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1.
J Pain Symptom Manage ; 66(5): 551-560.e1, 2023 11.
Article in English | MEDLINE | ID: mdl-37536524

ABSTRACT

CONTEXT: Despite the association of advance care planning (ACP) with improved patient and caregiver outcomes, Chinese American elders have low rates of ACP. OBJECTIVES: Assess ACP facilitators/barriers in the San Francisco (SF) Chinese community and codesign, implement, and test community-based ACP-promoting pilot events. METHODS: A Chinese Community Committee (N = 19 community-based organization leaders, health system representatives, community members) conducted focus groups in Cantonese and English with Chinese older adults (age ≥55), caregivers, and community leaders. The Committee designed and implemented pilot events in-person and online. We analyzed focus group data using thematic analysis; assessed pre-to-post-event readiness to engage in ACP (validated survey; 14 scale, 4 = most ready); and assessed event acceptability. RESULTS: A total of 34 people participated in six focus groups. Themes described Chinese community-specific importance of ACP (e.g., reduces family burden), barriers (e.g., younger generations lack tools to discuss ACP with elders and vice versa), and facilitators (e.g., intergenerational events, culturally/linguistically appropriate materials). Based on focus groups findings, the Committee developed a novel ACP tool and designed intergenerational events. A total of 195 participants attended 10 events; 95% were Chinese, 90% spoke Chinese languages, 80% were women. ACP readiness increased significantly (1.66 [SD 0.84] vs. 2.03 [SD 0.85]; P < 0.001); 94% of participants were comfortable attending and 96% would recommend events. CONCLUSION: Community-developed intergenerational events that highlight the value of ACP and address barriers are acceptable and increase ACP engagement in the Chinese community.


Subject(s)
Advance Care Planning , East Asian People , Aged , Female , Humans , Male , Asian , Focus Groups , Language , United States
2.
Article in English | MEDLINE | ID: mdl-34292147

ABSTRACT

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic, yellow-pigmented bacterium was isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic taxonomy study was used to describe and name the bacterial isolate, strain 1_F178T. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain 1_F178T was a member of the genus Chryseobacterium and was closely related to Chryseobacterium jejuense (99.1%) and Chryseobacterium nakagawai (98.7%). Overall genome similarity metrics (average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity) revealed greatest similarity to the C. jejuense and C. nakagawai type strains but were below the threshold for species delineation. Genome sequencing revealed a genome size of 6.18 Mbp and a G+C content of 35.6 mol%. The major respiratory quinone and most abundant polar lipid of strain 1_F178T were menaquinone-6 and phosphatidylethanolamine, respectively. Strain 1_F178T had a typical fatty acid composition for Chryseobacterium species. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic data, strain 1_F178T constitutes a novel species of Chryseobacterium, for which the name Chryseobacterium pennae sp. nov. is proposed. The type strain is 1_F178T (=LMG 30779T=KCTC 62759T).


Subject(s)
Chryseobacterium/classification , Feathers/microbiology , Phylogeny , Poultry/microbiology , Animals , Bacterial Typing Techniques , Base Composition , Chryseobacterium/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genome Size , Nucleic Acid Hybridization , Phosphatidylethanolamines/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , South Africa , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
3.
Chemosphere ; 263: 127708, 2021 Jan.
Article in English | MEDLINE | ID: mdl-33296998

ABSTRACT

In water treatment process, Microcystis colonies can be effectively removed by coagulants. However, the use of popular coagulants could cause adverse health effects in humans or increase the amount of sludge. Meanwhile, Microcystis unicells are much more difficult to remove than colonies, due to their small size and dispersed distribution. This study proposed and analyzed the flocculation of Microcystis unicells induced by pH regulation. The particle size, zeta potential, cell viability and integrity, cytochemical changes, and cell-to-cell connections were recorded during pH regulation. Results showed that when pH was adjusted in the range of 2.5 to 2 by HCl (1.2 M), Microcystis unicells aggregated to form flocs as large as 28 µm, which are easy to remove by filtration or sedimentation. The overwhelming majority of cells were intact and inactivated in the optimal pH range (2.5-2). Thus, pH regulation is an environment-friendly and cost-effective method to remove Microcystis unicells, which can be potentially applied to water treatment.


Subject(s)
Microcystis , Water Purification , Flocculation , Humans , Hydrogen-Ion Concentration , Sewage
5.
Int J Syst Evol Microbiol ; 70(9): 5093-5105, 2020 Sep.
Article in English | MEDLINE | ID: mdl-32809929

ABSTRACT

Two bacterial strains, 1NT and 5NT, were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1NT (0.65×1.85 µm) and 5NT (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5NT elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1NT and 5NT occurred at 25-30 °C, pH 6.5-7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1NT and 5NT were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11T, Paraburkholderia aspalathi LMG 27731T and Paraburkholderia caffeinilytica CF1T. The genomes of 1NT and 5NT had an average nucleotide identity (91.6 and 91.3%) and in silico DNA-DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1NT and 5NT from each other and their closest relatives. The only ubiquinone present in strains 1NT and 5NT was Q-8. The major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed features 2 (3OH-C14 : 0 / C16 : 1 iso I), 3 (C16 : 1 ω6c/ω7c) and 8 (C18 : 1 ω7c/ω6c). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana. Our polyphasic approach demonstrated that strains 1NT and 5NT represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1NT=DSM 110721T=LMG 31704T) and Paraburkholderia elongata sp. nov. (type strain 5NT=DSM 110722T=LMG 31705T) are proposed.


Subject(s)
Burkholderiaceae/classification , Forests , Phylogeny , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Burkholderiaceae/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Hydroxybenzoates , New York , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Ubiquinone/chemistry
6.
Int J Syst Evol Microbiol ; 70(8): 4432-4450, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32735208

ABSTRACT

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.


Subject(s)
Chryseobacterium/classification , Phylogeny , Amino Acids/chemistry , Extinction, Biological
7.
Microbiol Resour Announc ; 9(18)2020 Apr 30.
Article in English | MEDLINE | ID: mdl-32354966

ABSTRACT

Antimicrobial resistance is a significant issue, and it threatens the prevention and effective treatment of a range of bacterial infections. Here, we report the whole-genome sequence of the multidrug-resistant isolate Serratia sp. strain HRI. A hybrid assembly was created using sequences from a first (MiSeq) and second (PacBio) sequencing run. This work is imperative for understanding antimicrobial resistance and adds to the knowledge base for combating multidrug-resistant bacteria.

8.
Int J Syst Evol Microbiol ; 70(3): 2137-2146, 2020 Mar.
Article in English | MEDLINE | ID: mdl-32027304

ABSTRACT

RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731T, Paraburkholderia fungorum LMG 16225T and Paraburkholderia caffeinilytica CF1T. Strain RP11T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).


Subject(s)
Burkholderiaceae/classification , Forests , Hydroxybenzoates/metabolism , Phylogeny , Soil Microbiology , Bacterial Typing Techniques , Base Composition , Burkholderiaceae/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , New York , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Ubiquinone/chemistry
9.
PLoS One ; 14(11): e0224288, 2019.
Article in English | MEDLINE | ID: mdl-31738797

ABSTRACT

Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction is not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how bioinformatics is being included in biology education in the US by conducting a nationwide survey of faculty at two- and four-year institutions. The survey asked several open-ended questions that probed barriers to integration, the answers to which were analyzed using a mixed-methods approach. The barrier most frequently reported by the 1,260 respondents was lack of faculty expertise/training, but other deterrents-lack of student interest, overly-full curricula, and lack of student preparation-were also common. Interestingly, the barriers faculty face depended strongly on whether they are members of an underrepresented group and on the Carnegie Classification of their home institution. We were surprised to discover that the cohort of faculty who were awarded their terminal degree most recently reported the most preparation in bioinformatics but teach it at the lowest rate.


Subject(s)
Biology/education , Computational Biology/education , Curriculum , Faculty/statistics & numerical data , Female , Humans , Male , Motivation , Students/psychology , Surveys and Questionnaires/statistics & numerical data , United States
10.
Microorganisms ; 7(6)2019 Jun 04.
Article in English | MEDLINE | ID: mdl-31167433

ABSTRACT

Moraxella is an ocular bacterial pathogen isolated in cases of keratitis, conjunctivitis, and endophthalmitis. Gram-negative brick-shaped diplobacilli from ocular specimens, and slow growth in culture, are early indications of Moraxella ocular infection; however, identifying Moraxella to species can be complex and inconsistent. In this study, bacteria consistent with Moraxella were identified to species using: (1) DNA sequencing coupled with vancomycin susceptibility, (2) MALDI-TOF mass spectrometry, and (3) the Biolog ID system. Study samples consisted of nine ATCC Moraxella controls, 82 isolates from keratitis, 21 isolates from conjunctivitis, and 4 isolates from endophthalmitis. The ATCC controls were correctly identified. For keratitis, 66 (80.5%) were identified as M. nonliquefaciens, 7 (9.0%) as M. lacunata, 5 (6%) as M. osloensis, 2 (2.5%) as Acinetobacter lwoffii, 1 (1.0%) as M. bovis/nonliquefaciens, and 1 (1.0%) as M. osloensis/nonliquefaciens. For conjunctivitis, 9 (43.0%) were identified as M. osloensis, 6 (29.0%) as M. nonliquefaciens, 3 (14.3%) as Roseomonas, 2 (9.5%) as Acinetobacter (parvus, junii), and 1 (4.5%) as M. catarrhalis/nonliquefaciens. From endophthalmitis, 3 of 4 of the isolates were M. nonliquefaciens. Overall, M. nonliquefaciens and M. osloensis were identified in 70% (75 of 107) and 13% (14 of 107) of cases, respectively, totaling 83% (89 of 107). M. nonliquefaciens and M. osloensis are important bacterial pathogens of the eye as determined by DNA sequencing, MALDI-TOF MS, and Biolog. Although Moraxella catarrhalis is a clinical pathogen, other species of Moraxella appear to have a prominent role in eye infections.

11.
J Cardiothorac Surg ; 14(1): 61, 2019 Mar 15.
Article in English | MEDLINE | ID: mdl-30876459

ABSTRACT

BACKGROUND: A prospective, multi-center study (RECON) was conducted to evaluate the clinical outcomes of pericardial closure using a decellularized extracellular matrix (ECM) graft derived from porcine small intestinal submucosa. METHODS: Patients indicated for open cardiac surgery with pericardial closure using ECM were eligible for the RECON study cohort. Postoperative complications and readmission of the RECON patients were compared to the patient cohort in the Nationwide Readmissions Database (NRD). Inverse probability of treatment weighting was used to control the differences in patient demographics, comorbidities, and risk factors. RESULTS: A total of 1420 patients at 42 centers were enrolled, including 923 coronary artery bypass grafting (CABG) surgeries and 436 valve surgeries. Significantly fewer valve surgery patients in the RECON cohort experienced pleural effusion (3.1% vs. 13.0%; p < 0.05) and pericardial effusion (1.5% vs. 2.6%; p < 0.05) than in the NRD cohort. CABG patients in the RECON cohort were less likely to suffer bleeding (1.2% vs. 2.9%; p < 0.05) and pericardial effusion (0.2% vs. 2.2%, p < 0.05) than those in the NRD cohort. The 30-day all-cause hospital readmission rate was significantly lower among RECON patients than NRD patients following both valve surgery (HR: 0.34; p < 0.05) and CABG surgery (HR: 0.42; p < 0.05). In the RECON study, 14.4% of CABG patients and 27.0% of valve patients had postoperative atrial fibrillation as compared to previously reported risks, which generally ranges from 20 to 30% after CABG and from 35 to 50% after valve surgery. CONCLUSIONS: Pericardial closure with ECM following cardiac surgery is associated with a reduction in the proportion of patients with pleural effusion, pericardial effusion, and 30-day readmission compared to a nationwide database. TRIAL REGISTRATION: NCT02073331 , Registered on February 27, 2014.


Subject(s)
Cardiac Surgical Procedures/adverse effects , Extracellular Matrix/transplantation , Postoperative Hemorrhage/etiology , Tissue Scaffolds , Wound Closure Techniques , Aged , Animals , Atrial Fibrillation/etiology , Cardiac Surgical Procedures/methods , Cardiac Valve Annuloplasty/adverse effects , Coronary Artery Bypass/adverse effects , Female , Heart Valve Prosthesis Implantation/adverse effects , Humans , Male , Middle Aged , Patient Readmission , Pericardial Effusion/etiology , Pericardium/surgery , Pleural Effusion/etiology , Postoperative Complications/etiology , Prospective Studies , Swine , Transplantation, Heterologous
12.
Article in English | MEDLINE | ID: mdl-30637405

ABSTRACT

In an honors course on "Omics Sciences," draft genome sequences of Chryseobacterium elymi KCTC 22547T, Chryseobacterium flavum KCTC 12877T, Chryseobacterium hispanicum KCTC 22104T, Chryseobacterium lathyri KCTC 22544T, "Candidatus Chryseobacterium massiliae" CCUG 51329T, Chryseobacterium piscium CCUG 51923T, and Chryseobacterium rhizosphaerae KCTC 22548T were generated to facilitate phylogenomic comparisons within the genus.

13.
Int J Syst Evol Microbiol ; 69(2): 356-362, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30570477

ABSTRACT

As part of a study investigating the rhizosphere and endosphere of the Eastern cottonwood tree, Populus deltoides, a number of isolates were subjected to genome sequencing. The genome-derived 16S rRNA gene sequence of strain CF314T was 97.0 % similar to those of the Chryseobacterium daecheongense and Chryseobacterium polytrichastri type strains, but was essentially equidistant from many other Chryseobacterium type strains. Overall genome similarity metrics (average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity) revealed greatest similarity to the Chryseobacterium daecheongense, Chryseobacterium piperi and Chryseobacterium soldanellicola type strains, but were well below the species thresholds. Strain CF314T had a typical fatty acid composition for Chryseobacterium species and produced flexirubin pigments, but not carotenoids. The genome encodes a number of proteins such as a C-type lectin and terpene synthases that are also found in other plant-associated Bacteroidetes. Based on phenotypic and genomic characteristics of the strain, we propose the new species Chryseobacteriumpopuli. The type strain is CF314T=KCTC 62722T=LMG 30786T.


Subject(s)
Chryseobacterium/classification , Phylogeny , Populus/microbiology , Bacterial Typing Techniques , Base Composition , Chryseobacterium/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/chemistry , Nucleic Acid Hybridization , Pigmentation , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tennessee , Vitamin K 2/chemistry
14.
PLoS One ; 13(6): e0196878, 2018.
Article in English | MEDLINE | ID: mdl-29870542

ABSTRACT

Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent's degree of training, time since degree earned, and/or the Carnegie Classification of the respondent's institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.


Subject(s)
Computational Biology/education , Mental Competency , Problem-Based Learning , Adolescent , Adult , Female , Humans , Male , United States
15.
Int J Syst Evol Microbiol ; 66(12): 5452-5459, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27707434

ABSTRACT

Bordetella hinzii is known to cause respiratory disease in poultry and has been associated with a variety of infections in immunocompromised humans. In addition, there are several reports of B. hinzii infections in laboratory-raised mice. Here we sequenced and analysed the complete genome sequences of multiple B. hinzii-like isolates, obtained from vendor-supplied C57BL/6 mice in animal research facilities on different continents, and we determined their taxonomic relationship to other Bordetella species. The whole-genome based and 16S rRNA gene based phylogenies each identified two separate clades in B. hinzii, one was composed of strains isolated from poultry, humans and a rabbit whereas the other clade was restricted to isolates from mice. Distinctly different estimated DNA-DNA hybridization values, average nucleotide identity scores, gene content, metabolic profiles and host specificity all provide compelling evidence for delineation of the two species, B. hinzii - from poultry, humans and rabbit - and Bordetella pseudohinzii sp. nov. type strain 8-296-03T (=NRRL B-59942T=NCTC 13808T) that infect mice.


Subject(s)
Bordetella/classification , Mice, Inbred C57BL/microbiology , Phylogeny , Animals , Bacterial Typing Techniques , Base Composition , Bordetella/genetics , Bordetella/isolation & purification , DNA, Bacterial/genetics , Fatty Acids/analysis , Humans , Mice , Nucleic Acid Hybridization , Poultry , RNA, Ribosomal, 16S/genetics , Rabbits , Sequence Analysis, DNA
16.
Biosens Bioelectron ; 74: 243-62, 2015 Dec 15.
Article in English | MEDLINE | ID: mdl-26143465

ABSTRACT

Ten years on from a review in the twentieth issue of this journal, this contribution assess the direction research in the field of glucose sensing for diabetes is headed and various technologies to be seen in the future. The emphasis of this review was placed on the home blood glucose testing market. After an introduction to diabetes and glucose sensing, this review analyses state of the art and pipeline devices; in particular their user friendliness and technological advancement. This review complements conventional reviews based on scholarly published papers in journals.


Subject(s)
Biosensing Techniques/instrumentation , Blood Glucose Self-Monitoring/instrumentation , Blood Glucose/analysis , Smartphone/instrumentation , Diabetes Mellitus/blood , Equipment Design , Humans
17.
Int J Syst Evol Microbiol ; 64(Pt 11): 3804-3809, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25142211

ABSTRACT

While characterizing a related strain, it was noted that there was little difference between the 16S rRNA gene sequences of Bacillus indicus LMG 22858(T) and Bacillus cibi DSM 16189(T). Phenotypic characterization revealed differences only in the utilization of mannose and galactose and slight variation in pigmentation. Whole genome shotgun sequencing and comparative genomics were used to calculate established phylogenomic metrics and explain phenotypic differences. The full, genome-derived 16S rRNA gene sequences were 99.74% similar. The average nucleotide identity (ANI) of the two strains was 98.0%, the average amino acid identity (AAI) was 98.3%, and the estimated DNA-DNA hybridization determined by the genome-genome distance calculator was 80.3%. These values are higher than the species thresholds for these metrics, which are 95%, 95% and 70%, respectively, suggesting that these two strains should be classified as members of the same species. We propose reclassification of Bacillus cibi as a later heterotypic synonym of Bacillus indicus and an emended description of Bacillus indicus.


Subject(s)
Bacillus/classification , Phylogeny , Base Composition , DNA, Bacterial/genetics , Genome, Bacterial , Molecular Sequence Data , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
18.
Int J Syst Evol Microbiol ; 63(Pt 12): 4777-4783, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23996834

ABSTRACT

As part of an undergraduate microbiology course, a yellow-orange-pigmented, Gram-staining negative, rod-shaped, non-motile bacterial strain was isolated from a glass tank housing several red-spotted newts (Notophthalmus viridescens). The sequence of the 16S rRNA gene of this strain, designated KM(T), was 97.4-98.0 % similar to those of the type strains of Chryseobacterium luteum, C. shigense and C. vrystaatense, while the similarity levels for protein-coding genes were less than 94.7 % for rpoB, less than 92.1 % for groEL and less than 87.1 % for gyrB. These values are lower than for many other established distinct species. Polyphasic characterization and comparison to these relatives revealed that strain KM(T) was similar to other Chryseobacterium strains in that it contained MK-6 as its major respiratory quinone and phosphatidylethanolamine as the most abundant polar lipid, produced flexirubin-type pigments, oxidase and catalase and primarily contained the fatty acids iso-C15 : 0, iso-C17 : 1ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). Based on the results of this study, strain KM(T) represents a novel species, for which the name Chryseobacterium angstadtii sp. nov. is proposed. The type strain is KM(T) ( = ATCC BAA-2160(T) = NRRL B-59516(T) = KCTC 23297(T)).


Subject(s)
Chryseobacterium/classification , Phylogeny , Salamandridae , Animals , Bacterial Typing Techniques , Base Composition , Chaperonin 60/genetics , Chryseobacterium/genetics , Chryseobacterium/isolation & purification , DNA Gyrase/genetics , DNA, Bacterial/genetics , Fatty Acids/chemistry , Molecular Sequence Data , Phosphatidylethanolamines/chemistry , Polyenes/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
19.
J Palliat Med ; 16(11): 1362-7, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23971709

ABSTRACT

BACKGROUND/OBJECTIVE: Increased attention has been directed at the intersection of emergency and palliative medicine, since decisions made in the emergency department (ED) often determine the trajectory of subsequent medical treatments. Specifically, we examined whether inpatient admissions after palliative care (PC) consultation initiated in the ED were associated with decreased length of stay (LOS), compared with those in which consultations were initiated after hospital admission. METHODS: Education and training on PC and the consultation service were provided to ED physicians and nurses. The PC service evaluated patients in the ED during weekdays and provided telephone consultation nights and weekends with postadmission follow-up. We compared the outcomes of these patients with those whose PC needs were identified and addressed through consultation postadmission. PC consultation data between January 2006 and December 2010 were retrospectively collected from the administrative records system and analyzed using propensity scores within multivariate regression. RESULTS: Included in the analysis were 1435 PC consultations, 50 of which were initiated in the ED across the 4-year study period. Propensity scores were calculated using patient-level characteristics, including All Patient Refined Diagnostic Related Group (APRDRG) risk of mortality (ROM) and severity of illness (SOI), age, gender, readmission status, facility, and insurance type. Regression results showed that consultation in the ED was associated with a significantly shorter LOS by 3.6 days (p<0.01). CONCLUSIONS: Early initiation of PC consultation in the ED was associated with a significantly shorter LOS for patients admitted to the hospital, indicating that the patient- and family-centered benefits of PC are complemented by reduced inpatient utilization.


Subject(s)
Emergency Service, Hospital/organization & administration , Inpatients , Length of Stay/statistics & numerical data , Palliative Care , Referral and Consultation , Aged , Aged, 80 and over , Data Collection/methods , Decision Making , Female , Hospital Mortality , Humans , Male , Middle Aged , Propensity Score , Retrospective Studies , Risk Factors , Severity of Illness Index
20.
J Palliat Med ; 16(9): 1089-94, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23742686

ABSTRACT

BACKGROUND: The ambulatory care setting is a new frontier for advance care planning (ACP). While electronic health records (EHR) have been expected to make ACP documentation more retrievable, the literature is silent on the locations of ACP documentation in EHRs and how readily they can be found. OBJECTIVE: The study's objective is to identify the locations of ACP documentation in EpicCare EHR and to determine which patient and primary care provider (PCP) characteristics are associated with having a scanned ACP document. A scanned document (SD) is the only documentation containing signatures (unsigned documents are not legally valid). DESIGN: The study design is a retrospective review of EpicCare EHR records. The search of terms included advance directives, living will, Physician Orders for Life-Sustaining Treatments (POLST), power of attorney, and do-not-resuscitate. SETTING/SUBJECTS: Subjects were patients in a multispecialty practice in California age 65 or older who had at least one ACP documentation in the EHR. MEASUREMENTS: Measurements were types and locations of documentation, and characteristics of patients and physicians. RESULTS: About 50.9% of patients age 65 or older had at least one ACP documentation in the EHR (n=60,105). About 33.5% of patients with ACP documentation (n=30,566) had an SD. Patients' age, gender, race, illnesses, and when their physician started at the medical group were statistically significantly associated with the probability of having a scanned ACP document. CONCLUSIONS: Only 33.5% of patients with ACP documentation somewhere in the EHR had an SD. Standardizing the location of these documents should become a priority to improve care. Actions are needed to eliminate disparities.


Subject(s)
Advance Care Planning , Documentation/standards , Electronic Health Records , Aged , California , Female , Humans , Male , Primary Health Care , Retrospective Studies
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