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This essay examines relationships between agrarian ritual observances and specific maize cycle periodicities in Tepoztlan, Morelos. A comparison of the Tepoztecan data with descriptions of the solar/civil calendar contained in book 2 of the Florentine Codex reveals that identical periodicities occurred, albeit nearly three months earlier, for the sixteenth-century Aztecs. Our analysis raises questions concerning the origin, persistence, and mechanics of the Aztec calendar described by Sahagun.

A new compilation of historical observations and archaeomagnetic measurements of magnetic inclination for the last 1000 years from eastern Australia (the eastern Australian Inclination Record [eAIR2012]) has revealed the existence of a well-defined inclination anomaly in the region. Evidence of this magnetic feature has been preserved in sedimentary records from across eastern Australia, though this has not previously been recognised. Analyses of additional sedimentary sequences have confirmed the incidence and timing of this feature, revealing its presence between the 13th and 18th centuries ad. The inclination of the field during this episode appears to have been steeper than at any time since the start of the Holocene. Lake sediment evidence suggests that the anomaly is a composite feature, displaying a distinct peak at cal. ad 1270–1386 (±2 σ uncertainty), reappearing after cal. ad 1431–1651 (±2 σ uncertainty) and disappearing before cal. ad 1822±46 (±2 σ uncertainty). The disappearance of the anomaly is tightly bracketed in the historical record between ad 1770 and 1777. The rapid shift in inclination during the 18th century ad offers considerable potential as a means of dating a critical period of Australian environmental history, an episode that currently lies beyond the reach of established dating methods. This information also provides a valuable constraint on models of regional geomagnetic field change over centennial and millennial timescales. Our examination of the historical record has revealed that the inclination measurements made by the 18th-century French explorer La Pérouse are consistently erroneous. Since La Pérouse’s data make up 13% of the total body of pre-19th century inclination records, the inclusion of these measurements in global compendia of magnetic observations may seriously skew attempts to model the geomagnetic field. We advocate that La Pérouse’s inclination measurements should therefore be employed only with considerable caution. [ABSTRACT FROM PUBLISHER]

Abstract Background Physical activity is essential for older peoples’ physical and mental health and for maintaining independence. Guidelines recommend at least 150 minutes weekly, of at least moderate intensity physical activity, with activity on most days. Older people’s most common physical activity is walking, light intensity if strolling, moderate if brisker. Less than 20% of United Kingdom 65–74 year olds report achieving the guidelines, despite most being able to. Effective behaviour change techniques include strategies such as goal setting, self-monitoring, building self-efficacy and relapse prevention. Primary care physical activity consultations allow individual tailoring of advice. Pedometers measure step-counts and accelerometers measure physical activity intensity. This protocol describes an innovative intervention to increase walking in older people, incorporating pedometer and accelerometer feedback within a primary care nurse physical activity consultation, using behaviour change techniques. Methods/Design Design: Randomised controlled trial with intervention and control (usual care) arms plus process and qualitative evaluations. Participants: 300 people aged 60–74 years registered with 3 general practices within Oxfordshire and Berkshire West primary care trusts, able to walk outside and with no restrictions to increasing their physical activity. Intervention: 3 month pedometer and accelerometer based intervention supported by practice nurse physical activity consultations. Four consultations based on behaviour change techniques, physical activity diary, pedometer average daily steps and accelerometer feedback on physical activity intensity. Individual physical activity plans based on increasing walking and other existing physical activity will be produced. Outcomes: Change in average daily steps (primary outcome) and average time spent in at least moderate intensity physical activity weekly (secondary outcome) at 3 months and 12 months, assessed by accelerometry. Other outcomes include quality of life, mood, exercise self-efficacy, injuries. Qualitative evaluations will explore reasons for trial non-participation, the intervention’s acceptability to patients and nurses and factors enhancing or acting as barriers for older people in increasing their physical activity levels. Discussion The PACE-Lift trial will determine the feasibility and efficacy of an intervention for increasing physical activity among older primary care patients. Steps taken to minimise bias and the challenges anticipated will be discussed. Word count 341. Trial registration number ISRCTN42122561

Abstract Background Venous thromboembolism (VTE) is a common preventable cause of mortality in hospitalized medical patients. Despite rigorous randomized trials generating strong recommendations for anticoagulant use to prevent VTE, nearly 40% of medical patients receive inappropriate thromboprophylaxis. Knowledge-translation strategies are needed to bridge this gap. Methods We conducted a 16-week pilot cluster randomized controlled trial (RCT) to determine the proportion of medical patients that were appropriately managed for thromboprophylaxis (according to the American College of Chest Physician guidelines) within 24 hours of admission, through the use of a multicomponent knowledge-translation intervention. Our primary goal was to determine the feasibility of conducting this study on a larger scale. The intervention comprised clinician education, a paper-based VTE risk assessment algorithm, printed physicians’ orders, and audit and feedback sessions. Medical wards at six hospitals (representing clusters) in Ontario, Canada were included; three were randomized to the multicomponent intervention and three to usual care (i.e., no active strategies for thromboprophylaxis in place). Blinding was not used. Results A total of 2,611 patients (1,154 in the intervention and 1,457 in the control group) were eligible and included in the analysis. This multicomponent intervention did not lead to a significant difference in appropriate VTE prophylaxis rates between intervention and control hospitals (appropriate management rate odds ratio = 0.80; 95% confidence interval: 0.50, 1.28; p = 0.36; intra-class correlation coefficient: 0.022), and thus was not considered feasible. Major barriers to effective knowledge translation were poor attendance by clinical staff at education and feedback sessions, difficulty locating preprinted orders, and lack of involvement by clinical and administrative leaders. We identified several factors that may increase uptake of a VTE prophylaxis strategy, including local champions, support from clinical and administrative leaders, mandatory use, and a simple, clinically relevant risk assessment tool. Conclusions Hospitals allocated to our multicomponent intervention did not have a higher rate of medical inpatients appropriately managed for thromboprophylaxis than did hospitals that were not allocated to this strategy.

Abstract Background Swine origin influenza A/H1N1 infection (H1N1) emerged in early 2009 and rapidly spread to humans. For most infected individuals, symptoms were mild and self-limited; however, a small number developed a more severe clinical syndrome characterized by profound respiratory failure with hospital mortality ranging from 10 to 30%. While supportive care and neuraminidase inhibitors are the main treatment for influenza, data from observational and interventional studies suggest that the course of influenza can be favorably influenced by agents not classically considered as influenza treatments. Multiple observational studies have suggested that HMGCoA reductase inhibitors (statins) can exert a class effect in attenuating inflammation. The Collaborative H1N1 Adjuvant Treatment (CHAT) Pilot Trial sought to investigate the feasibility of conducting a trial during a global pandemic in critically ill patients with H1N1 with the goal of informing the design of a larger trial powered to determine impact of statins on important outcomes. Methods/Design A multi-national, pilot randomized controlled trial (RCT) of once daily enteral rosuvastatin versus matched placebo administered for 14 days for the treatment of critically ill patients with suspected, probable or confirmed H1N1 infection. We propose to randomize 80 critically ill adults with a moderate to high index of suspicion for H1N1 infection who require mechanical ventilation and have received antiviral therapy for ≤ 72 hours. Site investigators, research coordinators and clinical pharmacists will be blinded to treatment assignment. Only research pharmacy staff will be aware of treatment assignment. We propose several approaches to informed consent including a priori consent from the substitute decision maker (SDM), waived and deferred consent. The primary outcome of the CHAT trial is the proportion of eligible patients enrolled in the study. Secondary outcomes will evaluate adherence to medication administration regimens, the proportion of primary and secondary endpoints collected, the number of patients receiving open-label statins, consent withdrawals and the effect of approved consent models on recruitment rates. Discussion Several aspects of study design including the need to include central randomization, preserve allocation concealment, ensure study blinding compare to a matched placebo and the use novel consent models pose challenges to investigators conducting pandemic research. Moreover, study implementation requires that trial design be pragmatic and initiated in a short time period amidst uncertainty regarding the scope and duration of the pandemic. Trial Registration Number ISRCTN45190901

Abstract Background Lipopolysaccharide (LPS), the major component of the outer membrane of gram-negative bacteria, can activate immune cells including macrophages. Activation of macrophages in the central nervous system (CNS) contributes to neuronal injury. Bowman-Birk inhibitor (BBI), a soybean-derived protease inhibitor, has anti-inflammatory properties. In this study, we examined whether BBI has the ability to inhibit LPS-mediated macrophage activation, reducing the release of pro-inflammatory cytokines and subsequent neurotoxicity in primary cortical neural cultures. Methods Mixed cortical neural cultures from rat were used as target cells for testing neurotoxicity induced by LPS-treated macrophage supernatant. Neuronal survival was measured using a cell-based ELISA method for expression of the neuronal marker MAP-2. Intracellular reactive oxygen species (ROS) production in macrophages was measured via 2', 7'-dichlorofluorescin diacetate (DCFH2DA) oxidation. Cytokine expression was determined by quantitative real-time PCR. Results LPS treatment of macrophages induced expression of proinflammatory cytokines (IL-1β, IL-6 and TNF-α) and of ROS. In contrast, BBI pretreatment (1-100 μg/ml) of macrophages significantly inhibited LPS-mediated induction of these cytokines and ROS. Further, supernatant from BBI-pretreated and LPS-activated macrophage cultures was found to be less cytotoxic to neurons than that from non-BBI-pretreated and LPS-activated macrophage cultures. BBI, when directly added to the neuronal cultures (1-100 μg/ml), had no protective effect on neurons with or without LPS-activated macrophage supernatant treatment. In addition, BBI (100 μg/ml) had no effect on N-methyl-D-aspartic acid (NMDA)-mediated neurotoxicity. Conclusions These findings demonstrate that BBI, through its anti-inflammatory properties, protects neurons from neurotoxicity mediated by activated macrophages.

Abstract Background The influence of the family and home environment on childhood physical activity (PA) and whether this differs between ethnic groups remains uncertain. This paper investigates associations between family and home factors and childhood PA in a multi-ethnic population and explores whether associations differ between ethnic groups. Methods Cross-sectional study of 9-10 year-old schoolchildren, in which PA was objectively measured by Actigraph GT1 M accelerometers for ≤7 days to estimate average activity counts per minute (CPM). Information on 11 family and home environmental factors were collected from questionnaires. Associations between these factors and CPM were quantified using multi-level linear regression. Interactions with ethnicity were explored using likelihood ratio tests. Results 2071 children (mean ± SD age: 9.95 ± 0.38 years; 47.8% male) participated, including 25% white European, 28% black African-Caribbean, 24% South Asian, and 24% other ethnic origin. Family PA support and having a pet were associated with higher average CPM (adjusted mean difference: 6 (95%CI:1,10) and 13 (95%CI:3,23), respectively) while car ownership and having internet access at home were associated with lower average CPM (adjusted mean difference: -19 (95%CI:-30,-8) and -10 (95%CI:-19,0), respectively). These associations did not differ by ethnicity. Although the number of siblings showed no overall association with PA, there was some evidence of interaction with ethnicity (p for ethnicity interaction = 0.04, 0.05 in a fully-adjusted model); a positive significant association with number of siblings was observed in white Europeans (per sibling CPM difference 10.3 (95% CI 1.7, 18.9)) and a positive non-significant association was observed in black African-Caribbeans (per sibling CPM difference: 3.5 (-4.2, 11.2)) while a negative, non-significant association was observed in South Asians (per sibling CPM difference -6.0 (-15.5, 3.4)). Conclusions Some family and home environmental factors have modest associations with childhood PA and these are mostly similar across different ethnic groups. This suggests that targeting these factors in an intervention to promote PA would be relevant for children in different ethnic groups.

Abstract Background Passive smoke exposure increases the risk of lower respiratory infection (LRI) in infants, but the extensive literature on this association has not been systematically reviewed for nearly ten years. The aim of this paper is to provide an updated systematic review and meta-analysis of studies of the association between passive smoking and LRI, and with diagnostic subcategories including bronchiolitis, in infants aged two years and under. Methods We searched MEDLINE and EMBASE (to November 2010), reference lists from publications and abstracts from major conference proceedings to identify all relevant publications. Random effect pooled odds ratios (OR) with 95% confidence intervals (CI) were estimated. Results We identified 60 studies suitable for inclusion in the meta-analysis. Smoking by either parent or other household members significantly increased the risk of LRI; odds ratios (OR) were 1.22 (95% CI 1.10 to 1.35) for paternal smoking, 1.62 (95% CI 1.38 to 1.89) if both parents smoked, and 1.54 (95% CI 1.40 to 1.69) for any household member smoking. Pre-natal maternal smoking (OR 1.24, 95% CI 1.11 to 1.38) had a weaker effect than post-natal smoking (OR 1.58, 95% CI 1.45 to 1.73). The strongest effect was on bronchiolitis, where the risk of any household smoking was increased by an OR of 2.51 (95% CI 1.96 to 3.21). Conclusions Passive smoking in the family home is a major influence on the risk of LRI in infants, and especially on bronchiolitis. Risk is particularly strong in relation to post-natal maternal smoking. Strategies to prevent passive smoke exposure in young children are an urgent public and child health priority.

Abstract Background Randomized clinical trials (RCTs) stopped early for benefit often receive great attention and affect clinical practice, but pose interpretational challenges for clinicians, researchers, and policy makers. Because the decision to stop the trial may arise from catching the treatment effect at a random high, truncated RCTs (tRCTs) may overestimate the true treatment effect. The Study Of Trial Policy Of Interim Truncation (STOPIT-1), which systematically reviewed the epidemiology and reporting quality of tRCTs, found that such trials are becoming more common, but that reporting of stopping rules and decisions were often deficient. Most importantly, treatment effects were often implausibly large and inversely related to the number of the events accrued. The aim of STOPIT-2 is to determine the magnitude and determinants of possible bias introduced by stopping RCTs early for benefit. Methods/Design We will use sensitive strategies to search for systematic reviews addressing the same clinical question as each of the tRCTs identified in STOPIT-1 and in a subsequent literature search. We will check all RCTs included in each systematic review to determine their similarity to the index tRCT in terms of participants, interventions, and outcome definition, and conduct new meta-analyses addressing the outcome that led to early termination of the tRCT. For each pair of tRCT and systematic review of corresponding non-tRCTs we will estimate the ratio of relative risks, and hence estimate the degree of bias. We will use hierarchical multivariable regression to determine the factors associated with the magnitude of this ratio. Factors explored will include the presence and quality of a stopping rule, the methodological quality of the trials, and the number of total events that had occurred at the time of truncation. Finally, we will evaluate whether Bayesian methods using conservative informative priors to "regress to the mean" overoptimistic tRCTs can correct observed biases. Discussion A better understanding of the extent to which tRCTs exaggerate treatment effects and of the factors associated with the magnitude of this bias can optimize trial design and data monitoring charters, and may aid in the interpretation of the results from trials stopped early for benefit.

Abstract Background Higher exposure to outdoor air pollution is associated with increased cardiopulmonary deaths, but there is limited evidence about the association between outdoor air pollution and diagnosed cardiovascular disease. Our study aimed to estimate the size of the association between long term exposure to outdoor air pollution and prevalent cardiovascular disease. Methods We carried out a cross-sectional analysis of data on more than 19,000 white adults aged 45 and older who participated in three representative surveys of the English population in 1994, 1998 and 2003, examining the relationship between self-reported doctor-diagnosed cardiovascular disease and exposure to outdoor air pollutants using multilevel regression techniques and meta-analysis. Results The combined estimates suggested that an increase of 1 μg m-3 in concentration of particulate matter less than 10 microns in diameter was associated with an increase of 2.9% (95% CI -0.6% to 6.5%) in prevalence of cardiovascular disease in men, and an increase of 1.6% (95%CI -2.1% to 5.5%) in women. The year-specific analyses showed strongly positive associations in 2003 between odds of cardiovascular disease in both men and women and exposure to particulate matter but not in 1994 or 1998. We found no consistent associations between exposure to gaseous air pollutants and doctor-diagnosed cardiovascular disease. Conclusion The associations of prevalent cardiovascular disease with concentration of particulate matter less than 10 microns in diameter, while only weakly positive, were consistent with the effects reported in cohort studies. The results provide evidence of the size of the association between particulate air pollution and the prevalence of cardiovascular disease but no evidence for an association with gaseous pollutants. We found strongly positive associations between particulate matter and cardiovascular disease in 2003 only, which highlights the importance of replicating findings in more than one population.

Abstract Background Incomplete ascertainment of outcomes in randomized controlled trials (RCTs) is likely to bias final study results if reasons for unavailability of patient data are associated with the outcome of interest. The primary objective of this study is to assess the potential impact of loss to follow-up on the estimates of treatment effect. The secondary objectives are to describe, for published RCTs, (1) the reporting of loss to follow-up information, (2) the analytic methods used for handling loss to follow-up information, and (3) the extent of reported loss to follow-up. Methods We will conduct a systematic review of reports of RCTs recently published in five top general medical journals. Eligible RCTs will demonstrate statistically significant effect estimates with respect to primary outcomes that are patient-important and expressed as binary data. Teams of 2 reviewers will independently determine eligibility and extract relevant information from each eligible trial using standardized, pre-piloted forms. To assess the potential impact of loss to follow-up on the estimates of treatment effect we will, for varying assumptions about the outcomes of participants lost to follow-up (LTFU), calculate (1) the percentage of RCTs that lose statistical significance and (2) the mean change in effect estimate across RCTs. The different assumptions we will test are the following: (1) none of the LTFU participants had the event; (2) all LTFU participants had the event; (3) all LTFU participants in the treatment group had the event; none of those in the control group had it (worst case scenario); (4) the event incidence among LTFU participants (relative to observed participants) increased, with a higher relative increase in the intervention group; and (5) the event incidence among LTFU participants (relative to observed participants) increased in the intervention group and decreased in the control group. Discussion We aim to make our objectives and methods transparent. The results of this study may have important implications for both clinical trialists and users of the medical literature.

Abstract Background Physical activity studies in older people experience poor recruitment. We wished to assess the influence of activity levels and health status on recruitment to a physical activity study in older people. Methods Comparison of participants and non-participants to a physical activity study using accelerometers in patients aged ≥ 65 years registered with a UK primary care centre. Logistic regression was used to calculate odds ratios (OR) of participants in the accelerometer study with various adjustments. Analyses were initially adjusted for age, sex and household clustering; the health variables were then adjusted for physical activity levels and vice versa to look for independent effects. Results 43%(240/560) participated in the physical activity study. Age had no effect but males were more likely to participate than females OR 1.4(1.1–1.8). 46% (76/164) of non-participants sent the questionnaire returned it. The 240 participants reported greater physical activity than the 76 non-participants on all measures, eg faster walking OR 3.2(1.4–7.7), or 10.4(3.2–33.3) after adjustment for health variables. Participants reported more health problems; this effect became statistically significant after controlling for physical activity, eg disability OR 2.4(1.1–5.1). Conclusion Physical activity studies on older primary care patients may experience both a strong bias towards participants being more active and a weaker bias towards participants having more health problems and therefore primary care contact. The latter bias could be advantageous for physical activity intervention studies, where those with health problems need targeting.

Abstract Background Type 2 diabetes is an important cause of morbidity and mortality. Its prevalence appears to be increasing. Guidelines exist regarding its management. Recommendations regarding drug therapy have changed. Little is known about the influence of these guidelines and changed recommendations on the actual management of patients with type 2 diabetes. This study aims to document trends in the prevalence, drug treatment and recording of measures related to the management of type 2 diabetes; and to assess whether recommended targets can be met. Methods The population comprised subjects registered between 1994 and 2001 with 74 general practices in England and Wales which routinely contribute to the Doctors' Independent Network database. Approximately 500,000 patients and 10,000 type 2 diabetics were registered in each year. Results Type 2 diabetes prevalence rose from 17/1000 in 1994 to 25/1000 in 2001. Drug therapy has changed: use of long acting sulphonylureas is falling while that of short acting sulphonylureas, metformin and newer therapies including glitazones is increasing. Electronic recording of HbA1c, blood pressure, cholesterol and weight have risen steadily, and improvements in control of blood pressure and cholesterol levels have occurred. However, glycaemic control has not improved, and obesity has increased. The percentage with a BMI under 25 kg/m2 fell from 27.0% in 1994 to 19.4% in 2001 (p < 0.001). Conclusion Prevalence of type 2 diabetes is increasing. Its primary care management has changed in accordance with best evidence. Monitoring has improved, but further improvement is possible. Despite this, glycaemic control has not improved, while the prevalence of obesity in the diabetic population is rising.

Abstract Background The General Practice Research Database (GPRD) and Doctor's Independent Network Database (DIN), are large electronic primary care databases compiled in the UK during the 1990s. They provide a valuable resource for epidemiological and health services research. GPRD (based on VAMP) presents notes as a series of discrete episodes, whereas DIN is based on a system (MEDITEL) that used a Problem Orientated Medical Record (POMR) which links prescriptions to diagnostic problems. We have examined the implications for research of these different underlying philosophies. Methods Records of 40,183 children from 141 practices in DIN and 76,310 from 464 practices in GRPD who were followed to age 5 were used to compare the volume of recording of prescribing and diagnostic codes in the two databases. To assess the importance and additional value of the POMR within DIN, the appropriateness of diagnostic linking to skin emollient prescriptions was investigated. Results Variation between practices for both the number of days on which prescriptions were issued and diagnoses were recorded was marked in both databases. Mean number of "prescription days" during the first 5 years of life was similar in DIN (19.5) and in GPRD (19.8), but the average number of "diagnostic days" was lower in DIN (15.8) than in GPRD (22.9). Adjustment for linkage increased the average "diagnostic days" to 23.1 in DIN. 32.7% of emollient prescriptions in GPRD appeared with an eczema diagnosis on the same day compared to only 19.4% in DIN; however, 86.4% of prescriptions in DIN were linked to an earlier eczema diagnosis. More specifically 83% of emollient prescriptions appeared under a problem heading of eczema in the 121 practices that were using problem headings satisfactorily. Conclusion Prescribing records in DIN and GPRD are very similar, but the usage of diagnostic codes is more parsimonious in DIN because of its POMR structure. Period prevalence rates will be underestimated in DIN unless this structure is taken into account. The advantage of the POMR is that in 121 of 141 practices using problem headings as intended, most prescriptions can be linked to a problem heading providing a specific reason for their issue.

La Conferencia sobre Calidad de Elaboración de los Informes de los Metaanálisis (QUOROM) se convocó con el fin de abordar la mejora de la calidad de la elaboración de los informes de los metaanálisis de los ensayos clínicos controlados (ECC). El Grupo QUOROM estuvo integrado por 30 personas, entre epidemiólogos clínicos, estadísticos, editores e investigadores. Durante la conferencia se pidió al grupo que identificase aquellos elementos que, en su opinión, se deberían incluir en un protocolo de control de calidad por niveles. En la medida de lo posible, la elección de los elementos de dicho protocolo se guió por la evidencia científica, que sugería que el incumplimiento del elemento propuesto se podría traducir en resultados sesgados. Se utilizó una técnica Delphi modificada para valorar los elementos seleccionados a priori como parte del protocolo. La conferencia se tradujo en la declaración QUOROM, un protocolo de control de calidad y un diagrama de flujo. El protocolo de control de calidad describe la que creemos es la mejor forma de presentar el resumen, la introducción, los métodos, los resultados y la discusión del informe de un metaanálisis. Está organizada en 21 categorías y subcategorías relativas a búsquedas, selección, evaluación de la validez, análisis de los datos, características del estudio y síntesis de los datos cuantitativos, y en los resultados de "flujo de pruebas"; se identificó la documentación de la investigación con 18 elementos. El diagrama de flujo proporciona información tanto sobre el número de ensayos clínicos controlados identificados, incluidos y excluidos, como sobre las razones de su exclusión. Esperamos que este trabajo genere un mayor grado de reflexión sobre cómo mejorar la calidad de los informes de los metaanálisis de los ensayos clínicos controlados, y que los lectores, revisores, investigadores y editores utilicen la declaración QUOROM y generen ideas destinadas a su mejora.

This study investigated the generalizability of Arabidopsis thaliana immune responses across diverse pathogens, including Botrytis cinerea, Sclerotinia sclerotiorum, and Pseudomonas syringae, using a data-driven, machine learning approach. Machine learning models were trained to predict disease development from early transcriptional responses. Feature selection techniques based on network science and topology were used to train models employing only a fraction of the transcriptome. Machine learning models trained on one pathosystem where then validated by predicting disease development in new pathosystems. The identified feature selection gene sets were enriched for pathways related to biotic, abiotic, and stress responses, though the specific genes involved differed between feature sets. This suggests common immune responses to diverse pathogens that operate via different gene sets. The study demonstrates that machine learning can uncover both established and novel components of the plant's immune response, offering insights into disease resistance mechanisms. These predictive models highlight the potential to advance our understanding of multigenic outcomes in plant immunity and can be further refined for applications in disease prediction., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over-and under-polishing. Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacbio HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHARAOH (Phasing Reads in Areas Of Homozygosity), which uses ultra-long ONT data to ensure alignments are accurately phased and to correctly introduce heterozygous edits in falsely homozygous regions. We demonstrate that the DeepPolisher pipeline can reduce assembly errors by half, with a greater than 70% reduction in indel errors. We have applied our DeepPolisher-based pipeline to 180 assemblies from the next Human Pangenome Reference Consortium (HPRC) data release, producing an average predicted Quality Value (QV) improvement of 3.4 (54% error reduction) for the majority of the genome., Competing Interests: Conflict of interest A.C, D.E.C, P.C., A.K., L.B., M.N. and K.S. are employees of Google LLC and own Alphabet stock as part of the standard compensation package.

Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We present DeepSomatic, a deep learning method for detecting somatic SNVs and insertions and deletions (indels) from both short-read and long-read data, with modes for whole-genome and exome sequencing, and able to run on tumor-normal, tumor-only, and with FFPE-prepared samples. To help address the dearth of publicly available training and benchmarking data for somatic variant detection, we generated and make openly available a dataset of five matched tumor-normal cell line pairs sequenced with Illumina, PacBio HiFi, and Oxford Nanopore Technologies, along with benchmark variant sets. Across samples and technologies (short-read and long-read), DeepSomatic consistently outperforms existing callers, particularly for indels., Competing Interests: Competing interests K.S., D.E.C., P.C., A. Kolesnikov, L.B., J.C.M., and A.C. are employees of Google LLC and own Alphabet stock as part of the standard compensation package. M.S.F. is a part of the speakers bureau for Bayer and PacBio.

Phoresy is an interspecies interaction that facilitates spatial dispersal by attaching to a more mobile species. Hitchhiking species have evolved specific traits for physical contact and successful phoresy, but the regulatory mechanisms involved in such traits and their evolution are largely unexplored. The nematode Caenorhabditis elegans displays a hitchhiking behavior known as nictation during its stress-induced developmental stage. Dauer-specific nictation behavior has an important role in natural C. elegans populations, which experience boom-and-bust population dynamics. In this study, we investigated the nictation behavior of 137 wild C. elegans strains sampled throughout the world. We identified species-wide natural variation in nictation and performed a genome-wide association mapping. We show that the variants in the promoter of nta-1 , encoding a putative steroidogenic enzyme, underlie differences in nictation. This difference is due to the changes in nta-1 expression in glial cells, which implies that glial steroid metabolism regulates phoretic behavior. Population genetic analysis and geographic distribution patterns suggest that balancing selection maintained two nta-1 haplotypes that existed in ancestral C. elegans populations. Our findings contribute to further understanding of the molecular mechanism of species interaction and the maintenance of genetic diversity within natural populations., Competing Interests: Competing interests statement:The authors declare no competing interest.

Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility 1 . The X chromosome is vital for reproduction and cognition 2 . Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species., (© 2024. The Author(s).)

Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we established 48 PDX models from 22 patients enrolled in the TRACERx study. Multi-region tumor sampling increased successful PDX engraftment and most models were histologically similar to their parent tumor. Whole-exome sequencing enabled comparison of tumors and PDX models and we provide an adapted mouse reference genome for improved removal of NOD scid gamma (NSG) mouse-derived reads from sequencing data. PDX model establishment caused a genomic bottleneck, with models often representing a single tumor subclone. While distinct tumor subclones were represented in independent models from the same tumor, individual PDX models did not fully recapitulate intratumor heterogeneity. On-going genomic evolution in mice contributed modestly to the genomic distance between tumors and PDX models. Our study highlights the importance of considering primary tumor heterogeneity when using PDX models and emphasizes the benefit of comprehensive tumor sampling., (© 2024. The Author(s).)

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus., (© 2024. The Author(s).)

This comprehensive narrative review delves into the intricate interplay between diet and inflammatory bowel disease (IBD), shedding light on the potential impact of dietary interventions in disease management. By analyzing nutritional interventions, risks, challenges, and future perspectives, this review serves as a vital resource for clinicians, researchers, and patients alike. The amalgamation of evidence underscores the significance of customizing dietary strategies for individual patients, considering disease phenotype and cultural factors. Through an exploration of dietary components' effects on IBD, including exclusive enteral nutrition and omega-3 fatty acids, this review offers pragmatic implementation advice and outlines avenues for further research. Bridging the gap between research findings and clinical applications, the review facilitates informed decision-making and patient-centric care. In the face of escalating IBD prevalence, this review emerges as an indispensable guide for healthcare professionals, empowering them to navigate the complexities of dietary management while enabling patients to actively participate in their care trajectory. Ultimately, this narrative review advances the understanding of diet's pivotal role in IBD management, fostering a more integrated approach to patient care and paving the way for improved research and policy initiatives in the field of inflammatory bowel diseases., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2023, Saeed et al.)

Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Kramer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

This systematic review provides a qualitative summary of the risk factors, angiographic characteristics, treatment, and complications of young South Asians with coronary artery disease (CAD). PubMed, Embase, and Google Scholar were searched to identify research articles published between 1 January 2010 and 13 November 2022. Studies in patients aged 18 to 45 years that were conducted in South Asian countries, were published in the English language, and included information on patients' clinical profiles and at least two risk factors for young CAD were included in the review. Smoking, dyslipidemia, high body mass index, increased high-sensitivity C-reactive protein, and hyperhomocysteinemia were observed in high proportions in young patients with CAD. Single-vessel disease was more common than multi-vessel disease in young CAD. The complications of CAD such as arrhythmias, cardiogenic shock, and heart failure were also commonly observed in young patients. Large-scale health promotion activities that curb modifiable risk factors such as smoking, obesity, and a sedentary lifestyle should be conducted in South Asian countries.

Summary: RNA sequencing (RNA-seq) can be applied to diverse tasks including quantifying gene expression, discovering quantitative trait loci and identifying gene fusion events. Although RNA-seq can detect germline variants, the complexities of variable transcript abundance, target capture and amplification introduce challenging sources of error. Here, we extend DeepVariant, a deep-learning-based variant caller, to learn and account for the unique challenges presented by RNA-seq data. Our DeepVariant RNA-seq model produces highly accurate variant calls from RNA-sequencing data, and outperforms existing approaches such as Platypus and GATK. We examine factors that influence accuracy, how our model addresses RNA editing events and how additional thresholding can be used to facilitate our models' use in a production pipeline., Supplementary Information: Supplementary data are available at Bioinformatics Advances online., (© The Author(s) 2023. Published by Oxford University Press.)

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1 . These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample., (© 2023. The Author(s).)

Metastatic disease is responsible for the majority of cancer-related deaths 1 . We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse., (© 2023. The Author(s).)

Lung cancer is the leading cause of cancer-associated mortality worldwide 1 . Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource., (© 2023. The Author(s).)

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS) 1,2 . Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive 1,2 . Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma 3 . We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response., (© 2023. The Author(s).)

Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy 1 . The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study 2 . A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy., (© 2023. The Author(s).)