bluuebunny/crossref_metadata_2025 huggingface dataset:
Laparoscopic Cholecystectomy Versus Percutaneous Cholecystostomy: Suitability of APACHE-II Score, ASA Grade, and Tokyo Guidelines 18 Grade as Predictors of Outcome in Patients With Acute Cholecystitis
Authors: Latif Javed , Kushairi Anisa , Thurley Peter , Bhatti Imran , Awan Altaf
Published: March 2022

Introduction:

Intervention options in acute cholecystitis (AC) include drainage (percutaneous/endoscopic) or surgery. Several scoring systems have been used to risk stratify acute surgical patients, but few have been validated. This study investigated the suitability of Acute Physiology and Chronic Health Evaluation II (APACHE-II) score, American Society of Anesthesiologist (ASA) grade, and Tokyo Guidelines 2018 (TG18) grade as predictors of outcome and assess laparoscopic cholecystectomy versus percutaneous cholecystostomy (PC) as treatment options in patients with AC.

Materials and Methods:

Retrospective data was collected from patients that underwent acute inpatient cholecystectomy (index admission), urgent interval cholecystectomy (2 to 4 wk) and PC between 2016 and 2018. Data included baseline demographics, co-morbidities, ASA grade, APACHE-II score, TG18 grade, morbidity, and mortality. A P-value of <0.05 was statistically significant. Area under the receiver operating characteristic curve was calculated to compare accuracy of APACHE-II, ASA and TG18 in predicting morbidity.

Results:

A total of 344 consecutive patients (266 cholecystectomies and 84 PC) were included in the study. Significant difference in co-morbidities [median Charlson Co-Morbidity Index (CCI) 1 surgery and 4 cholecystostomy (PC) (P<0.05)], median APACHE-II score (3 surgery and 9 PC), median TG18 grade (1 surgery and 2 PC) and mortality rate [0% surgery and 7% cholecystostomy (PC)]. TG18 grade alone predicted postoperative/postprocedure morbidity (receiver operating characteristic; AUC=0.884; 95% confidence interval: 0.845-0.923; odds ratio: 4.38, 96% confidence interval, P<0.05).

Discussion:

Utilization of the TG18 grade have shown to be more accurate in risk stratifying and predicting outcomes in patients with AC and therefore may appropriately guide biliary intervention.

PC can be utilized in a select group of septic and co-morbid patients (myocardial infarction <6 weeks, chest infection and acute cerebrovascular accident) unable to withstand surgical intervention or in those with complex biliary disease (Mirizzi Syndrome). In a proportion, PC drains sepsis to improve critical state of the patient enough to consider an interval cholecystectomy with satisfactory outcomes.
Calcium homeostasis disruption initiates rapid growth after micro-fragmentation in the scleractinian coral Porites lobata
Authors: Lock Colin , Bentlage Bastian , Raymundo Laurie J
Published: March 2022

Coral reefs are ecosystems under increasing threat from global climate change. Coral restoration is a tool for preserving biological and ecological function of coral reefs by mitigating coral loss and maintaining the structural integrity and complexity of reefs. To generate the necessary stock for coral restoration, larger coral colonies are usually fragmented to generate smaller specimens for outplanting, taking advantage of the high regenerative ability of corals. In this study, we utilized RNA-seq technology to understand the physiological responses of Porites lobata colonies to physical fragmentation and outplanting, which have thus far not been characterized. Our results demonstrate that P. lobata fragments undergoing physical injury recover through two distinct phases: rapid wound regeneration of the cut margins, followed by a slower growth phase that cements the colony to the substrate. Our study found rapid physiological responses to acute physical injury and outplanting in the coral host that involved significantly increased energy production, calcium homeostasis disruption, and Endoplasmic Reticulum (ER) stress leading to increased antioxidant expression and rates of protein turnover. Our results suggest that phosphoinositide-mediated acute calcium homeostasis disruption stimulates wound recovery processes in response to physical injury. Symbiont gene expression revealed extremely low gene differences in response to fragmentation, growth, and outplanting. These results provide insight into the physiological mechanisms that allow for rapid wound healing and stabilization in response to physical injury in corals.
Temperature Stressed Caenorhabditis elegans Males Prioritize Feeding over Mating Resulting in Sterility
Authors: Sepulveda Nicholas B. , Petrella Lisa N.
Published: March 2022

Heat stress negatively impacts fertility in sexually reproducing organisms at sublethal temperatures. These temperature stress effects are typically more pronounced in males. In some species, sperm production, quality, and motility are the primary cause of male infertility under temperature stress. However, this is not the case in the model nematode Caenorhabditis elegans where changes in mating behavior are the primary cause of fertility loss. We report that temperature stressed C. elegans males experience a dramatic upset in the balance of their food drive and their mating drive such that they prioritize feeding over mating. This change in priorities is due partially to increased expression of the chemoreceptor odr-10 in the AWA sensory neurons. Increased odr-10 expression in the presence of ample food demonstrates that males are unable to experience satiety, thus they never leave a food source and engage in mate searching behavior. These results demonstrate that moderate temperature stress may have profound and previously underappreciated effects on reproductive behaviors. As climate change associated temperature variability becomes more commonplace, it will be imperative to understand how temperature stress affects conserved behavioral elements critical to reproduction.
Health indicators as a measure of individual health status: public perspectives
Authors: Sokoya Temiloluwa , Zhou Yuchun , Diaz Sebastian , Law Timothy , Himawan Lina , Lekey Francisca , Shi Lu , Gimbel Ronald W. , Jing Xia
Published: March 2022

Objective

We examined the perspectives of the general public on 29 health indicators to provide evidence for further prioritizing the indicators, which were obtained from the literature review. Health status is different from disease status, which can refer to different stages of cancer.

Design

This study uses a cross-sectional design.

Setting

An online survey was administered through Ohio University, ResearchMatch, and Clemson University.

Participants

Participants included the general public who are 18 years or older. A total of 1153 valid responses were included in the analysis.

Primary outcomes measures

Participants rated the importance of the 29 health indicators. The data were aggregated, cleaned, and analyzed in three ways: (1) to determine the agreement among the three samples on the importance of each indicator (IV = the three samples, DV = individual survey responses); (2) to examine the mean differences between the retained indicators with agreement across the three samples (IV = the identified indicators, DV = individual survey responses); and (3) to rank the groups of indicators after grouping the indicators with no mean differences (IV = the groups of indicators, DV = individual survey responses).

Results

The descriptive statistics indicate that the top-five rated indicators are drug or substance abuse, smoking or tobacco use, alcohol abuse, major depression, diet and nutrition. The importance of 13 of the 29 health indicators was agreed upon among the three samples. The 13 indicators were categorized into seven groups. Groups 1-3 were rated as significantly higher than Groups 4-7.

Conclusions

This study provides a baseline for prioritizing further the 29 health indicators, which can be used by electronic health records or personal health record system developers. Currently, self-rated health status is used predominantly. Our study provides a foundation to track and measure preventive services more accurately and to develop an individual health status index.

Strengths and limitations of this study

The work establishes the foundation to measure individual health status more comprehensively and objectively

The work reflects perspectives from three communities with a relatively large sample size

The work provides the foundation to prioritize the 29 health indicators further

With real-world longitudinal data, the public perspective data on individual health status measurement would be verified and validated further
Investigation of Genetic Variants and Causal Biomarkers Associated with Brain Aging
Authors: Kim Jangho , Lee Junhyeong , Lee Seunggeun
Published: March 2022

Delta age is a biomarker of brain aging that captures differences between the chronological age and the predicted biological brain age. Using multimodal data of brain MRI, genomics, and blood-based biomarkers and metabolomics in UK Biobank, this study investigates an explainable and causal basis of high delta age. A visual saliency map of brain regions showed that lower volumes in the fornix and the lower part of the thalamus are key predictors of high delta age. Genome-wide association analysis of the delta age using the SNP array data identified associated variants in gene regions such as KLF3-AS1 and STX1. Mendelian randomization (MR) for all metabolomic biomarkers and blood-related phenotypes showed that immune-related phenotypes have a causal impact on increasing delta age. Our analysis revealed regions in the brain that are susceptible to the aging process and provided evidence of the causal and genetic connections between immune responses and brain aging.
Efficacy of LD BioAspergillus ICT Lateral flow assay for serodiagnosis of chronic pulmonary aspergillosis
Authors: Ray Animesh , Chowdhury Mohit , Sachdev Janya , Sethi Prayas , Meena Ved Prakash , Singh Gagandeep , Xess Immaculata , Vyas Surabhi , Khan MA , Sinha Sanjeev , Denning David W. , Wig Naveet , Kabra SK
Published: March 2022

Background

The diagnosis of CPA relies on the detection of IgGAspergillusantibody which is not freely available, especially in resource-poor settings. Point-of-care tests like LDBioAspergillusICT lateral flow assay, evaluated in only a few studies, have shown promising results for diagnosis of CPA. However no study has compared the diagnostic performances of LDBio LFA in setting of tuberculosis endemic countries and have compared it with that of IgGAspergillus.

Objectives

This study aimed to evaluate the diagnostic performances of LDBio LFA in CPA and compare it with existing diagnostic algorithm utilising ImmunoCAP IgG Aspergillus.

Methods

Serial patients presenting with respiratory symptoms (cough, hemoptysis, fever etc) for > 4 weeks were screened for eligibility. Relevant investigations including direct microscopy and culture of respiratory secretions, IgGAspergillus, chest imaging etc were done according to existing algorithm. Serum of all patients were tested by LDBio LFA and IgGAspergillus(ImmunoCAP Asp IgG) and their diagnostic performances were compared.

Results

A total of 174 patients were included in the study with ∼66.7% patients having past history of tuberculosis. A diagnosis of CPA was made in 74 (42.5%) of patients. The estimated sensitivity and specificity of LDBio LFA was 67.6% (95% CI: 55.7%-78%) and 81% (95% CI: 71.9%-81%) respectively which increased to 73.3% (95% CI: 60.3%-83.9%) and 83.9% (95% CI: 71.7%-92.4%) respectively in patients with past history of tuberculosis. The sensitivity and specificity of IgGAspergilluswas 82.4% (95% CI: 71.8%-90.3%) and 82% (95% CI: 73.1-89%); 86.7% (95% CI: 75.4%-94.1%) and 80.4% (95% CI: 67.6%-89.8%) in the whole group and those with past history of tuberculosis respectively.

Conclusions

LDBio LFA is a point-of-care test with reasonable sensitivity and specificity. However, further tests may have to be done to rule-in or rule-out the diagnosis of CPA in the appropriate setting.
Impact of the COVID-19 pandemic on breast cancer screening indicators in a Spanish population-based program: a cohort study
Authors: Bosch Guillermo , Posso Margarita , Louro Javier , Roman Marta , Porta Miquel , Castells Xavier , Macià Francesc
Published: March 2022

Background

To assess the effect of the COVID-19 pandemic on performance indicators in the population-based breast cancer screening program of Parc de Salut Mar (PSMAR), Barcelona, Spain.

Methods

We conducted a before-and-after, quasi-experimental study to evaluate participation, recall, false-positives, cancer detection rate, and cancer characteristics in our screening population from March 2020 to March 2021 compared with the four previous rounds (2012-2019). Using independent logistic regression models, we estimated the adjusted odds ratios (aOR) of each of the performance indicators for the COVID-19 period, controlling by type of screening (prevalent or incident), socioeconomic index, family history of breast cancer, and menopausal status. We analyzed 144,779 observations from 47,571 women.

Results

During the COVID-19 period, the odds of participation were 11% lower in first-time invitees (aOR=0.89[95%CI=0.84-0.96]) and in those who had previously participated regularly and irregularly (aOR=0.65 [95%CI=0.61-0.69] and aOR=0.93 [95%CI=0.85-1.03], respectively). Participation showed a modest increase in women not attending any of the previous rounds (aOR=1.07 [95%CI=0.99-1.17]). The recall rate slightly decreased in both prevalent and incident screening (aOR=0.89 [95%CI=0.78-1.01] and aOR=0.89 [95%CI=0.79-1.00], respectively). No significant differences were observed in false-positives (prevalent - aOR=1.07 [95%CI=0.92-1.24] and incident screening -aOR=0.94 [95%CI=0.82-1.08]), cancer detection rate (aOR=0.91 [95%CI=0.69-1.18]), or cancer stages.

Conclusions

The COVID-19 pandemic negatively affected screening attendance, especially in previous participants and newcomers. We found no marked differences in recall, false-positives, or cancer detection, indicating the program’s resilience. There is a need for further evaluations of interval cancers and potential diagnostic delays.
Severity of SARS-CoV-2 Infection in Pregnancy in Ontario: A Matched Cohort Analysis
Authors: Murison Kiera R. , Grima Alicia A. , Simmons Alison E. , Tuite Ashleigh R. , Fisman David N.
Published: March 2022

Background

Pregnancy represents a physiological state associated with increased vulnerability to severe outcomes from infectious diseases, both for the pregnant person and developing infant. The SARS-CoV-2 pandemic may have important health consequences for pregnant individuals, who may also be more reluctant than non-pregnant people to accept vaccination. We sought to estimate the degree to which increased severity of SARS-CoV-2 outcomes can be attributed to pregnancy.

Methods

Our study made use of a population-based SARS-CoV-2 case file from Ontario, Canada. Due to both varying propensity to receive vaccination, and changes in dominant circulating viral strains over time, a time-matched cohort study was performed to evaluate the relative risk of severe illness in pregnant women with SARS-CoV-2 compared to other SARS-CoV-2 infected women of childbearing age (10 to 49 years old). Risk of severe SARS-CoV-2 outcomes (hospitalization or intensive care unit (ICU) admission) was evaluated in pregnant women and time-matched non-pregnant controls using multivariable conditional logistic regression.

Results

Compared to the rest of the population, non-pregnant women of childbearing age had an elevated risk of infection (standardized morbidity ratio (SMR) 1.28), while risk of infection was reduced among pregnant women (SMR 0.43). After adjustment for age, comorbidity, healthcare worker status, vaccination, and infecting viral variant, pregnant women had a markedly elevated risk of hospitalization (adjusted OR 4.96, 95% CI 3.86 to 6.37) and ICU admission (adjusted OR 6.58, 95% CI 3.29 to 13.18). The relative increase in hospitalization risk associated with pregnancy was greater in women without comorbidities than in those with comorbidities (P for heterogeneity 0.004).

Interpretation

A time-matched cohort study suggests that while pregnant women may be at a decreased risk of infection relative to the rest of the population, their risk of severe illness is markedly elevated if infection occurs. Given the safety of SARS-CoV-2 vaccines in pregnancy, risk-benefit calculus strongly favours SARS-CoV-2 vaccination in pregnant women.
Social capital, urbanization level, and COVID-19 vaccination uptake in the United States: A national level analysis
Authors: Qiao Shan , Li Zhenlong , Zhang Jiajia , Sun Xiaowen , Garrett Camryn , Li Xiaoming
Published: March 2022

Vaccination remains the most promising mitigation strategy for the COVID-19 pandemic. However, existing literature shows significant disparities in vaccination uptake in the United States. Using publicly available national-level data, we aimed to explore if county-level social capital can further explain disparities in vaccination uptake rate adjusting for demographic and social determinants of health (SDOH) variables; and if association between social capital and vaccination uptake may vary by urbanization level. Bivariate analyses and hierarchical multivariable quasi-binomial regression analysis were conducted, then the regression analysis was stratified by urban-rural status. The current study suggests that social capital contributes significantly to the disparities of vaccination uptake in the US. The results of stratification analysis show common predictors of vaccine uptake but also suggest various patterns based on urbanization level regarding the associations of COVID-19 vaccination uptake with SDOH and social capital factors. The study provides a new perspective to address disparities in vaccination uptake through fostering social capital within communities, which may inform tailored public health intervention efforts in enhancing social capital and promoting vaccination uptake.
Patients at risk of pulmonary fibrosis Post Covid-19: Epidemiology, pulmonary sequelaes and humoral response
Authors: Porto Miriam Hernández , Delgado Teresa , Aguirre-Jaime Armando , Ramos María Jose , Campos Silvia , Acosta Orlando , Llanos Ana Belén , Lecuona María
Published: March 2022

Background

The COVID-19 pandemic is one of the greatest public health problems. Our aims were to describe epidemiological characteristics, know the amount of protective antibodies and their permanence after a COVID-19 primary infection in patients with risk of pulmonary fibrosis.

Methods

Descriptive epidemiological and follow-up study of the humoral response in patients at risk of pulmonary fibrosis Post-Covid-19 hospitalized, between March and October 2020, and who were followed up for a one year after hospital discharge.

Results

72 patients participated in the study, 52 showed pre-existing chronic comorbidities. COVID-19 clinical severity was rated in 6% mild, 58% as moderate and 36% as severe. After a year of follow-up, the forty percent had pulmonary sequelae, the most frequent (20%) was mild pulmonary fibrosis. Any case of reinfection was detected. All patients presented RBD IgG antibodies and 88% presented IgA antibodies after 8-9 months. The amount of RBD IgG was similar at 4-5 and 8-9 months post-Covid. There was no difference when level of RBD IgG according to the severity of the COVID-19 (p=0.441, p=0.594).

Conclusions

Mild pulmonary fibrosis sequelae is exceptional but was detected in a high percentage. The amount of RBD IgG is maintained throughout the convalescent phase and seems to protect against new reinfections despite of emerging viral variants. However, seems not predict the developed or not of pulmonary fibrosis.
A new compartment model of COVID-19 transmission: The broken-link model
Authors: Ikeda Yoichi , Sasaki Kenji , Nakano Takashi
Published: March 2022

We propose a new compartment model of COVID-19 spread, the broken-link model, which includes the effect from unconnected infectious links of the transmission. The traditional SIR-type epidemic models are widely used to analyze the spread status, and the models show the exponential growth of the number of infected people. However, even in the early stage of the spread, it is proven by the actual data that the exponential growth did not occur all over the world. We consider this is caused by the suppression of secondary and higher transmissions of COVID-19. We find that the proposed broken-link model quantitatively describes the mechanism of this suppression and is consistent with the actual data.
Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
Authors: Edie Stewart M. , Collins Katie S. , Jablonski David
Published: March 2022

1.

Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak.’ Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. As the choice of homologous points for alignment can affect shape differences among specimens, so can the choice of orientation axes. Analysis of forty-five possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment implies a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we recognize one alignment in particular as a continuation of the historical approaches to morphometrics of shell form: orientation via the hinge line. Beyond bivalves, this axis-based approach to aligning specimens facilitates the comparison of continuous differences in shape among many other phylogenetically broad and morphologically disparate samples.
The multi-level regulation of clownfish metamorphosis by thyroid hormones
Authors: Roux Natacha , Miura Saori , Dussene Mélanie , Tara Yuki , Lee Fiona , de Bernard Simon , Reynaud Mathieu , Salis Pauline , Barua Agneesh , Boulahtouf Abdelhay , Balaguer Patrick , Gauthier Karine , Lecchini David , Gibert Yann , Besseau Laurence , Laudet Vincent
Published: March 2022

Most marine organisms have a biphasic life cycle during which a pelagic larva is transformed into a radically different juvenile. In vertebrates the role of thyroid hormones (TH) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrative analysis of metamorphosis of a marine teleost, the clownfish Amphiprion ocellaris. We reveal how TH coordinate a change in color vision as well as a major metabolic shift in energy production, hence highlighting its central integrative role in regulating this transformation. By manipulating the activity of LXR, a major regulator of metabolism, we also reveal a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild revealing how hormones coordinate energy needs with available resources during life cycle.
Tumor purity adjusted beta values improve biological interpretability of high-dimensional DNA methylation data
Authors: Johan Staaf , Mattias Aine
Published: March 2022

A common issue affecting DNA methylation analysis in tumor tissue is the presence of a substantial amount of non-tumor methylation signal derived from the surrounding microenvironment. Although approaches for quantifying and correcting for the infiltration component have been proposed previously, we believe these have not fully addressed the issue in a comprehensive and universally applicable way. We present a multi-population framework for adjusting DNA methylation beta values on the Illumina 450/850K platform using generic purity estimates to account for non-tumor signal. Our approach also provides an indirect estimate of the aggregate methylation state of the surrounding normal tissue. Using whole exome sequencing derived purity estimates and Illumina 450K methylation array data generated by The Cancer Genome Atlas project (TCGA), we provide a demonstration of this framework in breast cancer illustrating the effect of beta correction on the aggregate methylation beta value distribution, clustering accuracy, and global methylation profiles.
GWAS and meta-analysis identifies multiple new genetic mechanisms underlying severe Covid-19
Authors: Pairo-Castineira Erola , Rawlik Konrad , Klaric Lucija , Kousathanas Athanasios , Richmond Anne , Millar Jonathan , Russell Clark D , Malinauskas Tomas , Thwaites Ryan , Stuckey Alex , Odhams Christopher A , Walker Susan , Griffiths Fiona , Oosthuyzen Wilna , Morrice Kirstie , Keating Sean , Nichol Alistair , Semple Malcolm G , Knight Julian , Shankar-Hari Manu , Summers Charlotte , Hinds Charles , Horby Peter , Ling Lowell , McAuley Danny , Montgomery Hugh , Openshaw Peter J.M. , Walsh Timothy , Tenesa Albert ,   GenOMICC Investigators,   SCOURGE Consortium,   ISARIC4C Investigators,   23andMe, Scott Richard H , Caulfield Mark J , Moutsianas Loukas , Ponting Chris P , Wilson James F , Vitart Veronique , Pereira Alexandre C , Luchessi Andre , Parra Esteban , Cruz-Guerrero Raquel , Carracedo Angel , Fawkes Angie , Murphy Lee , Rowan Kathy , Law Andy , Hendry Sara Clohisey , Baillie J. Kenneth
Published: March 2022

Pulmonary inflammation drives critical illness in Covid-19, 1;2 creating a clinically homogeneous extreme phenotype, which we have previously shown to be highly efficient for discovery of genetic associations. 3;4 Despite the advanced stage of illness, we have found that immunomodulatory therapies have strong beneficial effects in this group. 1;5 Further genetic discoveries may identify additional therapeutic targets to modulate severe disease. 6 In this new data release from the GenOMICC (Genetics Of Mortality in Critical Care) study we include new microarray genotyping data from additional critically-ill cases in the UK and Brazil, together with cohorts of severe Covid-19 from the ISARIC4C 7 and SCOURGE 8 studies, and meta-analysis with previously-reported data. We find an additional 14 new genetic associations. Many are in potentially druggable targets, in inflammatory signalling (JAK1, PDE4A), monocyte-macrophage differentiation (CSF2), immunometabolism (SLC2A5, AK5), and host factors required for viral entry and replication (TMPRSS2, RAB2A). As with our previous work, these results provide tractable therapeutic targets for modulation of harmful host-mediated inflammation in Covid-19.
SARS-CoV-2 Spike evolution influences GBP and IFITM sensitivity
Authors: Mesner Dejan , Reuschl Ann-Kathrin , Whelan Matthew V.X , Bronzovich Taylor , Haider Tafhima , Thorne Lucy G. , Towers Greg J. , Jolly Clare
Published: March 2022

SARS-CoV-2 spike requires proteolytic processing for viral entry. The presence of a polybasic furin-cleavage site (FCS) in spike, and evolution towards an optimised FCS by dominant variants of concern (VOCs), are linked to enhanced infectivity and transmission. Here we show that interferon-inducible antiviral restriction factors Guanylate binding proteins (GBP) 2 and 5 interfere with furin-mediated cleavage of SARS-CoV-2 spike and inhibit the infectivity of early-lineage Wuhan-Hu-1, while VOCs Alpha and Delta have evolved to escape restriction. Strikingly, we find Omicron is unique amongst VOCs, being restricted by GBP2/5, and also IFITM1, 2 and 3. Replacing the spike S2 domain in Omicron with Delta shows S2 is the determinant of entry route and IFITM sensitivity. We conclude that VOC evolution under different selective pressures has influenced sensitivity to spike-targeting restriction factors, with Omicron selecting spike changes that not only mediate antibody escape, and altered tropism, but also sensitivity to innate immunity.
Species-specific cutaneous protein signatures upon incision injury and correlation with distinct pain-related phenotypes in humans
Authors: Segelcke Daniel , van der Burgt Max , Kappert Christin , Schmidt-Garcia Daniela , Sondermann Julia R. , Bigalke Stephan , Pradier Bruno , Gomez-Varela David , Zahn Peter K. , Schmidt Manuela , Pogatzki-Zahn Esther M.
Published: March 2022

Pain after surgery is common, and its management remains a clinical challenge. Severe acute and prolonged post-surgical pain impairs immediate recovery and leads to long-term consequences like chronic pain, opioid dependency, and reduced quality of life. Althought rodent pain incision models exist, translation to patients is still hampered. To bridge this gap, we combined sensory phenotyping with quantitative proteomics and protein networks in humans and mice after skin incision representing an established model for surgical pain. Initially, we revealed, for the first time, similarities and differences of protein-protein interaction (PPI) networks across both species. Next, we comprehensively phenotyped humans for pain-related symptoms and observed phenotypes with incision-induced proteome changes. Remarkably, post-incision PPI-networks differed between volunteers with small incision-related hyperalgesic areas (“Low responder”) versus those with large areas (“High responder”). The latter exhibited a pronounced proteolytic environment associated with persistent inflammation, while an anti-inflammatory protein signature was observed in Low responders. Taken together, we provide unprecedented insights into peripheral processes relevant for developing hyperalgesia and pain after incision. This knowledge will immensely facilitate bidirectional translational pain studies and guide future research on the pathophysiology of pain after surgery and the discovery of novel targets for its treatment and prevention.
Fish microbiomes 101: disentangling the rules governing marine fish mucosal microbiomes across 101 species
Authors: Minich Jeremiah , Härer Andreas , Vechinski Joseph , Frable Benjamin W , Skelton Zachary , Kunselman Emily , Shane Mike , Perry Daniela , Gonzalez Antonio , McDonald Daniel , Knight Rob , Michael Todd P. , Allen Eric E
Published: March 2022

Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence the fish microbiome. The microbiota from 101 species of Southern California marine fishes, spanning 22 orders, 55 families, and 83 genera representing ~25% of local marine fish diversity, was analyzed to identify patterns that explain microbial diversity patterns in a geographical subset of marine fish biodiversity. We compared fish microbiomes (gill, skin, midgut, and hindgut) using alpha, beta, and gamma diversity along with establishing a novel method to estimate microbial biomass (Qiime2 plugin katharoseq). For oceanic fishes from the neritic zone, host size and distance from shore were negatively associated with microbial biomass densities and diversity in the gills. Body site was the strongest driver for beta diversity with strong evidence of phylosymbiosis observed across the gill, skin, and hindgut, but not midgut. The majority of microbes from all fish body sites were of unknown origin but overall sea water generally contributes more microbes to fish mucus compared to marine sediment. In a meta-analysis of vertebrate hindguts (569 species), mammals had the highest gamma diversity when controlling for host species number while fishes had the highest percent of unique microbial taxa (92%). In fishes, the midgut, gill, and skin contains the majority of microbial diversity which collectively can be 5.5 times higher than the hindgut. The composite dataset will be useful to vertebrate microbiome researchers and fish biologists interested in microbial ecology with applications in aquaculture and fisheries management.
Resource use differences of two coexisting chironomid species at localized scales
Authors: McCormick Amanda R. , Phillips Joseph S. , Botsch Jamieson C. , Ólafsson Jón S. , Ives Anthony R.
Published: March 2022

The abundances of competing species may show positive correlations in time and space if they rely on a shared resource. Such positive correlations might obscure resource partitioning that facilitates coexistence of competitors and affects their abundances, spatial distributions, and population dynamics. Here, we examine the potential for resource partitioning between two ecologically similar midge species (Diptera: Chironomidae) in Lake Mývatn, Iceland.Tanytarsus gracilentusandChironomus islandicuslarvae coexist at high abundances in benthic habitats, and they have been previously described as feeding upon diatoms and detritus. Furthermore, both species show large, roughly synchronized population fluctuations, implying potential reliance on a shared fluctuating resource and posing the question of how these species coexist at high abundances. We first considered spatial partitioning of larvae; across multiple sites, abundances of both species were positively correlated. Thus, spatial partitioning across different sites in the lake did not appear to be strong. We then inferred differences in dietary resource use with stable carbon isotopes.T. gracilentuslarvae had higher δ13C values thanC. islandicus(mean difference = 5.39 ± 1.84‰), suggesting interspecific differences in resource use. Differences in resource selectivity, tube-building behavior, and feeding styles may facilitate resource partitioning between these two species. Relative to surface sediments,T. gracilentushad higher δ13C values (1.84 ± 0.96‰), suggesting that they selectively graze on13C-enriched resources such as productive algae from the surface of their tubes. In contrast,C. islandicushad lower δ13C values than surface sediments (−2.87 ± 1.95‰), suggesting reliance on isotopically depleted resources, which may include detrital organic matter and associated microbes that larvae selectively consume from the sediment surface or within their tube walls. Overall, our study illustrates that coexisting and ecologically similar species may show positive correlations in space and time while using different resources at fine spatial scales.
Morphofunctional changes at the active zone during synaptic vesicle exocytosis
Authors: Radecke Julika , Seeger Raphaela , Kádková Anna , Laugks Ulrike , Khosrozadeh Amin , Goldie Kenneth N. , Lučić Vladan , Sørensen Jakob B. , Zuber Benoît
Published: March 2022

The fusion of synaptic vesicles (SVs) with the plasma membrane (PM) proceeds through intermediate steps that remain poorly resolved. Additionally, the effect of persistent high or low exocytosis activity on intermediate steps remains unknown. Through time-resolved cryo-electron tomography, we ordered events into a sequence. Following stimulation, proximal tethered SVs rapidly form additional tethers with the PM. Simultaneously, fusion initiation occurs by membrane curvature (‘buckling’) of the SV and PM. It is followed by the formation of a fusion pore, and the collapse of SV membrane. At this time, membrane-proximal, but not membrane-distal, vesicles lose their interconnections, allowing them to move towards the PM. Two mutations of SNAP-25 that arrests or disinhibit spontaneous release, respectively, both caused a loss of interconnectors, while the disinhibiting mutant also caused a loss of membrane proximal multiple-tethered SVs. Overall, tether formation and connector dissolution is triggered by stimulation and respond to the spontaneous fusion rate. These morphological observations likely correspond to the transition of SVs from one functional pool to another.
Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments
Authors: Sugiyama Yuki , Uno Kohei , Matsui Yusuke
Published: March 2022

Two-dimensional video-based pose estimation is a technique that can estimate human skeletal coordinates from video data alone. It is also being applied to gait analysis and, particularly, due to its simplicity of measurement, it has the potential to be applied to the gait analysis of large populations. In contrast, it is considered difficult to completely homogenize the environment and settings during the measurement of large populations. Therefore, it is necessary to appropriately deal with technical errors that are not related to the biological factors of interest. In this study, by analyzing a large cohort database, we have identified four major types of anomalies that occur during gait analysis using OpenPose in uncontrolled environments: anatomical, biomechanical, and physical anomalies and errors due to estimation. We have also developed a workflow for identifying and correcting those anomalies and confirmed that the workflow is reproducible through simulation experiments. Our results will help obtain a comprehensive understanding of the anomalies to be addressed in a pre-processing for 2D video-based gait analysis of large populations.

Author summary

Gait is one of the important biomarkers of health conditions. With developing mobile health technologies, it is becoming easier to measure our health. However, to realize preventive medicine, establishing evidence is a critical issue, and we need to collect data from a large population. Two-dimensional video-based pose estimation can be a solution for the gait analysis of such a population. However, the technical accuracy and limitations of this analysis have not yet been sufficiently discussed. In this study, by analyzing the largest database currently available, we systematically identified four types of technical anomalies that occur during gait measurement: anatomical, biomechanical, and physical anomalies and errors dues to estimation. We have also shown how to deal with these issues and made solutions available as software so that researchers can reproduce them. In the future, increasing number of studies will use 2D video-based pose estimation to research health-related gait among large populations. We believe that our work will provide a guideline for researchers and clinicians involved in these studies to discuss design and algorithms.
Rapid identification of mosquito species, sex and age by mass spectrometric analysis
Authors: Wagner Iris , Grigoraki Linda , Enevoldson Peter , Clarkson Michael , Jones Sam , Hurst Jane L , Beynon Robert J , Ranson Hilary
Published: March 2022

Background:

A rapid, accurate method to identify and to age grade mosquito populations would be a major advance in predicting the risk of pathogen transmission and evaluating the public health impact of vector control interventions. Whilst other chemometric methods show promise, current approaches rely on challenging morphological techniques or simple binary classifications that cannot identify the subset of the population old enough to be infectious. In this study, the ability of Rapid Evaporative Ionisation Mass Spectrometry (REIMS) to identify the species, sex and age of mosquitoes reared in the laboratory and derived from the wild was investigated.

Results

The accuracy of REIMS in identifying morphologically identical species of theAnopheles gambiaecomplex exceeded 97 % using principal component/linear discriminant analysis (PC-LDA) and 84 % based on random forest analysis. Age separation into 3 different age categories (1 d, 5-6 d, 14-15 d.) was achieved with 99 % (PC-LDA) and 94 % (random forest) accuracy, after including three species and storing samples at room temperature for up to 11 days. When tested on wild mosquitoes from the UK, REIMS data could determine the species and age of the specimens with accuracies of 91 and 90 % respectively.

Conclusions

The accuracy of REIMS to resolve the species and age ofAnophelesmosquitoes is comparable to that achieved by chemometric approaches. The processing time and ease of use represent significant advantages over current, dissection-based methods. Importantly the accuracy was maintained when using wild mosquitoes reared under differing environmental conditions, and when mosquitoes were stored frozen or desiccated. This high throughput approach thus has potential to conduct rapid, real- time monitoring of vector populations, providing entomological evidence of the impact of alternative interventions.
Droplet size and surface hydrophobicity enhance bacterial plasmid transfer rates in microscopic surface wetness
Authors: Orevi Tomer , Sørensen Søren J. , Kashtan Nadav
Published: March 2022

Conjugal plasmids constitute a major engine for horizontal gene transfer in bacteria, and are key drivers of the spread of antibiotic resistance, virulence, and metabolic functions. Bacteria in terrestrial habitats often inhabit surfaces that are not constantly water-saturated, where microscopic surface wetness (MSW), comprised of thin liquid films and microdroplets, permanently or intermittently occurs. How physical properties of microdroplets, and of the surfaces they reside on, affect plasmid transfer rates is not well understood. Here, building on microscopy-based microdroplet experiments, we examined the relation between droplet properties (size and spread) and plasmid transfer rates at single-cell and individual droplet resolution, using Pseudomonas putida as a model species. We show that transfer rates increase with droplet size, due to higher densities of cells on the surface in larger droplets, resulting from lower ratio between the area of the liquid-solid interface and droplet volumes. We further show that surface hydrophobicity promotes transfer rates via the same mechanism. Our results provide new insights into how physical properties of surfaces and MSW affect plasmid transfer rates, and more generally, interactions mediated by cell-to-cell contact, with important implications for our understanding of the ecology and evolution of bacteria in unsaturated environments.
SOYBEAN RESPONSE TO INITIAL STAGE OF Fusarium virguliforme INFECTION
Authors: Giachero María Lorena , Marquez Nathalie , Ortega Leandro Ismael , Ducasse Daniel Adrian
Published: March 2022

Fusarium virguliforme causes the Sudden Death Syndrome, an important disease in soybean crops. In this work, we investigated the defensive response mechanisms in soybean root, at cell wall level, during F. virguliforme infection using an in vitro culture system. We measured total root lignin content by the acetyl bromide method and estimated the in-situ lignin and suberin deposition by confocal microscopy on local and systemic root tissues, i.e. adjacent and distant to the pathogen entry site respectively. Moreover, the expression dynamics of phenylalanine ammonia lyase (PAL), shikimate/quinate hydroxycinnamoyltransferase (HCT) and cinnamyl alcohol dehydrogenase (CAD) was evaluated by real-time quantitative PCR. The results showed that, although the most significant increment of lignin deposition was observed in the epidermal cells of local tissues, F. virguliforme also induced lignin deposition changes in a sistemic fashion. In fact, inoculated plants presented a higher deposition of lignin in hypodermis and cortex than the control ones, independently of the distance from the inoculum source, while suberin deposition was higher in local zones. Moreover, the gene expression analysis showed an up-regulation of PAL, HCT and CAD genes after the inoculation with the pathogen, which correlates with the cell wall modifications observed in the local tissues. The results presented here suggest that the increase in lignin and suberin deposition during soybean root/F. virguliforme interaction is probably a strategy not only to stop the pathogen entrance, but to provide the plant more time to prepare its defences as well.
Rapid phenotypic differentiation and local adaptation in Japanese knotweed s.l. (Reynoutria japonicaandR. ×bohemica, Polygonaceae) invading novel habitats
Authors: Yuan Wei , Pigliucci Massimo , Richards Christina L.
Published: March 2022

PREMISE

Many plant invaders like the Japanese knotweeds are thought to colonize new habitats with low genetic diversity. Such species provide an opportunity to study rapid adaptation to complex environmental conditions.

METHODS

Using replicate reciprocal transplants of clones across three habitats, we described patterns of phenotypic response and assessed degree of local adaptation.

KEY RESULTS

We found plants from beach habitats had decreased height, number of leaves, leaf area, and biomass allocation to roots and shoots compared to plants from marsh and roadside habitats when grown in their home habitat. In the marsh habitat, marsh plants were generally larger than beach plants, but not different from roadside plants. There were no differences among plants from different habitats grown in the roadside habitat. Despite this evidence of differentiation in beach and marsh habitats, we found mixed evidence for local adaptation. In their “home site” plants from the marsh habitat had greater biomass than plants from the beaches but not compared to plants from roadsides. Biomass comparisons in other habitats were either maladaptive or not significant. However, plants from the roadside had greater survival in their “home site” compared to foreign plants. There were no differences in survival in the other habitats.

CONCLUSIONS

We found phenotypic differentiation associated with habitats despite the low reported genetic diversity for these populations. Our results partially support the hypothesis of local adaptation in marsh and roadside habitats. Identifying whether these patterns of differentiation result from genetic or heritable non-genetic mechanisms will require further work.
Comparative metaproteomics demonstrates different views on the complex granular sludge microbiome
Authors: Kleikamp Hugo B.C. , Grouzdev Dennis , Schaasberg Pim , van Valderen Ramon , van der Zwaan Ramon , van de Wijgaart Roel , Lin Yuemei , Abbas Ben , Pronk Mario , van Loosdrecht Mark C.M. , Pabst Martin
Published: March 2022

The tremendous progress in sequencing technologies has made 16S amplicon and whole metagenome sequencing routine in microbiome studies. Furthermore, advances in mass spectrometric techniques has expanded conventional proteomics into the field of microbial ecology. Commonly referred to as metaproteomics, this approach measures the gene products (i.e., proteins) to subsequently identify the actively-expressed metabolic pathways and the protein-biomass composition of complete microbial communities.

However, more systematic studies on metaproteomic and genomic approaches are urgently needed, to determine the orthogonal character of these approaches. Here we describe a deep, comparative metaproteomic study on the complex aerobic granular sludge microbiome obtained from different wastewater treatment plants. Thereby, we demonstrate the different views that can be obtained on the central nutrient-removing organisms depending on the ‘omic’ approach and reference sequence databases. Furthermore, we demonstrate a ‘homogenized’ Genome Taxonomy Database (GTDB) that subsequently enables a more accurate interpretation of data from different omics approaches. Ultimately, our systematic study underscores the importance of metaproteomics in the characterization of complex microbiomes; and the necessity of accurate reference sequence databases to improve the comparison between approaches and accuracy in scientific reporting.