Small Population Size Research Articles

Identifying predictors of lymphatic leak after nephrectomy using American College of Surgeons-National Surgical Quality Improvement Program Targeted Data.

e16545 Background: Chylous ascites is a rare complication of nephrectomy with a reported incidence of up to 5.9%, caused by the disruption of lymphatic vessels in the retroperitoneum. Data from single institution retrospective reviews identify left-sided surgery, higher body mass index (BMI), and radical/donor nephrectomy as potential risk factors but are limited by small population size. We sought to identify predictors of lymphatic leak following nephrectomy using the American College of Surgeons-National Surgical Quality Improvement Program (ACS-NSQIP) Nephrectomy-Targeted database. Methods: Using the database from 2019 to 2022, we identified adult ( > 18 years old) patients who underwent nephrectomy. Patients were then dichotomized based on whether they developed lymph leak. We performed logistic regression to determine the association between baseline and perioperative covariates with development of lymph leak. Similarly, we evaluated the association between development of lymph leak and 30-day postoperative complications. Results: Our results yielded a total of 29,299 nephrectomies performed, of which 586 (2.0%) were documented to have a lymph leak. Open approach, left laterality, N1 or M1 staging, major visceral resection, lymph node sampling, unplanned conversion to open, nephrology related chemotherapy, prior pelvic surgery, higher preoperative creatinine, lower preoperative hemoglobin, lower preoperative albumin, ASA class, history of recent weight loss, steroid use, bleeding disorder, dialysis, disseminated cancer, or congestive heart failure. were associated with an increased likelihood of lymph leak. In our analysis, age, gender, ethnicity, BMI, history of smoking or diabetes were not statistically significantly associated with increased lymph leak. In the postoperative setting, there was association between development of lymph leak and myocardial infarction, cardiac arrest, postoperative ileus, postoperative bleeding, urinary tract infection, surgical site infection, clostridium difficile colitis, sepsis, pneumonia, venous thromboembolic event, renal insufficiency, unplanned reoperation, longer hospital stay, and readmissions. Conclusions: Chylous ascites is associated with worse postoperative outcomes. To our knowledge, this is the largest contemporary population-based analysis of risk factors for lymph leak following nephrectomy; our findings can be used to guide surgeons in determining which patients should be counseled to adhere to a postoperative prophylactic low fat diet and monitored closely for chylous ascites.

Constraints in the Integration of Gamification in Learning Management Systems in Higher Education

Rationale of Study – Integrating gamification in Learning Management Systems (LMSs) in higher education is a complex undertaking often flawed by several constraints. This study focused on determining the constraints in integrating gamification technologies in LMSs. Methodology – Descriptive survey research design and inferential and descriptive statistics were employed in data analysis. The census sampling technique was adopted because of the small population size of 81 respondents. Questionnaires integrated into a modular object-oriented dynamic learning environment were administered to 81 respondents for data collection. The secondary data was accessed and downloaded from the Dimensions research database, whose articles spanned from 2015 to 2024. VOSviewer and Bibliometrix packages in R, JASP, and SPSS software were used to analyse data, and the results were presented in tables, charts, and statistical narratives. Findings – The study confirmed constraints when integrating gamification elements in LMSs. For students' motivational learning experience, constraints are inexorable in integrating these innovative technologies that any higher education institution may not avoid. The study recommends that the university management support learners’ technical team and lecturers with the appropriate eLearning infrastructures, among other necessary resources, to proactively help the LMS stakeholders overcome any constraints that may arise in the integration of gamification in education. Implications – This study is significant to institutional policymakers and eLearning instructional designers in meeting the fourth sustainable development goal that ensures inclusive and equitable quality education and promotes lifelong learning opportunities for everybody. Originality - This paper contributes to the understanding of the various constraints facing the integration of gamification in the higher education through bibliometric analysis and experimental research design and consequently making its implementation successful.

Geobotanical Study and Preservation of Rare and Endangered Rosaceae Species.

The loss of plant species, especially endangered and endemic ones, poses a significant threat to global biodiversity. These species cannot easily be replaced when their populations decline or become extinct, which makes their loss particularly devastating. This study focuses on the geobotanical study of nine Rosaceae species (Cotoneaster karatavicus, Crataegus ambigua, Malus niedzwetzkyana, Malus sieversii, Prunus tenella, Prunus ulmifolia, Sibiraea laevigata, Sorbus persica, and Spiraeanthus schrenkianus) and the development of ex situ approaches for the conservation of Rosaceae species listed in the Red Book of Kazakhstan. The geobotanical study revealed an alarming trend of biodiversity loss in five regions of Kazakhstan. This loss is driven by threats from diseases and pests, as well as the aging of plants, small population sizes, weak in situ fruiting, and other factors, such as climate change. We have established an in vitro collection for the short- and medium-term conservation of seeds, embryos and shoots taken either directly from field-grown plants or from budwood cuttings forced indoors. We also use long-term sexual conservation methods, such as the cryopreservation of seed and embryonic axes, alongside conventional seed banking at -20 °C. Ex situ conservation efforts that use multiple propagules and storage methods for the same species are well-suited to a diverse genebank facility. These efforts enable future generations to use this valuable reservoir of genetic diversity for crop improvement and may also serve as a basis for propagating planting material to restore degraded populations.

Reproducibility of genetic risk factors identified for long COVID using combinatorial analysis across US and UK patient cohorts with diverse ancestries

BackgroundLong COVID is a major public health burden causing a diverse array of debilitating symptoms in tens of millions of patients globally. In spite of this overwhelming disease prevalence, staggering cost, severe impact on patients’ lives and intense global research efforts, study of the disease has proved challenging due to its complexity. Genome-wide association studies (GWAS) have identified only four loci potentially associated with the disease, although these results did not statistically replicate between studies. A previous combinatorial analysis study identified a total of 73 genes that were highly associated with two long COVID cohorts in the predominantly (> 91%) white European ancestry Sano GOLD population, and we sought to reproduce these findings in the independent and ancestrally more diverse All of Us (AoU) population.MethodsWe assessed the reproducibility of the 5343 long COVID disease signatures from the original study in the AoU population. Because the very small population sizes provide very limited power to replicate findings, we initially tested whether we observed a statistically significant enrichment of the Sano GOLD disease signatures that are also positively correlated with long COVID in the AoU cohort after controlling for population substructure.ResultsFor the Sano GOLD disease signatures that have a case frequency greater than 5% in AoU, we consistently observed a significant enrichment (77–83%, p < 0.01) of signatures that are also positively associated with long COVID in the AoU cohort. These encompassed 92% of the genes identified in the original study. At least five of the disease signatures found in Sano GOLD were also shown to be individually significantly associated with increased long COVID prevalence in the AoU population. Rates of signature reproducibility are strongest among self-identified white patients, but we also observe significant enrichment of reproducing disease associations in self-identified black/African-American and Hispanic/Latino cohorts. Signatures associated with 11 out of the 13 drug repurposing candidates identified in the original Sano GOLD study were reproduced in this study.ConclusionThese results demonstrate the reproducibility of long COVID disease signal found by combinatorial analysis, broadly validating the results of the original analysis. They provide compelling evidence for a much broader array of genetic associations with long COVID than previously identified through traditional GWAS studies. This strongly supports the hypothesis that genetic factors play a critical role in determining an individual's susceptibility to long COVID following recovery from acute SARS-CoV-2 infection. It also lends weight to the drug repurposing candidates identified in the original analysis. Together these results may help to stimulate much needed new precision medicine approaches to more effectively diagnose and treat the disease. This is also the first reproduction of long COVID genetic associations across multiple populations with substantially different ancestry distributions. Given the high reproducibility rate across diverse populations, these findings may have broader clinical application and promote better health equity. We hope that this will provide confidence to explore some of these mechanisms and drug targets and help advance research into novel ways to diagnose the disease and accelerate the discovery and selection of better therapeutic options, both in the form of newly discovered drugs and/or the immediate prioritization of coordinated investigations into the efficacy of repurposed drug candidates.

Beyond the (Geometric) Mean: Stochastic Models Undermine Deterministic Predictions of Bet Hedger Evolution

Beyond the (Geometric) Mean: Stochastic Models Undermine Deterministic Predictions of Bet Hedger Evolution

Implementation of Green Marketing on Buyer Decisions to Encourage Green Economy

The implementation of green marketing for coconut fiber utilization in Aceh, specifically in LhokseumaweCity, remains limited. Efforts to market environmental friendly products from coconut fiber have not been completely successful, leading to a low economic return. MSMEs working in this area continue to face challenges in promoting their products. Although MSME managers have previously tried different media to boost sales and sustain the use of coconut fiber, a limited understanding of green marketing strategies has been a barrier. This study aims to identify the factors influencing purchasing decisions for eco-friendly products made from coconut fiber waste. This research is quantitative, focusing on MSMEs selling agricultural or related products in Lhokseumawe City. A single MSME was sampled, chosen through the saturated sample technique due to the small population size, with 100 respondents selected for the study. Data analysis used multiple linear regression. Findings indicate that green products, green prices, green places, and green promotions all have a significant positive impact on consumer purchasing decisions for eco-friendly coir products in Lhokseumawe City. These results affirm that green marketing concepts play a role in influencing purchasing decisions for coir-based eco-products, highlighting the need for green marketing to enhance public awareness of eco-friendly products, reduce waste, and support a green economy.

Genomic and ecological divergence support recognition of a new species of endangered Satyrium butterfly (Lepidoptera, Lycaenidae).

We describe a highly isolated population of hairstreak butterfly from Waterton Lakes National Park, Alberta, Canada, as a new species, Satyriumcuriosolus sp. nov., previously recognized as Satyriumsemiluna (Half-moon Hairstreak). We propose "Curiously Isolated Hairstreak" as the common name due to its disjunct and unusual distribution. Previous whole-genome analyses revealed S.curiosolus has extremely low genomic diversity and is highly divergent from the nearest S.semiluna populations in British Columbia and Montana, more than 400 km distant. Further analysis suggested prolonged inbreeding and isolation for up to ~40,000 years BP. Ecological niche modeling indicated that S.curiosolus occupies environmental conditions that are distinct from S.semiluna, suggesting niche divergence driven by long-term geographical and ecological separation. While host plant and ant associations have not been definitively resolved, they likely differ between S.curiosolus and S.semiluna. As part of this description, we provide whole-genome consensus sequences for each individual of the type series and identify 21,985 single nucleotide polymorphisms (SNPs) that are divergently fixed between S.curiosolus and S.semiluna, including 117 unlinked SNPs distributed across the genome as putative diagnostic markers. Previously listed as Endangered in Canada as the Waterton population of S.semiluna, S.curiosolus should retain this conservation status due to its extreme isolation, small population size, and flatlined genomic diversity. We propose species recognition as a testable hypothesis under the General Lineage Concept and recommend further research to explore the taxonomy, ecological relationships, and conservation of the greater species complex, including S.curiosolus, S.semiluna, and S.fuliginosa.

Addressing the Unaddressed: Challenges in Geospatial Mapping of Typhoid Fever Cases in Ghana

BACKGROUND AND OBJECTIVES Geospatial mapping has been a valuable tool in public health interventions, yet its application in resource-limited settings remains challenging. This study aimed to map cases of typhoid fever intestinal perforations in northeastern Ghana and identify potential case clusters, while assessing the feasibility of conducting such analysis in a resource-limited setting. METHODS We conducted a retrospective analysis of 84 cases treated at a regional referral hospital from September 2023 to January 2024, and patient demographics and hometown locations were collected and mapped. When necessary, focused interviews with hospital staff and community members were conducted to approximate village locations. RESULTS Of the 84 cases, 88% (74 cases) were successfully mapped to the town or village level. However, precise neighborhood mapping was not possible due to the lack of standardized addressing systems. No significant disease clusters were identified, likely due to the small sample size and low population density. The study revealed specific challenges in conducting geospatial analysis in this setting, including duplicate village names, reliance on unpaved roads, and scarcity of detailed mapping systems. CONCLUSIONS While geospatial mapping of typhoid fever cases was largely successful at the town/village level, significant challenges remain in conducting precise analyses in resource-limited settings. This study emphasizes the need for improved mapping technologies, standardized addressing systems, and basic infrastructure enhancements to increase the effectiveness of public health interventions in similar settings worldwide.

Leveraging Synteny to Generate Reference Genomes for Conservation: Assembling the Genomes of Hector's and Māui Dolphins

ABSTRACTEscalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome‐level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterise long‐term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high‐quality genomes for species of conservation concern despite less‐than‐optimal samples and/or sequencing data, demonstrating its use on Hector's and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector's dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference‐guided techniques, utilising chromosome‐level genomes of closely related species. The pipeline assembled highly contiguous chromosome‐level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores &gt; 96.35%), despite non‐optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long‐term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector's and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high‐quality genomic resources to facilitate ongoing conservation genomics research.

Role of rare species in benthic diatom communities: patterns, processes and networks

Biodiversity loss in freshwater is five times higher compared to terrestrial ecosystems and especially threatens rare species. However, even basic knowledge about rarity is missing in aquatic algal ecology, which could be the base of their conservation strategies. Therefore, we investigated rare species in benthic diatom communities of the River Danube’s network system using different rarity concepts. We found that rare and common species are of similar quantities on a regional scale. Genera with fewer taxa provided more rare taxa. The majority of the rare diatom species had small population size among which 45–47% were habitat specialists and geographically restricted, locating streams and river sections whose protection would be outstandingly important. Rare diatom species provided 25–50% higher variability of the communities than common ones. Beta-diversity was also primarily determined by rare species and was mostly driven by species replacement especially in case of specialized and localized rare taxa. Benthic diatom communities established complex community structures. In this network organization, rare species have a core species role with a large impact on the structure and function of the ecological community. Study of rarity is not evident and a number of factors distract it, therefore, we have to carefully consider these uncertainties when dealing with rarity.

Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011to 2023: a retrospective, multicentre, clinical and genomic epidemiology study.

Defining the temporal dynamics of invasive Streptococcus pyogenes (group A Streptococcus) and differences between hyperendemic and lower-incidence regions provides crucial insights into pathogen evolution and, in turn, informs preventive measures. We aimed to examine the clinical and temporal lineage dynamics of Spyogenes across different disease settings in Australia to improve understanding of drivers of pathogen diversity. In this retrospective, multicentre, clinical and genomic epidemiology study, we identified cases of invasive Spyogenes infection from normally sterile sites between Jan 1, 2011, and Feb 28, 2023. Data were collected from fivehospital networks across low-incidence regions in temperate southeast Australia and the hyperendemic, tropical, and largely remote Top End of the Northern Territory of Australia. The crude incidence rate ratio (IRR) of bloodstream Spyogenes infection comparing the Top End and southeast Australia and in First Nations people compared with non-First Nations people was estimated by quasi-Poisson regression. We estimated odds ratios (ORs) of intensive care unit (ICU) admission, in-hospital mortality, and 30-day mortality for the Top End versus southeast Australia using logistic regression. Retrieved and successfully sequenced isolates were assigned lineages at whole-genome resolution. Temporal trends in the composition of co-circulating lineages were compared between the two regions. We used an S pyogenes-specific multistrain simulated transmission model to examine the relationship between host population-specific parameters and observed pathogen lineage dynamics. The prevalence of accessory genes (those present in 5-95% of all genomes) was compared across geographies and temporal periods to investigate genomic drivers of diversity. We identified 500cases of invasive Spyogenes infection in patients in the Top End and 495cases in patients in southeast Australia. The crude IRR of bloodstream infection for the Top End compared with southeast Australia was 5·97 (95% CI 4·61-7·73) across the entire study period; in the Top End, infection disproportionately affected First Nations people compared with non-First Nations people (5·41, 4·28-6·89). The odds of in-hospital mortality (OR 0·43, 95% CI 0·26-0·70), 30-day mortality (0·38, 0·23-0·63), and ICU admission (0·42, 0·30-0·59) were lower in the Top End than in southeast Australia. Longitudinal lineage analysis of 642 Spyogenes genomes identified waves of replacement with distinct lineages in the Top End, whereas southeast Australia had a small number of dominant lineages that persisted and cycled in frequency. The transmission model qualitatively reproduced a similar pattern of replacement with distinct lineages when using a high transmission rate, small population size, and high levels of human movement-characteristics similar to those of communities in the hyperendemic Top End. Using a lower transmission rate, larger population size, and lower levels of migration similar to those of communities in urbanised southeast Australia, the transmission model qualitatively reproduced a pattern of dominant lineages that cycled in frequency. Despite distinct circulating lineages, the prevalence of accessory genes in the bacterial population was maintained across geographies and temporal periods. In a hyperendemic setting, the replacement of distinct Spyogenes lineages occurred in waves, which could be linked to the disproportionate burden of disease and sparse human population in this setting. The maintenance of bacterial gene frequency could be consistent with multilocus selection. These findings suggest that lineage-specific interventions-such as vaccines under development-should consider disease setting and, without broad cross-protection, might lead to lineage replacement. National Health and Medical Research Council, and Leducq Foundation.

50 years of invertebrate conservation under the United States Endangered Species Act—history and threats to species

IntroductionThe United States Endangered Species Act celebrated its 50th anniversary in 2023. As a hallmark piece of environmental legislation, the Act has successfully prevented the extinction of hundreds of species. During these last 50 years, we have observed the decline of many species of invertebrates, resulting in the listing of 356 species.MethodsHere, we summarize the state of endangered invertebrates using text mining to review all listing documents, including listing decisions, species status assessments, critical habitat designations, and status reviews. In our review, we evaluate the most prevalent threats for aquatic and terrestrial invertebrates.ResultsWe found that invertebrates have been assessed and listed consistently in the past 50 years, and the last eight years have seen an uptick in status reviews. Further, we find that pollution, natural system modifications (such as dams), and intrinsic factors (such as small population sizes or number of populations) are the major contributing threats to aquatic invertebrates. On the other hand, problematic biotic factors (such as invasive species), climate change, residential and commercial development, and pollution are the major threats to terrestrial invertebrates.DiscussionOverall, our study reviews the current threats to invertebrates and provides a baseline for the next 50 years in the face of a shifting threat and conservation arena.

Genetic Diversity, Genetic Structure, and Demographic History of Black Snub-Nosed Monkey (Rhinopithecus strykeri) in the Gaoligong Mountains, Southwestern China.

The Gaoligong Mountains, located in the southeastern Tibetan Plateau, is one of the world's biodiversity hotspots and provides a refugium for many endangered endemic animals. In this study, we reported a population genetic study on black snub-nosed monkey (Rhinopithecus strykeri), a critically endangered primate endemic to the Gaoligong Mountains, yet their large-scale population genetic study remains underexplored. Here, we performed population genetic analyses from two geographical populations (Pianma and Luoma) based on targeted genomic single-nucleotide polymorphism (SNP) data (37.7 K) and mitochondrial DNA (mtDNA) control region (842 bp). Both nuclear SNP data and mtDNA revealed relatively low levels of genetic variation in both populations compared to other reported primates, which is most likely to be explained by loss of historical genetic diversity due to inbreeding and long-term small effective population size, thus potentially aggravating the effects of inbreeding and genetic depression. Phylogenetic and population structure analyses for mtDNA revealed two deep lineages (approximately 0.69 million years ago), but limited genetic differentiation in nuclear data, which might have been caused by the Late Cenozoic uplift of the Tibetan Plateau and glacial refuge, and subsequent secondary contact as a result of historically high and bidirectional gene flow between populations. Ecological niche modeling and landscape connectivity analyses also showed historical and recent connectivity between two geographical populations. The demographic history inferred from both mtDNA and nuclear data revealed at least two continuous declines in the effective population size occurring around 43 Kya and 8-10 Kya, respectively, probably due to Pleistocene glaciations and subsequent human activities. Our results provide the first detailed and comprehensive genetic insights into the genetic diversity, population structure, and demographic history of a critically endangered species, and provide essential baseline information to guide conservation efforts.

Immersive Virtual Reality for Enabling Patient Experience and Enrollment in Oncology Clinical Trials: A Feasibility Study.

Background/Objectives: Informed consent is a crucial part of the clinical trial enrollment process in which patients are asked to understand and provide approval for medical interventions. Consent forms can be complex and hinder patient comprehension, highlighting the need for novel tools to improve the patient enrollment experience. This feasibility study aimed to develop an immersive technology to enroll human subjects in oncology clinical trials and provide 3D avatar-based informed consent in a virtual reality (VR) environment. Methods: Clinical feasibility and the effects of head-mounted VR devices on motion sickness and educational quality were evaluated in adult oncology patients enrolled in an intravenous (IV) port placement intervention study. Participants received before- and after-questionnaires to measure their understanding of the information received in VR. A follow-up questionnaire was given four weeks post-consent to measure knowledge retention. Results: Clinical staff reported that VR technology was manageable to use. Among 16 adult participants, all reported that VR was well tolerated with no motion sickness. The mean pre-intervention knowledge score was 64.6%, with an immediate post-intervention knowledge score of 97.9%. A mean knowledge score of 93.3% four-weeks post-consent was observed among 10/16 participants who completed a follow-up questionnaire. Conclusions: These findings support that VR is well tolerated and effective at delivering information during the informed consent process for oncology clinical trials. Key limitations include the small sample size and single clinical population. Further trials are warranted to compare efficacy over traditional consenting mechanisms and include more diverse clinical populations among a wider participant pool.

Human deleterious mutation rate slows adaptation and implies high fitness variance.

Each new human has an expected new deleterious mutations. Using a novel approach to capture complex linkage disequilibria from high using genome-wide simulations, we confirm that fitness decline due to the fixation of many slightly deleterious mutations can be compensated by rarer beneficial mutations of larger effect. The evolution of increased genome size and complexity have previously been attributed to a similarly asymmetric pattern of fixations, but we propose that the cause might be high rather than the small population size posited as causal by drift barrier theory. High within-population variance in relative fitness is an inevitable consequence of high combined with inferred human deleterious effect sizes; two individuals will typically differ in fitness by 15-40%. The need to compensate for the deluge of deleterious mutations slows net adaptation (i.e. to the external environment) by ~13%-55%. The rate of beneficial fixations is more sensitive to changes in the mutation rate than the rate of deleterious fixations is. As a surprising consequence of this, an increase (e.g. 10%) in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.

Optimization of commercial SNP arrays and the generation of a high-efficiency GenoBaits Peanut 10K panel

To create a more comprehensive genetic analysis panel for peanuts, three high-density SNP panels were exploited. The refined SNP panel, PHR0301_Ah10K, comprises 10,000 SNP sites and demonstrated outstanding performance in sequence data analysis. It recorded the highest proportions of 99.53%, 96.48%, and 59.72% for the SNPs with minor allele frequency thresholds of MAF > 5%, MAF > 10%, and MAF > 20%, respectively. Moderate polymorphic information content (PIC) values were observed, with an average of 0.26, suggesting that the optimized SNP panel is informative. However, the PIC value for the four panels were skewed due to the small population size and limited genetic diversity (GD), as evidenced by the Kinship, PCA, and LD decay analyses. However, PHR0301_Ah10K demonstrated superior performance compared to the others in terms of variance explained in the PCA analysis while the outcomes of the genetic analyses confirmed its genotyping ability in peanut. The putative SNP sites associated with increased oleic acid levels have been integrated into this panel and validated, thus significantly enhancing its breeding potential. Moreover, the cost of genotyping by target sequencing (GBTS) using this panel is less than $9 per sample, making it more affordable. Due to its exceptional informativeness, cost-effectiveness, and breeding potential, we recommend this SNP panel for GBTS in peanut.

Challenges and Possible Strategies to Address Them in Rare Disease Drug Development: A Statistical Perspective.

Developing drugs for rare diseases presents unique challenges from a statistical perspective. These challenges may include slowly progressive diseases with unmet medical needs, poorly understood natural history, small population size, diversified phenotypes and genotypes within a disorder, and lack of appropriate surrogate endpoints to measure clinical benefits. The Real-World Evidence (RWE) Scientific Working Group of the American Statistical Association Biopharmaceutical Section has assembled a research team to assess the landscape including challenges and possible strategies to address these challenges and the role of real-world data (RWD) and RWE in rare disease drug development. This paper first reviews the current regulations by regulatory agencies worldwide and then discusses in more detail the challenges from a statistical perspective in the design, conduct, and analysis of rare disease clinical trials. After outlining an overall development pathway for rare disease drugs, corresponding strategies to address the challenges are presented. Other considerations are also discussed for generating relevant evidence for regulatory decision-making on drugs for rare diseases. The accompanying paper discusses how RWD and RWE can be used to improve the efficiency of rare disease drug development.

Short communication: exploring genetic associations with cryptorchidism in Wagyu cattle.

Wagyu cattle have seen an upsurge in popularity within the United States in recent years, as consumers seek improved meat quality and intramuscular fat, also known as marbling. The small effective population size of Wagyu cattle, paired with the growing interest in the breed, has led to increased inbreeding. As inbreeding has increased, the emergence of deleterious traits (i.e., progressive bovine myeloenecphaly, factor XI deficiency, and spherocytosis) has increased. Cryptorchidism, when one or both testes fail to descend into the scrotum, can lead to reduced fertility and is observed more frequently in certain cattle lines suggesting a genetic component to the disorder. This study hypothesized that cryptorchidism is recessively inherited. To test this hypothesis, a population of 18 Wagyu cattle from an extended family was genotyped, and a haplotype and genome-wide association analysis was completed to identify genomic regions associated with cryptorchidism. There were 218 haplotypes that trended toward an association (P < 0.05) though none were significant after multiple testing corrections were applied (false discovery rate <0.05). Two loci were associated (P < 1 × 10-5) with cryptorchidism on BTA4 and BTA13 in a dominant inheritance model and one locus on BTA4 was associated in an additive model. While this study identified loci associated with cryptorchidism in cattle, due to the small sample size, additional animals need to be evaluated to identify and validate the genomic regions associated with cryptorchidism.

Recombination and the role of pseudo-overdominance in polyploid evolution.

Natural selection is an imperfect force that can under some conditions fail to prevent the buildup of deleterious mutations. Small population sizes and the lack of recombination are two such scenarios that reduce the efficiency of selection. Under these conditions, the disconnect between deleterious genetic load and individual fitness due to the masking of recessive deleterious mutations in heterozygous individuals may result in the emergence of pseudo-overdominance, wherein the buildup of haplotypes with complementary sets of deleterious mutations results in apparent heterozygote advantage and an increase in linked neutral diversity. In polyploids, the presence of additional allelic copies magnifies this masking effect and may therefore increase the probability of pseudo-overdominance. Here, we simulate the evolution of small diploid and autotetraploid populations to identify the conditions that support the evolution of pseudo-overdominance. We discover that pseudo-overdominance evolves under a much wider range of parameters in autotetraploids than in diploids with identical population sizes, and that in many parts of parameter space there is an inverse relationship between fitness and recombination rate. These results imply that pseudo-overdominance may be more common than previously thought. We conclude by discussing the current evidence for pseudo-overdominance in species with polyploid histories, as well as its implications in agriculture due to the prevalence of polyploidy in crops.

Assessing the current distribution and potential habitat availability for Kaempfer's tody‐tyrant: a restricted‐range and threatened species from the Atlantic Rainforest

Human disturbances are threatening biodiversity worldwide, and species with restricted geographic distribution or small population sizes are more likely to become extinct. The prevention of extinctions is an urgent matter and knowledge on the ecology and distribution of threatened species is required to outline conservation strategies. In this study, we investigate the potential and current geographic distribution of the threatened endemic Atlantic Forest bird species Kaempfer's tody‐tyrant Hemitriccus kaempferi, to advance conservation efforts for this species. We used a species distribution model (SDM) to assess the potential geographic distribution of the species and to detect environmentally suitable areas to guide field survey efforts. We then established the current geographic distribution of H. kaempferi and estimated the proportion of habitat remaining and how much of it is located within protected areas. We found that suitable areas for H. kaempferi are restricted to low‐elevation lands of the south coast of Paraná state and the north and central coast of Santa Catarina state, southern Brazil. The predicted distribution encompasses an area of 7483 km2 of which 44% is currently covered by forest remnants and 15% is inside protected areas. The current geographic distribution was based on 166 occurrence records and encompasses an area of 5898 km2 of which 42% is covered by forest remnants and 13% by protected areas. Coverage of protected areas required to adequately protect the species was estimated as 71% of the predicted area. The species' presence was confirmed in only eight protected areas. Due to its restricted range, great habitat loss, and small coverage of protected areas, conservation actions need to urgently focus on the conservation of remaining forest fragments, habitat restoration programs, the establishment of new protected areas, and citizen awareness.