Multivariate Cluster Point Process to Quantify and Explore Multi-Entity Configurations: Application to Biofilm Image Data.

Clusters of similar or dissimilar objects are encountered in many fields. Frequently used approaches treat each cluster's central object as latent. Yet, often objects of one or more types cluster around objects of another type.

Integration of epidemiological and blood biomarker analysis links haem iron intake to increased type 2 diabetes risk.

Dietary haem iron intake is linked to an increased risk of type 2 diabetes (T2D), but the underlying plasma biomarkers are not well understood. We analysed data from 204,615 participants (79% females) in three large US cohorts over up to 36 years, examining the associations between iron intake and T2D risk. We also assessed plasma metabolic biomarkers and metabolomic profiles in subsets of 37,544 (82% females) and 9,024 (84% females) participants, respectively.

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.

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.

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.

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.

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.

Characterizing quantile-varying covariate effects under the accelerated failure time model.

An important task in survival analysis is choosing a structure for the relationship between covariates of interest and the time-to-event outcome. For example, the accelerated failure time (AFT) model structures each covariate effect as a constant multiplicative shift in the outcome distribution across all survival quantiles. Though parsimonious, this structure cannot detect or capture effects that differ across quantiles of the distribution, a limitation that is analogous to only permitting proportional hazards in the Cox model.

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.

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.

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.

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.

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 (H NMR) and confirmed the resulting oligomer ratio.

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.

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].

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 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.

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 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.

Improved Physicochemical Stability and High Ion Transportation of Poly(Arylene Ether Sulfone) Blocks Containing a Fluorinated Hydrophobic Part for Anion Exchange Membrane Applications.

A series of anion exchange membranes composed of partially fluorinated poly(arylene ether sulfone)s (PAESs) multiblock copolymers bearing quaternary ammonium groups were synthesized with controlled lengths of the hydrophilic precursor and hydrophobic oligomer via direct polycondensation. The chloromethylation and quaternization proceeded well by optimizing the reaction conditions to improve hydroxide conductivity and physical stability, and the fabricated membranes were very flexible and transparent. Atomic force microscope images of quaternized PAES (QN-PAES) membranes showed excellent hydrophilic/hydrophobic phase separation and distinct ion transition channels.

Facile Fabrication and Characterization of Improved Proton Conducting Sulfonated Poly(Arylene Biphenylether Sulfone) Blocks Containing Fluorinated Hydrophobic Units for Proton Exchange Membrane Fuel Cell Applications.

Sulfonated poly(arylene biphenylether sulfone)-poly(arylene ether) (SPABES-PAE) block copolymers by controlling the molar ratio of SPABES and PAE oligomers were successfully synthesized, and the performances of SPABES-PAE (1:2, 1:1, and 2:1) membranes were compared with Nafion 212. The prepared membranes including fluorinated hydrophobic units were stable against heat, nucleophile attack, and physio-chemical durability during the tests. Moreover, the polymers exhibited better solubility in a variety of solvents.

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.

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.

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).

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.

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.

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 H 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.