bluuebunny/crossref_metadata_2025 huggingface dataset:
Hemodynamic Analysis of a Three-Point Suture During Tapering Technique for Microanastomosis Using Computational Fluid Dynamics
Authors: Yagi Shunjiro , Sasaki Takafumi , Fukuhara Takahiro , Fujii Kaori , Morita Maki , Fukuoka Kohei , Ikuta Kento , Umeda Ryunosuke , Kanayama Haruka , Suyama Yoshiko
Published: July 2021

The tapering technique is one of the useful methods of anastomosing 2 vessels with large discrepancies during microanastomoses. When the tapering technique is used, a three-point suture is always present. The authors analyzed the most appropriate suture technique for this using computational fluid dynamics. This aspect has not previously been addressed. Three different suture techniques were simulated:

Vascular models of these 3 types were created. The streamline, wall shear stress, and oscillatory shear index at the anastomosis site were measured using a previously prepared venous model. Streamline disruption was most severe for Type II. In all 3 types, the highest wall shear stress was recorded at the suture peak protruding into the vessel. The maximum oscillatory shear index was highest in Type II, and lowest in Type III. The present results suggest that Type III is the best three-point suturing method for the tapering technique.
Association of Kidney Function With Major Postoperative Events After Noncardiac Ambulatory Surgeries
Authors: Harrison Tyrone G. , Hemmelgarn Brenda R. , James Matthew T. , Manns Braden J. , Tonelli Marcello , Brindle Mary E. , McCaughey Deirdre , Ruzycki Shannon M. , Zarnke Kelly B. , Wick James , Ronksley Paul E.
Published: July 2021

Objective:

The aim of this study was to estimate the association between estimated glomerular filtration rate (eGFR) and acute myocardial infarction (AMI) or death after ambulatory noncardiac surgery.

Summary Background Data:

People with chronic kidney disease (CKD) commonly undergo surgical procedures. Although most are performed in an ambulatory setting, the risk of major perioperative outcomes after ambulatory surgery for people with CKD is unknown.

Methods:

In this retrospective population-based cohort study using administrative health data from Alberta, Canada, we included adults with measured preoperative kidney function undergoing ambulatory noncardiac surgery between April 1, 2005 and February 28, 2017. Participants were categorized into 6 eGFR categories (in mL/min/1.73m2)of ≥60 (G1–2), 45 to 59 (G3a), 30 to 44 (G3b), 15 to 29 (G4), <15 not receiving dialysis (G5ND), and those receiving chronic dialysis (G5D). The odds of AMI or death within 30 days of surgery were estimated using multivariable generalized estimating equation models.

Results:

We identified 543,160 procedures in 323,521 people with a median age of 66 years (IQR 56–76); 52% were female. Overall, 2338 people (0.7%) died or had an AMI within 30 days of surgery. Compared with the G1–2 category, the adjusted odds ratio of death or AMI increased from 1.1 (95% confidence interval: 1.0–1.3) for G3a to 3.1 (2.6–3.6) for G5D. Emergency Department and Urgent Care Center visits within 30 days were frequent (17%), though similar across eGFR categories.

Conclusions:

Ambulatory surgery was associated with a low risk of major postoperative events. This risk was higher for people with CKD, which may inform their perioperative shared decision-making and management.
Postoperative opioid prescribing practices in US adult trauma patients: A systematic review
Authors: Rowe Scott , Zagales Israel , Fanfan Dino , Gargano Toria , Meneses Evander , Awan Muhammad , Zagales Ruth , McKenney Mark , Elkbuli Adel
Published: July 2021

BACKGROUND

Opioids have been proven effective in pain management, but overprescription can lead to addiction and abuse. Although current guidelines regarding opioid prescription for chronic and acute pain are available, they fail to address the use of opioids for pain management in traumatic injury patients who undergo operations. The primary objective of this study was to examine opioid prescribing practices for US adult trauma patients who require surgical management, based on prior history of opioid use, type of surgical practice, and age.

METHODS

PubMed and Cochrane Journals were used to identify relevant articles between October 2010 and December 29, 2020. Our primary outcome was discrepancies of morphine milligram equivalents (MMEs) prescribed to trauma patients. Significance was defined as p < 0.05.

RESULTS

Eleven studies on US trauma patients prescribed opioids were evaluated, creating a total of 30,249 patients stratified by prior opioid use, age, and race. Patterns seen among patients with prior opioid use include higher MMEs prescribed, lower likelihoods of opioid discontinuation, higher mortality rates, and higher complication rates. Orthopedic surgeons prescribed higher values of MMEs than nonorthopedic surgeons.

CONCLUSION

Higher incidences of opioid prescriptions are seen with orthopedic trauma surgery and prior opioid use by the patient. We recommend further development of national protocol implementation for acute pain management for the US trauma population.

LEVEL OF EVIDENCE

Systematic review, level III.
Nocardioides malaquae sp. nov., a novel actinobacterium isolated from sewage sludge of a fisheries processing factory
Authors: Zhang Xinyin , Wu Zhicheng , Yan Cen , Chen Can , Zheng Gang , Ye Yanghui , Sun Cong , Wu Min
Published: July 2021

A Gram-stain-positive, rod-shaped, strictly aerobic bacterial strain (Y6T) was isolated from a sewage sludge sample collected from a fisheries processing factory in Zhoushan, Zhejiang Province, PR China. The growth range of NaCl concentration was 0–6.0 % (w/v), with an optimum at 3.0 % (w/v). The temperature range for growth was 10–42 °C, with an optimum at 37 °C. The pH range for growth was pH 7.0–10.0, with an optimum at pH 9.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y6T belonged to the genus

Nocardioides

and showed the highest sequence similarity of 97.8 % to

Nocardioides jishulii

dk3136T. The average nucleotide identity and in silico DNA–DNA hybridization values between strain Y6T and the reference strains were 76.9–81.2 % and 20.6–23.6 %, respectively. Chemotaxonomic analysis indicated that the sole respiratory quinone was MK-8(H4) and the predominant cellular fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and C18 : 1
 ω9c. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified phospholipids, three unidentified aminolipids and five unidentified lipids. The peptidoglycan was ll-2,6-diaminopimelic acid. On the basis of the phenotypic, genotypic, phylogenetic and chemotaxonomic features, strain Y6T is considered to represent a novel species, for which the name Nocardioides malaquae sp. nov. is proposed. The type strain is Y6T (=KCTC 49504T=MCCC 1K04765T).
Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum
Authors: Oyunbileg Natsagdorj , Iizaka Yohei , Hamada Moriyuki , Davaapurev Bekh-Ochir , Fukumoto Atsushi , Tsetseg Baljinova , Kato Fumio , Tamura Tomohiko , Batkhuu Javzan , Anzai Yojiro
Published: July 2021

A novel actinomycete, designated NUM-2625T, was isolated as an endophytic bacterium in aerial parts of Comarum salesowianum, an endemic species in the Altai, Himalaya mountain chain area, collected from Khasagt Khairkhan Mountain in Mongolia. The 16S rRNA gene sequence of strain NUM-2625T showed the highest similarity to

Actinocatenispora thailandica

TT2-10T (99.4 %),

Actinocatenispora sera

KV-744T (99.3 %), and

Actinocatenispora rupis

CS5-AC17T (97.7 %). Chemotaxonomic properties of strain NUM-2625T were essentially consistent with those of the genus Actinocatenispora, such as the presence of meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, MK-9(H4) and MK-9(H6) as the major menaquinones, and iso-C16 : 0, iso-C15 : 0, iso-C14 : 0 3-OH, and anteiso-C17 : 0 as the major fatty acids. Meanwhile, digital DNA–DNA hybridization and average nucleotide identity values revealed a low relatedness between strain NUM-2625T and the other type strains of the genus

Actinocatenispora

. In addition, strain NUM-2625T exhibited several phenotypic properties that could be used to distinguish it from its closest relatives. Based on the results of polyphasic analyses, strain NUM-2625T represents a novel species in the genus

Actinocatenispora

, for which the name Actinocatenispora comari sp. nov. is proposed. The type strain is NUM-2625T (=NBRC 114660T=TBRC 13496T).
Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: Results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C)
Authors: Thomas Jason A. , Foraker Randi E. , Zamstein Noa , Payne Philip R.O. , Wilcox Adam B. ,   the N3C Consortium
Published: July 2021

Objective

To evaluate whether synthetic data derived from a national COVID-19 data set could be used for geospatial and temporal epidemic analyses.

Materials and Methods

Using an original data set (n=1,854,968 SARS-CoV-2 tests) and its synthetic derivative, we compared key indicators of COVID-19 community spread through analysis of aggregate and zip-code level epidemic curves, patient characteristics and outcomes, distribution of tests by zip code, and indicator counts stratified by month and zip code. Similarity between the data was statistically and qualitatively evaluated.

Results

In general, synthetic data closely matched original data for epidemic curves, patient characteristics, and outcomes. Synthetic data suppressed labels of zip codes with few total tests (mean=2.9±2.4; max=16 tests; 66% reduction of unique zip codes). Epidemic curves and monthly indicator counts were similar between synthetic and original data in a random sample of the most tested (top 1%; n=171) and for all unsuppressed zip codes (n=5,819), respectively. In small sample sizes, synthetic data utility was notably decreased.

Discussion

Analyses on the population-level and of densely-tested zip codes (which contained most of the data) were similar between original and synthetically-derived data sets. Analyses of sparsely-tested populations were less similar and had more data suppression.

Conclusion

In general, synthetic data were successfully used to analyze geospatial and temporal trends. Analyses using small sample sizes or populations were limited, in part due to purposeful data label suppression -an attribute disclosure countermeasure. Users should consider data fitness for use in these cases.
Association of socioeconomic and environmental factors with the spatio-temporal variability of suicide rates along a latitudinal gradient
Authors: Estay Sergio A. , Ruiz-Aravena Manuel , Baader Tomas , Gotelli Marcelo , Heskia Cristobal , Olivares Juan Carlos , Rivera Gerardo
Published: July 2021

Background

Suicide results from complex interactions between biological, psychological, and socioeconomic factors. At the population level, the study of suicide rates and their environmental and social determinants allows us to disentangle some of these complexities and provides support for policy design and preventive actions.

Objectives

To evaluate the associations between environmental and socioeconomic factors and demographically stratified suicide rates on large temporal and spatial scales.

Method

The dataset contains information about yearly suicides rates by sex and age from 2000 through 2017 along a 4,000 km latitudinal gradient. We used zero-inflated negative binomial models to evaluate the spatio-temporal influence of each environmental and socioeconomic variable on suicide rates at each sex/age combination.

Results

Overall, we found differential patterns of associations between suicide rates and explanatory variables by age and sex. Suicide rates in men increases in middle and high latitude regions and intermediate age classes. For adolescent and adult women, we found a similar pattern with an increase in suicide rates at middle and high latitudes. Sex differences measured by the male/female suicide rate ratio shows a marked increase with age. We found that cloudiness has a positive effect on suicide rates in both men and women 24 years old or younger. Regional poverty shows a major impact on men in age classes above 35 years old, an effect that was absent in women. Alcohol and marijuana consumption showed no significant effect sizes.

Conclusions

Our findings support high spatio-temporal variability in suicide rates in interaction with extrinsic factors. Several strong differential impacts of environmental and socioeconomic variables on suicide rates depending on sex and age were detected. These results suggest that the design of public policies and interventions to mitigate the impact of the studied variables need to consider the local social and environmental contexts of target populations.
COVID-19 Due to Wild-Type SARS-CoV-2 More Prevalent in Adolescents and Youth than in Older Adults Based on 19 US States in Fall 2020 Prior to Vaccine Availability
Authors: Rumain Barbara , Schneiderman Moshe , Geliebter Allan
Published: July 2021

PURPOSE

In a prior study, we examined data from six US states during Summer 2020, and found that prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p<.00001) as was a prevalence-related measure: Number of cases observed ÷ Number of cases expected (p<.005). We now extended our study to more states in Fall 2020 to confirm the prevalence relationships we found previously. Vaccines were still not available as of Fall 2020. Presumably, the SARS-CoV-2 strain circulating at the time was the wild-type lineage since no variants were reported in the US until the end of December 2020.

METHODS

We examined data from 19 U.S. states experiencing surges in cases to determine prevalence of COVID-19, and a prevalence-related measure: [Number of cases observed in a given age group] ÷ [Number of cases expected in the age group based on population demographics].

RESULTS

In 16 of the 19 states, we found that: (1) prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p-values ranged from p<0.00001 to p = 0.0175; (2) the ratio of cases observed to cases expected was significantly greater in adolescents and youth than in older adults (p-values ranging from p< 0.00001 to p = 0.004).

CONCLUSIONS

Our results are consistent with our previous study in Summer 2020. The finding of lower prevalence in older adults cannot be attributed to access to vaccination since our data are from Fall 2020 when vaccinations were not yet available. Our findings with the SARS-CoV-2 wild-type strain are consistent with the findings currently being reported in the UK for the delta variant. In both studies, prevalence in adolescents and youth exceeded that in older adults. The UK findings are more pronounced perhaps because that study transpired following months of vaccinations of older adults whereas ours occurred before vaccinations were available.
Elucidating Post-COVID-19 manifestations in India
Authors: Fatima Ghizal , Bhatt Divyansh , Idrees Jaserah , Khalid Bushra , Mahdi Farzana
Published: July 2021

Background

In India, a large number of patients with coronavirus disease-2019 (COVID-19), presented with common symptoms including fever, dyspnea, cough, musculoskeletal symptoms (fatigue, myalgia, joint pain) and gastrointestinal symptoms. However, information is lacking on symptoms that persist after recovery from COVID-19. In this study we assessed symptoms that persisted in patients even after their recovery and discharged from the hospital after one month from COVID-19.

Methods

This study is an observational cohort study. Participants in this study were enrolled between 30 to 40 days after recovery from COVID-19 of ≥18 years of age, who were hospitalized with laboratory-confirmed RT-PCR COVID-19 disease. Outcomes from post COVID-19 participants were elicited through questionnaire that consisted of three main parts beginning from subject’s demographical data, depicting about the status of COVID-19 and other co-morbidities of the subject, and about post-COVID-19 symptoms and manifestations.

Results

All subjects have reported some manifestation after recovery from COVID-19 whereas numerous symptoms and diseases were experienced by a great percentage of participants. Fatigue (56.25%), dyspnea (74.3%) and disturbed sleep (64.3%) were among the most common symptoms. However, more critical manifestations like renal failure and pulmonary fibrosis were reported by only a few percent of the subjects. Rating of worse physical and mental health after post-COVID recovery was also reported by subjects. There was a strong relationship found in between the presence of other co-morbidities before infection like diabetes, hypertension and in disease severity after infection. A total of 280 patients were enrolled and 160 completed the survey.

Conclusions

Post COVID-19 sufferers often experience symptoms that cause a disturbance in their physical health, mental health and their respiratory status for several weeks even after recovery from COVID-19. Therefore, all subjects after recovering from COVID-19 should undergo long-term monitoring programme for their symptoms and condition improvement.
Antibody response to SARS-CoV-2 infection and BNT162b2 vaccine in Israel
Authors: Shapira Guy , Hamad Ramzia Abu , Weiner Chen , Rainy Nir , Sorek-Abramovich Reut , Benveniste-Levkovitz Patricia , Chaim Adina Bar , Shomron Noam
Published: July 2021

Neutralizing antibodies targeting the Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) block viral entry to host cells, preventing disease and further spread of the pathogen. The presence of SARS-CoV-2 antibodies in serum is a reliable indicator of infection, used epidemiologically to estimate the prevalence of infection and clinically as a measurement of an antigen-specific immune response. In this study, we analyzed serum Spike protein-specific IgG antibodies from 26,170 samples, including convalescent individuals who had coronavirus disease 2019 (COVID-19) and recipients of the BNT162b2 vaccine. We find distinct serological patterns in COVID-19 convalescent and vaccinated individuals, correlated with age and gender and the presence symptoms.
POST-COVID-19 SYNDROME, INFLAMMATORY MARKERS AND SEX DIFFERENCES
Authors: Maamar Meryam , Artime Arancha , Pariente Emilio , Fierro Patricia , Ruiz Yolanda , Gutiérrez Silvia , González Roberto , Bustamante Elena , Pinedo Gabriel , Rodríguez Blanca , Peña Alvaro , Gómez Miguel A , Urarte Celeste , Pérez-Pajares Isabel , Tobalina Marian , Secada Carmen , Díaz-Salazar Sara , Pini Stefanie , Ramos Carmen , Olmos José M , Hernández José L
Published: July 2021

INTRODUCTION AND OBJECTIVE

Post-COVID syndrome (PCS) is a poorly-known entity. Underlying low-grade inflammation (LGI) has been theorized as one of its pathophysiological mechanisms. We aimed to investigate a possible relationship between PCS and an increase in inflammation markers, in a sex-stratified analysis.

PARTICIPANTS AND METHODS

Mild cases of COVID-19 according to the WHO classification followed-up in a Primary Care Center, were included. We collected epidemiological data (age, sex, body mass index -BMI-, smoking, and comorbidities -Charlson index-), variables of the acute COVID-19 episode, and data at 3 months of follow-up (clinical manifestations and inflammatory markers). Serum C-reactive protein (CRP), neutrophil and lymphocyte counts, neutrophil/lymphocyte ratio (NLR), lactate dehydrogenase (LDH), ferritin, fibrinogen, and D-dimer levels were analyzed. Low-grade inflammation (LGI) was defined as serum CRP between >0.3 and <1.0 mg/dL. Five composite indices were built combining the upper ranges of 4 markers. Bivariate and multivariate analyses (logistic regression and general linear models) were performed, stratified by sex.

RESULTS

We analyzed 121 subjects with mild COVID-19 (56.2% women; mean age 46 years). The most common symptom in the acute episode was fever (60.3%), while it was fatigue in PCS (42.8%). Prevalence of PCS was 35.8% in women and 20.8% in men (p = 0.07).

In women, after controlling for age, BMI, smoking, and comorbidities, the D1, D3, and D4 indices were consistently associated with PCS, with ORs of 5.14 (95% CI, 1.6-16.4), 4.20 (95% CI, 1.3-13.3), and 4.12 (95% CI, 1.3-13.1), respectively; in patients with post-COVID anosmia and ageusia, neutrophils were significantly elevated (3.43±0.3 vs 2.58±0.1; p = 0.014, and 3.89±0.3 vs 2.59±0.1; p = 0.002,respectively), after adjusting for confounders.

In men, the D2 and D5 indices were associated with PCS, with adjusted ORs of 10.1 (95% CI, 1.2-85) and 17.5 (95% CI, 2-153), respectively. Furthermore, serum CRP in the LGI range was associated with PCS [adjusted OR=12.9 (95% CI, 1.3-121)], and in post-COVID persistent fatigue, the neutrophil count was significantly elevated (4.68±0.6 vs 3.37±0.1; p = 0.041), after controlling for confounders.

CONCLUSIONS

Consistent associations among PCS, anosmia, ageusia, and fatigue, with slight -but significant-elevated levels of inflammatory markers, have been observed. The neutrophil count was the most frequently involved marker. Sex-stratified analyses showed relevant differences between women and men concerning PCS and serum inflammatory markers.
Loneliness among people with severe mental ill health during the COVID-19 pandemic: results from a linked UK population cohort study
Authors: Heron Paul N. , Spanakis Panagiotis , Crosland Suzanne , Johnston Gordon , Newbronner Elizabeth , Wadman Ruth , Walker Lauren , Gilbody Simon , Peckham Emily
Published: July 2021

Purpose

Population surveys underrepresent people with severe mental ill health. This paper aims to explore perceived social support and loneliness and factor associations during the Covid-19 pandemic in a sample of individuals with severe mental ill health.

Design/methodology/approach

We sampled an already existing cohort of people with severe mental ill health. Researchers contacted participants by phone or by post to invite them to take part in a survey about how the pandemic restrictions had impacted health, Covid-19 experiences, perceived social support, employment and loneliness. Loneliness was measured by the three item UCLA loneliness scale.

Findings

In the pandemic sub-cohort, 367 adults with a severe mental ill health diagnosis completed a remote survey. 29-34% of participants reported being lonely. Loneliness was associated with being younger in age (adjusted OR = -.98, p = .02), living alone (adjusted OR = 2.04, p = .01), high levels of social and economic deprivation (adjusted OR = 2.49, p = .04), and lower perceived social support (B = -5.86, p < .001). Living alone was associated with lower perceived social support. Being lonely was associated with a self-reported deterioration in mental health during the pandemic (adjusted OR = 3.46, 95%CI 2.03-5.91).

Practical implications

Intervention strategies to tackle loneliness in the severe mental ill health population are needed. Further research is needed to follow-up the severe mental ill health population after pandemic restrictions are lifted to understand perceived social support and loneliness trends.

Originality

Loneliness was a substantial problem for the severe mental ill health population before the Covid-19 pandemic but there is limited evidence to understand perceived social support and loneliness trends during the pandemic.
Soil conditions drive belowground trait space in temperate agricultural grasslands
Authors: Lachaise Tom , Bergmann Joana , Hölzel Norbert , Klaus Valentin H. , Kleinebecker Till , Rillig Matthias C. , van Kleunen Mark
Published: July 2021

Plant belowground organs perform essential functions, including water and nutrient uptake, anchorage, vegetative reproduction and recruitment of mutualistic soil microbiota. Determining how belowground traits jointly determine dimensions of the trait space and how these dimensions are linked to environmental conditions would further advance our understanding of plant functioning and community assembly.

Here, we investigated belowground plant-trait dimensionality and its variation along 10 soil and land-use parameters in 150 temperate grasslands plots. We used eight belowground traits collected in greenhouse and common garden experiments, as well as bud-bank size and specific leaf area from databases, for a total of 313 species, to calculate community weighted means (CWMs).

Using PCA, we found that about 55% of variance in CWMs was explained by two main dimensions, corresponding to a mycorrhizal ‘collaboration’ and a resource ‘conservation’ gradient. Frequently overlooked traits such as rooting depth, bud-bank size and root branching intensity were largely integrated in this bidimensional trait space. The two plant-strategy gradients were partially dependent on each other, with ‘outsourcing’ communities along the collaboration gradient being more often ‘slow’. These ‘outsourcing’ communities were also more often deep-rooting, and associated with soil parameters, such as low moisture and sand content, high topsoil pH, high C:N and low δ15N. ‘Slow’ communities had large bud-banks and were associated with low land-use intensity, high topsoil pH, and low nitrate but high ammonium concentrations in the soil. We did not find a substantial role of phosphorus-availability as an indicator along the ‘collaboration’ gradient.

In conclusion, the ‘collaboration’ and ‘conservation’ gradients previously identified at the species level scale up to community level in grasslands, encompass more traits than previously described, and vary with the environment.
A geospatial mapping pipeline for ecologists
Authors: van den Hoogen Johan , Robmann Niamh , Routh Devin , Lauber Thomas , van Tiel Nina , Danylo Olga , Crowther Thomas W.
Published: July 2021

Geospatial modelling can give fundamental insights in the biogeography of life, providing key information about the living world in current and future climate scenarios. Emerging statistical and machine learning approaches can help us to generate new levels of predictive accuracy in exploring the spatial patterns in ecological and biophysical processes. Although these statistical models cannot necessarily represent the essential mechanistic insights that are needed to understand global biogeochemical processes under ever-changing environmental conditions, they can provide unparalleled predictive insights that can be useful for exploring the variation in biophysical processes across space. As such, these emerging tools can be a valuable approach to complement existing mechanistic approaches as we aim to understand the biogeography of Earth’s ecosystems. Here, we present a comprehensive methodology that efficiently handles large datasets to produce global predictions. This mapping pipeline can be used to generate quantitative, spatially explicit predictions, with a particular emphasis on spatially-explicit insights into the evaluation of model uncertainties and inaccuracies.
Skilful decadal-scale prediction of fish habitat and distribution shifts
Authors: Payne Mark R. , Miesner Anna K. , Keenlyside Noel , Yang Shuting , Yeager Stephen G. , Danabasoglu Gokhan , Matei Daniela
Published: July 2021

Many fish and marine organisms are responding to our planet’s changing climate by shifting their distribution (i.e. where they are found). Such shifts can drive conflicts at the international scale and are highly problematic for the communities and businesses that depend on these living marine resources for income and nutrition. Advances in climate prediction mean that in some regions the state of the ocean, and thereby the drivers of these shifts, can be skilfully forecast up to a decade ahead. However, the potential for these forecasts to benefit ocean-dependent communities has yet to be realised. Here we show for the first time that marine climate predictions can be used to generate decadal-scale forecasts of shifts in the habitat and distribution of marine fish species, as exemplified by Atlantic mackerel, bluefin tuna and blue whiting. We show statistically significant forecast skill of individual years that outperform both persistence and climatological baseline forecasts for lead times of 3-10 years: multi-year averages perform even better, yielding correlation coefficients in excess of 0.90 in some cases. We also show that the habitat shifts underling recent conflicts over Atlantic mackerel fishing rights could have been foreseen on similar timescales. Our results show that climate predictions can be translated into information directly relevant to stakeholders and we anticipate that this tool will be critical in foreseeing, adapting to and coping with the challenges of a changing and variable future climate, particularly in the most ocean-dependent nations and communities.
DnoisE: Distance denoising by Entropy. An open-source parallelizable alternative for denoising sequence datasets
Authors: Antich Adrià , Palacín Creu , Turon Xavier , Wangensteen Owen S.
Published: July 2021

DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons are generated during amplification and sequencing procedures and constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE3 algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing run times on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
Mutualism-enhancing mutations dominate early adaptation in a microbial community
Authors: Venkataram Sandeep , Kuo Huan-Yu , Hom Erik F. Y. , Kryazhimskiy Sergey
Published: July 2021

Species interactions drive evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics, their outcomes and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this gap in a competitive mutualism between the yeastSaccharomyces cerevisiaeand the algaChlamydomonas reinhardtii. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular, those that increase and reduce the yields of both species. The presence of the alga does not change which mutations are adaptive in yeast (i.e., there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favor yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of the alga, adaptations contending for fixation in yeast are more likely to enhance the mutualism, even though cooperativity is not directly favored by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.
SPE-51, a sperm secreted protein with an Immunoglobulin-like domain, is required for sperm-egg fusion inC. elegans
Authors: Mei Xue , Druzhinina Marina , Dharia Sunny , Krauchunas Amber R. , Ni Julie , Singaravelu Gunasekaran , Gu Sam Guoping , Shakes Diane C. , Grant Barth D. , Singson Andrew W.
Published: July 2021

Despite the importance of fertilization, the molecular basis of sperm-egg interaction is not well understood. In a forward genetics screen for fertility mutants inCaenorhabditis eleganswe identifiedspe-51. Mutant worms make sperm that are unable to fertilize the oocyte but otherwise normal by all available measurements. Thespe-51gene encodes a secreted protein that includes an immunoglobulin (Ig)-like domain and a hydrophobic sequence of amino acids. The SPE-51 protein acts cell-autonomously and localizes to the surface of the spermatozoa. This is the first example of a secreted protein required for the interactions between the sperm and egg with genetic validation for a specific function in fertilization. Our analyses of these genes begin to build a paradigm for sperm-secreted or reproductive tract-secreted proteins that coat the sperm surface and influence their survival, motility, and/or the ability to fertilize the egg.
Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States
Authors: Tenforde Mark W. , Patel Manish M. , Ginde Adit A. , Douin David J. , Talbot H. Keipp , Casey Jonathan D. , Mohr Nicholas M. , Zepeski Anne , Gaglani Manjusha , McNeal Tresa , Ghamande Shekhar , Shapiro Nathan I. , Gibbs Kevin W. , Files D. Clark , Hager David N. , Shehu Arber , Prekker Matthew E. , Erickson Heidi L. , Exline Matthew C. , Gong Michelle N. , Mohamed Amira , Henning Daniel J. , Steingrub Jay S. , Peltan Ithan D. , Brown Samuel M. , Martin Emily T. , Monto Arnold S. , Khan Akram , Hough C. Terri , Busse Laurence , ten Lohuis Caitlin C. , Duggal Abhijit , Wilson Jennifer G. , Gordon Alexandra June , Qadir Nida , Chang Steven Y. , Mallow Christopher , Gershengorn Hayley B. , Babcock Hilary M. , Kwon Jennie H. , Halasa Natasha , Chappell James D. , Lauring Adam S. , Grijalva Carlos G. , Rice Todd W. , Jones Ian D. , Stubblefield William B. , Baughman Adrienne , Womack Kelsey N. , Lindsell Christopher J. , Hart Kimberly W. , Zhu Yuwei , Olson Samantha M. , Stephenson Meagan , Schrag Stephanie J. , Kobayashi Miwako , Verani Jennifer R. , Self Wesley H. ,   For the Influenza and Other Viruses in the Acutely Ill (IVY) Network
Published: July 2021

Background

As SARS-CoV-2 vaccination coverage increases in the United States (US), there is a need to understand the real-world effectiveness against severe Covid-19 and among people at increased risk for poor outcomes.

Methods

In a multicenter case-control analysis of US adults hospitalized March 11 - May 5, 2021, we evaluated vaccine effectiveness to prevent Covid-19 hospitalizations by comparing odds of prior vaccination with an mRNA vaccine (Pfizer-BioNTech or Moderna) between cases hospitalized with Covid-19 and hospital-based controls who tested negative for SARS-CoV-2.

Results

Among 1210 participants, median age was 58 years, 22.8% were Black, 13.8% were Hispanic, and 20.6% had immunosuppression. SARS-CoV-2 lineage B.1.1.7 was most common variant (59.7% of sequenced viruses). Full vaccination (receipt of two vaccine doses ≥14 days before illness onset) had been received by 45/590 (7.6%) cases and 215/620 (34.7%) controls. Overall vaccine effectiveness was 86.9% (95% CI: 80.4 to 91.2%). Vaccine effectiveness was similar for Pfizer-BioNTech and Moderna vaccines, and highest in adults aged 18-49 years (97.3%; 95% CI: 78.9 to 99.7%). Among 45 patients with vaccine-breakthrough Covid hospitalizations, 44 (97.8%) were ≥50 years old and 20 (44.4%) had immunosuppression. Vaccine effectiveness was lower among patients with immunosuppression (59.2%; 95% CI: 11.9 to 81.1%) than without immunosuppression (91.3%; 95% CI: 85.5 to 94.7%).

Conclusion

During March–May 2021, SARS-CoV-2 mRNA vaccines were highly effective for preventing Covid-19 hospitalizations among US adults. SARS-CoV-2 vaccination was beneficial for patients with immunosuppression, but effectiveness was lower in the immunosuppressed population.
Impact of the national test strategy on the development of the Covid-19 pandemic in Denmark
Authors: Busk Peter K. , Kristiansen Thomas Birk , Engsig-Karup Allan
Published: July 2021

During the Covid-19 pandemic, Denmark has pursued a unique mass testing strategy culminating in testing of more than 8,000 citizens per 100,000 inhabitants per day in the Spring 2021. The strategy includes free access to Covid-19 testing and since 2021, compulsory documentation for negative test or vaccination for access to workplace, educational institutions, restaurants, and many other places.

In the present study we analysed the effect of the Danish mass testing strategy throughout relevant stages of the pandemic. Mass testing was found not to have impact on the number of hospitalizations during the pandemic. Furthermore, during the highest level of testing in the spring 2021 the fraction of positive tests increased slightly on comparable days indicating that mass testing at best, did not reduce the prevalence of Covid-19.

The relationship between positives in antigen testing and in PCR testing indicated that many patients are not tested early in their infection where the risk of transmission is highest.

A likely explanation for the lack of impact of mass testing on hospitalizations and infections is that the testing increases risk-behaviour of the tested persons and that a high fraction of false negatives at low Covid-19 prevalence combined with increased risk-behaviour outweighs beneficial effects of mass testing.
Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning
Authors: Chang Yuzhou , He Fei , Wang Juexin , Chen Shuo , Li Jingyi , Liu Jixin , Yu Yang , Su Li , Ma Anjun , Allen Carter , Lin Yu , Sun Shaoli , Liu Bingqiang , Otero Jose , Chung Dongjun , Fu Hongjun , Li Zihai , Xu Dong , Ma Qin
Published: July 2021

Spatially resolved transcriptomics provides a new way to define spatial contexts and understand biological functions in complex diseases. Although some computational frameworks can characterize spatial context via various clustering methods, the detailed spatial architectures and functional zonation often cannot be revealed and localized due to the limited capacities of associating spatial information. We present RESEPT, a deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics. Given inputs as gene expression or RNA velocity, RESEPT learns a three-dimensional embedding with a spatial retained graph neural network from the spatial transcriptomics. The embedding is then visualized by mapping as color channels in an RGB image and segmented with a supervised convolutional neural network model. Based on a benchmark of sixteen 10x Genomics Visium spatial transcriptomics datasets on the human cortex, RESEPT infers and visualizes the tissue architecture accurately. It is noteworthy that, for the in-house AD samples, RESEPT can localize cortex layers and cell types based on a pre-defined region-or cell-type-specific genes and furthermore provide critical insights into the identification of amyloid-beta plaques in Alzheimer’s disease. Interestingly, in a glioblastoma sample analysis, RESEPT distinguishes tumor-enriched, non-tumor, and regions of neuropil with infiltrating tumor cells in support of clinical and prognostic cancer applications.
LptB2FG is an ABC transporter with Adenylate Kinase activity regulated by LptC/A recruitment
Authors: Baeta Tiago , Giandoreggio-Barranco Karine , Ayala Isabel , Moura Elisabete C. C. M. , Sperandeo Paola , Polissi Alessandra , Simorre Jean-Pierre , Laguri Cedric
Published: July 2021

Lipopolysaccharide (LPS) is an essential glycolipid covering the surface of gram-negative bacteria. Its transport involves a dedicated 7 protein transporter system, the Lpt machinery, that physically spans the entire cell envelope. LptB2FG complex is an ABC transporter that hydrolyses Adenosine Triphosphate (ATP) to extract LPS from the inner membrane (IM). LptB2FG was extracted directly from IM with its original lipid environment by Styrene-Maleic acids polymers(SMA). SMA-LptB2FG in nanodiscs displays ATPase activity and a previously uncharacterized Adenylate Kinase (AK) activity. It catalyzes phosphotransfer between two ADP molecules to generate ATP and AMP. ATPase and AK activities of LptB2FG are both stimulated by the interaction on the periplasmic side with LptC and LptA partners and inhibited by the presence of LptC transmembrane helix. Isolated ATPase module (LptB) has weak AK activity in absence of LptF and LptG, and one mutation, that weakens affinity for ADP, has AK activity similar to that of fully assembled complex. LptB2FG is thus capable of producing ATP from ADP depending on the assembly of the Lpt bridge and the AK activity might be important to ensure efficient LPS transport in fully assembled Lpt system.
Sequence Determines the Switch in the Fibril Forming Regions in the Low Complexity FUS Protein and Its Variants
Authors: Kumar Abhinaw , Chakraborty Debayan , Mugnai Mauro Lorenzo , Straub John E. , Thirumalai D.
Published: July 2021

Residues spanning distinct regions of the low-complexity domain of the RNA-binding protein, Fused in Sarcoma (FUS-LC), form fibril structures with different core morphologies. NMR experiments show that the 214 residue FUS-LC forms a fibril with an S-bend (core-1, residues 39-95), while the rest of the protein is disordered. In contrast, the fibrils of the C-terminal variant (FUS-LC-C; residues 111-214) has a U-bend topology (core-2, residues 112-150). Absence of the U-bend in FUS-LC implies that the two fibril cores do not coexist. Computer simulations show that these perplexing findings could be understood in terms of the population of sparsely-populated fibril-like excited states in the monomer. The propensity to form core-1 is higher compared to core-2. We predict that core-2 forms only in truncated variants that do not contain the core-1 sequence. At the monomer level, sequence-dependent enthalpic effects determine the relative stabilities of the core-1 and core-2 topologies.

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Large-scale deregulation of gene expression by artificial light at night in tadpoles of common toads
Authors: Touzot Morgane , Lefebure Tristan , Lengagne Thierry , Secondi Jean , Dumet Adeline , Konecny-Dupre Lara , Veber Philippe , Navratil Vincent , Duchamp Claude , Mondy Nathalie
Published: July 2021

Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems. Although gene-specific approaches have already shown the deleterious effect of ALAN on the circadian clock, immunity and reproduction, large-scale transcriptomic approaches with ecologically relevant light levels are still lacking to assess the global impact of ALAN on biological processes. Moreover, studies have focused mainly on variations in gene expression during the night in the presence of ALAN but never during the day. In a controlled laboratory experiment, transcriptome sequencing of Bufo bufo tadpoles revealed that ALAN affected gene expression at both night and daytime with a dose-dependent effect and globally induced a downregulation of genes. ALAN effects were detected at very low levels of illuminance (0.1 lux) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results indicate that a broad range of physiological pathways is impacted at the molecular level by very low levels of ALAN potentially resulting in reduced survival under environmental immune challenges.
Cellular toxicity of iHAP1 and DT-061 does not occur through PP2A-B56 targeting
Authors: Vit Gianmatteo , Duro Joana , Rajendraprasad Girish , Hertz Emil P.T. , Kauffeldt Holland Lya Katrine , Weisser Melanie Bianca , McEwan Brennan C. , Lopez-Mendez Blanca , Montoya Guillermo , Mailand Niels , Maeda Kenji , Kettenbach Arminja , Barisic Marin , Nilsson Jakob
Published: July 2021

PP2A is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The small molecule compounds iHAP1 and DT-061 have recently been reported by Leonard et al. (2020) and Morita et al. (2020) inCellto selectively stabilize specific PP2A-B56 complexes which mediate cell killing. Here, we show that this is not the case and question key findings in these papers. Through genome wide CRISPR-Cas9 screens, we uncover the biological pathways targeted by these compounds. We find that iHAP1 directly blocks microtubule assembly bothin vitroandin vivoand thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the endoplasmic reticulum and we directly visualize DT-061 in cytoplasmic granules that co-localize with Golgi markers. Our work demonstrates that iHAP1 and DT-061 cannot be used for dissecting PP2A-B56 biology.
Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria
Authors: Yunus Ian S. , Anfelt Josefine , Hudson Elton P. , Jones Patrik R.
Published: July 2021

The objective of this study was to implement direct sunlight-driven conversion of CO2 into a naturally excreted ready-to-use fuel. We engineered four different synthetic metabolic modules for biosynthesis of short-to medium-chain length hydrocarbons in the model cyanobacterium Synechocystis sp. PCC 6803. In module 1, the combination of a truncated clostridial n-butanol pathway with over-expression of the native cyanobacterial aldehyde deformylating oxygenase resulted in small quantities of propane when cultured under closed conditions. Direct conversion of CO2 into propane was only observed in strains with CRISPRi-mediated repression of three native putative aldehyde reductases. In module 2, three different pathways towards pentane were evaluated based on the polyunsaturated fatty acid linoleic acid as an intermediate. Through combinatorial evaluation of bioreaction ingredients it was concluded that linoleic acid undergoes a spontaneous non-enzymatic reaction to yield pentane and hexanal. When Synechocystis was added to the bioreaction, hexanal was converted into 1-hexanol, but there was no further stimulation of pentane biosynthesis. For modules 3 and 4, several different acyl-ACP thioesterases were evaluated in combination with two different decarboxylases. Small quantities of 1-heptene and 1-nonene were observed in strains expressing the desaturase-like enzyme UndB from Pseudomonas mendocina in combination with C8-C10 preferring thioestersaes. When UndB instead was combined with a C12-specific ‘UcFatB1 thioesterase, this resulted in ten-fold increase of alkene biosynthesis. When UndB was replaced with the light-dependent FAP decarboxylase, both undecane and tridecane accumulated, albeit with a 10-fold drop in productivity. Optimization of the RBS, promoter and gene order in these synthetic operons resulted in 1-alkene bioproductivity of 230 mg/L after 10 d with 15% carbon partitioning. In conclusion, the direct bioconversion of CO2 into secreted and ready-to-use hydrocarbon fuel was accomplished and optimal results were obtained with UndB and a C12 chain-length specific thioesterase.

Highlights

Multiple repression of endogenous aldehyde reductases/dehydrogenases by CRISPRi enabled propane biosynthesis

Biosynthesis of short-medium chain hydrocarbons (C7-C11) in a cyanobacterium was demonstrated for the first time

The final enzymes of the hydrocarbon pathways influenced both productivity and product profile

All volatile products were naturally secreted and accumulated outside of the cell