bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNALL: AN EFFICIENT ALGORITHM FOR PREDICTING RNA LOCAL SECONDARY STRUCTURAL LANDSCAPE IN GENOMES
Authors: WAN XIU-FENG , LIN GUOHUI , XU DONG 
Published: November 2006

Background: The information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study functions of RNA molecules. Most of the current RNA secondary structure prediction tools are not suitable for RNA LSS prediction on the genome scale due to high computational complexity. Methods: We developed a new computer package Rnall based on a dynamic programming technique, which scans an RNA sequence with a sliding window and extracts all RNA LSSs with sizes no larger than the window size using the nearest neighbor thermodynamic parameters. The worst case running time of Rnall is O(W3L), where W is the window size and L is the query sequence length. In practice we observed a running time of O(W2L). We further introduced the concept of energy landscape for illustrating RNA LSS, which may facilitate RNA motif mining on the genomic scale. Results: Rnall shows better prediction accuracy than two other prediction tools Lfold and Quickfold. Rnall is also applied to scan for RNA LSSs in three genomes, and the prediction maps well with known RNA motifs. Conclusions: Rnall is designed for RNA LSS prediction and together with the energy landscape, it has unique features that could be used for RNA structural motif mining. Rnall is freely available for download at or .
The role of sedation tests in identifying sedative drug effects in healthy volunteers and their power to dissociate sedative-related impairments from memory dysfunctions
Authors: Wezenberg E. , Sabbe B.G.C. , Hulstijn W. , Ruigt G.S.F. , Verkes R.J. 
Published: November 2006

The study investigated whether four specified drugs would show similar patterns on tests considered to measure sedation. In addition, their drug-effect patterns on sedation and memory performance were compared to determine whether the sedative effects could be differentiated from the memory effects. Two double-blind, placebo-controlled, crossover studies, each with 16 healthy volunteers, were performed, one testing lorazepam (2.5 mg) and mirtazapine (15 mg) and the other olanzapine (10 mg) and haloperidol (2.5 mg). Subjective sedation was assessed by means of visual analogue scales (VAS) and objective sedation using a simple-reaction-time (SRT) task and a choice-reaction-time (CRT) task, code substitution (symbol digit substitution test (SDST)) and the peak velocity of saccadic eye movements (SEM). A verbal memory test (VMT) was administered to evaluate memory capacity. Apart from haloperidol, all drugs proved to impair performance on all five sedation indices. Contrary to the VAS, the objective measures yielded different response profiles. Two types of drug-effect patterns emerged: one for greater impairments in response speed (SRT, SEM) and one for greater impairments in information processing (CRT, SDST). Lorazepam and olanzapine impeded memory performance, whereas mirtazapine did not. With the use of standardized scores it proved possible to differentiate between the size of the effects of the drugs on the sedation and memory tests. To accurately assess the level and nature of sedation and to differentiate sedation from memory impairments different types of sedation measures are required. Besides studying the subjective effects, it is recommended to also test psychomotor responses and information processing speed.
Malaria and anaemia among children in two communities of Kumasi, Ghana: a cross-sectional survey
Authors: Ronald Lisa A , Kenny Sarah L , Klinkenberg Eveline , Akoto Alex O , Boakye Isaac , Barnish Guy , Donnelly Martin J 
Published: November 2006

Abstract

Background
A survey in Kumasi, Ghana found a marked Plasmodium falciparum prevalence difference between two neighbouring communities (Moshie Zongo and Manhyia). The primary objective of this follow-up study was to determine whether this parasite rate difference was consistent over time. Secondary objectives were to compare prevalences of clinical malaria, anaemia, intestinal parasite infections, and malnutrition between these communities; and to identify potential risk factors for P. falciparum infection and anaemia.

Methods
A cross-sectional house-to-house survey of P. falciparum parasitaemia, clinical malaria, anaemia, anthropometric indices, and intestinal helminths was conducted in April-May 2005. Data collection included child and household demographics, mosquito avoidance practices, distance to nearest health facility, child's travel history, symptoms, and anti-malarial use. Risk factors for P. falciparum and anaemia (Hb < 11 g/dl) were identified using generalized linear mixed models.

Results
In total, 296 children were tested from 184 households. Prevalences of P. falciparum, clinical malaria, anaemia, and stunting were significantly higher in Moshie Zongo (37.8%, 16.9%, 66.2% and 21.1%, respectively) compared to Manhyia (12.8%, 3.4%, 34.5% and 7.4%). Of 197 children tested for helminths, four were positive for Dicrocoelium dendriticum. Population attributable risks (PAR%) of anaemia were 16.5% (P. falciparum) and 7.6% (malnutrition). Risk factors for P. falciparum infection were older age, rural travel, and lower socioeconomic status. Risk factors for anaemia were P. falciparum infection, Moshie Zongo residence, male sex, and younger age.

Conclusion
Heterogeneities in malariometric indices between neighbouring Kumasi communities are consistent over time. The low helminth prevalence, and the twofold higher PAR% of anaemia attributable to P. falciparum infection compared to malnutrition, indicate the importance of malaria as a cause of anaemia in this urban population.
Modification of the Tet-On regulatory system prevents the conditional-live HIV-1 variant from losing doxycycline-control
Authors: Zhou Xue , Vink Monique , Berkhout Ben , Das Atze T 
Published: November 2006

Abstract

Background
We have previously constructed a doxycycline (dox)-dependent HIV-1 variant by incorporating the Tet-On gene regulatory system into the viral genome. Replication of this HIV-rtTA virus is driven by the dox-inducible transactivator protein rtTA, and can be switched on and off at will. We proposed this conditional-live virus as a novel vaccine approach against HIV-1. Upon vaccination, replication of HIV-rtTA can be temporarily activated by transient dox administration and controlled to the extent needed for optimal induction of the immune system. However, subsequent dox-withdrawal may impose a selection for virus variants with reduced dox-dependence.

Results
We simulated this on/off switching of virus replication in multiple, independent cultures and could indeed select for HIV-rtTA variants that replicated without dox. Nearly all evolved variants had acquired a typical amino acid substitution at position 56 in the rtTA protein. We developed a novel rtTA variant that blocks this undesired evolutionary route and thus prevents HIV-rtTA from losing dox-control.

Conclusion
The loss of dox-control observed upon evolution of the dox-dependent HIV-1 variant was effectively blocked by modification of the Tet-On regulatory system.
Predicting domain-domain interactions using a parsimony approach
Authors: Guimarães Katia S , Jothi Raja , Zotenko Elena , Przytycka Teresa M 
Published: November 2006

AbstractWe propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts.
Treatment engagement and violence risk in mental disorders
Authors: Elbogen Eric B. , Van Dorn Richard A. , Swanson Jeffrey W. , Swartz Marvin S. , Monahan John 
Published: November 2006

BackgroundResearch has uncovered many characteristics related to violence committed by people with mental illness. However, relatively few studies have focused on understanding the connection between violence and dynamic, malleable variables such as a patient's level of treatment engagement.AimsTo explore the link between community violence and patients' beliefs about psychiatric treatment benefit.MethodA sample of 1011 adults receiving out-patient treatment for a psychiatric disorder in the public mental health systems of five US states were interviewed.ResultsBivariate analyses revealed community violence was inversely related to treatment adherence, perceived treatment need and perceived treatment effectiveness. Multivariate analyses showed these three variables were associated with reduced odds of violent and other aggressive acts.ConclusionsThe results suggest clinical consideration of patients' perceptions of treatment benefit can help enhance violence risk assessment in psychiatric practice settings.
The Face of Kosovar Albanian Nationalism: A Violent and Volatile Transformation of the Balkan Political Landscape
Authors: Graczyk Donald A. , Giannakos Symeon A. 
Published: November 2006

Donald Graczyk is a US Marine Corps lieutenant colonel who recently completed his graduate degree in international relations from Salve Regina University.
Symeon Giannakos is associate professor and director of the graduate program in international relations at Salve Regina University, Newport, Rhode Island.
Chemistry and Biochemistry of Insulin-Mimetic Vanadium and Zinc Complexes. Trial for Treatment of Diabetes Mellitus
Authors: Sakurai Hiromu , Katoh Akira , Yoshikawa Yutaka 
Published: November 2006

Abstract
The number of patients suffering from diabetes mellitus (DM), which is a chronic metabolic disorder and mainly classified as either insulin-dependent type 1 or non-insulin-dependent type 2, is increasing throughout the world. The sequence of DM progression makes this disease a major health risk in regard to microvascular disease that leads to kidney failure, blindness, and nerve damage as well as macrovascular disease that leads to amputations, cardiovascular disease, and stroke. To treat DM, several types of insulin preparations and synthetic drugs for type 1 and type 2 DM, respectively, are in clinical use. However, there are several problems concerning the insulin preparations and synthetic drugs, such as physical and mental pain due to daily insulin injections and defects involving several side effects, respectively. Thus, the disease demands extraordinary effects to define pathobiochemical pathways and strategies for prevention and to find new therapeutic approaches. For this purpose, oxovanadium(IV) (vanadyl, VO2+) and zinc(II) containing complexes have been explored as treatments for both types of DM. This article reviews the current state of research on insulin-mimetic and antidiabetic metal complexes, with special focus on paramagnetic vanadyl and diamagnetic zinc(II) complexes with different coordination modes, together with possible reaction mechanisms. New drug delivery systems involving enteric-coated capsulation and a biopolymer are also reviewed.
Electrocatalytic Activity of Metal-Loaded Reticulated Vitreous Carbon Electrodes for Hydrogen Evolution from Flowing Alkaline Solutions
Authors: Saleh Mahmoud M , El-Ankily Maher H , El-Deab Mohamed S , El-Anadouli B E 
Published: November 2006

Abstract
Reticulated vitreous carbon (RVC) electrodes have been used as possible porous cathodes, operating in flow-through mode for the purpose of the electrolytic generation of hydrogen gas from flowing alkaline solutions. The electrocatalytic performance of the RVC cathode was tested under different operating conditions, such as electrolyte flow regimes and temperature. Also, the effect of electroplating the RVC with copper metal or Watts nickel in flowing electrolytes has been assessed. Potentiodynamic and galvanostatic techniques along with SEM images were used to investigate the performance of the different cathodes: bare (uncoated) RVC, copper-coated RVC (RVC/Cu), and Ni-coated RVC (RVC/Ni). The hydrogen evolution reaction (HER) was found to be enhanced by coating RVC either with Cu or Ni. Polarization behavior had higher rates for HER using RVC/Ni than using RVC/Cu or bare RVC. This trend was confirmed by using a planar glassy carbon electrode (GC) coated with Cu and Ni under the same conditions. The activation energies for HER using RVC and RVC/Ni were estimated to be 32 and 14 kJ mol−1, respectively. Current transient and SEM micrographs showed good electrocatalytic and mechanical stability of the metal loadings. There was no indication of loss of the catalytic properties after operation for 30 h. Model calculations helped to extract kinetic parameters for the HER using different electrodes.
Use of 2,2′-Dibenzothiazolyl Disulfide-Triphenylphosphine and Lawesson’s Reagent in the Cyclization of β-Amino Acids
Authors: Kanwar Seema , Sharma S D 
Published: November 2006

Abstract
The disulfide reagents 2,2′-dithiobisbenzothiazole (MBTS) and 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide (Lawesson’s Reagent, LR) mediate the cyclization of β-amino acids with remarkable product yields. Compared to other cyclodehydrating agents, these have been found to be superior in terms of their cost, making them industrially viable. The advantageous properties of MBTS and LR make them useful and unique additions to the arsenal of cyclodehydrating agents.
Synthesis and Photochemical Properties of a New Water-Soluble Coumarin, Designed as a Chromophore for Highly Water-Soluble and Photolabile Protecting Group
Authors: Senda Naoko , Momotake Atsuya , Nishimura Yoshinobu , Arai Tatsuo 
Published: November 2006

Abstract
The absorption spectra and fluorescence spectra of a coumarin derivative (1), designed to be a water-soluble photolabile protecting group for caged compounds, were successfully observed in aqueous buffer solutions at pH 2.0–12.5 for the first time. Coumarin 1 is highly soluble (&gt;5 mM) in aqueous buffer at pH 7.2 and is stable in the dark at room temperature for up to a week. The pKa value for the protonation of anilino nitrogen in coumarin 1 was determined to be 4.5. Coumarin 1 has a fluorescence lifetime of 2.0 ns and undergoes intersystem crossing to the triplet state. Therefore, compound 1 can be used for the light absorbing part of the new water-soluble caged compounds, such as caged amino acids or caged nucleotides, which can release free amino acids or nucleotides, respectively, by excitation in the visible region.
Generation of an S-Peptide via an N–S Acyl Shift Reaction in a TFA Solution
Authors: Nakamura Ken’ichiroh , Sumida Megumi , Kawakami Toru , Vorherr Thomas , Aimoto Saburo 
Published: November 2006

Abstract
An N–S acyl shift reaction of thiol-containing peptides in a trifluoroacetic acid (TFA) solution was confirmed by a combination of 13C NMR spectroscopy, reversed-phase (RP) HPLC, and MS analyses. A model peptide containing a cysteine residue was transformed into an S-peptide in a TFA solution. The S-peptide was quickly transformed to the original peptide during RP-HPLC analysis even when an eluent that contained 0.1% TFA was used. A peptide that had an N-2-mercapto-4,5-dimethoxybenzyl (Dmmb) group was also transformed into an S-peptide, forming a thioester bond with the thiol of the Dmmb group by TFA treatment. The generated S-peptide was isolated by directly injecting the reaction mixture into a RP-HPLC and was readily converted to the corresponding 2-sulfoethyl thioester via an intermolecular thiol exchange reaction with sodium 2-mercaptoethanesulfonate. The 2-sulfoethyl peptide thioester is widely used as a building block in polypeptide synthesis. The N–S acyl shift reaction observed in peptides with or without an auxiliary group provides a new route for the preparation of peptide thioesters.
Ring Carbon Functionalization of N-Heterocyclic Carbene Ligand with Ester Groups. Electronic Effect of Ester Groups on Coordination Properties
Authors: Hara Kenji , Kanamori Yoshikazu , Sawamura Masaya 
Published: November 2006

Abstract
Palladium complexes with an imidazol-2-ylidene ligand functionalized with ester groups at its 4,5-positions were synthesized from a readily available imidazole derivative. σ-Donation from the carbene ligand to the palladium atom is considerably weakened by functionalization with the two ester moieties.
Determination of the thermodynamic quantities of complexation between Eu(III) and carboxylic acids by microcalorimetry
Authors: Kitano Hiroyuki , Onishi Yuko , Kirishima Akira , Sato Nobuaki , Tochiyama Osamu 
Published: November 2006

Potentiometric and microcalorimetric titration techniques were applied to determine the Gibbs free energies and enthalpies of the protonation of some carboxylic acids (acetic, glycolic, malonic and malic acids) and their complexation with Eu(III) in 1.0 M NaClO4 solution at 25 °C, where Eu(III) was used as a chemical analogue of radiologically important Am(III). By using the values of ΔG determined by potentiometric titrations, the results of calorimetric titrations were analyzed to give the values of ΔH and ΔS. To support the discussion on the obtained thermodynamic quantities, the hydration numbers of Eu(III) in the complexes were obtained by TRLFS measurement, where the luminescence lifetime of Eu(III) excited by 394 nm laser was measured.
A few to several kJ/mol of enthalpies were determined for the reactions within the uncertainties of ±0.01 to ±0.4. These enthalpy values indicated that the protonation of these carboxylates were entropy-driven, that is, |−TΔS|>>|ΔH| in ΔG=ΔH −TΔS. The complexations of Eu(III) were also shown to be controlled mainly by entropy term. The results of TRLFS measurement revealed that the number of dehydrated water molecule increased with the degree of complexation. A linear relation was found between total entropy change of the system (ΔS
T) and the net number of released molecules from the central Eu(III) ion. However, the values of ΔS
T for the hydroxy-carboxylates were smaller than that for simple carboxylates at the same net number of molecules released from Eu(III), suggesting that the dehydration occurred not only in the cation but also in the anion.
The uptake of radium by calcium silicate hydrates and hardened cement paste
Authors: Tits Jan , Iijima Kazuki , Wieland Erich , Kamei Gento 
Published: November 2006

In the present study the interaction of Ra(II) with calcium silicate hydrates (C-S-H) as well as with fresh and degraded hardened cement pastes (HCP) has been investigated using batch-type sorption tests. Synthetic C-S-H phases with varying CaO:SiO2 (C:S)mol ratios, relevant to non-degraded HCP and degraded HCP, were prepared in the absence of alkalis (Na(I), K(I)) and in an alkali-rich artificial cement pore water (ACW). The Ra(II) sorption kinetics, the effect of the solid to liquid ratio and the C:S mol ratio on the Ra(II) uptake were investigated. In addition, the reversibility of Ra(II) sorption was tested using dilution tests. Comparison with data on the uptake of Sr(II) by C-S-H phases obtained from previous in-house studies showed that the same model concept could be applied to interpret the immobilization of Sr(II) and Ra(II) in these systems. Ra(II) sorption on C-S-H in the absence of alkalis could be interpreted in terms of a Ra2+-Ca2+ cation exchange model. The Ra2+-Ca2+ exchange selectivity coefficient, Ra
CaKC, was determined to be (6±4). There are indications that, in the presence of alkalis, the Ra(II) sorption by C-S-H phases can only be described with the help of an ion-exchange model involving Ra2+, Ca2+ and the monovalent alkalis.
The cation exchange model developed for C-S-H phases in the absence of alkalis was successfully applied to predict the sorption of Ra(II) on degraded HCP, assuming that the Ra(II) sorbs solely on the C-S-H fraction of the HCP. Model predictions and experimental data were found to agree well in view of the simplified sorption model used.
Thermal diffusion of chlorine in uranium dioxide
Authors: Pipon Y. , Toulhoat N. , Moncoffre N. , Jaffrézic H. , Gavarini S. , Martin P. , Raimbault L. , Scheidegger A. M. 
Published: November 2006

In a nuclear reactor, isotopes such as 35Cl present as impurities in the nuclear fuel are activated by thermal neutron capture. During interim storage or geological disposal of nuclear fuel, the activation products such as 36Cl may be released from the fuel to the geo/biosphere and contribute to the “instant release fraction” as they are likely to migrate in defects and grain boundaries. In order to differentiate diffusion mechanisms due to “athermal” processes during irradiation from thermally activated diffusion, both irradiation and thermal effects must be assessed.
This work concerns the measurement of the thermal diffusion coefficient of chlorine in UO2.37Cl was implanted at a 1013 at/cm2 fluence in depleted UO2 samples which were then annealed in the 900−1200 °C temperature range and finally analyzed by Secondary Ion Mass Spectrometry (SIMS) to obtain 37Cl depth profiles. The migration process appears to be rather complex, involving mechanisms such as atomic, grain boundary, directed diffusion along preferential patterns as well as trapping into sinks before successive effusion. However, using a diffusion model based on general equation of transport, apparent diffusion coefficients could be calculated for 1000 and 1100 °C and a mean activation energy of 4.3 eV is proposed. This value is one of the lowest values compared to those found in literature for other radionuclides pointing out a great ability of chlorine to migrate in UO2 at relatively low temperatures.
In order to unequivocally determine the diffusion behaviour of both implanted and pristine chlorine before and after thermal annealing, the structural environment of chlorine in UO2 was examined using micro X-ray fluorescence (micro-XRF) and micro X-ray absorption spectroscopy (micro-XAS).
Comparison of Native and Introduced Flathead Catfish Populations in Alabama and Georgia: Growth, Mortality, and Management
Authors: Sakaris Peter C. , Irwin Elise R. , Jolley Jeffrey C. , Harrison Donald 
Published: November 2006

Abstract
We compared growth of flathead catfish Pylodictis olivaris from two native populations in Alabama (Coosa and Tallapoosa rivers) and two introduced populations in Georgia (Ocmulgee and Satilla rivers). We also compared mortality rates and potential outcomes of various management regimes (minimum length limits [MLLs]) among the populations. Total length–log10(age) regression slopes for introduced fish were higher than those for native fish, and von Bertalanffy growth coefficients (K) were greater for introduced fish (Ocmulgee: 0.195; Satilla: 0.201) than for native individuals (Coosa: 0.057; Tallapoosa: 0.059). Therefore, introduced flathead catfish grew more rapidly than those in their native range. Mortality (instantaneous mortality rate, Z) was higher in the Satilla River population (Z = −0.602) than in the Ocmulgee River (Z = −0.227) and Coosa River (Z = −0.156) populations. However, fish in the Satilla River population had been introduced for only 10 years and presumably did not reach their theoretical maximum age, potentially biasing the mortality estimate for that population. Simulation of management regimes in Fishery Analyses and Simulation Tools software predicted that maximum biomass of flathead catfish in the Ocmulgee (1,668 kg) and Satilla (1,137 kg) rivers was substantially larger than that in the Coosa (873 kg) and Tallapoosa (768 kg) populations. However, increased exploitation rates in the Ocmulgee and Satilla River populations resulted in dramatic declines in overall biomass, especially at lower MLLs (254 and 356 mm, respectively). Therefore, in systems where introduced flathead catfish represent an important recreational fishery but have dramatically reduced the abundance of native fishes through predation, minimal protection is recommended. We contend that rapid growth of introduced flathead catfish has major implications for their management and the conservation of native fishes.