The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely ...known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.
This study extends social capital to specific types of personal relationships that encourage residents’ collective action for rural tourism development. Two communities in South Korea were examined ...using face-to-face interviews with community leaders, and a structured questionnaire with residents. Five hypotheses that frame tourism development as a coordinated effort of social networks were identified. Findings indicate that the quality of one’s social networks are relevant to the propensity to participate in tourism development. The closer one’s relationship to a community leader of tourism development, the more likely they are to be part of community-based efforts for tourism development. In addition, compared to individualized personal ties among residents, already existing social organizations were critical to enhance collective action of residents. An implication for increased participation in tourism development is for community leaders to reach out and learn from residents who are isolated or less central within community leadership networks.
Cancer genomic heterogeneity presents significant challenges for understanding oncogenic processes and for cancer’s clinical management. Variation in driver mutation frequency between patients with ...the same tumor type as well as within an individual patients’ cancer can shape the use of mutations as diagnostic, prognostic, and predictive biomarkers. We have characterized genomic heterogeneity between and within canine splenic hemangiosarcoma (HSA), a common naturally occurring cancer in pet dogs that is similar to human angiosarcoma (AS). HSA is a clinically, physiologically, and genomically complex canine cancer that may serve as a valuable model for understanding the origin and clinical impact of cancer heterogeneity. We conducted a prospective collection of 52 splenic masses from 43 dogs (27 HSA, 15 benign masses, and 1 stromal sarcoma) presenting for emergency care with hemoperitoneum secondary to a ruptured splenic mass. Multi-platform genomic analysis included matched tumor/normal targeted sequencing panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/27 (52%) HSAs. Among recurrent candidate driver mutations,
TP53
was most commonly mutated (30%) followed by
PIK3CA
(15%),
AKT1
(11%), and
CDKN2AIP
(11%). We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary splenic tumors. These data provide new perspectives on the genomic landscape of this veterinary cancer and suggest a cross-species value for using HSA in pet dogs as a naturally occurring model of intratumoral heterogeneity.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Access to efficient enzymatic channeling is desired for improving all manner of designer biocatalysis. We demonstrate that enzymes constituting a multistep cascade can self-assemble with nanoparticle ...scaffolds into nanoclusters that access substrate channeling and improve catalytic flux by orders of magnitude. Utilizing saccharification and glycolytic enzymes with quantum dots (QDs) as a model system, nanoclustered-cascades incorporating from 4 to 10 enzymatic steps are prototyped. Along with confirming channeling using classical experiments, its efficiency is enhanced several fold more by optimizing enzymatic stoichiometry with numerical simulations, switching from spherical QDs to 2-D planar nanoplatelets, and by ordering the enzyme assembly. Detailed analyses characterize assembly formation and clarify structure-function properties. For extended cascades with unfavorable kinetics, channeled activity is maintained by splitting at a critical step, purifying end-product from the upstream sub-cascade, and feeding it as a concentrated substrate to the downstream sub-cascade. Generalized applicability is verified by extending to assemblies incorporating other hard and soft nanoparticles. Such self-assembled biocatalytic nanoclusters offer many benefits towards enabling minimalist cell-free synthetic biology.
Climate change pressures will influence marine planktonic systems globally, and it is conceivable that harmful algal blooms may increase in frequency and severity. These pressures will be manifest as ...alterations in temperature, stratification, light, ocean acidification, precipitation-induced nutrient inputs, and grazing, but absence of fundamental knowledge of the mechanisms driving harmful algal blooms frustrates most hope of forecasting their future prevalence. Summarized here is the consensus of a recent workshop held to address what currently is known and not known about the environmental conditions that favor initiation and maintenance of harmful algal blooms. There is expectation that harmful algal bloom (HAB) geographical domains should expand in some cases, as will seasonal windows of opportunity for harmful algal blooms at higher latitudes. Nonetheless there is only basic information to speculate upon which regions or habitats HAB species may be the most resilient or susceptible. Moreover, current research strategies are not well suited to inform these fundamental linkages. There is a critical absence of tenable hypotheses for how climate pressures mechanistically affect HAB species, and the lack of uniform experimental protocols limits the quantitative cross-investigation comparisons essential to advancement. A HAB “best practices” manual would help foster more uniform research strategies and protocols, and selection of a small target list of model HAB species or isolates for study would greatly promote the accumulation of knowledge. Despite the need to focus on keystone species, more studies need to address strain variability within species, their responses under multifactorial conditions, and the retrospective analyses of long-term plankton and cyst core data; research topics that are departures from the norm. Examples of some fundamental unknowns include how larger and more frequent extreme weather events may break down natural biogeographic barriers, how stratification may enhance or diminish HAB events, how trace nutrients (metals, vitamins) influence cell toxicity, and how grazing pressures may leverage, or mitigate HAB development. There is an absence of high quality time-series data in most regions currently experiencing HAB outbreaks, and little if any data from regions expected to develop HAB events in the future. A subset of observer sites is recommended to help develop stronger linkages among global, national, and regional climate change and HAB observation programs, providing fundamental datasets for investigating global changes in the prevalence of harmful algal blooms. Forecasting changes in HAB patterns over the next few decades will depend critically upon considering harmful algal blooms within the competitive context of plankton communities, and linking these insights to ecosystem, oceanographic and climate models. From a broader perspective, the nexus of HAB science and the social sciences of harmful algal blooms is inadequate and prevents quantitative assessment of impacts of future HAB changes on human well-being. These and other fundamental changes in HAB research will be necessary if HAB science is to obtain compelling evidence that climate change has caused alterations in HAB distributions, prevalence or character, and to develop the theoretical, experimental, and empirical evidence explaining the mechanisms underpinning these ecological shifts.
SWEMWBS is a popular measure of mental wellbeing, shown to be valid in clinical populations. Responsiveness to change has not yet been formally assessed.
Analysis of data from a clinical sample of ...172 clients undergoing up to 4 sessions of cognitive hypnotherapy. Cohen's D effect size (ES), Standardised response mean (SRM), probability of change statistic (P^) were used to evaluate whether SWEMWBS detected statistically important changes at the group level. Cohen's D effect size (ES) and Standard error of measurement (SEM) and were used to evaluate whether SWEMWBS detected statistically important changes at the individual level.
Mean (SD) SWEMWBS scores increased from baseline to therapy 4 from 19.28 (3.921) to 23.32 (4.873). At group level, using Cohen's D effect size, improvement ranges from ES = 0.20-1.41 and using SRM, ranged from 0.30-0.88, increasing with number of therapy sessions. (P^) ranged from 0.65-0.8. At individual level, use of Cohens D ES > 0.5 indicated statistically important improvement in 29.9-86.1% cf. 20.1-80.6% using a standard of 2.77 SEM (2.87 points). The lower threshold of 1 SEM (1.03 points) indicated statistically important improvement in 43.0-81.0%.
SWEMWBS is responsive to change at individual and group level. At individual level a change of between 1 and 3 points meets thresholds for statisticially important change, depending on standard used. Anchor based studies are necessary to confirm that such change represents minimally important change from the perspective of study participants.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Since the end of the second World War, the landscapes of the U.S. Corn Belt have increasingly been dominated by large-scale, industrialized agricultural production. Although not without its benefits, ...industrial agriculture has been shown to be detrimental to the social and ecological fabric of rural communities and beyond. In response, state and federal policy has encouraged farmers to adopt a limited number of strategies that may reduce the negative externalities of industrial agriculture. However, a growing body of research argues that to achieve transformative environmental and social change, the U.S. must transition to alternative food and farming systems. This study explores the potential of such transformative change by integrating the concept of the “good farmer” within a place-making framework to allow us to examine the shared understandings of place among farmers of an Illinois watershed. Through semi-structured interviews, we analyzed the experiences of 17 farmers, focusing on their management practices, connection to the land, and the centrality of farming to their lives. In addition, we interviewed eight non-farmers whose careers or family life were directly connected to local agriculture. The results of our analysis found that the farmers in our study have incorporated a good farmer identity that goes beyond the highly visible productivist notions of faming. The place-meanings of family legacy, stewarding a viable future, and caring for the land were found to be as important to farmers as profit-making and efficiency of their operations. Our findings suggest that a transition to alternative farming systems would likely align with the identity and shared place-meanings of the farmers in our study. Programs and policies intending to facilitate a transition away from productivist systems of farming in the Corn Belt should be designed to support the farmer-held meanings of family legacy, farm viability, and care.
•Sustainable agriculture programs have yet to stem land and social degradation.•Understandings of a good farmer are reproduced and reinforced through place-making.•Farmers have expanded good farmer identity to include non-productivist meanings.•Family legacy, viable futures, and care of land important to farmer identity.•Transformative change in ag systems must support core farmer meanings.
Agricultural lands in the north-central United States represent some of the most uniform and non-sustainable landscapes in human history. The conformity in land-use practices reflects a broad social ...agreement, albeit unspoken, of having an influence on agricultural practices and is referred to as a normative landscape. Implementing conservation agricultural practices requires engaging such social agreements in ways that question and disrupt them. By using a mixed methods approach to support the application of the influence of a normative landscape, this study examines two research questions: (1) How do regionally normative landscapes influence site-based farming practices? And (2) To what extent do aspects (i.e., crop areas, buffer areas, and living areas) of individual farms contribute to the development of those regionally normative landscape meanings? When examining the first research question, an analysis of 21 interviews with farmers in Wisconsin and Illinois’ Driftless Region revealed two recurrent themes: “road farming” was a common way in which farmers communicated with each other about farm practices, and land-based learning events were opportunities to foster dialogue about farming activities that shape normative ideals. The results from the thematic analysis connect site-based farming practices within a broader regional context. A quantitative analysis of a survey of 82 farmers in the same region indicates that social agreement to evaluate the farming practices of others is strongest for crop areas. Our findings suggest that farmers and professionals wanting to improve conservation outcomes should use local events that reflect sustainable practices to disrupt and re-envision regional norms to spread conservation farming practices.
Comparative studies of naturally occurring canine cancers have provided new insight into many areas of cancer research. Development and validation of circulating tumor DNA (ctDNA) analysis in pet ...dogs can help address diagnostic needs in veterinary as well as human oncology. Dogs have high incidence of naturally occurring spontaneous cancers, demonstrate molecular heterogeneity and clonal evolution during therapy, allow serial sampling of blood from the same individuals during the course of disease progression, and have relatively compressed intervals for disease progression amenable to longitudinal studies. Here, we present a feasibility study of ctDNA analysis performed in 48 dogs including healthy dogs and dogs with either benign splenic lesions or malignant splenic tumors (hemangiosarcoma) using shallow whole genome sequencing (sWGS) of cell-free DNA. To enable detection and quantification of ctDNA using sWGS, we adapted two informatic approaches and compared their performance for the canine genome. At the time of initial clinical presentation, mean ctDNA fraction in dogs with malignant splenic tumors was 11.2%, significantly higher than dogs with benign lesions (3.2%; p = 0.001). ctDNA fraction was 14.3% and 9.0% in dogs with metastatic and localized disease, respectively (p = 0.227). In dogs treated with surgical resection of malignant tumors, mean ctDNA fraction decreased from 11.0% prior to resection to 7.9% post-resection (p = 0.047 for comparison of paired samples). Our results demonstrate that ctDNA analysis is feasible in dogs with hemangiosarcoma using a cost-effective approach such as sWGS. Additional studies are needed to validate these findings, and determine the role of ctDNA to assess burden of disease and treatment response in dogs with cancer.
Zika virus (ZIKV) is currently undergoing pandemic emergence. While disease is typically subclinical, severe neurologic manifestations in fetuses and newborns after congenital infection underscore an ...urgent need for antiviral interventions. The adenosine analog BCX4430 has broad-spectrum activity against a wide range of RNA viruses, including potent in vivo activity against yellow fever, Marburg and Ebola viruses. We tested this compound against African and Asian lineage ZIKV in cytopathic effect inhibition and virus yield reduction assays in various cell lines. To further evaluate the efficacy in a relevant animal model, we developed a mouse model of severe ZIKV infection, which recapitulates various human disease manifestations including peripheral virus replication, conjunctivitis, encephalitis and myelitis. Time-course quantification of viral RNA accumulation demonstrated robust viral replication in several relevant tissues, including high and persistent viral loads observed in the brain and testis. The presence of viral RNA in various tissues was confirmed by an infectious culture assay as well as immunohistochemical staining of tissue sections. Treatment of ZIKV-infected mice with BCX4430 significantly improved outcome even when treatment was initiated during the peak of viremia. The demonstration of potent activity of BCX4430 against ZIKV in a lethal mouse model warrant its continued clinical development.
•Protective efficacy of BCX4430 in various cell lines and in a lethal mouse model, including therapeutic treatment.•Treatment with BCX4430 doesn't preclude antibody response.•Time-course detection of viral RNA and infectious virus in various tissues.•Pathology in the brain and spinal cord of infected mice.•Detection of persistent virus in the testis.
PDF
