Leveraging satellite observations to reveal ecological drivers of pest densities across landscapes

Landscape ecologists have long suggested that pest abundances increase in simplified, monoculture landscapes. However, tests of this theory often fail to predict pest population sizes in real-world agricultural fields. These failures may arise not only from variation in pest ecology, but also from the widespread use of categorical land-use maps that do not adequately characterize habitat-availability for pests. We used 1163 field-year observations of Lygus hesperus (Western Tarnished Plant Bug) densities in California cotton fields to determine whether integrating remotely-sensed metrics of vegetation productivity and phenology into pest models could improve pest abundance analysis and prediction. Because L. hesperus often overwinters in non-crop vegetation, we predicted that pest abundances would peak on farms surrounded by more non-crop vegetation, especially when the non-crop vegetation is initially productive but then dries down early in the year, causing the pest to disperse into cotton fields. We found that the effect of non-crop habitat on pest densities varied across latitudes, with a positive relationship in the north and a negative one in the south. Aligning with our hypotheses, models predicted that L. hesperus densities were 35 times higher on farms surrounded by high versus low productivity non-crop vegetation (EVI area 350 vs. 50) and 2.8 times higher when dormancy occurred earlier versus later in the year (May 15 vs. June 30). Despite these strong and significant effects, we found that integrating these remote-sensing variables into land-use models only marginally improved pest density predictions in cotton compared to models with categorical land cover metrics alone. Together, our work suggests that the remote sensing variables analyzed here can advance our understanding of pest ecology, but not yet substantively increase the accuracy of pest abundance predictions.

Global trends and scenarios for terrestrial biodiversity and ecosystem services from 1900 to 2050

Based on an extensive model intercomparison, we assessed trends in biodiversity and ecosystem services from historical reconstructions and future scenarios of land-use and climate change. During the 20th century, biodiversity declined globally by 2 to 11%, as estimated by a range of indicators. Provisioning ecosystem services increased several fold, and regulating services decreased moderately. Going forward, policies toward sustainability have the potential to slow biodiversity loss resulting from land-use change and the demand for provisioning services while reducing or reversing declines in regulating services. However, negative impacts on biodiversity due to climate change appear poised to increase, particularly in the higher-emissions scenarios. Our assessment identifies remaining modeling uncertainties but also robustly shows that renewed policy efforts are needed to meet the goals of the Convention on Biological Diversity.

Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care

Importance

Artificial intelligence (AI) tools are rapidly integrating into cancer care. Understanding stakeholder views on ethical issues associated with the implementation of AI in oncology is critical to optimal deployment.

Objective

To evaluate oncologists' views on the ethical domains of the use of AI in clinical care, including familiarity, predictions, explainability (the ability to explain how a result was determined), bias, deference, and responsibilities.

Design, Setting, and Participants

This cross-sectional, population-based survey study was conducted from November 15, 2022, to July 31, 2023, among 204 US-based oncologists identified using the National Plan & Provider Enumeration System.

Main Outcomes and Measures

The primary outcome was response to a question asking whether participants agreed or disagreed that patients need to provide informed consent for AI model use during cancer treatment decisions.

Results

Of 387 surveys, 204 were completed (response rate, 52.7%). Participants represented 37 states, 120 (63.7%) identified as male, 128 (62.7%) as non-Hispanic White, and 60 (29.4%) were from academic practices; 95 (46.6%) had received some education on AI use in health care, and 45.3% (92 of 203) reported familiarity with clinical decision models. Most participants (84.8% [173 of 204]) reported that AI-based clinical decision models needed to be explainable by oncologists to be used in the clinic; 23.0% (47 of 204) stated they also needed to be explainable by patients. Patient consent for AI model use during treatment decisions was supported by 81.4% of participants (166 of 204). When presented with a scenario in which an AI decision model selected a different treatment regimen than the oncologist planned to recommend, the most common response was to present both options and let the patient decide (36.8% [75 of 204]); respondents from academic settings were more likely than those from other settings to let the patient decide (OR, 2.56; 95% CI, 1.19-5.51). Most respondents (90.7% [185 of 204]) reported that AI developers were responsible for the medico-legal problems associated with AI use. Some agreed that this responsibility was shared by physicians (47.1% [96 of 204]) or hospitals (43.1% [88 of 204]). Finally, most respondents (76.5% [156 of 204]) agreed that oncologists should protect patients from biased AI tools, but only 27.9% (57 of 204) were confident in their ability to identify poorly representative AI models.

Conclusions and Relevance

In this cross-sectional survey study, few oncologists reported that patients needed to understand AI models, but most agreed that patients should consent to their use, and many tasked patients with choosing between physician- and AI-recommended treatment regimens. These findings suggest that the implementation of AI in oncology must include rigorous assessments of its effect on care decisions as well as decisional responsibility when problems related to AI use arise.

Unusual case of bullous emphysema with superimposed pneumonia

Bullous emphysema is a chronic obstructive pulmonary disease (COPD) that results from chronic inflammation of the lung parenchyma leading to alveolar destruction. Etiology includes tobacco smoking and alpha-1 antitrypsin deficiency. In this article, we present a rare case of bullous emphysema in a nonsmoker with no genetic predisposition or social risk factors presenting with productive cough, fatigue, and shortness of breath. The patient was diagnosed with bullous emphysema with superimposed pneumonia based on clinical and radiological findings. The patients acute complaints were treated successfully with antibiotics, supplemental oxygen, systemic steroids, and, nebulizer treatments. With this case report the authors highlight an unusual presentation of pneumonia in a patient with underlying bullous emphysema. Environmental exposure is often overlooked and the outcomes cannot be turned to favor without a comprehensive approach in patient management from history and physical to deciding the right treatment and follow-up protocols.

The Burnout PRedictiOn Using Wearable aNd ArtIficial IntelligEnce (BROWNIE) study: a decentralized digital health protocol to predict burnout in registered nurses

BACKGROUND

When job demand exceeds job resources, burnout occurs. Burnout in healthcare workers extends beyond negatively affecting their functioning and physical and mental health; it also has been associated with poor medical outcomes for patients. Data-driven technology holds promise for the prediction of occupational burnout before it occurs. Early warning signs of burnout would facilitate preemptive institutional responses for preventing individual, organizational, and public health consequences of occupational burnout. This protocol describes the design and methodology for the decentralized Burnout PRedictiOn Using Wearable aNd ArtIficial IntelligEnce (BROWNIE) Study. This study aims to develop predictive models of occupational burnout and estimate burnout-associated costs using consumer-grade wearable smartwatches and systems-level data.

METHODS

A total of 360 registered nurses (RNs) will be recruited in 3 cohorts. These cohorts will serve as training, testing, and validation datasets for developing predictive models. Subjects will consent to one year of participation, including the daily use of a commodity smartwatch that collects heart rate, step count, and sleep data. Subjects will also complete online baseline and quarterly surveys assessing psychological, workplace, and sociodemographic factors. Routine administrative systems-level data on nursing care outcomes will be abstracted weekly.

DISCUSSION

The BROWNIE study was designed to be decentralized and asynchronous to minimize any additional burden on RNs and to ensure that night shift RNs would have equal accessibility to study resources and procedures. The protocol employs novel engagement strategies with participants to maintain compliance and reduce attrition to address the historical challenges of research using wearable devices.

TRIAL REGISTRATION

NCT05481138.

Ethical Aspects of Prodromal Synucleinopathy Prognostic Counseling

Alpha-synucleinopathies can be identified in their prodromal phase, raising several ethical issues. In this review, we first provide definitions of prodromal α-synucleinopathies and discuss the importance of distinguishing between prodromes and risk factors. Next, we discuss the implications of a diagnosis of prodromal α-synucleinopathy and considerations regarding prognostic counseling in both clinical and research settings. We review available data on patient preferences regarding disclosure as well as providers' perspectives. We examine the pros and cons of disclosing a diagnosis of prodromal α-synucleinopathy, taking into consideration the differences between clinical and research settings. Asking about willingness to know in clinical and research settings and the shared decision-making process applied to prognostic counseling is discussed. Concerning research settings, ethical aspects regarding clinical trials are addressed. Availability of direct-to-consumer technologies will likely lead to novel contexts requiring prognostic counseling, and future neuroprotective or neuromodulating treatments may require further considerations on the timing, role, and importance of prognostic counseling. Recommendations on how to address ethical gaps should be a priority for patients, medical professional societies, and research workgroups. Ethical issues must be considered as an integral part of the overall clinical and research approach to prodromal synucleinopathies.

Single cell multi-omics characterise discrete human tendon cells populations that persist in vitro and on fibrous scaffolds

Chronic tendinopathy represents a growing healthcare burden in the ageing global population. Curative therapies remain elusive as the mechanisms that underlie chronic inflammation in tendon disease remain unclear. Identifying and isolating key pathogenic and reparative cells is essential in developing precision therapies and implantable materials for improved tendon healing. Multiple discrete human tendon cell populations have been previously described ex vivo. To determine if these populations persist in vitro, healthy human hamstring tenocytes were cultured for 8 d on either tissue culture plastic or aligned electrospun fibres of absorbable polydioxanone. Novel single-cell surface proteomics combined with unbiased single-cell transcriptomics (CITE-Seq) was used to identify discrete tenocyte populations. 6 cell populations were found, 4 of which shared key gene expression determinants with ex vivo human cell clusters: PTX3_PAPPA, POSTN_SCX, DCN_LUM and ITGA7_NES. Surface proteomics found that PTX3_PAPPA cells were CD10+CD26+CD54+. ITGA7_NES cells were CD146+ and POSTN_SCX cells were CD90+CD95+CD10+. Culture on the aligned electrospun fibres favoured 3 cell subtypes (DCN_LUM, POSTN_SCX and PTX3_ PAPPA), promoting high expression of tendon-matrix-associated genes and upregulating gene sets enriched for TNF-a and IL-6/STAT3 signalling. Discrete human tendon cell subpopulations persisted in in vitro culture and could be recognised by specific gene and surface-protein signatures. Aligned polydioxanone fibres promoted the survival of 3 clusters, including pro-inflammatory PTX3-expressing CD10+CD26+CD54+ cells found in chronic tendon disease. These results improved the understanding of preferred culture conditions for different tenocyte subpopulations and informed the development of in vitro models of tendon disease.

Computational identification of variables in neonatal vocalizations predictive for postpubertal social behaviors in a mouse model of 16p11.2 deletion

Autism spectrum disorder (ASD) is often signaled by atypical cries during infancy. Copy number variants (CNVs) provide genetically identifiable cases of ASD, but how early atypical cries predict a later onset of ASD among CNV carriers is not understood in humans. Genetic mouse models of CNVs have provided a reliable tool to experimentally isolate the impact of CNVs and identify early predictors for later abnormalities in behaviors relevant to ASD. However, many technical issues have confounded the phenotypic characterization of such mouse models, including systematically biased genetic backgrounds and weak or absent behavioral phenotypes. To address these issues, we developed a coisogenic mouse model of human proximal 16p11.2 hemizygous deletion and applied computational approaches to identify hidden variables within neonatal vocalizations that have predictive power for postpubertal dimensions relevant to ASD. After variables of neonatal vocalizations were selected by least absolute shrinkage and selection operator (Lasso), random forest, and Markov model, regression models were constructed to predict postpubertal dimensions relevant to ASD. While the average scores of many standard behavioral assays designed to model dimensions did not differentiate a model of 16p11.2 hemizygous deletion and wild-type littermates, specific call types and call sequences of neonatal vocalizations predicted individual variability of postpubertal reciprocal social interaction and olfactory responses to a social cue in a genotype-specific manner. Deep-phenotyping and computational analyses identified hidden variables within neonatal social communication that are predictive of postpubertal behaviors.

Neutral, Negative, or Negligible? Changes in Patient Perceptions of Disease Risk Following Receipt of a Negative Genomic Screening Result

Most individuals who undergo genomic screening will receive negative results or results not sufficient to warrant a clinical response. Even though a majority of individuals receive negative results, little is known about how negative results may impact individuals' perception of disease risk. Changes in risk perception (specifically reductions in perceived risk) may affect both probands and their family members if inaccurate information is communicated to family members. We surveyed patients who received negative results as part of their participation in a genomic screening study and assessed their perceptions of disease risk following receipt of results. Participants had either hyperlipidemia or colon polyps (or both) and received their negative genomic screening results by mail. Of 1712 total individuals recruited, 1442 completed the survey (84.2% completion rate). Approximately one quarter of individuals believed their risk for heart disease to be lower and approximately one third of individuals believed their risk for colon cancer to be lower after receiving and evaluating their negative genomic screening result. 78% of those who believed their risk for one or both diseases had declined had already shared or intended to share their result with family members. Our study suggests patients may interpret a negative genomic screening result as implying a reduction in their overall disease risk.

Ethical Tensions Resulting from Interpreter Involvement in the Consent Process

We describe how our institution responded when an interpreter who participated in the consent process involving an individual with limited English proficiency refused to cosign consent documents attesting that the individual enrolling in the study understood the consent information and that her consent to enroll was voluntary. In developing our approach, our institution took into account ethical tensions between the Belmont principles of respect for persons, beneficence, and justice that apply to the protection of research participants and the professional principles of beneficence, fidelity, and respect for the importance of culture that are outlined in ethical guidelines for medical interpreters.

Design and Pilot Testing of an English and Spanish Behavioral Health Patient Survey on Data Privacy

We piloted a Spanish and English survey on data privacy. Thirty-one Latino behavioral health patients completed the survey in person with a preference for paper (78%) over electronic questionnaire. Dialect variations across Latino countries and the lack of tools to assess reading level in Spanish affected comprehension. Our experience will help others address similar tasks more effectively and encourage inclusion of Latino populations in future research.

Perceptions and Preferences About Granular Data Sharing and Privacy of Behavioral Health Patients

Little is known about data sharing preferences for care and research of behavioral health patients. Eighty-six behavioral health patients (n = 37 Latinos; n = 32 with serious mental illness) completed questionnaires, in either English or Spanish, with items assessing their views on privacy and sensitivity of health record information. Most patients (82.5%) considered mental health information as sensitive. In general, there was a direct correspondence between perceived sensitivity of information and willingness to share with all or some providers. A main motivation for sharing data with providers was improving the patient's own care (77.8%). Most participants (96.5%) indicated they would be extremely to somewhat willing to share their data for research with their care facilities and universities. Follow-up patient interviews are being conducted to further elucidate these findings.

Cosmological Constraints from Multiple Probes in the Dark Energy Survey

The combination of multiple observational probes has long been advocated as a powerful technique to constrain cosmological parameters, in particular dark energy. The Dark Energy Survey has measured 207 spectroscopically confirmed type Ia supernova light curves, the baryon acoustic oscillation feature, weak gravitational lensing, and galaxy clustering. Here we present combined results from these probes, deriving constraints on the equation of state, w, of dark energy and its energy density in the Universe. Independently of other experiments, such as those that measure the cosmic microwave background, the probes from this single photometric survey rule out a Universe with no dark energy, finding w=-0.80_{-0.11}^{+0.09}. The geometry is shown to be consistent with a spatially flat Universe, and we obtain a constraint on the baryon density of Ω_{b}=0.069_{-0.012}^{+0.009} that is independent of early Universe measurements. These results demonstrate the potential power of large multiprobe photometric surveys and pave the way for order of magnitude advances in our constraints on properties of dark energy and cosmology over the next decade.

The Return of Actionable Variants Empirical (RAVE) Study, a Mayo Clinic Genomic Medicine Implementation Study: Design and Initial Results

OBJECTIVES

To identify clinically actionable genetic variants from targeted sequencing of 68 disease-related genes, estimate their penetrance, and assess the impact of disclosing results to participants and providers.

PATIENTS AND METHODS

The Return of Actionable Variants Empirical (RAVE) Study investigates outcomes following the return of pathogenic/likely pathogenic (P/LP) variants in 68 disease-related genes. The study was initiated in December 2016 and is ongoing. Targeted sequencing was performed in 2533 individuals with hyperlipidemia or colon polyps. The electronic health records (EHRs) of participants carrying P/LP variants in 36 cardiovascular disease (CVD) genes were manually reviewed to ascertain the presence of relevant traits. Clinical outcomes, health care utilization, family communication, and ethical and psychosocial implications of disclosure of genomic results are being assessed by surveys, telephone interviews, and EHR review.

RESULTS

Of 29,208 variants in the 68 genes, 1915 were rare (frequency <1%) and putatively functional, and 102 of these (60 in 36 CVD genes) were labeled P/LP based on the American College of Medical Genetics and Genomics framework. Manual review of the EHRs of participants (n=73 with P/LP variants in CVD genes) revealed that 33 had the expected trait(s); however, only 6 of 45 participants with non-familial hypercholesterolemia (FH) P/LP variants had the expected traits.

CONCLUSION

Expected traits were present in 13% of participants with P/LP variants in non-FH CVD genes, suggesting low penetrance; this estimate may change with additional testing performed as part of the clinical evaluation. Ongoing analyses of the RAVE Study will inform best practices for genomic medicine.

Current State of Electronic Consent Processes in Behavioral Health: Outcomes from an Observational Study

An integral element of value-based care is care team access to both physical and behavioral health data. Data release processes in both environments are governed by federal and state statutes. The requirements for obtaining consent are complex and often confusing. Little is known about the consent processes and practices in the behavioral health setting, specifically how patients and surrogates engage in the process and their interactions with electronic consent tools. This study analyzes the consent processes from the patient perspective at two community behavioral health clinics. Outcomes include description of the processes using electronic consent, workflows and consenter-provider interactions. Conclusions include need to streamline and standardize consent technologies and improve consenter engagement. This study supports the development of an electronic consent tool, My Data Choices (MDC), funded by the National Institute of Mental Health, that offers individuals with behavioral health conditions more control over their medical records.

National scale evaluation of the InVEST nutrient retention model in the United Kingdom

A wide variety of tools aim to support decision making by modelling, mapping and quantifying ecosystem services. If decisions are to be properly informed, the accuracy and potential limitations of these tools must be well understood. However, dedicated studies evaluating ecosystem service models against empirical data are rare, especially over large areas. In this paper, we report on the national-scale assessment of a new ecosystem service model for nutrient delivery and retention, the InVEST Nutrient Delivery Ratio model. For 36 river catchments across the UK, we modelled total catchment export of phosphorus (P) and/or nitrogen (N) and compared model outputs to measurements derived from empirical water chemistry data. The model performed well in terms of relative magnitude of nutrient export among catchments (best Spearman's rank correlation for N and P, respectively: 0.81 and 0.88). However, there was wide variation among catchments in the accuracy of the model, and absolute values of nutrient exports frequently showed high percentage differences between modelled and empirically-derived exports (best median absolute percentage difference for N and P, respectively: ±64%, ±44%). The model also showed a high degree of sensitivity to nutrient loads and hydrologic routing input parameters and these sensitivities varied among catchments. These results suggest that the InVEST model can provide valuable information on nutrient fluxes to decision makers, especially in terms of relative differences among catchments. However, caution is needed if using the absolute modelled values for decision-making. Our study also suggests particular attention should be paid to researching input nutrient loadings and retentions, and the selection of appropriate input data resolutions and threshold flow accumulation values. Our results also highlight how availability of empirical data can improve model calibration and performance assessment and reinforce the need to include such data in ecosystem service modelling studies.

A Study to Elicit Behavioral Health Patients' and Providers' Opinions on Health Records Consent

A main objective of this study is to assess the opinions of 50 behavioral health patients on selective control over their behavioral and physical health information. We explored patients' preferences regarding current consent models, what health information should be shared for care and research and whether these preferences vary based on the sensitivity of health information and/or the type of provider involved. The other objective of this study was to solicit opinions of 8 behavioral health providers on patient-driven granular control of health information and potential impact on care.

Electronic surveys were implemented at an outpatient Behavioral Health facility that provides care for behavioral health patients with non-serious mental illnesses. The Patient Survey included questions regarding patients' demographics and about their concerns and preferences for data sharing for care and research. The Provider Survey included questions about their view on the current consent process and perceptions on barriers and facilitators to implement patient-controlled granular consent models.

This novel study provides valuable preliminary data that can help guide future studies to better understand privacy choices of this underrepresented patient group.

Sediment delivery modeling in practice: Comparing the effects of watershed characteristics and data resolution across hydroclimatic regions

Geospatial models are commonly used to quantify sediment contributions at the watershed scale. However, the sensitivity of these models to variation in hydrological and geomorphological features, in particular to land use and topography data, remains uncertain. Here, we assessed the performance of one such model, the InVEST sediment delivery model, for six sites comprising a total of 28 watersheds varying in area (6-13,500km²), climate (tropical, subtropical, mediterranean), topography, and land use/land cover. For each site, we compared uncalibrated and calibrated model predictions with observations and alternative models. We then performed correlation analyses between model outputs and watershed characteristics, followed by sensitivity analyses on the digital elevation model (DEM) resolution. Model performance varied across sites (overall r²=0.47), but estimates of the magnitude of specific sediment export were as or more accurate than global models. We found significant correlations between metrics of sediment delivery and watershed characteristics, including erosivity, suggesting that empirical relationships may ultimately be developed for ungauged watersheds. Model sensitivity to DEM resolution varied across and within sites, but did not correlate with other observed watershed variables. These results were corroborated by sensitivity analyses performed on synthetic watersheds ranging in mean slope and DEM resolution. Our study provides modelers using InVEST or similar geospatial sediment models with practical insights into model behavior and structural uncertainty: first, comparison of model predictions across regions is possible when environmental conditions differ significantly; second, local knowledge on the sediment budget is needed for calibration; and third, model outputs often show significant sensitivity to DEM resolution.

The Sangre Por Salud Biobank: Facilitating Genetic Research in an Underrepresented Latino Community

BACKGROUND/AIMS

The Sangre Por Salud (Blood for Health; SPS) Biobank was created for the purpose of expanding precision medicine research to include underrepresented Latino patients. It is the result of a unique collaboration between Mayo Clinic and Mountain Park Health Center, a federally qualified community health center in Phoenix, Arizona. This report describes the rationale, development, implementation, and characteristics of the SPS Biobank.

METHODS

Latino adults (ages 18-85 years) who were active patients within Mountain Park Health Center's internal medicine practice in Phoenix, Ariz., and had no history of diabetes were eligible. Participants provided a personal and family history of chronic disease, completed a sociodemographic, psychosocial, and behavioral questionnaire, underwent a comprehensive cardiometabolic risk assessment (anthropometrics, blood pressure and labs), and provided blood samples for banking. Laboratory results of cardiometabolic testing were returned to the participants and their providers through the electronic health record.

RESULTS

During the first 2 years of recruitment into the SPS Biobank, 2,335 patients were approached and 1,432 (61.3%) consented to participate; 1,354 (94.5%) ultimately completed all requisite questionnaires and medical evaluations. The cohort is primarily Spanish-speaking (72.9%), female (73.3%), with a mean age of 41.3 ± 12.5 years. Most participants were born outside of the US (77.9%) and do not have health insurance (77.5%). The prevalence of overweight (35.5%) and obesity (45.0%) was high, as was previously unidentified prediabetes (55.9%), type 2 diabetes (7.4%), prehypertension (46.8%), and hypertension (16.2%). The majority of participants rated their health as good to excellent (72.1%) and, as a whole, described their overall quality of life as high (7.9/10).

CONCLUSION

Collaborative efforts such as the SPS Biobank are critical for ensuring that underrepresented minority populations are included in precision medicine initiatives and biomedical research that seeks to improve human health and reduce the burdens of disease.

The translational potential of research on the ethical, legal, and social implications of genomics

Federally funded research on the ethical, legal, and social implications (ELSI) of genomics includes a programmatic charge to consider policy-relevant questions and to communicate findings in venues that help inform the policy-making process. In addressing this goal, investigators must consider the range of policies that are relevant to human genetics; how foundational research in bioethics, law, and the social sciences might inform those policies; and the potential professional issues that this translational imperative raises for ELSI investigators. We review these questions in light of experiences from a consortium of federally funded Centers of Excellence in ELSI Research, and offer a set of policy recommendations for program design and evaluation of ELSI research. We conclude that it would be a mistake to require that ELSI research programs demonstrate a direct impact on science or health policy; however, ELSI researchers can take steps to increase the relevance of their work to policy makers. Similarly, funders of ELSI research who are concerned with facilitating policy development can help by building cross-disciplinary translational research capacities, and universities can take steps to make policy-relevant research more rewarding for scholars in the humanities, social sciences, and law.

Bacteriophages and Biofilms

Biofilms are an extremely common adaptation, allowing bacteria to colonize hostile environments. They present unique problems for antibiotics and biocides, both due to the nature of the extracellular matrix and to the presence within the biofilm of metabolically inactive persister cells. Such chemicals can be highly effective against planktonic bacterial cells, while being essentially ineffective against biofilms. By contrast, bacteriophages seem to have a greater ability to target this common form of bacterial growth. The high numbers of bacteria present within biofilms actually facilitate the action of bacteriophages by allowing rapid and efficient infection of the host and consequent amplification of the bacteriophage. Bacteriophages also have a number of properties that make biofilms susceptible to their action. They are known to produce (or to be able to induce) enzymes that degrade the extracellular matrix. They are also able to infect persister cells, remaining dormant within them, but re-activating when they become metabolically active. Some cultured biofilms also seem better able to support the replication of bacteriophages than comparable planktonic systems. It is perhaps unsurprising that bacteriophages, as the natural predators of bacteria, have the ability to target this common form of bacterial life.

The impact of climate change on water provision under a low flow regime: a case study of the ecosystems services in the Francoli river basin

Mediterranean basin is considered one of the most vulnerable regions of the world to climate change and with high probability to face acute water scarcity problem in the coming years. Francolí River basin (NE Spain), located in this vulnerable region is selected as a case study to evaluate the impact of climate change on the delivery of water considering the IPCC scenarios A2 and B1 for the time spans 2011-2040, 2041-2070 and 2071-2100. InVEST model is applied in a low flow river as a new case study, which reported successful results after its model validation. The studied hydrological ecosystem services will be highly impacted by climate change at Francolí River basin. Water yield is expected to be reduced between 11.5 and 44% while total drinking water provisioning will decrease between 13 and 50% having adverse consequences on the water quality of the river. Focusing at regional scale, Prades Mountains and Brugent Tributary provide most of the provision of water and also considered highly vulnerable areas to climate change. However, the most vulnerable part is the northern area which has the lowest provision of water. Francolí River basin is likely to experience desertification at this area drying Anguera and Vallverd tributaries.

The Manchester-Oxford Foot Questionnaire (MOXFQ): Development and validation of a summary index score

Objectives

The Manchester–Oxford Foot Questionnaire (MOXFQ) is a validated 16-item, patient-reported outcome measure for evaluating outcomes of foot or ankle surgery. The original development of the instrument identified three domains. This present study examined whether the three domains could legitimately be summed to provide a single summary index score.

Methods

The MOXFQ and Short-Form (SF)-36 were administered to 671 patients before surgery of the foot or ankle. Data from the three domains of the MOXFQ (pain, walking/standing and social interaction) were subjected to higher order factor analysis. Reliability and validity of the summary index score was assessed.

Results

The mean age of the participants was 52.8 years (sd 15.68; 18 to 89). Higher order principle components factor analysis produced one factor, accounting for 74.7% of the variance. The newly derived single index score was found to be internally reliable (α = 0.93) and valid, achieving at least moderate correlations (r ≥ 0.5, p < 0.001) with related (pain/function) domains of the SF-36.

Conclusions

Analyses indicated that data from the MOXFQ can be presented in summary form. The MOXFQ summary index score (MOXFQ-Index) provides an overall indication of the outcomes of foot and ankle surgery. Furthermore, the single index reduces the number of statistical comparisons, and hence the role of chance, when exploring MOXFQ data.

Relationships hold the key to trustworthy and productive translational science: recommendations for expanding community engagement in biomedical research

Good relationships between research institutions and communities are an essential, but often neglected, part of the infrastructure of translational science. In an effort to create greater interest among translational science researchers in cultivating relationships with community members, we report the results of a workshop we convened to learn how relationships vital to research are best created and sustained. We highlight common barriers and challenges that hinder relationships. We also provide recommendations that individual research institutions and teams can use to expand and strengthen their relationships with community members. The improved relationships between universities and communities that could result from their implementation should build greater public trust in biomedical research, lead to a stronger commitment to see it succeed, and engender shared values and commitments that will give rise to new rewards, recognition and admonishment to sustain those values and commitments over time, all of which would facilitate translational science.

Responsiveness of the Manchester-Oxford Foot Questionnaire (MOXFQ) compared with AOFAS, SF-36 and EQ-5D assessments following foot or ankle surgery

The responsiveness of the Manchester-Oxford Foot Questionnaire (MOXFQ) was compared with foot/ankle-specific and generic outcome measures used to assess all surgery of the foot and ankle. We recruited 671 consecutive adult patients awaiting foot or ankle surgery, of whom 427 (63.6%) were female, with a mean age of 52.8 years (18 to 89). They independently completed the MOXFQ, Short-Form 36 (SF-36) and EuroQol (EQ-5D) questionnaires pre-operatively and at a mean of nine months (3.8 to 14.4) post-operatively. Foot/ankle surgeons assessed American Orthopaedic Foot and Ankle Society (AOFAS) scores corresponding to four foot/ankle regions. A transition item measured perceived changes in foot/ankle problems post-surgery. Of 628 eligible patients proceeding to surgery, 491 (78%) completed questionnaires and 262 (42%) received clinical assessments both pre- and post-operatively. The regions receiving surgery were: multiple/whole foot in eight (1.3%), ankle/hindfoot in 292 (46.5%), mid-foot in 21 (3.3%), hallux in 196 (31.2%), and lesser toes in 111 (17.7%). Foot/ankle-specific MOXFQ, AOFAS and EQ-5D domains produced larger effect sizes (> 0.8) than any SF-36 domains, suggesting superior responsiveness. In analyses that anchored change in scores and effect sizes to patients' responses to a transition item about their foot/ankle problems, the MOXFQ performed well. The SF-36 and EQ-5D performed poorly. Similar analyses, conducted within foot-region based sub-groups of patients, found that the responsiveness of the MOXFQ was good compared with the AOFAS. This evidence supports the MOXFQ's suitability for assessing all foot and ankle surgery.

Comparative genome analysis suggests characteristics of yeast inverted repeats that are important for transcriptional activity

Inverted repeats are sequences of DNA that, when read in the 5' to 3' direction, have the same sequence on both strands (palindromic portion), with the exception of a small number of nucleotides in the exact center (nonpalindromic spacer). They have been implicated in various DNA-mediated processes including replication, transcription, and genomic instability. At least some of these sequences are capable of forming an alternative DNA structure, called a cruciform, that may be important for mediating these functions. We generated a list of inverted repeats in the Saccharomyces cerevisiae genome and determined which of them are conserved in three related yeasts. We have identified characterisitics of inverted repeats that make them more likely to be conserved than the surrounding DNA and characteristics, such as position and base composition, that make the genes they are associated with likely to be more actively transcribed. This is an important step in determining the functions of this group of genomic elements.

Genetic susceptibility testing for beryllium: worker knowledge, beliefs, and attitudes

BACKGROUND

We sought to gain insight into workers' knowledge, beliefs, and attitudes on the subject of testing for genetic susceptibility to beryllium.

METHODS

Five focus groups were held with 30 current and former beryllium workers and nine family members. Audio recordings were transcribed and assessed by hierarchical coding using an inductive approach.

RESULTS

Some workers were unclear about the distinction between genotoxicity and heritability. A key finding is that they perceived the benefits of a positive test result to be related to enhanced autonomous decision-making. The major concern cited by participants was potential abuse of genetic information by employers. Complete financial separation of a prospective testing entity from the employer was seen as crucial.

CONCLUSIONS

A window of opportunity exists to create regional partnerships for translational research on genetic susceptibility testing. Such partnerships would involve labor, management, public health scientists, primary care professionals, and other stakeholders. They would be critical to identifying testing strategies that maximize worker autonomy along with the public health advantages of genetic testing.

The MOXFQ patient-reported questionnaire: assessment of data quality, reliability and validity in relation to foot and ankle surgery

Previously validated for hallux valgus surgery, the Manchester-Oxford Foot Questionnaire (MOXFQ) is here evaluated for use with different regions of the foot and ankle. The study recruited 671 consecutive patients (87.8% of those eligible), mean age 52.8 years, 64% female, who completed the MOXFQ and SF-36 general health survey before foot or ankle surgery. Surgeons completed the American Orthopaedic Foot & Ankle Society (AOFAS) scales and indicated that the patients' main regions for surgery were: Hallux 210 (31.3%), Lesser toes 119 (17.7%), Mid foot 22 (3.3%), Ankle/hind foot 311 (46.3%), Multiple/whole foot 9 (1.3%). Individual MOXFQ items were assessed in terms of response rate and floor/ceiling effects, with the validity of the three MOXFQ scales (Walking/standing, Pain, and Social interaction) being assessed in terms of item-total correlations, internal and test-retest reliability, and construct validity. MOXFQ item response rates were high (all >98%). Cronbach's alphas of >0.7 confirmed internal consistency of all three scales. Test-retest ICCs were all ≥0.89. Correlations of >0.4 obtained with related SF-36 and AOFAS scales supported a priori hypotheses. Good measurement properties are confirmed for the MOXFQ in the context of baseline assessment of patients receiving surgery for a variety of foot or ankle problems.

Electroencephalography (EEG) and event-related potentials (ERPs) with human participants

Understanding the basic neural processes that underlie complex higher-order cognitive operations and functional domains is a fundamental goal of cognitive neuroscience. Electroencephalography (EEG) is a non-invasive and relatively inexpensive method for assessing neurophysiological function that can be used to achieve this goal. EEG measures the electrical activity of large, synchronously firing populations of neurons in the brain with electrodes placed on the scalp. This unit outlines the basics of setting up an EEG experiment with human participants, including equipment, and a step-by-step guide to applying and preparing an electrode cap. Also included are support protocols for two event-related potential (ERP) paradigms, P50 suppression, and mismatch negativity (MMN), which are measures of early sensory processing. These paradigms can be used to assess the integrity of early sensory processing in normal individuals and clinical populations, such as individuals with schizophrenia.

Electroencephalography (EEG) and event-related potentials (ERPs) with human participants

Understanding the basic neural processes that underlie complex higher-order cognitive operations and functional domains is a fundamental goal of cognitive neuroscience. Electroencephalography (EEG) is a non-invasive and relatively inexpensive method for assessing neurophysiological function that can be used to achieve this goal. EEG measures the electrical activity of large, synchronously firing populations of neurons in the brain with electrodes placed on the scalp. This unit outlines the basics of setting up an EEG experiment with human participants, including equipment, and a step-by-step guide to applying and preparing an electrode cap. Also included are support protocols for two event-related potential (ERP) paradigms, P50 suppression, and mismatch negativity (MMN), which are measures of early sensory processing. These paradigms can be used to assess the integrity of early sensory processing in normal individuals and clinical populations, such as individuals with schizophrenia.

Conservatively treated massive prolapsed discs: a 7-year follow-up

INTRODUCTION

The natural history of a lumbar hernia of the nucleus pulposus (HNP) is not fully known and clear indications for operative intervention cannot be established from the literature. Several studies have shown that the largest discs appear to have the greatest tendency to resolve. The aim of this study was to investigate whether massive prolapsed discs can be safely managed conservatively once clinical improvement has occurred.

PATIENTS AND METHODS

Thirty-seven patients were studied by clinical assessments and serial magnetic resonance imaging (MRI) over 2 years. Patients had severe sciatica at first, but began to show clinical improvement despite the large disc herniations. Clinical assessment included the Lasegue test and neurological appraisal. The Oswestry Disability Index was used to measure function and changes in function. Serial MRI studies allowed measurement of volume changes of the herniated disc material over a period of time.

RESULTS

Initial follow-up at an average of 23.2 months revealed that 83% had a complete and sustained recovery at the initial follow-up. Only four patients required a discectomy. The average Oswestry disability index improved from 58% to 15%. Volumetric analysis of serial MRI scans found an average reduction of 64% in disc size. There was a poor correlation between clinical improvement and the extent of disc resolution.

CONCLUSIONS

A massive disc herniation can pursue a favourable clinical course. If early progress is shown, the long-term prognosis is very good and even massive disc herniations can be treated conservatively.

Karma, reincarnation, and medicine: Hindu perspectives on biomedical research

Prior to the completion of the Human Genome Project, bioethicists and other academics debated the impact of this new genetic information on medicine, health care, group identification, and peoples' lives. A major issue is the potential for unintended and intended adverse consequences to groups and individuals. When conducting research in, for instance, American Indian and Alaskan native (AI/AN) populations, political, cultural, religious and historical issues must be considered. Among African Americans, the Tuskegee Syphilis Experiment is a reminder of racism and discrimination in this country. The goal of the current study is to understand reasons for participating, or not, in genetic research such as the HapMap project and other genetic/medical research from the perspective of the Indian American community in Houston, Texas. In this article, we report on a topic central to this discussion among Indian Americans: karma and reincarnation. Both concepts are important beliefs when considering the body and what should happen to it. Karma and reincarnation are also important considerations in participation in medical and genetic research because, according to karma, what is done to the body can affect future existences and the health of future descendants. Such views of genetic and medical research are culturally mediated. Spiritual beliefs about the body, tissue, and fluids and what happens to them when separated from the body can influence ideas about the utility and acceptability of genetic research and thereby affect the recruitment process. Within this community it is understood that genetic and environmental factors contribute to complex diseases such as diabetes, hypertension, and cancer; and acknowledgment of the significance of environmental stressors in the production of disease. A commitment to service, i.e. "betterment of humanity," karmic beliefs, and targeting environmental stressors could be prominent avenues for public health campaigns in this population. This study suggests that minority status does not automatically indicate unwillingness to participate in genetic or medical research. Indian Americans were not skeptical about the potential benefits of biomedical research in comparison to other ethnic minority communities in the United States.

The 5-choice continuous performance test: evidence for a translational test of vigilance for mice

Background

Attentional dysfunction is related to functional disability in patients with neuropsychiatric disorders such as schizophrenia, bipolar disorder, and Alzheimer's disease. Indeed, sustained attention/vigilance is among the leading targets for new medications designed to improve cognition in schizophrenia. Although vigilance is assessed frequently using the continuous performance test (CPT) in humans, few tests specifically assess vigilance in rodents.

Methods

We describe the 5-choice CPT (5C-CPT), an elaboration of the 5-choice serial reaction (5CSR) task that includes non-signal trials, thus mimicking task parameters of human CPTs that use signal and non-signal events to assess vigilance. The performances of C57BL/6J and DBA/2J mice were assessed in the 5C-CPT to determine whether this task could differentiate between strains. C57BL/6J mice were also trained in the 5CSR task and a simple reaction-time (RT) task involving only one choice (1CRT task). We hypothesized that: 1) C57BL/6J performance would be superior to DBA/2J mice in the 5C-CPT as measured by the sensitivity index measure from signal detection theory; 2) a vigilance decrement would be observed in both strains; and 3) RTs would increase across tasks with increased attentional load (1CRT task<5CSR task<5C-CPT).

Conclusions

C57BL/6J mice exhibited superior SI levels compared to DBA/2J mice, but with no difference in accuracy. A vigilance decrement was observed in both strains, which was more pronounced in DBA/2J mice and unaffected by response bias. Finally, we observed increased RTs with increased attentional load, such that 1CRT task<5CSR task<5C-CPT, consistent with human performance in simple RT, choice RT, and CPT tasks. Thus we have demonstrated construct validity for the 5C-CPT as a measure of vigilance that is analogous to human CPT studies.

An imaging workflow for characterizing phenotypical change in large histological mouse model datasets

MOTIVATION

This paper presents a workflow designed to quantitatively characterize the 3D structural attributes of macroscopic tissue specimens acquired at a micron level resolution using light microscopy. The specific application is a study of the morphological change in a mouse placenta induced by knocking out the retinoblastoma gene.

RESULT

This workflow includes four major components: (i) serial section image acquisition, (ii) image preprocessing, (iii) image analysis involving 2D pair-wise registration, 2D segmentation and 3D reconstruction, and (iv) visualization and quantification of phenotyping parameters. Several new algorithms have been developed within each workflow component. The results confirm the hypotheses that (i) the volume of labyrinth tissue decreases in mutant mice with the retinoblastoma (Rb) gene knockout and (ii) there is more interdigitation at the surface between the labyrinth and spongiotrophoblast tissues in mutant placenta. Additional confidence stem from agreement in the 3D visualization and the quantitative results generated.

AVAILABILITY

The source code is available upon request.

Reconstruction of cellular biological structures from optical microscopy data

Developments in optical microscopy imaging have generated large high-resolution data sets that have spurred medical researchers to conduct investigations into mechanisms of disease, including cancer at cellular and subcellular levels. The work reported here demonstrates that a suitable methodology can be conceived that isolates modality-dependent effects from the larger segmentation task and that 3D reconstructions can be cognizant of shapes as evident in the available 2D planar images. In the current realization, a method based on active geodesic contours is first deployed to counter the ambiguity that exists in separating overlapping cells on the image plane. Later, another segmentation effort based on a variant of Voronoi tessellations improves the delineation of the cell boundaries using a Bayesian formulation. In the next stage, the cells are interpolated across the third dimension thereby mitigating the poor structural correlation that exists in that dimension. We deploy our methods on three separate data sets obtained from light, confocal, and phase-contrast microscopy and validate the results appropriately.

Bacteriophage therapy: experience from the Eliava Institute, Georgia

The lysis of bacteria by bacteriophage was independently discovered by Frederick Twort and Felix d?Herelle but it was d?Herelle who proposed that bacteriophage might be applied to the control of bacterial diseases. Within the former Soviet Union (FSU), bacteriophage therapy was researched and applied extensively for the treatment of a wide range of bacterial infections. In the West, however, it was not explored with the same enthusiasm and was eventually discarded with the arrival of antibiotics. However, the increase in the incidence of multi-antibiotic-resistant bacteria and the absence of effective means for their control has led to increasing international interest in phage therapy and in the long experience of the Eliava Institute. The Eliava Institute of Bacteriophage, Microbiology and Virology (IBMV), which celebrates its 85th anniversary in 2008, was founded in Tbilisi in 1923 through the joint efforts of d?Herelle and the Georgian microbiologist, George Eliava.