bluuebunny/crossref_metadata_2025_split huggingface dataset:
HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences
Authors: Panjaworayan Nattanan , Roessner Stephan K , Firth Andrew E , Brown Chris M 
Published: December 2007

Abstract

Background
The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses.

Results
These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx). It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon) and RNA secondary structure predictions (e.g. Alidot) – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser) adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences.

Conclusion
HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.
Randomized Crossover Study Evaluating the Effect of Gemcitabine Infusion Dose Rate: Evidence of Auto-Induction of Gemcitabine Accumulation
Authors: Grimison Peter , Galettis Peter , Manners Susan , Jelinek Maria , Metharom Ekkaphon , de Souza Paul L. , Liauw Winston , Links Matthew J. 
Published: December 2007

Purpose Controversy exists over the optimal dose rate for administration of gemcitabine. There is a strong pharmacologic rationale for increased intracellular accumulation with prolonged infusions, but this failed to translate into a significant benefit in a large randomized study. The purpose of this study was to compare the intracellular pharmacokinetics of gemcitabine given for 30 minutes or for 100 minutes in a crossover design. Patients and Methods We randomly assigned 33 patients to a standard dose of 1,000 mg/m2 over either 30 minutes or 100 minutes. At the second week, they were transferred to the alternate schedule. Blood samples were collected at various times after the gemcitabine infusion. Gemcitabine and difluorodeoxyuridine were measured in plasma by high-performance liquid chromatography (HPLC), and gemcitabine-triphosphate was measured by HPLC in leukocytes. Results Intracellular accumulation was greater during the 100-minute infusion, which was consistent with previous data. This effect was confounded by an increase in gemcitabine-triphosphate accumulation between weeks 1 and 2, which was consistent with self-induction of gemcitabine accumulation. There was significant heterogeneity: 27% of patients had greater WBC accumulation during the 30-minute infusion (regardless of treatment order). Patients with relatively greater levels of gemcitabine-triphosphate in WBCs tended to have less under-dosing and a greater reduction in midcycle neutrophils. However, this observation did not correlate with plasma gemcitabine levels. Conclusion This work identifies significant variations in intracellular gemcitabine-triphosphate accumulation between and within individuals, and it provides evidence that this variation has potential clinical significance. The observed self-induction of gemcitabine metabolism has broad implications for the dosing of nucleoside analogs.
Colorectal Carcinoma in Childhood and Adolescence: A Clinicopathologic Review
Authors: Hill D. Ashley , Furman Wayne L. , Billups Catherine A. , Riedley Shannon E. , Cain Alvida M. , Rao Bhaskar N. , Pratt Charles B. , Spunt Sheri L. 
Published: December 2007

Purpose Pediatric colorectal carcinoma (CRC) is rare, but the available data suggest that it is more likely than adult CRC to be advanced at presentation and to have a poor outcome. We sought to better characterize pediatric CRC. Patients and Methods We reviewed the clinical and pathologic features, prognostic factors, and outcome of CRC in 77 children and adolescents (ages 7 to 19 years) referred to St Jude Children's Research Hospital between 1964 and 2003. Results At presentation, 76 patients had one or more signs or symptoms of CRC (abdominal pain, altered bowel habits, weight loss, anemia). Tumors were evenly distributed between the right and left colon; 62% were mucinous adenocarcinoma. At presentation, 86% of patients had advanced-stage disease; more than half had distant metastases. Overall outcome was poor. Advanced stage and mucinous histology were significant predictors of adverse outcome. Stage-specific survival at 10 years was 67% ± 27% (stage 1), 38% ± 15% (stage 2), 28% ± 11% (stage III), and 7% ± 4% (stage 4). Although no patient had a diagnosis of polyposis syndrome before diagnosis of CRC, 17 (22%) had colon polyps and eight (including two who previously underwent pelvic radiotherapy) had multiple polyps. Conclusion Initial signs and symptoms of CRC are similar in pediatric and adult patients. The strikingly higher frequency of mucinous histology suggests that the biology of CRC differs in pediatric and adult patients and may contribute to poor outcomes. Children should be included in prospective clinical trials for CRC.
Syntheses of Mesoporous and Microporous Materials via 2-Methylpentamethylenediamine
Authors: Ferdov Stanislav , Lin Zhi , Ferreira Rute A Sá 
Published: December 2007

Abstract
The hydrothermal syntheses of the high-silica microporous zeolite ZSM-48 and the mesoporous crystalline germanium oxide SU-M using 2-methylpentamethylenediamine (MPMD) are demonstrated.
Chemical Aminoacylation of RNA by an Intermolecular Adenosine Transfer Reaction
Authors: Liu Mingzhe , Jinmei Hiroshi , Abe Hiroshi , Ito Yoshihiro 
Published: December 2007

Abstract
RNA aminoacylation, based on an adenosine transfer mechanism, was achieved by the intermolecular transfer of phenylalaninyl adenosine from a donor probe to an acceptor RNA. This method can be applied to a wide variety of unnatural amino acids for tRNA aminoacylation.
Effect of an Asymmetrically Arranged Equatorial Chelate Ring in an Active Site of Nitrile Hydratase
Authors: Yano Takuma , Wasada-Tsutsui Yuko , Kajita Yuji , Shibayama Tomonori , Funahasi Yasuhiro , Ozawa Tomohiro , Masuda Hideki 
Published: December 2007

Abstract
A CoIII complex with a novel N2S2-type ligand, asymmetrically arranged with 6-5-5 chelate ring, was prepared as an active site model of nitrile hydratase and was found to show a higher stability constant in the axial ligation of t-butylisocyanide compared with the previously reported symmetric analog.
Synthesis and Properties of New Tetrathiapentalene Donors Composed of Vinylogous TTFs
Authors: Iwamoto Shintaro , Watanabe Shunsuke , Fueno Hiroyuki , Tanaka Kazuyoshi , Misaki Yohji 
Published: December 2007

Abstract
A bis-fused donor composed of TTF vinylogues, 2,5-bis(2-ethanediylidene-1,3-dithiole)-1,3,4,6-tetrathiapentalene (BisEDT, 1a) and its derivatives have been synthesized. Cyclic voltammograms of 1 consist of four-pairs of one-electron redox waves. X-ray structure analysis of tetrakis(methylthio)-1 (1b) reveals the donor adopts almost planar structure. The TCNQF4 complexes of 1 showed moderate conductivity of σrt=10−2 S cm−1 on a compressed pellet.
Estimating response times of Vadret da Morteratsch, Vadret da Palü, Briksdalsbreen and Nigardsbreen from their length records
Authors: Oerlemans J. 
Published: December 2007

AbstractLength records of two pairs of glaciers are used to reconstruct the equilibrium-line altitude (ELA) and to estimate glacier response times. The method is based on the assumption that neighbouring glaciers should be subject to the same climatic forcing, and that differences in the length records are thus caused by differences in response times and climate sensitivities. By means of a control method, in which the difference between the reconstructed histories of the ELA is minimized, realistic response times are found. The pairs of glaciers studied are: (i) Vadret da Morteratsch and Vadret da Palü in the Swiss Alps and (ii) Briksdalsbreen and Nigardsbreen in southern Norway. In both cases the reconstructed ELA histories of the individual glaciers are very similar, in spite of the large differences in the length records. Short e-folding response times are found for the steep glaciers: 4.4 years for Vadret da Palii, 5.0 years for Briksdalsbreen. For the larger glaciers with a more gentle slope the response times are substantially larger: 33.0 years for Vadret da Morteratsch, 34.8 years for Nigardsbreen.
Sub‐20 nm Magnetic Dots with Perpendicular Magnetic Anisotropy
Authors: Stillrich H. , Frömsdorf A. , Pütter S. , Förster S. , Oepen H. P. 
Published: December 2007

AbstractA new and simple method for the preparation of magnetic dot arrays is introduced. Diblock copolymer micelles with a silica core are used as template for the generation of nanostructure arrays. The silica cores are utilized as mask for ion milling preparation. The morphology and size of the silica and magnetic dot arrays are discussed. The magnetic dots are made from Co/Pt multilayer films. Ferromagnetic dots with a diameter well below 20 nm and perpendicular easy axis of magnetization are created. The switching behavior changes from domain wall motion, dominant in the film, to single domain particle switching in the dots. The magneto‐optic saturation signals and the evolution of magnetic anisotropy are discussed.
Green Synthesis and Property Characterization of Single‐Crystalline Perovskite Fluoride Nanorods
Authors: Zhang F. , Mao Y. , Park T.‐J. , Wong S. S. 
Published: December 2007

AbstractThe generalized green synthesis of single‐crystalline KMnF3 and NH4MnF3 nanorods as well as of their rare‐earth ion doped analogues, possessing reproducible shape and controllable size, has been achieved using a modified template‐directed approach under ambient room‐temperature conditions, with simple inorganic salts as functional precursors. Extensive characterization of the resulting nanorods has been performed using diffraction, electron microscopy, optical spectroscopy, as well as magnetic techniques. We have studied the antiferromagnetism of as‐prepared ternary metal fluoride nanorods as well as the luminescence of their as‐doped counterparts. Our collective data suggest the possibility of the incorporation of these high‐quality, chemically pure materials into functional nanoscale devices with various potential applications that exploit the interesting optomagnetic properties of these systems.
Preparation and characterization of polyamide 66/montmorillonite nanocomposites with methyl methacrylate as cointercalation agent
Authors: Yang Qing‐Quan , Guo Zhao‐Xia , Yu Jian 
Published: December 2007

AbstractThis study reports a simple and low‐cost preparation method for nearly exfoliated polyamide 66 (PA66)/montmorillonite (MMT) nanocomposites. Polymerizable methyl methacrylate (MMA) is used as cointercalation agent to take advantages of both in‐situ polymerization and melt mixing. Two preparation approaches, either direct melt compounding or dilution from a master‐batch, are investigated. The nano‐scale dispersion of organo‐MMT (OMMT) in PA66 is revealed by X‐ray diffraction and transmission electron microscopy. PA66/MMT nanocomposites having superior mechanical properties and heat distortion temperature (HDT) can be obtained by either of the two preparation approaches on condition that excess MMA, which is on the surface of PA66/OMMT is removed by ventilation before melt compounding. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Polymeric Zinc Ferrocenyl Sulfonate as a Molecular Aspirator for the Removal of Toxic Metal Ions
Authors: Mi Liwei , Hou Hongwei , Song Zhiyong , Han Huayun , Fan Yaoting 
Published: December 2007

AbstractA porous bilayered open coordination polymer [Zn(4,4′‐bpy)2(FcphSO3)2]n (1; FcphSO3Na=m‐ferrocenyl benzenesulfonate), has been assembled from Zn(NO3)2, m‐ferrocenyl benzenesulfonate, and the bridging ligand 4,4′‐bipyridine (4,4′‐bpy). Ion‐exchange induced products [Cd0.6Zn0.4(4,4′‐bpy)2(FcphSO3)2]n (2), [Zn0.75Pb0.25(4,4′‐bpy)2(FcphSO3)2]n (3), and [Cu0.5Zn0.5(4,4′‐bpy)2(FcphSO3)2]n (4) could be obtained directly by suspending a big single crystal of 1 into concentrated solutions of Cd(NO3)2, Pb(NO3)2, and Cu(NO3)2, respectively. Most importantly, the big single crystal of 1 could be partly regenerated after immersion into concentrated aqueous solutions of Zn(NO3)2. On the other hand, powdered 1 could also be used as a metal ion adsorbent because of the well‐defined pore size and pore shape. Ion exchange takes place along with the process of ion sorption. The big single crystal of 1 removes harmful metal ions by means of ion exchange, whereas powdered 1 removes toxic metal ions mainly through ion sorption. Also, compound 1 could be employed as a multi‐ion analysis fluorescent probe to detect dangerous metal ions, such as Pb2+, Cd2+, Ag+, and Cu2+. The compounds described in this study may have potential applications in the design of new molecular devices.
Modulatory effect of chiral nonsteroidal anti‐inflammatory drugs on apoptosis of human neutrophils
Authors: Zielińska‐Przyjemska Małgorzata , Główka Franciszek K. , Klaczyńska Joanna 
Published: December 2007

AbstractPolymorphonuclear neutrophils (PMNs) are short‐lived leukocytes that die by apoptosis. Although PMNs are crucial in the defense against infection, they have been implicated in the pathogenesis of tissue injury observed in inflammatory diseases. The induction or prevention of PMN apoptosis is currently discussed as a key event in the control of inflammation. Caspase‐3 activation is the first step in the execution phase of apoptosis. In the study, effect of racemic mixtures and enantiomers of 2‐arylpropionic acid derivatives: ketoprofen, flurbiprofen (FBP), and (+)‐S‐naproxen and 2‐arylbutyric acid: indobufen on apoptosis activation via caspase‐3 and phosphatidylserine (PS) translocation (annexin‐V binding) in human neutrophils in vitro has been investigated. Caspase‐3 activation was detected by Western blotting, fluorometric assay of DEVD‐AMC cleavage, and flow cytometry with carboxyfluorescein (FAM) labeled caspase inhibitor. PMNs were isolated and cultured up to 24 h. The chiral nonsteroidal anti‐inflammatory drugs (NSAIDs) were found to modulate human PMN apoptosis in a dose‐ and time‐dependent manner. The greater activation of caspase was found at 75–150 μg/ml concentration of racemates as well enantiomers, especially for FBP, whereas NSAIDs at smaller quantities (15 μg/ml) were inactive. At concentration of 75 μg/ml, NSAIDs increased the rate of PS externalization in PMA‐stimulated and non‐stimulated neutrophils. Additionally, no cytotoxic effect of the NSAIDs was observed at concentration up to 75 μg/ml that induce apoptosis. Regulation of caspase activity by NSAIDs may represent a potent target to trigger apoptosis and resolve inflammatory disorders. Chirality, 2008. © 2007 Wiley‐Liss, Inc.
Removal of Copper(II) Ions from Aqueous Solutions by Walnut‐, Hazelnut‐ and Almond‐Shells
Authors: Altun Türkan , Pehlivan Erol 
Published: December 2007

AbstractThe batch removal of Cu(II) ions from aqueous solution using low‐cost adsorbents such as walnut (WNS) (Juglans regia), hazelnut (HNS) (Corylus avellana), and almond (AS) (Prunus dulcis) shell under different experimental conditions was investigated in this study. The main parameters influencing Cu(II) ion sorption on WNS, HNS, and AS were: initial metal ion concentration, amount of adsorbent, contact time, and the pH value of the solution. The influences of initial Cu(II) ion concentration (0.005–0.05 mmol/mL), pH (2–9), contact time (10–240 min), and adsorbent amount (0.1–1.0 g) have been reported. WNS presented the highest adsorption capacities for the Cu(II) ion. Each of WNS, HNS, and AS as sorbents for the removal of Cu(II) ions showed that the sorption process was pH dependent. The greatest increase in the rate of adsorption of metal ion on the shells was observed for pH changes from 5.5–7.0. For WNS, HNS, and AS, the optimum pH value was 6 and the equilibrium time was 120 min. The metal ion sorption obeyed both the Langmuir and Freundlich isotherms. The sorption process conformed to the Langmuir isotherm with maximum Cu(II) ion sorption capacities of 6.74, 6.65, and 3.62 mg/g for WNS, HNS, and AS, respectively. The experimental results demonstrated that chelation and ion exchange is one of the major adsorption mechanisms for binding metal ions to the sorbents. The percentage removal Cu(II) ion was maximum at 10–3 mol/L solution concentration and initial pH of 6.0 (80.3, 75.6, and 75.0% by WNS, HNS, and AS, respectively).
Geotechnical Problems Experienced During the Construction of the Sludge Treatment Unit of the Main Wastewater Treatment Plant in Antalya
Authors: Acar Mustafa Hilmi 
Published: December 2007

AbstractThe treatment and disposal of wastewater still is a big problem of Antalya. The wastewater produced in the residential areas is biologically treated, the produced sludge, however, remains untreated. At the moment more than 60 t/day of dewatered sludge are buried at a landfill area located directly above the main groundwater resources of the city. As the area does not have any drainage and liner systems, it is believed that this kind of disposal constitutes a threat to the groundwater resources. Therefore, Antalya Metropolitan Municipality decided to add anaerobic sludge digestion units to the wastewater treatment plant. The sludge digestion tanks are considered to be built within the wastewater treatment plant area which is less than 1 km away from the beaches along the Mediterranean Sea. The purpose of this study is to examine the foundation soil in terms of its bearing capacity, consolidation settlement, and earthquake risks and to find out whether this construction site is suitable for building the sludge digestion tanks or not.
Abnormal cellular translocation of α‐internexin in spinal motor neurons of Dystonia musculorum mice
Authors: Tseng Kuang‐Wen , Chau Yat‐Pang , Yang Mei‐Fang , Lu Kuo‐Shyan , Chien Chung‐Liang 
Published: December 2007

AbstractDystonia musculorum (dt) is a mutant mouse with hereditary neuropathy where the dysfunction is mainly found in the dorsal root ganglia (DRG) neurons but not in the spinal motor neurons. However, the accumulation of intermediate filament (IF) proteins in the swelling axons of spinal motor neurons could be found in dt/dt mice. In order to understand the pathological role of neuronal IFs in the swelling axons of spinal motor neurons from dt/dt mice, we extensively examined the distribution of neuronal IF proteins. By immunofluorescence staining, our results indicated that α‐internexin was a major component in the swelling axon and showed abnormal translocation in the nuclei of spinal motor neurons in dt/dt mice. This abnormal translocation of α‐internexin in the nuclei of spinal motor neurons was also confirmed by Western blotting and immunoelectron microscopy. Instead of the 10‐nm filamentous structure, a diffuse immunopositive pattern of α‐internexin was observed in the nucleus of spinal motor neurons in dt/dt mutants. We further examined the cell death of spinal motor neurons by TUNEL assay, and no TUNEL‐positive cells could be identified from spinal motor neurons in dt/dt mice. From these observations we suggest that abnormal accumulation of neuronal IFs in the swelling axons and abnormal translocation of α‐internexin in the nuclei of the spinal motor neurons from dt/dt mice may not directly cause cell death of the spinal motor neurons. J. Comp. Neurol. 507:1053–1064, 2008. © 2007 Wiley‐Liss, Inc.
Prioritizing migraine biomarkers research
Authors: Gurwitz David , Diamond Seymour 
Published: December 2007

AbstractMigraine is among the most common chronic disorders in the developed countries, affecting up to 17% of adult women and 6% of adult men. It is also among the chronic disorders most commonly associated with recurring absence from work. It has been estimated that in the United States the indirect annual societal cost of migraine, mostly as lost work, is US$12 billion. Migraine diagnosis and treatment is hindered by the lack of reliable serum or genetic biomarkers that could potentially improve treatment choices. Research programs focused on identifying and developing migraine biomarkers for both prevention and treatment must be included in the national biomedical research agenda. Drug Dev Res 68:267–269, 2007. © 2007 Wiley‐Liss, Inc.
Effects of antiepileptic drugs on neurophysiologic abnormalities subtending migraine
Authors: de Tommaso Marina 
Published: December 2007

AbstractRecent theories about migraine pathogenesis have outlined migraine as a brain disorder. Migraine can be considered an aberrant physiological state with a low threshold for intermittent neuronal excitability. Neurophysiologic findings in migraine emphasized the presence of abnormal neuronal function during the asymptomatic phase, predisposing to attack occurrence, the main patterns being the loss of habituation of evoked and event related potentials and the hypersynchronization of electroencephalographic (EEG) activity. These studies confirmed the need of preventive agents able to act on neuronal excitability, with growing evidence in favor of the clinical efficacy of anti‐epileptic drugs (AED), though electrophysiological evidence supporting migraine as a state of neuronal hypoexcitability rendered the rationale of their use and their fundamental action mechanism in preventing migraine rather questionable. In the last years, many studies reported the efficacy of other preventive agents than AED, such as ‐blockers, in reversing neurophysiologic abnormalities of migraine, while reducing headache frequency. Our recent results showed a normalizing effects of levetiracetam and topiramate vs. placebo on the dishabituation pattern of the contingent negative variation (CNV) and the efficacy of levetiracetam vs. both topiramate and placebo in reversing the hypersynchronization of alpha rhythm under flash stimulation. All these effects concurred with the clinical efficacy on migraine frequency, and confirmed the action of AED on the basal mechanisms of migraine. Considering our and previous results, migraine may be considered as a state of “altered” excitability, where the AED are modulating agents able to reverse the electrophysiological patterns predisposing to the attack occurrence. The challenge for the future may be the identification of subgroups of migraine patients with pronounced expression of some neurophysiologic indexes of migraine predisposition, e.g., hypersynchronization, which may optimize the choice of the preventive agent. Drug Dev Res 68:369–375, 2007. © 2007 Wiley‐Liss, Inc.