Hamamsy Ismail 
Published: August 2022

Abstract

OBJECTIVES
Root reimplantation has been the favoured approach for patients with heritable aortic disorder requiring valve-sparring root replacement. In the past few years, root remodelling with annuloplasty has emerged as an alternative to root reimplantation in the general population. The aim of this study was to examine the late outcomes of patients with heritable aortic disorder undergoing valve-sparring root replacement and compare different techniques.

METHODS
Using the AVIATOR registry (Aortic Valve Insufficiency and ascending aorta Aneurysm InternATiOnal Registry), data were collected from 5 North American and European centres. Patients were divided into 4 groups according to the technique of valve-sparing used (root reimplantation, root remodelling with ring annuloplasty, root remodelling with suture annuloplasty and root remodelling alone). The primary endpoints were freedom from aortic regurgitation (AR) ≥2 and freedom from reintervention on the aortic valve. Secondary endpoints were survival and changes in annular dimensions over time.

RESULTS
A total of 237 patients were included in the study (reimplantation = 100, remodelling + ring annuloplasty = 76, remodelling + suture annuloplasty = 34, remodelling alone = 27). The majority of patients had Marfan syndrome (83%). Preoperative AR ≥2 was present in 41% of the patients. Operative mortality was 0.4% (n = 1). No differences were found between techniques in terms of postoperative AR ≥2 (P = 0.58), reintervention (P = 0.52) and survival (P = 0.59). Changes in aortic annulus dimension were significantly different at 10 years (P &lt; 0.05), a difference that started to emerge 4 years after surgery.

CONCLUSIONS
Overall, valve-sparring root replacement is a safe and durable procedure in patients with heritable aortic disorder. Nevertheless, root remodelling alone is associated with late annular dilatation. The addition of an annuloplasty, however, results in similar freedom from AR, reintervention, survival and changes in annulus size compared to reimplantation.
Nature versus nurture—on the origins of a specious argument
Authors: Wright Robert O 
Published: August 2022

Abstract
The concept of heritability parses out genetic and environmental causes of diseases and does not fit the underlying biology of complex diseases that arise from interactions among genetics and environment. Exposomics places environment on a similar scale as genomics and allows for more modern research approaches that estimate time-varying genome by exposome interactions. By addressing the biological underpinnings of disease comprehensively, we will find the “missing heritability” which is not solely based on genetic variation but is instead driven by time, life stage, and geographic variability in our exposome as it interacts with our genome.
Utilization of phosphonic acid compounds by marine bacteria of the genera Phaeobacter, Ruegeria, and Thalassospira (α-Proteobacteria)
Authors: Urata Shinpei , Kurosawa Yuki , Yamasaki Naoto , Yamamoto Hirofumi , Nishiwaki Nagatoshi , Hongo Yuki , Adachi Masao , Yamaguchi Haruo 
Published: July 2022

Abstract
Phosphonic acid (phosphonate) that possesses a carbon-phosphours bond is a chemically stable form of organic phosphorus. Various phosphonic acids are widely distributed in oceanic waters; in particular, methylphosphonic acid (namely methylphosphonate) is believed to be responsible for global methane production. To discuss the microbial degradation of phosphonic acids, we investigated the utilization of phosphonic acid compounds by cultures of marine bacteria, Phaeobacter sp., Ruegeria sp. (Rhodobacterales), and Thalassospira sp. (Rhodospirillales). These bacterial cultures were able to grow on methylphosphonic acid as well as on the tested alkyl-, carboxy-, aminoalkyl-, and hydroxyalkyl-phosphonic acid compounds. Cell yields and growth rates of Ruegeria and Thalassospira cultures grown on methyl-, ethyl-, propyl-, and butyl-phosphonic acid compounds tended to decrease with increasing alkyl chain length. In contrast, Phaeobacter sp. grew well on such alkyl-phosphonic acids. Our results suggest that these marine bacteria, which exhibit varied utilization, are involved in microbial degradation of various phosphonic acid compounds.
Preventing Falls Among Older Adults in Primary Care: A Mixed Methods Process Evaluation Using the RE-AIM Framework
Authors: Johnston Yvonne A , Reome-Nedlik Chelsea , Parker Erin M , Bergen Gwen , Wentworth Leah , Bauer Michael 
Published: August 2022

AbstractBackground and ObjectivesFalls are a leading cause of injuries and injury deaths for older adults. The Centers for Disease Control and Prevention’s Stopping Elderly Accidents Deaths and Injuries (STEADI) initiative, a multifactorial approach to fall prevention, was adapted for implementation within the primary care setting of a health system in upstate New York. The purpose of this article is to: (a) report process evaluation results for this implementation using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) framework and (b) examine the utility of RE-AIM for assessing barriers and facilitators.Research Design and MethodsThis evaluation used mixed methods. Qualitative evaluation involved semistructured interviews with key stakeholders and intercept interviews with health care providers and clinic staff. Quantitative methods utilized surveys with clinic staff. Process evaluation tools were developed based on the AIM dimensions of the RE-AIM framework. The study was conducted over a 2-month period, approximately 18 months postimplementation, and complements previously published results of the program’s reach and effectiveness.ResultsPrimary barriers by RE-AIM construct included competing organizational priorities (Adoption), competing patient care demands (Implementation), and staff turnover (Maintenance). Primary facilitators included having a physician champion (Adoption), preparing and training staff (Implementation), and communicating about STEADI and recognizing accomplishments (Maintenance).Discussion and ImplicationsResults revealed a high degree of concordance between qualitative and quantitative analyses. The framework supported assessments of various stakeholders, multiple organizational levels, and the sequence of practice change activities. Mixed methods yielded rich data to inform future implementations of STEADI-based fall prevention.
SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data
Authors: Zhang Yunwei , Wong Germaine , Mann Graham , Muller Samuel , Yang Jean Y H 
Published: July 2022

AbstractSurvival analysis is a branch of statistics that deals with both the tracking of time and the survival status simultaneously as the dependent response. Current comparisons of survival model performance mostly center on clinical data with classic statistical survival models, with prediction accuracy often serving as the sole metric of model performance. Moreover, survival analysis approaches for censored omics data have not been thoroughly investigated. The common approach is to binarize the survival time and perform a classification analysis.Here, we develop a benchmarking design, SurvBenchmark, that evaluates a diverse collection of survival models for both clinical and omics data sets. SurvBenchmark not only focuses on classical approaches such as the Cox model but also evaluates state-of-the-art machine learning survival models. All approaches were assessed using multiple performance metrics; these include model predictability, stability, flexibility, and computational issues. Our systematic comparison design with 320 comparisons (20 methods over 16 data sets) shows that the performances of survival models vary in practice over real-world data sets and over the choice of the evaluation metric. In particular, we highlight that using multiple performance metrics is critical in providing a balanced assessment of various models. The results in our study will provide practical guidelines for translational scientists and clinicians, as well as define possible areas of investigation in both survival technique and benchmarking strategies.