bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations
Authors: Schlum Katrina A. , Lamour Kurt , de Bortoli Caroline Placidi , Banerjee Rahul , Emrich Scott J. , Meagher Robert , Pereira Eliseu , Murua Maria Gabriela , Sword Gregory A. , Tessnow Ashley E. , Dillon Diego Viteri , Linares Ramirez Angela M. , Akutse Komivi S. , Schmidt-Jeffris Rebecca , Huang Fangneng , Reisig Dominic , Jurat-Fuentes Juan Luis
Published: September 2020

The fall armyworm (Spodoptera frugiperda(J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of >80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). In this study, the population structure and genetic diversity in 55S. frugiperdasamples from Argentina, Brazil, Kenya, Puerto Rico and the United States (USA) were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest panmixia in this population, other than a minor reduction in gene flow between the two overwintering populations in the continental USA that also corresponded to genetically distinct host strains. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Comparisons between laboratory-reared and field collectedS. frugiperdasupport similar genomic diversity, validating the experimental use of laboratory strains. Our research is the largest diverse collection of United StatesS. frugiperdawhole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level amongS. frugiperdapopulations.
A versatile toolkit for CRISPR-Cas13-based RNA manipulation inDrosophila
Authors: Huynh Nhan , Depner Noah , Larson Raegan , King-Jones Kirst
Published: September 2020

Advances in CRISPR technology have immensely improved our ability to manipulate nucleic acids, and the recent discovery of the RNA-targeting endonuclease Cas13 adds even further functionality. Here, we show that Cas13 works efficiently inDrosophila, bothex vivoandin vivo. We tested 44 different Cas13 variants to identify enzymes with the best overall performance and showed that Cas13 could target endogenousDrosophilatranscriptsin vivowith high efficiency and specificity. We also developed Cas13 applications to edit mRNAs and target mitochondrial transcripts. Our vector collection represents a versatile tool collection to manipulate gene expression at the post-transcriptional level.
Extreme variation in recombination rate and genetic variation along the Sylvioidea neo-sex chromosome
Authors: Ponnikas Suvi , Sigeman Hanna , Lundberg Max , Hansson Bengt
Published: September 2020

In the majority of bird species, recombination between the sex chromosome pairs in heterogametic females (ZW) is restricted to a small pseudoautosomal region (PAR), whereas recombination is ongoing along the entire Z chromosome in the homogametic males (ZZ). Recombination has a strong impact on the sequence evolution by affecting the extent of linkage, level of genetic diversity and efficacy of selection. Species within the Sylvioidea superfamily are unique among birds in having extended Z and W chromosomes (neo-sex chromosomes) formed by a fusion between the ancestral sex chromosomes and a part of chromosome 4A. So far the recombination landscape of the Sylvioidea neo-sex chromosomes remains unknown, despite its importance for understanding sequence evolution. Here, we use linkage mapping in a multi-generation pedigree to assemble, and assess the recombination rate along the entire Z chromosome of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). This resulted in an 87.54 Mbp and 90.19 cM large Z including the ancestral-Z, where the small PAR (0.89 Mbp) is located, and the added-Z. A striking result was an extreme variation in recombination rate along the Z in male great reed warblers with high rates at both telomeric ends, but an apparent lack of recombination over a substantial central section, covering 77% of the chromosome. This region showed a drastic loss of nucleotide diversity and accumulation of repeats compared to the highly recombining regions. Nonetheless, the evolutionary rate of genes (measured by dN/dS) did not differ between these regions, suggesting that the efficacy of selection on protein-coding sequences is not reduced by lack of recombination.
Droplet microfluidic sequencing of HIV genomes and integration sites
Authors: Sun Chen , Liu Leqian , Pérez Liliana , Li Xiangpeng , Liu Yifan , Xu Peng , Boritz Eli A. , Mullins James I. , Abate Adam R.
Published: September 2020

Sequencing individual HIV-proviruses and their adjacent cellular junctions can elucidate mechanisms of infected cell persistencein vivo. Here, we present a high throughput microfluidic method to sequence entire proviruses in their native integration site context. We used the method to analyze infected cells from people with HIV on suppressive antiretroviral therapy, demonstrating >90% capture and sequencing of paired proviral genomes and integration sites. This method should enable comprehensive genetic analysis of persistent HIV-infected cell reservoirs, providing important insights into the barriers to HIV cure.
Bleaching resistant corals retain heat tolerance following acclimatization to environmentally distinct reefs
Authors: Barott Katie L. , Huffmyer Ariana S. , Davidson Jennifer M. , Lenz Elizabeth A. , Matsuda Shayle B. , Hancock Joshua R. , Innis Teegan , Drury Crawford , Putnam Hollie M. , Gates Ruth D.
Published: September 2020

Urgent action is needed to prevent the demise of coral reefs as the climate crisis leads to an increasingly warmer and more acidic ocean. Propagating climate change resistant corals to restore degraded reefs is one promising strategy; however, empirical evidence is needed to determine if resistance is retained following transplantation within or beyond a coral’s natal reef. Here we assessed the performance of bleaching-resistant individuals of two coral species following reciprocal transplantation between environmentally distinct reefs (lowvshigh diel variability) to determine if stress resistance is retained following transplantation. Critically, transplantation to either environment had no influence on coral bleaching resistance, indicating that this trait was relatively fixed and is thus a useful metric for selecting corals for reef restoration within their native range. In contrast, growth was highly plastic, and native performance was not predictive of performance in the novel environment. Coral metabolism was also plastic, with cross transplants of both species matching the performance of native corals at both reefs within three months. Coral physiology (autotrophy, heterotrophy, and metabolism) and overall fitness (survival, growth, and reproduction) were higher at the reef with higher flow and fluctuations in diel pH and dissolved oxygen, and did not differ between native corals and cross-transplants. Conversely, cross-transplants at the low-variability reef had higher fitness than native corals, thus increasing overall fitness of the recipient population. This experiment was conducted during a non-bleaching year, which suggests that introduction of these bleaching-resistant individuals will provide even greater fitness benefits to recipient populations during bleaching years. In summary, this study demonstrates that propagating and transplanting bleaching-resistant corals can elevate the resistance of coral populations to ocean warming while simultaneously maintaining reef function as the climate crisis worsens.
Chromosomal instability accelerates the evolution of resistance to anti-cancer therapies
Authors: Lukow Devon A. , Sausville Erin L. , Suri Pavit , Chunduri Narendra Kumar , Leu Justin , Kendall Jude , Wang Zihua , Storchova Zuzana , Sheltzer Jason M.
Published: September 2020

Aneuploidy is a ubiquitous feature of human tumors, but the acquisition of aneuploidy is typically detrimental to cellular fitness. To investigate how aneuploidy could contribute to tumor growth, we triggered periods of chromosomal instability (CIN) in human cells and then exposed them to a variety of different culture environments. While chromosomal instability was universally detrimental under normal growth conditions, we discovered that transient CIN reproducibly accelerated the ability of cells to adapt and thrive in the presence of anti-cancer therapeutic agents. Single-cell sequencing revealed that these drug-resistant populations recurrently developed specific whole-chromosome gains and losses. We independently derived one aneuploidy that was frequently recovered in cells exposed to paclitaxel, and we found that this chromosome loss event was sufficient to decrease paclitaxel sensitivity. Finally, we demonstrated that intrinsic levels of CIN correlate with poor responses to a variety of systemic therapies in a collection of patient-derived xenografts. In total, our results show that while chromosomal instability generally antagonizes cell fitness, it also provides phenotypic plasticity to cancer cells that can allow them to adapt to diverse stressful environments. Moreover, our findings suggest that aneuploidy may function as an under-explored cause of therapy failure in human tumors.
Whole Genome Variation of Transposable Element Insertions in a Maize Diversity Panel
Authors: Qiu Yinjie , O’Connor Christine H. , Coletta Rafael Della , Renk Jonathan S. , Monnahan Patrick J. , Noshay Jaclyn M. , Liang Zhikai , Gilbert Amanda , Anderson Sarah N. , McGaugh Suzanne E. , Springer Nathan M. , Hirsch Candice N.
Published: September 2020

Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 non-redundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e. LTRs, Helitrons, TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 < 0.5) that potentially represent information that has not been well captured in previous SNP based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize, and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.
Genetic analyses link the conserved inner membrane protein CvpA to the σEextracytoplasmic stress response
Authors: Warr Alyson R. , Giorgio Rachel T. , Waldor Matthew K.
Published: September 2020

The function ofcvpA, a bacterial gene predicted to encode an inner membrane protein, is largely unknown. Early studies inE. colilinkedcvpAto Colicin V secretion and recent work revealed that it is required for robust intestinal colonization by diverse enteric pathogens. In enterohemorrhagicE. coli(EHEC),cvpAis required for resistance to the bile salt deoxycholate (DOC). Here, we carried out genome-scale transposon-insertion mutagenesis and spontaneous suppressor analysis to uncovercvpA’sgenetic interactions and identify common pathways that rescue the sensitivity of a ΔcvpAEHEC mutant to DOC. Collectively, these screens led to the hypothesis that the ΔcvpAmutant is impaired in its capacity to activate the σE-mediated stress response. This idea was supported by showing that mutations that activate σE, either indirectly or through its direct overexpression, can restore the ΔcvpAmutant’s resistance to DOC. Analysis of the distribution of CvpA homologs revealed that this inner membrane protein is conserved across bacterial phyla, in both enteric and non-enteric bacteria that are not exposed to bile. Together, our findings suggest that CvpA may function in triggering activation of the σEstress response pathway in response to DOC as well as additional stimuli.

Importance

Several enteric pathogens, including Enterohemorrhagic E. coli (EHEC), requirecvpAto robustly colonize the intestine. This inner membrane is also important for secretion of a colicin and EHEC resistance to the bile salt deoxycholate, but its function is unknown. Genetic analyses carried out here suggest thatcvpAis required to trigger the σE stress response pathway in response to deoxycholate. Since CvpA is conserved across diverse bacterial phyla, we propose that this inner membrane protein is important for activation of this stress response pathway in response to diverse perturbations of the cell envelope.
Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake
Authors: David Gwendoline M. , Moreira David , Reboul Guillaume , Annenkova Nataliia V. , Galindo Luis J. , Bertolino Paola , López-Archilla Ana I. , Jardillier Ludwig , López-García Purificación
Published: September 2020

Identifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world’s oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 µm cell size) along a North-South latitudinal gradient (∼600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities are much more interconnected than meso- and bathypelagic communities and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.

Originality and Significance Statement

Lake Baikal is the oldest, deepest and most voluminous freshwater lake on Earth, offering a unique opportunity to test the effects of horizontal versus vertical gradients on microbial community structure. Using a metabarcoding approach, we studied planktonic microbial eukaryotes from Baikal water columns (5 up to 1,400 m depth) across a North-South latitudinal gradient (∼600 km), including coastal and pelagic areas. Our results show that depth has a strong effect on protist community assemblage, but not latitude (minor effect) or coastal vs. open water sites (no effect). Co-occurrence analyses also point to specific biotic interactions as drivers of community structure. This comprehensive survey constitutes a useful reference for monitoring active climate change effects in this ancient lake.
The SPPL3-defined glycosphingolipid repertoire regulates immune responses by improving HLA class I access
Authors: Jongsma Marlieke L.M. , Raaben Matthijs , de Waard Antonius A. , Zhang Tao , Cabukusta Birol , Platzer René , Blomen Vincent A. , Xagara Anastasia , Verkerk Tamara , Bliss Sophie , Janssen Lennert , Stickel Elmer , Holst Stephanie , Plomp Rosina , Mulder Arend , Ferrone Soldano , Claas Frans H.J. , Heemskerk Mirjam H.M. , Griffioen Marieke , Overkleeft Hermen , Huppa Johannes B. , Wuhrer Manfred , Brummelkamp Thijn R. , Neefjes Jacques , Spaapen Robbert M.
Published: September 2020

HLA class I (HLA-I) drives immune responses by presenting antigen-derived peptides to cognate CD8+T cells. This process is often hijacked by tumors and pathogens for immune evasion. Since therapeutic options for restoring HLA-I antigen presentation are limited, we aimed to identify new HLA-I pathway targets. By iterative genome-wide screens we uncovered that the cell surface glycosphingolipid (GSL) repertoire determines effective HLA-I antigen presentation. We show that absence of the protease SPPL3 augments B3GNT5 enzyme activity, resulting in upregulated levels of surface (neo)lacto-series GSLs. These GSLs sterically impede molecular interactions with HLA-I and diminish CD8+T cell activation. In accordance, a disturbed SPPL3-B3GNT5 pathway in glioma associates with decreased patient survival. Importantly, we show that this immunomodulatory effect can be reversed through GSL synthesis inhibition using clinically approved drugs. Overall, our study identifies a GSL signature that functionally inhibits antigen presentation and represents a potential therapeutic target in cancer, infection and autoimmunity.
Intrarenal B cells integratein situinnate and adaptive immunity in human renal allograft rejection
Authors: Asano Yuta , Daccache Joe , Jain Dharmendra , Ko Kichul , Kinloch Andrew , Veselits Margaret , Wolfgeher Donald , Chang Anthony , Josephson Michelle , Cunningham Patrick , Tambur Anat , Khan Aly , Pillai Shiv , Chong Anita S. , Clark Marcus R.
Published: September 2020

In human allograft rejection, intrarenal B cell infiltrates identify those with a poor prognosis. However, how intrarenal B cells contribute to rejection is not known. Single cell RNA-sequencing of intrarenal class-switched B cells revealed a unique innate cell transcriptional state resembling murine peritoneal B1 cells (Bin cells). Comparison to the transcriptome of whole renal allograft rejecting tissue revealed that Bin cells existed within a complex autocrine and paracrine network of signaling axes. The immunoglobulins expressed by Bin cells did not bind donor specific antigens nor were they enriched for reactivity to ubiquitously expressed self-antigens. Rather, Bin cells frequently expressed antibodies reactive with renal expressed antigens. Furthermore, local antigens could drive Bin cell proliferation and differentiation into plasma cells expressing self-reactive antibodies. By contributing to local innate immune networks, and expressing antibodies reactive with renal expressed antigens, Bin cells are predicted to amplify local inflammation and tissue destruction.
Peripheral Taenia infection increases immunoglobulins in the central nervous system.
Authors: Van Belle Sylvia Carina , de Lange Anja , Tomes Hayley , Lucas Rodney , Naidoo Vinogran , Raimondo Joseph Valentino
Published: September 2020

Human cysticercosis is a disease caused by larvae of the cestode Taenia solium. It is the most common cause of adult-acquired epilepsy world-wide where it exacts a debilitating toll on the health and well-being of affected communities. It is commonly assumed that the major symptoms associated with cysticercosis are a result of the direct presence of larvae in the brain. As a result, the possible effect of peripherally located larvae on the central nervous system are not well understood. To address this question, we utilised the Taenia crassiceps intra-peritoneal murine model of cysticercosis, where larvae are restricted to the peritoneal cavity. In this model, previous research has observed behavioural changes in rodents but not the development of seizures. Here we used ELISAs, immunoblotting and the Evans Blue test for blood-brain barrier permeability to explore the central effects of peripheral infection of mice with Taenia crassiceps. We identified high levels of parasite-targeting immunoglobulins in the serum of Taenia crassiceps infected mice. We show that the Taenia crassciceps larvae themselves also contain and release host immunoglobulins over time. Additionally, we describe, for the first time, significantly increased levels of IgG within the hippocampi of infected mice, which are accompanied by changes in blood-brain barrier permeability. However, these Taenia crassiceps induced changes were not accompanied by alterations to the levels of proinflammatory, pro-seizure cytokines in the hippocampus. These findings contribute to the understanding of systemic and neuroimmune responses in the Taenia crassiceps model of cysticercosis, with implications for the pathogenesis of human cysticercosis.
Discovery of a newNeisseria gonorrhoeaeType IV pilus assembly factor, TfpC
Authors: Hu Linda I. , Yin Shaohui , Ozer Egon A. , Sewell Lee , Rehman Saima , Garnett James A , Seifert H Steven
Published: September 2020

Neisseria gonorrhoeaerely on Type IV pili (T4p) to promote colonization of their human host and to cause the sexually transmitted infection, gonorrhea. This organelle cycles through a process of extension and retraction back into the bacterial cell. Through a genetic screen, we identified the NGO0783 locus ofN. gonorrhoeaestrain FA1090 as containing a gene encoding a protein required to stabilize the Type IV pilus in its extended, non-retracted conformation. We have named the genetfpCand the protein TfpC. Deletion oftfpCproduces a nonpiliated colony morphology and immuno-transmission electron microscopy confirms that the pili are lost in the ΔtfpCmutant, although there is some pilin detected near the bacterial cell surface. A copy of thetfpCgene expressed from alacpromoter restores pilus expression and related phenotypes. A ΔtfpCmutant shows reduced levels of pilin protein, but complementation with atfpCgene restored pilin to normal levels. Bioinformatic searches show there are orthologues in numerous bacteria species but not all Type IV pilin expressing bacteria contain orthologous genes. Co-evolution and NMR analysis indicates that TfpC contains an N-terminal transmembrane helix, a substantial extended/unstructured region and a highly charge C-terminal coiled-coil domain.

Importance

Most bacterial species express one or more extracellular organelles called pili/fimbriae that are required for many properties of each bacterial cell. TheNeisseria gonorrhoeaeType IV pilus is a major virulence and colonization factor for the sexually transmitted infection, gonorrhea. We have discovered a new protein ofNeisseria gonorrhoeaecalled TfpC that is required to maintain the Type IV pili on the bacterial cell surface. There are similar proteins found in the other members of theNeisseriagenus and many other bacterial species important for human health.
Auditory-Visual Speech Behaviors are Resilient to Left pSTS Damage
Authors: Brang David , Plass John , Kakaizada Sofia , Hervey-Jumper Shawn L.
Published: September 2020

The ability to understand spoken language is essential for social, vocational, and emotional health, but can be disrupted by environmental noise, injury, or hearing loss. These auditory deficits can be ameliorated by visual speech signals that convey redundant or supplemental speech information, but the brain regions critically responsible for these audiovisual (AV) interactions remain poorly understood. Previous TMS and lesion-mapping studies suggest that the left posterior superior temporal sulcus (pSTS) is causally implicated in producing the McGurk effect, an AV illusion in which auditory and visual speech are perceptually “fused.” However, previous research suggests that the McGurk effect is neurally and behaviorally dissociable from other visual effects on speech perception and, therefore, may not provide a generalizable index of AV interactions in speech perception more broadly. To examine whether the left pSTS is critically responsible for AV speech integration more broadly, we measured the strength of the McGurk effect, AV facilitation effects, and AV conflict effects longitudinally over 2 years in patients undergoing surgery for intrinsic tumors in the left pSTS (n= 2) or frontal lobes (control;n= 14). Results demonstrated that left pSTS lesions impaired experience of the McGurk effect, but did not uniformly reduce visual influences on speech perception. Additionally, when multisensory behaviors were affected by a lesion, AV speech perception abilities could recover over time. Our results suggest a causal dissociation between perceptual benefits produced by congruent AV speech and perceptual modulations produced by incongruent AV speech (the McGurk effect).These data are consistent with models proposing that that the pSTS is only one of multiple critical areas necessary for AV speech interactions.
Dscam1 promotes blood cell survival inDrosophila melanogasterthrough a dual role in blood cells and neurons
Authors: Ouyang Debra , Xiao Xiaoyi , Mase Anjeli , Li Glenda , Corcoran Sean , Wang Fei , Brückner Katja
Published: September 2020

Down Syndrome Cell Adhesion Molecule 1 (Dscam1) is a receptor-like cell adhesion molecule that is conserved across the animal kingdom, but its roles in hematopoiesis remain unknown. Dscam1 related genes in vertebrates and invertebrates are key regulators of neuron morphogenesis and neuronal tiling. InDrosophila, Dscam1 in addition has roles in blood cells (hemocytes) in innate immunity and phagocytosis of pathogens. Given the anatomical and functional role of peripheral sensory neurons as microenvironments for resident hematopoietic sites in theDrosophilalarva, we sought to investigate the role of Dscam1 in this context. Interestingly, we find that Dscam1 fills the role of a previously anticipated factor in neuron-hemocyte communication that supports trophic survival: tissue specific silencing ofDscam1by in vivo RNAi in sensory neurons leads to neuron reduction, which in turn results in reduced hemocyte numbers due to apoptosis. Dscam1 silencing in hemocytes also results in a reduction of hemocytes and increased apoptosis. This cell-autonomous effect ofDscam1silencing can be mimicked by RNAi silencing ofdreadlocks(dock), suggesting that intracellular Dscam1 signaling relies on the adapter protein Dock in this system. Our findings reveal a dual role for Dscam1 inDrosophilahematopoiesis, by promoting survival of the sensory neuron microenvironments that in turn support hemocyte survival, and by promoting survival of hemocytes cell-autonomously. It will be interesting to explore possible functions of vertebrate Dscam1 related genes such as DSCAML1 in blood cells and their trophic survival.
From ovid to COVID: the metamorphosis of advanced decisions to refuse treatment into a safeguarding issue
Authors: Lyne Michael , Parker Jonathan
Published: September 2020

Purpose

This paper aims to examine advance decisions to refuse treatment (ADRTs) in the context of the COVID-19 (Coronavirus 2019) pandemic. This study considers the development of ADRTs, the lack of take up and confusion among the general public, clinicians and health and social care staff.

Design/methodology/approach

The paper is a conceptual piece that reflects on ADRTs in the particular context of COVID-19. It considers professional concerns and pronouncements on ADRTs.

Findings

ADRTs have a low take up currently. There is misunderstanding among public and professionals. There is a need for raising awareness, developing practice and a need to allay fears of misuse and abuse of ADRTs in clinical, health and social care settings.

Practical implications

The authors make recommendations that reflexive training and awareness become the norm in health and social care, that reform of ADRTs is undertaken to prevent misunderstandings and that the person becomes central in all decision-making processes.

Originality/value

This paper is original in considering ADRTs as a safeguarding issue from two perspectives: that of the person making the ADRT and being confident in respect for the decisions made; and that of clinicians and other professionals being reflexively aware of the need to accept advance decisions and not acting according to unconscious biases in times of crisis.
Rescuing intraspecific variation in human‐impacted environments
Authors: Carvalho Carolina da Silva , Lucas Marília Souza , Côrtes Marina Corrêa
Published: September 2020

Anthropogenic activities influence ongoing selective regimes leading to changes in phenotypic variation of plants and animals. The reduction of phenotypic variation may decrease populations' ability to cope with environmental changes. To counteract the increasing risk of extinction of affected populations, it is important to rescue intraspecific variability, assuring higher success of establishment and persistence under global changes.

We evaluated whether it is possible to revert phenotypic changes caused by humans using as study case a bird‐dispersed palm that presents seed size reduction due to defaunation of large‐gaped frugivores. We investigated how defaunation changes the seed size profile of each population by evaluating the coefficient of variation, mean and percentage of large phenotypes of produced and dispersed seed sizes. Simple theoretical models were used to simulate the success of two restoration strategies: (a) direct reintroduction of missing phenotypes that were originally found in the species and (b) reintroduction of large‐bodied frugivores to restore the ecological function of large‐seed dispersal. Here we discuss the importance of rescuing phenotype states in restoration strategies.

We found that defaunation changes the seed size profile by reducing the size of produced and dispersed seeds. By adding missing phenotypes one time, population mean seed size decreased back to phenotypically depauperated scenarios in eight generations. Conversely, large seed sizes could be rescued in approximately five generations after seed dispersal processes generated by large seed dispersers were re‐established.

To rescue and sustain phenotypes such as large seed sizes in palm populations is necessary to restore the seed dispersal processes by large frugivores or add missing phenotypes continuously over time. The restoration of the seed dispersal processes by large frugivores has additional value over seed addition because it would benefit other bird‐dispersed species and, therefore, may be crucial to face ongoing global change scenarios.

Synthesis and applications. Defaunation leads to character displacement within decades, having impact on populations, species and ecosystems. To prevent species extinction is paramount that phenotype variation is preserved. We propose the inclusion of phenotype restoration of wild populations as a goal for restoration framework.
Investigating the production and communication of evidence by the Productivity Commission: Apolitical, political, or somewhere in between?
Authors: Green Celia , Carey Gemma , Malbon Eleanor
Published: September 2020

The Australian Productivity Commission (PC) is an inquiry body of international renown, which Australian governments engage to obtain objective evidence‐informed recommendations regarding a wide range of policy issues. Despite its prominence in the Australian policy landscape, there has been little empirical investigation into its practices. This study sought to understand the processes by which evidence is produced and communicated by the PC, with an emphasis on understanding its role within the policy process. Our findings unsettle the notion of the PC as an arms‐length, independent body from government – revealing a more complex interplay of interpersonal strategies in both the production of evidence, shaping of recommendations, and communication of both. We identify practices undertaken by PC staff commonly attributed to policy entrepreneurs – or individuals seeking to influence policy and political processes. Our findings suggest that in different contexts and at different times, the PC shifts between being an apolitical or political actor.
Midwifery and Birth Centers Under State Medicaid Programs: Current Limits to Beneficiary Access to a High‐Value Model of Care
Authors: COURTOT BRIGETTE , HILL IAN , CROSS‐BARNET CAITLIN , MARKELL JENNY
Published: September 2020

Policy Points

Birth center services must be covered under Medicaid per federal mandate, but reimbursement and other policy barriers prevent birth centers from serving more Medicaid patients.

Midwifery care provided through birth centers improves maternal and infant outcomes and lowers costs for Medicaid beneficiaries. Birth centers offer an array of birth options and have resources to care for patients with medical and psychosocial risks.

Addressing the barriers identified in this study would promote birth centers’ participation in Medicaid, leading to better outcomes for Medicaid‐covered mothers and newborns and significant savings for the Medicaid program.

Context

Midwifery care, particularly when offered through birth centers, has shown promise in both improving pregnancy outcomes and containing costs. The national evaluation of Strong Start for Mothers and Newborns II, an initiative that tested enhanced prenatal care models for Medicaid beneficiaries, found that women receiving prenatal care at Strong Start birth centers experienced superior birth outcomes compared to matched and adjusted counterparts in typical Medicaid care. We use qualitative evaluation data to investigate birth centers’ experiences participating in Medicaid, and identify policies that influence Medicaid beneficiaries’ access to midwives and birth centers.

Methods

We analyzed data from more than 200 key informant interviews and 40 focus groups conducted during four case study rounds; a phone‐based survey of Medicaid officials in Strong Start states; and an Internet‐based survey of birth center sites. We identified themes related to access to midwives and birth centers, focusing on influential Medicaid policies.

Findings

Medicaid beneficiaries chose birth center care because they preferred midwife providers, wanted a more natural birth experience, or in some cases sought certain pain relief methods or birth procedures not available at hospitals. However, Medicaid enrollees currently have less access to birth centers than privately insured women. Many birth centers have difficulty contracting with managed care organizations and participating in Medicaid value‐based delivery system reforms, and birth center reimbursement rates are sometimes too low to cover the actual cost of care. Some birth centers significantly limit Medicaid business because of low reimbursement rates and threats to facility sustainability.

Conclusions

Medicaid beneficiaries do not have the same access to maternity care providers and birth settings as their privately insured counterparts. Medicaid policy barriers prevent some birth centers from serving more Medicaid patients, or threaten the financial sustainability of centers. By addressing these barriers, more Medicaid beneficiaries could access care that is associated with positive birth outcomes for mothers and newborns, and the Medicaid program could reap significant savings.
Effects of threat and efficacy messages on expected adherence to decontamination protocols in an immersive simulated chemical incident: A randomized controlled experiment
Authors: Symons Charles , Amlôt Richard , Carter Holly , Rubin G. James
Published: September 2020

The UK’s Initial Operational Response (IOR) decontamination protocol requires that chemically contaminated casualties remove contaminated clothing (disrobe) and then apply water or absorbent materials to skin. The health‐protective efficacy of the protocol is predicated on casualties quickly accepting both the need to act and the fact that this protocol is an effective action. The aim of this study was to test whether adherence is affected by the presentation of information by first responders about the severity and likelihood of contamination (Threat) and the health‐protective efficacy of IOR procedures (efficacy). A double‐blind randomized controlled experiment (N = 132) with a 3x2 independent measures design (registration number: ISRCTN17886859) was used to assess the effects of threat and efficacy on behavioural expectations during a simulated chemical incident, presented as an immersive video. Results indicated that addressing the threat of contamination made participants more likely to expect themselves to disrobe were the situation real. Emphasizing the efficacy of protective action made participants more likely to expect themselves to apply absorbent materials to skin and had an indirect positive effect on disrobing expectations, mediated by efficacy perceptions. We recommend that first responders explicitly address the threat of contamination and efficacy of decontamination when communicating with chemically contaminated casualties.
Controversies in the prevention of spontaneous preterm birth in asymptomatic women: an evidence summary and expert opinion
Authors: Goodfellow Laura , Care Angharad , Alfirevic Zarko
Published: September 2020

Preterm birth prevention is multifaceted and produces many nuanced questions. This review addresses six important clinical questions about preterm birth prevention as voted for by members of the UK Preterm Clinical Network. The questions cover the following areas: preterm birth prevention in ‘low‐risk’ populations; screening for asymptomatic genital tract infection in women at high risk of preterm birth; cervical length screening with cerclage or vaginal pessary in situ; cervical shortening whilst using progesterone; use of vaginal progesterone in combination with cervical cerclage; and optimal advice about intercourse for women at high risk of preterm birth.
The Heterogeneous Effects of Standards on Agricultural Trade Flows
Authors: Fiankor Dela‐Dem Doe , Haase Oliver‐Ken , Brümmer Bernhard
Published: September 2020

This article uses a theory‐based translog gravity model to investigate the heterogeneous effects of food standards on aggregate agricultural trade. We revisit the ‘standards‐as‐barriers‐to‐trade’ debate with a distinctive twist. In contrast to existing works, we show that standards reduce trade but even more so for countries that trade smaller volumes. Our identification strategy exploits the within‐country variation in specific trade concerns. We confirm that stricter importer standards are indeed trade‐restrictive. However, the estimated trade cost elasticity varies depending on how intensively two countries trade. Specifically, it decreases in magnitude with an increasing import share of the exporter in the importing country's total imports. The reason is simple but intuitive; bigger trading partners find it more profitable to invest in meeting the costs of importer‐specific standards. This work is novel in showing that the standards–trade debate misses out on an important heterogeneity driven by existing import shares. Liberalising non‐tariff measures will favour smaller trading partners more than well‐established ones.
Consumer preference for dried mango attributes: A conjoint study among Dutch, Chinese, and Indonesian consumers
Authors: Sulistyawati Ita , Dekker Matthijs , Verkerk Ruud , Steenbekkers Bea
Published: September 2020

One way to add value to tropical fruit and increase its availability in the global market is to develop new, less perishable, products from fresh fruit. The purpose of this study is to compare the perception of key quality attributes and preferences of dried mango between consumers with different familiarity and health consciousness. This study surveyed respondents from China, Indonesia, and the Netherlands via an adaptive choice‐based conjoint method (n = 483) to evaluate intrinsic quality attributes that influenced consumer preference for dried mango. Consumers in different countries have different texture, taste, and color preferences for dried mango. The most important attribute for the Dutch and Chinese was “free from extra ingredients”, while for Indonesians, it was the texture. Familiarity with dried mango and health consciousness do not influence consumer preference of intrinsic attributes of dried mango. Different preferences of intrinsic attributes of dried mango between countries are related to cultural differences. This study provides useful insights for food manufacturers into the significance of key intrinsic quality attributes in developing dried mango.

Practical Application

Intrinsic quality parameters of dried mango are not perceived in the same way by every consumer and this is related to cultural differences. Crispy texture is important only for Indonesian consumers, while “free from extra ingredients” is the most important for Dutch and Chinese consumers. This information is relevant when developing dried mango products for the respective markets.
Continuous spectrum of glucose dysmetabolism due to the KCNJ11 gene mutation—Case reports and review of the literature
Authors: He Binbin , Li Xia , Zhou Zhiguang
Published: September 2020

The KCNJ11 gene encodes the Kir6.2 subunit of the adenosine triphosphate‐sensitive potassium (KATP) channel, which plays a key role in insulin secretion. Monogenic diseases caused by KCNJ11 gene mutation are rare and easily misdiagnosed. It has been shown that mutations in the KCNJ11 gene are associated with neonatal diabetes mellitus (NDM), maturity‐onset diabetes of the young 13 (MODY13), type 2 diabetes mellitus (T2DM), and hyperinsulinemic hypoglycemia. We report four patients with KCNJ11 gene mutations and provide a systematic review of the literature. A boy with diabetes onset at the age of 1 month was misdiagnosed as type 1 diabetes mellitus (T1DM) for 12 years and received insulin therapy continuously, resulting in poor glycemic control. He was diagnosed as NDM with KCNJ11 E322K gene mutation, and glibenclamide was given to replace exogenous insulin. The successful transfer time was 4 months, much longer than the previous unsuccessful standard of 4 weeks. The other three patients were two sisters and their mother; the younger sister was misdiagnosed with T1DM at 13 years old, while the elder sister was diagnosed with diabetes (type undefined) at 16 years old. They were treated with insulin for 3 years, with poor glycemic control. Their mother was diagnosed with T2DM and achieved good glycemia control with glimepiride. They were diagnosed as MODY13 because of the autosomal dominant inheritance of two generations, early onset of diabetes before 25 years of age in the two sisters, and the presence of the KCNJ11 N48D gene mutation. All patients successfully transferred to sulfonylureas with excellent glycemic control. Therefore, the wide spectrum of clinical phenotypes of glucose dysmetabolism caused by KCNJ11 should be recognized to reduce misdiagnosis and implement appropriate treatment.
Is the Tone of Risk Disclosures in MD&As Relevant to Debt Markets? Evidence from the Pricing of Credit Default Swaps*
Authors: Wang Ke
Published: September 2020

This paper examines whether the tone of corporate textual disclosures related to risk and uncertainty conveys relevant information to the credit default swap (CDS) market. Prior studies largely focus on the amount of risk disclosures and provide inconclusive evidence on the usefulness of risk disclosures for investors in assessing firm risk. Using a large sample of textual risk disclosures in the Management's Discussion and Analysis (MD&A) section of 10‐K and 10‐Q filings, I predict and find that the change in CDS spreads over the three‐day window surrounding the 10‐K/Q filing date is positively associated with the pessimism of the language used in the risk disclosures. I conduct several analyses to show that the effect of the tone of risk disclosures is distinguishable from that of the amount of such disclosures. Cross‐sectional analyses reveal that the CDS market reaction to the tone of MD&A risk disclosures is more pronounced for reference entities closer to default, consistent with creditors' particular concern about downside risk. Further, the CDS market reacts more significantly to the tone of MD&A risk disclosures for reference entities with a weaker information environment. Overall, these results support the view that the tone of textual risk disclosures in MD&As has information content for investors in the CDS market in particular and debt markets in general. My findings improve the understanding of textual risk disclosures by showing that the tone and the amount of such disclosures have different implications for debt market investors' risk perceptions.
Scenarios for valuing sample information in natural resources
Authors: Williams Byron K. , Brown Eleanor D.
Published: September 2020

Uncertainty is ubiquitous in natural resource systems, science and management. Sample data are obtained in order to reduce uncertainty, thereby increasing knowledge and improving resource management, but sampling always comes at a cost of some sort. Is that cost worthwhile? Analysis of the value of sample information (VSI) addresses this question.

In this paper we develop the valuation of sample information in terms of five elements: (a) a system whose attributes are the focus of analysis; (b) a range of management actions that affect the system's status; (c) uncertainty about system status or structure, as characterized by initial (prior) probabilities of possible system states or structures; (d) an experiment or other information source that produces new data points and updated (posterior) probabilities; and (e) a value measure that is a function of the management action taken, conditional on either the system state or structure.

We describe five scenarios for analysing the VSI under uncertainty about system structure and state. Scenarios 1–3 comprise analyses of conditional, expected and optimal expected values of sample information. They focus primarily on choice of management adaptations with new information. Scenarios 4 and 5 involve pre‐selected management actions, and are useful for comparing designs of data collection rather than for choosing a management action. These last scenarios expand the framework for VSI to include actions that have been selected independently of the updating of uncertainty.

We discuss other extensions of VSI analysis, which include spatial applications, hybrid scenarios, applications involving dynamic systems, and a focus on costs rather than net benefits.

Value of sample information analysis holds promise in emerging areas of ecology such as ecological forecasting and the use of remote sensing in conservation, where potential new data from models and satellites can be evaluated in advance, thereby allowing more efficient prioritization of scientific efforts. More generally, VSI can contribute to better ecological understanding and more effective management in a wide range of ecological situations.