bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species associations and management intensity modulate the habitat niche breadth of forest birds
Authors: Basile Marco , Asbeck Thomas , Cordeiro Pereira João M. , Mikusiński Grzegorz , Storch Ilse 
Published: July 2021

AbstractSpecies associations can have profound effects on the realized habitat niche of species, indicating that habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organization in niche modelling, we developed multi-species abundance models, incorporating the local effect of potentially associated species, alongside with environmental ones, targeting mainly forest management intensity. We coupled it with a landscape-scale analysis to further examine the role of management intensity in modifying the habitat niche in connection with the landscape context. Using empirical data from the Black Forest in southern Germany, we focused on the forest bird assemblage and in particular on the cavity nester and canopy forager guilds. We included in the analysis species that co-occur and for which evidences suggest association is likely. Our findings show that the local effect of species associations can moderate the effects of management intensity. We also found that species express a larger habitat niche breadth in intensively managed forests, depending on the landscape context. Species associations may facilitate the utilization of a broader range of environmental conditions under intensive forest management, which benefits some species over others. Such network of associations may be a relevant factor in the effectiveness of conservation-oriented forest management.
Mutation of the nuclear pore complex component,aladin1, disrupts asymmetric cell division inZea mays(maize)
Authors: Best Norman B. , Addo-Quaye Charles , Kim Bong-Suk , Weil Clifford F. , Schulz Burkhard , Johal Guri , Dilkes Brian P. 
Published: July 2021

AbstractThe nuclear pore complex (NPC) regulates the movement of macromolecules between the nucleus and cytoplasm. Dysfunction of many components of the NPC results in human genetic diseases, including triple A syndrome (AAAS) as a result of mutations in ALADIN. Here we report a nonsense mutation in the maize ortholog,aladin1(ali1-1), at the orthologous amino acid residue of an AAAS allele from humans, alters plant stature, tassel architecture, and asymmetric divisions of subsidiary mother cells (SMCs). Crosses with the stronger nonsense alleleali1-2identified complex allele interactions for plant height and aberrant SMC division. RNA-seq analysis of theali1-1mutant identified compensatory transcript accumulation for other NPC components as well as gene expression consequences consistent with conservation of ALADIN1 functions between humans and maize. These findings demonstrate that ALADIN1 is necessary for normal plant development, shoot architecture, and asymmetric cell division in maize.
A versatile automated high-throughput drug screening platform for zebrafish embryos
Authors: Lubin Alexandra , Otterstrom Jason , Hoade Yvette , Bjedov Ivana , Stead Eleanor , Whelan Matthew , Gestri Gaia , Paran Yael , Payne Elspeth 
Published: July 2021

AbstractZebrafish provide a unique opportunity for drug screening in living animals, with the fast developing, transparent embryos allowing for relatively high throughput, microscopy-based screens. However, the limited availability of rapid, flexible imaging and analysis platforms has limited the use of zebrafish in drug screens. We have developed a easy-to-use, customisable automated screening procedure suitable for high-throughput phenotype-based screens of live zebrafish. We utilised the WiScan®HermesHigh Content Imaging System to rapidly acquire brightfield and fluorescent images of embryos, and the WiSoft®Athena Zebrafish Applicationfor analysis, which harnesses an Artificial Intelligence-driven algorithm to automatically detect fish in brightfield images, identify anatomical structures, partition the animal into regions, and exclusively select the desired side-oriented fish. Our initial validation combined structural analysis with fluorescence images to enumerate GFP-tagged haematopoietic stem and progenitor cells in the tails of embryos, which correlated with manual counts. We further validated this system to assess the effects of genetic mutations and x-ray irradiation in high content using a wide range of assays. Further, we performed simultaneous analysis of multiple cell types using dual fluorophores in high throughput. In summary, we demonstrate a broadly applicable and rapidly customisable platform for high content screening in zebrafish.
Distribution and functional potential of photoautotrophic bacteria in alkaline hot springs
Authors: Bennett Annastacia C. , Murugapiran Senthil K. , Kees Eric D. , Hamilton Trinity L. 
Published: July 2021

ABSTRACTAlkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on cyanobacteria (oxygenic phototrophs), but anoxygenic phototrophs are critical parts of the evolutionary history of life on Earth and and are abundant across temperature gradients in alkaline hot springs. However, many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. Here, we examined the distribution of genes involved in phototrophy and carbon and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites approaching the upper temperature limit of photosynthesis (~72°C) in YNP using metagenome sequencing. Genes associated with cyanobacteria are abundant throughout our data and more diverse at temperatures > 63°C, genes for autotrophic Chloroflexi are more abundant in sites > 63°C and genes associated with phototrophic Chloroflexi are abundant throughout. Additionally, we recovered deep branching nitrogen fixation genes from our metagenomes, which could inform the evolutionary history of nitrogen fixation. Lastly, we recovered 25 metagenome assembled genomes of Chloroflexi. We found distinct differences in carbon fixation genes inRoseiflexusandChloroflexusbins, in addition to several novel Chloroflexi bins. Our results highlight the physiological diversity and evolutionary history of the understudied, anoxygenic autotrophic Chloroflex. Furthermore, we provide evidence that genes involved in nitrogen fixation in Chloroflexi is more widespread than previously assumed.IMPORTANCEPhotosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology because they are responsible for the rise of oxygen and are critical to nutrient cycling. While a large body of work has focused on the oxygenic photosynthesis in cyanobacteria, many questions remain regarding the metabolic potential of anoxygenic phototrophs but are further compounded by their metabolic and taxonomic diversity. Here, we have recovered several novel metagenome bins and quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Together, our results add to the body of work focusing on photosynthetic bacteria in hot springs in Yellowstone National Park.
A midbrain - thalamus - cortex circuit reorganizes cortical dynamics to initiate planned movement
Authors: Inagaki Hidehiko K. , Chen Susu , Ridder Margreet C. , Sah Pankaj , Li Nuo , Yang Zidan , Hasanbegovic Hana , Gao Zhenyu , Gerfen Charles R. , Svoboda Karel 
Published: July 2021

AbstractMotor behaviors are often planned long before execution, but only released after specific sensory events. Planning and execution are each associated with distinct patterns of motor cortex activity. Key questions are how these dynamic activity patterns are generated and how they relate to behavior. Here we investigate the multi-regional neural circuits that link an auditory ‘go cue’ and the transition from planning to execution of directional licking. Ascending glutamatergic neurons in the midbrain reticular and pedunculopontine nuclei show short-latency and phasic changes in spike rate that are selective for the go cue. This signal is transmitted via the thalamus to the motor cortex, where it triggers a rapid reorganization of motor cortex state from planning-related activity to a motor command, which in turn drives appropriate movement. Our studies show how brainstem structures can control cortical dynamics via the thalamus for rapid and precise motor behavior.
Quantifying social contact patterns in Minnesota during Stay-at-Home social distancing order
Authors: Dorélien Audrey M. , Venkateswaran Narmada , Deng Jiuchen , Searle Kelly , Enns Eva , Kulasingam Shalini 
Published: July 2021

AbstractSARS-CoV-2 is primarily transmitted through person-to-person contacts. It is important to collect information on age-specific contact patterns because SARS-CoV-2 susceptibility, transmission, and morbidity vary by age. To reduce risk of infection, social distancing measures have been implemented. Social contact data, which identify who has contact with whom especially by age and place are needed to identify high-risk groups and serve to inform the design of non-pharmaceutical interventions.We estimated and used negative binomial regression to compare the number of daily contacts during the first wave (April-May 2020) of the Minnesota Social Contact Study, based on respondents age, gender, race/ethnicity, region, and other demographic characteristics. We used information on age and location of contacts to generate age-structured contact matrices. Finally, we compared the age-structured contact matrices during the stay-at-home order to pre-pandemic matrices.During the state-wide stay-home order, the mean daily number of contacts was 5.6. We found significant variation in contacts by age, gender, race, and region. Adults between 40 and 50 years had the highest number of contacts. Respondents in Black households had 2.1 more contacts than respondent in White households, while respondents in Asian or Pacific Islander households had approximately the same number of contacts as respondent in White households. Respondents in Hispanic households had approximately two fewer contacts compared to White households. Most contacts were with other individuals in the same age group. Compared to the pre-pandemic period, the biggest declines occurred in contacts between children, and contacts between those over 60 with those below 60.
COVID-19 Pandemic Analysis
Authors: van Lint Victor A.J. 
Published: July 2021

AbstractThe development of coronavirus disease (COVID-19) deaths in selected nations and states is compared to the result of calculations using a conventional SEIR model of pandemic development. The model is based on the infection multiplier, R0, defined as the number of people infected by each infectious person. The infection rate increases exponentially when R0 >1.0; it remains constant at R0 = 1.0 and decreases for R0 < 1.0. R0 is determined by population behavior (frequency and proximity of interactions) and the ease by which a victim is infected by an infectious person (virulence of the virus). It is reduced by herd immunity when a large fraction of the population acquires immunity by vaccination or by recovering from infection.The daily death rates in the U.S. and northern Europe exhibited peaks in April/May 2020 and Dec. 2020/Jan. 2021 with more a modest rate during the summer of 2020 and a gradually decreasing rate since Jan. 2021. The model produces this type of oscillatory response if it assumes that the population’s R0 responds to information reported about the pandemic, but with a delay between infections and resulting behavioral adjustments. Oscillatory behavior is typical of a control loop with delay in its feedback.The analysis concludes thatGiven the history of R0 the model predicts the development of pandemic deaths. However, since R0 is determined by the population’s behavior, control of the pandemic in democracies depends primarily on preparation and the persuasive power of political and scientific authorities. Data for S. Korea and New Zealand demonstrate the effectiveness of such methods.For each death in the U.S. about 169 persons were infected, but fewer than half of them were identified as cases.The pandemic was prolonged in the U.S. because the population chose to keep R0 near 1.0 by relaxing restrictions once the death rate subsided.Initial values of R0 as high as 5.0 were observed, leading to infections doubling about every 2 days. If unabated, the resulting exponential growth increases the infected population by a factor of about 5000 before the death from the first infections is recorded.Arrival from Italy probably initiated the pandemic in the eastern U.S., but, by the time the first death was recorded the number of domestic infections exceeded by far those that were imported. Import restrictions beyond this point are ineffective except in delaying the arrival of more virulent mutations.If no social restrictions had been adopted, approximately 1.6 million deaths would have resulted in the U.S. The vaccine, although developed and deployed at record speed, was too late to ameliorate this result.A third peak in death rate in Sept. 2021 may be prevented if more than 80% of the population is vaccinated.
Factors associated with transmission in COVID-19 outbreaks in long-term care facilities
Authors: Vijh Rohit , Ng Carmen H. , Shirmaleki Mehdi , Bharmal Aamir 
Published: July 2021

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a disproportionate impact on residents in long-term care facilities (LTCFs). Through our experience and data from managing COVID-19 exposures and outbreaks in LTCFs in the Fraser Health region in British Columbia, Canada, we identified risk factors associated with outbreak severity to inform current outbreak management strategies and future pandemic preparedness planning efforts.MethodsWe used a retrospective cohort study design to evaluate the association between non-modifiable factors (facility building, organization level, and resident population characteristics), modifiable factors (assessments for infection prevention and control (IPC) and public health measures), and severity of COVID-19 outbreaks (attack rate) in LTCFs. We modelled the COVID-19 attack rates in LTCF outbreaks using negative binomial regression models.ResultsFrom March 1, 2020 to January 10, 2021, a total of 145 exposures to at least one confirmed case of COVID-19 in 82 LTCFs occurred. For every item not met in the assessment tool, a 22% increase in the attack rate was observed (rate ratio 1.2 [95% CI 1.1 – 1.4]) after adjusting for other risk factors such as age of the facility, index case type (resident vs. staff) and proportion of single bed rooms.ConclusionOur findings highlight the importance of assessing IPC and public health measures for outbreak management. They also demonstrate the important modifiable and non-modifiable risk factors associated with COVID-19 outbreaks in our jurisdiction. We hope these findings will inform ongoing outbreak management and future pandemic planning efforts.
Increase in SARS-CoV-2 seroprevalence in healthy blood donors after the second wave of COVID-19 pandemic in South-Eastern Italy: evidence for asymptomatic young individuals as potential virus spreaders
Authors: Antonucci Francescopaolo , Fiore Josè Ramòn , De Feo Lucia , Granato Tommaso , Di Stefano Mariantonietta , Faleo Giuseppina , Farhan Mohamed Ahmed Mohamed , Margaglione Maurizio , Centra Michele , Santantonio Teresa Antonia 
Published: July 2021

AbstractBackgroundItaly has been the first among western countries to experience SARS-CoV-2 spread during which the southern regions were also heavily affected by the pandemic. To understand and monitor properly the evolution of COVID-19 pandemic, population based seroprevalence studies are a valid tool for the infection rates and effective prevalence of the SARS-CoV-2.AimIn this prospective study, we assessed the changes in SARS-CoV-2 seroprevalence rates among non-vaccinated blood donors in South-Eastern Italy over May 2020 to March 2021.Methods8,183 healthy blood donors referring to the Transfusion Center at the University Hospital “Riuniti” of Foggia (Italy) for blood donation in the period May 2020-March 2021 were tested for anti-SARS-CoV-2 antibodies by Ortho Clinical Diagnostics VITROS® 3600. None of the considered subjects had a diagnosed symptomatic COVID-19 infection.ResultsOverall, 516 resulted positive for anti-SARS-CoV-2 IgG antibodies (6.3%, 95% CI, 0.03-0.15%), 387 (4.7%) were male and 129 (1.7%) female. A statistically significant increase in the seropositive population was found from May 2020 to March 2021 (Fisher’s p<0.001). The difference of the seroprevalence was significant in terms of age but not sex (2-sided p<0.05 for age; 2-sided p>0.05 for sex) in both groups.ConclusionOur study shows a significant increase in the SARS-CoV-2 seroprevalence among blood donors and suggests a potential role of asymptomatic individuals in continuing the spread of the pandemic. These results may contribute to establishing containment measures and priorities in vaccine campaigns.
When time-dependence in disease outcome risk is not captured by impact evaluation modeling studies: a measles vaccination case study
Authors: Portnoy Allison , Hsieh Yuli Lily , Abbas Kaja , Klepac Petra , Santos Heather , Brenzel Logan , Jit Mark , Ferrari Matthew 
Published: July 2021

AbstractBackgroundIn modeling studies that evaluate the effects of health programs, the risk of secondary outcomes attributable to infection can vary with underlying disease incidence. Consequently, the impact of interventions on secondary outcomes would not be proportional to incidence reduction. Here we use a case study on measles vaccine program to demonstrate how failure to capture this non-linear relationship can lead to over- or under-estimation.MethodsWe used a published model of measles CFR that depends on incidence and vaccine coverage to illustrate the effects of: (1) assuming higher CFR in “no-vaccination” scenarios; (2) time-varying CFRs over the past; and (3) time-varying CFRs in future projections on measles impact estimation. We evaluated how different assumptions on vaccine coverage, measles incidence, and CFR levels in “no-vaccination” scenarios affect estimation of future deaths averted by measles vaccination.ResultsCompared to constant CFRs, aligning both “vaccination” and “no-vaccination” scenarios with time variant measles CFR estimates led to larger differences in mortality in historical years and lower in future years.ConclusionsTo assess consequences of interventions, impact estimates should consider the effect of “no-intervention” scenario assumptions on model parameters to project estimated impact for alternative scenarios according to intervention strategies and investment decisions.
Ethnic and sexual identities: inequalities in adolescent health and wellbeing in a national population-based study
Authors: Khanolkar Amal R. , Frost David M. , Tabor Evangeline , Redclift Victoria , Amos Rebekah , Patalay Praveetha 
Published: July 2021

AbstractPurposeThis study employed an intersectional framework to examine impact of inequities related to sexual and ethnic minority identities in risk for health, wellbeing, and health-related behaviors in a nationally representative sample.MethodsThe study sample comprised 9,789 (51% female) adolescents aged 17 years from the UK-wide Millennium Cohort Study, with data on self-identified sexual- and ethnic-identities. Adolescents were grouped into White-Heterosexual, White sexual minority (White-SM), ethnic minority (EM)-heterosexual, and ethnic- and sexual minority (EM-SM) categories.Mental health (e.g., self-reported psychological distress, doctor-diagnosed depression, attempted suicide, victimisation), general health (self-rated health, chronic illness, Body mass index) and a range of health-related behaviors (e.g., smoking, substance use) were assessed by questionnaires. Associations were analysed using logistic and linear regression (adjusted for sex and parental income).ResultsSexual minority individuals (White:18% and ethnic minority:3%) had increased odds for mental ill-health and attempted suicide, with higher odds in White-SM than EM-SM. Compared to White-heterosexual individuals, White-SM and EM-SM had higher risk for psychological distress (Odds ratios [OR]3.47/2.24 for White-SM/EM-SM respectively), and emotional problems (OR3.17/1.65). They had higher odds for attempted suicide (OR2.78/2.02), self-harm (OR3.06/1.52), and poor sleep quality (OR1.88/1.67). In contrast, White-Heterosexual and White-SM groups had similarly high proportions reporting risky behaviors except for drug use (OR1.34) and risky sex (OR1.40) which are more common in White-SM individuals. EM-Heterosexual and EM-SM individuals had decreased odds for health-related behaviors.ConclusionsSexual minority (White and EM) individuals had substantially worse mental health compared to their heterosexual peers. Adverse health-related behaviors were more common in White sexual minority individuals. Investigation into the mechanisms leading to these differences is needed.
Xeno-nucleic Acid (XNA) 2’-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding
Authors: Ferreira-Bravo Irani Alves , DeStefano Jeffrey J. 
Published: July 2021

AbstractThe causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2’-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~ 10-20 nM and a binding half-life for the RBD of 53 ± 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.