bluuebunny/crossref_metadata_2025_split huggingface dataset:
The STARD Statement for Reporting Studies of Diagnostic Accuracy: Explanation and Elaboration
Authors: Bossuyt Patrick M , Reitsma Johannes B , Bruns David E , Gatsonis Constantine A , Glasziou Paul P , Irwig Les M , Moher David , Rennie Drummond , de Vet Henrica C W , Lijmer Jeroen G 
Published: February 2004

Abstract
The quality of reporting of studies of diagnostic accuracy is less than optimal. Complete and accurate reporting is necessary to enable readers to assess the potential for bias in the study and to evaluate the generalisability of the results. A group of scientists and editors has developed the STARD (Standards for Reporting of Diagnostic Accuracy) statement to improve the reporting the quality of reporting of studies of diagnostic accuracy. The statement consists of a checklist of 25 items and flow diagram that authors can use to ensure that all relevant information is present. This explanatory document aims to facilitate the use, understanding and dissemination of the checklist. The document contains a clarification of the meaning, rationale and optimal use of each item on the checklist, as well as a short summary of the available evidence on bias and applicability. The STARD statement, checklist, flowchart and this explanation and elaboration document should be useful resources to improve reporting of diagnostic accuracy studies. Complete and informative reporting can only lead to better decisions in healthcare.
Human Kallikrein 13: Production and Purification of Recombinant Protein and Monoclonal and Polyclonal Antibodies, and Development of a Sensitive and Specific Immunofluorometric Assay
Authors: Kapadia Carl , Chang Albert , Sotiropoulou Georgia , Yousef George M , Grass Linda , Soosaipillai Antoninus , Xing Xuekun , Howarth David H C , Diamandis Eleftherios P 
Published: February 2004

AbstractBackground: The aims of this study were to develop immunologic reagents and a sensitive and specific immunoassay for human kallikrein 13 (hK13) and to examine the presence of hK13 in human tissues and biological fluids.Methods: Recombinant hK13 protein was produced and purified with use of a Pichia pastoris yeast expression system. The protein was used as an immunogen to generate mouse monoclonal and rabbit polyclonal anti-hK13 antibodies. A sandwich-type immunoassay was developed with these antibodies. The assay was used to measure hK13 in various biological fluids and tissue extracts. Immunohistochemical analysis was also performed on nondiseased and cancerous prostatic sections.Results: The hK13 immunoassay had a detection limit of 0.05 μg/L and showed no cross-reactivity with homologous kallikreins. The assay was linear at 0–20 μg/L, and within-and between-run CVs were &lt;10% (n = 12). hK13 was detected in tissues, including esophagus, tonsil, trachea, lung, cervix, and prostate. hK13 was also found in seminal plasma, amniotic fluid, follicular fluid, ascites of ovarian cancer patients, breast milk, and cytosolic extracts of ovarian cancer tissues. hK13 was immunohistochemically localized in epithelial cells of both nondiseased and cancerous prostate. hK13 appears to be overexpressed in 50% of ovarian cancer tissues compared with healthy ovarian tissues. Recovery of active enzyme added to milk or amniotic fluid was 70–98%, but was &lt;20% when added to serum, suggesting rapid sequestration by protease inhibitors. In fluids and tissue extracts, hK13 was found in its free (∼30 kDa) form.Conclusions: This immunofluorometric assay for hK13 may be used to examine the value of hK13 as a disease biomarker and to further explore the physiologic and pathobiologic role of this enzyme in human disease.
Human Kallikrein 8: Immunoassay Development and Identification in Tissue Extracts and Biological Fluids
Authors: Kishi Tadaaki , Grass Linda , Soosaipillai Antoninus , Shimizu-Okabe Chigusa , Diamandis Eleftherios P 
Published: February 2004

Abstract
Background: The serine protease human kallikrein 8 (hK8; neuropsin), a new member of the human kallikrein family, was predicted to be secreted; thus, it is expected to be present in biological fluids. The aim of this study was to develop a sensitive and specific immunoassay for hK8 (hK8-ELISA) and establish the distribution of hK8 in tissue extracts and biological fluids.
Methods: Recombinant hK8 was produced in a baculovirus expression system and purified with a three-step chromatographic procedure. Purified hK8 was injected into mice and rabbits for antibody generation. A highly specific and sensitive sandwich-type immunoassay (ELISA) was developed using the rabbit and mouse antisera to hK8. The hK8-ELISA was then used to study the distribution of hK8 in various biological fluids and tissue extracts.
Results: The dynamic range of the hK8-ELISA was 0.2 (detection limit) to 20 μg/L, and imprecision (CV) was &lt;10% within this range. This hK8-ELISA was specific for hK8 and had no detectable cross-reactivity with other members of the human kallikrein family. With this assay, hK8 was detected in tissue extracts of esophagus (highest concentrations), skin, testis, tonsil, kidney, breast, and salivary gland and in the biological fluids breast milk (highest concentrations), amniotic fluid, seminal plasma, and serum. Furthermore, in some cancer cell lines, the concentration of hK8 was regulated by steroid hormones.
Conclusions: We report for the first time production of recombinant hK8 protein, generation of antibodies, and development of a highly sensitive and specific immunoassay for quantification of hK8 in tissue extracts and biological fluids. This assay can be used to explore the potential of hK8 as a marker of cancer or other conditions.
Dual-Label Immunoassay for Simultaneous Measurement of Prostate-specific Antigen (PSA)-α1-Antichymotrypsin Complex Together with Free or Total PSA
Authors: Zhu Lei , Leinonen Jari , Zhang Wan-Ming , Finne Patrik , Stenman Ulf-Håkan 
Published: February 2004

Abstract
Background: A major portion of prostate-specific antigen exists in circulation as a complex with α1-antichymotrypsin (PSA-ACT), whereas a minor part is free (fPSA). The proportion of PSA-ACT is increased in prostate cancer (PCa), but immunologic determination of PSA-ACT is hampered by a background produced by nonspecific adsorption of ACT to the solid phase. To reduce the nonspecific interference, we produced an antibody specific for complexed ACT and developed immunofluorometric assays (IFMAs) for simultaneous measurement of fPSA + PSA-ACT (fPSA/PSA-ACT) and PSA-ACT + total PSA (tPSA, PSA-ACT/tPSA).
Methods: Monoclonal antibodies (MAbs) were produced by immunization with PSA-ACT. The dual-label time-resolved IFMAs for fPSA/PSA-ACT and PSA-ACT/tPSA used a capture MAb to tPSA, an Eu3+-labeled MAb to fPSA or complexed ACT, and an Sm3+-labeled MAb to complexed ACT or to tPSA as tracer antibodies. The clinical utility was evaluated using serum samples from individuals with or without PCa with PSA concentrations of 2.0–20.0 μg/L.
Results: One MAb (1D10) showed low cross-reactivity with free ACT and cathepsin G-ACT. A sandwich assay for PSA-ACT with 1D10 as tracer had a detection limit of 0.05 μg/L, and with this assay, PSA-ACT was undetectable in female sera. The detection limit for fPSA was 0.004 μg/L. Determinations of the ratio of fPSA to PSA-ACT and the proportions of fPSA/tPSA and PSA-ACT/tPSA provided the same clinical specificity for PCa and provided significantly better clinical specificity than did tPSA.
Conclusions: Background problems observed in earlier PSA-ACT assays are eliminated by the use of a MAb specific for complexed ACT as a tracer. The same clinical validity can be obtained by determination of fPSA or PSA-ACT together or in combination with tPSA.
Iron Deficiency and Erythropoiesis: New Diagnostic Approaches
Authors: Brugnara Carlo 
Published: February 2004

Abstract
Iron deficiency anemia is one of the most common diseases worldwide. In the majority of cases, the presence of hypochromic microcytic anemia and biochemical evidence for depletion of body iron stores makes the diagnosis relatively straightforward. However, in several clinical conditions, classic biochemical indices such as serum iron, transferrin saturation, and ferritin may not be informative or may not change rapidly enough to reflect transient iron-deficient states (functional iron deficiency), such as the ones that develop during recombinant human erythropoietin (r-HuEPO) therapy. The identification and treatment of iron deficiency in settings such as r-HuEPO therapy, anemia of chronic disease, and iron deficiency of early childhood may be improved by the use of red cell and reticulocyte cellular indices, which reflect in almost real time the development of iron deficiency and the response to iron therapy. In the anemia of chronic disease, measurements of plasma cytokines and iron metabolism regulators such as hepcidin (when available) may be helpful in the characterization of the pathophysiologic basis of this condition. The ratio of serum transferrin receptor (sTfR) to serum ferritin (R/F ratio) has been shown to have excellent performance in estimating body iron stores, but it cannot be used widely because of the lack of standardization for sTfR assays. The combination of hematologic markers such as reticulocyte hemoglobin content, which decreases with iron deficiency, and R/F ratio may allow for a more precise classification of anemias.
Potential Clinical Utility of Serum HER-2/neu Oncoprotein Concentrations in Patients with Breast Cancer
Authors: Carney Walter P , Neumann Rainer , Lipton Allan , Leitzel Kim , Ali Suhail , Price Christopher P 
Published: February 2004

AbstractBackground: The HER-2/neu oncogene and its p185 receptor protein are indicators of a more aggressive form of breast cancer. HER-2/neu status guides Herceptin therapy, specifically directed to the extracellular domain (ECD) of the HER-2/neu oncoprotein. The HER-2/neu ECD is shed from cancer cells into the circulation and is measurable by immunoassay.Methods: We performed a systematic review of the peer-reviewed literature on circulating ECD with respect to prevalence, prognosis, prediction of response to therapy, and monitoring of breast cancer.Results: The prevalence of increased ECD in patients with primary breast cancer varied between 0% and 38% (mean, 18.5%), whereas in metastatic disease the range was from 23% to 80% (mean, 43%). Some women with HER-2/neu-negative tumors by tissue testing develop increased ECD concentrations in metastatic disease. Increased ECD has been correlated with indicators of poor prognosis, e.g., overall survival and disease-free survival. Increased ECD predicts a poor response to hormone therapy and some chemotherapy regimens but can predict improved response to combinations of Herceptin and chemotherapy. Many studies support the value of monitoring ECD during breast cancer progression because serial increases precede the appearance of metastases and longitudinal ECD changes parallel the clinical course of disease.Conclusions: The monitoring of circulating HER-2/neu ECD provides a tool for assessing prognosis, for predicting response to therapy, and for earlier detection of disease progression and timely intervention with appropriate therapy.
Quality Control and Peak Finding for Proteomics Data Collected from Nipple Aspirate Fluid by Surface-Enhanced Laser Desorption and Ionization
Authors: Coombes Kevin R , Fritsche Herbert A , Clarke Charlotte , Chen Jeng-neng , Baggerly Keith A , Morris Jeffrey S , Xiao Lian-chun , Hung Mien-Chie , Kuerer Henry M 
Published: February 2004

Abstract
Background: Recently, researchers have been using mass spectroscopy to study cancer. For use of proteomics spectra in a clinical setting, stringent quality-control procedures will be needed.
Methods: We pooled samples of nipple aspirate fluid from healthy breasts and breasts with cancer to prepare a control sample. Aliquots of the control sample were used on two spots on each of three IMAC ProteinChip® arrays (Ciphergen Biosystems, Inc.) on 4 successive days to generate 24 SELDI spectra. In 36 subsequent experiments, the control sample was applied to two spots of each ProteinChip array, and the resulting spectra were analyzed to determine how closely they agreed with the original 24 spectra.
Results: We describe novel algorithms that (a) locate peaks in unprocessed proteomics spectra and (b) iteratively combine peak detection with baseline correction. These algorithms detected ∼200 peaks per spectrum, 68 of which are detected in all 24 original spectra. The peaks were highly correlated across samples. Moreover, we could explain 80% of the variance, using only six principal components. Using a criterion that rejects a chip if the Mahalanobis distance from both control spectra to the center of the six-dimensional principal component space exceeds the 95% confidence limit threshold, we rejected 5 of the 36 chips.
Conclusions: Mahalanobis distance in principal component space provides a method for assessing the reproducibility of proteomics spectra that is robust, effective, easily computed, and statistically sound.
Optimized Strategy for Rapid Cytochrome P450 2D6 Genotyping by Real-Time Long PCR
Authors: Müller Burkhardt , Zöpf Konstanze , Bachofer Julia , Steimer Werner 
Published: February 2004

Abstract
Background: Because of genetic polymorphisms, cytochrome P450 2D6 (Cyp2D6) activity in humans varies widely and alters the metabolism of commonly used drugs such as antidepressants, neuroleptics, and cardioactive agents. Severe adverse effects or resistance to therapy may result.
Methods: We performed long PCR on the LightCycler™ and used the product as a template for a previously validated multiplex PCR that examines the *3, *4, *6, *7, and *8 alleles of Cyp2D6. We used real-time PCR to identify the *5 null allele and duplication of Cyp2D6 with detection by either hybridization probes or SYBR Green®. The *2 −1584 C/G polymorphism and the *35 allele were identified by PCR with detection by hybridization probes. Products of all PCRs were visualized with gel electrophoresis using a 0.7–1.5% agarose gel and ethidium bromide. Samples containing the *35 allele were analyzed in parallel by digestion with NlaIII, MslI, and BstXI and SmaI. We analyzed samples from volunteers and patients (105 samples for deletion and duplication and 116 samples for preamplification). Of those samples, 59 were from depressive inpatients taking part in a trial not yet published.
Results: Identical genotyping results for both real-time and conventional PCR were obtained and verified by gel electrophoresis. Use of long-PCR methods on the LightCycler enabled comprehensive analysis of all relevant polymorphisms of the Cyp2D6 gene in 1 working day with a hands-on time of ∼3–4 h.
Conclusions: This is the first description of a successful long-PCR application on the LightCycler and the fastest technique for amplification and specific detection of a PCR product of comparable length. The method appears suitable for large clinical and epidemiologic studies.
Rapid Detection of Flt3 Mutations in Acute Myeloid Leukemia Patients by Denaturing HPLC
Authors: Bianchini Michele , Ottaviani Emanuela , Grafone Tiziana , Giannini Barbara , Soverini Simona , Terragna Carolina , Amabile Marilina , Piccaluga Pier Paolo , Malagola Michele , Rondoni Michela , Bosi Costanza , Baccarani Michele , Martinelli Giovanni 
Published: February 2004

Abstract
Background: fms-related tyrosine kinase 3 (Flt3) is the most commonly mutated gene in human acute myeloid leukemia (AML) and has been implicated in its pathogenesis. Because screening of Flt3 in AML patients by PCR followed by gel electrophoresis is time-consuming and fails to detect some very small internal tandem duplications (ITDs), we developed a method for screening of FLT3 receptor mutations with PCR plus denaturing HPLC (D-HPLC).
Methods: Total mRNAs extracted from 34 AML patients were first analyzed for the presence of juxtamembrane length mutations and tyrosine kinase domain point mutations by a conventional method involving PCR amplification, restriction enzyme digestion, and agarose gel electrophoresis (PCR-RED-AGE). Subsequently, the same patient panel was analyzed by D-HPLC, using specifically designed primers and optimized running temperatures for the length and point mutation analysis.
Results: Thirty-four patients were analyzed by PCR-RED-AGE; 9 were positive for known Flt3 mutations: 6 of 34 (18%) for ITDs in exon 14 and 3 of 34 (9%) for point mutations in exon 20. The same patient panel was analyzed by D-HPLC, and additional nucleotide changes were discovered; in total, 14 sequence variations were identified: 7 of 34 (21%) for ITDs in exon 14; 2 of 34 (6%) for point mutations in exon 20; 1 of 34 (3%) for a new point mutation in exon 16; and 4 of 34 (12%) for polymorphisms in exons 13 and 14. Direct sequencing analysis identified nucleotide alterations in each of the “D-HPLC positives” but in none of the “D-HPLC negatives”, yielding a specificity and sensitivity of 100% for D-HPLC-based screening.
Conclusions: This novel D-HPLC-based procedure, which is optimized for identification of new point mutations in the catalytic and regulatory domains of FLT3 receptor, could potentially be useful for studies involving precise genotype determination, which could be critical for selection of innovative AML therapies targeting the FLT3 protein.
Blood Loss from Laboratory Tests
Authors: Wisser Dirk , van Ackern Klaus , Knoll Ernst , Wisser Hermann , Bertsch Thomas 
Published: February 2004

Abstract
Background: Laboratory tests can be an important source of blood loss in hospitals, especially for newborns and patients in intensive care. The aim of this study was to quantify blood loss for laboratory diagnostic tests in a large number of patients in a teaching hospital.
Methods: We estimated blood loss by multiplying the number and volumes of sampling tubes collected from 2654 adult inpatients. We compared the number of tests per patient for all inpatients and intensive care unit patients during the first period and again in the same time period 1 year later when cumulative blood-loss volumes were being reported to physicians and educational information had been given to decrease blood loss from laboratory tests.
Results: For 95% of the patients, blood loss during hospitalization was &lt;196 mL. The largest proportion of the blood samples was used for clinical chemical tests (median, 45%), followed by hematologic (median, 26%) and coagulation (median, 17%) tests. In the surgical and cardiovascular surgical intensive care units, however, blood gas analyses accounted for 19–34% (medians) of the use. For 5% of the patients, all undergoing intensive care, blood loss was &gt;200 mL and for 0.7% was &gt;600 mL during their hospital stay. Such high blood losses were observed in patients with long-term ventilation, coagulation disorders, and repeated surgery. The largest median blood loss was in patients undergoing cardiovascular surgery (median, 201 mL). The mean number of tests was 44 per inpatient before cumulative blood loss was being reported and 46 when it was being reported.
Conclusions: Blood loss from laboratory diagnostic testing is not likely to pose a problem for most hospitalized patients. Blood loss is greater in intensive care patients and after cardiovascular surgical procedures. Reporting of the cumulative individual blood loss did not decrease blood loss for laboratory testing.
Justus Liebig and Animal Chemistry
Authors: Rosenfeld Louis 
Published: February 2004

Abstract
Justus Liebig was one of the individuals making chemistry almost a German monopoly in the 19th century. At Giessen he established the first organic chemistry laboratory and offered a systematic course for training new chemists. His comprehensive survey of plant nutrition changed the nature of scientific agriculture. In a study of animal chemistry, Liebig treated physiologic processes as chemical reactions and inferred the transformations from the chemical properties of the elements and compounds in laboratory reactions. He constructed hypothetical chemical equations derived from the formulae of the participating compounds. Liebig generalized that all organic nitrogenous constituents of the body are derived from plant protein and demonstrated how the application of quantitative methods of organic chemistry can be applied to the investigation of the animal organism. Liebig’s theories were attractive, but his method of converting one substance to another by moving atoms around on paper was speculative because of the lack of knowledge as to how the elements were arranged. His dynamic personality helped win widespread acceptance by many, but others were antagonized by his wishful thinking and speculative excesses. Liebig’s views on catalysis and fermentation brought him into a controversy with Louis Pasteur. Liebig’s Animal Chemistry stimulated an interest in clinical chemistry because it introduced a quantitative method into physiological chemistry. However, the isolated pieces of test results on blood and urine were unconnected and did not fit anywhere. Physicians found that chemistry was not helpful at the bedside and they lost interest in its application.
Familial Frontotemporal Dementia: From Gene Discovery to Clinical Molecular Diagnostics
Authors: Van Deerlin Vivianna M , Gill Lisa H , Farmer Jennifer M , Trojanowski John Q , Lee Virginia M-Y 
Published: February 2004

Abstract
Genetic testing is important for diagnosis and prediction of many diseases. The development of a clinical genetic test can be rapid for common disorders, but for rare genetic disorders this process can take years, if it occurs at all. We review the path from gene discovery to development of a clinical genetic test, using frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17) as an example of a complex, rare genetic condition. An Institutional Review Board-approved multidisciplinary research program was developed to identify patients with familial frontotemporal dementia. Genetic counseling is provided and DNA obtained to identify mutations associated with FTDP-17. In some cases it may be appropriate for individuals to be given the opportunity to learn information from the research study to prevent unnecessary diagnostic studies or the utilization of inappropriate therapies, and to make predictive testing possible. Mutations identified in a research laboratory must be confirmed in a clinical laboratory to be used clinically. To facilitate the development of clinical genetic testing for a rare disorder, it is useful for a research laboratory to partner with a clinical laboratory. Most clinical molecular assays are developed in research laboratories and must be properly validated. We conclude that the transition of genetic testing for rare diseases from the research laboratory to the clinical laboratory requires a validation process that maintains the quality-control elements necessary for genetic testing but is flexible enough to permit testing to be developed for the benefit of patients and families.