Advancing the microbiome research community.

The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology.

Pluripotency of a founding field: rebranding developmental biology.

The field of developmental biology has declined in prominence in recent decades, with off-shoots from the field becoming more fashionable and highly funded. This has created inequity in discovery and opportunity, partly due to the perception that the field is antiquated or not cutting edge. A 'think tank' of scientists from multiple developmental biology-related disciplines came together to define specific challenges in the field that may have inhibited innovation, and to provide tangible solutions to some of the issues facing developmental biology. The community suggestions include a call to the community to help 'rebrand' the field, alongside proposals for additional funding apparatuses, frameworks for interdisciplinary innovative collaborations, pedagogical access, improved science communication, increased diversity and inclusion, and equity of resources to provide maximal impact to the community.

The asymmetry of antimatter in the proton.

The fundamental building blocks of the proton-quarks and gluons-have been known for decades. However, we still have an incomplete theoretical and experimental understanding of how these particles and their dynamics give rise to the quantum bound state of the proton and its physical properties, such as its spin1. The two up quarks and the single down quark that comprise the proton in the simplest picture account only for a few per cent of the proton mass, the bulk of which is in the form of quark kinetic and potential energy and gluon energy from the strong force2. An essential feature of this force, as described by quantum chromodynamics, is its ability to create matter-antimatter quark pairs inside the proton that exist only for a very short time. Their fleeting existence makes the antimatter quarks within protons difficult to study, but their existence is discernible in reactions in which a matter-antimatter quark pair annihilates. In this picture of quark-antiquark creation by the strong force, the probability distributions as a function of momentum for the presence of up and down antimatter quarks should be nearly identical, given that their masses are very similar and small compared to the mass of the proton3. Here we provide evidence from muon pair production measurements that these distributions are considerably different, with more abundant down antimatter quarks than up antimatter quarks over a wide range of momenta. These results are expected to revive interest in several proposed mechanisms for the origin of this antimatter asymmetry in the proton that had been disfavoured by previous results4, and point to future measurements that can distinguish between these mechanisms.

Critical Assessment of Metagenome Interpretation: the second round of challenges.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

Long-term follow-up of liver-directed, adeno-associated vector-mediated gene therapy in the canine model of hemophilia A.

Questions remain concerning the long-term efficacy, safety, and site(s) of transgene expression following adeno-associated vector (AAV) therapy. We report a long-term follow-up of 8 (male = 4, hemizygous, and female = 4, homozygous) dogs with severe hemophilia A treated with a single portal vein infusion of a B-domain-deleted (BDD)-canine FVIII (cFVIII) AAV vector (median dose = 1.25 × 1013 vg/kg, AAV2 = 4, AAV6 = 3, and AAV8 = 1). After a median follow-up of 10.8 years (8.2-12.0 years), persistent FVIII:C (median one-stage = 12.7%, chromogenic = 7.2%) was seen in all responding dogs (n = 6), with improvement in annualized bleed rates (pre = 3.9 vs post = 0.3 event per year; P = .003). Anti-AAV capsid neutralizing antibodies (nAbs) toward the dosed capsid were detected throughout the study, with limited cross-reactivity to other capsids. nAb titers for all capsid serotypes declined with time, although they remained at levels precluding redosing with the same capsid. AAV-BDD-cFVIII DNA was detected in the liver of all dogs (median = 0.15 vg per diploid genome), with lower levels in the spleen in 4 dogs (median = 0.005 vg per diploid genome). Consistent with the liver-specific promoter, BDD-cFVIII mRNA was only detected in the liver. Postmortem examination demonstrated no evidence of chronic liver disease or liver malignancy. Persistent FVIII expression and an improved bleeding phenotype was seen for more than a decade after vector delivery. This is the longest follow-up reported in a preclinical model supporting long-term efficacy and safety of AAV-mediated gene therapy.

Are lateralized and bold fish optimistic or pessimistic?

Cognitive bias is defined as the influence of emotions on cognitive processes. The concept of the cognitive judgement bias has its origins in human psychology but has been applied to animals over the past 2 decades. In this study we were interested in determining if laterality and personality traits, which are known to influence learning style, might also be correlated with a cognitive bias in the three-spined sticklebacks (Gasterosteus aculeatus). We used the judgement bias test with the go/no-go procedure where fish were first trained to discriminate between a black and white card and, after reaching a minimum learning criterion, tested their response to an ambiguous card (grey). Optimistic subjects were expected to have a high expectation of reward associated with an ambiguous stimulus, whereas pessimistic subjects a high expectation of non-reward. We used an emergence and a mirror test to quantify boldness and laterality, respectively. We hypothesised that male, bolder and more strongly lateralized fish would be more optimistic than female, shy and less strongly lateralised fish. We found that males and more strongly lateralized fish were more optimistic than females and less strongly lateralized fish. In addition, bold males were more optimistic than shy males as we predicted, but females showed the opposite pattern. Finally, fish trained on the black colour card learned the training task faster than those trained on a white card. Our results indicate that both laterality and personality traits are linked to animals' internal states (pessimistic or optimistic outlooks) which likely has broad implications for understanding animal behaviour particularly in a welfare context.

An assessment of future rewilding potential in the United Kingdom.

Restoring ecosystems is an imperative for addressing biodiversity loss and climate change, and achieving the targets of the Kunming-Montreal Global Biodiversity Framework. One form of restoration, rewilding, may have particular promise but may also be precluded by requirements for other forms of land use now or in the future. This opportunity space is critical but challenging to assess. We explored the potential area available for rewilding in Great Britain until the year 2080 with a multisectoral land-use model with several distinct climatic and socioeconomic scenarios. By 2080, areas from 5000 to 7000 km2 were either unmanaged or managed in ways that could be consistent with rewilding across scenarios without conflicting with the provision of ecosystem services. Beyond these areas, another 24,000-42,000 km2 of extensive upland management could provide additional areas for rewilding if current patterns of implementation hold in the future. None of these areas, however, coincided reliably with ecosystems of priority for conservation: peatlands, ancient woodlands, or wetlands. Repeatedly, these ecosystems were found to be vulnerable to conversion. Our results are not based on an assumption of support for or benefits from rewilding and do not account for disadvantages, such as potential losses of cultural landscapes or traditional forms of management, that were beyond the modeled ecosystem services. Nevertheless, potential areas for rewilding emerge in a variety of ways, from intensification elsewhere having a substantial but inadvertent land-sparing effect, popular demand for environmental restoration, or a desire for exclusive recreation among the wealthy elite. Our findings therefore imply substantial opportunities for rewilding in the United Kingdom but also a need for interventions to shape the nature and extent of that rewilding to maintain priority conservation areas and societal objectives.

Una evaluación del potencial futuro de la resilvestración en el Reino Unido Resumen La restauración de ecosistemas es urgente para abordar la pérdida de biodiversidad y el cambio climático, así como para lograr los objetivos del Marco Mundial de Biodiversidad de Kunming­Montreal. Un método de restauración, la resilvestración, puede ser particularmente prometedor, aunque también puede ser excluido por los requerimientos para otras formas de uso de suelo actuales o en el futuro. Este espacio de oportunidad es crítico, pero también un reto para evaluar. Exploramos el área potencial disponible para el resilvestrado en Gran Bretaña hasta el año 2080 con un modelo multisectorial de uso de suelo con varios escenarios climáticos y socioeconómicos. Para este año, las áreas entre 5,000 y 7,000 km2 no estaban gestionadas o lo estaban, pero de manera que podían ser consistentes con el resilvestrado de los escenarios sin conflictuar el suministro de servicios ambientales. Más allá de estas áreas, otros 24,000­42,000 km2 de gestión extensiva tierra arriba podrían proporcionar áreas adicionales para el resilvestrado si los patrones actuales de implementación siguen en pie en el futuro. Sin embargo, ninguna de estas áreas coincidió de manera confiable con los ecosistemas de prioridad para la conservación: las turberas, bosques antiguos o humedales. Estos ecosistemas aparecieron varias veces como vulnerables a la conversión. Nuestros resultados no están basados en una suposición de apoyo para o los beneficios de la resilvestración y no consideran las desventajas, como la pérdida potencial de paisajes culturales o las maneras tradicionales de manejo, que estaban fuera del alcance de los servicios ambientales modelados. Sin embargo, las áreas potenciales para el resilvestrado emergen en una variedad de formas, desde la intensificación en otros lugares con un efecto de ahorro de tierras sustancial pero inadvertido, la demanda popular por la restauración ambiental o el deseo de una recreación exclusiva entre la elite acaudalada. Por lo tanto, nuestros descubrimientos implican una oportunidad sustancial para la resilvestración en el Reino Unido, aunque también una necesidad de intervenciones para moldear la naturaleza y la extensión de ese resilvestrado para mantener las áreas prioritarias de conservación y los objetivos sociales.

A cost-utility study of elective haemorrhoidectomies in Canada.

AIM: The aim was to estimate the 10-year cost-utility of haemorrhoidectomy surgery with preference-based measures of health using Canadian health utility measures and costs. METHODS: Patients undergoing elective haemorrhoidectomies by general and colorectal surgeons in British Columbia, Vancouver, between September 2015 and November 2022, completed preoperatively and postoperatively the EuroQol five-dimension five-level health-related quality of life questionnaire (EQ-5D-5L). Quality-adjusted life years (QALYs) attributable to surgery were calculated by discounting preoperative and postoperative health utility values derived from the EQ-5D-5L. Costs were measured from a health system perspective which incorporated costs of hospital stay and specialists' fees. Results are presented in 2021 Canadian dollars. RESULTS: Of 94 (47%) patients who completed both the preoperative and postoperative questionnaires, the mean gain in QALYs 10 years after surgery was 1.0609, assuming a 3.5% annual discounting rate. The average cost of the surgery was $3166. The average cost per QALY was $2985 when benefits of the surgery were assumed to accrue for 10 years. The cost per QALY was higher for women ($3821) compared with men ($2485). Participants over the age of 70 had the highest cost per QALY ($8079/QALY). CONCLUSIONS: Haemorrhoidectomies have been associated with significant gains in health status and are inexpensive relative to the associated gains in quality of life based on patients' perspectives of their improvement in health and well-being.

Acipenserid herpesvirus 2 genome and partial validation of a qPCR for its detection in white sturgeon Acipenser transmontanus.

White sturgeon Acipenser transmontanus is the primary species used for caviar and sturgeon meat production in the USA. An important pathogen of white sturgeon is acipenserid herpesvirus 2 (AciHV-2). In this study, 4 archived isolates from temporally discrete natural outbreaks spanning the past 30 yr were sequenced via Illumina and Oxford Nanopore Technologies platforms. Assemblies of approximately 134 kb were obtained for each isolate, and the putative ATPase subunit of the terminase gene was selected as a potential quantitative PCR (qPCR) target based on sequence conservation among AciHV-2 isolates and low sequence homology with other important viral pathogens. The qPCR was repeatable and reproducible, with a linear dynamic range covering 5 orders of magnitude, an efficiency of approximately 96%, an R2 of 0.9872, and an analytical sensitivity of 103 copies per reaction after 35 cycles. There was no cross-reaction with other known viruses or closely related sturgeon species, and no inhibition by sturgeon DNA. Clinical accuracy was assessed from white sturgeon juveniles exposed to AciHV-2 by immersion. Viral culture (gold standard) and qPCR were in complete agreement for both cell culture negative and cell culture positive samples, indicating that this assay has 100% relative accuracy compared to cell culture during an active outbreak. The availability of a whole-genome sequence for AciHV-2 and a highly specific and sensitive qPCR assay for detection of AciHV-2 in white sturgeon lays a foundation for further studies on host-pathogen interactions while providing a specific and rapid test for AciHV-2 in captive and wild populations.

Utilization of genetic testing in men with advanced prostate cancer.

BACKGROUND: Genetic evaluation of men with advanced prostate cancer is recognized as imperative both to guide treatment decisions and to trigger cascade genetic testing of family members. Here we investigate utilization patterns of genetic testing among a contemporary cohort of men with advanced prostate cancer at our institution. METHODS: We queried the Northwestern Electronic Data Warehouse from January 2021 to present for all men diagnosed with National Comprehensive Cancer Network high-risk/very high-risk, regional, or metastatic prostate cancer. Patients were excluded from analyses if treated at an outside institution and/or presented for a second opinion evaluation. Statistics were performed using t-test, Chi-squared test, and univariable and multivariable logistic regression with significance defined as p < 0.05. RESULTS: Atotal of 320 men (52.5%) had local/regional disease and 290 (47.5%) had metastatic disease, 53 (18.3%) of whom had castrate resistant prostate cancer. Rates of germline genetic testing rate were low in patients with localized disease (9.4%) and metastatic disease (34.1%). Only 19 (35.8%) men diagnosed with metastatic castrate resistant prostate cancer underwent germline genetic evaluation. Germline testing was most frequently discussed or ordered by medical oncologists (52%) followed by urologists (20%). Men who underwent germline testing were younger (p < 0.001), more likely to have Medicaid or private insurance (p = 0.002), and more likely to have metastatic disease (p < 0.001). There were no statistically significant differences in baseline PSA, ethnicity, race, or castration sensitivity status. Age (odds ratio [OR]: 0.94, 95% confidence interval [CI]: 0.91-0.97, p < 0.001) and metastatic disease (OR: 5.71, 95% CI: 3.63-9.22, p < 0.001) were significant independent predictors of genetic testing on multivariable logistic regression. CONCLUSIONS: Here we report that utilization of genetic testing is associated with metastatic disease and inversely associated with age. Overall, utilization rates of genetic testing remain low in all patient groups, including in the metastatic castrate resistant setting, where genetic testing can identify patients with homologous recombination repair deficiency who may benefit from use of targeted therapeutics such as PARP inhibitors. Genetic testing in men with aggressive prostate cancer is critical and barriers to routine implementation of testing require further study to develop strategies to improve utilization rates.

Superfluid Helium Drops Levitated in High Vacuum.

We demonstrate the trapping of millimeter-scale superfluid helium drops in high vacuum. The drops are sufficiently isolated that they remain trapped indefinitely, cool by evaporation to 330 mK, and exhibit mechanical damping that is limited by internal processes. The drops are also shown to host optical whispering gallery modes. The approach described here combines the advantages of multiple techniques, and should offer access to new experimental regimes of cold chemistry, superfluid physics, and optomechanics.

Implementation Barriers and Experiences of Eligible Patients Who Failed to Enroll in Collaborative Care for Depression and Anxiety.

BACKGROUND: Effective and efficient implementation of the Collaborative Care Model (CoCM) for depression and anxiety is imperative for program success. Studies examining barriers to implementation often omit patient perspectives. OBJECTIVES: To explore experiences and attitudes of eligible patients referred to CoCM who declined participation or were unable to be reached, and identify implementation barriers to inform strategies. DESIGN: Convergent mixed-methods study with a survey and interview. PARTICIPANTS: Primary care patients at an academic medical center who were referred to a CoCM program for anxiety and depression by their primary care clinician (PCC) but declined participation or were unable to be reached by the behavioral health care manager to initiate care (n = 80). Interviews were conducted with 45 survey respondents. MAIN MEASURES: Survey of patients' referral experiences and behavioral health preferences as they related to failing to enroll in the program. Interview questions were developed using the Consolidated Framework for Implementation Research version 2.0 (CFIR 2.0) to identify implementation barriers to enrollment. KEY RESULTS: Survey results found that patients were uncertain about insurance coverage, did not understand the program, and felt services were not necessary. Referred patients who declined participation were concerned about how their mental health information would be used and preferred treatment without medication. Men agreed more that they did not need services. Qualitative results exhibited a variety of implementation determinants (n = 23) across the five CFIR 2.0 domains. Barriers included mental health stigma, perceiving behavioral health as outside of primary care practice guidelines, short or infrequent primary care appointments, prioritizing physical health over mental health, receiving inaccurate program information, low motivation to engage, and a less established relationship with their PCC. CONCLUSIONS: Multiple barriers to enrollment led to failing to link patients to care, which can inform implementation strategies to address the patient-reported experiences and concerns.

Promoting Evidence-Based Practice: The Influence of Novel Structural Change to Accelerate Translational Rehabilitation.

OBJECTIVE: To evaluate changes in clinicians' use of evidence-based practice (EBP), openness toward EBP, and their acceptance of organizational changes after a rehabilitation hospital transitioned to a new facility designed to accelerate clinician-researcher collaborations. DESIGN: Three repeated surveys of clinicians before, 7-9 months, and 2.5 years after transition to the new facility. SETTING: Inpatient rehabilitation hospital. PARTICIPANTS: Physicians, nurses, therapists, and other health care professionals (n=410, 442, and 448 respondents at Times 1, 2, and 3, respectively). INTERVENTIONS: Implementation of physical (architecture, design) and team-focused (champions, leaders, incentives) changes in a new model of care to promote clinician-researcher collaborations. MAIN OUTCOME MEASURES: Adapted versions of the Evidence-Based Practice Questionnaire (EBPQ), the Evidence-Based Practice Attitudes Scale (EBPAS), and the Organizational Change Recipients' Beliefs Scale (OCRBS) were used. Open-ended survey questions were analyzed through exploratory content analysis. RESULTS: Response rates at Times 1, 2, and 3 were 67% (n=410), 69% (n=422), and 71% (n=448), respectively. After accounting for familiarity with the model of care, there was greater reported use of EBP at Time 3 compared with Time 2 (adjusted meant2=3.51, standard error (SE)=0.05; adj. meant3=3.64, SE=0.05; P=.043). Attitudes toward EBPs were similar over time. Acceptance of the new model of care was lower at Time 2 compared with Time 1, but rebounded at Time 3 (adjusted meant1=3.44, SE=0.04; adj. meant2=3.19, SE=0.04; P<.0001; adj. meant3=3.51, SE=0.04; P<.0001). Analysis of open-ended responses suggested that clinicians' optimism for the model of care was greater over time, but continued quality improvement should focus on cultivating communication between clinicians and researchers. CONCLUSIONS: Accelerating clinician-researcher collaborations in a rehabilitation setting requires sustained effort for successful implementation beyond novel physical changes. Organizations must be responsive to clinicians' changing concerns to adapt and sustain a collaborative translational medicine model and allow sufficient time, probably years, for such transitions to occur.

Retrospective Psychometrics and Effect Heterogeneity in Integrated Data Analysis: Commentary on the Special Issue.

The current special issue of Prevention Science indicates that momentum in using individual participant data (IPD) and integrative data analysis (IDA) to combine and synthesize findings in prevention science has accelerated over the past decade. In this commentary, we focus on two general themes involving methods for harmonizing measures and findings of effect heterogeneity. We describe methods for harmonization as retrospective psychometrics, requiring that we attend to the assumptions necessary for accurate measurement, but adjust our methods given the constraints of working with existing datasets that often involve different measures in different studies. We point to novel approaches for increasing confidence that semantic matching and empirical modeling used in these studies will yield accurate and valid measurements that can be combined in IDA. We also review findings about effect heterogeneity, emphasizing the importance of using etiologic and action theories to identify and evaluate sources of such effects. We note that all of the papers in this issue deserve careful attention, as they illustrate how prevention scientists are approaching the complexities of IDA and exploring novel methods for overcoming its challenges.

Normalization of Prevention Principles and Practices to Reduce Substance Use Disorders Through an Integrated Dissemination and Implementation Framework.

Major research breakthroughs over the past 30 years in the field of substance use prevention have served to: (1) enhance understanding of pharmacological effects on the central and peripheral nervous systems and the health and social consequences of use of psychoactive substances, particularly for children and adolescents; (2) delineate the processes that increase vulnerability to or protect from initiation of substance use and progression to substance use disorders (SUDs) and, based on this understanding, (3) develop effective strategies and practices to prevent the initiation and escalation of substance use. The challenge we now face as a field is to "normalize" what we have learned from this research so that it is incorporated into the work of those involved in supporting, planning, and delivering prevention programming to populations around the world, is integrated into health and social service systems, and helps to shape public policies. But we wish to go further, to incorporate these effective prevention practices into everyday life and the mind-sets of the public, particularly parents and educators. This paper reviews the advances that have been made in the field of prevention and presents a framework and recommendations to achieve these objectives generated during several meetings of prevention and implementation science researchers sponsored by the International Consortium of Universities for Drug Demand Reduction (ICUDDR) that guides a roadmap to achieve "normalization."

Effect of storage periods and conditions on embryonic mortalities and hatchability of artificially incubated ostrich eggs.

1. Despite substantial research, the hatching failure of ostrich eggs remains a key concern for many commercial breeding farms.2. This source of reproductive failure needs to be addressed for ostrich farming to become more profitable.3. Information from 2212 eggs were obtained from the ostrich resource flock at the Oudtshoorn Research Farm (2013-2014). Egg data were divided on a daily basis into two groups: Group 1 included eggs stored from 1 to 13 d in cold storage (CS) at a controlled temperature of 17°C and a relative humidity (RH) of 90%. Group 2 was stored for the same time interval as Group 1, but in a cool room (CR) at ambient temperature to simulate the uncontrolled storage conditions prevalent on most breeding farms.4. Overall embryonic mortalities (OEM) were significantly higher for eggs stored for 1 d (0.38 ± 0.04) and for 8 d or more (between 0.31 ± 0.04 and 0.43 ± 0.04) compared to eggs stored for between 2 and 7 d (between 0.20 ± 0.03 and 0.26 ± 0.04).5. The moisture loss during storage (ML) for eggs stored for 13 d in CS during spring was on average slightly higher (1.28%) than that during summer (0.95%). In contrast, the ML of eggs stored in the CR for 13 d was significantly higher, at 1.59% in spring and 2.08% in summer.6. A general reduction in chick weight occurred for all the seasons (winter, spring and summer) as the number of storage days increased. Ostrich eggs should be stored for between 2 and 8 d under controlled storage conditions for improved hatchability.

Peer Activate: A Feasibility Trial of a Peer-Delivered Intervention to Decrease Disparities in Substance Use, Depression, and Linkage to Substance Use Treatment.

Although effective evidence-based interventions (EBIs) exist, racial/ethnic minority individuals with lower income are less likely to have access to these interventions and may experience greater stigma in the health care system, resulting in disproportionate rates of morbidity and mortality. Peer recovery specialists (PRSs) may be uniquely suited to address barriers faced by those from impoverished areas; however, peers have not traditionally been trained in implementing EBIs. The current open-label trial (N = 8) was performed to evaluate implementation and preliminary effectiveness of an adapted EBI supporting recovery, linkage to treatment, and reduced depression. Results suggest the intervention was feasible, acceptable, and appropriate for linking individuals from a community setting to substance use treatment and could be delivered with fidelity by a peer interventionist. Participants who completed the intervention demonstrated clinically reliable decreases in substance use and depressive symptoms. Findings provide initial support for PRS dissemination of EBIs to increase linkage to care and support recovery in traditionally underserved populations. [Journal of Psychosocial Nursing and Mental Health Services, 61(11), 23-31.].

Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.

BACKGROUND: Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates. RESULTS: Our results show that long-read classifiers generally performed best. Several short-read classification and profiling methods produced many false positives (particularly at lower abundances), required heavy filtering to achieve acceptable precision (at the cost of reduced recall), and produced inaccurate abundance estimates. By contrast, two long-read methods (BugSeq, MEGAN-LR & DIAMOND) and one generalized method (sourmash) displayed high precision and recall without any filtering required. Furthermore, in the PacBio HiFi datasets these methods detected all species down to the 0.1% abundance level with high precision. Some long-read methods, such as MetaMaps and MMseqs2, required moderate filtering to reduce false positives to resemble the precision and recall of the top-performing methods. We found read quality affected performance for methods relying on protein prediction or exact k-mer matching, and these methods performed better with PacBio HiFi datasets. We also found that long-read datasets with a large proportion of shorter reads (< 2 kb length) resulted in lower precision and worse abundance estimates, relative to length-filtered datasets. Finally, for classification methods, we found that the long-read datasets produced significantly better results than short-read datasets, demonstrating clear advantages for long-read metagenomic sequencing. CONCLUSIONS: Our critical assessment of available methods provides best-practice recommendations for current research using long reads and establishes a baseline for future benchmarking studies.

Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?

The origins of sex-biased differences in disease and health are of growing interest to both medical researchers and health professionals. Several major factors have been identified that affect sex differences in incidence of diseases and mental disorders. These are: sex chromosomes, sex hormones and female immunity, sexual selection and antagonistic evolution, and differential susceptibility of sexes to environmental factors. These factors work on different time scales and are not exclusive of each other. Recently, a combined Sexual Selection-Sex Hormones (SS-SH) Theory was presented as an evolutionary mechanism to explain sex-biased differences in diseases and mental disorders (Singh in J Mol Evol 89:195-213, 2021). In that paper disease prevalence trends were investigated, and non-sex-specific diseases were hypothesized to be more common in males than in females in general. They showed signs of exceptions to this trend with inflammatory diseases and stress-related mental disorders that were more common in females. We believe that the SS-SH theory requires the consideration of psycho-social stress (PSS) to explain the predominance of female-biased mental disorders and some other exceptions in their findings. Here we present a theory of sex-differential experience of PSS and provide quantitative support for the combined SS-SH-PSS Theory using age-standardized incidence rates (ASIRs) recording the levels of male- and female-bias in data obtained from different countries. The grand theory provides an evolutionary framework for explaining patterns of sex-biased trends in the prevalence of disease and health. Further exploration of women's vulnerability to social factors may help to facilitate new treatments for female-biased diseases.