Patient-Engagement Health Information Technology and Quality Process Outcomes in Federally Qualified Health Centers.

BACKGROUND AND OBJECTIVES: Health information technology (HIT) for patient-engagement can positively influence the quality and efficiency of health care delivery. Although this topic is of significant importance, it has not been fully addressed in the federally qualified health center (FQHC) context. This research investigates the relationship between the level of patient-engagement HIT and FQHC preventive health care quality outcomes. METHOD: Based on the Uniform Data System (UDS), this study employed multivariable regression analysis to investigate the association between the level of patient-engagement HIT and FQHC preventive health care quality outcomes. FQHCs were placed in 4 mutually exclusive groups based on the level of FQHC use of patient-engagement HIT. RESULTS: The results indicate that compared with the most comprehensive patient-engagement HIT at FQHCs, less comprehensive patient-engagement HIT was associated with lower rates of preventive care provision. CONCLUSIONS: Comprehensive patient-engagement HIT across FQHCs may improve preventive health care quality outcomes. The results support policy incentives for FQHCs with less comprehensive levels of patient-engagement HIT to foster improved preventive care for their patients.

Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.

BACKGROUND: Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS: Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS: Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.

Flow states of two dimensional active gels driven by external shear.

Using a minimal hydrodynamic model, we theoretically and computationally study the Couette flow of active gels in straight and annular two-dimensional channels subject to an externally imposed shear. The gels are isotropic in the absence of externally- or activity-driven shear, but have nematic order that increases with shear rate. Using the finite element method, we determine the possible flow states for a range of activities and shear rates. Linear stability analysis of an unconfined gel in a straight channel shows that an externally imposed shear flow can stabilize an extensile fluid that would be unstable to spontaneous flow in the absence of the shear flow, and destabilize a contractile fluid that would be stable against spontaneous flow in the absence of shear flow. These results are in rough agreement with the stability boundaries between the base shear flow state and the nonlinear flow states that we find numerically for a confined active gel. For extensile fluids, we find three kinds of nonlinear flow states in the range of parameters we study: unidirectional flows, oscillatory flows, and dancing flows. To highlight the activity-driven spontaneous component of the nonlinear flows, we characterize these states by the average volumetric flow rate and the wall stress. For contractile fluids, we only find the linear shear flow and a nonlinear unidirectional flow in the range of parameters that we studied. For large magnitudes of the activity, the unidirectional contractile flow develops a boundary layer. Our analysis of annular channels shows how curvature of the streamlines in the base flow affects the transitions among flow states.

Chiral fluid membranes with orientational order and multiple edges.

We carry out Monte Carlo simulations on fluid membranes with orientational order and multiple edges in the presence and absence of external forces. The membrane resists bending and has an edge tension, the orientational order couples with the membrane surface normal through a cost for tilting, and there is a chiral liquid crystalline interaction. In the absence of external forces, a membrane initialized as a vesicle will form a disk at low chirality, with the directors forming a smectic-A phase with alignment perpendicular to the membrane surface except near the edge. At large chirality a catenoid-like shape or a trinoid-like shape is formed, depending on the number of edges in the initial vesicle. This shape change is accompanied by cholesteric ordering of the directors and multiple π walls connecting the membrane edges and wrapping around the membrane neck. If the membrane is initialized instead in a cylindrical shape and stretched by an external force, it maintains a nearly cylindrical shape but additional liquid crystalline phases appear. For large tilt coupling and low chirality, a smectic-A phase forms where the directors are normal to the surface of the membrane. For lower values of the tilt coupling, a nematic phase appears at zero chirality with the average director oriented perpendicular to the long axis of the membrane, while for nonzero chirality a cholesteric phase appears. The π walls are tilt walls at low chirality and transition to twist walls as chirality is increased. We construct a continuum model of the director field to explain this behavior.

Engaging and informing patients: Health information technology use in community health centers.

OBJECTIVE: This paper aims to address the relationship between the community health center (CHC) patient mix and the level of patient engagement health information technology (HIT) comprehensiveness. PARTICIPANTS: The study was conducted on sample CHCs (n = 3,592 CHC-years) active between 2016 and 2018. METHODS: Patient engagement HIT comprehensiveness was measured based on a framework of patient engagement through HIT that includes a two-part dichotomy of patient engagement and patient informing. Univariate analysis was used to describe CHC characteristics and multivariable ordered logistic regression analysis was used to test hypothesized relationships. RESULTS: The study identified four levels of patient engagement HIT comprehensiveness: 1) to neither engage nor inform, 2) to primarily inform, 3) to primarily engage, and 4) to engage and inform. It was found that CHCs serving disproportionate shares of patients with disadvantageous socioeconomic characteristics are less likely to incorporate more comprehensive patient engagement HIT. CONCLUSION: The results highlight the different levels of patient engagement HIT use among CHCs and a negative association between CHC's higher proportion of patients with a disadvantageous sociodemographic background and patient engagement HIT comprehensiveness.

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences.

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.

Development of an icIEF assay for monitoring AAV capsid proteins and application to gene therapy products.

Adeno-associated virus (AAV) gene therapy vectors, which contain a DNA transgene packaged into a protein capsid, have shown tremendous therapeutic potential in recent years. Methods traditionally used in quality control labs, such as high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE), do not provide a complete understanding of capsid viral protein (VP) charge heterogeneity. In the present study, we developed simple, one-step sample preparation and charge-based VP separation using imaged capillary isoelectric focusing (icIEF) for monitoring AAV products. The robustness of the method was confirmed through a design of experiments (DoE) exercise. An orthogonal reverse-phase (RP) HPLC method coupled with mass spectrometry was developed to separate and identify charge species. Additionally, capsid point mutants demonstrate the capability of the method to resolve deamidation at a single site on the viral proteins. Finally, case studies using two different AAV serotype vectors establish the icIEF method as stability indicating and demonstrate that increases in acidic species measured by icIEF correlate with increased deamidation, which, we show, results in decreased transduction efficiency. The addition of a rapid and robust icIEF method to the AAV capsid analytical toolkit enables development and consistent manufacturing of well-characterized gene therapy products.

Analysis of AAV-Extracted DNA by Charge Detection Mass Spectrometry Reveals Genome Truncations.

Adeno-associated virus (AAV) is a widely used gene therapy vector. The intact packaged genome is a critical quality attribute and necessary for an effective therapeutic. In this work, charge detection mass spectrometry (CDMS) was used to measure the molecular weight (MW) distribution for the genome of interest (GOI) extracted from recombinant AAV (rAAV) vectors. The measured MWs were compared to sequence masses for a range of rAAV vectors with different GOIs, serotypes, and production methods (Sf9 and HEK293 cell lines). In most cases, the measured MWs were slightly larger than the sequence masses, a result attributed to counterions. However, in a few cases, the measured MWs were significantly smaller than the sequence masses. In these cases, genome truncation is the only reasonable explanation for the discrepancy. These results suggest that direct analysis of the extracted GOI by CDMS provides a rapid and powerful tool to evaluate genome integrity in gene therapy products.

Nematode mitochondrial metagenomics: A new tool for biodiversity analysis.

DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.

MarkeTrak and EuroTrak: What We Can Learn by Looking Beyond the U.S. Market.

The MarkeTrak survey of the trends in hearing aid use, satisfaction and adoption in the United States has been conducted since 1989 by the Hearing Industries Association. It provide the hearing aid industry with valuable about the consumers view of the products and services within the industry. The EuroTrak survey is conducted by the European Hearing Instrument Manufactures Association. It is the counterpart to MarkeTrak and provides similar data for over a dozen countries in Europe, and Asia. While there are differences in the distribution models and reimbursement methods for these counties, many of the key metrics concerning hearing aid use and satisfaction can be compared.

Plectus of the Prairie: A Case Study of Taxonomic Resolution from a Nematode Biodiversity Survey.

Taxonomic resolution is a critical component of biodiversity assessments. In this case study, we examined a single taxon within a larger study of nematode diversity to evaluate the taxonomic resolution of different diversity assessment methods. The selected taxon was the microbial-feeding genus Plectus, a group considered to include multiple cosmopolitan species. The methods included a morphological evaluation by light microscopy, Sanger sequencing of PCR amplicons of COI and 18S gene regions, and 18S metabarcoding sequencing. The study sites were 15 remnant tallgrass prairie plots in eastern Nebraska. In the morphological analysis, we observed two basic morphotypes, a short-tailed form with a small amphid and a long-tailed form with a large amphid. Sanger sequencing of COI sorted Plectus diversity into six distinct clades. The largest two of these six clades keyed to P. parietinus and P. rhizophilus based on morphology. BLAST analysis with COI revealed no close matches in GenBank. Sanger sequencing of the 18S region did not differentiate the six clades. These results illustrate that the method of diversity assessment strongly influences estimates of biodiversity. An additional 95 Plectus specimens, from outside the remnant sites, added taxonomic breadth to the COI phylogenetic tree. There were no geographically widespread COI haplotypes and no evidence of cosmopolitan Plectus species.

Controlling the shape and topology of two-component colloidal membranes.

Changes in the geometry and topology of self-assembled membranes underlie diverse processes across cellular biology and engineering. Similar to lipid bilayers, monolayer colloidal membranes have in-plane fluid-like dynamics and out-of-plane bending elasticity. Their open edges and micrometer-length scale provide a tractable system to study the equilibrium energetics and dynamic pathways of membrane assembly and reconfiguration. Here, we find that doping colloidal membranes with short miscible rods transforms disk-shaped membranes into saddle-shaped surfaces with complex edge structures. The saddle-shaped membranes are well approximated by Enneper's minimal surfaces. Theoretical modeling demonstrates that their formation is driven by increasing the positive Gaussian modulus, which in turn, is controlled by the fraction of short rods. Further coalescence of saddle-shaped surfaces leads to diverse topologically distinct structures, including shapes similar to catenoids, trinoids, four-noids, and higher-order structures. At long timescales, we observe the formation of a system-spanning, sponge-like phase. The unique features of colloidal membranes reveal the topological transformations that accompany coalescence pathways in real time. We enhance the functionality of these membranes by making their shape responsive to external stimuli. Our results demonstrate a pathway toward control of thin elastic sheets' shape and topology-a pathway driven by the emergent elasticity induced by compositional heterogeneity.

Ecological and Morphological Differentiation Among COI Haplotype Groups in the Plant Parasitic Nematode Species Mesocriconema Xenoplax.

DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under "herbaceous," "woody wetlands," and "deciduous forest" were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.

Context-dependent role of abiotic and biotic factors structuring nematode communities along two environmental gradients.

Although abiotic environmental factors have been historically regarded as the dominant deterministic process in microbial community assembly, recent studies indicate that biotic interactions may be equally significant. However, the extent to which both processes are important in assembly of belowground communities is unknown. Along two environmental gradients: alkalinity (ranging from pH ~7 to ~11) and habitat type (lakes, shorelines, and prairies around lakes) present in the Western Nebraska Sandhills, we used 18S rRNA gene marker metabarcoding and statistical analyses, including generalized dissimilarity modelling (GDM), to evaluate the dynamics between abiotic and biotic factors that might play a role in nematode community assembly. Lakes supported the least diverse and prairies the most diverse communities with completely distinct compositions. We also observed a potential role of alkalinity in shaping these communities but only in lakes. Generally, GDMs indicated the influence of both abiotic and biotic factors. However, their relative importance in explaining community variability was dependent on the habitat. Biotic factors influenced the lake communities most, followed by shorelines and prairies, explaining ~47%, 27% and 8% of the variation, respectively. In contrast, the role of abiotic factors was relatively similar in lakes, shorelines and prairies (~15%, 18% and 14% of the variation, respectively). Most variation in the shorelines (62%) and prairies (82%) remained unexplained, suggesting the potential importance of factors associated with specific traits or a stronger role of stochastic processes. Nevertheless, our findings suggest both deterministic processes are important in nematode community assembly, but their specific contributions are context-dependent.

Identification of Recombinant Chimpanzee Adenovirus C68 Degradation Products Detected by AEX-HPLC.

Physicochemical tests represent important tools for the analytical control strategy of biotherapeutics. For adenoviral modalities, anion-exchange high performance liquid chromatography (AEX-HPLC) represents an important methodology, as it is able to simultaneously provide information on viral particle concentration, product purity and surface charge in a high-throughput manner. During product development of an adenoviral-based therapeutic, an accelerated stability study was performed and showed changes in each of the AEX-HPLC reportable attributes. These changes also correlated with a decrease in product infectivity prompting a detailed characterization of the impurity and mechanism of the surface charge change. Characterization experiments identified the impurity to be free hexon trimer, suggesting that capsid degradation could be contributing to both the impurity and reduced particle concentration. Additional mass spectrometry characterization identified deamidation of specific hexon residues to be associated with the external surface charge modification observed upon thermal stress conditions. To demonstrate a causal relationship between deamidation and surface charge changes observed by AEX-HPLC, site-directed mutagenesis experiments were performed. Through this effort, it was concluded that deamidation of asparagine 414 was responsible for the surface charge alteration observed in the AEX-HPLC profile but was not associated with the reduction in infectivity. Overall, this manuscript details critical characterization efforts conducted to enable understanding of a pivotal physicochemical test for adenoviral based therapeutics.

Antecedents of geographical expansion: The case of federally qualified health centers.

BACKGROUND: Federally qualified health centers (FQHCs) are pivotal safety net primary care providers for the medically underserved. FQHCs have complex organizational designs, with many FQHCs providing care at multiple physical locations ("sites"). The number of sites, however, varies considerably between FQHCs, which can have important implications for differential access that may perpetuate disparities in quality of care. PURPOSE: The objective of this study is to explore the organizational and environmental antecedents of the number of sites operated by each FQHC. The findings of this study contribute to a better understanding of FQHCs' expansion that has vital implications for cost and access outcomes. METHODOLOGY/APPROACH: The study is based on data between the years 2012 and 2018. Using multivariate growth curve modeling, we analyzed the final sample, consisting of 5,482 FQHC-years. RESULTS: The level of competition, measured as the number of FQHC sites in the Primary Care Service Area (PCSA) and the number of primary care physicians per 1,000 PCSA residents, was positively associated with the number of FQHC sites. The number of patients, the level of federal grant, and the year were also positively associated with the number of FQHC sites, whereas percentage of Medicaid patients; workforce supply, measured as primary care physician assistants per 1,000 PCSA residents; Medicaid expansion; and state/local funding available for FQHCs were not. CONCLUSION: Findings of this study indicate that competition, especially between peer FQHCs, is significantly associated with FQHC expansion. PRACTICE IMPLICATIONS: This result suggests that FQHC managers and policymakers may closely monitor cost, access, and quality implications of competition and FQHC expansion.

Assessment of genome packaging in AAVs using Orbitrap-based charge-detection mass spectrometry.

Adeno-associated viruses (AAVs) represent important gene therapy vectors with several approved clinical applications and numerous more in clinical trials. Genome packaging is an essential step in the bioprocessing of AAVs and needs to be tightly monitored to ensure the proper delivery of transgenes and the production of effective drugs. Current methods to monitor genome packaging have limited sensitivity, a high demand on labor, and struggle to distinguish between packaging of the intended genome or unwanted side-products. Here we show that Orbitrap-based charge-detection mass spectrometry allows the very sensitive quantification of all these different AAV bioprocessing products. A protocol is presented that allows the quantification of genome-packed AAV preparations in under half an hour, requiring only micro-liter quantities of typical AAV preparations with ∼1013 viral capsids per milliliter. The method quickly assesses the integrity and amount of genome packed AAV particles to support AAV bioprocessing and characterization of this rapidly emerging class of advanced drug therapies.

Pratylenchus smoliki, a new nematode species (Pratylenchidae: Tylenchomorpha) from the Great Plains region of North America.

Pratylenchus smoliki is a new species of root-lesion nematode described from corn-soybean production fields in the Central Great Plains of North America. It is characterized by populations with relatively abundant males, two lip annuli, females with a round functional spermatheca and a conoid to subcylindrical tail with a non-crenate, smooth terminus. In host preference tests, corn and wheat produce the largest nematode populations, whereas sorghum and soybeans produce less than 20% the numbers observed on corn. Scanning electron microscopy reveals that the en face patterns compare to those seen in Pratylenchus pseudocoffeae, P. scribneri, P. hexincisus, and P. alleni. The pattern is described as rectangular to trapezoidal subdorsal and subventral lips adjoining oral disc, but with a clear demarcation between the oral disc and the subdorsal and subventral sectors. A Maximum Likelihood COI tree recognizes P. smoliki as a moderately-well-supported clade with several haplotype subgroups. A Maximum Likelihood partial 28S tree provides strong support for the P. smoliki clade and reinforces the close relationships between species with similar en face patterns. Topotype specimens of P. alleni were demonstrably different from P. smoliki using DNA markers. The geographic range of P. smoliki overlaps with the ranges of P. alleni, P. scribneri, P. neglectus, P. hexicisus, and P. dakotaensis. The observed host range (corn, rye, sunflower, and wheat) suggests that P. smoliki may be native to the tallgrass prairie region of the Great Plains.

Characterization of Recombinant Chimpanzee Adenovirus C68 Low and High-Density Particles: Impact on Determination of Viral Particle Titer.

We observed differential infectivity and product yield between two recombinant chimpanzee adenovirus C68 constructs whose primary difference was genome length. To determine a possible reason for this outcome, we characterized the proportion and composition of the empty and packaged capsids. Both analytical ultracentrifugation (AUC) and differential centrifugation sedimentation (DCS, a rapid and quantitative method for measuring adenoviral packaging variants) were employed for an initial assessment of genome packaging and showed multiple species whose abundance deviated between the virus builds but not manufacturing campaigns. Identity of the packaging variants was confirmed by charge detection mass spectrometry (CDMS), the first known application of this technique to analyze adenovirus. The empty and packaged capsid populations were separated via preparative ultracentrifugation and then combined into a series of mixtures. These mixtures showed the oft-utilized denaturing A260 adenoviral particle titer method will underestimate the actual particle titer by as much as three-fold depending on the empty/full ratio. In contrast, liquid chromatography with fluorescence detection proves to be a superior viral particle titer methodology.

Quantitative analysis of genome packaging in recombinant AAV vectors by charge detection mass spectrometry.

Recombinant adeno-associated virus (rAAV) has emerged as an important gene therapy vector with many clinical trials currently in progress. Analytical characterization and quantitation of particle content remain challenges in both the development and production of rAAV vectors. In this study, charge detection mass spectrometry (CDMS) and gel electrophoresis are used to characterize the DNA content of recombinant AAV8 (rAAV8) vectors with a wide range of target genome sizes. We show that the differences between the masses of empty particles and particles with the genome of interest (GOI) are correlated with the expected genome mass. A small systematic deviation (around 2%) is attributed to the packaging of counterions along with the DNA. In addition to the GOI, a broad distribution of heterogeneous DNA is packaged. The distribution peaks are close to the packaging capacity of the rAAV8 vectors. There is also evidence for the co-packaging of small DNA fragments along with the GOI. Finally, we present evidence that incubation at an elevated temperature can reduce the heterogeneity of the packaged DNA. Taken together, these results show that CDMS is a viable tool for characterization of the packaged genome.