Defining infertility: a qualitative interview study of patients and physicians.

PURPOSE: To investigate if infertility patients and physicians apply a traditional biomedical model of disease in their conceptualisation of infertility, examine any contradictions and conflicts in conceptualisations, and examine areas of concordance and discordance between physicians and patients. METHODS: Semi-structured interviews were conducted with 20 infertility patients and 18 infertility physicians between September 2010 and April 2012. Interviews were analysed qualitatively to determine physician and patient conceptualisations of infertility, reactions to the definition of infertility as a disease, and potential benefits and concerns related to application of a disease label to the condition. RESULTS: Most physicians (n = 14/18) and a minority of patients (n = 6/20) were supportive of defining infertility as a disease. Many of the patients who agreed with classifying infertility as a disease expressed that they had not personally defined it as such previously. Physicians (n = 14) and patients (n = 13) described potential benefits of a disease label, including increases in research funding, insurance coverage, and social acceptability. Some patients (n = 10) described potential stigma as a negative consequence. When describing appraisals of infertility, both physicians (n = 7) and patients (n = 8) invoked religious/spiritual concepts. The potential for religious/spiritual appraisal to contribute to stigmatising or de-stigmatising infertility was discussed. CONCLUSION: Our findings contradict the assumption that infertility physicians and patients are fully supportive of defining infertility as a disease. While potential benefits of the disease label were recognised by both groups, caution against potential for stigmatisation and unsolicited invocation of religion/spirituality suggest a more holistic model may be appropriate.

Recombinase Polymerase Amplification Assay for Field Detection of Tomato Bacterial Spot Pathogens.

Bacterial spot of tomato is caused by Xanthomonas gardneri, X. euvesicatoria, X. perforans, and X. vesicatoria. Current diagnostic methods for the pathogens are not in-field assays. Recombinase polymerase amplification (RPA) is ideal for in-field detection assays, because it is an isothermal technique that is rapid and more tolerant to inhibitors compared with polymerase chain reaction. Hence, novel RPA probes and primers were designed to amplify regions of the hrcN gene of X. gardneri, X. euvesicatoria, and X. perforans. The X. gardneri RPA is specific to X. gardneri with a detection limit of 106 CFU/ml and detected X. gardneri in lesions from naturally (n = 6) or artificially (n = 18) infected plants. The X. euvesicatoria RPA detects both X. euvesicatoria and X. perforans with a detection limit of 106 CFU/ml and detected both pathogens in plants artificially infected (n = 36) or naturally infected (n = 85) with either X. euvesicatoria or X. perforans. The X. perforans RPA is specific to X. perforans with a detection limit of 107 CFU/ml. Although the X. perforans RPA assay was unable to detect X. perforans from lesions, the X. euvesicatoria RPA was successfully used in field to detect X. perforans from symptomatic field samples (n = 31). The X. perforans RPA was then used to confirm the pathogen in the laboratory. The X. euvesicatoria and X. gardneri RPA is promising for rapid, real-time in-field detection of bacterial spot and one of the first developed among plant pathogenic bacteria.

Nano-Magnesium Oxide: A Novel Bactericide Against Copper-Tolerant Xanthomonas perforans Causing Tomato Bacterial Spot.

Bacterial spot caused by Xanthomonas perforans causes significant damage on tomato in Florida. Due to the presence of copper (Cu)-tolerant X. perforans strains, Cu bactericides are not effective in disease management. Hence, there is a critical need to find alternatives for Cu. Antibacterial activity of magnesium oxide (Nano-MgO), and other metal oxide nanoparticles, were evaluated against a Cu-tolerant and -sensitive X. perforans strain. In vitro experiments demonstrated high antibacterial activity of Nano-MgO against both strains compared with the commercial Cu. The minimum inhibitory concentration of Nano-MgO is 25 µg/ml and the minimum bactericidal concentration is 100 µg/ml against a Cu-tolerant X. perforans strain after 4 h of exposure. Structural changes in the bacterial membrane following exposure to Nano-MgO treatments compared with the controls were observed using transmission electron microscopy. In two greenhouse experiments with a Cu-tolerant strain, bacterial spot severity was significantly reduced by Nano-MgO at 200 µg/ml compared with Cu-ethylene bis-dithiocarbamate (grower standard), and the untreated control (P = 0.05). In three field experiments, Nano-MgO at 200 µg/ml significantly reduced disease severity with no negative impact on yield compared with the untreated control. Inductively coupled plasma mass spectrometric analysis of the fruit confirmed that Nano-MgO application did not lead to the accumulation of Mg, Cu, Ca, K, Mn, P, and S. This study is the first to demonstrate the potential of Nano-MgO against bacterial spot of tomato.

Pediatric cervical epidural abscess in a 4-year-old patient: a case-based update.

PURPOSE: The purpose of this study was to review a case comprised of a cervical spinal epidural abscess, cervical and thoracic paraspinous edema, and widening of the right thoracic neural foramen secondary to a phlegmon. METHODS: We reviewed the case of a spinal epidural abscess managed medically in a 4-year-old male and performed a review of the literature with 15 other cases that have previously been reported. RESULTS: The current mainstay of treatment is largely variant but generally falls into a laminectomy-based surgical approach or longstanding antibiotics. Our review of the literature concluded that there are currently no clear guidelines established to recommend treatment, and current practice is largely based on the discretion of the pediatric neurosurgeon. CONCLUSIONS: Based on the literature review, and our personal case illustration, we conclude that an antibiotic-based treatment is a valid approach for therapy if initiated promptly in a pediatric patient with no neurological deficit.

Advanced Copper Composites Against Copper-Tolerant Xanthomonas perforans and Tomato Bacterial Spot.

Bacterial spot, caused by Xanthomonas spp., is a widespread and damaging bacterial disease of tomato (Solanum lycopersicum). For disease management, growers rely on copper bactericides, which are often ineffective due to the presence of copper-tolerant Xanthomonas strains. This study evaluated the antibacterial activity of the new copper composites core-shell copper (CS-Cu), multivalent copper (MV-Cu), and fixed quaternary ammonium copper (FQ-Cu) as potential alternatives to commercially available micron-sized copper bactericides for controlling copper-tolerant Xanthomonas perforans. In vitro, metallic copper from CS-Cu and FQ-Cu at 100 µg/ml killed the copper-tolerant X. perforans strain within 1 h of exposure. In contrast, none of the micron-sized copper rates (100 to 1,000 µg/ml) from Kocide 3000 significantly reduced copper-tolerant X. perforans populations after 48 h of exposure compared with the water control (P < 0.05). All copper-based treatments killed the copper-sensitive X. perforans strain within 1 h. Greenhouse studies demonstrated that all copper composites significantly reduced bacterial spot disease severity when compared with copper-mancozeb and water controls (P < 0.05). Although there was no significant impact on yield, copper composites significantly reduced disease severity when compared with water controls, using 80% less metallic copper in comparison with copper-mancozeb in field studies (P < 0.05). This study highlights the discovery that copper composites have the potential to manage copper-tolerant X. perforans and tomato bacterial spot.

[Internet resources for radiologists : a positive selection]. / Internetressourcen für Radiologen : Eine Positivauslese.

In radiology the use of internet resources is part of the daily routine. The critical selection of but not the access to radiologically relevant information is the key topic in internet use. We offer a selection of reviewed internet sources for radiologists. We present sources that offer guidance in decision-making in daily routine as well as internet sources on technical topics in radiology. Case selection and radiological search engines are helpful sites to begin an internet research. Online anatomy sites can be of assistance for interpretation of findings in radiology. Writing and publishing scientific works in radiology requires access to numerous internet services, a positive selection of which are reviewed in the present article. A variety of freeware is available on the internet, some of which may be a substantial benefit to projects in radiology.

Pitfalls in radiation oncology. "Myocardial metastasis" in PET-CT after palliative radiation treatment of the left 5th rib.

BACKGROUND: Positron emission tomography-computed tomography (PET-CT) is a useful diagnostic tool to detect metastases in patients with malignancy. False positives have been reported in cases of inflammation and tissue regeneration. CASE REPORT: Over a period of 2 years, a 32-year-old woman with hepatocellular carcinoma and multiple bone metastases received three treatments of radiation therapy to a bone metastasis in the 5th left rib. Restaging with [18F]fluorodeoxyglucose (FDG) PET-CT showed increased uptake within the cardiac apex highly suspicious for a myocardial metastasis. Because the patient was asymptomatic, additional magnetic resonance imaging (MRI) of the heart was performed demonstrating radiation-associated changes but no evidence for metastases. CONCLUSION: PET-CT is a well-established diagnostic tool in metastatic diseases but its results should always be correlated with the clinical picture of the patient and previous treatments to rule out false positives.

Gene expression is differently affected by pimecrolimus and betamethasone in lesional skin of atopic dermatitis.

BACKGROUND: Topical corticosteroids and calcineurin inhibitors are well-known treatments of atopic dermatitis (AD) but differ in their efficacy and side effects. We recently showed that betamethasone valerate (BM) although clinically more efficient impaired skin barrier repair in contrast to pimecrolimus in AD. OBJECTIVE: This study elucidates the mode of action of topical BM and pimecrolimus cream in AD. METHODS: Lesional AD skin samples after topical treatment with either BM or pimecrolimus were subjected to gene expression profile analysis. RESULTS: Betamethasone valerate resulted in a significant reduction in mRNA levels of genes encoding markers of immune cells and inflammation, dendritic cells, T cells, cytokines, chemokines, and serine proteases, whereas pimecrolimus exerted minor effects only. This corroborates the clinical finding that BM reduces inflammation more effectively than pimecrolimus. Genes encoding molecules important for skin barrier function were differently affected. Both BM and pimecrolimus normalized the expression of filaggrin and loricrin. BM, but not pimecrolimus, significantly reduced the expression of rate-limiting enzymes for lipid synthesis and the expression of involucrin and small proline-rich proteins, which covalently bind ceramides. This may explain the lack of restoration of functional stratum corneum layers observed after BM treatment. CONCLUSION: The gene expression profiles are consistent with our previous findings that corticosteroids may exert a more potent anti-inflammatory effect but may impair the restoration of the skin barrier. Corticosteroids are still the main treatment for severe and acutely exacerbated AD; pimecrolimus may be preferable for long-term treatment and stabilization.

[Magnetic resonance angiography in rheumatology]. / Magnetresonanzangiographie in der Rheumatologie.

The potentials and pitfalls of magnetic resonance imaging (MRI) and magnetic resonance angiography (MRA) in the diagnosis of large vessel vasculitis are summarized in this review article. With the ability to visualize the lumen and vessel walls of large and medium sized arteries, MRI and MRA have great potential to play a unique role in the diagnosis of large vessel vasculitis. This is underlined by the fact that mural inflammatory changes typically involve uptake of contrast agent that can be visualized with MRI. The cranial, intracranial and extracranial involvement pattern can be studied in a combined approach including an MRI examination of the superficial cranial arteries and an MRA examination of the thoracic aorta with its major supra-aortic branches. Typical MRI sequence parameters are given including monophasic MRA and time-resolved MRA protocols at 3 T. The MRI and MRA techniques have the potential to determine the most suitable (inflamed) segment for temporal artery biopsy and to monitor treatment. Initial results of multicenter studies for the diagnostic accuracy of these relatively new methods are expected soon. The MRA technique is recognized as an interesting alternative to invasive catheter angiography for the evaluation of central nervous system (CNS) vasculitis.

Simulated Leaching of Foliar Applied Copper Bactericides on the Soil Microbiome Utilizing Various Beta Diversity Resemblance Measurements.

Copper bactericides are routinely used to control Xanthomonas perforans (XP), causal agent of bacterial spot of tomato. Given the widespread tolerance to copper in XP strains in FL, USA, nanotechnology-based elemental composites have gained interest for their potential applications in agriculture in part due to their enhanced antimicrobial properties and toxicity to copper-tolerant strains. However, little is known about the potential impact of conventional copper bactericides as well as nano-based elemental composites on soil microbial communities, as determined by high-throughput sequencing of the 16S rDNA. We compared the effects of 2 and 200 µg/mL of core-shell (CS), a metallic copper composite, and a conventional copper bactericide + mancozeb (Cu+Man) on the soil microbiome. These treatments were compared to three controls, the microbial profile of the soil prior to application of copper products, a water application, and spiking the soil with a soilborne phytobacterium, Ralstonia solanacearum (RS). The RS treatment was included to determine if downstream analysis could detect the artificial inoculation. Utilizing multiple ß diversity measurements, each emphasizing various tenets of ecology, provided a greater perspective of the effects the treatments had on the microbiome. Analysis of HTS data revealed that the two treatments containing field applied rates of metallic copper, CS 200 and Cu+Man, had the largest impact on the soil microbiome at seven-days posttreatment compared to water. However, we simulated field applied rates of CS 200 entering the soil by treating soil with CS 2 and determined this concentration had a negligible effect on the soil microbiome. IMPORTANCE Nanotechnology-based elemental composites have gained popularity for their potential applications in plant disease management due to their enhanced antimicrobial properties. However, little is known about their potential impact on the environment. Foliar applications of nano metallic composites upon leaching into the soil have the potential to impact soil microbial populations that in turn influence soil health. Utilizing multiple ß diversity measurements, high-throughput sequencing analysis revealed that field applied rates of metallic copper (200 µg/mL) from an advanced copper composite (core-shell [CS]) and a conventional copper bactericide in combination with mancozeb had the largest impact on the soil microbiome compared to water and nontreated control. To simulate leaching from the leaf surface, a lower concentration (2 µg/mL) of CS was also applied to the soil and had a negligible effect on the soil microbiome. Thus, field applied rates of CS may have a minimal effect on soil microbial communities.

The effect of alcohol on radiographic progression in rheumatoid arthritis.

OBJECTIVE: Alcohol consumption reduces the risk of development of rheumatoid arthritis (RA) and significantly attenuates the development of erosive arthritis in animal models. It remains unknown whether alcohol consumption influences joint damage progression in RA. This study was undertaken to compare the rates of radiographic damage progression in alcohol drinkers and nondrinkers in a large prospective cohort of patients with RA. METHODS: All patients in the population-based Swiss Clinical Quality Management in RA registry database with at least 2 sequential radiographs were included. Joint erosions were assessed in 38 joints in the hands and feet using a validated scoring method. The rate of progression of erosions was analyzed using multivariate regression models for longitudinal data and was adjusted for potential confounders. RESULTS: The study included 2,908 patients with RA with a mean of 4 sequential radiographs and 3.9 years of followup. A trend toward reduced radiographic progression existed in drinkers compared with nondrinkers, with a mean rate of erosive progression of 0.99% (95% confidence interval [95% CI] 0.89-1.09) and 1.13% (95% CI 1.01-1.26) at 1 year, respectively. Alcohol consumption displayed a J-shaped dose-response effect, with a more favorable evolution in occasional consumers (P = 0.01) and daily consumers (P = 0.001) as compared with nondrinkers, while heavy drinkers demonstrated worse radiographic evolution (P = 0.0001). We found significant effect modification by sex, with male drinkers displaying significantly less erosive progression compared with male nondrinkers (mean 0.86% [95% CI 0.70-1.03] versus 1.35% [95% CI 1.02-1.67]; P = 0.007). CONCLUSION: Our findings indicate a trend toward reduced radiographic progression in alcohol drinkers compared with nondrinkers, specifically in occasional and daily alcohol consumers. In particular, male patients with RA who consume alcohol demonstrate less radiographic progression than do male nondrinkers.

The role of neoadjuvant and adjuvant treatment for adenocarcinoma of the upper gastrointestinal tract.

Both locally advanced adenocarcinoma of the stomach and gastro-esophageal junction are associated with poor prognosis due to the lack of effective treatment. Recently multimodal treatment consisting of neoadjuvant chemotherapy in combination with radiotherapy is reported to improve survival when compared to surgery alone. Neoadjuvant therapy in these locally advanced tumors allows for early tumor responses and the extent of tumor regression that can be achieved is considered a significant prognostic factor. This, in turn, increases the resectability of these tumors. Also due to the high frequency of lymph node metastasis, patients with locally advanced adenocarcinoma should undergo a D2 lymphadenectomy. Postoperative chemo?radiation and perioperative chemotherapy have been studied in gastric adenocarcinomas and showed a survival benefit. However, the surgical techniques used in these trials are no longer considered to be standard by today's surgical practice. In addition, there are no standard recommendations for adjuvant chemotherapy or chemoradiation after R0 resection and adequate lymph node dissection.

Trimodal therapy in squamous cell carcinoma of the esophagus.

Patients with ESCC (squamous cell carcinoma of the esophagus) are most commonly diagnosed with locally advanced tumor stages. Early metastatic disease and late diagnosis are common reasons responsible for this tumor's poor clinical outcome. The prognosis of esophageal cancer is very poor because patients usually do not have symptoms in early disease stages. Squamous cell carcinoma of the esophagus frequently complicates patients with multiple co-morbidities and these patients often require interdisciplinary diagnosis and treatment procedures. At present time, neoadjuvant radiation therapy and chemotherapy followed by surgery are regarded as the international standard of care. Meta-analyses have confirmed that this approach provides the patient with better local tumor control and an increased overall survival rate. It is recommended that patients with positive tumor response to neoadjuvant therapy and who are poor surgical candidates should consider definitive radiochemotherapy without surgery as a treatment option. In future, EGFR antibodies may also be administered to patients during therapy to improve the current treatment effectiveness. Positron-emission tomography proves to be an early response-imaging tool used to evaluate the effect of the neoadjuvant therapy and could be used as a predictive factor for the survival rate in ESCC. The percentage proportions of residual tumor cells in the histopathological analyses represent a gold standard for evaluating the response rate to radiochemotherapy. In the future, early response evaluation and molecular biological tests could be important diagnostic tools in influencing the treatment decisions of ESCC patients.

Do insulin-like growth factor associated proteins qualify as a tumor marker? Results of a prospective study in 163 cancer patients.

OBJECTIVE: Insulin-like growth factor (IGF)-1, -2 and Insulin like growth factor binding proteins (IGFBP) are involved in the proliferation and differentiation of cells. It has never been evaluated, if the IGF-system can serve as a tumor marker in neoplasms. METHODS: In our prospective study 163 patients with colorectal cancer (22), prostate cancer (21), head and neck tumors (17), lymphomas (20), lung cancer (34) and other entities (49) were analysed for their IGF and IGFBP serum levels at the beginning and the end of radiotherapy and compared to 13 healthy people. Subgroups of patients with local tumor disease versus metastatic disease, primary and recurrent therapy and curative versus palliative therapy were compared. RESULTS: The serum levels of IGF-2 were significantly elevated in patients with prostate and colorectal cancer. However, sensitivity and specificity were only 70%. IGFBP-2 serum levels were elevated in patients with head and neck tumors. Again sensitivity and specificity were only 73%. A difference between local disease and metastatic disease could not be found. A difference between IGF serum levels before and after radiotherapy could not be detected. CONCLUSION: The IGF-system cannot serve as a new tumor marker. The detected differences are very small, sensitivity and specificity are too low. IGF measurement is not useful for the evaluation of the success of radiotherapy in malignancies.

[Diagnosis of focal liver lesions in cirrhotic patients: comparison of contrast-enhanced ultrasound using sulphur hexafluoride (SF6) microbubbles and MRI using Gd-EOB-DTPA]. / Vergleich der kontrastverstärkten Sonografie und der MRT mit Gd-EOB-DTPA zur Diagnostik fokaler Leberläsionen bei Patienten mit Leberzirrhose.

AIM: The diagnostic accuracies of contrast-enhanced sonography and hepatobiliary contrast-enhanced MRI of the liver in evaluating focal liver lesions in patients with liver cirrhosis were compared. MATERIAL AND METHODS: In 33 patients (25 men, 8 women, mean age 63.2 ± 11.2 years) MRI of the liver using Gd-EOB-DTPA (Primovist®, Bayer Schering Pharma, Berlin) was performed. Axial T(2)-weighted, unenhanced T(1)-weighted and enhanced T(1)-weighted scans during arterial, portal venous and late phases were acquired, followed by coronary T(1)-weighted and axial fat-suppressed T(1)-weighted scans 15 minutes post contrast application. In all patients within 4 weeks contrast-enhanced sonography using sulfur hexafluoride microbubbles (SonoVue®, Nycomed, Germany) was obtained. RESULTS: Cirrhosis of the liver was related to viral infection in 45.4% and to alcoholism in 39.4%. All hepatic lesions were confirmed by histologic examination. Sensitivity and specificity of MRI were 90.2% and 83.3%, compared to contrast-enhanced sonography with 92.7 % and 50 %, respectively. Positive and negative predictive values were 97.4% and 55.5 % for MRI and 90.5% and 50% for contrast-enhanced sonography, respectively. DISCUSSION: In this retrospective study MRI using Gd-EOB-DTPA as well as contrast-enhanced sonography using sulfur hexafluoride microbubbles gave excellent results in detecting HCC in patients suffering from liver cirrhosis. Although the specificity was higher for MRI, the accuracy showed no significant difference between these two imaging techniques.

[Prevalence and clinical significance of incidental cardiac findings in non-ECG-gated chest CT scans]. / Prävalenz und klinische Bedeutung inzidenteller Herzbefunde im nicht EKG-getriggerten Thorax-CT.

BACKGROUND: The purpose of this study was to evaluate the prevalence and clinical significance of incidental cardiac findings in non-ECG-gated chest CT. PATIENTS AND METHODS: Non-ECG-gated chest CT examinations of 300 patients were retrospectively analyzed for incidental cardiac findings. Subsequently, these findings were evaluated for their clinical relevance by a cardiologist. RESULTS: A total of 107 out of 300 examined patients had 174 incidental cardiac findings including coronary calcification (90), aortic/mitral valve calcification (42), iatrogenic changes (23), pericardial effusion (6), dilatation of the heart (4), myocardial changes (3), thrombus in the left ventricle (2), constrictive pericarditis (2) and atrial myxoma (1). Of the cardiac findings 51% were described in the written report and in 53 out of the 107 patients the cardiac findings were unknown. Newly detected incidental findings from 8 patients were rated as clinically significant: pericardial effusion (4), constrictive pericarditis (1), thrombus in the left ventricle (1), atrial myxoma (1) and dilatation of the heart (1). CONCLUSION: Incidental cardiac findings are frequent in non-ECG-gated chest CT and may have a high clinical relevance.

[Case-based interactive PACS learning: introduction of a new concept for radiological education of students]. / Fallbasiertes interaktives "PACS-learning": Vorstellung eines neuen studentischen Lehrkonzepts für die Radiologie.

PURPOSE: Medical curricula are currently being reformed in order to establish superordinated learning objectives, including, e.g., diagnostic, therapeutic and preventive competences. This requires a shifting from traditional teaching methods towards interactive and case-based teaching concepts. Conceptions, initial experiences and student evaluations of a novel radiological course Co-operative Learning In Clinical Radiology (CLICR) are presented in this article. MATERIALS AND METHODS: A novel radiological teaching course (CLICR course), which combines different innovative teaching elements, was established and integrated into the medical curriculum. Radiological case vignettes were created for three clinical teaching modules. By using a PC with PACS (Picture Archiving and Communication System) access, web-based databases and the CASUS platform, a problem-oriented, case-based and independent way of learning was supported as an adjunct to the well established radiological courses and lectures. Student evaluations of the novel CLICR course and the radiological block course were compared. RESULTS: Student evaluations of the novel CLICR course were significantly better compared to the conventional radiological block course. Of the participating students 52% gave the highest rating for the novel CLICR course concerning the endpoint overall satisfaction as compared to 3% of students for the conventional block course. The innovative interactive concept of the course and the opportunity to use a web-based database were favorably accepted by the students. Of the students 95% rated the novel course concept as a substantial gain for the medical curriculum and 95% also commented that interactive working with the PACS and a web-based database (82%) promoted learning and understanding. CONCLUSION: Interactive, case-based teaching concepts such as the presented CLICR course are considered by both students and teachers as useful extensions to the radiological course program. These concepts fit well into competence-oriented curricula.

Meta-analyses qualify metzincins and related genes as acute rejection markers in renal transplant patients.

Definition of acute renal allograft rejection (AR) markers remains clinically relevant. Features of T-cell-mediated AR are tubulointerstitial and vascular inflammation associated with excessive extracellular matrix (ECM) remodeling, regulated by metzincins, including matrix metalloproteases (MMP). Our study focused on expression of metzincins (METS), and metzincins and related genes (MARGS) in renal allograft biopsies using four independent microarray data sets. Our own cases included normal histology (N, n = 20), borderline changes (BL, n = 4), AR (n = 10) and AR + IF/TA (n = 7). MARGS enriched in all data sets were further examined on mRNA and/or protein level in additional patients. METS and MARGS differentiated AR from BL, AR + IF/TA and N in a principal component analysis. Their expression changes correlated to Banff t- and i-scores. Two AR classifiers, based on METS (including MMP7, TIMP1), or on MARGS were established in our own and validated in the three additional data sets. Thirteen MARGS were significantly enriched in AR patients of all data sets comprising MMP7, -9, TIMP1, -2, thrombospondin2 (THBS2) and fibrillin1. RT-PCR using microdissected glomeruli/tubuli confirmed MMP7, -9 and THBS2 microarray results; immunohistochemistry showed augmentation of MMP2, -9 and TIMP1 in AR. TIMP1 and THBS2 were enriched in AR patient serum. Therefore, differentially expressed METS and MARGS especially TIMP1, MMP7/-9 represent potential molecular AR markers.

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data.

Batch effects are the systematic non-biological differences between batches (groups) of samples in microarray experiments due to various causes such as differences in sample preparation and hybridization protocols. Previous work focused mainly on the development of methods for effective batch effects removal. However, their impact on cross-batch prediction performance, which is one of the most important goals in microarray-based applications, has not been addressed. This paper uses a broad selection of data sets from the Microarray Quality Control Phase II (MAQC-II) effort, generated on three microarray platforms with different causes of batch effects to assess the efficacy of their removal. Two data sets from cross-tissue and cross-platform experiments are also included. Of the 120 cases studied using Support vector machines (SVM) and K nearest neighbors (KNN) as classifiers and Matthews correlation coefficient (MCC) as performance metric, we find that Ratio-G, Ratio-A, EJLR, mean-centering and standardization methods perform better or equivalent to no batch effect removal in 89, 85, 83, 79 and 75% of the cases, respectively, suggesting that the application of these methods is generally advisable and ratio-based methods are preferred.

Characterization of 1D photonic crystal nanobeam cavities using curved microfiber.

We investigate high-Q, small mode volume photonic crystal nanobeam cavities using a curved, tapered optical microfiber loop. The strength of the coupling between the cavity and the microfiber loop is shown to depend on the contact position on the nanobeam, angle between the nanobeam and the microfiber, and polarization of the light in the fiber. The results are compared to a resonant scattering measurement.