bluuebunny/crossref_metadata_2025 huggingface dataset:
On the relationship between serial interval, infectiousness profile and generation time
Authors: Lehtinen Sonja , Ashcroft Peter , Bonhoeffer Sebastian
Published: January 2021

The timing of transmission plays a key role in the dynamics and controllability of an epidemic. However, observing generation times—the time interval between the infection of an infector and an infectee in a transmission pair—requires data on infection times, which are generally unknown. The timing of symptom onset is more easily observed; generation times are therefore often estimated based on serial intervals—the time interval between symptom onset of an infector and an infectee. This estimation follows one of two approaches: (i) approximating the generation time distribution by the serial interval distribution or (ii) deriving the generation time distribution from the serial interval and incubation period—the time interval between infection and symptom onset in a single individual—distributions. These two approaches make different—and not always explicitly stated—assumptions about the relationship between infectiousness and symptoms, resulting in different generation time distributions with the same mean but unequal variances. Here, we clarify the assumptions that each approach makes and show that neither set of assumptions is plausible for most pathogens. However, the variances of the generation time distribution derived under each assumption can reasonably be considered as upper (approximation with serial interval) and lower (derivation from serial interval) bounds. Thus, we suggest a pragmatic solution is to use both approaches and treat these as edge cases in downstream analysis. We discuss the impact of the variance of the generation time distribution on the controllability of an epidemic through strategies based on contact tracing, and we show that underestimating this variance is likely to overestimate controllability.
Surface interactions and viability of coronaviruses
Authors: Aydogdu Mehmet Onur , Altun Esra , Chung Etelka , Ren Guogang , Homer-Vanniasinkam Shervanthi , Chen Biqiong , Edirisinghe Mohan
Published: January 2021

The recently emerged coronavirus pandemic (COVID-19) has become a worldwide threat affecting millions of people, causing respiratory system related problems that can end up with extremely serious consequences. As the infection rate rises significantly and this is followed by a dramatic increase in mortality, the whole world is struggling to accommodate change and is trying to adapt to new conditions. While a significant amount of effort is focused on developing a vaccine in order to make a game-changing anti-COVID-19 breakthrough, novel coronavirus (SARS-CoV-2) is also developing mutations rapidly as it transmits just like any other virus and there is always a substantial chance of the invented antibodies becoming ineffective as a function of time, thus failing to inhibit virus-to-cell binding efficiency as the spiked protein keeps evolving. Hence, controlling the transmission of the virus is crucial. Therefore, this review summarizes the viability of coronaviruses on inanimate surfaces under different conditions while addressing the current state of known chemical disinfectants for deactivation of the coronaviruses. The review attempts to bring together a wide spectrum of surface–virus–cleaning agent interactions to help identify material selection for inanimate surfaces that have frequent human contact and cleaning procedures for effective prevention of COVID-19 transmission.
First-order convergence of Milstein schemes for McKean–Vlasov equations and interacting particle systems
Authors: Bao Jianhai , Reisinger Christoph , Ren Panpan , Stockinger Wolfgang
Published: January 2021

In this paper, we derive fully implementable first-order time-stepping schemes for McKean–Vlasov stochastic differential equations, allowing for a drift term with super-linear growth in the state component. We propose Milstein schemes for a time-discretized interacting particle system associated with the McKean–Vlasov equation and prove strong convergence of order 1 and moment stability, taming the drift if only a one-sided Lipschitz condition holds. To derive our main results on strong convergence rates, we make use of calculus on the space of probability measures with finite second-order moments. In addition, numerical examples are presented which support our theoretical findings.
The mathematical foundations of anelasticity: existence of smooth global intermediate configurations
Authors: Goodbrake Christian , Goriely Alain , Yavari Arash
Published: January 2021

A central tool of nonlinear anelasticity is the multiplicative decomposition of the deformation tensor that assumes that the deformation gradient can be decomposed as a product of an elastic and an anelastic tensor. It is usually justified by the existence of an intermediate configuration. Yet, this configuration cannot exist in Euclidean space, in general, and the mathematical basis for this assumption is on unsatisfactory ground. Here, we derive a sufficient condition for the existence of global intermediate configurations, starting from a multiplicative decomposition of the deformation gradient. We show that these global configurations are unique up to isometry. We examine the result of isometrically embedding these configurations in higher-dimensional Euclidean space, and construct multiplicative decompositions of the deformation gradient reflecting these embeddings. As an example, for a family of radially symmetric deformations, we construct isometric embeddings of the resulting intermediate configurations, and compute the residual stress fields explicitly.
A new approach to integrable evolution equations on the circle
Authors: Fokas A. S. , Lenells J.
Published: January 2021

We propose a new approach for the solution of initial value problems for integrable evolution equations in the periodic setting based on the unified transform. Using the nonlinear Schrödinger equation as a model example, we show that the solution of the initial value problem on the circle can be expressed in terms of the solution of a Riemann–Hilbert problem whose formulation involves quantities which are defined in terms of the initial data alone. Our approach provides an effective solution of the problem on the circle which is conceptually analogous to the solution of the problem on the line via the inverse scattering transform.
A triple threat: high population density, high foraging intensity and flexible habitat preferences explain high impact of feral cats on prey
Authors: Hamer Rowena P. , Gardiner Riana Z. , Proft Kirstin M. , Johnson Christopher N. , Jones Menna E.
Published: January 2021

Alien mammalian carnivores have contributed disproportionately to global loss of biodiversity. In Australia, predation by the feral cat and red fox is one of the most significant causes of the decline of native vertebrates. To discover why cats have greater impacts on prey than native predators, we compared the ecology of the feral cat to a marsupial counterpart, the spotted-tailed quoll. Individual prey are 20–200 times more likely to encounter feral cats, because of the combined effects of cats' higher population densities, greater intensity of home-range use and broader habitat preferences. These characteristics also mean that the costs to the prey of adopting anti-predator behaviours against feral cats are likely to be much higher than adopting such behaviours in response to spotted-tailed quolls, due to the reliability and ubiquity of feral cat cues. These results help explain the devastating impacts of cats on wildlife in Australia and other parts of the world.
How do habitat amount and habitat fragmentation drive time-delayed responses of biodiversity to land-use change?
Authors: Semper-Pascual Asunción , Burton Cole , Baumann Matthias , Decarre Julieta , Gavier-Pizarro Gregorio , Gómez-Valencia Bibiana , Macchi Leandro , Mastrangelo Matías E. , Pötzschner Florian , Zelaya Patricia V. , Kuemmerle Tobias
Published: January 2021

Land-use change is a root cause of the extinction crisis, but links between habitat change and biodiversity loss are not fully understood. While there is evidence that habitat loss is an important extinction driver, the relevance of habitat fragmentation remains debated. Moreover, while time delays of biodiversity responses to habitat transformation are well-documented, time-delayed effects have been ignored in the habitat loss versus fragmentation debate. Here, using a hierarchical Bayesian multi-species occupancy framework, we systematically tested for time-delayed responses of bird and mammal communities to habitat loss and to habitat fragmentation. We focused on the Argentine Chaco, where deforestation has been widespread recently. We used an extensive field dataset on birds and mammals, along with a time series of annual woodland maps from 1985 to 2016 covering recent and historical habitat transformations. Contemporary habitat amount explained bird and mammal occupancy better than past habitat amount. However, occupancy was affected more by the past rather than recent fragmentation, indicating a time-delayed response to fragmentation. Considering past landscape patterns is therefore crucial for understanding current biodiversity patterns. Not accounting for land-use history ignores the possibility of extinction debt and can thus obscure impacts of fragmentation, potentially explaining contrasting findings of habitat loss versus fragmentation studies.
Machine Learning Forecast of Growth in COVID-19 Confirmed Infection Cases with Non-Pharmaceutical Interventions and Cultural Dimensions: Algorithm Development and Validation
Authors: Yeung Arnold YS , Roewer-Despres Francois , Rosella Laura , Rudzicz Frank
Published: January 2021

Background

National governments have implemented non-pharmaceutical interventions to control and mitigate against the COVID-19 pandemic. A deep understanding of these interventions is required.

Objective

We investigate the prediction of future daily national Confirmed Infection Growths – the percentage change in total cumulative cases across 14 days – using metrics representative of non-pharmaceutical interventions and cultural dimensions of each country.

Methods

We combine the OxCGRT dataset, Hofstede’s cultural dimensions, and COVID-19 daily reported infection case numbers to train and evaluate five non-time series machine learning models in predicting Confirmed Infection Growth. We use three validation methods – in-distribution, out-of-distribution, and country-based cross-validation – for evaluation, each applicable to a different use case of the models.

Results

Our results demonstrate high R2 values between the labels and predictions for the in-distribution, out-of-distribution, and country-based cross-validation methods (0.959, 0.513, and 0.574 respectively) using random forest and AdaBoost regression. While these models may be used to predict the Confirmed Infection Growth, the differing accuracies obtained from the three tasks suggest a strong influence of the use case.

Conclusions

This work provides new considerations in using machine learning techniques with non-pharmaceutical interventions and cultural dimensions data for predicting the national growth of confirmed infections of COVID-19.
Population dynamics of multi-host communities attacked by a common parasitoid
Authors: Singh Abhyudai
Published: January 2021

We model population dynamics of two host species attacked by a common parasitoid using a discrete-time formalism that captures their population densities from year to year. It is well known starting from the seminal work of Nicholson and Bailey that a constant parasitoid attack rate leads to an unstable host-parasitoid interaction. However, a Type III functional response, where the parasitoid attack rate accelerates with increasing host density stabilizes the population dynamics. We first consider a scenario where both host species are attacked by a parasitoid with the same Type III functional response. Our results show that sufficient fast acceleration of the parasitoid attack rate stabilizes the population dynamics of all three species. For two symmetric host species, the extent of acceleration needed to stabilize the three-species equilibrium is exactly the same as that needed for a single host-parasitoid interaction. However, asymmetry can lead to scenarios where the removal of a host species from a stable interaction destabilizes the interaction between the remaining host species and the parasitoid. Next, we consider a situation where one of the host species is attacked at a constant rate (i.e., Type I functional response), and the other species is attacked via a Type III functional response. We identify parameter regimes where a Type III functional response to just one of the host species stabilizes the three species interaction. In summary, our results show that a generalist parasitoid with a Type III functional response to one or many host species can play a key role in stabilizing population dynamics of host-parasitoid communities in apparent competition.
Pre-Settlement Forests of Southwest Washington: Witness Statements
Authors: Schroeder Tom
Published: January 2021

In the mid-nineteenth century overland immigration into western Washington State passed through lands bracketed by the lower Columbia River and the Pacific Ocean. Witness trees from the region’s first GLO surveys (General Land Office), which preceded settlement, are used to reconstruct the composition, character, and distribution of the region’s natural forests. As such, this investigation augments a similar study of early forests around Puget Sound, situated immediately to the north (Schroeder, 2019). A retrospective species map is constructed from locational information from more than thirty-five thousand witness trees; accompanying tree diameters elucidate size differences by species and geographic locales. Three principal forest types were noted: western hemlock in the rainy western hills, with some Sitka spruce near the coast; Douglas-fir with woodland tree species in the rain-shadowed central plains; and hemlock/Douglas-fir/redcedar mixtures on the lower flanks of the Cascade Range. Although the majority of trees were small or medium in size, a significant fraction was large. All forest types displayed significant amounts of old growth, as judged by screening witness trees against a quantitative model. Mensuration exercises estimate that the region’s pre-settlement tree population approached one-half billion specimens with a timber volume of nearly 50 billion cubic feet.
Predicting chemotherapy response using a variational autoencoder approach
Authors: Wei Qi , Ramsey Stephen A.
Published: January 2021

Motivation

Multiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemotherapy in cancer. While tumor transcriptome profiles are publicly available for thousands of tumors for many cancer types, a relatively modest number of tumor profiles are clinically annotated for response to chemotherapy. The paucity of labeled examples and high dimension of the feature data limit performance for predicting therapeutic response using fully-supervised classification methods. Recently, multiple studies have established the utility of a deep neural network approach, the variational autoencoder (VAE), for generating meaningful latent features from original data. Here, we report first study of a semi-supervised approach using VAE-encoded tumor transcriptome features and regularized gradient boosted decision trees (XGBoost) to predict chemotherapy drug response for five cancer types: colon adenocarcinoma, pancreatic adenocarcinoma, bladder carcinoma, sarcoma, and breast invasive carcinoma.

Results

We found: (1) VAE-encoding of the tumor transcriptome preserves the cancer type identity of the tumor, suggesting preservation of biologically relevant information; and (2) as a feature-set for supervised classification to predict response-to-chemotherapy, the unsupervised VAE encoding of the tumor’s gene expression profile leads to better area under the receiver operating characteristic curve (AUROC) classification performance than either the original gene expression profile or the PCA principal components of the gene expression profile, in four out of five cancer types that we tested.

Availability

github.com/ATHED/VAE_for_chemotherapy_drug_response_prediction

Contact

ramseyst@oregonstate.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Sexual dimorphism in mastoid process volumes measured from 3D models of dry crania from medieval Croatia
Authors: Petaros Anja , Sholts Sabrina B. , Čavka Mislav , Slaus Mario , Wärmländer Sebastian K.T.S.
Published: January 2021

3D analysis of skeletal volumes has become an important field in digital anthropology studies. The volume of the mastoid process has been proposed to display significant sexual dimorphism, but it has a complex shape and to date no study has quantified the full mastoid volume for sex estimation purposes. In this study we compared three different ways to isolate the volume of the mastoid process from digital 3D models of dry crania, and then evaluated the performance of the three different volume definitions for sex estimation purposes. A total of 170 crania (86 male, 84 females) excavated from five medieval Croatian sites were CT-scanned and used to produce 3D stereolitographic models. The three different isolation techniques were based on various anatomical landmarks and planes, as well as the anatomy of the mastoid process itself. Measurements of the three different mastoid volumes yielded different accuracies and precisions. Interestingly, anatomical structures were sometimes more useful than classical landmarks as demarcators of mastoid volume. For all three volume definitions, male mastoid volumes were significantly larger than female volumes, in both relative and absolute numbers. Sex estimation based on mastoid volume showed a slightly higher precision and better accuracy (71 % correct classifications) than visual scoring techniques (67 %) and linear distance measurements (69 %) of the mastoid process. Sex estimation based on cranial size performed even better (78 %), and multifactorial analysis (skull size + mastoid volume) reached up to 81% accuracy. These results show that measurements of the mastoid volume represent a promising metric to be used in multifactorial approaches for sex estimation of human remains.
Learning association for single-cell transcriptomics by integrating profiling of gene expression and alternative polyadenylation
Authors: Ji Guoli , Xuan Wujing , Zhuang Yibo , Ye Lishan , Zhu Sheng , Ye Wenbin , Wang Xi , Wu Xiaohui
Published: January 2021

Single-cell RNA-sequencing (scRNA-seq) has enabled transcriptome-wide profiling of gene expressions in individual cells. A myriad of computational methods have been proposed to learn cell-cell similarities and/or cluster cells, however, high variability and dropout rate inherent in scRNA-seq confounds reliable quantification of cell-cell associations based on the gene expression profile alone. Lately bioinformatics studies have emerged to capture key transcriptome information on alternative polyadenylation (APA) from standard scRNA-seq and revealed APA dynamics among cell types, suggesting the possibility of discerning cell identities with the APA profile. Complementary information at both layers of APA isoforms and genes creates great potential to develop cost-efficient approaches to dissect cell types based on multiple modalities derived from existing scRNA-seq data without changing experimental technologies. We proposed a toolkit called scLAPA forlearning association forsingle-cell transcriptomics by combing single-cell profiling of gene expression andalternativepolyadenylation derived from the same scRNA-seq data. We compared scLAPA with seven similarity metrics and five clustering methods using diverse scRNA-seq datasets. Comparative results showed that scLAPA is more effective and robust for learning cell-cell similarities and clustering cell types than competing methods. Moreover, with scLAPA we found two hidden subpopulations of peripheral blood mononuclear cells that were undetectable using the gene expression data alone. As a comprehensive toolkit, scLAPA provides a unique strategy to learn cell-cell associations, improve cell type clustering and discover novel cell types by augmentation of gene expression profiles with polyadenylation information, which can be incorporated in most existing scRNA-seq pipelines. scLAPA is available athttps://github.com/BMILAB/scLAPA.
Crystal structure of the classical MHC-I molecule: insights into the MHC-I system in antiviral diseases in dogs
Authors: Sun Yujiao , Ma Lizhen , Li Shen , Wang Yawen , Xiao Ruiqi , Yang Junqi , Xia Chun
Published: January 2021

Only one classical MHC-I locus (aka DLA-88) evolved in dogs, and thus far, a total of 76 DLA-88 alleles can be divided into two categories. The first category consists of 60 alleles, and the second category consists of 16 alleles. The main difference between the two categories is the insertion of an amino acid in the α2 region of DLA-88 alleles. To elucidate the structure of the first category, in this study, the crystal structure of pDLA-88*001:01 was determined for the first time. The 3D structure and topological characteristics of the ABG of pDLA-88*001:01 with a CDV peptide were analyzed. The viral presentation profile and the binding motif of viruses presented by pDLA-88*001:01 were determined. Most importantly, there were no amino acid insertions in the α2 region of the first category, which changed the conformation of the D pocket and the docking of the TCR. The results suggest obvious differences between the two categories. Because of the variation in the α2 region, pDLA-88*001:01 showed distinctive features in the two categories. Due to the peptide-binding motif of pDLA-88*001:01, more than 320 high-affinity viral peptides were predicted from dog H7N9, CPV, CMV, CMV, and CDV strains. The results reveal that there are two kinds of structural MHC-I systems in dogs that are responsible for CTL immunity against viral diseases. The results provide knowledge for designing viral epitope vaccines in canines.

Importance

DLA plays an important role in the acquired immunity of organism. In previous study, the pMHC-I structure of dog was analyzed with DLA-88 self-peptide. In this study, we screened several viral peptides which can bind to DLA-88 and resolved the structure of the DLA-88 complex binding the CDV peptide. This study enriches the study of canine MHC-I molecular-presenting polypeptide-activated TCR, which is of great significance for the study of canine cellular immunity and anti-viral vaccine development.
Adaptive immune responses to SARS-CoV-2 in recovered severe COVID-19 patients
Authors: Olea Beatriz , Albert Eliseo , Torres Ignacio , Amat Paula , Remigia María José , Gozalbo-Rovira Roberto , Rodríguez-Díaz Jesús , Buesa Javier , Blasco María Luisa , Redón Josep , Signes-Costa Jaime , Navarro David
Published: January 2021

Objectives

There is an imperative need to determine the durability of adaptive immunity to SARS-CoV-2. We enumerated SARS-CoV-2-reactive CD4+ and CD8+ T cells targeting S1 and M proteins and measured RBD-specific serum IgG over a period of 2-6 months after symptoms onset in a cohort of subjects who had recovered from severe clinical forms of COVID-19.

Methods

We recruited 58 patients (38 males and 20 females; median age, 62.5 years), who had been hospitalized with bilateral pneumonia, 60% with one or more comorbidities. IgG antibodies binding to SARS-CoV-2 RBD were measured by ELISA. SARS-CoV-2-reactive CD69+-expressing-IFNγ-producing-CD4+ and CD8+ T cells were enumerated in heparinized whole blood by flow cytometry for ICS.

Results

Detectable SARS-CoV-2-S1/M-reactive CD69+-IFN-γ CD4+ and CD8+ T cells were displayed in 17 (29.3%) and 6 (10.3%) subjects respectively, at a median of 84 days after onset of symptoms (range, 58-191 days). Concurrent comorbidities increased the risk (OR, 3.15; 95% CI, 1.03-9.61; P=0.04) of undetectable T-cell responses in models adjusted for age, sex and hospitalization ward. Twenty-one out of the 35 patients (60%) had detectable RBD-specific serum IgGs at a median of 118 days (range, 60 to 145 days) after symptoms onset. SARS-CoV-2 RBD-specific IgG serum levels were found to drop significantly over time.

Conclusion

A relatively limited number of subjects who developed severe forms of COVID-19 had detectable SARS-CoV-2-S1/M IFNγ CD4+ and CD8+ T cells at midterm after clinical diagnosis. Our data also indicated that serum levels of RBD-specific IgGs decline over time, becoming undetectable in some patients.
Histone H3K4me1 and H3K27ac play roles in nucleosome depletion and eRNA transcription, respectively, at enhancers
Authors: Kang Yujin , Kim Yea Woon , Kang Jin , Kim AeRi
Published: January 2021

Histone H3K4me1 and H3K27ac are enhancer specific modifications and are required for enhancers to activate transcription of target genes. However the reciprocal effects of these histone modifications on each other and their roles in enhancers are not clear. Here to comparatively analyze the role of these modifications, we inhibited H3K4me1 and H3K27ac by deleting SET domain of histone methyltransferases MLL3 and MLL4 and HAT domain of histone acetyltransferase p300, respectively, in erythroid K562 cells. The loss of H3K4me1 reduced H3K27ac at the β-globin enhancer LCR HSs, but H3K27ac reduction did not affect H3K4me1. This unequal relationship between two modifications was revealed in putative enhancers by genome-wide analysis using ChIP-seq. Histone H3 depletion at putative enhancers was weakened by the loss of H3K4me1 but not by the loss of H3K27ac. Chromatin remodeling complexes were recruited into the β-globin LCR HSs in a H3K4me1-dependent manner. In contrast, H3K27ac was required for enhancer RNA (eRNA) transcription, and H3K4me1 was not enough for it. Forced H3K27ac induced eRNA transcription without affecting H3K4me1 at the β-globin LCR HSs. These results indicate that H3K4me1 and H3K27ac affect each other in different ways and play more direct roles in nucleosome depletion and eRNA transcription, respectively, at enhancers.
Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling
Authors: Zheng Rikuan , Cai Ruining , Liu Rui , Shan Yeqi , Liu Ge , Sun Chaomin
Published: January 2021

Chloroflexi bacteria are abundant and globally distributed in various unexplored biospheres on Earth. However, only few Chloroflexi members have been cultivated, hampering further understanding of this important group. In the current study, we firstly clarify the high abundance of the phylum Chloroflexi in deep-sea sediments via the operational taxonomic units analysis. We further successfully isolate a novel Chloroflexi strain ZRK33 from cold seep sediments by using an enrichment medium constantly supplemented with rifampicin. Phylogenetic analyses based on 16S rRNA gene, genome, RpoB and EF-tu proteins indicate that strain ZRK33 represents a novel class, and the class is designated as Sulfochloroflexia because whole set of genes encoding key enzymes responsible for assimilatory sulfate reduction are identified in the genome of strain ZRK33. Indeed, assimilation of sulfate or thiosulfate by strain ZRK33 evidently benefits its growth and morphogenesis. Proteomic results suggest that metabolization of sulfate or thiosulfate significantly promotes the transport and degradation of various macromolecules and thereby stimulating the energy production. Notably, the putative genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the metagenome-assembled genomes of 27 Chloroflexi members derived from deep-sea sediments, strongly suggesting that Chloroflexi bacteria play undocumented key roles in deep-sea sulfur cycling.
Different translation dynamics of β- and γ-actin regulates cell migration
Authors: Vedula Pavan , Kurosaka Satoshi , MacTaggart Brittany , Ni Qin , Papoian Garegin A. , Jiang Yi , Dong Dawei , Kashina Anna
Published: January 2021

β- and γ-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different rolesin vivo. Their essential roles in embryogenesis and cell migration critically depend on the nucleotide sequences of their genes, rather than their amino acid sequence. However it is unclear which gene elements underlie this effect. Here we address the specific role of the coding sequence in β- and γ-cytoplasmic actins’ intracellular functions, using stable cell lines with exogenously expressed actin isoforms and their “codon-switched” variants. When targeted to the cell periphery using the β-actin 3′UTR, β-actin and γ-actin have differential effects on cell migration. These effects directly depend on the coding sequence. Single molecule measurements of actin isoform translation, combined with fluorescence recovery after photobleaching, demonstrate a pronounced difference in β- and γ-actins’ translation elongation rates, leading to changes in their dynamics at focal adhesions, impairments in actin bundle formation, and reduced cell anchoring to the substrate during migration. Our results demonstrate that coding sequence-mediated differences in actin translation play a key role in cell migration.
Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities
Authors: Brunet Maéva , de Bettignies Florian , Le Duff Nolwen , Tanguy Gwenn , Davoult Dominique , Leblanc Catherine , Gobet Angélique , Thomas François
Published: January 2021

Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6‐month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide‐degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.
Progression of cannabis withdrawal symptoms in people using medical cannabis for chronic pain
Authors: Coughlin Lara N. , Ilgen Mark A. , Jannausch Mary , Walton Maureen A. , Bohnert Kipling M.
Published: January 2021

Background and aims

Research from cohorts of individuals with recreational cannabis use indicates that cannabis withdrawal symptoms are reported by more than 40% of those using regularly. Withdrawal symptoms are not well understood in those who use cannabis for medical purposes. Therefore, we prospectively examined the stability of withdrawal symptoms in individuals using cannabis to manage chronic pain.

Design, Setting, Participants

Using latent class analysis (LCA) we examined baseline cannabis withdrawal to derive symptom profiles. Then, using latent transition analysis (LTA) we examined the longitudinal course of withdrawal symptoms across the time points. Exploratory analyses examined demographic and clinical characteristics predictive of withdrawal class and transitioning to more or fewer withdrawal symptoms over time.

A cohort of 527 adults with chronic pain seeking medical cannabis certification or re‐certification was recruited between February 2014 and June 2015. Participants were recruited from medical cannabis clinic waiting rooms in Michigan, USA. Participants were predominantly white (82%) and 49% identified as male, with an average age of 45.6 years (standard deviation = 12.8).

Measurements

Baseline, 12‐month and 24‐month assessments of withdrawal symptoms using the Marijuana Withdrawal Checklist–revised.

Findings

A three‐class LCA model including a mild (41%), moderate (34%) and severe (25%) symptom class parsimoniously represented withdrawal symptoms experienced by people using medical cannabis. Stability of withdrawal symptoms using a three‐class LTA at 12 and 24 months ranged from 0.58 to 0.87, with the most stability in the mild withdrawal class. Younger age predicted greater severity and worsening of withdrawal over time.

Conclusions

Adults with chronic pain seeking medical cannabis certification or re‐certification appear to experience mild to severe withdrawal symptoms. Withdrawal symptoms tend to be stable over a 2‐year period, but younger age is predictive of worse symptoms and of an escalating withdrawal trajectory.
Neutral effect of exenatide on serum testosterone in men with type 2 diabetes mellitus: A prospective cohort
Authors: Graybill Sky , Hatfield Jennifer , Kravchenko Maria , Beckman Darrick , Tate Joshua , Beauvais Alexis , Clerc Philip , Davila Desarae , Forbes Whitney , Wardian Jana , Kemm Matthew , Hubberd Abegail , True Mark
Published: January 2021

Background

Endogenous testosterone increases with weight loss from diet, exercise, and bariatric surgery. However, little is known about testosterone levels after weight loss from medication.

Objectives

Uncover the effects of Glucagon‐Like Peptide‐1 receptor agonist (GLP‐1 RA) therapy on serum testosterone.

Material and Methods

Prospective cohort study of men starting GLP‐1 RA therapy for type 2 diabetes mellitus.

Results

51 men lost 2.27 kg (p = 0.00162) and their HbA1c values improved by 0.7% (p = 0.000503) after 6 months of GLP‐1 RA therapy. There was no significant change in testosterone for the group as a whole. However, in subgroup analyses, there was a significant difference in total testosterone change between men starting with baseline total testosterone <320 ng/dL (238.5 ± 56.5 ng/dL to 272.2 ± 82.3 ng/dL) compared to higher values (438 ± 98.2 ng/dL to 412 ± 141.2 ng/dL) (p = 0.0172);free testosterone increased if the baseline total testosterone was <320 ng/dL (55.2 ± 12.8 pg/mL to 57.2 ± 17.6 pg/mL) and decreased if >320 ng/dL (74.7 ± 16.3 pg/mL to 64.2 ± 17.7 pg/mL) (p = 0.00807). Additionally, there were significant differences in testosterone change between men with HbA1c improvements ≥1% (351.6 ± 123.9 ng/dL to 394.4 ± 136.5 ng/dL) compared to men with HbA1c changes <1% (331.8 ± 128.6 ng/dL to 316.1 ± 126.2 ng/dL) (p = 0.0413).

Conclusion

GLP‐1 RA therapy improves weight and HbA1c without adverse effects on testosterone. Those starting with lower testosterone values or attaining greater improvement in HbA1c may see additional benefits.
Delivery of digestive surgery services during the COVID‐19 pandemic: Indonesian Society of Digestive Surgeons online survey
Authors: Nugroho Adianto , Arifin Fransicus , Wibowo Agung Ary , Handaya A. Yuda , Rivai M. Iqbal , Mulyawan Made , Niam Muhammad , Budiono Parish , Kristian Iwan , Putro Mamiek Dwi , Widianto Perwira , Warsinggih Warsinggih
Published: January 2021

Introduction

During the coronavirus disease 2019 (COVID‐19) pandemic, digestive surgery potentially exposes both health‐care professionals and vulnerable patients to COVID‐19. A survey was conducted with aim to determine the digestive surgery services provided during the COVID‐19 pandemic, optimize safety for patients and clinicians, and safeguard health‐care services.

Methods

An online survey was conceived and circulated to members of the Indonesian Society of Digestive Surgeons. The survey was conducted in two phases, in April 2020 and July 2020, to evaluate changes in response to the COVID‐19 pandemic.

Results

Early in the pandemic (April 2020), the median number of major digestive surgeries performed monthly declined from 20 cases (range. 3‐100 cases) to 1 case (range. 0‐10 cases) (P < .001; Wilcoxon signed‐rank test). Most of the cases in April 2020 addressed emergency problems, but more definitive surgeries were performed during the later period of the survey. The importance of screening for COVID‐19 with polymerase chain reaction has increased over time, and a more comprehensive screening methodology incorporating real‐time polymerase chain reaction, chest CT, and rapid antibody test were evident in 31.37% of July 2020 responses.

Conclusion

Our survey has shown that surgeons adapted to the evolving pandemic and continue to do so only with appropriate safety assurances.
Coronavirus disease 2019 and the revival of passive immunization: Antibody therapy for inhibiting severe acute respiratory syndrome coronavirus 2 and preventing host cell infection: IUPHAR review 31
Authors: Levi‐Schaffer Francesca , de Marco Ario
Published: January 2021

The coronavirus disease 2019 (COVID‐19) pandemic stimulated both the scientific community and healthcare companies to undertake an unprecedented effort with the aim of understanding the molecular mechanisms of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection and developing effective therapeutic solutions. The peculiar immune response triggered by this virus, which seems to last only few months, led to a search for alternatives such as passive immunization in addition to conventional vaccinations. Convalescent sera, monoclonal antibodies selected from the most potent neutralizing binders induced by the virus infection, recombinant human single‐domain antibodies, and binders of variable scaffold and different origin have been tested alone or in combination exploiting monovalent, multivalent and multispecific formats. In this review, we analyse the state of the research in this field and present a summary of the ongoing projects finalized to identify suitable molecules for therapies based on passive immunization.
Exclusion Expected? Cardiac Slowing Upon Peer Exclusion Links Preschool Parent Representations to School‐Age Peer Relationships
Authors: White Lars O. , Bornemann Boris , Crowley Michael J. , Sticca Fabio , Vrtička Pascal , Stadelmann Stephanie , Otto Yvonne , Klein Annette M. , von Klitzing Kai
Published: January 2021

Attachment theory proposes that children’s representations of interactions with caregivers guide information‐processing about others, bridging interpersonal domains. In a longitudinal study (N = 165), preschoolers (Mage = 5.19 years) completed the MacArthur Story Stem Battery to assess parent representations. At school‐age (Mage = 8.42 years), children played a virtual ballgame with peers who eventually excluded them to track event‐related cardiac slowing, a physiological correlate of rejection, especially when unexpected. At both ages, parents and teachers reported on peer and emotional problems. During exclusion versus inclusion‐related events, cardiac slowing was associated with greater positive parent representations and fewer emerging peer problems. Cardiac slowing served as a mediator between positive parent representations and peer problems, supporting a potential psychophysiological mechanism underlying the generalization of attachment‐related representations to peer relationships.
Topical corticosteroid allergy: Results of sequential testing to a corticosteroid series in New Zealand
Authors: Murphy Victoria L. , Patel Denesh C. , Lamb Steven R. , Cheng Harriet S.
Published: January 2021

Background

Our institution tests the European Baseline Series (EBS) and a steroid series sequentially in all patients presenting for patch testing. The rate of steroid sensitization in New Zealand has not previously been documented.

Objectives

To investigate the rate of corticosteroid sensitization and assess additional benefit of testing the full steroid series over the steroid allergy markers in the EBS.

Methods/Patients

Retrospective analysis of all patient demographics and patch test results over a 5‐year period (2014 to 2019) was performed at a tertiary patch test clinic in Auckland, New Zealand.

Results

A total of 319 patients completed patch testing, and 4.4% were sensitized to one or more corticosteroids. As much as 79% of positive reactions were of current relevance; 11/14 reactions were to tixocortol pivalate or budesonide. The “number needed to test” to detect one additional case of corticosteroid sensitization by using the full corticosteroid series over the EBS alone was 107.

Conclusions

Although corticosteroid sensitization was not uncommon in our population, the results suggest that sequential testing with the corticosteroid markers (budesonide and tixocortol) in the standard series alone is adequate. The additional corticosteroid series should be added if the markers are positive or where there is a clinical suspicion of corticosteroid allergy.
Evolutionary developmental biology and sustainability: A biology of resilience
Authors: Gilbert Scott F.
Published: January 2021

Evolutionary developmental biology, and especially ecological developmental biology, is essential for discussions of sustainability and the responses to global climate change. First, this paper explores examples of animals that have successfully altered their development to accommodate human‐made changes to their environments. We next document the ability of global warming to disrupt the development of those organisms with temperature‐dependent sex‐determination or with phenologies coordinating that organism's development with those of other species. The thermotolerance of Homo sapiens is also related to key developmental factors concerning brain development and maintenance, and the development of corals, the keystone organisms of tropical reefs, is discussed in relation to global warming as well as to other anthropogenic changes. While teratogenic and endocrine‐disrupting compounds are not discussed in this essay, the ability of glyphosate herbicides to block insect development is highlighted. Last, the paper discusses the need to creatively integrate developmental biology with ecological, political, religious, and economic perspectives, as the flourishing of contemporary species may require altering the ways that Western science has considered the categories of nature, culture, and self.
Delineating the breast cancer immune microenvironment in the era of multiplex immunohistochemistry/immunofluorescence
Authors: Tien Tracy Z , Lee Justina N L W , Lim Jeffrey C T , Chen Xiao‐Yang , Thike Aye Aye , Tan Puay Hoon , Yeong Joe P S
Published: January 2021

Breast cancer is the most common malignancy and the leading cause of cancer death in females worldwide. Treatment is challenging, especially for those who are triple‐negative. Increasing evidence suggests that diverse immune populations are present in the breast tumour microenvironment, which opens up avenues for personalised drug targets. Historically, our investigations into the immune constitution of breast tumours have been restricted to analyses of one or two markers at a given time. Recent technological advances have allowed simultaneous labelling of more than 35 markers and detailed profiling of tumour‐immune infiltrates at the single‐cell level, as well as determining the cellular composition and spatial analysis of the entire tumour architecture. In this review, we describe emerging technologies that have contributed to the field of breast cancer diagnosis, and discuss how to interpret the vast data sets obtained in order to effectively translate them for clinically relevant use.
Overused laboratory test of haemoglobin A1c at one medical centre in southern Taiwan
Authors: Hung Te‐Yu , Chan Kun‐Chen , Ma Li‐Jung
Published: January 2021

Aims

To investigate overused laboratory test of haemoglobin Ac1 (HbA1c) in one medicine centre in southern Taiwan.

Methods

Data were extracted from the database of the Medical Center from March 2013 to March 2015. These patients were classified into five groups, including group A (diabetic patients with HbA1c value ≥7), group B (healthy people with HbA1c value ≥7), group C (diabetic patients with HbA1c test value <7), group D (healthy people with HbA1c value <6.5) and group E (prediabetic people with HbA1c value 6.5‐7). The divisions requested for HbA1c test were divided into four categories, including endocrinology, internal medicine, surgery and the others. Repeat testing at the time of the second test was investigated using survival analysis.

Results

The percentage of overall inappropriate repeat testing was as high as 34%. The percentages among the five patient groups were relatively different. Group C had the largest percentage of inappropriate repeat testing (48%) and group A had the second largest (30%), followed by groups D (25%), E (13%) and B (10%). The percentages of inappropriate repeat testing of the five patient groups were also relatively different among the four categories of division, with Kaplan‐Meier curves showing significant differences. The time to repeat testing was the shortest for group A and was the second shortest for group C, followed by groups B, E and D.

Conclusions

The results provided detailed information about the percentages of inappropriate repeat testing of HbA1c of the five patient groups among the four categories of division.
Review Article: Hawai‘i's Cesspool Problem: Review and Recommendations for Water Resources and Human Health
Authors: Mezzacapo Michael , Donohue Mary J. , Smith Celia , El‐Kadi Aly , Falinski Kim , Lerner Darren T.
Published: January 2021

Cesspools as onsite sewage disposal systems (OSDS) are widespread in the Hawaiian Islands and of concern due to their lack of primary treatment and direct discharge of pathogens and nutrients into groundwater. Approximately 88,000 cesspools in Hawai‘i release nearly 55 million gallons per day (mgd) of sewage into the ground. Here, we review the status of wastewater pollution, with an emphasis on cesspools, and associated impacts to water resources, nearshore ecosystems, and human health. We present evidence supporting the creation of a cesspool conversion plan, highlighting the need to upgrade cesspools. Knowledge gaps in areas such as hydraulic/hydrologic modeling and technological limitations in identifying specific wastewater sources present barriers to addressing cesspool challenges. We show many of these constraints can be diminished. For example, limitations in identifying specific sources from wastewater indicators using %N and δ15N can be reduced with available land‐use information and potential pollution sources to clarify concentration and isotopic data. Resource management presents many challenges, including recognition of diverse societal views and values. To overcome discrepancies in available data, and varying societal values, the use of transparent, adaptable framework methods such as “structured decision‐making” offers approaches for problem solving. Such frameworks are consistent with a holistic management approach to OSDS that couple the natural and social sciences in identifying and addressing barriers to reduce negative impacts. Maintaining momentum through adoption of clearly articulated short‐, medium‐, and long‐term achievement benchmarks associated with such a management approach is recommended.