bluuebunny/crossref_metadata_2025 huggingface dataset:
SOFTDOCK application to protein–protein interaction benchmark and CAPRI
Authors: Li Nan , Sun Zhonghua , Jiang Fan
Published: September 2007

The success of molecular docking requires cooperation of sampling and scoring of various conformations. The SOFTDOCK package uses a coarse‐grained docking method to sample all possible conformations of complexes. SOFTDOCK uses a new Voronoi molecular surface and calculates several grid‐based scores. It is shown by the leave‐one‐out test that three geometry scores and an FTDOCK‐like electrostatics score contribute the most to the discrimination of near‐native conformations. However, an atom‐based solvation score is shown to be ineffective. It is also found that an increased Voronoi surface thickness greatly increases the accuracy of docking results. Finally, the clustering procedure is shown to improve the overall ranking, but leads to less accurate docking results. The application of SOFTDOCK in Critical Assessment of PRedicted Interactions involves four steps: (i) sampling with INTELEF; (ii) clustering; (iii) AMBER energy minimization; and (iv) manual inspection. Biological information from literature is used as filters in some of the sampling and manual inspection according to different targets. Two of our submissions have L_rmsd around 10 Å. Although they are not classified as acceptable solutions, they are considered successful because they are comparable to the accuracy of our method. Availability: SOFTDOCK is open source code and can be downloaded at http://bio.iphy.ac.cn Proteins 2007. © 2007 Wiley‐Liss, Inc.
Protein–protein docking: Progress in CAPRI rounds 6–12 using a combination of methods: The introduction of steered solvated molecular dynamics
Authors: Heifetz Alexander , Pal Sandeep , Smith Graham R.
Published: September 2007

In recent rounds of CAPRI, the Bii group has employed a combination of techniques for the prediction of the structure of protein–protein complexes. We currently use third‐party software for rigid‐body and semiflexible docking (MolFit, 3D‐Dock, RosettaDock), and our own steered molecular dynamics (SMD) technique for flexible refinement. SMD has also been found to be useful for discriminating near‐native from false positive docking decoys. In addition to this, a variety of sources of information, including multiple descriptors of interface quality combined with a QSAR‐like technique, published biological information, and continuum electrostatics calculations, are also used in the assessment of candidate complexes. We shall concentrate on results for CAPRI rounds 9–11 (targets 24–27). In these rounds, the Bii group has been successful in submitting a medium quality model for each of CAPRI targets 25 and 26, and a model of acceptable quality for target 27. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility
Authors: May Andreas , Zacharias Martin
Published: September 2007

A reduced protein model combined with a systematic docking approach has been employed to predict protein–protein complex structures in CAPRI rounds 6–11. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to the second protein starting from many thousand initial protein partner placements. It also allows for approximate inclusion of global flexibility of protein partners during systematic docking by conformational relaxation of the partner proteins in precalculated soft collective backbone degrees of freedom. We have submitted models for six targets, achieved acceptable docking solutions for two targets, and predicted >20% correct contacts for five targets. Possible improvements of the docking approach in particular at the scoring and refinement steps are discussed. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Assessing the energy landscape of CAPRI targets by FunHunt
Authors: London Nir , Schueler‐Furman Ora
Published: September 2007

RosettaDock has repeatedly created high‐resolution structures of protein complexes in the CAPRI experiment, thanks to the explicit modeling of conformational changes of the monomers at the side chain level. These models can be selected based on their energy. During the search for the lowest‐energy model, RosettaDock samples a deep funnel around the native orientation, but additional funnels may appear in the energy landscape, especially in cases where backbone conformational changes occur upon binding. We have previously developed FunHunt, a Support Vector Machine‐based classifier that distinguishes the energy funnels around the native orientation from other funnels in the energy landscape. Here we assess the ability of FunHunt to help in model selection in the CAPRI experiment. For all of 12 recent CAPRI targets, FunHunt clearly identifies a near‐native funnel in comparison to the funnel around the lowest energy model identified by the RosettaDock global search protocol. FunHunt is also able to choose a near‐native orientation among models submitted by predictor groups, demonstrating its general applicability for model selection. This suggests that FunHunt will be a valuable tool in coming CAPRI rounds for the selection of models, and for the definition of regions that need further refinement with restricted backbone flexibility. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI
Authors: Gong Xin Qi , Chang Shan , Zhang Qing Hua , Li Chun Hua , Shen Long Zhu , Ma Xiao Hui , Wang Ming Hui , Liu Bin , He Hong Qiu , Chen Wei Zu , Wang Cun Xin
Published: September 2007

Protein–protein docking is usually exploited with a two‐step strategy, i.e., conformational sampling and decoy scoring. In this work, a new filter enhanced sampling scheme was proposed and added into the RosettaDock algorithm to improve the conformational sampling efficiency. The filter term is based on the statistical result that backbone hydrogen bonds in the native protein structures are wrapped by more than nine hydrophobic groups to shield them from attacks of water molecules (Fernandez and Scheraga, Proc Natl Acad Sci USA 2003;100:113–118). A combinatorial scoring function, ComScore, specially designed for the other‐type protein–protein complexes was also adopted to select the near native docked modes. ComScore was composed of the atomic contact energy, van der Waals, and electrostatic interaction energies, and the weight of each item was fit through the multiple linear regression approach. To analyze our docking results, the filter enhanced sampling scheme was applied to targets T12, T20, and T21 after the CAPRI blind test, and improvements were obtained. The ligand least root mean square deviations (L_rmsds) were reduced and the hit numbers were increased. ComScore was used in the scoring test for CAPRI rounds 9–12 with good success in rounds 9 and 11. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Synthesis and antitumor activity of peptide‐paclitaxel conjugates
Authors: Papas Serafim , Akoumianaki Tonia , Kalogiros Christos , Hadjiarapoglou Lazaros , Theodoropoulos Panayiotis A. , Tsikaris Vassilios
Published: September 2007

Paclitaxel (Pac) is the most important anticancer drug used mainly in treatment of breast, lung, and ovarian cancer and is being investigated for use as a single agent for treatment of lung cancer, advanced head and neck cancers, and adenocarcinomas of the upper gastrointestinal tract. In this work, we present the synthesis of five 2′‐paclitaxel‐substituted analogs in which paclitaxel was covalently bound to peptides or as multiple copies to synthetic carriers. Ac‐Cys(CH2CO‐2′‐Pac)‐Arg‐Gly‐Asp‐Arg‐NH2, Folyl‐Cys(CH2CO‐2′‐Pac)‐Arg‐Gly‐Asp‐Ser‐NH2, Ac‐[Lys‐Aib‐Cys(CH2CO‐2′‐Pac)]2‐NH2, Ac‐[Lys‐Aib‐Cys(CH2CO‐2′‐Pac)]3‐NH2 and Ac‐[Lys‐Aib‐Cys(CH2CO‐2′‐Pac)]4‐NH2 were synthesized using 2′‐halogeno‐acetylated paclitaxel derivatives. Paclitaxel conjugates showed greater solubility in water than paclitaxel and inhibited the proliferation of human breast, prostate, and cervical cancer cell lines. Although all synthesized compounds had an antiproliferative activity, the Ac‐[Lys‐Aib‐Cys(CH2CO‐2′‐Pac)]4‐NH2 derivative showed improved biological activity in comparison with paclitaxel in cervical and prostate human cancer cells. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Loop propensity of the sequence YKGQP from staphylococcal nuclease: implications for the folding of nuclease
Authors: Patel Sunita , Sasidhar Yellamraju U.
Published: September 2007

Recently we performed molecular dynamics (MD) simulations on the folding of the hairpin peptide DTVKLMYKGQPMTFR from staphylococcal nuclease in explicit water. We found that the peptide folds into a hairpin conformation with native and nonnative hydrogen‐bonding patterns. In all the folding events observed in the folding of the hairpin peptide, loop formation involving the region YKGQP was an important event. In order to trace the origins of the loop propensity of the sequence YKGQP, we performed MD simulations on the sequence starting from extended, polyproline II and native type I' turn conformations for a total simulation length of 300 ns, using the GROMOS96 force field under constant volume and temperature (NVT) conditions. The free‐energy landscape of the peptide YKGQP shows minima corresponding to loop conformation with Tyr and Pro side‐chain association, turn and extended conformational forms, with modest free‐energy barriers separating the minima. To elucidate the role of Gly in facilitating loop formation, we also performed MD simulations of the mutated peptide YKAQP (Gly → Ala mutation) under similar conditions starting from polyproline II conformation for 100 ns. Two minima corresponding to bend/turn and extended conformations were observed in the free‐energy landscape for the peptide YKAQP. The free‐energy barrier between the minima in the free‐energy landscape of the peptide YKAQP was also modest. Loop conformation is largely sampled by the YKGQP peptide, while extended conformation is largely sampled by the YKAQP peptide. We also explain why the YKGQP sequence samples type II turn conformation in these simulations, whereas the sequence as part of the hairpin peptide DTVKLMYKGQPMTFR samples type I' turn conformation both in the X‐ray crystal structure and in our earlier simulations on the folding of the hairpin peptide. We discuss the implications of our results to the folding of the staphylococcal nuclease. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
A general goodness‐of‐fit test for Markov and hidden Markov models
Authors: Titman Andrew C. , Sharples Linda D.
Published: September 2007

Markov models are a convenient and useful method of estimating transition rates between levels of a categorical response variable, such as a disease stage, which changes over time. In medical applications the response variable is typically observed at irregular intervals. A Pearson‐type goodness‐of‐fit test for such models was proposed by Aguirre‐Hernandez and Farewell (Statist. Med. 2002; 21:1899–1911), but this test is not applicable in the common situation where the process includes an absorbing state, such as death, for which the time of entry is known precisely nor when the data include censored state observations. This paper presents a modification to the Pearson‐type test to allow for these cases. An extension of the method, to allow for the class of hidden Markov models where the response variable is subject to misclassification error, is given. The method is applied to data on cardiac allograft vasculopathy in post‐heart‐transplant patients. Copyright © 2007 John Wiley & Sons, Ltd.
A comparison of methods for determining HIV viral set point
Authors: Mei Y. , Wang L. , Holte S. E.
Published: September 2007

During a course of human immunodeficiency virus (HIV‐1) infection, the viral load usually increases sharply to a peak following infection and then drops rapidly to a steady state, where it remains until progression to AIDS. This steady state is often referred to as the viral set point. It is believed that the HIV viral set point results from an equilibrium between the HIV virus and immune response and is an important indicator of AIDS disease progression. In this paper, we analyze a real data set of viral loads measured before antiretroviral therapy is initiated, and propose two‐phase regression models to utilize all available data to estimate the viral set point. The advantages of the proposed methods are illustrated by comparing them with two empirical methods, and the reason behind the improvement is also studied. Our results illustrate that for our data set, the viral load data are highly correlated and it is cost effective to estimate the viral set point based on one or two measurements obtained between 5 and 12 months after HIV infection. The utility and limitations of this recommendation will be discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Anterior sacral meningocele: management in gynecological practice
Authors: Manson F. , Comalli‐Dillon K. , Moriaux A.
Published: September 2007

We describe the case of a young woman with anterior sacral meningocele (ASM), initially identified during a routine ultrasound examination and subsequently diagnosed using magnetic resonance imaging (MRI). ASM is a rare disorder characterized by uni‐ or multilocular extensions of the meninges from the sacral spinal canal to the retroperitoneal presacral space. Common symptoms include lower back and pelvic pain, constipation, difficulties in defecation, dysmenorrhea and dyspareunia, and urinary incontinence, retention or urgency. Perineal and lower‐extremity paresthesias may present when nerve roots are affected. Despite its more posterior location, ASM can mimic an ovarian cyst or other adnexal cystic mass, and in the obstetric patient can present a mechanical obstacle to delivery with a risk of rupture and infection during labor and delivery. Although it is a rare condition, we feel that awareness of the etiology, presentation and imaging characteristics of ASM is of importance and have therefore carried out a review of the literature, taking into account case findings and the obstetric and gynecological management of this disorder. Copyright © 2007 ISUOG. Published by John Wiley & Sons, Ltd.
Aeroelastic instability problems for wind turbines
Authors: Hansen M. H.
Published: September 2007

This paper deals with the aeroelastic instabilities that have occurred and may still occur for modern commercial wind turbines: stall‐induced vibrations for stall‐turbines, and classical flutter for pitch‐regulated turbines. A review of previous works is combined with derivations of analytical stability limits for typical blade sections that show the fundamental mechanisms of these instabilities. The risk of stall‐induced vibrations is mainly related to blade airfoil characteristics, effective direction of blade vibrations and structural damping; whereas the blade tip speed, torsional blade stiffness and chordwise position of the center of gravity along the blades are the main parameters for flutter. These instability characteristics are exemplified by aeroelastic stability analyses of different wind turbines. The review of each aeroelastic instability ends with a list of current research issues that represent unsolved aeroelastic instability problems for wind turbines. Copyright © 2007 John Wiley & Sons, Ltd.
“Workers’ Self-Management and Social Property”: A Comment
Authors: Reed Adolph L.
Published: September 2007

The tradition of all the dead generations weighs like a nightmare on the brain of the living. And just when they seem engaged in revolutionizing themselves and things, in creating something that has never existed, precisely in such periods of revolutionary crisis they anxiously conjur up the spirits of the past to their service and borrow from them names, battle cries and costumes in order to present the new scene of world history in this time-honoured disguise and this borrowed language.1
Treatment of Scaphoid Nonunions with Closed-Wedge Osteotomy of the Distal Radius: Report of Six Cases
Authors: Monreal Ricardo
Published: September 2007

Background The ideal treatment of nonunion of the scaphoid remains unresolved and controversial. It was hypothesized that scaphoid nonunion could be treated successfully using a closed-wedge osteotomy of the distal radius which reduces the inclination of the joint surface and decreases the pressure between the radial and scaphoid surfaces with a reduction of the force applied by the styloid process. We present a preliminary report in six patients with nonunion of the carpal scaphoid using this procedure. The main objective of the osteotomy is to achieve fusion, alleviate pain, and improve function.

Materials and Methods Six closed-wedge osteotomies to reduce the inclination of the distal radial surface were performed in patients with scaphoid waist nonunion and a viable proximal pole, without posttrauma osteoarthritis or with moderate posttraumatic osteoarthritis confined to the radio-scaphoid joint. The present series of six patients (all men) were followed for at least 8 months (mean follow-up 14.2 months, range 8–21 months).

Results Solid union was achieved in five patients. Postoperatively, three patients were pain-free, two presented mild pain for heavy work, and one had moderate pain. This type of osteotomy reduced the inclination of the joint surface (radial angulation) 6.2° on average. There was an improvement in joint flexion from a preoperative mean of 40° to 52.5° at last follow-up, in extension from 40.8° to 66.7°, in radial deviation from 15° to 22.5°, and in ulnar deviation from 30.8° to 41.7°.

Conclusions This preliminary study suggests that a closed-wedge osteotomy of the distal radius could be an alternative approach for patients with scaphoid waist nonunion and a viable proximal pole, without posttrauma osteoarthritis or with moderate posttraumatic osteoarthritis confined to the radio-scaphoid joint. The number of cases was small; however, further studies with a much larger series are needed before routine use of wedge osteotomy in scaphoid nonunion can be recommended.
A Novel Cryo‐SEM Technique for Imaging Vegetable Oil Based Organogels
Authors: Rogers Michael A. , Smith Alexandra K. , Wright Amanda J. , Marangoni Alejandro G.
Published: September 2007

Gels were prepared by cooling dilute solutions (2% wt/wt) of 12‐hydroxystearic acid (12‐HSA) in canola oil and storing them at 30 °C for 24 h. The gel's in‐situ supramolecular network structure was imaged using four techniques: polarized light microscopy (PLM), 3‐dimensional deconvolution polarized light microscopy (3DPLM), and cryo‐scanning electron microscopy (cryo‐SEM) of the xerogel and of an osmium tetroxide vapor fixed gel washed with isobutanol. Most of the canola oil was immobilized in the gel by fixation with osmium tetroxide therefore very little of the canola oil was removed during washing unlike the xerogel where all of the canola oil has been displaced. The in‐situ supramolecular network structure as observed by PLM, was comparable to that seen through the new cryo‐SEM method for fixed organogel. Cryo‐SEM images of the xerogel did not show similar length scales or strand thickness as compared to the PLM images. The lengths of the network strands were much shorter for the xerogel as compared to the osmium tetroxide treated sample and the structures visualized by PLM. Furthermore, the thickness of the strands observed using PLM or cryo‐SEM were in the size range of 3–10 μm while the xerogels had strands in the range of 0.01–0.1 μm thick. Therefore, the removal of canola oil from the gel using 80/20% v/v hexane/acetone with no fixation disrupted the supramolecular network.
Reviews
Authors: Beckwith Helen , Overman Susan , Frydendall Jodi , O'Connor Ellen
Published: September 2007

The Stem Cell Divide, Michael Bellomo 2006, 272 pages, $24.95 hardcover

Unplugged: Reclaiming Our Right to Die in America, William H. Colby, 2006, 272 pages, $24.95 hardcover

Mosby's Diagnostic and Laboratory Test Reference, eighth edition, Kathleen D. Pagana and Timothy J. Pagana, 2007; 1,120 pages, $39.95 softcover

A Daybook for Nurse Leaders and Mentors, Sigma Theta Tau International, 2006, 180 pages, $19.95 softcover
Chromatin extrusion in resting encystment of Colpoda cucullus: A possible involvement of apoptosis‐like nuclear death
Authors: Akematsu Takahiko , Matsuoka Tatsuomi
Published: September 2007

The extrusion of macronuclear chromatin is a remarkable characteristic during encystment in Colpoda, but the biological significance of this phenomenon has not been fully elucidated. Here we demonstrate that chromatin extrusion occurs with high frequency when encystment was induced by increasing Ca2+ in growing cells in various stages of the cell cycle. The Feulgen‐DNA reaction revealed that vegetatively growing cells have more macronuclear DNA than cells in the stationary phase, suggesting an association of macronuclear DNA content with the execution of chromatin extrusion. Using 4′,6‐diamidino‐2‐phenylindole (DAPI), we found that the size of the macronuclear extrusion body was reduced with time and eventually disappeared approximately 24 h after encystment induction. In addition, oligonucleosome‐sized DNA cleavage was confirmed to occur concomitant with the size reduction, suggesting that the extrusion body is selectively degraded, while the normal macronucleus remains alive. Combined use of acridine orange and Hoechst 33342 demonstrated that the extruded body was increasingly acidified before final resorption. These features are reminiscent of the nuclear degradation process in conjugating Tetrahymena, and therefore we conclude that chromatin extrusion in Colpoda might occur to adjust the macronuclear DNA content prior to encystment. In this way, it is similar to the apoptotic‐like nuclear death that occurs during the conjugation of other ciliates.
Cancer: A matter of life cycle?
Authors: Erenpreisa Jekaterina , Cragg Mark S.
Published: September 2007

In the last decade, the concept of “cancer stem cells” has emerged, recognised by the fact that only a small fraction of tumour cells appears to retain the stem cell properties of self‐renewal and unlimited proliferation. At the same time, it is well known that cancer is an age‐related disease developing at the limit of proliferating cell senescence. The apparent need to link senescence and the capacity for self‐renewal has lead some authors to suggest that cancers develop from amongst senescing stem cells. However, an alternative solution has recently been proffered by Sundaram M, Guernsey DL, Rajaraman MM, Rajaraman R [Neosis: a novel type of cell division in cancer. Cancer Biol Ther 2004;3:207–18], who suggest that stemness may be a transient, cyclic property afforded by de‐polyploidisation of senescing cells which have undergone polyploidisation. In this mini‐review, we attempt to reconcile both of these views by the idea that cycling polyploidy intermitting senescence and rejuvenation may be features of a life cycle analogous to the life cycles of certain unicellular organisms. Furthermore, we suggest that mitotic catastrophe may represent a mechanism through which the cell can switch from the usual mitotic cell‐cycle to this evolutionarily conserved life cycle. Intriguingly, some most recent data suggest that cell senescence may be reversible and that stem cells are tolerant to polyploidy caused by genotoxic stress.
Plasma level of cardiotrophin‐1 as a prognostic predictor in patients with chronic heart failure
Authors: Tsutamoto Takayoshi , Asai Shigeru , Tanaka Toshinari , Sakai Hiroshi , Nishiyama Keizo , Fujii Masanori , Yamamoto Takashi , Ohnishi Masato , Wada Atsuyuki , Saito Yoshihiko , Horie Minoru
Published: September 2007

Background:

Cardiotrophin‐1 (CT‐1) is a member of the interleukin (IL‐6) family of cytokines and is increased in patients with chronic heart failure (CHF).

Aims:

To evaluate the prognostic role of CT‐1 in patients with CHF.

Methods and results:

We measured the plasma levels of CT‐1, brain natriuretic peptide (BNP), and IL‐6 in 125 patients with CHF. Patients were monitored for a mean follow‐up period of 2.9years. Plasma levels of CT‐1 increased with severity of CHF. There was a significant negative correlation between plasma CT‐1 and left ventricular ejection fraction. There was a significant correlation between plasma CT‐1 and log IL‐6. During the follow‐up period, 37 patients died. High plasma levels of CT‐1, BNP, and IL‐6 were independent predictors of mortality on stepwise multivariate analysis. The hazard ratio for mortality in patients with plasma BNP>170pg/mL and CT‐1>658fmol/mL was 2.48 (95% confidence interval, 1.217–5.060) compared to those with plasma BNP>170pg/mL and CT‐1<658fmol/mL (p=0.0124).

Conclusion:

These findings indicate that plasma CT‐1 measurement provides additional prognostic information and that combined levels of CT‐1 and BNP are more accurate at predicting mortality in patients with CHF than either marker alone.
Impact of levetiracetam on mood and cognition during prednisone therapy
Authors: Brown E. Sherwood , Frol Alan B. , Khan David A. , Larkin Gregory L. , Bret Mary Ellen
Published: September 2007

Purpose

Corticosteroid excess is associated with impairment in declarative memory and hippocampal changes. in animals, phenytoin blocks the effects of stress on memory and hippocampal histology. Levetiracetam also shows neuroprotective properties in some animal models. This report examines whether levetiracetam prevents mood or cognitive changes secondary to prescription corticosteroids.

Materials and methods

Thirty outpatients given systemic corticosteroid therapy for asthma were randomized to either levetiracetam (1500 mg/day) or placebo given concurrently with the corticosteroids. Mood was assessed with the Hamilton rating scale for depression (HRSD), Young mania rating scale (YMRS) and activation (ACT) subscale of the internal state scale, declarative memory with the Rey auditory verbal learning test (RAVLT), and attention and executive functioning with the Stroop color and word test at baseline and after approximately 7 days of corticosteroid plus levetiracetam or placebo therapy.

Results

Levetiracetam and placebo groups showed significant improvement from baseline to exit on RAVLT total words recalled with a non-significant change on other outcomes. No significant between-group differences were found. initial prednisone dose showed a significant correlation with change in some cognitive domains.

Conclusions

Levetiracetam was well tolerated when combined with prednisone. Significant between-group differences in mood and cognition were not found.
Eye‐open at birth phenotype with reduced keratinocyte motility in LGR4 null mice
Authors: Kato Shigeki , Mohri Yasuaki , Matsuo Tsuyoshi , Ogawa Eisaku , Umezawa Akihiro , Okuyama Ryuhei , Nishimori Katsuhiko
Published: September 2007

We observed a consistent eye‐open at birth (EOB) phenotype in mouse pups homozygous for a leucine‐rich repeat containing G‐protein coupled receptor 4 (Lgr4) allele deleting the whole transmembrane domain coding region. An in vitro wound‐healing scratch assay showed notably reduced keratinocyte motility in the null mice. Phalloidin staining of F‐actin in the eyelid epidermis was also reduced. We also generated keratinocyte‐specific Lgr4 deficient mice, circumventing the embryonic/neonatal lethality and kidney abnormalities. Most of the conditional Lgr4 knockout mice showed the EOB phenotype. Thus, Lgr4 might be a novel gene class regulating cell motility.
A specific binding site for neoxanthin in the monomeric antenna proteins CP26 and CP29 of Photosystem II
Authors: Caffarri Stefano , Passarini Francesca , Bassi Roberto , Croce Roberta
Published: September 2007

The location of the neoxanthin binding site in CP26 and CP29 was investigated by site‐directed mutagenesis. The crystallographic structure of LHCII shows that the binding of neoxanthin to the N1 site is stabilised by an H bond with a tyrosine in the lumenal loop. This residue is conserved in CP26 and CP29. Mutation of this tyrosine into phenylalanine induced specific loss of neoxanthin without affecting violaxanthin binding. In contrast to previous proposals, it is thus concluded that also in these minor antenna complexes neoxanthin is accommodated in the N1 site. The characteristics of this binding site in the different antenna complexes are discussed.
Obstetric fistula: Clinical considerations in the creation of a new urethra and the management of a subsequent pregnancy
Authors: Browning A.
Published: September 2007

The paper presents two case studies to illustrate the complexity of repairing obstetric fistula (OF) with neourethral construction when complete circumferential destruction occurred. Using fictitious names, the author describes the personal story and contexts leading to OF development and depression, surgical options, and the prognosis of repair. These cases were documented at the Barhirdar Hamlin Fistula Center in Northern Ethiopia.
Complications of treatment of obstetric fistula in the developing world: Gynatresia, urinary incontinence, and urinary diversion
Authors: Gutman R.E. , Dodson J.L. , Mostwin J.L.
Published: September 2007

Objective: To provide a comprehensive review of the pathophysiology, evaluation, and treatment of gynatresia and urinary incontinence, 2 conditions that can arise following the repair of obstetric fistulas. The article discusses relevant issues with respect to urinary diversion in the treatment of obstetrical fistula and associated urinary incontinence. Methods: A review was conducted of the existing literature and of the expert recommendations issued at the Gates Institute fistula meeting held in July 2005 at the Johns Hopkins Bloomberg School of Public Health. Results: Gynatresia and urinary incontinence develop in approximately 10% and 16% of patients, respectively, after the first repair. Urinary diversion may be necessary when fistulas cannot be closed vaginally or in cases of severe urinary incontinence following successful closure. Gynatresia, urinary incontinence, and urinary diversion are all associated with morbidity, and they require surgical and nonsurgical expertise for proper management. Conclusions: Closing the anatomical fistula is not always sufficient, and treatment paradigms must shift toward the prevention and repair of gynatresia and urinary incontinence at the time of the primary operation.
Evaluation of the association of Bartonella species, feline herpesvirus 1, feline calicivirus, feline leukemia virus and feline immunodeficiency virus with chronic feline gingivostomatitis
Authors: Quimby Jessica M. , Elston Thomas , Hawley Jennifer , Brewer Melissa , Miller Arianne , Lappin Michael R.
Published: September 2007

Gingivostomatitis (GS) is a significant condition in cats because of oral discomfort and associated periodontal disease. Several infectious agents have been associated with the presence of GS, but a causal relationship is unclear. The cats in this study were housed together, had a history of flea exposure, and were vaccinated with a modified live FVRCP product. There were nine cats with active GS and 36 unaffected cats at the time of sample collection. Serum was tested for feline leukemia virus (FeLV) antigen and antibodies against feline immunodeficiency virus, feline calicivirus (FCV), feline herpesvirus 1 (FHV-1), and Bartonella species (enzyme-linked immunosorbent assay and Western blot immunoassay). PCR assays for Bartonella species and FHV-1 and a reverse transcriptase PCR assay for FCV were performed on blood and throat swabs. All cats were negative for FeLV. Assay results failed to correlate to the presence of GS in the group of cats studied.
Radiographic measurement of vertebral heart size in healthy stray cats
Authors: Ghadiri Alireza , Avizeh Reza , Rasekh Abdolrahman , Yadegari Ali
Published: September 2007

The aims of this study were to determine vertebral heart size (VHS) in stray cats and to compare different radiographic views. This study was performed on 50 adult stray cats. All cats were short-haired and non-obese and were considered to be healthy based on physical examination and electrocardiography. Left and right lateral, dorsoventral and ventrodorsal radiographs were taken. The long and short axes of the heart were measured in millimetres. The thoracic vertebral length spanned by each dimension was measured caudally from the fourth thoracic vertebra. Mean ± SD and the correlation coefficient between the measurements were calculated with standard statistical software. The sum of the long and short axes of the heart expressed as VHS was 7.3 ± 0.49 vertebrae in right lateral, 7.3 ± 0.55 vertebrae in left lateral, 7.5 ± 0.68 vertebrae in dorsoventral and 7.5 ± 0.53 vertebrae in ventrodorsal. The differences between right and left lateral as well as dorsoventral and ventrodorsal views were not significant ( P > 0.05). Absolute measurements and vertebral heart scale values were slightly smaller than those reported in the literature for mixed population of cats. It is, therefore, important to take the breed in to account.
Immunohistochemical features of proliferative marker and basement membrane components of two feline inductive odontogenic tumours
Authors: Sakai Hiroki , Mori Takashi , Iida Tsuneyoshi , Tokuma Yanai , Maruo Kouji , Masegi Toshiaki
Published: September 2007

Feline inductive odontogenic tumour (FIOT) is a rare and interesting odontogenic neoplasm in which the odontogenic epithelium has inductive potential to form aggregated foci of dental pulp-like mesenchymal cells. Two male cats aged 11 and 10 months presented with nasal swelling and a left maxillary mass. Histopathologically, the masses consisted of non-encapsulated invasive neoplasms exhibiting proliferation of epithelial and mesenchymal components with local infiltration into the maxillary bone in both cases. The epithelial component formed islands, anastomosing strands, and solid sheets of polygonal epithelial cells. Occasionally, these cells formed circular aggregates, resembling the cap stage of odontogenesis. Type IV collagen and laminin were constantly positive around the foci of epithelial cells, and Ki-67 positive indices were extremely low; therefore, these findings consistent with the benign clinical presentation of FIOT.
ETHNICITY AND NATIONALISM IN URBAN COLONIAL ZIMBABWE: BULAWAYO, 1950 TO 1963
Authors: MSINDO ENOCENT
Published: September 2007

Zimbabwean historians have not yet fully assessed the interaction of two problematic identities, ethnicity and nationalism, to determine whether the two can work as partners and successfully co-exist. This essay argues that, in Bulawayo during the period studied, ethnicity co-existed with and complemented nationalism rather than the two working as polar opposite identities. Ethnic groups provided both the required leaders who became prominent nationalist figures and the precolonial history, personalities and monuments that sparked the nationalist imagination. From the 1950s, ethnic groups expanded their horizons and provided platforms from which emerging African nationalists launched their agenda. Understanding these interrelationships will reshape our understanding of the workings of these two identities in a cosmopolitan town.
CYCLICAL HISTORY IN THE GAMBIA/CASAMANCE BORDERLANDS: REFUGE, SETTLEMENT AND ISLAM FROM c. 1880 TO THE PRESENT
Authors: NUGENT PAUL
Published: September 2007

This article begins with a quotation from a local informant highlighting a perception in the Gambia/Casamance borderlands that there is a pattern linking the violence of the later nineteenth century with more recent troubles. It argues that there is some merit in this thesis, which is encapsulated in a concatenation of events: systematic raiding by Fodé Sylla led to the creation of a relatively depopulated colonial border zone which was later filled by Jola immigrants from Buluf to the southeast. In the perception of some, it is these immigrants who attracted the MFDC rebels. Mandinkas and Jolas of Fogny Jabankunda and Narang, and Karoninkas from the islands of Karone have therefore been largely unreceptive to appeals to Casamance nationalism. The article also argues that there are more twisted historical connections. Whereas in the later nineteenth century, the Jolas associated Islam with violent enslavement, they later converted en masse. Their attitude towards Fodé Sylla remained negative, whilst the Mauritanian marabout, Cheikh Mahfoudz, was credited with the introduction of a pacific form of Islam that valorized hard work and legitimated physical migration. This legacy has posed a further barrier to militant nationalism. Islam and violence remain linked, but the signs have been reversed.
Habituieren oder sensitivieren Patienten mit Alkoholabhängigkeit an suchtassoziierte Stimuli?
Authors: Wingenfeld Katja , Lewitzky Miriam , Mensebach Christoph , Beblo Thomas , Driessen Martin
Published: September 2007

Zusammenfassung: Der emotionale Stroop Test ist ein in der Forschung häufig eingesetztes Verfahren, um Interferenzeffekte durch emotionale oder krankheitsrelevante Stimuli zu untersuchen. So konnte gezeigt werden, dass Patienten mit Alkoholabhängigkeit verlangsamte Reaktionszeiten auf alkoholspezifische Reize aufweisen. Inwieweit dieser Effekt bei Wiederholungsmessungen stabil ist, wurde bisher weniger intensiv untersucht. Dies ist insofern erstaunlich, als dass sowohl Theorien existieren, die eine Normalisierung der Reaktionszeiten nahe legen (Habituation), als auch Konzepte, die gleich bleibende oder zunehmend verlangsamte Reaktionszeiten erwarten lassen (Sensitivierung), möglicherweise assoziiert mit verstärktem oder neu entstehendem Craving. In dieser Studie wurden 20 Patienten mit Alkoholabhängigkeit nach abgeschlossenem Alkoholentzug mit einem Stroop Test untersucht, in dem u. a. individuell bedeutsame alkoholbezogene Wörter präsentiert wurden. Zunächst konnten frühere Befunde einer verstärkten Interferenz durch alkoholassoziierte Wörter repliziert werden. Weiterhin konnte gezeigt werden, dass Patienten mit einer Alkoholerkrankung an diese Stimuli habituieren. In weiteren Studien sollte untersucht werden, inwieweit dieser Habituationseffekt auch auf physiologischer Ebene nachweisbar ist.
Prospektives Gedächtnis bei Patienten mit Schädel-Hirn-Trauma
Authors: Louda Johanna , Loseva Darja , Mielke Rüdiger
Published: September 2007

Zusammenfassung: Das prospektive Gedächtnis ist eine kognitive Funktion, deren Erforschung zunehmendes Interesse findet. Der Begriff “prospektives Gedächtnis” bezeichnet die Fähigkeit, sich zur richtigen Zeit daran zu erinnern, zuvor gefasste Handlungsabsichten in die Tat umzusetzen (z. B. Termine einzuhalten) und ist von sehr hoher Alltagsrelevanz. Liegen nach einer Hirnschädigung Defizite des prospektiven Gedächtnisses vor, so kann dies zu erheblichen Problemen bei der beruflichen Wiedereingliederung und bei der Bewältigung alltäglicher Anforderungen führen. Der vorliegende Artikel gibt einen Überblick über Studien zum prospektiven Gedächtnis bei Patienten mit Schädel-Hirn-Trauma (SHT). In allen Untersuchungen konnten Beeinträchtigungen der prospektiven Gedächtnisleistungen bei SHT-Patienten nachgewiesen werden. Darüber hinaus legen einige Studien nahe, dass die Patienten ihre prospektiven Gedächtnisfähigkeiten überschätzen. Ergebnisse von Interventionsstudien zur Behandlung prospektiver Gedächtnisdefizite berechtigen zu vorsichtigem Optimismus.
Exhuming Norwegian ultrahigh‐pressure rocks: Overprinting extensional structures and the role of the Nordfjord‐Sogn Detachment Zone
Authors: Johnston Scott M. , Hacker Bradley R. , Andersen Torgeir B.
Published: September 2007

The Nordfjord‐Sogn Detachment Zone (NSDZ) is widely cited as one of the primary structures responsible for the exhumation of Norwegian (ultra)high‐pressure (UHP) rocks. Here we review data from the considerable volume of research describing this shear zone, and compile a strike‐parallel cross section along the NSDZ from the Solund Basin in the south to the Sørøyane UHP domain in the north. This cross section highlights several previously unrecognized patterns, revealing a shear zone with top‐to‐the‐west asymmetric fabrics that (1) initiated at amphibolite facies, (2) overprints metamorphic breaks and tectonostratigraphic contacts, and (3) has a gradational continuum of muscovite cooling ages. These patterns constrain the kinematic evolution of the NSDZ and suggest a new three‐step model for the exhumation of Norwegian (U)HP rocks. The initial stages of exhumation were characterized by the rise of crustal rocks from (U)HP depths to the base of the crust by buoyancy‐driven mechanisms not specified in this paper. Mantle exhumation was followed by top‐to‐the‐west, normal‐sense displacement within a broad noncoaxial ductile shear zone near the base of the crust that overprinted tectonostratigraphic contacts formed previously during mantle exhumation. In the final stages of crustal exhumation, top‐W brittle‐ductile detachments soled into and partially excised this ductile shear zone, dropping the Devonian basins into contact with rocks of varying tectonostratigraphic levels. This new interpretation of the NSDZ is significant as it accounts for the extreme crustal excision observed in western Norway using three sequentially overprinting structures active at different stages of UHP rock exhumation.
Eddy statistics from Lagrangian drifters and hydrography for the northern Gulf of Mexico slope
Authors: Hamilton Peter
Published: September 2007

Cyclones and anticyclones on the northern Gulf of Mexico slope have been statistically characterized using upper layer drifter orbits and repeated hydrographic surveys. A total of 243 slope eddy drifter orbits (151 cyclones and 92 anticyclones) were analyzed in terms of size (mean radius and eccentricity) and rotation period. Orbits in large Loop Current anticyclones were excluded. Eddies of both signs scale approximately as the baroclinic radius of deformation with relatively smaller radii on the upper slope, where water depths are less than 1000 m. The median radius for all eddies was ∼30 km, and median periods were 12 and 13.5 days for cyclones and anticyclones, respectively. Anticyclones also tend to be more circular than cyclones. Relative vorticity maps were constructed for seven hydrographic surveys, which mapped the slope at 4–5 month intervals. A total of 26 cyclones and 15 anticyclones had statistics that were consistent with drifter orbit analyses. The surveys indicate that at any one time, between 2 and 5 cyclones and 1 and 3 anticyclones may be present. Both drifters and surveys indicate that cyclones have a slight numerical dominance.
Threshold wind speed for dust emission in east Asia and its seasonal variations
Authors: Kurosaki Y. , Mikami M.
Published: September 2007

We present maps of threshold wind speed for dust emission in east Asia, which are statistically evaluated from synoptic surface meteorological data. We define threshold wind speeds as ut5% and ut50%, which can be identified as threshold wind speeds at close to the most favorable land surface condition for dust emission and under normal land surface conditions, respectively. Spatial distributions of ut5% and ut50% are similar and roughly correspond to the land cover type. The threshold wind speed is low in desert regions such as the Taklimakan Desert (ut5% = 4.4 ± 0.6 m s−1 and ut50% = 6.7 ± 1.5 m s−1) and the Loess Plateau (ut5% = 6.9 ± 1.2 m s−1 and ut50% = 9.4 ± 1.6 m s−1). On the other hand, the highest is seen in northern Mongolia (ut5% = 9.8 ± 2.2 m s−1 and ut50% = 16.2 ± 2.5 m s−1), whose land cover type is grassland. One exception is the high threshold wind speed recorded in the Gobi Desert (ut5% = 8.9 ± 2.2 m s−1 and ut50% = 13.8 ± 2.0 m s−1). Seasonal variations in the threshold wind speed are narrow in desert regions such as the Taklimakan Desert, the Gobi Desert and Loess Plateau, but wide in grassland regions such as northern Mongolia. This suggests that land surface conditions are the similar throughout the year in desert regions, but seasonally variable in grassland regions.
Acidic gases (HCOOH, CH3COOH, HNO3, HCl, and SO2) and related aerosol species at a high mountain Alpine site (4360 m elevation) in Europe
Authors: Preunkert S. , Legrand M. , Jourdain B. , Dombrowski‐Etchevers I.
Published: September 2007

During a field campaign performed at 4360 m elevation in the French Alps in summer 2004, atmospheric levels of acidic gases (HCOOH, CH3COOH, HNO3, HCl, and SO2) and related aerosol species were investigated using mist chamber and denuder tube samplings. Sulfate aerosol levels greatly exceeded those of gaseous SO2. Conversely, chloride, nitrate and particularly monocarboxylates were much more present in the gas phase than in the aerosol phase. On a molar basis, formic and acetic acids are the most abundant acidic gases (∼14 nmol m−3 STP), followed by nitric acid (7 nmol m−3 STP), hydrochloric acid (1.7 nmol m−3 STP) and sulfur dioxide (0.8 nmol m−3 STP). These data gained in the free troposphere over Europe in summer are discussed and compared to those obtained during aircraft missions conducted over North America and the northwest Pacific near China. It is concluded that the concentrations of acidic gases and related aerosol species are quite similar in the free troposphere in summer over Europe and North America. Concentrations of sulfur and nitrogen species in the free troposphere are lower over Europe (and North America) than over the Pacific region located near China (a factor 5 and 2, respectively). Finally, measurements achieved in this study tend to indicate that secondary production is important for the atmospheric budget of carboxylic acids.
Bacterial diversity in hyperarid Atacama Desert soils
Authors: Connon Stephanie A. , Lester Elizabeth D. , Shafaat Hannah S. , Obenhuber Donald C. , Ponce Adrian
Published: September 2007

Surface and subsurface soil samples analyzed for this investigation were collected from the hyperarid Yungay region in the Atacama Desert, Chile. This report details the bacterial diversity derived from DNA and PLFA extracted directly from these extremely desiccated soils. Actinobacteria, Proteobacteria, Firmicutes and TM7 division bacteria were detected. Ninety‐four percent of the 16S rRNA genes cloned from these soils belong to the Actinobacteria phylum, and the majority of these were most closely related to the genus Frankia. A 24‐hour water activity (aw) time course showed a diurnal cycle that peaked at 0.52 in the early predawn hours, and ranged from 0.01–0.08 during the day. All measured water activity values were below the levels required for microbial growth or enzyme activity. Total organic carbon (TOC) concentrations were above the limit of detection and below the limit of quantification (i.e., 200 μg/g < TOC < 1000 μg/g), and phospholipid fatty acid (PLFA) concentrations ranged from 2 × 105 to 7 × 106 cell equivalents per gram of soil. Soil extracts analyzed for culturable biomass yielded mostly no growth on R2A media; the highest single extract yielded 47 colony forming units (CFU) per gram of soil.