bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of ENSO and the North American monsoon on mast seeding in two Rocky Mountain conifer species
Authors: Wion Andreas P. , Pearse Ian S. , Rodman Kyle C. , Veblen Thomas T. , Redmond Miranda D. 
Published: October 2021

We aimed to disentangle the patterns of synchronous and variable cone production (i.e. masting) and its relationship to climate in two conifer species native to dry forests of western North America. We used cone abscission scars to reconstructca15 years of recent cone production inPinus edulisandPinus ponderosa, and used redundancy analysis to relate time series of annual cone production to climate indices describing the North American monsoon and the El Niño Southern Oscillation (ENSO). We show that the sensitivity to climate and resulting synchrony in cone production varies substantially between species. Cone production among populations ofP. eduliswas much more spatially synchronous and more closely related to large-scale modes of climate variability than among populations ofP. ponderosa. Large-scale synchrony inP. eduliscone production was associated with the North American monsoon and we identified a dipole pattern of regional cone production associated with ENSO phase. InP. ponderosa, these climate indices were not strongly associated with cone production, resulting in asynchronous masting patterns among populations. This study helps frame our understanding of mast seeding as a life-history strategy and has implications for our ability to forecast mast years in these species.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
Climate change and plant reproduction: trends and drivers of mast seeding change
Authors: Hacket-Pain Andrew , Bogdziewicz Michał 
Published: October 2021

Climate change is reshaping global vegetation through its impacts on plant mortality, but recruitment creates the next generation of plants and will determine the structure and composition of future communities. Recruitment depends on mean seed production, but also on the interannual variability and among-plant synchrony in seed production, the phenomenon known as mast seeding. Thus, predicting the long-term response of global vegetation dynamics to climate change requires understanding the response of masting to changing climate. Recently, data and methods have become available allowing the first assessments of long-term changes in masting. Reviewing the literature, we evaluate evidence for a fingerprint of climate change on mast seeding and discuss the drivers and impacts of these changes. We divide our discussion into the main characteristics of mast seeding: interannual variation, synchrony, temporal autocorrelation and mast frequency. Data indicate that masting patterns are changing but the direction of that change varies, likely reflecting the diversity of proximate factors underlying masting across taxa. Experiments to understand the proximate mechanisms underlying masting, in combination with the analysis of long-term datasets, will enable us to understand this observed variability in the response of masting. This will allow us to predict future shifts in masting patterns, and consequently ecosystem impacts of climate change via its impacts on masting.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
Modes of climate variability bridge proximate and evolutionary mechanisms of masting
Authors: Ascoli Davide , Hacket-Pain Andrew , Pearse Ian S. , Vacchiano Giorgio , Corti Susanna , Davini Paolo 
Published: October 2021

There is evidence that variable and synchronous reproduction in seed plants (masting) correlates to modes of climate variability, e.g. El Niño Southern Oscillation and North Atlantic Oscillation. In this perspective, we explore the breadth of knowledge on how climate modes control reproduction in major masting species throughout Earth's biomes. We posit that intrinsic properties of climate modes (periodicity, persistence and trends) drive interannual and decadal variability of plant reproduction, as well as the spatial extent of its synchrony, aligning multiple proximate causes of masting through space and time. Moreover, climate modes force lagged but in-phase ecological processes that interact synergistically with multiple stages of plant reproductive cycles. This sets up adaptive benefits by increasing offspring fitness through either economies of scale or environmental prediction. Community-wide links between climate modes and masting across plant taxa suggest an evolutionary role of climate variability. We argue that climate modes may ‘bridge’ proximate and ultimate causes of masting selecting for variable and synchronous reproduction. The future of such interaction is uncertain: processes that improve reproductive fitness may remain coupled with climate modes even under changing climates, but chances are that abrupt global warming will affect Earth's climate modes so rapidly as to alter ecological and evolutionary links.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
Natural disturbances and masting: from mechanisms to fitness consequences
Authors: Vacchiano Giorgio , Pesendorfer Mario B. , Conedera Marco , Gratzer Georg , Rossi Lorenzo , Ascoli Davide 
Published: October 2021

The timing of seed production and release is highly relevant for successful plant reproduction. Ecological disturbances, if synchronized with reproductive effort, can increase the chances of seeds and seedlings to germinate and establish. This can be especially true under variable and synchronous seed production (masting). Several observational studies have reported worldwide evidence for co-occurrence of disturbances and seed bumper crops in forests. Here, we review the evidence for interaction between disturbances and masting in global plant communities; we highlight feedbacks between these two ecological processes and posit an evolutionary pathway leading to the selection of traits that allow trees to synchronize seed crops with disturbances. Finally, we highlight relevant questions to be tested on the functional and evolutionary relationship between disturbances and masting.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
Delayed fertilization facilitates flowering time diversity in Fagaceae
Authors: Satake Akiko , Kelly Dave 
Published: October 2021

Fagaceae includes typical masting species that exhibit highly synchronized and fluctuating acorn production. Fagaceae shows an interesting feature in that fertilization is delayed by several weeks to more than 1 year after pollination. Although delayed fertilization was recorded over a century ago, the evolutionary advantage of delayed fertilization is still poorly understood. Here, we present a new hypothesis that delayed fertilization facilitates temporal niche differentiation via non-overlapping flowering times among species. Comparing flowering and fruiting times in 228 species from five genera in Fagaceae, we first show that there is a close association between a wider spread of flowering times and the likelihood of a 2-year fruiting habit in which there is a long delay from pollination to fertilization. To study the coevolution of flowering time and delayed fertilization, we developed a mathematical model that incorporates the effects of competition for pollinators, seed predator satiation and unfavourable season for reproduction on fitness. The model shows that delayed fertilization facilitates the diversification of flowering time in a population, which is advantageous for animal-pollinated trees that compete over pollinators. Our new hypothesis about the coevolution of delayed fertilization and flowering time will provide new insight into the evolution of masting.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
Studying the genetic basis of masting
Authors: Satake Akiko , Kelly Dave 
Published: October 2021

The mechanisms underlying mast seeding have traditionally been studied by collecting long-term observational data on seed crops and correlating seedfall with environmental variables. Significant progress in ecological genomics will improve our understanding of the evolution of masting by clarifying the genetic basis of masting traits and the role of natural selection in shaping those traits. Here, we summarize three important aspects in studying the evolution of masting at the genetic level: which traits govern masting, whether those traits are genetically regulated, and which taxa show wide variation in these traits. We then introduce recent studies on the molecular mechanisms of masting. Those studies measure seasonal changes in gene expression in natural conditions to quantify how multiple environmental factors combine to regulate floral initiation, which in many masting plant species is the single largest contributor to among-year variation in seed crops. We show that Fagaceae offers exceptional opportunities for evolutionary investigations because of its diversity at both the phenotypic and genetic levels and existing documented genome sequences.This article is part of the theme issue ‘The ecology and evolution of synchronized seed production in plants’.
‘I had no life. I was only existing’. Factors shaping the mental health and wellbeing of people experiencing long Covid: a qualitative study
Authors: Burton Alexandra , Aughterson Henry , Fancourt Daisy , Philip Keir EJ 
Published: October 2021

AbstractBackgroundAround one in 10 people who have COVID-19 report persistent symptoms or ‘long Covid’. Impaired mental health and wellbeing is commonly reported including anxiety, depression and reduced quality of life. There is however, limited in-depth research exploring why mental health and wellbeing have been impacted among people experiencing long Covid.AimsTo explore factors impacting mental health and wellbeing, from the perspective of people with long Covid.MethodSemi-structured qualitative interviews that were audio-recorded and transcribed. Data were analysed using reflexive thematic analysis. 21 people with long Covid participated in the study. Participants were eligible to take part if they self-reported a positive swab test/antibody test, or one or more commonly reported COVID-19 symptoms at illness onset and experiences of one or more long Covid symptom three or more weeks following illness onset.ResultsFive themes were identified across participant accounts regarding factors impacting mental health and wellbeing including i) experiences of care and understanding from others; ii) lack of service and treatment options; iii) severe disruption to daily life iv) uncertainty of illness trajectories and v) changes to identity.ConclusionsPeople with long Covid experience a range of factors that negatively impact their mental health and wellbeing. Providing patient centred health services that integrate the rapidly evolving research in this area is important, as are peer support groups and supported approaches to self-management.
Photoacoustic monitoring of angiogenesis predicts response to therapy in healing wounds
Authors: Mantri Yash , Tsujimoto Jason , Donovan Brian , Fernandes Christopher C. , Garimella Pranav S. , Penny William F. , Anderson Caesar A. , Jokerst Jesse V. 
Published: October 2021

AbstractChronic wounds are a major health problem that cause the medical infrastructure billions of dollars every year. Chronic wounds are often difficult to heal and cause significant discomfort. Although wound specialists have numerous therapeutic modalities at their disposal, tools that could 3D-map wound bed physiology and guide therapy do not exist. Visual cues are the current standard but are limited to surface assessment; clinicians rely on experience to predict response to therapy. Photoacoustic (PA) ultrasound (US) is a non-invasive, hybrid imaging modality that can solve these major limitations. PA relies on the contrast generated by hemoglobin in blood which allows it to map local angiogenesis, tissue perfusion and oxygen saturation—all critical parameters for wound healing. This work evaluates the use of PA-US to monitor angiogenesis and stratify patients respondingvs. not-responding to therapy. We imaged 19 patients with 22 wounds once a week for at least three weeks. Our findings suggest that PA imaging directly visualizes angiogenesis. Patients responding to therapy showed clear signs of angiogenesis and an increased rate of PA increase (p = 0.002). These responders had a significant and negative correlation between PA intensity and wound size. Hypertension was correlated to impaired angiogenesis in non-responsive patients. The rate of PA increase and hence the rate of angiogenesis was able to predict healing times within 30 days from the start of monitoring (power = 88%, alpha = 0.05) This early response detection system could help inform management and treatment strategies while improving outcomes and reducing costs.
Memory B cell and humoral responses elicited by Sputnik V in naïve and COVID-19-recovered vaccine recipients
Authors: Byazrova Maria G , Kulemzin Sergey V , Astakhova Ekaterina A , Belovezhets Tatyana N , Efimov Grigory A , Chikaev Anton N , Kolotygin Ilya O , Gorchakov Andrey A , Taranin Alexander V , Filatov Alexander V 
Published: October 2021

ABSTRACTThe development of effective vaccines against SARS-CoV-2 remains a global health priority. Despite extensive use, the effects of Sputnik V on B cell immunity need to be explored in detail. We show that B memory cell (MBC) and antibody responses to Sputnik V were heavily dependent on whether the vaccinee had a history of SARS-CoV-2 infection or not. In vitro stimulated MBCs from previously infected recipients of Sputnik V secreted a significant amount of anti-RBD IgG both on days 28 and 85 from the beginning of vaccination. These antibodies demonstrated robust neutralization of the Wuhan Spike-pseudotyped lentivirus. In the naïve group of vaccinees, the level of anti-RBD IgG secretion was five- to six-fold reduced compared to that of the recovered group, and maximum virus neutralization (Wuhan spike) was achieved only on day 85. Sera from all the recovered and most naïve Sputnik V recipients were neutralizing against the ancestral Wuhan and mutant B.1.351 viruses. Thus, our in-depth analysis of MBC responses in Sputnik V vaccinees complements traditional serological approaches and may provide important outlook into future B cell responses upon re-encounter with the emerging variants of SARS-CoV-2.
Duration of viral shedding and culture positivity with post-vaccination breakthrough delta variant infections
Authors: Siedner Mark J. , Boucau Julie , Gilbert Rebecca , Uddin Rockib , Luu Jonathan , Haneuse Sebastien , Vyas Tammy , Reynolds Zahra , Iyer Surabhi , Chamberlin Grace , Goldstein Robert H. , North Crystal M. , Sacks Chana A. , Regan James , Flynn James P. , Choudhary Manish C. , Vyas Jatin M. , Barczak Amy , Lemieux Jacob , Li Jonathan Z. 
Published: October 2021

AbstractIsolation guidelines for SARS-CoV-2 are largely derived from data collected prior to emergence of the delta variant. We followed a cohort of ambulatory patients with post-vaccination breakthrough SARS-CoV-2 infections with longitudinal collection of nasal swabs for SARS-CoV-2 viral load quantification, whole genome sequencing, and viral culture. All delta variant infections (8/8, 100%) in our cohort were symptomatic, compared with 64% (9/14) of non-delta variant infections. Delta variant breakthrough infections were characterized by higher initial viral load, longer duration of virologic shedding by PCR (median 13.5 vs 4 days, hazard ratio [HR] 0.45, 95%CI 0.17-1.17), greater likelihood of replication-competent virus at early stages of infection (6/8 [75%] vs 3/14 [23%], P=0.03), and longer duration of culturable virus (median 7 vs 3 days, HR 0.38, 95%CI 0.14-1.02) compared to non-delta variants. Nonetheless, no individuals with delta variant infections had replication-competent virus by day 10 after symptom onset or 24 hours after resolution of symptoms. These data support current US Center for Disease Control isolation guidelines and reinforce the importance of prompt testing and isolation among symptomatic individuals with delta variant breakthrough infections. Additional data are needed to evaluate these relationships among asymptomatic and more severe delta variant breakthrough infections.
Interactions among common non-SARS-CoV-2 respiratory viruses and influence of the COVID-19 pandemic on their circulation in New York City
Authors: Yuan Haokun , Yeung Alice , Yang Wan 
Published: October 2021

AbstractBackgroundNon-pharmaceutical interventions (NPIs) and voluntary behavioral changes during the COVID-19 pandemic have influenced the circulation of non-SARS-CoV-2 respiratory infections. We aimed to examine interactions among common non-SARS-CoV-2 respiratory virus and further estimate the impact of the COVID-19 pandemic on these viruses.MethodsWe analyzed incidence data for seven groups of respiratory viruses in New York City (NYC) during Oct 2015 - May 2021 (i.e., before and during the COVID-19 pandemic). We first used elastic net regression to identify potential virus interactions and further examined the robustness of the found interactions by comparing the performance of Auto Regressive Integrated Moving Average (ARIMA) models with and without the interactions. We then used the models to compute counterfactual estimates of cumulative incidence and estimate the reduction during the COVID-19 pandemic period from March 2020 to May 2021, for each virus.ResultsWe identified potential interactions for three endemic human coronaviruses (CoV-NL63, CoV-HKU, and CoV-OC43), parainfluenza (PIV)-1, rhinovirus, and respiratory syncytial virus (RSV). We found significant reductions (by ~70-90%) in cumulative incidence of CoV-OC43, CoV-229E, human metapneumovirus, PIV-2, PIV-4, RSV, and influenza virus during the COVID-19 pandemic. In contrast, the circulation of adenovirus and rhinovirus was less affected.ConclusionsCirculation of several respiratory viruses has been low during the COVID-19 pandemic, which may lead to increased population susceptibility. It is thus important to enhance monitoring of these viruses and promptly enact measures to mitigate their health impacts (e.g., influenza vaccination campaign and hospital infection prevention) in the coming months.
Novel point-of-care ultrasound (POCUS) technique to modernize the JVP exam and rule out elevated right atrial pressures
Authors: Istrail Larry , Stepanova Maria 
Published: October 2021

ABSTRACTAccurate assessment of the jugular venous pressure (JVP) and right atrial pressure (RAP) has relied on the same bedside examination method since 1930. While this technique provides a rough estimate of right sided pressures, it is limited by poor sensitivity and overall diagnostic inaccuracy. The internal jugular vein (IJV) is difficult to visualize in many patients and relies on an incorrect assumption that the right atrium lies 5 centimeters below the sternum. Point-of-care ultrasound (POCUS) offers an alternative method for more precisely estimating JVP and RAP. We propose a novel method of measuring the right atrial depth (RAD) using a sonographic measurement of the depth of the posterior left ventricular outflow tract as a surrogate landmark to the center of the right atrium when viewed in the parasternal long axis view. This is combined with determination if JVD was present at the supraclavicular point. Sensitivity, specificity, PPV, NPV of JVD at the supraclavicular point was 70%, 76%, 59%, 91% respectively. These values were confounded by the lack of standardization of zero reference landmarks (ZRLs) used during the right heart catheterizations. When the RAD measurement was adjusted to account for measurement error the sensitivity of JVD at supraclavicular point for elevated RAP improved to 90% with negative predictive value of 96%. This may offer a rapid and reliable method for ruling out elevated RAP and increase objectivity in our volume status assessment.
Progression Free Survival Prediction for Head and Neck Cancer using Deep Learning based on Clinical and PET-CT Imaging Data
Authors: Naser Mohamed A. , Wahid Kareem A. , Mohamed Abdallah S.R. , Abdelaal Moamen Abobakr , He Renjie , Dede Cem , van Dijk Lisanne V. , Fuller Clifton D. 
Published: October 2021

AbstractDetermining progression-free survival (PFS) for head and neck squamous cell carcinoma (HNSCC) patients is a challenging but pertinent task that could help stratify patients for improved overall outcomes. PET/CT images provide a rich source of anatomical and metabolic data for potential clinical biomarkers that would inform treatment decisions and could help improve PFS. In this study, we participate in the 2021 HECKTOR Challenge to predict PFS in a large dataset of HNSCC PET/CT images using deep learning approaches. We develop a series of deep learning models based on the DenseNet architecture using a negative log-likelihood loss function that utilizes PET/CT images and clinical data as separate input channels to predict PFS in days. Internal model validation based on 10-fold cross-validation using the training data (N=224) yielded C-index values up to 0.622 (without) and 0.842 (with) censoring status considered in C-index computation, respectively. We then implemented model ensembling approaches based on the training data cross-validation folds to predict the PFS of the test set patients (N=101). External validation on the test set for the best ensembling method yielded a C-index value of 0.694. Our results are a promising example of how deep learning approaches can effectively utilize imaging and clinical data for medical outcome prediction in HNSCC, but further work in optimizing these processes is needed.
A Systematic Review of the Methodological Quality of Economic Evaluations in Genetic Screening and Testing for Monogenic Disorders
Authors: Johnson Karl , Saylor Kate , Guynn Isabella , Hicklin Karen , Berg Jonathan S. , Lich Kristen Hassmiller 
Published: October 2021

ABSTRACTPurposeUnderstanding the value of genetic screening and testing for monogenic disorders requires high-quality, methodologically robust economic evaluations. This systematic review sought to assess the methodological quality among such studies and examine opportunities for improvement.MethodsWe searched Pubmed, Cochrane, Embase, and Web of Science for economic evaluations of genetic screening/testing (2013-2019). Methodological rigor and adherence to best practices were systematically assessed using the BMJ checklist.ResultsAcross 47 identified studies, there was substantial variation in modeling approaches, reporting detail, and sophistication. Models ranged from simple decision trees to individual-level microsimulation, comparing between two and >20 alternative interventions. Many studies failed to report sufficient detail to enable replication or did not justify modeling assumptions, especially for costing methods and utility values. Meta-analyses, systematic reviews, or calibration were rarely used to derive parameter estimates. Nearly all studies conducted some sensitivity analysis, and more sophisticated studies implemented probabilistic sensitivity/uncertainty analysis, threshold analysis, and value of information analysis.ConclusionWe describe a heterogeneous body of work and present recommendations and exemplar studies across the methodological domains of (1) perspective, scope, and parameter selection, (2) use of uncertainty/sensitivity analyses, and (3) reporting transparency for improvement in the economic evaluation of genetic screening/testing.