bluuebunny/crossref_metadata_2025 huggingface dataset:
A testbed for geomagnetic data assimilation
Authors: Gwirtz K , Morzfeld M , Kuang W , Tangborn A
Published: August 2021

Geomagnetic data assimilation merges past and present-day observations of the Earth’s magnetic field with numerical geodynamo models and the results are used to initialize forecasts. We present a new ‘proxy model’ that can be used to test, or rapidly prototype, numerical techniques for geomagnetic data assimilation. The basic idea for constructing a proxy is to capture the conceptual difficulties one encounters when assimilating observations into high-resolution, 3-D geodynamo simulations, but at a much lower computational cost. The framework of using proxy models as ‘gate-keepers’ for numerical methods that could/should be considered for more extensive testing on operational models has proven useful in numerical weather prediction, where advances in data assimilation and, hence, improved forecast skill, are at least in part enabled by the common use of a wide range of proxy models. We also present a large set of systematic data assimilation experiments with the proxy to reveal the importance of localization and inflation in geomagnetic data assimilation.
Poor feeding opportunities and reduced condition factor for salmon post-smolts in the Northeast Atlantic Ocean
Authors: Utne Kjell Rong , Pauli Beatriz Diaz , Haugland Monika , Jacobsen Jan Arge , Maoileidigh Niall , Melle Webjørn , Broms Cecilie Thorsen , Nøttestad Leif , Holm Marianne , Thomas Katie , Wennevik Vidar
Published: August 2021

During the last few decades, many wild Atlantic salmon populations have declined dramatically. One possible contributing factor for the decline is reduced prey availability at sea. Here, we examine post-smolt diet and investigate if post-smolts show signs of selective feeding based on 2546 post-smolts sampled from west of Ireland to the northern Norwegian Sea over a 25-year period. We also test for changes over time in stomach fullness, diet, condition factor and body length. There was a clear reduction in condition factor for post-smolts sampled in the Norwegian Sea in the period 2003–2012. The post-smolt stomach fullness was also reduced in the same period. The reduction in condition factor is partly explained by reduced stomach fullness, including a reduction of highly energetic fish larvae and Amphipoda in the diet. Feeding on other prey, such as meso-zooplankton and insects, cannot substitute the high-quality fish larvae and Amphipoda in the post-smolt diet. This is the first study to document how salmon post-smolts feeding in the Norwegian Sea are affected by reduced feeding conditions. Possible causes for the observed changes in post-smolt feeding are ocean warming, decreased primary productivity, and reduced recruitment of important fish larvae.
Crohn’s and Colitis Canada’s 2021 Impact of COVID-19 and Inflammatory Bowel Disease in Canada: Epidemiology—The Trends of Disease Over Time
Authors: Coward Stephanie , Windsor Joseph W , Kuenzig M Ellen , Bitton Alain , Bernstein Charles N , Jones Jennifer L , Khanna Reena , Lee Kate , Murthy Sanjay K , Targownik Laura , Benchimol Eric , Huang James Guoxian , Mukhtar Mariam S , Tandon Parul , Kaplan Gilaad G
Published: August 2021

At the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there were many unknowns: transmission vectors of the virus, appropriate intervention strategies and if being immunocompromised due to inflammatory bowel disease (IBD), for example, or medications put a person at increased risk for severe COVID-19. Imposing and relaxing of public health restrictions at different times and in different regions in Canada led to different epidemiologies of the virus in different provinces and territories. In order to understand the waxing and waning of waves of the COVID-19 pandemic, it is necessary to understand the effective reproductive number (Rt) and the countervailing forces that exert upward or downward pressure on the spread of the virus at a given point in time. As many regions in Canada deal with a third wave, the primary forces affecting the Rt of severe acute respiratory syndrome coronavirus 2 are variants of concern and the increasing vaccinations of Canadians leading to increased population-level immunity. Fortunately, for the IBD population, current research suggests that those with IBD are not at increased risk of contracting COVID-19, nor of having a more severe disease course when compared to the general population.
Factors affecting antler growth period and casting date in red deer
Authors: Gómez José Ángel , Pérez-Barbería Javier , García Andrés José , Cappelli Jamil , Chonco Louis , Ceacero Francisco , Pérez-Serrano Martina , Landete-Castillejos Tomás
Published: August 2021

Antlers are unique structures because they grow rapidly and are cast annually, representing an important energetic and mineral cost for deer. Variables related to the timing of antler growth, such as date of antler casting and length of growth period, therefore, should be affected by somatic resources and availability of food. We examined the effects of body and antler weight, age, and climatic variables, on antler casting date and the period of time antlers were grown as well as possible random effects of individual, year, cohort, and pedigree, based on 244 antlers in a population of 109 males of Iberian red deer (Cervus elaphus) over a 17-year study from 1999 to 2016. Body weight affected casting date, with heavier males casting antlers earlier than lighter males. Antlers also grew faster and were cast earlier among older males than young males. Antler weight influenced casting date and the duration of the growth period: males with heavier antlers cast them earlier and grow them faster than males with light antlers. Nevertheless, age and antler weight interacted; as such, older males grew their antlers slower and delay casting date because they produce heavier antlers, in contrast to younger males, where those with the heaviest antlers grow them faster and cast first. The date of the end of antler growth also influenced casting date, so that antlers that took the longest to develop were cast later than those that finished growing early. We conclude that older and heavier males cast their antlers earlier and grow them faster than younger and lighter males, likely to correlate the subsequent antler growth with the spring peak in plant nutrients, but that this early development is limited physiologically by the size of the antlers.
Invasive wild boar’s distribution overlap with threatened native ungulate in Patagonia
Authors: Bercê William , Bello Carolina , Mendes Calebe P , Vancine Maurício H , Galetti Mauro , Ballari Sebastián A
Published: August 2021

Wild boar (Sus scrofa) is one of the most damaging invasive species in the world and can have a profound impact on the distribution of native species. Nevertheless, there still are limitations on the species’ current fine-scale spatial information, which is needed to develop effective management measures. Here, we used Species Distribution Models (SDMs) and niche overlap analysis to estimate potential conflict areas between the wild boar and the native southern pudu (Pudu puda), which is a bioindicator of the forest conservation status within the Nahuel Huapi National Park (NHNP), Argentina. The two species’ environmental niche overlaps by 40%, which results in a wide geographical overlap between wild boar and pudu distributions. The distribution model predicted that the wild boar potential distribution occupies 22% of the national park and overlaps up to 67% with the pudu distribution, which in turn occupies 20% of the park. Based on our models, we classified 12% of the park as extreme management priority areas, because both species are present. High priority areas, where wild boars have the potential to invade but will not overlap with pudu populations, represent 10% of the park. Medium priority areas, where wild boars do not threaten pudu populations, and low priority areas, with no potential presence of either species, are 8% and 68%, respectively. The results of this study show how SDMs developed at local scales can support the management and monitoring of native and invasive species and help guide the allocation of efforts and resources for management actions focused on protected areas.
Rapid, midline retroperitoneal exposure for four-level anterior lumbar interbody fusion—technical case atlas
Authors: Malik Rema J , Falahee Mark H , Kahn Elyne N , Heidenreich Michael J , Springstead David , Aziz Abdulhameed
Published: August 2021

We describe a novel, rapid midline retroperitoneal operative technique in a patient, with multi-level degenerative scoliosis, who underwent an extensive L2-S1 anterior lumbar interbody fusion in addition to posterior instrumentation. Uniquely, our approach enables an essentially midline approach to the rectus muscle and uses the diminution of the transversalis fascia-to-peritoneum transition in the pelvis to provide expedited exposure—making it particularly helpful for ALIF exposure, retraction and intraoperative radiography. We minimize morbidity around the rectus sheath by dissecting only the medial rectus muscle and then gently, bluntly mobilizing the retroperitoneum from the deep pelvis cranially.
Reconstruction for rupture of profunda femoris artery aneurysm in a patient with sarcopenia
Authors: Tanaka Chiharu , Furuya Hidekazu , Yamaguchi Masaomi , Kanabuchi Kazuo , Kuwaki Kenji
Published: August 2021

Profunda femoris artery aneurysm (PFAA) is rare and has a high incidence of rupture. Herein, we report the case of an 80-year-old man who developed sarcopenia after gastric surgery. The patient presented to our hospital with a reddish thigh and was diagnosed with PFAA rupture. We performed aneurysmectomy and graft interposition in emergency. Postoperative enhanced computed tomography revealed an interposed graft, and the patient was discharged on postoperative Day 7. We considered that the PFAA patients with sarcopenia has a high risk of rupture because the muscles surrounding the profunda femoris artery became weak, and should be followed-up closely.
The circularization time-scales of late–type binary stars
Authors: Terquem Caroline , Martin Scott
Published: August 2021

We examine the consequences of, and apply, the formalism developed in Terquem (2021) for calculating the rate DR at which energy is exchanged between fast tides and convection. In this previous work, DR (which is proportional to the gradient of the convective velocity) was assumed to be positive in order to dissipate the tidal energy. Here we argue that, even if energy is intermittently transferred from convection to the tides, it must ultimately return to the convective flow and transported efficiently to the stellar surface on the convective time-scale. This is consistent with, but much less restrictive than, enforcing DR > 0. Our principle result is a calculation of the circularization time-scale of late–type binaries, taking into account the full time evolution of the stellar structure. We find that circularization is very efficient during the PMS phase, inefficient during the MS, and once again efficient when the star approaches the RGB. These results are in much better agreement with observations than earlier theories. We also apply our formalism to hot Jupiters, and find that tidal dissipation in a Jupiter mass planet yields a circularization time-scale of 1 Gyr for an orbital period of 3 d, also in good overall agreement with observations. The approach here is novel, and the apparent success of the theory in resolving longstanding time-scale puzzles is compelling.
Improving the reliability of photometric redshift with machine learning
Authors: Razim Oleksandra , Cavuoti Stefano , Brescia Massimo , Riccio Giuseppe , Salvato Mara , Longo Giuseppe
Published: August 2021

In order to answer the open questions of modern cosmology and galaxy evolution theory, robust algorithms for calculating photometric redshifts (photo-z) for very large samples of galaxies are needed. Correct estimation of the various photo-z algorithms’ performance requires attention to both the performance metrics and the data used for the estimation. In this work, we use the supervised machine learning algorithm MLPQNA (Multi-Layer Perceptron with Quasi-Newton Algorithm) to calculate photometric redshifts for the galaxies in the COSMOS2015 catalogue and the unsupervised Self-Organizing Maps (SOM) to determine the reliability of the resulting estimates. We find that for zspec < 1.2, MLPQNA photo-z predictions are on the same level of quality as spectral energy distribution fitting photo-z. We show that the SOM successfully detects unreliable zspec that cause biases in the estimation of the photo-z algorithms’ performance. Additionally, we use SOM to select the objects with reliable photo-z predictions. Our cleaning procedures allow us to extract the subset of objects for which the quality of the final photo-z catalogues is improved by a factor of 2, compared to the overall statistics.
COTAN: scRNA-seq data analysis based on gene co-expression
Authors: Galfrè Silvia Giulia , Morandin Francesco , Pietrosanto Marco , Cremisi Federico , Helmer-Citterich Manuela
Published: August 2021

Estimating the co-expression of cell identity factors in single-cell is crucial. Due to the low efficiency of scRNA-seq methodologies, sensitive computational approaches are critical to accurately infer transcription profiles in a cell population. We introduce COTAN, a statistical and computational method, to analyze the co-expression of gene pairs at single cell level, providing the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts’ distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can assess the correlated or anti-correlated expression of gene pairs, providing a new correlation index with an approximate p-value for the associated test of independence. COTAN can evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Similarly to correlation network analysis, it provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions, becoming a new tool to identify cell-identity markers. We assayed COTAN on two neural development datasets with very promising results. COTAN is an R package that complements the traditional single cell RNA-seq analysis and it is available at https://github.com/seriph78/COTAN.
Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows
Authors: Lemoine Frédéric , Gascuel Olivier
Published: August 2021

Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables easily installable, integrable in workflow environments, and parallelizable when possible. Moreover, Go is a compiled language, which accelerates computations compared to interpreted languages. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386) on GitHub at https://github.com/evolbioinfo/gotree, Bioconda and DockerHub.
Multimodal platform for assessing drug distribution and response in clinical trials
Authors: Lopez Begoña G C , Kohale Ishwar N , Du Ziming , Korsunsky Ilya , Abdelmoula Walid M , Dai Yang , Stopka Sylwia A , Gaglia Giorgio , Randall Elizabeth C , Regan Michael S , Basu Sankha S , Clark Amanda R , Marin Bianca-Maria , Mladek Ann C , Burgenske Danielle M , Agar Jeffrey N , Supko Jeffrey G , Grossman Stuart A , Nabors Louis B , Raychaudhuri Soumya , Ligon Keith L , Wen Patrick Y , Alexander Brian , Lee Eudocia Q , Santagata Sandro , Sarkaria Jann , White Forest M , Agar Nathalie Y R
Published: August 2021

Background

Response to targeted therapy varies between patients for largely unknown reasons. Here, we developed and applied an integrative platform using mass spectrometry imaging (MSI), phosphoproteomics, and multiplexed tissue imaging for mapping drug distribution, target engagement, and adaptive response to gain insights into heterogeneous response to therapy.

Methods

Patient-derived xenograft (PDX) lines of glioblastoma were treated with adavosertib, a Wee1 inhibitor, and tissue drug distribution was measured with MALDI-MSI. Phosphoproteomics was measured in the same tumors to identify biomarkers of drug target engagement and cellular adaptive response. Multiplexed tissue imaging was performed on sister sections to evaluate spatial co-localization of drug and cellular response. The integrated platform was then applied on clinical specimens from glioblastoma patients enrolled in the phase 1 clinical trial.

Results

PDX tumors exposed to different doses of adavosertib revealed intra- and inter-tumoral heterogeneity of drug distribution and integration of the heterogeneous drug distribution with phosphoproteomics and multiplexed tissue imaging revealed new markers of molecular response to adavosertib. Analysis of paired clinical specimens from patients enrolled in the phase 1 clinical trial informed the translational potential of the identified biomarkers in studying patient’s response to adavosertib.

Conclusions

The multimodal platform identified a signature of drug efficacy and patient-specific adaptive responses applicable to preclinical and clinical drug development. The information generated by the approach may inform mechanisms of success and failure in future early phase clinical trials, providing information for optimizing clinical trial design and guiding future application into clinical practice.
Corticosteroids Do Not Increase the Likelihood of Primary Clostridioides difficile Infection in the Setting of Broad-Spectrum Antibiotic Use
Authors: Carlson Travis J , Gonzales-Luna Anne J , Wilcox Melissa F , Theriault Sarah G , Alnezary Faris S , Patel Pankaj , Ahn Bumhee K , Zasowski Evan J , Garey Kevin W
Published: August 2021

Background

The pathogenesis of Clostridioides difficile infection (CDI) involves a significant host immune response. Generally, corticosteroids act by suppressing the host inflammatory response, and their anti-inflammatory effects are used to treat gastrointestinal disorders. Although previous investigations have demonstrated mixed results regarding the effect of corticosteroids on CDI, we hypothesized that the anti-inflammatory effect of corticosteroids would decrease the risk of CDI in hospitalized patients.

Methods

This was a case–control study of hospitalized adults. The case population included patients diagnosed with primary CDI who received at least 1 dose of a high-risk antibiotic (cefepime, meropenem, or piperacillin-tazobactam) in the 90 days before CDI diagnosis. The control population included patients who received at least 1 dose of the same high-risk antibiotic but did not develop CDI in the 90 days following their first dose of antibiotic. The primary study outcome was the development of CDI based on receipt of corticosteroids.

Results

The final study cohort consisted of 104 cases and 153 controls. Those who received corticosteroids had a lower odds of CDI after adjusting for age, proton pump inhibitor use, and antibiotic days of therapy (odds ratio, 0.54; 95% CI, 0.30–0.97; P = .04). We did not observe an association between corticosteroid dose or duration and CDI.

Conclusions

We demonstrated a 46% relative reduction in the odds of developing CDI in patients who received corticosteroids in the past 90 days. We believe that our results provide the best clinical evidence to further support mechanistic studies underlying this phenomenon.
Vertex operator superalgebra/sigma model correspondences: The four-torus case
Authors: Anagiannis Vassilis , Cheng Miranda C N , Duncan John , Volpato Roberto
Published: August 2021

We propose a correspondence between vertex operator superalgebras and families of sigma models in which the two structures are related by symmetry properties and a certain reflection procedure. The existence of such a correspondence is motivated by previous work on ${\cal N}=(4,4)$ supersymmetric non-linear sigma models on K3 surfaces, and on a vertex operator superalgebra with Conway group symmetry. Here we present an example of the correspondence for ${\cal N}=(4,4)$ supersymmetric non-linear sigma models on four-tori, and compare it to the K3 case.
Trusts and beneficiary ownership concept in Russian law and practice
Authors: Kanachevsky Vladimir
Published: August 2021

This article outlines the regulatory landscape of the use of trusts by Russian residents and the implementation of the concept of beneficial ownership by the Russian legal system. The researcher describes an attempt to introduce trusts into the Russian legal system. The article also deals with trusts created by Russian residents abroad. In addition, the approaches of the Russian courts to the beneficial ownership concept, in the context of trusts and offshore companies are also discussed. The author analyses a number of cases which shed light on the issue of recognition of beneficiary owners’ rights in Russia.
The development of an intervention to support uptake and adherence to antiretroviral therapy in people living with HIV: the SUPA intervention. A brief report
Authors: King Kathryn , Horne Rob , Cooper Vanessa , Glendinning Elizabeth , Michie Susan , Chalder Trudie ,   SUPA Group, Jane Anderson , Campbell Lucy J , Chalder Trudie , Collins Simon , Cooper Vanessa , Glendinning Elizabeth , Fisher Martin , Harfield Scott , Horne Rob , King Kathryn , Leake-Date Heather , McCrone Paul , Michie Susan , Nelson Mark , Perry Nicky , Sabin Caroline , Smith Jonathan A , Sseruma Winnie , Walker Sarah
Published: August 2021

The effectiveness of antiretroviral therapy (ART) depends on prompt uptake of treatment and a high level of adherence over the long-term, yet these behaviors are suboptimal. Previous interventions have significantly improved adherence but effect sizes are generally small. The aim of this article is to describe the design and content of an intervention to support uptake and adherence to treatment in HIV positive patients (SUPA intervention), utilizing cognitive behavioral and motivational interviewing (MI) techniques. The intervention was developed in line with Medical Research Council (MRC) guidance for the development of complex interventions and informed by the NICE (National Institute for Health and Care Excellence) Guidelines for adherence, empirical evidence and focus groups. Behavior change techniques were mapped to perceptual and practical barriers to uptake and adherence to ART, identified in previous research. Intervention materials were designed and later discussed within focus groups, where feedback enabled an iterative process of development.

We conclude it is possible to transparently report the design and content of a theory-based intervention to increase uptake and adherence to ART. The intervention has been evaluated within a randomized controlled trial (RCT) at 10 HIV clinics in England, the results of which will be reported elsewhere.
Integrated transcriptome and proteome analysis of developing embryo reveals the mechanisms underlying the high levels of oil accumulation in Carya cathayensis Sarg.
Authors: Huang Chunying , Li Yan , Wang Ketao , Xi Jianwei , Xu Yifan , Hong Junyan , Si Xiaolin , Ye Hongyu , Lyu Shiheng , Xia Guohua , Wang Jianhua , Li Peipei , Xing Yulin , Wang Yige , Huang Jianqin
Published: August 2021

Hickory (Carya cathayensis Sarg.) is an extraordinary nut-bearing deciduous arbor with high content of oil in its embryo. However, the molecular mechanism underlying high oil accumulation is mostly unknown. Here, we reported that the lipid droplets and oil accumulation gradually increased with the embryo development and the oil content was up to ~76% at maturity. Furthermore, transcriptome and proteome analysis of developing hickory embryo identified 32,907 genes and 9857 proteins. Time-series analysis of gene expressions showed that these genes were divided into 12 clusters and lipid metabolism-related genes were enriched in Cluster 3, with the highest expression levels at 95 days after pollination (S2). Differentially expressed genes and proteins indicated high correlation, and both were enriched in the lipid metabolism. Notably, the genes involved in biosynthesis, transport of fatty acid/lipid and lipid droplets formation had high expression levels at S2, while the expression levels of other genes required for suberin/wax/cutin biosynthesis and lipid degradation were very low at all the sampling time points, ultimately promoting the accumulation of oil. Quantitative reverse-transcription PCR analysis also verified the results of RNA-seq. The co-regulatory networks of lipid metabolism were further constructed and WRINKLED1 (WRI1) was a core transcriptional factor located in the nucleus. Of note, CcWRI1A/B could directly activate the expression of some genes (CcBCCP2A, CcBCCP2B, CcFATA and CcFAD3) required for fatty acid synthesis. These results provided in-depth evidence for revealing the molecular mechanism of high oil accumulation in hickory embryo.
Research on pumped two-phase single-sided cold plate of IGBT for rail transit applications
Authors: Wu Hui , Zhang Gang , Feng Zhaozan , He Kai , Yao Lei , Li Wei , Yao Shichune
Published: August 2021

The use of pumped two-phase cooling to improve the thermal management of insulated gate bipolar transistor (IGBT) in rail transportation is a novel cooling technology. An experimental investigation on pumped two-phase cold plate of IGBT used in HXD1C locomotives was conducted at a mass flow rate of 0.1 kg/s–0.29 kg/s and a heat flux of 6.2 W/cm2, with R245fa as the working fluid. The experimental results showed that the base temperature nonuniformity can be controlled within 2.2 °C at flow rates of 0.14 kg/s and 0.19 kg/s, which is of great benefit to the reliability of IGBT. Based on well known correlations for saturated flow boiling in tubes, an analytical model was developed and compared with the experimental data. The model could predict the base temperature data within an error band of ±3 °C, as well as capture the trend of base temperature as a function of vapour quality and mass flow rate. The performance of the pumped two-phase cold plate of IGBT could be further improved with the aid of the developed model.
Anthropogenic evolution in an insect wing polymorphism following widespread deforestation
Authors: Foster Brodie J. , McCulloch Graham A. , Vogel Marianne F. S. , Ingram Travis , Waters Jonathan M.
Published: August 2021

Anthropogenic environmental change can underpin major shifts in natural selective regimes, and can thus alter the evolutionary trajectories of wild populations. However, little is known about the evolutionary impacts of deforestation—one of the most pervasive human-driven changes to terrestrial ecosystems globally. Absence of forest cover (i.e. exposure) has been suggested to play a role in selecting for insect flightlessness in montane ecosystems. Here, we capitalize on human-driven variation in alpine treeline elevation in New Zealand to test whether anthropogenic deforestation has caused shifts in the distributions of flight-capable and flightless phenotypes in a wing-polymorphic lineage of stoneflies from theZelandoperla fenestrataspecies complex. Transect sampling revealed sharp transitions from flight-capable to flightless populations with increasing elevation. However, these phenotypic transitions were consistently delineated by the elevation of local treelines, rather than by absolute elevation, providing a novel example of human-driven evolution in response to recent deforestation. The inferred rapid shifts to flightlessness in newly deforested regions have implications for the evolution and conservation of invertebrate biodiversity.
Intra-specific differences in cognition: bumblebee queens learn better than workers
Authors: Muth Felicity
Published: August 2021

Species’ cognitive traits are shaped by their ecology, and even within a species, cognition can reflect the behavioural requirements of individuals with different roles. Social insects have a number of discrete roles (castes) within a colony and thus offer a useful system to determine how ecological requirements shape cognition. Bumblebee queens are a critical point in the lifecycle of their colony, since its future success is reliant on a single individual's ability to learn about floral stimuli while finding a suitable nest site; thus, one might expect particularly adept learning capabilities at this stage. I compared wild
Bombus vosnesenskii
queens and workers on their ability to learn a colour association and found that queens performed better than workers. In addition, queens of another species,
B. insularis,
a cuckoo species with a different lifecycle but similar requirements at this stage, performed equally well as the non-parasitic queens. To control for differences in foraging experience, I then repeated this comparison with laboratory-based
B. impatiens
and found that unmated queens performed better than workers. These results add to the body of work on how ecology shapes cognition and opens the door to further research in comparative cognition using wild bees.
Resource exchange and partner recognition mediate mutualistic interactions between prey and their would-be predators
Authors: Camacho Luis F. , Avilés Leticia
Published: August 2021

Animals may develop mutualistic associations with other species, whereby prey offer resources or services in exchange for protection from predators. Alternatively, prey may offer resources or services directly to their would-be predators in exchange for their lives. The latter may be the case of hemipterans that engage in mutualistic interactions with ants by offering a honeydew reward. We test the extent to which a honeydew offering versus partner recognition may play a role as proximate mechanisms deterring ants from predating upon their hemipteran partners. We showed that, when presented with a choice between a hemipteran partner and an alternative prey type, mutualist ants were less likely to attack and more likely to remain probing their hemipteran partners. This occurred even in the absence of an immediate sugary reward, suggesting either an evolved or learned partner recognition response. To a similar extent, however, ants were also less likely to attack the alternative prey type when laced with honey as a proxy for a honeydew reward. This was the case even after the honey had been depleted, suggesting an ability of ants to recognize new potential sources of sugars. Either possibility suggests a degree of innate or learned partner recognition.
Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
Authors: Harvey Virginia L. , Keating Joseph N. , Buckley Michael
Published: August 2021

Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the ‘gold standard’ for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250–283 Ma and ∼120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with theα3 (I) sequence evolving the fastest, followed by theα2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.
Wallpaper group kirigami
Authors: Liu Lucy , Choi Gary P. T. , Mahadevan L.
Published: August 2021

Kirigami, the art of paper cutting, has become a paradigm for mechanical metamaterials in recent years. The basic building blocks of any kirigami structures are repetitive deployable patterns that derive inspiration from geometric art forms and simple planar tilings. Here, we complement these approaches by directly linking kirigami patterns to the symmetry associated with the set of 17 repeating patterns that fully characterize the space of periodic tilings of the plane. We start by showing how to construct deployable kirigami patterns using any of the wallpaper groups, and then design symmetry-preserving cut patterns to achieve arbitrary size changes via deployment. We further prove that different symmetry changes can be achieved by controlling the shape and connectivity of the tiles and connect these results to the underlying kirigami-based lattice structures. All together, our work provides a systematic approach for creating a broad range of kirigami-based deployable structures with any prescribed size and symmetry properties.
Epidemics on hypergraphs: spectral thresholds for extinction
Authors: Higham Desmond J. , de Kergorlay Henry-Louis
Published: August 2021

Epidemic spreading is well understood when a disease propagates around a contact graph. In a stochastic susceptible–infected–susceptible setting, spectral conditions characterize whether the disease vanishes. However, modelling human interactions using a graph is a simplification which only considers pairwise relationships. This does not fully represent the more realistic case where people meet in groups. Hyperedges can be used to record higher order interactions, yielding more faithful and flexible models and allowing for the rate of infection of a node to depend on group size and also to vary as a nonlinear function of the number of infectious neighbours. We discuss different types of contagion models in this hypergraph setting and derive spectral conditions that characterize whether the disease vanishes. We study both the exact individual-level stochastic model and a deterministic mean field ODE approximation. Numerical simulations are provided to illustrate the analysis. We also interpret our results and show how the hypergraph model allows us to distinguish between contributions to infectiousness that (i) are inherent in the nature of the pathogen and (ii) arise from behavioural choices (such as social distancing, increased hygiene and use of masks). This raises the possibility of more accurately quantifying the effect of interventions that are designed to contain the spread of a virus.
Uniform asymptotic expansions for the Whittaker functions
M

κ
,
μ

(
z
) and
W

κ
,
μ

(
z
) with
μ
large
Authors: Dunster T. M.
Published: August 2021

Uniform asymptotic expansions are derived for Whittaker’s confluent hypergeometric functions

M

κ
,
μ

(
z
)

and

W

κ
,
μ

(
z
)

, as well as the numerically satisfactory companion function

W

−
κ
,
μ

(
z
 

e

−
π

i

)

. The expansions are uniformly valid for

μ
→
∞

,

0
≤
κ

/

μ
≤
1
−
δ
<
1

and

0
≤
arg
⁡
(
z
)
≤
π

. By using appropriate connection and analytic continuation formulae, these expansions can be extended to all unbounded non-zero complex

z

. The approximations come from recent asymptotic expansions involving elementary functions and Airy functions, and explicit error bounds are either provided or available.
Ruminococcus bovis sp. nov., a novel species of amylolytic Ruminococcus isolated from the rumen of a dairy cow
Authors: Gaffney James , Embree Jordan , Gilmore Sean , Embree Mallory
Published: August 2021

This study describes JE7A12T (=ATCC TSD-225T=NCTC 14479T), an isolate from the ruminal content of a dairy cow. Phenotypic and genotypic traits of the isolate were explored. JE7A12T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that grows in chains. The API 50 CH carbon source assay detected fermentation of d-glucose, d-fructose, d-galactose, glycogen and starch. HPLC showed acetate to be the major fermentation product as a result of carbohydrate fermentation. Phylogenetic analysis of JE7A12T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome indicated a divergent lineage from the closest neighbours in the genus

Ruminococcus

. The results of 16S rRNA sequence comparison, whole genome average nucleotide identity (ANI) and DNA G+C content data indicate that JE7A12T represents a novel species which we propose the name Ruminococcus bovis with JE7A12T as the type strain.
Taxonomic status of the species Clostridium methoxybenzovorans Mechichi et al. 1999
Authors: Kobayashi Hisami , Tanizawa Yasuhiro , Sakamoto Mitsuo , Ohkuma Moriya , Tohno Masanori
Published: August 2021

The taxonomic status of the species

Clostridium methoxybenzovorans

was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection (

C. methoxybenzovorans

ATCC 700855T) is a member of the species

Eubacterium callanderi

. Hence,

C. methoxybenzovorans

ATCC 700855T cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182T) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3T showed high sequence identity with those of

Lacrimispora indolis

(recently reclassified from

Clostridium indolis

) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on blast and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results,

C. methoxybenzovorans

SR3T was considered to be a member of

L. indolis

.
SARS-CoV-2 Seroprevalence and Drug Use in Trauma Patients from Six Sites in the United States
Authors: Ngo Tran B. , Karkanitsa Maria , Adusei Kenneth M. , Graham Lindsey A. , Ricotta Emily E. , Darrah Jenna R. , Blomberg Richard D. , Spathies Jacquelyn , Pauly Kyle J. , Klumpp-Thomas Carleen , Travers Jameson , Mehalko Jennifer , Drew Matthew , Hall Matthew D , Memoli Matthew J , Esposito Dominic , Kozar Rosemary A. , Griggs Christopher , Cunningham Kyle W. , Schulman Carl I. , Crandall Marie , Neavyn Mark , Dorfman Jon D. , Lai Jeffrey T. , Whitehill Jennifer M. , Babu Kavita M. , Mohr Nicholas M. , Van Heukelom Jon , Fell James C. , Rooke Whit , Kalish Heather , Thomas F. Dennis , Sadtler Kaitlyn
Published: August 2021

In comparison to the general patient population, trauma patients show higher level detections of bloodborne infectious diseases, such as Hepatitis and Human Immunodeficiency Virus. In comparison to bloodborne pathogens, the prevalence of respiratory infections such as SARS-CoV-2 and how that relates with other variables, such as drug usage and trauma type, is currently unknown in trauma populations. Here, we evaluated SARS-CoV-2 seropositivity and antibody isotype profile in 2,542 trauma patients from six Level-1 trauma centers between April and October of 2020 during the first wave of the COVID-19 pandemic. We found that the seroprevalence in trauma victims 18-44 years old (9.79%, 95% confidence interval/CI: 8.33 11.47) was much higher in comparison to older patients (45-69 years old: 6.03%, 4.59-5.88; 70+ years old: 4.33%, 2.54 – 7.20). Black/African American (9.54%, 7.77 – 11.65) and Hispanic/Latino patients (14.95%, 11.80 – 18.75) also had higher seroprevalence in comparison, respectively, to White (5.72%, 4.62 7.05) and Non-Latino patients (6.55%, 5.57 – 7.69). More than half (55.54%) of those tested for drug toxicology had at least one drug present in their system. Those that tested positive for narcotics or sedatives had a significant negative correlation with seropositivity, while those on anti-depressants trended positive. These findings represent an important consideration for both the patients and first responders that treat trauma patients facing potential risk of respiratory infectious diseases like SARS-CoV-2.
Building Prediction Models for 30-Day Readmissions Among ICU Patients Using Both Structured and Unstructured Data in Electronic Health Records
Authors: Moerschbacher Alex , He Zhe
Published: August 2021

ICU readmissions are associated with poor outcomes for patients and poor performance of hospitals. Patients who are readmitted have an increased risk of in-hospital deaths; hospitals with a higher readmission rate have a reduced profitability, due to an increase in cost and reduced payments from Medicare and Medicaid programs. Predicting a patient’s likelihood of being readmitted to the ICU can help reduce early discharges, the risk of in-hospital deaths, and help increase profitability. In this study, we built and evaluated multiple machine learning models to predict 30-day readmission rates of ICU patients in the MIMIC-III database. We used both the structured data including demographics, laboratory tests, comorbidities, and unstructured discharge summaries as the predictors and evaluated different combinations of features. The best performing model in this study Logistic Regression achieved an AUROC of 75.7%. This study shows the potential of leveraging machine learning and deep learning for predicting ICU readmissions.
Infectious SARS-CoV-2 is emitted in aerosols
Authors: Hawks Seth A. , Prussin Aaron J. , Kuchinsky Sarah C. , Pan Jin , Marr Linsey C. , Duggal Nisha K.
Published: August 2021

Respiratory viruses such as SARS-CoV-2 are transmitted in respiratory droplets and aerosols, which are released during talking, breathing, coughing, and sneezing. Non-contact transmission of SARS-CoV-2 has been demonstrated, suggesting transmission in aerosols. Here we demonstrate that golden Syrian hamsters emit infectious SARS-CoV-2 in aerosols, prior to and concurrent with the onset of mild clinical signs of disease. The average emission rate is 25 infectious virions/hour on days 1 and 2 post-inoculation, with average viral RNA levels 200-fold higher than infectious virus in aerosols. Female hamsters have delayed kinetics of viral shedding in aerosols compared to male hamsters, with peak viral emission for females on dpi 2 and for males on dpi 1. The majority of virus is contained within aerosols <8 µm in size. Thus, we provide direct evidence that, in hamsters, SARS-CoV-2 is an airborne virus.
Concentration and quantification of Tilapia tilapinevirus from water using a simple iron flocculation coupled with probe-based RT-qPCR
Authors: Taengphu Suwimon , Kayansamruaj Pattanapon , Kawato Yasuhiko , Delamare-Deboutteville Jerome , Mohan Chadag Vishnumurthy , Dong Ha Thanh , Senapin Saengchan
Published: August 2021

Tilapia tilapinevirus (also known as tilapia lake virus, TiLV) is an important virus responsible for die-off of farmed tilapia globally. Detection and quantification of the virus from environmental DNA/RNA (eDNA/eRNA) using pond water represents a potential, noninvasive routine approach for pathogen monitoring and early disease forecasting in aquaculture systems. Here, we report a simple iron flocculation method for viral concentration from water combined with a newly developed hydrolysis probe quantitative RT-qPCR method for detection and quantification of TiLV. The RT-qPCR method targeting a conserved region of TiLV genome segment 9 has a detection limit of 10 viral copies per µL of template. The method had a 100% analytical specificity and sensitivity for TiLV. The optimized iron flocculation method was able to recover 16.11 ± 3.3% of virus from water samples spiked with viral cultures. During disease outbreak cases from an open-caged system and a closed hatchery system, both tilapia and water samples were collected for detection and quantification of TiLV. The results revealed that TiLV was detected from both clinically sick fish and asymptomatic fish. Most importantly, the virus was successfully detected from water samples collected from different locations in the affected farms e.g. river water samples from affected cages (8.50 × 102 to 2.79 × 104 copies/L) and fish-rearing water samples, sewage, and reservoir (4.29 × 102 to 3.53 × 103 copies/L) from affected and unaffected ponds of the hatchery. In summary, this study suggests that the eRNA detection system using iron flocculation coupled with probe based-RT-qPCR is feasible for concentration and quantification of TiLV from water. This approach might be useful for noninvasive monitoring of TiLV in tilapia aquaculture systems and facilitating appropriate decisions on biosecurity interventions needed.