Review and further developments in statistical corrections for Winner's Curse in genetic association studies

Genome-wide association studies (GWAS) are commonly used to identify genomic variants that are associated with complex traits, and estimate the magnitude of this association for each variant. However, it has been widely observed that the association estimates of variants tend to be lower in a replication study than in the study that discovered those associations. A phenomenon known as Winner's Curse is responsible for this upward bias present in association estimates of significant variants in the discovery study. We review existing Winner's Curse correction methods which require only GWAS summary statistics in order to make adjustments. In addition, we propose modifications to improve existing methods and propose a novel approach which uses the parametric bootstrap. We evaluate and compare methods, first using a wide variety of simulated data sets and then, using real data sets for three different traits. The metric, estimated mean squared error (MSE) over significant SNPs, was primarily used for method assessment. Our results indicate that widely used conditional likelihood based methods tend to perform poorly. The other considered methods behave much more similarly, with our proposed bootstrap method demonstrating very competitive performance. To complement this review, we have developed an R package, 'winnerscurse' which can be used to implement these various Winner's Curse adjustment methods to GWAS summary statistics.

Early Stopping Criterion for Recursive Least Squares Training of Behavioural Models

The necessity of the rapid evolution of wireless communications, with continuously increasing demands for higher data rates and capacity Zheng (Big datadriven optimization for mobile networks toward 5g 30:44-51, 2016), is constantly augmenting the complexity of radio frequency (RF) transceiver architecture. A significant component in the configuration of such complex radio transceivers is the power amplifier(PA). Multiple distributed PAs are now common in proposed RF architectures. PAs exhibit non linear behaviour, causing signal distortion in transmission. Behavioural models offer a concise representation of a PAs characteristic performance which is extremely useful in simulating performance of multiple nonlinear power amplifiers. A considerable drawback with using the Recursive Least Squares (RLS) technique is that the instability of the coefficients during the training of the model. This manuscript provides a computationally efficient technique to detect the onset of instability during adaptive RLS training and subsequently to inform the decision to cease training of dynamic memory polynomial based behavioural models, to avoid the onset of instability. The proposed technique does not require modification of the RLS algorithm, merely an observation of the pre-exsisting autocorrelation function based update. This technique is experimentally validated using four different signal modulation schemes, LTE OFDM, 5G-NR, DVBS2X and WCDMA.

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

BACKGROUND

The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals.

RESULTS

Here we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance.

CONCLUSION

Long-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.

How recreational marathon runners hit the wall: A large-scale data analysis of late-race pacing collapse in the marathon

Introduction

In the marathon, how runners pace and fuel their race can have a major impact on race outcome. The phenomenon known as hitting the wall (HTW) refers to the iconic hazard of the marathon distance, in which runners experience a significant slowing of pace late in the race, typically after the 20-mile mark, and usually because of a depletion of the body’s energy stores.

Aim

This work investigates the occurrence of significant late-race slowing among recreational marathoners, as a proxy for runners hitting the wall, to better understand the likelihood and nature of such slowdowns, and their effect on race performance.

Methods

Using pacing data from more than 4 million race records, we develop a pacing-based definition of hitting the wall, by identifying runners who experience a sustained period of slowing during the latter stages of the marathon. We calculate the cost of these slowdowns relative to estimates of the recent personal-best times of runners and compare slowdowns according to runner sex, age, and ability.

Results

We find male runners more likely to slow significantly (hit the wall) than female runners; 28% of male runners hit the wall compared with 17% of female runners, χ²(1, N = 1, 928, 813) = 27, 693.35, p < 0.01, OR = 1.43. Such slowdowns are more frequent in the 3 years immediately before and after a recent personal-best (PB) time; for example, 36% of all runners hit the wall in the 3 years before a recent PB compared with just 23% in earlier years, χ²(1, N = 509, 444) = 8, 120.74, p < 0.01, OR = 1.31. When runners hit the wall, males slow more than females: a relative slowdown of 0.40 vs. 0.37 is noted, for male and female runners, when comparing their pace when they hit the wall to their earlier race (5km-20km) pace, with t(475, 199) = 60.19, p < 0.01, d = 0.15. And male runners slow over longer distances than female runners: 10.7km vs. 9.6km, respectively, t(475, 199) = 68.44, p < 0.01, d = 0.17. Although, notably the effect size of these differences is small. We also find the finish-time costs of hitting the wall (lost minutes) to increase with ability; r²(7) = 0.91, p < 0.01 r²(7) = 0.81, p < 0.01 for male and female runners, respectively.

Conclusions

While the findings from this study are consistent with qualitative results from earlier single-race or smaller-scale studies, the new insights into the risk and nature of slowdowns, based on the runner sex, age, and ability, have the potential to help runners and coaches to better understand and calibrate the risk/reward trade-offs that exist as they plan for future races.

Heritable epigenetic diversity for conservation and utilization of epigenetic germplasm resources of clonal East African Highland banana (EAHB) accessions

KEY MESSAGE

Genetically identical East African Highland banana (EAHB) clones are epigenetically diverse with heritable epialleles that can contribute to morphological diversity. Heritable epigenetic variation can contribute to agronomic traits in crops and should be considered in germplasm conservation. Despite the genetic uniformity arising from a genetic bottleneck of one ancestral clone, followed by subsequent vegetative propagation, East African Highland bananas (EAHBs) display significant phenotypic diversity potentially arising from somatic mutations, heritable epialleles and/or genotype-by-environment interactions. Here, we use DNA methylation profiling across EAHB accessions representing most of the primary EAHB genepool to demonstrate that the genetically uniform EAHB genepool harbours significant epigenetic diversity. By analysing 724 polymorphic DNA methylation sites by methylation-sensitive AFLP across 90 EAHB cultivars, we could differentiate the EAHB varieties according to their regions (Kenya and Uganda). In contrast, there was minimal association of DNA methylation variation with the five morphological groups that are used to classify EAHBs. We further analysed DNA methylation patterns in parent-offspring cohort, which were maintained in offspring generated by sexual (seed) and asexual (vegetative) propagation, with higher levels of altered DNA methylation observed in vegetatively generated offspring. Our results indicate that the phenotypic diversity of near-isogenic EAHBs is mirrored by considerable DNA methylation variation, which is transmitted between generations by both vegetative reproduction and seed reproduction. Genetically uniform vegetatively propagated crops such as EAHBs harbour considerable heritable epigenetic variation, where heritable epialleles could arise in offspring and contribute to functional traits. This study provides a basis for developing strategies for conservation of epigenetic resources and for integration of epimarkers into crop breeding programmes.

Accelerated discovery of new magnets in the Heusler alloy family

Magnetic materials underpin modern technologies, ranging from data storage to energy conversion to contactless sensing. However, the development of a new high-performance magnet is a long and often unpredictable process, and only about two dozen magnets are featured in mainstream applications. We describe a systematic pathway to the design of novel magnetic materials, which demonstrates a high throughput and discovery speed. On the basis of an extensive electronic structure library of Heusler alloys containing 236,115 prototypical compounds, we filtered those displaying magnetic order and established whether they can be fabricated at thermodynamic equilibrium. Specifically, we carried out a full stability analysis of intermetallic Heusler alloys made only of transition metals. Among the possible 36,540 prototypes, 248 were thermodynamically stable but only 20 were magnetic. The magnetic ordering temperature, TC, was estimated by a regression calibrated on the experimental TC of about 60 known compounds. As a final validation, we attempted the synthesis of a few of the predicted compounds and produced two new magnets: Co2MnTi, which displays a remarkably high TC in perfect agreement with the predictions, and Mn2PtPd, which is an antiferromagnet. Our work paves the way for large-scale design of novel magnetic materials at potentially high speed.

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions

While basic and clinical research over the last several decades has recognized a number of modifiable risk factors associated with cardiometabolic disease progression, additional and alternative biological perspectives may offer novel targets for prevention and treatment of this disease set. There is mounting preclinical and emerging clinical evidence indicating that the mass of metabolically diverse microorganisms which inhabit the human gastrointestinal tract may be implicated in initiation and modulation of cardiovascular and metabolic disease outcomes. The following review will discuss this gut microbiome-host metabolism axis and address newly proposed bile-mediated signaling pathways through which dysregulation of this homeostatic axis may influence host cardiovascular risk. With a central focus on the major nuclear and membrane-bound bile acid receptor ligands, we aim to review the putative impact of microbial bile acid modification on several major phenotypes of metabolic syndrome, from obesity to heart failure. Finally, attempting to synthesize several separate but complementary hypotheses, we will review current directions in preclinical and clinical investigation in this evolving field.

Use of Fluorescence Lifetime Imaging Microscopy (FLIM) as a Timer of Cell Cycle S Phase

Incorporation of thymidine analogues in replicating DNA, coupled with antibody and fluorophore staining, allows analysis of cell proliferation, but is currently limited to monolayer cultures, fixed cells and end-point assays. We describe a simple microscopy imaging method for live real-time analysis of cell proliferation, S phase progression over several division cycles, effects of anti-proliferative drugs and other applications. It is based on the prominent (~ 1.7-fold) quenching of fluorescence lifetime of a common cell-permeable nuclear stain, Hoechst 33342 upon the incorporation of 5-bromo-2'-deoxyuridine (BrdU) in genomic DNA and detection by fluorescence lifetime imaging microscopy (FLIM). We show that quantitative and accurate FLIM technique allows high-content, multi-parametric dynamic analyses, far superior to the intensity-based imaging. We demonstrate its uses with monolayer cell cultures, complex 3D tissue models of tumor cell spheroids and intestinal organoids, and in physiological study with metformin treatment.

May the Force Be With You: The Light and Dark Sides of the Microbiota-Gut-Brain Axis in Neuropsychiatry

The role of the gut microbiota in health and disease is becoming increasingly recognized. The microbiota-gut-brain axis is a bi-directional pathway between the brain and the gastrointestinal system. The bacterial commensals in our gut can signal to the brain through a variety of mechanisms, which are slowly being resolved. These include the vagus nerve, immune mediators and microbial metabolites, which influence central processes such as neurotransmission and behaviour. Dysregulation in the composition of the gut microbiota has been identified in several neuropsychiatric disorders, such as autism, schizophrenia and depression. Moreover, preclinical studies suggest that they may be the driving force behind the behavioural abnormalities observed in these conditions. Understanding how bacterial commensals are involved in regulating brain function may lead to novel strategies for development of microbiota-based therapies for these neuropsychiatric disorders.

Quinoline Alkaloids Isolated from Choisya Aztec-Pearl and Their Contribution to the Overall Antinociceptive Activity of This Plant

Choisya 'Aztec-Pearl', a hybrid of Choisya ternata and Choisya dumosa var. arizonica, had the antinociceptive activity in the ethanol extract (EECA) of its leaves evaluated. Two quinoline alkaloids, anhydroevoxine (A) and choisyine (C), isolated from these leaves were also tested. The results obtained pointed out to a very high antinociceptive activity measured by the hot plate model for EECA (at doses of 10, 30 and 100 mg/kg) as well as for A and C (at doses of 1, 3 and 10 mg/kg). The magnitude of the activity was two-fold higher than the one observed for the morphine treated animals for the higher doses of extracts/compounds (30, 100 mg/kg and 3, 10 mg/kg respectively). The mechanism of action for this activity was also investigated and it seems that for EECA as well as A and C, the opiate system plays an important role. Results have also shown that the nitric oxide (NO) system also play a pivotal role in the case of EECA and A while for C it seems that the cholinergic system have some involvement. The acute toxicity was evaluated for EECA with results showing no important toxic effect.

Coffee extraction kinetics in a well mixed system

The extraction of coffee solubles from roasted and ground coffee is a complex operation, the understanding of which is key to the brewing of high quality coffee. This complexity stems from the fact that brewing of coffee is achieved through a wide variety of techniques each of which depends on a large number of process variables. In this paper, we consider a recent, experimentally validated model of coffee extraction, which describes extraction from a coffee bed using a double porosity model. The model incorporates dissolution and transport of coffee in the coffee bed. The model was shown to accurately describe extraction of coffee solubles from grains in two situations: extraction from a dilute suspension of coffee grains and extraction from a packed coffee bed. The full model equations can only be solved numerically. In this work we consider asymptotic solutions, based on the dominant mechanisms, in the case of coffee extraction from a dilute suspension of coffee grains. Extraction in this well mixed system, can be described by a set of ordinary differential equations. This allows analysis of the extraction kinetics from the coffee grains independent of transport processes associated with flow through packed coffee beds. Coffee extraction for an individual grain is controlled by two processes: a rapid dissolution of coffee from the grain surfaces in conjunction with a much slower diffusion of coffee through the tortuous intragranular pore network to the grain surfaces. Utilising a small parameter resulting from the ratio of these two timescales, we construct asymptotic solutions using the method of matched asymptotic expansions. The asymptotic solutions are compared with numerical solutions and data from coffee extraction experiments. The asymptotic solutions depend on a small number of dimensionless parameters, so the solutions facilitate quick investigation of the influence of various process parameters on the coffee extraction curves.

Synthesis of indium nanoparticles at ambient temperature; simultaneous phase transfer and ripening

The synthesis of size-monodispersed indium nanoparticles via an innovative simultaneous phase transfer and ripening method is reported. The formation of nanoparticles occurs in a one-step process instead of well-known two-step phase transfer approaches. The synthesis involves the reduction of InCl₃ with LiBH₄ at ambient temperature and although the reduction occurs at room temperature, fine indium nanoparticles, with a mean diameter of 6.4 ± 0.4 nm, were obtained directly in non-polar n-dodecane. The direct synthesis of indium nanoparticles in n-dodecane facilitates their fast formation and enhances their size-monodispersity. In addition, the nanoparticles were highly stable for more than 2 months. The nanoparticles were characterised by dynamic light scattering (DLS), small angle X-ray scattering (SAXS), transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDS) and Fourier transform infrared (FT-IR) spectroscopy to determine their morphology, structure and phase purity.

KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome

BACKGROUND

Joubert syndrome (JBTS) and related disorders are defined by cerebellar malformation (molar tooth sign), together with neurological symptoms of variable expressivity. The ciliary basis of Joubert syndrome related disorders frequently extends the phenotype to tissues such as the eye, kidney, skeleton and craniofacial structures.

RESULTS

Using autozygome and exome analyses, we identified a null mutation in KIAA0556 in a multiplex consanguineous family with hallmark features of mild Joubert syndrome. Patient-derived fibroblasts displayed reduced ciliogenesis potential and abnormally elongated cilia. Investigation of disease pathophysiology revealed that Kiaa0556 (-/-) null mice possess a Joubert syndrome-associated brain-restricted phenotype. Functional studies in Caenorhabditis elegans nematodes and cultured human cells support a conserved ciliary role for KIAA0556 linked to microtubule regulation. First, nematode KIAA0556 is expressed almost exclusively in ciliated cells, and the worm and human KIAA0556 proteins are enriched at the ciliary base. Second, C. elegans KIAA0056 regulates ciliary A-tubule number and genetically interacts with an ARL13B (JBTS8) orthologue to control cilium integrity. Third, human KIAA0556 binds to microtubules in vitro and appears to stabilise microtubule networks when overexpressed. Finally, human KIAA0556 biochemically interacts with ciliary proteins and p60/p80 katanins. The latter form a microtubule-severing enzyme complex that regulates microtubule dynamics as well as ciliary functions.

CONCLUSIONS

We have identified KIAA0556 as a novel microtubule-associated ciliary base protein mutated in Joubert syndrome. Consistent with the mild patient phenotype, our nematode, mice and human cell data support the notion that KIAA0556 has a relatively subtle and variable cilia-related function, which we propose is related to microtubule regulation.

Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation

A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.