bluuebunny/crossref_metadata_2025 huggingface dataset:
Managing the risk of a COVID-19 outbreak from border arrivals
Authors: Steyn Nicholas , Plank Michael J. , James Alex , Binny Rachelle N. , Hendy Shaun C. , Lustig Audrey
Published: April 2021

In an attempt to maintain the elimination of COVID-19 in New Zealand, all international arrivals are required to spend 14 days in government-managed quarantine and to return a negative test result before being released. We model the testing, isolation and transmission of COVID-19 within quarantine facilities to estimate the risk of community outbreaks being seeded at the border. We use a simple branching process model for COVID-19 transmission that includes a time-dependent probability of a false-negative test result. We show that the combination of 14-day quarantine with two tests is highly effective in preventing an infectious case entering the community, provided there is no transmission within quarantine facilities. Shorter quarantine periods, or reliance on testing only with no quarantine, substantially increases the risk of an infectious case being released. We calculate the fraction of cases detected in the second week of their two-week stay and show that this may be a useful indicator of the likelihood of transmission occurring within quarantine facilities. Frontline staff working at the border risk exposure to infected individuals and this has the potential to lead to a community outbreak. We use the model to test surveillance strategies and evaluate the likely size of the outbreak at the time it is first detected. We conclude with some recommendations for managing the risk of potential future outbreaks originating from the border.
Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter
Authors: Pérez-Rodríguez Ileana , Choi Jessica K. , Abuyen Karla , Tyler Madeline , Ronkowski Cynthia , Romero Eric , Trujillo Anthony , Tremblay Jason , Viney Isabella , Savalia Pratixaben , Amend Jan P.
Published: April 2021

A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5–40 °C), 10 and 50 g l−1 NaCl (optimum, 15–20 g l−1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5–40 °C), 10 and 50 g l−1 NaCl (optimum, 15–25 g l−1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4
3-, SO4
2-, SeO4
2-, S2O3
2-, S0 and NO3
- were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to

Geothermobacter ehrlichii

, within the class δ-

Proteobacteria

(now within the class

Desulfuromonadia

). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus

Geothermobacter

, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).
Unlocking low- and middle-income countries to detect SARS-CoV-2
Authors: Alcántara Roberto , Peñaranda Katherin , Mendoza Gabriel , Nakamoto Jose A. , Martins-Luna Johanna , del Valle Juana , Adaui Vanessa , Milón Pohl
Published: April 2021

Low- and middle-income countries (LMICs) are significantly affected by SARS-CoV-2, partially due to their limited capacity for local development of molecular testing and accentuated by the international supply shortage. Here, we describe a molecular toolkit that can be readily produced and deployed in LMICs using minimal laboratory equipment. Our results show that mid-scale production of enzymes and nucleic acids can supply thousand tests per production batch. One-step RT-PCR was optimized for two SARS-CoV-2 loci and coupled to CRISPR/Cas12a detection. The clinical validation indicated a sensitivity near 100% for mid and high viral load samples (Cq ≤ 33). The specificity was around 100% regardless of viral load. The toolkit was used with the mobile laboratory BentoLab, potentially unlocking LMICs to implement detection services in unattended regions. Altogether, we provide detailed methods and performance evidence of molecular tools aiming to aid LMICs to deploy molecular testing for current or future pathogenic outbreaks.

One Sentence Summary

We describe a molecular toolkit for the detection of SARS-CoV-2 that is compatible with available facilities in low- and middle-income countries (LMICs).
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics
Authors: Chen Shengquan , Zhang Boheng , Chen Xiaoyang , Zhang Xuegong , Jiang Rui
Published: April 2021

Motivation

Single-cell RNA sequencing (scRNA-seq) techniques have revolutionized the investigation of tran-scriptomic landscape in individual cells. Recent advancements in spatial transcriptomic technologies further enable gene expression profiling and spatial organization mapping of cells simultaneously. Among the tech-nologies, imaging-based methods can offer higher spatial resolutions, while they are limited by either the small number of genes imaged or the low gene detection sensitivity. Although several methods have been proposed for enhancing spatially resolved transcriptomics, inadequate accuracy of gene expression prediction and in-sufficient ability of cell-population identification still impede the applications of these methods.

Results

We propose stPlus, a reference-based method that leverages information in scRNA-seq data to enhance spatial transcriptomics. Based on an auto-encoder with a carefully tailored loss function, stPlus performs joint embedding and predicts spatial gene expression via a weightedk-NN. stPlus outperforms baseline meth-ods with higher gene-wise and cell-wise Spearman correlation coefficients. We also introduce a clustering-based approach to assess the enhancement performance systematically. Using the data enhanced by stPlus, cell populations can be better identified than using the measured data. The predicted expression of genes unique to scRNA-seq data can also well characterize spatial cell heterogeneity. Besides, stPlus is robust and scalable to datasets of diverse gene detection sensitivity levels, sample sizes, and number of spatially meas-ured genes. We anticipate stPlus will facilitate the analysis of spatial transcriptomics.

Availability

stPlus with detailed documents is freely accessible athttp://health.tsinghua.edu.cn/software/stPlus/and the source code is openly available onhttps://github.com/xy-chen16/stPlus.

Contact

ruijiang@tsinghua.edu.cn

Supplementary information

Supplementary data are available atBioinformaticsonline.
A computational solution for bolstering reliability of epigenetic clocks: Implications for clinical trials and longitudinal tracking
Authors: Higgins-Chen Albert T. , Thrush Kyra L. , Wang Yunzhang , Kuo Pei-Lun , Wang Meng , Minteer Christopher J. , Moore Ann Zenobia , Bandinelli Stefania , Vinkers Christiaan H. , Vermetten Eric , Rutten Bart P.F. , Geuze Elbert , Okhuijsen-Pfeifer Cynthia , van der Horst Marte Z. , Schreiter Stefanie , Gutwinski Stefan , Luykx Jurjen J. , Ferrucci Luigi , Crimmins Eileen M. , Boks Marco P. , Hägg Sara , Hu-Seliger Tina T. , Levine Morgan E.
Published: April 2021

Epigenetic clocks are widely used aging biomarkers calculated from DNA methylation data. Unfortunately, measurements for individual CpGs can be surprisingly unreliable due to technical noise, and this may limit the utility of epigenetic clocks. We report that noise produces deviations up to 3 to 9 years between technical replicates for six major epigenetic clocks. The elimination of low-reliability CpGs does not ameliorate this issue. Here, we present a novel computational multi-step solution to address this noise, involving performing principal component analysis on the CpG-level data followed by biological age prediction using principal components as input. This method extracts shared systematic variation in DNAm while minimizing random noise from individual CpGs. Our novel principal-component versions of six clocks show agreement between most technical replicates within 0 to 1.5 years, equivalent or improved prediction of outcomes, and more stable trajectories in longitudinal studies and cell culture. This method entails only one additional step compared to traditional clocks, does not require prior knowledge of CpG reliabilities, and can improve the reliability of any existing or future epigenetic biomarker. The high reliability of principal component-based epigenetic clocks will make them particularly useful for applications in personalized medicine and clinical trials evaluating novel aging interventions.
Megapixel camera arrays for high-resolution animal tracking in multiwell plates
Authors: Barlow Ida , Feriani Luigi , Minga Eleni , McDermott-Rouse Adam , O’Brien Thomas , Liu Ziwei , Hofbauer Maximilian , Stowers John R. , Andersen Erik C. , Ding Siyu Serena , Brown André E.X.
Published: April 2021

Tracking small laboratory animals such as flies, fish, and worms is used for phenotyping in neuroscience, genetics, disease modelling, and drug discovery. Current imaging systems are limited either in spatial resolution or throughput. A system capable of imaging a large number of animals with sufficient resolution to estimate their pose would enable a new class of experiments where detailed behavioural differences are quantified but at a scale where hundreds of treatments can be tested simultaneously. Here we report a new imaging system consisting of an array of six 12-megapixel cameras that can simultaneously record from all the wells of a 96-well plate with a resolution of 80 pixels/mm at 25 frames per second. We show that this resolution is sufficient to estimate the pose of nematode worms including head identification and to extract high-dimensional phenotypic fingerprints. We use the system to study behavioural variability across wild isolates, the sensitisation of worms to repeated blue light stimulation, the phenotypes of worm disease models, and worms’ behavioural responses to drug treatment. Because the system is compatible with standard multiwell plates, it makes computational ethological approaches accessible in existing high-throughput pipelines and greatly increases the scale of possible phenotypic screening experiments inC. elegans.
Speed tuning in head coordinates as an alternative explanation of depth selectivity from motion parallax in area MT
Authors: Xu Zhe-Xin , DeAngelis Gregory C.
Published: April 2021

There are two distinct sources of retinal image motion: motion of objects in the world and movement of the observer. In cases where an object moves in a scene and the eyes also move, a coordinate transformation that involves smooth eye movements and retinal motion will be needed in order to estimate object motion in world coordinates. More recently, interactions between retinal and eye velocity signals have also been suggested to generate depth selectivity from motion parallax (MP) in the macaque middle temporal (MT) area. We explored whether the nature of the interaction between eye and retinal velocities in MT neurons favors one of these two possibilities or a mixture of both. We analyzed responses of MT neurons to retinal and eye velocities in a viewing context in which the observer translates laterally while maintaining visual fixation on a world-fixed target. In this scenario, the depth of an object can be inferred from the ratio between retinal velocity and eye velocity, according to the motion-pursuit law. Previous studies have shown that MT responses to retinal motion are gain-modulated by the direction of eye movement, suggesting a potential mechanism for depth tuning from MP. However, our analysis of the joint tuning profile for retinal and eye velocities reveals that some MT neurons show a partial coordinate transformation toward head coordinates. We formalized a series of computational models to predict neural spike trains as well as selectivity for depth, and we used factorial model comparisons to quantify the relative importance of each model component. Our findings for many MT neurons reveal that the data are equally well explained by gain modulation or a partial coordinate transformation toward head coordinates, although some responses can only be well fit by the coordinate transform model. Our results highlight the potential role of MT neurons in representing multiple higher-level sensory variables, including depth from MP and object motion in the world.
Evidence that faecal carriage of resistantEscherichia coliby 16-week-old dogs in the United Kingdom is associated with raw feeding
Authors: Mounsey Oliver , Wareham Kezia , Hammond Ashley , Findlay Jacqueline , Gould Virginia C. , Morley Katy , Cogan Tristan A. , Turner Katy M.E. , Avison Matthew B. , Reyher Kristen K.
Published: April 2021

We report a survey (August 2017 to March 2018) and risk factor analysis of faecal carriage of antibacterial-resistant (ABR)Escherichia coliin 223 sixteen-week-old dogs in the United Kingdom. Raw feeding was associated with the presence ofE. coliresistant to fluoroquinolones, tetracycline, amoxicillin, and streptomycin, but not to cefalexin or cefotaxime. Whole genome sequencing of 30 fluoroquinolone-resistant (FQ-R), 22 cefotaxime-resistant (CTX-R) and seven dual FQ-R/CTX-RE. coliisolates showed a wide range of sequence types (STs), an approximately 50:50 split of CTX-M:AmpC-mediated CTX-R, and almost exclusively mutational FQ-R dominated by ST744 and ST162. Comparisons betweenE. coliisolates from puppies known to be located within a 50 x 50 km region with those isolated from human urinary tract and bloodstream infections (isolated in parallel in the same region) identified a clone of ST963E. colicarrying chromosomalblaCMY.2in two puppies and causing two urinary tract infections and one bloodstream infection. Furthermore, an ST744 FQ-R clone was carried by one puppy and caused one urinary tract infection. Accordingly, we conclude that raw feeding is associated with carriage of ABRE. coliin dogs even at sixteen weeks of age and that bacteria carried by dogs are shared with humans.
Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes
Authors: Joh Richard I. , Lawrence Michael S. , Aryee Martin J. , Motamedi Mo
Published: April 2021

The establishment of distinct transcriptional states entails coordinated transcriptional coregulation of several disparate biological processes (BP), involving thousands of genes scattered throughout the genome. Linear clustering of genes in a single BP is one strategy for their transcriptional coregulation. However, whether such gene clustering also plays a role in transcriptional coherence of several disparate BPs remains unexplored. Here, by analyzing the genomes of eukaryotes ranging from yeast to human, we report the identification of thousands of conserved and species-specific disparate clustered BP pairs, many of which in normal human tissues are transcriptionally correlated. Strikingly, our results reveal that often this system-level transcriptional coordination is achieved in part by the genic proximity of regulatory nodes of disparate BPs whose coregulation drives the transcriptional coherence of their respective pathways. This, we hypothesize, is one strategy for creating coregulated, tunable modulons in eukaryotes.
Intestinal helminth infection transforms the CD4+ T cell composition of the skin
Authors: Classon C H , Li M , Ma J , Clavero A Lerma , Feng X , Tibbitt C A , Stark J M , Cardoso R , Ringqvist E , Boon L , Villablanca E J , Rothfuchs A Gigliotti , Eidsmo L , Coquet J M , Nylén S
Published: April 2021

Intestinal helminth parasites can alter immune responses to vaccines, other infections, allergens and autoantigens, indicating effects on host immune responses in distal barrier tissues. We herein show that C57BL/6 mice infected with the strictly intestinal nematodeHeligmosomoides polygyrushave impaired capacity to initiate skin immune responses and develop skin-resident memory cells to mycobacterial antigens, both during infection and months after deworming therapy. Surprisingly, and in contrast to a previously noted loss of T cells in peripheral lymph nodes, the skin of worm-infected mice harboured higher numbers of CD4+ T cells compared to skin of uninfected controls.H. polygyrus-specific TH2 cells accumulated during infection and remained after worm expulsion. Accumulation of TH2 cells in the skin was associated with increased expression of the skin-homing chemokine receptors CCR4 and CCR10 on CD4+ T cells in blood and mesenteric lymph nodes draining intestinal tissues, indicating gut-to-skin trafficking of cells. In conclusion, we show that infection by a strictly intestinal helminth has long-term effects on immune cell composition and local immune responses to unrelated antigens in the skin, revealing a novel mechanism for T cell colonization and worm-mediated immunosuppression in this organ.
Sequence determinants ofin cellcondensate assembly morphology, dynamics, and oligomerization as measured by number and brightness analysis
Authors: Emenecker Ryan J. , Holehouse Alex S. , Strader Lucia C.
Published: April 2021

Background

Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo.

Methods

In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), which is a transcription factor integral to the signaling pathway for the plant hormone auxin. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates.

Results

Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity.

Conclusions

IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate.
Exosome component 1 cleaves single-stranded DNA and sensitizes kidney renal clear cell carcinoma cells to poly(ADP-ribose) polymerase inhibitor
Authors: Xiao Qi , Liu Qiaoling , Wang Lina , Wang Na , Wang Kai , Song Chengli , Yang Qingkai
Published: April 2021

Targeting DNA repair pathway offers an important therapeutic strategy for cancers. However, the failure of DNA repair inhibitors to markedly benefit patients necessitates the development of new strategies. Here, we show that exosome component 1 (EXOSC1) promotes DNA damages and sensitizes kidney renal clear cell carcinoma (KIRC) cells to DNA repair inhibitor. Considering that endogenous source of mutation (ESM) constantly assaults genomic DNA and likely sensitize cancer cells to the inhibitor, we first analyzed the statistical relationship between the expression of individual genes and the mutations for KIRC. Among the candidates, EXOSC1 most notably promoted DNA damages and subsequent mutations via preferentially cleaving C site(s) in single-stranded DNA. Consistently, EXOSC1 was more significantly correlated with C>A transversions in coding strands than these in template strands in KIRC. Notably, KIRC patients with high EXOSC1 showed a poor prognosis, and EXOSC1 sensitized cancer cells to poly(ADP-ribose) polymerase inhibitor. These results show that EXOSC1 acts as an ESM in KIRC, and targeting EXOSC1 might be a potential therapeutic strategy.
Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses
Authors: West Johanna , Röder Juliane , Matrosovich Tatyana , Beicht Jana , Baumann Jan , Kouassi Nancy Mounogou , Doedt Jennifer , Bovin Nicolai , Zamperin Gianpiero , Gastaldelli Michele , Salviato Annalisa , Bonfante Francesco , Pond Sergei Kosakovsky , Herfst Sander , Fouchier Ron , Wilhelm Jochen , Klenk Hans-Dieter , Matrosovich Mikhail
Published: April 2021

The hemagglutinin (HA) of A/H3N2 pandemic influenza viruses (IAVs) of 1968 differed from its inferred avian precursor by eight amino acid substitutions. To determine their phenotypic effects, we studied recombinant variants of A/Hong Kong/1/1968 virus containing either human-type or avian-type amino acids in the corresponding positions of HA. The precursor HA displayed receptor binding profile and high conformational stability typical for duck IAVs. Substitutions Q226L and G228S, in addition to their known effects on receptor specificity and replication, marginally decreased HA stability. Substitutions R62I, D63N, D81N and N193S reduced HA binding avidity. Substitutions R62I, D63N, D81N and A144G promoted virus replication in human airway epithelial cultures. Analysis of HA sequences revealed that substitutions D63N and D81N accompanied by the addition of N-glycans represent common markers of avian H3 HA adaptation to mammals. Our results advance understanding of genotypic and phenotypic changes in IAV HA required for avian-to-human adaptation and pandemic emergence.
Computer-Vision Stabilized Intravital Imaging Reveals Lung Capillary Neutrophil Dynamics Crucial for Lung Host-Defense Function
Authors: Tsukasaki Yoshikazu , Bachmaier Kurt , Joshi Jagdish C. , Joshi Bhagwati , Toth Peter T. , Hong Zhigang , Nepal Saroj , Gunzer Matthias , Cho Jaehyung , Mehta Dolly , Tiruppathi Chinnaswamy , Pinho Sandra , Mo Gary , Rehman Jalees , Malik Asrar B.
Published: April 2021

Polymorphonuclear neutrophils (PMN) are highly dynamic innate immune cells which are essential for lung host defense. However,in vivointravital imaging in moving organs such as the lung remains challenging due to motion artifacts. Here we describe a novel intravital imaging method with high-throughput analytical capability based on a computer vision stabilization algorithm, Computer-vision-Assisted STabilized intravital imaging (CASTii). The sub-micron precision of this approach enables analysis of compartmentalized intravital PMN dynamics. We quantified in real-time a novel patrolling function of lung intracapillary circulating PMN. We also describe the dynamics of intracapillary PMN pooling (marginated PMN pool) using direct imaging of PMNs. The pool was formed by repeated catch-and-release kinetics involving PMN deformation inside microvessels during the passage of PMNs in vessels. We observed rapid PMN recruitment into the lung tissue compartments from pooled PMNs in response to alveolar chemoattract exposure. In contrast, endotoxemia-induced intracapillary sequestration of PMN impaired PMN transmigration into the alveolar space and defective phagocytosis of live bacteria. Intravital imaging of PMN dynamics with CASTii provides fundamental insights into host-defense functions of lung capillary PMN.
The SARS CoV-1 3a protein disrupts Golgi complex morphology and cargo trafficking
Authors: Gonzales Rex R. , Machamer Carolyn E.
Published: April 2021

Coronaviruses assemble by budding into the endoplasmic reticulum-Golgi intermediate compartment, but the pathway of egress from infected cells is not well understood. Efficient egress of infectious bronchitis virus (a gamma coronavirus, CoV) requires neutralization of Golgi pH by the envelope (E) protein. This results in reduced rates of cargo traffic and disrupts Golgi morphology, but it protects the spike protein from aberrant proteolysis. The severe acute respiratory syndrome (SARS) CoV-1 E protein does not disrupt the Golgi, however. We show here that in transfected cells, the ORF3a protein of SARS CoV-1 disrupts Golgi morphology, cargo trafficking and luminal pH. Unlike the infectious bronchitis virus E protein, these functions of the SARS CoV-1 3a protein appear to require its viroporin activity. Thus, neutralization of acidic compartments may be a universal feature of CoV infection, although different viral proteins and mechanisms may be used to achieve this outcome.
Cumulative effects of spruce budworm and moose herbivory on boreal forest ecosystems
Authors: Leroux Shawn J. , Charron Louis , Hermanutz Luise , Feltham Janet
Published: April 2021

Ungulate herbivory is a key natural disturbance in many ecosystems. In forest ecosystems, ungulate herbivory often co‐occurs with other disturbances yet there are few studies looking at the cumulative impacts of ungulates and other natural disturbances on forest dynamics.

We report on an 18‐year experiment to investigate the combined effects of introduced, non‐native moose and native spruce budworm herbivory on balsam fir forest recruitment and regeneration. Specifically, we measured inputs into early life‐history components of balsam fir dominant boreal forest ecosystems such as seed density, seedbed quality, seedling and sapling height and density, as well as adult density in eight paired moose exclosure and control sites across a spruce budworm disturbance gradient (i.e. no outbreak, recent outbreak, old outbreak) that resulted in closed, partially open and open canopies.

Piecewise structural equation models (SEMs) revealed a strong negative effect of spruce budworm disturbance on balsam fir adult density and indirect effects of this budworm disturbance on balsam fir seedling and sapling density mediated through adult density. We observed a similar pattern of budworm disturbance effects on balsam fir seed density with the lowest densities in sites with open canopy, then partially open and closed canopies. As expected, the SEM showed a positive effect of bryophyte seedbed cover on balsam fir seedling density. The SEM showed support for a positive effect of moose exclusion on balsam fir sapling height and density. Specifically, saplings were on average taller and denser in exclosure than control plots and these differences are most pronounced at sites with partially open canopies created by spruce budworm disturbance and undisturbed or closed canopy sites. Overall, we show evidence for cumulative and interactive effects of spruce budworm and moose herbivory on all life stages of balsam fir and such effects are negatively affecting regeneration of balsam fir forests.

Human activities are creating conditions that facilitate the expansion and increased impacts of herbivores on boreal ecosystem functioning. A greater understanding of how ungulate herbivory interacts with other disturbances is needed to improve our predictions of forest ecosystem dynamics under global change.

A free Plain Language Summary can be found within the Supporting Information of this article.
Global resorption efficiencies of trace elements in leaves of terrestrial plants
Authors: Chen Hao , Reed Sasha C. , Lü Xiaotao , Xiao Kongcao , Wang Kelin , Li Dejun
Published: April 2021

Leaf nutrient resorption is a critical nutrient conservation strategy. Previous studies focus mainly on resorption patterns of macronutrients, but resorption patterns of trace elements remain poorly understood.

A meta‐analysis was conducted to explore the general patterns of the leaf resorption of eight trace elements [i.e. copper (Cu), molybdenum (Mo), zinc (Zn), boron (B), manganese (Mn), sodium (Na), aluminium (Al) and iron (Fe)], and a macronutrient [i.e. sulphur (S)] using data collected from 53 published studies.

Sulphur (49.6%) had the highest average resorption efficiency followed by Cu (30.3%), Mo (29.5%), Zn (19.5%) and B (17.6%). Two structural elements, Na and Mn, were not resorbed, whereas two potentially toxic elements, Al (−55.6%) and Fe (−25.4%), were accumulated in senesced leaves. Both climatic factors and growth types affected leaf nutrient resorption efficiency, but the magnitudes and directions of the effects differed greatly between S and the trace elements. The resorption efficiencies of S, Cu, Mo and Zn decreased as leaf nutrient concentrations increased, but the structural or potentially toxic elements (i.e. B, Mn, Na, Fe and Al) presented no response or opposite trends.

Our results provide global mean resorption efficiencies of trace elements for the first time, and highlight that structural and potentially toxic elements have relatively lower or no leaf resorption, which should be fully considered in biogeochemical models.

A free Plain Language Summary can be found within the Supporting Information of this article.
How grazing management can maximize erosion resistance of salt marshes
Authors: Marin‐Diaz Beatriz , Govers Laura L. , van der Wal Daphne , Olff Han , Bouma Tjeerd J.
Published: April 2021

Combining natural saltmarsh habitats with conventional barriers can provide a sustainable and cost‐effective alternative for fully engineered flood protection, provided that a minimal salt marsh width can be guaranteed for a long period. Hence, it is essential to understand both the key factors and management options driving the lateral erodibility/stability of salt marshes.

We aimed to determine how salt marsh management (i.e. grazing by large vs. small grazers vs. artificial mowing), marsh elevation and marsh age affect soil stability (i.e. soil collapse) and intrinsic lateral erodibility of salt marshes (i.e. particle‐by‐particle detachment). Soil cores were collected in high and low marshes (above and below 0.5 m MHWL, respectively) of different ages. At these locations, we compared cores from grazed areas to cores inside grazer exclosures, with and without artificial mowing. All cores were exposed to waves in flumes to test their stability and lateral erodibility.

All soil cores were characterized by a stable fine‐grained layer deposited on top of readily erodible sand. The thickness of the fine‐grained layer was a key parameter in reducing salt marsh instability (cliff collapse). This layer thickness increased with marsh age and at lower elevations, but decreased with cattle grazing due to compaction.

The erosion resistance of the fine‐grained layer increased with (a) large grazers that compacted the soil by trampling, (b) mowing that excluded soil‐bioturbating species, and (c) grazing by small grazers that promoted vegetation types with higher root density.

Synthesis and applications. Overall, marshes with thinner cohesive and/or fine‐grained top layers are more sensitive to lateral erosion than marshes with deep cohesive soils, independently of the management. Grazing and artificial mowing can reduce the erodibility of fine‐grained soils, making salt marshes more resilient to lateral erosion. However, compaction by large grazers simultaneously leads to thinner fine‐grained layers and lower elevation, potentially leading to more inundation under sea‐level rise. Hence, to effectively manage salt marshes to enhance their contribution to coastal protection, we recommend (a) moderate/rotational livestock grazing, avoiding high intensity grazing in sediment‐poor systems sensitive to sea‐level rise and (b) investigating measures to preserve small grazers.
Detecting early‐warning signals of concern in plant populations with a Citizen Science network. Are threatened and other priority species for conservation performing worse?
Authors: García María B. , Silva José L. , Tejero Pablo , Pardo Iker
Published: April 2021

Long‐term monitoring of biodiversity is a fundamental part of environmental management, and Citizen Science (CS) approaches are increasing their contribution to such endeavour. CS plant monitoring programmes, however, almost exclusively report on the species presence, which can be used to detect changes in distribution or occupancy areas, but not to assess their local extinction risk. To anticipate the collapse of local populations, we need information on population sizes, trends, temporal fluctuations and threats. This is particularly important in the case of priority species (threatened, endangered and those that need special protection).

Here we describe the working protocol of the ‘Adopt a plant’ programme, a collaborative network that is currently monitoring 332 populations of 204 plant taxa (threatened, of community interest, common, rare and habitat indicators) across a heterogeneous landscape in NE Spain. Coordinated by scientists, participants estimate population sizes, record disturbances and follow scientifically rigorous sampling methods to track plant abundances year after year in fixed representative areas within populations. Two simple indices are estimated from that information: the overall trend (mean population abundance change, as percentage; PAch) and temporal fluctuations (standard deviation of annual changes; PAchsd).

The potential of this ongoing high‐quality dataset is demonstrated through the analysis of 242 populations monitored over 3–10 years. Stability is the dominant trend (mean PAch: +0.14%), with priority species having similar PAch and lower PAchsd than non‐priority ones. Regardless of the priority status, small populations performed worse than large ones. Only 8% of studied populations faced direct human threats.

Synthesis and applications. The ‘Adopt a plant’ collaborative monitoring programme was launched in NE of Spain to produce standardized indices of abundance change and other early‐warning signals of concern or risk of population collapse. Such information is crucial to report the conservation status of threatened plants, and plants of Community interest (Habitats Directive). By analysing hundreds of populations, we found that priority plants experienced few threats and did not perform worse than non‐priority ones. This unexpected finding evidences the importance of gathering massive demographic information to refine conservation priorities and to achieve a more comprehensive assessment of flora's vulnerability.
Unravelling physiological signatures of tomato bacterial wilt and xylem metabolites exploited by Ralstonia solanacearum
Authors: Gerlin Léo , Escourrou Antoine , Cassan Cédric , Maviane Macia Felicià , Peeters Nemo , Genin Stéphane , Baroukh Caroline
Published: April 2021

The plant pathogen Ralstonia solanacearum uses plant resources to intensely proliferate in xylem vessels and provoke plant wilting. We combined automatic phenotyping and tissue/xylem quantitative metabolomics of infected tomato plants to decipher the dynamics of bacterial wilt. Daily acquisition of physiological parameters such as transpiration and growth were performed. Measurements allowed us to identify a tipping point in bacterial wilt dynamics. At this tipping point, the reached bacterial density brutally disrupts plant physiology and rapidly induces its death. We compared the metabolic and physiological signatures of the infection with drought stress, and found that similar changes occur. Quantitative dynamics of xylem content enabled us to identify glutamine (and asparagine) as primary resources R. solanacearum consumed during its colonization phase. An abundant production of putrescine was also observed during the infection process and was strongly correlated with in planta bacterial growth. Dynamic profiling of xylem metabolites confirmed that glutamine is the favoured substrate of R. solanacearum. On the other hand, a triple mutant strain unable to metabolize glucose, sucrose and fructose appears to be only weakly reduced for in planta growth and pathogenicity.
Reaching out in anticipation: bacterial membrane extensions represent a permanent investment in polysaccharide sensing and utilization
Authors: Dürwald Alexandra , Zühlke Marie‐Katherin , Schlüter Rabea , Gebbe Rebecca , Bartosik Daniel , Unfried Frank , Becher Dörte , Schweder Thomas
Published: April 2021

Outer membrane extensions are common in many marine bacteria. However, the function of these surface enlargements or extracellular compartments is poorly understood. Using a combined approach of microscopy and subproteome analyses, we therefore examined Pseudoalteromonas distincta ANT/505, an Antarctic polysaccharide degrading gamma‐proteobacterium. P. distincta produced outer membrane vesicles (MV) and vesicle chains (VC) on polysaccharide and non‐polysaccharide carbon sources during the exponential and stationary growth phase. Surface structures of carbohydrate‐grown cells were equipped with increased levels of highly substrate‐specific proteins. At the same time, proteins encoded in all other polysaccharide degradation‐related genomic regions were also detected in MV and VC samples under all growth conditions, indicating a basal expression. In addition, two alkaline phosphatases were highly abundant under non‐limiting phosphate conditions. Surface structures may thus allow rapid sensing and fast responses in nutritionally deprived environments. It may also facilitate efficient carbohydrate processing and reduce loss of substrates and enzymes by diffusion as important adaptions to the aquatic ecosystem.
Gang‐related crime in Los Angeles remained stable following COVID‐19 social distancing orders
Authors: Jeffrey Brantingham Paul , Tita George E. , Mohler George
Published: April 2021

Research Summary

The onset of extreme social distancing measures is expected to have a dramatic impact on crime. Here, we examine the impact of mandated, city‐wide social distancing orders aimed at limiting the spread of COVID‐19 on gang‐related crime in Los Angeles. We hypothesize that the unique subcultural processes surrounding gangs may supersede calls to shelter in place and allow gang‐related crime to persist. If the normal guardianship of people and property is also disrupted by social distancing, then we expect gang violence to increase. Using autoregressive time series models, we show that gang‐related crime remained stable and crime hot spots largely stationary following the onset of shelter in place.

Policy Implications

In responding to disruptions to social and economic life on the scale of the present pandemic, both police and civilian organizations need to anticipate continued demand, all while managing potential reductions to workforce. Police are faced with this challenge across a wide array of crime types. Civilian interventionists tasked with responding to gang‐related crime need to be prepared for continued peacekeeping and violence interruption activities, but also an expansion of responsibilities to deal with “frontline” or “street‐level” management of public health needs.
Refugee recruitment and workplace integration: An opportunity for human resource management scholarship and impact
Authors: Hirst Giles , Curtis Sally , Nielsen Ingrid , Smyth Russell , Newman Alexander , Xiao Ning
Published: April 2021

Employment underpins the successful resettlement and integration of refugees, and human resource (HR) professionals are integral to successful employee–employer relationships. Until recently, research has largely overlooked the role of HR professionals in the recruitment and integration of employees at work. Reviewing the literature on refugee employment through an HR lens, this review offers insights and practical solutions that contribute to the effective recruitment and workplace integration of refugees. We identify strategies such as onboarding programs, job enrichment and internships that offer realistic job previews, and the opportunity for people from a refugee background to validate and demonstrate their credentials. In addition, we describe the benefits of organisations’ engagement in external relationship management to champion changes in industrial relations and foster cross‐sector partnerships that aid refugee employment. In the discussion, we describe the practical implications of our review, and highlight directions for future research that addresses different stakeholder needs and priorities.
Awareness of traditional knowledge and attitudes towards wildlife conservation among Maasai communities: The case of Enkusero Sampu Conservancy, Kajiado County in Kenya
Authors: Ochieng Christine Nyangweso , Thenya Thuita , Shah Parita , Odwe George
Published: April 2021

Traditional wildlife conservation methods and attitude towards wildlife conservation are key for the success of wildlife conservation intervention. This study examined awareness of traditional wildlife conservation measures and socio‐demographic factors associated with attitudes towards wildlife conservation among the Maasai communities living in Enkusero Sampu Conservancy (ESC) in Kajiado County, Kenya. Data were based on a cross‐sectional household survey conducted from 02 February to 23 March 2018, among 278 heads of households. Analysis entails cross‐tabulation with chi‐square test and estimation of a multivariate logistic regression model. Awareness of traditional wildlife conservation methods and attitude towards wildlife conservation were significantly (p < 0.05) associated with gender and household size. Heads of household who were aware of traditional wildlife conservation methods were aged 50 or more years. While people from smaller household size (<6 persons) were more likely to have a positive attitude towards wildlife conservation. Those who experienced livestock predation or crop destruction by wild animals were less likely to have a positive attitude towards wildlife conservation. The findings underscore the need for conservation managers to factor in local people's traditional knowledge and attitudes to foster sustainable wildlife conservation in areas surrounding and within wildlife conservation areas.
Aqueous eye drops containing drug/cyclodextrin nanoparticles deliver therapeutic drug concentrations to both anterior and posterior segment
Authors: Loftsson Thorsteinn , Stefánsson Einar
Published: April 2021

Using topical application to deliver therapeutic concentrations of drugs to the posterior segment of the eye remains very challenging. As a result, posterior segment diseases are usually treated by intravitreal injection or implant. While topical treatments are commonly used for anterior segment conditions, they sometimes require frequent applications. Eye drop formulations based on γ‐cyclodextrin (γCD)‐based nanoparticle aggregates were developed, which in animal models and clinical studies deliver therapeutic concentrations of drugs (dorzolamide and dexamethasone) to both anterior and posterior segments of the eye. An early study in humans showed dorzolamide/γCD eye drops could achieve comparable intraocular pressure decreases to commercial dorzolamide eye drops, but with less frequent application. Pilot studies with dexamethasone/γCD eye drops suggested that they could be effective in a range of conditions, including diabetic macular oedema, cystoid macular oedema and vitritis secondary to uveitis, postcataract surgery inflammation and postoperative treatment in trabeculectomy. Phase II studies with similar dexamethasone/γCD nanoparticle eye drops in diabetic macular oedema and postcataract surgery inflammation have recently been completed. This technology has the potential to be used with other classes of drug molecules and to replace or complement invasive treatments, providing safer, non‐invasive therapies, particularly for posterior segment conditions, that can be self‐administered as eye drops by patients.
Half of the children with overweight or obesity and attention‐deficit/hyperactivity disorder reach normal weight with stimulants
Authors: Fast Karin , Björk Anna , Strandberg Maxwell , Johannesson Elias , Wentz Elisabet , Dahlgren Jovanna
Published: April 2021

Aim

Treatment of childhood obesity is often insufficient and may be aggravated by high co‐occurrence of attention‐deficit/hyperactivity disorder (ADHD). We aimed to investigate whether children with overweight or obesity normalised in weight when receiving stimulant treatment for ADHD.

Methods

Growth data of 118 children were obtained from medical records at outpatient paediatric and children’s psychiatric services in the Gothenburg area, Sweden. The children were diagnosed with ADHD and were between 6 and 17 years at the start of stimulant treatment. The pre‐treatment data act as an internal control where every child is their own control.

Results

At the start of treatment, 74 children had normal weight and 44 had either overweight or obesity. During the year with stimulants, the mean (SD) body mass index (BMI) in standard deviation score (SDS) decreased significantly: −0.72 (0.66) compared with 0.17 (0.43) during the year before treatment (p < 0.01). After one year with treatment, 43% of those with overweight or obesity had reached normal weight.

Conclusions

Stimulant treatment for ADHD yields significant weight loss. In children with overweight or obesity and ADHD, this is an important finding showing additional benefit in terms of weight management.
Spatialising illicit commodity chains: Comparing coffee and cocaine
Authors: Dávila Anayansi , Magliocca Nicholas , McSweeney Kendra , Rueda Ximena
Published: April 2021

Among geographers, recent focus on the illicit and illegal has tended to fall into two camps. Economic geographers focus on regimes of illicitness and corresponding production of specific forms of economic space; political ecologists and land change scholars, on the other hand, scrutinised how illicit commodity flows shape land and resource use, especially in the global South. This paper offers an initial integration of these two relatively separate subfields, specifically in terms of their complementary attention to uneven development. We use the concept of “global commodity chains” to explore the ways in which the regulation of agricultural commodities shapes how they are trafficked and embed in space, with particular attention to sites of international transshipment. When a commodity is illegal, spaces of transit take on significant analytical importance. As a heuristic, we present a comparative mapping of two agricultural commodity chains linking Colombia and the USA: coffee and cocaine. Their comparison highlights how “illicitness” fundamentally transforms cocaine’s spatiality, requiring risk evasion that results in characteristically enlarged transit spaces and huge differentials between producer and consumer price. We show how rents circulate in those transit spaces, socially and ecologically embedding in diffuse, fluid networks with severe consequences for people and environments. We conclude with implications for work on illicit commodities and the collateral social and environmental harms they produce.