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.

Acceptability of psilocybin-assisted group therapy in patients with cancer and major depressive disorder: Qualitative analysis.

BACKGROUND: The present study explored the acceptability of psilocybin-assisted group therapy from the perspective of patients with cancer and depression who participated in a clinical trial assessing the safety and efficacy of this novel intervention. METHODS: Guided by the conceptual framework of acceptability, the authors conducted semi-structured interviews with participants of the psilocybin trial. Data were analyzed using template and thematic analyses. RESULTS: Participants' (n = 28) perspectives on the acceptability of the group and simultaneous sessions was generally positive, both in terms of safety and efficacy: first, the groups contributed to increase participants' sense of safety and preparedness as they were engaging in the therapy; and second, the groups fostered a sense of connection and of belonging, which served to enrich and deepen the meaning of participants' experience, ultimately opening a dimension of self-transcendence and compassion. Other subthemes related to factors influencing the acceptability of the group approach included: 1) the importance of the therapeutic framework, 2) the complementary value of individual sessions, 3) disruptive factors related to the group and/or simultaneous setting, and 4) opportunities and challenges related to group size and how to structure interactions. CONCLUSIONS: This study enhances understanding of what promotes acceptability of the psilocybin-assisted therapy group model for the treatment of MDD in cancer patients. PLAIN LANGUAGE SUMMARY: We conducted exit interviews with participants of a phase 2 trial of psilocybin-assisted therapy (PAT) conducted in a community cancer center, to assess the acceptability of a novel psilocybin delivery model combining simultaneous individual therapy and group sessions. Our findings support the acceptability of this intervention and suggest that in addition to being feasible, it might also enhance participants' perceived safety and efficacy compared to uniquely individual or group delivery models of PAT. Our analysis highlights critical factors conditioning acceptability and suggests new ways PAT may be scaled and integrated into cancer care.

Advance Care Planning and Palliative Care Consultation in Kidney Transplantation.

RATIONALE & OBJECTIVE: Because of the high risk of waitlist mortality and posttransplant complications, kidney transplant (KT) patients may benefit from advance care planning (ACP) and palliative care consultation (PCC). We quantified the prevalence and racial disparities in ACP and PCC among KT candidates and recipients. STUDY DESIGN: Prospective cohort study. SETTING & PARTICIPANTS: 2,575 adult KT candidates and 1,233 adult recipients (2008-2020). EXPOSURE: Race and ethnicity. OUTCOMES: All reports of ACP and PCC were abstracted from chart review. ACP was defined as patient self-report of an advance directive, presence of an advance directive in the medical record, or a documented goals-of-care conversation with a provider. PCC was defined as an ordered referral or a documented palliative care note in the medical record. ANALYTICAL APPROACH: Racial/ethnic disparities in ACP/PCC were estimated using adjusted logistic regression. RESULTS: 21.4% of KT candidates and 34.9% of recipients engaged in ACP. There were racial/ethnic disparities in ACP among KT candidates (White, 24.4%; Black, 19.1%; Hispanic, 15%; other race and ethnicity, 21.1%; P=0.008) and recipients (White, 39.5%; Black, 31.2%; Hispanic, 26.3%; other race and ethnicity, 26.6%; P=0.007). After adjustment, Black KT recipients had a 29% lower likelihood of engaging in ACP (OR, 0.71; 95% CI, 0.55-0.91) than White KT recipients. Among older (aged≥65 years) recipients, those who were Black had a lower likelihood of engaging in ACP, but there was no racial disparity among younger recipients (P=0.020 for interaction). 4.2% of KT candidates and 5.1% of KT recipients engaged in PCC; there were no racial disparities in PCC among KT candidates (White, 5.3%; Black, 3.6%; Hispanic, 2.5%; other race and ethnicity, 2.1%; P=0.13) or recipients (White, 5.5%; Black, 5.6%; Hispanic, 0.0%; other race and ethnicity, 1.3%; P = 0.21). LIMITATIONS: Generalizability may be limited to academic transplant centers. CONCLUSIONS: ACP is not common among KT patients, and minoritized transplant patients are least likely to engage in ACP; PCC is less common. Future efforts should aim to integrate ACP and PCC into the KT process. PLAIN-LANGUAGE SUMMARY: Kidney transplant (KT) candidates and recipients are at elevated risk of morbidity and mortality. They may benefit from completing a document or conversation with their palliative care provider that outlines their future health care wishes, known as advance care planning (ACP), which is a component of palliative care consultation (PCC). We wanted to determine how many KT candidates and recipients have engaged in ACP or PCC and identify potential racial disparities. We found that 21.4% of candidates and 34.9% of recipients engaged in ACP. After adjustment, Black recipients had a 29% lower likelihood of engaging in ACP. We found that 4.2% of KT candidates and 5.1% of KT recipients engaged in PCC, with no racial disparities found in PCC.

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.

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.

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.

Aeromonas salmonicida, causative agent of salmonid furunculosis, isolated from the freshwater parasitic copepod, Salmincola californiensis.

Here, we provide evidence that the freshwater parasitic copepod, Salmincola californiensis, acts as a vector for Aeromonas salmonicida. While investigating the effects of S. californiensis on Chinoook salmon (Oncorhynchus tshawytscha), we tangentially observed that fish infected with the copepod developed furunculosis, caused by A. salmonicida. This occurred despite being reared in pathogen-free well water in a research facility with no prior history of spontaneous infection. We further investigated the possibility of S. californiensis to serve as a vector for the bacterium via detection of fluorescently labelled A. salmonicida inside the egg sacs from copepods in which the fish hosts were experimentally infected with GFP-A449 A. salmonicida. We then evaluated copepod egg sacs that were collected from adult Chinook salmon from a freshwater hatchery with A. salmonicida infections confirmed by either culture or PCR. The bacterium was cultured on tryptic soy agar plates from 75% of the egg sacs, and 61% were positive by PCR. These three separate experiments indicate an alternative tactic of transmission in addition to direct transmission of A. salmonicida in captivity. The copepod may play an important role in transmission of the bacterium when fish are more dispersed, such as in the wild.

Integrating evidence-based communication principles into routine cancer care.

PURPOSE: The global incidence of cancer and available cancer-directed therapy options is increasing rapidly, presenting patients and clinicians with more complex treatment decisions than ever before. Despite the dissemination of evidence-based communication training tools and programs, clinicians cite barriers to employing effective communication in cancer care (e.g., discomfort of sharing serious news, concern about resource constraints to meet stated needs). We present two composite cases with significant communication challenges to guide clinicians through an application of evidence-based approaches to achieve quality communication. METHODS: Composite cases, communication skills blueprint, and visual conceptualization. RESULTS: High-stakes circumstances in each case are described, including end-of-life planning, advanced pediatric illness, strong emotions, and health inequities. Three overarching communication approaches are discussed: (1) content selection and delivery; (2) rapport development; and (3) empathic connection. The key takeaways following each case provide succinct summaries of challenges encountered and approaches used. A communication blueprint from the Memorial Sloan Kettering Cancer Center Communication Skills Training Program and Research Laboratory has been adapted and is comprised of strategies, skills, process tasks, and sample talking points. A visually concise tool - the Communication Blueprint Traffic Circle - illustrates these concepts and demonstrates the iterative, holistic, and agile considerations inherent to effective communication. CONCLUSION: Evidence-based communication is foundational to person-centeredness, associated with improved clinician and patient/caregiver outcomes, and can be integrated throughout routine oncology care. When used by clinicians, evidence-based communication can improve patient and caregiver experiences and assist in ensuring goal-concordant cancer care delivery.

Improving serious illness communication: a qualitative study of clinical culture.

OBJECTIVE: Communication about patients' values, goals, and prognosis in serious illness (serious illness communication) is a cornerstone of person-centered care yet difficult to implement in practice. As part of Serious Illness Care Program implementation in five health systems, we studied the clinical culture-related factors that supported or impeded improvement in serious illness conversations. METHODS: Qualitative analysis of semi-structured interviews of clinical leaders, implementation teams, and frontline champions. RESULTS: We completed 30 interviews across palliative care, oncology, primary care, and hospital medicine. Participants identified four culture-related domains that influenced serious illness communication improvement: (1) clinical paradigms; (2) interprofessional empowerment; (3) perceived conversation impact; (4) practice norms. Changes in clinicians' beliefs, attitudes, and behaviors in these domains supported values and goals conversations, including: shifting paradigms about serious illness communication from 'end-of-life planning' to 'knowing and honoring what matters most to patients;' improvements in psychological safety that empowered advanced practice clinicians, nurses and social workers to take expanded roles; experiencing benefits of earlier values and goals conversations; shifting from avoidant norms to integration norms in which earlier serious illness discussions became part of routine processes. Culture-related inhibitors included: beliefs that conversations are about dying or withdrawing care; attitudes that serious illness communication is the physician's job; discomfort managing emotions; lack of reliable processes. CONCLUSIONS: Aspects of clinical culture, such as paradigms about serious illness communication and inter-professional empowerment, are linked to successful adoption of serious illness communication. Further research is warranted to identify effective strategies to enhance clinical culture and drive clinician practice change.

Application of an eDNA assay for the detection of Pseudoloma neurophilia (Microsporidia) in zebrafish (Danio rerio) facilities.

Environmental DNA (eDNA) water assays are beginning to be implemented for many important pathogens in confined aquaculture systems. Recirculating systems are rapidly being developed for fin fish aquaculture. Zebrafish (Danio rerio) are reared in these systems, and Pseudoloma neurophilia (Microsporidia) represents a serious challenge for zebrafish research facilities. Diagnosis of the pathogen has traditionally used histology or PCR of tissues with lethal sampling. However, with the development of a nonlethal assay to detect P. neurophilia in tank water, facilities will be able to integrate the assay into routine surveillance efforts to couple with their established protocols. Here, we first describe a modified protocol to extract and quantify parasite DNA from the environment for nonlethal detection of P. neurophilia in adult zebrafish populations. Using this modified assay, we then evaluated water samples from a longitudinal experimental infection study, targeting timepoints during initial infection. The parasite was detectable in the water immediately after initial exposure until week 4 post exposure (pe), when the parasite was undetectable until 7 weeks pe. After that time, the parasite was sporadically detected in the water for the 10-month study, likely correlating with the lifecycle of the parasite. Using water samples from the Zebrafish International Resource Center, we also validated the clinical relevance of the assay in a large zebrafish facility. The integration of this assay at ZIRC will significantly compliment surveillance and control efforts for the microsporidian parasite.

Evidence for infection influencing survival of the freshwater copepod Salmincola californiensis, a parasite of Pacific salmon and trout.

OBJECTIVE: We explore apparent infection of Salmincola californiensis arising during investigations involving this lernaeopodid copepod parasitic on Pacific salmon and trout Oncorhynchus spp. METHODS: We noted occasional unusual coloration of adult female copepods collected from the wild. These females were bright blue and pink in contrast to the cream white coloration characteristic of the copepod. We also observed that similar color patterns developed under laboratory settings when copepod eggs were held for hatching. In paired egg cases, we found consistent hatching failure of blue and pink eggs and patterns in apparent disease development that would be consistent with both vertical and horizontal transmission. RESULT: Attempts to identify the cause of the apparent infection using genetic methods and transmission electron microscopy were inconclusive. CONCLUSION: Iridovirus infection was initially suspected, but bacterial infection is also plausible. This apparent reduced hatching success of S. californiensis warrants further exploration as it could reduce local abundances. Given the potential importance of a disease impacting this copepod, a parasite that itself affects endangered and commercially important Pacific salmon and trout, future research would benefit from clarification of the apparent infection through additional sequencing, primer development, visualization, and exploration into specificity and transmission.

Disruption as an opportunity or threat: A qualitative analysis of factors influencing the attitudes of experts in serious illness care toward psychedelic-assisted therapies.

BACKGROUND: Psychedelic-assisted therapies (PAT) are emerging as a promising treatment for psycho-existential distress in patients with serious illness. A recent qualitative analysis of perspectives of 17 experts in serious illness care and/or PAT research identified divergent views on the therapeutic potential and safety of PAT in patients with serious illness. This paper further analyzes the factors that may influence these views. OBJECTIVES: To identify factors underlying the attitudes of experts in serious illness care and/or PAT toward PAT and its potential role in serious illness care. METHODS: Semi-structured interviews of 17 experts in serious illness care and/or PAT from the United States and Canada were analyzed to identify factors cited as influencing their views on PAT. RESULTS: Five factors were identified as influencing experts' attitudes toward PAT: perception of unmet need, knowledge of empirical studies of PAT, personal experience with psychedelics, professional background, and age/generation. In addition, an integrative theme emerged from the analysis, namely PAT's disruptive potential at 4 levels relevant to serious illness care: patient's experience of self, illness, and death; relationships with loved ones and health-care providers; existing clinical models of serious illness care; and societal attitudes toward death. Whether this disruptive potential was viewed as a therapeutic opportunity, or an undue risk, was central in influencing experts' level of support. Experts' perception of this disruptive potential was directly influenced by the 5 identified factors. SIGNIFICANCE OF RESULTS: Points of disruption potentially invoked by PAT in serious illness care highlight important practical and philosophical considerations when working to integrate PAT into serious illness care delivery in a safe and effective way.

Acceptability of a Serious Illness Conversation Guide to Black Americans: Results from a focus group and oncology pilot study.

OBJECTIVES: Serious illness conversations (SICs) can improve the experience and well-being of patients with advanced cancer. A structured Serious Illness Conversation Guide (SICG) has been shown to improve oncology patient outcomes but was developed and tested in a predominantly White population. To help address disparities in advanced cancer care, we aimed to assess the acceptability of the SICG among African Americans with advanced cancer and their clinicians. METHODS: A two-phase study conducted in Charleston, SC, included focus groups to gather perspectives on the SICG in Black Americans and a single-arm pilot study of a revised SICG with surveys and qualitative exit interviews to evaluate patient and clinician perspectives. We used descriptive analysis of survey results and thematic analysis of qualitative data. RESULTS: Community-based and patient focus group participants (N = 20) reported that a simulated conversation using an adapted SICG built connection, promoted control, and fostered consideration of religious faith and family. Black patients with advanced cancer (N = 23) reported that SICG-guided conversations were acceptable, helpful, and promoted conversations with loved ones. Oncologists found conversations feasible to implement and skill-building, and also identified opportunities for training and implementation that could support meeting the needs of their patients with low health literacy. An adapted SICG includes language to assess the strength and affirm the clinician-patient relationship. SIGNIFICANCE OF RESULTS: An adapted structured communication tool to facilitate SIC, the SICG, appears acceptable to Black Americans with advanced cancer and seems feasible for use by oncology clinicians working with this population. Further testing in other marginalized populations may address disparities in advanced cancer care.

Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites.

Poly-N-acetyl-lactosamine (poly-LacNAc) structures are composed of repeating [-Galß(1,4)-GlcNAcß(1,3)-]n glycan extensions. They are found on both N- and O-glycoproteins and glycolipids and play an important role in development, immune function, and human disease. The majority of mammalian poly-LacNAc is synthesized by the alternating iterative action of ß1,3-N-acetylglucosaminyltransferase 2 (B3GNT2) and ß1,4-galactosyltransferases. B3GNT2 is in the largest mammalian glycosyltransferase family, GT31, but little is known about the structure, substrate recognition, or catalysis by family members. Here we report the structures of human B3GNT2 in complex with UDP:Mg2+ and in complex with both UDP:Mg2+ and a glycan acceptor, lacto-N-neotetraose. The B3GNT2 structure conserves the GT-A fold and the DxD motif that coordinates a Mg2+ ion for binding the UDP-GlcNAc sugar donor. The acceptor complex shows interactions with only the terminal Galß(1,4)-GlcNAcß(1,3)- disaccharide unit, which likely explains the specificity for both N- and O-glycan acceptors. Modeling of the UDP-GlcNAc donor supports a direct displacement inverting catalytic mechanism. Comparative structural analysis indicates that nucleotide sugar donors for GT-A fold glycosyltransferases bind in similar positions and conformations without conserving interacting residues, even for enzymes that use the same donor substrate. In contrast, the B3GNT2 acceptor binding site is consistent with prior models suggesting that the evolution of acceptor specificity involves loops inserted into the stable GT-A fold. These observations support the hypothesis that GT-A fold glycosyltransferases employ coevolving donor, acceptor, and catalytic subsite modules as templates to achieve the complex diversity of glycan linkages in biological systems.

Detection of SARS-CoV-2 B.1.351 (Beta) Variant through Wastewater Surveillance before Case Detection in a Community, Oregon, USA.

Genomic surveillance has emerged as a critical monitoring tool during the SARS-CoV-2 pandemic. Wastewater surveillance has the potential to identify and track SARS-CoV-2 variants in the community, including emerging variants. We demonstrate the novel use of multilocus sequence typing to identify SARS-CoV-2 variants in wastewater. Using this technique, we observed the emergence of the B.1.351 (Beta) variant in Linn County, Oregon, USA, in wastewater 12 days before this variant was identified in individual clinical specimens. During the study period, we identified 42 B.1.351 clinical specimens that clustered into 3 phylogenetic clades. Eighteen of the 19 clinical specimens and all wastewater B.1.351 specimens from Linn County clustered into clade 1. Our results provide further evidence of the reliability of wastewater surveillance to report localized SARS-CoV-2 sequence information.

The relationship between dietary trophic level, parasites and the microbiome of Pacific walrus (Odobenus rosmarus divergens).

Arctic species are likely to experience rapid shifts in prey availability under climate change, which may alter their exposure to microbes and parasites. Here, we describe fecal bacterial and macroparasite communities and assess correlations with diet trophic level in Pacific walruses harvested during subsistence hunts by members of the Native Villages of Gambell and Savoonga on St Lawrence Island, Alaska. Fecal bacterial communities were dominated by relatively few taxa, mostly belonging to phyla Fusobacteriota and Firmicutes. Members of parasite-associated phyla Nematoda, Acanthocephala and Platyhelminthes were prevalent in our study population. We hypothesized that high versus low prey trophic level (e.g. fish versus bivalves) would result in different gut bacterial and macroparasite communities. We found that bacterial community structure correlated to diet, with nine clades enriched in walruses consuming higher-trophic-level prey. While no parasite compositional differences were found at the phylum level, the cestode genus Diphyllobothrium was more prevalent and abundant in walruses consuming higher-trophic-level prey, probably because fish are the intermediate hosts for this genus. This study suggests that diet is important for structuring both parasite and microbial communities of this culturally and ecologically important species, with potential implications for population health under climate change.

HiCRep.py: fast comparison of Hi-C contact matrices in Python.

MOTIVATION: Hi-C is the most widely used assay for investigating genome-wide 3D organization of chromatin. When working with Hi-C data, it is often useful to calculate the similarity between contact matrices in order to assess experimental reproducibility or to quantify relationships among Hi-C data from related samples. The HiCRep algorithm has been widely adopted for this task, but the existing R implementation suffers from run time limitations on high-resolution Hi-C data or on large single-cell Hi-C datasets. RESULTS: We introduce a Python implementation of HiCRep and demonstrate that it is much faster and consumes much less memory than the existing R implementation. Furthermore, we give examples of HiCRep's ability to accurately distinguish replicates from non-replicates and to reveal cell type structure among collections of Hi-C data. AVAILABILITY AND IMPLEMENTATION: HiCRep.py and its documentation are available with a GPL license at https://github.com/Noble-Lab/hicrep. The software may be installed automatically using the pip package installer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

"I was not able to keep myself away from tending to her immediate needs": Primary Care Physicians' Perspectives of Serious Illness Conversations at Community Health Centers.

PURPOSE: Seriously ill patients in low-income and minority populations have lower rates of advance care planning. Initiatives that promote serious illness (SI) conversations in community health centers (CHCs) can reach broad, diverse patient populations. This qualitative study explored the experiences of primary care physicians in conducting SI conversations at CHCs in order to understand challenges and needs in this setting. METHODS: An initiative to increase SI conversations was implemented at two CHCs in the Bronx, NY. Eleven participating family physicians who together conducted 37 SI conversations underwent semi-structured in-depth interviews. The 11 interviews were analyzed using inductive thematic analysis. RESULTS: Eight themes emerged: (1) Structured approaches to SI conversations are useful even in longstanding patient-doctor relationships; (2) Discussion of prognosis is meaningful but difficult; (3) Emotional work is humanizing but draining; (4) Poverty and underinsurance are high priorities; (5) Social context affects patient readiness; (6) Communication barriers take multiple forms; (7) Patient characteristics make it "easier" or "harder" to initiate the SI conversation; (8) Time constraints limit the ability to meet multiple patient needs. CONCLUSIONS: Physicians at CHCs identified challenges in SI conversations at personal, interpersonal, organizational, and societal levels. These challenges should be addressed by initiatives that aim to increase SI conversations in primary care, and especially at CHCs.

Asian American Medicare Beneficiaries Disproportionately Receive Invasive Mechanical Ventilation When Hospitalized at the End-of-Life.

BACKGROUND: Asian Americans are the fastest-growing ethnic minority in the USA, but we know little about the end-of-life care for this population. OBJECTIVE: Compare invasive mechanical ventilation (IMV) use between older Asian and White decedents with hospitalization in the last 30 days of life. DESIGN: Population-based retrospective cohort study. PARTICIPANTS: A 20% random sample of 2000-2017 Medicare fee-for-service decedents who were 66 years or older and had a hospitalization in the last 30 days of life. EXPOSURE: White and Asian ethnicity as collected by the Social Security Administration. MAIN MEASURES: We identified IMV using validated procedural codes. We compared IMV use between Asian and White fee-for-service decedents using random-effects logistic regression analysis, adjusting for sociodemographics, admitting diagnosis, comorbidities, and secular trends. KEY RESULTS: From 2000 to 2017, we identified 2.1 million White (54.5% female, 82.4±8.1 mean age) and 28,328 Asian (50.8% female, 82.6±8.1 mean age) Medicare fee-for-service decedents hospitalized in the last 30 days. Compared to White decedents, Asian fee-for-service decedents have an increased adjusted odds ratio (AOR) of 1.42 (95%CI: 1.38-1.47) for IMV. In sub-analyses, Asians' AOR for IMV differed by admitting diagnoses (cancer AOR=1.32, 95%CI: 1.15-1.51; congestive heart failure AOR=1.75, 95%CI: 1.47-2.08; dementia AOR=1.93, 95%CI: 1.70-2.20; and chronic obstructive pulmonary disease AOR=2.25, 95%CI: 1.76-2.89). CONCLUSIONS: Compared to White decedents, Asian Medicare decedents are more likely to receive IMV when hospitalized at the end-of-life, especially among patients with non-cancer admitting diagnoses. Future research to better understand the reasons for these differences and perceived quality of end-of-life care among Asian Americans is urgently needed.

"I think that she would have wanted. . .": Qualitative interviews with bereaved caregivers reveal complexity in measuring goal-concordant care at the end of life.

BACKGROUND: Experts consider goal-concordant care an important healthcare outcome for individuals with serious illness. Despite their relationship to the patient and knowledge about the patient's wishes and values, little is known about bereaved family caregivers' perceptions of how end-of-life care aligns with patient goals and preferences. AIM: To understand caregivers' perceptions about patients' care experiences, the extent to which care was perceived as goal-concordant, and the factors that contextualized the end-of-life care experience. DESIGN: Qualitative interview study employing a semi-structured interview guide based on the National Health and Aging Trends Survey end-of-life planning module. Template analysis was used to identify themes. SETTING/PARTICIPANTS: Nineteen recently bereaved family caregivers of people with serious illness in two academic medical centers in the Northeastern United States. RESULTS: Most caregivers reported goal-concordant care, though many also recalled experiences of goal discordance. Three themes characterized care perceptions and related to perceived quality: communication, relationships and humanistic care, and care transitions. Within communication, caregivers described the importance of clear communication, inadequate prognostic communication, and information gaps that undermined caregiver confidence in decision making. Patient-clinician relationships enriched care and were considered higher-quality when felt to be humanistic. Finally, care transitions impacted goal discordance when marked by logistical barriers, a need to establish relationships with new providers, inadequate information transfer, and poor care coordination. CONCLUSIONS: Bereaved caregivers commonly rated care as goal-concordant while also identifying areas of disappointing and low-quality care. Communication, relationships and humanistic care, and care transitions are modifiable quality improvement targets for patients with advanced cancer.