A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy.

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens, including those from the herpes, retro-, and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant and could play a key role in regulation of the immune response. Using 121 infection- and inflammation-related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates hematopoietic pathways and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation.

Genome-wide association study of leprosy in Malawi and Mali.

Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.

Yield stress-enabled microencapsulation of field responsive microparticle suspensions.

Try and encapsulate microparticles inside the cores of microcapsules and you will often find that particles adhere to the liquid-liquid interface in a phenomenon known as Pickering stabilization. Particles will remain irreversibly trapped and embedded within the subsequently formed microcapsule membrane. In cases where the encapsulant particles must remain suspended inside the microcapsule core to retain their desired properties or behaviours, Pickering stabilization is detrimental. Here we demonstrate a general procedure using yield stress materials as the core material, where the yield stress of the gel is strong enough to suspend particles against sedimentation, but weak enough to allow spatial manipulation of encapsulant particles using an external field. This external field imparts enough force on particles to disrupt the supporting network and allow particle mobility after encapsulation.

Three-Dimensional Sag Tracking in Falling Liquid Films.

Coating defects often arise during application in the flash stage, which constitutes the ∼10 min interval immediately following film application when the solvent evaporates. Understanding the transient rheology and kinematics of a coating system is necessary to avoid defects such as sag, which results in undesirable appearance. A new technique named variable angle inspection microscopy (VAIM) aimed at measuring these phenomena was developed and is summarized herein. The essence of this new, non-invasive, rheological technique is the measurement of a flow field in response to a known gravitational stress. VAIM was used to measure the flow profile through a volume of a liquid thin film at an arbitrary orientation. Flow kinematics of the falling thin film was inferred from particle tracking measurements. Initial benchmarking measurements in the absence of drying tracked the velocity of silica probe particles in ∼140 µm thick films of known viscosity, much greater than water, at incline angles of 5° and 10°. Probe particles were tracked through the entire thickness of the film and at speeds as high as ∼100 µm/s. The sag flow field was well resolved in ∼10 µm thick cross sections, and in general the VAIM measurements were highly reproducible. Complementary profilometer measurements of film thinning were utilized to predict sag velocities with a known model. The model predictions showed good agreement with measurements, which validated the effectiveness of this new method in relating material properties and flow kinematics.

Precision, reliability and application of the Wilkins Rate of Reading Test.

BACKGROUND: The Wilkins Rate of Reading Test (WRRT) enables rapid measurement of reading speed using text passages that have no semantic content and demand minimal word recognition skills. It is suited to applications where the primary interest is in the influence of visual and ocular motor factors on reading rate. METHODS: We obtained estimates of precision and reliability of WRRT from four data samples (A-D) collected independently by the authors: (A) n = 118 adults; (B) n = 90 adults; (C) n = 787 children; (D) n = 134 children. Each participant was asked to read aloud as quickly and accurately as possible, for 1 min, and results were recorded as number of words read correctly per minute (wcpm). RESULTS: Estimates of precision are given by the within-subjects standard deviation sw , and reliability by the intraclass correlation coefficient for single measurements r1 . For each sample these estimates were (A) sw  = 11.5 wcpm, r1  = 0.85; (B) sw  = 3.8 wcpm, r1  = 0.98; (C) sw  = 6.7 wcpm, r1  = 0.93; (D) sw  = 6.2 wcpm, r1  = 0.94. CONCLUSION: The reliability of WRRT reflects large variation in reading rate between individuals compared to within-individual variability, indicating that it is a good test for discriminating differences in reading speed between individuals. The precision of the test varies from 3.8 wcpm to 11.5 wcpm among samples, and the pooled value of 7.2 wcpm, provides a basis for setting a population-wide criterion for minimum detectable change of reading rate in individuals over time. Nevertheless, a preferable way of monitoring change in an individual would be to use a criterion determined from estimates of that individual's baseline variation in WRRT scores.

Risk of pneumococcal bacteremia in Kenyan children with glucose-6-phosphate dehydrogenase deficiency.

BACKGROUND: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency state in humans. The clinical phenotype is variable and includes asymptomatic individuals, episodic hemolysis induced by oxidative stress, and chronic hemolysis. G6PD deficiency is common in malaria-endemic regions, an observation hypothesized to be due to balancing selection at the G6PD locus driven by malaria. G6PD deficiency increases risk of severe malarial anemia, a key determinant of invasive bacterial disease in malaria-endemic settings. The pneumococcus is a leading cause of invasive bacterial infection and death in African children. The effect of G6PD deficiency on risk of pneumococcal disease is undefined. We hypothesized that G6PD deficiency increases pneumococcal disease risk and that this effect is dependent upon malaria. METHODS: We performed a genetic case-control study of pneumococcal bacteremia in Kenyan children stratified across a period of falling malaria transmission between 1998 and 2010. RESULTS: Four hundred twenty-nine Kenyan children with pneumococcal bacteremia and 2677 control children were included in the study. Among control children, G6PD deficiency, secondary to the rs1050828 G>A mutation, was common, with 11.2% (n = 301 of 2677) being hemi- or homozygotes and 33.3% (n = 442 of 1329) of girls being heterozygotes. We found that G6PD deficiency increased the risk of pneumococcal bacteremia, but only during a period of high malaria transmission (P = 0.014; OR 2.33, 95% CI 1.19-4.57). We estimate that the population attributable fraction of G6PD deficiency on risk of pneumococcal bacteremia in areas under high malaria transmission is 0.129. CONCLUSIONS: Our data demonstrate that G6PD deficiency increases risk of pneumococcal bacteremia in a manner dependent on malaria. At the population level, the impact of G6PD deficiency on invasive pneumococcal disease risk in malaria-endemic regions is substantial. Our study highlights the infection-associated morbidity and mortality conferred by G6PD deficiency in malaria-endemic settings and adds to our understanding of the potential indirect health benefits of improved malaria control.

Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.

Bacteremia (bacterial bloodstream infection) is a major cause of illness and death in sub-Saharan Africa but little is known about the role of human genetics in susceptibility. We conducted a genome-wide association study of bacteremia susceptibility in more than 5,000 Kenyan children as part of the Wellcome Trust Case Control Consortium 2 (WTCCC2). Both the blood-culture-proven bacteremia case subjects and healthy infants as controls were recruited from Kilifi, on the east coast of Kenya. Streptococcus pneumoniae is the most common cause of bacteremia in Kilifi and was thus the focus of this study. We identified an association between polymorphisms in a long intergenic non-coding RNA (lincRNA) gene (AC011288.2) and pneumococcal bacteremia and replicated the results in the same population (p combined = 1.69 × 10(-9); OR = 2.47, 95% CI = 1.84-3.31). The susceptibility allele is African specific, derived rather than ancestral, and occurs at low frequency (2.7% in control subjects and 6.4% in case subjects). Our further studies showed AC011288.2 expression only in neutrophils, a cell type that is known to play a major role in pneumococcal clearance. Identification of this novel association will further focus research on the role of lincRNAs in human infectious disease.

Methylthioadenosine Suppresses Salmonella Virulence.

In order to deploy virulence factors at appropriate times and locations, microbes must rapidly sense and respond to various metabolite signals. Previously, we showed a transient elevation of the methionine-derived metabolite methylthioadenosine (MTA) concentration in serum during systemic Salmonella enterica serovar Typhimurium infection. Here we explored the functional consequences of increased MTA concentrations on S Typhimurium virulence. We found that MTA, but not other related metabolites involved in polyamine synthesis and methionine salvage, reduced motility, host cell pyroptosis, and cellular invasion. Further, we developed a genetic model of increased bacterial endogenous MTA production by knocking out the master repressor of the methionine regulon, metJ Like MTA-treated S Typhimurium, the ΔmetJ mutant displayed reduced motility, host cell pyroptosis, and invasion. These phenotypic effects of MTA correlated with suppression of flagellar and Salmonella pathogenicity island 1 (SPI-1) networks. S Typhimurium ΔmetJ had reduced virulence in oral and intraperitoneal infection of C57BL/6J mice independently of the effects of MTA on SPI-1. Finally, ΔmetJ bacteria induced a less severe inflammatory cytokine response in a mouse sepsis model. Together, these data indicate that exposure of S Typhimurium to MTA or disruption of the bacterial methionine metabolism pathway suppresses S Typhimurium virulence.

Genetic variants associated with non-typhoidal Salmonella bacteraemia in African children.

BACKGROUND: Non-typhoidal Salmonella (NTS) causes invasive and frequently fatal disease in African children. Existing strategies to prevent, diagnose, and treat NTS disease are inadequate. An improved understanding of the biology of invasive Salmonella infection will facilitate the development of novel NTS control measures. Despite evidence in mice and man showing a clear role for host genetics in NTS susceptibility, there are no published studies investigating host genetic susceptibility to NTS in African populations. METHODS: We conducted a genome-wide association study (SNP Array 6.0, Affymetrix, CA, USA) of NTS bacteraemia in Kenyan children, with replication in Malawian children. We assessed the function of NTS-associated variants in an expression quantitative trait locus (eQTL) dataset of interferon γ (IFNγ) and lipopolysaccharide-stimulated monocytes from 432 healthy European adults. Serum IFNγ (Bio-Plex immunoassay, Bio-Rad Laboratories, CA, USA) in Malawian NTS cases (n=106) during acute disease was correlated with genotype by linear regression. FINDINGS: After whole-genome imputation and quality control, 180 Kenyan cases and 2677 controls were included in an association analysis at 7 951 614 (additive model) and 4 669 537 (genotypic model) loci. After quality control, 143 Malawian cases and 336 controls were included in the replication analysis. An intronic variant in STAT4 was associated (recessive model) with NTS in both Kenyan and Malawian children (Kenya p=5·6 × 10(-9), Malawi p=0·02, combined p=1·4 × 10(-9); odds ratio 7·2, 95% CI 3·8-13·5). The NTS-associated variant was an eQTL for STAT4 expression in IFNγ-stimulated monocytes (p=9·59 × 10(-6)), the NTS risk allele being associated with lower STAT4 expression. In Malawian children with NTS bacteraemia, the same NTS risk allele was associated with lower serum concentrations of IFNγ (p=0·02) at presentation. INTERPRETATION: STAT4 is highly plausible as a susceptibility locus for invasive NTS disease. STAT4 mediates IFNγ release in T cells and natural killer cells in response to interleukin 12 (IL12). Individuals with rare mutations elsewhere in the IL12-IFNγ axis are at risk of disseminated NTS infection. We provide the first evidence, to our knowledge, of a host genetic determinant of NTS disease in African children, and of a STAT4 variant conferring susceptibility to an infectious disease in man. FUNDING: Wellcome Trust.

Large-Area Nanoparticle Films by Continuous Automated Langmuir-Blodgett Assembly and Deposition.

The operating parameters and resulting surface morphology of automated Langmuir-Blodgett deposition of monosized micrometer-scale silica colloids from an aqueous suspension are investigated. This apparatus allows continuous roll-to-roll deposition of particles into well-ordered arrays. The reproducible deposition of particle monolayers at low to moderate deposition rates at web speeds of less than 10 mm/s is possible and accurately characterized by a simple mass balance of particles deposited from solution. At faster deposition rates, Landau-Levich flow increases the film thickness such that flow instabilities hinder uniform particle deposition. A simple phase diagram outlines transitions from dispersed to multilayer coatings and from uniform to erratic deposition patterns. While the threshold of maximum deposition rate is well-defined for these conditions, changing operating parameters, particle size, and fluid viscosity and evaporation rate, the maximum speed can be increased significantly.

Effect of Ionic Strength and Surface Charge on Convective Deposition.

Particle-particle and particle-substrate interactions play a crucial role in capillary driven convective self-assembly for continuous deposition of particles. This systematic study demonstrates the nontrivial effects of varying surface charge and ionic strength of monosized silica microspheres in water on the quality of the deposited monolayer. Increase in particle surface charge results a broader range of parameters that result in monolayer deposition which can be explained considering the particle-substrate electrostatic repulsion in solution. Resulting changes in the coating morphology and microstructure at different solution conditions were observed using confocal microscopy enabling correlation of order to disorder transitions with relative particle stability. These results, in part, may explain similar results seen by Muangnapoh et al., 2013 in vibration-assisted convective deposition.

Repetitive nerve stimulation and single-fiber electromyography in the evaluation of patients with suspected myasthenia gravis or Lambert-Eaton myasthenic syndrome: Review of recent literature.

INTRODUCTION: Our aim in this study was to provide an updated literature review of electrodiagnostic testing in myasthenia gravis and Lambert-Eaton myasthenic syndrome. METHODS: A systematic review of the recent literature was performed using the following key words: myasthenia gravis (MG); Lambert-Eaton myasthenic syndrome (LEMS); electromyography (EMG); repetitive nerve stimulation (RNS); single-fiber electromyography (SFEMG); nerve conduction study; and normative values. RESULTS: Several articles supported testing of facial, bulbar, and respiratory muscles in the diagnosis of neuromuscular junction (NMJ) disorders, including muscle-specific kinase antibody (MuSK)-seropositive MG. Several articles supported use of concentric needle EMG as an alternative to SFEMG jitter in disorders of neuromuscular transmission. A limited number of articles addressed measurement of area (vs. amplitude) decrement in RNS and decreasing the threshold of post-exercise facilitation. CONCLUSIONS: Electrodiagnostic testing continues to be useful for diagnosis of MG and LEMS, although the quality of the evidence is not great. This literature review summarizes RNS and jitter measurement of facial and respiratory muscles and use of concentric needle EMG for SFEMG.

Spacing of Seeded and Spontaneous Streaks during Convective Deposition.

Convective deposition is widely used to deposit a highly ordered and uniform layer of monosized particles from solution by drawing the particles into an advancing thin film that uses capillary forces to define their local orientation. This process is often plagued by the formation of streaks, the regions where particles accumulate due to a local flux inhomogeneity. Flow occurs in the direction orthogonal to the deposition direction and parallel to the substrate near the streaks due to enhanced evaporation where particles have accumulated. This study investigates the formation of streaks nucleated from seeds or defects having prescribed dimensions and spacing across the substrate. The formation and spacing of both seeded and spontaneous streaks are characterized and were observed to be roughly dictated by the suspending fluid capillary length. Thus, spontaneously forming streaks can be suppressed by reducing the spacing to less than twice the critical length. Likewise, the conditions for maximum density or minimal spacing of streaks are also shown.

Flow-induced alignment of (100) fcc thin film colloidal crystals.

The realization of structural diversity in colloidal crystals obtained by self-assembly techniques remains constrained by thermodynamic considerations and current limits on our ability to alter structure over large scales using imposed fields and confinement. In this work, a convective-based procedure to fabricate multi-layer colloidal crystal films with extensive square-like symmetry is enabled by periodic substrate motion imposed during the continuous assembly. The formation of film-spanning domains of (100) fcc symmetry as a result of added vibration is robust across a range of micron-scale monosized spherical colloidal suspensions (e.g., polystyrene, silica) as well as substrate surface chemistries (e.g., hydrophobic, hydrophilic). The generation of extensive single crystalline (100) fcc domains as large as 15 mm(2) and covering nearly 40% of the colloidal crystalline film is possible by simply tuning coating conditions and multi-layer film thickness. Preferential orientation of the square-packed domains with respect to the direction of deposition is attributed to domain generation based upon a shear-related mechanism. Visualization during assembly gives clues toward the mechanism of this flow-driven self-assembly method.

Sequential acquisition of T cells and antibodies to nontyphoidal Salmonella in Malawian children.

BACKGROUND: Salmonella Typhimurium (STm) remain a prominent cause of bacteremia in sub-Saharan Africa. Complement-fixing antibodies to STm develop by 2 years of age. We hypothesized that STm-specific CD4⁺ T cells develop alongside this process. METHODS: Eighty healthy Malawian children aged 0-60 months were recruited. STm-specific CD4⁺ T cells producing interferon γ, tumor necrosis factor α, and interleukin 2 were quantified using intracellular cytokine staining. Antibodies to STm were measured by serum bactericidal activity (SBA) assay, and anti-STm immunoglobulin G antibodies by enzyme-linked immunosorbent assay. RESULTS: Between 2006 and 2011, STm bacteremias were detected in 449 children <5 years old. STm-specific CD4⁺ T cells were acquired in infancy, peaked at 14 months, and then declined. STm-specific SBA was detectable in newborns, declined in the first 8 months, and then increased to a peak at age 35 months. Acquisition of SBA correlated with acquisition of anti-STm-lipopolysaccharide (LPS) immunoglobulin G (r = 0.329 [95% confidence interval, .552-.062]; P = .01) but not anti-STm-outer membrane protein or anti-STm-flagellar protein (FliC). CONCLUSIONS: Acquisition of STm-specific CD4⁺ T cells in early childhood is consistent with early exposure to STm or cross-reactive protein antigens priming this T-cell development. STm-specific CD4⁺ T cells seem insufficient to protect against invasive nontyphoidal Salmonella disease, but sequential acquisition of SBA to STm LPS is associated with a decline in its incidence.

Small-fiber degeneration in alcohol-related peripheral neuropathy.

BACKGROUND: Alcohol-related peripheral neuropathy (ALN) is generally characterized as an axonal large-fiber polyneuropathy caused by thiamine deficiency. We hypothesized, based on clinical observations, that ALN is associated with a small-fiber polyneuropathy that can be diagnosed with skin biopsy in heavy alcohol drinking subjects with normal thiamine status. METHODS: Eighteen individuals (9 heavy alcohol drinking subjects and 9 healthy control subjects) were assessed for the potential utility of skin biopsies in detecting ALN-associated small nerve fiber degeneration. Heavy drinking was defined as greater than 4 drinks/d and 5 drinks/d in women and men, respectively, as determined by the Timeline Follow-Back and lifetime drinking history. All subjects underwent neurological examination, nerve conduction studies, and skin biopsies to quantify end nerve fiber densities (ENFD). Other causes of neuropathy were excluded and thiamine status was assessed. RESULTS: Average ENFD were significantly decreased at the calf in the alcohol group as compared with control group (p < 0.0001). Histological sections demonstrated striking attrition and architectural simplification of intraepidermal nerve fibers in the heavy alcohol drinking subjects. There were no significant intergroup differences with respect to clinical assessments of neuropathy or thiamine status. CONCLUSIONS: ALN is associated with a small-fiber neuropathy that can be detected with skin biopsy in heavy alcohol drinking individuals with normal thiamine status. Skin biopsy is a useful, minimally invasive biomarker that could extend studies to understand the effect of alcohol on the peripheral nerves and to evaluate potential therapeutic agents in larger clinical trials.

Microstructure of sheared monosized colloidal suspensions resulting from hydrodynamic and electrostatic interactions.

Hydrodynamic and near-particle interactions in sheared suspensions are communicated through suspension microstructure to produce a wide variety of rheological behaviors. To characterize this microstructure, the individual positions of monosized silica particles flowing through a microchannel are obtained with near simulation-level detail. The pair distribution functions of the microstructure at moderate to high Péclet number shear rates are very similar to previous numerical studies. Viscometric functions calculated based on the detailed microstructure obtained through this technique show qualitative agreement with computational results. These results elucidate the origins of shear-thickening of suspensions at high shear rates. While efforts are taken to screen electrostatic interactions to study hydrodynamic and Brownian interactions, the role of electrostatic interaction between particles is also investigated by reducing suspension ionic strength. These non-hydrodynamic electrostatic interactions result in a loss of anisotropy that generally agrees with previous findings of "soft" particle systems.

Density Matching for Microencapsulation of Field Responsive Suspensions of Non-Brownian Microparticles.

When forming composite microcapsules through the emulsification of a dispersed phase laden with microparticles, one will find that the microparticles become irreversibly embedded in the resulting microcapsule membrane. This phenomenon, known as Pickering stabilization, is detrimental when the end function of the microcapsules relies on the mobility of encapsulated microparticles within the capsule core. In this work, a robust microencapsulation route using density matching of non-Brownian microparticles in a binary solvent is shown to easily and effectively encapsulate particles, with >90% of particles retaining mobility within the microcapsules, without the necessity for prior chemical/physical modifications to the microparticles. This is proposed as a generalized method to be used for all manner of particle chemistries, shapes, and sizes.

Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture.

The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p<5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.