bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
Authors: Freeman Timothy M. ,   Genomics England Research Consortium, Wang Dennis , Harris Jason
Published: June 2019

Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloguing population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilise consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations and alternative methods are required to overcome these.

We have developed a novel statistical method based on summarising sequenced reads from whole genome clinical samples and cataloguing them in “Incremental Databases” that maintain individual confidentiality. Allele statistics were catalogued for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at ∼1-3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio=23.29-33.69) and the NIST high confidence genomic regions (odds ratio=0.154-0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels.

Our results recommend increased caution to address systematic biases in whole genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.
FOXO mediates organismal hypoxia tolerance by regulating NF-κB inDrosophila
Authors: Barretto Elizabeth C , Polan Danielle M , Beever-Potts Amy N , Lee Byoungchun , Grewal Savraj S
Published: June 2019

Exposure of tissues and organs to low oxygen (hypoxia) occurs in both physiological and pathological conditions in animals. Under these conditions, organisms have to adapt their physiology to ensure proper functioning and survival. Here we define a role for the transcription factor FOXO as a mediator of hypoxia tolerance inDrosophila. We find that upon hypoxia exposure, FOXO transcriptional activity is rapidly induced in both larvae and adults. Moreover, we see thatfoxomutant animals show misregulated glucose metabolism in low oxygen and subsequently exhibit reduced hypoxia survival. We identify the innate immune transcription factor, NF-KappaB/Relish, as a key FOXO target in the control of hypoxia tolerance. We find that expression of Relish and its target genes are increase in a FOXO-dependent manner in hypoxia, and thatrelishmutant animals show reduced survival in hypoxia. Together, these data indicate that FOXO is a hypoxia inducible factor that mediates tolerance to low oxygen by inducing immune-like responses.
Multi-session visual cortex transcranial random noise stimulation in adults with amblyopia
Authors: Donkor Richard , Silva Andrew E. , Teske Caroline , Wallis-Duffy Margaret , Johnson Aaron , Thompson Benjamin
Published: June 2019

Purpose

We tested the hypothesis that five daily sessions of visual cortex transcranial random noise stimulation would improve contrast sensitivity, crowded and uncrowded visual acuity in adults with amblyopia.

Methods

Nineteen adults with amblyopia (44.2 ± 14.9yrs, 10 female) were randomly allocated to active or sham tRNS of the visual cortex (active, n = 9; sham, n = 10). tRNS was delivered for 25 minutes across five consecutive days. Monocular contrast sensitivity, uncrowded and crowded visual acuity were measured before, during, 5 minutes and 30 minutes post stimulation on each day.

Results

Active tRNS significantly improved contrast sensitivity and uncrowded visual acuity for both amblyopic and fellow eyes whereas sham stimulation had no effect. An analysis of the day by day effects revealed large within session improvements on day 1 for the active group that waned across subsequent days. No long-lasting (multi-day) improvements were observed for contrast sensitivity, however a long-lasting improvement in amblyopic eye uncrowded visual acuity was observed for the active group. This improvement remained at 28 day follow up. However, between-group differences in baseline uncrowded visual acuity complicate the interpretation of this effect. No effect of tRNS was observed for amblyopic eye crowded visual acuity.

Conclusions

In agreement with previous non-invasive brain stimulation studies using different techniques, tRNS induced short-term contrast sensitivity improvements in adult amblyopic eyes, however, multiple sessions of tRNS did not lead to enhanced or long-lasting effects for the majority of outcome measures.
Sustained Co-evolution in a Stochastic Model of the Cancer-Immune Interaction
Authors: George Jason T. , Levine Herbert
Published: June 2019

The dynamical interaction between a growing cancer population and the adaptive immune system generates diverse evolutionary trajectories which ultimately result in tumor clearance or immune escape. Here, we create a simple mathematical model coupling T-cell recognition with an evolving cancer population which may randomly produce evasive subclones, imparting transient protection against the effector T-cells. We demonstrate that T-cell turnover declines and evasion rates together explain differential probabilities in early incidence data for almost all cancer types. Fitting the model to TRACERx evolutionary data argues in favor of substantial and sustained immune pressure exerted on a developing tumor, suggesting that measured incidence is a small proportion of all cancer initiation events. Most generally, dynamical models promise to increase our quantitative understanding of many immune escape contexts, with applications to cancer and intracellular pathogenic infections.
Comparison of marker selection methods for high throughput scRNA-seq data
Authors: Gilbert Anna C. , Vargo Alexander
Published: June 2019

Here, we evaluate the performance of a variety of marker selection methods on scRNA-seq UMI counts data. We test on an assortment of experimental and synthetic data sets that range in size from several thousand to one million cells. In addition, we propose several performance measures for evaluating the quality of a set of markers when there is no known ground truth. According to these metrics, most existing marker selection methods show similar performance on experimental scRNA-seq data; thus, the speed of the algorithm is the most important consid-eration for large data sets. With this in mind, we introduce RANKCORR, a fast marker selection method with strong mathematical underpinnings that takes a step towards sensible multi-class marker selection.
Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif
Authors: Wood Kelsey , Nur Munir , Gil Juliana , Fletcher Kyle , Lakeman Kim , Gothberg Ayumi , Khuu Tina , Kopetzky Jennifer , Pandya Archana , Pel Mathieu , Michelmore Richard
Published: June 2019

Pathogens infecting plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen, Bremia lactucae, using comparative genomics and bioinformatics to search for the WY domain. This conserved structural element is found in Phytophthora effectors and some other oomycete pathogens; it has been implicated in the immune-suppressing function of these effectors as well as their recognition by host resistance proteins. We predicted 54 WY domain containing proteins in isolate SF5 of B. lactucae that have substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis effectors containing WY domains revealed eleven out of 21 that triggered necrosis, which is characteristic of the immune response on wild accessions and domesticated lettuce lines containing resistance genes. Only two of the eleven recognized effectors contained a canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.

Author Summary

There is a microscopic battle that takes place at the molecular level during infection of plants and animals by pathogens. Some of the weapons that pathogens battle with are known as “effectors,” which are secreted proteins that enter host cells to alter physiology and suppress the immune system. Effectors can also be a liability for plant pathogens because plants have evolved ways to recognize these effectors, triggering a defense response leading to localized cell death, which prevents the spread of the pathogen. Here we used computer models to predict effectors from the genome of Bremia lactucae, the causal agent of lettuce downy mildew. Three effectors were demonstrated to suppress the basal immune system of lettuce. Eleven effectors were recognized by one or more resistant lines of lettuce. In addition to contributing to our understanding of the mechanisms of pathogenesis, this study of effectors is useful for breeding disease resistant lettuce, decreasing agricultural reliance on fungicides.
A receptor for herbivore-associated molecular patterns mediates plant immunity
Authors: Steinbrenner Adam D. , Muñoz-Amatriaín Maria , Aguilar Venegas Jessica Montserrat , Lo Sassoum , Shi Da , Holton Nicholas , Zipfel Cyril , Abagyan Ruben , Huffaker Alisa , Close Timothy J. , Schmelz Eric A.
Published: June 2019

Plant-herbivore interactions are ubiquitous across nature and drive major agricultural losses. Inducible defense responses triggered through immune recognition aid in host plant protection; however, specific ligand-receptor pairs mediating the initial perception of herbivory remain unknown. Plants in the subtribe Phaseolinae detect herbivore-associated peptides in caterpillar oral secretions and the defined ligands are proteolytic fragments of chloroplastic ATP synthase termed inceptins. Using forward genetic mapping of inceptin-induced responses, we identify a cowpea (Vigna unguiculata) leucine-rich repeat receptor-like protein as an inceptin receptor (INR) sufficient for elicitor-induced responses and enhanced defense against armyworms (Spodoptera exigua). INR defines a receptor by which plants perceive herbivore-associated molecular patterns (HAMPs) and expands the paradigm of surface immune recognition to attack with mandibles.

One Sentence Summary

A plant cell surface receptor directly perceives peptides associated with caterpillar herbivory.
Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors
Authors: Bubie Adrian , Gonzalez-Kozlova Edgar , Akers Nicholas , Villanueva Augusto , Losic Bojan
Published: June 2019

Recently proposed tumor fitness measures, based on profiling neoepitopes for reactive viral epitope similarity, have been proposed to predict response to immune checkpoint inhibitors in melanoma and small-cell lung cancer. Here we apply these checkpoint based fitness measures measures to the matched checkpoint treatment naive TCGA samples where cytolytic activity imparts a known survival benefit. We observed no significant survival predictive power beyond that of overall patient tumor mutation burden, and furthermore, found no association between checkpoint based fitness and tumor T-cell infiltration, cytolytic activity (CYT), and abundance (TIL burden). In addition, we investigated the key assumption of viral epitope similarity driving immune response in the hepatitis B virally infected liver cancer TCGA cohort, and uncover suggestive evidence that tumor neoepitopes actually dominate viral epitopes in putative immunogenicity and plausibly drive immune response and recruitment.
Elizabethkingia anophelisresponse to iron stress: physiologic, genomic, and transcriptomic analyses
Authors: Chen Shicheng , Johnson Benjamin K. , Yu Ting , Nelson Brooke N. , Walker Edward D.
Published: June 2019

Elizabethkingia anophelisbacteria encounter fluxes of iron in the midgut of mosquitoes, where they live as symbionts. They also establish bacteremia with severe clinical manifestations in humans, and live in water service lines in hospitals. In this study, we investigated the global gene expression responses ofE. anophelisto iron fluxes in the midgut of femaleAnopheles stephensimosquitoes fed sucrose or blood, and in iron-poor or iron-rich culture conditions. Of 3,686 transcripts revealed by RNAseq technology, 218 were upregulated while 112 were down-regulated under iron-poor conditions. Most of these differentially expressed genes (DEGs) were enriched in functional groups assigned within “biological process,” “cell component” and “molecular function” categories.E. anophelispossessed 4 iron/heme acquisition systems. Hemolysin gene expression was significantly repressed when cells were grown under iron-rich or high temperature (37°C) conditions. Furthermore, hemolysin gene expression was down-regulated after a blood meal, indicating thatE. anopheliscells responded to excess iron and its associated physiological stress by limiting iron loading. By contrast, genes encoding respiratory chain proteins were up-regulated under iron-rich conditions, allowing these iron-containing proteins to chelate intracellular free iron.In vivostudies showed that growth ofE. anopheliscells increased 3-fold in blood-fed mosquitoes over those in sucrose-fed ones. Deletion of aerobactin synthesis genes led to impaired cell growth in both iron-rich and iron-poor media. Mutants showed more susceptibility to H2O2toxicity and less biofilm formation than did wild-type cells. Mosquitoes withE. anophelisexperimentally colonized in their guts produced more eggs than did those treated with erythromycin or left unmanipulated, as controls. Results reveal thatE. anophelisbacteria respond to varying iron concentration in the mosquito gut, harvest iron while fending off iron-associated stress, contribute to lysis of red blood cells, and positively influence mosquito host fecundity.
Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs
Authors: Champer Samuel E. , Oh Suh Yeon , Liu Chen , Wen Zhaoxin , Clark Andrew G. , Messer Philipp W. , Champer Jackson
Published: June 2019

CRISPR homing gene drives potentially have the capacity for large-scale population modification or suppression. However, resistance alleles formed by the drives can prevent them from successfully spreading. Such alleles have been found to form at high rates in most studies, including those in both insects and mammals. One possible solution to this issue is the use of multiple guide RNAs (gRNAs), thus allowing cleavage by the drive even if resistance sequences are present at some of the gRNA target sequences. Here, we develop a high-fidelity model incorporating several factors affecting the performance of drives with multiple gRNAs, including timing of cleavage, reduction in homology-directed repair efficiency due to imperfect homology around the cleavage site, Cas9 activity saturation, variance in the activity level of individual gRNAs, and formation of resistance alleles due to incomplete homology-directed repair. We parameterize the model using data from homing drive experiments designed to investigate these factors and then use it to analyze several types of homing gene drives. We find that each type of drive has an optimal number of gRNAs, usually between two and eight, dependent on drive type and performance parameters. Our model indicates that utilization of multiple gRNAs is insufficient for construction of successful gene drives, but that it provides a critical boost to drive efficiency when combined with other strategies for population modification or suppression.
Fitness and productivity increase with ecotypic diversity amongE. colievolved in a simple, constant environment
Authors: Yang Dong-Dong , Alexander Ashley , Kinnersley Margie , Cook Emily , Caudy Amy , Rosebrock Adam , Rosenzweig Frank
Published: June 2019

Community productivity often correlates with diversity. In the microbial world this phenomenon can sometimes be explained by highly-specific metabolic interactions that include cross-feeding and syntrophy. Such interactions help account for the astonishing variety of microbial life, and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new ‘species.’ We have previously shown that in a simple, constant environment a single clone ofE. colican give rise to a consortium of genetically-and physiologically-differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes. We then used flow cytometry to show that each strain by itself is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts resources to offspring than its ancestor or any member acting in isolation.

Importance

In the microbial world, diversity and productivity of communities and consortia often correlate positively. However, it is challenging to tease apart a consortium whose members have co-evolved, and connect estimates of their fitness and the fitness of their ancestor(s) with estimates of productivity. Such analyses are prerequisite to understanding the evolutionary origins of all biological communities. Here we dissect anE. coliconsortium that evolved in the laboratory and show that cooperative interactions are favored under continuous glucose limitation because a partnership of ecotypes is better able to scavenge all available resources and more efficiently convert those resources to offspring than any single individual. Such interactions may be a prelude to a special form of syntrophy, and are likely to be key determinants of microbial community structure in nature, including those having clinical significance, such as chronic infections.
Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss
Authors: Wang Qi , Sun Qiang , Li Xiaoping , Wang Zhefeng , Zheng Haotian , Ju Yanmei , Guo Ruijin , Peng Songlin , Jia Huijue
Published: June 2019

Bone mass loss contributes to the risk of bone fracture in the elderly. Many factors including age, obesity, estrogen and diet, are associated with bone mass loss. Mice studies suggest that the intestinal microbiome might influence the bone mass by regulating the immune system, however there has been little evidence from human studies.

We have recruited 361 Chinese elderly women to collect data for a metagenomic-wide association study (MWAS) to investigate the influence of the gut microbiome on bone health. Gut microbiome data were produced using BGISEQ500 sequencing, BMD was calculated using Hologic dual energy X-ray machine, BMI (Body Mass Index) and age were also provided. This therefore data allows exploration of gut microbiome diversity and links to bone mass loss, as well as microbial species and modules as markers for bone mineral density. Making these data potentially useful in studying the role the gut microbiota might play in bone mass loss and offering exploration into the bone mass loss process.
On the mechanistic roots of an ecological law: parasite aggregation
Authors: Rabajante Jomar F. , Anzia Elizabeth L. , Gokhale Chaitanya S.
Published: June 2019

Parasite aggregation, a recurring pattern in macroparasite infections, is considered one of the “laws” of parasite ecology. Few hosts have a large number of parasites while most hosts have a low number of parasites. Phenomenological models of host-parasite systems thus use the negative-binomial distribution. However, to infer the mechanisms of aggregation, a mechanistic model that does not make any a priori assumptions is essential. Here we formulate a mechanistic model of parasite aggregation in hosts without assuming a negative-binomial distribution. Our results show that a simple model of parasite accumulation still results in an aggregated pattern, as shown by the derived mean and variance of the parasite distribution. By incorporating the derived statistics in host-parasite interactions, we can predict how aggregation affects the population dynamics of the hosts and parasites through time. Thus, our results can directly be applied to observed data as well as can inform the designing of statistical sampling procedures. Overall, we have shown how a plausible mechanistic process can result in the often observed phenomenon of parasite aggregation occurring in numerous ecological scenarios, thus providing a basis for a “law” of ecology.
Integrated analysis of different non-coding features across the Sox2 locus implicates a diencephalic enhancer in adult brain expression
Authors: Carter D.A.
Published: June 2019

SOX2 is a prominent member of the SOX family of transcription factors that has many different functional roles. This pleiotropy is made possible by multiple regulatory mechanisms that direct appropriate spatial and temporal patterns of expression, and therefore action. The current study concerns the mechanisms that determine Sox2 gene expression in the adult mammalian brain, where SOX2 protein is absent in general, but is selectively and abundantly expressed in a majority of neurons within a ventral diencephalic brain structure, the suprachiasmatic nucleus (SCN). In this study, a comparative bioinformatic and biochemical analysis of different adult rat brain regions was conducted in order to identify SCN-selective (immaturity-related) regulatory mechanisms. The approach incorporated an integrated analysis of Sox2 enhancers, CTCF binding sites, and also expression of the Sox2-overlapping, long non-coding (lnc)RNA, Sox2ot. Initial experiments revealed brain region-specific Sox2ot expression (including region-specific novel transcripts), indicating a significant diversity of Sox2ot expression across the adult brain. However, the pattern and abundance of Sox2ot expression in the SCN, relative to selected control areas of the brain, did not indicate an overt relationship to Sox2 gene expression. Furthermore, although multiple individual Sox2ot exon sequences were shown to overlap annotated Sox2 gene enhancers at different sites across the Sox2 locus, again there was no indication of a SCN-specific functional correlation. Further integration with an analysis of selectively-active CTCF sites within the Sox2 locus directed attention to one site with both a prominent peak of activity in immature brain, and proximity to a functionally-characterized, ventral diencephalic, Sox2 enhancer termed U6 (upstream enhancer 6). Ex vivo analysis of the U6-associated CTCF site revealed SCN-selective CTCF binding, and these sequences were both localized within a known (brain region-selective) super-enhancer. Bioinformatic analysis of the U6 enhancer sequence revealed an abundance of consensus sites for the SCN-selective transcription factor LHX1, and over-expression of this factor enhanced the activity of cloned U6 sequence in transfected cells. However, despite this compelling evidence for a molecular mechanism that underlies adult brain expression of SOX2, further analysis of LHX1-SOX2 co-expression in the SCN confounded this view, indicating the presence of other concurrent mechanisms in the different cell populations of the SCN.
Polyhyrdoxybutyrate production by Bacillus marcorestinctum using a Cheaper substrate and its electrospinned blends with polymer
Authors: Narayankumar Swetha , Shaji Neethu K. , Krishnaswamy Veena gayathri
Published: June 2019

Poly(hydroxybutyric acid) (PHB) and other biodegradable polyesters are promising candidates for the development of environment-friendly and completely biodegradable plastics. One of the major drawbacks in the production of PHB is production costs, since it requires large amount of carbon source. This calls for cheaper substrates that can be used as an alternative carbon source such as agro-industrial residues. In this study, cane molasses was used as an additional carbon source at 2% concentration along with glucose for large scale production of PHB. Ammonium nitrate was used as the nitrogen source and the C:N ratio was maintained at 1:15. The maximum production of PHB was obtained at 24hours of growth which was found to be 0.5g/L and had a dry cell weight of 3.7g/ L.The PHB produced was further analysed by GC-MS Analysis and Transmission Electron Microscopy (TEM).The obtained PHB from scale-up studies were further electrospinned using different blends of polymers.
Criticality of plasma membrane lipids reflects activation state of macrophage cells
Authors: Cammarota Eugenia , Soriani Chiara , Taub Raphaelle , Morgan Fiona , Sakai Jiro , Veatch Sarah L. , Bryant Clare E. , Cicuta Pietro
Published: June 2019

Signalling is of particular importance in immune cells, and upstream in the signalling pathway many membrane receptors are functional only as complexes, co-locating with particular lipid species. Work over the last 15 years has shown that plasma membrane lipid composition is close to a critical point of phase separation, with evidence that cells adapt their composition in ways that alter the proximity to this thermodynamical point. Macrophage cells are a key component of the innate immune system, responsive to infections, regulating the local state of inflammation. We investigate changes in the plasma membrane’s proximity to the critical point, as a response to stimulation by various pro- and anti-inflammatory agents. Pro-inflammatory (IFN-γ, Kdo-LipidA, LPS) perturbations induce an increase in the transition temperature of the GMPVs; anti-inflammatory IL4 has the opposite effect. These changes recapitulate complex plasma membrane composition changes, and are consistent with lipid criticality playing a master regulatory role: being closer to critical conditions increases membrane protein activity.
Repurposing protein degradation for optogenetic modulation of protein activities
Authors: Mondal Payel , Krishnamurthy Vishnu V. , Sharum Savanna R. , Haack Neeka , Zhang Kai
Published: June 2019

Non-neuronal optogenetic approaches empower precise regulation of protein dynamics in live cells but often require target-specific protein engineering. To address this challenge, we developed a generalizable light modulated protein stabilization system (GLIMPSe) to control intracellular protein level independent of its functionality. We applied GLIMPSe to control two distinct classes of proteins: mitogen-activated protein kinase phosphatase 3 (MKP3), a negative regulator of the extracellular signal-regulated kinase (ERK) pathway, as well as a constitutively active form of MEK (CA MEK), a positive regulator of the same pathway. Kinetics study showed that light-induced protein stabilization could be achieved within 1 minute of blue light stimulation. GLIMPSe enables target-independent optogenetic control of protein activities and therefore minimizes the systematic variation embedded within different photoactivatable proteins. Overall, GLIMPSe promises to achieve light-mediated post-translational stabilization of a wide array of target proteins in live cells.
Intramolecular interactions dominate the autoregulation ofEscherichia colistringent factor RelA
Authors: Turnbull Kathryn Jane , Dzhygyr Ievgen , Lindemose Søren , Hauryliuk Vasili , Roghanian Mohammad
Published: June 2019

Amino acid starvation inEscherichia coliactivates the enzymatic activity of the stringent factor RelA, leading to accumulation of the alarmone nucleotide (p)ppGpp. The alarmone acts as an intercellular messenger to regulate transcription, translation and metabolism to mediate bacterial stress adaptation. The enzymatic activity of RelA is subject to multi-layered allosteric control executed both by ligands – such as ‘starved’ ribosomal complexes, deacylated tRNA and pppGpp – and by individual RelA domains. The auto-regulation of RelA is proposed to act eitherin cis(inhibition of the enzymatic activity of the N-terminal region, NTD, by regulatory C-terminal region, CTD) orin trans(CTD-mediated dimerization leading to enzyme inhibition). In this report, we probed the regulatory roles of the individual domains ofE. coliRelA and our results are not indicative of RelA dimerization being the key regulatory mechanism. First, at growth-permitting levels, ectopic expression of RelA CTD does not interfere with activation of native RelA, indicating lack of regulationviainhibitory complex formation in the cell. Second, in our biochemical assays, increasing RelA concentration does not decrease the enzyme activity, as would be expected in the case of efficient auto-inhibitionviadimerization. Third, while high-level CTD expression efficiently inhibits the growth, the effect is independent of native RelA and is mediated by direct inhibition of protein synthesis, likelyviadirect interaction with the ribosomal A-site. Finally, deletion of the RRM domain of the CTD region leads to growth inhibition mediated by accumulation of (p)ppGpp, suggesting de-regulation of the synthetic activity in this mutant.
Using Automated Detection and Classification of Interictal HFOs to Improve the Identification of Epileptogenic Zones in Preparation for Epilepsy Surgery
Authors: Farahmand Sina , Sobayo Tiwalade , Mogul David J.
Published: June 2019

Objective

For more than 25 million drug-resistant epilepsy patients, surgical intervention aiming at resecting brain regions where seizures arise is often the only alternative therapy. However, the identification of this epileptogenic zone (EZ) is often imprecise which may affect post-surgical outcomes (PSOs). Interictal high-frequency oscillations (HFOs) have been revealed to be reliable biomarkers in delineating EZ. In this paper, an analytical methodology aiming at automated detection and classification of interictal HFOs is proposed to improve the identification of EZ. Furthermore, the detected high-rate HFO areas were compared with the seizure onset zones (SOZs) and resected areas to investigate their clinical relevance in predicting PSOs.

Methods

FIR band-pass filtering as well as a combination of time-series local energy, peak, and duration analysis were utilized to identify high-rate HFO areas in interictal, multi-channel intracranial electroencephalographic (iEEG) recordings. The detected HFOs were then classified into fast-ripple (FR), ripple (R), and fast-ripple concurrent with ripple (FRandR) events.

Results

The proposed method resulted in sensitivity of 91.08% and false discovery rate of 7.32%. Moreover, it was found that the detected HFO-FRandR areas in concordance with the SOZs would have better delineated the EZ for each patient, while limiting the area of the brain required to be resected.

Conclusion

Testing on a dataset of 20 patients has supported the feasibility of using this method to provide an automated algorithm to better delineate the EZ.

Significance

The proposed methodology may significantly improve the precision by which pathological brain tissue can be identified.
Killer Immunoglobulin-like Receptor-Ligand Interactions Predict Clinical Outcomes Following Unrelated Donor Transplants
Authors: Krieger Elizabeth , Sabo Roy , Moezzi Sanauz , Cain Caitlin , Roberts Catherine , Kimball Pamela , Chesney Alden , McCarty John , Keating Armand , Romee Rizwan , Wiedl Christina , Qayyum Rehan , Toor Amir
Published: June 2019

Killer immunoglobulin-like receptor (KIR) and KIR-ligand (KIRL) interactions play an important role in natural killer (NK) cell mediated graft versus leukemia effect following hematopoietic cell transplantation (HCT). However, there is considerable heterogeneity in the KIR gene and KIRL content in individuals, making it difficult to estimate the full clinical impact of NK cell reconstitution following HCT. Herein a novel mathematical model designed to quantify these interactions is presented to better assess the influence of NK cell-mediated alloreactivity on transplant outcomes. Ninety-eight HLA matched unrelated donor (URD) HCT recipients were retrospectively studied. The KIR-KIRL interactions were quantified using a system of matrix equations. Unit values were ascribed to each KIR-KIRL interaction and directionality of interactions was denoted by, either a positive (activating) or negative symbol (inhibition); these interactions were then summed. The absolute values of both the missing KIRL as well as inhibitory KIR-KIRL interactions were significantly associated with overall survival and relapse. These score components were initially used to develop a weighted (w-KIR Score) and subsequently a simplified, non-weighted KIR-KIRL interaction scores (IM-KIR Score). Increased w-KIR Score and IM-KIR Score were both predictive of all-cause mortality and relapse; w-KIR score HR of 0.37 (P=0.001) and 0.44 (P=0.044) respectively; IM-KIR score HR of 0.5 (P=0.049) and 0.44 (P=0.002) respectively. IM-KIR score was also associated with NK cell reconstitution post HCT. KIR-KIRL interactions as reflected by the w-KIR and IM-KIR scores influence both relapse risk and survival in recipients of HLA matched URD HCT with hematological malignancies.

Highlights

Killer immunoglobulin-like receptor (KIR) – KIR-ligand (KIRL) interactions display a high degree of variability in HLA matched stem cell transplant (SCT) recipients.

Individually, the magnitude of inhibitory and missing KIR-KIRL interactions predicts overall survival and relapse risk following SCT.

Taken together the known KIR-KIRL interactions also predict clinical outcomes after HLA matched unrelated donor stem cell transplantation.
Opioid prescribing in the emergency department of a tertiary hospital: A retrospective audit of hospital discharge data
Authors: Stanley Beata , Collins Lisa J , Norman Amanda F , Karro Jonathon , Jung Monica , Bonomo Yvonne A
Published: June 2019

Objective

EDs are a common source of prescription opioids on discharge. We explored opioid prescribing practices in an ED at a tertiary hospital in Victoria, Australia.

Methods

A retrospective audit over a 6 month period of patients discharged from the ED to the community with the maximum allowable quantities of prescription opioids.

Results

There was a total of 3301 patient‐episodes discharged with a prescription from the ED. Of these, 766 (23.2%, 95% confidence interval [CI] 21.8–24.6) were prescribed opioids, with over half discharged with the maximum allowable quantities of prescription opioids. Immediate‐release opioids were prescribed in 362 (85.8%, 95% CI 82.5–89.1) patient‐episodes, a combination of immediate‐release and slow‐release preparations were prescribed in 29 (6.9%, 95% CI 4.5–9.3) and 31 (7.3%, 95% CI 4.8–9.8) were prescribed as slow‐release opioids alone. Co‐prescription of other analgesia with opioids occurred in 152 (36.0%, 95% CI 31.4–40.6) patient‐episodes. Possible drug interactions between opioids and other medications were noted in 117 (27.7%, 95% CI 23.4–32.0) patient‐episodes. Discharge summaries were prepared for 360 (85.3%, 95% CI 81.9–88.7) patient‐episodes, but only 171 (40.5%, 95% CI 35.8–45.2) included a plan to address the opioids, be that an opioid‐weaning regimen, analgesia review or referral to a pain specialist on discharge.

Conclusion

Opioid prescribing was common in this ED, with almost one‐quarter of discharge prescriptions being for a prescription opioid. This audit highlights potential areas for practice improvement including review of the quantity of opioid tablets prescribed as well as an opioid plan on discharge from the ED.
A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth
Authors: Zhou Qian , Gao Haoyang , Zhang Yong , Fan Guangyi , Xu Hao , Zhai Jieming , Xu Wenteng , Chen Zhangfan , Zhang He , Liu Shanshan , Niu Yipeng , Li Wensheng , Li Weiming , Lin Haoran , Chen Songlin
Published: June 2019

The giant grouper (Epinephelus lanceolatus) is the largest coral reef teleost, with a native range that spans temperate and tropical waters in the Pacific and the Indian Oceans. It is cultured artificially and used as a breeding species in aquaculture due to its rapid growth rate. Here we report a giant grouper genome assembled at the chromosome scale from sequences generated using Illumina and high‐throughput chromatin conformation capture (Hi‐C) technology. The assembly comprised 1.086 Gb, with 98.4% of the scaffold sequences anchored into 24 chromosomes. The contig and scaffold N50 values were 119.9 kb and 46.2 Mb, respectively. The assembly is of high integrity, including 96.4% universal single‐copy orthologues based on BUSCO analysis. Through chromosome‐scale evolution analysis, we identified alignments of six giant grouper chromosomes to three stickleback chromosomes and some of the genes located within the breakpoints of reshuffling events may related to development and growth. From the 24,718 protein‐coding genes, we found that several gene families related to innate immunity and glycan biosynthesis were significantly expanded in the giant grouper genome compared to other teleost genomes. In addition, we identified several genes related to the hormone signalling pathway and innate immunity that have experienced positive selection or accelerated evolution, implicating their roles in immune defence and fast growth of the species. The high‐quality genome assembly will provide a valuable genomic resource for further biological and evolutionary studies, and useful genomic tools for breeding of the giant grouper.
Multiple roles of Bet v 1 ligands in allergen stabilization and modulation of endosomal protease activity
Authors: Soh Wai Tuck , Aglas Lorenz , Mueller Geoffrey A. , Gilles Stefanie , Weiss Richard , Scheiblhofer Sandra , Huber Sara , Scheidt Tamara , Thompson Peter M. , Briza Peter , London Robert E. , Traidl‐Hoffmann Claudia , Cabrele Chiara , Brandstetter Hans , Ferreira Fatima
Published: June 2019

Background

Over 100 million people worldwide suffer from birch pollen allergy. Bet v 1 has been identified as the major birch pollen allergen. However, the molecular mechanisms of birch allergic sensitization, including the roles of Bet v 1 and other components of the birch pollen extract, remain incompletely understood. Here, we examined how known birch pollen–derived molecules influence the endolysosomal processing of Bet v 1, thereby shaping its allergenicity.

Methods

We analyzed the biochemical and immunological interaction of ligands with Bet v 1. We then investigated the proteolytic processing of Bet v 1 by endosomal extracts in the presence and absence of ligands, followed by a detailed kinetic analysis of Bet v 1 processing by individual endolysosomal proteases as well as the T‐cell epitope presentation in BMDCs.

Results

We identified E1 phytoprostanes as novel Bet v 1 ligands. Pollen‐derived ligands enhanced the proteolytic resistance of Bet v 1, affecting degradation kinetics and preferential cleavage sites of the endolysosomal proteases cathepsin S and legumain. E1 phytoprostanes exhibited a dual role by stabilizing Bet v 1 and inhibiting cathepsin protease activity.

Conclusion

Bet v 1 can serve as a transporter of pollen‐derived, bioactive compounds. When carried to the endolysosome, such compounds can modulate the proteolytic activity, including its processing by cysteine cathepsins. We unveil a paradigm shift from an allergen‐centered view to a more systemic view that includes the host endolysosomal enzymes.
The role of mobile health technologies in allergy care: An EAACI position paper
Authors: Matricardi Paolo Maria , Dramburg Stephanie , Alvarez‐Perea Alberto , Antolín‐Amérigo Darío , Apfelbacher Christian , Atanaskovic‐Markovic Marina , Berger Uwe , Blaiss Michael S. , Blank Simon , Boni Elisa , Bonini Matteo , Bousquet Jean , Brockow Knut , Buters Jeroen , Cardona Victoria , Caubet Jean‐Christoph , Cavkaytar Özlem , Elliott Tania , Esteban‐Gorgojo Ignacio , Fonseca Joao A. , Gardner James , Gevaert Philippe , Ghiordanescu Ileana , Hellings Peter , Hoffmann‐Sommergruber Karin , Fusun Kalpaklioglu A. , Marmouz Farid , Meijide Calderón Ángela , Mösges Ralph , Nakonechna Alla , Ollert Markus , Oteros José , Pajno Giovanni , Panaitescu Catalina , Perez‐Formigo Daniel , Pfaar Oliver , Pitsios Constantinos , Rudenko Michael , Ryan Dermot , Sánchez‐García Silvia , Shih Jennifer , Tripodi Salvatore , Van der Poel Lauri‐Ann , van Os‐Medendorp Harmieke , Varricchi Gilda , Wittmann Jörn , Worm Margitta , Agache Ioana
Published: June 2019

Mobile health (mHealth) uses mobile communication devices such as smartphones and tablet computers to support and improve health‐related services, data and information flow, patient self‐management, surveillance, and disease management from the moment of first diagnosis to an optimized treatment. The European Academy of Allergy and Clinical Immunology created a task force to assess the state of the art and future potential of mHealth in allergology. The task force endorsed the “Be He@lthy, Be Mobile” WHO initiative and debated the quality, usability, efficiency, advantages, limitations, and risks of mobile solutions for allergic diseases. The results are summarized in this position paper, analyzing also the regulatory background with regard to the “General Data Protection Regulation” and Medical Directives of the European Community. The task force assessed the design, user engagement, content, potential of inducing behavioral change, credibility/accountability, and privacy policies of mHealth products. The perspectives of healthcare professionals and allergic patients are discussed, underlining the need of thorough investigation for an effective design of mHealth technologies as auxiliary tools to improve quality of care. Within the context of precision medicine, these could facilitate the change in perspective from clinician‐ to patient‐centered care. The current and future potential of mHealth is then examined for specific areas of allergology, including allergic rhinitis, aerobiology, allergen immunotherapy, asthma, dermatological diseases, food allergies, anaphylaxis, insect venom, and drug allergy. The impact of mobile technologies and associated big data sets are outlined. Facts and recommendations for future mHealth initiatives within EAACI are listed.
Interleukin‐13: Targeting an underestimated cytokine in atopic dermatitis
Authors: Bieber Thomas
Published: June 2019

Atopic dermatitis (AD) is a common inflammatory skin condition that has traditionally been considered a paradigmatic type 2 immunity (T2)‐driven disease. Interleukin (IL)‐4 and IL‐13 are both pivotal cytokines involved in the generation of allergic diseases. Currently, besides dupilumab, which blocks the binding of both cytokines to their receptors, a number of new pharmacologic entities have been designed to target both T2 cytokines and/or their receptors and/or receptor‐associated signal transduction machinery such as Janus kinases. Recently, IL‐13 has been suggested to be the key T2 cytokine driving inflammation in the periphery, while IL‐4 may merely have a central effect. There is increasing evidence that this concept holds true for the inflammatory reaction underlying AD, where IL‐13 is overexpressed locally and has a significant impact on skin biology, including the recruitment of inflammatory cells, the alteration of the skin microbiome, and the decrease in the epidermal barrier function. This review provides an update on the role of IL‐13 in AD and discusses the different strategies aimed at interfering with its biologic activity as well as their potential in a precision medicine approach in the management of AD.
Opioid prescribing improvement in orthopaedic specialty unit in a tertiary hospital: a retrospective audit of hospital discharge data pre‐ and post‐intervention for better opioid prescribing practice
Authors: Stanley Beata , Jackson Aidan , Norman Amanda , Collins Lisa , Bonomo Anthony , Bonomo Yvonne
Published: June 2019

Background

This study aimed to investigate the effects of an intervention focusing on better opioid prescription practice in a tertiary metropolitan hospital orthopaedic unit.

Methods

Following a previous audit of opioid prescribing in the orthopaedics unit, an intervention comprising the (i) Expert Advisory Group oversight of opioid prescribing, (ii) development of a prescription opioid guideline for various hospital contexts and (iii) a series of education sessions was undertaken to improve opioid prescription practice. A re‐audit was subsequently carried out to determine whether the intervention had had an impact on the previously audited orthopaedic unit.

Results

Each audit period was 6 months. There were 281 orthopaedic patients in the original audit (1 January 2017–30 June 2017) and 289 in the re‐audit (1 March 2018–31 August 2018). In both audits, a high proportion of patients were discharged to the community on opioids, 82.2% (n = 231) pre‐intervention and 79.6% (n = 230) post‐intervention. Statistically significant differences in opioid prescribing were found between audits, including: a reduction in the number of patients discharged on combination opioids from 71.4% to 45.7% (P < 0.001), a reduction in the provision of full pharmaceutical quantities of opioid on discharge from 29.4% to 6.1% (P < 0.001) and an increase in opioid weaning plans included in discharge summaries from 6.9% to 87.4% (P < 0.001).

Conclusion

Raised awareness across the organization and education for staff more than halved the post‐operative opioid prescription levels. This highlights the capacity for change in hospitals and the ability to work towards safer prescribing of post‐operative opioid therapy.