bluuebunny/crossref_metadata_2025_split huggingface dataset:
The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI
Authors: Wiehe Kevin , Pierce Brian , Tong Wei Wei , Hwang Howook , Mintseris Julian , Weng Zhiping 
Published: September 2007

AbstractWe present an evaluation of our protein–protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6–11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium‐accuracy predictions. In the new scoring portion of the CAPRI exercise, we were able to attain at least one acceptable prediction for the three targets submitted and achieved three medium‐accuracy predictions for Target 26. Scoring was performed using ZRANK, a new algorithm for reranking initial‐stage docking predictions using a weighted energy function and no structural refinement. Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A holistic approach to protein docking
Authors: Qin Sanbo , Zhou Huan‐Xiang 
Published: September 2007

AbstractDocking of unbound protein structures into a complex has gained significant progress in recent years, but nonetheless still poses a great challenge. We have pursued a holistic approach to docking which brings together effective methods at different stages. First, protein‐protein interaction sites are predicted or obtained from experimental studies in the literature. Interface prediction/experimental data are then used to guide the generation of docked poses or to rank docked poses generated from an unbiased search. Finally, selected models are refined by lengthy molecular dynamics (MD) simulations in explicit water. For CAPRI target T27, we used information on interaction sites as input to drive docking and as a filter to rank docked poses. Lead candidates were then clustered according to RMSD among them. From the clustering, 10 models were selected and subject to refinement by MD simulations. Our Model 7 is rated number one among all submissions according to L_rmsd. Six of our other submissions are rated acceptable. As scorer, eight of our submissions are rated acceptable. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A theory for the spinup of tropical depressions
Authors: Raymond D. J. , Sessions S. L. , Fuchs Ž. 
Published: September 2007

AbstractRecent advances in our understanding of the physics of precipitation over tropical oceans is married with vorticity dynamics to produce a simple theory for the development or non‐development of tropical depressions. This early phase of tropical cyclogenesis is perhaps the least understood part of the whole process. The theory predicts a finite amplitude threshold for intensification, with weaker disturbances decaying. Furthermore, only disturbances with radii larger than a critical value develop. Rough estimates of this critical radius place it near 1600 km, though better estimates of various parameters could change this value significantly. Copyright © 2007 Royal Meteorological Society
Role of nocturnal turbulence and advection in the formation of shallow cumulus over land
Authors: Vilà‐Guerau de Arellano Jordi 
Published: September 2007

AbstractShallow cumuli over land are normally studied from a diurnal perspective. However, the thermodynamic vertical profiles of the morning transition may play an important role in setting up favourable conditions for the formation of shallow cumuli. In turn, these profiles are highly dependent on the evolution of the nocturnal boundary characteristics and of their layer aloft.By analysing thermodynamic profiles measured by radiosondes launched every three hours at four different stations, we are able to determine how horizontal advection and turbulent mixing modify the atmospheric stability and the differences in potential temperature and specific humidity at the interface between the atmospheric boundary layer and the layer above it. Two consecutive nights are studied. They show very similar boundary‐layer development; but variations in the layer aloft by a low‐level‐jet advection event during the second night, and intense turbulent mechanical mixing, lead to the development of two diurnal boundary layers with very different characteristics: the first one clear, the second cloudy.To complete the observational study, we perform a sensitivity analysis using a mixed‐layer model to examine the role of the morning initial conditions in the formation of shallow cumuli over land. The complexity and subtlety of the observed situation—namely, the interaction of a strongly‐mixed nocturnal boundary layer and horizontal advection—make this case suitable for testing the capacity of mesoscale models to reproduce cloudy boundary layers that are largely dependent on conditions during the previous night. Copyright © 2007 Royal Meteorological Society
Prenatal ultrasound detection of talipes equinovarus in a non‐selected population of 49 314 deliveries in Norway
Authors: Offerdal K. , Jebens N. , Blaas H. G. K. , Eik‐Nes S. H. 
Published: September 2007

AbstractObjectivesTo evaluate prenatal ultrasound detection of talipes equinovarus (TEV) in a large non‐selected population and to study trends in detection rates over time, as well as the prevalence and outcome of isolated TEV and TEV with associated anomalies.MethodsAll cases of pre‐ or postnatally diagnosed TEV between 1987 and 2004 within a non‐selected population of 49 314 deliveries were investigated. The study period was divided into three 6‐year periods to shed light on changes in detection rates and other aspects of the anomaly over time.ResultsA total of 113 cases of TEV were registered during the 18‐year period, of which 49% had isolated TEV and 51% had associated anomalies. During the three 6‐year periods, there was a significant improvement (P = 0.006) in the overall detection of TEV from 43% to 67% and 77%, respectively. The detection rate for isolated TEV increased over time. Isolated bilateral TEV cases were detected more than twice as often as isolated unilateral TEV. The three largest groups of associated anomalies were syndromes/sequences (26%), chromosome aberrations (26%), and musculoskeletal disorders (24%). Pregnancies were terminated in 23% of the cases, all with severe additional anomalies. Treatment of TEV included surgery in 86% of the cases.ConclusionThe overall detection rate of TEV improved significantly over time. Prenatal detection was higher when TEV was bilateral and when other associated anomalies were present. Parents should be informed that, in suspected isolated TEV, associated anomalies might remain undetected prenatally. Copyright © 2007 ISUOG. Published by John Wiley & Sons, Ltd.
Modeling the effect of fire on the demography ofDicerandra frutescensssp.frutescens(Lamiaceae), an endangered plant endemic to Florida scrub
Authors: Evans Margaret E. K. , Holsinger Kent E. , Menges Eric S. 
Published: September 2007

AbstractManaging populations, either for conservation, harvesting, or control, requires a mechanistic or semi‐mechanistic understanding of population dynamics. Here, we investigate how time‐since‐fire affects demographic transitions in an endangered plant,Dicerandra frutescensssp.frutescens(Lamiaceae), which is specialized to gaps created by fire. We used a hierarchical Bayesian model to estimate transition probabilities (i.e., the elements of population projection matrices) as a function of time‐since‐fire and random effects, from 13 years of data on marked individuals in five populations. Using a standard Bayesian criterion to compare models, we find that death becomes increasingly probable and progression increasingly improbable with time‐since‐fire. The magnitude of some of the time‐since‐fire effects is substantial: death is 3–5 times more likely for flowering plants >6 years versus 3–6 years post‐fire, 3‐step progression is almost 7 times less likely, and large flowering plants are more than 6 times more likely to stop flowering. These insights inspire new hypotheses about the underlying cause of decline with time‐since‐fire, and how it can be managed. Our approach can be used by others who wish to model the effect of an exogenous factor on demography, while rigorously accounting for uncertainty and variability.
Kinetics of Palm Oil Methanolysis
Authors: Narváez P. C. , Rincón S. M. , Sánchez F. J. 
Published: September 2007

AbstractA kinetics study of palm oil methanolysis was conducted at three different temperatures and three different concentrations of catalyst, sodium hydroxide, keeping constant the molar ratio of methanol to oil and the rotational speed of the impeller (6:1 and 400 rpm). The maximum conversion of palm oil and productivity to methyl esters were obtained at 60 °C and 1 wt% of NaOH based on palm oil, and they were 100 and 97.6%, respectively. The statistical analysis of conversions of palm oil and productivities to methyl esters as functions of temperature and concentration of catalyst, after 80 min of reaction, allowed them to fit second order polynomial equations, which adequately describe the experimental behavior. The experimental data appear to be a good fit into a second order kinetic model for the three stepwise reactions, and the reaction rate constants and the activation energies were determined. In this article we present the kinetic constant and activation energies for the experiments with 0.2% wt of NaOH. The effect of molar ratio on the concentration of products was investigated, while the temperature (55 °C), the concentration of catalyst (0.60 wt% of NaOH), and the rotational speed (400 rpm), were held constant. The results showed that the conversion and the productivity increased due to methanol excess, and were higher for the reactions with a molar ratio of 6:1.
Intramuscular administration of morphine reduces mustard oil‐induced craniofacial muscle pain behavior in lightly anesthetized rats
Authors: Han Seung R. , Lee Min K. , Lim Koang H. , Yang Gwi Y. , Jeon Hye J. , Ju Jin S. , Yoon Young W. , Kim Sung K. , Ahn Dong K. 
Published: September 2007

AbstractThe present study investigated the role of peripheral opioid receptors in mustard oil‐induced nociceptive behavior and inflammation in the masseter muscles of lightly anesthetized rats. Experiments were carried out on male Sprague–Dawley rats weighing between 300 and 400g. After initial anesthesia with sodium pentobarbital (40mg/kg, i.p.), one femoral vein was cannulated and connected to an infusion pump for the intravenous infusion of sodium pentobarbital. The rate of infusion was adjusted to provide a constant level of anesthesia. Mustard oil (MO, 30μl) was injected into the mid‐region of the left masseter muscle via a 30‐gauge needle. Intramuscularly‐administered morphine significantly reduced shaking behavior but not MO‐induced inflammation. Intramuscular pretreatment with naloxone, an opioid receptor antagonist, reversed antinociception produced by intramuscularly‐administered morphine, while intracisternal administration of naloxone did not affect the antinociception of peripheral morphine. Pretreatment withd‐Pen‐Cys‐Tyr‐d‐Trp‐Orn‐Thr‐Pen‐Thr‐NH2 (CTOP), a μ opioid receptor antagonist, but not naltrindole, a δ opioid receptor antagonist, nor norbinaltorphimine (nor‐BNI), a κ opioid receptor antagonist, reversed intramuscularly‐administered morphine‐induced antinociception. These results indicate that intramuscularly‐administered morphine produces antinociception in craniofacial muscle nociception and that this intramuscularly‐administered morphine‐induced antinociception is mediated by a peripheral μ opioid receptor. Our observations further support the clinical approach of administering opioids in the periphery for the treatment of craniofacial muscle nociception.
Sex mediates dopamine and adrenergic receptor expression in adult rats exposed prenatally to cocaine
Authors: Ferris Mark J. , Mactutus Charles F. , Silvers Janelle M. , Hasselrot Ulla , Beaudin Stephane A. , Strupp Barbara J. , Booze Rosemarie M. 
Published: September 2007

AbstractThe extent of catecholaminergic receptor and respective behavioral alterations associated with prenatal cocaine exposure varies according to exogenous factors such as the amount, frequency, and route of maternal exposure, as well as endogenous factors such as specific brain regions under consideration and sex of the species. The goal of the current study was to use autoradiography to delineate possible moderators of dopaminergic and adrenergic receptor expression in adult rat offspring exposed to cocaine in utero. The current study demonstrated sex‐dependent D1 receptor, α2, and noradrenergic transporter binding alterations in prelimbic, hippocampus, and anterior cingulate regions of adult rat brains exposed to cocaine during gestational days 8–21. Of further interest was the lack of alterations in the nucleus accumbens for nearly all receptors/transporters investigated, as well as the lack of alterations in D3 receptor binding in nearly all of the regions investigated (nucleus accumbens, prelimbic region, hippocampus, and cingulate gyrus).Thus, the current investigation demonstrated persistent receptor and transporter alterations that extend well into adulthood as a result of cocaine exposure in utero. Furthermore, the demonstration that sex played a mediating role in prenatal cocaine‐induced, aberrant receptor/transporter expression is of primary importance for future studies that seek to control for sex in either design or analysis.
Genetic and pharmacologic manipulation of oxidative stress after neonatal hypoxia‐ischemia
Authors: Sheldon R. Ann , Christen Stephan , Ferriero Donna M. 
Published: September 2007

AbstractOxidative stress is a critical component of the injury response to hypoxia‐ischemia (HI) in the neonatal brain, and this response is unique and at times paradoxical to that seen in the mature brain. Previously, we showed that copper‐zinc superoxide‐dismutase (SOD1) over‐expression is not beneficial to the neonatal mouse brain with HI injury, unlike the adult brain with ischemic injury. However, glutathione peroxidase 1 (GPx1) over‐expression is protective to the neonatal mouse brain with HI injury. To further test the hypothesis that an adequate supply of GPx is critical to protection from HI injury, we crossed SOD1 over‐expressing mice (hSOD‐tg) with GPx1 over‐expressing mice (hGPx‐tg). Resulting litters contained wild‐type (wt), hGPx‐tg, hSOD‐tg and hybrid hGPx‐tg/hSOD‐tg pups, which were subjected to HI at P7. Confirming previous results, the hGPx‐tg mice had reduced injury compared to both Wt and hSOD‐tg littermates. Neonatal mice over‐expressing both GPx1 and SOD1 also had less injury compared to wt or hSOD‐tg alone. A result of oxidative stress after neonatal HI is a decrease in the concentration of reduced (i.e. antioxidant‐active) glutathione (GSH). In this study, we tested the effect of systemic administration of α‐lipoic acid on levels of GSH in the cortex after HI. Although GSH levels were restored by 24 h after HI, injury was not reduced compared to vehicle‐treated mice. We also tested two other pharmacological approaches to reducing oxidative stress in hSOD‐tg and wild‐type littermates. Both the specific inhibitor of neuronal nitric oxide synthase, 7‐nitroindazole (7NI), and the spin‐trapping agent alpha‐phenyl‐tert‐butyl‐nitrone (PBN) did not reduce HI injury, however. Taken together, these results imply that H2O2 is a critical component of neonatal HI injury, and GPx1 plays an important role in the defense against this H2O2 and is thereby neuroprotective.
Recent trends in erythropoietin‐mediated neuroprotection
Authors: McPherson Ronald J. , Juul Sandra E. 
Published: September 2007

AbstractFifteen years of evidence have established that the cytokine erythropoietin offers promise as a treatment for brain injury. In particular, neonatal brain injury may be reduced or prevented by early treatment with recombinant erythropoietin. Extreme prematurity and perinatal asphyxia are common conditions associated with poor neurodevelopmental outcomes including cerebral palsy, mental retardation, hearing or visual impairment, and attention deficit hyperactivity disorder. When high doses of erythropoietin are administered systemically, a small proportion crosses the blood–brain barrier and can protect against hypoxic–ischemic brain injury. In addition to other protective effects, erythropoietin can specifically protect dopaminergic neurons. Since reduced dopamine neurotransmission contributes to attention deficit hyperactivity disorder, this condition may be amenable to erythropoietin treatment. This review focuses on the potential application of erythropoietin as a neuroprotectant with regard to neurologic complications of extreme prematurity, including attention deficit hyperactivity disorder. Recent concerns that early erythropoietin might exacerbate the pathologic neovascularization associated with retinopathy of prematurity are addressed.
Reflections on the knowledge base for obstetric fistula
Authors: Kelly J. , Winter H.R. 
Published: September 2007

AbstractThis article presents the reflections of an experienced fistula surgeon and an epidemiologist on the current knowledge base for obstetric fistula. The incidence, prevention, and management of vesico‐vaginal and recto‐vaginal fistula are discussed. The authors call for more randomized controlled trials to determine the effectiveness of surgical interventions for fistula repair.
THE POLITICAL ECOLOGY OF THE COPAL TRADE IN THE TANZANIAN COASTAL HINTERLAND, c. 1820–1905
Authors: SUNSERI THADDEUS 
Published: September 2007

ABSTRACTBetween 1830 and 1880 copal was the major trade commodity from mainland Tanzania apart from ivory. Unlike ivory, copal was a product of a distinct environment, the lowland forests of the East African coastal hinterland. This region's copal was the best in the world for making high-value carriage varnish. It therefore found a ready market in the West, especially New England, whose traders brought cotton textiles to trade with East Africans for copal. The monopolization by hinterland polities of the copal–cloth trade nexus enabled them to consolidate politically as a sub-entrepôt of the Zanzibar commercial state. After 1880 a global demand for wild rubber, a product of far more diverse landscapes, posed a threat to the copal economy, and in part ushered in German colonialism. New colonial tax, labor and conservationist policies spelled the decline of the copal economy and its communities as they lost access to the coastal forests.
THE ELEPHANT SHOOTING: COLONIAL LAW AND INDIRECT RULE IN KAOKO, NORTHWESTERN NAMIBIA, IN THE 1920s AND 1930s
Authors: RIZZO LORENA 
Published: September 2007

ABSTRACTThe law as a means of sociopolitical control in colonial states has gained significance as an issue in the recent historiography of Africa. This article discusses the making of a criminal case in colonial Kaoko, northwestern Namibia in the 1920s and 30s. It focuses on the problem of African voice and narrative and the ways in which they have been transformed into written evidence in the course of legal investigation. It demonstrates that the archival documents which emerged from this case require careful methodological scrutiny if they are to be used for the reconstruction of the region's past. It goes beyond colonial law as constituting a particular discourse to conceive colonial law as a space for intervention and agency for both colonized and colonizers. The central argument raised in the article is that while the South African administration in northwestern Namibia allegedly aimed at prosecuting culprits and securing evidence for their transgressions, men and women in Kaoko used colonial law as an arena for the negotiation of social and political issues. Concerned with the case's impact on the configuration of gender, the article shows how colonial law became both a site of male representation and power, and a space for female contestation of male claims to sociopolitical mastery.
THE ENEMY WITHIN: LOYALISTS AND THE WAR AGAINST MAU MAU IN KENYA
Authors: BRANCH DANIEL 
Published: September 2007

ABSTRACTBetween 1952 and 1960, the British colonial government of Kenya waged a violent counter-insurgency campaign against the Mau Mau rebels. In this effort the regime was assisted by collaborators, known as loyalists, drawn from the same communities as the insurgents. Based primarily on new archival sources, this article sets out the history of loyalism, stresses the ambiguity of allegiances during the conflict and argues that loyalism was a product of the same intellectual debates that had spawned the Mau Mau insurgency. The article concludes by stressing the significance for postcolonial Kenya of this history.
An Alternative Scoring System to Predict Risk for Surgical Site Infection Complicating Coronary Artery Bypass Graft Surgery
Authors: Friedman N. Deborah , Bull Ann L. , Russo Philip L. , Leder Karin , Reid Christopher , Billah Baki , Marasco Silvana , McBryde Emma , Richards Michael J. 
Published: September 2007

Objective.To analyze the risk factors for surgical site infection (SSI) complicating coronary artery bypass graft (CABG) surgery and to create an alternative SSI risk score based on the results of multivariate analysis.Methods.A prospective cohort study involving inpatient and laboratory-based surveillance of patients who underwent CABG surgery over a 27-month period from January 1, 2003 through March 31, 2005. Data were obtained from 6 acute care hospitals in Victoria, Australia, that contributed surveillance data for SSI complicating CABG surgery to the Victorian Hospital Acquired Infection Surveillance System Coordinating Centre and the Australasian Society of Cardiac and Thoracic Surgeons, also in Victoria.Results.A total of 4,633 (93%) of the 4,987 patients who underwent CABG surgery during this period were matched in the 2 systems databases. There were 286 SSIs and 62 deep or organ space sternal SSIs (deep or organ space sternal SSI rate, 1.33%). Univariate analysis revealed that diabetes mellitus, body mass index (BMI) greater than 35, and receipt of blood transfusion were risk factors for all types of SSI complicating CABG surgery. Six multivariate analysis models were created to examine either preoperative factors alone or preoperative factors combined with operative factors. All models revealed diabetes and BMI of 30 or greater as risk factors for SSI complicating CABG surgery. A new preoperative scoring system was devised to predict sternal SSI, which assigned 1 point for diabetes, 1 point for BMI of 30 or greater but less than 35, and 2 points for BMI of 35 or greater. Each point in the scoring system represented approximately a doubling of risk of SSI. The new scoring system performed better than the National Nosocomial Infections Surveillance System (NNIS) risk index at predicting SSI.Conclusion.A new weighted scoring system based on preoperative risk factors was created to predict sternal SSI risk following CABG surgery. The new scoring system outperformed the NNIS risk index. Future studies are needed to validate this scoring system.