bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of soil frost on soil respiration and its radiocarbon signature in a Norway spruce forest soil
Authors: MUHR JAN , BORKEN WERNER , MATZNER EGBERT 
Published: September 2008

AbstractApart from a general increase of mean annual air temperature, climate models predict a regional increase of the frequency and intensity of soil frost with possibly strong effects on C cycling of soils. In this study, we induced mild soil frost (up to −5 °C in a depth of 5 cm below surface) in a Norway spruce forest soil by removing the natural snow cover in the winter of 2005/2006. Soil frost lasted from January to April 2006 and was detected down to 15 cm depth. Soil frost effectively reduced soil respiration in the snow removal plots in comparison to undisturbed control plots. On an annual basis 6.2 t C ha−1 a−1 were emitted in the control plots compared with 5.1 t C ha−1 a−1 in the snow removal plots. Only 14% of this difference was attributed to reduced soil respiration during the soil frost period itself, whereas 63% of this difference originated from differences during the summer of 2006. Radiocarbon (Δ14C) signature of CO2 revealed a considerable reduction of heterotrophic respiration on the snow removal plots, only partly compensated for by a slight increase of rhizosphere respiration. Similar CO2 concentrations in the uppermost mineral horizons of both treatments indicate that differences between the treatments originated from the organic horizons. Extremely low water contents between June and October of 2006 may have inhibited the recovery of the heterotrophic organisms from the frost period, thereby enhancing the differences between the control and snow removal plots. We conclude that soil frost triggered a change in the composition of the microbial community, leading to an increased sensitivity of heterotrophic respiration to summer drought. A CO2 pulse during thawing, such as described for arable soils several times throughout the literature, with the potential to partly compensate for reduced soil respiration during soil frost, appears to be lacking for this soil. Our results from this experiment indicate that soil frost reduces C emission from forest soils, whereas mild winters may enhance C losses from forest soils.
Telephone helpline for parents of children with congenital anomalies
Authors: Gischler Saskia J. , Mazer Petra , Poley Marten J. , Tibboel Dick , Van Dijk Monique 
Published: September 2008

AbstractTitle.  Telephone helpline for parents of children with congenital anomalies. Aim.  This paper is a report of a study to evaluate how often and for what reason parents of children born with severe anatomical congenital anomalies use a 24‐hour telephone helpline, and to identify differences between callers and non‐callers.Background.  Children born with severe congenital anomalies often remain dependent on medical care and technology after discharge. Adequate medical consultation in the home situation may lower parental burden.Method.  Observational study of telephone contacts from 2000 to 2006 with parents of congenital anomaly patients discharged home after neonatal intensive care admission. Frequency of telephone calls was categorized per type of anomaly. Resulting interventions in terms of consultation and hospital admission were recorded. Finally, costs of personnel needed to provide 24‐hour telephone helpline availability were calculated.Findings.  A total of 670 calls occurred outside office hours, from 34·4% of all parents; 23·7% of these calls concerned feeding problems. Parents of children with oesophageal atresia, urogenital malformation and congenital diaphragmatic hernia called most frequently (44·3–50·6%). Non‐callers were more often first‐time parents, divorced/separated or immigrants. Nurses handled 24·5% of calls by themselves and 20·2% of calls led to emergency room consultations resulting in 4·9% admissions. First contact took place at median age 3 months, last contact at median age 8 months. Total personnel costs amounted to €27,191 per year.Conclusion.  A 24‐hour telephone helpline provides easy access to medical and supportive care for parents of children with congenital anomalies at relatively low cost. Nurses can effectively run this telephone helpline with paediatrician back‐up.
Quantifying cell–matrix adhesion dynamics in living cells using interference reflection microscopy
Authors: HOLT M.R. , CALLE Y. , SUTTON D.H. , CRITCHLEY D.R. , JONES G.E. , DUNN G.A. 
Published: September 2008

SummaryFocal adhesions and podosomes are integrin‐mediated cell‐substratum contacts that can be visualized using interference reflection microscopy (IRM). Here, we have developed automated image‐processing procedures to quantify adhesion turnover from IRM images of live cells. Using time sequences of images, we produce adhesion maps that reveal the spatial changes of adhesions and contain additional information on the time sequence of these changes. Such maps were used to characterize focal adhesion dynamics in mouse embryo fibroblasts lacking one or both alleles of the vinculin gene. Loss of vinculin expression resulted in increased assembly, disassembly and/or in increased translocation of focal adhesions, suggesting that vinculin is important for stabilizing focal adhesions. This method is also useful for studying the rapid dynamics of podosomes as observed in primary mouse dendritic cells.
Mechanical properties of plasma membrane and nuclear envelope measured by scanning probe microscope
Authors: YOKOKAWA M. , TAKEYASU K. , YOSHIMURA S.H. 
Published: September 2008

SummaryAtomic force microscopy has been used to visualize nano‐scale structures of various cellular components and to characterize mechanical properties of biomolecules. In spite of its ability to measure non‐fixed samples in liquid, the application of AFM for living cell manipulation has been hampered by the lack of knowledge of the mechanical properties of living cells. In this study, we successfully combine AFM imaging and force measurement to characterize the mechanical properties of the plasma membrane and the nuclear envelope of living HeLa cells in a culture medium. We examine cantilevers with different physical properties (spring constant, tip angle and length) to find out the one suitable for living cell imaging and manipulation. Our results of elasticity measurement revealed that both the plasma membrane and the nuclear envelope are soft enough to absorb a large deformation by the AFM probe. The penetrations of the plasma membrane and the nuclear envelope were possible when the probe indents the cell membranes far down close to a hard glass surface. These results provide useful information to the development of single‐cell manipulation techniques.
Image matching between experimental and simulated high‐resolution electron micrographs of sapphire on the orientation
Authors: DU K. , RÜHLE M. 
Published: September 2008

SummaryThe effects of imaging parameters have been studied on their roles of the severe mismatches between experimental and simulated high‐resolution transmission electron micrographs of sapphire along the direction. Image simulation and convergent‐beam electron diffraction techniques have been performed on misalignments of the electron beam and the crystal specimen. Based on this study, we have introduced an approach to achieve reliable simulation for experimental images of sapphire on the projection by the use of iterative digital image matching.
Sub‐100‐nanometre resolution in total internal reflection fluorescence microscopy
Authors: BECK M. , ASCHWANDEN M. , STEMMER A. 
Published: September 2008

SummaryCombining total internal reflection fluorescence microscopy with structured illumination allows optical wide‐field imaging with sub‐100‐nanometre resolution. We present a novel objective‐launch set‐up for standing wave illumination that takes advantage of a tunable transmission diffraction grating and transparent phase shifters actuated by electro‐active polymers to control the excitation pattern in three dimensions. Image acquisition is completed in less than 1 s. To reconstruct the extended image spectrum, we apply a new apodization function that results in a lateral resolution of 89 nm for green emission wavelength.
Alignment with sub‐pixel accuracy for images of multi‐modality microscopes using automatic calibration
Authors: TSAI C.‐L. , WARGER II W.C. , LAEVSKY G.S. , DIMARZIO C.A. 
Published: September 2008

SummaryA biological specimen is often imaged with various imaging modalities, and it is crucial that such images are well aligned to best reveal physiological structures and functions of the specimen for in‐depth analyses. In this paper, we present a methodology for automatic calibration of multiple optical imaging modalities within the x–y detector plane using a custom chrome‐on‐glass target and an automatic and accurate registration algorithm. The target contains lines crossing at random angles, and our method of registration is based on the alignment of salient features extracted from the lines within the individual images. Once spatial relationships are found between the various detectors and applied to the resultant images, no further registration is required for all static samples, and the registered images serve as the starting point for registration of dynamic samples, where the remaining misalignment is caused by sample movement. We have validated our algorithm with 40 inter‐modal and 30 intra‐modal image pairs, and the success rates are 95 and 100%, respectively, with sub‐pixel accuracy. This methodology is widely applicable to any multi‐modal microscope that combines a number of imaging modalities on a common platform assuming images of the target can be obtained.
Quantitative tomography of early mouse embryos: laser scanning microscopy and 3D reconstruction
Authors: POGORELOV A.G. , POGORELOVA V.N. 
Published: September 2008

SummaryThe cell volume alteration participates in a wide variety of cellular functions that may interfere with intra‐cellular homeostasis. The most adequate approach of estimation of the volume changes induced by osmotic misbalance, alteration in shape and size due to the action shape forming substances, etc., is the direct measurement of volumetric parameters of embryos. In the given research, the volume magnitude and kinetics of changes in volume and surface area of blastomere and polar bodies of early mouse embryos were determined using three‐dimensional reconstruction of the optical section stack obtained with laser scanning microscope (LSM). The size and surface area were determined for isotonic and anisosmotic conditions. The physiological significance of the findings is discussed.
Advantages and pitfalls of using free‐hand sections of frozen needles for three‐dimensional analysis of mesophyll by stereology and confocal microscopy
Authors: LHOTÁKOVÁ Z. , ALBRECHTOVÁ J. , JANÁČEK J. , KUBÍNOVÁ L. 
Published: September 2008

SummaryThe anatomical structure of mesophyll tissue in the leaf is tightly connected with many physiological processes in plants. One of the most important mesophyll parameters related to photosynthesis is the internal leaf surface area, i.e. the surface area of mesophyll cell walls exposed to intercellular spaces. An efficient design‐based stereological method can be applied for estimation of this parameter, using software‐randomized virtual fakir test probes in stacks of optical sections acquired by a confocal microscope within thick physical free‐hand sections (i.e. acquired using a hand microtome), as we have shown in the case of fresh Norway spruce needles recently. However, for wider practical use in plant ecophysiology, a suitable form of sample storage and other possible technical constraints of this methodology need to be checked. We tested the effect of freezing conifer needles on their anatomical structure as well as the effect of possible deformations due to the cutting of unembedded material by a hand microtome, which can result in distortions of cutting surfaces. In the present study we found a higher proportion of intercellular spaces in mesophyll in regions near to the surface of a physical section, which means that the measurements should be restricted only to the middle region of the optical section series. On the other hand, the proportion of intercellular spaces in mesophyll as well as the internal needle surface density in mesophyll did not show significant difference between fresh and frozen needles; therefore, we conclude that freezing represents a suitable form of storage of sampled material for proposed stereological evaluation.
Stereological estimation for layered structures based on slabs perpendicular to a surface
Authors: LEGLAND D. , DEVAUX M.‐F. , KIÊU K. , BOUCHET B. 
Published: September 2008

SummaryThis paper deals with the characterization of layered structures sampled with respect to a reference surface. A scheme where thick slabs are sampled perpendicular to a curved surface is considered, resulting in a non‐uniform sampling of the structure. We present an estimation procedure based on the Horvitz–Thompson principle. An approximation of the sampling probability is proposed, which depends on the local surface curvatures, on the slab dimensions and on the intensity function of slab anchors. The practical determination of local parameters is detailed for the case of a revolution surface. The procedure is applied to the estimation of surface area density of cell walls in tomato pericarp.
Subcellular imaging of RNA distribution and DNA replication in single mammalian cells with SIMS: the localization of heat shock induced RNA in relation to the distribution of intranuclear bound calcium
Authors: CHANDRA S. 
Published: September 2008

SummaryThe subcellular localization of RNA for understanding transcriptional activity by using RNA precursors, like 5‐bromouridine (BrU), generally requires chemical fixation and staining of cells with monoclonal antibody for imaging BrU‐containing RNA in individual cells. Although effective for RNA localization, the native chemical composition of diffusible ions and molecules is destroyed in this approach and one cannot study their spatial relationship with RNA localization sites in this sample type. This work presents a novel secondary ion mass spectrometry approach in cryogenically prepared cells, which allows the same cell imaging of RNA (and/or replicating DNA) distribution in relation to intracellular chemical composition. The heat shock treatment of HeLa cells was used as a model system because the transcription of heat shock genes is activated during heat shock while other transcriptional activities of the cell are suppressed. The HeLa cells were heat‐shocked for 1 h at 42°C in presence of 100 μM BrU and/or 100 μM IdU (5‐iododeoxyuridine). Following the heat shock treatments, the cells were cryogenically prepared with our sandwich freeze‐fracture method and freeze‐dried prior to secondary ion mass spectrometry analysis. A CAMECA IMS 3f secondary ion mass spectrometry ion microscope (CAMECA, Paris, France) capable of producing elemental (isotopic) distributions with a spatial resolution of 500 nm was used in the study. Secondary ion mass spectrometry analysis of fractured freeze‐dried HeLa cells revealed well‐preserved intracellular 39K and 23Na concentrations in heat‐shocked cells. Both DNA replication and RNA distribution (total RNA) were imaged directly in the same cell by secondary ion mass spectrometry imaging of masses 127I (from IdU) and 81Br (from BrU), respectively. Surprisingly, the nucleus of heat‐shocked cells contained spatially resolved regions with elevated levels of bound calcium (approximately 0.75 mM total calcium instead of 0.50 mM total calcium in the nucleoplasm). These regions spatially correlated with depleted levels of BrU‐RNA in 81Br secondary ion mass spectrometry images. The remainder of intranuclear regions displayed the presence of BrU‐RNA with heterogeneous distribution. These observations indicate that calcium in its bound form may play a fundamental role in processes such as transcription and/or processing and storage of RNA. The shape of intranuclear regions with elevated levels of bound calcium resembled the heat shock induced nuclear bodies in HeLa cells. The analysis of cryogenically prepared frozen freeze‐dried cells provides an ideal sample type for further understanding of the role of bound calcium in transcription of genes under physiological and pathological conditions.
Comparison of three cell fixation methods for high content analysis assays utilizing quantum dots
Authors: WILLIAMS Y. , BYRNE S. , BASHIR M. , DAVIES A. , WHELAN Á. , GUN’KO Y. , KELLEHER D. , VOLKOV Y. 
Published: September 2008

SummarySemiconductor nanoparticles or quantum dots are being increasingly utilized as fluorescent probes in cell biology both in live and fixed cell assays. Quantum dots possess an immense potential for use in multiplexing assays that can be run on high content screening analysers. Depending on the nature of the biological target under investigation, experiments are frequently required on cells retaining an intact cell membrane or also on those that have been fixed and permeabilized to expose intracellular antigens. Fixation of cell lines before or after the addition of quantum dots may affect their localization, emission properties and stability. Using a high content analysis platform we perform a quantitative comparative analysis of three common fixation techniques in two different cell lines exposed to carboxylic acid stabilized CdTe quantum dots.Our study demonstrates that in prefixed and permeabilized cells, quantum dots are readily internalized regardless of cell type, and their intracellular location is primarily determined by the properties of the quantum dots themselves. However, if the fixation procedures are preformed on live cells previously incubated with quantum dots, other important factors have to be considered. The choice of the fixative significantly influences the fluorescent characteristics of the quantum dots. Fixatives, regardless of their chemical nature, negatively affected quantum dots fluorescence intensity. Comparative analysis of gluteraldehyde, methanol and paraformaldehyde demonstrated that 2% paraformaldehyde was the fixative of choice. The presence of protein in the media did not significantly alter the quantum dot fluorescence.This study indicates that multiplexing assays utilizing quantum dots, despite being a cutting edge tool for high content cell imaging, still require careful consideration of the basic steps in biological sample processing.
TEM analysis of centreline sulphide precipitates modified by titanium additions to low carbon steel
Authors: AMINORROAYA S. , DIPPENAAR R. 
Published: September 2008

SummaryElongated inclusions, particularly MnS, contribute significantly to reduced ductility and toughness in hot rolled steel but earlier research indicated that these properties can be improved by titanium additions. Such additions to a steel result in titanium being dissolved in manganese sulphide or MnS being replaced by TiS and/or titanium carbosulphides. In the present study, a steel was designed to decrease alloying element segregation and to evaluate the effect of titanium on centreline sulphide precipitates. Precipitates were identified by using scanning electron microscopy and characterized by the use of transmission electron microscopy following sample preparation by focused ion beam milling techniques. Iron–titanium‐sulphides form in close proximity to MnS precipitates that contain iron. Evidence is provided that an increase in the titanium content of steel leads to an increase in the percentage of titanium contained in the iron sulphides and a decrease in the iron content of MnS inclusions.
Second‐harmonic microscopy of ex vivo porcine corneas
Authors: VOHNSEN B. , ARTAL P. 
Published: September 2008

SummaryThe ex vivo cornea of porcine eyes has been studied with second‐harmonic microscopy with a laboratory‐built system to examine the structure of collagen fibrils at different length scales, as well as the image dependence on polarization and wavelength of the illumination source. We found that collagen fibrils can effectively be visualized with second‐harmonic microscopy, in agreement with previous findings, at different wavelengths of the illumination. The same laser source used for imaging may also be used to induce changes to the corneal tissues that are observable both in the linear and second‐harmonic imaging channels. Such studies are essential first steps towards a future high‐resolution optical characterization technique for simultaneous corneal surgery and wound healing of the human eye.
Performance of a gradient‐based shift estimator in a spatially sparse data environment: tracking the sub‐pixel motion of fluorescent particles
Authors: KIRKPATRICK S.J. , DUNCAN D.D. 
Published: September 2008

SummaryThrough a series of numerical simulations, we investigate the suitability of a relatively new gradient‐based particle‐tracking algorithm for efficiently quantifying sub‐pixel shifts of fluorescently labelled cells or particles from a sequence of video microscopy images. The algorithm excels at estimating sub‐0.5 pixel per frame shifts in both data‐dense (e.g. laser speckle imaging) and data‐sparse (e.g. fluorescence imaging) applications. No upsampling (i.e. interpolation) is required to achieve the sub‐pixel shift resolution, and thus the approach avoids the complexity and potential errors associated with the interpolation process. An efficient matlab sub‐routine is provided for implementing the algorithm.
EM 3D contour maps provide protein assembly at the nanoscale within the neuronal porosome complex
Authors: CHO W.J. , REN G. , JENA B.P. 
Published: September 2008

SummaryThe neuronal porosome complex, the secretory machinery at the plasma membrane of nerve terminals, is a 12–17‐nm cup‐shaped lipoprotein structure possessing a central plug. Since the porosome is a membrane associated, multi‐protein complex measuring >650 kD, it has precluded generation of 3D crystals for x‐ray diffraction studies, nor structural analysis at the atomic level using solution magnetic resonance spectroscopy. These limitations were partially overcome in the current studies, furthering our understanding of the porosome structure. Using atomic force microscopy, electron microscopy and electron density and 3D contour mapping, finally provides at the nanoscale, the structure and assembly of proteins within the neuronal porosome complex. Results from this study demonstrate a set of eight protein units lining the porosome cup, each connected via spoke‐like elements to a central plug region within the structure. The isolation of intact porosomes for near‐atomic resolution using cryo‐electron diffraction measurements, is finally possible.
Mirrored pyramidal wells for simultaneous multiple vantage point microscopy
Authors: SEALE K.T. , REISERER R.S. , MARKOV D.A. , GES I.A. , WRIGHT C. , JANETOPOULOS C. , WIKSWO J.P. 
Published: September 2008

SummaryWe report a novel method for obtaining simultaneous images from multiple vantage points of a microscopic specimen using size‐matched microscopic mirrors created from anisotropically etched silicon. The resulting pyramidal wells enable bright‐field and fluorescent side‐view images, and when combined with z‐sectioning, provide additional information for 3D reconstructions of the specimen. We have demonstrated the 3D localization and tracking over time of the centrosome of a live Dictyostelium discoideum. The simultaneous acquisition of images from multiple perspectives also provides a five‐fold increase in the theoretical collection efficiency of emitted photons, a property which may be useful for low‐light imaging modalities such as bioluminescence, or low abundance surface‐marker labelling.