Shortcut citations in the methods section: Frequency, problems, and strategies for responsible reuse.

Methods sections are often missing essential details. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used 3 approaches to examine shortcut citation use in neuroscience, biology, and psychiatry. First, we assessed current practices in more than 750 papers. More than 90% of papers used shortcut citations. Other common reasons for using citations in the methods included giving credit or specifying what was used (who or what citation) and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, they can also deprive readers of essential methodological details. Problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and shortcut citation chains. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report previously described methods. We propose that methodological shortcut citations should meet 3 criteria; cited resources should provide (1) a detailed description of (2) the method used by the citing authors', and (3) be open access. Resources that do not meet these criteria should be cited to give credit, but not as shortcut citations. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting.

IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques.

The regulation of inflammatory responses and pulmonary disease during SARS-CoV-2 infection is incompletely understood. Here we examine the roles of the prototypic pro- and anti-inflammatory cytokines IFNγ and IL-10 using the rhesus macaque model of mild COVID-19. We find that IFNγ drives the development of 18fluorodeoxyglucose (FDG)-avid lesions in the lungs as measured by PET/CT imaging but is not required for suppression of viral replication. In contrast, IL-10 limits the duration of acute pulmonary lesions, serum markers of inflammation and the magnitude of virus-specific T cell expansion but does not impair viral clearance. We also show that IL-10 induces the subsequent differentiation of virus-specific effector T cells into CD69+CD103+ tissue resident memory cells (Trm) in the airways and maintains Trm cells in nasal mucosal surfaces, highlighting an unexpected role for IL-10 in promoting airway memory T cells during SARS-CoV-2 infection of macaques.

Ceramide as an endothelial cell surface receptor and a lung-specific lipid vascular target for circulating ligands.

The vascular endothelium from individual organs is functionally specialized, and it displays a unique set of accessible molecular targets. These serve as endothelial cell receptors to affinity ligands. To date, all identified vascular receptors have been proteins. Here, we show that an endothelial lung-homing peptide (CGSPGWVRC) interacts with C16-ceramide, a bioactive sphingolipid that mediates several biological functions. Upon binding to cell surfaces, CGSPGWVRC triggers ceramide-rich platform formation, activates acid sphingomyelinase and ceramide production, without the associated downstream apoptotic signaling. We also show that the lung selectivity of CGSPGWVRC homing peptide is dependent on ceramide production in vivo. Finally, we demonstrate two potential applications for this lipid vascular targeting system: i) as a bioinorganic hydrogel for pulmonary imaging and ii) as a ligand-directed lung immunization tool against COVID-19. Thus, C16-ceramide is a unique example of a lipid-based receptor system in the lung vascular endothelium targeted in vivo by circulating ligands such as CGSPGWVRC.

Blind spots on western blots: Assessment of common problems in western blot figures and methods reporting with recommendations to improve them.

Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader's ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n = 151) and cell biology (n = 400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps, and antibody labeling protocol. Important antibody identifiers like company or supplier, catalog number, or RRID were omitted frequently for primary antibodies and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers, and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish, and an antibody reporting template.

Recommendations for empowering early career researchers to improve research culture and practice.

Early career researchers (ECRs) are important stakeholders leading efforts to catalyze systemic change in research culture and practice. Here, we summarize the outputs from a virtual unconventional conference (unconference), which brought together 54 invited experts from 20 countries with extensive experience in ECR initiatives designed to improve the culture and practice of science. Together, we drafted 2 sets of recommendations for (1) ECRs directly involved in initiatives or activities to change research culture and practice; and (2) stakeholders who wish to support ECRs in these efforts. Importantly, these points apply to ECRs working to promote change on a systemic level, not only those improving aspects of their own work. In both sets of recommendations, we underline the importance of incentivizing and providing time and resources for systems-level science improvement activities, including ECRs in organizational decision-making processes, and working to dismantle structural barriers to participation for marginalized groups. We further highlight obstacles that ECRs face when working to promote reform, as well as proposed solutions and examples of current best practices. The abstract and recommendations for stakeholders are available in Dutch, German, Greek (abstract only), Italian, Japanese, Polish, Portuguese, Spanish, and Serbian.

Chatting Beyond ChatGPT: Advancing Equity Through AI-Driven Language Interpretation.

Medical interpretation is an underutilized resource, despite its legal mandate and proven efficacy in improving health outcomes for populations with low English proficiency. This disconnect can often be attributed to the costs and wait-times associated with traditional means of interpretation, making the service inaccessible and burdensome. Technology has improved access to translation through phone and video interpretation; with the acceleration of artificial intelligence (AI) large language models, we have an opportunity to further improve interpreter access through real-time, automated translation. The impetus to utilize this burgeoning tool for improved health equity must be combined with a critical view of the safety, privacy, and clinical decision-making risks involved. Physicians must be active participants and collaborators in both the mobilization of AI tools to improve clinical care and the development of regulations to mitigate harm.

Incorporating Anti-racist Principles Throughout the Research Lifecycle: A Position Statement from the Society of General Internal Medicine (SGIM).

Biomedical research has advanced medicine but also contributed to widening racial and ethnic health inequities. Despite a growing acknowledgment of the need to incorporate anti-racist objectives into research, there remains a need for practical guidance for recognizing and addressing the influence of ingrained practices perpetuating racial harms, particularly for general internists. Through a review of the literature, and informed by the Research Lifecycle Framework, this position statement from the Society of General Internal Medicine presents a conceptual framework suggesting multi-level systemic changes and strategies for researchers to incorporate an anti-racist perspective throughout the research lifecycle. It begins with a clear assertion that race and ethnicity are socio-political constructs that have important consequences on health and health disparities through various forms of racism. Recommendations include leveraging a comprehensive approach to integrate anti-racist principles and acknowledging that racism, not race, drives health inequities. Individual researchers must acknowledge systemic racism's impact on health, engage in self-education to mitigate biases, hire diverse teams, and include historically excluded communities in research. Institutions must provide clear guidelines on the use of race and ethnicity in research, reject stigmatizing language, and invest in systemic commitments to diversity, equity, and anti-racism. National organizations must call for race-conscious research standards and training, and create measures to ensure accountability, establishing standards for race-conscious research for research funding. This position statement emphasizes our collective responsibility to combat systemic racism in research, and urges a transformative shift toward anti-racist practices throughout the research cycle.

How Are We Teaching Advocacy? A National Survey of Internal Medicine Residency Program Directors.

BACKGROUND: Although internal medicine (IM) physicians accept public advocacy as a professional responsibility, there is little evidence that IM training programs teach advocacy skills. The prevalence and characteristics of public advocacy curricula in US IM residency programs are unknown. OBJECTIVES: To describe the prevalence and characteristics of curricula in US IM residencies addressing public advocacy for communities and populations; to describe barriers to the provision of such curricula. DESIGN: Nationally representative, web-based, cross-sectional survey of IM residency program directors with membership in an academic professional association. PARTICIPANTS: A total of 276 IM residency program directors (61%) responded between August and December 2022. MAIN MEASUREMENTS: Percentage of US IM residency programs that teach advocacy curricula; characteristics of advocacy curricula; perceptions of barriers to teaching advocacy. KEY RESULTS: More than half of respondents reported that their programs offer no advocacy curricula (148/276, 53.6%). Ninety-five programs (95/276, 34.4%) reported required advocacy curricula; 33 programs (33/276, 12%) provided curricula as elective only. The content, structure, and teaching methods of advocacy curricula in IM programs were heterogeneous; experiential learning in required curricula was low (23/95, 24.2%) compared to that in elective curricula (51/65, 78.5%). The most highly reported barriers to implementing or improving upon advocacy curricula (multiple responses allowed) were lack of faculty expertise in advocacy (200/276, 72%), inadequate faculty time (190/276, 69%), and limited curricular flexibility (148/276, 54%). CONCLUSION: Over half of US IM residency programs offer no formal training in public advocacy skills and many reported lack of faculty expertise in public advocacy as a barrier. These findings suggest many IM residents are not taught how to advocate for communities and populations. Further, less than one-quarter of required curricula in public advocacy involves experiential learning.

Learning from the past to develop data analysis curricula for the future.

Problems with statistical analyses and the shift toward big data have prompted many researchers to call for improvements in statistics education. A recent study in PLOS Biology assesses changes in the use of data analysis techniques over time to determine which skills young scientists might need.

Training early career researchers to use meta-research to improve science: A participant-guided "learn by doing" approach.

Meta-research, or the science of science, is a powerful technique that scientists can use to improve science, however most scientists are unaware that meta-research exists and courses are rare. This initiative demonstrates the feasibility of a participant-guided "learn by doing" approach, in which a multidisciplinary, global team of early career researchers learned meta-research skills by working together to design, conduct and publish a meta-research study.

Creating clear and informative image-based figures for scientific publications.

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

Ten simple rules for implementing open and reproducible research practices after attending a training course.

Open, reproducible, and replicable research practices are a fundamental part of science. Training is often organized on a grassroots level, offered by early career researchers, for early career researchers. Buffet style courses that cover many topics can inspire participants to try new things; however, they can also be overwhelming. Participants who want to implement new practices may not know where to start once they return to their research team. We describe ten simple rules to guide participants of relevant training courses in implementing robust research practices in their own projects, once they return to their research group. This includes (1) prioritizing and planning which practices to implement, which involves obtaining support and convincing others involved in the research project of the added value of implementing new practices; (2) managing problems that arise during implementation; and (3) making reproducible research and open science practices an integral part of a future research career. We also outline strategies that course organizers can use to prepare participants for implementation and support them during this process.

WHS guidelines for the treatment of pressure ulcers-2023 update.

The major populations at risk for developing pressure ulcers are older adults who have multiple risk factors that increase their vulnerability, people who are critically ill and those with spinal cord injury/disease. The reported prevalence of pressure ulcers in the United States is 2.5 million. However, this estimate is derived from acute care facilities and does not include people who are living at home or in nursing facilities. Despite the implementation of hospital and facility-based preventive measures, the incidence of pressure ulcers has not decreased in decades. In addition to the burden of pain, infection and death, it is estimated that hospital-acquired pressure ulcers cost the health system $26.8 billion annually with over 50% of the cost attributed to treating Stage 3 and 4 pressure injuries. Thus, it is critical to examine the literature and develop guidelines that will improve the outcomes of this complex and costly condition. This guideline update is a compendium of the best available evidence for the treatment of Pressure Ulcers published since the last update in 2015 and includes a new section based on changing demographics entitled 'Palliative wound care for seriously ill patients with pressure ulcers'. The overall goal of the Wound Healing Society Guideline project is to present clear, concise and commercial free guidelines that clinicians can use to guide care, that researchers can use to develop studies that will improve treatment and that both clinicians and researchers can use to understand the gaps in our knowledge base.

How to Create a Diversity, Equity, and Inclusion Curriculum: More Than Checking a Box.

We are beginning to accept and address the role that medicine as an institution played in legitimizing scientific racism and creating structural barriers to health equity. There is a call for greater emphasis in medical education on explaining our role in perpetuating health inequities and educating learners on how bias and racism lead to poor health outcomes for historically marginalized communities. Diversity, equity, and inclusion (DEI; also referred to as EDI) and antiracism are key parts of patient care and medical education as they empower health professionals to be advocates for their patients, leading to better health care outcomes and more culturally and socially humble health care professionals. The Liaison Committee on Medical Education has set forth standards to include structural competency and other equity principles in the medical curriculum, but medical schools are still struggling with how to specifically do so. Here, we highlight a stepwise approach to systematically developing and implementing medical educational curriculum content with a DEI and antiracism lens. This article serves as a blueprint to prepare institution leadership, medical faculty, staff, and learners in how to effectively begin or scale up their current DEI and antiracism curricular efforts.

Disrupted in schizophrenia 1 regulates neuronal progenitor proliferation via modulation of GSK3beta/beta-catenin signaling.

The Disrupted in Schizophrenia 1 (DISC1) gene is disrupted by a balanced chromosomal translocation (1; 11) (q42; q14.3) in a Scottish family with a high incidence of major depression, schizophrenia, and bipolar disorder. Subsequent studies provided indications that DISC1 plays a role in brain development. Here, we demonstrate that suppression of DISC1 expression reduces neural progenitor proliferation, leading to premature cell cycle exit and differentiation. Several lines of evidence suggest that DISC1 mediates this function by regulating GSK3beta. First, DISC1 inhibits GSK3beta activity through direct physical interaction, which reduces beta-catenin phosphorylation and stabilizes beta-catenin. Importantly, expression of stabilized beta-catenin overrides the impairment of progenitor proliferation caused by DISC1 loss of function. Furthermore, GSK3 inhibitors normalize progenitor proliferation and behavioral defects caused by DISC1 loss of function. Together, these results implicate DISC1 in GSK3beta/beta-catenin signaling pathways and provide a framework for understanding how alterations in this pathway may contribute to the etiology of psychiatric disorders.

Prehabilitation in radiation therapy: a scoping review.

PURPOSE/OBJECTIVES: Radiation therapy (RT) is a central component of cancer treatment with survival and long-term quality-of-life benefits across a spectrum of oncologic diagnoses. However, RT has been associated with varying levels of fatigue, pain, weight loss, and changes in mental health both during and post-treatment. Prehabilitation aims to optimize health prior to anti-neoplastic therapy in order to reduce side effects, increase adherence to treatment, expedite post-treatment recovery, and improve long-term outcomes. Though prehabilitation has been studied in those undergoing cancer-related surgery, literature on prehabilitation in individuals undergoing RT has not been comprehensively explored. Thus, this scoping review aims to summarize the existing literature focused on prehabilitation interventions for patients receiving RT. MATERIALS/METHODS: The PRISMA-ScR checklist for conducting scoping reviews was adopted to identify and evaluate studies investigating the efficacy of prehabilitation before and during RT for cancer over the past 21 years (10/2002-10/2022). A search of prehabilitation and RT was performed to identify studies investigating prehabilitation interventions in adult cancer patients undergoing RT. RESULTS: A total of 30 articles met inclusion criteria, yielding 3657 total participants. Eighteen (60%) studies were randomized controlled trials (RCTs) with sample sizes ranging from 21 to 221. The most commonly studied populations were patients with head and neck cancer, followed by rectal, breast, and lung cancer. A majority (80%) of studies evaluated one prehabilitation intervention (i.e., unimodal). Targeted physical exercises were the most common intervention, followed by general physical exercises and technology/apps. Adherence/feasibility was the most common primary outcome, representing 30% of studies. All studies reported data on sex, and 5 (17%) reported data on race and/or ethnicity. CONCLUSIONS: Prehabilitation interventions have been successfully implemented in patients with cancer undergoing surgical treatment. Based on limited current literature, prehabilitation appears to have a promising effect in reducing morbidity in adult cancer patients requiring RT. Though our review identified many RCTs, they were frequently small sample trials with primary outcomes focused on feasibility, rather than functional status or quality of life. Thus, there is a need for adequately powered, randomized controlled intervention trials to investigate the efficacy of prehabilitation and maximize the treatment outcomes for patients undergoing RT.

CRISPR Immunological Memory Requires a Host Factor for Specificity.

Bacteria and archaea employ adaptive immunity against foreign genetic elements using CRISPR-Cas systems. To generate immunological memory, the Cas1-Cas2 protein complex captures 30-40 base pair segments of foreign DNA and catalyzes their integration into the host genome as unique spacer sequences. Although spacers are inserted strictly at the A-T-rich leader end of CRISPR loci in vivo, the molecular mechanism of leader-specific spacer integration remains poorly understood. Here we show that the E. coli integration host factor (IHF) protein is required for spacer acquisition in vivo and for integration into linear DNA in vitro. IHF binds to the leader sequence and induces a sharp DNA bend, allowing the Cas1-Cas2 integrase to catalyze the first integration reaction at the leader-repeat border. Together, these results reveal that Cas1-Cas2-mediated spacer integration requires IHF-induced target DNA bending and explain the elusive role of CRISPR leader sequences during spacer acquisition.

The impact of peritoneal dialysis on oxypurinol and urate elimination in people with gout.

Gout affects 15%-30% of individuals with advanced kidney disease. Allopurinol which is rapidly and extensively metabolised to an active metabolite, oxypurinol, is the most commonly prescribed urate-lowering therapy. Oxypurinol is almost entirely eliminated by the kidneys (>95%) and has an elimination half-life of 18-30 h in those with normal kidney function. However, oxypurinol pharmacokinetics are poorly understood in individuals with kidney failure on peritoneal dialysis. This study characterised the elimination of oxypurinol and urate in people with gout receiving peritoneal dialysis. Oxypurinol steady-state oral clearance (CL/F), elimination half-life as well as kidney (CLk) and peritoneal (CLpd) clearances for oxypurinol and urate were calculated from the plasma, urine and dialysate concentration data for each individual. Our results demonstrate that oxypurinol and urate are removed by peritoneal dialysis, accounting for more than 50% of oxypurinol and urate clearances. An allopurinol dose about 50%-60% lower than the usual dose used for a patient with normal kidney function will provide adequate urate-lowering therapy.

Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain.

Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursued. Engineered filamentous bacteriophage (phage) particles have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans. Herein we report the development and initial evaluation of two targeted phage-based vaccination approaches against SARS-CoV-2: dual ligand peptide-targeted phage and adeno-associated virus/phage (AAVP) particles. For peptide-targeted phage, we performed structure-guided antigen design to select six solvent-exposed epitopes of the SARS-CoV-2 spike (S) protein. One of these epitopes displayed on the major capsid protein pVIII of phage induced a specific and sustained humoral response when injected in mice. These phage were further engineered to simultaneously display the peptide CAKSMGDIVC on the minor capsid protein pIII to enable their transport from the lung epithelium into the systemic circulation. Aerosolization of these "dual-display" phage into the lungs of mice generated a systemic and specific antibody response. In the second approach, targeted AAVP particles were engineered to deliver the entire S protein gene under the control of a constitutive CMV promoter. This induced tissue-specific transgene expression, stimulating a systemic S protein-specific antibody response in mice. With these proof-of-concept preclinical experiments, we show that both targeted phage- and AAVP-based particles serve as robust yet versatile platforms that can promptly yield COVID-19 vaccine prototypes for translational development.

Reduced length of stay after implementation of a clinical pathway following repair of ventricular septal defect.

BACKGROUND: There is variation in care and hospital length of stay following surgical repair of ventricular septal defects. The use of clinical pathways in a variety of paediatric care settings has been shown to reduce practice variability and overall length of stay without increasing the rate of adverse events. METHODS: A clinical pathway was created and used to guide care following surgical repair of ventricular septal defects. A retrospective review was done to compare patients two years prior and three years after the pathway was implemented. RESULTS: There were 23 pre-pathway patients and 25 pathway patients. Demographic characteristics were similar between groups. Univariate analysis demonstrated a significantly shorter time to initiation of enteral intake in the pathway patients (median time to first enteral intake after cardiac ICU admission was 360 minutes in pre-pathway patients and 180 minutes in pathway patients, p < 0.01). Multivariate regression analyses demonstrated that the pathway use was independently associated with a decrease in time to first enteral intake (-203 minutes), hospital length of stay (-23.1 hours), and cardiac ICU length of stay (-20.5 hours). No adverse events were associated with the use of the pathway, including mortality, reintubation rate, acute kidney injury, increased bleeding from chest tube, or readmissions. CONCLUSIONS: The use of the clinical pathway improved time to initiation of enteral intake and decreased length of hospital stay. Surgery-specific pathways may decrease variability in care while also improving quality metrics.