bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of an image simulation technique for two computed radiography systems: An application to neonatal imaging
Authors: Smans Kristien , Vandenbroucke Dirk , Pauwels Herman , Struelens Lara , Vanhavere Filip , Bosmans Hilde
Published: April 2010

Purpose:

The purpose of this study is to develop a computer model to simulate the image acquisition for two computed radiography (CR) imaging systems used for neonatal chest imaging: (1) The Agfa ADC Compact, a flying spot reader with powder phosphor image plates (MD 40.0); and (2) the Agfa DX‐S, a line‐scanning CR reader with needle crystal phosphor image plates (HD 5.0). The model was then applied to compare the image quality of the two CR imaging systems.

Methods:

Monte Carlo techniques were used to simulate the transport of primary and scattered x rays in digital x‐ray systems. The output of the Monte Carlo program was an image representing the energy absorbed in the detector material. This image was then modified using physical characteristics of the CR imaging systems to account for the signal intensity variations due to the heel effect along the anode‐cathode axis, the spatial resolution characteristics of the imaging system, and the various sources of image noise. The simulation was performed for typical acquisition parameters of neonatal chest x‐ray examinations. To evaluate the computer model, the authors compared the threshold‐contrast detectability in simulated and experimentally acquired images of a contrast‐detail phantom. Threshold‐contrast curves were computed using a commercially available scoring program.

Results:

The threshold‐contrast curves of the simulated and experimentally acquired images show good agreement; for the two CR systems, 93% of the threshold diameters calculated from the simulated images fell within the confidence intervals of the threshold diameter calculated from the experimentally assessed images. Moreover, the superiority of needle based CR plates for neonatal imaging was confirmed.

Conclusions:

The good agreement between simulated and experimental acquired results indicates that the computer model is accurate.
MR‐based attenuation correction for hybrid PET‐MR brain imaging systems using deformable image registration
Authors: Schreibmann Eduard , Nye Jonathon A. , Schuster David M. , Martin Diego R. , Votaw John , Fox Tim
Published: April 2010

Purpose:

Realization of combined positron emission tomography (PET)—magnetic resonance (MR) scanners has the potential to significantly change healthcare and revolutionize clinical practice as it allows, simultaneously, visualization of molecular imaging and anatomical imaging. PET‐MR, acquired in one imaging study, will likely become the advanced imaging modality of choice for neurological studies, certain forms of cancer, stroke, and the emerging study of stem cell therapy. A challenge toward the implementation and operation of combined PET‐MR scanners is that attenuation corrections maps are not directly available due to space and cost constraints. This article presents a method to obtain accurate patient‐specific PET attenuation coefficients maps in head imaging by warping an atlas computed tomography (CT) data set to the patient‐specific MR data set using a deformable registration model.

Methods:

A multimodality optical flow deformable model has been developed that establishes a voxel‐to‐voxel correspondence between the CT atlas and patient MR images. Once the mapping is established, the atlas is warped with the deformation field obtained by the registration to create a simulated CT image study that matches the patient anatomy, which could be used for attenuation correction.

Results:

To evaluate the accuracy of the deformable‐based attenuation correction, 17 clinical brain tumor cases were studied using acquired MR‐CT images. A simulated CT was compared to the patient's true CT to assess geometrical accuracy of the deformation module as well as voxel‐to‐voxel comparison of Hounsfield units (HUs). In all cases, mapping from the atlas CT to the individual MR was achieved with geometrical accuracy as judged using quantitative inspection tools. The mean distance between simulated and true CT external contour and bony anatomy was 1.26 and 2.15 mm, respectively. In terms of HU unit comparison, the mean voxel‐to‐voxel difference was less than 2 HU for all cases.

Conclusions:

Attenuation correction for hybrid PET‐MR scanners was easily achieved by individualizing an atlas CT to the MR data set using a deformable model without requiring user interaction. The method provided clinical accuracy while eliminating the need for an additional CT scan for PET attenuation correction.
Skeletal dosimetry in a voxel‐based rat phantom for internal exposures to photons and electrons
Authors: Xie Tianwu , Han Dao , Liu Yang , Sun Wenjuan , Liu Qian
Published: April 2010

Purpose:

The skeleton makes a significant contribution to the whole body absorbed dose evaluation of rats, since the bone marrow and bone surface in the skeleton express high radiosensitivity and are considered to be important dose‐limiting tissues. The bone marrow can be categorized as red bone marrow (RBM) and yellow bone marrow (YBM). It is important to investigate the bone marrow in skeletal dosimetry.

Methods:

Cryosectional color images of the skeleton of a 156 g rat were segmented into mineral bone (including cortical bone and trabecular bone), RBM, and YBM. These three tissue types were identified at 40 different bone sites and integrated into a previously developed voxel‐based rat computational phantom. Photon and electron skeletal absorbed fractions were then calculated using the MCNPX Monte Carlo code.

Results:

Absorbed fraction (AF) and specific absorbed fraction (SAF) for mineral bone, RBM, and YBM at the 40 different bone sites were established for monoenergetic photon and electron sources placed in 18 organs and seven bone sites. Discrete photon energy was varied from 0.01 to 5.0 MeV in 21 discrete steps, while 21 discrete electron energies were studied, from 0.1 to 10.0 MeV. The trends and values found were consistent with the results of other researchers [M. G. Stabin, T. E. Peterson, G. E. Holburn, and M. A. Emmons, “Voxel‐based mouse and rat models for internal dose calculations,” J. Nucl. Med. 47, 655–659 (2006)]. ‐factors for the radionuclides , , , , and , located in 18 organs and seven bone sites for the skeleton, were calculated and are provided in detail.

Conclusions:

For internal dose calculations, the AF data reveal that the mineral bone in the rat skeletal system is responsible for significant attenuation of gamma rays, especially at low energies. The photon SAF curves of RBM show that, for photon energies greater than 0.6 MeV, there is an increase in secondary photons emitted from the mineral bone as photon energy increases. The SAF values calculated in this study can also be used to determine the absorbed dose to the skeletal system of rats. The‐factors generated here will be useful in preclinical targeted radiotherapy experiments.
Brushed permanent magnet DC MLC motor operation in an external magnetic field
Authors: Yun J. , St. Aubin J. , Rathee S. , Fallone B. G.
Published: April 2010

Purpose:

Linac‐MR systems for real‐time image‐guided radiotherapy will utilize the multileaf collimators (MLCs) to perform conformal radiotherapy and tumor tracking. The MLCs would be exposed to the external fringe magnetic fields of the linac‐MR hybrid systems. Therefore, an experimental investigation of the effect of an external magnetic field on the brushed permanent magnet DC motors used in some MLC systems was performed.

Methods:

The changes in motor speed and current were measured for varying external magnetic field strengths up to 2000 G generated by an EEV electromagnet. These changes in motor characteristics were measured for three orientations of the motor in the external magnetic field, mimicking changes in motor orientations due to installation and/or collimator rotations. In addition, the functionality of the associated magnetic motor encoder was tested. The tested motors are used with the Varian 120 leaf Millennium MLC (Maxon Motor half leaf and full leaf motors) and the Varian 52 leaf MKII MLC (MicroMo Electronics leaf motor) including a carriage motor (MicroMo Electronics).

Results:

In most cases, the magnetic encoder of the motors failed prior to any damage to the gearbox or the permanent magnet motor itself. This sets an upper limit of the external magnetic field strength on the motor function. The measured limits of the external magnetic fields were found to vary by the motor type. The leaf motor used with a Varian 52 leaf MKII MLC system tolerated up to. The carriage motor tolerated up to field. The motors used with the Varian 120 leaf Millennium MLC system were found to tolerate a maximum of .

Conclusions:

The current Varian MLC system motors can be used for real‐time image‐guided radiotherapy coupled to a linac‐MR system, provided the fringe magnetic fields at their locations are below the determined tolerance levels. With the fringe magnetic fields of linac‐MR systems expected to be larger than the tolerance levels determined, some form of magnetic shielding would be required.
Planning tools for modulated electron radiotherapy
Authors: Surucu Murat , Klein Eric E. , Mamalui‐Hunter Maria , Mansur David B. , Low Daniel A.
Published: April 2010

Purpose:

To develop tools to plan modulated electron radiotherapy (MERT) and to compare the MERT plans to conventional or intensity modulated radiotherapy (IMRT) treatment plans.

Methods:

Monte Carlo dose calculations of electron fields shaped with the inherent photon multileaf collimators (MLCs) were investigated in this study. Treatment plans for four postmastectomy breast cancer patients were generated using MERT. The distances from the patient skin surfaces to the distal planning target volume surfaces were computed along the beam axis direction to determine the physical depth. Electron beam energies were selected to provide target coverage at these depths and energy bins were generated. A custom built MERT treatment planning graphical user interface (MERTgui) was used to shape the electron bins into deliverable electron segments. Monte Carlo dose distribution simulations were performed using the MLC‐defined segments generated from the MERTgui. A custom built superpositiongui was used to combine doses for each segment using relative weights and final MERT treatment plans were compared to the conventional or IMRT treatment plans. In addition, a demonstration of combined MERT and IMRT treatment plans was performed.

Results:

The MERT treatment plans provided acceptable target organ coverage in all cases. Relative to 3D conventional or IMRT treatment plans, the MERT plans predicted lower heart doses in all cases; average of the heart of all plans was reduced from 14.1 to 3.3 Gy. The contralateral breast and contralateral lung doses decreased substantially with MERT planning compared to IMRT (on average, contralateral breast heart was reduced from 8.7 to 0.7 Gy and contralateral lung was reduced from 8.4 to 1.2 Gy with MERT). Ipsilateral lung was lower with MERT than with the conventional plans (44.6 vs 29.2 Gy with MERT), but greater when compared against IMRT treatment plans (25.4 vs 28.9 Gy with MERT). A MERT and IMRT combination plan was generated to benefit from the complementary advantages of MERT and IMRT, resulting in satisfactory target coverage and reduced organ at risk doses.

Conclusions:

MERT tools can facilitate treatment planning and provide plans for treatment of shallow targets such as the postmastectomy chest wall.
Computerized image analysis: Texture‐field orientation method for pectoral muscle identification on MLO‐view mammograms
Authors: Zhou Chuan , Wei Jun , Chan Heang‐Ping , Paramagul Chintana , Hadjiiski Lubomir M. , Sahiner Berkman , Douglas Julie A.
Published: April 2010

Purpose:

To develop a new texture‐field orientation (TFO) method that combinesa priori knowledge, local and global information for the automated identification of pectoral muscle on mammograms.

Methods:

The authors designed a gradient‐based directional kernel (GDK) filter to enhance the linear texture structures, and a gradient‐based texture analysis to extract a texture orientation image that represented the dominant texture orientation at each pixel. The texture orientation image was enhanced by a second GDK filter for ridge point extraction. The extracted ridge points were validated and the ridges that were less likely to lie on the pectoral boundary were removed automatically. A shortest‐path finding method was used to generate a probability image that represented the likelihood that each remaining ridge point lay on the true pectoral boundary. Finally, the pectoral boundary was tracked by searching for the ridge points with the highest probability lying on the pectoral boundary. A data set of 130 MLO‐view digitized film mammograms (DFMs) from 65 patients was used to train the TFO algorithm. An independent data set of 637 MLO‐view DFMs from 562 patients was used to evaluate its performance. Another independent data set of 92 MLO‐view full field digital mammograms (FFDMs) from 92 patients was used to assess the adaptability of the TFO algorithm to FFDMs. The pectoral boundary detection accuracy of the TFO method was quantified by comparison with an experienced radiologist's manually drawn pectoral boundary using three performance metrics: The percent overlap area (POA), the Hausdorff distance (Hdist), and the average distance (AvgDist).

Results:

The mean and standard deviation of POA, Hdist, and AvgDist were, , and , respectively. For the POA measure, 91.5%, 97.3%, and 98.9% of the computer detected pectoral muscles had POA larger than 90%, 85%, and 80%, respectively. For the distance measures, 85.4% and 98.0% of the computer detected pectoral boundaries had Hdist within 5 and 10 mm, respectively, and 99.4% of computer detected pectoral muscle boundaries had AvgDist within 5 mm from the radiologist's manually drawn boundaries.

Conclusions:

The pectoral muscle on DFMs can be detected accurately by the automated TFO method. The preliminary study of applying the same pectoral muscle identification algorithm to FFDMs without retraining demonstrates that the TFO method is reasonably robust against the differences in the image properties between the digitized and digital mammograms.
Global Biodiversity: Indicators of Recent Declines
Authors: Butchart Stuart H. M. , Walpole Matt , Collen Ben , van Strien Arco , Scharlemann Jörn P. W. , Almond Rosamunde E. A. , Baillie Jonathan E. M. , Bomhard Bastian , Brown Claire , Bruno John , Carpenter Kent E. , Carr Geneviève M. , Chanson Janice , Chenery Anna M. , Csirke Jorge , Davidson Nick C. , Dentener Frank , Foster Matt , Galli Alessandro , Galloway James N. , Genovesi Piero , Gregory Richard D. , Hockings Marc , Kapos Valerie , Lamarque Jean-Francois , Leverington Fiona , Loh Jonathan , McGeoch Melodie A. , McRae Louise , Minasyan Anahit , Morcillo Monica Hernández , Oldfield Thomasina E. E. , Pauly Daniel , Quader Suhel , Revenga Carmen , Sauer John R. , Skolnik Benjamin , Spear Dian , Stanwell-Smith Damon , Stuart Simon N. , Symes Andy , Tierney Megan , Tyrrell Tristan D. , Vié Jean-Christophe , Watson Reg
Published: April 2010

Global Biodiversity Target Missed

In 2002, the Convention on Biological Diversity (CBD) committed to a significant reduction in the rate of biodiversity loss by 2010. There has been widespread conjecture that this target has not been met.

Butchart
et al.

(p.
1164
, published online 29 April) analyzed over 30 indicators developed within the CBD's framework. These indicators include the condition or state of biodiversity (e.g., species numbers, population sizes), the pressures on biodiversity (e.g., deforestation), and the responses to maintain biodiversity (e.g., protected areas) and were assessed between about 1970 and 2005. Taken together, the results confirm that we have indeed failed to meet the 2010 targets.
Endosomal Chloride-Proton Exchange Rather Than Chloride Conductance Is Crucial for Renal Endocytosis
Authors: Novarino Gaia , Weinert Stefanie , Rickheit Gesa , Jentsch Thomas J.
Published: April 2010

Chloride Balancing Act

The ionic composition of the cytosol and intracellular organelles must be regulated in the face of ongoing membrane traffic into and out of the cell. Now, two papers address the consequences of a change in the transport phenotype of an intracellular Cl
−
transport protein from a coupled exchanger to a passive Cl
−
conductor (see the Perspective by

Smith and Schwappach

).

Novarino
et al.

(p.
1398
, published online 29 April) investigated the consequence of a knock-in of the uncoupled ClC-5 transporter into mouse. The knock-out mouse of this endosomal kidney transporter has a severe endocytic phenotype believed to be due to a defect in vesicular acidification. The current study shows a similarly impaired endocytic phenotype for the uncoupled mutant, but the acidification of endosomes was unaffected.

Weinert
et al.

(p.
1401
, published online 29 April) used a similar strategy to investigate the consequence of the equivalent mutation in the lysosomal transporter ClC-7, which is highly expressed in the resorption lacuna of osteoclasts and whose knock-out in mice produces lysosomal storage disease and severe osteopetrosis. A similar (though less severe) phenotype was observed in the knock-in mice containing the uncoupled ClC-7, indicating that coupled transport plays a critical role in lysosomes.
Self-Assembled M
24
L
48
Polyhedra and Their Sharp Structural Switch upon Subtle Ligand Variation
Authors: Sun Qing-Fu , Iwasa Junji , Ogawa Daichi , Ishido Yoshitaka , Sato Sota , Ozeki Tomoji , Sei Yoshihisa , Yamaguchi Kentaro , Fujita Makoto
Published: April 2010

Two Molecular Spheres

Viruses form highly symmetrical coat structures, capsids, through the assembly of multiple lower-symmetry protein precursors. Recently, chemists have sought to emulate this process on a smaller scale, relying on the assembly of organic molecular struts and metal ions, rather than proteins.

Sun
et al.

(p.
1144
, published online 29 April; see the Perspective by

Stefankiewicz and Sanders

) now demonstrate that a mixture of palladium ions and V-shaped bridging ligands can self-assemble into a hollow, nearly spherical polyhedron with 24 vertices and a central diameter of 4 nanometers. The assembly process was highly sensitive to the ligand angle; a subtle average decrease generated instead a smaller 12-vertex product.
Eruption-related lahars and sedimentation response downstream of Mount Hood
Authors: Pierson Thomas C. , Scott William E. , Vallance James W. , Pringle Patrick T.
Published: April 2010

Late Holocene dome-building eruptions at Mount Hood during the Timberline and Old Maid eruptive periods resulted in numerous dome-collapse pyroclastic flows and lahars that moved large volumes of volcaniclastic sediment into temporary storage in headwater canyons of the Sandy River. During each eruptive period, accelerated sediment loading to the river through erosion and remobilization of volcanic fragmental debris resulted in very high sediment-transport rates in the Sandy River during rain- and snowmelt-induced floods. Large sediment loads in excess of the river's transport capacity led to channel aggradation, channel widening, and change to a braided channel form in the lowermost reach of the river, between 61 and 87 km downstream from the volcano. The post-eruption sediment load moved as a broad bed-material wave, which in the case of the Old Maid eruption took ~2 decades to crest 83 km downstream. Maximum post-eruption aggradation levels of at least 28 and 23 m were achieved in response to Timberline and Old Maid eruptions. In each case, downstream aggradation cycles were initiated by lahars, but the bulk of the aggradation was achieved by fluvial sediment transport and deposition. When the high rates of sediment supply began to diminish, the river degraded, incising the channel fills and forming progressively lower sets of degradational terraces. A variety of debris-flow, hyperconcentrated-flow, and fluvial (upper and lower flow regime) deposits record the downstream passage of the sediment waves that were initiated by these eruptions. The deposits also presage a hazard that may be faced by communities along the Sandy River when volcanic activity at Mount Hood resumes.
Cataclysms and controversy—Aspects of the geomorphology of the Columbia River Gorge
Authors: O’Connor Jim E. , Burns Scott F.
Published: April 2010

Landslides and floods of lava and water tremendously affected the Columbia River during its long history of transecting the Cascade Volcanic Arc. This field trip touches on aspects of the resulting geology of the scenic Columbia River Gorge, including the river-blocking Bonneville landslide of ~550 years ago and the great late-Pleistocene Missoula floods. Not only did these events create great landscapes, but they inspired great geologists. Mid-nineteenth century observations of the Columbia River and Pacific Northwest by James Dwight Dana and John Strong Newberry helped germinate the “school of fluvial” erosion later expanded upon by the southwestern United States topographic and geologic surveys. Later work on features related to the Missoula floods framed the career of J Harlen Bretz in one of the great geologic controversies of the twentieth century.
The dynamic landscape on the north flank of Mount St. Helens
Authors: Austin Steven A.
Published: April 2010

The dynamic landscape on the north flank of Mount St. Helens includes the largest debris avalanche deposit to accumulate within human history, covering more than 45 km2 on the upper North Fork of the Toutle River on 18 May 1980. Most land-forms on the debris avalanche are now relatively stable and only affected significantly by geomorphic processes exceeding certain energy thresholds. Following the debris avalanche, the most significant landscape-forming event has been the mudflow of 19 March 1982. This mudflow overtopped the rim of the largest explosion pit, formed and deepened channels, and largely formed the present landscape of the debris avalanche surface. Now that the power of geomorphic processes has diminished, only finer sediment is being moved. Channels are armored with coarser clasts, and valleys are plugging with sediment. Hikers can observe the new landscape from two selected overlooks. Johnston Ridge Observatory is the staging area for a recommended roundtrip hike of 13.6 km (8.4 mi).
Hydrogeology of the Columbia River Basalt Group in the northern Willamette Valley, Oregon
Authors: Burt Walter , Conlon Terrence , Tolan Terry L. , Wells Ray E. , Melady Jason
Published: April 2010

Basalt flows of the Columbia River Basalt Group (CRBG) host a series of regionally extensive aquifers between western Idaho and the Pacific Ocean that serve as an important source for domestic, municipal, agricultural, and industrial water supply throughout much of this area, and are the sole source for some communities in the Willamette Valley. Rapid growth and increased pumping have resulted in significant water level declines in some locales in the Willamette Valley, forcing some communities to develop other water sources, and/or develop aquifer storage and recovery projects to store water in CRBG aquifers.

The CRBG generally consists of multiple concordant, tabular sheet flows. The primary water-bearing horizons within the CRBG are associated the vesicular and/ or brecciated flow top and flow bottom (pillow/hyaloclastite) structures that form the interflow zone between two flows. The interiors of the CRBG flows typically have limited vertical permeability and act as aquitards, creating a series of layered confined aquifers. The dominant groundwater flow pathway in the CRBG aquifer system is along these individual, laterally extensive, interflow zones. Tectonic structures may modify the dominant flow regime in the CRBG by offsetting or otherwise disturbing originally laterally continuous interflow zones. Faults result in a wide spectrum of effects on flow in the CRBG aquifers depending on the nature of the fault.

The hydraulic properties inherent to CRBG aquifers, including high degree of confinement, low bulk permeability and limited recharge have led to overdraft conditions in many areas. Conversely, these characteristics create favorable conditions for aquifer storage and recovery system development in the central Willamette Valley and Tualatin Basin.
Developing a global research agenda on violence and injury prevention: a modest proposal
Authors: Villaveces Andrés , Christiansen Ann , Hargarten Stephen W
Published: April 2010

The need for the development of a global injury prevention research agenda is examined. Literature was reviewed in public health and selected policy strategies outside of public health that address the development of research agendas both for specific injury topics as well as for other health related areas; the benefits of creating a global research agenda are highlighted. There are examples of successful strategies where the development of a global research agenda on an injury specific topic has improved knowledge and prevention activities in that subfield. There are also examples that consolidate larger health topics and follow an agenda. Such efforts can benefit from wider governmental and institutional support. It is concluded that the development of a global injury prevention research agenda focused on collaborative efforts and with emphasis in implementation and dissemination research could be a useful tool to improve the quantity and quality of research in the field.
Anadromy in Arctic populations of lake trout (Salvelinus namaycush): otolith microchemistry, stable isotopes, and comparisons with Arctic char (Salvelinus alpinus)
Authors: Swanson Heidi K. , Kidd Karen A. , Babaluk John A. , Wastle Rick J. , Yang Panseok P. , Halden Norman M. , Reist James D.
Published: April 2010

In the family Salmonidae, lake trout ( Salvelinus namaycush ) are considered the least tolerant of salt water. There are, however, sporadic reports of lake trout in coastal, brackish habitats in the Canadian Arctic. Otolith microchemistry analyses conducted on lake trout and Arctic char ( Salvelinus alpinus ) from four Arctic lakes in the West Kitikmeot region of Nunavut, Canada, revealed that 37 of 135 (27%) lake trout made annual marine migrations. Anadromous lake trout were in significantly better condition (K = 1.17) and had significantly higher C:N ratios (3.71) than resident lake trout (K = 1.05 and C:N = 3.34). Anadromous lake trout also had significantly higher δ15N (mean = 16.4‰), δ13C (mean = –22.3‰), and δ34S (mean = 13.43‰) isotope ratios than resident lake trout (means = 12.84‰, –26.21‰, and 1.93‰ for δ15N, δ13C, and δ34S, respectively); results were similar for Arctic char and agree with results from previous studies. Mean age of first migration for lake trout was 13 years, which was significantly older than that for Arctic char (5 years). This could be a reflection of size-dependent salinity tolerance in lake trout, but further research is required. These are the first detailed scientific data documenting anadromy in lake trout.
Modeling migratory energetics of Connecticut River American shad (Alosa sapidissima): implications for the conservation of an iteroparous anadromous fish
Authors: Castro-Santos Theodore , Letcher Benjamin H.
Published: April 2010

We present a simulation model in which individual adult migrant American shad ( Alosa sapidissima ) ascend the Connecticut River and spawn, and survivors return to the marine environment. Our approach synthesizes bioenergetics, reproductive biology, and behavior to estimate the effects of migratory distance and delays incurred at dams on spawning success and survival. We quantified both the magnitude of effects and the consequences of uncertainty in the estimates of input variables. Behavior, physiology, and energetics strongly affected both the distribution of spawning effort and survival to the marine environment. Delays to both upstream and downstream movements had dramatic effects on spawning success, determining total fecundity and spatial extent of spawning. Delays, combined with cues for migratory reversal, also determined the likelihood of survival. Spawning was concentrated in the immediate vicinity of dams and increased with greater migratory distance and delays to downstream migration. More research is needed on reproductive biology, behavior, energetics, and barrier effects to adequately understand the interplay of the various components of this model; it does provide a framework, however, that suggests that provision of upstream passage at dams in the absence of expeditious downstream passage may increase spawning success — but at the expense of reduced iteroparity.
Substock variation in reproductive traits in North Sea cod (Gadus morhua)
Authors: Harrald Marion , Wright Peter J. , Neat Francis C.
Published: April 2010

The North Sea stock of Atlantic cod ( Gadus morhua ) is comprised of a number of subcomponents that differ both genetically and phenotypically. A potential cause for such spatial variability is adaptive divergence, which may be linked to differences in thermal environment and (or) historical fishing pressure. Here we present evidence that spatial variation in maturity–size relationships in the wild has a significant intrinsic component. Using a common-environment experiment on wild-caught juveniles raised through to maturity, we demonstrate that cod from the southern North Sea (SNS) mature at larger sizes than those from the northwestern North Sea (NWNS) despite broadly similar growth rates. Consistent with these experimental results, year-class-specific maturity ogives for recent maturing year classes (1999–2001) suggested that the length at which 50% of females reached maturity was 11 cm greater for SNS than for NWNS cod. Under a common environment, smaller female size at maturity partly reflected higher relative liver weight, with NWNS females having a higher relative liver weight than SNS females. By investigating maturation under controlled conditions, our study provides evidence for life history trade-offs in energy allocation between growth, energy storage, and reproduction that may underlie the spatial variation observed in the field.
A general model for reconstructing salmon runs
Authors: Branch Trevor A. , Hilborn Ray
Published: April 2010

A general model is developed for salmon run reconstruction based on catch, escapement, and age composition data. The model is based on “groups” of salmon, each of which share the same characteristics but can differ from other groups in run timing, abundance, gear selectivity, and migration routes. The model is highly flexible so that it can be adapted to a variety of fisheries and can compare the fits of alternative hypotheses to available data. The model is applied to three sockeye salmon ( Oncorhynchus nerka ) districts in Bristol Bay, Alaska, USA, to show the effect of allowing age classes to arrive at different times and the impact of including process errors to mimic day-to-day arrival variability. The model predicts that in 2005, Wood River salmon comprised only 54% of the catch in the Nushagak fishing district (but 71% of the escapement), although these predictions are contradicted by genetic data for 2006–2008 showing high harvest rates of Wood River and Nushagak River fish but only light harvest rates of Igushik River fish. The genetics highlight the importance of including stock-specific availability parameters in future versions of the model to account for differences in harvest rates among stocks caught in the same fishing district.
Size-based variation in intertissue comparisons of stable carbon and nitrogen isotopic signatures of bull sharks (Carcharhinus leucas) and tiger sharks (Galeocerdo cuvier)
Authors: Matich Philip , Heithaus Michael R. , Layman Craig A.
Published: April 2010

Stable isotopes are important tools for understanding the trophic roles of elasmobranchs. However, whether different tissues provide consistent stable isotope values within an individual are largely unknown. To address this, the relationships among carbon and nitrogen isotope values were quantified for blood, muscle, and fin from juvenile bull sharks ( Carcharhinus leucas ) and blood and fin from large tiger sharks ( Galeocerdo cuvier ) collected in two different ecosystems. We also investigated the relationship between shark size and the magnitude of differences in isotopic values between tissues. Isotope values were significantly positively correlated for all paired tissue comparisons, but R2 values were much higher for δ13C than for δ15N. Paired differences between isotopic values of tissues were relatively small but varied significantly with shark total length, suggesting that shark size can be an important factor influencing the magnitude of differences in isotope values of different tissues. For studies of juvenile sharks, care should be taken in using slow turnover tissues like muscle and fin, because they may retain a maternal signature for an extended time. Although correlations were relatively strong, results suggest that correction factors should be generated for the desired study species and may only allow coarse-scale comparisons between studies using different tissue types.
The fine structure of Rhodopseudomonas acidophila
Authors: Tauschel H.-D. , Hoeniger Judith F. M.
Published: April 2010

The morphology of the photosynthetic bacterium Rhodopseudomonas acidophila strain P18aF1 1.2 has been investigated with the electron microscope. The cells grow by budding, the sessile buds eventually separating from the mother cells by constriction. In some dividing stages a belt-like structure was observed in the zone of division. Motile cells possess a subpolar tuft of unsheathed flagella. At the site of insertion of the flagella, the cell wall bears 12- to 14-nm wide holes or annuli through which the flagella probably pass. Motile cells readily lose their flagella.The structure of the surface revealed two distinct types: cells with a hexagonally patterned outer layer composed of ring-shaped elements and cells possessing a thick, fibrous capsule. Thin sections showed a well-developed thylakoid system arranged in piles and similar to that of other budding photosynthetic bacteria.The morphology of R. acidophila has been compared with that of R. palustris to show similarities and differences between the two species.
Gluconeogenesis by Veillonella parvula M4: evidence for the indirect conversion of pyruvate to P-enolpyruvate
Authors: Ng Stephen K. C. , Hamilton Ian R.
Published: April 2010

Cells of Veillonella parvula M4 growing in complex medium with lactate-U-14C as the carbon source were shown to synthesize complex cellular components with lactate carbon. Of the original labeled substrate, 69% of the label appeared in the metabolic end products (acetate, propionate, and CO2) while 25% was distributed among the products of biosynthesis. Of this latter radioactivity, the lipopolysaccharide (LPS2) fraction contained 22% of the total, 6% of which was found in lipid material and 16% in a carbohydrate fraction; this latter material was analyzed and shown to contain labeled glucosamine, galactosamine, galactose, glucose, and ribose. The remaining 2.6% was distributed in DNA (0.6%), cellular amino acids (0.6%), and the extracellular polysaccharide (LPS1) fraction (1.4%). Further analysis showed that this latter fraction was composed of only glucose and galactose. Of the cellular amino acids, arginine, aspartate, glutamate, alanine, and serine were labeled.Since the above results indicated that gluconeogenesis in V. parvula M4 proceeds, at least in part, from lactate, enzyme studies were undertaken with dialyzed crude extracts of the organism to determine the possible route of lactate conversion to P-enolpyruvate. Evidence is presented for the presence of pyruvate kinase and PEP carboxykinase activity in the organism. Since extract preparations produced significant quantities of (32P)ADP, but negligible quantities of (32P)AMP, during assays containing (α-32P)ATP and pyruvate, it was concluded that PEP synthetase or pyruvate, phosphate dikinase are absent in the organism. Thus, from these and previous results, it was concluded that in V. parvula M4, lactate is converted to P-enolpyruvate via the intermediate, oxaloacetate.
Production and control of extracellular enzymes in Micrococcus sodonensis
Authors: Mills Cecily , Campbell J. N.
Published: April 2010

Micrococcus sodonensis has been shown to produce several extracellular enzymes: an alkaline phosphatase, at least two forms of phosphodiesterase, a 5′-nucleotidase, and an alkaline proteinase. The quantitative release of these enzymes into the culture medium during logarithmic growth under all the various culture conditions tested indicates that these enzymes are truly extracellular in nature. Inorganic phosphate repressed the production of the alkaline phosphatase in synthetic as well as in complex media, whereas, the repression of the production of active diesterase and 5′-nucleotidase by inorganic phosphate was partly reversed by the addition of supplemental organic nutrients to the culture medium. Proteinase production was independent of the culture conditions used. A mutant strain of M. sodonensis with an altered production of diesterase was obtained; the other extracellular enzymes were unaffected. These results suggest that the extracellular enzymes of M. sodonensis are not produced in a pleiotropic fashion since the level of one of the enzymes can be changed without affecting a corresponding change in the levels of the other enzymes. An extracellular high molecular weight carbohydrate fraction was shown to be produced by M. sodonensis in synthetic medium. The fraction was also shown to contain glycoprotein.
Replication of virus-like particles in Penicillium stoloniferum mycelia
Authors: Detroy R. W. , Lillehoj E. B. , Hesseltine C. W.
Published: April 2010

Direct extraction of nucleic acid from mycelium of Penicillium stoloniferum yielded five viral double-stranded ribonucleic acid (dsRNA) components, transfer RNA (tRNA), and a deoxyribonuclease-sensitive fraction of deoxyribonucleic acid. Analysis of fungal cells from a submerged fermentation demonstrated detectable viral dsRNA and both types of virus-like particles (VLP) at 36 h with an increase in viral RNA synthesis for both VLP parallel to fungal growth up to 72 h followed by mycelial autolysis and loss of viral RNA. Replication of nucleic acid from VLP was measured by (i) incorporation of 14C-2-uracil into viral dsRNA, (ii) purification of viral dsRNA by cellulose column chromatography and subsequent ultraviolet absorption determination, and (iii) analysis of nucleic acid species by poly-acrylamide gel electrophoresis.
Study of mycorrhizae by means of fluorescent antibody
Authors: Schmidt E. L. , Biesbrock J. A. , Bohlool B. B. , Marx D. H.
Published: April 2010

The fluorescent antibody technique was found to be highly promising as a new approach to the study of mycorrhizae. Fluorescent antibodies prepared against two mycorrhizal fungi, Thelephora terrestris and Pisolithus tinctorius, were effective and specific as microscopic stains for those fungi and their corresponding mycorrhizae. Thelephora terrestris antibody gave zero, and P. tinctorius antibody gave five cross-reactions of moderate intensity, in tests with 31 diverse nonmycorrhizal fungi. Armillaria mellea reacted nonspeciflcally with several fluorescent antibodies.
The laboratory diagnosis of dermatophytosis complicated with Candida albicans
Authors: Fischer J. B. , Kane Julius
Published: April 2010

When scrapings of skin and nails containing Candida albicans and a dermatophyte are cultured, the more rapidly growing C. albicans may prevent the growth of the dermatophyte. Studies have shown that C. albicans has a complete requirement for biotin but the common dermatophytes such as Trichophyton rubrum and T. mentagrophytes and Epidermophyton floccosum are able to produce their requirements of this growth factor when cultured on a suitable medium in which the biotin has been inactivated. Advantage has been taken of this to restrict the growth of C. albicans by inactivating with egg albumen the biotin naturally present in the culture medium. The active principal in egg albumen is avidin.To further discourage the growth of C. albicans and encourage the growth of a dermatophyte, erythritol was used in place of dextrose in the isolation medium. This carbohydrate is not used by C. albicans but is used by T. rubrum and T. mentagrophytes.The new medium formulated to impede the growth of C. albicans but encourage the growth of a dermatophyte is casamino acids erythritol albumen agar. It minimizes the chance of sending an incomplete and misleading report to the physician.
Minimum nutritional requirements for growth of host-independent derivatives of Bdellovibrio bacteriovorus strain 109 Davis
Authors: Ishiguro Edward E.
Published: April 2010

A chemically defined medium for host-independent (H-I) derivatives of Bdellovibrio bacteriovorus strain 109 Davis has been developed. Carbon-source utilization studies indicated that H-I cells can assimilate a wider variety of compounds than host-dependent bdellovibrios. The defined medium did not support growth of freshly isolated H-I strains which required unidentified growth factors present in Escherichia coli cell-free extracts and in yeast extract.
The isolation of blue-green bacteria in pure culture
Authors: McCurdy Jr. Howard D. , Hodgson Walter
Published: April 2010

Omnimixer treatment followed by surface plating of colonies from membrane filters provides a convenient means for the isolation of pure cultures of blue-green bacteria.
Bark degradation by Aspergillus fumigatus. Growth studies
Authors: Nordström U. Marie
Published: April 2010

A fungus, Aspergillus fumigatus Fres., which used bark as its sole carbon and energy source, was isolated. Difficulties arose in measuring fungal growth, since the hyphae and the bark could not be separated. Measurement of the weight loss of the solid material did not quantitatively estimate fungal growth. Therefore, two methods were developed to estimate fungal mass when the carbon and energy source is particulate and contributes to the parameter used as a measure of growth. They were based on determination of nitrogen either in the solid material or in the medium. The nitrogen concentration in A. fumigatus was found to be nearly constant throughout the growth cycle and to be independent of the carbon and nitrogen concentrations in the medium but to vary with the carbon source used.Aspergillus fumigatus was grown at 37C as a submerged culture in salts medium with finely ground bark from Picea abies as sole carbon and energy source. The bark medium was heat-sterilized before inoculation with spores. The fungus utilized cellulose and hemicellulose but not lignin. Substances solubilized from the bark contributed to the growth. The yield was the same on unextracted as on water-extracted bark, although growth was delayed on the former. Growth was rapid and comparable to growth on other polymeric polysaccharides, i.e. starch. Aspergillus fumigatus degraded 32–40% of the polymeric part of the bark within 4 days and with an economic coefficient of about 50%.
Some nitrogen considerations of wood ecology and preservation
Authors: Sharp R. F.
Published: April 2010

Several kinds of nutrients were perfused to soil-inoculated veneers and were found not to change significantly the frequencies of microfungi isolation, but to have more effect on the rate of strength loss. Woods supplied with small amounts of nitrogen nutrient had slight strength reductions and thus indicated the adaptability of these microfungi to such conditions.The presence of nitrogenase activity within deteriorated wood was demonstrated and this suggested that over a long period of time nitrogen-fixing microorganisms might increase the wood nitrogen content.Amino compounds present in wood were altered with nitrous acid and shown not to upset the colonization patterns or the rate of decay. Some depolymerization of the cellulose fraction with further treatment by dilute alkali and ammonia gave varied results and no apparent decay when perfused with water.Leaching the wood with dilute acid gave a decrease in nitrogen content and this again did not affect the fungal growth, but it did prevent a loss of strength when perfused with water. It might provide a method of preserving timber used in certain conditions.
Metabolism of Dyfonate by soil fungi
Authors: Flashinski S. J. , Lichtenstein E. P.
Published: April 2010

The metabolism and detoxication of 14C-(ethoxy) and 14C-(ring)-Dyfonate were demonstrated with isolated soil fungi. Quantitative and qualitative differences in the production of insecticide metabolites were observed. Among the nine fungal species tested, Mucor plumbeus and Rhizopus arrhizus were most active in degrading the insecticide, while Penicillium notatum was the least active. This activity was evidenced by the production of increasing amounts of water-soluble 14C-compounds in the culture media and the disappearance (degradation) of the originally applied insecticide from the fungal cultures. The water-soluble metabolites were non-toxic to mosquito larvae. Hexane-extractable compounds from cultures of the most active species were non-toxic to fruit flies, while those from cultures of the less active fungal species were insecticidal. Among the metabolites produced and detected by thin-layer chromatography were primarily dyfoxon, ethylethoxyphosphonothioic acid, ethylethoxyphosphonic acid, methyl phenyl sulfoxide, and methyl phenyl sulfone. With Aspergillus niger and 14C-(ring)-Dyfonate, most of the radiocarbon recovered from the TLC-plates was associated with an unknown compound. Production of the metabolites by the fungi was a function of the live mycelia, followed by excretion of water-soluble 14C-compounds into the culture media.
The production of aphidicolin by Nigrospora sphaerica
Authors: Starratt A. N. , Loschiavo S. R.
Published: April 2010

A tetrol isolated from culture filtrates of the fungus Nigrospora sphaerica has been shown to be identical with aphidicolin, an antiviral diterpenoid.
Incorporation of amino acid carbon into prodigiosin synthesized by nonproliferating cells of Serratia marcescens
Authors: Qadri S. M. Hussain , Williams Robert P.
Published: April 2010

We investigated incorporation into prodigiosin of carbon from amino acids after addition of U-14C-amino acids to suspensions of nonpigmented, nonproliferating cells (NPC) of Serratia marcescens incubated at 25C. Biosynthesis of prodigiosin was initiated by addition of unlabeled proline (17 mM) at 0 h followed by 42.5 mM more at 14 h to promote rapid formation of the pigment. Then, 1 to 2 h later, trace amounts of various U-14C-amino acids were added. Radioactivity of prodigiosin and of protein was measured while cultures incubated for 36 h. Radioactive carbon from amino acids that caused prodigiosin biosynthesis in NPC was incorporated approximately in the order of their effectiveness for production of prodigiosin. In addition, isotope from cysteine, glycine, methionine, threonine, and, to a small extent, tyrosine was incorporated. Incorporation of carbon from other amino acids contained in casein hydrolysate was insignificant, although all contributed carbon to cellular protein. Kinetics of incorporation paralleled kinetics for formation of prodigiosin, but the amount of isotope incorporated was low, probably because of the large amount of cold proline added to cultures and because the amino acids were used for other biosyntheses in addition to pigment formation. The data established that several amino acids contributed carbon to the prodigiosin molecule, but the biosynthetic pathways that are used must still be determined.
A rapid quantitative microtitration of Pseudomonas aeruginosa antibody
Authors: Sato H. , Diena B. B.
Published: April 2010

A concavity slide agglutination technique is described which compares favorably with the test tube agglutination method. The new method is based on the serological reactivity of heat-stable somatic "O" antigens, and gives satisfactory results; it is also timesaving.