bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi contact-based folding method forde novoprotein structure prediction
Authors: Hou Minghua , Peng Chunxiang , Zhou Xiaogen , Zhang Biao , Zhang Guijun
Published: October 2021

Meta contact, which combines different contact maps into one to improve contact prediction accuracy and effectively reduce the noise from a single contact map, is a widely used method. However, protein structure prediction using meta contact cannot fully exploit the information carried by original contact maps. In this work, a multi contact-based folding method under the evolutionary algorithm framework, MultiCFold, is proposed. In MultiCFold, the thorough information of different contact maps is directly used by populations to guide protein structure folding. In addition, noncontact is considered as an effective supplement to contact information and can further assist protein folding. MultiCFold is tested on a set of 120 nonredundant proteins, and the average TM-score and average RMSD reach 0.617 and 5.815 Å, respectively. Compared with the meta contact-based method, MetaCFold, average TM-score and average RMSD have a 6.62 and 8.82% improvement. In particular, the import of noncontact information increases the average TM-score by 6.30%. Furthermore, MultiCFold is compared with four state-of-the-art methods of CASP13 on the 24 FM targets, and results show that MultiCFold is significantly better than other methods after the full-atom relax procedure.
Intravital imaging of the murine subventricular zone with three photon microscopy
Authors: Sun Bin , Wang Mengran , Hoerder-Suabedissen Anna , Xu Chris , Packer Adam M , Szele Francis G
Published: October 2021

The mouse subventricular zone (SVZ) produces neurons throughout life. It is useful for mechanism discovery and is relevant for regeneration. However, the SVZ is deep, significantly restricting live imaging since current methods do not extend beyond a few hundred microns. We developed and adapted three-photon microscopy (3PM) for non-invasive deep brain imaging in live mice, but its utility in imaging the SVZ niche was unknown. Here, with fluorescent dyes and genetic labeling, we show successful 3PM imaging in the whole SVZ, extending to a maximum depth of 1.5 mm ventral to the dura mater. 3PM imaging distinguished multiple SVZ cell types in postnatal and juvenile mice. We also detected fine processes on neural stem cells interacting with the vasculature. Previous live imaging removed overlying cortical tissue or lowered lenses into the brain, which could cause inflammation and alter neurogenesis. We found that neither astrocytes nor microglia become activated in the SVZ, suggesting 3PM does not induce major damage in the niche. Thus, we show for the first time 3PM imaging of the SVZ in live mice. This strategy could be useful for intravital visualization of cell dynamics, molecular, and pathological perturbation and regenerative events.
Health, Wealth, and Voting Trajectories in Later Life
Authors: Engelman Michal , Joo Won-tak , Fletcher Jason , Burden Barry
Published: October 2021

Objectives

Much of what we know about voting behaviors is based on cross-sectional comparisons of voters at different ages. This study draws on a unique linkage between the Wisconsin Longitudinal Study and state voter files to characterize voting trajectories in later life and explore their determinants.

Methods

Using sequence analysis, we identify 5 voting typologies based on turnout and voting methods over 8 biennial elections. Using multinomial logistic and Poisson regressions, we examine the role of physical, cognitive, and mental health and wealth in shaping enfranchisement and civic participation at older ages.

Results

Health and wealth are both positively associated with voter turnout, but the negative impact of poor health on voting declines with increasing wealth. Voting at the polls and early voting are more common among healthier older adults, whereas absentee voting is more common among older voters who are more affluent, less healthy, or both. Among those less wealthy, absentee methods mitigate the impact of poor health for previously active voters, but do not compensate for a lower turnout rate. In addition to physical and cognitive limitations, emotional difficulties and depression reduce turnout, particularly among the least wealthy.

Discussion

In this sample of older, largely White, primarily Midwestern committed voters, civic participation at older ages is shaped by individual experiences with wealth and health across the life course as well as political structures that facilitate or restrict the ability of individuals to consistently participate in elections.
Chest wall stabilization and rib fixation using a nitinol screwless system in selected patients after blunt trauma: long-term results in a single-centre experience
Authors: Hojski Aljaz , Xhambazi Arben , Wiese Mark Nikolaj , Subotic Dragan , Bachmann Helga , Lardinois Didier
Published: October 2021

OBJECTIVES

First experiences with rib fixation using nitinol, in terms of reliability and morbidity, influence on pain control and quality of life (QOL), in a large series of selected patients after blunt chest trauma.

METHODS

Data of all patients who had undergone rib fixation by the use of nitinol were retrospectively analysed in terms of indications, morbidity and in-hospital mortality. Pain status and health-related QOL were assessed preoperatively, when possible, at discharge and at 1, 3, 6 and 12 months post-surgery using visual analogous scale and short form 12 questionnaires.

RESULTS

From September 2017 to April 2019, 70 patients underwent rib fixation using the nitinol device, of which 47 (67%) had dislocated, painful fractures, 6 (8.5%) had flail chest injuries, 6 (8.5%) were emergencies with haemodynamical instability and 11 (16%) had pseudoarthrosis. Morbidity was 21% without wound infection; in-hospital mortality was 3%. Fracture of the material occurred in 6% of the patients during the first year, but removal of the material was not required. Analysis of the pain score showed a statistically significant decrease in pain for both the whole collective and the group with a series of dislocated and painful fractured ribs (P < 0.001, Tukey contrast on the linear mixed-effects models). Assessment of health-related QOL revealed a significant improvement in the physical score for the mid- and long-term analysis.

CONCLUSIONS

Our results suggest that rib fixation using the nitinol device is reliable, associated with an acceptable morbidity, while significantly decreasing pain and improving health-related QOL.
Varicella Zoster Virus Impairs Expression of the Nonclassical Major Histocompatibility Complex Class I–Related Gene Protein (MR1)
Authors: Purohit Shivam K , Samer Carolyn , McWilliam Hamish E G , Traves Renee , Steain Megan , McSharry Brian P , Kinchington Paul R , Tscharke David C , Villadangos Jose A , Rossjohn Jamie , Abendroth Allison , Slobedman Barry
Published: October 2021

The antigen presentation molecule MR1 (major histocompatibility complex, class I–related) presents ligands derived from the riboflavin (vitamin B) synthesis pathway, which is not present in mammalian species or viruses, to mucosal-associated invariant T (MAIT) cells. In this study, we demonstrate that varicella zoster virus (VZV) profoundly suppresses MR1 expression. We show that VZV targets the intracellular reservoir of immature MR1 for degradation, while preexisting, ligand-bound cell surface MR1 is protected from such targeting, thereby highlighting an intricate temporal relationship between infection and ligand availability. We also identify VZV open reading frame (ORF) 66 as functioning to suppress MR1 expression when this viral protein is expressed during transient transfection, but this is not apparent during infection with a VZV mutant virus lacking ORF66 expression. This indicates that VZV is likely to encode multiple viral genes that target MR1. Overall, we identify an immunomodulatory function of VZV whereby infection suppresses the MR1 biosynthesis pathway.
Differential use of p24 family members as cargo receptors for the transport of glycosylphosphatidylinositol-anchored proteins and Wnt1
Authors: Tashima Yuko , Hirata Tetsuya , Maeda Yusuke , Murakami Yoshiko , Kinoshita Taroh
Published: October 2021

Complexes of p24 proteins act as cargo receptors for the transport of COPII vesicles from the endoplasmic reticulum (ER). The major cargos of p24 complexes are hydrophilic proteins tethered to the ER membrane via a covalently attached glycosylphosphatidylinositol (GPI) or fatty acid. Each p24 complex is known to contain members from all four p24 subfamilies (p24α, p24β, p24γ and p24δ). However, it remains unclear how the cargo specificities of p24 complexes are influenced by member stoichiometry. Here, we report the subunit compositions of mammalian p24 complexes involved in the transport of GPI-anchored proteins and Wnt1. We show that at least one p24α is required for the formation of p24 complexes and that a p24 complex consisting of p24α2, p24β1, p24γ2 and p24δ1 is required for the efficient transport of GPI-anchored proteins. On the other hand, a p24 complex containing p24α2, p24α3, p24β1, p24γ and p24δ1 is involved in the transport of Wnt1. Further, interactions between p24α2 and p24α3 are critical for Wnt1 transport. Thus, p24α and p24γ subfamily members are important for cargo selectivity. Lastly, our data fit with an octamer, rather than a tetramer, model of p24 complexes, where each complex consists of two proteins from each p24 subfamily.
Completion lower lobectomy after basal segmentectomy for pulmonary sclerosing pneumocytoma with lymph node metastasis
Authors: Komatsu Hiroaki , Izumi Nobuhiro , Tsukioka Takuma , Inoue Hidetoshi , Ito Ryuichi , Nishiyama Noritoshi
Published: October 2021

A 20-year-old man was referred to our hospital because of a tumor in his left lung. Chest computed tomography showed a 35-mm nodule in the left lower lung lobe. Bronchoscopic examination and cryobiopsy were performed, which revealed suspicion for sclerosing pneumocytoma. We performed basal segmentectomy, and intraoperative-frozen pathological examination revealed no metastases in the segmental lymph nodes. However, the postoperative pathological diagnosis revealed metastasis in these nodes. We performed additional resection of segment 6 (completion lower lobectomy) and hilar and mediastinal lymph node dissection 2 weeks after the first surgery. The postoperative course was favorable, and the patient was discharged 13 days after the second surgery. Pathological examination of the additional resected specimens revealed lymph node metastases in the interlobar and mediastinal lymph nodes. Pulmonary sclerosing pneumocytoma with lymph node metastasis is extremely rare, and its prognosis is unclear. Recurrence has been reported rarely, and long-term follow-up is required.
Feasibility of implementing a first aid training programme (COOPERA-UGR) for medical students who plan to volunteer: a pilot study
Authors: Parrilla-Ruiz Francisco M , Martín-Aragón-García María , Redruello-Guerrero Pablo , García-Calatayud Sandra , Gómez-Macías Pilar , Rivera-Izquierdo Mario , Cárdenas-Cruz Antonio
Published: October 2021

The COOPERA-UGR project presents the first results of a pilot evaluation of a novel undergraduate curriculum initiative in a single medical school in Spain. The first aid maneuvers taught to participants showed high acquisition and the information collected supports the feasibility of the project.
Successful Orthotopic Heart Transplantation in a Patient with Anti-U Antibody
Authors: Hughes Caitlin , Sterling Brent , Andrews Jennifer
Published: October 2021

Objective

The U (universal) antigen is part of the MNS blood group present at a frequency of nearly 100% in Caucasians and 98% of African Americans. The anti-U antibody is clinically significant and has been reported to cause hemolytic transfusion reactions and hemolytic disease of the fetus and newborn.

Methods

Routine forward and backward typing, direct antiglobulin testing, and an antibody screen were performed. In addition, red blood cell phenotype and adsorption studies were also performed.

Results

The patient was found to have a rare anti-U antibody, rendering all available inventory in our hospital incompatible for transfusion.

Conclusion

This is the first reported case of solid organ transplantation in a patient with an anti-U alloantibody. Appropriate pretransplant evaluation and coordination between the clinical team and transfusion medicine service must be optimized to procure rare packed red blood cell units in a timely manner.
Atmospheric characterization of hot Jupiters using hierarchical models of Spitzer observations
Authors: Keating Dylan , Cowan Nicolas B
Published: October 2021

The field of exoplanet atmospheric characterization is trending towards comparative studies involving many planetary systems, and using Bayesian hierarchical modelling is a natural next step. Here we demonstrate two use cases. We first use hierarchical modelling to quantify variability in repeated observations by reanalysing a suite of 10 Spitzer secondary eclipse observations of the hot Jupiter XO-3 b. We compare three models: one where we fit 10 separate eclipse depths, one where we use a single eclipse depth for all 10 observations, and a hierarchical model. By comparing the widely applicable information criterion of each model, we show that the hierarchical model is preferred over the others. The hierarchical model yields less scatter across the suite of eclipse depths – and higher precision on the individual eclipse depths – than does fitting the observations separately. We find that the hierarchical eclipse depth uncertainty is larger than the uncertainties on the individual eclipse depths, which suggests either slight astrophysical variability or that single eclipse observations underestimate the true eclipse depth uncertainty. Finally, we fit a suite of published dayside brightness measurements for 37 planets using a hierarchical model of brightness temperature versus irradiation temperature. The hierarchical model gives tighter constraints on the individual brightness temperatures than the non-hierarchical model. Although we tested hierarchical modelling on Spitzer eclipse data of hot Jupiters, it is applicable to observations of smaller planets like hot Neptunes and super-Earths, as well as for photometric and spectroscopic transit or phase-curve observations.
Giant Metrewave Radio Telescope unveils steep-spectrum antique filaments in the galaxy cluster Abell 725
Authors: Pandge M B , Kale Ruta , Dabhade Pratik , Mahato Mousumi , Raychaudhury Somak
Published: October 2021

We present original Giant Metrewave Radio Telescope (GMRT) radio observations of the galaxy cluster Abell 725, at a redshift (z) of 0.09, along with other archival observations. Our GMRT maps reveal two steep-spectrum diffuse filaments in the cluster, along with a previously reported arc-like structure, and a wide-angle-tail (WAT) radio source associated with the brightest cluster galaxy (BCG) at the periphery of the cluster. The bent morphology of the WAT indicates that its jets have been swept back by the dynamic pressure resulting from the motion of the BCG through the surrounding intracluster medium. The BCG associated with the WAT hosts a black hole whose mass we estimate to be 1.4 $\ \pm\ 0.4 \times 10^{9}\,\rm M_{\odot }$. We observe a 2 arcmin (195 kpc in projection) offset between the BCG and the X-ray centroid of the galaxy cluster, which, along with other dynamic features, indicates the cluster’s early stage of evolution. The WAT radio galaxy, the arc, and the filaments have spectral indices $\alpha _{612}^{240}= -0.46\ \pm\ 0.15$, −0.8 ± 0.3, and (−1.13 ± 0.48, −1.40 ± 0.50), respectively. The WAT and the arc are connected structures, while the filaments are detached from them, but are found to be along the trail of the WAT. Based on the morphology of the components, and the progressive steepening of the components from the core of the WAT to the filaments, we propose that this system is a radio galaxy with trailing antique filaments.
Application of the Shannon entropy in the planar (non-restricted) four-body problem: the long-term stability of the Kepler-60 exoplanetary system
Authors: Kővári E , Érdi B , Sándor Zs
Published: October 2021

In this paper, we present an application of the Shannon entropy in the case of the planar (non-restricted) four-body problem. Specifically, the Kepler-60 extrasolar system is being investigated with a primary interest in the resonant configuration of the planets that exhibit a chain of mean-motion commensurabilities with the ratios 5:4:3. In the dynamical maps provided, the Shannon entropy is utilized to explore the general structure of the phase space, while, based on the time evolution of the entropy, we also determine the extent and rate of the chaotic diffusion as well as the characteristic times of stability for the planets. Two cases are considered: (i) the pure Laplace resonance when the critical angles of the two-body resonances circulate and that of the three-body resonance librates; and (ii) the chain of two two-body resonances when all the critical angles librate. Our results suggest that case (ii) is the more favourable configuration, but we state too that, in either case, the relevant resonance plays an important role in stabilizing the system. The derived stability times are no shorter than 108 yr in the central parts of the resonances.
Orbital and physical parameters of eclipsing binaries from the ASAS catalogue – XII. A sample of systems with K2 photometry
Authors: Hełminiak K G , Moharana A , Pawar T , Ukita N , Sybilski P , Espinoza N , Kambe E , Ratajczak M , Jordán A , Maehara H , Brahm R , Kozłowski S K , Konacki M
Published: October 2021

We present results of the analysis of light and radial velocity (RV) curves of eight detached eclipsing binaries observed by the All-Sky Automated Survey, which we have followed up with high-resolution spectroscopy, and were later observed by the Keplersatellite as part of the K2mission. The RV measurements came from spectra obtained with OAO-188/HIDES, MPG-2.2 m/FEROS, SMARTS 1.5 m/CHIRON, Euler/CORALIE, ESO-3.6 m/HARPS, and OHP-1.93/ELODIE instruments. The K2 time-series photometry was analysed with the jktebop code, with out-of-eclipse modulations of different origin taken into account. Individual component spectra were retrieved with the fd3 code, and analysed with the code ispec in order to determine effective temperatures and metallicities. Absolute values of masses, radii, and other stellar parameters are calculated, as well as ages, found through isochrone fitting. For five systems, such analysis has been done for the first time. The presented sample consists of a variety of stars, from low-mass dwarfs, through G- and F-type main sequence objects, to evolved active sub-giants, one of which is found to be crossing the Hertzsprung gap. One target may contain a γ Dor-type pulsator, two more are parts of higher-order multiples, and spectra of their tertiaries were also retrieved and used to constrain the properties of these systems.
Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats
Authors: Bernard Guillaume , Teulière Jérôme , Lopez Philippe , Corel Eduardo , Lapointe François-Joseph , Bapteste Eric
Published: October 2021

How, when, and why do organisms, their tissues, and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel the ultimate causes of organismal aging. A central hypothesis of these theories is that the strength of natural selection decreases with age. However, empirical evidence on when, why, and how organisms age is phylogenetically limited, especially in natural populations. Here, we developed generic comparisons of gene co-expression networks that quantify and dissect the heterogeneity of gene co-expression in conspecific individuals from different age-classes to provide topological evidence about some mechanical and fundamental causes of organismal aging. We applied this approach to investigate the complexity of some proximal and ultimate causes of aging phenotypes in a natural population of the greater mouse-eared bat Myotis myotis, a remarkably long-lived species given its body size and metabolic rate, with available longitudinal blood transcriptomes. M. myotis gene co-expression networks become increasingly fragmented with age, suggesting an erosion of the strength of natural selection and a general dysregulation of gene co-expression in aging bats. However, selective pressures remain sufficiently strong to allow successive emergence of homogeneous age-specific gene co-expression patterns, for at least 7 years. Thus, older individuals from long-lived species appear to sit at an evolutionary crossroad: as they age, they experience both a decrease in the strength of natural selection and a targeted selection for very specific biological processes, further inviting to refine a central hypothesis in evolutionary aging theories.
Positive Selection and Horizontal Gene Transfer in the Genome of a Male-Killing Wolbachia
Authors: Hill Tom , Unckless Robert L , Perlmutter Jessamyn I
Published: October 2021

Wolbachia are a genus of widespread bacterial endosymbionts in which some strains can hijack or manipulate arthropod host reproduction. Male killing is one such manipulation in which these maternally transmitted bacteria benefit surviving daughters in part by removing competition with the sons for scarce resources. Despite previous findings of interesting genome features of microbial sex ratio distorters, the population genomics of male-killers remain largely uncharacterized. Here, we uncover several unique features of the genome and population genomics of four Arizonan populations of a male-killing Wolbachia strain, wInn, that infects mushroom-feeding Drosophila innubila. We first compared the wInn genome with other closely related Wolbachia genomes of Drosophila hosts in terms of genome content and confirm that the wInn genome is largely similar in overall gene content to the wMel strain infecting D. melanogaster. However, it also contains many unique genes and repetitive genetic elements that indicate lateral gene transfers between wInn and non-Drosophila eukaryotes. We also find that, in line with literature precedent, genes in the Wolbachia prophage and Octomom regions are under positive selection. Of all the genes under positive selection, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes. These dynamics of selection and horizontal gene transfer across the genomes of several Wolbachia strains and diverse host species may be important underlying factors in Wolbachia’s success as a male-killer of divergent host species.
The lupus autoantigen La/Ssb is anXist-binding protein involved inXistfolding and cloud formation
Authors: Ha Norbert , Ding Nan , Hong Ru , Liu Rubing , Roca Xavier , Luo Yingyuan , Duan Xiaowei , Wang Xiao , Ni Peiling , Wu Haiyang , Zhang Li-Feng , Chen Lingyi
Published: October 2021

Using the programmable RNA-sequence binding domain of the Pumilio protein, we FLAG-tagged Xist (inactivated X chromosome specific transcript) in live mouse cells. Affinity pulldown coupled to mass spectrometry was employed to identify a list of 138 candidate Xist-binding proteins, from which, Ssb (also known as the lupus autoantigen La) was validated as a protein functionally critical for X chromosome inactivation (XCI). Extensive XCI defects were detected in Ssb knockdown cells, including chromatin compaction, death of female mouse embryonic stem cells during in vitro differentiation and chromosome-wide monoallelic gene expression pattern. Live-cell imaging of Xist RNA reveals the defining XCI defect: Xist cloud formation. Ssb is a ubiquitous and versatile RNA-binding protein with RNA chaperone and RNA helicase activities. Functional dissection of Ssb shows that the RNA chaperone domain plays critical roles in XCI. In Ssb knockdown cells, Xist transcripts are unstable and misfolded. These results show that Ssb is critically involved in XCI, possibly as a protein regulating the in-cell structure of Xist.
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

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

We 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

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

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

Recent 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

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 <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

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.
Contemporary Mechanical Circulatory Support With Continuous-Flow Biventricular Assist Devices: A Systematic Review
Authors: Meece Lauren E. , Yu Julia , Jeng Eric I. , Ahmed Mustafa M.
Published: October 2021

As the incidence of heart failure increases, so too has that of biventricular failure. While transplantation remains the gold standard therapy for end-stage heart failure, the limited organ supply has increased the need for durable mechanical circulatory support. We therefore sought to conduct a systematic review of continuous-flow ventricular assist devices in a biventricular configuration (CF-BiVAD). An electronic search of PubMed and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases was performed using the keyword “BIVAD.” Studies were reviewed to identify discrete variables, including implant indication, INTERMACs profile, timing of implant, mean age and BMI, and the anticoagulation/antiplatelet regimens employed post implant. Outcomes of interest included mortality and the incidence of thrombus, bleeding, infection, stroke, and renal failure. A total of 25 studies met inclusion criteria. No single variable was consistently reported, with only 4 studies reporting all 5 adverse effects. INTERMACs profile at implant and anticoagulation/antiplatelet regimen were reported in less than 50% of studies. Of those reporting mortality, there was a wide range of follow-up, from less than 6 months to >10 years, and the survival rate was similarly widely variable. Additionally, more than 50% of studies failed to isolate CF-BiVAD from alternative means of biventricular support, such as temporary support platforms, TAH, and pulsatile VADs. Therefore, high-quality quantitative analysis is not possible. In summary, the CF-BiVAD literature has a very heterogenous reporting of data. Standard reporting criteria may allow for future analyses to determine which patient characteristics portend a favorable outcome with CF-BiVAD implantation.
New developments in the diagnosis of primary immune thrombocytopenia
Authors: Lozano Maria L.
Published: October 2021

Immune thrombocytopenia is an acquired autoimmune disorder, which can affect both adults and children, characterized by lower than normal platelet counts (below 100 × 109/l). Thrombocytopenia may result in an increased risk of bleeding and puts patients at risk for serious complications. In the last decade, the multifactorial pathogenesis of ITP has become apparent, leading to greater understanding that different immune-mediated mechanisms could be involved in each patient, explaining the variable clinical presentation and response to therapies. The management of ITP patients has changed considerably in these past 10 years, but diagnosis of the disease has changed little, and remains clinical and possible only with the exclusion of other causes of thrombocytopenia. Although the search for such a test continues, to date, there is no reliable biomarker or gold-standard diagnostic test, which contributes to the high rate of misdiagnosis of the disease. This review presents the current limitations in the identification of the molecular disease underlying this disorder.
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

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

Several 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

Background

It 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.

Objective

Utilizing 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.

Results

We 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.

Conclusion

Based 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

Using 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.