bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of provider satisfaction with specialty pharmacy services in integrated health-system and external practice models: A multisite survey
Authors: Anguiano Rebekah H , Zuckerman Autumn D , Hall Elizabeth , Diamantides Erica , Kumor Lisa , Duckworth Deborah L , Peter Megan , Sorgen Patrick J , Nathanson Amy , Kandah Huda-Marie , Dura Jillian , Campbell Udobi 
Published: March 2021

Abstract

Purpose
The purpose of this study is to obtain insight into providers’ satisfaction with services offered by health-system integrated specialty pharmacies and to determine whether providers’ perceptions of services offered under an integrated model differ from perceptions of external specialty pharmacy services.

Methods
A multi-site, cross-sectional, online survey of specialty clinic healthcare providers at 10 academic health systems with integrated specialty pharmacies was conducted. The questionnaire was developed by members of the Vizient Specialty Pharmacy Outcomes and Benchmarking Workgroup and was pretested at 3 pilot sites prior to dissemination. Prescribers of specialty medications within each institution were identified and sent an email invitation to participate in the study that included a link to the anonymous questionnaire. Respondents were asked to rate their agreement with 10 statements regarding quality of services of integrated and external specialty pharmacies on a 5-point scale (1 = strongly disagree, 5 = strongly agree). An analysis to determine differences in providers’ overall satisfaction with the integrated and external specialty pharmacy practice models, as well as differences in satisfaction scores for each of the 10 statements, was performed using paired-samples t tests.

Results
The mean (SD) score for overall satisfaction with integrated specialty pharmacies was significantly higher than the score for satisfaction with external specialty pharmacies: 4.72 (0.58) vs 2.97 (1.20); 95% confidence interval, 1.64-1.87; P &lt; 0.001. Provider ratings of the integrated specialty pharmacy model were also higher for all 10 items evaluating the quality of services (P &lt; 0.05 for all comparisons).

Conclusion
The study results confirm that the health-system integrated specialty pharmacy practice model promotes high rates of provider satisfaction with services and perceived benefits.
Innovation, Resiliency, and Genius in Intensive English Programs: Decolonializing Recruitment and Contradictory Advocacy
Authors: Litzenberg Jason 
Published: March 2021

AbstractThis article considers Intensive English Programs (IEPs) affiliated with higher education institutions of the Global North from the perspective of a decolonial option in which English is viewed as a tool of modernity used for colonization and the maintenance of unequal socioeconomic and power structures. Via nuanced description (Pennycook and Makoni 2020) of two colonizing practices typical to IEPs—namely, recruitment and advocacy—the article argues that the traits of resiliency, innovation, and genius commonly ascribed to IEPs are qualities that lend themselves to the refoundation, reconfiguration, and reconstruction (de Sousa Santos 2019) of alternative visions. In this way, IEPs have the opportunity to promote the liberatory visions of applied linguistics’ practitioners and to positively influence decolonialization of the field. Because of their historical involvement in English language teaching and the industry it has spawned, applied linguists have an obligation to foster these changes, which need not affect the ability of IEPs to conduct language pedagogy or to provide the field with opportunities for research, teacher training, and professional development.
Information content of trees: three-taxon statements, inference rules and dependency
Authors: Rineau Valentin , Zaragüeta Rene , Bardin Jérémie 
Published: March 2021

Abstract
The three-taxon statement is the fundamental unit of rooted trees in cladistics, stating that for three terminal taxa, two are more related to each other than to a third. Because of their fundamental role in phylogenetics, three-taxon statements are present in methodological research of various disciplines in evolutionary biology; for example consensus methods, supertree methods, species-tree methods, distance metrics and even phylogenetic reconstruction. However, three-taxon statement methods are subject to important flaws related to information redundancy. Here we aim to study the behaviour of three-taxon statements and the interactions among them in order to enhance their performance in evolutionary studies. We show how specific interactions between three-taxon statements are responsible for the emergence of redundancy and dependency within trees, and how they can be used for the improvement of weighting procedures. Our proposal is subsequently tested empirically in the supertree framework using simulations. We show that three-taxon statements using fractional weights perform much better than classical methods such as MRP (matrix representation with parsimony) or methods using unweighted statements. Our study shows that appropriate fractional weighting of three-taxon statements is of critical importance for removing redundancy in any method using them, such as in consensus, supertrees, distance metrics, and phylogenetic or biogeographical analyses.
Radiomics: a new tool to differentiate adrenocortical adenoma from carcinoma
Authors: Torresan F , Crimì F , Ceccato F , Zavan F , Barbot M , Lacognata C , Motta R , Armellin C , Scaroni C , Quaia E , Campi C , Iacobone M 
Published: March 2021

Abstract

Background
The main challenge in the management of indeterminate incidentally discovered adrenal tumours is to differentiate benign from malignant lesions. In the absence of clear signs of invasion or metastases, imaging techniques do not always precisely define the nature of the mass. The present pilot study aimed to determine whether radiomics may predict malignancy in adrenocortical tumours.

Methods
CT images in unenhanced, arterial, and venous phases from 19 patients who had undergone resection of adrenocortical tumours and a cohort who had undergone surveillance for at least 5 years for incidentalomas were reviewed. A volume of interest was drawn for each lesion using dedicated software, and, for each phase, first-order (histogram) and second-order (grey-level colour matrix and run-length matrix) radiological features were extracted. Data were revised by an unsupervised machine learning approach using the K-means clustering technique.

Results
Of operated patients, nine had non-functional adenoma and 10 carcinoma. There were 11 patients in the surveillance group. Two first-order features in unenhanced CT and one in arterial CT, and 14 second-order parameters in unenhanced and venous CT and 10 second-order features in arterial CT, were able to differentiate adrenocortical carcinoma from adenoma (P &lt; 0.050). After excluding two malignant outliers, the unsupervised machine learning approach correctly predicted malignancy in seven of eight adrenocortical carcinomas in all phases.

Conclusion
Radiomics with CT texture analysis was able to discriminate malignant from benign adrenocortical tumours, even by an unsupervised machine learning approach, in nearly all patients.
Partial effects in non-linear panel data models with correlated random effects
Authors: Abrevaya Jason , Hsu Yu-Chin 
Published: March 2021

Summary
Nonlinearity and heterogeneity are known to cause difficulties in estimating and interpreting partial effects. This paper provides a systematic characterization of the various partial effects in nonlinear panel data models that might be of interest to empirical researchers. The interpretation of the partial effects depends upon (i) whether the distribution of unobserved heterogeneity is treated as fixed or allowed to vary with covariates, and (ii) whether one is interested in particular covariate values or an average over such values. The characterization covers partial-effects concepts already in the literature but also includes new concepts for partial effects. A simple panel probit design highlights that the different partial effects can be quantitatively very different.
Diversified Bund Vegetation Coupled With Flowering Plants Enhances Predator Population and Early-Season Pest Control
Authors: Qian Ping , Bai Yueliang , Zhou Wenwu , Yu Hang , Zhu Zijie , Wang Guiyao , Quais Md Khairul , Li Feiqiang , Chen Yue , Tan Ye , Shi Xiaoxiao , Wang Xueqin , Zhong Xueming , Zhu Zeng-Rong 
Published: March 2021

AbstractInsecticide overuse in crop production systems often results in detrimental effects on predators and parasitoids, which regulate important insect pests. The natural enemies are also unable to survive in monocrop landscapes with the absence of shelter or food sources. Diversified vegetation, especially with flowering plants, can enhance natural enemy abundance and diversity, thus strengthening biological control, enabling farmers to reduce insecticides. In this study, we conserved bund vegetation and manipulated the existing rice landscapes with flowering plants to provide food and shelter for the biological control agents. Our study revealed significant positive relationships between predator densities and bund plant diversity. The abundance of predators significantly increased in the eco-engineered plots, especially at the flowering peaks compared to the insecticide-treated and control plots, while parasitoids were more diverse in both the eco-engineered and control plots. There were no significant differences in planthopper and leafhopper densities among the treatments during the rice early and maximum tillering stages, suggesting effective natural control of these herbivore pests in the eco-engineered plots at the early rice-growing season. However, at the heading stage relatively higher planthopper and leafhopper populations in the control and eco-engineered plots than in the insecticide-sprayed plots were recorded, suggesting perhaps the need for insecticide interventions if exceeding the threshold at this time. Our study indicates that manipulating the habitats surrounding the rice fields to enhance natural enemies is a sustainable practice in rice production as it can enhance the natural suppression of pests and thus reducing the need for insecticide.
Severe chronic aortic regurgitation after percutaneous coronary intervention: a case report and literature review
Authors: Wedin Johan O , Vikholm Per , Alström Ulrica , Schiller Petter 
Published: March 2021

Abstract

Background
Severe aortic regurgitation (AR) is an extremely rare complication after coronary catheterization and percutaneous coronary intervention (PCI), where most reported cases have required relatively urgent surgical intervention due to acute-onset AR and cardiac decompensation.

Case summary
We report a case of a 60-year-old woman that previously presented with a non-ST-elevation myocardial infarction (NSTEMI) due to an ostial right coronary artery stenosis. During the course of 2 years, she developed five recurrent NSTEMI due to in-stent thrombosis, necessitating either a new coronary stent or balloon. She developed a chronic severe AR due to a drug-eluting coronary stent protruding from the right coronary artery and underwent successful aortic valve replacement and coronary artery by-pass grafting.

Discussion
We performed a literature review and identified 16 reported cases of iatrogenic severe aortic regurgitation related to coronary catheterization or percutaneous coronary intervention. All patients developed an acute aortic regurgitation and, thus, we report the first case of a delayed complication caused by a protruding coronary stent. The surgical strategy is related to the extent of the damage, where smaller perforations or lacerations seems to be feasible for aortic valve repair and larger defects more often lead to aortic valve replacement. Our patient developed a fibrotic right coronary cusp which could not be used to perform a successful aortic valve repair.
Capecitabine-mediated heart failure in colorectal cancer: a case series
Authors: McAndrew Erin N , Jassal Davinder S , Goldenberg Benjamin A , Kim Christina A 
Published: March 2021

AbstractBackgroundCapecitabine is a pyrimidine antimetabolite that inhibits thymidylate synthase and is commonly used in the treatment of colorectal cancer. Adverse cardiac side effects are reported in 1–18% of patients receiving Capecitabine. The most commonly proposed mechanism of cardiotoxicity in the setting of Capecitabine use is vasospasm of the coronary arteries. However, cardiotoxicity can also present as an acute coronary syndrome, arrhythmia, hypertension, and/or sudden cardiac death. Profound non-vasospastic cardiotoxicity is rare.Case summaryWe describe two cases of acute heart failure leading to cardiogenic shock in patients shortly after exposure to Capecitabine. Both patients did not demonstrate the characteristic transient ST elevation seen in patients with coronary artery vasospasms secondary to Capecitabine. Both patients required admission to the Acute Cardiac Care Unit requiring vasopressor and inotropic support. Thorough diagnostic investigations including echocardiography, cardiac magnetic resonance imaging, and cardiac computed tomography did not identify infarction, myocarditis, or any infiltrative process to explain their symptoms. Both patients had complete resolution of cardiac function, with no long-term sequalae.DiscussionIn patients receiving Capecitabine, reversible heart failure leading to cardiogenic shock should be considered as a potential cardiotoxic side effect.
T cell responses toChlamydia
Authors: D. Helble Jennifer , N. Starnbach Michael 
Published: March 2021

ABSTRACTChlamydia trachomatis is the most commonly reported sexually transmitted infection in the United States. The high prevalence of infection and lack of a vaccine indicate a critical knowledge gap surrounding the host's response to infection and how to effectively generate protective immunity. The immune response to C. trachomatis is complex, with cells of the adaptive immune system playing a crucial role in bacterial clearance. Here, we discuss the CD4+ and CD8+ T cell response to Chlamydia, the importance of antigen specificity and the role of memory T cells during the recall response. Ultimately, a deeper understanding of protective immune responses is necessary to develop a vaccine that prevents the inflammatory diseases associated with Chlamydia infection.
The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health
Authors: Brose Julia , Lau Kin H , Dang Thu Thuy Thi , Hamilton John P , Martins Lívia do Vale , Hamberger Britta , Hamberger Bjoern , Jiang Jiming , O’Connor Sarah E , Buell C Robin 
Published: March 2021

Abstract
Mitragyna speciosa (kratom) produces numerous compounds with pharmaceutical properties including the production of bioactive monoterpene indole and oxindole alkaloids. Using a linked-read approach, a 1,122,519,462 bp draft assembly of M. speciosa “Rifat” was generated with an N50 scaffold size of 1,020,971 bp and an N50 contig size of 70,448 bp that encodes 55,746 genes. Chromosome counting revealed that “Rifat” is a tetraploid with a base chromosome number of 11, which was further corroborated by orthology and syntenic analysis of the genome. Analysis of genes and clusters involved in specialized metabolism revealed genes putatively involved in alkaloid biosynthesis. Access to the genome of M. speciosa will facilitate an improved understanding of alkaloid biosynthesis and accelerate the production of bioactive alkaloids in heterologous hosts.
High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain
Authors: Wu Di , Tanaka Ryokei , Li Xiaowei , Ramstein Guillaume P , Cu Suong , Hamilton John P , Buell C Robin , Stangoulis James , Rocheford Torbert , Gore Michael A 
Published: March 2021

AbstractDespite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.
X-ray microtomography–based atlas of mouse cranial development
Authors: Matula Jan , Tesarova Marketa , Zikmund Tomas , Kaucka Marketa , Adameyko Igor , Kaiser Jozef 
Published: March 2021

Abstract

Background
X-ray microtomography (μCT) has become an invaluable tool for non-destructive analysis of biological samples in the field of developmental biology. Mouse embryos are a typical model for investigation of human developmental diseases. By obtaining 3D high-resolution scans of the mouse embryo heads, we gain valuable morphological information about the structures prominent in the development of future face, brain, and sensory organs. The development of facial skeleton tracked in these μCT data provides a valuable background for further studies of congenital craniofacial diseases and normal development.

Findings
In this work, reusable tomographic data from 7 full 3D scans of mouse embryo heads are presented and made publicly available. The ages of these embryos range from E12.5 to E18.5. The samples were stained by phosphotungstic acid prior to scanning, which greatly enhanced the contrast of various tissues in the reconstructed images and enabled precise segmentation. The images were obtained on a laboratory-based μCT system. Furthermore, we provide manually segmented masks of mesenchymal condensations (for E12.5 and E13.5) and cartilage present in the nasal capsule of the scanned embryos.

Conclusion
We present a comprehensive dataset of X-ray 3D computed tomography images of the developing mouse head with high-quality manual segmentation masks of cartilaginous nasal capsules. The provided μCT images can be used for studying any other major structure within the developing mouse heads. The high quality of the manually segmented models of nasal capsules may be instrumental to understanding the complex process of the development of the face in a mouse model.
Oxygenation as a driving factor in epithelial differentiation at the air–liquid interface
Authors: Kouthouridis Sonya , Goepp Julie , Martini Carolina , Matthes Elizabeth , Hanrahan John W , Moraes Christopher 
Published: March 2021

AbstractCulture at the air–liquid interface is broadly accepted as necessary for differentiation of cultured epithelial cells towards an in vivo-like phenotype. However, air–liquid interface cultures are expensive, laborious and challenging to scale for increased throughput applications. Deconstructing the microenvironmental parameters that drive these differentiation processes could circumvent these limitations, and here we hypothesize that reduced oxygenation due to diffusion limitations in liquid media limits differentiation in submerged cultures; and that this phenotype can be rescued by recreating normoxic conditions at the epithelial monolayer, even under submerged conditions. Guided by computational models, hyperoxygenation of atmospheric conditions was applied to manipulate oxygenation at the monolayer surface. The impact of this rescue condition was confirmed by assessing protein expression of hypoxia-sensitive markers. Differentiation of primary human bronchial epithelial cells isolated from healthy patients was then assessed in air–liquid interface, submerged and hyperoxygenated submerged culture conditions. Markers of differentiation, including epithelial layer thickness, tight junction formation, ciliated surface area and functional capacity for mucociliary clearance, were assessed and found to improve significantly in hyperoxygenated submerged cultures, beyond standard air–liquid interface or submerged culture conditions. These results demonstrate that an air–liquid interface is not necessary to produce highly differentiated epithelial structures, and that increased availability of oxygen and nutrient media can be leveraged as important strategies to improve epithelial differentiation for applications in respiratory toxicology and therapeutic development.
ImmuneDEX: a strategy for the genetic improvement of immune competence in Australian Angus cattle
Authors: Reverter Antonio , Hine Brad C , Porto-Neto Laercio , Li Yutao , Duff Christian J , Dominik Sonja , Ingham Aaron B 
Published: March 2021

Abstract
In animal breeding and genetics, the ability to cope with disease, here defined as immune competence (IC), with minimal detriment to growth and fertility is a desired objective which addresses both animal production and welfare considerations. However, defining and objectively measuring IC phenotypes using testing methods which are practical to apply on-farm has been challenging. Based on previously described protocols, we measured both cell-mediated immune response (Cell-IR) and antibody-mediated immune response (Ab-IR) and combined these measures to determine an animal’s IC. Using a population of 2,853 Australian Angus steers and heifers, we compared 2 alternative methods to combine both metrics into a single phenotype to be used as a tool for the genetic improvement of IC. The first method, named ZMEAN, is obtained by taking the average of the individual metrics after subjecting each to a Z-score standardization. The second, ImmuneDEX (IDEX), is a weighted average that considers the correlation between Cell-IR and Ab-IR, as well as the difference in ranking of individuals by each metric, and uses these as weights in the averaging. Both simulation and real data were used to understand the behavior of ZMEAN and IDEX. To further ascertain the relationship between IDEX and other traits of economic importance, we evaluated a range of traits related to growth, feedlot performance, and carcass characteristics. We report estimates of heritability of 0.31 ± 0.06 for Cell-IR, 0.42 ± 0.06 for Ab-IR, 0.42 ± 0.06 for ZMEAN and 0.370 ± 0.06 for IDEX, as well as a unity genetic correlation (rg) between ZMEAN and IDEX. While a moderately positive rg was estimated between Cell-IR and Ab-IR (rg = 0.33 ± 0.12), strongly positive estimates were obtained between IDEX and Cell-IR (rg = 0.80 ± 0.05) and between IDEX and Ab-IR (rg = 0.85 ± 0.04). We obtained a moderately negative rg between IC traits and growth including an rg = −0.38 ± 0.14 between IDEX and weaning weight, and negligible with carcass fat measurements, including an rg = −0.03 ± 0.12 between IDEX and marbling. Given that breeding with a sole focus on production might inadvertently increase susceptibility to disease and associated antibiotic use, our analyses suggest that ImmuneDEX will provide a basis to breed animals that are both highly productive and with an enhanced ability to resist disease.