Accounting for Digestion Enzyme Bias in Casanovo.

A key parameter of any bottom-up proteomics mass spectrometry experiment is the identity of the enzyme that is used to digest proteins in the sample into peptides. The Casanovo de novo sequencing model was trained using data that was generated with trypsin digestion; consequently, the model prefers to predict peptides that end with the amino acids "K" or "R". This bias is desirable when Casanovo is used to analyze data that was also generated using trypsin but can be problematic if the data was generated using some other digestion enzyme. In this work, we modify Casanovo to take as input the identity of the digestion enzyme alongside each observed spectrum. We then train Casanovo with data generated by using several different enzymes, and we demonstrate that the resulting model successfully learns to capture enzyme-specific behavior. However, we find, surprisingly, that this new model does not yield a significant improvement in sequencing accuracy relative to a model trained without enzyme information but using the same training set. This observation may have important implications for future attempts to make use of experimental metadata in de novo sequencing models.

Race Dialogues and Potential Application in Clinical Environments: A Scoping Review.

BACKGROUND: Race dialogues, conversations about race and racism among individuals holding different racial identities, have been proposed as one component of addressing racism in medicine and improving the experience of racially minoritized patients. Drawing on work from several fields, we aimed to assess the scope of the literature on race dialogues and to describe potential benefits, best practices, and challenges of conducting such dialogues. Ultimately, our goal was to explore the potential role of race dialogues in medical education and clinical practice. METHODS: Our scoping review included articles published prior to June 2, 2022, in the biomedicine, psychology, nursing and allied health, and education literatures. Ultimately, 54 articles were included in analysis, all of which pertained to conversations about race occurring between adults possessing different racial identities. We engaged in an interactive group process to identify key takeaways from each article and synthesize cross-cutting themes. RESULTS: Emergent themes reflected the processes of preparing, leading, and following up race dialogues. Preparing required significant personal introspection, logistical organization, and intentional framing of the conversation. Leading safe and successful race dialogues necessitated trauma-informed practices, addressing microaggressions as they arose, welcoming participation and emotions, and centering the experience of individuals with minoritized identities. Longitudinal experiences and efforts to evaluate the quality of race dialogues were crucial to ensuring meaningful impact. DISCUSSION: Supporting race dialogues within medicine has the potential to promote a more inclusive and justice-oriented workforce, strengthen relationships amongst colleagues, and improve care for patients with racially minoritized identities. Potential levers for supporting race dialogues include high-quality racial justice curricula at every level of medical education and valuation of racial consciousness in admissions and hiring processes. All efforts to support race dialogues must center and uplift those with racially minoritized identities.

Review of Pseudoloma neurophilia (Microsporidia): A common neural parasite of laboratory zebrafish (Danio rerio).

Zebrafish (Danio rerio) is now the second most used animal model in biomedical research. As with other vertebrate models, underlying diseases and infections often impact research. Beyond mortality and morbidity, these conditions can compromise research end points by producing nonprotocol induced variation within experiments. Pseudoloma neurophilia, a microsporidium that targets the central nervous system, is the most frequently diagnosed pathogen in zebrafish facilities. The parasite undergoes direct, horizontal transmission within populations, and is also maternally transmitted with spores in ovarian fluid and occasionally within eggs. This transmission explains the wide distribution among research laboratories as new lines are generally introduced as embryos. The infection is chronic, and fish apparently never recover following the initial infection. However, most fish do not exhibit outward clinical signs. Histologically, the parasite occurs as aggregates of spores throughout the midbrain and spinal cord and extends to nerve roots. It often elicits meninxitis, myositis, and myodegeneration when it infects the muscle. There are currently no described therapies for the parasite, thus the infection is best avoided by screening with PCR-based tests and removal of infected fish from a facility. Examples of research impacts include reduced fecundity, behavioral changes, transcriptome alterations, and autofluorescent lesions.

A Comparison of Palliative Care Delivery between Ethnically Chinese and Non-Chinese Canadians in the Last Year of Life.

BACKGROUND: Ethnically Chinese adults in Canada and the United States face multiple barriers in accessing equitable, culturally respectful care at the end-of-life. Palliative care (PC) is committed to supporting patients and families in achieving goal-concordant, high-quality serious illness care. Yet, current PC delivery may be culturally misaligned. Therefore, understanding ethnically Chinese patients' use of palliative care may uncover modifiable factors to sustained inequities at the end-of-life. OBJECTIVE: To compare the use and delivery of PC in the last year of life between ethnically Chinese and non-Chinese adults. DESIGN: Population-based cohort study. PARTICIPANTS: All Ontario adults who died between January 1st, 2012, and October 31st, 2022, in Ontario, Canada. EXPOSURES: Chinese ethnicity. MAIN MEASURES: Elements of physician-delivered PC, including model of care (generalist; specialist; mixed), timing and location of initiation, and type of palliative care physician at initial consultation. KEY RESULTS: The final study cohort included 527,700 non-Chinese (50.8% female, 77.9 ± 13.0 mean age, 13.0% rural residence) and 13,587 ethnically Chinese (50.8% female, 79.2 ± 13.6 mean age, 0.6% rural residence) adults. Chinese ethnicity was associated with higher likelihoods of using specialist (adjusted odds ratio [aOR] 1.53, 95%CI 1.46-1.60) and mixed (aOR 1.32, 95%CI 1.26-1.38) over generalist models of PC, compared to non-Chinese patients. Chinese ethnicity was also associated with a higher likelihood of PC initiation in the last 30 days of life (aOR 1.07, 95%CI 1.03-1.11), in the hospital setting (aOR 1.24, 95%CI 1.18-1.30), and by specialist PC physicians (aOR 1.33, 95%CI 1.28-1.38). CONCLUSIONS: Chinese ethnicity was associated with a higher likelihood of mixed and specialist models of PC delivery in the last year of life compared to adults who were non-Chinese. These observed differences may be due to later initiation of PC in hospital settings, and potential differences in unmeasured needs that suggest opportunities to initiate early, community-based PC to support ethnically Chinese patients with serious illness.

A learned score function improves the power of mass spectrometry database search.

MOTIVATION: One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide sequence that was responsible for generating the spectrum. Two primary classes of methods are used to solve this problem: database search and de novo peptide sequencing. State-of-the-art methods for de novo sequencing use machine learning methods, whereas most database search engines use hand-designed score functions to evaluate the quality of a match between an observed spectrum and a candidate peptide from the database. We hypothesized that machine learning models for de novo sequencing implicitly learn a score function that captures the relationship between peptides and spectra, and thus may be re-purposed as a score function for database search. Because this score function is trained from massive amounts of mass spectrometry data, it could potentially outperform existing, hand-designed database search tools. RESULTS: To test this hypothesis, we re-engineered Casanovo, which has been shown to provide state-of-the-art de novo sequencing capabilities, to assign scores to given peptide-spectrum pairs. We then evaluated the statistical power of this Casanovo score function, Casanovo-DB, to detect peptides on a benchmark of three mass spectrometry runs from three different species. In addition, we show that re-scoring with the Percolator post-processor benefits Casanovo-DB more than other score functions, further increasing the number of detected peptides.

Palliative Care for Patients With Cancer: ASCO Guideline Update.

PURPOSE: To provide evidence-based guidance to oncology clinicians, patients, nonprofessional caregivers, and palliative care clinicians to update the 2016 ASCO guideline on the integration of palliative care into standard oncology for all patients diagnosed with cancer. METHODS: ASCO convened an Expert Panel of medical, radiation, hematology-oncology, oncology nursing, palliative care, social work, ethics, advocacy, and psycho-oncology experts. The Panel conducted a literature search, including systematic reviews, meta-analyses, and randomized controlled trials published from 2015-2023. Outcomes of interest included quality of life (QOL), patient satisfaction, physical and psychological symptoms, survival, and caregiver burden. Expert Panel members used available evidence and informal consensus to develop evidence-based guideline recommendations. RESULTS: The literature search identified 52 relevant studies to inform the evidence base for this guideline. RECOMMENDATIONS: Evidence-based recommendations address the integration of palliative care in oncology. Oncology clinicians should refer patients with advanced solid tumors and hematologic malignancies to specialized interdisciplinary palliative care teams that provide outpatient and inpatient care beginning early in the course of the disease, alongside active treatment of their cancer. For patients with cancer with unaddressed physical, psychosocial, or spiritual distress, cancer care programs should provide dedicated specialist palliative care services complementing existing or emerging supportive care interventions. Oncology clinicians from across the interdisciplinary cancer care team may refer the caregivers (eg, family, chosen family, and friends) of patients with cancer to palliative care teams for additional support. The Expert Panel suggests early palliative care involvement, especially for patients with uncontrolled symptoms and QOL concerns. Clinicians caring for patients with solid tumors on phase I cancer trials may also refer them to specialist palliative care.Additional information is available at www.asco.org/supportive-care-guidelines.

Implementing the Serious Illness Care Program in Safety Net Health Systems: A Qualitative Study.

CONTEXT: Interventions to improve the quality of care for people affected by serious illness commonly fail to reach patients from marginalized and underserved communities, which include those characterized by racialized or indigenous identity, sexual and gender minority status, and rural living. Interventions to improve care through serious illness conversations have demonstrated benefit, but little is known about their implementation in health systems that predominantly serve these patient groups. OBJECTIVES: The study aimed to understand factors influencing implementation of a serious illness communication-focused intervention-the Serious Illness Care Program in health systems who primarily provide care to marginalized and underserved communities. METHODS: Qualitative interviews (16) and focus groups (3) were conducted with 19 interdisciplinary team members from six geographically diverse U.S. healthcare systems. Using a template analysis approach, investigators coded data inductively and deductively to identify themes. RESULTS: Three themes emerged: patient factors, intervention elements, and health system contextual factors. Participants highlighted mission-driven efforts, creativity, interprofessional practice, and trainees as enablers of success. They identified weaknesses in the intervention's communication tool-the Serious Illness Conversation Guide as barriers to implementation of conversations. Resource constraints, socio-economic vulnerability, and mistrust in the health system were seen as additional barriers. CONCLUSIONS: Health systems that provide care to underserved and marginalized communities face unique challenges implementing the Serious Illness Care Program. They also possess assets, some unique to these settings, that support program adoption. Findings suggest that implementation of similar programs in low-resource healthcare settings may help address unmet needs among marginalized populations.