Community Consortium Research Articles

Goal-Oriented Metropolis Ecosystem Development

Enterprise architecture (EA) modelling is understood as a system of architecture defined in ISO42010 and EA is intended to ensure a holistic view of business organization. This study analyses the goal-oriented approach to EA development. Justification of selection of this topic results from studies on EA modelling methods. Enterprise architects mainly focus on process modelling as well as on the application of UML language. There is still an open question of what the goals of EA modelling are. This paper presents an application of ArchiMate language and i* notation for goal-oriented EA modelling. The paper methodology covers a literature survey as well as a case study presenting ArchiMate and i* models for goal-oriented EA development by example of metropolis system architecture modelling. In this paper, a metropolis is defined as a consortium of cooperative communities and it is considered as a business organization for which the system architecture is modelled. The paper aims to develop the metropolis architecture model consisting of system components, i.e. business issues, data, software and hardware. The metropolis architecture models are provided to support development of a metropolis strategy. The main findings include the identification of business goals and EA goals, goal mapping, and specification of the key performance indicators (KPIs) to control the achievement of the goals.

No biological effect on magnesium isotope fractionation during stromatolite growth

The growth and morphology of stromatolites have been previously linked to diverse microbial activities. However, the role of microbial metabolisms on carbonate formation during stromatolite growth remains controversial. Magnesium isotopes have been proposed to serve as a tracer of microbial carbonate formation, implying a potential biological isotope fractionation. To further elucidate whether Mg isotope fractionation is modified during microbial carbonate formation, this study reports Mg isotope compositions of Holocene stromatolites and pore waters from Lagoa Salgada, a coastal ephemeral lake in Brazil. The stromatolitic carbonates are composed of high-Mg calcites characterized by extremely positive inorganic δ13C values, up to +20‰, and variable δ26Mg values, ranging from −2.98‰ to −0.68‰. Multiple pieces of evidence consistently demonstrate changes in microbial metabolism resulting from ecosystem fluid chemistry evolution. However, the direction of Mg isotope fractionation associated with carbonate precipitation remained invariable despite the changes in microbial activity. Mineralogical features indicate that the stromatolitic carbonates formed via 2-D nucleation. An isotopic mass balance calculation based on the observed variations in δ26Mg values and Mg concentrations of associated pore waters argues for an Mg isotopic equilibrium fractionation factor of −2.60‰ associating with the carbonate formation at Lagoa Salgada, well-matching experimental values for abiotic calcite precipitation. Thus, the observed δ26Mg variability of stromatolitic carbonates is primarily controlled by the changes of physicochemical conditions in the ambient fluid. We infer that during the formation of stromatolites, a consortium of different microbial communities produces extracellular polymeric substances, which serve as a substrate for carbonate nucleation from ambient fluid without significantly affecting the fractionation of Mg-isotopes. Our findings shed light on the effects of microbial processes on carbonate formation during stromatolite growth and improve the current understanding of the Mg isotope record in microbial carbonates.

Dataverse Community Survey 2022 – Report

This report presents some of the results from the Dataverse Community Survey 2022.
 The main goal of the survey was to help the Global Dataverse Community Consortium (GDCC; https://dataversecommunity.global/) and the Dataverse Project (https://dataverse.org/) decide on what actions to take to improve the Dataverse software and the larger ecosystem of integrated tools and services as well as better support community members. The results from the survey may also be of interest to other communities working on software and services for managing research data.
 The survey was designed to map out the current status as well as the roadmaps and priorities of Dataverse installations around the world.
 The main target group for participating in the survey were the people/teams responsible for operating Dataverse installations around the world. A secondary target group were people/teams at organizations that are planning to deploy or considering deploying a Dataverse installation. There were 34 existing and planned Dataverse installations participating in the survey.

Interview with RD Hinshelwood

PurposeA one-day conference organised by the University of Essex and the Consortium of Therapeutic Communities, 10 December, 2021 with the theme, “The Unconscious and Organisations”. Presentations and discussions throughout the conference had the aim of generating ideas and sharing knowledge about the unconscious and how this can inform practitioners working in therapeutic communities and other organisations meeting the challenge of emotional distress.Design/methodology/approachInterview with Professor Robert (Bob) Hinshelwood (RH), now 83 years old, who has been involved in therapeutic communities (TCs) since 1969, part of the initial founding of the Association of Therapeutic Communities in 1974, is presented. He qualified as a psychoanalyst in 1976. In 1980 he instigated the founding of the International Journal of Therapeutic Communities along with Nick Manning, David Kennard, Jeff Roberts and Barry Shenkar. In 1984 he founded the British Journal of Psychotherapy, and edited it for 10 years. He was Director of the Cassel Hospital 1993–1997. In 1999 he founded the journal Psychoanalysis and History. He was part of the Free Associations Group (founded by Bob Young and others) which ran the journal Free Associations, and with Mike Rustin and the University of East London, the “Psychoanalysis and Public Sphere” conferences in the 1990s. He has written a great deal about the dynamics of organisational cultures in complex settings. He is Fellow of the British Psychoanalytical Society, Fellow of the Royal College of Psychiatrists and Professor Emeritus of the University of Essex. The interviewer was conducted by Dr Gary Winship (GW) is an associate professor at the University of Nottingham where he leads the MA in Trauma Informed Practice, visiting professor Moscow Institute of Psychoanalysis, and also visiting professor at the Russian State Humanities University, editor of the International Journal of Therapeutic Communities.FindingsHinshelwood reflects on the question of the unconscious and the impact of destructive tendencies on organisational process. He shares his personal experience being a young evacuee during the Second World War and considers the impact of trauma, losing his religion and his subsequent career choices in medicine, psychiatry and psychoanalysis. He discusses his experience of supervision with Isabel Menzies Lyth and reflects on the different groups in the Institute of Psychoanalysis. He turns to the question tribalism in TCs and regrets that there had not been more bridge building and collaboration. He talks about his own prolific writing and publishing career which he describes as obsessional rather than passionate, and finally candidly reflects on the prospect of facing death.Originality/valueThe interview was transcribed.

Characterization of a microbial consortium with potential for biological degradation of cactus pear biomass for biofuel production

Cactus pear (Opuntia ficus-indica) is a crassulacean acid metabolism (CAM) species that serves as a food, feed, and bioenergy crop. O. ficus-indica is an attractive alternative biofuel feedstock due to its low water demand and high biomass productivity. Current ethanol yields from O. ficus-indica are not commercially viable due to low concentrations of released fermentable carbohydrates. Axenic strains of bacteria and fungi were isolated and characterized from a soil microbial community consortium that effectively degrades cladodes into soluble components. The consortium consisted of species representing 14 genera of eubacteria and four genera of fungi. The digestion efficiency of each axenic isolate was evaluated by measuring the release of soluble material after aerobic digestion of cladodes and direct measurement of cellulase and pectinase activities in the culture supernatants. Pectobacterium cacticida was the most effective eubacterial species identified for degrading cladodes among all isolates evaluated. Thus, P. cacticida holds great promise for increasing the release of fermentable sugars and improving overall ethanol yields.

Performance of microbial community dominated by Bacillus spp. in acid mine drainage remediation systems: A focus on the high removal efficiency of SO42-, Al3+, Cd2+, Cu2+, Mn2+, Pb2+, and Sr2+

A consortium of microbial community was used for the treatment of acid mine drainage wastewater laden with sulphate and heavy metals. The wastewater was treated in an anaerobic continuously stirred tank bioreactor. The microbial community activity increased the pH from 5.6 to 6.5, and improved sulphate removal up to 85% from an initial sulphate concentration of 8080 mg SO42−/L in a continuous mode, following enrichment for 21 d. The maximum heavy metal removal percentage was observed for Cd (98%), Al (97%), Mn (95%), Pb (94%), Sr (94%) and Cu (91%). The microbial community showed synergy between strictly anaerobic and facultative Firmicutes sp., which were responsible for the bioreactor performance. The biochemical reaction indicated the microbial community has a wider range of substrates dominated by metallo-aminopeptidases.

Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture.

Dynamic consortium of microbial communities (bacteria, fungi, protists, viruses, and nematodes) colonizing multiple tissue types and coevolving conclusively with the host plant is designated as a plant microbiome. The interplay between plant and its microbial mutualists supports several agronomic functions, establishing its crucial role in plant beneficial activities. Deeper functional and mechanistic understanding of plant-microbial ecosystems will render many “ecosystem services” by emulating symbiotic interactions between plants, soil, and microbes for enhanced productivity and sustainability. Therefore, microbiome engineering represents an emerging biotechnological tool to directly add, remove, or modify properties of microbial communities for higher specificity and efficacy. The main goal of microbiome engineering is enhancement of plant functions such as biotic/abiotic stresses, plant fitness and productivities, etc. Various ecological-, biochemical-, and molecular-based approaches have come up as a new paradigm for disentangling many microbiome-based agromanagement hurdles. Furthermore, multidisciplinary approaches provide a predictive framework in achieving a reliable and sustainably engineered plant-microbiome for stress physiology, nutrient recycling, and high-yielding disease-resistant genotypes.

Core Mycobiome and Their Ecological Relevance in the Gut of Five Ips Bark Beetles (Coleoptera: Curculionidae: Scolytinae).

Bark beetles are destructive forest pests considering their remarkable contribution to forest depletion. Their association with fungi is useful against the challenges of survival on the noxious and nutritionally limited substrate, i.e., conifer tissues. Fungal symbionts help the beetles in nutrient acquisition and detoxification of toxic tree secondary metabolites. Although gut is the prime location for food digestion and detoxification, limited information is available on gut-mycobiome of bark beetles. The present study screened the gut-mycobiont from six bark beetles (five Ips and one non-Ips) from Scolytinae subfamily using high-throughput sequencing and explored their putative role in symbiosis with the host insect. Results revealed the predominance of four fungal classes- Sordariomycetes, Saccharomycetes, Eurothiomycetes, and Dothidomycetes in all bark beetles. Apart from these, Agaricomycetes, Leothiomycetes, Incertae sedis Basidiomycota, Tremellomycetes, Lecanoromycetes, and Microbotryomycetes were also documented in different beetles. Five Ips bark beetles share a consortium of core fungal communities in their gut tissues consisting of 47 operational taxonomic units (OTUs) belonging to 19 fungal genera. The majority of these core fungal genera belong to the phylum Ascomycota. LEfSe analysis revealed a set of species-specific fungal biomarkers in bark beetles. The present study identified the gut mycobiont assemblage in bark beetles and their putative ecological relevance. An enriched understanding of bark beetle-fungal symbiosis is not only filling the existing knowledge gap in the field but may also unleash an unforeseen potential for future bark beetle management.

The use of epilithic biofilms as bioaccumulators of pesticides and pharmaceuticals in aquatic environments.

Biofilms are a consortium of communities of organisms that live in syntrophic relationships and present a higher organization level than that of individual cells. Biofilms dominate microbial life in streams and rivers, enable crucial ecosystem processes, contribute to global biogeochemical flows and represent the main active bacterial life form. Epilithic biofilms are the main biomass found in rivers; their exposure to contaminants can lead to changes in their structure and composition. The composition of these communities is influenced by physicochemical factors, temperature, light and prior exposure to pollutants, among other factors, and it can be used for water quality monitoring purposes. The heterogenous composition of biofilms enables them to accumulate compounds in an integrative manner. Moreover, the availability of several sorption sites and their likely saturation can contribute to bioaccumulation. In aquatic environments, biofilms are also susceptible to the acquisition of antibiotic resistance genes and participate in their dissemination. Anthropic pressure intensification processes continuously expose water resources and, consequently, biofilm communities to different contamination sources. Therefore, the use of biofilms to indicate environmental pollution is reinforced by the progress of studies on the subject. Biofilm communities' response to pollutants in aquatic environments can be mainly influenced by the presence of different organisms, which may change due to community development or age. The current research aims to review studies about biofilm contamination and highlight the importance of biofilm use to better evaluate and maintain the quality of water bodies.

Gut bacteria of the cowpea beetle mediate its resistance to dichlorvos and susceptibility to Lippia adoensis essential oil

Bacteria inhabiting the gut of insects provide many benefits to their hosts, such as aiding in food digestion, reproduction, and immunity, tissue homeostasis, adaptation to environment and resistance to pathogen and pesticides. The cowpea beetle, Callosobruchus maculatus, is a serious cosmopolitan pest of pulses. This beetle has lent itself as a guinea pig for several ecological studies. It harbors a consortium of bacterial communities in its gut, but the evidence for their role in its physiology is fragmentary. In this work, we hypothesized that gut microbiota mediates C. maculatus resistance to dichlorvos (DDVP or O,O-dimethyl O-2,2-dichlorovinylphosphate) and represent the target of Lippia adoensis (Gambian Tea Bush) essential oil (EO). Symbiotic and aposymbiotic beetles were exposed to artificial cowpea seeds earlier treated with DDVP or EO. Adult mortality and changes in gut bacterial community composition and abundance were examined at F1 and F5 generations. The susceptibility of experimental beetles to DDVP was significantly affected by their symbiotic status. The adult mortality decreased across generations in DDVP treatments, and remained significantly higher in aposymbiotic groups. In EO treatments, the mortality was consistent irrespective of symbiotic status and experimental generations. When compared to DDVP and the Control, EO treatments had significantly lower bacterial richness and diversity, as well as lower abundance of Proteobacteria, Firmicutes, and Bacteroidetes. These results support our hypothesis and describe the responses of gut microbial communities to pesticide treatments. This could be of interest for developing new management strategies of this pest.

Microbiome and disease in the upper airway.

Microbiome refers to the genetic potential of resident microorganisms that inhabit a given niche. The exact role of the microbiome and its relation to chronic disease processes remains largely unknown, although various associations have been observed. We reviewed current literature investigating the microbiome of the upper airway by subsite (nasal cavity, sinus cavities, nasopharynx, and larynx) and its relation to chronic inflammatory disease processes. The disruption of indigenous microbiota at a specific subsite may lead to pathogen overgrowth and increased susceptibility to infection. This has previously been demonstrated in the gastrointestinal tract and lower airways. The role of the microbiome and its relation to pathogenesis of disease in the upper airway, however, is less clearly understood. The present review discusses the recent studies that appear to link dysbiosis to upper airway chronic inflammatory diseases. Despite mounting research, the role of microbiota in the upper airway remains poorly understood. Based on review of the current literature comparing healthy versus diseased patients with site-specific inflammatory conditions, a complex consortium of microbial communities inhabits the upper airway. Fluctuations in the baseline microbiome may contribute to disease pathogenesis, and improved understanding of the dynamics between shifting microbiota may be critical to guiding future medical therapy.

Community-Based Participatory Research and Sustainability: The Petersburg Wellness Consortium

The principle and practice of sustainability is critical in community-based participatory research. Actively planning for and building community capacity to ensure sustainability is even more critical in research involving underserved populations and underrepresented minorities. The perception of researchers engaging with the community until their research needs have been met, then leaving the community with minimal, if any benefits, has all too often been the reality in these communities. This paper offers a case study of how an independent community consortium was borne from an academic/community research partnership in Petersburg, Virginia. We discuss lessons learned and practice implications as we describe the evolution of, and challenges associated with, cultivating a sustainable independent coalition.

Exploring the Association between Alzheimer's Disease, Oral Health, Microbial Endocrinology and Nutrition.

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer’s disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis, a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host’s inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual’s diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD.

Antecedents to Collaborative Relationship Development among the Organizations in a Policy Network: An Evidence from the South Los Angeles Community Consortium

Antecedents to Collaborative Relationship Development among the Organizations in a Policy Network: An Evidence from the South Los Angeles Community Consortium

Using Participatory System Dynamics Modeling to Examine the Local HIV Test and Treatment Care Continuum in Order to Reduce Community Viral Load.

Achieving community-level goals to eliminate the HIV epidemic requires coordinated efforts through community consortia with a common purpose to examine and critique their own HIV testing and treatment (T&T) care system and build effective tools to guide their efforts to improve it. Participatory system dynamics (SD) modeling offers conceptual, methodological, and analytical tools to engage diverse stakeholders in systems conceptualization and visual mapping of dynamics that undermine community-level health outcomes and identify those that can be leveraged for systems improvement. We recruited and engaged a 25-member multi-stakeholder Task Force, whose members provide or utilize HIV-related services, to participate in SD modeling to examine and address problems of their local HIV T&T service system. Findings from the iterative model building sessions indicated Task Force members' increasingly complex understanding of the local HIV care system and demonstrated their improved capacity to visualize and critique multiple models of the HIV T&T service system and identify areas of potential leverage. Findings also showed members' enhanced communication and consensus in seeking deeper systems understanding and options for solutions. We discuss implications of using these visual SD models for subsequent simulation modeling of the T&T system and for other community applications to improve system effectiveness.

Mechanistic modeling of salmonellosis: Update and future directions

ABSTRACTMicrobial risk assessors often make simplifying assumptions that lead to the selection of simple concave functions with low-dose linearity, consistent with no-threshold and single-hit hypotheses, as default dose–response model forms. However, evidence is accumulating as the “microbiome revolution” progresses that challenge these assumptions that influence the estimates of the nature and magnitude of uncertainties associated with microbial risks. Scientific advances in the knowledge of the human “superorganism” (hybrid consortium of human plus microbial communities that cooperatively regulates health and disease) enable the design of definitive studies to estimate the pathogen doses overcome by the innate defenses, including the protective microbiota. The systematic investigation of the events of non-typhoid salmonellosis in humans undertaken nearly 2 decades ago was updated to incorporate recent scientific advances in the understanding of impact of the healthy superorganism that strengthens and extends the biological motivations for sublinear or convex dose–response curves in microbial risk assessment. The knowledge of colonization resistance (innate protection of the human superorganism from low doses of ingested pathogens) and microbiota-mediated clearance is advancing mechanistically for many pathosystems. However, until more detailed mechanistic data become available for salmonellosis, the consideration of a variety of empirical model forms is essential for depicting the uncertainty of the “true” dose–response model.

Predictors of Heart Dose From Lung Radiation Therapy in a Large Consortium of Community and Academic Practices

Predictors of Heart Dose From Lung Radiation Therapy in a Large Consortium of Community and Academic Practices

Time Trends and Predictors of Heart Dose From Breast Radiation Therapy in a Large Consortium of Community and Academic Practices

Time Trends and Predictors of Heart Dose From Breast Radiation Therapy in a Large Consortium of Community and Academic Practices

Interferon-free therapy for genotype 1 hepatitis C in liver transplant recipients: Real-world experience from the hepatitis C therapeutic registry and research network.

Recurrent infection with the hepatitis C virus (HCV) after liver transplantation (LT) is associated with decreased graft and patient survival. Achieving sustained virological response (SVR) with antiviral therapy improves survival. Because interferon (IFN)-based therapy has limited efficacy and is poorly tolerated, there has been rapid transition to IFN-free direct-acting antiviral (DAA) regimens. This article describes the experience with DAAs in the treatment of posttransplant genotype (GT) 1 HCV from a consortium of community and academic centers (Hepatitis C Therapeutic Registry and Research Network [HCV-TARGET]). Twenty-one of the 54 centers contributing to the HCV-TARGET consortium participated in this study. Enrollment criteria included positive posttransplant HCV RNA before treatment, HCV GT 1, and documentation of use of a simeprevir (SMV)/sofosbuvir (SOF) containing DAA regimen. Safety and efficacy were assessed. SVR was defined as undetectable HCV RNA 64 days or later after cessation of treatment. A total of 162 patients enrolled in HCV-TARGET started treatment with SMV+SOF with or without ribavirin (RBV) following LT. The study population included 151 patients treated with these regimens for whom outcomes and safety data were available. The majority of the 151 patients were treated with SOF and SMV alone (n = 119; 79%) or with RBV (n = 32; 21%), The duration of therapy was 12 weeks for most patients, although 15 patients received 24 weeks of treatment. Of all patients receiving SOF/SMV with or without RBV, 133/151 (88%) achieved sustained virological response at 12 weeks after therapy and 11 relapsed (7%). One patient had virological breakthrough (n = 1), and 6 patients were lost to posttreatment follow-up. Serious adverse events occurred in 11.9%; 3 patients (all cirrhotic) died due to aspiration pneumonia, suicide, and multiorgan failure. One experienced LT rejection. IFN-free DAA treatment represents a major improvement over prior IFN-based therapy. Broader application of these and other emerging DAA regimens in the treatment of posttransplant hepatitis C is warranted.

Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle.

Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters—polyketide synthase, nonribosomal peptide synthetase and siderophore—affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host’s immune response. The genome also harbored a large number of mobile elements (∼5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.