Macrophage immunomodulation through new polymers that recapitulate functional effects of itaconate as a power house of innate immunity.

Itaconate (ITA) is an emerging powerhouse of innate immunity with therapeutic potential that is limited in its ability to be administered in a soluble form. We developed a library of polyester materials that incorporate ITA into polymer backbones resulting in materials with inherent immunoregulatory behavior. Harnessing hydrolytic degradation release from polyester backbones, ITA polymers resulted in the mechanism specific immunoregulatory properties on macrophage polarization in vitro. In a functional assay, the polymer-released ITA inhibited bacterial growth on acetate. Translation to an in vivo model of biomaterial associated inflammation, intraperitoneal injection of ITA polymers demonstrated a rapid resolution of inflammation in comparison to a control polymer silicone, demonstrating the value of sustained biomimetic presentation of ITA.

Using Machine Learning of Clinical Data to Diagnose COVID-19

The recent pandemic of Coronavirus Disease 2019 (COVID-19) has placed severe stress on healthcare systems worldwide, which is amplified by the critical shortage of COVID-19 tests. In this study, we propose to generate a more accurate diagnosis model of COVID-19 based on patient symptoms and routine test results by applying machine learning to reanalyzing COVID-19 data from 151 published studies. We aimed to investigate correlations between clinical variables, cluster COVID-19 patients into subtypes, and generate a computational classification model for discriminating between COVID -19 patients and influenza patients based on clinical variables alone. We discovered several novel associations between clinical variables, including correlations between being male and having higher levels of serum lymphocytes and neutrophils. We found that COVID-19 patients could be clustered into subtypes based on serum levels of immune cells, gender, and reported symptoms. Finally, we trained an XGBoost model to achieve a sensitivity of 92.5% and a specificity of 97.9% in discriminating COVID-19 patients from influenza patients. We demonstrated that computational methods trained on large clinical datasets could yield ever more accurate COVID-19 diagnostic models to mitigate the impact of lack of testing. We also presented previously unknown COVID-19 clinical variable correlations and clinical subgroups.

Age and multiparity related urethral sphincter muscle dysfunction in a rabbit model: Potential roles of TGF-ß and Wnt-ß catenin signaling pathways.

AIMS: Prior studies demonstrate increased incidence of urinary incontinence (UI) in the geriatric population which affects their quality of life. Pathophysiology of UI in the geriatric population and the underlying molecular mechanisms are still unclear. To elucidate these mechanisms, we performed a pre-clinical study in a rabbit model and the objectives were to (i) determine the effect of aging as well as multiparity on urethral sphincter muscle thickness and urethral closing pressure (UCP); (ii) examine the role of fibrosis and atrophy; and (iii) elucidate the molecular pathways that mediate fibrosis and atrophy in the urethral tissue. METHODS: New Zealand White female rabbits (n = 6 each; young 6-12 months and old over 30 months of age) were anesthetized and urethral muscle thickness and sphincter closure function were measured. Rabbits were then sacrificed and urethral tissues (bladder neck and mid-urethra) were collected to process for immunostaining as well as for molecular studies for markers for fibrosis (ß-catenin which is an important mediator of Wnt signaling, Collagen-1, and TGF-ß) and atrophy (MuRF-1). RESULTS: Our studies showed a significant decrease in the urethral sphincter muscle thickness and closure function with age. Age-related increase in protein and mRNA expression levels of fibrosis, as well as atrophy markers were observed in the bladder neck and mid-urethral tissues. CONCLUSIONS: Age and multiparity related increase in fibrosis and atrophy of urethral sphincter muscles may contribute to impaired urethral closure function seen in old animals.

A Paradigm shift in the concept for making dental impressions.

Digital dental impression is a revolutionary technological advancement that so surpasses the accuracy and efficiency of former techniques for obtaining replicas of prepared teeth for the purpose of fabricating restorations that its adoption by dentists is rapidly eclipsing the use of elastomeric impression materials. The ultimate goals of dentists dedicated to quality restorative dentistry are to make their treatment of patients as accurate, stressless, and efficient as possible. By elimination of the everyday problems described above, there is no question that the significant advantages of digital impressions will make intraoral digital scanning standard procedure in most dental offices within the next several years. Furthermore, digital impressions have proven to reduce remakes and returns, as well as increase overall efficiency. The patient also benefits by being provided a far more positive experience. Finally, through the use of digital impression making, it has been determined that laboratory products become more consistent and require less chair time at insertion.

Combination restoration in full mouth rehabilitation.

Successful restoration of the dentition requires plenty of contemporary and conventional treatment techniques and planning and attachment retained partial dentures are one such kind of treatment modality in prosthodontics. Satisfactory restoration in a patient with a partially edentulous situation can be challenging especially when unilateral or bilateral posterior segment of teeth is missing. One such treatment modality is attachment-retained cast partial dentures. The purpose of this article is to provide an overview of a case with maxillary complete denture and opposing cast partial denture with precision attachment.

Relationship between occlusal plane and ala-tragus line in dentate individuals: A Clinical pilot study.

Many methods have been used to establish the occlusal plane in complete denture prosthodontics. However, no single method seems to be fully accepted. Anteriorly, esthetic considerations help define the occlusal plane, and posteriorly the tongue, retromolar pad, and Stenson's duct are considered. Some dentists bisect the space between the residual ridges. The technique of using the ala-tragus line (Camper's line) to establish the occlusal plane is well documented. However, definitions of the ala-tragus line cause confusion, because the exact points of reference do not agree. For example, the glossary of prosthodontic terms states that the ala-tragus line runs from the inferior border of the ala of the nose to the superior border of the tragus of the ear while Spratley' describes it as running from the center of the ala to the center of the tragus. This article concerns us the exact relationship between the occlusal plane and ala-tragus line in dentate individuals.

Length tension function of puborectalis muscle: implications for the treatment of fecal incontinence and pelvic floor disorders.

BACKGROUND/AIMS: External anal sphincter (EAS) and puborectalis muscle (PRM) play important role in anal continence function. Based on length-tension measurement, we recently reported that the human EAS muscle operates at short sarcomere length under phys-iological conditions. Goal of our study was to determine if PRM also operates at the short sarcomere length. METHODS: Length-tension relationship of the PRM muscle was studied in vivo in 10 healthy nullipara women. Length was altered by vagi-nal distension using custom-designed probes of 5, 10, 15, 20, 25 and 30 mm diameters as well as by distending a poly-ethylene bag with different volumes of water. Probes were equipped with a reverse perfuse sleeve sensor to measure vaginal pressure (surrogate of PRM tension). PRM electromyogram (EMG) was recorded using wire electrodes. Three-dimensional ultra-sound images were obtained to determine effect of vaginal distension on PRM length. RESULTS: Ultrasound images demonstrate distension volume dependent increase in PRM length. Rest and squeeze pressures of vaginal bag increased with the increase in bag volume. Similarly, the change in vaginal pressure, which represents the PRM contraction increased with the increase in the probe size. Increase in probe size was not associated with an increase in EMG activity (a marker of neural drive) of the PRM. CONCLUSIONS: Probe size dependent increase in PRM contraction pressure, in the presence of constant EMG (neural input) proves that the hu-man PRM operates at short sarcomere length. Surgically adjusting the PRM length may represent a novel strategy to improve treat anal continence and possibly other pelvic floor disorders.(J Neurogastroenterol Motil 2014;20:539-546).

Length Tension Function of Puborectalis Muscle: Implications for the Treatment of Fecal Incontinence and Pelvic Floor Disorders

BACKGROUND/AIMS: External anal sphincter (EAS) and puborectalis muscle (PRM) play important role in anal continence function. Based on length-tension measurement, we recently reported that the human EAS muscle operates at short sarcomere length under physiological conditions. Goal of our study was to determine if PRM also operates at the short sarcomere length. METHODS: Length-tension relationship of the PRM muscle was studied in vivo in 10 healthy nullipara women. Length was altered by vaginal distension using custom-designed probes of 5, 10, 15, 20, 25 and 30 mm diameters as well as by distending a polyethylene bag with different volumes of water. Probes were equipped with a reverse perfuse sleeve sensor to measure vaginal pressure (surrogate of PRM tension). PRM electromyogram (EMG) was recorded using wire electrodes. Three-dimensional ultra-sound images were obtained to determine effect of vaginal distension on PRM length. RESULTS: Ultrasound images demonstrate distension volume dependent increase in PRM length. Rest and squeeze pressures of vaginal bag increased with the increase in bag volume. Similarly, the change in vaginal pressure, which represents the PRM contraction increased with the increase in the probe size. Increase in probe size was not associated with an increase in EMG activity (a marker of neural drive) of the PRM. CONCLUSIONS: Probe size dependent increase in PRM contraction pressure, in the presence of constant EMG (neural input) proves that the human PRM operates at short sarcomere length. Surgically adjusting the PRM length may represent a novel strategy to improve treat anal continence and possibly other pelvic floor disorders.

Effect of ascophyllan from brown algae Padina tetrastromatica on inflammation and oxidative stress in carrageenan-induced rats.

Sulfated polysaccharide ascophyllan was isolated from the brown algae Padina tetrastromatica and purified by ion-exchange chromatography. Anti-inflammatory effect of ascophyllan fraction against carrageenan-induced paw edema in rats was studied. Paw edema in rats was induced by injecting 0.1 ml, 1 % carrageenan suspension in 0.9 % NaCl solution into the sub-plantar tissue of the right hind paw. Carrageenan caused a significant increase in the activity of inflammatory marker enzymes like lipoxygenases and cyclooxygenase in peripheral blood mononuclear cells and paw tissue and also increased the concentration of prostaglandin E2 (PGE2) and myeloperoxidase (MPO) in paw tissue. When compared to the reference drug diclofenac, ascophyllan fraction-3 (AF3) treatment significantly reduced the activities of anti-inflammatory enzymes, concentration of PGE2 and MPO. AF3 treatment decreased the mRNA level expression of TNF-α and IL-6. Concentration of thiobarbituric acid reactive substances was decreased. Activities of antioxidant enzymes and reduced glutathione level were increased on treatment with AF3. Histopathology of paw tissue showed decreased edema formation and cellular infiltration on supplementation with AF3. Thus the results demonstrated the potential beneficiary effect of ascophyllan fraction on carrageenan-treated rats.

Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation.

Uranium contamination is a serious concern at several sites motivating the development of novel treatment strategies such as the Geobacter-mediated reductive immobilization of uranium. However, this bioremediation strategy has not yet been optimized for the sustained uranium removal. While several reactive-transport models have been developed to represent Geobacter-mediated bioremediation of uranium, these models often lack the detailed quantitative description of the microbial process (e.g., biomass build-up in both groundwater and sediments, electron transport system, etc.) and the interaction between biogeochemical and hydrological process. In this study, a novel multi-scale model was developed by integrating our recent model on electron capacitance of Geobacter (Zhao et al., 2010) with a comprehensive simulator of coupled fluid flow, hydrologic transport, heat transfer, and biogeochemical reactions. This mechanistic reactive-transport model accurately reproduces the experimental data for the bioremediation of uranium with acetate amendment. We subsequently performed global sensitivity analysis with the reactive-transport model in order to identify the main sources of prediction uncertainty caused by synergistic effects of biological, geochemical, and hydrological processes. The proposed approach successfully captured significant contributing factors across time and space, thereby improving the structure and parameterization of the comprehensive reactive-transport model. The global sensitivity analysis also provides a potentially useful tool to evaluate uranium bioremediation strategy. The simulations suggest that under difficult environments (e.g., highly contaminated with U(VI) at a high migration rate of solutes), the efficiency of uranium removal can be improved by adding Geobacter species to the contaminated site (bioaugmentation) in conjunction with the addition of electron donor (biostimulation). The simulations also highlight the interactive effect of initial cell concentration and flow rate on U(VI) reduction.

Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments.

In situ stimulation of the metabolic activity of Geobacter species through acetate amendment has been shown to be a promising bioremediation strategy to reduce and immobilize hexavalent uranium [U(VI)] as insoluble U(IV). Although Geobacter species are reducing U(VI), they primarily grow via Fe(III) reduction. Unfortunately, the biogeochemistry and the physiology of simultaneous reduction of multiple metals are still poorly understood. A detailed model is therefore required to better understand the pathways leading to U(VI) and Fe(III) reduction by Geobacter species. Based on recent experimental evidence of temporary electron capacitors in Geobacter we propose a novel kinetic model that physically distinguishes planktonic cells into electron-loaded and -unloaded states. Incorporation of an electron load-unload cycle into the model provides insight into U(VI) reduction efficiency, and elucidates the relationship between U(VI)- and Fe(III)-reducing activity and further explains the correlation of high U(VI) removal with high fractions of planktonic cells in subsurface environments. Global sensitivity analysis was used to determine the level of importance of geochemical and microbial processes controlling Geobacter growth and U(VI) reduction, suggesting that the electron load-unload cycle and the resulting repartition of the microbes between aqueous and attached phases are critical for U(VI) reduction. As compared with conventional Monod modeling approaches without inclusion of the electron capacitance, the new model attempts to incorporate a novel cellular mechanism that has a significant impact on the outcome of in situ bioremediation.

The degree of redundancy in metabolic genes is linked to mode of metabolism.

An understanding of the factors favoring the maintenance of duplicate genes in microbial genomes is essential for developing models of microbial evolution. A genome-scale flux-balance analysis of the metabolic network of Saccharomyces cerevisiae has suggested that gene duplications primarily provide increased enzyme dosage to enhance metabolic flux because the incidence of gene duplications in essential genes is no higher than that in nonessential genes. Here, we used genome-scale metabolic models to analyze the extent of genetic and biochemical redundancy in prokaryotes that are either specialists, with one major mode of energy generation, or generalists, which have multiple metabolic strategies for conservation of energy. Surprisingly, the results suggest that generalists, such as Escherichia coli and Bacillus subtilis, are similar to the eukaryotic generalist, S. cerevisiae, in having a low percentage (<10%) of essential genes and few duplications of these essential genes, whereas metabolic specialists, such as Geobacter sulfurreducens and Methanosarcina barkeri, have a high percentage (>30%) of essential genes and a high degree of genetic redundancy in these genes compared to nonessential genes. Furthermore, the specialist organisms appear to rely more on gene duplications rather than alternative-but-equivalent metabolic pathways to provide resilience to gene loss. Generalists rely more on alternative pathways. Thus, the concept that the role of gene duplications is to boost enzymatic flux rather than provide metabolic resilience may not be universal. Rather, the degree of gene duplication in microorganisms may be linked to mode of metabolism and environmental niche.

Serotonin transporter polymorphism, memory and hippocampal volume in the elderly: association and interaction with cortisol.

The s allele variant of the serotonin transporter gene (5-HTT) has recently been observed to moderate the relationship of stress to depression and anxiety. To date no study has considered interactive effects of 5-HTT genotype, stress and hypothalamic-pituitary-adrenal (HPA) function on cognition in healthy, older adults, which may reflect developmental, functional or neurodegenerative effects of the serotonin transporter polymorphism. We investigated whether 5-HTT genotype interacts with cumulative life stress and HPA-axis measures of waking and diurnal cortisol slope to impact cognition in 154 non-depressed, older adults. Structural images of hippocampal volume were acquired on a subsample of 56 participants. The 5-HTT s allele was associated with both significantly lower delayed recall and higher waking cortisol levels. Presence of the s allele interacted with higher waking cortisol to negatively impact memory. We also observed a significant interaction of higher waking cortisol and the s allele on lower hippocampal volume. Smaller hippocampi and higher cortisol were associated with lower delayed recall only in s allele carriers. No impact or interactions of cumulative life stress with 5-HTT or cortisol were observed. This is the first investigation to identify an association of the 5-HTT s allele with poorer memory function in older adults. The interactive effects of the s allele and waking cortisol levels on reduced hippocampal volume and lower memory suggest that the negative effect of the serotonin polymorphism on memory is mediated by the HPA axis. Further, given the significant association of the s allele with higher waking cortisol in our investigation, future studies may be needed to evaluate the impact of the serotonin transporter polymorphism on any neuropsychiatric or behavioral outcome which is influenced by HPA axis function in older adults.

Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.

Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated with intracellular acceptors. This limitation was attributed to lack of cytoplasmic proton consumption during reduction of extracellular electron acceptors. Model-based analysis of the metabolic cost of producing an extracellular electron shuttle to promote electron transfer to insoluble Fe(III) oxides demonstrated why Geobacter species, which do not produce shuttles, have an energetic advantage over shuttle-producing Fe(III) reducers in subsurface environments. In silico analysis also revealed that the metabolic network of G. sulfurreducens could synthesize amino acids more efficiently than that of Escherichia coli due to the presence of a pyruvate-ferredoxin oxidoreductase, which catalyzes synthesis of pyruvate from acetate and carbon dioxide in a single step. In silico phenotypic analysis of deletion mutants demonstrated the capability of the model to explore the flexibility of G. sulfurreducens central metabolism and correctly predict mutant phenotypes. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications.

Properties of metabolic networks: structure versus function.

Biological data from high-throughput technologies describing the network components (genes, proteins, metabolites) and their associated interactions have driven the reconstruction and study of structural (topological) properties of large-scale biological networks. In this article, we address the relation of the functional and structural properties by using extensively experimentally validated genome-scale metabolic network models to compute observable functional states of a microorganism and compare the "structure versus function" attributes of metabolic networks. It is observed that, functionally speaking, the essentiality of reactions in a node is not correlated with node connectivity as structural analyses of other biological networks have suggested. These findings are illustrated with the analysis of the genome-scale biochemical networks of three species with distinct modes of metabolism. These results also suggest fundamental differences among different biological networks arising out of their representation and functional constraints.

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.

Genome-scale constraint-based models of several organisms have now been constructed and are being used for model driven research. A key issue that may arise in the use of such models is the existence of alternate optimal solutions wherein the same maximal objective (e.g., growth rate) can be achieved through different flux distributions. Herein, we investigate the effects that alternate optimal solutions may have on the predicted range of flux values calculated using currently practiced linear (LP) and quadratic programming (QP) methods. An efficient LP-based strategy is described to calculate the range of flux variability that can be present in order to achieve optimal as well as suboptimal objective states. Sample results are provided for growth predictions of E. coli using glucose, acetate, and lactate as carbon substrates. These results demonstrate the extent of flux variability to be highly dependent on environmental conditions and network composition. In addition we examined the impact of alternate optima for growth under gene knockout conditions as calculated using QP-based methods. It was observed that calculations using QP-based methods can show significant variation in growth rate if the flux variability among alternate optima is high. The underlying biological significance and general source of such flux variability is further investigated through the identification of redundancies in the network (equivalent reaction sets) that lead to alternate solutions. Collectively, these results illustrate the variability inherent in metabolic flux distributions and the possible implications of this heterogeneity for constraint-based modeling approaches. These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data.

Unexceptional spatial memory in an exceptional memorist.

Rajan Mahadevan evidences an exceptional memory for arrays of digits. We tested whether Rajan's spatial memory was likewise exceptional. Eight control Ss and Rajan were instructed to remember the position and orientation of 48 images of common objects shown either to the left or the right of fixation and facing either left or right. Rajan's accuracy for judging whether the position and orientation of these pictures had changed when they were shown in a different sequence was lower than that of control Ss for both judgments. Rajan's exceptional memory capacity apparently does not extend to spatial relations.

Osmolar relationships in infantile dehydration.

We studied serum osmolality in 167 consecutive infants admitted for gastroenteritis with 5% or more dehydration. Osmolality was determined by the freezing-point method in a 0.2-mL sample of serum immediately on admission. Forty-one patients (24.6%) had hypo-osmolar dehydration, with a mean osmolality of 257 mOsm/kg (range, 234 to 270 mOsm/kg). Eleven patients (6.5%) had hyperosmolar dehydration, with a mean osmolality of 329 mOsm/kg (range, 312 to 369 mOsm/kg). Simultaneous serum and CSF osmolalities were determined in 14 patients with hypo-osmolar and eight with hyperosmolar dehydration. In patients with hyperosmolar dehydration, serum osmolality correlated well with CSF osmolality, but a poor correlation was seen between serum and CSF sodium levels. Convulsions occurred in two patients in whom the CSF osmolality was greater than the serum osmolality by more than 10 mOsm/kg. Convulsions also occurred in two patients with hypo-osmolar dehydration in whom the CSF osmolality was lower than the serum osmolality by more than 13 mOsm/kg.