bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aluminum, Iron, Lead, Cadmium, Copper, Zinc, Chromium, Magnesium, Strontium, and Calcium Content in Bone of End-Stage Renal Failure Patients
Authors: D’Haese Patrick C , Couttenye Marie-Madeleine , Lamberts Ludwig V , Elseviers Monique M , Goodman William G , Schrooten Iris , Cabrera Walter E , De Broe Marc E 
Published: January 2020

AbstractBackground: Little is known about trace metal alterations in the bones of dialysis patients or whether particular types of renal osteodystrophy are associated with either increased or decreased skeletal concentrations of trace elements. Because these patients are at risk for alterations of trace elements as well as for morbidity from skeletal disorders, we measured trace elements in bone of patients with end-stage renal disease.Methods: We analyzed bone biopsies of 100 end-stage renal failure patients enrolled in a hemodialysis program. The trace metal contents of bone biopsies with histological features of either osteomalacia, adynamic bone disease, mixed lesion, normal histology, or hyperparathyroidism were compared with each other and with the trace metal contents of bone of subjects with normal renal function. Trace metals were measured by atomic absorption spectrometry.Results: The concentrations of aluminum, chromium, and cadmium were increased in bone of end-stage renal failure patients. Comparing the trace metal/calcium ratio, significantly higher values were found for the bone chromium/calcium, aluminum/calcium, zinc/calcium, magnesium/calcium, and strontium/calcium ratios. Among types of renal osteodystrophy, increased bone aluminum, lead, and strontium concentrations and strontium/calcium and aluminum/calcium ratios were found in dialysis patients with osteomalacia vs the other types of renal osteodystrophy considered as one group. Moreover, the concentrations of several trace elements in bone were significantly correlated with each other. Bone aluminum was correlated with the time on dialysis, whereas bone iron, aluminum, magnesium, and strontium tended to be associated with patient age. Bone trace metal concentrations did not depend on vitamin D intake nor on the patients’ gender.Conclusions: The concentration of several trace elements in bone of end-stage renal failure patients is disturbed, and some of the trace metals under study might share pathways of absorption, distribution, and accumulation. The clinical significance of the increased/decreased concentrations of several trace elements other than aluminum in bone of dialysis patients deserves further investigation.
Urine Antibody Tests: New Insights into the Dynamics of HIV-1 Infection
Authors: Urnovitz Howard B , Sturge Jerrilyn C , Gottfried Toby D , Murphy William H 
Published: January 2020

AbstractBackground: Noninvasive methodologies provide alternatives to diagnostic blood tests and have high patient acceptance, increased safety, and reduced costs. Such tests may supplement or replace blood diagnostic assays currently in use.Methods: Using a licensed urine-based test for antibody to HIV-1, we performed 25 991 HIV-1 urine antibody enzyme immunoassay (EIA) screening tests [confirmable by HIV-1 Western blot (WB)] on paired urine and blood specimens obtained from high- and low-risk HIV-1 subjects collected at six sites representative of the US population.Results: Using HIV-1 urine EIA tests confirmed by urine Western blot, a compartmentalized immune response (urine positive/serum negative) occurred in 0.24% of a cohort of 11 896 subjects. In the same cohort, specimens that were urine negative/serum positive occurred in 0.17% of subjects. In a second study of 25 991 subjects that included 859 high-risk individuals, the false-positive urine EIA frequency (urine WB negative or indeterminate) was 1.3%. This false-positive frequency in the high-risk cohort was attributed, in part, to an IgA antibody response. We tabulated urine and serum indeterminate reactivities and examined their possible causes. Data are presented showing that antibodies from a seroindeterminate HIV-1vau group O subject were reactive in urine EIA and urine WB tests. An analysis of the HIV-1vau strain group O env nucleotide sequence disclosed a high frequency of homology with human chromosome 7q31, a fragile site implicated in many human malignancies.Conclusions: These results demonstrate the utility of urine for alternative HIV-1 antibody testing and provide new insights into the pathogenesis of HIV-1 infection and into potential application of this approach in investigation of other microbial pathogens and toxic compounds.
Causes of Unsatisfactory Performance in Proficiency Testing
Authors: Jenny Richard W , Jackson-Tarentino Kathryn Y 
Published: January 2020

Abstract
Background: Proficiency testing (PT) provides a measure of the effectiveness of laboratory quality assurance programs. Test reports are released from processes that the laboratory judges to be in conformance with quality specifications; an evaluation of unsatisfactory performance (UNSAT) by a PT provider is an unexpected outcome for the laboratory. An understanding of the root cause(s) of testing errors provides an opportunity for the continuous improvement of laboratory services.
Methods: We used participant data from the New York State Department of Health PT program to characterize the quality of testing in the toxicology specialty. Outcomes from laboratory investigations into causes of UNSAT and information on quality control practices collected from all program participants were used to identify the root causes of error.
Results: Two classes of error were encountered: spurious test results caused by lapses in standard operating procedures and instrument malfunctions (300 per million assays) and common-cause analytic error (7000 per million assays or 0.7% rate of UNSAT). Causes of spurious results included inaccurate mathematical correction for specimen dilution, misinterpretation of instrument codes, and instrument sampling errors. Calibration drift was most frequently cited as the common-cause analytic error. Approximately one-half of the laboratories used an allowable error for the quality control of analytical systems that exceeded the threshold error specified by manufacturers for stable instrument performance.
Conclusions: The causes of spurious results suggest the need for ongoing competency testing of analysts where analyst intervention is required in an otherwise automated process, and for continued diligence in mistake-proofing instrument design. The intrinsic quality of laboratory testing is unlikely to improve until the allowable error in quality control is consistent with manufacturer specifications for stable system performance.
Evaluation of the Performance of a p53 Sequencing Microarray Chip Using 140 Previously Sequenced Bladder Tumor Samples
Authors: Wikman Friedrik P , Lu Ming-Lan , Thykjaer Thomas , Olesen Sanne H , Andersen Lars D , Cordon-Cardo Carlos , Ørntoft Torben F 
Published: January 2020

Abstract
Background: Testing for mutations of the TP53 gene in tumors is a valuable predictor for disease outcome in certain cancers, but the time and cost of conventional sequencing limit its use. The present study compares traditional sequencing with the much faster microarray sequencing on a commercially available chip and describes a method to increase the specificity of the chip.
Methods: DNA from 140 human bladder tumors was extracted and subjected to a multiplex-PCR before loading onto the p53 GeneChip from Affymetrix. The same samples were previously sequenced by manual dideoxy sequencing. In addition, two cell lines with two different homozygous mutations at the TP53 gene locus were analyzed.
Results: Of 1464 gene chip positions, each of which corresponded to an analyzed nucleotide in the sequence, 251 had background signals that were not attributable to mutations, causing the specificity of mutation calling without mathematical correction to be low. This problem was solved by regarding each chip position as a separate entity with its own noise and threshold characteristics. The use of background plus 2 SD as the cutoff improved the specificity from 0.34 to 0.86 at the cost of a reduced sensitivity, from 0.92 to 0.84, leading to a much better concordance (92%) with results obtained by traditional sequencing. The chip method detected as little as 1% mutated DNA.
Conclusions: Microarray-based sequencing is a novel option to assess TP53 mutations, representing a fast and inexpensive method compared with conventional sequencing.
Rapid Real-Time Fluorescent PCR Gene Dosage Test for the Diagnosis of DNA Duplications and Deletions
Authors: Ruiz-Ponte Clara , Loidi Lourdes , Vega Ana , Carracedo Angel , Barros Francisco 
Published: January 2020

Abstract
Background: Current methods to determine gene dosage are time-consuming and labor-intensive. We describe a new and rapid method to assess gene copy number for identification of DNA duplications or deletions occurring in Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), respectively.
Methods: We studied 16 patients with HNPP, 4 with CMT1A, and 49 control subjects. We used real-time PCR on the LightCycler system with use of a single capillary tube and no post-PCR handling. A polymorphic fragment of the PMP22 gene was amplified to determine gene dosage for heterozygous samples. The presence of two alleles was used to indicate that no deletion was present in HNPP samples. The ratio obtained between the areas under each allele melting curve of heterozygous CMT1A samples was used to determine whether the sequence was duplicated or normal. Homozygous samples required a competitive gene dosage test, where the ratio between the areas under the melting curves of the target DNA of samples and of the competitor molecule was used to determine whether the target sequence was duplicated, deleted, or normal. Samples from HNPP, CMT1A, and controls were analyzed.
Results: Area ratios were ∼0.6, 1.0, and 2.0 for HNPP, control, and CMT1A samples, respectively. The results agreed with those obtained by Southern blotting and microsatellite analysis in the same samples.
Conclusions: Direct and competitive real-time fluorescent PCR can differentiate one, two, or three copies of the target DNA. The method described is sensitive and accurate for detection of CMT1A duplications and HNPP deletions and is faster and easier than current methods.
Genotyping of Eight Thiopurine Methyltransferase Mutations: Three-Color Multiplexing, “Two-Color/Shared” Anchor, and Fluorescence-quenching Hybridization Probe Assays Based on Thermodynamic Nearest-Neighbor Probe Design
Authors: Schütz Ekkehard , von Ahsen Nicolas , Oellerich Michael 
Published: January 2020

Abstract
Background: The inherited deficiency of thiopurine methyltransferase (TPMT) leads to severe myelosuppression in homozygous patients treated with thiopurine derivatives. One in 300 Caucasians has a homozygous TPMT deficiency with no measurable enzyme activity. To date, eight single-point mutations have been characterized; one group (TPMT*3) accounts for 75% of these.
Methods: We used four LightCyclerTM capillaries to investigate all eight mutations. The three mutations on exon 10 were detected in one capillary with a single “shared” anchor labeled 5′ with Cy5.5 and 3′ with fluorescein. A wild-type-compatible 3′-fluorescein-labeled probe 5′ adjacent to the anchor covered the TPMT*7 mutation, and a 5′-LC-RED640-labeled probe 3′ adjacent to the anchor covered the TPMT*3C mutation. For TPMT*4, the forward amplification primer was internally labeled with a fluorescence quencher [6-carboxytetramethylrhodamine (TAMRA)], and a 3′-fluorescein-labeled antisense wild-type-compatible probe was placed at the mutation. For TPMT*2 and TPMT*3D, located on exon 5, a shared anchor approach was chosen. TPMT*3B and TPMT*6 were detected in multiplex technique and TPMT*5 in conventional manner. Anchors and probes were designed using a thermodynamic nearest-neighbor model.
Results: All mutations were detected using four capillaries with one amplification protocol in 40 min. The concentrations of the shared anchors had to be decreased to reduce their intrinsic fluorescence resonance energy transfer signals. The quenching approach using TAMRA produced a very reproducible upside-down-shaped melting curve in channel 1 of the LightCycler. Deviations from wild type were easily detected because the smallest melting point shift for any possible mutation under the core of the probes was 1.5 °C.
Conclusions: This total TPMT genotyping approach shows that it is possible to use double site-labeled anchor oligonucleotides, that channel 1 of the LightCycler can be used as detection channel for mutations using a quenching design, and that the designed probes enable detection of wild types with 100% likelihood.
Should We Use Carbohydrate-deficient Transferrin instead of γ-Glutamyltransferase for Detecting Problem Drinkers? A Systematic Review and Metaanalysis
Authors: Scouller Kay , Conigrave Katherine M , Macaskill Petra , Irwig Les , Whitfield John B 
Published: January 2020

Abstract
Background: Carbohydrate-deficient transferrin (CDT) has been used as a test for excessive alcohol consumption in research, clinical, and medico-legal settings, but there remain conflicting data on its accuracy, with sensitivities ranging from &lt;20% to 100%. We examined evidence of its benefit over a conventional and less expensive test, γ-glutamyltransferase (GGT), and compared the accuracy of different CDT assay methods.
Methods: We performed a systematic review using summary ROC analysis of 110 studies prior to June 1998 on the use of CDT in the detection of alcohol dependence or hazardous/harmful alcohol use.
Results: We identified several potential sources of bias in studies. In studies examining CDT and GGT in the same subjects, subject characteristics were less likely to influence the comparison. In such paired studies, the original Pharmacia CDT assay was significantly more accurate than GGT, but the modified CDTect assay did not perform as well as the original and was not significantly better than GGT. The accuracy of the AXIS %CDT assay was statistically indistinguishable from modified CDTect. Several CDT assay methods appeared promising, in particular, liquid chromatography (chromatofocusing, HPLC, fast protein liquid chromatography) and isoelectric focusing, but there were insufficient paired studies from which to draw firm conclusions.
Conclusions: In studies published before June 1998, the results obtained with commercially available CDT assays were not significantly better than GGT as markers of excessive alcohol use in paired studies. Further high-quality studies comparing CDTect (modified) and other CDT assays with GGT in the same subjects are needed.
Fetal DNA in Maternal Plasma: Biology and Diagnostic Applications
Authors: Lo Y M Dennis 
Published: January 2020

Abstract
Background: Molecular analysis of plasma DNA during human pregnancy has led to the discovery that maternal plasma contains both fetal and maternal DNA. This valuable source of fetal DNA opens up new possibilities for noninvasive prenatal diagnosis.
Approach: Published data from the last 3 years demonstrating the feasibility and utility of analyzing fetal DNA in maternal plasma are reviewed.
Content: The detection of fetal DNA in maternal plasma is much simpler and more robust than detecting fetal nucleated cells in maternal blood, and does not require prior enrichment. This approach has been shown to have application in the prenatal diagnosis of fetal rhesus D status, sex-linked disorders, and other paternally inherited genetic disorders. Abnormal fetal DNA concentrations in maternal plasma and serum have been found in common pregnancy-associated disorders, including preterm labor and preeclampsia, as well as in pregnancies complicated by fetal trisomy 21. After delivery, fetal DNA is cleared rapidly from maternal plasma, with a half-life in the order of minutes. These clearance kinetics exhibit an important difference from fetal cell clearance, where long-term persistence has been demonstrated.
Summary: It has been only 3 years since fetal DNA was first detected in maternal plasma, and much remains to be learned about the biology of this phenomenon. In addition, additional diagnostic applications beyond those discussed here can be expected in the near future.
Determination of the Designer Drugs 3,4-Methylenedioxymethamphetamine, 3,4-Methylenedioxyethylamphetamine, and 3,4-Methylenedioxyamphetamine with HPLC and Fluorescence Detection in Whole Blood, Serum, Vitreous Humor, and Urine
Authors: Clauwaert Karine M , Van Bocxlaer Jan F , De Letter Els A , Van Calenbergh Serge , Lambert Willy E , De Leenheer André P 
Published: January 2020

Abstract
Background: The popular designer drugs 3,4-methylenedioxymethamphetamine (MDMA) and 3,4-methylenedioxyethylamphetamine (MDEA) can be determined in serum, whole blood, and urine, but also in vitreous humor. The latter matrix is interesting when dealing with decomposed bodies in a toxicological setting.
Methods: After extraction, chromatographic separation was achieved on a narrow-bore C18 column by gradient elution with fluorometric detection; results were confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS).
Results: The method was linear over the range of 2–1000 μg/L for whole blood, serum, and vitreous humor, and 0.1–5 mg/L for urine. Extraction recoveries were &gt;70%, imprecision (CV) was 2.5–19%, and analytical recoveries were 95.5–104.4%. The limit of detection (LOD) and the limit of quantification (LOQ) were 0.8 and 2 μg/L, respectively, for whole blood, serum, and vitreous humor, and 2.5 μg/L and 0.1 mg/L, respectively, for urine. Excellent correlations between the quantitative LC-fluorescence and LC-MS/MS results were obtained. We found the following concentrations in a thanatochemical distribution study in rabbits: in serum, 5.3–685 μg/L for MDMA and from the LOQ to 14.5 μg/L for 3,4-methylenedioxyamphetamine (MDA); in whole blood, 19.7–710 μg/L for MDMA and from the LOQ to 17.8 μg/L for MDA; in vitreous humor, 12.1–97.8 μg/L for MDMA and from the LOQ to 3.86 μg/L for MDA. In routine toxicological urine samples, concentrations ranged from LOQ to 14.62 mg/L for MDA, from LOQ to 157 mg/L for MDMA, and from LOQ to 32.54 mg/L for MDEA.
Conclusions: The HPLC method described is sensitive, specific, and suitable for the determination of MDMA, MDEA, and MDA in whole blood, serum, vitreous humor, and urine.
Diagnosis and Monitoring of Hepatic Injury. I. Performance Characteristics of Laboratory Tests
Authors: Dufour D Robert , Lott John A , Nolte Frederick S , Gretch David R , Koff Raymond S , Seeff Leonard B 
Published: January 2020

AbstractPurpose: To review information on performance characteristics for tests that are commonly used to identify acute and chronic hepatic injury.Data Sources and Study Selection: A MEDLINE search was performed for key words related to hepatic tests, including quality specifications, aminotransferases, alkaline phosphatase, γ-glutamyltransferase, bilirubin, albumin, ammonia, and viral markers. Abstracts were reviewed, and articles discussing performance of laboratory tests were selected for review. Additional articles were selected from the references.Guideline Preparation and Review: Drafts of the guidelines were posted on the Internet, presented at the AACC Annual Meeting in 1999, and reviewed by experts. Areas requiring further amplification or literature review were identified for further analysis. Specific recommendations were made based on analysis of published data and evaluated for strength of evidence and clinical impact. The drafts were also reviewed by the Practice Guidelines Committee of the American Association for the Study of Liver Diseases and approved by the committee and the Association’s Council.Recommendations: Although many specific recommendations are made in the guidelines, some summary recommendations are discussed here. Alanine aminotransferase is the most important test for recognition of acute and chronic hepatic injury. Performance goals should aim for total error of &lt;10% at the upper reference limit to meet clinical needs in monitoring patients with chronic hepatic injury. Laboratories should have age-adjusted reference limits for enzymes in children, and gender-adjusted reference limits for aminotransferases, γ-glutamyltransferase, and total bilirubin in adults. The international normalized ratio should not be the sole method for reporting results of prothrombin time in liver disease; additional research is needed to determine the reporting mechanism that best correlates with functional impairment. Harmonization is needed for alanine aminotransferase activity, and improved standardization for hepatitis C viral RNA measurements.
Diagnosis and Monitoring of Hepatic Injury. II. Recommendations for Use of Laboratory Tests in Screening, Diagnosis, and Monitoring
Authors: Dufour D Robert , Lott John A , Nolte Frederick S , Gretch David R , Koff Raymond S , Seeff Leonard B 
Published: January 2020

AbstractPurpose: To review information on the use of laboratory tests in screening, diagnosis, and monitoring of acute and chronic hepatic injury.Data Sources and Study Selection: A MEDLINE search was performed for key words related to hepatic diseases, including acute hepatitis, chronic hepatitis, alcoholic hepatitis, cirrhosis, hepatocellular carcinoma, and etiologic causes. Abstracts were reviewed, and articles discussing use of laboratory tests selected for review. Additional articles were selected from the references.Guideline Preparation and Review: Drafts of the guidelines were posted on the Internet, presented at the AACC Annual Meeting in 1999, and reviewed by experts. Areas requiring further amplification or literature review were identified for further analysis. Specific recommendations were made based on analysis of published data and evaluated for strength of evidence and clinical impact.Recommendations: Although many specific recommendations are made in the guidelines, only some summary recommendations are listed here. In acute hepatic injury, prothrombin time and, to a lesser extent, total bilirubin are the best indicators of severity of disease. Although ALT is useful for detecting acute and chronic hepatic injury, it is not related to severity of acute hepatic injury and only weakly related to severity of chronic hepatic injury. Specific tests of viral markers should be the initial differential tests in both acute and chronic hepatic injury; when positive, they are also useful for monitoring recovery from hepatitis B and C.