bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modification of a melanoma discrimination index derived from hyperspectral data: a clinical trial conducted in 2 centers between March 2011 and December 2013
Authors: Nagaoka T. , Kiyohara Y. , Koga H. , Nakamura A. , Saida T. , Sota T. 
Published: August 2014

BackgroundThe morphology of pigmented skin lesions (PSLs) is predominantly a result of varying concentrations and distributions of pigmented molecules such as melanin and hemoglobin. Based on these differences and the fact that their information is contained in cutaneous spectra, a hyperspectral imager (HSI) for pigmented melanoma and a single discrimination index derived from the resultant hyperspectral data are proposed.ObjectiveTo develop and evaluate a new discrimination index for melanomas, compared to the previous index.MethodsA HSI, which is convenient for both patients and clinicians, was newly developed and used in a clinical trial conducted in 2 centers with 80 patients with primary lesions and 17 volunteers between March 2011 and December 2013. There were 24 melanomas and 110 other PSLs. A previously proposed discrimination index was used without modifications. A new index, which emphasized the essential features of melanoma, was proposed, and its performance was examined. For each index, a threshold value was set to minimize the average value of the false positive and false negative fractions. The performances of both indices were compared.ResultsThe sensitivity and specificity of the old index were 75% and 97%, respectively, while those of the new index were 96% and 87%.ConclusionThe new index had a higher sensitivity and adequate specificity, indicating that it is more useful than the old index.
The movement of the non‐cell‐autonomous transcription factor, SHORT‐ROOT relies on the endomembrane system
Authors: Wu Shuang , Gallagher Kimberly L. 
Published: August 2014

SummaryPlant cells are able to convey positional and developmental information between cells through the direct transfer of transcription factors. One well studied example of this is the SHORT‐ROOT (SHR) protein, which moves from the stele into the neighboring ground tissue layer to specify endodermis. While it has been shown that SHR trafficking relies on plasmodesmata (PD), and interaction with the SHR INTERACTING EMBRYONIC LETHAL (SIEL) protein, little information is known about how SHR trafficking is controlled or how SIEL promotes the movement of SHR. Here we show that SHR can move from multiple different cell types in the root. Analysis of subcellular localization indicates that in the cytoplasm of root or leaf cells, SHR localizes to endosomes in a SIEL‐dependent manner. Interference of early and late endosomes disrupts intercellular movement of SHR. Our findings reveal an essential role for the plant endomembrane, independent of secretion, in the intercellular trafficking of SHR.
The effect of immunoadsorption with the Immusorba TR‐350 column on coagulation compared to plasma exchange
Authors: Koessler J. , Kobsar A. , Kuhn S. , Koessler A. , Yilmaz P. , Weinig E. , Putz E. , Boeck M. , Klinker E. 
Published: August 2014

Background and ObjectivesPlasma exchange (PE) and immunoadsorption with the Immusorba TR‐350 column (IA) are used to remove autoantibodies from plasma in acute neurological autoimmune disorders. The impact of IA on coagulation and on low molecular weight heparin (LMWH) levels in comparison with PE was investigated.Patients and MethodsIn five patients with neurological autoimmune disorders, coagulation parameters (global tests, coagulation factors) were measured before and after PE or IA (Part A). In five other patients under anticoagulation with LMWH, anti‐Xa activity and global tests were measured before and after the treatments (Part B).ResultsAfter PE, coagulation factors were significantly reduced by 50–70%. After IA, a distinct reduction was observed for fibrinogen, but not for antithrombin and most of the other coagulation factors. Anti‐Xa activity was reduced after PE (from 0·57 ± 0·10 to 0·13 ± 0·05 IU/ml) and almost unchanged after IA.ConclusionIt is advisable to discontinue or to reduce LMWH doses and to monitor coagulation parameters and anti‐Xa activity after PE or IA to decide about further LMWH dosing.
The constructive membership problem for discrete free subgroups of rank 2 of
Authors: Eick B. , Kirschmer M. , Leedham-Green C. 
Published: August 2014

AbstractWe exhibit a practical algorithm for solving the constructive membership problem for discrete free subgroups of rank $2$ in $\mathrm{PSL}_2(\mathbb{R})$ or $\mathrm{SL}_2(\mathbb{R})$. This algorithm, together with methods for checking whether a two-generator subgroup of $\mathrm{PSL}_2(\mathbb{R})$ or $\mathrm{SL}_2(\mathbb{R})$ is discrete and free, have been implemented in Magma for groups defined over real algebraic number fields.Supplementary materials are available with this article.
A system to detect cerebral aneurysms in multimodality angiographic data sets
Authors: Hentschke Clemens M. , Beuing Oliver , Paukisch Harald , Scherlach Cordula , Skalej Martin , Tönnies Klaus D. 
Published: August 2014

Purpose:The early detection of cerebral aneurysms plays a major role in preventing subarachnoid hemorrhage. The authors present a system to automatically detect cerebral aneurysms in multimodal 3D angiographic data sets. The authors’ system is parametrizable for contrast‐enhanced magnetic resonance angiography (CE‐MRA), time‐of‐flight magnetic resonance angiography (TOF‐MRA), and computed tomography angiography (CTA).Methods:Initial volumes of interest are found by applying a multiscale sphere‐enhancing filter. Several features are combined in a linear discriminant function (LDF) to distinguish between true aneurysms and false positives. The features include shape information, spatial information, and probability information. The LDF can either be parametrized by domain experts or automatically by training. Vessel segmentation is avoided as it could heavily influence the detection algorithm.Results:The authors tested their method with 151 clinical angiographic data sets containing 112 aneurysms. The authors reach a sensitivity of 95% with CE‐MRA data sets at an average false positive rate per data set (FPDS) of 8.2. For TOF‐MRA, we achieve 95% sensitivity at 11.3 FPDS. For CTA, we reach a sensitivity of 95% at 22.8 FPDS. For all modalities, the expert parametrization led to similar or better results than the trained parametrization eliminating the need for training. 93% of aneurysms that were smaller than 5 mm were found. The authors also showed that their algorithm is capable of detecting aneurysms that were previously overlooked by radiologists.Conclusions:The authors present an automatic system to detect cerebral aneurysms in multimodal angiographic data sets. The system proved as a suitable computer‐aided detection tool to help radiologists find cerebral aneurysms.
Image‐guided transorbital procedures with endoscopic video augmentation
Authors: DeLisi Michael P. , Mawn Louise A. , Galloway Robert L. 
Published: August 2014

Purpose:Surgical interventions to the orbital space behind the eyeball are limited to highly invasive procedures due to the confined nature of the region along with the presence of several intricate soft tissue structures. A minimally invasive approach to orbital surgery would enable several therapeutic options, particularly new treatment protocols for optic neuropathies such as glaucoma. The authors have developed an image‐guided system for the purpose of navigating a thin flexible endoscope to a specified target region behind the eyeball. Navigation within the orbit is particularly challenging despite its small volume, as the presence of fat tissue occludes the endoscopic visual field while the surgeon must constantly be aware of optic nerve position. This research investigates the impact of endoscopic video augmentation to targeted image‐guided navigation in a series of anthropomorphic phantom experiments.Methods:A group of 16 surgeons performed a target identification task within the orbits of four skull phantoms. The task consisted of identifying the correct target, indicated by the augmented video and the preoperative imaging frames, out of four possibilities. For each skull, one orbital intervention was performed with video augmentation, while the other was done with the standard image guidance technique, in random order.Results:The authors measured a target identification accuracy of 95.3% and 85.9% for the augmented and standard cases, respectively, with statistically significant improvement in procedure time (Z = −2.044, p = 0.041) and intraoperator mean procedure time (Z = 2.456, p = 0.014) when augmentation was used.Conclusions:Improvements in both target identification accuracy and interventional procedure time suggest that endoscopic video augmentation provides valuable additional orientation and trajectory information in an image‐guided procedure. Utilization of video augmentation in transorbital interventions could further minimize complication risk and enhance surgeon comfort and confidence in the procedure.
A Raman cell based on hollow core photonic crystal fiber for human breath analysis
Authors: Chow Kam Kong , Short Michael , Lam Stephen , McWilliams Annette , Zeng Haishan 
Published: August 2014

Purpose:Breath analysis has a potential prospect to benefit the medical field based on its perceived advantages to become a point‐of‐care, easy to use, and cost‐effective technology. Early studies done by mass spectrometry show that volatile organic compounds from human breath can represent certain disease states of our bodies, such as lung cancer, and revealed the potential of breath analysis. But mass spectrometry is costly and has slow‐turnaround time. The authors’ goal is to develop a more portable and cost effective device based on Raman spectroscopy and hollow core‐photonic crystal fiber (HC‐PCF) for breath analysis.Methods:Raman scattering is a photon‐molecular interaction based on the kinetic modes of an analyte which offers unique fingerprint type signals that allow molecular identification. HC‐PCF is a novel light guide which allows light to be confined in a hollow core and it can be filled with a gaseous sample. Raman signals generated by the gaseous sample (i.e., human breath) can be guided and collected effectively for spectral analysis.Results:A Raman‐cell based on HC‐PCF in the near infrared wavelength range was developed and tested in a single pass forward‐scattering mode for different gaseous samples. Raman spectra were obtained successfully from reference gases (hydrogen, oxygen, carbon dioxide gases), ambient air, and a human breath sample. The calculated minimum detectable concentration of this system was ∼15 parts per million by volume, determined by measuring the carbon dioxide concentration in ambient air via the characteristic Raman peaks at 1286 and 1388 cm−1.Conclusions:The results of this study were compared to a previous study using HC‐PCF to trap industrial gases and backward‐scatter 514.5 nm light from them. The authors found that the method presented in this paper has an advantage to enhance the signal‐to‐noise ratio (SNR). This SNR advantage, coupled with the better transmission of HC‐PCF in the near‐IR than in the visible wavelengths led to an estimated seven times improvement in the detection sensitivity. The authors’ prototype device also demonstrated a 100‐fold improvement over a recently reported detection limit of a reflective capillary fiber‐based Raman cell for breath analysis. Continued development is underway to increase the detection sensitivity further to reach practical clinical applications.
Amorphous In–Ga–Zn–O thin‐film transistor active pixel sensor x‐ray imager for digital breast tomosynthesis
Authors: Zhao Chumin , Kanicki Jerzy 
Published: August 2014

Purpose:The breast cancer detection rate for digital breast tomosynthesis (DBT) is limited by the x‐ray image quality. The limiting Nyquist frequency for current DBT systems is around 5 lp/mm, while the fine image details contained in the high spatial frequency region (>5 lp/mm) are lost. Also today the tomosynthesis patient dose is high (0.67–3.52 mGy). To address current issues, in this paper, for the first time, a high‐resolution low‐dose organic photodetector/amorphous In–Ga–Zn–O thin‐film transistor (a‐IGZO TFT) active pixel sensor (APS) x‐ray imager is proposed for next generation DBT systems.Methods:The indirect x‐ray detector is based on a combination of a novel low‐cost organic photodiode (OPD) and a cesium iodide‐based (CsI:Tl) scintillator. The proposed APS x‐ray imager overcomes the difficulty of weak signal detection, when small pixel size and low exposure conditions are used, by an on‐pixel signal amplification with a significant charge gain. The electrical performance of a‐IGZO TFT APS pixel circuit is investigated by SPICE simulation using modified Rensselaer Polytechnic Institute amorphous silicon (a‐Si:H) TFT model. Finally, the noise, detective quantum efficiency (DQE), and resolvability of the complete system are modeled using the cascaded system formalism.Results:The result demonstrates that a large charge gain of 31–122 is achieved for the proposed high‐mobility (5–20 cm2/V s) amorphous metal‐oxide TFT APS. The charge gain is sufficient to eliminate the TFT thermal noise, flicker noise as well as the external readout circuit noise. Moreover, the low TFT (<10−13 A) and OPD (<10−8 A/cm2) leakage currents can further reduce the APS noise. Cascaded system analysis shows that the proposed APS imager with a 75 μm pixel pitch can effectively resolve the Nyquist frequency of 6.67 lp/mm, which can be further improved to ∼10 lp/mm if the pixel pitch is reduced to 50 μm. Moreover, the detector entrance exposure per projection can be reduced from 1 to 0.3 mR without a significant reduction of DQE. The signal‐to‐noise ratio of the a‐IGZO APS imager under 0.3 mR x‐ray exposure is comparable to that of a‐Si:H passive pixel sensor imager under 1 mR, indicating good image quality under low dose. A threefold reduction of current tomosynthesis dose is expected if proposed technology is combined with an advanced DBT image reconstruction method.Conclusions:The proposed a‐IGZO APS x‐ray imager with a pixel pitch <75 μm is capable to achieve a high spatial frequency (>6.67 lp/mm) and a low dose (<0.4 mGy) in next generation DBT systems.
Decorin Binding Proteins A and B in the Serodiagnosis of Lyme Disease in North America
Authors: Arnaboldi Paul M. , Sambir Mariya , Dattwyler Raymond J. 
Published: August 2014

ABSTRACT

The laboratory diagnosis of Lyme disease is based upon the detection of antibodies generated against
Borrelia burgdorferi
using a two-tier assay, typically consisting of an enzyme-linked immunosorbent assay (ELISA), followed by a Western blot. This system, put into place to address the nonspecificity associated with standalone first-tier assays, is insensitive for diagnosing early infection, when most people seek care. The use of bacterial lysates or whole-protein antigens as first-tier assay targets contributes to nonspecificity due, in part, to the presence of cross-reactive epitopes that are also found in other bacteria. This precludes their use as sensitive standalone assays. The use of peptides containing linear epitopes that are highly specific for
B. burgdorferi
offers a method for reducing this cross-reactivity. In the present study, we mapped the linear epitopes of the prominently expressed
Borrelia
adhesins decorin binding protein A (DbpA) and DbpB. We identified several epitopes in each protein that were highly conserved among North American strains of
B. burgdorferi
, and we screened peptides containing specific epitopes using serum panels from early and late Lyme disease patients. The individual peptides primarily detected IgM but not IgG, while the proteins efficiently detected both IgM and IgG. While no individual peptide demonstrated better utility for antibody detection than its respective whole protein, an assay containing a combination of a DbpA and a DbpB peptide adequately detected both IgM and IgG, accurately identifying 87.5% (84/96) of the early Lyme disease patients and 80.0% (16/20) of the late Lyme disease patients.
Laboratory Detection of Clostridium difficile in Piglets in Australia
Authors: Knight Daniel R. , Squire Michele M. , Riley Thomas V. 
Published: August 2014

ABSTRACT

Clostridium difficile
is a well-known enteric pathogen of humans and the causative agent of high-morbidity enteritis in piglets aged 1 to 7 days.
C. difficile
prevalence in Australian piglets is as high as 70%. The current diagnostic assays have been validated only for human infections, and there are no published studies assessing their performance in Australian piglets. We evaluated the suitability of five assays for detecting
C. difficile
in 157 specimens of piglet feces. The assays included a loop-mediated isothermal amplification (LMIA)-PCR for
tcdA
(illumigene
C. difficile
; Meridian), a real-time PCR for
tcdB
(GeneOhm Cdiff; Becton Dickinson), two-component enzyme immunoassays (EIA) for
C. difficile
glutamate dehydrogenase (GDH) (EIA-GDH) and TcdA/TcdB (EIA-TcdA/TcdB) (C. diff Quik Chek; Alere), and direct culture (DC) (
C. difficile
chromID agar; bioMérieux). The assays for detection of the organism were compared against enrichment culture (EC), and assays for detection of toxins/toxin genes were compared against EC followed by PCR for toxin genes (toxigenic EC [TEC]). The recovery of
C. difficile
by EC was 39.5% (
n
= 62/157), and TEC revealed that 58.1% (
n
= 36/62) of isolates were positive for at least one toxin gene (
tcdA
/
tcdB
). Compared with those for EC/TEC, the sensitivities, specificities, positive predictive values, and negative predictive values were, respectively, as follows: DC, 91.9, 100.0, 100.0, and 95.0%; EIA-GDH, 41.9, 92.6, 78.8, and 71.0%; EIA-TcdA/TcdB, 5.6, 99.2, 66.7, and 77.9%; real-time PCR, 42.9, 96.7, 78.9, and 85.4% and LMIA-PCR, 25.0, 95.9, 64.3, and 81.1%. The performance of the molecular methods was poor, suggesting that the current commercially available assays for diagnosis of
C. difficile
in humans are not suitable for use in piglets.
C. difficile
recovery by the DC provides a cost-effective alternative.
PCR in Diagnosis of Invasive Aspergillosis: a Meta-Analysis of Diagnostic Performance
Authors: Arvanitis Marios , Ziakas Panayiotis D. , Zacharioudakis Ioannis M. , Zervou Fainareti N. , Caliendo Angela M. , Mylonakis Eleftherios 
Published: August 2014

ABSTRACT

Invasive aspergillosis is a difficult-to-diagnose infection with a high mortality rate that affects high-risk groups such as patients with neutropenia and hematologic malignancies. We performed a bivariate meta-analysis of diagnostic data for an
Aspergillus
sp. PCR assay with blood specimens from high-risk hematology patients. We included all studies involving human subjects that assessed the performance of any PCR assay for invasive aspergillosis in whole blood or serum and that used the European Organization for the treatment of Cancer/Mycoses Study Group criteria as a reference standard. Three investigators independently searched the literature for eligible studies and extracted the data. Out of a total of 37 studies, 25 met strict quality criteria and were included in our evidence synthesis. Twenty-five studies with 2,595 patients were analyzed. The pooled diagnostic performance of whole-blood and serum PCR assays was moderate, with a sensitivity and specificity of 84% (95% confidence interval [CI], 75 to 91%) and 76% (95% CI, 65 to 84%), respectively, suggesting that a positive or negative result is unable, on its own, to confirm or exclude a suspected infection. The performance of a PCR assay of serum was not significantly different from that of whole blood. Notably, at least two positive PCR test results were found to have a specificity of 95% and a sensitivity of 64% for invasive infection, achieving a high positive likelihood ratio of 12.8. Importantly, the European
Aspergillus
PCR Initiative (EAPCRI) recommendations improved the performance of the PCR even further when at least two positive specimens were used to define PCR positivity. In conclusion, two positive PCR results should be considered highly indicative of an active
Aspergillus
sp. infection. Use of the EAPCRI recommendations by clinical laboratories can further enhance PCR performance.
Comparative Evaluation of Three Commercial Systems for Detection of High-Risk Human Papillomavirus in Cervical and Vaginal ThinPrep PreservCyt Samples and Correlation with Biopsy Results
Authors: Binnicker M. J. , Pritt B. S. , Duresko B. J. , Espy M. J. , Grys T. E. , Zarka M. A. , Kerr S. E. , Henry M. R. 
Published: August 2014

ABSTRACT

Genital human papillomavirus (HPV) is the etiologic agent of more than 99% of all cervical cancers worldwide, with 14 genotypes being considered oncogenic or “high risk” because of their association with severe dysplasia and cervical carcinoma. Among these 14 high-risk types, HPV-16 and -18 account for approximately 70% of cervical cancers. The aim of this study was to evaluate three FDA-approved HPV nucleic acid-based tests for the ability to predict high-grade cervical intraepithelial neoplasias (CIN2 or worse) in corresponding tissue biopsy specimens. Residual specimens (total
n
= 793, cervical
n
= 743, vaginal
n
= 50) collected in ThinPrep PreservCyt medium with a cytologic result of ≥atypical squamous cells of undetermined significance were tested by the Hybrid Capture 2 (HC2) assay (Qiagen, Gaithersburg, MD), the cobas HPV test (Roche Diagnostics, Indianapolis, IN), and the APTIMA HPV assay (Hologic, San Diego, CA). Genotyping for HPV-16 and HPV-18 was simultaneously performed by the cobas HPV test. Results were compared to cervical or vaginal biopsy findings, when they were available (
n
= 350). Among the 350 patients with corresponding biopsy results, 81 (23.1%) showed ≥CIN2 by histopathology. The ≥CIN2 detection sensitivity was 91.4% by the cobas and APTIMA assays and 97.5% by HC2 assay. The specificities of the cobas, APTIMA, and HC2 assays were 31.2, 42.0, and 27.1%, respectively. When considering only positive HPV-16 and/or HPV-18 genotype results, the cobas test showed a sensitivity and a specificity of 51.9 and 86.6%, respectively. While the HC2, cobas, and APTIMA assays showed similar sensitivities for the detection of ≥CIN2 lesions, the specificities of the three tests varied, with the greatest specificity (86.6%) observed when the HPV-16 and/or HPV-18 genotypes were detected.