bluuebunny/crossref_metadata_2025 huggingface dataset:
Sclerostin and DKK1 circulating levels associate with low bone turnover in patients with chronic kidney disease Stages 3 and 4
Authors: Neto Ricardo , Pereira Luciano , Magalhães Juliana , Quelhas-Santos Janete , Martins Sandra , Carvalho Catarina , Frazão João Miguel
Published: May 2021

Background

Disordered mineral and bone metabolism is a common complication of chronic kidney disease (CKD). Bone biopsy remains the gold standard tool for evaluating renal osteodystrophy (ROD), but it is an invasive procedure. Despite a growing interest in the ability of newer bone biomarkers to discriminate between different forms of ROD, data on pre-dialysis patients are scarce.

Methods

A cross-sectional study was conducted in a cohort of 56 patients with CKD Stages 3 and 4. Participants underwent a transiliac bone biopsy after a course of double tetracycline labelling. Circulating levels of Wnt signalling inhibitors sclerostin and Dickkopf-1 (DKK1), soluble receptor activator of nuclear factor-κB ligand (sRANKL) and osteoprotegerin were measured and correlated with histomorphometric analysis results.

Results

Most patients had abnormal bone histology and low-turnover bone disease was the predominant form of ROD. Characteristics associated with high bone turnover were worse renal function, lower serum calcium and higher intact parathyroid hormone and fibroblast growth factor-23 levels. Patients with low bone turnover, on the other hand, presented with higher sclerostin along with lower DKK1 and sRANKL levels. In the multivariable logistic regression analysis, sclerostin and DKK1 levels were independently associated with low-turnover bone disease.

Conclusions

Our results suggest that circulating levels of Wnt signalling inhibitors sclerostin and DKK1 are predictive of low-turnover bone disease in patients not yet on dialysis. Further research is needed to assess the performance of these bone turnover biomarkers, compared with histomorphometric analysis, in the diagnosis and treatment monitoring of ROD.
Pushing against an open door: Agamben on Hadot and Foucault
Authors: Sharpe Matthew J , Stettler Matteo J
Published: May 2021

This article provides a rejoinder to Giorgio Agamben’s interpretation of the Hadot-Foucault dialogue, which appeared in the pivotal ‘Intermezzo’ of The Use of Bodies. In ‘Pushing against the open door’ section, we provide a close reading of Agamben’s claims about Hadot’s alleged misreadings of Foucault on the ancients and on subjectivity more widely. We demonstrate how, far from rebutting Hadot, these claims end up confirming the latter’s positions on Foucault malgré Agamben. In ‘Wisdom, the cosmic dimension, and the “objectivist-exercisant” self’ section, we draw on classicist Christopher Gill’s notion of the ‘objectivist-participant’ self in Greco-Roman Antiquity, to argue that the deepest stakes of the debate between Foucault and Hadot do not implicate Hadot’s incompetence, as Agamben suggests. They concern Foucault’s unease, as well as Agamben’s misunderstanding, of the objective and participative dimensions of ancient conceptions of selfhood. In ‘The ghosts of christianities past’ section, we contest the recurrent tendency of commentators, like Agamben, to assume latent carry-overs of Hadot’s early religiosity in his later works on Greek and Roman philosophy and spiritual exercises as reflecting the long shadow of Christianity in postmodern thought.
Attribution and Knowledge Creation Assemblages in Cybersecurity Politics
Authors: Egloff Florian J , Dunn Cavelty Myriam
Published: May 2021

Attribution is central to cybersecurity politics. It establishes a link between technical occurrences and political consequences by reducing the uncertainty about who is behind an intrusion and what the likely intent was, ultimately creating cybersecurity “truths” with political consequences. In a critical security studies’ spirit, we purport that the “truth” about cyber-incidents that is established through attribution is constructed through a knowledge creation process that is neither value-free nor purely objective but built on assumptions and choices that make certain outcomes more or less likely. We conceptualize attribution as a knowledge creation process in three phases – incident creation, incident response, and public attribution – and embark on identifying who creates what kind of knowledge in this process, when they do it, and on what kind of assumptions and previous knowledge this is based on. Using assemblage theory as a backdrop, we highlight attribution as happening in complex networks that are never stable but always shifting, assembled, disassembled and reassembled in different contexts, with multiple functionalities. To illustrate, we use the intrusions at the US Office of Personnel Management (OPM) discovered in 2014 and 2015 with a focus on three factors: assumptions about threat actors, entanglement of public and private knowledge creation, and self-reflection about uncertainties. When it comes to attribution as knowledge creation processes, we critique the strong focus on existing enemy images as potentially crowding out knowledge on other threat actors, which in turn shapes the knowledge structure about security in cyberspace. One remedy, so we argue, is to bring in additional data collectors from the academic sector who can provide alternative interpretations based on independent knowledge creation processes.
An overview of graph databases and their applications in the biomedical domain
Authors: Timón-Reina Santiago , Rincón Mariano , Martínez-Tomás Rafael
Published: May 2021

Over the past couple of decades, the explosion of densely interconnected data has stimulated the research, development and adoption of graph database technologies. From early graph models to more recent native graph databases, the landscape of implementations has evolved to cover enterprise-ready requirements. Because of the interconnected nature of its data, the biomedical domain has been one of the early adopters of graph databases, enabling more natural representation models and better data integration workflows, exploration and analysis facilities. In this work, we survey the literature to explore the evolution, performance and how the most recent graph database solutions are applied in the biomedical domain, compiling a great variety of use cases. With this evidence, we conclude that the available graph database management systems are fit to support data-intensive, integrative applications, targeted at both basic research and exploratory tasks closer to the clinic.
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies
Authors: Andrés-Hernández Liliana , Halimi Razlin Azman , Mauleon Ramil , Mayes Sean , Baten Abdul , King Graham J
Published: May 2021

Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systematic description of metadata often limits integration and sharing. We therefore aimed to understand some of the challenges facing findable, accesible, interoperable and reusable (FAIR) curation and annotation of phenotypic data from minor and underutilized crops. We used bambara groundnut (Vigna subterranea) as an exemplar underutilized crop to assess the ability of the Crop Ontology system to facilitate curation of trait datasets, so that they are accessible for comparative analysis. This involved generating a controlled vocabulary Trait Dictionary of 134 terms. Systematic quantification of syntactic and semantic cohesiveness of the full set of 28 crop-specific COs identified inconsistencies between trait descriptor names, a relative lack of cross-referencing to other ontologies and a flat ontological structure for classifying traits. We also evaluated the Minimal Information About a Phenotyping Experiment and FAIR compliance of bambara trait datasets curated within the CropStoreDB schema. We discuss specifications for a more systematic and generic approach to trait controlled vocabularies, which would benefit from representation of terms that adhere to Open Biological and Biomedical Ontologies principles. In particular, we focus on the benefits of reuse of existing definitions within pre- and post-composed axioms from other domains in order to facilitate the curation and comparison of datasets from a wider range of crops.

Database URL: https://www.cropstoredb.org/cs_bambara.html
Impact of standardized clinical pathways on esophagectomy: a systematic review and meta-analysis
Authors: Puccetti Francesco , Wijnhoven Bas P L , Kuppusamy MadhanKumar , Hubka Michal , Low Donald E
Published: May 2021

Esophageal surgery is historically associated with adverse postoperative outcomes. Selected high-volume centers have previously reported the effect on clinical outcomes following the adoption of a standardized clinical pathway (SCP). This meta-analysis aims to evaluate the current literature to document the effect of SCP and enhanced recovery after surgery (ERAS) on esophagectomy outcomes. A literature search was conducted through the main search engines (PubMed, Embase, Medline, and Cochrane database) in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. All eligible comparative studies (randomized control trial, prospective, retrospective, and combined) were identified and assessed based on Methodological Index for Non-Randomized Studies and Jadad quality criteria. Data concerning overall morbidity, early mortality, and length of stay (LOS) were primarily collected and compared. Secondary outcomes included anastomotic leaks, pulmonary complications, and readmission rate. Twenty-six articles (including five randomized controlled trials and six prospective trials) were included in the analysis. Overall study quality was moderate and the included studies utilized a variable approach to SCP. No statistically significant differences were found between groups in terms of overall morbidity, postoperative mortality, anastomotic leak, and readmission rates. Significant improvements included pulmonary complications (odds ratios [OR] 0.66, 95% confidence interval [CI] 0.49–0.94) and hospital LOS (OR −3.68, 95% CI −4.49 to −2.87). Previous reports of SCP within esophagectomy programs have demonstrated clinical improvements in postoperative pulmonary complications and LOS. Given the high heterogeneity historically demonstrated within SCPs, further improvement in outcomes should be expected following the adoption of standardized ERAS guidelines.
Immunological Networks Defining the Heterogeneity of Inflammatory Bowel Diseases
Authors: Selin Katja A , Hedin Charlotte R H , Villablanca Eduardo J
Published: May 2021

Current practice in IBD is to classify patients based on clinical signs and symptoms and provide treatments accordingly. However, the response of IBD patients to available treatments is highly variable, highlighting clinically significant heterogeneity among patients. Thus, more accurate patient stratification is urgently needed to more effectively target therapeutic interventions to specific patients. Here we review the degree of heterogeneity in IBD, discussing how the microbiota, genetics, and immune system may contribute to the variation among patients. We highlight how molecular heterogeneity may relate to clinical phenotype, but in other situations may be independent of clinical phenotype, encouraging future studies to fill the gaps. Finally, we discuss novel stratification methodologies as a foundation for precision medicine, in particular a novel stratification strategy based on conserved genes across species. All of these dimensions of heterogeneity have potential to provide strategies for patient stratification and move IBD practice towards personalised medicine.
Pre-hospital heparin use for ST-elevation myocardial infarction is safe and improves angiographic outcomes
Authors: Bloom Jason E , Andrew Emily , Nehme Ziad , Dinh Diem T , Fernando Himawan , Shi William Y , Vriesendorp Pieter , Nanayakarra Shane , Dawson Luke P , Brennan Angela , Noaman Samer , Layland Jamie , William Jeremy , Al-Fiadh Ali , Brooks Matthew , Freeman Melanie , Hutchinson Adam , McGaw David , Van Gaal William , Willson William , White Anthony , Prakash Roshan , Reid Christopher , Lefkovits Jeffrey , Duffy Stephen J , Chan William , Kaye David M , Stephenson Michael , Bernard Stephen , Smith Karen , Stub Dion
Published: May 2021

Aims

This study aims to evaluate if pre-hospital heparin administration by paramedics is safe and improves clinical outcomes.

Methods and results

Using the multicentre Victorian Cardiac Outcomes Registry, linked with state-wide ambulance records, we identified consecutive patients undergoing primary percutaneous coronary intervention for STEMI between January 2014 and December 2018. Information on thrombolysis in myocardial infarction (TIMI) flow at angiography was available in a subset of cases. Patients receiving pre-hospital heparin were compared to those who did not receive heparin. Findings at coronary angiography and 30-day clinical outcomes were compared between groups. Propensity-score matching was performed for risk adjustment. We identified a total of 4720 patients. Of these, 1967 patients had TIMI flow data available. Propensity-score matching in the entire cohort yielded 1373 matched pairs. In the matched cohort, there was no observed difference in 30-day mortality (no-heparin 3.5% vs. heparin 3.0%, P = 0.25), MACCE (no-heparin 7% vs. heparin 6.2%, P = 0.44), and major bleeding (no-heparin 1.9% vs. heparin 1.4%, P = 0.64) between groups. Propensity-score analysis amongst those with TIMI data produced 552 matched pairs. The proportion of cases with TIMI 0 or 1 flow in the infarct-related artery (IRA) was lower among those receiving pre-hospital heparin (66% vs. 76%, P < 0.001) compared to those who did not.

Conclusion 

In this multicentre, propensity-score matched study, the use of pre-hospital heparin by paramedics was safe and is associated with fewer occluded IRAs in patients presenting with STEMI.
Directly measured vs. calculated remnant cholesterol identifies additional overlooked individuals in the general population at higher risk of myocardial infarction
Authors: Varbo Anette , Nordestgaard Børge G
Published: May 2021

Aims 

We tested the hypothesis that high directly measured remnant cholesterol is associated with increased risk of ischaemic heart disease (IHD) and myocardial infarction (MI) in the general population. We also explored whether directly measured vs. calculated remnant cholesterol is superior in identifying individuals at increased risk.

Methods and results 

Overall, 16 207 individuals from the Copenhagen General Population Study with both directly measured and calculated remnant cholesterol, both representing cholesterol content in triglyceride-rich lipoproteins, were followed up for 14 years to analyse the risk for IHD and MI. For directly measured and calculated remnant cholesterol, hazard ratios for individuals with concentrations ≥95th percentile vs. <40th percentile were 1.75 (95% confidence interval 1.42–2.15) and 1.76 (1.42–2.17) for IHD and 2.05 (1.50–2.80) and 1.93 (1.40–2.66) for MI. Compared to individuals with both directly measured and calculated remnant cholesterol <80th percentile (75% of the whole population), those with only directly measured remnant cholesterol ≥80th percentile (5%) had hazard ratios of 1.42 (1.15–1.75) for IHD and 1.83 (1.35–2.47) for MI. Corresponding hazard ratios for individuals with only calculated remnant cholesterol ≥80th percentile (5%) were 1.14 (0.91–1.44) and 1.14 (0.80–1.62), respectively, and corresponding hazard ratios for individuals with both directly measured and calculated remnant cholesterol ≥80th percentiles (15%) were 1.48 (1.30–1.68) and 1.67 (1.38–2.01), respectively. In individuals with high directly measured or high calculated remnant cholesterol, the median directly measured remnant cholesterol was 1.9 and 1.5 mmol/L, the median plasma triglycerides were 2.0 and 2.7 mmol/L, and the median plasma apolipoprotein B was 132 and 142 mg/dL, respectively.

Conclusions 

Directly measured vs. calculated remnant cholesterol identifies 5% overlooked individuals in the general population with cholesterol-rich, triglyceride-poor remnants and 1.8-fold increased risk of MI.
Effectiveness and safety of a single freeze strategy of cryoballoon ablation of atrial fibrillation: an EHRA systematic review and meta-analysis
Authors: Farkowski Michal Miroslaw , Karlinski Michal , Barra Sergio , Providencia Rui , Golicki Dominik , Pytkowski Mariusz , Anic Ante , Chun Julian Kyoung Ryul , de Asmundis Carlo , Lane Deirdre Anne , Boveda Serge
Published: May 2021

To conduct a systematic review and meta-analysis to compare the effectiveness and safety of cryoballoon ablation of atrial fibrillation (AF) performed using a single freeze strategy in comparison to an empiric double (‘bonus’) freeze strategy. We systematically searched MEDLINE, EMBASE, and CENTRAL databases from inception to 12 July 2020, for prospective and retrospective studies of patients undergoing cryoballoon for paroxysmal or persistent AF comparing a single vs. bonus freeze strategy. The main outcome was atrial arrhythmia-free survival and eligible studies required at least 12 months of follow-up; the primary safety outcome was a composite of all complications. Study quality was assessed using the Cochrane risk of bias tool and the Newcastle–Ottawa Scale. Thirteen studies (3 randomized controlled trials and 10 observational studies) comprising 3163 patients were eligible for inclusion (64% males, 71.5% paroxysmal AF, mean CHA2DS2-VASc score 1.3 ± 0.9). There was no significant difference in pooled effectiveness between single freeze strategy compared to double freeze strategy [relative risk (RR) 1.03; 95% confidence interval (CI): 0.98–1.07; I2 = 0%]. Single freeze procedures were associated with a significantly lower adverse event rate (RR 0.72; 95% CI: 0.53–0.98; I2 = 0%) and shorter average procedure time (90 ± 27 min vs. 121 ± 36 min, P < 0.001). A trend for lower risk of persistent phrenic nerve palsy was observed (RR 0.61; 95% CI: 0.37–1.01; I2 = 0%). The quality of included studies was moderate/good, with no evidence of significant publication bias. Single freeze strategy for cryoballoon of AF is as effective as an empiric double (‘bonus’) freeze strategy while appearing safer and probably quicker (PROSPERO registration number CRD42020158696).
Fe-S coordination defects in the replicative DNA polymerase delta cause deleterious DNA replication in vivo and subsequent DNA damage in the yeast Saccharomyces cerevisiae
Authors: Chanet Roland , Baïlle Dorothée , Golinelli-Cohen Marie-Pierre , Riquier Sylvie , Guittet Olivier , Lepoivre Michel , Huang Meng-Er , Vernis Laurence
Published: May 2021

B-type eukaryotic polymerases contain a [4Fe-4S] cluster in their C-terminus domain, whose role is not fully understood yet. Among them, DNA polymerase delta (Polδ) plays an essential role in chromosomal DNA replication, mostly during lagging strand synthesis. Previous in vitro work suggested that the Fe-S cluster in Polδ is required for efficient binding of the Pol31 subunit, ensuring stability of the Polδ complex. Here, we analyzed the in vivo consequences resulting from an impaired coordination of the Fe-S cluster in Polδ. We show that a single substitution of the very last cysteine coordinating the cluster by a serine is responsible for the generation of massive DNA damage during S phase, leading to checkpoint activation, requirement of homologous recombination for repair, and ultimately to cell death when the repair capacities of the cells are overwhelmed. These data indicate that impaired Fe-S cluster coordination in Polδ is responsible for aberrant replication. More generally, Fe-S in Polδ may be compromised by various stress including anti-cancer drugs. Possible in vivo Polδ Fe-S cluster oxidation and collapse may thus occur, and we speculate this could contribute to induced genomic instability and cell death, comparable to that observed in pol3-13 cells.
Construction of a high-density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing
Authors: Popowski Elizabeth , Thomson Susan J , Knäbel Mareike , Tahir Jibran , Crowhurst Ross N , Davy Marcus , Foster Toshi M , Schaffer Robert J , Tustin D Stuart , Allan Andrew C , McCallum John , Chagné David
Published: May 2021

Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
Rampant Genome-Wide Admixture across theHeliconiusRadiation
Authors: Kozak Krzysztof M , Joron Mathieu , McMillan W Owen , Jiggins Chris D
Published: May 2021

How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a genomic representation of 40 out of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of Heliconius erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of Heliconius melpomene and relatives. We identify Heliconius hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.
A bioenergetic model to address carbon sequestration potential of shellfish farming: example from Ruditapes philippinarum in the Venice lagoon
Authors: Bertolini C , Bernardini I , Brigolin D , Matozzo V , Milan M , Pastres R
Published: May 2021

Shellfish are increasingly been looked at as sustainable food sources that provide additional ecosystem services. However, their role as CO2 sinks or sources is still debated. To quantify it, shell accretion dynamics should be accounted for. However, the shell component is usually calculated with allometric scaling, in most bivalve models. With this study, shell accretion was added to a bioenergetic model of the Manilla clam (Ruditapes philippinarum), and a parameter linking assimilated energy towards shell growth (KSH) was calibrated for four sites, where clams from the same cohort were monitored during a transplant experiment. The model was then used to calculate CO2 fluxes resulting from respiration and shell calcification, taking into account CaCO3 stocked in the shell and CO2 emission. The findings show that KSH varied slightly among sites and that clams played a role as a moderate sink of CO2 over a whole year. CO2 fluxes were characterized by a seasonal variability: clams were net sources in wintertime and sinks in summer time, suggesting the need of accounting for seasonality and growth should shellfish farming be included in carbon markets.
Ensuring quality qualitative research reporting in community pharmacy: a systematic literature review
Authors: Aref Heba A T , Witry Matthew , Olufemi-Yusuf Damilola , Guirguis Lisa M
Published: May 2021

Objectives

To evaluate the reporting quality for a sample of community pharmacy qualitative research articles based on the Standards for Reporting Qualitative Research (SRQR) guidelines, data interpretation and use of theory.

Methods

A systematic literature search was conducted using Ovid MEDLINE to identify qualitative research related to community pharmacy. Data were extracted and evaluated based on the SRQR standards, data interpretation level and use of theory. Adherence to standards was analysed using descriptive statistics.

Key findings

Eighty-one studies were retrieved through the database search (n = 81). Then, 31 studies met the inclusion criteria after screening abstracts and full texts. Twelve out of 21 SRQR were present in more than 80% of the studies. However, essential standards, such as research approach, reflexivity and trustworthiness techniques, were absent or partially present in 30 (97%) studies, 30 (97%) studies and 21 (68%) studies, respectively. Data interpretation level was descriptive in 27 (87%) studies and interpretive or partially interpretive in 4 (13%) studies. Theory was absent in 19 (60%) and implied, partially integrated or retrospectively applied in 12 (40%) of the studies.

Conclusion

Trustworthiness and quality of qualitative inferences within community pharmacy research could be enhanced with increasing awareness about reporting; the approach and paradigm, reflexivity, trustworthiness techniques, data interpretation level and theoretical use.
The Rankings Game: A Relational Approach to Country Performance Indicators
Authors: Beaumont Paul , Towns Ann E
Published: May 2021

As the number of international rankings has risen dramatically since the 1990s, a large body of scholarship has emerged to examine and understand them. The aim of this article is to provide an overview of this body of work and to chart out fruitful directions for future research. In short, prior scholarship has been surprisingly quiet on the relations among multiple actors and their economic dimensions at the core of country performance indicator (CPI) activities. To foreground crucial socioeconomic relations, we develop a relational heuristic based upon a sports analogy: the actors involved in the creation and maintenance of CPIs can fruitfully be approached as a complex of players, referees, coaches, and audiences. Such an account helps us better understand how CPIs emerge and are sustained, even when they rely on dodgy data and their effects are perverse. We use nation brand rankings—overlooked in international relations research—as empirical illustration.
Between the Prophetic and Priestly: The Role of Black Pastoral Authority in Health and Science Promotion
Authors: Schneider Rachel C , Bolger Daniel
Published: May 2021

Health researchers often seek to leverage pastoral authority in Black churches to forge community partnerships that address racial health disparities in the United States. Yet, researchers have not fully recognized the range (and limits) of pastoral authority as well as the complex role of religion in African American health. Here we explore how health and science are engaged in Black Church contexts and what role pastoral authority plays in this process. Drawing on focus groups with Black pastors and interviews with congregants, we outline three different dimensions of pastoral authority: gatekeeper, connector, and moral exemplar. We argue that these dimensions create tensions between the priestly and prophetic mandates of Black pastors, which in turn impact how church members engage with health resources and scientific knowledge. These results complicate current understandings of how authority functions in Black churches while underscoring the need to seriously consider Black Religion in studies of religion, health, and science.
Temporal Trends in Pollination Deficits and Its Potential Impacts on Chinese Agriculture
Authors: Mashilingi Shibonage K , Zhang Hong , Chen Wenfeng , Vaissière Bernard E , Garibaldi Lucas A , An Jiandong
Published: May 2021

Worldwide, there is increasing evidence that shows a decline in pollinators, limiting crop pollination and production. However, it is unclear to what extent Chinese agriculture could be impacted by pollinator deficits. Data for 84 major crops in China between 1961 and 2018 were analyzed for the temporal trends in crop area and production, agricultural economic contribution of pollination, crop yield deficits, and honey bee pollination demand. We found a rapid increase in agricultural dependence on insect pollinators: both the cultivated area and total production of pollinator-dependent crops increased faster than those of pollinator-independent crops during 1961–2018. The total economic value of pollination amounted to US$ 106.08 billion in 2010, representing 19.12% of the total production value of Chinese agriculture, approximately twice the 9.5% value estimated for global agriculture. Crops with higher pollinator dependence showed greater mean growth in cultivated area than those with lower dependence, but lower mean growth of crop production and yield. Crop yield growth was also more unstable with increasing pollinator dependence. The minimum pollination demand for honey bee colonies was about three times the stock of honey bee colonies available in 2018. Furthermore, we found a decline in crop yield deficit with the increase in honey bee colony pollination service capacity. We considered that the shortage of pollinators resulted in the yield deficits for pollinator-dependent crops. Future increase in the area of pollinator-dependent crops will increase the need for more pollinators, suggesting the importance of implementing measures to protect pollinators to ensure a better-secured future for agricultural production in China.
“So delightful a temporary home”: The Material Culture of Domesticity in Late Nineteenth-century English Convalescent Institutions
Authors: Anders Eli Osterweil
Published: May 2021

This article examines the material culture of domesticity in late nineteenth-century English convalescent institutions. Convalescent homes drew on powerful Victorian ideas about the physical and moral benefits of “home-like” domestic comfort, which they contrasted with the “institutional” environment of hospitals and the degrading surroundings of urban slums. Administrative records, press accounts, photographs, and patient letters reveal how convalescent homes cultivated temporary home-like environments through architecture, interior decoration, and behavioral expectations and routines. Convalescent homes drew on heterogeneous models of domesticity, including the grand architecture of country estates, the possession-packed spaces of middle-class homes, and the recreational spaces of male social clubs. Nevertheless, they shared a belief in the power of domestic spaces, comforts, and practices to support the recovery of convalescents and to influence their identity and behavior. The material culture and practices of domesticity deployed in convalescent homes encouraged reflection, self-improvement, and self-control—qualities essential to the cultivation of respectable, self-governing, liberal citizens. Nevertheless, the meanings and experiences of these spaces were also shaped by inmates, whose expectations and experiences did not always align with the ideal image of home that authorities wished to create.
Treatment outcomes of molecular targeted therapy following nivolumab in metastatic renal cell carcinoma
Authors: Bando Yukari , Furukawa Junya , Terakawa Tomoaki , Harada Kenichi , Hinata Nobuyuki , Nakano Yuzo , Fujisawa Masato
Published: May 2021

Objective

The purpose of this study was to assess the therapeutic efficacy of molecular targeted therapies following nivolumab in metastatic renal cell carcinoma and to examine the relationship between therapeutic efficacy and the specific molecular targeted therapy used.

Methods

We retrospectively reviewed the medical records of 115 metastatic renal cell carcinoma patients who were treated with nivolumab at our institution and five affiliated hospitals. Among them, 52 patients who received subsequent molecular targeted therapy following nivolumab were selected to survey treatment outcomes. Progression-free survival and overall survival were estimated with Kaplan-Meier curves, and differences were analyzed by the log-rank test.

Results

Among the 52 eligible patients, 40 (76.9%) were treated with tyrosine kinase inhibitors and 12 (23.1%) were treated with mammalian target of rapamycin inhibitor. The median time to treatment failure and progression-free survival of subsequent molecular targeted therapy were 5.6 and 8.0 months, respectively. The median overall survival from the initiation of first-line therapy was not reached. The disease control rate of subsequent molecular targeted therapy was 69.2% (partial response: 25.0%, stable disease: 44.2%). The median progression-free survival of subsequent tyrosine kinase inhibitor and mammalian target of rapamycin inhibitor were 9.2 and 8.0 months, respectively (P = 0.37). The progression-free survival of patients whose best response to prior nivolumab was either progressive disease or stable disease/partial response were 6.3 and 11.3 months, respectively (P = 0.36).

Conclusions

Molecular targeted therapies following nivolumab had comparatively better therapeutic efficacy, which was confirmed regardless of the type of molecular targeted agent used.
Radical surgery for anal canal neuroendocrine carcinoma with pagetoid spread: a case report
Authors: Fukuhara Sotaro , Yoshimitsu Masanori , Yano Takuya , Oshita Ko , Bekku Kensuke , Okamoto Hitoshi , Toi Yoichiro , Ichimura Koichi , Okamoto Wataru , Okajima Masazumi
Published: May 2021

Anal canal neuroendocrine carcinoma (NEC) with pagetoid spread (PS) is a rare disease, and its treatment strategy remains unclear. The prognosis of anal canal NEC with PS is poor. Resection margin status is very important for anorectal carcinoma because it affects survival. When accompanied by PS, the defect of the resulting perineal wound following radical surgical intervention may be necessarily enlarged to ensure the appropriate margin status. This case report discusses the treatment of a patient with advanced anal canal NEC with PS, inguinal lymph node metastasis and sphincter infiltration in which total pelvic exenteration with plastic surgery was successfully performed. The plastic surgery incorporated a gracilis muscle flap that was useful for the reconstruction of the enlarged perineal defect.
Formation of light-harvesting complex II aggregates from LHCII–PSI–LHCI complexes in rice plants under high light
Authors: Wu Guangxi , Ma Lin , Yuan Cai , Dai Jiahao , Luo Lai , Poudyal Roshan Sharma , Sayre Richard T , Lee Choon-Hwan
Published: May 2021

During low light- (LL) induced state transitions in dark-adapted rice (Oryza sativa) leaves, light-harvesting complex (LHC) II become phosphorylated and associate with PSI complexes to form LHCII–PSI–LHCI supercomplexes. When the leaves are subsequently transferred to high light (HL) conditions, phosphorylated LHCII complexes are no longer phosphorylated. Under the HL-induced transition in LHC phosphorylation status, we observed a new green band in the stacking gel of native green–PAGE, which was determined to be LHCII aggregates by immunoblotting and 77K chlorophyll fluorescence analysis. Knockout mutants of protein phosphatase 1 (PPH1) which dephosphorylates LHCII failed to form these LHCII aggregates. In addition, the ability to develop non-photochemical quenching in the PPH1 mutant under HL was less than for wild-type plants. As determined by immunoblotting analysis, LHCII proteins present in LHCII–PSI–LHCI supercomplexes included the Lhcb1 and Lhcb2 proteins. In this study, we provide evidence suggesting that LHCII in the LHCII–PSI–LHCI supercomplexes are dephosphorylated and subsequently form aggregates to dissipate excess light energy under HL conditions. We propose that this LHCII aggregation, involving LHCII L-trimers, is a newly observed photoprotective light-quenching process operating in the early stage of acclimation to HL in rice plants.
Binary–binary close encounters in the Kuiper Belt
Authors: López María C , Brunini A
Published: May 2021

Trans-Neptunian binaries are among the objects carrying the most relevant information on the conditions that prevailed in the primitive outer Solar system. However, their present orbital architecture not necessarily reflects those conditions, because it is the result of complex evolutionary processes. There is evidence suggesting that binary systems dominated the primitive trans-Neptunian populations. Therefore, binary–binary interactions could be an important evolutionary path. In this paper, a series of numerical experiments of binary–binary close encounters were carried out, varying specific parameters related to their physical and orbital characteristics. The relative speeds with which the encounters occur play an important role in the relative variation of orbital elements, showing a good agreement with impulsive approximation models involving a binary and a single intruder. However, simulations varying the mass, semimajor axis, and closest approach distance between pairs of binaries, showed marked deviations from this model.
On the structure of the Enceladus plume
Authors: Fu Menghao , Gu Hao , Cui Jun , Xiao Zhiyong , He Fei , Wei Yong , Ren Zhipeng
Published: May 2021

The detection of a water-rich plume erupting from ‘tiger stripes’ near the Enceladus south polar region is an important discovery of geologically active satellites within the Solar system. In this work, we apply an analytical approach to model the plume structure, using as a diagnostic the CO2 distribution extracted from the Cassini Ion and Neutral Mass Spectrometer measurements made during the E14, E17, and E18 flybys. Special focus is placed on the modelling of the spike-like structures by including only sources with substantial contributions to the plume densities. Such a procedure reduces greatly the model complexity and helps to better constrain the source parameters. Both the model source rate and Mach number are found to vary considerably among different sources during the same flyby and also among different flybys for the same source, revealing a complicated spatio-temporal variability in the plume structure. Our analysis suggests a total escape rate of (1.0–7.1) × 1026 s−1 for CO2 and (2.4–6.6) × 1028 s−1 for H2O, in broad agreement with previous estimates. Of particular interest is our identification of a tentative correlation between the Mach number and thermal brightness, of which the latter is a tracer of the geological activity of the emission source. Such a relation should be able to provide more insights into the nature of geyser emission along the ‘tiger stripes’.
Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes
Authors: Fan Kaili , Moore Jill E , Zhang Xiao-ou , Weng Zhiping
Published: May 2021

Gene expression is controlled by regulatory elements within accessible chromatin. Although most regulatory elements are cell type-specific, a subset is accessible in nearly all the 517 human and 94 mouse cell and tissue types assayed by the ENCODE consortium. We systematically analyzed 9000 human and 8000 mouse ubiquitously-accessible candidate cis-regulatory elements (cCREs) with promoter-like signatures (PLSs) from ENCODE, which we denote ubi-PLSs. These are more CpG-rich than non-ubi-PLSs and correspond to genes with ubiquitously high transcription, including a majority of cell-essential genes. ubi-PLSs are enriched with motifs of ubiquitously-expressed transcription factors and preferentially bound by transcriptional cofactors regulating ubiquitously-expressed genes. They are highly conserved between human and mouse at the synteny level but exhibit frequent turnover of motif sites; accordingly, ubi-PLSs show increased variation at their centers compared with flanking regions among the ∼186 thousand human genomes sequenced by the TOPMed project. Finally, ubi-PLSs are enriched in genes implicated in Mendelian diseases, especially diseases broadly impacting most cell types, such as deficiencies in mitochondrial functions. Thus, a set of roughly 9000 mammalian promoters are actively maintained in an accessible state across cell types by a distinct set of transcription factors and cofactors to ensure the transcriptional programs of cell-essential genes.
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
Authors: Shaikh Bilal , Marupilla Gnaneswara , Wilson Mike , Blinov Michael L , Moraru Ion I , Karr Jonathan R
Published: May 2021

Comprehensive, predictive computational models have significant potential for science, bioengineering, and medicine. One promising way to achieve more predictive models is to combine submodels of multiple subsystems. To capture the multiple scales of biology, these submodels will likely require multiple modeling frameworks and simulation algorithms. Several community resources are already available for working with many of these frameworks and algorithms. However, the variety and sheer number of these resources make it challenging to find and use appropriate tools for each model, especially for novice modelers and experimentalists. To make these resources easier to use, we developed RunBioSimulations (https://run.biosimulations.org), a single web application for executing a broad range of models. RunBioSimulations leverages community resources, including BioSimulators, a new open registry of simulation tools. These resources currently enable RunBioSimulations to execute nine frameworks and 44 algorithms, and they make RunBioSimulations extensible to additional frameworks and algorithms. RunBioSimulations also provides features for sharing simulations and interactively visualizing their results. We anticipate that RunBioSimulations will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models.
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing
Authors: Harrison Peter W , Lopez Rodrigo , Rahman Nadim , Allen Stefan Gutnick , Aslam Raheela , Buso Nicola , Cummins Carla , Fathy Yasmin , Felix Eloy , Glont Mihai , Jayathilaka Suran , Kadam Sandeep , Kumar Manish , Lauer Katharina B , Malhotra Geetika , Mosaku Abayomi , Edbali Ossama , Park Young Mi , Parton Andrew , Pearce Matt , Estrada Pena Jose Francisco , Rossetto Joseph , Russell Craig , Selvakumar Sandeep , Sitjà Xènia Pérez , Sokolov Alexey , Thorne Ross , Ventouratou Marianna , Walter Peter , Yordanova Galabina , Zadissa Amonida , Cochrane Guy , Blomberg Niklas , Apweiler Rolf
Published: May 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.
De Novo Pial Arteriovenous Fistula Associated With Cerebral Infarction and Venous Hypertension: Report of 2 Cases Suggesting a “Second Hit Theory”
Authors: Terada Tomoaki , Nakayama Sadayoshi , Wada Akira , Tanaka Yuko , Yabuzaki Hajime , Matsuda Yoshikazu , Tsumoto Tomoyuki
Published: May 2021

BACKGROUND AND IMPORTANCE

The etiology of de novo pial arteriovenous fistula (AVF) is unknown. We found 2 cases of de novo pial AVF, which appeared after cerebral infarction and which was associated with venous hypertension secondary to venous sinus thrombosis with a dural AVF (dAVF). Additional angiogenic stimuli (second hit) were considered as one of the mechanisms of de novo pial AVF.

CLINICAL PRESENTATION

A 63-yr-old male was admitted to our hospital due to an intraventricular hemorrhage. He had a history of cerebral infarction 2 yr before. Angiography demonstrated multiple dAVFs with bilateral occlusion of the distal transverse sinus associated with prominent retrograde cortical venous drainage. A pial AVF was found at the border of his previous cerebral infarction. Both lesions were successfully treated using endovascular technique.

A second case involved a 47-yr-old female who was admitted to our hospital due to venous infarction also associated with sinus thrombosis. De novo pial AVF at the border of the venous infarction and dAVF at the transverse sigmoid junction were demonstrated on angiography 6 mo later.

CONCLUSION

We speculate that venous hypertension associated with additional angiogenic stimuli (second hit) due to brain ischemia and/or brain injury related to infarction caused de novo pial AVF in these 2 cases.