Small Felids Coexist in Mixed-Use Landscape in the Bolivian Amazon.

In the face of global species loss, it is paramount to understand the effects of human activity on vulnerable species, particularly in highly diverse, complex systems. The Greater Madidi Landscape in the Bolivian Amazon includes several biodiverse protected areas that were created with the goal of sustaining healthy and diverse ecosystems while not impeding the livelihoods of local indigenous peoples. In this study, we sought to use camera trap data and single-species occupancy analysis to assess the impacts of different forms of human activity on four species of small felids: ocelots (Leopardus pardalis), margays (Leopardus wiedii), jaguarundi (Herpailurus yagouaroundi), and oncilla (Leopardus tigrinus). We modeled both human variables (proximity to indigenous communities, roads, and tourist camps) and non-human variables (terrain ruggedness, proximity to rivers, canopy height, prey availability, and large cat abundance). Margay occupancy was unaffected by any of these human variables and ocelots showed only weak evidence of being affected by tourism. Ocelots were particularly pervasive throughout the study area and were consistently estimated to have high occupancy probability. We did not obtain sufficient data on jaguarundi or oncilla to reliably model these effects. Our results indicate that small cats successfully coexist both with each other and with the surrounding human activity in this unique landscape, which serves as a model for global protected area management.

Data Sharing to Combat Segregation.

Data sharing between housing and education agencies will provide housing agencies with resources to assist them with efforts to decrease segregation and mitigate the adverse health outcomes experienced by people of color. The Fair Housing Act has the potential to fulfill its original integrationist purpose if housing and education agencies combine resources and data to create and implement fair housing plans. The Biden Administration's restored rule to affirmatively further fair housing pursuant to the Fair Housing Act of 1968 which seeks to reduce segregation and increase housing equity. However, it omits most of the processes set forth by the Obama Administration whereby federal agencies provide the proper tools to housing agencies so that they are able to make data-based decisions about housing policies. This article advocates for the sharing of data between housing and education agencies to optimize the positive impact of fair housing not only within housing, but also on the education, employment, and health opportunities for communities of color.

The Invariant NKT Cell Response Has Differential Signaling Requirements during Antigen-Dependent and Antigen-Independent Activation.

Invariant NKT (iNKT) cells are an innate-like population characterized by their recognition of glycolipid Ags and rapid cytokine production upon activation. Unlike conventional T cells, which require TCR ligation, iNKT cells can also be stimulated independently of their TCR. This feature allows iNKT cells to respond even in the absence of glycolipid Ags, for example, during viral infections. Although the TCR-dependent and -independent activation of iNKT cells have been relatively well established, the exact contributions of IL-12, IL-18, and TLRs remain unclear for these two activation pathways. To definitively investigate how these components affect the direct and indirect stimulation of iNKT cells, we used mice deficient for either MyD88 or the IL-12Rß2 in the T cell lineage. Using these tools, we demonstrate that IL-12, IL-18, and TLRs are completely dispensable for the TCR activation pathway when a strong agonist is used. In contrast, during murine CMV infection, when the TCR is not engaged, IL-12 signaling is essential, and TLR signaling is expendable. Importantly, to our knowledge, we discovered an intrinsic requirement for IL-18 signaling by splenic iNKT cells but not liver iNKT cells, suggesting that there might be diversity, even within the NKT1 population.

Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing.

In this work, we report 2 cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin resistance in 2 patients with acute myeloid leukemia and myelodysplastic syndrome. Mutations related to daptomycin-nonsusceptible phenotype in liaSR genes were found in all strains of the study, including those with a minimum inhibitory concentration <1 µg/mL collected before daptomycin therapy. Epidemiological investigation using core genome single nucleotide polymorphism and core genome multilocus sequence typing revealed clonality of all the isolates. In this study, we conclude that real-time genome sequencing of clinical isolates can provide rapid access to timely information on daptomycin-resistant genotypes that would help clinicians speed up and optimize the selection of the antibiotic for treatment.

Simultaneous Visualization of RNA and Protein Expression in Tissue Using a Combined RNAscope™ In Situ Hybridization and Immunofluorescence Protocol.

Gene expression analysis is critical to precisely characterize complex tissues and provide insight into a disease condition. Techniques like PCR, sequencing, and northern blotting are highly sensitive and specific but are unable to provide information about spatial positioning of target genes. Visualization of gene expression with a spatial context can be critical in identifying complex milieus in heterogenous tissues like tumors. The RNAscope in situ hybridization (ISH) technology detects target RNA expression with high sensitivity and specificity at single-cell resolution. To understand the cellular cross talk between different cell populations, it is essential to simultaneously study gene and protein expression within a complex tissue. This chapter details combining the RNAscope ISH assay with immunofluorescence (IF) in one protocol to simultaneously visualize gene expression and protein expression in human tumor tissue and mouse brain tissue.

Planning for Implementation Success Using RE-AIM and CFIR Frameworks: A Qualitative Study.

Background: RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) and CFIR (Consolidated Framework for Implementation Research) dissemination and implementation frameworks define theory-based domains associated with the adoption, implementation and maintenance of evidence-based interventions. Used together, the two frameworks identify metrics for evaluating implementation success, i.e., high reach and effectiveness resulting in sustained practice change (RE-AIM), and modifiable factors that explain and enhance implementation outcomes (CFIR). We applied both frameworks to study the implementation planning process for a technology-delivered asthma care intervention called Breathewell within an integrated care organization. The goal of the Breathewell intervention is to increase the efficiency of delivering resource-intensive asthma care services. Methods: We reviewed historical documents (i.e., meeting agendas; minutes) from 14 months of planning to evaluate alignment of implementation team priorities with RE-AIM domains. Key content was extracted and analyzed on topics, frequency and amount of discussion within each RE-AIM domain. Implementation team members were interviewed using questions adapted from the CFIR Interview Guide Tool to focus their reflection on the process and contextual factors considered during pre-implementation planning. Documents and transcripts were initially coded using RE-AIM domain definitions, and recoded using CFIR constructs, with intent to help explain how team decisions and actions can contribute to adoption, implementation and maintenance outcomes. Results: Qualitative analysis of team documents and interviews demonstrated strong alignment with the RE-AIM domains: Reach, Effectiveness, and Implementation; and with the CFIR constructs: formal inclusion of provider and staff stakeholders in implementation planning, compatibility of the intervention with workflows and systems, and alignment of the intervention with organizational culture. Focus on these factors likely contributed to RE-AIM outcomes of high implementation fidelity. However, team members expressed low confidence that Breathewell would be adopted and maintained post-trial. A potential explanation was weak alignment with several CFIR constructs, including tension for change, relative priority, and leadership engagement that contribute to organizational receptivity and motivation to sustain change. Conclusions: While RE-AIM provides a practical framework for planning and evaluating practice change interventions to assure their external validity, CFIR explains why implementation succeeded or failed, and when used proactively, identifies relevant modifiable factors that can promote or undermine adoption, implementation, and maintenance.

Adults With Asthma Experience No Increase in Asthma-related Exacerbations When Digital Communication Technology Tools Are Employed to Offset Provider Workload: A Pragmatic Randomized Trial.

BACKGROUND: Challenges to health care efficiency are increasingly addressed with the help of digital communication technology tools (DCTs). OBJECTIVE: The objective of this study was to test whether DCT, compared with Usual Care, can reduce health care clinician burden without increasing asthma-related exacerbations among patients with asthma in a large integrated health care system. RESEARCH DESIGN: The (Breathewell) program was a pragmatic, randomized trial at (Kaiser Permanente Colorado), where asthma nurses screen patients for poor symptom control when beta2-agonist refill requests came within 60 days of previous fill or in the absence of a controller medication fill within 4 months (beta2-agonist overfill). A total of 14,978 adults with asthma were randomized to Usual Care or 1 of 2 DCT intervention groups (Text/Phone call or Email). SUBJECTS: Participants included adults 18 and older with an asthma diagnosis at the time of randomization and no history of chronic obstructive pulmonary disease. MEASURES: Primary outcome measures included asthma-related health care resource utilization (eg, asthma nurse contacts), medication use, and exacerbations. RESULTS: A total of 1933 patients had 4337 events which met beta2-agonist overfill criteria. Of the 2874 events in the intervention arm, 1188 (41%) were resolved by DCT contact and did not require additional clinician contact. Asthma medication use and exacerbations over 12 months did not differ among the 3 groups. CONCLUSIONS: DCT tools can successfully contact adult asthma patients to screen for symptoms and facilitate intervention. The absence of differences in medication fills and health care utilization indicates that the strategic replacement of nursing interventions by digital outreach did not reduce treatment adherence or compromise health care outcomes.

Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia.

Here, we present complete genome sequences of four Enterococcus faecium isolates, obtained from two patients with apparent vancomycin-resistant Enterococcus faecium bacteremia; these isolates also carried two mutations known to be associated with daptomycin resistance. Sequences were obtained using de novo and hybrid assembly of Oxford Nanopore and Illumina sequence data.

Refill Reminder Preference and Inhaled Corticosteroid Adherence Among Patients with Asthma.

CONTEXT: Refill reminders can help patients improve adherence to inhaled corticosteroid (ICS) therapy. However, little is known about patient preferences for reminder type or whether patients who express a preference differ from patients who do not. OBJECTIVES: To describe patient preferences for ICS prescription refill reminder type and to compare baseline ICS therapy adherence, measured as proportion of days covered (PDC) 1 year before initiating preference-based reminders, between patients who did and did not express a preference. DESIGN: This substudy within a randomized multi-intervention study was conducted at Kaiser Permanente Colorado. Adults with asthma randomized to intervention were offered the opportunity to choose text, telephone, or email reminders. Patients who did and did not provide a preference were compared by baseline characteristics using log-binomial models. MAIN OUTCOME MEASURE(S): The primary outcomes were reminder preference and type. RESULTS: A total of 1497 of 4545 patients (32.9%) expressed a preference; 789 (52.7%) chose text. The adjusted relative risk (aRR) of not providing a preference increased with decreasing PDC (PDC of 0.50 to < 0.80: aRR, 1.14; 95% confidence interval [CI], 1.04-1.25; PDC < 0.5: aRR, 1.76; 95% CI, 1.59-1.95) compared with patients with a PDC of 0.80 or greater. CONCLUSION: Among patients who expressed a preference, text reminders were preferred. Patients who expressed a preference had higher baseline adherence. Further research is needed to determine whether expressing a preference for a refill reminder type is itself associated with adherence. Given that offering the opportunity to choose a reminder type only engaged a subset of patients, further work is needed to understand how best to leverage technology-enabled communication outreach to help patients optimize adherence.

A standardized approach to bereavement risk-screening: a quality improvement project.

Objectives: Identifying family members at-risk of poor bereavement outcomes poses a challenge for clinicians, resulting in inconsistent bereavement follow-up. The current quality improvement study tests a method for identification of at-risk family members, and describes follow-up they received from the bereavement service at Dana-Farber Cancer Institute.Design: A standardized bereavement risk assessment, referral and follow-up process was piloted as part of a quality improvement project using a plan-do-study-act approach (PDSA).Methods: A convenience sample of eleven clinical social workers completed paper and pencil bereavement risk-screening assessments using the Bereavement Risk-Screening Tool (BRST) on a sample of bereaved family members known to them. The results of the BRST were passed onto the bereavement program for follow-up.Findings: Eleven out of a total of 17 social workers participated in the study. Social workers screened 100% (52/52) of identified bereaved family members, corresponding to 52 patient deaths. Approximately half (28/52) were identified as being 'at-risk' of a poor bereavement outcome based on the social worker's consideration of the presence of potential risk-factors and their response to a prediction-type question about the bereaved individual's future coping. 'Lack of preparation for the death', 'unexpected death within the context of an illness' and 'witnessing a difficult death' were the most commonly identified risk factors. Of those individuals who were identified to be 'at-risk', 89% received an outreach attempt by telephone from the director of bereavement services, surpassing our project target of 80%. Conclusions: The BRST has the potential to help clinicians in health care settings identify those family members who might be considered at heightened risk of a poor bereavement outcome, facilitating early outreach and recommendations for support. The tool was easy to complete and helped streamline the referral process to the bereavement program.

Qa-1-Restricted CD8+ T Cells Can Compensate for the Absence of Conventional T Cells during Viral Infection.

The role of non-classical T cells during viral infection remains poorly understood. Using the well-established murine model of CMV infection (MCMV) and mice deficient in MHC class Ia molecules, we found that non-classical CD8+ T cells robustly expand after MCMV challenge, become highly activated effectors, and are capable of forming durable memory. Interestingly, although these cells are restricted by MHC class Ib molecules, they respond similarly to conventional T cells. Remarkably, when acting as the sole component of the adaptive immune response, non-classical CD8+ T cells are sufficient to protect against MCMV-induced lethality. We also demonstrate that the MHC class Ib molecule Qa-1 (encoded by H2-T23) restricts a large, and critical, portion of this population. These findings reveal a potential adaptation of the host immune response to compensate for viral evasion of classical T cell immunity.

Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection.

Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of nosocomial infections of the bloodstream and urinary tract. Here, we report the draft genome sequences of 48 vancomycin-resistant E. faecium isolates recovered from inpatients exhibiting clinical signs of bacteremia at the University of Arkansas for Medical Sciences (UAMS).

The characterization of androstenone transport in boar plasma.

The transport of steroids by plasma proteins influences the amount of steroid available for uptake by the target tissue. In the boar, androstenone is transported to the adipose tissue where it accumulates to cause an off-odour or off-flavour in pork, known as boar taint. The mechanism of the transport of androstenone in the boar remains unclear, and the plasma protein responsible for binding androstenone has yet to be identified. Therefore, the purpose of the present study was to characterize the binding of androstenone to plasma proteins in the boar. The binding specificity of androstenone to plasma proteins was first investigated using a HPLC gel filtration method. [3H]-androstenone was incubated with plasma in the presence or absence of unlabeled competitors and the displacement of androstenone from plasma proteins was measured. In the presence of excess unlabeled competitors, [3H]-androstenone was only partially displaced from plasma proteins, indicating it binds to a low affinity high capacity plasma protein. Binding kinetics studies were also conducted to characterize the binding of androstenone and dehydroepiandrosterone (DHEA) to plasma proteins. The Bmax of androstenone and DHEA was approximately the same (89.1% and 92.3%, respectively). However, the binding affinity (K) of androstenone was 6.5 fold greater than DHEA (0.39 nmol/ml and 0.06 nmol/ml, respectively). Affinity chromatography was used to remove albumin from the plasma proteins. Following incubations with androstenone and DHEA, the binding observed in the albumin free protein fraction was reduced 2.6 and 2.1 fold, respectively relative to the binding in the albumin protein fractions. These results provide direct evidence that androstenone is transported non-specifically by albumin in the plasma of the boar.

Implementing Health Care Technology Research into Practice to Improve Adult Asthma Management.

BACKGROUND: Use of health technology has shown potential to improve asthma adherence and outcomes. Few studies have looked at the implementation of such research within larger asthma populations. OBJECTIVE: This report examines the process of translating results from a pragmatic trial using speech recognition (SR) in children with persistent asthma into the standard operating procedure within a large health maintenance organization. Medication adherence and outcomes in adults with asthma were examined. METHODS: The SR protocol was implemented for the total Kaiser Permanente Colorado (KPCO) patient population of 480,142, of whom 36,356 had asthma. Patients had persistent asthma, filled 1 or more inhaled corticosteroid prescriptions in the prior 6 months, and remained continuously enrolled with KPCO for 2 years. Documented exacerbations included the presence of a hospitalization, emergency department visit, or course of oral corticosteroid where asthma was the principal diagnosis. Adherence and exacerbation events were compared 1 year before and 1 year after intervention for 4,510 adults aged 19 to 64. RESULTS: Patient adherence demonstrated a small but significant improvement from 39.5% to 41.7% (P < .0001). Although not significant, data trends suggested greater improvement for patients with lower socioeconomic status. When an outlier month was removed from both the pre- and postintervention time periods, courses of oral corticosteroids decreased. Emergency department visits and hospitalizations were infrequent in both time periods and did not decrease over time. CONCLUSIONS: A low-cost SR intervention reminding patients to fill and take their daily controller asthma medication can improve treatment adherence and decrease the need for oral corticosteroids due to asthma exacerbations, but not decrease emergency department visits or hospitalizations.

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay.

Because precision medicine is highly dependent on the accurate detection of biomarkers, there is an increasing need for standardized and robust technologies that measure RNA biomarkers in situ in clinical specimens. While grind-and-bind assays like RNAseq and quantitative RT-PCR enable highly sensitive gene expression measurements, they also require RNA extraction and thus prevent valuable expression analysis within the morphological tissue context. The in situ hybridization (ISH) assay described here can detect RNA target sequences as short as 50 nucleotides at single-nucleotide resolution and at the single-cell level. This assay is complementary to the previously developed commercial assay and enables sensitive and specific in situ detection of splice variants, short targets, and point mutations within the tissue. In this protocol, probes were designed to target unique exon junctions for two clinically important splice variants, EGFRvIII and METΔ14. The detection of short target sequences was demonstrated by the specific detection of CDR3 sequences of T-cell receptors α and ß in the Jurkat T-cell line. Also shown is the utility of this ISH assay for the distinction of RNA target sequences at single-nucleotide resolution (point mutations) through the visualization of EGFR L858R and KRAS G12A single-nucleotide variations in cell lines using automated staining platforms. In summary, the protocol shows a specialized RNA ISH assay that enables the detection of splice variants, short sequences, and mutations in situ for manual performance and on automated stainers.

Novel Junction-specific and Quantifiable In Situ Detection of AR-V7 and its Clinical Correlates in Metastatic Castration-resistant Prostate Cancer.

BACKGROUND: Androgen receptor splice variant 7 (AR-V7) has been implicated in resistance to abiraterone and enzalutamide treatment in men with metastatic castration-resistant prostate cancer (mCRPC). Tissue- or cell-based in situ detection of AR-V7, however, has been limited by lack of specificity. OBJECTIVE: To address current limitations in precision measurement of AR-V7 by developing a novel junction-specific AR-V7 RNA in situ hybridization (RISH) assay compatible with automated quantification. DESIGN, SETTING, AND PARTICIPANTS: We designed a RISH method to visualize single splice junctions in cells and tissue. Using the validated assay for junction-specific detection of the full-length AR (AR-FL) and AR-V7, we generated quantitative data, blinded to clinical data, for 63 prostate tumor biopsies. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We evaluated clinical correlates of AR-FL/AR-V7 measurements, including association with prostate-specific antigen progression-free survival (PSA-PFS) and clinical and radiographic progression-free survival (PFS), in a subset of patients starting treatment with abiraterone or enzalutamide following biopsy. RESULTS AND LIMITATIONS: Quantitative AR-FL/AR-V7 data were generated from 56 of the 63 (88.9%) biopsy specimens examined, of which 44 were mCRPC biopsies. Positive AR-V7 signals were detected in 34.1% (15/44) mCRPC specimens, all of which also co-expressed AR-FL. The median AR-V7/AR-FL ratio was 11.9% (range 2.7-30.3%). Positive detection of AR-V7 was correlated with indicators of high disease burden at baseline. Among the 25 CRPC biopsies collected before treatment with abiraterone or enzalutamide, positive AR-V7 detection, but not higher AR-FL, was significantly associated with shorter PSA-PFS (hazard ratio 2.789, 95% confidence interval 1.12-6.95; p=0.0081). CONCLUSIONS: We report for the first time a RISH method for highly specific and quantifiable detection of splice junctions, allowing further characterization of AR-V7 and its clinical significance. PATIENT SUMMARY: Higher AR-V7 levels detected and quantified using a novel method were associated with poorer response to abiraterone or enzalutamide in prostate cancer.

Ultrasensitive automated RNA in situ hybridization for kappa and lambda light chain mRNA detects B-cell clonality in tissue biopsies with performance comparable or superior to flow cytometry.

The assessment of B-cell clonality is a critical component of the evaluation of suspected lymphoproliferative disorders, but analysis from formalin-fixed, paraffin-embedded tissues can be challenging if fresh tissue is not available for flow cytometry. Immunohistochemical and conventional bright field in situ hybridization stains for kappa and lambda are effective for evaluation of plasma cells but are often insufficiently sensitive to detect the much lower abundance of light chains present in B-cells. We describe an ultrasensitive RNA in situ hybridization assay that has been adapted for use on an automated immunohistochemistry platform and compare results with flow cytometry in 203 consecutive tissues and 104 consecutive bone marrows. Overall, in 203 tissue biopsies, RNA in situ hybridization identified light chain-restricted B-cells in 85 (42%) vs 58 (29%) by flow cytometry. Within 83 B-cell non-Hodgkin lymphomas, RNA in situ hybridization identified restricted B-cells in 74 (89%) vs 56 (67%) by flow cytometry. B-cell clonality could be evaluated in only 23/104 (22%) bone marrow cases owing to poor RNA preservation, but evaluable cases showed 91% concordance with flow cytometry. RNA in situ hybridization allowed for recognition of biclonal/composite lymphomas not identified by flow cytometry and highlighted unexpected findings, such as coexpression of kappa and lambda RNA in 2 cases and the presence of lambda light chain RNA in a T lymphoblastic lymphoma. Automated RNA in situ hybridization showed excellent interobserver reproducibility for manual evaluation (average K=0.92), and an automated image analysis system showed high concordance (97%) with manual evaluation. Automated RNA in situ hybridization staining, which can be adopted on commonly utilized immunohistochemistry instruments, allows for the interpretation of clonality in the context of the morphological features in formalin-fixed, paraffin-embedded tissues with a clinical sensitivity similar or superior to flow cytometry.

Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution.

Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones. Computational modeling suggests that subclones must arise sufficiently early, or carry a considerable fitness advantage, to form large or spatially disparate subclones. Examples of putative treatment-resistant cells isolated in small topographical areas are observed. The BaseScope assay represents a significant technical advance for in situ mutation detection that provides new insight into tumor evolution, and could have ramifications for selecting patients for treatment.