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1.
GigaByte ; 2023: gigabyte84, 2023.
Article in English | MEDLINE | ID: mdl-37408731

ABSTRACT

'Chambourcin' is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like 'Chambourcin'. Here, we assembled the genome of 'Chambourcin' using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for 'Chambourcin' with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between 'Chambourcin', V. vinifera 'PN40024' 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of 'Chambourcin'. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.

2.
Antibiotics (Basel) ; 12(4)2023 Apr 10.
Article in English | MEDLINE | ID: mdl-37107097

ABSTRACT

Pseudomonas aeruginosa (PsA) is an opportunistic bacterial pathogen that causes life-threatening infections in individuals with compromised immune systems and exacerbates health concerns for those with cystic fibrosis (CF). PsA rapidly develops antibiotic resistance; thus, novel therapeutics are urgently needed to effectively combat this pathogen. Previously, we have shown that a novel cationic Zinc (II) porphyrin (ZnPor) has potent bactericidal activity against planktonic and biofilm-associated PsA cells, and disassembles the biofilm matrix via interactions with eDNA In the present study, we report that ZnPor caused a significant decrease in PsA populations in mouse lungs within an in vivo model of PsA pulmonary infection. Additionally, when combined with an obligately lytic phage PEV2, ZnPor at its minimum inhibitory concentration (MIC) displayed synergy against PsA in an established in vitro lung model resulting in greater protection of H441 lung cells versus either treatment alone. Concentrations above the minimum bactericidal concentration (MBC) of ZnPor were not toxic to H441 cells; however, no synergy was observed. This dose-dependent response is likely due to ZnPor's antiviral activity, reported herein. Together, these findings show the utility of ZnPor alone, and its synergy with PEV2, which could be a tunable combination used in the treatment of antibiotic-resistant infections.

3.
BMC Plant Biol ; 23(1): 211, 2023 Apr 22.
Article in English | MEDLINE | ID: mdl-37085756

ABSTRACT

BACKGROUND: Grafting is a horticultural practice used widely across woody perennial crop species to fuse together the root and shoot system of two distinct genotypes, the rootstock and the scion, combining beneficial traits from both. In grapevine, grafting is used in nearly 80% of all commercial vines to optimize fruit quality, regulate vine vigor, and enhance biotic and abiotic stress-tolerance. Rootstocks have been shown to modulate elemental composition, metabolomic profiles, and the shape of leaves in the scion, among other traits. However, it is currently unclear how rootstock genotypes influence shoot system gene expression as previous work has reported complex and often contradictory findings. RESULTS: In the present study, we examine the influence of grafting on scion gene expression in leaves and reproductive tissues of grapevines growing under field conditions for three years. We show that the influence from the rootstock genotype is highly tissue and time dependent, manifesting only in leaves, primarily during a single year of our three-year study. Further, the degree of rootstock influence on scion gene expression is driven by interactions with the local environment. CONCLUSIONS: Our results demonstrate that the role of rootstock genotype in modulating scion gene expression is not a consistent, unchanging effect, but rather an effect that varies over time in relation to local environmental conditions.


Subject(s)
Gene-Environment Interaction , Plant Roots , Plant Roots/metabolism , Plant Leaves/genetics , Genotype , Gene Expression
4.
Am J Respir Cell Mol Biol ; 68(1): 75-89, 2023 01.
Article in English | MEDLINE | ID: mdl-36125351

ABSTRACT

The mechanisms by which excessive systemic activation of adaptive T lymphocytes, as in cytokine release syndrome (CRS), leads to innate immune cell-mediated acute lung injury (ALI) or acute respiratory distress syndrome, often in the absence of any infection, remains unknown. Here, we investigated the roles of IFN-γ and IL-17A, key T-cell cytokines significantly elevated in patients with CRS, in the immunopathogenesis of CRS-induced extrapulmonary ALI. CRS was induced in wild-type (WT), IL-17A- and IFN-γ knockout (KO) human leukocyte antigen-DR3 transgenic mice with 10 µg of the superantigen, staphylococcal enterotoxin B, given intraperitoneally. Several ALI parameters, including gene expression profiling in the lungs, were studied 4, 24, or 48 hours later. Systemic T-cell activation with staphylococcal enterotoxin B resulted in robust upregulation of several chemokines, S100A8/A9, matrix metalloproteases, and other molecules implicated in tissue damage, granulocyte as well as agranulocyte adhesion, and diapedesis in the lungs as early as 4 hours, which was accompanied by subsequent neutrophil/eosinophil lung infiltration and severe ALI in IFN-γ KO mice. These pathways were significantly underexpressed in IL-17A KO mice, which manifested mildest ALI and intermediate in WT mice. Neutralization of IFN-γ worsened ALI in WT and IL-17A KO mice, whereas neutralizing IL-17A did not mitigate lung injury in IFN-γ KO mice, suggesting a dominant protective role for IFN-γ in ALI and that IL-17A is dispensable. Ruxolitinib, a Janus kinase inhibitor, increased ALI severity in WT mice. Thus, our study identified novel mechanisms of ALI in CRS and its differential modulation by IFN-γ and IL-17A.


Subject(s)
Acute Lung Injury , Interleukin-17 , Humans , Mice , Animals , Cytokine Release Syndrome , Interferon-gamma , Cytokines , Lung/pathology , Acute Lung Injury/pathology , Mice, Knockout , Mice, Inbred C57BL
5.
Clin Chest Med ; 43(4): 757-771, 2022 12.
Article in English | MEDLINE | ID: mdl-36344079

ABSTRACT

The development of formal transition models emerged to reduce variability in care, including cystic fibrosis (CF) responsibility, independence, self-care, and education (RISE), which provides a standardized transition program, including knowledge assessments, self-management checklists, and milestones for people with CF. Despite these interventions, the current landscape of health care transition (HCT) remains suboptimal, and additional focused attention on HCT is necessary. Standardization of assessment tools to gauge the efficacy of transfer from pediatric to adult care is a high priority. Such tools should incorporate both clinical and patient-centered outcomes to provide a comprehensive picture of progress and deficiencies of the HCT process.


Subject(s)
Cystic Fibrosis , Transition to Adult Care , Adult , Child , Humans , Cystic Fibrosis/therapy , Self Care
6.
Oxid Med Cell Longev ; 2022: 9518592, 2022.
Article in English | MEDLINE | ID: mdl-36193076

ABSTRACT

Aims: Studies have linked severe hyperoxia, or prolonged exposure to very high oxygen levels, with worse clinical outcomes. This study investigated the role of epidermal growth factor receptor (EGFR) in hyperoxia-induced lung injury at very high oxygen levels (>95%). Results: Effects of severe hyperoxia (100% oxygen) were studied in mice with genetically inhibited EGFR and wild-type littermates. Despite the established role of EGFR in lung repair, EGFR inhibition led to improved survival and reduced acute lung injury, which prompted an investigation into this protective mechanism. Endothelial EGFR genetic knockout did not confer protection. EGFR inhibition led to decreased levels of cleaved caspase-3 and poly (ADP-ribosyl) polymerase (PARP) and decreased terminal dUTP nick end labeling- (TUNEL-) positive staining in alveolar epithelial cells and reduced ERK activation, which suggested reduced apoptosis in vivo. EGFR inhibition decreased hyperoxia (95%)-induced apoptosis and ERK in murine alveolar epithelial cells in vitro, and CRISPR-mediated EGFR deletion reduced hyperoxia-induced apoptosis and ERK in human alveolar epithelial cells in vitro. Innovation. This work defines a protective role of EGFR inhibition to decrease apoptosis in lung injury induced by 100% oxygen. This further characterizes the complex role of EGFR in acute lung injury and outlines a novel hyperoxia-induced cell death pathway that warrants further study. Conclusion: In conditions of severe hyperoxia (>95% for >24 h), EGFR inhibition led to improved survival, decreased lung injury, and reduced cell death. These findings further elucidate the complex role of EGFR in acute lung injury.


Subject(s)
Acute Lung Injury , Hyperoxia , Lung Injury , Acute Lung Injury/metabolism , Adenosine Diphosphate/pharmacology , Animals , Apoptosis , Caspase 3/metabolism , ErbB Receptors/metabolism , Humans , Hyperoxia/complications , Hyperoxia/metabolism , Lung/metabolism , Lung Injury/etiology , Lung Injury/metabolism , Mice , Mice, Inbred C57BL , Oxygen/metabolism , Poly(ADP-ribose) Polymerase Inhibitors/metabolism , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
7.
Plant Direct ; 6(8): e440, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35999957

ABSTRACT

Plants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above-ground plant tissues, such as leaves, reflects both above- and below-ground activities of the plant, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study how genetically distinct root systems influence the elemental composition of a common shoot system. We measured elemental composition of over 7,000 leaves in the grapevine cultivar "Chambourcin" growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition, and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above-ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.

8.
Gigascience ; 10(12)2021 12 29.
Article in English | MEDLINE | ID: mdl-34966928

ABSTRACT

BACKGROUND: Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown. RESULTS: Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season. CONCLUSIONS: These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.


Subject(s)
Plant Leaves , Plant Roots , Genotype , Phenotype , Plant Leaves/genetics , Plant Roots/genetics , Seasons
9.
Chest ; 159(5): e325-e329, 2021 05.
Article in English | MEDLINE | ID: mdl-33965157

ABSTRACT

CASE PRESENTATION: An 84-year-old physician was seen in the pulmonary clinic with 10 days of progressive exertional dyspnea, night sweats, and dry cough. For the past 5 months, he had been taking ibuprofen for lumbar radiculopathy from spinal stenosis. Ten days earlier, ibuprofen was switched to naproxen 250 mg twice daily because of its longer half-life. He denied fever, weight loss, rash, dysphagia, proximal muscle weakness, wheeze, sinus congestion, and peripheral numbness/tingling. Medical history included paroxysmal atrial fibrillation, hypertension, Hashimoto's thyroiditis, and OSA. Long-term medications included aspirin, flecainide, atorvastatin, amlodipine, levothyroxine, and candesartan. He was a lifelong nonsmoker. There was no history of recent travel.


Subject(s)
Anti-Inflammatory Agents, Non-Steroidal/adverse effects , Naproxen/adverse effects , Pulmonary Eosinophilia/chemically induced , Pulmonary Eosinophilia/diagnostic imaging , Aged , Cough , Diagnosis, Differential , Dyspnea , Humans , Male , Tomography, X-Ray Computed
10.
Microorganisms ; 9(1)2021 Jan 02.
Article in English | MEDLINE | ID: mdl-33401756

ABSTRACT

Grafting connects root and shoot systems of distinct individuals, bringing microbial communities of different genotypes together in a single plant. How do root system and shoot system genotypes influence plant microbiota in grafted grapevines? To address this, we utilized clonal replicates of the grapevine 'Chambourcin', growing ungrafted and grafted to three different rootstocks in three irrigation treatments. Our objectives were to (1) characterize the microbiota (bacteria and fungi) of below-ground compartments (roots, adjacent soil) and above-ground compartments (leaves, berries), (2) determine how rootstock genotype, irrigation, and their interaction influences grapevine microbiota in different compartments, and (3) investigate abundance of microorganisms implicated in the late-season grapevine disease sour rot (Acetobacterales and Saccharomycetes). We found that plant compartment had the largest influence on microbial diversity. Neither rootstock genotype nor irrigation significantly influenced microbial diversity or composition. However, differential abundance of bacterial and fungal taxa varied as a function of rootstock and irrigation treatment; in particular, Acetobacterales and Saccharomycetes displayed higher relative abundance in berries of grapevines grafted to '1103P' and 'SO4' rootstocks and varied across irrigation treatments. This study demonstrates that grapevine compartments retain distinct microbiota and identifies associations between rootstock genotypes, irrigation treatment, and the relative abundance of agriculturally relevant microorganisms in the berries.

11.
Psychodyn Psychiatry ; 48(3): 259-270, 2020.
Article in English | MEDLINE | ID: mdl-32996847

ABSTRACT

Coronavirus disease 2019 (COVID-19) is currently ravaging health systems across the world. Psychiatric trainees are at risk of exposure to patients with COVID-19 given their clinical roles in emergency and inpatient psychiatric settings. This article represents a case study of group dynamics in which we reflect on our own experience as psychiatric residents at a Boston-area hospital system in the era of COVID-19 and apply Wilfred Bion's concepts of the "work group" and the "basic assumption group" processes of group operation. We assess dynamics between trainees and administrative leadership both at baseline and in the current pandemic. Since navigation through crises is more effective if group leadership recognizes and responds to basic assumption behaviors, we propose suggestions to enable health system administration to successfully lead health care organizations through periods of societal turmoil. We posit that these principles apply across settings, specialties, and provider types. In addition, we use our observations to indicate future directions for expanding Bion's theories in the contemporary context.


Subject(s)
Coronavirus Infections , Internship and Residency , Leadership , Pandemics , Pneumonia, Viral , Psychiatry/education , Betacoronavirus , COVID-19 , Group Processes , Humans , SARS-CoV-2
12.
Chest ; 158(4): 1397-1408, 2020 10.
Article in English | MEDLINE | ID: mdl-32553536

ABSTRACT

BACKGROUND: Tocilizumab, an IL-6 receptor antagonist, can be used to treat cytokine release syndrome (CRS), with observed improvements in a coronavirus disease 2019 (COVID-19) case series. RESEARCH QUESTION: The goal of this study was to determine if tocilizumab benefits patients hospitalized with COVID-19. STUDY DESIGN AND METHODS: This observational study of consecutive COVID-19 patients hospitalized between March 10, 2020, and March 31, 2020, and followed up through April 21, 2020, was conducted by chart review. Patients were treated with tocilizumab using an algorithm that targeted CRS. Survival and mechanical ventilation (MV) outcomes were reported for 14 days and stratified according to disease severity designated at admission (severe, ≥ 3 L supplemental oxygen to maintain oxygen saturation > 93%). For tocilizumab-treated patients, pre/post analyses of clinical response, biomarkers, and safety outcomes were assessed. Post hoc survival analyses were conducted for race/ethnicity. RESULTS: Among the 239 patients, median age was 64 years; 36% and 19% were black and Hispanic, respectively. Hospital census increased exponentially, yet MV census did not. Severe disease was associated with lower survival (78% vs 93%; P < .001), greater proportion requiring MV (44% vs 5%; P < .001), and longer median MV days (5.5 vs 1.0; P = .003). Tocilizumab-treated patients (n = 153 [64%]) comprised 90% of those with severe disease; 44% of patients with nonsevere disease received tocilizumab for evolving CRS. Tocilizumab-treated patients with severe disease had higher admission levels of high-sensitivity C-reactive protein (120 vs 71 mg/L; P < .001) and received tocilizumab sooner (2 vs 3 days; P < .001), but their survival was similar to that of patients with nonsevere disease (83% vs 91%; P = .11). For tocilizumab-treated patients requiring MV, survival was 75% (95% CI, 64-89). Following tocilizumab treatment, few adverse events occurred, and oxygenation and inflammatory biomarkers (eg, high-sensitivity C-reactive protein, IL-6) improved; however, D-dimer and soluble IL-2 receptor (also termed CD25) levels increased significantly. Survival in black and Hispanic patients, after controlling for age, was significantly higher than in white patients (log-rank test, P = .002). INTERPRETATION: A treatment algorithm that included tocilizumab to target CRS may influence MV and survival outcomes. In tocilizumab-treated patients, oxygenation and inflammatory biomarkers improved, with higher than expected survival. Randomized trials must confirm these findings.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Betacoronavirus , Coronavirus Infections/complications , Coronavirus Infections/therapy , Cytokine Release Syndrome/drug therapy , Cytokine Release Syndrome/virology , Pneumonia, Viral/complications , Pneumonia, Viral/therapy , Adult , Aged , Aged, 80 and over , Algorithms , COVID-19 , Coronavirus Infections/mortality , Cytokine Release Syndrome/mortality , Female , Hospitalization , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/mortality , Respiration, Artificial , SARS-CoV-2 , Survival Rate , Treatment Outcome , Young Adult
13.
J Occup Environ Med ; 61(12): 1019-1029, 2019 12.
Article in English | MEDLINE | ID: mdl-31592942

ABSTRACT

: Noise-induced hearing loss (NIHL) represents the second most common occupational disease in the United States. Although the Occupational Safety and Health Administration (OSHA) has promulgated an occupational noise exposure standard and associated recordkeeping requirements, OSHA inspections increasingly document practices that violate both the noise standard and recordkeeping regulation. This article describes five deviations from good clinical practices masking the true societal costs of NIHL, leading to missed prevention opportunities, and creating burdens for individuals and society. These include attributing NIHL to nonoccupational sources, exculpating the workplace because of audiogram patterns without careful documentation, ignoring symptoms or physical examination findings, and simply denying work-relatedness, leading to employers inappropriately lining out cases from the OSHA 300 log. The practices identified by OSHA suggest that many individuals are not following widely recognized and accepted practices when administering hearing conservation programs.


Subject(s)
Noise, Occupational , Occupational Medicine , Practice Patterns, Physicians' , Adult , Female , Hearing Loss, Noise-Induced/epidemiology , Humans , Male , Middle Aged , National Institute for Occupational Safety and Health, U.S. , Occupational Exposure/statistics & numerical data , Practice Patterns, Physicians'/statistics & numerical data , Surveys and Questionnaires , United States/epidemiology , United States Occupational Safety and Health Administration
14.
Biol Direct ; 14(1): 12, 2019 08 01.
Article in English | MEDLINE | ID: mdl-31370905

ABSTRACT

BACKGROUND: Metagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms that live in diverse ecosystems. In order to understand the metagenomic profile of one of the densest interaction spaces for millions of people, the public transit system, the MetaSUB international Consortium has collected and sequenced metagenomes from subways of different cities across the world. In collaboration with CAMDA, MetaSUB has made the metagenomic samples from these cities available for an open challenge of data analysis including, but not limited in scope to, the identification of unknown samples. RESULTS: To distinguish the metagenomic profiling among different cities and also predict unknown samples precisely based on the profiling, two different approaches are proposed using machine learning techniques; one is a read-based taxonomy profiling of each sample and prediction method, and the other is a reduced representation assembly-based method. Among various machine learning techniques tested, the random forest technique showed promising results as a suitable classifier for both approaches. Random forest models developed from read-based taxonomic profiling could achieve an accuracy of 91% with 95% confidence interval between 80 and 93%. The assembly-based random forest model prediction also reached 90% accuracy. However, both models achieved roughly the same accuracy on the testing test, whereby they both failed to predict the most abundant label. CONCLUSION: Our results suggest that both read-based and assembly-based approaches are powerful tools for the analysis of metagenomics data. Moreover, our results suggest that reduced representation assembly-based methods are able to simultaneous provide high-accuracy prediction on available data. Overall, we show that metagenomic samples can be traced back to their location with careful generation of features from the composition of microbes and utilizing existing machine learning algorithms. Proposed approaches show high accuracy of prediction, but require careful inspection before making any decisions due to sample noise or complexity. REVIEWERS: This article was reviewed by Eugene V. Koonin, Jing Zhou and Serghei Mangul.


Subject(s)
Data Analysis , Machine Learning , Metagenome , Metagenomics/methods , Microbiota/genetics
15.
Hortic Res ; 6: 64, 2019.
Article in English | MEDLINE | ID: mdl-31069086

ABSTRACT

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine 'Chambourcin' (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in 'Chambourcin' grown ungrafted as well as grafted to three different rootstocks ('SO4', '1103P' and '3309C') across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on 'Chambourcin' leaf morphology, ionomics, and gene expression.

16.
Dig Dis Sci ; 64(7): 1809-1814, 2019 07.
Article in English | MEDLINE | ID: mdl-30746632

ABSTRACT

BACKGROUND AND AIMS: IBD patients with inadequately treated disease often relapse and require hospitalizations for further management. The purpose of this practice review was to determine whether personalized IBD care improved patient outcomes as measured by IBD-related hospitalizations. METHODS: A dedicated IBD clinic was created for personalized patient care in a tertiary veterans health care center in 2014. In the first year, the care program consisted of patient-centered medical home (PCMH). In the second year, personalized biologic therapy was incorporated into the program, based on the severity of mucosal barrier dysfunction measured by probe-based confocal laser endomicroscopy (pCLE) analysis of the terminal ileum during colonoscopy. IBD-related hospitalizations during these 2 years were compared to the year before the care program. RESULTS: The IBD-related admissions at baseline, year 1 and 2 of the program were: total number of admissions of 25, 24, 8 (P = 0.03) per year, total number of hospital days of 177, 144, 31 days per year (P < 0.01), median length of stay 7, 4, and 2 days per visit (P = 0.013), respectively. Patients had significant increases in serum hemoglobin (11.5 ± 2.7, 11.9 ± 2.6, 14.0 ± 1.4 g/dl; P = 0.035), albumin (2.7 ± 0.7, 3.0 ± 0.6 g/dl 3.7 ± 0.8 g/dl; P = 0.031) and body mass index (26.6 ± 2.9, 28.1 ± 5.9; 34.0 ± 10.8; P = 0.047). CONCLUSIONS: Personalized IBD care incorporating a PCMH model and tailored biologic therapy based on pCLE findings of mucosal barrier dysfunction significantly reduced IBD-related hospitalizations.


Subject(s)
Ambulatory Care Facilities , Biological Products/therapeutic use , Inflammatory Bowel Diseases/drug therapy , Intestinal Mucosa/drug effects , Outcome and Process Assessment, Health Care , Patient Admission , Patient-Centered Care , Veterans Health Services , Adult , Aged , Aged, 80 and over , Biological Products/adverse effects , Clinical Decision-Making , Colonoscopy , Female , Humans , Inflammatory Bowel Diseases/diagnosis , Intestinal Mucosa/pathology , Length of Stay , Male , Microscopy, Confocal , Middle Aged , Patient Selection , Predictive Value of Tests , Program Evaluation , Quality Indicators, Health Care , Severity of Illness Index , Time Factors , Treatment Outcome
17.
Micron ; 118: 43-49, 2019 03.
Article in English | MEDLINE | ID: mdl-30583220

ABSTRACT

It is well known that damage induced by impinging Ga+ ions during focused ion beam (FIB) milling of transmission electron microscopy (TEM) specimens can obfuscate subsequent TEM characterization, especially in the near-surface region of the TEM foil. Numerous strategies for minimizing this damage have been invoked, with the most common being the deposition of a Pt 'strap' at the area of interest. However, damage can still occur in the near-surface region during this Pt deposition step and the variation in the character and extent of this damage with applied Pt deposition parameter, especially in complex structural alloys, is not well characterized. In this study, the damage induced in an aerospace Al alloy (AA7075-T651) during five different Pt deposition protocols is examined using TEM. Results indicate significant variations in damage character and depth amongst the applied Pt deposition protocols, with damage being effectively eliminated using a combined electron-beam/ion-beam Pt deposition strategy. These experimental results are found to be in good agreement with Monte Carlo-based simulations of ion implantation and the implications of these findings on recent experiments in the fracture mechanics community are explored.

18.
BMC Genomics ; 18(1): 937, 2017 Dec 02.
Article in English | MEDLINE | ID: mdl-29197332

ABSTRACT

BACKGROUND: The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar 'Riesling' to improve annotation of the grapevine reference genome sequence. RESULTS: Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy. CONCLUSIONS: In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species.


Subject(s)
Genome, Plant , Models, Genetic , Molecular Sequence Annotation , RNA, Long Noncoding/genetics , Vitis/genetics , High-Throughput Nucleotide Sequencing/methods , Reference Values , Vitis/growth & development
19.
Gastrointest Endosc Clin N Am ; 26(3): 553-62, 2016 Jul.
Article in English | MEDLINE | ID: mdl-27372777

ABSTRACT

Recent development and expansion of endoscopy units has necessitated similar progress in the quality assurance of procedure sedation and monitoring. The large number of endoscopic procedures performed annually underlies the need for standardized quality initiatives focused on mitigating patient risk before, during, and immediately after endoscopic sedation, as well as improving procedure outcomes and patient satisfaction. Specific standards are needed for newer sedation modalities, including propofol administration. This article reviews the current guidelines and literature concerning quality assurance and endoscopic procedure sedation.


Subject(s)
Conscious Sedation/standards , Deep Sedation/standards , Endoscopy, Gastrointestinal/statistics & numerical data , Monitoring, Intraoperative/standards , Quality Assurance, Health Care , Clinical Competence , Gastroenterology/education , Gastroenterology/standards , Guideline Adherence , Humans , Informed Consent/standards , Medical History Taking , Patient Education as Topic , Patient Satisfaction , Physical Examination , Practice Guidelines as Topic , Risk Assessment , Time Out, Healthcare/standards
20.
Case Rep Crit Care ; 2016: 9693653, 2016.
Article in English | MEDLINE | ID: mdl-27006838

ABSTRACT

Stress (Takotsubo) cardiomyopathy is a form of reversible left ventricular dysfunction with a heightened risk of ventricular arrhythmia thought to be caused by high circulating catecholamines. We report a case of stress cardiomyopathy that developed during severe alcohol withdrawal successfully treated with dexmedetomidine. The case involves a 53-year-old man with a significant history of alcohol abuse who presented to a teaching hospital with new-onset seizures. His symptoms of acute alcohol withdrawal were initially treated with benzodiazepines, but the patient later developed hypotension, and stress cardiomyopathy was suspected based on ECG and echocardiographic findings. Adjunctive treatment with the alpha-2-adrenergic agonist, dexmedetomidine, was initiated to curtail excessive sympathetic outflow of the withdrawal syndrome, thereby targeting the presumed pathophysiology of the cardiomyopathy. Significant clinical improvement was observed within one day of initiation of dexmedetomidine. These findings are consistent with other reports suggesting that sympathetic dysregulation during alcohol withdrawal produces ideal pathobiology for stress cardiomyopathy and leads to ventricular arrhythmogenicity. Stress cardiomyopathy should be recognized as a complication of alcohol withdrawal that significantly increases cardiac-related mortality. By helping to correct autonomic dysregulation of the withdrawal syndrome, dexmedetomidine may be useful in the treatment of stress-induced cardiomyopathy.

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