PULSE - Fall 2015, Issue Two

PULSE is the bi-quarterly student-run lifestyle magazine of Central Washington University.https://digitalcommons.cwu.edu/pulse/1001/thumbnail.jp

Comparison of methods for donor-derived cell-free DNA quantification in plasma and urine from solid organ transplant recipients.

In allograft monitoring of solid organ transplant recipients, liquid biopsy has emerged as a novel approach using quantification of donor-derived cell-free DNA (dd-cfDNA) in plasma. Despite early clinical implementation and analytical validation of techniques, direct comparisons of dd-cfDNA quantification methods are lacking. Furthermore, data on dd-cfDNA in urine is scarce and high-throughput sequencing-based methods so far have not leveraged unique molecular identifiers (UMIs) for absolute dd-cfDNA quantification. Different dd-cfDNA quantification approaches were compared in urine and plasma of kidney and liver recipients: A) Droplet digital PCR (ddPCR) using allele-specific detection of seven common HLA-DRB1 alleles and the Y chromosome; B) high-throughput sequencing (HTS) using a custom QIAseq DNA panel targeting 121 common polymorphisms; and C) a commercial dd-cfDNA quantification method (AlloSeq® cfDNA, CareDx). Dd-cfDNA was quantified as %dd-cfDNA, and for ddPCR and HTS using UMIs additionally as donor copies. In addition, relative and absolute dd-cfDNA levels in urine and plasma were compared in clinically stable recipients. The HTS method presented here showed a strong correlation of the %dd-cfDNA with ddPCR (R 2 = 0.98) and AlloSeq® cfDNA (R 2 = 0.99) displaying only minimal to no proportional bias. Absolute dd-cfDNA copies also correlated strongly (τ = 0.78) between HTS with UMI and ddPCR albeit with substantial proportional bias (slope: 0.25; 95%-CI: 0.19-0.26). Among 30 stable kidney transplant recipients, the median %dd-cfDNA in urine was 39.5% (interquartile range, IQR: 21.8-58.5%) with 36.6 copies/μmol urinary creatinine (IQR: 18.4-109) and 0.19% (IQR: 0.01-0.43%) with 5.0 copies/ml (IQR: 1.8-12.9) in plasma without any correlation between body fluids. The median %dd-cfDNA in plasma from eight stable liver recipients was 2.2% (IQR: 0.72-4.1%) with 120 copies/ml (IQR: 85.0-138) while the median dd-cfDNA copies/ml was below 0.1 in urine. This first head-to-head comparison of methods for absolute and relative quantification of dd-cfDNA in urine and plasma supports a method-independent %dd-cfDNA cutoff and indicates the suitability of the presented HTS method for absolute dd-cfDNA quantification using UMIs. To evaluate the utility of dd-cfDNA in urine for allograft surveillance, absolute levels instead of relative amounts will most likely be required given the extensive variability of %dd-cfDNA in stable kidney recipients

Adequação de medicamentos prescritos em pacientes em uso de sonda enteral em um hospital público no sul do Brasil

Patients receiving enteral nutritional therapy are fed via enteral feeding tubes, which are also routes of medical administration. Nutrients and drugs interact with each other and with the gastrointestinal tract; care is needed to ensure that this therapy is properly performed in order to avoid adverse effects related to enteral nutritional therapy. The professionals involved in prescribing, dispensing and administrating drugs by feeding tubes should have the technical ability and skills that ensure the adequacy of the drug treatment in patients who use this type of therapy. There are few clinical protocols that refer to drug use in solid pharmaceutical form via enteral catheter. This study aimed to verify the inadequacy of the prescription of the solid pharmaceutical form through enteral feeding tube in patients hospitalized in a clinical unit in a public hospital in the south of Brazil. This is an observational, cross-sectional study whose data were analyzed from medical prescriptions of patients using enteral tubes. Among the drugs with pharmaceutical form of oral use prescribed via enteral feeding tubes, 94% (604) were prescribed in a solid dosage form, of which 42% (253) were inadequately prescribed. The high prevalence of inadequately prescribed drugs for tube administration demonstrates the importance of the pharmaceutical activity among the multidisciplinary team who assists patients with enteral nutritional therapy

Antifungal activity against Alternaria solani and control of early blight in tomato by essential oil of citronella

ABSTRACT An alternative to the agrochemicals is the use of essential oils that can act in plant defense against phytopathogens. The objective of work was to evaluate the antifungal activity, the early blight control, and the enzymatic defense in tomato treated with citronella essential oil. Mycelial disks of the pathogen were added in Petri dishes, with treatments 0, 500, 1000, 1500, 2000 and 2500 μL L-1 of essential oil and a control treatment with fungicide, thus evaluated mycelial growth and sporulation. The treatments were applied in the second pair of leaves of plants (treated) and after 72 hours the pathogen was inoculated on the second pair (treated) and also on the third pair leaves (untreated). The severity was expressed through the area under the disease progress curve (AUDPC). The enzymatic activity of peroxidase, polyphenoloxidase, and phenylalanine ammonia-lyase were evaluated. The essential oil reduced the mycelial growth and sporulation of the pathogen. The AUDPC was reduced up to 38.14% in the treated leaves and 51.32% in the untreated, and increases in the activities of enzymes were found. The essential oil of citronella could be an alternative in the control of tomato early blight by antimicrobial activity and/or resistance induction local and systemically

Comparison of methods for donor-derived cell-free DNA quantification in plasma and urine from solid organ transplant recipients

In allograft monitoring of solid organ transplant recipients, liquid biopsy has emerged as a novel approach using quantification of donor-derived cell-free DNA (dd-cfDNA) in plasma. Despite early clinical implementation and analytical validation of techniques, direct comparisons of dd-cfDNA quantification methods are lacking. Furthermore, data on dd-cfDNA in urine is scarce and high-throughput sequencing-based methods so far have not leveraged unique molecular identifiers (UMIs) for absolute dd-cfDNA quantification. Different dd-cfDNA quantification approaches were compared in urine and plasma of kidney and liver recipients: A) Droplet digital PCR (ddPCR) using allele-specific detection of seven common HLA-DRB1 alleles and the Y chromosome; B) high-throughput sequencing (HTS) using a custom QIAseq DNA panel targeting 121 common polymorphisms; and C) a commercial dd-cfDNA quantification method (AlloSeq® cfDNA, CareDx). Dd-cfDNA was quantified as %dd-cfDNA, and for ddPCR and HTS using UMIs additionally as donor copies. In addition, relative and absolute dd-cfDNA levels in urine and plasma were compared in clinically stable recipients. The HTS method presented here showed a strong correlation of the %dd-cfDNA with ddPCR (R2 = 0.98) and AlloSeq® cfDNA (R2 = 0.99) displaying only minimal to no proportional bias. Absolute dd-cfDNA copies also correlated strongly (τ = 0.78) between HTS with UMI and ddPCR albeit with substantial proportional bias (slope: 0.25; 95%-CI: 0.19–0.26). Among 30 stable kidney transplant recipients, the median %dd-cfDNA in urine was 39.5% (interquartile range, IQR: 21.8–58.5%) with 36.6 copies/μmol urinary creatinine (IQR: 18.4–109) and 0.19% (IQR: 0.01–0.43%) with 5.0 copies/ml (IQR: 1.8–12.9) in plasma without any correlation between body fluids. The median %dd-cfDNA in plasma from eight stable liver recipients was 2.2% (IQR: 0.72–4.1%) with 120 copies/ml (IQR: 85.0–138) while the median dd-cfDNA copies/ml was below 0.1 in urine. This first head-to-head comparison of methods for absolute and relative quantification of dd-cfDNA in urine and plasma supports a method-independent %dd-cfDNA cutoff and indicates the suitability of the presented HTS method for absolute dd-cfDNA quantification using UMIs. To evaluate the utility of dd-cfDNA in urine for allograft surveillance, absolute levels instead of relative amounts will most likely be required given the extensive variability of %dd-cfDNA in stable kidney recipients

ENCODE whole-genome data in the UCSC genome browser (2011 update)

The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA digestion and others. This data helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, DNA methylation, RNA expression, RNA binding and other cell-state indicators. It includes sequences with quality scores, alignments, signals calculated from the alignments, and in most cases, element or peak calls calculated from the signal data. Each data set is available for visualization and download via the UCSC Genome Browser (http://genome.ucsc.edu/). ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access

GEOGRAPHICAL DISTRIBUTION OF EREMOTHERIUM (XENARTHRA, MEGATHERIIDAE) RECORDS IN MIDWEST BRAZIL

The aim of this article was to present the current fossil record and geographical distribution of Eremotherium in midwest Brazil. The methodology employed here included a bibliographic survey and mapping of specimens. On the last years, new information has been revealed on these ground sloths mainly due to new fossil discoveries in the western region of Goiás and Mato Grosso states. The temporal distribution shows that these records range from the Pliocene to Holocene. This taxon is an important representative of the Brazilian megafauna, and despite its wide Pan-American distribution during the Pliocene-Holocene, there are few known Eremotherium records from this large geographic region of Brazil

GEOGRAPHICAL DISTRIBUTION OF EREMOTHERIUM (XENARTHRA, MEGATHERIIDAE) RECORDS IN MIDWEST BRAZIL

The aim of this article was to present the current fossil record and geographical distribution of Eremotherium in midwest Brazil. The methodology employed here included a bibliographic survey and mapping of specimens. On the last years, new information has been revealed on these ground sloths mainly due to new fossil discoveries in the western region of Goiás and Mato Grosso states. The temporal distribution shows that these records range from the Pliocene to Holocene. This taxon is an important representative of the Brazilian megafauna, and despite its wide Pan-American distribution during the Pliocene-Holocene, there are few known Eremotherium records from this large geographic region of Brazil

VISIONS:the VISTA Star Formation Atlas I. Survey overview

VISIONS is an ESO public survey of five nearby (d < 500 pc) star-forming molecular cloud complexes that are canonically associated with the constellations of Chamaeleon, Corona Australis, Lupus, Ophiuchus, and Orion. The survey was carried out with the Visible and Infrared Survey Telescope for Astronomy (VISTA), using the VISTA Infrared Camera (VIRCAM), and collected data in the near-infrared passbands J (1.25 μm), H (1.65 μm), and KS (2.15 μm). With a total on-sky exposure time of 49.4h VISIONS covers an area of 650 deg2, it is designed to build an infrared legacy archive with a structure and content similar to the Two Micron All Sky Survey (2MASS) for the screened star-forming regions. Taking place between April 2017 and March 2022, the observations yielded approximately 1.15 million images, which comprise 19 TB of raw data. The observations undertaken within the survey are grouped into three different subsurveys. First, the wide subsurvey comprises shallow, large-scale observations and it has revisited the star-forming complexes six times over the course of its execution. Second, the deep subsurvey of dedicated high-sensitivity observations has collected data on areas with the largest amounts of dust extinction. Third, the control subsurvey includes observations of areas of low-to-negligible dust extinction. Using this strategy, the VISIONS observation program offers multi-epoch position measurements, with the ability to access deeply embedded objects, and it provides a baseline for statistical comparisons and sample completeness – all at the same time. In particular, VISIONS is designed to measure the proper motions of point sources, with a precision of 1 mas yr−1 or better, when complemented with data from the VISTA Hemisphere Survey (VHS). In this way, VISIONS can provide proper motions of complete ensembles of embedded and low-mass objects, including sources inaccessible to the optical ESA Gaia mission. VISIONS will enable the community to address a variety of research topics from a more informed perspective, including the 3D distribution and motion of embedded stars and the nearby interstellar medium, the identification and characterization of young stellar objects, the formation and evolution of embedded stellar clusters and their initial mass function, as well as the characteristics of interstellar dust and the reddening law