Planetary Health Diet Index and risk of total and cause-specific mortality in three prospective cohorts.

BACKGROUND: In 2019, the EAT-Lancet Commission proposed a healthy dietary pattern that, along with reductions in food waste and improved agricultural practices, could feed the increasing global population sustainably. We developed a Planetary Health Diet Index (PHDI) to quantify adherence to the EAT-Lancet reference diet. OBJECTIVES: We aimed to assess associations between PHDI and total and cause-specific mortality in 3 prospective cohorts of males and females in the United States. METHODS: We followed 66,692 females from the Nurses' Health Study (1986-2019), 92,438 females from the Nurses' Health Study II (1989-2019), and 47,274 males from the Health Professionals Follow-up Study (1986-2018) who were free of cancer, diabetes, and major cardiovascular diseases at baseline. The PHDI was calculated every 4 y using a semiquantitative food frequency questionnaire. Hazard ratios (HRs) were calculated using multivariable proportional-hazards models. RESULTS: During follow-up, we documented 31,330 deaths among females and 23,206 among males. When comparing the highest with the lowest quintile of PHDI, the pooled multivariable-adjusted HRs were 0.77 [95% confidence interval (CI): 0.75, 0.80] for all-cause mortality (P-trend < 0.0001). The PHDI was associated with lower risk of deaths from cardiovascular diseases (HR: 0.86; 95% CI: 0.81, 0.91), cancer (HR: 0.90; 95% CI: 0.85, 0.95), respiratory diseases (HR: 0.53; 95% CI: 0.48, 0.59), and neurodegenerative diseases (HR: 0.72; 95% CI: 0.67, 0.78). In females, but not males, the PHDI was also significantly associated with a lower risk of deaths from infectious diseases (HR: 0.62; 95% CI: 0.51, 0.76). PHDI scores were also associated inversely with greenhouse gas emissions and other environmental impacts. CONCLUSIONS: In 3 large United States-based prospective cohorts of males and females with up to 34 y of follow-up, a higher PHDI was associated with lower risk of total and cause-specific mortality and environment impacts.

Group lasso priors for Bayesian accelerated failure time models with left-truncated and interval-censored data.

An important task in health research is to characterize time-to-event outcomes such as disease onset or mortality in terms of a potentially high-dimensional set of risk factors. For example, prospective cohort studies of Alzheimer's disease (AD) typically enroll older adults for observation over several decades to assess the long-term impact of genetic and other factors on cognitive decline and mortality. The accelerated failure time model is particularly well-suited to such studies, structuring covariate effects as "horizontal" changes to the survival quantiles that conceptually reflect shifts in the outcome distribution due to lifelong exposures. However, this modeling task is complicated by the enrollment of adults at differing ages, and intermittent follow-up visits leading to interval-censored outcome information. Moreover, genetic and clinical risk factors are not only high-dimensional, but characterized by underlying grouping structures, such as by function or gene location. Such grouped high-dimensional covariates require shrinkage methods that directly acknowledge this structure to facilitate variable selection and estimation. In this paper, we address these considerations directly by proposing a Bayesian accelerated failure time model with a group-structured lasso penalty, designed for left-truncated and interval-censored time-to-event data. We develop an R package with a Markov chain Monte Carlo sampler for estimation. We present a simulation study examining the performance of this method relative to an ordinary lasso penalty and apply the proposed method to identify groups of predictive genetic and clinical risk factors for AD in the Religious Orders Study and Memory and Aging Project prospective cohort studies of AD and dementia.

An augmented illness-death model for semi-competing risks with clinically immediate terminal events.

Preeclampsia is a pregnancy-associated condition posing risks of both fetal and maternal mortality and morbidity that can only resolve following delivery and removal of the placenta. Because in its typical form preeclampsia can arise before delivery, but not after, these two events exemplify the time-to-event setting of "semi-competing risks" in which a non-terminal event of interest is subject to the occurrence of a terminal event of interest. The semi-competing risks framework presents a valuable opportunity to simultaneously address two clinically meaningful risk modeling tasks: (i) characterizing risk of developing preeclampsia, and (ii) characterizing time to delivery after onset of preeclampsia. However, some people with preeclampsia deliver immediately upon diagnosis, while others are admitted and monitored for an extended period before giving birth, resulting in two distinct trajectories following the non-terminal event, which we call "clinically immediate" and "non-immediate" terminal events. Though such phenomena arise in many clinical contexts, to-date there have not been methods developed to acknowledge the complex dependencies between such outcomes, nor leverage these phenomena to gain new insight into individualized risk. We address this gap by proposing a novel augmented frailty-based illness-death model with a binary submodel to distinguish risk of immediate terminal event following the non-terminal event. The model admits direct dependence of the terminal event on the non-terminal event through flexible regression specification, as well as indirect dependence via a shared frailty term linking each submodel. We develop an efficient Bayesian sampler for estimation and corresponding model fit metrics, and derive formulae for dynamic risk prediction. In an extended example using pregnancy outcome data from an electronic health record, we demonstrate the proposed model's direct applicability to address a broad range of clinical questions.

Interplay between diet, circulating indolepropionate concentrations and cardiometabolic health in US populations.

OBJECTIVES: To identify indolepropionate (IPA)-predicting gut microbiota species, investigate potential diet-microbiota interactions, and examine the prospective associations of circulating IPA concentrations with type 2 diabetes (T2D) and coronary heart disease (CHD) risk in free-living individuals. DESIGN: We included 287 men from the Men's Lifestyle Validation Study, a substudy of the Health Professionals Follow-Up Study (HPFS), who provided up to two pairs of faecal samples and two blood samples. Diet was assessed using 7-day diet records. Associations between plasma concentrations of tryptophan metabolites and T2D CHD risk were examined in 13 032 participants from Nurses' Health Study (NHS), NHSII and HPFS. RESULTS: We identified 17 microbial species whose abundance was significantly associated with plasma IPA concentrations. A significant association between higher tryptophan intake and higher IPA concentrations was only observed among men who had higher fibre intake and a higher microbial species score consisting of the 17 species (p-interaction<0.01). Dietary and plasma concentrations of tryptophan and most kynurenine pathway metabolites were positively associated with T2D risk (HRQ5 vs Q1 ranged from 1.17 to 1.46) while a significant inverse association was found for IPA (HRQ5 vs Q1 (95% CI) 0.70 (0.56 to 0.88)). No associations were found in CHD for any plasma tryptophan metabolites. CONCLUSIONS: Specific microbial species and dietary fibre jointly predicted significantly higher circulating IPA concentrations at higher tryptophan intake. Dietary and plasma tryptophan, as well as its kynurenine pathway metabolites, demonstrated divergent associations from those for IPA, which was significantly predictive of lower risk of T2D.

Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals.

Experimental studies reported biochemical actions underpinning aging processes and mortality, but the relevant metabolic alterations in humans are not well understood. Here we examine the associations of 243 plasma metabolites with mortality and longevity (attaining age 85 years) in 11,634 US (median follow-up of 22.6 years, with 4288 deaths) and 1878 Spanish participants (median follow-up of 14.5 years, with 525 deaths). We find that, higher levels of N2,N2-dimethylguanosine, pseudouridine, N4-acetylcytidine, 4-acetamidobutanoic acid, N1-acetylspermidine, and lipids with fewer double bonds are associated with increased risk of all-cause mortality and reduced odds of longevity; whereas L-serine and lipids with more double bonds are associated with lower mortality risk and a higher likelihood of longevity. We further develop a multi-metabolite profile score that is associated with higher mortality risk. Our findings suggest that differences in levels of nucleosides, amino acids, and several lipid subclasses can predict mortality. The underlying mechanisms remain to be determined.

MEASURING PERFORMANCE FOR END-OF-LIFE CARE.

Although not without controversy, readmission is entrenched as a hospital quality metric with statistical analyses generally based on fitting a logistic-Normal generalized linear mixed model. Such analyses, however, ignore death as a competing risk, although doing so for clinical conditions with high mortality can have profound effects; a hospital's seemingly good performance for readmission may be an artifact of it having poor performance for mortality. in this paper we propose novel multivariate hospital-level performance measures for readmission and mortality that derive from framing the analysis as one of cluster-correlated semi-competing risks data. We also consider a number of profiling-related goals, including the identification of extreme performers and a bivariate classification of whether the hospital has higher-/lower-than-expected readmission and mortality rates via a Bayesian decision-theoretic approach that characterizes hospitals on the basis of minimizing the posterior expected loss for an appropriate loss function. in some settings, particularly if the number of hospitals is large, the computational burden may be prohibitive. To resolve this, we propose a series of analysis strategies that will be useful in practice. Throughout, the methods are illustrated with data from CMS on N = 17,685 patients diagnosed with pancreatic cancer between 2000-2012 at one of J = 264 hospitals in California.

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men.

OBJECTIVES: Gut-produced trimethylamine N-oxide (TMAO) is postulated as a possible link between red meat intake and poor cardiometabolic health. We investigated whether gut microbiome could modify associations of dietary precursors with TMAO concentrations and cardiometabolic risk markers among free-living individuals. DESIGN: We collected up to two pairs of faecal samples (n=925) and two blood samples (n=473), 6 months apart, from 307 healthy men in the Men's Lifestyle Validation Study. Diet was assessed repeatedly using food-frequency questionnaires and diet records. We profiled faecal metagenome and metatranscriptome using shotgun sequencing and identified microbial taxonomic and functional features. RESULTS: TMAO concentrations were associated with the overall microbial compositions (permutational analysis of variance (PERMANOVA) test p=0.001). Multivariable taxa-wide association analysis identified 10 bacterial species whose abundance was significantly associated with plasma TMAO concentrations (false discovery rate <0.05). Higher habitual intake of red meat and choline was significantly associated with higher TMAO concentrations among participants who were microbial TMAO-producers (p<0.05), as characterised based on four abundant TMAO-predicting species, but not among other participants (for red meat, P-interaction=0.003; for choline, P-interaction=0.03). Among abundant TMAO-predicting species, Alistipes shahii significantly strengthened the positive association between red meat intake and HbA1c levels (P-interaction=0.01). Secondary analyses revealed that some functional features, including choline trimethylamine-lyase activating enzymes, were associated with TMAO concentrations. CONCLUSION: We identified microbial taxa that were associated with TMAO concentrations and modified the associations of red meat intake with TMAO concentrations and cardiometabolic risk markers. Our data underscore the interplay between diet and gut microbiome in producing potentially bioactive metabolites that may modulate cardiometabolic health.

Enhancing Physicochemical Properties and Single Cell Performance of Sulfonated Poly(arylene ether) (SPAE) Membrane by Incorporation of Phosphotungstic Acid and Graphene Oxide: A Potential Electrolyte for Proton Exchange Membrane Fuel Cells.

The development of potential and novel proton exchange membranes (PEMs) is imperative for the further commercialization of PEM fuel cells (PEMFCs). In this work, phosphotungstic acid (PWA) and graphene oxide (GO) were integrated into sulfonated poly(arylene ether) (SPAE) through a solution casting approach to create a potential composite membrane for PEMFC applications. Thermal stability of membranes was observed using thermogravimetric analysis (TGA), and the SPAE/GO/PWA membranes exhibited high thermal stability compared to pristine SPAE membranes, owing to the interaction between SPAEK, GO, and PWA. By using a scanning electron microscope (SEM) and atomic force microscope (AFM), we observed that GO and PWA were evenly distributed throughout the SPAE matrix. The SPAE/GO/PWA composite membrane comprising 0.7 wt% GO and 36 wt% PWA exhibited a maximum proton conductivity of 186.3 mS cm-1 at 90 °C under 100% relative humidity (RH). As a result, SPAE/GO/PWA composite membrane exhibited 193.3 mW cm-2 of the maximum power density at 70 °C under 100% RH in PEMFCs.

Enhanced Hydroxide Conductivity and Dimensional Stability with Blended Membranes Containing Hyperbranched PAES/Linear PPO as Anion Exchange Membranes.

A series of novel blended anion exchange membranes (AEMs) were prepared with hyperbranched brominated poly(arylene ether sulfone) (Br-HB-PAES) and linear chloromethylated poly(phenylene oxide) (CM-PPO). The as-prepared blended membranes were fabricated with different weight ratios of Br-HB-PAES to CM-PPO, and the quaternization reaction for introducing the ionic functional group was performed by triethylamine. The Q-PAES/PPO-XY (quaternized-PAES/PPO-XY) blended membranes promoted the ion channel formation as the strong hydrogen bonds interconnecting the two polymers were maintained, and showed an improved hydroxide conductivity with excellent thermal behavior. In particular, the Q-PAES/PPO-55 membrane showed a very high hydroxide ion conductivity (90.9 mS cm-1) compared to the pristine Q-HB-PAES membrane (32.8 mS cm-1), a result supported by the morphology of the membrane as determined by the AFM analysis. In addition, the rigid hyperbranched structure showed a suppressed swelling ratio of 17.9-24.9% despite an excessive water uptake of 33.2-50.3% at 90 °C, and demonstrated a remarkable alkaline stability under 2.0 M KOH conditions over 1000 h.

Ameliorated Performance of Sulfonated Poly(Arylene Ether Sulfone) Block Copolymers with Increased Hydrophilic Oligomer Ratio in Proton-Exchange Membrane Fuel Cells Operating at 80% Relative Humidity.

We designed and synthesized a series of sulfonated poly(arylene ether sulfone) (SPES) with different hydrophilic or hydrophobic oligomer ratios using poly-condensation strategy. Afterward, we fabricated the corresponding membranes via a solution-casting approach. We verified the SPES membrane chemical structure using nuclear magnetic resonance (1H NMR) and confirmed the resulting oligomer ratio. Field-emission scanning electron microscope (FE-SEM) and atomic force microscope (AFM) results revealed that we effectively attained phase separation of the SPES membrane along with an increased hydrophilic oligomer ratio. Thermal stability, glass transition temperature (Tg) and membrane elongation increased with the ratio of hydrophilic oligomers. SPES membranes with higher hydrophilic oligomer ratios exhibited superior water uptake, ion-exchange capacity, contact angle and water sorption, while retaining reasonable swelling degree. The proton conductivity results showed that SPES containing higher amounts of hydrophilic oligomers provided a 74.7 mS cm-1 proton conductivity at 90 °C, which is better than other SPES membranes, but slightly lower than that of Nafion-117 membrane. When integrating SPES membranes with proton-exchange membrane fuel cells (PEMFCs) at 60 °C and 80% relative humidity (RH), the PEMFC power density exhibited a similar increment-pattern like proton conductivity pattern.

Bayesian variable selection for multivariate zero-inflated models: Application to microbiome count data.

Microorganisms play critical roles in human health and disease. They live in diverse communities in which they interact synergistically or antagonistically. Thus for estimating microbial associations with clinical covariates, such as treatment effects, joint (multivariate) statistical models are preferred. Multivariate models allow one to estimate and exploit complex interdependencies among multiple taxa, yielding more powerful tests of exposure or treatment effects than application of taxon-specific univariate analyses. Analysis of microbial count data also requires special attention because data commonly exhibit zero inflation, i.e., more zeros than expected from a standard count distribution. To meet these needs, we developed a Bayesian variable selection model for multivariate count data with excess zeros that incorporates information on the covariance structure of the outcomes (counts for multiple taxa), while estimating associations with the mean levels of these outcomes. Though there has been much work on zero-inflated models for longitudinal data, little attention has been given to high-dimensional multivariate zero-inflated data modeled via a general correlation structure. Through simulation, we compared performance of the proposed method to that of existing univariate approaches, for both the binary ("excess zero") and count parts of the model. When outcomes were correlated the proposed variable selection method maintained type I error while boosting the ability to identify true associations in the binary component of the model. For the count part of the model, in some scenarios the univariate method had higher power than the multivariate approach. This higher power was at a cost of a highly inflated false discovery rate not observed with the proposed multivariate method. We applied the approach to oral microbiome data from the Pediatric HIV/AIDS Cohort Oral Health Study and identified five (of 44) species associated with HIV infection.

Unjamming and collective migration in MCF10A breast cancer cell lines.

Each cell comprising an intact, healthy, confluent epithelial layer ordinarily remains sedentary, firmly adherent to and caged by its neighbors, and thus defines an elemental constituent of a solid-like cellular collective [1,2]. After malignant transformation, however, the cellular collective can become fluid-like and migratory, as evidenced by collective motions that arise in characteristic swirls, strands, ducts, sheets, or clusters [3,4]. To transition from a solid-like to a fluid-like phase and thereafter to migrate collectively, it has been recently argued that cells comprising the disordered but confluent epithelial collective can undergo changes of cell shape so as to overcome geometric constraints attributable to the newly discovered phenomenon of cell jamming and the associated unjamming transition (UJT) [1,2,5-9]. Relevance of the jamming concept to carcinoma cells lines of graded degrees of invasive potential has never been investigated, however. Using classical in vitro cultures of six breast cancer model systems, here we investigate structural and dynamical signatures of cell jamming, and the relationship between them [1,2,10,11]. In order of roughly increasing invasive potential as previously reported, model systems examined included MCF10A, MCF10A.Vector; MCF10A.14-3-3ζ; MCF10.ErbB2, MCF10AT; and MCF10CA1a [12-15]. Migratory speed depended on the particular cell line. Unsurprisingly, for example, the MCF10CA1a cell line exhibited much faster migratory speed relative to the others. But unexpectedly, across different cell lines higher speeds were associated with enhanced size of cooperative cell packs in a manner reminiscent of a peloton [9]. Nevertheless, within each of the cell lines evaluated, cell shape and shape variability from cell-to-cell conformed with predicted structural signatures of cell layer unjamming [1]. Moreover, both structure and migratory dynamics were compatible with previous theoretical descriptions of the cell jamming mechanism [2,10,11,16,17]. As such, these findings demonstrate the richness of the cell jamming mechanism, which is now seen to apply across these cancer cell lines but remains poorly understood.

Variation in zygotic CRISPR/Cas9 gene editing outcomes generates novel reporter and deletion alleles at the Gdf11 locus.

Recent advances in CRISPR/Cas gene editing technology have significantly expanded the possibilities and accelerated the pace of creating genetically engineered animal models. However, CRISPR/Cas-based strategies designed to precisely edit the genome can often yield unintended outcomes. Here, we report the use of zygotic CRISPR/Cas9 injections to generate a knock-in GFP reporter mouse at the Gdf11 locus. Phenotypic and genomic characterization of founder animals from these injections revealed a subset that contained the correct targeting event and exhibited GFP expression that, within the hematopoietic system, was restricted predominantly to lymphoid cells. Yet, in another subset of founder mice, we detected aberrant integration events at the target site that dramatically and inaccurately shifted hematopoietic GFP expression from the lymphoid to the myeloid lineage. Additionally, we recovered multiple Gdf11 deletion alleles that modified the C-terminus of the GDF11 protein. When bred to homozygosity, most of these alleles recapitulated skeletal phenotypes reported previously for Gdf11 knockout mice, suggesting that these represent null alleles. However, we also recovered one Gdf11 deletion allele that encodes a novel GDF11 variant protein ("GDF11-WE") predicted to contain two additional amino acids (tryptophan (W) and glutamic acid (E)) at the C-terminus of the mature ligand. Unlike the other Gdf11 deletion alleles recovered in this study, homozygosity for the Gdf11WE allele did not phenocopy Gdf11 knockout skeletal phenotypes. Further investigation using in vivo and in vitro approaches demonstrated that GDF11-WE retains substantial physiological function, indicating that GDF11 can tolerate at least some modifications of its C-terminus and providing unexpected insights into its biochemical activities. Altogether, our study confirms that one-step zygotic injections of CRISPR/Cas gene editing complexes provide a quick and powerful tool to generate gene-modified mouse models. Moreover, our findings underscore the critical importance of thorough characterization and validation of any modified alleles generated by CRISPR, as unintended on-target effects that fail to be detected by simple PCR screening can produce substantially altered phenotypic readouts.

Mapping the Tooth Enamel Proteome and Amelogenin Phosphorylation Onto Mineralizing Porcine Tooth Crowns.

Tooth enamel forms in an ephemeral protein matrix where changes in protein abundance, composition and posttranslational modifications are critical to achieve healthy enamel properties. Amelogenin (AMELX) with its splice variants is the most abundant enamel matrix protein, with only one known phosphorylation site at serine 16 shown in vitro to be critical for regulating mineralization. The phosphorylated form of AMELX stabilizes amorphous calcium phosphate, while crystalline hydroxyapatite forms in the presence of the unphosphorylated protein. While AMELX regulates mineral transitions over space and time, it is unknown whether and when un-phosphorylated amelogenin occurs during enamel mineralization. This study aims to reveal the spatiotemporal distribution of the cleavage products of the most abundant AMLEX splice variants including the full length P173, the shorter leucine-rich amelogenin protein (LRAP), and the exon 4-containing P190 in forming enamel, all within the context of the changing enamel matrix proteome during mineralization. We microsampled permanent pig molars, capturing known stages of enamel formation from both crown surface and inner enamel. Nano-LC-MS/MS proteomic analyses after tryptic digestion rendered more than 500 unique protein identifications in enamel, dentin, and bone. We mapped collagens, keratins, and proteolytic enzymes (CTSL, MMP2, MMP10) and determined distributions of P173, LRAP, and P190 products, the enamel proteins enamelin (ENAM) and ameloblastin (AMBN), and matrix-metalloprotease-20 (MMP20) and kallikrein-4 (KLK4). All enamel proteins and KLK4 were near-exclusive to enamel and in excellent agreement with published abundance levels. Phosphorylated P173 and LRAP products decreased in abundance from recently deposited matrix toward older enamel, mirrored by increasing abundances of testicular acid phosphatase (ACPT). Our results showed that hierarchical clustering analysis of secretory enamel links closely matching distributions of unphosphorylated P173 and LRAP products with ACPT and non-traditional amelogenesis proteins, many associated with enamel defects. We report higher protein diversity than previously published and Gene Ontology (GO)-defined protein functions related to the regulation of mineral formation in secretory enamel (e.g., casein α-S1, CSN1S1), immune response in erupted enamel (e.g., peptidoglycan recognition protein, PGRP), and phosphorylation. This study presents a novel approach to characterize and study functional relationships through spatiotemporal mapping of the ephemeral extracellular matrix proteome.

Outcome of early dental implant placement versus other dental implant placement protocols: A systematic review and meta-analysis.

BACKGROUND: The aim of this systematic review and meta-analysis was to compare the clinical efficacy of the early dental implant placement protocol with immediate and delayed dental implant placement protocols. METHODS: An electronic and manual search of literature was made to identify clinical studies comparing early implant placement with immediate or delayed placement. Data from the included studies were pooled and quantitative analyses were performed for the implant outcomes reported as the number of failed implants (primary outcome variable) and for changes in peri-implant marginal bone level, peri-implant probing depth, and peri-implant soft tissue level (secondary outcome variables). RESULTS: Twelve studies met the inclusion criteria. Significant difference in risk of implant failure was found neither between the early and immediate placement protocols (risk difference = -0.018; 95% confidence interval [CI] = -0.06, 0.025; P = 0.416) nor between early and delayed placement protocols (risk difference = -0.008; 95% CI = -0.044, 0.028; P = 0.670). Pooled data of changes in peri-implant marginal bone level demonstrated significantly less marginal bone loss for implants placed using the early placement protocol compared with those placed in fresh extraction sockets (P = 0.001; weighted mean difference = -0.14 mm; 95% CI = -0.22, -0.05). No significant differences were found between the protocols for the other variables. CONCLUSIONS: The available evidence supports the clinical efficacy of the early implant placement protocol. Present findings indicate that the early implant placement protocol results in implant outcomes similar to immediate and delayed placement protocols and a superior stability of peri-implant hard tissue compared with immediate implant placement.

Dimensional accuracy of cone beam CT with varying angulation of the jaw to the X-ray beam.

OBJECTIVES: Cone beam CT (CBCT) machines do not always allow for patients to be scanned in the ideal position for image acquisition. This study aimed to investigate the influence of the position/angulation of the mandible relative to the X-ray beam of a CBCT machine. METHODS: Five sequential CBCT scans were captured of a human mandible at each angulation of 10°, 20°, 30°, and 40° using a coronal and sagittal positioning. Inspection software utilized a best-fit alignment to automatically calculate the three-dimensional variation at 15 standardized points of interest. RESULTS: Statistically significant differences were found between the dimensional accuracy of CBCT scans taken at 10° (26.3 µm) of coronal angulation, as well as those taken at 20° (-17.3 mm) and 30° (35.2 mm) of sagittal angulations (p < 0.001, 0.016, and <0.001, respectively). The largest deviations in accuracy included an overall maximum deviation of 490 mm. CONCLUSIONS: The position of the mandible with respect to the X-ray beam has a clinically insignificant effect on dimensional accuracy, up to the maximum angle of 40° assessed.

SemiCompRisks: An R Package for the Analysis of Independent and Cluster-correlated Semi-competing Risks Data.

Semi-competing risks refer to the setting where primary scientific interest lies in estimation and inference with respect to a non-terminal event, the occurrence of which is subject to a terminal event. In this paper, we present the R package SemiCompRisks that provides functions to perform the analysis of independent/clustered semi-competing risks data under the illness-death multi-state model. The package allows the user to choose the specification for model components from a range of options giving users substantial flexibility, including: accelerated failure time or proportional hazards regression models; parametric or non-parametric specifications for baseline survival functions; parametric or non-parametric specifications for random effects distributions when the data are cluster-correlated; and, a Markov or semi-Markov specification for terminal event following non-terminal event. While estimation is mainly performed within the Bayesian paradigm, the package also provides the maximum likelihood estimation for select parametric models. The package also includes functions for univariate survival analysis as complementary analysis tools.

Geometric constraints during epithelial jamming.

As an injury heals, an embryo develops, or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively whereas variability of shape from cell-to-cell is regarded most often as biological noise. But where do cell shape and its variability come from? Here we report that cell shape and shape variability are mutually constrained through a relationship that is purely geometrical. That relationship is shown to govern processes as diverse as maturation of the pseudostratified bronchial epithelial layer cultured from non-asthmatic or asthmatic donors, and formation of the ventral furrow in the Drosophila embryo. Across these and other epithelial systems, shape variability collapses to a family of distributions that is common to all. That distribution, in turn, is accounted for by a mechanistic theory of cell-cell interaction showing that cell shape becomes progressively less elongated and less variable as the layer becomes progressively more jammed. These findings suggest a connection between jamming and geometry that spans living organisms and inert jammed systems, and thus transcends system details. Although molecular events are needed for any complete theory of cell shape and cell packing, observations point to the hypothesis that jamming behavior at larger scales of organization sets overriding geometrical constraints.

Oral microbiota in youth with perinatally acquired HIV infection.

BACKGROUND: Microbially mediated oral diseases can signal underlying HIV/AIDS progression in HIV-infected adults. The role of the oral microbiota in HIV-infected youth is not known. The Adolescent Master Protocol of the Pediatric HIV/AIDS Cohort Study is a longitudinal study of perinatally HIV-infected (PHIV) and HIV-exposed, uninfected (PHEU) youth. We compared oral microbiome levels and associations with caries or periodontitis in 154 PHIV and 100 PHEU youth. RESULTS: Species richness and alpha diversity differed little between PHIV and PHEU youth. Group differences in average counts met the significance threshold for six taxa; two Corynebacterium species were lower in PHIV and met thresholds for noteworthiness. Several known periodontitis-associated organisms (Prevotella nigrescens, Tannerella forsythia, Aggregatibacter actinomycetemcomitans, and Filifactor alocis) exhibited expected associations with periodontitis in PHEU youth, associations not observed in PHIV youth. In both groups, odds of caries increased with counts of taxa in four genera, Streptococcus, Scardovia, Bifidobacterium, and Lactobacillus. CONCLUSIONS: The microbiomes of PHIV and PHEU youth were similar, although PHIV youth seemed to have fewer "health"-associated taxa such as Corynebacterium species. These results are consistent with the hypothesis that HIV infection, or its treatment, may contribute to oral dysbiosis.

Enhanced Performance of a Sulfonated Poly(arylene ether ketone) Block Copolymer Bearing Pendant Sulfonic Acid Groups for Polymer Electrolyte Membrane Fuel Cells Operating at 80% Relative Humidity.

The series of sulfonated poly(arylene ether ketone) (SPAEK) block copolymers with controlled F-oligomer length bearing pendant diphenyl unit were synthesized via a polycondensation reaction. Sulfonation was verified by 1H NMR analysis to introduce sulfonic acid group selectively and intensively on the pendant diphenyl unit of polymer backbones. The SPAEK membranes fabricated by the solution casting approach were very transparent and flexible with the thickness of ∼50 µm. These membranes with different F-oligomer lengths were investigated to the physiochemical properties such as water absorption, dimensional stability, ion exchange capacity, and proton conductivity. As a result, the SPAEK membranes (X4.8Y8.8, X7.5Y8.8, and X9.1Y8.8) in accordance to increasing the length of hydrophilic oligomer showed excellent proton conductivity in range of 131-154 mS cm-1 compared to Nafion-115 (131 mS cm-1) at 90 °C under 100% relative humidity (RH). Among the SPAEK membranes, proton conductivity of SPAEK X9.1Y8.8 (140.7 mS cm-1) is higher than that of Nafion-115 (102 mS cm-1) at 90 °C under 80% RH. The atomic force microscopy image demonstrated that number of ion transport channels is increased with increase in the length of hydrophilic oligomer in the main chains, and the morphology is proved to be related to the proton conductivity. The synthesized SPAEK membrane exhibited a maximum power density of 324 mW cm-2, which is higher than that of Nafion-115 (291 mW cm-2) at 60 °C under 100% RH.