bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatty acid composition, extraction, fractionation, and stabilization of bullfrog (Rana catesbeiana) oil
Authors: Méndez Eduardo , Sanhueza Julio , Nieto Susana , Speisky Hernán , Valenzuela Alfonso
Published: June 2007

The oil extracted from the fat‐storage organ (fat body) of the bullfrog (Rana catesbeiana) was characterized for its fatty acid composition. The main fatty acids were palmitic (18.1%), stearic (4.1%), myristic (2.7%), oleic (31.7%), and linoleic (12.9%) acids. Long‐chain polyunsaturated fatty acids were also present in significant amounts, i.e., eicosapentaenoic (1.5%) and docosahexaenoic (4.7%), and were probably derived from the fish meal content of the diet. A partially fractionated oil was extracted from the homogenized and frozen fat body with an oleic acid content of 43.2%. The natural alkaloid boldine, added at 0.5 mg/g oil level, improved the oxidative stability by a factor ranging from 1.7 to 2.4, as assessed by the Oil Stability Index method between 90 and 110°C. The stabilization effect of boldine was higher than that of naringenin, morin, and quercitin and for the synthetic antioxidant butylated hydroxytoluene at the same concentration level.
Pathologic evaluation of uterine leiomyoma treated with radiofrequency ablation
Authors: Luo Xin , Shen Yuan , Song Wen‐Xia , Chen Pei‐wen , Xie Xing‐mei , Wang Xiao‐yu
Published: June 2007

Objective: To explore the mechanism by which radiofrequency ablation (RFA) treats uterine leiomyoma by observing the features of the lesions caused by RFA to leiomyoma tissue. Methods: Specimens from treated lesions were observed after hysterectomy was performed immediately (acute test) or on the third day (chronic test) following treatment in 2 groups of 30 patients. Histopathologic studies were also performed for all specimens, with untreated specimens as controls. Results: For the acute and chronic tests, specimens from the RFA‐treated lesions included the center segment (group 1); the marginal segment (group 2); the segment 1‐cm away from the margin (group 3); and the segment 2‐cm away from the margin (group 4). In the acute test, group 1 showed a sharply demarcated area of coagulative necrosis that did not express estrogen receptor (ER) or progesterone receptor (PR); group 2 showed a severe hydropic degeneration or necrosis; and group 3 showed regular leiomyoma cells. The expression of ER and PR was significantly less in groups 2 and 3 than in the control group (P < 0.05), but ER and PR expression in group 4, which had normal leiomyoma cells, was the same as in the control group (P > 0.05). In the chronic test, group 1 showed carbonization and coagulation necrosis without ER or PR expression. There was severe hemorrhage and thrombosis in group 2; hyaline degeneration and tissue granulation in group 3; and mild degeneration in group 4. The expression of ER and PR was significantly lower in groups 2, 3, and 4 than in the control group (P < 0.05). Conclusion: Radiofrequency ablation might treat uterine leiomyomas by inducing coagulative necrosis and depressing ER and PR expression.
Birth Attendants Trained in “Prevention of Mother‐to‐Child HIV Transmission” Provide Care in Rural Cameroon, Africa
Authors: Wanyu Benjamin , Diom Emmanuel , Mitchell Patricia , Tih Pius M. , Meyer Dorothy J.
Published: June 2007

Since 1984, Cameroon Baptist Convention Health Board's Life Abundant Primary health care program has established primary health centers in remote villages and trained literate women in these villages as birth attendants to offer antenatal care, low‐risk delivery, and triage of high‐risk mothers to larger health facilities. In 2002, the birth attendants were trained to provide Prevention of Maternal‐to‐Child HIV Transmission (PMTCT) services, including counseling, voluntary testing, performing oral rapid HIV tests (OraQuick; OraSure Technologies, Inc., Bethlehem, PA), posttest counseling, and administering single‐dose nevirapine to HIV‐positive women, to be taken in labor, and to their newborns. Ongoing supervision is provided by nurse supervisors. Between July 2002 and June 2005, 30 PMTCT‐trained birth attendants in 20 villages counseled 2331 pregnant women and tested 2310 (99.1%) for HIV. Eighty‐two women had a positive OraQuick HIV test (3.5%). Forty‐two of these mothers were delivered by the trained birth attendants, with 88.1% of mothers and 85.7% of newborns receiving single‐dose nevirapine prophylaxis. Nevirapine‐treated babies were tested after 15 months of age, and two of 13 HIV‐exposed infants had a positive rapid HIV antibody test (15.3% transmission rate with treatment). Program challenges include: maintaining adequate supplies of HIV tests kits and medications, supervising and supporting the PMCT‐trained birth attendants on a regular basis, and achieving exclusive breastfeeding and early weaning.
Meeting Health Care Needs of Women Experiencing Complications of Miscarriage and Unsafe Abortion: USAID's Postabortion Care Program
Authors: Curtis Carolyn
Published: June 2007

Each year, an estimated 210 million women become pregnant. Worldwide, more than one fourth of these pregnancies will end in abortion or an unplanned birth. While many abortions may result from the desire to delay or avoid pregnancy, 15% to 20% of pregnancies will end in miscarriage or stillbirth with some causative agents being malaria, HIV/AIDS, and physical violence. Postabortion care (PAC) is needed to provide treatment for complications caused by incomplete or spontaneous abortion and critical family planning counseling and services to prevent future unplanned pregnancies that may result in repeat abortions. In 2003, the United States Agency for International Development (USAID) initiated a 5‐year strategy wherein seven countries were provided financial funding and technical assistance. Since 2003, more than 3000 women have been seen in health centers and health posts for PAC services; more than 14,000 community members have received messages on unsafe abortion; family planning, and complications of unsafe abortion and miscarriage; and more than 600 documents were reviewed for inclusion in a global PAC resource package. This package has been used for developing Cambodia's national PAC policy and for developing patient education materials and provider job aids in Cambodia and Tanzania. These promising methodologies will be replicated in other countries.
Eventful Transformations: Al-Futuwwa between History and the Everyday
Authors: Jacob Wilson Chacko
Published: June 2007

A special correspondent for the leading Egyptian newspaper al-Ahram wrote from Alexandria on 28 May 1936: “One of the effects of the Al-Bosfur nightclub murder in Cairo is that its circumstances have led to an interest in the problem of ‘al-futuwwat’ [sing., al-futuwwa] and how much power and influence (al-sat˙wa) they have in the capital and in other Egyptian cities.” The murder referred to was that of a popular singer and dancer, Imtithal Fawzi, by a band of assassins led by failed businessman and weight-trainer Fuad al-Shami. I argue here that this murder can be read as an instance of a larger event, which might be inscribed in the following way: a moment that irrevocably branded the public figure of futuwwa with the additional meanings of thug, mobster, and nefarious villain—bal ˙tagi. This is not the conventional way of registering this moment; indeed, the modern transformation of al-futuwwa is rarely considered as a historical event. It is not my aim here to affirm or deny the outcome of this transformation, nor am I suggesting that the normative conception of al-futuwwa as an Islamic ideal of masculinity had never before had any negative connotations. Rather, I posit—and want to interrogate—a changed historical relationship in the constitution of al-futuwwa, in which the nature of history itself was radically transformed and contributed to the formation of a new politics and a new subject of politics. As part of the hegemonic rise of this field of politics and its subject, history typically shows, or simply presumes, that other life-worlds, like that of the futuwwat and their particular form of power, were rendered exceptional and ultimately obsolete. In a larger project from which this article is drawn, I explored the gendered constitution of that new cultural and political hegemony. I labeled the gender norm that emerged at the intersection of colonial modernity and nationalism as effendi (bourgeois) masculinity, which I located in a new constellation of practices and discourses around the desirable, modern body. The present essay is in part an effort to de-center this bourgeois figure and the terms of its narration, which I unwittingly reproduced in the original study by rendering the event of the futuwwa's transformation as a bit part within a larger story of ostensibly greater national and historical import.
Virgil the Grammarian and Bede: a preliminary study
Authors: Bracken Damian
Published: June 2007

The chapters in Bede's De temporum ratione begin with an etymology for the name of the subject to be examined. Sources and analogues for some have not hitherto been identified. This article shows that some of these etymologies of words for the divisions of time come ultimately, though perhaps not directly, from bk XI of Virgil the Grammarian's Epitomae. These accounts of the origins of calendrical and cosmological terms wound their way through early western computistical works and eventually into Bede's De temporum ratione. The article identifies examples of Virgil's influence on anonymous early medieval biblical commentaries and discusses their significance as pointers towards their place of composition.
Mycobacteria causing human cervical lymphadenitis in pastoral communities in the Karamoja region of Uganda
Authors: OLOYA J. , OPUDA-ASIBO J. , KAZWALA R. , DEMELASH A. B. , SKJERVE E. , LUND A. , JOHANSEN T. B. , DJONNE B.
Published: June 2007

Mycobacteria from lymph node biopsies of patients with cervical lymphadenitis reporting for tuberculosis treatment in Matany and Moroto Hospitals in the transhumant areas of Karamoja, Uganda were isolated and characterized. The AccuProbe®culture identification kits forMycobacterium tuberculosiscomplex (MTC),M. aviumcomplex (MAC) andM. aviumwere used to identify the isolates. Spoligotyping, IS901PCR and IS1311and IS1245restriction fragment length polymorphism (RFLP) were used to characterize the isolates. Of the 43 biopsies, tenM. avium, sevenM. tuberculosis, threeM. bovis, and twoM. intracellularewere isolated. Two isolates could not be identified with AccuProbe®and from 19 samples no mycobacteria could be isolated. Three isolates with the Beijing spoligotype were identified from the sevenM. tuberculosisisolates. The spoligopatterns of theM. bovisisolates had previously been detected in cattle in Uganda. Isolation of members of the MAC group reflects the complex interaction between the transhumant communities, water sources and their cattle. None of theM. aviumisolates harboured IS901, and all showed several bands on IS1311and IS1245RFLP, in accordance withM. aviumsubsp.hominissuis. Composite dendrograms of IS1311and IS1245RFLP showed that the isolates were similar and identical patterns were found. The isolation ofM. bovisconfirms the human infection with zoonotic mycobacteria in areas where consumption of raw milk and meat is routine. Isolation of environmental mycobacteria also confirms their increasing role in human disease and the occupational risk of infection in the transhumant ecosystem in the absence of safe drinking water and environmental contamination.
Trace metals in cyanobacterial mats, phytoplankton and sediments of the Lake Vanda region, Antarctica
Authors: Webster-Brown J.G. , Webster K.S.
Published: June 2007

The degree and nature of association between trace metals (Cu, Pb, Zn, Ni, Ag, & Cd) and cyanobacterial mats, phytoplankton and sediments has been assessed in the Lake Vanda region of the Wright Valley, Victoria Land. Trace metal:Fe ratios and SEM imaging confirmed that apparent trace metal enrichment in cyanobacterial mats, relative to the sediment beneath, was due to incorporation of fine (sub-micron) sediment particles in the muciligenous matrix of the mat. In suspended particulate material (SPM) filtered from the oxic water of Lake Vanda and the Onyx River, the degree of trace metal binding to the SPM did not appear to correlate with phytoplankton content. Instead a positive correlation was observed between Fe and trace metal content. The SPM at the top of the lake water column, where only the finest sediment remains suspended, had the highest trace metal concentrations. It is concluded that the trace metal content of cyanobacterial mats and phytoplankton samples is primarily due to incorporation of fine sediment particles of high surface area which therefore enhance trace metal adsorption capacity. This reinforces the existing hypothesis that trace metal solubility in this environment is primarily controlled by abiotic processes.
Chemical and pharmacological chaperones as new therapeutic agents
Authors: Loo Tip W. , Clarke David M.
Published: June 2007

Proteins that are exported from the cell, or targeted to the cell surface or other organelles, are synthesised and assembled in the endoplasmic reticulum and then delivered to their destinations. Point mutations – the most common cause of human genetic diseases – can inhibit folding and assembly of the protein in the endoplasmic reticulum. The unstable or partially folded mutant protein does not undergo trafficking and is usually rapidly degraded. A potential therapy for protein misfolding is to correct defective protein folding and trafficking using pharmacological chaperones. Pharmacological chaperones are substrates or modulators that appear to function by directly binding to the partially folded biosynthetic intermediate to stabilise the protein and allow it to complete the folding process to yield a functional protein. Initial clinical studies with pharmacological chaperones have successfully reduced clinical symptoms of disease. Therefore, pharmacological chaperones show great promise as a new class of therapeutic agents that can be specifically tailored for a particular genetic disease.
Deglacial laminated facies on the NW European continental margin: The hydrographic significance of British‐Irish Ice Sheet deglaciation and Fleuve Manche paleoriver discharges
Authors: Eynaud F. , Zaragosi S. , Scourse J. D. , Mojtahid M. , Bourillet J. F. , Hall I. R. , Penaud A. , Locascio M. , Reijonen A.
Published: June 2007

We have compiled results obtained from four high sedimentation rate hemipelagic sequences from the Celtic sector of the NW European margin (NE Atlantic) to investigate the paleoceanographic and paleoclimatic evolution of the area over the last few climatic cycles. We focus on periods characteristic of deglacial transitions. We adopt a multiproxy sedimentological, geochemical, and micropaleontological approach, applying a sampling resolution down to ten microns for specific intervals. The investigation demonstrates the relationships between the Bay of Biscay hydrography and the glacial/deglacial history of both the proximal British‐Irish Ice Sheet (BIIS) and the western European continent. We identify recurrent phases of laminae deposition concurrent with major BIIS deglacial episodes in all the studied cores. Evidence for abrupt freshwater discharges into the open ocean highlights the influence of such events at a regional scale. We discuss their impact at a global scale considering the present and past key location of the Bay of Biscay versus the Atlantic Meridional Overturning Circulation (AMOC).
Insights on coccolith chemistry from a new ion probe method for analysis of individually picked coccoliths
Authors: Stoll Heather , Shimizu Nobumichi , Arevalos Alicia , Matell Nora , Banasiak Adam , Zeren Seth
Published: June 2007

The elemental chemistry of calcareous nannofossils may provide valuable information on past ocean conditions and coccolithophorid physiology, but artifacts from noncoccolith particles and from changing nannofossil assemblages may bias geochemical records from coccolith size fractions. We describe the first method for picking individual coccoliths using a tungsten needle in micromanipulator. Epoxy‐mounted individuals and populations of coccoliths can be analyzed by secondary ion mass spectrometry (SIMS). For Paleocene sediments the technique distinguishes the high Sr/Ca ratios of coccoliths (0.3 to 2.8 mmol/mol) from low ratios in abiogenic calcite blades (0.1 mmol/mol). The large heterogeneity of Sr/Ca ratios among different genera suggests that primary geochemical differences have not been homogenized by diagenetic overgrowth and the thick massive coccoliths of the late Paleocene are a primary feature of biomineralization. Sr/Ca ratios for modern genera are on average higher than those of Paleogene genera but exhibit a comparable level of variability.
Ionospheric climatology and variability from long‐term and multiple incoherent scatter radar observations: Climatology in eastern American sector
Authors: Zhang Shun‐Rong , Holt John M.
Published: June 2007

Ionospheric climatology and variability studies are conducted using long‐term incoherent scatter radar (ISR) observations from seven sites around the world. These studies result in an empirical model system, the ISR Ionospheric Model (ISRIM), which represents local and regional ionospheric climatology and variability of the ionosphere. This paper addresses some new climatological features revealed by the model for latitudes spanning 18–70°N over the eastern American sector. The latitudinal change of the F2‐layer electron density exhibits a clear depletion near Millstone Hill latitudes when solar activity is median or low, accompanied by a Te enhancement, and electron density peaks at ∼10° both to the north and south of Millstone Hill. Possible explanations are discussed. We also characterize several types of variation in plasma temperatures in this region, including ion temperature elevation for quiet conditions in the auroral zone and electron temperature increases toward higher latitudes.
Uncertainties in gridded air temperature fields and effects on predictive active layer modeling
Authors: Anisimov Oleg A. , Lobanov Vladimir A. , Reneva Svetlana A. , Shiklomanov Nikolay I. , Zhang Tingjun , Nelson Frederick E.
Published: June 2007

Several model‐based assessments predict a discernible increase in the depth of seasonal thawing and circumpolar‐scale warming of permafrost by the mid‐21st century. Quantitative estimates of the environmental and socioeconomic impacts of changing climate in northern regions require robust projection of changes in permafrost, which in turn depend on the availability of appropriate models and forcing data. We examined four high‐resolution, hemispheric‐scale gridded sets of monthly temperature and precipitation constructed using different interpolation routines and reanalysis of data from a large number of weather stations. At many of 455 Russian weather stations, the four data sets depart from empirical mean annual air temperatures averaged over the 15‐year period by 1–2°C and in cumulative daily positive temperature sums (degree days of thawing) by more than 200°C days. A permafrost model, forced with the gridded climatic data sets, was used to calculate the large‐scale characteristics of permafrost in northern Eurasia. We analyzed zonal‐mean air and ground temperatures, depth of seasonal thawing, and area occupied by near‐surface permafrost in Eurasia north of 45°N. The 0.5–1.0 °C difference in zonal‐mean air temperature between the data sets translates into a range of uncertainty of 10–20% in estimates of near‐surface permafrost area, which is comparable to the extent of changes projected for the following several decades. We conclude that more observations and theoretical studies are needed to improve characterization of baseline climatic conditions and to narrow the range of uncertainties in model‐based permafrost projections.
Anticorrelated multidecadal variations between surface and subsurface tropical North Atlantic
Authors: Zhang Rong
Published: June 2007

In this paper for the first time I show that the multidecadal variations of observed tropical North Atlantic (TNA) sea surface temperature (SST) are strongly anticorrelated with those of the observed TNA subsurface ocean temperature, with long‐term trends removed. I further show that the anticorrelated change between the TNA surface and subsurface temperature is a distinctive signature of the Atlantic meridional overturning circulation (AMOC) variations, using water‐hosing experiments with the GFDL state‐of‐art coupled climate model (CM2.1). External radiative forced simulations with the same model do not provide a significant relationship between the TNA surface and subsurface temperature variations. The observed detrended multidecadal TNA subsurface temperature anomaly may be taken as a proxy for the AMOC variability. Various mechanisms proposed for the multidecadal TNA SST variations, which are crucial for multidecadal variations of Atlantic hurricane activities, should take into account the observed anticorrelation between the TNA surface and subsurface temperature variations.
Polycomb protein Cbx4 promotes SUMO modification of de novo DNA methyltransferase Dnmt3a
Authors: Li Bing , Zhou Jing , Liu Peng , Hu Jialei , Jin Hong , Shimono Yohei , Takahashi Masahide , Xu Guoliang
Published: June 2007

The ‘de novo methyltransferase’ Dnmt3a (DNA methyltransferase 3a) has been shown to mediate transcriptional repression. Post-translational modification of Dnmt3a by SUMOylation affects its ability to transcriptionally repress. However, very little is known about how the SUMOylation process is regulated. In the present study, we identified a PcG (Polycomb group) protein, Cbx4 (chromobox 4), as a specific interaction partner of Dnmt3a. Co-expression of Cbx4 and SUMO-1 (small ubiquitin-related modifier-1) along with Dnmt3a in transfected cells results in enhanced modification of Dnmt3a with SUMO-1. Purified Cbx4 also promotes SUMOylation of Dnmt3a in vitro. The modification occurs in the N-terminal regulatory region, including the PWWP (Pro-Trp-Trp-Pro) domain. Our results suggest that Cbx4 functions as a SUMO E3 ligase for Dnmt3a and it might be involved in the functional regulation of DNA methyltransferases by promoting their SUMO modification.
Relative sensitivity of soluble guanylate cyclase and mitochondrial respiration to endogenous nitric oxide at physiological oxygen concentration
Authors: Rodríguez-Juárez Félix , Aguirre Enara , Cadenas Susana
Published: June 2007

Nitric oxide (NO) is a widespread biological messenger that has many physiological and pathophysiological roles. Most of the physiological actions of NO are mediated through the activation of sGC (soluble guanylate cyclase) and the subsequent production of cGMP. NO also binds to the binuclear centre of COX (cytochrome c oxidase) and inhibits mitochondrial respiration in competition with oxygen and in a reversible manner. Although sGC is more sensitive to endogenous NO than COX at atmospheric oxygen tension, the more relevant question is which enzyme is more sensitive at physiological oxygen concentration. Using a system in which NO is generated inside the cells in a finely controlled manner, we determined cGMP accumulation by immunoassay and mitochondrial oxygen consumption by high-resolution respirometry at 30 μM oxygen. In the present paper, we report that the NO EC50 of sGC was approx. 2.9 nM, whereas that required to achieve IC50 of respiration was 141 nM (the basal oxygen consumption in the absence of NO was 14±0.8 pmol of O2/s per 106 cells). In accordance with this, the NO–cGMP signalling transduction pathway was activated at lower NO concentrations than the AMPKs (AMP-activated protein kinase) pathway. We conclude that sGC is approx. 50-fold more sensitive than cellular respiration to endogenous NO under our experimental conditions. The implications of these results for cell physiology are discussed.
Proteasome-mediated CCAAT/enhancer-binding protein δ (C/EBPδ) degradation is ubiquitin-independent
Authors: Zhou Shanggen , DeWille James W.
Published: June 2007

C/EBPδ (CCAAT/enhancer-binding protein δ) is a member of the C/EBP family of nuclear proteins that function in the control of cell growth, survival, differentiation and apoptosis. We previously demonstrated that C/EBPδ gene transcription is highly induced in G0 growth-arrested mammary epithelial cells but the C/EBPδ protein exhibits a t1/2 of only ∼120 min. The goal of the present study was to investigate the role of C/EBPδ modification by ubiquitin and C/EBPδ proteasome-mediated degradation. Structural and mutational analyses demonstrate that an intact leucine zipper is required for C/EBPδ ubiquitination; however, the leucine zipper does not provide lysine residues for ubiquitin conjugation. C/EBPδ ubiquitination is not required for proteasome-mediated C/EBPδ degradation and the presence of ubiquitin does not increase C/EBPδ degradation by the proteasome. Instead, the leucine zipper stabilizes the C/EBPδ protein by forming homodimers that are poor substrates for proteasome degradation. To investigate the cellular conditions associated with C/EBPδ ubiquitination we treated G0 growth-arrested mammary epithelial cells with DNA-damage- and oxidative-stress-inducing agents and found that C/EBPδ ubiquitination is induced in response to H2O2. However, C/EBPδ protein stability is not influenced by H2O2 treatment. In conclusion, our results demonstrate that proteasome-mediated protein degradation of C/EBPδ is ubiquitin-independent.
Decomposition of density matrix renormalization group states into a Slater determinant basis
Authors: Moritz Gerrit , Reiher Markus
Published: June 2007

The quantum chemical density matrix renormalization group (DMRG) algorithm is difficult to analyze because of the many numerical transformation steps involved. In particular, a decomposition of the intermediate and the converged DMRG states in terms of Slater determinants has not been accomplished yet. This, however, would allow one to better understand the convergence of the algorithm in terms of a configuration interaction expansion of the states. In this work, the authors fill this gap and provide a determinantal analysis of DMRG states upon convergence to the final states. The authors show that upon convergence, DMRG provides the same complete-active-space expansion for a given set of active orbitals as obtained from a corresponding configuration interaction calculation. Additional insight into DMRG convergence is provided, which cannot be obtained from the inspection of the total electronic energy alone. Indeed, we will show that the total energy can be misleading as a decrease of this observable during DMRG microiteration steps may not necessarily be taken as an indication for the pickup of essential configurations in the configuration interaction expansion. One result of this work is that a fine balance can be shown to exist between the chosen orbital ordering, the guess for the environment operators, and the choice of the number of renormalized states. This balance can be well understood in terms of the decomposition of total and system states in terms of Slater determinants.
Enhanced antiferromagnetic saturation in amorphous CoFeB-Ru-CoFeB synthetic antiferromagnets by ion-beam assisted deposition
Authors: Huang J. C. A. , Hsu C. Y. , Chen S. F. , Liu C. P. , Liao Y. F. , Lin M. Z. , Lee C. H.
Published: June 2007

The interlayer coupling of CoFeB-based synthetic antiferromagnets (SyAFs), modulated by the ion-beam assisted deposition (IBAD) has been systematically investigated under different assisted deposition voltage from 0 to 140 V. We observe that proper IBAD voltage can significantly enhance the antiferromagnetically coupled saturation field from 280 to 1000 Oe and retain the amorphous structure of CoFeB layers. This approach provides a convenient method to enhance the magnetic coupling of SyAFs, which is useful for the magnetic tunnel junctions fabrication and magnetoresistive random access memory development.
Magnetic and structural properties of spin-reorientation transitions in orthoferrites
Authors: Tsymbal L. T. , Bazaliy Ya. B. , Derkachenko V. N. , Kamenev V. I. , Kakazei G. N. , Palomares F. J. , Wigen P. E.
Published: June 2007

Magnetic and structural characteristics of ErFeO3, TmFeO3, and YbFeO3 single crystals were studied over a wide temperature range. Magnetic measurements found that the spin-rotation transitions in all crystals are well described by the earlier proposed theory with no fitting parameters. Additionally, they have shown the absence of the magnetic compensation point in TmFeO3 and a noticeable growth of the c-axis magnetization at low temperatures in TmFeO3 and ErFeO3. The x-ray measurements found no symmetry-lowering lattice distortions during the reorientation. Overall, the measurements cover a wide range of material parameters and demonstrate the generality of the modified mean field theory of the Γ4→Γ24→Γ2 orientation phase transitions in orthoferrites.
The Flash-Lag Effect during Illusory Chopstick Rotation
Authors: Anstis Stuart
Published: June 2007

In the ‘flash-lag’ effect, a static object that is briefly flashed next to a moving object appears to lag behind the moving object. A flash was put up next to an intersection that appeared to be moving clockwise along a circular path but was actually moving counterclockwise [the chopstick illusion; Anstis, 1990, in AI and the Eye Eds A Blake, T Troscianko (London: John Wiley) pp 105–117; 2003, in Levels of Perception Eds L Harris, M Jenkin (New York: Springer) pp 90–93]. As a result, the flash appeared displaced clockwise. This was appropriate to the physical, not the subjective, direction of rotation, and it suggests that the flash-lag illusion occurs early in the visual system, before motion signals are parsed into moving objects.
Cueing Attention by Relative Motion in the Periphery of the Visual Field
Authors: Poggel Dorothe A , Strasburger Hans , MacKeben Manfred
Published: June 2007

Sudden changes of visual stimulation attract attention. The observer's body motion generates retinal-flow field patterns containing information about his/her own speed and trajectory and relative motion of other objects. We investigated the effectiveness of relative motion as an attentional cue and compared it with conventional cueing by appearance of a frame in the far periphery of the visual field. In a group of ten subjects, contrast thresholds for the perception of static Gabor grating orientation [four alternative non-forced-choice (4ANFC)] task were determined at 20°, 30°, 40°, and 60° eccentricity. Subsequently, near-threshold discrimination performance of Gabor pattern orientation without versus with a ring-shaped cue was measured at the same positions. The same Gabor patterns were then presented embedded in a random-dot flow field, and uncued discrimination performance was compared with performance after presentation of a relative-motion cue (RMC), ie a small random-dot field with motion in the opposite direction of the flow field. Both the conventional ring cue and the RMC induced significantly increased discrimination performance at all test locations. With the parameters chosen for this study, the RMC was slightly less effective than the conventional cue, but its effects were somewhat more pronounced in the far periphery of the visual field. Thus, relative motion is a powerful cue to attract attention to peripheral visual objects and improves performance as effectively as a conventional ring cue. The findings have practical relevance for everyday life, in particular for tasks like driving and navigation.
Size, shape and development time are plastic traits in salt lake ostracods of the Mytilocypris mytiloides (Ostracoda:Cyprididae) species complex
Authors: Finston Terrie
Published: June 2007

The taxonomy of the ostracod genus Mytilocypris is based in part on characters of shell morphology. Specifically, M. minuta, M. mytiloides and M. tasmanica chapmani lack distinctive internal characters and are differentiated largely on size and shape of the shell. The three taxa also differ in the salinity of the habitats they occupy. A field study showed a steady decrease in adult size, spanning the size range of all three taxa, over the course of a season within single lakes, in association with changing salinity and other environmental variables. The present study was conducted to investigate whether each phenotype could be produced under laboratory conditions of variable salinity. Offspring of the three parental phenotypes were raised under high and low salinity. Regardless of parental type, offspring grew more quickly, but reached a smaller size at high salinity, and grew more slowly, but reached a larger size at low salinity. The shape of the shell was found to have a significant size component. Plasticity in size and shape suggests these are unreliable characters for taxonomy. Accelerated development may be an adaptation to living in an ephemeral habitat, with salinity being one of the cues Mytilocypris uses to gauge habitat duration.
Area requirements and pelagic protected areas: is size an impediment to implementation?
Authors: Alpine J. E. , Hobday A. J.
Published: June 2007

Global oceans are experiencing not only increased levels of human exploitation, but also major changes to their physics, chemistry and biology. These alarming changes have prompted calls for new and improved conservation and management tools if the future sustainability of oceanic ecosystems is to be assured. Spatial management, although widely used in coastal and nearshore environments, is one strategy yet to be adequately considered for open ocean systems. Resistance to both investigation and implementation of this management approach stems predominantly from the perception that given the highly dynamic nature of the ocean, adequate protection of both its biological and physical components would require regulation of vast regions. To examine this assertion, a series of reserve networks were modelled using the reserve design tool Marxan for an oceanic region off eastern Australia. Consideration was given to a set of biological, physical and social features. Three distinct management approaches were evaluated; fisheries priority, conservation priority, and equal fisheries-conservation priority. Reserve solution area requirements ranged from 7% to 26% of the focus area, falling within the lower end of the range of areas suggested in the published reports. This analysis suggests that percentage area requirements for oceanic protected areas should not be an impediment to further consideration.
Geographic range, population structure and conservation status of the green python (Morelia viridis), a popular snake in the captive pet trade
Authors: Wilson David , Heinsohn Robert
Published: June 2007

Accurate knowledge of distribution and population size is required for effective conservation and management of wild species. Here we report on the first estimates of the distribution and density of the green python (Morelia viridis), an iconic rainforest species widely kept in captivity. We used climatic modelling to predict its distribution in Papua New Guinea, and both climate and vegetation mapping to predict its Australian distribution. We used mark–recapture methods to estimate the density and population structure of green pythons at Iron Range, northern Australia. Bioclimatic analyses suggested that there is extensive climatically suitable habitat in Papua New Guinea (≥200 000 km2), but very little in Australia (~300 km2). However, use of vegetation maps increases the predicted suitable area of occupancy in Australia to 3127 km2, including nine regional ecosystems. Density estimates at Iron Range were 4–5 ha–1 in the complex vine forest regional ecosystem; however, only half of these were mature adults. The large predicted area of occurrence and the high density in the one intensively studied area suggest that the species is not vulnerable to extinction in the short term. However, more studies are needed in both New Guinea and Australia, especially to quantify the impact of harvesting green pythons for the pet trade.
Differential rates of offspring provisioning in Gould's petrels: are better feeders better breeders
Authors: O'Dwyer Terence W. , Buttemer William A. , Priddel David M.
Published: June 2007

Procellariiformes (albatrosses and petrels) must accumulate substantial energy reserves to sustain them while incubating their single egg. They then produce a chick that is often more than 130% of their own body mass. Thus, despite the variable nature of resource availability in the marine environment, successful reproduction requires a considerable increase in foraging rates. Birds that are better foragers are, therefore, likely to be better parents. As surrogates of foraging ability, we assessed two parental traits that are separated temporally over the breeding season, body condition during incubation and provisioning performance, in Gould’s petrel (Pterodroma leucoptera). Although parental condition did not influence hatching success, we found significant positive correlations between the average body condition of a breeding pair and both the growth rate of chicks (g day–1) and the body condition of chicks at peak mass. Provisioning rate also correlated positively with chick condition. Chick condition was positively correlated with haemoglobin concentration [Hb] at peak mass, which was positively correlated with [Hb] at fledging. Because the probability of survival after fledging may be influenced by chick body condition and [Hb], the ability of parents to acquire additional resources for breeding is likely to be an important determinant of reproductive success.
Neural correlates of attentional expertise in long-term meditation practitioners
Authors: Brefczynski-Lewis J. A. , Lutz A. , Schaefer H. S. , Levinson D. B. , Davidson R. J.
Published: June 2007

Meditation refers to a family of mental training practices that are designed to familiarize the practitioner with specific types of mental processes. One of the most basic forms of meditation is concentration meditation, in which sustained attention is focused on an object such as a small visual stimulus or the breath. In age-matched participants, using functional MRI, we found that activation in a network of brain regions typically involved in sustained attention showed an inverted u-shaped curve in which expert meditators (EMs) with an average of 19,000 h of practice had more activation than novices, but EMs with an average of 44,000 h had less activation. In response to distracter sounds used to probe the meditation, EMs vs. novices had less brain activation in regions related to discursive thoughts and emotions and more activation in regions related to response inhibition and attention. Correlation with hours of practice suggests possible plasticity in these mechanisms.
Generation of reactive oxygen species by fungal NADPH oxidases is required for rice blast disease
Authors: Egan Martin J. , Wang Zheng-Yi , Jones Mark A. , Smirnoff Nicholas , Talbot Nicholas J.
Published: June 2007

One of the first responses of plants to microbial attack is the production of extracellular superoxide surrounding infection sites. Here, we report that
Magnaporthe grisea
, the causal agent of rice blast disease, undergoes an oxidative burst of its own during plant infection, which is associated with its development of specialized infection structures called appressoria. Scavenging of these oxygen radicals significantly delayed the development of appressoria and altered their morphology. We targeted two superoxide-generating NADPH oxidase-encoding genes, Nox1 and Nox2, and demonstrated genetically, that each is independently required for pathogenicity of
M. grisea
. Δ
nox1
and Δ
nox2
mutants are incapable of causing plant disease because of an inability to bring about appressorium-mediated cuticle penetration. The initiation of rice blast disease therefore requires production of superoxide by the invading pathogen.
The network of sequence flow between protein structures
Authors: Meyerguz Leonid , Kleinberg Jon , Elber Ron
Published: June 2007

Sequence–structure relationships in proteins are highly asymmetric because many sequences fold into relatively few structures. What is the number of sequences that fold into a particular protein structure? Is it possible to switch between stable protein folds by point mutations? To address these questions, we compute a directed graph of sequences and structures of proteins, which is based on 2,060 experimentally determined protein shapes from the Protein Data Bank. The directed graph is highly connected at native energies with “sinks” that attract many sequences from other folds. The sinks are rich in β-sheets. The number of sequences that transition between folds is significantly smaller than the number of sequences retained by their fold. The sequence flow into a particular protein shape from other proteins correlates with the number of sequences that matches this shape in empirically determined genomes. Properties of strongly connected components of the graph are correlated with protein length and secondary structure.
Non-parametric quantification of protein lysate arrays
Authors: Hu Jianhua , He Xuming , Baggerly Keith A. , Coombes Kevin R. , Hennessy Bryan T.J. , Mills Gordon B.
Published: June 2007

Motivation: Proteins play a crucial role in biological activity, so much can be learned from measuring protein expression and post-translational modification quantitatively. The reverse-phase protein lysate arrays allow us to quantify the relative expression levels of a protein in many different cellular samples simultaneously. Existing approaches to quantify protein arrays use parametric response curves fit to dilution series data. The results can be biased when the parametric function does not fit the data.

Results: We propose a non-parametric approach which adapts to any monotone response curve. The non-parametric approach is shown to be promising via both simulation and real data studies; it reduces the bias due to model misspecification and protects against outliers in the data. The non-parametric approach enables more reliable quantification of protein lysate arrays.

Availability: Code to implement the proposed method in the statistical package R is available at: http://odin.mdacc.tmc.edu/jhu/lysatearray-analysis/

Contact:  jhu@mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.
A Higher Plant Δ8 Sphingolipid Desaturase with a Preference for (Z)-Isomer Formation Confers Aluminum Tolerance to Yeast and Plants
Authors: Ryan Peter R. , Liu Qing , Sperling Petra , Dong Bei , Franke Stefan , Delhaize Emmanuel
Published: June 2007

Three plant cDNA libraries were expressed in yeast (Saccharomyces cerevisiae) and screened on agar plates containing toxic concentrations of aluminum. Nine cDNAs were isolated that enhanced the aluminum tolerance of yeast. These cDNAs were constitutively expressed in Arabidopsis (Arabidopsis thaliana) and one cDNA from the roots of Stylosanthes hamata, designated S851, conferred greater aluminum tolerance to the transgenic seedlings. The protein predicted to be encoded by S851 showed an equally high similarity to Δ6 fatty acyl lipid desaturases and Δ8 sphingolipid desaturases. We expressed other known Δ6 desaturase and Δ8 desaturase genes in yeast and showed that a Δ6 fatty acyl desaturase from Echium plantagineum did not confer aluminum tolerance, whereas a Δ8 sphingobase desaturase from Arabidopsis did confer aluminum tolerance. Analysis of the fatty acids and sphingobases of the transgenic yeast and plant cells demonstrated that S851 encodes a Δ8 sphingobase desaturase, which leads to the accumulation of 8(Z/E)-C18-phytosphingenine and 8(Z/E)-C20-phytopshingenine in yeast and to the accumulation of 8(Z/E)-C18-phytosphingenine in the leaves and roots of Arabidopsis plants. The newly formed 8(Z/E)-C18-phytosphingenine in transgenic yeast accounted for 3 mol% of the total sphingobases with a 8(Z):8(E)-isomer ratio of approximately 4:1. The accumulation of 8(Z)-C18-phytosphingenine in transgenic Arabidopsis shifted the ratio of the 8(Z):8(E) isomers from 1:4 in wild-type plants to 1:1 in transgenic plants. These results indicate that S851 encodes the first Δ8 sphingolipid desaturase to be identified in higher plants with a preference for the 8(Z)-isomer. They further demonstrate that changes in the sphingolipid composition of cell membranes can protect plants from aluminum stress.
Long-Term Response toward Inorganic Carbon Limitation in Wild Type and Glycolate Turnover Mutants of the Cyanobacterium Synechocystis sp. Strain PCC 6803
Authors: Eisenhut Marion , von Wobeser Eneas Aguirre , Jonas Ludwig , Schubert Hendrik , Ibelings Bas W. , Bauwe Hermann , Matthijs Hans C.P. , Hagemann Martin
Published: June 2007

Concerted changes in the transcriptional pattern and physiological traits that result from long-term (here defined as up to 24 h) limitation of inorganic carbon (Ci) have been investigated for the cyanobacterium Synechocystis sp. strain PCC 6803. Results from reverse transcription-polymerase chain reaction and genome-wide DNA microarray analyses indicated stable up-regulation of genes for inducible CO2 and HCO3  − uptake systems and of the rfb cluster that encodes enzymes involved in outer cell wall polysaccharide synthesis. Coordinated up-regulation of photosystem I genes was further found and supported by a higher photosystem I content and activity under low Ci (LC) conditions. Bacterial-type glycerate pathway genes were induced by LC conditions, in contrast to the genes for the plant-like photorespiratory C2 cycle. Down-regulation was observed for nitrate assimilation genes and surprisingly also for almost all carboxysomal proteins. However, for the latter the observed elongation of the half-life time of the large subunit of Rubisco protein may render compensation. Mutants defective in glycolate turnover (ΔglcD and ΔgcvT) showed some transcriptional changes under high Ci conditions that are characteristic for LC conditions in wild-type cells, like a modest down-regulation of carboxysomal genes. Properties under LC conditions were comparable to LC wild type, including the strong response of genes encoding inducible high-affinity Ci uptake systems. Electron microscopy revealed a conspicuous increase in number of carboxysomes per cell in mutant ΔglcD already under high Ci conditions. These data indicate that an increased level of photorespiratory intermediates may affect carboxysomal components but does not intervene with the expression of majority of LC inducible genes.
Solution structure of the general transcription factor 2I domain in mouse TFII‐I protein
Authors: Doi‐Katayama Yukiko , Hayashi Fumiaki , Inoue Makoto , Yabuki Takashi , Aoki Masaaki , Seki Eiko , Matsuda Takayoshi , Kigawa Takanori , Yoshida Mayumi , Shirouzu Mikako , Terada Takaho , Hayashizaki Yoshihide , Yokoyama Shigeyuki , Hirota Hiroshi
Published: June 2007

The general transcription factor TFII‐I, with the corresponding gene name GTF2I, is an unusual transcriptional regulator that associates with both basal and signal‐induced transcription factors. TFII‐I consists of six GTF2I repeat domains, called I‐repeats R1–R6. The structure and function of the GTF2I domain are not clearly understood, even though it contains a helix‐loop‐helix motif, which is considered to be the protein–protein interaction area, based on biochemical analyses. Here, we report the solution structure of the fifth repeat of the six GTF2I repeat domains from murine TFII‐I, which was determined by heteronuclear multidimensional NMR spectroscopy (PDB code 1Q60). The three‐dimensional structure of the GTF2I domain is classified as a new fold, consisting of four helices (residues 8–24, 34–39, 63–71, and 83–91), two antiparallel beta strands (residues 44–47 and 77–80), and a well‐defined loop containing two β‐turns between sheet 1 and helix 3. All of the repeats probably have similar folds to that of repeat 5, because the conserved residues in the GTF2I repeat domains are assembled on the hydrophobic core, turns, and secondary structure elements, as revealed by a comparison of the sequences of the first through the sixth GTF2I repeats in TFII‐I.