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Abstract Metal-organic frameworks (MOFs) are currently widely investigated for a number of potential biomedicinal applications, with particular focus on nanoscale drug delivery. Nanomedicine in general comes with specific challenges to ensure reproducibility of results, including batch-to-batch variations in ostensibly the same nanomaterial, differences in synthetic and analytical practices, intrinsic issues with in vitro culturing and assaying, and a lack of availability of raw data for comparative analysis. This perspective provides an overview of reproducibility issues in the context of MOFs in nanomedicine, covering their preparation and in vitro analysis. The commonly studied UiO-66 is used as an exemplar to highlight variability in synthetic and characterisation practices, as well as in the publication and availability of data. Some common roadblocks to reproducibility are highlighted, alongside suggestions and resources for best practice.

ABSTRACTWhat cultural ecosystem services (CES) do people perceive in their immediate surroundings, and what sensory experiences are linked to these ecosystem services? And how are these CES and experiences expressed in natural language? In this study, we used data generated through a gamified application called Window Expeditions, where people uploaded short descriptions of landscapes they were able to experience through their windows during the COVID-19 pandemic. We used a combination of annotation, close reading and distant reading using natural language processing and graph analysis to extract CES and sensory experiences and link these to biophysical landscape elements. In total, 272 users contributed 373 descriptions in English across more than 40 countries. Of the cultural ecosystem services, recreation was the most prominently described, followed by heritage, identity and tranquility. Descriptions of sensory experiences focused on the visual but also included auditory experiences and touch and feel. Sensory experiences and cultural ecosystem services varied according to biophysical landscape elements, with, for example, animals being more associated with sound and touch/feel and heritage being more associated with moving objects and the built environment. Sentiments also varied across the senses, with the visual being more strongly associated with positive experiences than other senses. This study showed how a hybrid approach combining manual analysis and natural language processing can be productively applied to landscape descriptions generated by members of the public, and how CES on everyday lived landscapes can be extracted from such data sources.

City Walking Tour Videos (CWTVs) are a novel source of Volunteered Geographic Information providing street-level imagery through video sharing platforms such as YouTube. We demonstrate that these videos contain rich information for urban analytical applications, by conducting a mobility study. We detect transport modes with a focus on active (pedestrians and cyclists) and motorised mobility (cars, motorcyclists and trucks). We chose the City of Paris as our area of interest given the rapid expansion of the bicycle network as a response to the Covid-19 pandemic and compiled a video corpus encompassing more than 66 hours of video footage. Through the detection of street names in the video and placename containing timestamps we extracted and georeferenced 1169 locations at which we summarise the detected transport modes. Our results show high potential of CWTVs for studying urban mobility applications. We detected significant shifts in the mobility mix before and during the pandemic as well as weather effects on the volumes of pedestrians and cyclists. Combined with the observed increase in data availability over the years we suggest that CWTVs have considerable potential for other applications in the field of urban analytics.

ABSTRACT The two species that account for most cases of Acinetobacter-associated bacteremia in the United Kingdom are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and Acinetobacter baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii, and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health. This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30, respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defense systems and harbored a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm, and infect both in vivo and in in vitro models of infection. This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesize that the fact that it only harbors a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram-negative bacteria.IMPORTANCEAcinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived bloodstream infections in England and Wales. In contrast to the well-studied and often highly drug-resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not, and could inform future novel treatment strategies.

Blastocystis is a genus of intestinal stramenopiles that infect vertebrates, and may cause disease of the alimentary tract. Currently, at least 40 genotypes (“subtypes”) of Blastocystis are recognised worldwide based on sequence data for the small subunit of the nuclear ribosomal RNA (SSU-rRNA) gene. Despite the numerous studies of Blastocystis worldwide, very few studies have explored Blastocystis in wild animals, particularly in Australia. Here, we used a PCR-based next generation sequencing (NGS)–phylogenetic approach to genetically characterise and classify Blastocystis variants from selected wildlife in the Australian state of Victoria. In total, 1658 faecal samples were collected from nine host species, including eastern grey kangaroo, swamp wallaby, common wombat, deer, European rabbit, canines and emu. Genomic DNA was extracted from these samples, a 500 bp region of the SSU-rRNA gene amplified by polymerase chain reaction (PCR) and, then, a subset of samples sequenced using Illumina technology. Primary PCR detected Blastocystis in 482 of the 1658 samples (29%), with the highest percentage in fallow deer (63%). Subsequent, Illumina-based sequencing of a subset of 356 samples revealed 55 distinct amplicon sequence variants (ASVs) representing seven currently-recognised subtypes (STs) [ST13 (prominent in marsupials), ST10, ST14, ST21, ST23, ST24 and ST25 (prominent in deer)] and two novel STs (ST45 and ST46) in marsupials. Mixed infections of different STs were observed in macropods, deer, emu and canids (fox, feral dog or dingo), but no infection was detected in rabbits or wombats. This study reveals marked genetic diversity within Blastocystis in a small number of species of wild animals in Australia, suggesting complexity in the genetic composition and transmission patterns of members of the genus Blastocystis in this country.

The applicability of electrical impedance tomography (EIT) in birds is unknown. This study aimed to evaluate the use of EIT in anaesthetised chickens in four recumbency positions. Four adult Hyline chickens were anaesthetised with isoflurane in oxygen, and intubated endotracheally for computed tomography (CT). A rubber belt was placed around the coelom caudal to the shoulder joint. A chicken-specific finite element (FE) model, which is essential to generate anatomically accurate functional EIT images for analysis, was constructed based on the CT images obtained at the belt level. Ten additional chickens were anaesthetised with the same protocol. An EIT electrode belt was placed at the same location. The chickens were breathing spontaneously and positioned in dorsal, ventral, right and left lateral recumbency in a randomised order. For each recumbency, raw EIT data were collected over 2 min after 13 min of stabilisation. The data were reconstructed into functional EIT images. EIT variables including tidal impedance variation (TIV), centre of ventilation right to left (CoVRL) and ventral to dorsal (CoVVD), right to left (RL) ratio, impedance change (ΔZ) and eight regional impedance changes including the dorsal, central-dorsal, central-ventral and ventral regions of the right and left regions were analysed. Four breathing patterns (BrP) were observed and categorised based on the expiratory curve. A linear mixed model was used to compare EIT variables between recumbencies. Fisher's exact test was used to compare the frequencies of breathing patterns for each recumbency. The ΔZ observed was synchronous to ventilation, and represented tidal volume of the cranial air sacs as confirmed by CT. Significant differences were found in CoVVD and regional impedance changes between dorsal and ventral recumbencies (P < 0.05), and in CoVRL, RL ratio and regional impedance changes between right and left recumbencies (P < 0.05), which suggested a tendency for the distribution of ventilation to shift towards non-dependent air sacs. No differences were found for TIV and respiratory rate between recumbencies. Recumbency had a significant effect on the frequencies of each of the four BrPs (P = 0.001). EIT can monitor the magnitude and distribution of ventilation of the cranial air sacs in different recumbencies in anaesthetised chickens.

Abstract Background Frailty is prevalent in older people with chronic kidney disease (CKD) and robust evidence supporting the benefit of dialysis in this setting is lacking. We aimed to measure frailty and quality of life (QOL) longitudinally in older people with advanced CKD and assess the impact of dialysis initiation on frailty, QOL and mortality. Methods Outpatients aged ≥65 with an eGFR ≤ 20ml/minute/1.73m2 were enrolled in a prospective observational study and followed up four years later. Frailty status was measured using a Frailty Index (FI), and QOL was evaluated using the EuroQol 5D-5L instrument. Mortality and dialysis status were determined through inspection of electronic records. Results Ninety-eight participants were enrolled. Between enrolment and follow-up, 36% of participants commenced dialysis and 59% died. Frailty prevalence increased from 47% at baseline to 86% at follow-up (change in median FI = 0.22, p

Studies assessing animal pain in veterinary research are often performed primarily for the benefit of animals. Frequently, the goal of these studies is to determine whether the analgesic effect of a novel treatment is clinically meaningful, and therefore has the capacity to improve the welfare of treated animals. To determine the treatment effect of a potential analgesic, control groups are necessary to allow comparison. There are negative control groups (where pain is unattenuated) and positive control groups (where pain is attenuated). Arising out of animal welfare concerns, there is growing reluctance to use negative control groups in pain studies. But for studies where pain is experimentally induced, the absence of a negative control group removes the opportunity to demonstrate that the study methods could differentiate a positive control intervention from doing nothing at all. For studies that are controlled by a single comparison group, the capacity to distinguish treatment effects from experimental noise is more difficult; especially considering that pain studies often involve small sample sizes, small and variable treatment effects, systematic error and use pain assessment measures that are unreliable. Due to these limitations, and with a focus on farm animals, we argue that many pain studies would be enhanced by the simultaneous inclusion of positive and negative control groups. This would help provide study-specific definitions of pain and pain attenuation, thereby permitting more reliable estimates of treatment effects. Adoption of our suggested refinements could improve animal welfare outcomes for millions of animals globally.

The use of bicycles can provide myriad benefits to society, especially in crowded urban centres where other modes of transport are at or near capacity. However, integrating cycling into policy and planning requires more comprehensive data about their use in space and time. Current approaches, using sparse networks of counters provide one possible route to more comprehensive data. In this paper we investigate another, using data collected from Paris’ bicycle sharing system to explore use during 2020. We chose 2020 as a test year because the use of bicycles was strongly influenced by the COVID-19 pandemic, allowing us to explore how bicycle use adapted to both legal and environmental influences. We used interactive visualization to allow hypothesis generation and data exploration, before analysing bicycle use as a function of weather and COVID-19 restrictions. Our results show that bicycle sharing system data and Paris’ counters both capture very similar behaviour patterns, and therefore bicycle sharing system data are a reliable proxy for overall cycling behaviour, providing finer spatial granularity than existing sparse counter networks. Seasonally, precipitation influenced bicycle use more strongly in 2020 than COVID-19 measures.

Background. Clinical Practice Guidelines suggest that frailty be measured during kidney transplant eligibility assessments. Yet it is not known how frailty is best assessed in this setting or whether its assessment is acceptable to patients. We aimed to examine the construct validity and feasibility of Frailty Index (FI) assessment among patients attending a kidney transplant assessment clinic and to explore patients’ perspectives on frailty and the acceptability of its routine assessment. Methods. A 58-item FI was calculated for 147 clinic patients. Semistructured interviews were conducted with a subgroup of 29 patients. The FI was validated against normative FI characteristics (mean, distribution, limit), age, and the Estimated Post-Transplant Survival Score. Feasibility was assessed using descriptive statistics. Qualitative data were analyzed using reflexive thematic analysis. Results. The mean FI was 0.23 (±0.10, normal distribution, limit 0.53). FI increased with age and Estimated Post-Transplant Survival score. The FI was completed for 62.8% of eligible patients (147/234). The median completion time was 10 min, and completion rate (with no missing data) was 100%. Four themes were identified: perceptions of frailty, acceptability, perceived benefits, and risks of frailty measurement. Patients linked frailty with age and adverse outcomes, and most did not consider themselves frail. Patients reported that the FI was quick, simple, and efficient. They felt that frailty assessment is relevant to transplant eligibility and should be used to address potentially reversible factors. Conclusions. The FI demonstrated construct validity and was feasible and acceptable in this clinic setting. The challenge is ensuring that routine assessments lead to better care.

Abstract Background Modulating the microbiota in the large intestine of kidney transplant recipients through prebiotic supplementation may prevent infectious complications from occurring. To date, there have been no interventional trials which have investigated this novel treatment in kidney transplantation. The aim of PREBIOTIC is to assess the feasibility of performing a randomised controlled trial of prebiotics in reducing infections and gastrointestinal symptoms in kidney transplant recipients. Methods Sixty kidney transplant patients will be recruited to a double-blind, placebo-controlled, randomised feasibility trial. Patients will be provided with prebiotic therapy or placebo for 4 to 6 weeks. Outcomes will include recruitment, adherence, tolerance, retention, laboratory parameters (including serum indoxyl sulphate, ρ-cresyl sulphate and stool collection), patients’ self-assessed quality of life, gastrointestinal symptoms and clinical outcomes. Discussion This trial will assess the feasibility of prebiotic supplementation in kidney transplant recipients. Prebiotics not only may alter the gut microbiota and their inherent metabolism and production of uraemic toxins but also may prevent infections from occurring in kidney transplant recipients. Trial registration Australian New Zealand Clinical Trials Registry number ACTRN12618001057279p. The date of registration was 25th June 2018, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375370&isReview=true .

Abstract Objective There are few multinational studies on gestational trophoblastic neoplasia (GTN) treatment outcomes in South America. The purpose of this study was to assess the clinical presentation, treatment outcomes, and factors associated with chemoresistance in low-risk postmolar GTN treated with first-line single-agent chemotherapy in three South American centers. Methods Multicentric, historical cohort study including women with International Federation of Gynecology and Obstetrics (FIGO)-staged low-risk postmolar GTN attending centers in Argentina, Brazil, and Colombia between 1990 and 2014. Data were obtained on patient characteristics, disease presentation, and treatment response. Logistic regression was used to assess the relationship between clinical factors and resistance to first-line single-agent treatment. A multivariate analysis of the clinical factors significant in univariate analysis was performed. Results A total of 163 women with low-risk GTN were included in the analysis. The overall rate of complete response to first-line chemotherapy was 80% (130/163). The rates of complete response to methotrexate or actinomycin-D as first-line treatment, and actinomycin-D as second-line treatment postmethotrexate failure were 79% (125/157), 83% (⅚), and 70% (23/33), respectively. Switching to second-line treatment due to chemoresistance occurred in 20.2% of cases (33/163). The multivariate analysis demonstrated that patients with a 5 to 6 FIGO risk score were 4.2-fold more likely to develop resistance to first-line single-agent treatment (p= 0.019). Conclusion 1) At presentation, most women showed clinical characteristics favorable to a good outcome, 2) the overall rate of sustained complete remission after first-line single-agent treatment was comparable to that observed in developed countries, 3) a FIGO risk score of 5 or 6 is associated with development of resistance to first-line single-agent chemotherapy.

Androgen deprivation therapy is a cornerstone of treatment for advanced prostate cancer, and the development of castrate-resistant prostate cancer (CRPC) is the primary cause of prostate cancer-related mortality. While CRPC typically develops through a gain in androgen receptor (AR) signaling, a subset of CRPC will lose reliance on the AR. This process involves genetic, epigenetic, and hormonal changes that promote cellular plasticity, leading to AR-indifferent disease, with neuroendocrine prostate cancer (NEPC) being the quintessential example. NEPC is enriched following treatment with second-generation anti-androgens and exhibits resistance to endocrine therapy. Loss of RB1, TP53, and PTEN expression and MYCN and AURKA amplification appear to be key drivers for NEPC differentiation. Epigenetic modifications also play an important role in the transition to a neuroendocrine phenotype. DNA methylation of specific gene promoters can regulate lineage commitment and differentiation. Histone methylation can suppress AR expression and promote neuroendocrine-specific gene expression. Emerging data suggest that EZH2 is a key regulator of this epigenetic rewiring. Several mechanisms drive AR-dependent castration resistance, notably AR splice variant expression, expression of the adrenal-permissive 3βHSD1 allele, and glucocorticoid receptor expression. Aberrant epigenetic regulation also promotes radioresistance by altering the expression of DNA repair- and cell cycle-related genes. Novel therapies are currently being developed to target these diverse genetic, epigenetic, and hormonal mechanisms promoting lineage plasticity-driven NEPC.

Events profoundly influence human-environment interactions. Through repetition, some events manifest and amplify collective behavioral traits, which significantly affects landscapes and their use, meaning, and value. However, the majority of research on reaction to events focuses on case studies, based on spatial subsets of data. This makes it difficult to put observations into context and to isolate sources of noise or bias found in data. As a result, inclusion of perceived aesthetic values, for example, in cultural ecosystem services, as a means to protect and develop landscapes, remains problematic. In this work, we focus on human behavior worldwide by exploring global reactions to sunset and sunrise using two datasets collected from Instagram and Flickr. By focusing on the consistency and reproducibility of results across these datasets, our goal is to contribute to the development of more robust methods for identifying landscape preference using geo-social media data, while also exploring motivations for photographing these particular events. Based on a four facet context model, reactions to sunset and sunrise are explored for Where, Who, What, and When. We further compare reactions across different groups, with the aim of quantifying differences in behavior and information spread. Our results suggest that a balanced assessment of landscape preference across different regions and datasets is possible, which strengthens representativity and exploring the How and Why in particular event contexts. The process of analysis is fully documented, allowing transparent replication and adoption to other events or datasets.

Abstract Background Patients with multiple myeloma (MM) were excluded from the original SARS-CoV-2 mRNA vaccine trials, which may influence vaccine hesitancy in this population. We prospectively characterized the safety and immunogenicity of two-dose SARS-CoV-2 mRNA vaccination in 44 patients with MM, who underwent vaccination from 12/17/2020 to 3/18/2021. Results Rates adverse reactions were low and consistent with those documented in vaccine trials. Among those on MM therapy, 93% developed detectable anti-receptor binding domain (RBD) antibodies after dose 2, while 94% of patients not on MM therapy seroconverted. Conclusions Two-dose SARS-CoV-2 mRNA vaccination is mildly reactogenic and leads to high rates of seroconversion in patients with MM. These findings can provide reassurance to MM patients who are hesitant to receive SARS-CoV-2 mRNA vaccines.

IntroductionEvidence of animal personality and behavioral syndromes is widespread across animals, yet the development of these traits remains poorly understood. Previous research has shown that exposure to predators, heterospecifics, and urbanized environments can influence personality and behavioral syndromes. Yet, to date, the influence of early social experiences with conspecifics on the development of adult behavioral traits is far less known. We use swordtail fish (Xiphophorus nigrensis), a species with three genetically-determined male mating strategies (courtship display, coercion, or mixed strategy) to assess how different early-life social experiences shape adult behavioral development.MethodsWe raised female swordtails from birth to adulthood in density-controlled sexual-social treatments that varied in the presence of the type of male mating tactics (coercers only, displayers only, coercers and displayers, and mixed-strategists only). At adulthood, we tested females’ boldness, shyness, aggression, sociality, and activity.ResultsWe found that the number of different mating strategies females were raised with (social complexity) shaped behavioral development more than any individual mating strategy. Females reared in complex environments with two male mating tactics were bolder, less shy, and less aggressive than females reared with a single male mating tactic (either courtship only or coercion only). Complex sexual-social environments produced females with behavioral syndromes (correlations between aggression and activity, shyness and aggression, and social interaction and activity), whereas simple environments did not.DiscussionImportantly, the characteristics of these socially-induced behavioral syndromes differ from those driven by predation, but converge on characteristics emerging from animals found in urban environments. Our findings suggest that complexity of the sexual-social environment shapes the development of personality and behavioral syndromes to facilitate social information gathering. Furthermore, our research highlights the previously overlooked influence of sexual selection as a significant contributing factor to diverse behavioral development.

This study proposes a method that can help in identifying potential locations for improvements of cycling infrastructures. It addresses the need for simple and effective methods to support decision-making in bicycle planning. The city of Paris is used as a case study area because it has made considerable efforts to improve cycling infrastructures and to become more bicycle-friendly in recent years. The method (1) identifies potential locations for improvements of bicycle infrastructures on a street level and (2) on a city level considering accessibility to important destinations. The main data used in this project is street data from OpenStreetMap (OSM) and cycling infrastructure data from the Atelier parisien d’urbanisme (Apur). The proposed method can be applied with commonly available data, has clear outcomes, is reproducible, and can be applied to different case study areas. We produced a map of bicycle suitability across all of Paris, and validated it for the 30 longest segments in the city with lower bike suitability. Our validation showed that combining OSM and Apur data led to a reliable dataset, with which we modelled bikeability using the underlying network overlain on a 250 m resolution grid and destinations representing leisure activities, education, shopping, city functions and public transport. The resulting map identifies regions of the city with poor bikeability, where improvements to cycling infrastructure should be investigated.

Computing trajectory similarity is a fundamental operation in movement analytics, required in search, clustering, and classification of trajectories, for example. Yet the range of different but interrelated trajectory similarity measures can be bewildering for researchers and practitioners alike. This paper describes a systematic comparison and methodical exploration of trajectory similarity measures. Specifically, this paper compares five of the most important and commonly used similarity measures: dynamic time warping (DTW), edit distance (EDR), longest common subsequence (LCSS), discrete Fréchet distance (DFD), and Fréchet distance (FD). The paper begins with a thorough conceptual and theoretical comparison. This comparison highlights the similarities and differences between measures in connection with six different characteristics, including their handling of a relative versus absolute time and space, tolerance to outliers, and computational efficiency. The paper further reports on an empirical evaluation of similarity in trajectories with contrasting properties: data about constrained bus movements in a transportation network, and the unconstrained movements of wading birds in a coastal environment. A set of four experiments: a. creates a measurement baseline by comparing similarity measures to a single trajectory subjected to various transformations; b. explores the behavior of similarity measures on network-constrained bus trajectories, grouped based on spatial and on temporal similarity; c. assesses similarity with respect to known behavioral annotations (flight and foraging of oystercatchers); and d. compares bird and bus activity to examine whether they are distinguishable based solely on their movement patterns. The results show that in all instances both the absolute value and the ordering of similarity may be sensitive to the choice of measure. In general, all measures were more able to distinguish spatial differences in trajectories than temporal differences. The paper concludes with a high-level summary of advice and recommendations for selecting and using trajectory similarity measures in practice, with conclusions spanning our three complementary perspectives: conceptual, theoretical, and empirical.

Abstract A mouse model of human Familial Adenomatous Polyposis responds favorably to pharmacological inhibition of 5′-methylthioadenosine phosphorylase (MTAP). Methylthio-DADMe-Immucillin-A (MTDIA) is an orally available, transition state analogue inhibitor of MTAP. 5′-Methylthioadenosine (MTA), the substrate for MTAP, is formed in polyamine synthesis and is recycled by MTAP to S-adenosyl-l-methionine (SAM) via salvage pathways. MTDIA treatment causes accumulation of MTA, which inhibits growth of human head and neck (FaDu) and lung (H359, A549) cancers in immunocompromised mouse models. We investigated the efficacy of oral MTDIA as an anti-cancer therapeutic for intestinal adenomas in immunocompetent APCMin/+ mice, a murine model of human Familial Adenomatous Polyposis. Tumors in APCMin/+ mice were decreased in size by MTDIA treatment, resulting in markedly improved anemia and doubling of mouse lifespan. Metabolomic analysis of treated mice showed no changes in polyamine, methionine, SAM or ATP levels when compared with control mice but indicated an increase in MTA, the MTAP substrate. Generation of an MTDIA-resistant cell line in culture showed a four-fold amplification of the methionine adenosyl transferase (MAT2A) locus and expression of this enzyme. MAT2A is downstream of MTAP action and catalyzes synthesis of the SAM necessary for methylation reactions. Immunohistochemical analysis of treated mouse intestinal tissue demonstrated a decrease in symmetric dimethylarginine, a PRMT5-catalyzed modification. The anti-cancer effects of MTDIA indicate that increased cellular MTA inhibits PRMT5-mediated methylations resulting in attenuated tumor growth. Oral dosing of MTDIA as monotherapy has potential for delaying the onset and progression of colorectal cancers in Familial Adenomatous Polyposis (FAP) as well as residual duodenal tumors in FAP patients following colectomy. MTDIA causes a physiologic inactivation of MTAP and may also have efficacy in combination with inhibitors of MAT2A or PRMT5, known synthetic-lethal interactions in MTAP −/− cancer cell lines.

Abstract Background Larvae of the Australian sheep blowfly, Lucilia cuprina, parasitise sheep by feeding on skin excretions, dermal tissue and blood, causing severe damage known as flystrike or myiasis. Recent advances in -omic technologies and bioinformatic data analyses have led to a greater understanding of blowfly biology and should allow the identification of protein families involved in host-parasite interactions and disease. Current literature suggests that proteins of the SCP (Sperm-Coating Protein)/TAPS (Tpx-1/Ag5/PR-1/Sc7) (SCP/TAPS) superfamily play key roles in immune modulation, cross-talk between parasite and host as well as developmental and reproductive processes in parasites. Methods Here, we employed a bioinformatics workflow to curate the SCP/TAPS protein gene family in L. cuprina. Protein sequence, the presence and number of conserved CAP-domains and phylogeny were used to group identified SCP/TAPS proteins; these were compared to those found in Drosophila melanogaster to make functional predictions. In addition, transcription levels of SCP/TAPS protein-encoding genes were explored in different developmental stages. Results A total of 27 genes were identified as belonging to the SCP/TAPS gene family: encoding 26 single-domain proteins each with a single CAP domain and a solitary double-domain protein containing two conserved cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domains. Surprisingly, 16 SCP/TAPS predicted proteins formed an extended tandem array spanning a 53 kb region of one genomic region, which was confirmed by MinION long-read sequencing. RNA-seq data indicated that these 16 genes are highly transcribed in all developmental stages (excluding the embryo). Conclusions Future work should assess the potential of selected SCP/TAPS proteins as novel targets for the control of L. cuprina and related parasitic flies of major socioeconomic importance.

Abstract Background The parasitic flatworm Clonorchis sinensis inhabits the biliary tree of humans and other piscivorous mammals. This parasite can survive and thrive in the bile duct, despite exposure to bile constituents and host immune attack. Although the precise biological mechanisms underlying this adaptation are unknown, previous work indicated that Niemann-pick type C2 (NPC2)-like sterol-binding proteins might be integral in the host-parasite interplay. Expansions of this family in some invertebrates, such as arthropods, have shown functional diversification, including novel forms of chemoreception. Thus, here we curated the NPC2-like protein gene complement in C. sinensis, and predicted their conserved and/or divergent functional roles. Methods We used an established comparative genomic-bioinformatic approach to curate NPC2-like proteins encoded in published genomes of Korean and Chinese isolates of C. sinensis. Protein sequence and structural homology, presence of conserved domains and phylogeny were used to group and functionally classify NPC2-like proteins. Furthermore, transcription levels of NPC2-like protein-encoding genes were explored in different developmental stages and tissues. Results Totals of 35 and 32 C. sinensis NPC2-like proteins were predicted to be encoded in the genomes of the Korean and Chinese isolates, respectively. Overall, these proteins had low sequence homology and high variability of sequence alignment coverage when compared with curated NPC2s. Most C. sinensis proteins were predicted to retain a conserved ML domain and a conserved fold conformation, with a large cavity within the protein. Only one protein sequence retained the conserved amino acid residues required in bovine NPC2 to bind cholesterol. Non-canonical C. sinensis NPC2-like protein-coding domains clustered into four distinct phylogenetic groups with members of a group frequently encoded on the same genome scaffolds. Interestingly, NPC2-like protein-encoding genes were predicted to be variably transcribed in different developmental stages and adult tissues, with most being transcribed in the metacercarial stage. Conclusions The results of the present investigation confirms an expansion of NPC2-like proteins in C. sinensis, suggesting a diverse array of functions beyond sterol binding and transport. Functional explorations of this protein family should elucidate the mechanisms enabling the establishment and survival of C. sinensis and related flukes in the biliary systems of mammalian hosts.

Abstract Increasing access to next‐generation sequencing (NGS) technologies is revolutionizing the life sciences. In disease ecology, NGS‐based methods have the potential to provide higher‐resolution data on communities of parasites found in individual hosts as well as host populations. Here, we demonstrate how a novel analytical method, utilizing high‐throughput sequencing of PCR amplicons, can be used to explore variation in blood‐borne parasite (Theileria—Apicomplexa: Piroplasmida) communities of African buffalo at higher resolutions than has been obtained with conventional molecular tools. Results reveal temporal patterns of synchronized and opposite fluctuations of prevalence and relative abundance of Theileria spp. within the host population, suggesting heterogeneous transmission across taxa. Furthermore, we show that the community composition of Theileria spp. and their subtypes varies considerably between buffalo, with differences in composition reflected in mean and variance of overall parasitemia, thereby showing potential to elucidate previously unexplained contrasts in infection outcomes for host individuals. Importantly, our methods are generalizable as they can be utilized to describe blood‐borne parasite communities in any host species. Furthermore, our methodological framework can be adapted to any parasite system given the appropriate genetic marker. The findings of this study demonstrate how a novel NGS‐based analytical approach can provide fine‐scale, quantitative data, unlocking opportunities for discovery in disease ecology.

ObjectiveTo relate preevacuation platelet count and leukogram findings, especially neutrophil/lymphocyte ratios (NLR) and platelet/lymphocyte ratios with the occurrence of gestational trophoblastic neoplasia (GTN) after complete hydatidiform mole (CHM) among Brazilian women.MethodsRetrospective cohort study of patients with CHM followed at Rio de Janeiro Federal University, from January/2015-December/2020. Before molar evacuation, all patients underwent a medical evaluation, complete blood count and hCG measurement, in addition to other routine preoperative tests. The primary outcome was the occurrence of postmolar GTN.ResultsFrom 827 cases of CHM treated initially at the Reference Center, 696 (84.15%) had spontaneous remission and 131 (15.85%) developed postmolar GTN. Using optimal cut-offs from receiver operating characteristic curves and multivariable logistic regression adjusted for the possible confounding variables of age and preevacuation hCG level (already known to be associated with the development of GTN) we found that ≥2 medical complications at presentation (aOR: 1.96, CI 95%: 1.29-2.98, pConclusionAlthough blood count is a widely available test, being a low-cost test and mandatory before molar evacuation, and prognostic for outcome in other neoplasms, its findings were not able to predict the occurrence of GTN after CHM. In contrast, the occurrence of medical complications at presentation and higher preevacuation hCG levels were significantly associated with postmolar GTN and may be useful to guide individualized clinical decisions in post-molar follow-up and treatment of these patients.

Abstract Anterior cruciate ligament reconstruction is the preferred treatment to anterior cruciate ligament injury. With the increase in anterior cruciate ligament injuries in both adults and skeletally immature patients comes the need for individualized anterior cruciate ligament reconstruction graft selection whether it is the type of graft (auto vs. allograft) or the harvesting site (hamstrings, iliotibial band, quadriceps, patella). Several factors need to be considered preoperatively in order to optimize the patients’ recovery and restore anterior cruciate ligament strength and function. These include age and bone maturity, preoperative knee flexor/extensor strength, sport participation, patient’s needs and anatomical characteristics. This paper aims at bringing evidence supporting the use of a personalized approach in graft selection for faster and more efficient return to sport and propose a theoretical framework to support the approach.

Objective To assess in ART-naïve pregnant women randomized to efavirenz- versus raltegravir-based ART (IMPAACT P1081) whether pretreatment drug resistance (PDR) with minority frequency variants (Design A case-control study design compared PDR minority variants in cases with virologic non-suppression (plasma HIV RNA >200 copies/mL) at delivery to randomly selected ART-suppressed controls. Methods HIV pol genotypes were derived from pretreatment plasma specimens by Illumina sequencing. Resistance mutations were assessed using the HIV Stanford Database, and the proportion of cases versus controls with PDR to their ART regimens was compared. Results PDR was observed in 7 participants (11.3%; 95% CI 4.7, 21.9) and did not differ between 21 cases and 41 controls (4.8% vs 14.6%, p = 0.4061). PDR detected only as minority variants was less common (3.2%; 95% CI 0.2, 11.7) and also did not differ between groups (0% vs. 4.9%; p = 0.5447). Cases’ median plasma HIV RNA at delivery was 347c/mL, with most (n = 19/22) showing progressive diminution of viral load but not ≤200c/mL. Among cases with viral rebound (n = 3/22), none had PDR detected. Virologic non-suppression at term was associated with higher plasma HIV RNA at study entry (pConclusions We observed a moderate frequency of PDR that did not significantly contribute to virologic non-suppression at term. Rather, higher pretreatment plasma HIV RNA, randomization to efavirenz-based ART, and shorter duration of ART were associated with non-suppression. These findings support early prenatal care engagement of pregnant women and initiation of integrase inhibitor-based ART due to its association with more rapid suppression of plasma RNA levels. Furthermore, because minority variants appeared infrequent in ART-naïve pregnant women and inconsequential to ART-suppression, testing for minority variants may be unwarranted.

Australasian marsupials harbour a diverse group of gastrointestinal strongyloid nematodes. These nematodes are currently grouped into two subfamilies, namely the Cloacininae and Phascolostrongylinae. Based on morphological criteria, the Cloacininae and Phascolostrongylinae were defined as monophyletic and placed in the family Cloacinidae, but this has not been supported by molecular data and they are currently placed in the Chabertiidae. Although molecular data (internal transcribed spacers of the nuclear ribosomal RNA genes or mitochondrial protein-coding genes) have been used to verify morphological classifications within the Cloacininae and Phascolostrongylinae, the phylogenetic relationships between the subfamilies have not been rigorously tested. This study determined the phylogenetic relationships of the subfamilies Cloacininae and Phascolostrongylinae using amino acid sequences conceptually translated from the twelve concatenated mitochondrial protein-coding genes. The findings demonstrated that the Cloacininae and Phascolostrongylinae formed a well-supported monophyletic assemblage, consistent with their morphological classification as an independent family, Cloacinidae. Unexpectedly, however, the subfamily Phascolostrongylinae was split into two groups comprising the genera from macropodid hosts (kangaroos and wallabies) and those from vombatid hosts (wombats). Genera of the Cloacininae and Phascolostrongylinae occurring in macropodid hosts were more closely related compared to genera of the Phascolostrongylinae occurring in wombats that formed a sister relationship with the remaining genera from macropods. These findings provide molecular evidence supporting the monophyly of the family Cloacinidae and an alternative hypothesis for the origin of marsupial strongyloid nematodes in vombatid hosts that requires further exploration using molecular approaches and additional samples

Conditions have been identified in which phenolic aldoximes and ketoximes of the types used in commercial solvent extraction processes can be doubly deprotonated and generate polynuclear Cu complexes with lower extractant:Cu molar ratios than those found in commercial operations. Electrospray mass spectrometry has provided an insight into the solution speciation in extraction experiments and has identified conditions to allow isolation and characterization of polynuclear Cu-complexes. Elevation of pH is effective in enhancing the formation of trinuclear complexes containing planar {Cu3-μ3-O}4+ or {Cu3-μ3-OH}5+ units. DFT calculations suggest that such trinuclear complexes are more stable than other polynuclear species. Solid structures of complexes formed by a salicylaldoxime with a piperidino substituent ortho to the phenolic OH group (L9H2) contain two trinuclear units in a supramolecular assembly, {[Cu3OH(L9H)3(ClO4)](ClO4)} 2, formed by H-bonding between the central {Cu3-μ3-OH}5+ units and oxygen atoms in the ligands of an adjacent complex. Whilst the lower ligand:Cu molar ratios provide more efficient Cu-loading in solvent extraction processes, the requirement to raise the pH of the aqueous phase to achieve this will make it impractical in most commercial operations because extraction will be accompanied by the precipitation (as oxyhydroxides) of Fe(III) which is present in significant quantities in feed solutions generated by acid leaching of most Cu ores.

OBJECTIVES: This study aimed to determine the effects of age, race/ethnicity, body mass index, and contraception on human chorionic gonadotropin (hCG) regression following the evacuation of a molar pregnancy. METHODS: This was a retrospective cohort study of 277 patients with molar pregnancies between January 1, 1994 and December 31, 2015. The rate of hCG regression was estimated using mixed-effects linear regression models on daily log-transformed serum hCG levels after evacuation. RESULTS: There were no differences in hCG half-lives among age (p=0.13) or race/ethnicity (p=0.16) groups. Women with obesity and hormonal contraceptive use demonstrated faster hCG regression than their counterparts (3.2 versus. 3.7 days, p=0.02 and 3.4 versus. 4.0 days, p=0.002, respectively). CONCLUSION: Age and race/ethnicity were not associated with hCG regression rates. Hormonal contraceptive use and obesity were associated with shorter hCG half-lives, but with unlikely clinical significance. It is important to understand whether the clinical characteristics of patients may influence the hCG regression curve, as it has been proposed as a way to predict the risk of gestational trophoblastic neoplasia.

Summary: The erythropoietin receptor (EPOR) plays an essential role in erythropoiesis and other cellular processes by forming distinct signaling complexes composed of EPOR homodimers or hetero-oligomers between the EPOR and another receptor, but the mechanism of heteroreceptor assembly and signaling is poorly understood. We report here a 46-residue, artificial transmembrane protein aptamer, designated ELI-3, that binds and activates the EPOR and induces growth factor independence in murine BaF3 cells expressing the EPOR. ELI-3 requires the transmembrane domain and JAK2-binding sites of the EPOR for activity, but not the cytoplasmic tyrosines that mediate canonical EPOR signaling. Instead, ELI-3-induced proliferation and activation of JAK/STAT signaling requires the transmembrane and cytoplasmic domains of the cytokine receptor β-common subunit (βcR) in addition to the EPOR. Moreover, ELI-3 fails to induce erythroid differentiation of primary human hematopoietic progenitor cells but inhibits nonhematopoietic cell death induced by serum withdrawal. : Biological Sciences; Cell Biology; Functional Aspects of Cell Biology Subject Areas: Biological Sciences, Cell Biology, Functional Aspects of Cell Biology

Abstract Background People in close contact with tuberculosis should have screening and appropriate management, as an opportunity for active case detection and prevention. However, implementation of tuberculosis contact screening and management is limited in high-burden settings. Behaviour change is needed across three levels of the healthcare system—policymakers, healthcare providers, and patients. To bridge the wide policy-practice gap, this study draws on the Consolidated Framework for Implementation Research, the Behaviour Change Wheel, and the RE-AIM model (Reach, Effectiveness, Adoption, Implementation, Maintenance) to respectively understand barriers, implement change, and evaluate process and outcome. Methods This methods paper describes a mixed-methods intervention study in Eastern Indonesia. Quantitative data will be collected during baseline, intervention, and sustainability periods and analyzed using time series analysis. The primary outcome is the number of individuals completing tuberculosis preventive therapy by the end of the two-year intervention phase. Of an estimated 10,000 contacts during this period, we anticipate that a minimum of 416 will be found to have active TB or will complete preventive therapy. Qualitative data (semi-structured interviews, focus group discussions, and observations) will be collected from consenting healthcare providers, patients, and contacts. Activities to promote policy implementation include healthcare provider training, quarterly continuous quality improvement workshops, a social media discussion forum, and promotional materials. The Consolidated Framework for Implementation Research will be used to identify reasons for limited policy implementation at baseline. The Behaviour Change Wheel will be used to ensure that a suitable range of activities are implemented to facilitate change. The RE-AIM model will be used as the evaluation framework. Discussion Use of theoretical frameworks in combination can ensure a comprehensive understanding of, and robust response to, health policy underimplementation. The selected frameworks are highly applicable to this pragmatic intervention study, in a setting where End TB Strategy targets will not be met without substantial behavior change within health systems. Continuous quality improvement cycles will provide a way to engage staff and stakeholders in understanding local data to motivate behavior change. If successful, up to 500 people could be prevented from developing complications of tuberculosis through early case-finding or receiving preventive therapy over a two-year period. Study registration Australian New Zealand Clinical Trials Register 375803.

Information from Magnetic Resonance Imaging (MRI) is useful for diagnosis and treatment management of human neurological patients. MRI monitoring might also prove useful for non-human animals involved in neuroscience research provided that MRI is available and feasible and that there are no MRI contra-indications precluding scanning. However, MRI monitoring is not established in macaques and a resource is urgently needed that could grow with scientific community contributions. Here we show the utility and potential benefits of MRI-based monitoring in a few diverse cases with macaque monkeys. We also establish a PRIMatE MRI Monitoring (PRIME-MRM) resource within the PRIMatE Data Exchange (PRIME-DE) and quantitatively compare the cases to normative information drawn from MRI data from typical macaques in PRIME-DE. In the cases, the monkeys presented with no or mild/moderate clinical signs, were well otherwise and MRI scanning did not present a significant increase in welfare impact. Therefore, they were identified as suitable candidates for clinical investigation, MRI-based monitoring and treatment. For each case, we show MRI quantification of internal controls in relation to treatment steps and comparisons with normative data in typical monkeys drawn from PRIME-DE. We found that MRI assists in precise and early diagnosis of cerebral events and can be useful for visualising, treating and quantifying treatment response. The scientific community could now grow the PRIME-MRM resource with other cases and larger samples to further assess and increase the evidence base on the benefits of MRI monitoring of primates, complementing the animals’ clinical monitoring and treatment regime.

We develop and apply analytically tractable generative models of livestock movements at national scale. These go beyond current models through mechanistic modelling of heterogeneous trade partnership network dynamics and the trade events that occur on them. Linking resulting animal movements to disease transmission between farms yields analytical expressions for the basic reproduction number R0. We show how these novel modelling tools enable systems approaches to disease control, using R0 to explore impacts of changes in trading practices on between-farm prevalence levels. Using the Scottish cattle trade network as a case study, we show our approach captures critical complexities of real-world trade networks at the national scale for a broad range of endemic diseases. Changes in trading patterns that minimize disruption to business by maintaining in-flow of animals for each individual farm reduce R0, with the largest reductions for diseases that are most challenging to eradicate. Incentivizing high-risk farms to adopt such changes exploits ‘scale-free’ properties of the system and is likely to be particularly effective in reducing national livestock disease burden and incursion risk. Encouragingly, gains made by such targeted modification of trade practices scale much more favourably than comparably targeted improvements to more commonly adopted farm-level biosecurity.

Scientific articles often contain relevant geographic information such as where field work was performed or where patients were treated. Most often, this information appears in the full-text article contents as a description in natural language including place names, with no accompanying machine-readable geographic metadata. Automatically extracting this geographic information could help conduct meta-analyses, find geographical research gaps, and retrieve articles using spatial search criteria. Research on this problem is still in its infancy, with many works manually processing corpora for locations and few cross-domain studies. In this paper, we develop a fully automatic pipeline to extract and represent relevant locations from scientific articles, applying it to two varied corpora. We obtain good performance, with full pipeline precision of 0.84 for an environmental corpus, and 0.78 for a biomedical corpus. Our results can be visualized as simple global maps, allowing human annotators to both explore corpus patterns in space and triage results for downstream analysis. Future work should not only focus on improving individual pipeline components, but also be informed by user needs derived from the potential spatial analysis and exploration of such corpora.

BackgroundThe need for kidney transplantation drives efforts to expand organ donation. The decision to accept organs from donors with acute kidney injury (AKI) can result in a clinical dilemma in the context of conflicting reports from published literature.Material and methodsThis observational study included all deceased donor kidney transplants performed in Australia and New Zealand between 1997 and 2017. The association of donor-AKI, defined according to KDIGO criteria, with all-cause graft failure was evaluated by multivariable Cox regression. Secondary outcomes included death-censored graft failure, death, delayed graft function (DGF) and acute rejection.ResultsThe study included 10,101 recipients of kidneys from 5,774 deceased donors, of whom 1182 (12%) recipients received kidneys from 662 (11%) donors with AKI. There were 3,259 (32%) all-cause graft failures, which included 1,509 deaths with functioning graft. After adjustment for donor, recipient and transplant characteristics, donor AKI was not associated with all-cause graft failure (adjusted hazard ratio [HR] 1.11, 95% CI 0.99-1.26), death-censored graft failure (HR 1.09, 95% CI 0.92-1.28), death (HR 1.15, 95% CI 0.98-1.35) or graft failure when death was evaluated as a competing event (sub-distribution hazard ratio [sHR] 1.07, 95% CI 0.91-1.26). Donor AKI was not associated with acute rejection but was associated with DGF (adjusted odds ratio [OR] 2.27, 95% CI 1.92-2.68).ConclusionDonor AKI stage was not associated with any kidney transplant outcome, except DGF. Use of kidneys with AKI for transplantation appears to be justified.

Despite advances in high-throughput sequencing and bioinformatics, molecular investigations of snail intermediate hosts that transmit parasitic trematodes are scant. Here, we report the first transcriptome for Bulinus truncatus – a key intermediate host of Schistosoma haematobium – a blood fluke that causes urogenital schistosomiasis in humans. We assembled this transcriptome from short- and long-read RNA-sequence data. From this transcriptome, we predicted 12,998 proteins, 58% of which had orthologs in Biomphalaria glabrata – an intermediate host of Schistosoma mansoni – a blood fluke that causes hepato-intestinal schistosomiasis. We predicted that select protein groups are involved in signal transduction, cell growth and death, the immune system, environmental adaptation and/or the excretory/secretory system, suggesting roles in immune responses, pathogen defence and/or parasite-host interactions. The transcriptome of Bu. truncatus provides a useful resource to underpin future molecular investigations of this and related snail species, and its interactions with pathogens including S. haematobium. The present resource should enable comparative investigations of other molluscan hosts of socioeconomically important parasites in the future.

Abstract In mice, both androgens and the gut microbiota modify pulmonary responses to ozone. We hypothesized that androgens affect gut microbiota and thereby impact pulmonary responses to ozone. To address this hypothesis, we transferred cecal microbiota from male castrated or sham castrated C57BL/6J mice into female germ‐free recipient C57BL/6J mice. Four weeks later mice were exposed to ozone (2 ppm) or room air for 3 hr. The gut microbiomes of castrated versus sham castrated donors differed, as did those of recipients of microbiota from castrated versus sham castrated donors. In recipients, ozone‐induced airway hyperresponsiveness was not affected by donor castration status. However, compared to mice receiving microbiota from sham castrated donors, mice receiving microbiota from castrated donors had elevated numbers of bronchoalveolar lavage (BAL) neutrophils despite evidence of reduced lung injury as measured by BAL protein. Serum concentrations of IL‐17A and G‐CSF were significantly greater in recipients of castrated versus sham castrated microbiota. Furthermore, BAL neutrophils correlated with both serum IL‐17A and serum G‐CSF. Our data indicate that androgen‐mediated effects on the gut microbiota modulate pulmonary inflammatory responses to ozone and suggest a role for circulating IL‐17A and G‐CSF in these events.

Clonorchiasis is a neglected tropical disease caused by the Chinese liver fluke, Clonorchis sinensis, and is often associated with a malignant form of bile duct cancer (cholangiocarcinoma). Although some aspects of the epidemiology of clonorchiasis are understood, little is known about the genetics of C. sinensis populations. Here, we conducted a comprehensive genetic exploration of C. sinensis from endemic geographic regions using complete mitochondrial protein gene sets. Genomic DNA samples from C. sinensis individuals (n = 183) collected from cats and dogs in China (provinces of Guangdong, Guangxi, Hunan, Heilongjiang and Jilin) as well as from rats infected with metacercariae from cyprinid fish from the Russian Far East (Primorsky Krai region) were deep sequenced using the BGISEQ-500 platform. Informatic analyses of mitochondrial protein gene data sets revealed marked genetic variation within C. sinensis; significant variation was identified within and among individual worms from distinct geographical locations. No clear affiliation with a particular location or host species was evident, suggesting a high rate of dispersal of the parasite across endemic regions. The present work provides a foundation for future biological, epidemiological and ecological studies using mitochondrial protein gene data sets, which could aid in elucidating associations between particular C. sinensis genotypes/haplotypes and the pathogenesis or severity of clonorchiasis and its complications (including cholangiocarcinoma) in humans.

Summary: The Sc(III) MOF-type MFM-300(Sc) is demonstrated in this study to be stable under physiological conditions (PBS), biocompatible (to human skin cells), and an efficient drug carrier for the long-term controlled release (through human skin) of antioxidant ferulate. MFM-300(Sc) also preserves the antioxidant pharmacological effects of ferulate while enhancing the bio-preservation of dermal skin fibroblasts, during the delivery process. These discoveries pave the way toward the extended use of Sc(III)-based MOFs as drug delivery systems (DDSs).

Background: Pre-treatment HIV-drug-resistance (PDR) to WHO-recommended 1st-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral treatment (ART) is increasing in low-resource communities. We evaluated the risk of PDR on treatment failure if detected at single or multiple codons, at minority (2–9%) or higher (≥10%) frequencies during efavirenz- vs. nevirapine-ART. Methods: We conducted a pooled analysis across three cohorts of Kenyans initiating 1st-line NNRTI-ART between 2006 and 2014. Mutations K103N, Y181C, G190A, M184V and K65R were detected by an oligonucleotide ligation assay (OLA) and confirmed by Sanger and next-generation sequencing (NGS). PDR was defined as detection of any mutation by OLA when confirmed by NGS. Treatment failure, defined as plasma HIV RNA ≥400 copies/mL at month-12 of ART, was compared by PDR genotypes. Findings: PDR was detected in 59/1231 (4·8%) participants. Compared to wild-type genotypes, PDR in participants prescribed nevirapine-ART was associated with increased treatment failure [PDR 69·2% (27/39) vs. wild-type 10·4% (70/674); p = 0·0001], whether detected as minority [66·7% (4/6)] or higher [69·7% (23/33)] frequencies in an individual's HIV quasispecies (p = 0·002 and p

Abstract Objectives Cellular immunity against BK polyomavirus (BKV)‐encoded antigens plays a crucial role in long‐term protection against virus‐associated pathogenesis in transplant recipients. However, in‐depth understanding on dynamics of these cellular immune responses is required to develop better immune monitoring and immunotherapeutic strategies. Methods Here, we have conducted a proteome‐wide analysis of BKV‐specific T‐cell responses in a cohort of 53 healthy individuals and 26 kidney transplant recipients to delineate the functional and transcriptional profile of these effector cells and compared these characteristics to T cells directed against cytomegalovirus, which is also known to cause significant morbidity in transplant recipients. Results Profiling of BKV‐specific CD4+ and CD8+ T cells revealed that kidney transplant recipients with high levels of circulating viraemia showed significantly reduced T‐cell reactivity against large T and/or small T antigens when compared to healthy donors. Interestingly, T cells specific for these antigens showed strong cross‐recognition to orthologous JC virus (JCV) peptides, including those exhibiting varying degrees of sequence identity. Ex vivo functional and phenotypic characterisation revealed that the majority of BKV‐specific T cells from renal transplant recipients expressed low levels of the key transcriptional regulators T‐bet and eomesodermin, which was coincident with undetectable expression of granzyme B and perforin. However, in vitro stimulation of T cells with BKV epitopes selectively enhanced the expression of T‐bet, granzyme B and cellular trafficking molecules (CCR4, CD49d and CD103) with minimal change in eomesodermin and perforin. Conclusions These observations provide an important platform for the future development of immune monitoring and adoptive T‐cell therapy strategies for BKV‐associated diseases in transplant recipients, which may also be exploited for similar therapeutic value in JCV‐associated clinical complications.

Abstract Background Human schistosomiasis is a neglected tropical disease caused by parasitic worms of the genus Schistosoma that still affects some 200 million people. The mainstay of schistosomiasis control is a single drug, praziquantel. The reliance on this drug carries a risk of resistance emerging to this anthelmintic, such that research towards alternative anti-schistosomal drugs is warranted. In this context, a number of studies have employed computational approaches to prioritise proteins for investigation as drug targets, based on extensive genomic, transcriptomic and small-molecule data now available. Methods Here, we established a customisable, online application for the prioritisation of drug targets and applied it, for the first time, to the entire inferred proteome of S. haematobium. This application enables selection of weighted and ranked proteins representing potential drug targets, and integrates transcriptional data, orthology and gene essentiality information as well as drug-drug target associations and chemical properties of predicted ligands. Results Using this application, we defined 25 potential drug targets in S. haematobium that associated with approved drugs, and 3402 targets that (although they could not be linked to any compounds) are conserved among a range of socioeconomically important flatworm species and might represent targets for new trematocides. Conclusions The online application developed here represents an interactive, customisable, expandable and reproducible drug target ranking and prioritisation approach that should be useful for the prediction of drug targets in schistosomes and other species of parasitic worms in the future. We have demonstrated the utility of this online application by predicting potential drug targets in S. haematobium that can now be evaluated using functional genomics tools and/or small molecules, to establish whether they are indeed essential for parasite survival, and to assist in the discovery of novel anti-schistosomal compounds.

The prevalent porcine helminth, Ascaris suum, compromises pig health and reduces farm productivity worldwide. The closely related human parasite, A. lumbricoides, infects more than 800 million people representing a disease burden of 1.31 million disability-adjusted life years. The infections are often chronic in nature, and the parasites have a profound ability to modulate their hosts’ immune responses. This study provides the first in-depth characterisation of extracellular vesicles (EVs) from different developmental stages and body parts of A. suum and proposes the role of these vesicles in the host–parasite interplay. The release of EVs from the third- (L3) and fourth-stage (L4) larvae and adults was demonstrated by transmission electron microscopy (TEM), and sequencing of EV-derived RNA identified a number of microRNAs (miRNAs) and transcripts of potential host immune targets, such as IL-13, IL-25 and IL-33, were identified. Furthermore, proteomics of EVs identified several proteins with immunomodulatory properties and other proteins previously shown to be associated with parasite EVs. Taken together, these results suggest that A. suum EVs and their cargo may play a role in host–parasite interactions. This knowledge may pave the way to novel strategies for helminth infection control and knowledge of their immune modulatory potential.

Background: Northern New South Wales in Australia is a “hotspot” for natural disaster declarations with recent extensive flooding in early 2017. With limited knowledge about how climate change affects mental health and resilience, robust local assessments are required to better understand long-term impact, particularly in communities prone to extreme weather events.Methods: Six months post-flood, a cross-sectional survey of adults living in the region during the flood was conducted to quantify associations between flood impact and psychological morbidity (post-traumatic stress (PTSD), anxiety, depression, suicidal ideation) for different exposure scenarios, and respondent groups. We adopted a community-academic partnership approach and purposive recruitment to increase participation from marginalized groups.Results: Of 2,180 respondents, almost all (91%) were affected by some degree of flood-related exposure at an individual and community level (ranging from suburb damage to home or business inundated). Socio-economically marginalized respondents were more likely to have their homes inundated and to be displaced. Mental health risk was significantly elevated for respondents: whose home/business/farm was inundated [e.g., home inundation: PTSD adjusted odds ratio (AOR) 13.72 (99% CI 4.53–41.56)]; who reported multiple exposures [e.g., three exposures: PTSD AOR 6.43 (99% CI 2.11–19.60)]; and who were still displaced after 6 months [e.g., PTSD AOR 24.43 (99% CI 7.05–84.69)].Conclusion: The 2017 flood had profound impact, particularly for respondents still displaced and for socio-economically marginalized groups. Our community-academic partnership approach builds community cohesion, informs targeted mental health disaster preparedness and response policies for different sectors of the community and longer-term interventions aimed at improving community adaptability to climate change.

User-Generated Content (UGC) provides a potential data source which can help us to better describe and understand how places are conceptualized, and in turn better represent the places in Geographic Information Science (GIScience). In this article, we aim at aggregating the shared meanings associated with places and linking these to a conceptual model of place. Our focus is on the metadata of Flickr images, in the form of locations and tags. We use topic modeling to identify regions associated with shared meanings. We choose a grid approach and generate topics associated with one or more cells using Latent Dirichlet Allocation. We analyze the sensitivity of our results to both grid resolution and the chosen number of topics using a range of measures including corpus distance and the coherence value. Using a resolution of 500 m and with 40 topics, we are able to generate meaningful topics which characterize places in London based on 954 unique tags associated with around 300,000 images and more than 7000 individuals.

Deep layer auditory cortex neurons project to a number of limbic and subcortical auditory structures. Here, the authors show how these corticofugal projections adjust response gain following noise-induced cochlear damage.

Abstract Background Extracellular vesicles (EVs) are considered as a new class of resources for potential biomarkers. We analyzed expression of specific mRNA and miRNA in EVs derived from ovarian cancer ascites and the ideal controls, peritoneal fluids from benign patients for potential early detection and prognostic biomarkers. Methods Fluids were collected from subjects with benign cysts or endometrioma (n = 10), or low/high grade serous ovarian carcinoma (n = 8). EV particles were captured using primarily ExoComplete filterplate or ultracentrifugation and analyzed by nanoparticle tracking analysis, ELISA, and scanning electron microscopy. EV RNAs extracted from two ascites and three peritoneal fluids were submitted for next-generation sequencing. The expression of 34 mRNA and 18 miRNAs in the EVs isolated from patient fluids and cell line media was determined using qPCR. Results EVs isolated from patient samples had concentrations greater than 1010 EV particles/mL and 30% were EpCAM-positive based on ELISA. EV particle sizes averaged 113 ± 11.5 nm. The qPCR studies identified five mRNA (CA11, MEDAG, LAMA4, SPINT2, NANOG) and six miRNA (let-7b, miR23b, miR29a, miR30d, miR205, miR720) that were significantly differentially expressed between cancer ascites and peritoneal fluids. In addition, CA11 mRNA was decreased to 0.5-fold and SPINT2 and NANOG mRNA were significantly increased up to 100-fold in conditioned media of cancer cells compared to immortalized ovarian surface and fallopian tube epithelial cell lines, the hypothesized cells of origin for ovarian cancer development. Conclusions This study indicates that EV mRNA profiles can reflect the disease stage and may provide a potentially novel source for discovery of biomarkers in ovarian cancer.