A Data-Analytic Strategy for Protein-Biomarker Discovery: Profiling of High-Dimensional Proteomic Data for Cancer Detection

With recent advances in mass spectrometry techniques, it is now possible to investigate proteins over a wide range of molecular weights in small biological specimens. This advance has generated data-analytic challenges in proteomics, similar to those created by microarray technologies in genetics, namely, discovery of "signature" protein profiles specific to each pathologic state (e.g., normal vs. cancer) or differential profiles between experimental conditions (e.g., treated by a drug of interest vs. untreated) from high-dimensional data. We propose a data analytic strategy for discovering protein biomarkers based on such high-dimensional mass-spectrometry data. A real biomarker-discovery project on prostate cancer is taken as a concrete example throughout the paper: the project aims to identify proteins in serum that distinguish cancer, benign hyperplasia, and normal states of prostate using the Surface Enhanced Laser Desorption/Ionization (SELDI) technology, a recently developed mass spectrometry technique. Our data analytic strategy takes properties of the SELDI mass-spectrometer into account: the SELDI output of a specimen contains about 48,000 (x, y) points where x is the protein mass divided by the number of charges introduced by ionization and y is the protein intensity of the corresponding mass per charge value, x, in that specimen. Given high coefficients of variation and other characteristics of protein intensity measures (y values), we reduce the measures of protein intensities to a set of binary variables that indicate peaks in the y-axis direction in the nearest neighborhoods of each mass per charge point in the x-axis direction. We then account for a shifting (measurement error) problem of the x-axis in SELDI output. After these pre-analysis processing of data, we combine the binary predictors to generate classification rules for cancer, benign hyperplasia, and normal states of prostate. Our approach is to apply the boosting algorithm to select binary predictors and construct a summary classifier. We empirically evaluate sensitivity and specificity of the resulting summary classifiers with a test dataset that is independent from the training dataset used to construct the summary classifiers. The proposed method performed nearly perfectly in distinguishing cancer and benign hyperplasia from normal. In the classification of cancer vs. benign hyperplasia, however, an appreciable proportion of the benign specimens were classified incorrectly as cancer. We discuss practical issues associated with our proposed approach to the analysis of SELDI output and its application in cancer biomarker discovery.

Acute testicular torsion in children: the role of sonography in the diagnostic workup

Acute testicular torsion in children is an emergency and has to be diagnosed urgently. Doppler sonography is increasingly used in imaging the acute scrotum. Nevertheless, in uncertain cases, surgical exploration is required. In this study, we attempted to define the role of Doppler sonography in the diagnostic workup of the acutely painful scrotum. All patients admitted between 1999 and 2005 with acute scrotal pain were included. After clinical assessment, patients were imaged by Doppler sonography with a ''high-end'' instrument. In cases of absent arterial perfusion of the testis in Doppler sonography, surgical exploration was carried out. Patients with unaffected perfusion were followed clinically by ultrasound for up to 2 years. Sixty-one infants and children aged 1 day to 17 years (median: 7.9 years) were included. In 14 cases, sonography demonstrated absent central perfusion, with abnormal parenchymal echogenicity in six. Absence of venous blood flow together with reduction of central arterial perfusion was found in one infant. In these 15 patients, surgical exploration confirmed testicular torsion. Among the other 46 patients, we found four cases with increased testicular perfusion and 27 with increased perfusion of the epididymis. In one infant, a testicular tumour was found sonographically, and orchiectomy confirmed diagnosis of a teratoma. Follow-up examinations of the conservatively treated patients showed good clinical outcome with physiologic central perfusion as well as normal echogenic pattern of both testes. No case of testicular torsion was missed. By means of Doppler sonography, an unequivocal statement regarding testicular perfusion was possible in all cases. The initial Doppler diagnosis was confirmed by operative evaluation and follow-up ultrasound. Testicular torsion can therefore be excluded by correctly performed ultrasound with modern equipment.

Identifying mechanisms of treatment effects and recovery in rehabilitation of schizophrenia: longitudinal analytic methods

The longitudinal dimension of schizophrenia and related severe mental illness is a key component of theoretical models of recovery. However, empirical longitudinal investigations have been underrepresented in the psychopathology of schizophrenia. Similarly, traditional approaches to longitudinal analysis of psychopathological data have had serious limitations. The utilization of modern longitudinal methods is necessary to capture the complexity of biopsychosocial models of treatment and recovery in schizophrenia. The present paper summarizes empirical data from traditional longitudinal research investigating recovery in symptoms, neurocognition, and social functioning. Studies conducted under treatment as usual conditions are compared to psychosocial intervention studies and potential treatment mechanisms of psychosocial interventions are discussed. Investigations of rehabilitation for schizophrenia using the longitudinal analytic strategies of growth curve and time series analysis are demonstrated. The respective advantages and disadvantages of these modern methods are highlighted. Their potential use for future research of treatment effects and recovery in schizophrenia is also discussed.

Biomechanical analysis of torsion and shear forces in lumbar and lumbosacral spine segments of nonchondrodystrophic dogs

OBJECTIVE: To determine stiffness and load-displacement curves as a biomechanical response to applied torsion and shear forces in cadaveric canine lumbar and lumbosacral specimens. STUDY DESIGN: Biomechanical study. ANIMALS: Caudal lumbar and lumbosacral functional spine units (FSU) of nonchondrodystrophic large-breed dogs (n=31) with radiographically normal spines. METHODS: FSU from dogs without musculoskeletal disease were tested in torsion in a custom-built spine loading simulator with 6 degrees of freedom, which uses orthogonally mounted electric motors to apply pure axial rotation. For shear tests, specimens were mounted to a custom-made shear-testing device, driven by a servo hydraulic testing machine. Load-displacement curves were recorded for torsion and shear. RESULTS: Left and right torsion stiffness was not different within each FSU level; however, torsional stiffness of L7-S1 was significantly smaller compared with lumbar FSU (L4-5-L6-7). Ventral/dorsal stiffness was significantly different from lateral stiffness within an individual FSU level for L5-6, L6-7, and L7-S1 but not for L4-5. When the data from 4 tested shear directions from the same specimen were pooled, level L5-6 was significantly stiffer than L7-S1. CONCLUSIONS: Increased range of motion of the lumbosacral joint is reflected by an overall decreased shear and rotational stiffness at the lumbosacral FSU. CLINICAL RELEVANCE: Data from dogs with disc degeneration have to be collected, analyzed, and compared with results from our chondrodystrophic large-breed dogs with radiographically normal spines.

Mechano-Biologie von bovinen Bandscheiben belastet unter Kompression und Torsion

Einleitung: Bandscheiben wirken als Schockabsorbierer in der Wirbelsäule und auf diese wirken meistens komplexe Kräfte, zusammengesetzt aus Kompression, Torsion und Flexion. Die biomechanishe Umgebung einer Bandscheibe ist denn auch geprägt von komplexen Belastungen. Die Forschung über die in vitro Bandscheibenbiologie hat sich bisher um die axiale Kompression konzentriert, wobei die Bedeutung von Torsion und insbesondere dem Zusammenspiel von Kompression und Torsion (="Twisting") praktisch noch nie untersucht wurde an lebenden Organkultur-Explantaten. Wir präsentieren neue mechanobiologische Daten über die Überlebenswahrscheinlichkeit von Bandscheibenzellen kultiviert in einem neuartigen, kompakten Design eines bi-axialen Bioreaktors, um die Bedeutung von Kompression und Torsion zu verstehen. Material/Methode: Bovine Schwanzbandscheiben mit den Endplatten wurden isoliert wie bereits beschrieben [2] und mechanische Belastung wurde angewendet mit einem 2 DoF Bioreaktor für 14 Tage [3]. Die Bandscheiben wurden in verschiedene Belastungsgruppen eingeteilt: 1) Keine Belastung (NL), 2) zyklische Kompression (CC) [8h: axiale Kompression mit 0.6 ± 0.2 MPa, 0.2 Hz], 3) zyklische Torsion (CT) [8h: ± 2° torsion, 0.2 Hz, 0.2 MPa compression], 4) zyklische Kompression und Torsion (CCT) [8h: 0.6 ± 0.2 MPa, 0.2 Hz & ± 2° torsion, 0.2 Hz]. Das Bandscheibengewebe wurde mit LIVE/DEAD gefärbt und miteinem konfokalen Mikroskop visualisiert um die Überlebensrate zu bestimmen. Zell Apoptosis wurde quantifiziert mit einem Caspase 3/7 Kit normalisiert zum totalen Proteingehalt (Bradford). Relative Gen-Expression von wichtigen Genen für die Bandscheibe wurde bestimmt von anabolischen, katabolischen und inflammatorischen Genen mittels real-time RT-PCR. Die Morphologie der Bandscheibenzellen wurde mittels Histologie bestimmt. Ergebnisse: Die Resultate zeigten einen starken Abfall der Zellüberlebenswahrscheinlichkeit im Zentrum der Bandscheiben, dem Nulceus Pulposus (NP), i.e. 10%, in der Gruppe mit CCT. Hingegen die Überlebenswahrscheinlichkeit im Annulus fibrosus (AF) war stabilisiert bei über 60% im NP und im AF in allen anderen Gruppen (Fig 1). Apoptotische Aktivität war statistisch signifikant erhöht in der CC-Gruppe, aber nicht in der CCT-Gruppe, was die Vermutung nahe legt, dass der erhöhte Zellverlust im NP nicht mit Apoptose sondern mit Nekrose erklärt werden kann. Die Gen Expression der anabolischen Gene COL1, COL2 und Biglycan war signifikant erhöht im AF in der CCT Gruppe, ebenfalls waren Remodeling-Gene angeschaltet wie ADAMTS4 und MMP-13 in der CCT Gruppe (Fig. 2). Der Glykosaminoglykan (GAG) Gehalt war generell im AF erhöht in den Gruppen unter mechanischer Belastung, jedoch nicht statistisch signifikant. Schlussfolgerung: Zyklische Torsion kombiniert mit zyklischer Kompression waren in dieser Studie erfolgreich und nach unserem besten Wissen zum ersten Mal an Bandscheibenexplantaten in einer 14- tägigen Organkultur angewendet worden in einem dafür speziell konzipierten Bioreaktor. Die Resultezeigten überraschend einen negativen Effekt bei physiologischen Parametern, was die Belastung (0.6MPa ± 0.2MPa) und die Torsion (± 2°) angeht. Dieser negative Effekt des "Twistings" auf die Überlebenswahrscheinlichkeit der Zellen war jedoch nur regional im NP von Bedeutung, wohingegen im AF keine Effekte zu detektieren waren.

Region Specific Response of Intervertebral Disc Cells to Complex Dynamic Loading: An Organ Culture Study Using a Dynamic Torsion-Compression Bioreactor

The spine is routinely subjected to repetitive complex loading consisting of axial compression, torsion, flexion and extension. Mechanical loading is one of the important causes of spinal diseases, including disc herniation and disc degeneration. It is known that static and dynamic compression can lead to progressive disc degeneration, but little is known about the mechanobiology of the disc subjected to combined dynamic compression and torsion. Therefore, the purpose of this study was to compare the mechanobiology of the intervertebral disc when subjected to combined dynamic compression and axial torsion or pure dynamic compression or axial torsion using organ culture. We applied four different loading modalities 1. control: no loading (NL), 2. cyclic compression (CC), 3. cyclic torsion (CT), and 4. combined cyclic compression and torsion (CCT) on bovine caudal disc explants using our custom made dynamic loading bioreactor for disc organ culture. Loads were applied for 8 h/day and continued for 14 days, all at a physiological magnitude and frequency. Our results provided strong evidence that complex loading induced a stronger degree of disc degeneration compared to one degree of freedom loading. In the CCT group, less than 10\% nucleus pulposus (NP) cells survived the 14 days of loading, while cell viabilities were maintained above 70\% in the NP of all the other three groups and in the annulus fibrosus (AF) of all the groups. Gene expression analysis revealed a strong up-regulation in matrix genes and matrix remodeling genes in the AF of the CCT group. Cell apoptotic activity and glycosaminoglycan content were also quantified but there were no statistically significant differences found. Cell morphology in the NP of the CCT was changed, as shown by histological evaluation. Our results stress the importance of complex loading on the initiation and progression of disc degeneration.