Temporal multispectral and 3D analysis of Cerro de Pasco, Peru.

Mining operations across the world often lead to contamination of land, water resources, ecosystems and in some cases, entire communities.Results of recent health and ground sampling studies revealed extensive lead contamination within the populace and around the City of Cerro de Pasco, Peru. Tailings excavated from a large open pit zinc mine in the center of the city have been aggregated in four large stockpiles within close proximity to neighborhoods, schools, and hospitals. Visual comparison of ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) imagery from 2001 and Sentinel-2 imagery from 2018 suggests a size increase in one tailing stockpile in particular near the neighborhood of Paragsha. Due to ongoing mining efforts, the hypothesis motivating the work presented here is that Pb-bearing minerals would be detectable through multispectral analysis, an increase in Pb mineral percent abundance would be observed and tailing stockpile volume would be detectable between 2001 and 2016. This hypothesis is tested using Spectral Angle Mapper (SAM), Adaptive Coherence Estimator (ACE), and Jeffries-Matusita distance calculation on ASTER (2001) and Sentinel-2 (2018) VNIR and SWIR bands. Volume and area estimate of tailing stockpiles were calculated using a photogrammetrically derived point cloud. SAM detected the presence of five Pb-bearing minerals around Cerro de Pasco and Paragsha. The results of the temporal SAM analysis displayed an increase of approximately 17% of Pb-bearing minerals around the greater Cerro de Pasco city area and approximately 11% for the neighborhood of Paragsha. Jeffries-Matusita distance results suggest clear correlation between contamination sources and affected locations. Total tailing stockpile volume was measured to be approximately 200,300,000 m3. Volume for Pile 4 was estimated to have increased by approximately 46,000,000 m3 between 2001 and 2018. These presented results will hopefully inspire and guide future remote sensing campaigns, perhaps involving a UAV or aircraft-based hyperspectral instrument.

A pharmacogenetic investigation of intravenous furosemide in decompensated heart failure: a meta-analysis of three clinical trials.

We conducted a meta-analysis of pharmacogenomic substudies of three randomized trials conducted in patients with decompensated heart failure (HF) that were led by National Heart Lung and Blood Institute (NHLBI)-funded HF Network to test the hypothesis that candidate genes modulate net fluid loss and weight change in patients with decompensated HF treated with a furosemide-based diuretic regimen. Although none of the genetic variants previously shown to modulate the effects of loop diuretics in healthy individuals were associated with net fluid loss after 72 h of treatment, a set of rare variants in the APOL1 gene, which codes for apolipoprotein L1 (P=0.0005 in the random effects model), was associated with this end point. Moreover, a common variant in the multidrug resistance protein-4 coding gene (ABCC4, rs17268282) was associated with weight loss with furosemide use (P=0.0001). Our results suggest that both common and rare genetic variants modulate the response to a furosemide-based diuretic regimen in patients with decompensated HF.

Incidence and risk factors for hospital-acquired Clostridium difficile infection among inpatients in an orthopaedic tertiary care hospital.

The aim of this retrospective study was to identify risk factors for hospital-acquired Clostridium difficile infection (HA-CDI) in orthopaedic patients. Thirty-two HA-CDI cases were each matched with two controls. Incidence rate was 0.33 cases per 1000 patient-days. Univariate analyses showed that surgery >24 h after admission, antibiotics for treatment, and proton pump inhibitors were associated with HA-CDI. Multivariate analyses revealed that surgery >24 h after admission was associated with HA-CDI. Patients hospitalized before surgery had a greater risk of HA-CDI, suggesting opportunities to reduce environmental exposure to C. difficile by timelier preoperative medical optimization in the outpatient setting.

Elevated stricture rate following the use of fully covered self-expandable metal biliary stents for biliary leaks following liver transplantation.

BACKGROUND: Biliary leaks and strictures are common complications after liver transplantation and can be managed surgically or endoscopically. Endoscopic management using fully covered self-expandable metal stents (FCSEMS) might provide some advantages over the commonly used plastic stents in the management of bile leaks after liver transplantation. METHODS: Between December 2006 and January 2009, 17 liver transplant recipients underwent placement of a FCSEMS for treatment of biliary leaks. RESULTS: FCSEMS were deployed at median of 18 days (range: 6 - 160) after liver transplantation and left in place for a median of 102 days (range: 35 - 427), with a median follow-up after FCSEMS removal of 407 days (range: 27 - 972). Long-term leak control was obtained in all but one patient. Complications included 6 clinically significant biliary strictures (35 %), which were treated with repeat stent placement, and two clinically insignificant strictures (12 %) which required no intervention. Additionally, three patients (18 %) had biliary ulcerations after stent removal, confirmed by choledochoscopy, and were managed conservatively. Two patients required repeat liver transplantation due to hepatic artery thrombosis, and one patient died from sepsis unrelated to FCSEMS stenting. CONCLUSIONS: FCSEMS treat biliary leaks effectively, but carry a relatively high stricture risk in patients who have received liver transplants. FCSEMS cannot be recommended for management of biliary leaks following liver transplantation at this point.

Overview of methods for flexible endoscopic training and description of a simple explant model.

The question of how to train surgeons in flexible endoscopy has been debated over the years as these skills have become an essential part of residency and practice. As many as two-thirds of surgeons perform flexible endoscopy, and for many, endoscopy represents up to 50% of their practice. Training in flexible endoscopy has evolved over many decades from an apprenticeship-type model to a more formal training program. Surgical residencies vary widely in their approach, with some having dedicated endoscopy rotations and others using an integrated approach. Innate to a good training program are faculty dedicated to teaching, an established curriculum, and adequate exposure of residents to proper training tools, whether as patient-based learning or supplemented by simulators. Hands-on models for teaching surgical endoscopy include mechanical, animal, and computer-based platforms. Herein, we describe our experience with a low-cost approach using porcine stomach explants that offers a breadth of endoscopic training including scope navigation, band ligation, endoscopic mucosal resection, hemostasis management, esophageal stenting, foreign body extraction, and ERCP. Simulation-based learning must be validated from a construct and internal validity perspective to be considered useful. Correlation between simulator learning and improvement in clinically relevant skills must then be shown using a validated scale, such as the Global Assessment of Gastrointestinal Endoscopy Skills. Competency in flexible endoscopy, which is currently measured by case volume, may be replaced by objective programs, such as Fundamentals of Endoscopic Surgery, that combine didactic teaching, cognitive assessment, and hands-on technical skills evaluation to determine a minimum level of proficiency.

Application of principal component analysis to pharmacogenomic studies in Canada.

Ethnicity can confound results in pharmacogenomic studies. Allele frequencies of loci that influence drug metabolism can vary substantially between different ethnicities and underlying ancestral genetic differences can lead to spurious findings in pharmacogenomic association studies. We evaluated the application of principal component analysis (PCA) in a pharmacogenomic study in Canada to detect and correct for genetic ancestry differences using genotype data from 2094 loci in 220 key drug biotransformation genes. Using 89 Coriell worldwide reference samples, we observed a strong correlation between principal component values and geographic origin. We further applied PCA to accurately infer the genetic ancestry in our ethnically diverse Canadian cohort of 524 patients from the GATC study of severe adverse drug reactions. We show that PCA can be successfully applied in pharmacogenomic studies using a limited set of markers to detect underlying differences in genetic ancestry thereby maximizing power and minimizing false-positive findings.

Identification and characterization of CYP2D6*56B, an allele associated with the poor metabolizer phenotype.

A 5-year-old African-American girl presented with a CYP2D6*4xN/*10 genotype that was discordant with her poor metabolizer phenotype determined with the probe drug dextromethorphan. Both phenotype and genotype were confirmed in repeat assessments, suggesting that the CYP2D6*10 allele carried a novel debilitating sequence variation(s). The rationale for this study was to resolve the discordance and to describe the novel non-functional allelic variant of CYP2D6 and its frequency in populations of different ethnic backgrounds.

Real-time PCR detection and quantification of vector trichodorid nematodes and Tobacco rattle virus.

This report describes a novel diagnostic method for virus-vector trichodorid nematodes and associated Tobacco rattle virus (TRV) based on a real-time fluorogenic 5' nuclease PCR assay (TaqMan). Two independent primer/probe sets were designed targeting the 18S gene of the ribosomal cistron for the trichodorid species, Paratrichodorus pachydermus and Trichodorus similis. Assays using purified plasmid DNA containing clones of the 18S region and genomic DNA extracted from individuals from both nematode species displayed high specificity as no cros s-reaction was observed between the species or with two non-target trichodorid species Paratrichodorus anemones and Trichodorus primitivus. Relative quantification of target DNA present in unknown samples was performed by comparison of the fluorescence signals of the samples to those obtained from plasmid standard dilutions. Three primer/probe sets were also used to target TRV; one set for RNA1 and the two other sets for RNA2 of specific isolates (TRV-PpK20 and TRV-TpO1). Detection of both trichodorid species and TRV RNA1 and RNA2 from a single sample was achieved and field samples were used to demonstrate the potential of this assay to provide rapid, accurate and sensitive molecular information in relation to risk assessment in the field.

Molecular variation in the potato cyst nematode, Globodera pallida, in relation to virulence.

The potato cyst nematode Globodera pallida poses a challenge for potato growers. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida cause damage valued at over pounds 50m per annum in the U.K. and problems in controlling PCN are growing due to the increase in populations and spread of G. pallida, the lack of many commercially attractive cultivars with resistance to this species and the pressure to reduce nematicide use. Over 60% of potato fields in the U.K. are infected with G. pallida (Minnis et al. 2000). The Scottish Agricultural Science Agency (SASA) figures show that the incidence of both species of PCN on Scottish seed potato land, though low, has been increasing. The proportion of potato land in ware production in Scotland is also increasing and now represents 50% of the potato growing area. This situation potentially increases the risk of the spread of PCN unless it is very carefully monitored and managed.

Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.

Recent studies of human populations suggest that the genome consists of chromosome segments that are ancestrally conserved ('haplotype blocks'; refs. 1-3) and have discrete boundaries defined by recombination hot spots. Using publicly available genetic markers, we have constructed a first-generation haplotype map of chromosome 19. As expected for this marker density, approximately one-third of the chromosome is encompassed within haplotype blocks. Evolutionary modeling of the data indicates that recombination hot spots are not required to explain most of the observed blocks, providing that marker ascertainment and the observed marker spacing are considered. In contrast, several long blocks are inconsistent with our evolutionary models, and different mechanisms could explain their origins.

Ribosomal Intergenic Spacer: A Polymerase Chain Reaction Diagnostic for Meloidogyne chitwoodi, M. fallax, and M. hapla.

ABSTRACT Polymerase chain reaction amplification of the intergenic spacer region between the 5S and 18S genes from Meloidogyne chitwoodi, M. fallax, and M. hapla enabled these three important temperate species to be differentiated. Length polymorphism was found between M. chitwoodi and M. fallax as a result of differing numbers of short repeats located between the 5S and 18S genes. The presence of the 5S gene within the rDNA cistrons was confirmed in the Meloidogyne spp. included in this study. The region between the 28S and 5S genes for M. chitwoodi and M. fallax was short and lacked variability in repeated sequences compared with the main tropical Meloidogyne spp. and M. hapla. Differences in the number of these repeats resulted in intraspecific length polymorphism for M.hapla.

Mapping by genetic interaction: high-resolution congenic mapping of the type 1 diabetes loci Idd10 and Idd18 in the NOD mouse.

As many of the linked chromosome regions that predispose to type 1 diabetes in the NOD mouse have been dissected, it has become apparent that the initially observed effect is in fact attributable to several loci. One such cluster of loci on distal chromosome 3, originally described as Idd10, is now known to comprise three separate loci, Idd10, Idd17, and Idd18. Although these loci have a significant combined effect on diabetes development, their individual effects are barely detectable when diabetes is used as a read-out, which makes fine-mapping them by use of a conventional congenic approach impractical. In this study, we demonstrate that it is possible to map loci, with modest effects, to regions small enough for systematic gene identification by capitalizing on the fact that the combined loci provide more profound, measurable protection. We have mapped the Idd10 and Idd18 loci to 1.3- and 2.0-cM intervals, respectively, by holding the Idd3 allele constant. In addition, we have excluded Csf1 and Nras as candidates for both loci.

Nosocomial infections due to nontuberculous mycobacteria.

Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and cause colonization, infection, and pseudo-outbreaks in health care settings. Data suggest that the frequency of nosocomial outbreaks due to NTM may be increasing, and reduced hot water temperatures may be partly responsible for this phenomenon. Attention to adequate high-level disinfection of medical devices and the use of sterile reagents and biologicals will prevent most outbreaks. Because NTM cannot be eliminated from the hospital environment, and because they present an ongoing potential for infection, NTM should be considered in all cases of nosocomial infection, and careful surveillance must be used to identify potential outbreaks. Analysis of the species of NTM and the specimen source may assist in determining the significance of a cluster of isolates. Once an outbreak or pseudo-outbreak is suspected, molecular techniques should be applied promptly to determine the source and identify appropriate control measures.

Cuticle heterogeneity as exhibited by Pasteuria spore attachment is not linked to the phylogeny of parthenogenetic root-knot nematodes (Meloidogyne spp.).

The cuticle is a major barrier prohibiting the infection of nematodes against micro-organisms. The attachment of bacterial spores of the nematode hyperparasite Pasteuria penetrans (PP1) to field populations of root-knot nematodes (RKN, Meloidogyne spp.) from Burkino Faso, Ecuador, Greece, Malawi, Senegal and Trinidad and Tobago were assayed in standard attachment tests. The attachment of spore population PP1 to different field populations of root-knot nematode showed that the rates of attachment differed between countries. Similar tests were also undertaken on P. penetrans spores from these countries against 2 species of RKN, M. incognita and M. arenaria. The results showed a high degree of variability in spore attachment with no clear distinction between the 2 species of nematode. It has been hypothesized that Pasteuria spore attachment is linked to nematode species designations and this study clearly shows that this is not the case. Further tests showed that variation in spore attachment was not linked to nematode phylogeny. The results therefore beg the question of how do parthenogenetic root-knot nematodes maintain cuticle variability in the face of such an aggressive hyperparasite.

The NOD Idd9 genetic interval influences the pathogenicity of insulitis and contains molecular variants of Cd30, Tnfr2, and Cd137.

Previous analyses of NOD mice have shown that some genes control the development of both insulitis and diabetes, while other loci influence diabetes without reducing insulitis. Evidence for the existence of a gene only influencing diabetes, Idd9 on mouse chromosome 4, is provided here by the development of a novel congenic mouse strain, NOD.B10 Idd9. NOD.B10 Idd9 mice display profound resistance to diabetes even though nearly all develop insulitis. Subcongenic analysis has demonstrated that alleles of at least three B10 genes, Idd9.1, Idd9.2, and Idd9.3 are required to produce Idd9-mediated diabetes resistance. Candidate genes with amino acid differences between the NOD and B10 strains have been localized to the 5.6 cM Idd9.2 interval (Tnfr2, Cd30) and to the 2.0 cM Idd9.3 interval (Cd137).

Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation.

Large-scale pharmacogenetics and complex disease association studies will require typing of thousands of single-nucleotide polymorphisms (SNPs) in thousands of individuals. Such projects would benefit from a genotyping system with accuracy >99% and a failure rate <5% on a simple, reliable, and flexible platform. However, such a system is not yet available for routine laboratory use. We have evaluated a modification of the previously reported Invader SNP-typing chemistry for use in a genotyping laboratory and tested its automation. The Invader technology uses a Flap Endonuclease for allele discrimination and a universal fluorescence resonance energy transfer (FRET) reporter system. Three hundred and eighty-four individuals were genotyped across a panel of 36 SNPs and one insertion/deletion polymorphism with Invader assays using PCR product as template, a total of 14,208 genotypes. An average failure rate of 2.3% was recorded, mostly associated with PCR failure, and the typing was 99.2% accurate when compared with genotypes generated with established techniques. An average signal-to-noise ratio (9:1) was obtained. The high degree of discrimination for single base changes, coupled with homogeneous format, has allowed us to deploy liquid handling robots in a 384-well microtitre plate format and an automated end-point capture of fluorescent signal. Simple semiautomated data interpretation allows the generation of approximately 25,000 genotypes per person per week, which is 10-fold greater than gel-based SNP typing and microsatellite typing in our laboratory. Savings on labor costs are considerable. We conclude that Invader chemistry using PCR products as template represents a useful technology for typing large numbers of SNPs rapidly and efficiently.

A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida.

The mitochondrial genome (mtDNA) of the plant parasitic nematode Globodera pallida exists as a population of small, circular DNAs that, taken individually, are of insufficient length to encode the typical metazoan mitochondrial gene complement. As far as we are aware, this unusual structural organization is unique among higher metazoans, although interesting comparisons can be made with the multipartite mitochondrial genome organizations of plants and fungi. The variation in frequency between populations displayed by some components of the mtDNA is likely to have major implications for the way in which mtDNA can be used in population and evolutionary genetic studies of G. pallida.

Clinical research: ASHP guidelines and future directions for pharmacists.

ASHP guidelines on the pharmacist's role in clinical drug research and future directions for pharmacists in clinical drug research are described. Health-system pharmacists have a responsibility to the patient and to the institution to ensure that clinical research systems are sound, that patients are protected, and that research is conducted in a safe, effective way. ASHP guidelines list minimum standards that are essential for improving performance. The ASHP Guidelines on Clinical Drug Research, approved in November 1997, update information previously found in the ASHP Guidelines for the Use of Investigational Drugs in Organized Health-Care Settings, approved in 1990, but have an expanded focus. Additions include recognition of relevant business practices, implications of technology, and the expansion of clinical research beyond the academic health center. At a minimum, all pharmacists involved in clinical research should handle the record keeping for drug accountability, provide drug information to patients and to other health care providers, ensure the appropriate care of patients at sites not involved in the study, and provide accountability at nonpharmacy locations. Managing and coordinating clinical drug research is an area of growth that represents a great opportunity for clinical drug research. By providing baseline and higher-level pharmaceutical services for clinical research projects, pharmacists can help to ensure data accuracy and completeness and patient safety.

Cloning of a novel member of the low-density lipoprotein receptor family.

A gene encoding a novel transmembrane protein was identified by DNA sequence analysis within the insulin-dependent diabetes mellitus (IDDM) locus IDDM4 on chromosome 11q13. Based on its chromosomal position, this gene is a candidate for conferring susceptibility to diabetes. The gene, termed low-density lipoprotein receptor related protein 5 (LRP5), encodes a protein of 1615 amino acids that contains conserved modules which are characteristic of the low-density lipoprotein (LDL) receptor family. These modules include a putative signal peptide for protein export, four epidermal growth factor (EGF) repeats with associated spacer domains, three LDL-receptor (LDLR) repeats, a single transmembrane spanning domain, and a cytoplasmic domain. The encoded protein has a unique organization of EGF and LDLR repeats; therefore, LRP5 likely represents a new category of the LDLR family. Both human and mouse LRP5 cDNAs have been isolated and the encoded mature proteins are 95% identical, indicating a high degree of evolutionary conservation.

Evidence for a Dosage Effect of the Mi gene on Partially Virulent Isolates of Meloidogyne javanica.

The reproduction of single egg-mass isolates of Meloidogyne javanica from Crete that differed in virulence were compared on tomato (Lycopersicon esculentum) genotypes homozygous or heterozygous for the Mi gene. The reproduction of three isolates with partial virulence was much greater on tomato genotypes heterozygous for the Mi gene (cultivars Scala, Bermuda, and 7353) than on two homozygous genotypes (F8 inbred lines derived from Scala). The reproduction of a highly virulent isolate on the homozygous and heterozygous genotypes was similar to that on a susceptible cultivar. These results pose questions regarding the nature of partial virulence and indicate a quantitative effect of the Mi gene in relation to such virulence.