bluuebunny/crossref_metadata_2025_split huggingface dataset:
XuvTools: free, fast and reliable stitching of large 3D datasets
Authors: EMMENLAUER M. , RONNEBERGER O. , PONTI A. , SCHWARB P. , GRIFFA A. , FILIPPI A. , NITSCHKE R. , DRIEVER W. , BURKHARDT H. 
Published: January 2009

SummaryCurrent biomedical research increasingly requires imaging large and thick 3D structures at high resolution. Prominent examples are the tracking of fine filaments over long distances in brain slices, or the localization of gene expression or cell migration in whole animals like Caenorhabditis elegans or zebrafish. To obtain both high resolution and a large field of view (FOV), a combination of multiple recordings (‘tiles’) is one of the options. Although hardware solutions exist for fast and reproducible acquisition of multiple 3D tiles, generic software solutions are missing to assemble (‘stitch’) these tiles quickly and accurately.In this paper, we present a framework that achieves fully automated recombination of tiles recorded at arbitrary positions in 3D space, as long as some small overlap between tiles is provided. A fully automated 3D correlation between all tiles is achieved such that no manual interaction or prior knowledge about tile positions is needed. We use (1) phase‐only correlation in a multi‐scale approach to estimate the coarse positions, (2) normalized cross‐correlation of small patches extracted at salient points to obtain the precise matches, (3) find the globally optimal placement for all tiles by a singular value decomposition and (4) accomplish a nearly seamless stitching by a bleaching correction at the tile borders. If the dataset contains multiple channels, all channels are used to obtain the best matches between tiles. For speedup we employ a heuristic method to prune unneeded correlations, and compute all correlations via the fast Fourier transform (FFT), thereby achieving very good runtime performance.We demonstrate the successful application of the proposed framework to a wide range of different datasets from whole zebrafish embryos and C. elegans, mouse and rat brain slices and fine plant hairs (trichome). Further, we compare our stitching results to those of other commercially and freely available software solutions.The algorithms presented are being made available freely as an open source toolset ‘XuvTools’ at the corresponding author's website (http://lmb.informatik.uni‐freiburg.de/people/ronneber), licensed under the GNU General Public License (GPL) v2. Binaries are provided for Linux and Microsoft Windows. The toolset is written in templated C++, such that it can operate on datasets with any bit‐depth. Due to the consequent use of 64bit addressing, stacks of arbitrary size (i.e. larger than 4 GB) can be stitched. The runtime on a standard desktop computer is in the range of a few minutes. A user friendly interface for advanced manual interaction and visualization is also available.
Dental enamel birefringence for a wide mineral content range and for different immersion media's refractive indexes: an improved mathematical interpretation
Authors: SOUSA F.B. , VIANNA S.S. , SANTOS‐MAGALHÃES N.S. 
Published: January 2009

SummaryThe aim of this study is to extend, for a larger range of mineral volume (V1) and different aqueous immersion media, the model for calculating the refractive index of the non‐mineral phase of the human dental enamel proposed by Sousa et al. Published experimental birefringence data of carious and developing human enamel in air and aqueous immersion media with different refractive indexes were interpreted. For 48%≤V1≤ 95%, quantitative estimates on the non‐mineral contents consistent with the values described in the literature were derived. New polynomial relationships of the non‐mineral contents as a function of the mineral content (48%≤V1≤ 95%) are introduced, which allows computing the theoretical mean enamel birefringence in water and air for most of the points of developing, carious and mature enamel with a difference of one order of magnitude in relation to the classical model for the non‐mineral content's refractive index and closer to the experimental data. For enamel birefringence in immersion media other than water and air, a less expressive improvement was obtained. Perspectives for future studies are discussed.
Simple 3D images from fossil and Recent micromaterial using light microscopy
Authors: HAUG J.T. , HAUG C. , MAAS A. , FAYERS S.R. , TREWIN N.H. , WALOSZEK D. 
Published: January 2009

AbstractWe present a technique for extracting 3D information from small‐scale fossil and Recent material and give a summary of other contemporary techniques for 3D methods of investigation. The only hardware needed for the here‐presented technique is a microscope that can perform dark field and/or differential interference contrast with a mounted digital camera and a computer. Serial images are taken while the focus is successively shifted from the uppermost end of the specimen to the lowermost end, resulting in about 200 photographs. The data are then processed almost completely automatically by successive use of three freely available programs. Firstly, the stack of images is aligned by the use of CombineZM, which is used to produce a combined image with a high depth of field. Secondly, the aligned images are cropped and sharp edges extracted with the aid of ImageJ. Thirdly, although ImageJ is also capable of producing 3D representations, we preferred to process the image stack further using osirix as it has the facility to export various formats. One of the interesting export formats is a virtual Quicktime movie file (QTVR), which can be used for documentation, and stereo images can also be produced from this Quicktime VR. This method is easy to apply and can be used for documenting specimens in 3D (at least some aspects) without having to prepare them. Therefore, it is particularly useful as a safe method for documenting limited material, before using methods that may destroy the specimen of interest, or to investigate type material that cannot be treated with any preparatory technique. As light microscopes are available in most labs and free computer programs are easily accessible, this method can be readily applied.
Interface study by dual‐beam FIB‐TEM in a pressureless infiltrated Al(Mg)–Al2O3 interpenetrating composite
Authors: CHANG H. , HIGGINSON R.L. , BINNER J.G.P. 
Published: January 2009

SummaryThis paper considers the microstructures of an Al(Mg)–Al2O3 interpenetrating composite produced by a pressureless infiltration technique. It is well known that the governing principle in pressureless infiltration in Al–Al2O3 system is the wettability between the molten metal and the ceramic phase; however, the infiltration mechanism is still not well understood. The objective of this research was to observe the metal–ceramic interface to understand the infiltration mechanism better. The composite was produced using an Al‐8 wt% Mg alloy and 15% dense alumina foams at 915°C in a flowing N2 atmosphere. After infiltration, the composite was characterized by a series of techniques. Thin‐film samples, specifically produced across the Al(Mg)–Al2O3 interface, were prepared using a dual‐beam focussed ion beam and subsequently observed using transmission electron microscopy. XRD scan analysis shows that Mg3N2 formed in the foam at the molten alloy–ceramic infiltration front, whereas transmission electron microscopy analysis revealed that fine AlN grains formed at the metal–ceramic interface and MgAl2O4 and MgSi2 grains formed at specific points. It is concluded that it is the reactions between Al, Mg and the N2 atmosphere that improve the wettability between molten Al and Al2O3 and induce spontaneous infiltration.
Confocal mosaicing microscopy in skin excisions: a demonstration of rapid surgical pathology
Authors: GAREAU D.S. , PATEL Y.G. , LI Y. , ARANDA I. , HALPERN A.C. , NEHAL K.S. , RAJADHYAKSHA M. 
Published: January 2009

SummaryPrecise micro‐surgical removal of tumour with minimal damage to the surrounding normal tissue requires a series of excisions, each guided by an examination of frozen histology of the previous. An example is Mohs surgery for the removal of basal cell carcinomas (BCCs) in skin. The preparation of frozen histology is labour‐intensive and slow. Confocal microscopy may enable rapid detection of tumours directly in surgical excisions with minimal need for frozen histology. Mosaicing of images enables observation of nuclear and cellular morphology in large areas of surgically excised tissue. In skin, the use of 10–1% acetic acid as a reflectance contrast agent brightens nuclei in 0.5–5 min and enhances nuclear‐to‐dermis contrast and detectability of BCCs. A tissue fixture was engineered for precisely mounting surgical excisions to enable mosaicing of 36 × 36 images to create a field of view of 12 × 12 mm. This large field of view displays the excision at 2× magnification, similar to that routinely used by Mohs surgeons when examining frozen histology. Comparison of mosaics to histology demonstrates detectability of BCCs. Confocal mosaicing presently requires 9 min, instead of 20–45 min per excision for preparing frozen histology, and thus may provide a means for rapid pathology‐at‐the‐bedside to expedite and guide surgery.
An automatic system forin vitrocell migration studies
Authors: DEGERMAN J. , THORLIN T. , FAIJERSON J. , ALTHOFF K. , ERIKSSON P.S. , PUT R.V.D. , GUSTAVSSON T. 
Published: January 2009

SummaryThis paper describes a system forin vitrocell migration analysis. Adult neural stem/progenitor cells are studied using time‐lapse bright‐field microscopy and thereafter stained immunohistochemically to find and distinguish undifferentiated glial progenitor cells and cells having differentiated into type‐1 or type‐2 astrocytes. The cells are automatically segmented and tracked through the time‐lapse sequence. An extension to the Chan‐Vese Level Set segmentation algorithm, including two new terms for specialized growing and pruning, made it possible to resolve clustered cells, and reduced the tracking error by 65%. We used a custom‐built manual correction module to form a ground truth used as a reference for tracked cells that could be identified from the fluorescence staining. On average, the tracks were correct 95% of the time, using our new segmentation. The tracking, or association of segmented cells, was performed using a 2‐state Hidden Markov Model describing the random behaviour of the cells. By re‐estimating the motion model to conform with the segmented data we managed to reduce the number of tracking parameters to essentially only one. Upon characterization of the cell migration by the HMM state occupation function, it was found that glial progenitor cells were moving randomly 2/3 of the time, while the type‐2 astrocytes showed a directed movement 2/3 of the time. This finding indicates possibilities for cell‐type specific identification and cell sorting of live cells based on specific movement patterns in individual cell populations, which would have valuable applications in neurobiological research.
Robust approaches to quantitative ratiometric FRET imaging of CFP/YFP fluorophores under confocal microscopy
Authors: TADROSS M.R. , PARK S.A. , VEERAMANI B. , YUE D.T. 
Published: January 2009

SummaryRatiometric quantification of CFP/YFP FRET enables live‐cell time‐series detection of molecular interactions, without the need for acceptor photobleaching or specialized equipment for determining fluorescence lifetime. Although popular in widefield applications, its implementation on a confocal microscope, which would enable sub‐cellular resolution, has met with limited success. Here, we characterize sources of optical variability (unique to the confocal context) that diminish the accuracy and reproducibility of ratiometric FRET determination and devise practical remedies. Remarkably, we find that the most popular configuration, which pairs an oil objective with a small pinhole aperture, results in intractable variability that could not be adequately corrected through any calibration procedure. By quantitatively comparing several imaging configurations and calibration procedures, we find that significant improvements can be achieved by combining a water objective and increased pinhole aperture with a uniform‐dye calibration procedure. The combination of these methods permitted remarkably consistent quantification of sub‐cellular FRET in live cells. Notably, this methodology can be readily implemented on a standard confocal instrument, and the dye calibration procedure yields a time savings over traditional live‐cell calibration methods. In all, identification of key technical challenges and practical compensating solutions promise robust sub‐cellular ratiometric FRET imaging under confocal microscopy.
Birch pollen allergen Bet v 1 binds to and is transported through conjunctival epithelium in allergic patients
Authors: Renkonen J. , Mattila P. , Lehti S. , Mäkinen J. , Sormunen R. , Tervo T. , Paavonen T. , Renkonen R. 
Published: January 2009

Background:  Previous work in type‐I pollen allergies has mainly focused on lymphocytes and immune responses. Here, we begin to analyse with a systems biology view the differences in conjunctival epithelium obtained from healthy and allergic subjects.Methods:  Transcriptomics analysis combined with light and electron microscopic analysis of birch pollen allergen Bet v 1 located within conjunctival epithelial cells and tissues from birch allergic subjects and healthy controls was carried out.Results:  Bet v 1 pollen allergen bound to conjunctival epithelial cells within minutes after the exposure even during the nonsymptomatic winter season only in allergic, but not in healthy individuals. Light‐ and electron microscopy showed that Bet v 1 was transported through the epithelium within lipid rafts/caveolae and reached mast cells only in allergic patients, but not in healthy individuals. Transcriptomics yielded 22 putative receptors expressed at higher levels in allergic epithelium compared with healthy specimens. A literature search indicated that out of these receptors, eight (i.e. 37%) were associated with lipid rafts/caveolae, which suggested again that Bet v 1 transport is lipid raft/caveola‐dependent.Conclusions:  We show a clear difference in the binding and uptake of Bet v 1 allergen by conjunctival epithelial cells in allergic vs healthy subjects and several putative lipid raft/caveolar receptors were identified, which could mediate or be co‐transported with this entry. The application of discovery driven methodologies on human conjunctival epithelial cells and tissues can provide new hypotheses worth a further analysis to the molecular mechanisms of a complex multifactorial disease such as type‐I birch pollen allergy.
Monitoring of fluid absorption with nitrous oxide during transurethral resection of the prostate
Authors: DROBIN D. , HJELMQVIST H. , PIROS D. , HAHN R. G. 
Published: January 2009

Background: The fluid absorption that occurs during transurethral resection of the prostate (TURP) can be indicated and quantified by the ethanol method. Recently, nitrous oxide (N2O) was tested in animals and volunteers and seemed to be more accurate and safe. The present study compared these two methods in surgical patients.Methods: Eighty‐six TURPs were performed at two hospitals using an irrigating fluid that contained 3% mannitol, 1% ethanol and 0.004% N2O (40 ml/l). The ethanol concentration was measured by end‐expiratory tests every 10 min. The N2O concentration was measured by a flared nasal cannula every second. Fluid absorption was calculated based on a regression equation (ethanol method) from the area under the curve based on the samples where CO2 >median (N2O method).Results: Thirteen patients (15%) absorbed >300 ml of fluid as indicated by the ethanol method. The median volume was 707 ml (range 367–1422). Ethanol yielded higher figures for fluid absorption up to 700–800 ml, whereafter the N2O method indicated that the absorption was larger. Over the entire range, the mean difference between the two methods at the end of any 10‐min period of TURP was only +45 ml, although the 95% limits of agreement were quite separated (−479 to +569 ml).Conclusions: The N2O method does not require forced breath sampling and was successfully apply clinically. However, there was a dose‐dependent difference in result between the ethanol and N2O methods, which markedly separated the limits of agreement for a wider range of fluid absorption events.
Addition of ketamine to propofol for initiation of procedural anesthesia in children reduces propofol consumption and preserves hemodynamic stability
Authors: AOUAD M. T. , MOUSSA A. R. , DAGHER C. M. , MUWAKKIT S. A. , JABBOUR‐KHOURY S. I. , ZBEIDY R. A. , ABBOUD M. R. , KANAZI G. E. 
Published: January 2009

Background: There is no ideal anesthesia protocol to perform short invasive procedures in pediatric oncology. The combination of propofol and ketamine may offer advantages over propofol alone.Methods: In a prospective, randomized, double‐blind study, we analyzed 63 consecutive procedures performed in 47 oncology children. All patients received 1 μg/kg fentanyl, followed by propofol 1 mg/kg in group P (n=33) or propofol 0.5 mg/kg and ketamine 0.5 mg/kg in group PK (n=30) for the initiation of anesthesia. The need for supplementation with propofol and/or fentanyl to maintain an adequate level of anesthesia was recorded. The hemodynamic and respiratory profile, recovery time and the occurrence of side effects were compared.Results: Significantly more children required propofol (100% vs. 83.3%) and fentanyl (75.5% vs. 43.3%) rescue doses, and developed hypotension (63.6% vs. 23.4%) and bradycardia (48.5 vs. 23.4%) in group P compared with group PK, with a comparable incidence of respiratory adverse events and recovery times. However, 40% of children in group PK were agitated following recovery compared with 6% in group P.Conclusions: The combination of propofol and ketamine for invasive procedures in pediatric oncology resulted in reduced propofol and fentanyl consumption and preserved hemodynamic stability, but more children in the combination group recovered with agitation.
Bupivacaine inhibits COX‐2 expression, PGE2, and cytokine production in endotoxin‐activated macrophages
Authors: HUANG Y. H. , TSAI P. S. , HUANG C. J. 
Published: January 2009

Background:Upregulation of cyclooxygenase‐2 (COX‐2) and resultant prostaglandin E2(PGE2) overproduction has been shown to play a crucial role in initiating a systemic inflammatory response during sepsis. Sepsis also induces robust production of pro‐inflammatory cytokines tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β), and IL‐6 as well as anti‐inflammatory cytokine IL‐10. We sought to elucidate the effects of bupivacaine on COX‐2 expression and production of PGE2and cytokines using an endotoxin‐activated murine macrophages model.Methods:Confluent murine macrophages (RAW264.7 cells) were treated with lipopolysaccharide (LPS, 100 ng/ml) or LPS plus bupivacaine (1, 10, or 100 μM). Bupivacaine was added immediately after LPS. After reacting for 18 h, cell cultures were harvested for subsequent analysis.Results:LPS significantly upregulated COX‐2 transcription and PGE2production in macrophages. LPS also significantly increased the production of TNF‐α, IL‐1β, IL‐6 and IL‐10 in macrophages. Bupivacaine significantly inhibited the effects of LPS on COX‐2 transcription and PGE2production in a dose‐dependent manner. In a dose‐dependent manner, bupivacaine also significantly inhibited the effects of LPS on the production of TNF‐α, IL‐1β, and IL‐6. However, bupivacaine exerted no significant effects on LPS‐induced IL‐10 production.Conclusion:Bupivacaine significantly inhibited COX‐2 expression, PGE2and cytokine production in endotoxin‐activated macrophages.
THIS ARTICLE HAS BEEN RETRACTED Interaction between a NMDA receptor antagonist, AP‐5 and an AMPA receptor antagonist, YM 872 in antinociception in the spinal cord
Authors: NISHIYAMA T. 
Published: January 2009

Background:The intrathecalN‐methyl‐d‐aspartate (NMDA) receptor antagonist, AP‐5 and the α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid (AMPA) receptor antagonist, YM 872 showed inhibition on both acute and facilitated nociception in our previous study. The present study was performed to investigate the interaction between intrathecal AP‐5 and YM 872 in antinociception for acute and chronic nociception.Methods:Sprague–Dawley rats with lumbar intrathecal catheters were tested for their thermal tail withdrawal response and for their paw flinches by formalin injection after intrathecal administration of AP‐5 or YM 872. The effects of the combination were tested by an isobolographic analysis using 50% effective dose (ED50). Total fractional dose was calculated as (ED50 dose of AP‐5 in combination)/(ED50 dose of AP‐5 alone)+(ED50 dose of YM 872 in combination)/(ED50 dose of YM 872 alone).Results:Intrathecally administered AP‐5, YM 872, and their combination produced dose‐dependent increases of the tail‐flick latency and decreases in the number of flinches in both phase 1 and 2 of the formalin test. The ED50 values of the combination were significantly lower than the calculated additive values (P<0.01). Total fractional dose value was 0.22 in the tail flick test, 0.12 in the phase 1 and 0.14 in the phase 2 of the formalin test.Conclusion:An NMDA receptor antagonist, AP‐5 and an AMPA receptor antagonist, YM 872 had synergistic antinociceptive effects on both acute thermal and inflammatory induced acute and facilitated nociception.
N‐Methyl‐d‐aspartate receptor antagonist MK‐801 attenuates morphine tolerance and associated glial fibrillary acid protein up‐regulation: a proteomic approach
Authors: WEN Z.‐H. , WU G.‐J. , HSU L.‐C. , CHEN W.‐F. , CHEN J.‐Y. , SHUI H.‐A. , CHOU A.‐K. , WONG C.‐S. 
Published: January 2009

Background: It is well known that long‐term morphine administration results in tolerance, which limits the clinical use of this drug in pain management.Methods: Male Wistar rats were randomly assigned to receive one of four different infusions: morphine [15 μg/h, intrathecal (i.t.)], saline, MK‐801 (5 μg/h, i.t.) plus morphine (15 μg/h, i.t.), or MK‐801 (5 μg/h, i.t.) alone.Results: Morphine infusion induced a maximal antinociceptive effect on day 1 and tolerance on day 3, and the maximal anti‐receptive tolerance was observed on day 5. Co‐infusing MK‐801 with morphine attenuated morphine's anti‐receptive tolerance. Two‐dimensional gel electrophoretic analysis of spinal proteins revealed that eight protein spots were up‐regulated in morphine‐tolerant rats, and that they were significantly inhibited by MK‐801 co‐infusion. Among the up‐regulated proteins, glial fibrillary acid protein (GFAP), a glial‐specific maker, was identified by mass spectrometry. This finding was also confirmed by Western blot analysis.Conclusion: Using proteomic analysis, we identified eight GFAP protein spots that were up‐regulated in the dorsal horn of morphine‐tolerant rat spinal cords. This up‐regulation was partly inhibited by N‐methyl‐d‐aspartate receptor antagonist MK‐801 co‐infusion, which suggests that GFAP protein can be considered to be a pathogenesis marker of morphine tolerance.