Impact of Hospital Characteristics and Governance Structure on the Adoption of Tracking Technologies for Clinical and Supply Chain Use: Longitudinal Study of US Hospitals.

BACKGROUND: Despite the increasing adoption rate of tracking technologies in hospitals in the United States, few empirical studies have examined the factors involved in such adoption within different use contexts (eg, clinical and supply chain use contexts). To date, no study has systematically examined how governance structures impact technology adoption in different use contexts in hospitals. Given that the hospital governance structure fundamentally governs health care workflows and operations, understanding its critical role provides a solid foundation from which to explore factors involved in the adoption of tracking technologies in hospitals. OBJECTIVE: This study aims to compare critical factors associated with the adoption of tracking technologies for clinical and supply chain uses and examine how governance structure types affect the adoption of tracking technologies in hospitals. METHODS: This study was conducted based on a comprehensive and longitudinal national census data set comprising 3623 unique hospitals across 50 states in the United States from 2012 to 2015. Using mixed effects population logistic regression models to account for the effects within and between hospitals, we captured and examined the effects of hospital characteristics, locations, and governance structure on adjustments to the innate development of tracking technology over time. RESULTS: From 2012 to 2015, we discovered that the proportion of hospitals in which tracking technologies were fully implemented for clinical use increased from 36.34% (782/2152) to 54.63% (1316/2409), and that for supply chain use increased from 28.58% (615/2152) to 41.3% (995/2409). We also discovered that adoption factors impact the clinical and supply chain use contexts differently. In the clinical use context, compared with hospitals located in urban areas, hospitals in rural areas (odds ratio [OR] 0.68, 95% CI 0.56-0.80) are less likely to fully adopt tracking technologies. In the context of supply chain use, the type of governance structure influences tracking technology adoption. Compared with hospitals not affiliated with a health system, implementation rates increased as hospitals affiliated with a more centralized health system-1.9-fold increase (OR 1.87, 95% CI 1.60-2.13) for decentralized or independent hospitals, 2.4-fold increase (OR 2.40, 95% CI 2.07-2.80) for moderately centralized health systems, and 3.1-fold increase for centralized health systems (OR 3.07, 95% CI 2.67-3.53). CONCLUSIONS: As the first of such type of studies, we provided a longitudinal overview of how hospital characteristics and governance structure jointly affect adoption rates of tracking technology in both clinical and supply chain use contexts, which is essential for developing intelligent infrastructure for smart hospital systems. This study informs researchers, health care providers, and policy makers that hospital characteristics, locations, and governance structures have different impacts on the adoption of tracking technologies for clinical and supply chain use and on health resource disparities among hospitals of different sizes, locations, and governance structures.

Chromatin reader L(3)mbt requires the Myb-MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment.

Lethal malignant brain tumors (lmbt) result from the loss of the conserved transcriptional repressor l(3)mbt, in Drosophila melanogaster. Similar mutations in the human homolog L3MBTL1 correlate with some cancers. The protein's C-terminal MBT repeats bind mono and dimethylated histones in vitro, which could influence recruitment of L3MBTL1 to its target sites. The L(3)mbt chromatin targeting mechanism, however, is controversial and several studies suggest insufficiency or a minor role for histone methylation in determining the site specificity for recruitment. We report that L(3)mbt colocalizes with core members of the Myb-MuvB/DREAM (MMB/DREAM) transcriptional regulatory complex genome-wide, and that L(3)mbt-mediated repression requires this complex in salivary glands and larval brains. Loss of l(3)mbt or of MMB components through mutation cause similar spurious expression of genes, including the transposon regulatory gene piwi, in terminally differentiated cells. The DNA-binding MMB core component Mip120 (Lin54) is required for L(3)mbt recruitment to chromosomes, whereas Mip130 (Lin9) (an MMB core protein) and E2f2 (an MMB transcriptional repressor) are not, but are essential for repression. Cytolocalization experiments suggest the presence of site-specific differential composition of MMB in polytene chromosomes where some loci were bound by a Myb-containing or alternatively, an E2f2 and L(3)mbt form of the complex.

High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available.

DNA barcodes of Asian Houbara Bustard (Chlamydotis undulata macqueenii).

Populations of Houbara Bustards have dramatically declined in recent years. Captive breeding and reintroduction programs have had limited success in reviving population numbers and thus new technological solutions involving molecular methods are essential for the long term survival of this species. In this study, we sequenced the 694 bp segment of COI gene of the four specimens of Asian Houbara Bustard (Chlamydotis undulata macqueenii). We also compared these sequences with earlier published barcodes of 11 individuals comprising different families of the orders Gruiformes, Ciconiiformes, Podicipediformes and Crocodylia (out group). The pair-wise sequence comparison showed a total of 254 variable sites across all the 15 sequences from different taxa. Three of the four specimens of Houbara Bustard had an identical sequence of COI gene and one individual showed a single nucleotide difference (G > A transition at position 83). Within the bustard family (Otididae), comparison among the three species (Asian Houbara Bustard, Great Bustard (Otis tarda) and the Little Bustard (Tetrax tetrax)), representing three different genera, showed 116 variable sites. For another family (Rallidae), the intra-family variable sites among the individuals of four different genera were found to be 146. The COI genetic distances among the 15 individuals varied from 0.000 to 0.431. Phylogenetic analysis using 619 bp nucleotide segment of COI clearly discriminated all the species representing different genera, families and orders. All the four specimens of Houbara Bustard formed a single clade and are clearly separated from other two individuals of the same family (Otis tarda and Tetrax tetrax). The nucleotide sequence of partial segment of COI gene effectively discriminated the closely related species. This is the first study reporting the barcodes of Houbara Bustard and would be helpful in future molecular studies, particularly for the conservation of this threatened bird in Saudi Arabia.

Identification and Removal of Potential Contaminants in 16S rRNA Gene Sequence Data Sets from Low-Microbial-Biomass Samples: an Example from Mosquito Tissues.

The bacterial microbiota of the mosquito influences numerous physiological processes of the host. As low-microbial-biomass ecosystems, mosquito tissues are prone to contamination from the laboratory environment and from reagents commonly used to isolate DNA from tissue samples. In this report, we analyzed nine 16S rRNA data sets, including new data obtained by us, to gain insight into the impact of potential contaminating sequences on the composition, diversity, and structure of the mosquito tissue microbial community. Using a clustering-free approach based on the relative abundance of amplicon sequence variants (ASVs) in tissue samples and negative controls, we identified candidate contaminating sequences that sometimes differed from, but were consistent with, results found using established methodologies. Some putative contaminating sequences belong to bacterial taxa previously identified as contaminants that are commonly found in metagenomic studies but that have also been identified as part of the mosquito core microbiota, with putative physiological relevance for the host. Using different relative abundance cutoffs, we show that contaminating sequences have a significant impact on tissue microbiota diversity and structure analysis. IMPORTANCE The study of tissue-associated microbiota from mosquitoes (primarily from the gut) has grown significantly in the last several years. Mosquito tissue samples represent a challenge for researchers given their low microbial biomass and similar taxonomic composition commonly found in the laboratory environment and in molecular reagents. Using new and published data sets that identified mosquito tissue microbiota from gut and reproductive tract tissues (and their respective negative controls), we developed a simple method to identify contamination microbiota. This approach uses an initial taxonomic identification without operational taxonomic unit (OTU) clustering and evaluates the relative abundance of control sample sequences, allowing the identification and removal of purported contaminating sequences in data sets obtained from low-microbial-biomass samples. While it was exemplified with the analysis of tissue microbiota from mosquitos, it can be extended to other data sets dealing with similar technical artifacts.

Phylogeny of Canadian ergot fungi and a detection assay by real-time polymerase chain reaction.

The ergot disease of cereals has become increasingly important in agricultural areas of Canada since 1999. Generally, this disease is considered to be caused by Claviceps purpurea, but the taxonomy of Claviceps from these areas has not been well studied. The objectives of this study were (i) to determine the phylogenetic lineages (phylogenetic species) present in agricultural areas of Canada and (ii) to develop a molecular assay that can separate the lineages on crops from other lineages. Genetic diversity of Claviceps collected from agriculture areas in Canada were investigated using multilocus sequence typing. The loci sequenced include nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), partial fragments of translation elongation factor 1-α (TEF1), RNA polymerase II second largest subunit (RPB2), ß-tubulin (tubB), and two ergot alkaloid synthesis genes (easA, easE). Based on individual locus and concatenated alignments, phylogenetic analyses revealed seven lineages within the premolecular concept of C. purpurea, of which five corresponded with undescribed species (G2b and G4-7). Although lineages G2-7 had narrow host ranges, lineage G1 (= C. purpurea s.s.) had a broad host range that overlapped with other lineages. A molecular diagnostic quantitative polymerase chain reaction (qPCR) assay was developed and validated with 185 samples from a wide range of host plants and geographic origins, including 10 phylogenetic species in C. sect. Claviceps, 8 in C. sect. Pusillae, 1 in C. sect. Citrinae, and 1-2 species from Alternaria, Fusarium, and Penicillium. The assay can detect lineage G1 at a concentration of 7.5 pg/µL and distinguish it from other Claviceps species and lineages. This facilitates disease management by detecting the inocula from nonagriculture host plants.

Mapping of Standards to Facilitate Immunization Information Exchange through Two-Dimensional Bar Coding of Vaccine Products.

Purpose: A two-dimensional barcode that includes both static information (vaccine identifier) and variable information (expiration date and lot number) can facilitate streamlined documentation and sharing of vaccine administration. We sought to identify how vaccine tracking information in the two-dimensional barcode is represented in systems that are used by pharmacies, providers, and public health agencies. Methods: We identified and reviewed relevant information technology standards that govern data storage and exchange for providers, pharmacy systems, billing systems, and manufacturers to identify how each system codes the vaccine identifier, expiration date, and lot number. We selected standards commonly used by manufacturers, providers, and pharmacies and mapped the critical vaccine data elements across them. We shared the mapping with stakeholders to identify areas of alignment across standards and discussed how to address misalignment going forward. Results: Data elements were not consistently formatted in each type of information system. The vaccine lot number and expiration date were consistent, which would facilitate sharing across information systems. However, the way to identify a given vaccine is not consistent in each standard and would require manual entry. This inconsistency is related to the segmentation of the National Drug Code into three components. Therefore, vaccine identification methods differ across the systems governed by different standards. Conclusion: Patient safety can be enhanced by automated verification of the vaccine ordered versus the vaccine administered. Immunizers' back-end systems would benefit from automated documentation and reporting.

Wild and native plants and mushrooms sold in the open-air markets of south-eastern Poland.

BACKGROUND: The study of plants and fungi sold in open-air markets is an important part of ethnobotanical enquiry. Only few such studies were carried out in Europe. METHODS: Four of the largest open-air markets of south-eastern Poland were visited regularly, and the plants sold in them were recorded between 2013 and 2015. The aim of the study was to record native and/or wild species sold in the markets. All the plants sold in the markets were photographed regularly. In each market, 25 sellers were interviewed. Voucher specimens were collected and fungi were identified using DNA barcoding. RESULTS: Altogether, 468 species of plants were recorded, 117 of them native to south-eastern Poland - 19 only collected from the wild and 11 both wild and cultivated. Seventeen of the species are under legal protection. Most protected plants were sold from cultivation, although proper authorization procedures had not been performed. Thirty-two species of fungi were sold (including two cultivated species), all of them for culinary purposes. Two species (Lactarius quieticolor, Leccinum schistophilum) are new to the mycobiota of Poland. Ornamental plants constituted a large section of the market, and they dominated the group of native species. Food plants dominated among wild-collected plants and were sold mainly as fruits for jams, juices and alcoholic drinks, or as culinary herbs. Very few medicinal or green vegetable plants were sold. An interesting feature of the markets was the sale of Ledum palustre as an insect repellent. CONCLUSIONS: Finding two species of fungi which are new to Poland highlights the importance of DNA barcoding in ethnomycological studies. Most items in the markets are ornamental plants, or edible fruits and mushrooms. Very few medicinal plants and green vegetables are sold, which differentiates the markets from southern European ones. Such a pattern is probably the model for most central European markets.

Predicting a novel pathogenicity island in Helicobacter pylori by genomic barcoding.

AIM: To apply a new, integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori (H. pylori). METHODS: A genomic barcode imaging method (converting frequency matrices to grey-scale levels) was designed to visually distinguish origin-specific genomic regions in H. pylori. The complete genome sequences of the six H. pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned, and compared to the genome barcodes of Escherichia coli (E. coli) O157:H7 strain EDL933 and a random nucleotide sequence. The following criteria were applied to identify potential pathogenicity islands (PAIs): (1) barcode distance distinct from that of the general background; (2) length greater than 10000 continuous base pairs; and (3) containing genes with known virulence-related functions (as determined by PfamScan and Blast2GO). RESULTS: Comparison of the barcode images generated for the 26695, HPAG1, J99, Shi470, G27 and P12 H. pylori genomes with those for the E. coli and random sequence controls revealed that H. pylori genomes contained fewer anomalous regions. Among the H. pylori-specific continuous anomalous regions (longer than 20 kbp in each strain's genome), two fit the criteria for identifying candidate PAIs. The bioinformatic-based functional analyses revealed that one of the two anomalous regions was the known pathogenicity island cag-PAI, this finding also served as proof-of-principle for the utility of the genomic barcoding approach for identifying PAIs, and characterized the other as a novel PAI, which was designated as tfs3-PAI. Furthermore, the cag-PAI and tfs3-PAI harbored genes encoding type IV secretion system proteins and were predicted to have potential for functional synergy. CONCLUSION: Genomic barcode imaging represents an effective bioinformatic-based approach for scanning bacterial genomes, such as H. pylori, to identify candidate PAIs.

Identification of plants in Euphorbiaceae in Hainan by ITS2 barcoding sequence / 中草药

Objective: To evaluate the ability of ITS2 region as a DNA barcode for identifying the plants in Euphorbiaceae in Hainan. Methods: The ITS2 of ribosomal DNA was amplified and sequenced by bidirectional sequencing of PCR products. Sequence assembly and consensus sequence generation were performed by using Codon Code Aligner. Phylogenetic study was performed using software MEGA 6.0 in accordance with Kimura-2-parameter (K2P) model, and the phylogenetic tree was constructed by using the Neighbor-joining (NJ) method. The ITS2 secondary structure was predicted using the ITS2 Database server. The distribution of intra-versus inter-specific variability was compared using DNA bar coding gaps. Results: The variable sites and the informative sites were accounted for 84% and 69.67% of the ITS2 regions length. In the cluster dendrogram, all species showed monophyletic. The maximum intra-specific distance was 0.067 3, and the minimum inter-specific distance was 0.119 1. There was significant bar coding gap between intra-specific and inter-specific variation. To compare the ITS2 secondary structure, we noticed that it had no obvious distinguishment of intra-specific, while had obvious distinguishment of inter-specific. Conclusion: ITS2 sequence can be used as a DNA barcode for the rapid identification of the plants in Euphorbiaceae in Hainan.

Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).

Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs (