Text mining for contexts and relationships in cancer genomics literature.

MOTIVATION: Scientific advances build on the findings of existing research. The 2001 publication of the human genome has led to the production of huge volumes of literature exploring the context-specific functions and interactions of genes. Technology is needed to perform large-scale text mining of research papers to extract the reported actions of genes in specific experimental contexts and cell states, such as cancer, thereby facilitating the design of new therapeutic strategies. RESULTS: We present a new corpus and Text Mining methodology that can accurately identify and extract the most important details of cancer genomics experiments from biomedical texts. We build a Named Entity Recognition model that accurately extracts relevant experiment details from PubMed abstract text, and a second model that identifies the relationships between them. This system outperforms earlier models and enables the analysis of gene function in diverse and dynamically evolving experimental contexts. AVAILABILITY AND IMPLEMENTATION: Code and data are available here: https://github.com/cambridgeltl/functional-genomics-ie.

Extreme Paralysis Following Rocuronium Administration in a Myasthenia Gravis Patient: A Case Report.

INTRODUCTION: The use of paralytics during rapid sequence intubation (RSI) in patients with myasthenia gravis (MG) remains a controversial topic in emergency medicine. Due to fewer functional acetylcholine receptors, these patients can be both sensitive and resistant to different types of neuromuscular blocking agents (NMBA). Their atypical sensitivity to non-depolarizing NMBAs such as rocuronium can increase both the duration and depth of paralysis after its use at typical RSI doses. However, the extent of rocuronium's prolonged duration of effect in patients with MG has yet to be quantified in an emergency department setting. CASE REPORT: We describe a case wherein a full RSI dose of 1.2 milligrams per kilogram of rocuronium led to a prolonged 232-minute duration of paralysis in a patient with MG. This sustained paralysis was suspected but only confirmed after the patient received the reversal agent sugammadex. Once administered, an acute change in neurologic function was seen, and the patient was emergently taken to the operating room for neurosurgical intervention. CONCLUSION: When intubating patients with MG, many emergency physicians are aware that using paralytics during RSI provides several challenges. If not properly dose-reduced, rocuronium may exert its paralytic effects for up to four hours in patients with MG. This unique case highlights the importance of personalizing care for this patient population before, during, and after RSI.

Effects of a Dietitian-Led, Telehealth Lifestyle Intervention on Blood Pressure: Results of a Randomized, Controlled Trial.

Background Limited data exist on the benefits of lifestyle behavior change delivered using telehealth and web-based applications with varied support on blood pressure (BP). Methods and Results We conducted a 2-site randomized controlled trial at Geisinger (January 2019-March 2021) to compare the efficacy of 2 remotely delivered strategies using web-based applications in participants with 24-hour systolic BP 120-160 mm Hg and body mass index ≥25 kg/m2. Both arms received access to web-based applications and the same lifestyle guidance per American Heart Association guidelines. One arm received minimal nonclinical staff support, and the other arm received dietitian support with motivational interviewing during weekly calls. The primary outcome was 12-week change in 24-hour systolic BP. A total of 187 participants were randomly assigned, with 156 (83.4%) completing the trial. In both arms, 24-hour systolic BP was reduced at follow-up, but the difference in BP change was not significant (dietitian-led arm, -6.73 mm Hg [95% CI, -8.64 to -4.82]; minimal-support arm, -4.92 [95% CI, -7.01 to -2.77]; P comparing groups=0.2). The dietitian-support arm had greater 12-week improvements in the secondary outcomes sleep systolic BP (mean, -6.92 versus -1.45; P=0.004), sleep diastolic BP (-3.31 versus 0.73; P=0.001), and self-reported physical activity (866 versus -243 metabolic equivalent task minutes per week; P=0.01) and tended to have improvements in weight loss (-5.11 versus -3.89 kg; P=0.1) and Healthy Eating Index-2015 score (9.23 versus 6.43 units; P=0.09). Conclusions Both the dietitian- and minimal-support interventions reduced 24-hour systolic BP similarly, although the dietitian-led intervention led to greater improvements in several secondary cardiometabolic outcomes. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT03700710.

Urban green space interaction and wellbeing - investigating the experience of international students in Berlin during the first COVID-19 lockdown.

This qualitative study explores the topic of mental health/wellbeing with reference to exposure to urban green space (UGS). It builds on previous research, which has highlighted the potential for green space interaction for supporting positive emotional and mental wellbeing, particularly in times of stress and uncertainty. Using this basis, the paper explores whether UGS interaction also helped to mitigate the negative mental health impacts brought about by the first COVID-19 lockdown. The specific focus is on students and expatriates living in Berlin, Germany as this population groupbecame increasingly vulnerable during this time as a result of uncertainty and restrictions in their daily lives brought about the enforced lockdown measures. More specifically, this paper investigates how a change in their daily routines created opportunities to interact with and experience UGS differently and how their emotional response and perception towards these spaces changed. Semi-structured interviews allowed for stories, experiences and emotions to unfold, which revealed that the participants' gained an appreciation for the potential of UGS to support their wellbeing during a stressful and isolating time. UGS interaction also allowed them to form tangible memories of summer 2020 as it provided a safe arena for them to maintain social contact with friends outdoors, or to escape their home environment and experience respite and relaxation in a natural setting. The findings demonstrate that for this sub-group of the population UGS became a reliable constant and a valuable public health resource, which may also help to mitigate the long-term adverse mental health impacts of the pandemic.

Comparing Smoking Cessation Interventions among Underserved Patients Referred for Lung Cancer Screening: A Pragmatic Trial Protocol.

Smoking burdens are greatest among underserved patients. Lung cancer screening (LCS) reduces mortality among individuals at risk for smoking-associated lung cancer. Although LCS programs must offer smoking cessation support, the interventions that best promote cessation among underserved patients in this setting are unknown. This stakeholder-engaged, pragmatic randomized clinical trial will compare the effectiveness of four interventions promoting smoking cessation among underserved patients referred for LCS. By using an additive study design, all four arms provide standard "ask-advise-refer" care. Arm 2 adds free or subsidized pharmacologic cessation aids, arm 3 adds financial incentives up to $600 for cessation, and arm 4 adds a mobile device-delivered episodic future thinking tool to promote attention to long-term health goals. We hypothesize that smoking abstinence rates will be higher with the addition of each intervention when compared with arm 1. We will enroll 3,200 adults with LCS orders at four U.S. health systems. Eligible patients include those who smoke at least one cigarette daily and self-identify as a member of an underserved group (i.e., is Black or Latinx, is a rural resident, completed a high school education or less, and/or has a household income <200% of the federal poverty line). The primary outcome is biochemically confirmed smoking abstinence sustained through 6 months. Secondary outcomes include abstinence sustained through 12 months, other smoking-related clinical outcomes, and patient-reported outcomes. This pragmatic randomized clinical trial will identify the most effective smoking cessation strategies that LCS programs can implement to reduce smoking burdens affecting underserved populations. Clinical trial registered with clinicaltrials.gov (NCT04798664). Date of registration: March 12, 2021. Date of trial launch: May 17, 2021.

Effects of Dietary App-Supported Tele-Counseling on Sodium Intake, Diet Quality, and Blood Pressure in Patients With Diabetes and Kidney Disease.

OBJECTIVES: The aim of this study is to examine the effect of a telehealth intervention that used a dietary app, educational website, and weekly dietitian tele-counseling on sodium intake, diet quality, blood pressure, and albuminuria among individuals with diabetes and early-stage chronic kidney disease. DESIGN AND METHODS: We examined the effects of a dietary app-supported tele-counseling intervention in a single center, single arm study of 44 participants with type 2 diabetes and stage 1-3a chronic kidney disease. Participants recorded and shared dietary data via MyFitnessPal with registered dietitians, who used motivational interviewing to provide telephone counseling weekly for 8 weeks. After the 8-week intensive intervention, participants were followed at 6 and 12 months. Outcomes included 24-hour urine sodium (2 collections per timepoint), Healthy Eating Index 2015 score (three 24-hour dietary recalls per timepoint), 24-hour systolic blood pressure (SBP) and diastolic blood pressure (DBP), and 24-hour urine albumin excretion. RESULTS: Out of 44 consented participants (mean age 60.3 ± 11.9 years, 43% female, 89% white, median estimated glomerular filtration rate was 78.5 mL/min/1.73 m2, median urine albumin excretion 52.9 mg/day, 84% hypertension), 32 (73%) completed 8-week follow-up, 27 (61%) completed 6-month follow-up, and 25 (57%) completed 12-month follow-up. Among participants who completed 12-month follow-up, reported sodium intake decreased by 638 mg/day from baseline of 2,919 mg/day (P < .001). The 24-hour mean urine sodium and albumin excretion did not decline over the study period. Healthy Eating Index 2015 score improved by 7.76 points at 12 months from a mean baseline of 54.6 (P < .001). Both 24-hour SBP and DBP declined at 12 months from baseline (SBP -5.7 mm Hg, 95% confidence interval -10.5 to -1.0, P = .02; DBP -4.1 mm Hg, 95% confidence interval -7.2 to -1.1, P = .01). CONCLUSIONS: Overall, this study demonstrates that a short, intensive, remotely delivered dietary intervention for adults with type 2 diabetes and early chronic kidney disease at high risk for disease progression and cardiovascular complications led to improvement in blood pressure and self-reported sodium intake and diet quality, but no improvement in albuminuria. Future research studies are needed to examine whether remotely delivered dietary interventions can ultimately improve kidney health over time.

BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine.

BACKGROUND: Recent advances in representation learning have enabled large strides in natural language understanding; However, verbal reasoning remains a challenge for state-of-the-art systems. External sources of structured, expert-curated verb-related knowledge have been shown to boost model performance in different Natural Language Processing (NLP) tasks where accurate handling of verb meaning and behaviour is critical. The costliness and time required for manual lexicon construction has been a major obstacle to porting the benefits of such resources to NLP in specialised domains, such as biomedicine. To address this issue, we combine a neural classification method with expert annotation to create BioVerbNet. This new resource comprises 693 verbs assigned to 22 top-level and 117 fine-grained semantic-syntactic verb classes. We make this resource available complete with semantic roles and VerbNet-style syntactic frames. RESULTS: We demonstrate the utility of the new resource in boosting model performance in document- and sentence-level classification in biomedicine. We apply an established retrofitting method to harness the verb class membership knowledge from BioVerbNet and transform a pretrained word embedding space by pulling together verbs belonging to the same semantic-syntactic class. The BioVerbNet knowledge-aware embeddings surpass the non-specialised baseline by a significant margin on both tasks. CONCLUSION: This work introduces the first large, annotated semantic-syntactic classification of biomedical verbs, providing a detailed account of the annotation process, the key differences in verb behaviour between the general and biomedical domain, and the design choices made to accurately capture the meaning and properties of verbs used in biomedical texts. The demonstrated benefits of leveraging BioVerbNet in text classification suggest the resource could help systems better tackle challenging NLP tasks in biomedicine.

Telehealth versus self-directed lifestyle intervention to promote healthy blood pressure: a protocol for a randomised controlled trial.

INTRODUCTION: Weight loss, consumption of a Dietary Approaches to Stop Hypertension dietary pattern, reduced sodium intake and increased physical activity have been shown to lower blood pressure (BP). Use of web-based tools and telehealth to deliver lifestyle counselling could be potentially scalable solutions to improve BP through behavioural modification though limited data exists to support these approaches in clinical practice. METHODS AND ANALYSIS: This randomised controlled trial will compare the efficacy of a telehealth versus self-directed lifestyle intervention in lowering 24-hour SBP in patients with overweight/obesity (body mass index ≥25 kg/m2) and 24-hour SBP 120-160 mm Hg. All participants receive personalised recommendations to improve dietary quality based on a web-based Food Frequency Questionnaire, access to an online comprehensive weight management programme and a smartphone dietary app. The telehealth arm additionally includes weekly calls with registered dietitian nutritionists who use motivational interviewing. The primary outcome is change from baseline to 12 weeks in 24-hour SBP. Secondary outcomes include changes from baseline in 24-hour diastolic BP, daytime SBP, nighttime SP, daytime diastolic BP, nighttime diastolic BP, total Healthy Eating Index-2015 score, weight, waist circumference and physical activity. Other prespecified outcomes will include change in individual components of the Healthy Eating Index-2015 score, and satisfaction with the Healthy BP research study measured on a 5-point Likert scale. ETHICS AND DISSEMINATION: The study has been approved by the Geisinger Institutional Review Board. Results will be disseminated through peer-reviewed publications and conference presentations. TRIAL REGISTRATION NUMBER: NCT03700710.

A Program to Provide Clinicians with Feedback on Their Diagnostic Performance in a Learning Health System.

PROBLEM: Reducing diagnostic errors requires improving both systems and individual clinical reasoning. One strategy to achieve diagnostic excellence is learning from feedback. However, clinicians remain uncomfortable receiving feedback on their diagnostic performance. Thus, a team of researchers and clinical leaders aimed to develop and implement a diagnostic performance feedback program for learning that mitigates potential clinician discomfort. APPROACH: The program was developed as part of a larger project to create a learning health system around diagnostic safety at Geisinger, a large, integrated health care system in rural Pennsylvania. Steps included identifying potential missed opportunities in diagnosis (MODs) from various sources (for example, risk management, clinician reports, patient complaints); confirming MODs through chart review; and having trained facilitators provide feedback to clinicians about MODs as learning opportunities. The team developed a guide for facilitators to conduct effective diagnostic feedback sessions and surveyed facilitators and recipients about their experiences and perceptions of the feedback sessions. OUTCOMES: 28 feedback sessions occurred from January 2019 to June 2020, involving MODs from emergency medicine, primary care, and hospital medicine. Most facilitators (90.6% [29/32]) reported that recipients were receptive to learning and discussing MODs. Most recipients reported that conversations were constructive and nonpunitive (83.3% [25/30]) and allowed them to take concrete steps toward improving diagnosis (76.7% [23/30]). Both groups believed discussions would improve future diagnostic safety (93.8% [30/32] and 70.0% [21/30], respectively). KEY INSIGHTS AND NEXT STEPS: An institutional program was developed and implemented to deliver diagnostic performance feedback. Such a program may facilitate learning and improvement to reduce MODs. Future efforts should assess long-term effects on diagnostic performance and patient outcomes.

Remote Dietary Counseling Using Smartphone Applications in Patients With Stages 1-3a Chronic Kidney Disease: A Mixed Methods Feasibility Study.

OBJECTIVE(S): Although healthy dietary patterns are associated with decreased mortality in patients with chronic kidney disease (CKD), few patients receive dietitian counseling due to concerns such as dietitian availability, travel distance, and cost. Our objective was to determine the feasibility of dietary smartphone application-supported telecounseling to reduce sodium intake and improve dietary quality in patients with early CKD. METHODS: This was a pre-post, mixed methods feasibility study of 16 patients with Stage 1-3a CKD in central/northeast Pennsylvania. Patients recorded and shared dietary data via smartphone applications with registered dietitians, who used motivational interviewing to provide telephone counseling weekly for 8 weeks. Seven patients were assigned to a customized study-specific application and nine patients to a commercially available, free application (MyFitnessPal). Participant satisfaction was assessed via survey, and participants were invited to complete a semistructured interview. Outcomes assessed included sodium intake, Healthy Eating Index 2015 score, weight, and 24-hour blood pressure (BP). RESULTS: Mean age was 64.7 years, 31% were female, 100% were white, 13% had income <$25,000. Adherence was excellent with 14 (88%) entering dietary data at least 75% of total days. Patients reported high satisfaction with the intervention and dietitian telecounseling. Use of dietary apps was viewed positively for allowing tracking of sodium and energy intake although some participants experienced functionality issues with the customized application that were not generally experienced by those using the commercially available free application. Sodium intake (-604 mg/day, 95% confidence interval [CI]: -1,104 to -104), Healthy Eating Index 2015 score (3.97, 95% CI: 0.03-7.91), weight (-3.4, 95% CI: -6.6 to -0.1), daytime systolic BP (-5.8, 95% CI: -12.1 to 0.6), and daytime diastolic BP (-4.1, 95% CI: -7.9 to -0.2) improved after the intervention. CONCLUSIONS: An application-supported telecounseling program with a registered dietitian appears to be a feasible and well-accepted strategy to improve dietary quality and improve cardiovascular risk factors in patients with early kidney disease.

Evaluating the effectiveness and implementation of evidence-based treatment: A multisite hybrid design.

The gap between treatment development and efficacy testing to scaled up implementations of evidence-based treatment (EBT) is an estimated 20 years, and hybrid research designs aim to reduce the gap. One was used for a multisite study in cancer control, testing coprimary aims: (a) determine the feasibility and utility of a flexible EBT implementation strategy and (b) determine the clinical effectiveness of an EBT as implemented by newly trained providers. Therapists from 15 diverse sites implemented the biobehavioral intervention (BBI) for cancer patients (N = 158) as part of standard care. For implementation, therapists determined treatment format, number of sessions, and so forth and reported session-by-session fidelity. Patients completed fidelity and outcome assessments. Results showed therapists BBI implementation was done with fidelity, for example, session "dose" (59%), core content coverage (60-70%), and others. Patient reported fidelity was favorable and comparable to the BBI efficacy trial. Effectiveness data show the primary outcome, patients' scores on the Profile of Mood States total mood disturbance, significantly improved (R² = 0.06, ß = -0.24, p < .01) as did a secondary outcome, physical activity (R² = 0.02, ß = 0.13, p < .05). This first use of a hybrid design in health psychology provided support for a novel strategy that allowed providers implementation flexibility. Still, the EBT was delivered with fidelity and in addition, therapists generated novel procedures to enhance setting-specific usage of BBI and its ultimate effectiveness with patients. This research is an example of translational research spanning theory and efficacy tests to dissemination and implementation. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Benefits of reminiscence therapy.

During my second placement in my first year of training, I was working in a community hospital where I helped to care for an older male patient, who I will call Ben.

See the person behind the patient.

During my first clinical placement on a surgical ward, I helped care for a female patient with peritoneal cancer. The patient, who I will call Jane, was about 60 years old and was receiving palliative care.

ß-Catenin Stabilization in Skin Fibroblasts Causes Fibrotic Lesions by Preventing Adipocyte Differentiation of the Reticular Dermis.

The Wnt/ß-catenin pathway plays a central role in epidermal homeostasis and regeneration, but how it affects fibroblast fate decisions is unknown. We investigated the effect of targeted ß-catenin stabilization in dermal fibroblasts. Comparative gene expression profiling of stem cell antigen 1(-) (Sca1(-)) and Sca1(+) neonatal fibroblasts from upper and lower dermis, respectively, confirmed that Sca1(+) cells had a preadipocyte signature and showed differential expression of Wnt/ß-catenin-associated genes. By targeting all fibroblasts or selectively targeting Dlk1(+) lower dermal fibroblasts, we found that ß-catenin stabilization between developmental stages E16.5 and P2 resulted in a reduction in the dermal adipocyte layer with a corresponding increase in dermal fibrosis and an altered hair cycle. The fibrotic phenotype correlated with a reduction in the potential of Sca1(+) fibroblasts to undergo adipogenic differentiation ex vivo. Our findings indicate that Wnt/ß-catenin signaling controls adipogenic cell fate within the lower dermis, which potentially contributes to the pathogenesis of fibrotic skin diseases.

Examination of the Beck Depression Inventory-II Factor Structure Among Bariatric Surgery Candidates.

BACKGROUND: The Beck Depression Inventory-II (BDI-II) is frequently used to evaluate bariatric patients in clinical and research settings; yet, there are limited data regarding the factor structure of the BDI-II with a bariatric surgery population. METHODS: Exploratory factor analysis (EFA) using principal axis factoring with oblimin rotation was employed with data from 1228 consecutive presurgical bariatric candidates. Independent t tests were used to examine potential differences between sexes. Confirmatory factor analysis (CFA) was conducted with the next 383 consecutive presurgical patients to evaluate the proposed model based on EFA results. RESULTS: EFA revealed three factors: negative perceptions, diminished vigor, and cognitive dysregulation, each with adequate internal consistency. Six BDI-II items did not load significantly on any of the three factors. CFA results largely supported the proposed model. CONCLUSIONS: Results suggest that dimensions of depression for presurgical bariatric candidates vary from other populations and raise important caveats regarding the utility of the BDI-II in bariatric research.

Internalized weight bias in weight-loss surgery patients: psychosocial correlates and weight loss outcomes.

PURPOSE: In this study, we examined the relationship between pre-operative internalized weight bias and 12-month post-operative weight loss in adult bariatric surgery patients. METHODS: Bariatric surgery patients (n=170) from one urban and one rural medical center completed an internalized weight bias measure (the weight bias internalization scale, WBIS) and a depression survey (Beck depression inventory-II, BDI-II) before surgery, and provided consent to access their medical records. RESULTS: Participants (BMI=47.8 kg/m2, age=45.7 years) were mostly female (82.0 %), White (89.5 %), and underwent gastric bypass (83.6 %). The average WBIS score by item was 4.54 ± 1.3. Higher pre-operative WBIS scores were associated with diminished weight loss at 12 months after surgery (p=0.035). Pre-operative WBIS scores were positively associated with depressive symptoms (p<0.001). CONCLUSION: Greater internalized weight bias was associated with more depressive symptoms before surgery and less weight loss 1 year after surgery.

Engaging patients in public policy advocacy.

Health professionals can and should be game-changing influencers of U.S. health policies. The American Thoracic Society (ATS) is enabling its members to advocate on important issues through such initiatives as the Breathing Better Alliance network and the annual ATS Hill Day. Patients are also organizing to make their voices heard by participating in the member organizations of the ATS Public Advisory Roundtable and by accompanying ATS members and staff on visits to legislators and government regulators. If we join together, we can amplify our messages and promote better health policies. Doing so will require us to embrace a partnership steeped in trust and hope.