Data Harmonization for a Molecularly Driven Health System.

Data commons have emerged as the best current method for enabling data aggregation across multiple projects and multiple data sources. Good data harmonization techniques are critical to maintain quality of data within a data commons, as well as to allow future meta-analysis across different data commons. We present some of the current best practices for data harmonization.

Earliest known human burial in Africa.

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1-3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1-6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya7,8. Recent excavations have revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the pit was deliberately excavated. Taphonomical evidence, such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction, support the in-place decomposition of the fresh body. The presence of little or no displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth), making the PYS finding the oldest known human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to Homo sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual assembly of modern traits during the emergence of our species. The PYS burial sheds light on how MSA populations interacted with the dead.

Cell line authentication: a necessity for reproducible biomedical research.

Immortalized or continuous cell lines are invaluable tools in basic and preclinical research. However, the widespread use of misidentified cell lines is a serious threat to scientific reproducibility. Based on the experiences of mandatory cell line authentication at the International Journal of Cancer (IJC), we provide an overview of the issues pertinent to misidentified cell lines and discuss available solutions. We also summarize the lessons learned, revealing that at least 5% of the human cell lines used in manuscripts considered for peer review are misidentified. About 4% of the considered manuscripts are rejected for severe cell line problems, and most are subsequently published in other journals. In order to diminish such malpractice and its consequences for the scientific record, we postulate that strict multi-layered quality control is essential. Besides journals and publishers, we encourage scientists, research institutions, and funders to take action on the matter and revise their respective policies. Hence, we provide concrete recommendations on introducing regular authentication schemes and staff training, and discuss future steps for enhancing good cell culture practices.

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics.

Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.

Artifacts and biases of the reverse transcription reaction in RNA sequencing.

RNA sequencing has spurred a significant number of research areas in recent years. Most protocols rely on synthesizing a more stable complementary DNA (cDNA) copy of the RNA molecule during the reverse transcription reaction. The resulting cDNA pool is often wrongfully assumed to be quantitatively and molecularly similar to the original RNA input. Sadly, biases and artifacts confound the resulting cDNA mixture. These issues are often overlooked or ignored in the literature by those that rely on the reverse transcription process. In this review, we confront the reader with intra- and intersample biases and artifacts caused by the reverse transcription reaction during RNA sequencing experiments. To fight the reader's despair, we also provide solutions to most issues and inform on good RNA sequencing practices. We hope the reader can use this review to their advantage, thereby contributing to scientifically sound RNA studies.

What is the role of current mass spectrometry in pharmaceutical analysis?

The role of mass spectrometry (MS) has become more important in most application domains in recent years. Pharmaceutical analysis is specific due to its stringent regulation procedures, the need for good laboratory/manufacturing practices, and a large number of routine quality control analyses to be carried out. The role of MS is, therefore, very different throughout the whole drug development cycle. While it dominates within the drug discovery and development phase, in routine quality control, the role of MS is minor and indispensable only for selected applications. Moreover, its role is very different in the case of analysis of small molecule pharmaceuticals and biopharmaceuticals. Our review explains the role of current MS in the analysis of both small-molecule chemical drugs and biopharmaceuticals. Important features of MS-based technologies being implemented, method requirements, and related challenges are discussed. The differences in analytical procedures for small molecule pharmaceuticals and biopharmaceuticals are pointed out. While a single method or a small set of methods is usually sufficient for quality control in the case of small molecule pharmaceuticals and MS is often not indispensable, a large panel of methods including extensive use of MS must be used for quality control of biopharmaceuticals. Finally, expected development and future trends are outlined.

Banking on virus-specific T cells to fulfill the need for off-the-shelf cell therapies.

Adoptively transferred virus-specific T cells (VSTs) have shown remarkable safety and efficacy for the treatment of virus-associated diseases and malignancies in hematopoietic stem cell transplant (HSCT) recipients, for whom VSTs are derived from the HSCT donor. Autologous VSTs have also shown promise for the treatment of virus-driven malignancies outside the HSCT setting. In both cases, VSTs are manufactured as patient-specific products, and the time required for procurement, manufacture, and release testing precludes their use in acutely ill patients. Further, Good Manufacturing Practices-compliant products are expensive, and failures are common in virus-naive HSCT donors and patient-derived VSTs that are rendered anergic by immunosuppressive tumors. Hence, highly characterized, banked VSTs (B-VSTs) that can be used for multiple unrelated recipients are highly desirable. The major challenges facing B-VSTs result from the inevitable mismatches in the highly polymorphic and immunogenic human leukocyte antigens (HLA) that present internally processed antigens to the T-cell receptor, leading to the requirement for partial HLA matching between the B-VST and recipient. HLA mismatches lead to rapid rejection of allogeneic T-cell products and graft-versus-host disease induced by alloreactive T cells in the infusion product. Here, we summarize the clinical outcomes to date of trials of B-VSTs used for the treatment of viral infections and malignancies and their potential as a platform for chimeric antigen receptors targeting nonviral tumors. We will highlight the properties of VSTs that make them attractive off-the-shelf cell therapies, as well as the challenges that must be overcome before they can become mainstream.

Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club.

Despite advances and social progress, the exclusion of diverse groups in academia, especially science, technology, engineering, and mathematics (STEM) fields, across the US and Europe persists, resulting in the underrepresentation of diverse people in higher education. There is extensive literature about theory, observation, and evidence-based practices that can help create a more equitable, inclusive, and diverse learning environment. In this article, we propose the implementation of a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club as a strategic initiative to foster education and promote action towards making academia a more equitable institution. By creating a space for people to engage with DEIJ theories* and strategize ways to improve their learning environment, we hope to normalize the practice and importance of analyzing academia through an equity lens. Guided by restorative justice principles, we offer 10 recommendations for fostering community cohesion through education and mutual understanding. This approach underscores the importance of appropriate action and self-education in the journey toward a more diverse, equitable, inclusive, and just academic environment. *Authors' note: We understand that "DEIJ" is a multidisciplinary organizational framework that relies on numerous fields of study, including history, sociology, philosophy, and more. We use this term to refer to these different fields of study for brevity purposes.

FAIR-USE4OS: Guidelines for creating impactful open-source software.

This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding "USE" (User-Centered, Sustainable, Equitable), software development can adhere to open source best practice by incorporating user-input early on, ensuring front-end designs are accessible to all possible stakeholders, and planning long-term sustainability alongside software design. The FAIR-USE4OS guidelines will allow funders and researchers to more effectively evaluate and plan open-source software projects. There is good evidence of funders increasingly mandating that all funded research software is open source; however, even under the FAIR guidelines, this could simply mean software released on public repositories with a Zenodo DOI. By creating FAIR-USE software, best practice can be demonstrated from the very beginning of the design process and the software has the greatest chance of success by being impactful.

Limitation of life sustaining therapy in disorders of consciousness: ethics and practice.

Clinical conversations surrounding the continuation or limitation of life-sustaining therapies (LLST) are both challenging and tragically necessary for patients with disorders of consciousness (DoC) following severe brain injury. Divergent cultural, philosophical and religious perspectives contribute to vast heterogeneity in clinical approaches to LLST-as reflected in regional differences and inter-clinician variability. Here we provide an ethical analysis of factors that inform LLST decisions among patients with DoC. We begin by introducing the clinical and ethical challenge and clarifying the distinction between withdrawing and withholding life-sustaining therapy. We then describe relevant factors that influence LLST decision-making including diagnostic and prognostic uncertainty, perception of pain, defining a 'good' outcome, and the role of clinicians. In concluding sections, we explore global variation in LLST practices as they pertain to patients with DoC and examine the impact of cultural and religious perspectives on approaches to LLST. Understanding and respecting the cultural and religious perspectives of patients and surrogates is essential to protecting patient autonomy and advancing goal-concordant care during critical moments of medical decision-making involving patients with DoC.

What is happening to immunohistochemistry?

Immunohistochemistry is a commonly used technique in research and pathology laboratories worldwide. However, in recent years, there has been a significant decrease in the number of Pubmed entries using the term immunohistochemistry. This decline can be attributed to two factors: increased awareness of the issue of unreliable research antibodies and the availability of novel RNA in situ hybridization techniques. Using the example of immunohistochemistry, this text discusses the factors that can affect good laboratory and publishing practices, or their lack thereof.

Lung Disease and Social Justice: Chronic Obstructive Pulmonary Disease as a Manifestation of Structural Violence.

Lung health, the development of lung disease, and how well a person with lung disease is able to live all depend on a wide range of societal factors. These systemic factors that adversely affect people and cause injustice can be thought of as "structural violence." To make the causal processes relating to chronic obstructive pulmonary disease (COPD) more apparent, and the responsibility to interrupt or alleviate them clearer, we have developed a taxonomy to describe this. It contains five domains: 1) avoidable lung harms (processes impacting lung development, processes that disadvantage lung health in particular groups across the life course), 2) diagnostic delay (healthcare factors; norms and attitudes that mean COPD is not diagnosed in a timely way, denying people with COPD effective treatment), 3) inadequate COPD care (ways in which the provision of care for people with COPD falls short of what is needed to ensure they are able to enjoy the best possible health, considered as healthcare resource allocation and norms and attitudes influencing clinical practice), 4) low status of COPD (ways COPD as a condition and people with COPD are held in less regard and considered less of a priority than other comparable health problems), and 5) lack of support (factors that make living with COPD more difficult than it should be, i.e., socioenvironmental factors and factors that promote social isolation). This model has relevance for policymakers, healthcare professionals, and the public as an educational resource to change clinical practices and priorities and stimulate advocacy and activism with the goal of the elimination of COPD.

A practical guide for implementing omalizumab therapy for food allergy.

The recent approval of omalizumab for the treatment of IgE-mediated food allergy is an important step forward for the millions of food allergy patients in the United States. Through the depletion of circulating IgE and the subsequent reduction of FcεR1 on key effector cells, patients increase their tolerance to food allergens. However, omalizumab does not permit patients to eat foods that they are allergic to with impunity. Rather, it protects them from most accidental exposures. In addition, omalizumab does not cure food allergy and has not demonstrated true immunomodulation. Thus, omalizumab might be a lifelong therapy for some patients. Furthermore, there are many important questions and issues surrounding the appropriate administration of omalizumab to treat food allergy, which we discuss. Managing treatment of patients with disease that falls outside the dosing range, assessing treatment response or nonresponse, addressing its appropriateness for patients older than 55, and determining whether immunotherapy plus omalizumab provides any advantage over omalizumab alone all need to be examined. Identifying appropriate patients for this therapy is critical given the cost of biologics. Indeed, not all food allergy patients are good candidates for this therapy. Also, when and how to stop omalizumab therapy in patients who may have outgrown their food allergy needs to be elucidated. Thus, although this therapy provides a good option for patients with food allergies, much information is needed to determine how best to use this therapy. Despite many unanswered questions and issues, we provide clinicians with some practical guidance on implementing this therapy in their patients.

The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines.

The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.

VXX-401, a novel anti-PCSK9 vaccine, reduces LDL-C in cynomolgus monkeys.

Atherosclerotic cardiovascular disease (ASCVD) remains the leading cause of disease burden in the world and is highly correlated with chronic elevations of LDL-C. LDL-C-lowering drugs, such as statins or monoclonal antibodies against proprotein convertase subtilisin/kexin type 9 (PCSK9), are known to reduce the risk of cardiovascular diseases; however, statins are associated with limited efficacy and poor adherence to treatment, whereas PCSK9 inhibitors are only prescribed to a "high-risk" patient population or those who have failed other therapies. Based on the proven efficacy and safety profile of existing monoclonal antibodies, we have developed a peptide-based vaccine against PCSK9, VXX-401, as an alternative option to treat hypercholesterolemia and prevent ASCVD. VXX-401 is designed to trigger a safe humoral immune response against PCSK9, resulting in the production of endogenous antibodies and a subsequent 30-40% reduction in blood LDL-C. In this article, VXX-401 demonstrates robust immunogenicity and sustained serum LDL-C-lowering effects in nonhuman primates. In addition, antibodies induced by VXX-401 bind to human PCSK9 with high affinity and block the inhibitory effect of PCSK9 on LDL-C uptake in a hepatic cell model. A repeat-dose toxicity study conducted in nonhuman primates under good laboratory practices toxicity indicated a suitable safety and tolerability profile, with injection site reactions being the main findings. As a promising safe and effective LDL-C-lowering therapy, VXX-401 may represent a broadly accessible and convenient option to treat hypercholesterolemia and prevent ASCVD.

Physician knowledge, practice patterns, and barriers encountered regarding guideline-concordant use of bone modifying agents for prostate cancer.

BACKGROUND: Guidelines recommend bone-modifying agents (BMAs) for patients with castrate-resistant prostate cancer (CRPC) and bone metastasis, but not for castrate-sensitive prostate cancer (CSPC). Physicians beliefs and practices regarding BMA therapy are poorly understood. METHODS: This was a qualitative interview study with embedded Likert-scale elements. Study participants were physicians who treat prostate cancer, located within an academic cancer center or an affiliated community-based network. Participants were asked about their experiences and practice patterns regarding BMA therapy. Participants used Likert-scale items to identify the most common barriers to guideline-concordant BMA use and the most effective potential interventions. Participants were subsequently asked to rank the three most common barriers and the three most effective interventions to reduce underuse (for CRPC) and overuse (for CSPC). RESULTS: Nineteen physicians were invited and 15 participated; one physician did not answer some questions as outside of their practice scope. All were aware of the recommendation for BMAs in CRPC. 14% (2/14) were unaware of the recommendation against BMA use for CSPC; an additional 29% (4/14) believed that BMA use could be appropriate for CSPC depending on the metastatic disease burden. 36% (5/14) were unaware of recommendations for screening and treatment of low bone mineral density. The most common barriers (occurring "often" or "sometimes") were obtaining dental clearance (11/15) and insufficient clinic time (6/15). The interventions identified as most effective to reduce underuse were dental navigation (11/15) and electronic medical record (EMR)-based guidance (9/15). The interventions identified as most effective to reduce overuse were peer-to-peer education (14/15) and EMR-based guidance (13/15). CONCLUSIONS: Awareness of guideline recommendations for screening and treatment of low bone mineral density and against BMA use for CSPC was good, but not complete. Dental navigation, peer-to-peer education, and EMR-based guidance were preferred intervention strategies to improve guideline-concordant use.

Acute chest syndrome in children with sickle cell disease: Data from a national AIEOP cohort identify priority areas of intervention in a hub-and-spoke system.

Acute chest syndrome (ACS) is a frequent cause of hospitalization in sickle cell disease (SCD). Despite advances in acute care, many settings still lack knowledge about ACS best practices. After the AIEOP Guidelines were published in 2012, suggesting standardized management in Italy, a retrospective study was performed to assess the diagnostic and therapeutic pathways of ACS in children. From 2013 to 2018, 208 ACS episodes were presented by 122/583 kids in 11 centres. 73 were male, mean age 10.9 years, 85% African, 92% HbSS or Sß°. In our hub-and-spoke system, a good adherence to Guidelines was documented, but discrepancies between reference centres and general hospitals were noted. Improvement is needed for timely transfer to reference centres, use of incentive spirometry, oxygen therapy and pain management.

Business leaders' perceptions of how workplace charters can reduce health inequalities for employees in West Yorkshire, England: a qualitative study.

BACKGROUND: Workplace interventions to increase the number of good quality jobs can help reduce widening health inequalities in England and are an important area for public health research. Over the past decade, workplace charters led by local and regional government authorities have become increasingly popular. Charters typically include commitments on workplace practices-such as job security, pay, wellbeing, and employee voice-and an assessment and award process. Still, there is limited knowledge on how this intervention works. We aimed to understand the views of business leaders on how workplace charters can reduce health inequalities for employees. METHODS: In this qualitative study, 12 business leaders in West Yorkshire were purposively recruited (seven [58%] female, and five [42%] male) through the West Yorkshire Combined Authority, covering different business sizes and sectors. Business leaders were recruited, as key stakeholders who decide whether to engage with charters. Semi-structured interviews were conducted between Aug 3, and Sept 7, 2022. Interviews were transcribed and analysed using reflexive thematic analysis to identify perceived charter mechanisms to reduce health inequalities, alongside emergent barriers to charter implementation. Ethics approval was granted by the University of Sheffield Research Ethics Committee. Participants gave written informed consent. FINDINGS: Business leaders perceived multiple charter mechanisms to reduce health inequalities: the charter to benchmark workplace practices, facilitate a business community, act as a credible badge for fair employers, and open a dialogue with partners. Three key emergent barriers to charter implementation were also identified, including different perceptions of fair work among business leaders, concern about significant charter demands for smaller businesses, and perceived external constraints from the political, social, and economic environment. INTERPRETATION: Business leaders' views affirmed that workplace charters are collectively perceived as a potential tool to address differential workplace practices and reduce health inequalities. However, due to substantial barriers identified, this study suggested that workplace charters could also exclude particular organisations and generate health inequalities. Charter providers must reconcile the tension between the collective aspiration, and practical reality of workplace charters. If reconciled, workplace charters could potentially be a timely and meaningful intervention to help reduce health inequalities in England. FUNDING: None.

Factors affecting the delivery of community-based salon interventions to prevent cardiovascular disease and breast cancer among ethnically diverse women in South London: a concept-mapping approach.

BACKGROUND: In the UK, women from ethnically diverse and socioeconomically deprived communities are at increased risk of underdiagnosis of cardiovascular disease (CVD) and breast cancer. Promoting CVD prevention and awareness of breast cancer screening via community salons and primary health care partnerships can improve uptake of screening services and early detection. METHODS: Concept mapping is a multistage mixed methods participatory approach comprised of six stages: preparation, brainstorming, structuring of statements, representing statements, interpretation and utilisation of maps using Group wisdom software. A target of 20 salons, excluding male-only salons were approached. Salons included Salons included hairdressing or hairdressing and beauty salons. Purposeful and convenience sampling (online and face to face) among UK salons (hair and beauty) was conducted. Participants were given a focus prompt "What would be some factors that can influence the ability of salons to deliver this service?" and required to generate statements, which were sorted into categories based on similarity and rated for importance and feasibility. Concept maps using multidimensional scaling and hierarchical cluster analyses were produced. FINDINGS: Of 35 participants invited, 25 (71%) consented and agreed to take part in concept mapping. Reported ages were 26-35 years (n=5, 20%), 36-45 years (n=12, 48%), 46-55 years (n=3, 12%), 56-65 years (n=5, 20%), and no age reported (n=10, 40%). Around 36% (n=9) of participants were from non-White ethnic groups, with 12% (n=3) being male and 88% (n=22) female. Seven clusters emerged. Salon staff capabilities and capacities and engaging in health conversations in community salons scored average bridging values of 0·09 and 0·2 respectively, indicating good cluster homogeneity (similar meaning statements were closely sorted). Facilitating health-care access with GP practices was rated highly important to effectively promote the intervention. Engaging in health conversations in community salons and salon incentives for participation were examples of factors that were highly feasible to address. The r correlation coefficient was 0·68 between importance and feasibility to address factors affecting community health interventions. INTERPRETATION: Salons are well positioned to support health promotion interventions. Actionable priorities were identified for a salon-GP surgery partnership to promote CVD prevention through lifestyle changes and health check uptake, raising breast cancer screening awareness and address issue of equity. FUNDING: National Institute of Health and Care Research (NIHR), Research for Patient Benefit (RfPB) Programme NIHR202769.

A practical guide to cross-cultural and multi-sited data collection in the biological and behavioural sciences.

Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.