The NCI/NIH Cancer Moonshot BioBank (CMB) and the Maine Cancer Genetics/Genomics Education Core (ME-CGEC) Collaborate to Improve Cancer Care in Maine

Goal: To better understand drug resistance and sensitivity in patients with late stage (Stage III & IV) cancers that are receiving standard of care molecularly targeted therapies through next generation sequencing (NGS) of biopsy and blood samples collected longitudinally (diagnosis-- treatment--progression).https://knowledgeconnection.mainehealth.org/lambrew-retreat-2021/1053/thumbnail.jp

A Period Seroprevalence (SARS-CoV-2) Survey in MHCCN Cancer Healthcare Workers (HCWs) Providing Patient Care during the Height of the Outbreak: A Registry Study (Initial Progress)

Introduction: There is little information on the basic epidemiologic and serologic profile(s) of the novel SARSCoV- 2 coronavirus especially in HCWs employed in rural settings. We embarked on a period seroprevalence study in the MaineHealth Cancer Network (MHCCN) to document Covid-19 exposure in our rural cancer care workforce. Our fundamental hypothesis is that despite implementing procedures to safeguard patients and the use of appropriate PPE in the care of known source patients/PUIs in both the inpatient and outpatient cancer care settings a small, but not insignificant number of cancer care providers (hereafter referred to as cancer HCWs) will have evidence of exposure by virtue of plasma antibody seroconversion.https://knowledgeconnection.mainehealth.org/lambrew-retreat-2021/1001/thumbnail.jp

A multi-centre study of interactional style in nurse specialist- and physician-led Rheumatology clinics in the UK

Background: Nurse-led care is well established in Rheumatology in the UK and provides follow-up care to people with inflammatory arthritis including treatment, monitoring, patient education and psychosocial support. Aim: The aim of this study is to compare and contrast interactional style with patients in physician-led and nurse-led Rheumatology clinics. Design: A multi-centre mixed methods approach was adopted. Settings: Nine UK Rheumatology out-patient clinics were observed and audio-recorded May 2009-April 2010. Participants: Eighteen practitioners agreed to participate in clinic audio-recordings, researcher observations, and note-taking. Of 9 nurse specialists, 8 were female and 5 of 9 physicians were female. Eight practitioners in each group took part in audio-recorded post-clinic interviews. All patients on the clinic list for those practitioners were invited to participate and 107 were consented and observed. In the nurse specialist cohort 46% were female 71% had a diagnosis of Rheumatoid Arthritis (RA). The physician cohort comprised 31% female 40% with RA and 16% unconfirmed diagnosis. Nineteen (18%) of the patients observed were approached for an audio-recorded telephone interview and 15 participated (4 male, 11 female). Methods: Forty-four nurse specialist and 63 physician consultations with patients were recorded. Roter's Interactional Analysis System (RIAS) was used to code this data. Thirty-one semi-structured interviews were conducted (16 practitioner, 15 patients) within 24 h of observed consultations and were analyzed using thematic analysis. Results: RIAS results illuminated differences between practitioners that can be classified as 'socio-emotional' versus 'task-focussed'. Specifically, nurse specialists and their patients engaged significantly more in the socio-emotional activity of 'building a relationship'. Across practitioners, the greatest proportion of 'patient initiations' were in 'giving medical information' and reflected what patients wanted the practitioner to know rather than giving insight into what patients wanted to know from practitioners. Interviews revealed that continuity of practitioner was highly valued by patients as offering the benefits of an established relationship and of emotional support beyond that of the clinical encounter. This fostered familiarity not only with their particular medical history, but also their individual personal circumstances, and this encouraged patient participation. In contrast, practitioners (mis)perceived waiting times to have a greater impact on patient satisfaction. However, practitioner interviews also revealed that clinic structure is often outside of the practitioner control and can undermine the possibility of maintaining patient-practitioner continuity. Conclusions: This research enhances understanding of nurse specialist consultation styles in Rheumatology, specifically the value of their socio-emotional communication skills to enhance patient participation

The prevention of progression of arterial disease and diabetes (POPADAD) trial: factorial randomised placebo controlled trial of aspirin and antioxidants in patients with diabetes and asymptomatic peripheral arterial disease

Objective To determine whether aspirin and antioxidant therapy, combined or alone, are more effective than placebo in reducing the development of cardiovascular events in patients with diabetes mellitus and asymptomatic peripheral arterial disease

White paper: Preserving the Integrity of Manoomin in Minnesota

White paper: Preserving the Integrity of Manoomin in Minnesota 2011White paper: Preserving the Integrity of Manoomin in Minnesota 2011Andow, David; Bauer, Theresa; Belcourt, Mark; Bloom, Paul; Child, Brenda; Doerfler, Jill; Eule-Nashoba, Amber; Heidel, Thelma; Kokotovich, Adam; Lodge, Alexandra; LaGarde, Joe; Lorenz, Karl; Mendoza, Louis; Mohl, Emily; Osborne, Jake; Prescott, Kristina; Schultz, Paul; Smith, David; Solarz, Susan; Walker, Rachel. (2011). White paper: Preserving the Integrity of Manoomin in Minnesota. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/220342

Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests

Our understanding of the long-lasting effects of human land use on soil fungal communities in tropical forests is limited. Yet, over 70% of all remaining tropical forests are growing in former agricultural or logged areas. We investigated the relationship among land use history, biotic and abiotic factors, and soil fungal community composition and diversity in a second-growth tropical forest in Puerto Rico. We coupled high-throughput DNA sequencing with tree community and environmental data to determine whether land use history had an effect on soil fungal community descriptors. We also investigated the biotic and abiotic factors that underlie such differences and asked whether the relative importance of biotic (tree diversity, basal tree area, and litterfall biomass) and abiotic (soil type, pH, iron, and total carbon, water flow, and canopy openness) factors in structuring soil fungal communities differed according to land use history. We demonstrated long-lasting effects of land use history on soil fungal communities. At our research site, most of the explained variation in soil fungal composition (R2 = 18.6%), richness (R2 = 11.4%), and evenness (R2 = 10%) was associated with edaphic factors. Areas previously subject to both logging and farming had a soil fungal community with lower beta diversity and greater evenness of fungal operational taxonomic units (OTUs) than areas subject to light logging. Yet, fungal richness was similar between the two areas of historical land use. Together, these results suggest that fungal communities in disturbed areas are more homogeneous and diverse than in areas subject to light logging. Edaphic factors were the most strongly correlated with soil fungal composition, especially in areas subject to light logging, where soils are more heterogenous. High functional tree diversity in areas subject to both logging and farming led to stronger correlations between biotic factors and fungal composition than in areas subject to light logging. In contrast, fungal richness and evenness were more strongly correlated with biotic factors in areas of light logging, suggesting that these metrics might reflect long-term associations in old-growth forests. The large amount of unexplained variance in fungal composition suggests that these communities are structured by both stochastic and niche assemblage processes

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year

Ten-year mortality, disease progression, and treatment-related side effects in men with localised prostate cancer from the ProtecT randomised controlled trial according to treatment received

Background The ProtecT trial reported intention-to-treat analysis of men with localised prostate cancer randomly allocated to active monitoring (AM), radical prostatectomy, and external beam radiotherapy. Objective To report outcomes according to treatment received in men in randomised and treatment choice cohorts. Design, setting, and participants This study focuses on secondary care. Men with clinically localised prostate cancer at one of nine UK centres were invited to participate in the treatment trial comparing AM, radical prostatectomy, and radiotherapy. Intervention Two cohorts included 1643 men who agreed to be randomised and 997 who declined randomisation and chose treatment. Outcome measurements and statistical analysis Analysis was carried out to assess mortality, metastasis and progression and health-related quality of life impacts on urinary, bowel, and sexual function using patient-reported outcome measures. Analysis was based on comparisons between groups defined by treatment received for both randomised and treatment choice cohorts in turn, with pooled estimates of intervention effect obtained using meta-analysis. Differences were estimated with adjustment for known prognostic factors using propensity scores. Results and limitations According to treatment received, more men receiving AM died of PCa (AM 1.85%, surgery 0.67%, radiotherapy 0.73%), whilst this difference remained consistent with chance in the randomised cohort (p = 0.08); stronger evidence was found in the exploratory analyses (randomised plus choice cohort) when AM was compared with the combined radical treatment group (p = 0.003). There was also strong evidence that metastasis (AM 5.6%, surgery 2.4%, radiotherapy 2.7%) and disease progression (AM 20.35%, surgery 5.87%, radiotherapy 6.62%) were more common in the AM group. Compared with AM, there were higher risks of sexual dysfunction (95% at 6 mo) and urinary incontinence (55% at 6 mo) after surgery, and of sexual dysfunction (88% at 6 mo) and bowel dysfunction (5% at 6 mo) after radiotherapy. The key limitations are the potential for bias when comparing groups defined by treatment received and changes in the protocol for AM during the lengthy follow-up required in trials of screen-detected PCa. Conclusions Analyses according to treatment received showed increased rates of disease-related events and lower rates of patient-reported harms in men managed by AM compared with men managed by radical treatment, and stronger evidence of greater PCa mortality in the AM group. Patient summary More than 95 out of every 100 men with low or intermediate risk localised prostate cancer do not die of prostate cancer within 10 yr, irrespective of whether treatment is by means of monitoring, surgery, or radiotherapy. Side effects on sexual and bladder function are better after active monitoring, but the risks of spreading of prostate cancer are more common

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe