Best practices for data management and sharing in experimental biomedical research.

Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building on results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers' careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers.

Toward clinical exomes in diagnostics and management of male infertility.

Infertility, affecting ∼10% of men, is predominantly caused by primary spermatogenic failure (SPGF). We screened likely pathogenic and pathogenic (LP/P) variants in 638 candidate genes for male infertility in 521 individuals presenting idiopathic SPGF and 323 normozoospermic men in the ESTAND cohort. Molecular diagnosis was reached for 64 men with SPGF (12%), with findings in 39 genes (6%). The yield did not differ significantly between the subgroups with azoospermia (20/185, 11%), oligozoospermia (18/181, 10%), and primary cryptorchidism with SPGF (26/155, 17%). Notably, 19 of 64 LP/P variants (30%) identified in 28 subjects represented recurrent findings in this study and/or with other male infertility cohorts. NR5A1 was the most frequently affected gene, with seven LP/P variants in six SPGF-affected men and two normozoospermic men. The link to SPGF was validated for recently proposed candidate genes ACTRT1, ASZ1, GLUD2, GREB1L, LEO1, RBM5, ROS1, and TGIF2LY. Heterozygous truncating variants in BNC1, reported in female infertility, emerged as plausible causes of severe oligozoospermia. Data suggested that several infertile men may present congenital conditions with less pronounced or pleiotropic phenotypes affecting the development and function of the reproductive system. Genes regulating the hypothalamic-pituitary-gonadal axis were affected in >30% of subjects with LP/P variants. Six individuals had more than one LP/P variant, including five with two findings from the gene panel. A 4-fold increased prevalence of cancer was observed in men with genetic infertility compared to the general male population (8% vs. 2%; p = 4.4 × 10-3). Expanding genetic testing in andrology will contribute to the multidisciplinary management of SPGF.

The impact of clinical genome sequencing in a global population with suspected rare genetic disease.

There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.

Solving the 250-year-old mystery of the origin and global spread of the German cockroach, Blattella germanica.

The origin of the German cockroach, Blattella germanica, is enigmatic, in part because it is ubiquitous worldwide in human-built structures but absent from any natural habitats. The first historical records of this species are from ca. 250 years ago (ya) from central Europe (hence its name). However, recent research suggests that the center of diversity of the genus is Asian, where its closest relatives are found. To solve this paradox, we sampled genome-wide markers of 281 cockroaches from 17 countries across six continents. We confirm that B. germanica evolved from the Asian cockroach Blattella asahinai approximately 2,100 ya, probably by adapting to human settlements in India or Myanmar. Our genomic analyses reconstructed two primary global spread routes, one older, westward route to the Middle East coinciding with various Islamic dynasties (~1,200 ya), and another younger eastward route coinciding with the European colonial period (~390 ya). While Europe was not central to the early domestication and spread of the German cockroach, European advances in long-distance transportation and temperature-controlled housing were likely important for the more recent global spread, increasing chances of successful dispersal to and establishment in new regions. The global genetic structure of German cockroaches further supports our model, as it generally aligns with geopolitical boundaries, suggesting regional bridgehead populations established following the advent of international commerce.

Significant challenges to the sustainability of the California coast considering climate change.

Climate change is an existential threat to the environmental and socioeconomic sustainability of the coastal zone and impacts will be complex and widespread. Evidence from California and across the United States shows that climate change is impacting coastal communities and challenging managers with a plethora of stressors already present. Widespread action could be taken that would sustain California's coastal ecosystems and communities. In this perspective, we highlight the main threat to coastal sustainability: the compound effects of episodic events amplified with ongoing climate change, which will present unprecedented challenges to the state. We present two key challenges for California's sustainability in the coastal zone: 1) accelerating sea-level rise combined with storm impacts, and 2) continued warming of the oceans and marine heatwaves. Cascading effects from these types of compounding events will occur within the context of an already stressed system that has experienced extensive alterations due to intensive development, resource extraction and harvesting, spatial containment, and other human use pressures. There are critical components that could be used to address these immediate concerns, including comanagement strategies that include diverse groups and organizations, strategic planning integrated across large areas, rapid implementation of solutions, and a cohesive and policy relevant research agenda for the California coast. Much of this has been started in the state, but the scale could be increased, and timelines accelerated. The ideas and information presented here are intended to help expand discussions to sharpen the focus on how to encourage sustainability of California's iconic coastal region.

Sex bias in pain management decisions.

In the pursuit of mental and physical health, effective pain management stands as a cornerstone. Here, we examine a potential sex bias in pain management. Leveraging insights from psychological research showing that females' pain is stereotypically judged as less intense than males' pain, we hypothesize that there may be tangible differences in pain management decisions based on patients' sex. Our investigation spans emergency department (ED) datasets from two countries, including discharge notes of patients arriving with pain complaints (N = 21,851). Across these datasets, a consistent sex disparity emerges. Female patients are less likely to be prescribed pain-relief medications compared to males, and this disparity persists even after adjusting for patients' reported pain scores and numerous patient, physician, and ED variables. This disparity extends across medical practitioners, with both male and female physicians prescribing less pain-relief medications to females than to males. Additional analyses reveal that female patients' pain scores are 10% less likely to be recorded by nurses, and female patients spend an additional 30 min in the ED compared to male patients. A controlled experiment employing clinical vignettes reinforces our hypothesis, showing that nurses (N = 109) judge pain of female patients to be less intense than that of males. We argue that the findings reflect an undertreatment of female patients' pain. We discuss the troubling societal and medical implications of females' pain being overlooked and call for policy interventions to ensure equal pain treatment.

Structure-based identification of a G protein-biased allosteric modulator of cannabinoid receptor CB1.

Cannabis sativa is known for its therapeutic benefit in various diseases including pain relief by targeting cannabinoid receptors. The primary component of cannabis, Δ9-tetrahydrocannabinol (THC), and other agonists engage the orthosteric site of CB1, activating both Gi and ß-arrestin signaling pathways. The activation of diverse pathways could result in on-target side effects and cannabis addiction, which may hinder therapeutic potential. A significant challenge in pharmacology is the design of a ligand that can modulate specific signaling of CB1. By leveraging insights from the structure-function selectivity relationship (SFSR), we have identified Gi signaling-biased agonist-allosteric modulators (ago-BAMs). Further, two cryoelectron microscopy (cryo-EM) structures reveal the binding mode of ago-BAM at the extrahelical allosteric site of CB1. Combining mutagenesis and pharmacological studies, we elucidated the detailed mechanism of ago-BAM-mediated biased signaling. Notably, ago-BAM CB-05 demonstrated analgesic efficacy with fewer side effects, minimal drug toxicity and no cannabis addiction in mouse pain models. In summary, our finding not only suggests that ago-BAMs of CB1 provide a potential nonopioid strategy for pain management but also sheds light on BAM identification for GPCRs.

Private management of African protected areas improves wildlife and tourism outcomes but with security concerns in conflict regions.

Protected areas can conserve wildlife and benefit people when managed effectively. African governments increasingly delegate the management of protected areas to private, nongovernmental organizations, hoping that private organizations' significant resources and technical capacities actualize protected areas' potential. Does private sector management improve outcomes compared to a counterfactual of government management? We leverage the transfer of management authority from governments to African Parks (AP)-the largest private manager of protected areas in Africa-to show that private management significantly improves wildlife outcomes via reduced elephant poaching and increased bird abundances. Our results also suggest that AP's management augments tourism, while the effect on rural wealth is inconclusive. However, AP's management increases the risk of armed groups targeting civilians, which could be an unintended outcome of AP's improved monitoring and enforcement systems. These findings reveal an intricate interplay between conservation, economic development, and security under privately managed protected areas in Africa.

FAIR Header Reference genome: a TRUSTworthy standard.

The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.

Anaerobes in diabetic foot infections: pathophysiology, epidemiology, virulence, and management.

SUMMARYDiabetic foot infections (DFI) are a public health problem worldwide. DFI are polymicrobial, biofilm-associated infections involving complex bacterial communities organized in functional equivalent pathogroups, all including anaerobes. Indeed, multiple pathophysiological factors favor the growth of anaerobes in this context. However, the prevalence, role, and contribution of anaerobes in wound evolution remain poorly characterized due to their challenging detection. Studies based on culture reviewed herein showed a weighted average of 17% of patients with anaerobes. Comparatively, the weighted average of patients with anaerobes identified by 16S rRNA gene sequencing was 83.8%. Culture largely underestimated not only the presence but also the diversity of anaerobes compared with cultivation-independent approaches but both methods showed that anaerobic Gram-negative bacilli and Gram-positive cocci were the most commonly identified in DFI. Anaerobes were more present in deeper lesions, and their detection was associated with fever, malodorous lesions, and ulcer depth and duration. More specifically, initial abundance of Peptoniphilus spp. was associated with ulcer-impaired healing, Fusobacterium spp. detection was significantly correlated with the duration of DFI, and the presence of Bacteroides spp. was significantly associated with amputation. Antimicrobial resistance of anaerobes in DFI remains slightly studied and warrants more consideration in the context of increasing resistance of the most frequently identified anaerobes in DFI. The high rate of patients with DFI-involving anaerobes, the increased knowledge on the species identified, their virulence factors, and their potential role in wound evolution support recommendations combining debridement and antibiotic therapy effective on anaerobes in moderate and severe DFI.

Equitable Care for Hypertension: Blood Pressure and Patient-Reported Outcomes of the RICH LIFE Cluster Randomized Trial.

BACKGROUND: Disparities in hypertension control are well documented but underaddressed. METHODS: RICH LIFE (Reducing Inequities in Care of Hypertension: Lifestyle Improvement for Everyone) was a 2-arm, cluster randomized trial comparing the effect on blood pressure (BP) control (systolic BP ≤140 mm Hg, diastolic BP ≤90 mm Hg), patient activation, and disparities in BP control of 2 multilevel interventions, standard of care plus (SCP) and collaborative care/stepped care (CC/SC). SCP included BP measurement standardization, audit and feedback, and equity-leadership training. CC/SC added roles to address social or medical needs. Primary outcomes were BP control and patient activation at 12 months. Generalized estimating equations and mixed-effects regression models with fixed effects of time, intervention, and their interaction compared change in outcomes at 12 months from baseline. RESULTS: A total of 1820 adults with uncontrolled BP and ≥1 other risk factors enrolled in the study. Their mean age was 60.3 years, and baseline BP was 152.3/85.5 mm Hg; 59.4% were women; 57.4% were Black, 33.2% were White, and 9.4% were Hispanic; 74% had hyperlipidemia; and 45.1% had type 2 diabetes. CC/SC did not improve BP control rates more than SCP. Both groups achieved statistically and clinically significant BP control rates at 12 months (CC/SC: 57.3% [95% CI, 52.7%-62.0%]; SCP: 56.7% [95% CI, 51.9%-61.5%]). Pairwise comparisons between racial and ethnic groups showed overall no significant differences in BP control at 12 months. Patients with coronary heart disease showed greater achievement of BP control in CC/SC than in SCP (64.0% [95% CI, 54.1%-73.9%] versus 50.8% [95% CI, 42.6%-59.0%]; P=0.04), as did patients in rural areas (67.3% [95% CI, 49.8%-84.8%] versus 47.8% [95% CI, 32.4%-63.2%]; P=0.01). Individuals in both arms experienced statistically and clinically significant reductions in mean systolic BP (CC/SC: -13.8 mm Hg [95% CI, -15.2 to -12.5]; SCP: -14.6 mm Hg [95% CI, -15.9 to -13.2]) and diastolic BP (CC/SC: -6.9 mm Hg [95% CI, -7.8 to -6.1]; SCP: -5.5 mm Hg [95% CI, -6.4 to -4.6]) over time. The difference in diastolic BP reduction between CC/SC and SCP over time was statistically significant (-1.4 mm Hg [95% CI, -2.6 to -0.2). Patient activation did not differ between arms. CC/SC showed greater improvements in patient ratings of chronic illness care (Patient Assessment of Chronic Illness Care score) over 12 months (0.12 [95% CI, 0.02-0.22]). CONCLUSIONS: Adding a collaborative care team to enhanced standard of care did not improve BP control but did improve patient ratings of chronic illness care.

Evaluation and Management of Chronic Heart Failure in Children and Adolescents With Congenital Heart Disease: A Scientific Statement From the American Heart Association.

With continued medical and surgical advancements, most children and adolescents with congenital heart disease are expected to survive to adulthood. Chronic heart failure is increasingly being recognized as a major contributor to ongoing morbidity and mortality in this population as it ages, and treatment strategies to prevent and treat heart failure in the pediatric population are needed. In addition to primary myocardial dysfunction, anatomical and pathophysiological abnormalities specific to various congenital heart disease lesions contribute to the development of heart failure and affect potential strategies commonly used to treat adult patients with heart failure. This scientific statement highlights the significant knowledge gaps in understanding the epidemiology, pathophysiology, staging, and outcomes of chronic heart failure in children and adolescents with congenital heart disease not amenable to catheter-based or surgical interventions. Efforts to harmonize the definitions, staging, follow-up, and approach to heart failure in children with congenital heart disease are critical to enable the conduct of rigorous scientific studies to advance our understanding of the actual burden of heart failure in this population and to allow the development of evidence-based heart failure therapies that can improve outcomes for this high-risk cohort.

2024 ACC/AHA/AACVPR/APMA/ABC/SCAI/SVM/SVN/SVS/SIR/VESS Guideline for the Management of Lower Extremity Peripheral Artery Disease: A Report of the American College of Cardiology/American Heart Association Joint Committee on Clinical Practice Guidelines.

AIM: The "2024 ACC/AHA/AACVPR/APMA/ABC/SCAI/SVM/SVN/SVS/SIR/VESS Guideline for the Management of Lower Extremity Peripheral Artery Disease" provides recommendations to guide clinicians in the treatment of patients with lower extremity peripheral artery disease across its multiple clinical presentation subsets (ie, asymptomatic, chronic symptomatic, chronic limb-threatening ischemia, and acute limb ischemia). METHODS: A comprehensive literature search was conducted from October 2020 to June 2022, encompassing studies, reviews, and other evidence conducted on human subjects that was published in English from PubMed, EMBASE, the Cochrane Library, CINHL Complete, and other selected databases relevant to this guideline. Additional relevant studies, published through May 2023 during the peer review process, were also considered by the writing committee and added to the evidence tables where appropriate. STRUCTURE: Recommendations from the "2016 AHA/ACC Guideline on the Management of Patients With Lower Extremity Peripheral Artery Disease" have been updated with new evidence to guide clinicians. In addition, new recommendations addressing comprehensive care for patients with peripheral artery disease have been developed.

Diagnosis and Management of Acute Pancreatitis.

Acute pancreatitis (AP) is increasing in incidence across the world, and in all age groups. Major changes in management have occurred in the last decade. Avoiding total parenteral nutrition and prophylactic antibiotics, avoiding overly aggressive fluid resuscitation, initiating early feeding, avoiding endoscopic retrograde cholangiopancreatography in the absence of concomitant cholangitis, same-admission cholecystectomy, and minimally invasive approaches to infected necrosis should now be standard of care. Increasing recognition of the risk of recurrence of AP, and progression to chronic pancreatitis, along with the unexpectedly high risk of diabetes and exocrine insufficiency after AP is the subject of large ongoing studies. In this review, we provide an update on important changes in management for this increasingly common disease.

AGA Clinical Practice Update on Pain Management in Inflammatory Bowel Disease: Commentary.

DESCRIPTION: Pain is a common symptom among patients with inflammatory bowel disease (IBD). Although pain typically occurs during episodes of inflammation, it is also commonly experienced when intestinal inflammation is quiescent. Many gastroenterologists are at a loss how to approach pain symptoms when they occur in the absence of gut inflammation. We provide guidance in this area as to the evaluation, diagnosis, and treatment of pain among patients with IBD. METHODS: This CPU was commissioned and approved by the AGA Institute Clinical Practice Updates Committee (CPUC) and the AGA Governing Board to provide timely guidance on a topic of high clinical importance to the AGA membership and underwent internal peer review by the CPUC and external peer review through standard procedures of Gastroenterology. This expert commentary incorporates important as well as recently published studies in this field, and it reflects the experiences of the authors. Formal ratings regarding the quality of evidence or strength of the presented considerations were not included because systematic reviews were not performed.

Tiam1-mediated maladaptive plasticity underlying morphine tolerance and hyperalgesia.

Opioid pain medications, such as morphine, remain the mainstay for treating severe and chronic pain. Prolonged morphine use, however, triggers analgesic tolerance and hyperalgesia (OIH), which can last for a long period after morphine withdrawal. How morphine induces these detrimental side effects remains unclear. Here, we show that morphine tolerance and OIH are mediated by Tiam1-coordinated synaptic structural and functional plasticity in the spinal nociceptive network. Tiam1 is a Rac1 GTPase guanine nucleotide exchange factor that promotes excitatory synaptogenesis by modulating actin cytoskeletal dynamics. We found that prolonged morphine treatment activated Tiam1 in the spinal dorsal horn and Tiam1 ablation from spinal neurons eliminated morphine antinociceptive tolerance and OIH. At the same time, the pharmacological blockade of Tiam1-Rac1 signalling prevented the development and reserved the established tolerance and OIH. Prolonged morphine treatment increased dendritic spine density and synaptic NMDA receptor activity in spinal dorsal horn neurons, both of which required Tiam1. Furthermore, co-administration of the Tiam1 signalling inhibitor NSC23766 was sufficient to abrogate morphine tolerance in chronic pain management. These findings identify Tiam1-mediated maladaptive plasticity in the spinal nociceptive network as an underlying cause for the development and maintenance of morphine tolerance and OIH and provide a promising therapeutic target to reduce tolerance and prolong morphine use in chronic pain management.