bluuebunny/crossref_metadata_2025 huggingface dataset:
Short‐term immunosuppression after rat parathyroid allotransplantation
Authors: Timm Stephan , Otto Christoph , Begrich Daniel , Illert Bertram , Hamelmann Wulf , Ulrichs Karin , Thiede Arnulf , Timmermann Wolfgang
Published: October 2003

The aim of this study was to evaluate whether short‐term postoperative immunosuppression is able to sufficiently prolong graft survival after experimental allogeneic parathyroid transplantation. Heterotopic parathyroid transplantation was performed in 6 groups: 1) syngeneic control Lewis (LEW) to LEW; 2) allogeneic control Wistar‐Furth (WF) to LEW; 3–5) WF to LEW plus short‐term immunosuppression, postoperative days 1–13 (cyclosporine 5/10/20 mg/kg); and 6) WF to LEW plus 10 mg/kg CyA from preoperative day 7 to postoperative day 7. Graft function was examined up to 60 days; histological and immunohistological examination was performed on all grafts with impaired function. Graft function after syngeneic transplantation was indefinite, while recipients of allogeneic grafts turned hypocalcemic after 13 ± 2 days. With immunosuppression, graft function was 21 ± 2 days (groups 5 and 6) and 28 ± 3 days (groups 3 and 4). Histologically, a cellular infiltrate responsible for graft destruction was found. The results show that indefinite parathyroid allograft survival cannot be achieved by short‐term immunosuppression alone. Whether the combination of an additional graft pretreatment and immunosuppression has an impact on graft function will be further examined. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:503–507 2003
Needles to promote ventricular blood into the schemic myocardium applied in a rat heart transplant model: An acute observation
Authors: Lee S. , Pivetti C.D. , Hong I.C. , Yoo C.H. , Kim K. , Nam S. , Bai S. , Niewiadomski S.T. , Wolf P. , Gittes R.F.
Published: October 2003

Two needles were designed in order to revascularize an ischemic myocardium in the event of left coronary artery occlusion. This study was conducted by performing the Lee modified Fox‐Montorsi heart‐lung transplant on 25 San Diego Microsurgical Institute‐bred Sprague Dawley rats that were subjected to left coronary artery ligation in each case. Of these 25 rats, a straight‐porous (SP) needling procedure was applied to 9 heterotopically transplanted rat hearts, and a distinct horseshoe (HS)‐shaped needle application was performed on the remaining 16 heterotopically transplanted rat hearts. This report represents an acute study on the efficiency of these two needles to transmit oxygen‐rich blood from the left ventricle into the ischemic myocardium. Doppler readings for male vs. female transplants showed that the control peak (PK) and mean (MN) kHz values are on the average of 0.20 kHz higher in males than in females. However, control heart rate values in both sexes are approximately equal. Ligation of the left coronary artery caused a dramatic decrease of PK and MN kHz values in both sexes, while heart rate showed no significant decrease from the original control values in response to ischemia. Application of the SP needle showed only a slight return of PK and MN values in both sexes, but heart rate values increased to levels higher than the original control values. The HS needling procedure was able to recover approximately 80% of the control PK and MN kHz values in both sexes. Thus, these data indicate that the HS needle can successfully transmit left ventricular blood into the myocardium. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:443–449 2003
Consecutive en‐bloc liver (30%)‐pancreas‐duodenum‐spleen‐stomach transplant in Lewis rats
Authors: Yoo C.H. , Hong I.C. , Lee S. , Nam S. , Bai S. , Kim K. , Pivetti C.D. , Niewiadomski S.T. , Wolf P. , Gittes R.F.
Published: October 2003

It is well‐known that 30% of the remaining liver mass, following partial hepatectomy, regenerates to full original mass within 2 weeks in rats. In order to carry the transplanted rat liver to repeated transplantation, a technique of combining 30% of the liver with the pancreaticoduodenum and spleen transplantation is performed in this consecutive organ transplantation study. Our laboratory observed several 37‐month‐old transplanted rats by carrying through 2–3 generations, and histological disclosure were made. Because the partial liver transplants did not regenerate after the transplantation with other splanchnic organs, this technique is not so difficult though subsequent surgical maneuvers are needed and the liver histology proved entirely normal in every aspect when followed beyond the rat's life span of 24 months. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:440–442 2003
Changes in microcirculation after ischemic process in rat skeletal muscle
Authors: Nemeth Norbert , Lesznyak Tamas , Brath Endre , Acs Gabor , Nagy Arpad , Pap‐Szekeres Jozsef , Furka Istvan , Miko Iren
Published: October 2003

Laser Doppler flowmetry (LDF) is a good method to investigate tissue microcirculation, but it has many standardization and measuring problems. To exclude these effects, we performed a test using LDF on rat skeletal muscle. In 12 CD outbred anesthetized rats, bilateral femoral vessels and the quadriceps femoris muscle were exposed. The left femoral artery and vein were clamped for 1 h by microvascular clips (ischemic side). On the right side, no other intervention was made (control side). An LDF probe was applied on the medial vastus muscle. Short‐term occlusions (2–3 s) were performed before and after the 1‐h clamping and on the control side while LDF curves were registered. The halftimes of ascending curves on the ischemic side were significantly elongated vs. the condition before clamping (P = 0.0007) or the control side (P = 0.0017). Microcirculatory changes caused by 1‐h ischemia were shown by this simple, quick, and well‐reproducible test on rat skeletal muscle.

A lézer Doppler (LD) áramlásmérés elfogadott módszer a szöveti mikrokeringés vizsgálatára, bár számos standardizációs és mérési problémája lehet. E nehézségek kizárására kifejlesztettünk egy tesztet patkány harántcsíkolt izomszöveten. 12 CD outbred patkány a. és v. femoralisát és a m. quadriceps femorist feltártuk mindkét oldalon. A bal oldali femoralis ereket microvascularis clippekkel 1 órára leszorítottuk (ischaemiás oldal), míg a jobb oldalon egyéb beavatkozás nem történt (kontroll oldal). A LD mérőfejet a m. vastus medialisra helyeztük. Az 1 órás leszorítás előtt és után illetve a kontroll oldalon rövid időtartamú (2–3 s) occlusiót idéztünk elő, miközben a LD jelet folyamatosan rögzítettük. A felszálló LD görbék 50%‐os értékénél mért idő szignifikánsan hosszabb volt a kontroll oldalhoz (P = 0.0017) illetve a beavatkozás előtti állapothoz képest (P = 0.0007). Ezzel az egyszerű, gyors és jól reprodukálható teszttel az 1 órás ischaemia indukálta mikrocirculációs változásokat sikerült kimutatni patkány vázizomban. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:419–423 2003
Prolonged survival of heart allografts transduced with AAV‐CTLA4Ig
Authors: Chen Zongyou , Lu Lina , Li Juan , Xiao Xiao , Fung John J. , Qian Shiguang
Published: October 2003

Organ grafts transduced with gene‐encoding immunosuppressive molecules are a less toxic approach to preventing graft rejection. Adenovirus vectors have been widely tested with unsatisfactory results, while adeno‐associated virus (AAV) is smaller and elicits a low host humoral response. We constructed an AAV vector containing the mouse CTLA4Ig gene. B10 (H2b) cardiac grafts were transduced with AAV‐CTLA4Ig by coronary infusion. AAV‐LacZ vectors were used as reporters and controls, and the expression of β‐gal was determined by X‐gal staining. Thirty percent to 40% of myocytes displayed strongly positive X‐gal staining after infusion with AAV‐LacZ. Additional infusion with vascular dilator reagents did not improve the transduction rate. Survival of B10 heart allografts transduced with AAV‐CTLA4‐Ig was significantly prolonged in C3H (H2k) recipients. These data demonstrate that AAV vectors can efficiently be transduced into the mouse myocardium by coronary infusion. Graft transduction with AAV‐CTLA4Ig may be a novel approach to preventing allograft rejection. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:489–493 2003
Comparison of in vivo lymphocyte proliferation between allogeneic and xenogeneic heart transplantation in mice
Authors: Kellersmann Richard , Kellersmann Anne , Thiede Arnulf , Ulrichs Karin
Published: October 2003

There are controversial in vitro data comparing the strength of the cellular immune response between allogeneic and xenogeneic stimulator/responder combinations. The present study therefore compares in vivo lymphocyte proliferation using heart transplantation (HTx) models in mice. Heterotopic HTx into BALB/c mice was performed using donor organs from mice (BALB/c and C57BL/6) or Lewis rats. Intraperitoneally given bromodeoxyuridine (BrdU) was incorporated into the DNA and was subsequently analyzed by flow cytometry. On postoperative days 3 and 5, proliferation of splenocytes, CD4+ T‐lymphocytes, and CD19+ B‐lymphocytes was significantly higher after xenogeneic than after allogeneic and isogeneic HTx. No significant difference was observed when proliferation of CD8+ lymphocytes was determined. The increased in vivo proliferation after xenotransplantation may reflect an earlier and probably stronger cellular immune response compared to allogeneic transplantation. The higher CD4+ lymphocyte proliferation underscores the importance of this cell population in xenograft rejection. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:498–502 2003
Optimization of a metastasizing human gastric cancer model in nude mice
Authors: Illert Bertram , Otto Christoph , Braendlein Stephanie , Thiede Arnulf , Timmermann Wolfgang
Published: October 2003

Our purpose was to optimize the surgical orthotopic implantation (SOI) technique to create a reproducible gastric cancer model in nude mice with stable tumor growth and metastasizing course. We performed xenotransplantation of primary human tumor specimens from patients with gastric cancer (series 1) and orthotopic transplantation of tumor specimens originating from the gastric cancer cell line 23132/87 (series 2). All specimens were transplanted using microsurgical techniques. The two series were compared with regard to tumor growth rates and kinetics, development of metastases, and induction of minimal residual disease (MRD), as determined by histology and PCR techniques. In series 1 mice, the tumor growth rate was slow; in series 2 mice, it was both fast and reproducible. Unlike animals in series 1, animals in series 2 developed metastases and MRD. In conclusion, the optimized SOI technique presented here represents a reproducible and reliably metastasizing gastric cancer model. © 2003 Wiley‐Liss, Inc. MICROSURGERY 23:508–512 2003
Processable photonic polymers with controllable properties
Authors: Kallitsis J. K. , Andreopoulou A. K.
Published: October 2003

A series of polyethers consisting of a conjugated segment connected with a nonconjugated spacer were synthesized and characterized. On the basis of the chemical structure of the conjugated moiety, controllable light emission was obtained. The thermal properties were influenced from the structure of the conjugated segment, the type of substituents used, and the length of the flexible spacer used. Additionally, coil‐rod‐coil block copolymers having conjugated segments as the rod block were prepared with atom transfer radical polymerization of α,ω‐modified conjugated oligomers. The optical properties of these copolymers were examined with respect to their aggregation behavior. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2485–2491, 2003
Negative differential mobility in pentacene
Authors: Conwell E. M. , Basko D. M.
Published: October 2003

Despite narrow bands and large energy gaps, which result in a negligible number of intrinsic carriers, high‐quality molecular crystals, such as pentacene and naphthalene, show high mobilities at low temperatures. As a result, injected carriers can have their “temperature” increased by easily attainable electric fields. Their mobility is then expected to decrease with an increasing field, both because of the increased scattering rate and the increase in the effective mass due to the nonparabolicity of the energy bands. Using Poisson's equation, we investigate the effect on the current voltage characteristic of the mobility decrease being so steep over some field range that the drift velocity (vd) decreases with an increasing field; that is, the sample displays negative differential mobility (NDM) over that range. NDM is expected for samples in which the effective mass increases. We find that, with increasing voltage, V, after the Ohm's law region, there is a region in which J ∝ V2, as expected for a space‐charge‐limited value of J. When V is large enough to cause heating of the carriers, J increases less rapidly than V2, tending toward a linear dependence on V in the hot carrier region. Thus, V/J tends to saturate at high fields. It is shown that the data of Schön et al. for pentacene, when properly interpreted, show saturation of V/J rather than that of vd, as they claimed. The direct measurement of vd versus the field by the time‐of‐flight method for naphthalene at low temperatures by Warta and Karl was interpreted by them as indicating saturation of vd. We point out that the determination of vd by the time‐of‐flight method in a situation with varying mass and trapping is not straightforward. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2595–2600, 2003
Energy transfer and triplet exciton confinement in polymeric electrophosphorescent devices
Authors: Chen Fang‐Chung , Chang Shun‐Chi , He Gufeng , Pyo Seungmoon , Yang Yang , Kurotaki Masayuki , Kido Junji
Published: October 2003

Energy transfer and triplet exciton confinement in polymer/phosphorescent dopant systems have been investigated. Various combinations of host‐guest systems have been studied, consisting of two host polymers, poly(vinylcarbazole) (PVK) and poly[9,9‐bis(octyl)‐fluorene‐2,7‐diyl] (PF), blended with five different phosphorescent iridium complexes with different triplet energy levels. These combinations of hosts and dopants provide an ideal situation for studying the movement of triplet excitons between the host polymers and dopants. The excitons either can be confined at the dopant sites or can flow to the host polymers, subject to the relative position of the triplet energy levels of the material. For PF, because of its low triplet energy level, the exciton can flow back from the dopants to PF when the dopant has a higher triplet energy and subsequently quench the device efficiency. In contrast, efficient electrophosphorescence has been observed in doped PVK films because of the high triplet energy level of PVK. Better energy transfer from PVK to the dopants, as well as triplet exciton confinement on the dopants, leads to higher device performance than found in PF devices. Efficiencies as high as 16, 8.0, and 2.6 cd/A for green, yellow, and red emissions, respectively, can be achieved when PVK is selected as the host polymer. The results in this study show that the energy transfer and triplet exciton confinement have a pronounced influence on the device performance. In addition, this study also provides material design and selection rules for the efficient phosphorescent polymer light‐emitting diodes. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2681–2690, 2003
Thermoelectric power of sulphur at high pressure up to 40 GPa
Authors: Shchennikov Vladimir V. , Ovsyannikov Sergey V.
Published: October 2003

From the thermoelectric power S measurements on sulphur at high pressure P, a hole‐type electrical conductivity has been established above 25 GPa. A correlation of the pressure dependence of S with the previously published optical reflectance data has been found. The positive value of S and its decrease with pressure have shown the similarity of the electron structure of sulphur and its neighbours from Group VI – Te and Se. However, a negative magnetoresistance (MR) established at P ≈ 30 GPa points to low mobility of holes and implies an indirect semiconductor gap for sulphur in contrast to the direct gap for Te and Se in the vicinity of the semiconductor–metal phase transition.
Modelling and simulation of multi‐phase effects on X‐ray elasticity constants
Authors: Fréour S. , Gloaguen D. , François M. , Guillén R.
Published: October 2003

This paper deals with the calculation of X‐ray Elasticity Constants (XEC) of phases embedded in multi‐phase polycrystals. A three scales (macroscopic, pseudo‐macroscopic, mesoscopic) model based on the classical self‐consistent formalism is developed in order to analyse multi‐phase effects on XEC values. Simulations are performed for cubic or hexagonal crystallographic structure phases embedded in several two‐phases materials. In fact, it is demonstrated that XEC vary with the macroscopic stiffness of the whole polycrystal. In consequence, the constants of one particular phase depend on the elastic behaviour and the volume fraction of all the phases constituting the material. Now, XEC play a leading role in pseudo‐macroscopic stresses determination by X‐Ray Diffraction (XRD) methods. In this work, a quantitative analysis of the multi‐phase effects on stresses determination by XRD methods was performed. Numerical results will be compared and discussed.
Electronic structure of CeBa2Cu3O7
Authors: Łuszczek M. , Laskowski R.
Published: October 2003

The linearized augmented plane wave (LAPW) method was used for spin‐polarized self‐consistent electronic structure calculations of CeBa2Cu3O7 (not synthesized as a single phase yet) and compared with three other members of the ReBa2Cu3O7 (denoted as Re123) family of compounds: Y123 (superconducting), Nd123 (superconducting) and Pr123 (potentially‐superconducting). The obtained band structures are qualitatively similar. We hypothesize that the spin‐split band structure observed in Pr123 and Ce123 could indicate the potential off‐stoichiometry, substitutional defects and as a consequence the suppression of superconductivity in the former, and the failure of single phase synthesis in the last system.
First‐principle simulations of the electronic structure of copper‐based oxide superconductors
Authors: Yutoh Y. , Sugihara S.
Published: October 2003

The relationship between the transition temperature (Tc) of an oxide superconductor and strain has been studied by means of experiments, with a focus an specimens that include an interface between a superconductor and a substrate. In the current study, we performed calculations on the bulk and the surface in order to investigate the electronic structures of the above systems. We calculated the electronic structure of La2CuO4 bulk by employment of three‐dimensional boundary conditions and that of a La2CuO4 surface by employment of two‐dimensional boundary conditions. The results for the bulk indicate that a relationship exists between the lattice parameters and Tc of La2CuO4. We discuss the calculated results for the bulk and surface on the basis of the results of investigation of the differences in electronic structures. The results indicate that the surface retained the electronic structures of the bulk.
ESD thresholds for KCl
Authors: Gołek F.
Published: October 2003

Electron stimulated desorption (ESD) energy thresholds for thin KCl layers are measured relative to the target current onset. The applied procedure allow to correct electron beam energy for the contact potential difference in the system. The results show that the energy threshold for ESD of cations and anions (or neutral Cl) coincides with the fundamental absorption edge. The measured threshold energies are about 20 eV for Cl+ and about 8 eV for K+ and Cl (or Cl−) ESD. The 20 eV threshold for Cl+ signal confirms the involvement of an Auger transition in positive halogen ion emission while the 8 eV threshold for the other species is consistent with the so‐called “defect‐mediated desorption” model of ESD. It is proposed that the near surface lattice instability induced by electronic transition results in a local heating capable of ejecting constituent ion or neutral atom.
Origin of electron spin resonance in La0.7Ca0.3MnO3
Authors: Joh Keon Woo , Lee Chang Hoon , Lee Cheol Eui , Jeong Yoon Hee
Published: October 2003

An electron spin resonance study was carried out for a La0.7Ca0.3MnO3 bulk sample above the ferromagnetic ordering temperature. From careful analysis on the ESR parameters, it is shown that itinerant spins interacting with magnetic spin clusters in bottleneck regime are responsible for the ESR signals.
Guiding Students Toward Solutions in Field Experiences
Authors: Beckett Julia , Grant Nancy K.
Published: October 2003

Professors who supervise students in field experiences have a unique challenge in helping students solve the problems that they face. The authors offer strategies for helping students analyze and solve problems that they experience in field experiences.
Ecological considerations support color physicalism
Authors: Clark James J.
Published: October 2003

We argue that any theory of color physicalism must include consideration of ecological interactions. Ecological and sensorimotor contingencies resulting from relative surface motion and observer motion give rise to measurable effects on the spectrum of light reflecting from surfaces. These contingencies define invariant manifolds in a sensory-spatial space, which is the physical underpinning of all subjective color experiences.
True color only exists in the eye of the observer
Authors: Cornelissen Frans W. , Brenner Eli , Smeets Jeroen
Published: October 2003

The colors we perceive are the outcome of an attempt to meaningfully order the spectral information from the environment. These colors are not the result of a straightforward mapping of a physical property to a sensation, but arise from an interaction between our environment and our visual system. Thus, although one may infer from a surface’ reflectance characteristics that it will be perceived as “colored,” true colors only arise by virtue of the interaction of the reflected light with the eye (and brain) of an observer.
Mechanisms of disrupted language comprehension in schizophrenia
Authors: Condray Ruth , Steinhauer Stuart R.
Published: October 2003

Mechanisms that contribute to perceptual processing dysfunction in schizophrenia were examined by Phillips & Silverstein, and formulated as involving disruptions in both local and higher-level coordination of signals. We agree that dysfunction in the coordination of cognitive functions (disconnection) is also indicated for many of the linguistic processing deficits documented for schizophrenia. We suggest, however, that it may be necessary to add a timing mechanism to the theoretical account.
Orange laser beams are not illusory: The need for a plurality of “real” color ontologies
Authors: Decock Lieven , van Brakel Jaap
Published: October 2003

Reflectance physicalism only provides a partial picture of the ontology of color. Byrne & Hilbert’ account is unsatisfactory because the replacement of reflectance functions by productance functions is ad hoc, unclear, and only leads to new problems. Furthermore, the effects of color contrast and differences in illumination are not really taken seriously: Too many “real” colors are tacitly dismissed as illusory, and this for arbitrary reasons. We claim that there cannot be an all-embracing ontology for color.
Productance physicalism and a posteriori necessity
Authors: Dedrick Don
Published: October 2003

The problem of nonreflectors perceived as colored is the central problem for Byrne & Hilbert's (B&H's) physicalism. Vision scientists and other interested parties need to consider the motivation for their account of “productance physicalism.” Is B&H's theory motivated by scientific concerns or by philosophical interests intended to preserve a physicalist account of color as a posteriori necessary?
Cognitive coordination deficits: A necessary but not sufficient factor in the development of schizophrenia
Authors: Gooding Diane C. , Braun Jacqueline G.
Published: October 2003

The Phillips & Silverstein model of NMDA-mediated coordination deficits provides a useful heuristic for the study of schizophrenic cognition. However, the model does not specifically account for the development of schizophrenia-spectrum disorders. The P&S model is compared to Meehl's seminal model of schizotaxia, schizotypy, and schizophrenia, as well as the model of schizophrenic cognitive dysfunction posited by McCarley and colleagues.
Linking brain to mind in normal behavior and schizophrenia
Authors: Grossberg Stephen
Published: October 2003

To understand schizophrenia, a linking hypothesis is needed that shows how brain mechanisms lead to behavioral functions in normals, and also how breakdowns in these mechanisms lead to behavioral symptoms of schizophrenia. Such a linking hypothesis is now available that complements the discussion offered by Phillips & Silverstein (P&S).
Parallels between hearing and seeing support physicalism
Authors: Handel Stephen , Erickson Molly L.
Published: October 2003

There are 2,000 hair cells in the cochlea, but only three cones in the retina. This disparity can be understood in terms of the differences between the physical characteristics of the auditory signal (discrete excitations and resonances requiring many narrowly tuned receptors) and those of the visual signal (smooth daylight excitations and reflectances requiring only a few broadly tuned receptors). We argue that this match supports the physicalism of color and timbre.
Theory of mind in schizophrenia: Damaged module or deficit in cognitive coordination?
Authors: Leiser David , Bonshtein Udi
Published: October 2003

Schizophrenics exhibit a deficit in theory of mind (ToM), but an intact theory of biology (ToB). One explanation is that ToM relies on an independent module that is selectively damaged. Phillips & Silverstein's analyses suggest an alternative: ToM requires the type of coordination that is impaired in schizophrenia, whereas ToB is spared because this type of coordination is not involved.
Hue magnitudes and Revelation
Authors: Kulvicki John
Published: October 2003

Revelation, the thesis that the full intrinsic nature of colors is revealed to us by color experiences, is false in Byrne & Hilbert's (B&H's) view, but in an interesting and nonobvious way. I show what would make Revelation true, given B&H's account of colors, and then show why that situation fails to obtain, and why that is interesting.
No blind schizophrenics: Are NMDA-receptor dynamics involved?
Authors: Sanders Glenn S. , Platek Steven M. , Gallup Gordon G.
Published: October 2003

Numerous searches have failed to identify a single co-occurrence of total blindness and schizophrenia. Evidence that blindness causes loss of certain NMDA-receptor functions is balanced by reports of compensatory gains. Connections between visual and anterior cingulate NMDA-receptor systems may help to explain how blindness could protect against schizophrenia.
Spatial position and perceived color of objects
Authors: Nijhawan Romi
Published: October 2003

Visual percepts are called veridical when a “real” object can be identified as their cause, and illusions otherwise. The perceived position and color of a flashed object may be called veridical or illusory depending on which viewpoint one adopts. Since “reality” is assumed to be fixed (independent of viewpoint) in the definition of veridicality (or illusion), this suggests that “perceived” position and color are not properties of “real” objects.
Reflectance-to-color mappings depend critically on spatial context
Authors: Rudd Michael E.
Published: October 2003

In visual science, color is usually regarded as a subjective phenomenon. The relationship between the specific color experiences that are evoked by a visual scene and the physical properties of the surfaces viewed in that scene are complex and highly dependent on spatial context. There is no simple correspondence between experienced color and a stable class of physical reflectances.
Depression, anxiety and psychoses in later life: more challenges for primary care
Authors: Iliffe Steve , Manthorpe Jill
Published: October 2003

The current focus on dementia risks eclipsing other mental health problems of later life. While the National Service Framework for Older People (NSF) has highlighted depression as an important disorder meriting special consideration,1 anxiety and psychoses in older people remain difficult problems for practitioners to manage. This paper reviews the prevalence and impact, recognition, complexity and prognosis and treatment for these three clinical problems, and proposes a framework for ‘good enough practice’
An assessment of biofuel use and burning of agricultural waste in the developing world
Authors: Yevich Rosemarie , Logan Jennifer A.
Published: October 2003

We present an assessment of biofuel use and agricultural field burning in the developing world. We used information from government statistics, energy assessments from the World Bank, and many technical reports, as well as from discussions with experts in agronomy, forestry, and agro‐industries. We estimate that 2060 Tg biomass fuel was used in the developing world in 1985; of this, 66% was burned in Asia, and 21% and 13% in Africa and Latin America, respectively. Agricultural waste supplies about 33% of total biofuel use, providing 39%, 29%, and 13% of biofuel use in Asia, Latin America, and Africa, and 41% and 51% of the biofuel use in India and China. We find that 400 Tg of crop residues are burned in the fields, with the fraction of available residue burned in 1985 ranging from 1% in China, 16–30% in the Middle East and India, to about 70% in Indonesia; in Africa about 1% residue is burned in the fields of the northern drylands, but up to 50% in the humid tropics. We distributed this biomass burning on a spatial grid with resolution of 1° × 1°, and applied emission factors to the amount of dry matter burned to give maps of trace gas emissions in the developing world. The emissions of CO from biofuel use in the developing world, 156 Tg, are about 50% of the estimated global CO emissions from fossil fuel use and industry. The emission of 0.9 Pg C (as CO2) from burning of biofuels and field residues together is small, but nonnegligible when compared with the emissions of CO2 from fossil fuel use and industry, 5.3 Pg C. The biomass burning source of 10 Tg/yr for CH4 and 2.2 Tg N/yr of NOx are relatively small when compared with total CH4 and NOx sources; this source of NOx may be important on a regional basis.
Neogene extension and volcanism in the Kunlun Fault Zone, northern Tibet: New constraints on the age of the Kunlun Fault
Authors: Jolivet M. , Brunel M. , Seward D. , Xu Z. , Yang J. , Malavieille J. , Roger F. , Leyreloup A. , Arnaud N. , Wu C.
Published: October 2003

The geology of the Jingyu basin (north Tibet) provides constraints on the relationship between localized E‐W extension in the Qiangtang block and strike‐slip motion along the Kunlun fault. Eocene to Oligocene SW‐NE compression formed topographic relief in the present western Kunlun Shan. Pull‐apart basins started forming in the western Kunlun ranges around 15 Ma, possibly coincident with the initiation of subduction of the Tarim‐Qaidam lithosphere under the Kunlun Shan. Extensional tectonism is still active, and the Jingyu basin is extending, as a normal fault connected with the Kunlun fault was recently active. Localized extension allows Tertiary and Quaternary shoshonitic magmas to reach the surface from crustal depths of 50 to 60 km. Miocene strike‐slip faulting indicates that the initiation of the Kunlun strike‐slip fault is early Neogene in age and that the total amount of horizontal movement that occurred along the fault has to be reconsidered.
Variability of atmospheric dimethylsulphide over the southern Indian Ocean due to changes in ultraviolet radiation
Authors: Kniveton D. R. , Todd M. C. , Sciare J. , Mihalopoulos N.
Published: October 2003

Dimethylsulphide (DMS) is a climatically important component of global biogeochemical cycles, through its role in the sulphur cycle. Changes in ultraviolet radiation (UV) exhibit both positive and negative forcings on the dynamics of production and turnover of DMS and its precursor dimethylsulphoniopropionate (DMSP). In this study we investigate the net forcing of UV on atmospheric DMS. The work is based on a 10‐year record of observed DMS at Amsterdam Island in the southern Indian Ocean, and satellite‐based retrievals of surface UV and photosynthetically active radiation (PAR). The results show an inverse relationship between UV radiation and atmospheric DMS associated with extreme changes (defined as the greatest 5%) in daily UV, independent of changes in wind speed, sea surface temperature, and PAR.
A parameterization of sea‐salt aerosol source function for sub‐ and super‐micron particles
Authors: Gong S. L.
Published: October 2003

A parameterization of a sea‐salt source function for both sub‐ and super‐micron particles was developed based on the semi‐empirical formulation of Monahan et al. [1986]. This new parameterization extends the range of Monahan's equation to below 0.2 μm in diameter where it has been found to overestimate submicron sea‐salt aerosols, especially the sea‐salt number concentrations. The new parameterization was used in a one‐dimensional (1‐D) column model to predict the number size distributions and compared with reasonable agreement to the observed distributions at various wind speeds reported by O'Dowd et al. [1997]. A global 3‐D sea‐salt simulation with this parameterization was also made and a much better dependence of sea‐salt on surface wind speed was predicted than other schemes compared to observations. For an indirect impact assessment of sea‐salt aerosols on climate where submicron particles may have a dominant contribution to aerosol‐cloud interactions, this scheme provides the most realistic number flux of sea‐salt particles between ocean and atmosphere.
Geochemistry of lavas from Negros Arc, west central Philippines: Insights into the contribution from the subducting slab
Authors: Solidum Renato U. , Castillo Paterno R. , Hawkins James W.
Published: October 2003

The Negros Arc in west central Philippines is comprised of six Pliocene to Quaternary stratovolcanoes that have erupted calc‐alkaline to slightly shoshonitic basalts to dacites. Petrographic, major and trace element, and Sr, Nd, and Pb isotope data suggest that crustal level differentiation processes have likely generated the range in composition of lavas. Several silicic lavas from the southern volcanoes have high Sr and moderate Sr/Y similar to melts presumed to be derived from subducted basaltic crust (adakites). However, these silicic lavas have low La/Yb unlike typical adakites, and have other incompatible trace element ratios (e.g., Nb/Ta, Ba/La, Pb/Ce) which are opposite to those expected of adakites. Modeling results also indicate that partial melting of the subducting Southeast Sulu Sea crust cannot satisfactorily reproduce the adakite‐like characteristics or account for the other incompatible trace element ratios. Fractionation of amphibole (± apatite) together with variable fractionation and accumulation of plagioclase have likely imparted the adakite‐like features. Trace element and isotopic variations indicate a three‐component mixing, whereby variable proportions of melted sediment and aqueous fluids derived from basaltic crust were added to the subarc MORB‐source type mantle to form the source of Negros Arc lavas. Southern Negros lavas reflect the strongest fluid contribution whereas northern Negros lavas best exhibit the sediment melt contribution.
Bursty Pi1 activity at the South American equatorial zone during the 29 October 1994 magnetic storm
Authors: Padilha Antonio L. , Alves M. Virginia , Trivedi Nalin B. , Kitamura Tai‐I. , Shinohara Manabu
Published: October 2003

The effects of the great magnetic storm of 29 October 1994 on the daytime equatorial ionosphere have been studied by a ground‐based array of fluxgate magnetometers in South America. The array covers around 2 h in magnetic local time and spans dip angles from 6.7°N to 10.8°S, with additional very‐low latitude and nightside dip equator stations as reference. Following an abrupt increase in the AE index during the storm main phase, bursty Pi1 activity is seen over a wide region around the prenoon dip equator. This is the first observation of such pulsations at these latitudes. The pulsations are strongly attenuated not propagating outside the equatorial zone and sometimes may present differences in time onset at different longitudes. It is proposed that they may have been originated by instabilities in the equatorial electrojet currents triggered by prompt penetration of high latitude electric fields.
Evidence for the buried rim of Campi Flegrei caldera from 3‐d active seismic imaging
Authors: Zollo A. , Judenherc S. , Auger E. , D'Auria L. , Virieux J. , Capuano P. , Chiarabba C. , de Franco R. , Makris J. , Michelini A. , Musacchio G.
Published: October 2003

An extended marine, active seismic survey has been performed on September, 2001 in the gulfs of Naples and Pozzuoli by recording about 5000 shots at a network of 62 sea bottom and 72 on shore seismographs. 3‐D images of the shallow caldera structure are obtained from the tomographic inversion of about 77000 first P arrival times using the Benz et al. [1996] tomographic technique. The buried rim of the Campi Flegrei caldera is clearly detected at about 800–2000 m depth, as an anular high P‐velocity and high density body. It has a diameter of about 8–12 km and a height of 1–2 km. According to stratigraphic and sonic log data from deep boreholes and tomographic P velocities, the rim is likely formed by solidified lavas and/or tuffs with interbedded lava. This study confirms the existence for a depressed limestone basement beneath the caldera at less than 4 km depth, while no evidence are found for shallower magmatic bodies.
Sensitivity of deep lake temperature to past and future climatic changes: A modeling study for Lac d'Annecy, France, and Ammersee, Germany
Authors: Danis P.‐A. , von Grafenstein U. , Masson‐Delmotte V.
Published: October 2003

Oxygen isotope ratios (δ18O) of deep‐lake ostracod valves can provide excellent estimates of the oxygen isotopic composition of past atmospheric precipitation (δ18OP). One of the major steps of such a δ18OP reconstruction is the calculation of the δ18O of the lake water (δ18OL) from the valve δ18O, which includes an appropriate estimate of the past water temperature during valve formation. In order to simulate changes in lake vertical temperature profile and specifically the bottom water temperature during ostracod valve formation, we have redeveloped a one‐dimensional eddy diffusion thermal lake model including a lake ice model and refined it by including a seasonal light extinction model. This model was tested for two different sites, Lac d'Annecy and Ammersee. Sensitivity studies show that the ostracod calcification temperature is approaching constant 3.7°C for colder, but may significantly vary for warmer than present conditions. In Lac d'Annecy, such temperature effects can lead to a significant underestimation of positive δ18OP excursions. In Ammersee the underestimation is smaller because the hypolimnic temperatures are less sensitive to surface temperature changes. Our model can be used to better constrain such temperature effects and such further increase the quality of the δ18OL and δ18OP reconstruction.
GCHap: fast MLEs for haplotype frequencies by gene counting
Authors: Thomas Alun
Published: October 2003

Summary: GCHap quickly finds maximum likelihood estimates (MLEs) of frequencies of haplotypes given genotype information on a random sample of individuals. It uses the gene counting method but by excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.

Availability: The Java classes and Javadocs pages for GCHap can be obtained from bioinformatics.med.utah.edu/~alun
Intersect: identification and visualization of overlaps in database search results
Authors: Pegg Scott C.-H. , Novak Walter R. P. , Babbitt Patricia C.
Published: October 2003

Summary: The determination of distant evolutionary relationships remains an important biological problem, and distant homologs often appear in statistically insignificant regions of sequence similarity searches. Intersect is a computer program designed to identify and visualize the overlaps between sets of sequences reported by multiple database searches. This capability extends the usefulness of database search results and aids researchers in identifying the individual sequences that best bridge sequence families and superfamilies.

Availability: The Intersect program is available from the Babbitt laboratory website at http://www.babbittlab.ucsf.edu/software/intersect
Modes and clustering for time-warped gene expression profile data
Authors: Liu Xueli , Müller Hans-Georg
Published: October 2003

Motivation: The study of the dynamics of regulatory processes has led to increased interest for the analysis of temporal gene expression level data. To address the dynamics of regulation, expression data are collected repeatedly over time. It is difficult to statistically represent the resulting high-dimensional data. When regulatory processes determine gene expression, time-warping is likely to be present, i.e. the sample of gene expression trajectories reflects variation not only in terms of the expression amplitudes, but also in terms of the temporal structure of gene expression.

Results: A non-parametric time-synchronized iterative mean updating technique is proposed to find an overall representation that corresponds to a mode of a sample of expression profiles, viewed as a random sample in function space. The proposed algorithm explores the application of previous work of Hall and Heckman to genome-wide expression data and provides an extension that includes random time-warping with the aim to synchronize timescales across genes. The proposed algorithm is universally applicable for the construction of modes for functional data with time-warping. We demonstrate the construction of mode functions for a sample of Drosophila gene expression data. The algorithm can be applied to define clusters among the observed trajectories of gene expression, without any kind of prior non-time-warped clustering, as illustrated in the numerical example.
A computational pipeline for protein structure prediction and analysis at genome scale
Authors: Shah Manesh , Passovets Sergei , Kim Dongsup , Ellrott Kyle , Wang Li , Vokler Inna , LoCascio Philip , Xu Dong , Xu Ying
Published: October 2003

Motivation: Experimental techniques alone cannot keep up with the production rate of protein sequences, while computational techniques for protein structure predictions have matured to such a level to provide reliable structural characterization of proteins at large scale. Integration of multiple computational tools for protein structure prediction can complement experimental techniques.

Results: We present an automated pipeline for protein structure prediction. The centerpiece of the pipeline is our threading-based protein structure prediction system PROSPECT. The pipeline consists of a dozen tools for identification of protein domains and signal peptide, protein triage to determine the protein type (membrane or globular), protein fold recognition, generation of atomic structural models, prediction result validation, etc. Different processing and prediction branches are determined automatically by a prediction pipeline manager based on identified characteristics of the protein. The pipeline has been implemented to run in a heterogeneous computational environment as a client/server system with a web interface. Genome-scale applications on Caenorhabditis elegans, Pyrococcus furiosus and three cyanobacterial genomes are presented.

Availability: The pipeline is available at http://compbio.ornl.gov/proteinpipeline/
Topology of gene expression networks as revealed by data mining and modeling
Authors: Lukashin Alexander V. , Lukashev Matvey E. , Fuchs Rainer
Published: October 2003

Motivation: Interpretation of high-throughput gene expression profiling requires a knowledge of the design principles underlying the networks that sustain cellular machinery. Recently a novel approach based on the study of network topologies has been proposed. This methodology has proven to be useful for the analysis of a variety of biological systems, including metabolic networks, networks of protein–protein interactions, and gene networks that can be derived from gene expression data. In the present paper, we focus on several important issues related to the topology of gene expression networks that have not yet been fully studied.

Results: The networks derived from gene expression profiles for both time series experiments in yeast and perturbation experiments in cell lines are studied. We demonstrate that independent from the experimental organism (yeast versus cell lines) and the type of experiment (time courses versus perturbations) the extracted networks have similar topological characteristics suggesting together with the results of other common principles of the structural organization of biological networks. A novel computational model of network growth that reproduces the basic design principles of the observed networks is presented. Advantage of the model is that it provides a general mechanism to generate networks with different types of topology by a variation of a few parameters. We investigate the robustness of the network structure to random damages and to deliberate removal of the most important parts of the system and show a surprising tolerance of gene expression networks to both kinds of disturbance.
A fast layout algorithm for protein interaction networks
Authors: Han Kyungsook , Ju Byong-Hyon
Published: October 2003

Motivation: Graph drawing algorithms are often used for visualizing relational information, but a naive implementation of a graph drawing algorithm encounters real difficulties when drawing large-scale graphs such as protein interaction networks.

Results: We have developed a new, extremely fast layout algorithm for visualizing large-scale protein interaction networks in the three-dimensional space. The algorithm (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of this algorithm over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases and (3) it provides several abstraction and comparison operations for effectively analyzing large-scale protein interaction networks.

Availability:  http://wilab.inha.ac.kr/interviewer/