bluuebunny/crossref_metadata_2025 huggingface dataset:
Partner’s age, not social environment, predicts extrapair paternity in wild great tits (Parus major)
Authors: Roth Allison M , Firth Josh A , Patrick Samantha C , Cole Ella F , Sheldon Ben C
Published: August 2019

An individual’s fitness is not only influenced by its own phenotype, but by the phenotypes of interacting conspecifics. This is likely to be particularly true when considering fitness gains and losses caused by extrapair matings, as they depend directly on the social environment. While previous work has explored effects of dyadic interactions, limited understanding exists regarding how group-level characteristics of the social environment affect extrapair paternity (EPP) and cuckoldry. We use a wild population of great tits (Parus major) to examine how, in addition to the phenotypes of focal parents, two neighborhood-level traits—age and personality composition—predict EPP and cuckoldry. We used the well-studied trait “exploration behavior” as a measure of the reactive-proactive personality axis. Because breeding pairs inhabit a continuous “social landscape,” we first established an ecologically relevant definition of a breeding “neighborhood” through genotyping parents and nestlings in a 51-ha patch of woodland and assessing the spatial predictors of EPP events. Using the observed decline in likelihood of EPP with increasing spatial separation between nests, we determined the relevant neighborhood boundaries, and thus the group phenotypic composition of an individual’s neighborhood, by calculating the point at which the likelihood of EPP became negligible. We found no evidence that “social environment” effects (i.e., neighborhood age or personality composition) influenced EPP or cuckoldry. We did, however, find that a female’s own age influenced the EPP of her social mate, with males paired to older females gaining more EPP, even when controlling for the social environment. These findings suggest that partner characteristics, rather than group phenotypic composition, influence mating activity patterns at the individual level.
Age differences in the temporal stability of a male African elephant (Loxodonta africana) social network
Authors: Murphy Derek , Mumby Hannah S , Henley Michelle D
Published: August 2019

Social animals live in complex and variable socio-ecological environments where individuals adapt their behavior to local conditions. Recently, there have been calls for studies of animal social networks to take account of temporal dynamics in social relationships as these have implications for the spread of information and disease, group cohesion, and the drivers of sociality, and there is evidence that maintaining stable social relationships has fitness benefits. It has recently been recognized that male elephants form strong social bonds with other males. The nature of these relationships, and thus network structure, may vary over time in response to varying environmental conditions and as individuals age. Using social network analysis, we examine the stability of relationships and network centrality in a population of male African elephants. Our results suggest that males may maintain stable social relationships with others over time. Older males show greater stability in network centrality than younger males, suggesting younger males face uncertainty in transitioning to adult society. For elephants, where older individuals function as social repositories of knowledge, maintaining a social network underpinned by older males could be of particular importance.
Cardioinformatics: the nexus of bioinformatics and precision cardiology
Authors: Khomtchouk Bohdan B , Tran Diem-Trang , Vand Kasra A , Might Matthew , Gozani Or , Assimes Themistocles L
Published: August 2019

Cardiovascular disease (CVD) is the leading cause of death worldwide, causing over 17 million deaths per year, which outpaces global cancer mortality rates. Despite these sobering statistics, most bioinformatics and computational biology research and funding to date has been concentrated predominantly on cancer research, with a relatively modest footprint in CVD. In this paper, we review the existing literary landscape and critically assess the unmet need to further develop an emerging field at the multidisciplinary interface of bioinformatics and precision cardiovascular medicine, which we refer to as ‘cardioinformatics’.
Truncation of MYH8 tail in AML: a novel prognostic marker with increase cell migration and epithelial–mesenchymal transition utilizing RAF/MAPK pathway
Authors: Park Hyejoo , Kim Daeyoon , Kim Dongchan , Park Jihyun , Koh Youngil , Yoon Sung-Soo
Published: August 2019

MYH8 is an actin-based motor protin involved in integrin-mediated cell adhesion and migration. Heretofore, the association of MYH8 mutation and cancer is unclear. In this study, we investigated the biologic significance of novel MYH8 tail truncation mutation, R1292X, in acute myeloid leukemia (AML) which was discovered by whole-exome sequencing and targeted re-sequencing of 209 AML patients. The patients harboring the mutation all relapsed within 3.8–20.9 months. To explore the functional consequence of the mutation in AML progress, we established knock-in cell lines using CRISPR-Cas9 genome editing. Using the established mutant model, we assessed traits of cancer progress. The mutant cells had improved motility, which was confirmed by immunofluorescence staining, wound healing, transwell migration and adhesion assay. The cell morphology and cell cycle were altered to be accessible to migration and epithelial-to-mesenchymal transition (EMT) transcription factors were also increased. The Raf and p44/42 MAPK pathway was a major regulator of these characteristics proved by a screening of signal transduction and inhibitor assay. Further, a public cancer genome database (cBioPortal) shows that MYH8 tail truncation mutations occurring near the R1292 position of the genome may have a significant function in cancer. In conclusion, truncation of MYH8 could be a novel prognostic marker related to poor prognosis by inducing cell migration and EMT features, and inhibition of the Raf/MAPK pathway would be a therapeutic strategy for AML patients with MYH8 tail truncation.
Mass-transfer studies of solid-base catalyst-aided CO2 absorption and solid-acid catalyst-aided CO2 desorption for CO2 capture in a pilot plant using aqueous solutions of MEA and blends of MEA-MDEA and BEA-AMP
Authors: Coker James , Afari Daniel Boafo , Narku-Tetteh Jessica , Idem Raphael
Published: August 2019

Mass-transfer studies of catalyst-aided CO2 absorption and desorption were performed in a full-cycle, bench-scale pilot plant to improve CO2 absorption using 5M MEA, 5M MEA-2M MDEA and 2M BEA-2M AMP. A solid-base catalyst, K/MgO, and an acid catalyst, HZSM-5, were used to facilitate absorption and desorption, respectively. Absorption and desorption mass-transfer performance was presented in terms of the overall mass-transfer coefficient of the gas side (KGav) and liquid side (KLav), respectively. For non-catalytic runs, the highest KGaV and KLaV were 0.086 Kmolm3.kPa.hr  and 0.785 1hr for 2M BEA-2M AMP solvent. The results showed 38.7% KGav and 23.6% KLav increase for 2M BEA-2M AMP with only HZSM-5 catalyst in desorber and a 95% KGaV and 45% KLaV increase for both K/MgO catalyst and HZSM-5 catalyst. This was attributed to the role of K/MgO in bonding loosely with CO2 and making it available for the amine reaction.
How Task Interactivity Shapes Action Observation
Authors: Sacheli L M , Verga C , Arcangeli E , Banfi G , Tettamanti M , Paulesu E
Published: August 2019

Action observation triggers imitation, a powerful mechanism permitting interpersonal coordination. Coordination, however, also occurs when the partners’ actions are nonimitative and physically incongruent. One influential theory postulates that this is achieved via top-down modulation of imitation exerted by prefrontal regions. Here, we rather argue that coordination depends on sharing a goal with the interacting partner: this shapes action observation, overriding involuntary imitation, through the predictive activity of the left ventral premotor cortex (lvPMc). During functional magnetic resonance imaging (fMRI), participants played music in turn with a virtual partner in interactive and noninteractive conditions requiring 50% of imitative/nonimitative responses. In a full-factorial design, both perceptual features and low-level motor requirements were kept constant throughout the experiment. Behaviorally, the interactive context minimized visuomotor interference due to the involuntary imitation of physically incongruent movements. This was paralleled by modulation of neural activity in the lvPMc, which was specifically recruited during the interactive task independently of the imitative/nonimitative nature of the social exchange. This lvPMc activity reflected the predictive decoding of the partner’s actions, as revealed by multivariate pattern analysis. This demonstrates that, during interactions, we process our partners’ behavior to prospectively infer their contribution to the shared goal achievement, generating motor predictions for cooperation beyond low-level imitation.
Movement and Performance Explain Widespread Cortical Activity in a Visual Detection Task
Authors: Salkoff David B , Zagha Edward , McCarthy Erin , McCormick David A
Published: August 2019

Recent studies in mice reveal widespread cortical signals during task performance; however, the various task-related and task-independent processes underlying this activity are incompletely understood. Here, we recorded wide-field neural activity, as revealed by GCaMP6s, from dorsal cortex while simultaneously monitoring orofacial movements, walking, and arousal (pupil diameter) of head-fixed mice performing a Go/NoGo visual detection task and examined the ability of task performance and spontaneous or task-related movements to predict cortical activity. A linear model was able to explain a significant fraction (33–55% of variance) of widefield dorsal cortical activity, with the largest factors being movements (facial, walk, eye), response choice (hit, miss, false alarm), and arousal and indicate that a significant fraction of trial-to-trial variability arises from both spontaneous and task-related changes in state (e.g., movements, arousal). Importantly, secondary motor cortex was highly correlated with lick rate, critical for optimal task performance (high d′), and was the first region to significantly predict the lick response on target trials. These findings suggest that secondary motor cortex is critically involved in the decision and performance of learned movements and indicate that a significant fraction of trial-to-trial variation in cortical activity results from spontaneous and task-related movements and variations in behavioral/arousal state.
Effects of Developmental Nicotine Exposure on Frontal Cortical GABA-to-Non-GABA Neuron Ratio and Novelty-Seeking Behavior
Authors: Martin Melissa M , McCarthy Deirdre M , Schatschneider Chris , Trupiano Mia X , Jones Sara K , Kalluri Aishani , Bhide Pradeep G
Published: August 2019

Cigarette smoking during pregnancy is a major public health concern, resulting in detrimental health effects in the mother and her offspring. The adverse behavioral consequences for children include increased risk for attention deficit hyperactivity disorder, working memory deficits, epilepsy, novelty-seeking, and risk-taking behaviors. Some of these behavioral conditions are consistent with an imbalance in frontal cortical excitatory (glutamate) and inhibitory (GABA) neurotransmitter signaling. We used a GAD67-GFP knock-in mouse model to examine if developmental nicotine exposure alters frontal cortical GABA neuron numbers, GABA-to-non-GABA neuron ratio and behavioral phenotypes. Female mice were exposed to nicotine (100 or 200 μg/mL) in drinking water beginning 3 weeks prior to breeding and until 3 weeks postpartum. Male and female offspring were examined beginning at 60 days of age. The nicotine exposure produced dose-dependent decreases in GABA-to-non-GABA neuron ratios in the prefrontal and medial prefrontal cortices without perturbing the intrinsic differences in cortical thickness and laminar distribution of GABA or non-GABA neurons between these regions. A significant increase in exploratory behavior and a shift toward “approach” in the approach–avoidance paradigm were also observed. Thus, developmental nicotine exposure shifts the cortical excitation–inhibition balance toward excitation and produces behavioral changes consistent with novelty-seeking behavior.
Recurrence and Occurrence of Kaposi’s Sarcoma in Patients Living With Human Immunodeficiency Virus (HIV) and on Antiretroviral Therapy, Despite Suppressed HIV Viremia
Authors: Palich Romain , Veyri Marianne , Valantin Marc-Antoine , Marcelin Anne-Geneviève , Guihot Amélie , Pourcher Valérie , Jary Aude , Solas Caroline , Makinson Alain , Poizot-Martin Isabelle , Costagliola Dominique , Spano Jean-Philippe , Katlama Christine ,   for the CancerVIH Study Group, Autran B , Boué F , Choquet S , Cadranel J , Costagliola D , Garraffo R , Guihot A , Jary A , Katlama C , Lambotte O , Lavolé A , Makinson A , Marcelin A-G , Palich R , Poizot-Martin I , Solas C , Spano J-P , Valantin M-A , Veyri M , Ait-Mohand H , Baillat V , Belhouari K , Canestri A , Chiarello P , El Hajj Lise , Gras G , Hitoto H , Makhloufi D , Pourcher V , Pacanowski J , Patrat-Delon S , Pavel S , Psomas C , Vareil M-O
Published: August 2019

In 21 cutaneous and/or visceral Kaposi’s sarcoma cases, occurring in patients living with human immunodeficiency virus (HIV) who were on antiretroviral therapy with suppressed HIV viremia and high CD4 T cell counts, the efficacy of conventional chemotherapies was limited due to cumulative toxicities, comedications, and a lack of immune improvement.
Natural History and Evolution of Anti-Interferon-γ Autoantibody-Associated Immunodeficiency Syndrome in Thailand and the United States
Authors: Hong Gloria H , Ortega-Villa Ana M , Hunsberger Sally , Chetchotisakd Ploenchan , Anunnatsiri Siriluck , Mootsikapun Piroon , Rosen Lindsey B , Zerbe Christa S , Holland Steven M
Published: August 2019

Background

The natural history of anti-interferon-γ (IFN-γ) autoantibody-associated immunodeficiency syndrome is not well understood.

Methods

Data of 74 patients with anti-IFN-γ autoantibodies at Srinagarind Hospital, Thailand, were collected annually (median follow-up duration, 7.5 years). Annual data for 19 patients and initial data for 4 patients with anti-IFN-γ autoantibodies at the US National Institutes of Health were collected (median follow-up duration, 4.5 years). Anti-IFN-γ autoantibody levels were measured in plasma samples.

Results

Ninety-one percent of US patients were of Southeast Asian descent; there was a stronger female predominance (91%) in US than Thai (64%) patients. Mycobacterium abscessus (34%) and Mycobacterium avium complex (83%) were the most common nontuberculous mycobacteria in Thailand and the United States, respectively. Skin infections were more common in Thailand (P = .001), whereas bone (P < .0001), lung (P = .002), and central nervous system (P = .03) infections were more common in the United States. Twenty-four percent of Thai patients died, most from infections. None of the 19 US patients with follow-up data died. Anti-IFN-γ autoantibody levels decreased over time in Thailand (P < .001) and the United States (P = .017), with either cyclophosphamide (P = .01) or rituximab therapy (P = .001).

Conclusions

Patients with anti-IFN-γ autoantibodies in Thailand and the United States had distinct demographic and clinical features. While titers generally decreased with time, anti-IFN-γ autoantibody disease had a chronic clinical course with persistent infections and death. Close long-term surveillance for new infections is recommended.
Clinical Manifestations of Nipah Virus–Infected Patients Who Presented to the Emergency Department During an Outbreak in Kerala State in India, May 2018
Authors: Chandni Radhakrishnan , Renjith T P , Fazal Arshad , Yoosef Noufel , Ashhar C , Thulaseedharan N K , Suraj K P , Sreejith M K , Sajeeth Kumar K G , Rajendran V R , Remla Beevi A , Sarita R L , Sugunan Attayur P , Arunkumar Govindakarnavar , Mourya D T , Murhekar Manoj
Published: August 2019

Background

An outbreak of Nipah virus (NiV) disease occurred in the Kozhikode district of Kerala State in India in May 2018. Several cases were treated at the emergency medicine department (ED) of the Government Medical College, Kozhikode (GMCK). The clinical manifestations and outcome of these cases are described.

Methods

The study included 12 cases treated in the ED of GMCK. Detailed clinical examination, laboratory investigations, and molecular testing for etiological diagnosis were performed.

Results

The median age of the patients was 30 years and the male to female ratio was 1.4:1.0. All the cases except the index case contracted the infection from hospitals. The median incubation period was 10 days, and the case fatality ratio was 83.3%. Ten (83.3%) patients had encephalitis and 9 out of 11 patients whose chest X-rays were obtained had bilateral infiltrates. Three patients had bradycardia and intractable hypotension requiring inotropes. Encephalitis, acute respiratory distress syndrome, and myocarditis were the clinical prototypes, but there were large overlaps between these. Ribavirin therapy was given to a subset of the patients. Although there was a 20% reduction in NiV encephalitis cases treated with the drug, the difference was not statistically significant. The outbreak ended soon after the introduction of total isolation of patients and barrier nursing.

Conclusion

The outbreak of NiV disease in Kozhikode in May 2018 presented as encephalitis, acute respiratory distress and myocarditis or combinations of these. The CFR was high. Ribavirin therapy was tried but no evidence for its benefit could be obtained.
Frequent Methicillin-Resistant Staphylococcus aureus Introductions Into an Inner-city Jail: Indications of Community Transmission Networks
Authors: Popovich Kyle J , Snitkin Evan S , Zawitz Chad , Aroutcheva Alla , Payne Darjai , Thiede Stephanie N , Schoeny Michael , Green Stefan J , Hayden Mary K , Hota Bala , Weinstein Robert A
Published: August 2019

Background

Jails may facilitate spread of methicillin-resistant Staphylococcus aureus (MRSA) in urban areas. We examined MRSA colonization upon entrance to a large urban jail to determine if there are MRSA transmission networks preceding incarceration.

Methods

Males incarcerated in Cook County Jail (Chicago) were enrolled, with enrichment for people living with human immunodeficiency virus (PLHIV), within 72 hours of intake. Surveillance cultures assessed prevalence of MRSA colonization. Whole-genome sequencing (WGS) identified preincarceration transmission networks.

We examined methicillin-resistant Staphylococcus aureus (MRSA) isolates to determine if there are transmission networks that precede incarceration. A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to community reservoirs for MRSA.

Results

There were 718 individuals (800 incarcerations) enrolled; 58% were PLHIV. The prevalence of MRSA colonization at intake was 19%. In multivariate analysis, methamphetamine use, unstable housing, current/recent skin infection, and recent injection drug use were predictors of MRSA. Among PLHIV, recent injection drug use, current skin infection, and HIV care at outpatient clinic A that emphasizes comprehensive care to the lesbian, gay, bisexual, transgender community were predictors of MRSA. Fourteen (45%) of 31 detainees with care at clinic A had colonization. WGS revealed that this prevalence was not due to clonal spread in clinic but rather to an intermingling of distinct community transmission networks. In contrast, genomic analysis supported spread of USA500 strains within a network. Members of this USA500 network were more likely to be PLHIV (P < .01), men who have sex with men (P < .001), and methamphetamine users (P < .001).

Conclusions

A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to identify colonized detainees entering jail and potential community reservoirs of MRSA.
Sri Lanka’s Quest for a Reformed Constitution: Lessons from a Lost Opportunity
Authors: Pullé Austin I , Ratnapala Suri
Published: August 2019

The history of Sri Lanka is highly instructive of the dynamics of constitutional evolution in a post-colonial, multi-ethnic, and economically challenged Asian nation. Sri Lanka is one of the few ex-colonies where constitutional change has happened without military involvement. Citizens have changed their government 10 times by generally fair and free elections. In the first three decades after independence, the country’s judiciary enjoyed an enviable reputation for independence, integrity, and competence. The public service, though poorly rewarded and resourced, maintained a praiseworthy standard of administrative impartiality and competence. Sri Lanka had, and still has, one of the highest rates of literacy in the developing world and scores creditably on human development indicators. Despite these impressive achievements, the country has a chequered record of constitutional government since independence. It has been ruled for long periods under emergency rule, and the nation’s two republican constitutions have a poor record of maintaining constitutional democracy and basic rights and freedoms. The nation’s most recent efforts at constitutional reform, despite some notable successes, have stalled as a consequence of hyper-partisanship and opportunistic political strategizing. This article examines the post-independence constitutional history of the nation, prognosticates its prospects of constitutional revival, and draws important lessons from the failure of the current constitutional project.
Hydrographical Flow Modelling of the River Severn Using Particle Swarm Optimization
Authors: Kenny Ian
Published: August 2019

A model is presented to model hydrographical flow, which we apply to flood forecasting in the River Severn catchment area. The approach uses Particle Swarm Optimization (PSO), a swarm computation heuristic, to produce a predictive model of hydrographical flow. Hydrological flow data from 1980 to 1990 are considered, comprising the daily average flow through the River Severn and its tributaries. PSO models are developed from each year of data and are applied to predict flow in the other 10 years; model performance is shown to be largely independent of the training year, suggesting the catchment system is stable and the approach is robust. Importantly, and in contrast to most of the existing alternatives, flow is derived from data measurements taken 2 days previously, as demanded for early-warning flood prediction. The cross-validated model for prediction of extreme (Q95) events R2 = 0.96, significantly improving upon multiple linear regression R2 = 0.93, the best performing of current existing methods.
Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids
Authors: Houde Aimee Lee S , Günther Oliver P , Strohm Jeffrey , Ming Tobi J , Li Shaorong , Kaukinen Karia H , Patterson David A , Farrell Anthony P , Hinch Scott G , Miller Kristina M
Published: August 2019

Early marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr–smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.
Prolonged exposure to low oxygen improves hypoxia tolerance in a freshwater fish
Authors: Gilmore Kayla L , Doubleday Zoe A , Gillanders Bronwyn M
Published: August 2019

Lay summary

It is poorly understood whether fish can acclimate to prolonged low-oxygen conditions (or hypoxia). Our study shows that prior long-term exposure to low-oxygen conditions improves tolerance to low-oxygen in a freshwater fish. The results of our study aid our understanding of long-term responses of freshwater fish to low-oxygen to hypoxic events.
Effects of traffic noise exposure on corticosterone, glutathione and tonic immobility in chicks of a precocial bird
Authors: Flores Romina , Penna Mario , Wingfield John C , Cuevas Elfego , Vásquez Rodrigo A , Quirici Verónica
Published: August 2019

Repeated exposure to traffic noise may be perceived as a succession of stressors, and therefore, noisy urban environments could lead to a state of chronic stress. In developing animals, glucocorticoids can have organizational effects on the hypothalamic–pituitary–adrenal axis in addition to the classic activation effects, so evaluating the effect of traffic noise during development is urgently needed. To our knowledge, to date six studies have investigated the effects of traffic noise on baseline corticosterone (CORT) and/or the stress response in birds during development; however, these studies were performed in nestling (altricial species), where confounding factors (e.g. communication between nestlings and parents) could mask the real impact of traffic noise on stress. In this study, we evaluated the effect of traffic noise (traffic noise group vs. rural noise group) on baseline levels of CORT and stress responses in chicks of a precocial bird species, the Japanese quail (Coturnix japonica). Because CORT can also decrease glutathione (GSH) levels (antioxidant and neurotransmitter/modulator), secondly by means of path analysis we investigated whether the strength of the association between CORT levels, GSH levels and tonic immobility (TI) varied in relation to treatment. We observed (i) similar baseline levels of CORT in both groups, (ii) a trend toward higher stress response in the traffic noise group (P = 0.08), (iii) similar TI duration in both groups, (iv) higher GSH levels in the traffic noise group and (v) differences in the strength and sign of the associations in relation to the treatment (traffic vs. rural). We conclude that the acoustic environment perceived during development has implications for physiology and behaviour; as more research is done on this topic, the need for sustainable urban planning will become clearer.
Preservation of fecal glucocorticoid metabolites and immunoglobulin A through silica gel drying for field studies in horses
Authors: Krueger Konstanze , Marr Isabell , Dobler Andrea , Palme Rupert
Published: August 2019

Stability of stress hormone metabolites, fecal glucocorticoid metabolites (FGMs), and immunoglobulin A (IgA) was evaluated in horse feces dried in an air tight tube on silica gel, for improving stress analysis with fecal samples collected under field conditions with uncontrollable humidity. IgA showed a significant loss, but FGMs were stable and appeared to be reliably preserved.
A Flattened Protagonist: Sleep and Environmental Mitigation in Lydia Millet’s How the Dead Dream
Authors: Bateman Benjamin
Published: August 2019

Thinking with contemporary American novelist Lydia Millet’s How the Dead Dream (2007), this essay explores sleep as a form of ecological relief and argues that the form of the novel can critically expose the limitations of a “set-aside” approach to environmental conservation. As the protagonist T. loses the ability to sequester personal losses, he pursues co-sleeping opportunities with critically endangered animals both in zoos and in the wild. Through his somnolent form, the novel imagines sustainable and rehabilitative alternatives to traditional character development.
RumimiR: a detailed microRNA database focused on ruminant species
Authors: Bourdon Céline , Bardou Philippe , Aujean Etienne , Le Guillou Sandrine , Tosser-Klopp Gwenola , Le Provost Fabienne
Published: August 2019

The ever-increasing use of next-generation sequencing technologies to explore the genome has generated large quantities of data in recent years. Numerous publications have described several thousand sequences of microRNAs, all species included. A new database (RumimiR) has been created from the literature to provide a detailed description of microRNAs for three ruminant species: cattle, goats and sheep. To date, 2887, 2733 and 5095 unique microRNAs from bovine, caprine and ovine species, respectively, are included. In addition to the most recent reference genomic position and sequence of each microRNA, this database contains details about the animals, tissue origins and experimental conditions mentioned in the publications. Identity to human or mouse microRNA is also indicated. The RumimiR database allows data filtering by selecting microRNAs on the basis of defined criteria such as animal status or tissue origin. For ruminant studies, RumimiR supplements the widely used miRBase database, by using complementary criteria to allow browsing and filtering, and integrates all newly described published sequences. The principal goal of this database is to provide easy access to all the ruminant microRNAs described in the literature.
KOFFI and Anabel 2.0—a new binding kinetics database and its integration in an open-source binding analysis software
Authors: Norval Leo William , Krämer Stefan Daniel , Gao Mingjie , Herz Tobias , Li Jianyu , Rath Christin , Wöhrle Johannes , Günther Stefan , Roth Günter
Published: August 2019

The kinetics of featured interactions (KOFFI) database is a novel tool and resource for binding kinetics data from biomolecular interactions. While binding kinetics data are abundant in literature, finding valuable information is a laborious task. We used text extraction methods to store binding rates (association, dissociation) as well as corresponding meta-information (e.g. methods, devices) in a novel database. To date, over 270 articles were manually curated and binding data on over 1705 interactions was collected and stored in the (KOFFI) database. Moreover, the KOFFI database application programming interface was implemented in Anabel (open-source software for the analysis of binding interactions), enabling users to directly compare their own binding data analyses with related experiments described in the database.
PopTargs: a database for studying population evolutionary genetics of human microRNA target sites
Authors: Hatlen Andrea , Helmy Mohab , Marco Antonio
Published: August 2019

There is an increasing interest in the study of polymorphic variants at gene regulatory motifs, including microRNA target sites. Understanding the effects of selective forces at specific microRNA target sites, together with other factors like expression levels or evolutionary conservation, requires the joint study of multiple datasets. We have compiled information from multiple sources and compared it with predicted microRNA target sites to build a comprehensive database for the study of microRNA targets in human populations. PopTargs is a web-based tool that allows the easy extraction of multiple datasets and the joint analyses of them, including allele frequencies, ancestral status, population differentiation statistics and site conservation. The user can also compare the allele frequency spectrum between two groups of target sites and conveniently produce plots. The database can be easily expanded as new data becomes available and the raw database as well as code for creating new custom-made databases is available for downloading. We also describe a few illustrative examples.
BioSCOOP – Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks
Authors: Jarczak J , Lach J , Borówka P , Gałka M , Bućko M , Marciniak B , Strapagiel D
Published: August 2019

Dynamic development of biobanking industry (both business and science) resulted in an increased number of IT systems for samples and data management. The most difficult and complicated case for the biobanking community was cooperation between institutions, equipped with different IT systems, in the field of scientific research, mainly data interchange and information flow. Tools available on the market relate mainly to the biobank or collection level. Efficient and universal protocols including the detailed information about the donor and the sample are still very limited. Here, we have developed BioSCOOP, a communication protocol in the form of a well documented JSON API. The main aim of this study was to harmonize and standardize the rules of communication between biobanks on the level of information about the donor together with information about the sample. The purpose was to create a communication protocol for two applications: to transfer the information between different biobanks and to allow the searching and presentation of the sample and data sets.
Enabling semantic queries across federated bioinformatics databases
Authors: Sima Ana Claudia , Mendes de Farias Tarcisio , Zbinden Erich , Anisimova Maria , Gil Manuel , Stockinger Heinz , Stockinger Kurt , Robinson-Rechavi Marc , Dessimoz Christophe
Published: August 2019

Motivation: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.

Results: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.
‘One DB to rule them all’—the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs
Authors: Politano Gianfranco , Di Carlo Stefano , Benso Alfredo
Published: August 2019

In the last decade, genomics data have been largely adopted to sketch, study and better understand the complex mechanisms that underlie biological processes. The amount of publicly available data sources has grown accordingly, and several types of regulatory interactions have been collected and documented in literature. Unfortunately, often these efforts do not follow any data naming/interoperability/formatting standards, resulting in high-quality but often uninteroperable heterogeneous data repositories. To efficiently take advantage of the large amount of available data and integrate these heterogeneous sources of information, we built the RING (Regulatory Interaction Graph), an integrative standardized multilevel database of biological interactions able to provide a comprehensive and unmatched high-level perspective on several phenomena that take place in the regulatory cascade and that researchers can use to easily build regulatory networks around entities of interest.
SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)
Authors: Masonbrink Rick , Maier Tom R , Seetharam Arun S , Juvale Parijat S , Baber Levi , Baum Thomas J , Severin Andrew J
Published: August 2019

Soybean is an important worldwide crop, and farmers continue to experience significant yield loss due to the soybean cyst nematode (SCN), Heterodera glycines. This soil-borne roundworm parasite is rated the most important pathogen problem in soybean production. The infective nematodes enter into complex interactions with their host plant by inducing the development of specialized plant feeding cells that provide the parasites with nourishment. Addressing the SCN problem will require the development of genomic resources and a global collaboration of scientists to analyze and use these resources. SCNBase.org was designed as a collaborative hub for the SCN genome. All data and analyses are downloadable and can be analyzed with three integrated genomic tools: JBrowse, Feature Search and BLAST. At the time of this writing, a number of genomic and transcriptomic data sets are already available, with 43 JBrowse tracks and 21 category pages describing SCN genomic analyses on gene predictions, transcriptome and read alignments, effector-like genes, expansion and contraction of genomic repeats, orthology and synteny with related nematode species, Single Nucleotide Polymorphism (SNPs) from 15 SCN populations and novel splice sites. Standard functional gene annotations were supplemented with orthologous gene annotations using a comparison to nine related plant-parasitic nematodes, thereby enabling functional annotations for 85% of genes. These annotations led to a greater grasp on the SCN effectorome, which include over 3324 putative effector genes. By designing SCNBase as a hub, future research findings and genomic resources can easily be uploaded and made available for use by others with minimal needs for further curation. By providing these resources to nematode research community, scientists will be empowered to develop novel, more effective SCN management tools.
Outcomes and Strategies to Support a Treat-to-target Approach in Inflammatory Bowel Disease: A Systematic Review
Authors: Colombel Jean-Frédéric , D’haens Geert , Lee Wan-Ju , Petersson Joel , Panaccione Remo
Published: August 2019

Background and Aims

Management of Crohn’s disease and ulcerative colitis has typically relied upon treatment intensification driven by symptoms alone. However, a ‘treat-to-target’ management approach may help to address underlying inflammation, minimise disease activity at early stages of inflammatory bowel disease, limit progression, and improve long-term outcomes.

Methods

A systematic literature review was conducted to identify data relevant to a treat-to-target approach in inflammatory bowel disease, published between January 1, 2007 and May 15, 2017.

Results

Consistent with recommendations of the Selecting Therapeutic Targets in Inflammatory Bowel Disease [STRIDE] working group, studies have investigated factors influencing the achievement of both endoscopic and histological mucosal healing and patient-level outcomes in inflammatory bowel disease [IBD]. Histological healing and biomarker levels have also been shown to be modifiable outcomes. Although there is a lack of prospectively derived evidence validating mucosal healing as a treatment target, data are emerging to suggest that targeting mucosal healing or inflammation rather than symptoms may be cost-effective in some settings. The review highlighted several strategies that may support the implementation of a treat-to-target approach in IBD. The prospective randomised CALM study demonstrated how tight control [whereby treatment decisions are based on close monitoring of inflammatory biomarkers] leads to improvements in endoscopic and clinical outcomes. The review also considered the influence of coordinated care from a multidisciplinary team and patient engagement with improved adherence, as well as the role of therapeutic drug monitoring in inflammatory bowel disease management.

Conclusions

A treat-to-target strategy may impact on disease progression and improve outcomes in inflammatory bowel disease. Prospective studies including long-term data are required to ensure that the most appropriate targets and strategies are identified.
The Safety Profile of Vedolizumab in Ulcerative Colitis and Crohn’s Disease: 4 Years of Global Post-marketing Data
Authors: Cohen Russell D , Bhayat Fatima , Blake Aimee , Travis Simon
Published: August 2019

Background and Aims

Vedolizumab is a gut-selective antibody to α 4  β 7 integrin, approved to treat moderate-to-severe ulcerative colitis and Crohn’s disease in adults. Clinical trial data on patients meeting protocol-specified criteria may not reflect real-world clinical practice. This is a descriptive analysis of 4 years of post-marketing safety data on vedolizumab.

Methods

The Vedolizumab Global Safety Database contains all adverse event reports collated by Takeda Pharmaceutical Company Ltd since vedolizumab approval [May 20, 2014]. Adverse event reports received between approval and May 19, 2018 were identified using Medical Dictionary for Regulatory Activities version 21.0 Preferred Terms. Adverse event frequencies were calculated and categorised.

Results

In approximately 208 050 patient-years of vedolizumab exposure, 32 752 patients reported 80 218 events. In patients with Crohn’s disease or ulcerative colitis, 37 662 and 34 259 events occurred in 14 191 and 14 042 patients, respectively, and 8297 events occurred in 4519 individuals with other [off-label] or unreported indications. Overall, 5230 [14%; Crohn’s disease] and 3580 [10%; ulcerative colitis] events were serious. Most frequently reported were gastrointestinal events (Crohn’s disease, 6156 [16%]; ulcerative colitis, 5701 [17%]). Patients with Crohn’s disease or ulcerative colitis reported 251 malignancies [<1%], 402 hepatobiliary events [<1%], and 5876 infections (1137 serious [19%], 301 opportunistic [5%]). Patients aged ≥70 years [2326 patients] reported <10% of events.

Conclusions

Adverse event patterns were consistent with clinical trials, with no new safety concerns. Most reported events were non-serious and event frequency was low, considering patient-years of exposure. Although limitations of post-marketing safety reports require acknowledgement, these real-world data support a favourable safety profile of vedolizumab.
Imaging in ESC clinical guidelines: chronic coronary syndromes
Authors: Saraste Antti , Barbato Emanuele , Capodanno Davide , Edvardsen Thor , Prescott Eva , Achenbach Stephan , Bax Jeroen J , Wijns William , Knuuti Juhani
Published: August 2019

The European Society of Cardiology (ESC) has recently published new guidelines on the diagnosis and management of chronic coronary syndromes (CCS). The 2019 guideline identified six common clinical scenarios of CCS defined by the different evolutionary phases of coronary artery disease (CAD), excluding the situations in which an acute coronary event, often with coronary thrombus formation, dominates the clinical presentation. This review aims at providing a summary of novel or revised concepts in the guidelines together with the recent data underlying the major changes on the use of cardiac imaging in patients with suspected or known CCS.

Based on data from contemporary cohorts of patients referred for diagnostic testing, the pre-test probabilities of CAD based on age, sex and symptoms have been adjusted substantially downward as compared with 2013 ESC guidelines. Further, the impact of various risk factors and modifiers on the pre-test probability was highlighted and a new concept of ‘Clinical likelihood of CAD’ was introduced. Recommendations regarding diagnostic tests to establish or rule-out obstructive CAD have been updated with recent data on their diagnostic performance in different patient groups and impact on patient outcome. As the initial strategy to diagnose CAD in symptomatic patients, non-invasive functional imaging for myocardial ischaemia, coronary computed tomography angiography or invasive coronary angiography combined with functional evaluation may be used, unless obstructive CAD can be excluded by clinical assessment alone. When available, imaging tests instead of the exercise electrocardiogram are recommended when following the non-invasive diagnostic strategy.
Morpho-metabolic post-surgical patterns of non-infected prosthetic heart valves by [18F]FDG PET/CTA: “normality” is a possible diagnosis
Authors: Roque Albert , Pizzi María N , Fernández-Hidalgo Nuria , Permanyer Eduard , Cuellar-Calabria Hug , Romero-Farina Guillermo , Ríos Remedios , Almirante Benito , Castell-Conesa Joan , Escobar Manuel , Ferreira-González Ignacio , Tornos Pilar , Aguadé-Bruix Santiago
Published: August 2019

Aims

To define characteristic PET/CTA patterns of FDG uptake and anatomic changes following prosthetic heart valves (PVs) implantation over time, to help not to misdiagnose post-operative inflammation and avoid false-positive cases.

Methods and results

Prospective evaluation of 37 post-operative patients without suspected infection that underwent serial cardiac PET/CTA examinations at 1, 6, and 12 months after surgery, in which metabolic features (FDG uptake distribution pattern and intensity) and anatomic changes were evaluated. Standardized uptake values (SUVs) were obtained and a new measure, the valve uptake index (VUI), (SUVmax–SUVmean)/SUVmax, was tested to homogenize SUV results.

In total, 111 PET/CTA scans were performed in 37 patients (19 aortic and 18 mitral valves). FDG uptake was visually detectable in 79.3% of patients and showed a diffuse, homogeneous distribution pattern in 93%. Quantitative analysis yielded a mean maximum standardized uptake value (SUVmax) of 4.46 ± 1.50 and VUI of 0.35 ± 0.10. There were no significant differences in FDG distribution or uptake values between 1, 6, or 12 months. No abnormal anatomic changes or endocarditis lesions were detected in any patient during follow-up.

Conclusions

FDG uptake, often seen in recently implanted PVs, shows a characteristic pattern of post-operative inflammation and, in the absence of associated anatomic lesions, could be considered a normal finding. These features remain stable for at least 1 year after surgery, so questioning the recommended 3-month safety period. A new measure, the VUI, can be useful for evaluating the FDG distribution pattern.