bluuebunny/crossref_metadata_2025 huggingface dataset:
Chest drainage after oesophageal resection: A systematic review
Authors: Bull Alexander , Pucher Philip H , Lagergren Jesper , Gossage James A
Published: September 2021

Background

Modern enhanced recovery protocols discourage drain use due to negative impacts on patient comfort, mobility, and recovery, and lack of proven clinical benefit. After oesophagectomy, however, drains are still routinely placed. This review aimed to assess the evidence for, and how best to use chest drains after oesophageal surgery.

Methods

A systematic literature search was performed in Medline, Embase and Cochrane collaboration databases. Studies reporting outcomes for different types or uses of thoracic drainage, or outcomes related to drains after trans-thoracic oesophagectomy were included. Studies were collated into domains based on variations in number, position, type, removal criteria, diagnostic use and complications of drains. Methodological quality was assessed with Newcastle-Ottawa and Jadad scores.

Results

Among 434 potentially relevant studies, 27 studies met the inclusion criteria and these included 2564 patients. Studies that examined the number of drains showed pain reduction with a single drain compared to multiple drains (3 studies, n = 103), and transhiatal placement compared to intercostal (6 studies, n = 425). Amylase levels may aid diagnosis of anastomotic leak (9 studies, n = 888). Narrow calibre Blake drains may effectively drain both air and fluid (2 studies, n = 163). Drain removal criteria by daily drainage volumes of up to 300 mL did not impact subsequent effusion rates (2 studies, n = 130). Complications related directly to drains were reported by 3 studies (n = 59).

Conclusion

Available evidence on the impact of thoracic drainage after oesophagectomy is limited, but has the potential to negatively affect outcomes. Further research is required to determine optimum drainage strategies.
Genetic mapping of host resistance to the Pyrenophora teres f. maculata isolate 13IM8.3
Authors: Alhashel Abdullah Fahad , Sharma Poudel Roshan , Fiedler Jason , Carlson Craig H , Rasmussen Jack , Baldwin Thomas , Friesen Timothy L , Brueggeman Robert S , Yang Shengming
Published: September 2021

Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm), is a foliar disease of barley that results in significant yield losses in major growing regions worldwide. Understanding the host-parasite interactions between pathogen virulence/avirulence genes and the corresponding host susceptibility/resistance genes is important for the deployment of genetic resistance against SFNB. Two recombinant inbred mapping populations were developed to characterize genetic resistance/susceptibility to the Ptm isolate 13IM8.3, which was collected from Idaho (ID). An Illumina Infinium array was used to produce a genome-wide marker set. Quantitative trait loci (QTL) analysis identified ten significant resistance/susceptibility loci, with two of the QTL being common to both populations. One of the QTL on 5H appears to be novel, while the remaining loci have been reported previously. Single nucleotide polymorphisms (SNPs) closely linked to or delimiting the significant QTL have been converted to user-friendly markers. Loci and associated molecular markers identified in this study will be useful in genetic mapping and deployment of the genetic resistance to SFNB in barley.
Repeatability enhancement of time-lapse seismic data via a convolutional autoencoder
Authors: Jun Hyunggu , Cho Yongchae
Published: September 2021

In an ideal case, the time-lapse differences in 4-D seismic data should only reflect the changes of the subsurface geology. Practically, however, undesirable discrepancies are generated because of various reasons. Therefore, proper time-lapse processing techniques are required to improve the repeatability of time-lapse seismic data and to capture accurate seismic information to analyse target changes. In this study, we propose a machine learning-based time-lapse seismic data processing method improving repeatability. A training data construction method, training strategy and machine learning network architecture based on a convolutional autoencoder are proposed. Uniform manifold approximation and projection are applied to the training and target data to analyse the features corresponding to each data point. When the feature distribution of the training data is different from the target data, we implement data augmentation to enhance the diversity of the training data. The method is verified through numerical experiments using both synthetic and field time-lapse seismic data, and the results are analysed with several methods, including a comparison of repeatability metrics. From the results of the numerical experiments, we can conclude that the proposed convolutional autoencoder can enhance the repeatability of the time-lapse seismic data and increase the accuracy of observed variations in seismic signals generated from target changes.
The Logic of Negative Appeals: Graphic Imagery, Affective Empathy, and Foreign Development Aid
Authors: Bayram A Burcu , Holmes Marcus
Published: September 2021

The use of negative visual imagery of the poor to conjure feelings of pity, guilt, and empathy (also called “poverty porn”) is premised on an emotional mechanism that is supposed to elicit compassion and giving behavior, and yet the very emotional nature of the response to this kind of negative imagery can have the exact opposite effect by evoking compassion fatigue and psychological numbing. Our study interrogates this puzzle. Leveraging original data from survey experiments, we show that exposure to negative and personalized images of aid recipients in despair actually increases support for foreign development aid. In contrast, descriptive statistical information about global poverty moves people very little, or not at all. Our findings have implications for understanding the role imagery plays in shaping public opinion on foreign aid and for development communication. This study builds a bridge between research on foreign aid and humanitarian communication.
The Side Effects of Safe Asset Creation
Authors: Acharya Sushant , Dogra Keshav
Published: September 2021

We present an incomplete markets model to understand the costs and benefits of increasing government debt when an increased demand for safety pushes the natural rate of interest below zero. A higher demand for safe assets causes the zero lower bound (ZLB) to bind, increasing unemployment. Higher government debt satiates the demand for safe assets, raising the natural rate, and restoring full employment. However, this entails permanently lower investment, which reduces welfare, since our economy is dynamically efficient even when the natural rate is negative. Despite this, increasing debt until the ZLB no longer binds raises welfare when alternative instruments are unavailable. Higher inflation targets instead allow for negative real interest rates and achieve full employment without reducing investment.
Consensus on the Diagnosis and Treatment of Melasma in China (2021 Version)#
Authors: Gao Tian-Wen , Gu Hua , He Li , Lei Tie-Chi , Li Ming , Li Tie-Nan , Li Chun-Ying , Lin Tong , Mu Kuan-Hou , Tu Cai-Xia , Wen Hai , Wu Ji-Yuan , Xu Ai-E , Zhang Jun-Ling , Zhen Zhi-Zhong
Published: September 2021

The pathogenesis of melasma is believed to be related to heredity, sun exposure, sex hormones, and other factors. The mechanisms underlying the development of melasma include increased melanin synthesis, vascular proliferation within the skin lesions, inflammation, and skin barrier dysfunction. The diagnosis of melasma is mainly based on clinical manifestations and noninvasive techniques. Coupling with recent research progress in melasma, the present consensus comprehensively elaborates the etiology, pathogenesis, clinical manifestations, staging, classification, diagnosis, and treatment of melasma to improve the diagnostic and therapeutic skills of Chinese dermatologists.
Universal deformations in inhomogeneous isotropic nonlinear elastic solids
Authors: Yavari Arash
Published: September 2021

Universal (controllable) deformations of an elastic solid are those deformations that can be maintained for all possible strain-energy density functions and suitable boundary tractions. Universal deformations have played a central role in nonlinear elasticity and anelasticity. However, their classification has been mostly established for homogeneous isotropic solids following the seminal works of Ericksen. In this article, we extend Ericksen’s analysis of universal deformations to inhomogeneous compressible and incompressible isotropic solids. We show that a necessary condition for the known universal deformations of homogeneous isotropic solids to be universal for inhomogeneous solids is that inhomogeneities respect the symmetries of the deformations. Symmetries of a deformation are encoded in the symmetries of its pulled-back metric (the right Cauchy–Green strain). We show that this necessary condition is sufficient as well for all the known families of universal deformations except for Family 5.
Fur colour in the Arctic fox: genetic architecture and consequences for fitness
Authors: Tietgen Lukas , Hagen Ingerid J. , Kleven Oddmund , Bernardi Cecilia Di , Kvalnes Thomas , Norén Karin , Hasselgren Malin , Wallén Johan Fredrik , Angerbjörn Anders , Landa Arild , Eide Nina E. , Flagstad Øystein , Jensen Henrik
Published: September 2021

Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified theMC1Rgene as the sole causal gene underlying Arctic foxVulpes lagopusfur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations.MC1Ris located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.
Species ecology explains the spatial components of genetic diversity in tropical reef fishes
Authors: Donati Giulia Francesca Azzurra , Zemp Niklaus , Manel Stéphanie , Poirier Maude , Claverie Thomas , Ferraton Franck , Gaboriau Théo , Govinden Rodney , Hagen Oskar , Ibrahim Shameel , Mouillot David , Leblond Julien , Julius Pagu , Velez Laure , Zareer Irthisham , Ziyad Adam , Leprieur Fabien , Albouy Camille , Pellissier Loïc
Published: September 2021

Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the
α
,
β
and
γ
components of genetic diversity, which we subsequently link to six ecological traits. We find that the
α
and
γ
components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The
α
and
γ
diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic
β
diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.
Between the devil and the deep blue sea: herbivory induces foraging for and uptake of cadmium in a metal hyperaccumulating plant
Authors: Mohiley Anubhav , Laaser Tanja , Höreth Stephan , Clemens Stephan , Tielbörger Katja , Gruntman Michal
Published: September 2021

Plants have been shown to change their foraging behaviour in response to resource heterogeneity. However, an unexplored hypothesis is that foraging could be induced by environmental stressors, such as herbivory, which might increase the demand for particular resources, such as those required for herbivore defence. This study examined the way simulated herbivory affects both root foraging for and uptake of cadmium (Cd), in the metal-hyperaccumulating plant
Arabidopsis halleri
, which uses this heavy metal as herbivore defence. Simulated herbivory elicited enhanced relative allocation of roots to Cd-rich patches as well as enhanced Cd uptake, and these responses were exhibited particularly by plants from non-metalliferous origin, which have lower metal tolerance. By contrast, plants from a metalliferous origin, which are more tolerant to Cd, did not show any preference in root allocation, yet enhanced Cd sharing between ramets when exposed to herbivory. These results suggest that foraging for heavy metals, as well as their uptake and clonal-sharing, could be stimulated in
A. halleri
by herbivory impact. Our study provides first support for the idea that herbivory can induce not only defence responses in plants but also affect their foraging, resource uptake and clonal sharing responses.
JMM Profile: Vibrio cholerae: an opportunist of human crises
Authors: Grant Trudy-Ann , Balasubramanian Deepak , Almagro-Moreno Salvador
Published: September 2021

Vibrio cholerae

O1 is the aetiological agent of the severe diarrhoeal disease cholera. Annually, there are an estimated 1–4 million cholera cases worldwide and over 140 000 deaths. The primary mode of disease transmission is through the consumption of water or food contaminated with the bacterium. Although cholera patients can be treated effectively using rehydration therapy, the disease remains a major scourge in areas with limited access to clean water and proper sanitation. Its continued prevalence highlights the failure of socioeconomic policies leading to wealth disparities, fragile and dated public infrastructure, and lack of appropriate health surveillance.
SARS-CoV-2 vaccine effectiveness and breakthrough infections in maintenance dialysis patients
Authors: Manley Harold J. , Aweh Gideon N. , Hsu Caroline M. , Weiner Daniel E. , Miskulin Dana , Harford Antonia M. , Johnson Doug , Lacson Eduardo K.
Published: September 2021

Among patients receiving maintenance dialysis with a national US dialysis provider, fully vaccinated dialysis patients were significantly less likely to be diagnosed with COVID-19 or be hospitalized than unvaccinated patients. Ad26.COV2.S/Janssen vaccine had significantly worse outcomes, and mRNA-1273/Moderna the best. Among the 27 patients with breakthrough COVID-19 and anti-spike IgG antibodies measured, 23/27 (85%) breakthrough COVID-19 cases occurred at titers <2 U/L (lower limit of a positive response); 14 of these patients never developing Ab titers above 2 U/L. Only 3/27 were receiving immunosuppression. The potential use of antibody titers to guide vaccinations should be explored.
Measuring Subjective Cognitive Decline in Older Adults: Harmonization between the Cognitive Change Index and the Measurement of Everyday Cognition Instruments
Authors: Wells Lindsey F , Risacher Shannon L , McDonald Brenna C , Farlow Martin R , Brosch Jared , Gao Sujuan , Apostolova Liana G , Saykin Andrew J
Published: September 2021

Background

Self and informant (proxy or study partner) reports of everyday cognitive functioning have been shown to be associated with incipient neurodegenerative disease. The 20-item Cognitive Change Index (CCI) and the 39-item Measurement of Everyday Cognition (ECog) were each developed to characterize early subjective changes in cognitive function.

Objective

We examined the relationship between CCI and ECog self and informant evaluations to determine content overlap and provide a co-calibration for converting between these widely used instruments.

Methods

950 participants (57.1% female, mean age=71.2yrs) from ADNI and the Indiana ADRC with self evaluations and 279 participants (60.9% female, mean age=71.8yrs) with informant evaluations (Indiana ADRC) were included. Analyzed variables for the CCI and ECog included domain mean scores, memory domain total scores, and total scores for all items. Pearson correlations, regression analyses, and frequency distributions were used to assess the relationship between CCI and ECog. Sex, years of education, race, APOE ε4 carrier status, and baseline diagnosis were also analyzed as potentially relevant covariates.

Results

CCI and ECog total scores were highly correlated for the self (r=0.790, p<0.001) and informant (r=0.860, p<0.001) versions. Frequency distributions of total scores were generated and self and informant histograms were plotted separately. Quadratic regressions for self (r2=0.682) and informant (r2=0.863) scores were used to create a translation table between the CCI and ECog total scores.

Conclusion

Self and informant total scores can be harmonized and translated between the CCI and ECog to facilitate cross-study and longitudinal assessment of perceived cognitive change, an important patient-reported outcome.
Human lung tissue resident memory T cells are re-programmed but not eradicated with systemic glucocorticoids after acute cellular rejection
Authors: Snyder Mark E. , Moghbeli Kaveh , Bondonese Anna , Craig Andrew , Popescu Iulia , Fan Li , Tabib Tracy , Lafyatis Robert , Chen Kong , Trejo Bittar Humberto E. , Lendermon Elizabeth , Pilewski Joseph , Johnson Bruce , Kilaru Silpa , Zhang Yingze , Sanchez Pablo G. , Alder Jonathan K. , Sims Peter A. , McDyer John F.
Published: September 2021

Acute cellular rejection is common after lung transplantation and is associated with an increased risk of early chronic rejection. We present combined single cell RNA and T cell receptor sequencing on recipient derived T cells obtained from the bronchoalveolar lavage of three lung transplant recipients with acute cellular rejection and compare them with T cells obtained from the same three patients after clinical treatment of rejection with high-dose, systemic glucocorticoids. At the time of acute cellular rejection, we find an oligoclonal expansion of cytotoxic CD8+T cells, that all persist as tissue resident memory T cells following successful treatment. Persisting CD8+allograft-resident T cells have reduced gene expression for cytotoxic mediators following therapy with glucocorticoids. This clonal expansion is discordant with circulating T cell clonal expansion at the time of rejection, suggesting in-situ expansion. These findings pose a potential biological mechanism linking acute cellular rejection to chronic allograft damage.
Assessing inertial measurement unit locations for freezing of gait detection and patient preference
Authors: O’Day Johanna , Lee Marissa , Seagers Kirsten , Hoffman Shannon , Jih-Schiff Ava , Kidziński Łukasz , Delp Scott , Bronte-Stewart Helen
Published: September 2021

Background

Freezing of gait, a common symptom of Parkinson’s disease, presents as sporadic episodes in which an individual’s feet suddenly feel stuck to the ground. Inertial measurement units (IMUs) promise to enable at-home monitoring and personalization of therapy, but there is a lack of consensus on the number and location of IMUs for detecting freezing of gait. The purpose of this study was to assess IMU sets in the context of both freezing of gait detection performance and patient preference.

Methods

Sixteen people with Parkinson’s disease were surveyed about sensor preferences. Raw IMU data from seven people with Parkinson’s disease, wearing up to eleven sensors, were used to train convolutional neural networks to detect freezing of gait. Models trained with data from different sensor sets were assessed for technical performance; a best technical set and minimal IMU set were identified. Clinical utility was assessed by comparing model- and human-rater-determined percent time freezing and number of freezing events.

Results

The best technical set consisted of three IMUs (lumbar and both ankles, AUROC = 0.83), all of which were rated highly wearable. The minimal IMU set consisted of a single ankle IMU (AUROC = 0.80). Correlations between these models and human raters were good to excellent for percent time freezing (ICC = 0.93, 0.89) and number of freezing events (ICC = 0.95, 0.86) for the best technical set and minimal IMU set, respectively.

Conclusions

Several IMU sets consisting of three IMUs or fewer were highly rated for both technical performance and wearability, and more IMUs did not necessarily perform better in FOG detection. We openly share our data and software to further the development and adoption of a general, open-source model that uses raw signals and a standard sensor set for at-home monitoring of freezing of gait.
Young adults vulnerability to COVID-19 in Brazil: an overview across the country
Authors: de Souza Fernanda Sumika Hojo , Hojo-Souza Natália Satchiko , de Oliveira Daniela Carine Ramires , da Silva Cristiano Maciel , Guidoni Daniel Ludovico
Published: September 2021

Brazil is a country of continental dimensions, where many smaller countries would fit. In addition to demographic, socioeconomic, and cultural differences, hospital infrastructure and healthcare varies across all 27 federative units. Therefore, the evolution of COVID-19 pandemic did not manifest itself in a homogeneous and predictable trend across the nation. In late 2020 and early 2021, new waves of the COVID-19 outbreak have caused an unprecedented sanitary collapse in Brazil. Unlike the first COVID-19 wave, in subsequent waves, preliminary evidence has pointed to an increase in the daily reported cases among younger people being hospitalized, overloading the healthcare system. In this comprehensive retrospective study, confirmed cases of hospitalization, ICU admission, IMV requirement and in-hospital death from Brazilian COVID-19 patients throughout 2020 until the beginning of 2021 were analyzed through a spatio-temporal study for patients aged 20-59 years. All Brazilian federative units had their data disaggregated in six periods of ten epidemiological weeks each. We found that there is a wide variation in the waves dynamic due to SARS-CoV-2 infection, both in the first and in subsequent outbreaks in different federative units over the analyzed periods. As a result, atypical waves can be seen in the Brazil data as a whole. The analysis showed that Brazil is experiencing a numerical explosion of hospitalizations and deaths for patients aged 20-59 years, especially in the state of São Paulo, with a similar proportion of hospitalizations for this age group but higher proportion of deaths compared to the first wave.
Perfusate metabolomics content and tubular transporters expression during kidney graft preservation by hypothermic machine perfusion
Authors: Faucher Quentin , Alarcan Hugo , Sauvage François-Ludovic , Forestier Lionel , Miquelestorena-Standley Elodie , Nadal-Desbarats Lydie , Arnion Hélène , Venhard Jean-Christophe , Brichart Nicolas , Bruyère Franck , Marquet Pierre , Guellec Chantal Barin-Le
Published: September 2021

Background

Ischemia-related injury during the pre-implantation period impacts kidney graft outcome. Evaluating these lesions by a non-invasive approach before transplantation could help to understand the mechanisms of graft injury and identify potential biomarkers predictive of graft outcomes. This study aims to determine metabolomic content of graft perfusion fluids and its dependence on preservation time and to explore whether tubular transporters are possibly involved in the metabolomics variations observed.

Methods

Kidneys were stored on hypothermic perfusion machines. We evaluated the metabolomic profiles of perfusion fluids (n=35) using Liquid Chromatography coupled with tandem Mass Spectrometry and studied the transcriptional expression of tubular transporters on pre-implantation biopsies (n=26). We used univariate and multivariate analyses to assess the impact of perfusion time on these parameters and their relationship with graft outcome.

Results

Seventy-two metabolites were found in preservation fluids at the end of perfusion, of which 40% were already present in the native conservation solution. We observed an increase of 23 metabolites with longer perfusion time and a decrease for 8. The predictive model for time-dependent variation of metabolomics content showed good performance (R2= 76%, Q2= 54%, accuracy= 41%, permutations test significant). Perfusion time had no effect on the mRNA expression of transporters. We found no correlation between metabolomics and transporters expression. Neither the metabolomics profile nor the transporters expression were predictive of graft outcome.

Conclusion

Our results open the way for further studies, focusing on both intra- and extra-tissue metabolome, to investigate whether transporter alterations can explain the variations observed in pre-implantation period.
Metric selection and promotional language in health artificial intelligence
Authors: Graham S. Scott , Ghotra Trisha
Published: September 2021

Background

Recent advances in Artificial intelligence (AI) have the potential to substantially improve healthcare across clinical areas. However, there are concerns health AI research may overstate the utility of newly developed systems and that certain metrics for measuring AI system performance may lead to an overly optimistic interpretation of research results. The current study aims to evaluate the relationship between researcher choice of AI performance metric and promotional language use in published abstracts.

Methods and findings

This cross-sectional study evaluated the relationship between promotional language and use of composite performance metrics (AUC or F1). A total of 1200 randomly sampled health AI abstracts drawn from PubMed were evaluated for metric selection and promotional language rates. Promotional language evaluation was accomplished through the development of a customized machine learning system that identifies promotional claims in abstracts describing the results of health AI system development. The language classification system was trained with an annotated dataset of 922 sentences. Collected sentences were annotated by two raters for evidence of promotional language. The annotators achieved 94.5% agreement (κ = 0.825). Several candidate models were evaluated and, the bagged classification and regression tree (CART) achieved the highest performance at Precision = 0.92 and Recall = 0.89. The final model was used to classify individual sentences in a sample of 1200 abstracts, and a quasi-Poisson framework was used to assess the relationship between metric selection and promotional language rates. The results indicate that use of AUC predicts a 12% increase (95% CI: 5-19%, p = 0.00104) in abstract promotional language rates and that use of F1 predicts a 16% increase (95% CI: 4% to 30%, p = 0. 00996).

Conclusions

Clinical trials evaluating spin, hype, or overstatement have found that the observed magnitude of increase is sufficient to induce misinterpretation of findings in researchers and clinicians. These results suggest that efforts to address hype in health AI need to attend to both underlying research methods and language choice.
Predictors of parents’ intention to vaccinate their children against the COVID-19 in Greece: a cross-sectional study
Authors: Galanis Petros , Vraka Irene , Siskou Olga , Konstantakopoulou Olympia , Katsiroumpa Aglaia , Moisoglou Ioannis , Kaitelidou Daphne
Published: September 2021

Background

Parents’ intention to vaccinate their children against the COVID-19 is envisaged as critical strategy to control the pandemic.

Objective

To investigate the intention of parents to vaccinate their children against the COVID-19 and the factors influencing this intention.

Methods

We conducted an online cross-sectional study in Greece and we collected data during the first week of September 2021. A convenience sample was used by collecting questionnaires through social media. Our study population included adult parents with children aged 12-17 years who were eligible for a COVID-19 vaccine.

Results

Study population included 813 parents with a mean age of 42.3 years. Among parents, 36% reported that they will vaccinate their children against the COVID-19, 33.5% denied vaccination and 30.5% were undecided. Concerns about the safety, effectiveness and side effects of COVID-19 vaccines were the most important reasons for decline of COVID-19 vaccination. Parents who took the flu vaccine in 2020 and those who had more knowledge and fewer concerns about COVID-19 vaccines had a greater probability to vaccinate their children against the COVID-19. Increased self-perceived severity of COVID-19, and increased trust in COVID-19 vaccines and the government regarding the information about the COVID-19 vaccines were associated with parents’ intention to vaccinate their children. However, increased knowledge regarding COVID-19 was associated with decreased intention of parents to vaccinate their children.

Conclusions

Parents’ intention to vaccinate their children against the COVID-19 was low. Our findings could contribute to the development of target strategies to implement adherence to COVID-19 vaccination campaigns.
Does Time to Theatre Affect The Ability to Achieve Fracture Reduction in Tibial Plateau Fractures?
Authors: Kitchen David S. , Richards Jack , Smitham Peter J. , Atkins Gerald J. , Solomon Lucian B.
Published: September 2021

Aims

The primary aim of this study was to assess the effect of time to surgery on fracture reduction, assessed as residual articular step, in cases of tibial plateau fracture (TPF). The secondary aim was to assess the effect of pre-operative demographics and residual articular step on patient reported outcomes (PROMs) following TPF.

Method

Between 2006 and 2017 all surgically treated TPF patients managed by a single surgeon at our institution were prospectively consented for the study of fracture outcomes. Timing to surgical intervention, reduction of articular step, age, gender, medical background, fracture classification, mechanism of injury and PROMs (Lysholm Scores and Knee Injury and Osteoarthritis Outcome Scores (KOOS)) were recorded and analysed. Reduction of articular step, defined as <2mm, was assessed by a single blinded examiner using measurements on plain radiographs on PACS.

Results

One hundred seventeen patients were enrolled, 52 with Schatzker II, four with Schatzker IV and 61 with Schatzker VI fractures. Patients were followed-up to a mean time of 3.9 years. The ability to achieve fracture reduction was negatively influenced by time to theatre with the odds of achieving reduction decreasing 17% each day post-injury (p = 0.002). An increased time to theatre was associated with reduced Lysholm scores at the one-year mark (p = 0.01). The ability to achieve fracture reduction did not influence PROMs within the study period.

Conclusion

Delay in surgical fixation negatively affects fracture reduction in TPF and may delay recovery. However, residual articular step did not influence the investigated PROMs in the cohort investigated over the mid-term (mean of 3.9 years).
Re-evaluation of ethylene role in Arabidopsis cauline leaf abscission induced by water stress and rewatering
Authors: Meir Shimon , Philosoph-Hadas Sonia , Salim Shoshana , Segev Adi , Riov Joseph
Published: September 2021

Patharkar and Walker (2016) reported that cauline leaf abscission in Arabidopsis is induced by a cycle of water stress and rewatering, which is regulated by the complex of INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), HAESA (HAE), and HAESA-LIKE2 (HSL2) kinases. However, they stated without presenting experimental results that ethylene is not involved in this process. Since this statement contradicts the well-established role of ethylene in organ abscission induced by a cycle of water stress and rewatering, our present study was aimed to re-evaluate the possible involvement of ethylene in this process. For this purpose, we examined the endogenous ethylene production during water stress and following rewatering, as well as the effects of exogenous ethylene and 1-methylcyclopropene (1-MCP), on cauline leaf abscission of Arabidopsis wild type. Additionally, we examined whether this stress induces cauline leaf abscission in ethylene-insensitive Arabidopsis mutants. The results of the present study demonstrated that ethylene production rates increased significantly in cauline leaves at 4 h after rewatering of stressed plants, and remained high for at least 24 h in plants water-stressed to 40 and 30% of system weight. Ethylene treatment applied to well-watered plants induced cauline leaf abscission, which was inhibited by 1-MCP. Cauline leaf abscission was also inhibited by 1-MCP applied during a cycle of water stress and rewatering. Finally, no abscission occurred in two ethylene-insensitive mutants,ein2-1andein2-5, following a cycle of water stress and rewatering. Taken together, these results clearly indicate that ethylene is involved in Arabidopsis cauline leaf abscission induced by water stress.

One sentence summary

Unlike Patharker and Walker (2016), our results show that ethylene is involved in Arabidopsis cauline leaf abscission induced by water stress and rewatering, similar to leaf abscission in other plants.
Mapping Spatial Frequency Preferences Across Human Primary Visual Cortex
Authors: Broderick William F. , Simoncelli Eero P. , Winawer Jonathan
Published: September 2021

Abstract

Neurons in primate visual cortex (area V1) are tuned for spatial frequency, in a manner that depends on their position in the visual field. Several studies have examined this dependency using fMRI, reporting preferred spatial frequencies (tuning curve peaks) of V1 voxels as a function of eccentricity, but their results differ by as much as two octaves, presumably due to differences in stimuli, measurements, and analysis methodology. Here, we characterize spatial frequency tuning at a millimeter resolution within human primary visual cortex, across stimulus orientation and visual field locations. We measured fMRI responses to a novel set of stimuli, constructed as sinusoidal gratings in log-polar coordinates, which include circular, radial, and spiral geometries. For each individual stimulus, the local spatial frequency varies inversely with eccentricity, and for any given location in the visual field, the full set of stimuli span a broad range of spatial frequencies and orientations. Over the measured range of eccentricities, the preferred spatial frequency is well-fit by a function that varies as the inverse of the eccentricity plus a small constant. We also find small but systematic effects of local stimulus orientation, defined in both absolute coordinates and relative to visual field location. Specifically, peak spatial frequency is higher for pinwheel than annular stimuli and for horizontal than vertical stimuli.
PhycoMine: A Microalgae Data Warehouse
Authors: Goitia Rodrigo R. D. , Riaño-Pachón Diego M. , Fassio Alexandre Victor , Winck Flavia V.
Published: September 2021

PhycoMine is data warehouse system created to fostering the analysis of complex and integrated data from microalgae species in a single computational environment. The PhycoMine was developed on top of the InterMine software system, and it has implemented an extended database model, containing a series of tools that help the users in the analysis and mining of individual data and group data. The platform has widgets created to facilitate simultaneous data mining of different datasets. Among the widgets implemented in PhycoMine, there are options for mining chromosome distribution, gene expression variation via transcriptomics, proteomics sets, Gene Onthology enrichment, KEGG enrichment, publication enrichment, EggNOG, Transcription factors and transcriptional regulators enrichment and phenotypical data. These widgets were created to facilitate data visualization of the gene expression levels in different experimental setups, for which RNA-seq experimental data is available in data repositories. For comparative purposes, we have reanalyzed 200 RNA-seq datasets from Chlamydomonas reinhardtii, a model unicellular microalga, for optimizing the performance and accuracy of data comparisons. We have also implemented widgets for metabolic pathway analysis of selected genes and proteins and options for biological network analysis. The option for analysis of orthologue genes was also included. With this platform, the users can perform data mining for a list of genes or proteins of interest in an integrated way through accessing the data from different sources and visualizing them in graphics and by exporting the data into table formats. The PhycoMine platform is freely available and can be visited through the URL https://PhycoMine.iq.usp.br.
Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing
Authors: Tabatabaei S. Kasra , Pham Bach , Pan Chao , Liu Jingqian , Chandak Shubham , Shorkey Spencer A. , Hernandez Alvaro G. , Aksimentiev Aleksei , Chen Min , Schroeder Charles M. , Milenkovic Olgica
Published: September 2021

DNA is a promising next-generation data storage medium, but the recording latency and synthesis cost of oligos using the four natural nucleotides remain high. Here, we describe an improved DNA-based storage system that uses an extended 11-letter molecular alphabet combining natural and chemically modified nucleotides. Our extended-alphabet molecular storage paradigm offers a nearly two-fold increase in storage density and potentially the same order of reduction in the recording time. Experimental results involving a library of 77 custom-designed hybrid sequences reveal that one can readily detect and discriminate different combinations and orders of monomers via MspA nanopores. Furthermore, a neural network architecture designed to classify raw current signals generated by Oxford Nanopore Technologies sequencing ensures an average accuracy exceeding 60%, which is 39 times higher than that of random guessing. Molecular dynamics simulations reveal that the majority of modified nucleotides do not induce dramatic disruption of the DNA double helix, making the extended alphabet system potentially compatible with PCR-based random access data retrieval. The methodologies proposed provide a forward path for new implementations of molecular recorders.
Long read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod
Authors: Pearman William S. , Wells Sarah J. , Dale James , Silander Olin K. , Freed Nikki E.
Published: September 2021

Most animal mitochondrial genomes are small, circular, and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod,Isocladus armatus. Data from long and short read DNA sequencing, suggests thatI. armatushas two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that a heteroplasmic site previously observed across many species within Isopoda is absent inI. armatus,but confirm the presence of two heteroplasmic sites recently reported in two other isopod species.
A combination of two human neutralizing antibodies prevents SARS-CoV-2 infection in rhesus macaques
Authors: Cobb Ronald R. , Nkolola Joseph , Gilchuk Pavlo , Chandrashekar Abishek , House Robert V. , Earnhart Christopher G. , Dorsey Nicole M. , Hopkins Svetlana A. , Snow Doris M. , Chen Rita E. , VanBlargan Laura A. , Hechenblaikner Manuel , Hoppe Brian , Collins Laura , Tomic Milan T. , Nonet Genevieve H. , Hackett Kyal , Slaughter James C. , Diamond Michael S. , Carnahan Robert H. , Barouch Dan H. , Crowe James E.
Published: September 2021

Human monoclonal antibody (mAb) treatments are promising for COVID-19 prevention, post-exposure prophylaxis, or therapy. However, the titer of neutralizing antibodies required for protection against SARS-CoV-2 infection remains poorly characterized. We previously described two potently neutralizing mAbs COV2-2130 and COV2-2381 targeting non-overlapping epitopes on the receptor-binding domain of SARS-CoV-2 spike protein. Here, we engineered the Fc-region of these mAbs with mutations to extend their persistence in humans and reduce interactions with Fc gamma receptors. Passive transfer of individual or combinations of the two antibodies (designated ADM03820) given prophylactically by intravenous or intramuscular route conferred virological protection in a non-human primate (NHP) model of SARS-CoV-2 infection, and ADM03820 potently neutralized SARS-CoV-2 variants of concernin vitro. We defined 6,000 as a protective serum neutralizing antibody titer in NHPs against infection for passively transferred human mAbs that acted by direct viral neutralization, which corresponded to a concentration of 20 μg/mL of circulating mAb.
PD-1 checkpoint blockade activates germinal center follicular T cell programs that disrupt type 2 isotype-specific antibody homeostasis
Authors: Shuparski Andrew G. , Higgins Brett W. , Miller Karen B. , McHeyzer-Williams Louise J. , McHeyzer-Williams Michael G.
Published: September 2021

Multiple CD4 T cell dependent tolerance mechanisms control adaptive B cell immunity to environmental antigens. We recently demonstrated a PD-1 checkpoint within steady-state splenic germinal centers (GC) that constrains the maturation of type 2 IgG1 isotype-specific antibody homeostasis. Here, we utilized single cell-indexed custom RNA-sequencing to probe the follicular T cell mechanisms directly targeted by acute PD-1 blockade. We find a pre-existing subset of follicular helper T (TFH) cells that express type 2 immune response properties (TFH2) with exaggerated pathways of TCR activation, cytokine signaling, and enhanced cell-cell contact upon acute PD-1 blockade. This selective amplification of the TFH2 program significantly increases predicted molecular connections to type 2 IgG1 GC B cells that dominate limited changes in GC localized follicular regulatory T (GC TFR) cell programs. These studies demonstrate how type 2 isotype-specific adaptive B cell tolerance is selectively disrupted by acute PD-1 blockade to reveal the modular regulatory mechanisms that control splenic GC dynamics at homeostasis.

One Sentence Summary

Acute PD-1 blockade alters the regulatory dynamic of the steady state germinal center to drive the maturation of IgG1 GC B cells towards PC differentiation in a process mediated by type 2 like TFH effector molecules.

HIGHLIGHTS

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Acute PD-1 blockade enhances the steady state splenic TFH program

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PD-1 blockade selectively exaggerates a Type 2 like TFH module

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GC TFR cells are minimally impacted by blockade

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PD-1 restrains predicted TFH2 functional contacts with IgG1 GC B Cells
picd-1, a gene that encodes CABIN1 domain-containing protein, interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans
Authors: Mallick Avijit , Taylor Shane K. B. , Mehta Sakshi , Gupta Bhagwati P.
Published: September 2021

AXIN family members control diverse biological processes in eukaryotes. As a scaffolding protein, AXIN facilitates interactions between cellular components and provides specificity to signaling pathways. Despite its crucial roles in metazoans and discovery of a large number of family members, the mechanism of AXIN function is not very well understood. The C. elegans AXIN homolog PRY-1 provides a powerful tool to identify interacting genes and downstream effectors that function in a conserved manner to regulate AXIN-mediated signaling. Previous work demonstrated pry-1’s essential role in developmental processes such as reproductive system, seam cells, and a P lineage cell P11.p. More recently, our lab carried out a transcriptome profiling of pry-1 mutant and uncovered the essential role of the gene in lipid metabolism, stress response, and aging. In this study, we have extended the work on pry-1 by reporting a novel interacting gene picd-1 (pry-1-interacting CABIN1 domain containing). Our findings have revealed that picd-1 plays an essential role in C. elegans and is involved in several pry-1-mediated processes including regulation of stress response and lifespan maintenance. In support of this, picd-1 expression overlaps with pry-1 in multiple tissues throughout the lifespan of animals. Further experiments showed that picd-1 inhibits CREB-regulated transcriptional coactivator homolog CRTC-1 function, which promotes longevity in a calcineurin-dependent manner. These data provide evidence for an essential role of the CABIN1 domain protein PICD-1 in mediating PRY-1 signaling in C. elegans.
Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia
Authors: Yagound Boris , West Andrea J. , Richardson Mark F. , Selechnik Daniel , Shine Richard , Rollins Lee A.
Published: September 2021

Understanding the mechanisms underlying rapid adaptation of invasive species in novel environments is key to improving our ability to manage these species. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk-taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads (Rhinella marina) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads’ dispersal ability. Common-garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. However, genetic diversity is greatly reduced across the invasive range due to a strong founder effect, and the genetic basis underlying dispersal-related behavioural changes remains unknown. Here we used RNA-seq to compare the brain transcriptomes of toads from the Hawai’ian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, cane toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between range-core and range-front populations. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.