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Scientific discovery has advanced human society in countless ways, but research requires the expenditure of energy and resources. This Scientific Life article details one laboratory's efforts to reduce the environmental impact of wet-lab research and provides a series of resources to improve lab sustainability.
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The past 15 y has seen much development in documentation of domestication of plants and animals as gradual traditions spanning millennia. There has also been considerable momentum in understanding the dispersals of major domesticated taxa across continents spanning thousands of miles. The two processes are often considered within different theoretical strains. What is missing from our repertoire of explanations is a conceptual bridge between the protracted process over millennia and the multiregional, globally dispersed nature of domestication. The evidence reviewed in this paper bears upon how we conceptualize domestication as an episode or a process. By bringing together the topics of crop domestication and crop movement, those complex, protracted, and continuous outcomes come more clearly into view.
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Productos Agrícolas , Domesticación , Animales , Productos Agrícolas/genéticaRESUMEN
Climate-sensitive infectious diseases are an issue of growing concern due to global warming and the related increase in the incidence of extreme weather and climate events. Diarrhea, which is strongly associated with climatic factors, remains among the leading causes of child death globally, disproportionately affecting populations in low- and middle-income countries (LMICs). We use survey data for 51 LMICs between 2000 and 2019 in combination with gridded climate data to estimate the association between precipitation shocks and reported symptoms of diarrheal illness in young children. We account for differences in exposure risk by climate type and explore the modifying role of various social factors. We find that droughts are positively associated with diarrhea in the tropical savanna regions, particularly during the dry season and dry-to-wet and wet-to-dry transition seasons. In the humid subtropical regions, we find that heavy precipitation events are associated with increased risk of diarrhea during the dry season and the transition from dry-to-wet season. Our analysis of effect modifiers highlights certain social vulnerabilities that exacerbate these associations in the two climate zones and present opportunities for public health intervention. For example, we show that stool disposal practices, child feeding practices, and immunizing against the rotavirus modify the association between drought and diarrhea in the tropical savanna regions. In the humid subtropical regions, household's source of water and water disinfection practices modify the association between heavy precipitation and diarrhea. The evidence of effect modification varies depending on the type and duration of the precipitation shock.
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Clima , Diarrea , Humanos , Niño , Preescolar , Diarrea/epidemiología , Estaciones del Año , Salud Pública , AguaRESUMEN
Advocates of transparency in science often point to the benefits of open practices for the scientific process. Here, we focus on a possibly underappreciated effect of standards for transparency: their influence on non-scientific decisions. As a case study, we consider the current state of probabilistic genotyping software in forensics.
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Genética Forense , Ciencias Forenses , HumanosRESUMEN
Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) literate programming, (2) code version control and sharing, (3) compute environment control, (4) persistent data sharing and (5) documentation. These practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatics data analysts and bioinformaticians in training, but should be relevant to other domains of study.
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Biología Computacional , Difusión de la Información , Reproducibilidad de los Resultados , Programas InformáticosRESUMEN
BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS: We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS: Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.
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Enfermedades Raras , Humanos , Enfermedades Raras/genética , Enfermedades Raras/diagnóstico , Genoma Humano/genética , Variación Genética/genética , Biología Computacional/métodos , FenotipoRESUMEN
Intensive crop production on grassland-derived Mollisols has liberated massive amounts of carbon (C) to the atmosphere. Whether minimizing soil disturbance, diversifying crop rotations, or re-establishing perennial grasslands and integrating livestock can slow or reverse this trend remains highly uncertain. We investigated how these management practices affected soil organic carbon (SOC) accrual and distribution between particulate (POM) and mineral-associated (MAOM) organic matter in a 29-y-old field experiment in the North Central United States and assessed how soil microbial traits were related to these changes. Compared to conventional continuous maize monocropping with annual tillage, systems with reduced tillage, diversified crop rotations with cover crops and legumes, or manure addition did not increase total SOC storage or MAOM-C, whereas perennial pastures managed with rotational grazing accumulated more SOC and MAOM-C (18 to 29% higher) than all annual cropping systems after 29 y of management. These results align with a meta-analysis of data from published studies comparing the efficacy of soil health management practices in annual cropping systems on Mollisols worldwide. Incorporating legumes and manure into annual cropping systems enhanced POM-C, microbial biomass, and microbial C-use efficiency but did not significantly increase microbial necromass accumulation, MAOM-C, or total SOC storage. Diverse, rotationally grazed pasture management has the potential to increase persistent soil C on Mollisols, highlighting the key role of well-managed grasslands in climate-smart agriculture.
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Agricultura/métodos , Alimentación Animal , Carbono/química , Productos Agrícolas/fisiología , Pradera , Suelo/química , Animales , Bovinos , Industria LecheraRESUMEN
SignificanceDue to market and system failures, policies and programs at the local level are needed to accelerate the renewable energy transition. A voluntary environmental program (VEP), such as SolSmart, can encourage local governments to adopt solar-friendly best practices. Unlike previous research, this study uses a national sample, more recent data, and a matched control group for difference-in-differences estimation to quantify the causal impact of a VEP in the public, rather than private, sector. We offer empirical evidence that SolSmart increased installed solar capacity and, with less statistical significance, the number of solar installations. The results inform the design of sustainability-focused VEPs and future research to understand the causal pathways between local governments' voluntary actions and solar market development.
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The interplay between academics and society within the environment of the COVID-19 pandemic has impacted on scientists across the world, prompting reevaluation of how virtual toolboxes can be used to support responsible collaborative research practices. We provide awareness of virtual resources and activities that enable scientific discovery using safe and efficient practices.
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Investigación Biomédica/organización & administración , COVID-19/epidemiología , COVID-19/psicología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/psicología , Prácticas Interdisciplinarias/organización & administración , Pandemias , Neumonía Viral/epidemiología , Neumonía Viral/psicología , Interfaz Usuario-Computador , Betacoronavirus/patogenicidad , COVID-19/transmisión , COVID-19/virología , Infecciones por Coronavirus/transmisión , Infecciones por Coronavirus/virología , Humanos , Difusión de la Información , Distanciamiento Físico , Neumonía Viral/transmisión , Neumonía Viral/virología , Salud Pública , SARS-CoV-2 , Medios de Comunicación SocialesRESUMEN
To prevent doping practices in sports, the World Anti-Doping Agency implemented the Athlete Biological Passport (ABP) program, monitoring biological variables over time to indirectly reveal the effects of doping rather than detect the doping substance or the method itself. In the context of this program, a highly multiplexed mass spectrometry-based proteomics assay for 319 peptides corresponding to 250 proteins was developed, including proteins associated with blood-doping practices. "Baseline" expression profiles of these potential biomarkers in capillary blood (dried blood spots (DBS)) were established using multiple reaction monitoring (MRM). Combining DBS microsampling with highly multiplexed MRM assays is the best-suited technology to enhance the effectiveness of the ABP program, as it represents a cost-effective and robust alternative analytical method with high specificity and selectivity of targets in the attomole range. DBS data were collected from 10 healthy athlete volunteers over a period of 140 days (28 time points per participant). These comprehensive findings provide a personalized targeted blood proteome "fingerprint" showcasing that the targeted proteome is unique to an individual and likely comparable to a DNA fingerprint. The results can serve as a baseline for future studies investigating doping-related perturbations.
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Proteínas Sanguíneas , Doping en los Deportes , Pruebas con Sangre Seca , Proteómica , Humanos , Doping en los Deportes/prevención & control , Proteómica/métodos , Proteínas Sanguíneas/análisis , Pruebas con Sangre Seca/métodos , Pruebas con Sangre Seca/normas , Masculino , Valores de Referencia , Adulto , Biomarcadores/sangre , Espectrometría de Masas/métodos , Detección de Abuso de Sustancias/métodos , Proteoma/análisis , Atletas , FemeninoRESUMEN
There is a growing shift from the use of conventional pharmaceutical oral care products to the use of herbal extracts and traditional remedies in dental caries prevention. This is attributed to the potential environmental and health implications of contemporary oral products. This comprehensive review aims at the analysis of plant-derived compounds as preventive modalities in dental caries research. It focuses on data collected from 2019 until recently, trying to emphasize current trends in this topic. The research findings suggest that several plant-derived compounds, either aqueous or ethanolic, exhibit notable antibacterial effects against Streptococcus mutans and other bacteria related to dental caries, with some extracts demonstrating an efficacy comparable to that of chlorhexidine. Furthermore, in vivo studies using plant-derived compounds incorporated in food derivatives, such as lollipops, have shown promising results by significantly reducing Streptococcus mutans in high-risk caries children. In vitro studies on plant-derived compounds have revealed bactericidal and bacteriostatic activity against S. mutans, suggesting their potential use as dental caries preventive agents. Medicinal plants, plant-derived phytochemicals, essential oils, and other food compounds have exhibited promising antimicrobial activity against oral pathogens, either by their anti-adhesion activity, the inhibition of extracellular microbial enzymes, or their direct action on microbial species and acid production. However, further research is needed to assess their antimicrobial activity and to evaluate the cytotoxicity and safety profiles of these plant-derived compounds before their widespread clinical use can be recommended.
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OBJECTIVES: To estimate the association of dietary practices with early life weight among children born in 2001 in the U.S. METHODS: The Early Childhood Longitudinal Study (ECLS-B) is a population-based cohort followed from 9 months to Kindergarten entry (n~5000). We employed an auto-regressive cross-lagged model to assess the impacts of dietary practices on weight stability over time. We calculated age- and sex-standardized BMI z-scores using WHO growth curves. RESULTS: BMI z-scores had a stable increase over time. Later age of solid food introduction was associated with lower BMI z-score at age 2y [-0.03(-0.05,-0.004)]; having dinners more times per week with family at age 2y was associated with higher BMI z-score at 4y [0.03(0.01,0.05)]. These changes, of <0.05 BMI z-score, are small. Children with higher birthweight were introduced to solid foods at younger ages [-0.39 months(-0.45,-0.32)] and were breast fed longer [0.13 months(0.04,0.22)]. For girls, having dinner at a regular time at ages 2y and 4y was associated with lower BMI at ages 4y and 5y. CONCLUSIONS: Dietary practices in early childhood affect weight trajectories. However, these effects are small and are largely overshadowed by prior weight. Children's weight in infancy is associated with subsequent dietary practices but also small effects.
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Enrollment in cancer clinical trials cannot occur without first successfully identifying trials for which patients are a match based on their clinical characteristics. A lack of onsite matching trials has been identified as the single largest barrier preventing patients from participating in clinical trials. The site-agnostic cancer clinical trial matching environment is a mix of public and private tools and infrastructure that are not designed to work together to facilitate trial matching in an efficient manner. To identify policy and infrastructure solutions that could enable more effective and more frequent use of third-party site-agnostic matching, the American Cancer Society Cancer Action Network held a summit to examine challenges and propose consensus recommendations that could address those challenges. At this 2019 summit, stakeholders in this field examined these barriers and challenges and made a number of policy and infrastructure recommendations to improve the ability of this environment to work in a more coordinated and efficient manner.
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Neoplasias , Humanos , Consenso , Neoplasias/terapia , Cuidados Paliativos , Ensayos Clínicos como AsuntoRESUMEN
BACKGROUND: Provider and institutional practices have been shown to have a large impact on cancer clinical trial enrollment. Understanding provider perspectives on screening for trial eligibility is necessary to improve enrollment. METHODS: A questionnaire about incentives, barriers, process tools, and infrastructure related to opening trials and referring patients to onsite and offsite trials was administered to diverse stakeholders, including professional societies, advocacy organizations, and industry networks. Descriptive statistics were used to summarize findings. RESULTS: Overall, 693 responses were received, primarily from physicians (42.7%) and nurses (35.6%) employed at hospital health systems (43.7%) and academic centers (36.5%). Approximately half (49.2%) screened all patients for onsite clinical trials with screening typically done by manual chart review (81.9%). The greatest incentive reported for offering trials was providing the best treatment options for patients (67.7%). Contracting and paperwork (48.5%) were the greatest barriers to opening more onsite trials. Offsite referrals were rare. CONCLUSIONS: Screening for trial eligibility is a largely manual and ad hoc process, with screening and referral to offsite trials occurring infrequently. Administrative and infrastructure barriers commonly prevent sites from opening more onsite trials. These findings suggest that automated trial screening tools built into workflows that screen in a site-agnostic manner could result in more frequent trial eligibility screening, especially for offsite trials. With recent momentum, in part in response to the COVID-19 pandemic, to improve clinical trial efficiencies and broaden access and participant diversity, implementing tools to improve screening and referral processes is timely and essential. PLAIN LANGUAGE SUMMARY: There are many factors that contribute to low adult enrollment in cancer clinical trials, but previous research has indicated that provider and institutional barriers are the largest contributors to low cancer clinical trial enrollment. In this survey, we sought to gain insight into cancer clinical trial enrollment practices from the perspective of health care providers such as physicians and nurses. We found that only approximately half of respondents indicated their institution systematically screens their patients for clinical trials and this process is manual and time consuming. Furthermore, we found that providers infrequently search for and refer patients to clinical trials at other sites. Creating better screening methods could improve enrollment in clinical trials.
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Motivación , Neoplasias , Adulto , Humanos , Detección Precoz del Cáncer , Neoplasias/diagnóstico , Neoplasias/terapia , Pandemias , Derivación y Consulta , Encuestas y Cuestionarios , Ensayos Clínicos como AsuntoRESUMEN
PURPOSE: Given the relatively high incidence of both endometriosis and breast cancer, investigating the potential connection between these gynecological diseases is of substantial clinical significance. However, there is no clear consensus in the literature on the extent to which the risk of breast cancer is increased in patients with endometriosis. Therefore, we conducted a large-scale observational study investigating the association between endometriosis and breast cancer risk. METHODS: This study included women aged ≥ 18 years with an initial endometriosis diagnosis from one of 315 office-based gynecologists in Germany between January 2005 and December 2021. Non-endometriosis patients were matched 1:1 to patients with endometriosis based on age, index year, average yearly consultation frequency, and predefined co-diagnoses within 12 months before or on the index date, including obesity and benign breast disorders. The association between endometriosis and the 10-year incidence of breast cancer was studied using Kaplan-Meier curves and log-rank tests. Finally, a univariable Cox regression analysis was conducted to assess the association between endometriosis and breast cancer. RESULTS: Over a follow-up period of up to 10 years, no significant difference was observed between the endometriosis (2.4%) and the matched non-endometriosis group (2.5%) with regard to breast cancer diagnoses. Furthermore, the regression analysis revealed no significant association between endometriosis and subsequent breast cancer. CONCLUSION: In summary, our comprehensive 10-year study involving a substantial sample of women indicates that endometriosis is not significantly associated with an increased risk of subsequent breast cancer.
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Neoplasias de la Mama , Endometriosis , Femenino , Humanos , Endometriosis/complicaciones , Endometriosis/epidemiología , Endometriosis/diagnóstico , Estudios Retrospectivos , Neoplasias de la Mama/complicaciones , Neoplasias de la Mama/epidemiología , Riesgo , Alemania/epidemiologíaRESUMEN
Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective observational study examines mNGS results from two academic medical centers employing different stewardship approaches. Eighty mNGS orders [54 cerebrospinal fluid (CSF) and 26 plasma] were identified from 2019 to 2021 at the University of Washington (UW), which requires director-level approval for mNGS orders, and the University of Utah (Utah), which does not restrict ordering. The impact of mNGS results and the relationship to traditional microbiology orders were evaluated. Nineteen percent (10/54) of CSF and 65% (17/26) of plasma studies detected at least one organism. Compared to CSF results, plasma results more frequently identified clinically significant organisms (31% vs 7%) and pathogens not detected by traditional methods (12% vs 0%). Antibiotic management was more frequently impacted by plasma versus CSF results (31% vs 4%). These outcome measures were not statistically different between study sites. The number and cumulative cost of traditional microbiology tests at UW were greater than Utah for CSF mNGS testing (UW: 46 tests, $6,237; Utah: 26 tests, $2,812; P < 0.05) but similar for plasma mNGS (UW: 31 tests, $3,975; Utah: 21 tests, $2,715; P = 0.14). mNGS testing accounted for 30%-50% of the total microbiology costs. Improving the diagnostic performance of mNGS by stewardship remains challenging due to low positivity rates and difficulties assessing clinical impact. From a fiscal perspective, stewardship efforts should focus on reducing testing in low-yield populations given the high costs of mNGS relative to overall microbiology testing expenditures. IMPORTANCE: Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly standardized. This study aims to provide actionable insights for institutions that seek to reduce the unnecessary usage of mNGS. Importantly, we highlight that clinical impact remains challenging to measure without standardized guidelines, and we provide an actual cost estimate of microbiology expenditures on individuals undergoing mNGS.
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Food insecurity affects an estimated 691-783 million people globally and is disproportionately high in Africa and Asia. It arises from poverty, armed conflict, and climate change, among other demographic and globalization forces. This review summarizes evidence for policies and practices across five elements of the agrifood system framework and identifies gaps that inform an agenda for future research. Under availability, imbalanced agriculture policies protect primarily staple food producers, and there is limited evidence on food security impacts for smallholder and women food producers. Evidence supports the use of cash transfers and food aid for affordability and school feeding for multiple benefits. Food-based dietary guidelines can improve the nutritional quality of dietary patterns, yet they may not reflect the latest evidence or food supplies. Evidence from the newer food environment elements, promotion and sustainability, while relatively minimal, provides insight into achieving long-term impacts. To eliminate hunger, our global community should embrace integrated approaches and bring evidence-based policies and practices to scale.
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Inseguridad Alimentaria , Humanos , Salud Global , Abastecimiento de Alimentos/normas , Política Nutricional , Agricultura , Asistencia Alimentaria/organización & administraciónRESUMEN
This "Best Practices in User Consultation" article is the result of a 2022 International Society for the Advancement of Cytometry (ISAC) membership survey that collected valuable insights from the shared research laboratory (SRL) community and of a group discussion at the CYTO 2022 workshop of the same name. One key takeaway is the importance of initiating a consultation at the outset of a flow cytometry project, particularly for trainees. This approach enables the improvement and standardization of every step, from planning experiments to interpreting data. This proactive approach effectively mitigates experimental bias and avoids superfluous trial and error, thereby conserving valuable time and resources. In addition to guidelines, the optimal approaches for user consultation specify communication channels, methods, and critical information, thereby establishing a structure for productive correspondence between SRL and users. This framework functions as an exemplar for establishing robust and autonomous collaborative relationships. User consultation adds value by providing researchers with the necessary information to conduct reproducible flow cytometry experiments that adhere to scientific rigor. By following the steps, instructions, and strategies outlined in these best practices, an SRL can readily tailor them to its own setting, establishing a personalized workflow and formalizing user consultation services. This article provides a pragmatic guide for improving the caliber and efficacy of flow cytometry research and aggregates the flow cytometry SRL community's collective knowledge regarding user consultation.
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The Kidney Disease: Improving Global Outcomes (KDIGO) guideline for diabetes management in chronic kidney disease (CKD) was updated in 2022, just 2 years after the previous update. The need for this rapid update is reflective of the recent and unprecedented positive results of numerous clinical trials aimed at reducing kidney and cardiovascular morbidity and mortality in people with diabetes. The Kidney Disease Outcomes Quality Initiative (KDOQI) work group for diabetes in CKD, convened by the National Kidney Foundation, provides herein a commentary on these changes, particularly the implications for health care in the United States. Changes to the KDIGO guideline mirror the evolution of sodium/glucose cotransporter 2 (SGLT2) inhibitors and glucagon-like peptide 1 receptor agonists from purely antihyperglycemic agents to cardiorenal-metabolic therapeutics, and the lower estimated glomerular filtration rate of≥20mL/min/1.73m2 for SGLT2 inhibitor initiation. New data have also brought the addition of the first-in-class, Federal Drug Administration-approved nonsteroidal mineralocorticoid receptor antagonist finerenone as an agent to reduce cardiorenal end points. While there has been significant progress in innovation, there remain serious challenges to implementation, particularly in the United States where inequities in insurance coverage and high costs limit their use, particularly in vulnerable populations, ultimately widening health care disparities.
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Diabetes Mellitus Tipo 2 , Diabetes Mellitus , Insuficiencia Renal Crónica , Humanos , Estados Unidos , Insuficiencia Renal Crónica/tratamiento farmacológico , Hipoglucemiantes/uso terapéutico , Progresión de la Enfermedad , Riñón , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/tratamiento farmacológicoRESUMEN
OBJECTIVES: Existing guidelines for psoriatic arthritis (PsA) cover many aspects of management. Some gaps remain relating to routine practice application. An expert group aimed to enhance current guidance and develop recommendations for clinical practice that are complementary to existing guidelines. METHODS: A steering committee comprising experienced, research-active clinicians in rheumatology, dermatology and primary care agreed on themes and relevant questions. A targeted literature review of PubMed and Embase following a PICO framework was conducted. At a second meeting, recommendations were drafted and subsequently an extended faculty comprising rheumatologists, dermatologists, primary care clinicians, specialist nurses, allied health professionals, non-clinical academic participants and members of the Brit-PACT patient group, was recruited. Consensus was achieved via an online voting platform when 75% of respondents agreed in the range of 7-9 on a 9-point scale. RESULTS: The guidance comprised 34 statements covering four PsA themes. Diagnosis focused on strategies to identify PsA early and refer appropriately, assessment of diagnostic indicators, use of screening tools and use of imaging. Disease assessment centred on holistic consideration of disease activity, physical functioning and impact from a patient perspective, and on how to implement shared decision-making. For comorbidities, recommendations included specific guidance for high-impact conditions such as depression and obesity. Management statements (which excluded extant guidance on pharmacological therapies) covered multidisciplinary team working, implementation of lifestyle modifications and treat-to-target strategies. Minimising corticosteroid use was recommended where feasible. CONCLUSION: The consensus group have made evidence-based best practice recommendations for the management of PsA to enhance the existing guidelines.