bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test–Retest Reliability of a Computerized Neurocognitive Battery in School-Age Children with HIV in Botswana
Authors: Tsima Billy M , Lowenthal Elizabeth D , Van Pelt Amelia E , Moore Tyler M , Matshaba Mogomotsi , Gur Ruben C , Tshume Ontibile , Thuto Boitumelo , Scott J Cobb 
Published: August 2022

Abstract
Human immunodeficiency virus (HIV) infection is prevalent among children and adolescents in Botswana, but standardized neurocognitive testing is limited. The Penn Computerized Neurocognitive Battery (PennCNB) attempts to streamline evaluation of neurocognitive functioning and has been culturally adapted for use among youth in this high-burden, low-resource setting. However, its reliability across measurements (i.e., test–retest reliability) is unknown. This study examined the test–retest reliability of the culturally adapted PennCNB in 65 school-age children (age 7–17) living with HIV in Botswana. Intraclass correlation coefficients (ICCs) for PennCNB summary scores (ICCs &gt; 0.80) and domain scores (ICCs = 0.66–0.88) were higher than those for individual tests, which exhibited more variability (ICCs = 0.50–0.82), with the lowest reliability on memory tests. Practice effects were apparent on some measures, especially within memory and complex cognition domains. Taken together, the adapted PennCNB exhibited adequate test–retest reliability at the domain level but variable reliability for individual tests. Differences in reliability should be considered in implementation of these tests.
CD30 Regulation of IL-13–STAT6 Pathway in Breast Implant–Associated Anaplastic Large Cell Lymphoma
Authors: Kadin Marshall E , Morgan John , Wei Wei , Song Zhihui , Yang Yibin 
Published: August 2022

Abstract

Background
Breast implant–associated anaplastic large cell lymphoma (BIA-ALCL) is a rare, usually indolent CD30+ T-cell lymphoma with tumor cells, often surrounded by eosinophils, expressing IL-13 and pSTAT6.

Objectives
The aim of this study was to understand the unique tumor pathology and growth regulation of BIA-ALCL, leading to potential targeted therapies.

Methods
We silenced CD30 and analyzed its effect on IL-13 signaling and tumor cell viability. IL-13 signaling receptors of BIA-ALCL cell lines were evaluated by flow cytometry and pSTAT6 detected by immunohistochemistry. CD30 was deleted by CRISPR/Cas9 editing. Effects of CD30 deletion on transcription of IL-13 and IL-4, and phosphorylation of STAT6 were determined by real-time polymerase chain reaction and western blotting. The effect of CD30 deletion on p38 mitogen-activated protein kinase (MAPK) phosphorylation was determined. Suppression of IL-13 transcription by a p38 MAPK inhibitor was tested. Tumor cell viability following CD30 deletion and treatment with a pSTAT6 inhibitor were measured in cytotoxicity assays.

Results
BIA-ALCL lines TLBR1 and TLBR2 displayed signaling receptors IL-4Rα, IL-13Rα1 and downstream pSTAT6. Deletion of CD30 by CRISPR/Cas9 editing significantly decreased transcription of IL-13, less so Th2 cytokine IL-4, and phosphorylation of STAT6. Mechanistically, we found CD30 expression is required for p38 MAPK phosphorylation and activation, and IL-13–STAT6 signaling was reduced by an inhibitor of p38 MAPK in BIA-ALCL tumor cells. Tumor cell viability was decreased by silencing of CD30, and a specific inhibitor of STAT6, indicating STAT6 inhibition is cytotoxic to BIA-ALCL tumor cells.

Conclusions
These findings suggest reagents targeting the IL-13 pathway, pSTAT6 and p38 MAPK, may become useful for treating BIA-ALCL patients.
SPRoBERTa: protein embedding learning with local fragment modeling
Authors: Wu Lijun , Yin Chengcan , Zhu Jinhua , Wu Zhen , He Liang , Xia Yingce , Xie Shufang , Qin Tao , Liu Tie-Yan 
Published: August 2022

Abstract
Well understanding protein function and structure in computational biology helps in the understanding of human beings. To face the limited proteins that are annotated structurally and functionally, the scientific community embraces the self-supervised pre-training methods from large amounts of unlabeled protein sequences for protein embedding learning. However, the protein is usually represented by individual amino acids with limited vocabulary size (e.g. 20 type proteins), without considering the strong local semantics existing in protein sequences. In this work, we propose a novel pre-training modeling approach SPRoBERTa. We first present an unsupervised protein tokenizer to learn protein representations with local fragment pattern. Then, a novel framework for deep pre-training model is introduced to learn protein embeddings. After pre-training, our method can be easily fine-tuned for different protein tasks, including amino acid-level prediction task (e.g. secondary structure prediction), amino acid pair-level prediction task (e.g. contact prediction) and also protein-level prediction task (remote homology prediction, protein function prediction). Experiments show that our approach achieves significant improvements in all tasks and outperforms the previous methods. We also provide detailed ablation studies and analysis for our protein tokenizer and training framework.
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction
Authors: Liu Xuan , Song Congzhi , Liu Shichao , Li Menglu , Zhou Xionghui , Zhang Wen 
Published: August 2022

Abstract

Motivation
Drug combinations have exhibited promise in treating cancers with less toxicity and fewer adverse reactions. However, in vitro screening of synergistic drug combinations is time-consuming and labor-intensive because of the combinatorial explosion. Although a number of computational methods have been developed for predicting synergistic drug combinations, the multi-way relations between drug combinations and cell lines existing in drug synergy data have not been well exploited.

Results
We propose a multi-way relation-enhanced hypergraph representation learning method to predict anti-cancer drug synergy, named HypergraphSynergy. HypergraphSynergy formulates synergistic drug combinations over cancer cell lines as a hypergraph, in which drugs and cell lines are represented by nodes and synergistic drug–drug–cell line triplets are represented by hyperedges, and leverages the biochemical features of drugs and cell lines as node attributes. Then, a hypergraph neural network is designed to learn the embeddings of drugs and cell lines from the hypergraph and predict drug synergy. Moreover, the auxiliary task of reconstructing the similarity networks of drugs and cell lines is considered to enhance the generalization ability of the model. In the computational experiments, HypergraphSynergy outperforms other state-of-the-art synergy prediction methods on two benchmark datasets for both classification and regression tasks and is applicable to unseen drug combinations or cell lines. The studies revealed that the hypergraph formulation allows us to capture and explain complex multi-way relations of drug combinations and cell lines, and also provides a flexible framework to make the best use of diverse information.

Availability and implementation
The source data and codes of HypergraphSynergy can be freely downloaded from https://github.com/liuxuan666/HypergraphSynergy.

Supplementary information
Supplementary data are available at Bioinformatics online.
Vitamin K1 and progression of cardiovascular calcifications in hemodialysis patients: The VitaVasK randomized controlled trial
Authors: Saritas Turgay , Reinartz Sebastian , Krüger Thilo , Ketteler Markus , Liangos Orfeas , Labriola Laura , Stenvinkel Peter , Kopp Christoph , Westenfeld Ralf , Evenepoel Pieter , Siepmann Robert , Wied Stephanie , Hilgers Ralf-Dieter , Schurgers Leon , Floege Jürgen ,   for the VitaVasK Investigators
Published: August 2022

Abstract

Background
Cardiovascular calcifications are prevented by matrix Gla protein (MGP), a vitamin K-dependent protein. Hemodialysis patients exhibit marked vitamin K deficiency. The randomized, prospective, open-label, multicenter VitaVasK trial analyzed whether vitamin K1 supplementation reduces progression of coronary artery calcifications (CAC) and thoracic aortic calcifications (TAC).

Methods
Patients with preexisting CAC were randomized to continue on standard care or to additionally receive 5 mg vitamin K1 orally thrice weekly. Hierarchically ordered primary end points were progression of TAC and CAC in computed tomography scans at 18 months. Linear mixed effects models with repeated measures at baseline, 12 and 18 months assessed treatment effects after adjusting for study site.

Results
Of 60 randomized patients, 20 dropped out for reasons unrelated to vitamin K1, resulting in 23 control and 17 vitamin K1 patients. The trial was stopped early due to slow recruitment. At 18 months, the average TAC progression was 56% lower in the vitamin K1 compared to the control group (p = 0.039). CAC significantly progressed within the control group, but not within the vitamin K1 group. Average progression at 18 months was 68% lower in the vitamin K1 compared to the control group (p = 0.072). Vitamin K1 reduced plasma levels of pro-calcific uncarboxylated-MGP by 69% at 18 months. No treatment-related adverse events were noted.

Conclusion
Vitamin K1 intervention is a potent, safe and cost-effective approach to correct vitamin K deficiency and to potentially reduce cardiovascular calcification in this high-risk population.
SGLT-2 inhibitors in nephrotic-range proteinuria: emerging clinical evidence
Authors: Kalay Zeynepgul , Sahin Ozgun E , Copur Sidar , Danacı Senem , Ortiz Alberto , Yau Kevin , Cherney David Z I , Kanbay Mehmet 
Published: August 2022

ABSTRACT
Sodium-glucose cotransporter-2 (SGLT-2) inhibitors are a class of novel oral anti-hyperglycemic agents which are increasingly used in clinical practice. SGLT-2 inhibitors improve glycemic control and cardiorenal outcomes, promote weight loss, and reduce blood pressure. Randomized controlled trials have demonstrated that SGLT-2 inhibitors reduce proteinuria and delay progression of kidney disease in patients with albuminuria. However, whether SGLT-2 inhibitors have similar benefits in patients with nephrotic-range proteinuria has not been well established. Evidence to date has been limited to case reports, case series and secondary analyses of randomized controlled trials. This is the first comprehensive review on the effectiveness of SGLT-2 inhibitors for the treatment of patients with nephrotic-range albuminuria or proteinuria. Overall findings support a likely beneficial role of SGLT-2 inhibitors in reducing proteinuria and delaying chronic kidney disease progression in patients with nephrotic-range proteinuria.
Intravascular molecular imaging: translating pathophysiology of atherosclerosis into human disease conditions
Authors: Seguchi Masaru , Aytekin Alp , Lenz Tobias , Nicol Philipp , Klosterman Grace R , Beele Alicia , Sabic Emina , Utsch Léa , Alyaqoob Aseel , Gorpas Dimitris , Ntziachristos Vasilis , Jaffer Farouc A , Rauschendorfer Philipp , Joner Michael 
Published: August 2022

Abstract
Progression of atherosclerotic plaque in coronary arteries is characterized by complex cellular and non-cellular molecular interactions. Within recent years, atherosclerosis has been recognized as inflammation-driven disease condition, where progressive stages are characterized by morphological changes in plaque composition but also relevant molecular processes resulting in increased plaque vulnerability. While existing intravascular imaging modalities are able to resolve key morphological features during plaque progression, they lack capability to characterize the molecular profile of advanced atherosclerotic plaque. Because hybrid imaging modalities may provide incremental information related to plaque biology, they are expected to provide synergistic effects in detecting high risk patients and lesions. The aim of this article is to review existing literature on intravascular molecular imaging approaches, and to provide clinically oriented proposals of their application. In addition, we assembled an overview of future developments in this field geared towards detection of patients at risk for cardiovascular events.
‘This was the better way’: The Restoration Afterlives of Ben Jonson’s Comic Designs
Authors: Cameron John H , Goossen Jonathan 
Published: August 2022

Abstract
The dramatists of the Restoration stage reveal the guiding influence of Ben Jonson, giving his plays a strong comedic afterlife, particularly with respect to his construction of his plots and his sense of comedic design. This article explores that influence by first considering the influences on Jonson’s own concept of comic design, particularly as derived from Aristotle, and the late-antique grammarians Euanthius and Donatus. Jonson follows Aristotle’s distinction of comedy from tragedy on the basis of the ‘laughable’ moral quality of its characters. When paired with Jonson’s own didactic bent, this distinction shaped his ‘humours’-based approach to character, and his plots’ exposure and mockery of those characters. Daniël Heinsius’s commentaries on Aristotle’s Poetics show clear consonance with Jonson’s tight integration of his humorous characters into densely unified plots by way of the trickster characters’ hoaxes. Jonson also finds in Scaliger’s unique concept of catastasis, the penultimate movement of comic plot, a definitive tactic for achieving that integration and exposure. In the light of these claims, we look at three of Jonson’s plays, Every Man Out of His Humour (1599), Volpone (1605) and Epicene, or the Silent Woman (1609), which depict his developing techniques of character, exposure hoaxes and catastasis. This leads to the later seventeenth century and John Dryden’s attentive analysis of Jonson’s comic plots, especially that of Epicene. We then show how the Jonsonian traits singled out by Dryden were used and adapted by William Wycherley in The Country Wife (1675) and William Congreve in The Way of the World (1700).
Productivity of ClonalIlex paraguariensisGenotypes in a Semi-Hydroponic System Is Reduced by Shading
Authors: de Aguiar Natália Saudade , Moreno Gabira Mônica , de Cássia Tomasi Jéssica , Mendes Duarte Manoela , Marcolino Vieira Leandro , José Lavoranti Osmir , Wendling Ivar 
Published: August 2022

AbstractYerba mate (Ilex paraguariensis A. St.-Hil.) is a South American tree cultivated in systems with or without shading at different intensities; however, there is no consensus about shading effect on leaf biomass production. Therefore, we evaluated yerba mate clones under different shading levels over one year to determine the influence of shading and genotype on biomass production. Two yerba mate genotypes (EC22 and EC40), cultivated in a semi-hydroponic system, were subjected to five shading levels (0%, 40%, 51%, 76%, and 82%) in a greenhouse. We determined total fresh biomass (branches and leaves) and fresh biomass of young and mature leaves on six harvests. Biomass production was influenced by harvest season, genotype, and shading levels. Spring and summer harvests provided higher biomass production than the other seasons. EC40 genotype produced higher total fresh and young leaf biomass than EC22. Although we observed differences among genotypes and harvest seasons, shading was the factor that most influenced biomass production. Total fresh biomass productivity was reduced 6.8 times between 0% and 82% shading for the EC40 genotype. Thus, we do not recommend high levels of shade, such as 76% and 82%, in this new yerba mate cultivation system.
Ecoregional Variation of Crimean Pine (Pinus nigrasubspeciespallasiana[Lamb.] Holmboe) Stand Growth
Authors: Seki Mehmet , Sakici Oytun Emre 
Published: August 2022

AbstractInvestigation and numerical determination of the effects of ecologically different regions on forest growth are important issues to be considered for sustainable forest management. In this study, differences in growth patterns of Crimean pine (Pinus nigra subsp. pallasiana [Lamb.] Holmboe) stands among the ecoregions located in the Kastamonu region of northwestern Turkey were investigated. For this purpose, stand-level growth models for dominant height, number of trees, basal area, and volume were fitted using the data from 274 sample plots and 293 stem analysis in even-aged, pure, and productive Crimean pine stands. The nonlinear extra sum of squares method and graphical examinations revealed that growth characteristics of these Crimean pine stands were affected by ecoregional differences. Ecoregion-based growth models, which are more flexible and have the ability to reflect the ecoregional differences in growth patterns, were found to be superior to regional models. Applying general models without any ecoregional classification resulted in biases of 5.3%, 23.1%, 5.5%, and 6.2% in the estimates of dominant height, number of trees, basal area, and volume of Crimean pine stands, respectively. The results showed that ecological differences must be considered in studies on forest growth modeling and forest management.
The measurement and modification of hypoxia in colorectal cancer: overlooked but not forgotten
Authors: Fletcher Teddy , Thompson Alex J , Ashrafian Hutan , Darzi Ara 
Published: August 2022

Abstract
Tumour hypoxia is the inevitable consequence of a tumour’s rapid growth and disorganized, inefficient vasculature. The compensatory mechanisms employed by tumours, and indeed the absence of oxygen itself, hinder the ability of all treatment modalities. The clinical consequence is poorer overall survival, disease-free survival, and locoregional control. Recognizing this, clinicians have been attenuating the effect of hypoxia, primarily with hypoxic modification or with hypoxia-activated pro-drugs, and notable success has been demonstrated. However, in the case of colorectal cancer (CRC), there is a general paucity of knowledge and evidence surrounding the measurement and modification of hypoxia, and this is possibly due to the comparative inaccessibility of such tumours. We specifically review the role of hypoxia in CRC and focus on the current evidence for the existence of hypoxia in CRC, the majority of which originates from indirect positron emission topography imaging with hypoxia selective radiotracers; the evidence correlating CRC hypoxia with poorer oncological outcome, which is largely based on the measurement of hypoxia inducible factor in correlation with clinical outcome; the evidence of hypoxic modification in CRC, of which no direct evidence exists, but is reflected in a number of indirect markers; the prognostic and monitoring implications of accurate CRC hypoxia quantification and its potential in the field of precision oncology; and the present and future imaging tools and technologies being developed for the measurement of CRC hypoxia, including the use of blood-oxygen-level-dependent magnetic resonance imaging and diffuse reflectance spectroscopy.
Immigration Experience and Cognitive Function Trajectories Among Older Chinese Immigrants
Authors: Tang Fengyan , Li Ke , Rauktis Mary E , Buckley Tommy D , Chi Iris 
Published: August 2022

AbstractObjectivesAlthough a number of studies have documented cognitive health among older immigrants in the United States, little is known about how the life-course immigration experiences are associated with cognitive trajectories among older Chinese immigrants. We assess patterns of cognitive functioning and change over time and examine whether age at migration, reasons for migration, acculturation, perceived discrimination, and preferred dialects are related to cognitive trajectories.MethodsThe sample comprised 2,075 participants from the Population Study of Chinese Elderly (PINE), who completed a battery of cognitive tests at four time points (2011–2019). Latent class growth analysis and multinomial logistic regression were utilized.ResultsThree latent classes of cognitive trajectories were identified: the low functioning with the fastest decline (LCF, 12%), the moderate functioning with a medium decline rate (MCF, 39%), and the high functioning with the slowest decline (HCF, 48%). Perceiving more discrimination reduced, whereas speaking Taishanese increased the odds of being in the LCF and MCF. High acculturation only distinguished MCF from HCF after controlling for the known factors of cognitive health such as age, education, and social engagement.DiscussionThis study identifies a group of older Chinese immigrants who are especially vulnerable to cognitive impairment and indicates that the risk of cognitive decline appears to be elevated with lower levels of acculturation and unidentified racial discrimination. More research is needed to fully understand the underlying mechanisms that link the life-course immigration experiences to cognitive health outcomes in later life.
Memory, community and the end of empire on the Isle of Dogs, 1980–2004
Authors: Gleeson Finn 
Published: August 2022

Abstract
How might we best understand the place of imperial memory in contemporary British history? Recent scholarship has tended to characterize this through one of two binary categories, pointing to either imperial ‘amnesia’ or imperial ‘nostalgia’. This article contends that sustained and detailed case studies can offer us a more sophisticated and nuanced understanding of the production of memory. It uses the example of the Island History Trust, established to help local residents of London’s Docklands protest and later adjust to the losses brought about by deindustrialization, outward migration and financialized redevelopment overseen by Margaret Thatcher’s Conservative government. Within this narrative of social and economic displacement, however, was hidden another story: residents’ lament for the empowerment and enrichment that they had in earlier life derived from their proximity to the imperial port. The Trust’s left-wing practitioners had a complex relationship with the foundational place of empire in local identity; while they perceived it as being connected to an ‘endemic’ racism among residents, they also knew it signified great pride and dignity for many. This article traces the Trust’s shifting representations of empire over time. They celebrated the imperial port when it signified residents’ enrichment, criticized it when addressing the far-right British National Party’s popularity and obscured its connection to racism when mourning the disappearing community for posterity. The article argues that case studies like this can help begin the vital work of moving past simplistic and binary analyses of imperial ‘amnesia’ or ‘nostalgia’, and towards a history of imperial memory that appreciates its fluidity, messiness and political contingency. This, it argues, is vital if we are to effectively understand the politics of imperial memory in the present.
About a Play: Stanley Middleton’s Pentrich Revolution
Authors: Steedman Carolyn 
Published: August 2022

Abstract
A school play about the Pentrich Revolution (1817) and Jeremiah Brandreth its ‘leader’, scripted in 1970–71 by teacher and novelist Stanley Middleton, reveals the history of teaching about Pentrich, to adults and children, over the previous century. Middleton’s use of the Nottinghamshire dialect to write history, in the play and his many novels, is a focus of the article.