bluuebunny/crossref_metadata_2025 huggingface dataset:
Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes
Authors: Shepherd Jack W , Payne-Dwyer Alex L , Lee Ji-Eun , Syeda Aisha , Leake Mark C
Published: May 2021

Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.
Grassroots Glasnost: Experimental Art, Participation, and Civic Life in 1980s East Berlin
Authors: Smith Briana J.
Published: May 2021

This article examines how experimental art staged in East Berlin galleries and city streets from the mid-1970s through the 1980s was used to rethink the relationship between art, social life, and citizenship under socialism. Experimental artists took advantage of the gaps in party control in order to access a second public sphere in which open communication, imagination, and critique were possible—and encouraged. The article situates East Berlin’s experimental practitioners as part of a broader pattern in East-Central Europe in which unconventional art incited a localized grassroots glasnost parallel to top-down reforms emanating from the USSR. These conceptual installations, performances, and actions challenged viewers’ traditional forms of perceiving reality and, thus, the status quo. Moreover, general audiences were often invited to participate in the process of artistic production as a form of collective action. These practices contributed to a spirit of political ferment across East-Central Europe in which more expansive and participatory forms of socialist citizenship were tested, and later contributed to the possibility for revolution. They retained their relevance in the aftermath of revolutionary change and during the postsocialist transformation as artists continued to insist on art fulfilling a social, critical, and public purpose.
Contributions of Glucose and Hemoglobin A1c Measurements in Diabetes Screening
Authors: Hilborne Lee H , Bi Caixia , Radcliff Jeff , Kroll Martin H , Kaufman Harvey W
Published: May 2021

Objectives

Given the long-term consequences of untreated diabetes, patients benefit from timely diagnoses. Payer policies often recognize glucose but not hemoglobin A1c (HbA1c) for diabetes screening. This study evaluates the different information that glucose and HbA1c provide for diabetes screening.

Methods

We conducted a retrospective review of national clinical laboratory testing during 2020 when glucose and HbA1c were ordered for routine diabetes screening, excluding patients with known diabetes, out-of-range glucose, or metabolic syndrome.

Results

Of 15.47 million glucose and HbA1c tests ordered simultaneously, 672,467 (4.35%) met screening inclusion criteria; 116,585 (17.3%) were excluded because of diabetes-related conditions or the specimen was nonfasting, leaving 555,882 result pairs. More than 1 in 4 patients 60 years of age or older with glucose within range had an elevated HbA1c level. HbA1c claims were denied more often for Medicare beneficiaries (38,918/65,273 [59.6%]) than for other health plans combined (23,234/291,764 [8.0%]).

Conclusions

Although many health plans do not cover HbA1c testing for diabetes screening, more than 1 in 4 glucose screening patients 60 years of age or older with an in-range glucose result had a concurrent elevated HbA1c result. Guideline developers and health plans should explicitly recognize that glucose and HbA1c provide complementary information and together offer improved clinical utility for diabetes screening.
Access to direct-acting antivirals for hepatitis C–negative transplant recipients receiving organs from hepatitis C–viremic donors
Authors: Bova Sarah , Cameron Andrew , Durand Christine , Katzianer Jennifer , LeGrand Meighan , Boyer Lauren , Glorioso Jaime , Toman Lindsey P
Published: May 2021

Purpose

A barrier to using organs from hepatitis C virus (HCV)-viremic donors is the high cost of direct-acting antivirals (DAAs) and concerns about access for recipients after transplantation. The purpose of this study was to evaluate access, cost, and timing for HCV DAAs following transplantation.

Methods

This was a single-center, retrospective study of HCV-negative adult transplant recipients from June 2017 to December 2019 who received grafts from HCV-viremic and/or HCV-seropositive individuals and became HCV viremic after transplantation.

Results

Between June 2017 and December 2019, there were 60 HCV-negative transplant recipients who became viremic after receiving grafts from HCV-viremic or HCV-seropositive donors. Thirty-eight patients met the inclusion criteria (n = 25 with liver transplants, n = 6 with lung transplants, n = 4 with simultaneous liver and kidney transplants, and n = 3 with kidney transplants). Of these patients, 23 had commercial insurance, 13 had Medicare, and 2 had Medicaid. All patients ultimately received insurance coverage for treatment; however, 36 (95%) required prior authorization and 9 (24%) required appeals to obtain insurance coverage. The median time from DAA prescription to insurance approval was 6 days. The median time from transplantation to start of treatment was 29 days (range, 0-84 days). Patients with Medicaid insurance had a significantly longer time to insurance approval (31.5 vs 6 days, P = 0.007). The average out-of-pocket cost to patients was less than $10 a month after patient assistance. All patients who completed treatment and 12-week follow-up after treatment achieved a sustained virologic response (n = 36).

Conclusion

In this study, all HCV-negative recipients who developed HCV following transplantation had access to DAA therapy, with the majority starting treatment in the first month after transplantation.
HEAL: an automated deep learning framework for cancer histopathology image analysis
Authors: Wang Yanan , Coudray Nicolas , Zhao Yun , Li Fuyi , Hu Changyuan , Zhang Yao-Zhong , Imoto Seiya , Tsirigos Aristotelis , Webb Geoffrey I , Daly Roger J , Song Jiangning
Published: May 2021

Motivation

Digital pathology supports analysis of histopathological images using deep learning methods at a large-scale. However, applications of deep learning in this area have been limited by the complexities of configuration of the computational environment and of hyperparameter optimization, which hinder deployment and reduce reproducibility.

Results

Here, we propose HEAL, a deep learning-based automated framework for easy, flexible and multi-faceted histopathological image analysis. We demonstrate its utility and functionality by performing two case studies on lung cancer and one on colon cancer. Leveraging the capability of Docker, HEAL represents an ideal end-to-end tool to conduct complex histopathological analysis and enables deep learning in a broad range of applications for cancer image analysis.

Availability and implementation

The docker image of HEAL is available at https://hub.docker.com/r/docurdt/heal and related documentation and datasets are available at http://heal.erc.monash.edu.au.

Supplementary information

Supplementary data are available at Bioinformatics online.
A More ‘Child-Centred’ System? Child Protection Social Workers’ Willingness to Employ Discretion
Authors: Murphy Ciarán
Published: May 2021

The Munro Review highlighted obstacles hindering the realisation of an ‘effective’ and ‘child-centred’ English child protection system, including the ‘risk’ associated with the social worker’s discretionary space. The review called for reform to enable practicing social workers to exercise their discretion in the best interests of the individual child. This article reports on the results of an iterative qualitative mixed-methods case study of one local authority child protection team, utilising focus group, questionnaire, interview, observation, documentary analysis and critical realist grounded theory, to explore whether, on encountering a discretionary space, social workers were willing to employ discretion, and the factors influencing this decision. The main findings included that social workers were experiencing discretionary space in an entrepreneurial, de jure and de facto sense and that practitioners were more likely to choose to exercise their discretion within the managerially sanctioned discretionary space. Whilst the research does offer some evidence in favour of Munro’s image for discretion within the system, it also suggests that further efforts may be required to better imbed ‘sanctioned’ discretionary space into local policy and procedures so that child protection social workers can more consistently employ their discretion in the interests of the individual child.
Use of high-content imaging to quantify transduction of AAV-PHP viruses in the brain following systemic delivery
Authors: Smith Edward J , Farshim Pamela P , Flomen Rachel , Jones Samuel T , McAteer Sean J , Deverman Benjamin E , Gradinaru Viviana , Bates Gillian P
Published: May 2021

The engineering of the AAV-PHP capsids was an important development for CNS research and the modulation of gene expression in the brain. They cross the blood brain barrier and transduce brain cells after intravenous systemic delivery, a property dependent on the genotype of Ly6a, the AAV-PHP capsid receptor. It is important to determine the transduction efficiency of a given viral preparation, as well as the comparative tropism for different brain cells; however, manual estimation of adeno-associated viral transduction efficiencies can be biased and time consuming. Therefore, we have used the Opera Phenix high-content screening system, equipped with the Harmony processing and analysis software, to reduce bias and develop an automated approach to determining transduction efficiency in the mouse brain. We used R Studio and ‘gatepoints’ to segment the data captured from coronal brain sections into brain regions of interest. C57BL/6J and CBA/Ca mice were injected with an AAV-PHP.B virus containing a green fluorescent protein reporter with a nuclear localization signal. Coronal sections at 600 μm intervals throughout the entire brain were stained with Hoechst dye, combined with immunofluorescence to NeuN and green fluorescent protein to identify all cell nuclei, neurons and transduced cells, respectively. Automated data analysis was applied to give an estimate of neuronal percentages and transduction efficiencies throughout the entire brain as well as for the cortex, striatum and hippocampus. The data from each coronal section from a given mouse were highly comparable. The percentage of neurons in the C57BL/6J and CBA/Ca brains was approximately 40% and this was higher in the cortex than striatum and hippocampus. The systemic injection of AAV-PHP.B resulted in similar transduction rates across the entire brain for C57BL/6J mice. Approximately 10–15% of all cells were transduced, with neuronal transduction efficiencies ranging from 5% to 15%, estimates that were similar across brain regions, and were in contrast to the much more localized transduction efficiencies achieved through intracerebral injection. We confirmed that the delivery of the AAV-PHP.B viruses to the brain from the vasculature resulted in widespread transduction. Our methodology allows the rapid comparison of transduction rates between brain regions producing comparable data to more time-consuming approaches. The methodology developed here can be applied to the automated quantification of any parameter of interest that can be captured as a fluorescent signal.
Queen Caroline, music and Handel revisited
Authors: Gardner Matthew
Published: May 2021

Queen Caroline (1683–1737) was a long-term supporter of Handel and his music. Her connection to the composer began in 1710 when he was appointed Kapellmeister to the Hanoverian court. In London from 1714 Caroline continued to show interest in music and Handel in particular, helping him to further develop his career. She regularly attended the opera, organized private performances at court, and ensured that her children received a good musical education—with Handel employed as a music master to her daughters. Although some royal support of music did continue after Caroline’s death, it is evident from a general decline in these years that she had been the driving force behind royal patronage, rather than her husband George II. Handel’s anthem for the funeral of Queen Caroline, The ways of Zion do mourn (1737), and individual aspects of her support of music and Handel, as well as her general interest in the arts, have received some scholarly attention. Her broader support of music in connection with Handel’s London career has, however, not been addressed in one place. This article therefore revisits Queen Caroline’s interests in music, providing new context surrounding her role in the Hanoverians’ patronage of Handel.
Statin associated lower cancer risk and related mortality in patients with heart failure
Authors: Ren Qing-Wen , Yu Si-Yeung , Teng Tiew-Hwa Katherine , Li Xue , Cheung Ka-Shing , Wu Mei-Zhen , Li Hang-Long , Wong Pui-Fai , Tse Hung-Fat , Lam Carolyn S P , Yiu Kai-Hang
Published: May 2021

Aims 

Patients with heart failure (HF) have an increased risk of incident cancer. Data relating to the association of statin use with cancer risk and cancer-related mortality among patients with HF are sparse.

Methods and results 

Using a previously validated territory-wide clinical information registry, statin use was ascertained among all eligible patients with HF (n = 87 102) from 2003 to 2015. Inverse probability of treatment weighting was used to balance baseline covariates between statin nonusers (n = 50 926) with statin users (n = 36 176). Competing risk regression with Cox proportional-hazard models was performed to estimate the risk of cancer and cancer-related mortality associated with statin use. Of all eligible subjects, the mean age was 76.5 ± 12.8 years, and 47.8% was male. Over a median follow-up of 4.1 years (interquartile range: 1.6–6.8), 11 052 (12.7%) were diagnosed with cancer. Statin use (vs. none) was associated with a 16% lower risk of cancer incidence [multivariable adjusted subdistribution hazard ratio (SHR) = 0.84; 95% confidence interval (CI), 0.80–0.89]. This inverse association with risk of cancer was duration dependent; as compared with short-term statin use (3 months to <2 years), the adjusted SHR was 0.99 (95% CI, 0.87–1.13) for 2 to <4 years of use, 0.82 (95% CI, 0.70–0.97) for 4 to <6 years of use, and 0.78 (95% CI, 0.65–0.93) for ≥6 years of use. Ten-year cancer-related mortality was 3.8% among statin users and 5.2% among nonusers (absolute risk difference, −1.4 percentage points [95% CI, −1.6% to −1.2%]; adjusted SHR = 0.74; 95% CI, 0.67–0.81).

Conclusion 

Our study suggests that statin use is associated with a significantly lower risk of incident cancer and cancer-related mortality in HF, an association that appears to be duration dependent.
Age-related functional changes of intestinal flora in rats
Authors: Yang Yuping , Chen Tianlu , Zhang Xia , Wang Xiaoyan
Published: May 2021

Intestinal flora structure and function change with age and have been associated with a variety of aging-related diseases. Until now, how age affects the functions of gut bacteria has not been fully understood. We used 16S-rRNA-sequencing technology and PICRUSt2 analysis to predict the functions encoded by intestinal flora in male Wistar rats across lifespan. We found that the abundance of gut microbiota genes encoding the L-tryptophan, L-histidine, L-leucine, inositol and catechol degradation pathways as well as L-arginine, ectoine, flavin and ubiquinol synthesis pathways increased with age. Differential analysis of the associated genera revealed that Rhodococcus spp. were significantly abundant during middle-old aged stage. This genus contributed greatly to the L-tryptophan, catechol and inositol degradation pathways as well as ectoine and L-arginine biosynthesis pathways. We concluded that gut bacteria-encoded functions such as amino acid metabolism, B vitamin metabolism, aromatic compound metabolism and energy metabolism varied in an age-dependent manner, and Rhodococcus spp. were the most associated functional bacteria in middle-old aged rats. These may be closely associated with the physiological phenotype of the aging process, which offers new insights for evaluating the relationship between intestinal flora and aging.
DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing
Authors: Dimond James L , Nguyen Nhung , Roberts Steven B
Published: May 2021

Symbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species.
DNA templates with blocked long 3ʹ end single-stranded overhangs (BL3SSO) promote bona fide Cas9-stimulated homology-directed repair of long transgenes into endogenous gene loci
Authors: Bandyopadhyay Saptaparni , Douglass Joseph , Kapell Sebastian , Khan Nazimuddin , Feitosa-Suntheimer Fabiana , Klein Jenny A , Temple Jasmine , Brown-Culbertson Jayce , Tavares Alexander H , Saeed Mohsan , Lau Nelson C
Published: May 2021

Knock-in of large transgenes by Cas9-mediated homology-directed repair (HDR) is an extremely inefficient process. Although the use of single-stranded oligonucleotides (ssODN) as an HDR donor has improved the integration of smaller transgenes, they do not support efficient insertion of large DNA sequences. In an effort to gain insights into the mechanism(s) governing the HDR-mediated integration of larger transgenes and to improve the technology, we conducted knock-in experiments targeting the human EMX1 locus and applied rigorous genomic PCR analyses in the human HEK293 cell line. This exercise revealed an unexpected molecular complication arising from the transgene HDR being initiated at the single homology arm and the subsequent genomic integration of plasmid backbone sequences. To pivot around this problem, we devised a novel PCR-constructed template containing blocked long 3' single-stranded overhangs (BL3SSO) that greatly improved the efficiency of bona fide Cas9-stimulated HDR at the EMX1 locus. We further refined BL3SSO technology and successfully used it to insert GFP transgenes into two important interferon-stimulated genes (ISGs) loci, Viperin/RSAD2, and ISG15. This study demonstrates the utility of the BL3SSO platform for inserting long DNA sequences into both constitutive and inducible endogenous loci to generate novel human cell lines for the study of important biological processes.
Environmentally contingent control of Candida albicans cell wall integrity by transcriptional regulator Cup9
Authors: Ichikawa Yuichi , Bruno Vincent M , Woolford Carol A , Kim Hannah , Do Eunsoo , Brewer Grace C , Mitchell Aaron P
Published: May 2021

The fungal pathogen Candida albicans is surrounded by a cell wall that is the target of caspofungin and other echinocandin antifungals. Candida albicans can grow in several morphological forms, notably budding yeast and hyphae. Yeast and hyphal forms differ in cell wall composition, leading us to hypothesize that there may be distinct genes required for yeast and hyphal responses to caspofungin. Mutants in 27 genes reported previously to be caspofungin hypersensitive under yeast growth conditions were all caspofungin hypersensitive under hyphal growth conditions as well. However, a screen of mutants defective in transcription factor genes revealed that Cup9 is required for normal caspofungin tolerance under hyphal and not yeast growth conditions. In a hyphal-defective efg1Δ/Δ background, Cup9 is still required for normal caspofungin tolerance. This result argues that Cup9 function is related to growth conditions rather than cell morphology. RNA-seq conducted under hyphal growth conditions indicated that 361 genes were up-regulated and 145 genes were down-regulated in response to caspofungin treatment. Both classes of caspofungin-responsive genes were enriched for cell wall-related proteins, as expected for a response to disruption of cell wall integrity and biosynthesis. The cup9Δ/Δ mutant, treated with caspofungin, had reduced RNA levels of 40 caspofungin up-regulated genes, and had increased RNA levels of 8 caspofungin down-regulated genes, an indication that Cup9 has a narrow rather than global role in the cell wall integrity response. Five Cup9-activated surface-protein genes have roles in cell wall integrity, based on mutant analysis published previously (PGA31 and IFF11) or shown here (ORF19.3499, ORF19.851, or PGA28), and therefore may explain the hypersensitivity of the cup9Δ/Δmutant to caspofungin. Our findings define Cup9 as a new determinant of caspofungin susceptibility.
Parallel and population-specific gene regulatory evolution in cold-adapted fly populations
Authors: Huang Yuheng , Lack Justin B , Hoppel Grant T , Pool John E
Published: May 2021

Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
Care, Dementia, and the Fourth Age in Erica Jong’s Later Work
Authors: Stončikaitė Ieva
Published: May 2021

Background and Objectives

This article addresses the representations of dementia and caregiving in the fourth age as depicted in Erica Jong’s later-life work. It shows how the experience of parental care leads to the discovery of new ways of human interaction and expressions of personhood.

Research Design and Methods

Framed within literary–cultural age studies, this article shows how humanities-based inquiry can illuminate important aspects of aging and care of the oldest old, which are significant and revealing, but often hidden under the dark shadow of dementia.

Results

Newly discovered ways of communication challenge the notion of the loss of agency as they demonstrate that the body itself has the power of creative and intentional capacities and self-expression.

Discussion and Implications

Care-related narratives offer new insights into aging, dementia, and subjectivity that can help pursue a better analysis of the “deep” old age, strengthen collective solidarity, and manage increasing ageism, especially pronounced during the coronavirus disease 2019 pandemic.
Modeling gap junction beta 2 gene-related deafness with human iPSC
Authors: Fukunaga Ichiro , Oe Yoko , Danzaki Keiko , Ohta Sayaka , Chen Cheng , Shirai Kyoko , Kawano Atsushi , Ikeda Katsuhisa , Kamiya Kazusaku
Published: May 2021

There are >120 forms of non-syndromic deafness associated with identified genetic loci. In particular, mutation of the gap junction beta 2 gene (GJB2), which encodes connexin (CX)26 protein, is the most frequent cause of hereditary deafness worldwide. We previously described an induction method to develop functional CX26 gap junction-forming cells from mouse-induced pluripotent stem cells (iPSCs) and generated in vitro models for GJB2-related deafness. However, functional CX26 gap junction-forming cells derived from human iPSCs or embryonic stem cells (ESCs) have not yet been reported. In this study, we generated human iPSC-derived functional CX26 gap junction-forming cells (iCX26GJCs), which have the characteristics of cochlear supporting cells. These iCX26GJCs had gap junction plaque-like formations at cell–cell borders and co-expressed several markers that are expressed in cochlear supporting cells. Furthermore, we generated iCX26GJCs derived from iPSCs from two patients with the most common GJB2 mutation in Asia, and these cells reproduced the pathology of GJB2-related deafness. These in vitro models may be useful for establishing optimal therapies and drug screening for various mutations in GJB2-related deafness.
NovelLRRK2mutations and other rare, non-BAP1-related candidate tumor predisposition gene variants in high-risk cancer families with mesothelioma and other tumors
Authors: Cheung Mitchell , Kadariya Yuwaraj , Sementino Eleonora , Hall Michael J , Cozzi Ilaria , Ascoli Valeria , Ohar Jill A , Testa Joseph R
Published: May 2021

There is irrefutable evidence that germline BRCA1-associated protein 1 gene (BAP1) mutations contribute to malignant mesothelioma (MM) susceptibility. However, BAP1 mutations are not found in all cases with evidence of familial MM or in other high-risk cancer families affected by various cancers, including MM. The goal of this study was to use whole genome sequencing (WGS) to determine the frequency and types of germline gene variants occurring in 12 MM patients who were selected from a series of 141 asbestos-exposed MM patients with a family history of cancer but without a germline BAP1 mutation. WGS was also performed on two MM cases, a proband and sibling, from a previously reported family with multiple cases of MM without the inheritance of a predisposing BAP1 mutation. Altogether, germline DNA sequencing variants were identified in 21 cancer-related genes in 10 of the 13 probands. Germline indel, splice site and missense mutations and two large deletions were identified. Among the 13 MM index cases, 6 (46%) exhibited one or more predicted pathogenic mutations. Affected genes encode proteins involved in DNA repair (ATM, ATR, BRCA2, BRIP1, CHEK2, MLH3, MUTYH, POLE, POLE4, POLQ and XRCC1), chromatin modification (ARID1B, DNMT3A, JARID2 and SETD1B) or other cellular pathways: leucine-rich repeat kinase 2 gene (LRRK2) (two cases) and MSH4. Notably, somatic truncating mutation or deletions of LRRK2 were occasionally found in MMs in The Cancer Genome Atlas, and the expression of LRRK2 was undetectable or downregulated in a majority of primary MMs and MM cell lines we examined, implying that loss of LRRK2 expression is a newly recognized tumor suppressor alteration in MM.
High-altitude pulmonary edema is aggravated by risk loci and associated transcription factors in HIF-prolyl hydroxylases
Authors: Sharma Kavita , Mishra Aastha , Singh Himanshu N , Parashar Deepak , Alam Perwez , Thinlas Tashi , Mohammad Ghulam , Kukreti Ritushree , Syed Mansoor Ali , Pasha M A Qadar
Published: May 2021

High-altitude (HA, >2500 m) hypoxic exposure evokes several physiological processes that may be abetted by differential genetic distribution in sojourners, who are susceptible to various HA disorders, such as high-altitude pulmonary edema (HAPE). The genetic variants in hypoxia-sensing genes influence the transcriptional output; however the functional role has not been investigated in HAPE. This study explored the two hypoxia-sensing genes, prolyl hydroxylase domain protein 2 (EGLN1) and factor inhibiting HIF-1α (HIF1AN) in HA adaptation and maladaptation in three well-characterized groups: highland natives, HAPE-free controls and HAPE-patients. The two genes were sequenced and subsequently validated through genotyping of significant single nucleotide polymorphisms (SNPs), haplotyping and multifactor dimensionality reduction. Three EGLN1 SNPs rs1538664, rs479200 and rs480902 and their haplotypes emerged significant in HAPE. Blood gene expression and protein levels also differed significantly (P < 0.05) and correlated with clinical parameters and respective alleles. The RegulomeDB annotation exercises of the loci corroborated regulatory role. Allele-specific differential expression was evidenced by luciferase assay followed by electrophoretic mobility shift assay, liquid chromatography with tandem mass spectrometry and supershift assays, which confirmed allele-specific transcription factor (TF) binding of FUS RNA-binding protein (FUS) with rs1538664A, Rho GDP dissociation inhibitor 1 (ARHDGIA) with rs479200T and hypoxia upregulated protein 1 (HYOU1) with rs480902C. Docking simulation studies were in sync for the DNA-TF structural variations. There was strong networking among the TFs that revealed physiological consequences through relevant pathways. The two hydroxylases appear crucial in the regulation of hypoxia-inducible responses.
HG-9-91-01 Attenuates Murine Experimental Colitis by Promoting Interleukin-10 Production in Colonic Macrophages Through the SIK/CRTC3 Pathway
Authors: Fu Yong , Ma Gailing , Zhang Yuqian , Wang Wenli , Shi Tongguo , Zhu Jie , Zhang Junfeng , Huang Zhen , Chen Jiangning
Published: May 2021

Background

Interleukin-10 (IL-10) is a potent immunoregulatory cytokine that plays a pivotal role in maintaining mucosal immune homeostasis. As a novel synthetic inhibitor of salt-inducible kinases (SIKs), HG-9-91-01 can effectively enhance IL-10 secretion at the cellular level, but its in vivo immunoregulatory effects remain unclear. In this study, we investigated the effects and underlying mechanism of HG-9-91-01 in murine colitis models.

Methods

The anti-inflammatory effects of HG-9-91-01 were evaluated on 2, 4, 6-trinitrobenzene sulfonic acid (TNBS)-, dextran sulfate sodium–induced colitis mice, and IL-10 knockout chronic colitis mice. The in vivo effector cell of HG-9-91-01 was identified by fluorescence-activated cell sorting and quantitative real-time polymerase chain reaction. The underlying mechanism of HG-9-91-01 was investigated via overexpressing SIKs in ANA-1 macrophages and TNBS colitis mice.

Results

Treatment with HG-9-91-01 showed favorable anticolitis effects in both TNBS- and DSS-treated mice through significantly promoting IL-10 expression in colonic macrophages but failed to protect against IL-10 KO murine colitis. Further study indicated that HG-9-91-01 markedly enhanced the nuclear level of cAMP response element-binding protein (CREB)-regulated transcription coactivator 3 (CRTC3), whereas treatment with lentiviruses encoding SIK protein markedly decreased the nuclear CRTC3 level in HG-9-91-01–treated ANA-1 macrophages. In addition, intracolonic administration with lentiviruses encoding SIK protein significantly decreased the nuclear CRTC3 level in the lamina propria mononuclear cells and ended the anti-inflammatory activities of HG-9-91-01.

Conclusions

We found that HG-9-91-01 promoted the IL-10 expression of colonic macrophages and exhibited its anticolitis activity through the SIK/CRTC3 axis, and thus it may represent a promising strategy for inflammatory bowel disease therapy.
The Impact of Alcohol in Inflammatory Bowel Diseases
Authors: White Bradley A , Ramos Guilherme Piovezani , Kane Sunanda
Published: May 2021

Several environmental factors have been implicated in the pathogenesis of inflammatory bowel diseases (IBD); however, the evidence for alcohol is sparse, as is its implications on disease activity and overall management. Here, we examine the available evidence for the effect of alcohol on IBD, including its association with the development of IBD, role in exacerbations, and potential medication interactions. Several mechanisms have been demonstrated to mediate the effects of ethanol in the gastrointestinal tract. Alcohol has been shown to alter the gut microbiome, disrupt intestinal barrier, and increase intestinal permeability, directly and indirectly promoting immune activation. Conversely, specific alcoholic beverages, notably red wine, may have anti-inflammatory properties capable of assisting in disease control and affecting disease monitoring. Nonetheless, most alcohol-mediated effects seem to facilitate intestinal inflammation and consequently impact disease onset, recurrence, and symptom control. Furthermore, alcohol use interferes with the metabolism of several medications leading to increased side effect profiles or even loss of effect. Notably, mesalamine, azathioprine, methotrexate, and biologic medications can all be affected by concomitant alcohol intake via a variety of mechanisms.
Influenza Vaccines: Successes and Continuing Challenges
Authors: Becker Tanja , Elbahesh Husni , Reperant Leslie A , Rimmelzwaan Guus F , Osterhaus Albert D M E
Published: May 2021

Influenza vaccines have been available for over 80 years. They have contributed to significant reductions in influenza morbidity and mortality. However, there have been limitations in their effectiveness, in part due to the continuous antigenic evolution of seasonal influenza viruses, but also due to the predominant use of embryonated chicken eggs for their production. The latter furthermore limits their worldwide production timelines and scale. Therefore today, alternative approaches for their design and production are increasingly pursued, with already licensed quadrivalent seasonal influenza vaccines produced in cell cultures, including based on a baculovirus expression system. Next-generation influenza vaccines aim at inducing broader and longer-lasting immune responses to overcome seasonal influenza virus antigenic drift and to timely address the emergence of a new pandemic influenza virus. Tailored approaches target mechanisms to improve vaccine-induced immune responses in individuals with a weakened immune system, in particular older adults.
Hyperglycemia minimally alters primary self-renewing human colonic epithelial cells while TNFα-promotes severe intestinal epithelial dysfunction
Authors: Dutton Johanna S , Hinman Samuel S , Kim Raehyun , Attayek Peter J , Maurer Mallory , Sims Christopher S , Allbritton Nancy L
Published: May 2021

Hyperglycemia is thought to increase production of inflammatory cytokines and permeability of the large intestine. Resulting intestinal inflammation is then often characterized by excess secretion of tumor necrosis factor alpha (TNFα). Thus, hyperglycemia in hospitalized patients suffering from severe trauma or disease is frequently accompanied by TNFα secretion, and the combined impact of these insults on the intestinal epithelium is poorly understood. This study utilized a simple yet elegant model of the intestinal epithelium, comprised of primary human intestinal stem cells and their differentiated progeny, to investigate the impact of hyperglycemia and inflammatory factors on the colonic epithelium. When compared to epithelium cultured under conditions of physiologic glucose, cells under hyperglycemic conditions displayed decreased mucin-2 (MUC2), as well as diminished alkaline phosphatase (ALP) activity. Conditions of 60 mM glucose potentiated secretion of the cytokine IL-8 suggesting that cytokine secretion during hyperglycemia may be a source of tissue inflammation. TNFα measurably increased secretion of IL-8 and IL-1β, which was enhanced at 60 mM glucose. Surprisingly, intestinal permeability and paracellular transport were not altered by even extreme levels of hyperglycemia. The presence of TNFα increased MUC2 presence, decreased ALP activity, and negatively impacted monolayer barrier function. When TNFα hyperglycemia and ≤30 mM glucose and were combined, MUC2 and ALP activity remained similar to that of TNFα alone, although synergistic effects were seen at 60 mM glucose. An automated image analysis pipeline was developed to assay changes in properties of the zonula occludens-1 (ZO-1)-demarcated cell boundaries. While hyperglycemia alone had little impact on cell shape and size, cell morphologic properties were extraordinarily sensitive to soluble TNFα. These results suggest that TNFα acted as the dominant modulator of the epithelium relative to glucose, and that control of inflammation rather than glucose may be key to maintaining intestinal homeostasis.
Automated production of research data marts from a canonical fast healthcare interoperability resource data repository: applications to COVID-19 research
Authors: Lenert Leslie A , Ilatovskiy Andrey V , Agnew James , Rudisill Patricia , Jacobs Jeff , Weatherston Duncan , Deans Jr Kenneth R
Published: May 2021

Objective

The rapidly evolving COVID-19 pandemic has created a need for timely data from the healthcare systems for research. To meet this need, several large new data consortia have been developed that require frequent updating and sharing of electronic health record (EHR) data in different common data models (CDMs) to create multi-institutional databases for research. Traditionally, each CDM has had a custom pipeline for extract, transform, and load operations for production and incremental updates of data feeds to the networks from raw EHR data. However, the demands of COVID-19 research for timely data are far higher, and the requirements for updating faster than previous collaborative research using national data networks have increased. New approaches need to be developed to address these demands.

Methods

In this article, we describe the use of the Fast Healthcare Interoperability Resource (FHIR) data model as a canonical data model and the automated transformation of clinical data to the Patient-Centered Outcomes Research Network (PCORnet) and Observational Medical Outcomes Partnership (OMOP) CDMs for data sharing and research collaboration on COVID-19.

Results

FHIR data resources could be transformed to operational PCORnet and OMOP CDMs with minimal production delays through a combination of real-time and postprocessing steps, leveraging the FHIR data subscription feature.

Conclusions

The approach leverages evolving standards for the availability of EHR data developed to facilitate data exchange under the 21st Century Cures Act and could greatly enhance the availability of standardized datasets for research.
Application and evaluation of a K-Medoids-based shape clustering method for an articulated design space
Authors: Yousif Shermeen , Yan Wei
Published: May 2021

Research on articulating the design space in computational generative systems is ongoing, to overcome the issue of possible overwhelming multiplicity and redundancy of emerging design options. The article contributes to this line of research of design space articulation, in order to facilitate designers’ successful exploration in computational design. We have recently developed a method for shape clustering using K-Medoids, a machine learning-based strategy. The method performs clustering of similar design shapes and retrieves a representative shape for each cluster in 2D grid-based representation. In this paper, we present a progress in our project where the method has been applied to a new test case, and empirically verified using clustering evaluation methods. Our clustering evaluation results show comparable accuracy when assessed against an external study and provide insight into the evaluation criteria for machine learning methods, as presented in the paper.
Comparison of Artificial Diets and Natural Prey for Mass Rearing of Orius strigicollis (Hemiptera: Anthocoridae) Using Demographic Characteristics to Optimize Cost-Efficiency
Authors: Hung Yi-Ting , Yang Chin-Cheng Scotty , Saska Pavel , Tuan Shu-Jen
Published: May 2021

Orius strigicollis (Poppius) has been commonly released to control minute pests due to its remarkable foraging and predation ability. Despite decades long history of mass-rearing using eggs of Cadra cautella Walker (Lepidoptera: Pyralidae) as food, the cost of this food impeded the predator’s marketing potential. Finding cost-effective artificial diets for mass rearing programs is, therefore, the key to promote the use of this generalist predator in practice. The aim of this study was to explore suitability of alternative diets for mass rearing of this predator, using the age-stage, two-sex life table. Eight recipes of artificial diets were initially screened, and the candidate diets were subsequently evaluated using the population parameters of O. strigicollis. The highest intrinsic rate of increase was found in the O. strigicollis fed on the meridic combined Diet 1, where nymphs and adults were fed different diets. However, the intensive period of oviposition by females reared on oligidic Diet O3 contributed to the shorter rearing period (42 d) and lower rearing cost than that on combined Diet 1 (60 d). Besides, with the harvest rate of 0.919, the minimal population size of 10,774 individuals with a stable age-stage distribution was needed for daily harvesting 1,000 third instars of O. strigicollis reared on Diet O3 at the rearing cost of 0.295 NTD (new Taiwanese dollar) per nymph. Thus, Diet O3 was determined to be the most cost-effective recipe for the mass-rearing of O. strigicollis among those used in this study.
Intraday Trades Profile Estimation: An Intensity Approach
Authors: Sancetta Alessio
Published: May 2021

The intraday trades profile is the expected intensity of a counting process where the counts measure the number of trades over an interval. It needs to capture the salient features of the trading activity, its spikes, and periods of relative quietness. This calls for an estimator with a time varying resolution that allows us to identify jumps. The problem can be recast as a regression one, using a fused Lasso penalty. The framework allows us to identify jumps within possibly thousands different locations within a day when the number of trading days at disposal is in the order of hundreds. This can be done without imposing any conditions on the counting process except for certain regularity conditions on the expected intensity. The empirical results suggest that much of the trading activity in some liquid futures can be captured by a deterministic seasonal component in the trade arrival process.
How US Private Foundations Change Payouts Based on Financial Shocks: Revealed Publicness or Revealed Privateness?
Authors: Calabrese Thad D , Ely Todd L
Published: May 2021

This article asks what distribution behavior of private foundations in the United States reveals about their motivations and strategy. Do private foundations intentionally distribute additional money to grantees to help them manage through business cycles and maintain services during economic downturns? Such behavior would be consistent with revealed publicness with respect to distributions. Do they retrench during difficult economic times to protect their endowments? Or do they simply distribute money independent from the larger economy? The current study considers these conflicting expectations, and empirically tests whether private foundation distributions vary with endowment returns and the larger economy as suggested by competing theories. Using administrative data filed with the Internal Revenue Service, fixed effects regression models indicate that private foundations change distributions in a manner consistent with retrenchment or independently from the larger economy, depending on the sample used. The results do not support the notion that private foundations act with prosocial-countercyclical motivations about distributions—in which more money is distributed during economic downturns—despite their receiving significant public subsidies.