bluuebunny/crossref_metadata_2025_split huggingface dataset:
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms
Authors: Arshinoff Bradley I , Cary Gregory A , Karimi Kamran , Foley Saoirse , Agalakov Sergei , Delgado Francisco , Lotay Vaneet S , Ku Carolyn J , Pells Troy J , Beatman Thomas R , Kim Eugene , Cameron R Andrew , Vize Peter D , Telmer Cheryl A , Croce Jenifer C , Ettensohn Charles A , Hinman Veronica F 
Published: October 2021

Abstract
Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying the user interface to adapt to multispecies echinoderm content. This approach leveraged over 15 years of previous database and web application development to generate a new fully featured informatics resource in a single year. In addition to the software stack, Echinobase uses the private cloud and physical hosts that support Xenbase. Echinobase currently supports six echinoderm species, focused on those used for genomics, developmental biology and gene regulatory network analyses. Over 38 000 gene pages, 18 000 publications, new improved genome assemblies, JBrowse genome browser and BLAST + services are available and supported by the development of a new echinoderm anatomical ontology, uniformly applied formal gene nomenclature, and consistent orthology predictions. A novel feature of Echinobase is integrating support for multiple, disparate species. New genomes from the diverse echinoderm phylum will be added and supported as data becomes available. The common code development design of the integrated knowledgebases ensures parallel improvements as each resource evolves. This approach is widely applicable for developing new model organism informatics resources.
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses
Authors: Walsh Amy T , Triant Deborah A , Le Tourneau Justin J , Shamimuzzaman Md , Elsik Christine G 
Published: October 2021

AbstractWe report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.
Presupposing Legal Authority
Authors: Mullins Robert 
Published: October 2021

Abstract
The thesis that law necessarily claims authority is popular amongst legal philosophers. Some distinguished legal philosophers, including the late John Gardner, Joseph Raz and Scott Shapiro, have suggested that support for this thesis is found in legal officials’ use of deontic language. This article begins by considering the merits of this suggestion. I discuss two unpromising arguments for the claim thesis based on the use of deontic language in law. I then suggest that a more plausible basis for the claim thesis lies in the felicity conditions of the speech acts that legal officials perform. In the absence of an explicit claim to authority, legal officials make a presupposition to authority over their subjects. The presupposition arises from interaction between the felicity conditions of legal speech acts and basic norms of cooperative communication. I consider some implications of this conclusion for our understanding of legal authority.
Toward predicting photosynthetic efficiency and biomass gain in crop genotypes over a field season
Authors: Keller Beat , Zimmermann Lars , Rascher Uwe , Matsubara Shizue , Steier Angelina , Muller Onno 
Published: October 2021

Abstract
Photosynthesis acclimates quickly to the fluctuating environment in order to optimize the absorption of sunlight energy, specifically the photosynthetic photon fluence rate (PPFR), to fuel plant growth. The conversion efficiency of intercepted PPFR to photochemical energy (ɛe) and to biomass (ɛc) are critical parameters to describe plant productivity over time. However, they mask the link of instantaneous photochemical energy uptake under specific conditions, that is, the operating efficiency of photosystem II (Fq′/Fm′), and biomass accumulation. Therefore, the identification of energy- and thus resource-efficient genotypes under changing environmental conditions is impeded. We long-term monitored Fq′/Fm′ at the canopy level for 21 soybean (Glycine max (L.) Merr.) and maize (Zea mays) genotypes under greenhouse and field conditions using automated chlorophyll fluorescence and spectral scans. Fq′/Fm′ derived under incident sunlight during the entire growing season was modeled based on genotypic interactions with different environmental variables. This allowed us to cumulate the photochemical energy uptake and thus estimate ɛe noninvasively. ɛe ranged from 48% to 62%, depending on the genotype, and up to 9% of photochemical energy was transduced into biomass in the most efficient C4 maize genotype. Most strikingly, ɛe correlated with shoot biomass in seven independent experiments under varying conditions with up to r = 0.68. Thus, we estimated biomass production by integrating photosynthetic response to environmental stresses over the growing season and identified energy-efficient genotypes. This has great potential to improve crop growth models and to estimate the productivity of breeding lines or whole ecosystems at any time point using autonomous measuring systems.
The responsibilization paradox: The legal route from deresponsibilization to systemic corruption in the Australian financial sector
Authors: Pasculli Lorenzo 
Published: October 2021

AbstractRecent corruption scandals suggest that the legal structures developed to responsibilize corporations might paradoxically enable the systematization of corruption across entire industry sectors. This study uses grounded theory methodology to develop a preliminary theoretical model of the correlations between the law, responsibilization, and the causes of systemic corruption. Through a qualitative examination of documental evidence from the case study of the recent Australian banking scandal, this article conceptualizes a two-way process of ‘legal deresponsibilization’. On the one hand, legal dysfunctions fail to effectively support the situational and cultural goals of responsibilization. On the other hand, the pursuit of such goals transforms the law in ways that can lead to the deresponsibilization of both corporations and the state. The article suggests that structural reforms are needed to correct this process and the underlying systemic imbalances between the legal promotion of financial interests and that of countervailing values of integrity and accountability.
History of proliferative glomerulonephritis predicts end stage kidney disease in pure membranous lupus nephritis
Authors: Fava Andrea , Fenaroli Paride , Rosenberg Avi , Bagnasco Serena , Li Jessica , Monroy-Trujillo Jose , Fine Derek , Atta Mohamed G , Petri Michelle 
Published: October 2021

Abstract

Objectives
Pure membranous (class V) LN is considered a less aggressive phenotype, but tissue fibrosis and chronic kidney disease may still develop. This study aimed to elucidate the prognostic value of a history of class switch in pure membranous LN.

Methods
We included LN patients with at least two clinically indicated kidney biopsies. New onset of end stage kidney disease (ESKD) was defined as estimated glomerular filtration rate &lt;15 ml/min/1.73 m2, initiation of dialysis or kidney transplantation.

Results
Among 220 patients (542 biopsies), 199 (90%) were female, and 118 (54%) were African American, 59 (27%) Caucasian, with median age of 28 years at the first kidney biopsy. Patients with pure class V in a first biopsy converted to proliferative LN in 41% of cases. Pure class V in a repeat biopsy was preceded by proliferative LN in 52%. Trajectory analysis of up to four repeat biopsies revealed that ISN class switch may happen at any time, even after multiple biopsies with the same class. New onset ESKD was observed within 2 years in 5/56 (9%) patients with pure class V in a repeat biopsy. All five patients had proliferative LN in the first biopsy (log rank P = 0.024).

Conclusions
The conversion from proliferative to membranous (and vice-versa) is frequent in SLE. It can occur at any time in the course of disease, limiting the prognostic value of the first biopsy. Evidence of prior proliferative LN is key as it is associated with higher risk of ESKD in non-proliferative LN.
Integrated serological surveillance of acute febrile illness in the context of a lymphatic filariasis survey in Timor-Leste: a pilot study using dried blood spots
Authors: Arkell Paul , Angelina Julia , do Carmo Vieira Alberina , Wapling Johanna , Marr Ian , Monteiro Merita , Matthews Alexander , Amaral Salvador , da Conceicao Virginia , Kim Sung Hye , Bailey Daniel , Yan Jennifer , Fancourt's Nicholas S S , Vaz Nery Susana , Francis Joshua R 
Published: October 2021

Abstract

Background
Acute febrile illnesses (AFIs), including dengue, scrub typhus and leptospirosis, cause significant morbidity and mortality in Southeast Asia. Serological surveillance can be used to investigate the force and distribution of infections. Dried blood spot (DBS) samples are an attractive alternative to serum because they are easier to collect and transport and require less cold storage. We conducted a pilot study to determine the feasibility of integrating serological surveillance for dengue, scrub typhus and leptospirosis into a population-representative lymphatic filariasis seroprevalence survey in Timor-Leste using DBSs.

Methods
A total of 272 DBSs were collected from healthy community participants. DBSs were analysed at the National Health Laboratory using commercially available enzyme-linked immunosorbent assays. To validate assays for DBSs, 20 anonymised serum samples of unknown serostatus were used to create dried serum spots (DSSs). These were analysed with optical densities compared with those of serum. Where low variance was observed (dengue assay) the published kit cut-offs for serum were applied to the analysis of DBSs. For the other assays (scrub typhus and leptospirosis), index values (IVs) were calculated and cut-offs were determined to be at 2 standard deviations (SDs) above the mean.

Results
Of the 272 samples analysed, 19 (7.0% [95% confidence interval {CI} 4.3 to 10.7]) were positive for dengue immunoglobulin G (IgG), 11 (4.0% [95% CI 2.1 to 7.1]) were positive for scrub typhus IgG and 16 (5.9% [95% CI 3.4 to 9.4%]) were positive for leptospira IgG.

Conclusions
While dengue seroprevalence was lower than in nearby countries, results represent the first evidence of scrub typhus and leptospirosis transmission in Timor-Leste. Integrated programmes of serological surveillance could greatly improve our understanding of infectious disease epidemiology in remote areas and would incur minimal additional fieldwork costs. However, when planning such studies, the choice of assays, their validation for DBSs and the laboratory infrastructure and technical expertise at the proposed location of analysis must be considered.
The Concept of Pain Inventory for Adults (COPI-Adult)
Authors: Pate Joshua W. , Simons Laura E. , Rush Gillian , Hancock Mark J. , Hush Julia M. , Verhagen Arianne , Pacey Verity 
Published: October 2021

Objectives:
Assessing knowledge and beliefs regarding pain science can identify gaps and misconceptions. The Concept of Pain Inventory (COPI) was recently developed in children with the intent to guide targeted pain science education. We utilized the original COPI item pool to (1) develop a tool to assess an adult’s concept of pain in a cohort who had not received pain science education, (2) evaluate its psychometric properties, (3) examine distribution of scores in a cohort of adults who had received pain science education, and (4) examine associations between scores and clinical variables.

Materials and Methods:
A total cohort of 627 adults were recruited through social media for an online survey. Initial development was conducted on those who had not received prior pain science education (n=125), then the COPI-Adult tool was tested in those who had received prior pain science education (n=502).

Results:
The resulting unidimensional 13-item COPI-Adult had acceptable internal consistency (α=0.78) and good test-retest reliability at 1 week (Intraclass Correlation Coefficient3,1=0.84 (95% confidence interval: 0.71-0.91). Higher COPI-Adult scores reflect greater alignment with contemporary pain science. COPI-Adult scores were correlated with revised Neurophysiology of Pain Questionnaire (rNPQ) scores and inversely correlated with average and current pain intensity, and pain interference. Adults who reported having received pain science education had significantly higher mean COPI-Adult scores than those who had not, and this difference exceeded the smallest detectable change.

Discussion:
The COPI-Adult is a brief questionnaire with promising psychometric properties to identify conceptual gaps or misconceptions to inform individualized pain science education.
Dexmedetomidine Added to Ropivacaine for Ultrasound-guided Erector Spinae Plane Block Prolongs Analgesia Duration and Reduces Perioperative Opioid Consumption After Thoracotomy
Authors: Wang Qiang , Li Huixian , Wei Shijing , Zhang Guohua , Ni Cheng , Sun Li , Zheng Hui 
Published: October 2021

Objectives:
Single-injection erector spinae plane block (ESPB) provides good control of pain relief after open thoracotomy surgeries. However, the duration of pain relief does not last long. For this purpose, we hypothesized that adding α2-adrenoceptor agonist, dexmedetomidine, for interfascial nerve blockade may increase the duration of analgesia. There are only few studies using dexmedetomidine for interfasical nerve blocks in humans. In this study, our aim is to investigate whether addition of dexmedetomidine to ropivacaine for ESPB could effectively prolong the duration of postoperative analgesia and reduce opioid consumption after open thoracotomy.

Materials and Methods:
Sixty patients with esophageal cancer were randomized to receive ESPB using 28 mL of 0.5% ropivacaine, with 2 mL of normal saline (group R) or 0.5 µg/kg dexmedetomidine in 2 mL (group RD) administered interfascially. ESPB was performed at the fifth thoracic level under ultrasound guidance. The primary outcome was the duration of analgesia. The secondary outcomes were total postoperative sufentanil consumption, Numeric Rating Scale pain scores, Ramsay Sedation Scale scores and adverse effects.

Results:
The duration of analgesia in group RD (505.1±113.9) was longer than that in group R (323.2±75.4) (P<0.001). The total postoperative sufentanil consumption was lower in group RD (23.3±10.0) than in group R (33.8±13.8) (P=0.001). There was no significant difference in the incidence of adverse effects between the 2 groups.

Conclusion:
After open thoracotomy, addition of dexmedetomidine to ropivacaine for ESPB effectively prolonged the duration of postoperative analgesia and reduced opioid consumption without increasing additional incidence of adverse effects.
Spontaneous Resolution of Ear Lidding in Newborns: A Prospective Observational Cohort Study
Authors: Pauwels Julie , Lu D.Y.D. , Kozak Frederick K. , Chadha Neil K. 
Published: October 2021

Abstract
Ear lidding is a cosmetic outer ear shape deformity commonly observed in newborns. Although lidding is considered a benign condition, psychological concerns such as bullying and depression have been observed in older children supporting correction of the condition. Nonsurgical correction of lidding using molding and splinting techniques has become increasingly popular, achieving successful outcomes in the majority of cases. Spontaneous resolution of the condition has also been reported in the literature however there is minimal prospective data available on the natural progression of ear lidding. In our case series of 11 closely followed newborns, we aimed to characterize the natural progression and resolution of lidding. Ten consecutive newborns participated in the observation plan and all 10 had complete spontaneous resolution of lidding within an average of 40 days. One other newborn's parents self-selected to have molding and splinting treatment. These results suggest that cosmetic treatment for less severe cases of ear lidding may be unnecessary as they have the potential to resolve on their own. Future research in this area could include controlled study designs and more work is needed to identify, which infants will require treatment. Our study may provide helpful reassurance to families and physicians that many newborns may see complete resolution of lidding without intervention.
SARS-CoV-2 infects and replicates in photoreceptor and retinal ganglion cells of human retinal organoids
Authors: Menuchin-Lasowski Yotam , Schreiber André , Lecanda Aarón , Mecate-Zambrano Angeles , Brunotte Linda , Psathaki Olympia E. , Ludwig Stephan , Rauen Thomas , Schöler Hans R. 
Published: October 2021

AbstractSeveral studies have pointed to retinal involvement in COVID-19 disease, yet many questions remain regarding the ability of SARS-CoV-2 to infect and replicate in retinal cells and its effects on the retina. Here we have used human stem cell–derived retinal organoids to study retinal infection by the SARS-CoV-2 virus. Indeed, SARS-CoV-2 can infect and replicate in retinal organoids, as it is shown to infect different retinal lineages, such as retinal ganglion cells and photoreceptors. SARS-CoV-2 infection of retinal organoids also induces the expression of several inflammatory genes, such as interleukin 33, a gene associated with acute COVID-19 disease and retinal degeneration. Finally, we show that the use of antibodies to block the ACE2 receptor significantly reduces SARS-CoV-2 infection of retinal organoids, indicating that SARS-CoV-2 infects retinal cells in an ACE2-dependent manner. These results suggest a retinal involvement in COVID-19 and emphasize the need to monitor retinal pathologies as potential sequelae of “long COVID”.
Genetically determined serum testosterone level and Covid-19 illness level: A mendelian randomization study
Authors: Xiong Juan , Kong Xuejun , Ma Ziyong , Qu Yifei , Yang Xu , Miao Ruicheng , Huang Jie 
Published: October 2021

AbstractBackgroundIt is hypothesized that different levels of hormones especially serum testosterone level could explain the sex differences between men and women on the susceptibility and case fatality rate of COVID-19. However, traditional observational studies that support this hypothesis could not effectively establish the causal effects.ObjectiveUtilizing recently published genome-wide associations studies (GWAS) on serum Testosterone level and on COVID-19 related phenotypes, we sought to assess the causality through Mendelian Randomization (MR) analyses. We further applied a suite of statistical genomics methods to further explore the biological mechanisms.ResultsWe found that testosterone level is significantly associated with Covid-19 critical illness. All six MR methods yielded significant associations. There is no significant association between Testosterone and COVID-19 respiratory failure or COVID-19 susceptibility.ConclusionBased on the GWAS currently available, we provide support for a causal role of Testosterone on COVID-19 critical illness.Nevertheless, we recognize that the COVID-19 susceptibility GWAS effort is still ongoing and there is no such strong locus as CCR5 for HIV discovered for COVID-19.
On the Use of Z-Scores for Fine-Mapping with Related Individuals
Authors: Jiang Jicai 
Published: October 2021

AbstractUsing summary statistics from genome-wide association studies (GWAS) has been widely used for fine-mapping complex traits in humans. The statistical framework was largely developed for unrelated samples. Though it is possible to apply the framework to fine-mapping with related individuals, extensive modifications are needed. Unfortunately, this has often been ignored in summary-statistics-based fine-mapping with related individuals. In this paper, we show in theory and simulation what modifications are necessary to extend the use of summary statistics to related individuals. The analysis also demonstrates that though existing summary-statistics-based fine-mapping methods can be adapted for related individuals, they appear to have no computational advantage over individual-data-based methods.
Is 7-days home BP measurement comparable to 24-hours Ambulatory BP Measurement?
Authors: Islam Sheikh Mohammed Shariful , Karmakar Chandan , Ahmed Imran , Maddison Ralph 
Published: October 2021

ABSTRACTHigh blood pressure (BP) or hypertension is a significant risk factor for the global burden of cardiovascular diseases. Home blood pressure measurements (HBPM) have been recommended for hypertension diagnosis, treatment initiation and medication titration, but guidelines for the number of measurements and duration are inconsistent. This study compared the accuracy of 3 home BP measurements per day for seven days with 24-hour ambulatory BP measurements. We examined 24-hour ambulatory BP measurements (ABPM) and HBPM during-morning, afternoon, and evening each day for seven days in healthy community living volunteers. Standardized Bland-Altman scatterplots and limits of agreement (LOA) were used to assess absolute reliability and the variability of measurement biases. We used nonparametric Mann-Whitney U-tests to compare the mean (SD) of the devices. Correlations between HBPM and 24-hour ABPM measurements were statistically significant at p<0.05. The high correlation coefficient (r=0.75) was observed between the systolic BP retrieved from two devices compared to moderate correlation (r=0.46) among diastolic BP. A significant difference was found for systolic BP (P<0.05) between the HBPM and ABPM but was non-significant for diastolic BP (P>0.05). In Bland-Altman plots, the LOA between HBPM and ABPM was 0.07-26.23 mmHg for SBP and 11.24 -16.20 mmHg for DBP. The overall mean difference (bias) in SBP and DBP was 13.08 and 2.48, respectively. Our results suggest that HBPM three times per day for seven days can potentially be used where ABPM is unavailable. Further studies in a diverse group of people with hypertension are needed.