bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steriltechnik in der Herstellung pharmazeutischer Produkte
Authors: Winter G. 
Published: October 2006

AbstractDie den Pharmabereich kennzeichnenden Besonderheiten in der Steriltechnik sollen in diesem Beitrag herausgearbeitet werden. Dabei wird auf Neuerungen und aktuelle Trends sowie auf die für den Pharmabereich typischen behördlichen Regulierungen eingegangen. Der verstärkte Einsatz von Isolatortechnik und der neuen „RABS”︁‐Konzepte zur vollständigen Trennung von Produkt und Personal werden kommentiert ebenso wie Weiterentwicklungen von automatischen Abfüllprozessen. Im Bereich der Reinigung Produkt berührender Oberflächen zeichnen sich neue Trends ab. Außerdem stehen die Reinigungsvalidierung an „Multi‐Purpose”︁‐Anlagen und der fortschreitende Einsatz von Einmalsystemen im Mittelpunkt. Einen weiteren Schwerpunkt bilden neue Packmittelkonzepte, insbesondere sog. „RTF”︁ = „ready to fill”︁‐Einheiten und moderne Devices. Abschließend wird kurz die Initiative der FDA zum Thema „Process Analytical Technologies”︁ (PAT) kommentiert.
Phenotypic diversity is the cornerstone of evolution: Variation in cortical field size within short‐tailed opossums
Authors: Karlen Sarah J. , Krubitzer Leah 
Published: October 2006

AbstractNatural selection operates on phenotypic variation that exists within a population. Variable aspects of cortical organization, such as the size and connections of a cortical field, can generate differences in behavior, which is a target of natural selection. Yet studies pertaining to within‐species variability in cortical organization are limited. In the present investigation, we examined variation in brain size, cortical sheet size, and primary sensory cortical field sizes in the adult short‐tailed opossum (Monodelphis domestica). Within individuals, we found no significant difference between the right and left hemispheres in the overall size of the dorsolateral cortex or in primary cortical field sizes. Between individuals, we found relatively little intraspecies variation in brain weight, brain volume, and cortical sheet area for the dorsolateral neocortex and pyriform cortex; however, we observed a large degree of variability in body weight and primary sensory cortical field size, as defined by myeloarchitecture. Further, we found that the size of each cortical field correlated with the size of the other cortical fields as well as with the total size of the dorsolateral cortex. Here we discuss the possible sources of variation and examine the relationship between cortical field size and sensory processing abilities and behaviors across species. Since behavior is the target of natural selection, variation in cortical field size across individuals may supply the raw material necessary for cortical field evolution. J. Comp. Neurol. 499:990–999, 2006. © 2006 Wiley‐Liss, Inc.
Ectopic expression of the homeobox gene Cux‐1 rescues calcineurin inhibition in mouse embryonic kidney cultures
Authors: Alcalay Neal I. , Brantley Jennifer G. , Sharma Madhulika , Gooch Jennifer L. , Vanden Heuvel Gregory B. 
Published: October 2006

AbstractCux‐1 is a murine homeobox gene structurally related to Drosophila cut. Cux‐1 is highly expressed in the nephrogenic zone of the developing kidney, where its expression coincides with cell proliferation. Cux‐1 functions as a transcriptional repressor of the cyclin kinase inhibitors (CKI) p21 and p27. Cux‐1 DNA binding activity is negatively regulated by phosphorylation, and dephosphorylation of Cux‐1 results in increased DNA binding. Transgenic mice ectopically expressing Cux‐1 develop renal hyperplasia associated with the down‐regulation of the CKI p27. Calcineurin A (CnA) α (−/−) mice display renal hypoplasia associated with the ectopic expression of p27. CnA is a serine/threonine phosphatase activated by intracellular calcium. Inhibiting CnA with cyclosporin A (CsA) leads to nephron deficit in rat metanephric organ cultures and apoptosis in various renal cell lines. To determine whether the ectopic expression of p27 in CnA‐α −/− kidneys results from the down‐regulation of Cux‐1, metanephroi from embryonic Cux‐1 transgenic and wild‐type mice were harvested and cultured with CsA for 5 days. CsA treatment significantly inhibited growth of wild‐type metanephroi. In contrast, CsA‐treated Cux‐1 transgenic kidney cultures were not growth inhibited, but showed high levels of cell proliferation in the nephrogenic zone. Moreover, in CsA‐treated Cux‐1 transgenic kidney cultures, p27 was not expressed in the nephrogenic zone, but only up‐regulated in maturing glomeruli and tubules. Taken together, our results demonstrate that ectopic expression of Cux‐1 can rescue the effects of CsA inhibition of CnA and suggest that Cux‐1 may be regulated by calcineurin A. Developmental Dynamics 236:184–191, 2007. © 2006 Wiley‐Liss, Inc.
Computational Determination of Iron Hyperfine Interactions in Organometallics Using Small Transverse External Magnetic Fields
Authors: Nowik Israel , Herber Rolfe H. 
Published: October 2006

AbstractA number of organometallic and related iron‐containing compounds have been examined by transmission 57Fe Mössbauer spectroscopy in modest (0–2.4 T) magnetic fields in order to determine the sign of the quadrupole‐splitting hyperfine parameter (QS) as well as the internal magnetic field in derived paramagnetic solids. A computer program has been developed to extract these parameters from the spectroscopic data. The sign of the QS is found to be positive in the neutral ferrocenoid solids and negative in the derived cationic complexes. The internal hyperfine field makes a positive contribution in the cationic ferrocenoids and a negative contribution in FeF2 and Fe(phen)2(SCN)2. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Borax as an Efficient Metal‐Free Catalyst for Hetero‐Michael Reactions in an Aqueous Medium
Authors: Hussain Sahid , Bharadwaj Saitanya K. , Chaudhuri Mihir K. , Kalita Harjyoti 
Published: October 2006

AbstractBorax, a naturally occurring material, very efficiently catalyzed the conjugate addition of thiols, dithiols and amines to α,β‐unsaturated ketones, nitriles, amides, aldehydes and esters in an aqueous medium to afford the corresponding Michael adducts in good yields at room temperature. Recycling of the catalyst and scaling up of the reactions are important attributes of this catalysis. The reactions of thiols and dithiols were relatively more facile than those of the corresponding amines. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Material surfaces affect the protein expression patterns of human macrophages: A proteomics approach
Authors: Dinnes Donna Lee M. , Marçal Helder , Mahler Stephen M. , Santerre J. Paul , Labow Rosalind S. 
Published: October 2006

AbstractMonocyte‐derived macrophages (MDM) are key inflammatory cells and are central to the foreign body response to implant materials. MDM have been shown to exhibit changes in actin cytoskeleton, multinucleation, cell size, and function in response to small alterations in polycarbonate‐urethane (PCNU) surface chemistry. Although PCNU chemistry has an influence on de novo protein synthesis, no assessments of the protein expression profiles of MDM have yet been reported. The rapid emerging field of expression proteomics facilitates the study of changes in cellular protein profiles in response to their microenvironment. The current study applied proteomic techniques, 2‐dimensional electrophoresis (2‐DE) combined with MALDI‐ToF (matrix assisted laser desorption ionization–time of flight) mass spectrometry, to determine differences in MDM protein expression influenced by PCNU. Results indicated that MDM responded to material chemistry by modulation of structural proteins (i.e. actin, vimentin, and tubulin). Additionally, intracellular protein modulation which requires proteins responsible for trafficking (i.e. chaperone proteins) and protein structure modification (i.e. bond rearrangement and protein folding) were also altered. This study demonstrated for the first time that a proteomics approach was able to detect protein expression profile changes in MDM cultured on different material surfaces, forming the basis for utilizing further quantitative proteomics techniques that could assist in elucidation of the mechanisms involved in MDM–material interaction. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Development of leiomyosarcoma of the uterus in MMTV‐CR‐1 transgenic mice
Authors: Strizzi L , Bianco C , Hirota M , Watanabe K , Mancino M , Hamada S , Raafat A , Lawson S , Ebert AD , D'Antonio A , Losito S , Normanno N , Salomon DS 
Published: October 2006

AbstractOverexpression of Cripto‐1 (CR‐1) in FVB/N mice using the MMTV‐LTR promoter results in increased mammary tumourigenesis in these female transgenic mice (MMTV‐CR‐1). Here, we characterize uterine tumours that developed in 15/76 (19.7%) of MMTV‐CR‐1 female nulliparous or multiparous mice during 24 months of observation compared with 0/33 (0%) of FVB/N normal control mice observed during the same time period (p < 0.01). The uterine tumours collected from the MMTV‐CR‐1 mice were classified as leiomyosarcomas and found to express the CR‐1 transgene by polymerase chain reaction analysis and immunohistochemistry. Detection by western blot analysis showed higher levels of phosphorylated (P) forms of c‐src, Akt, GSK‐3β, and dephosphorylated (DP)‐β‐catenin in lysates from MMTV‐CR‐1 uterine leiomyosarcomas in comparison with lysates from normal control FVB/N uteri. Immunostaining showed increased nuclear localization of β‐catenin in the MMTV‐CR‐1 uterine leiomyosarcomas. Increased immunostaining for CR‐1 was detected in 9/13 (69.2%) cases of human leiomyosarcoma compared with staining in 3/15 (20%) human leiomyoma sections. Stronger immunostaining for P‐src, P‐Akt, P‐GSK‐3β and increased nuclear localization of β‐catenin was also seen in human leiomyosarcomas in comparison with leiomyomas. Normal human uterine smooth muscle (UtSM) cells treated with exogenous soluble rhCR‐1 showed increased levels of P‐src, P‐Akt, P‐GSK‐3β and dephosphorylated (DP)‐β‐catenin and increased proliferation (p < 0.05) and migration (p < 0.01) in comparison with untreated control UtSM cells. Inhibitors against c‐src, Akt or β‐catenin, individually or in combination, significantly reduced CR‐1‐induced migration. These results suggest a role for CR‐1 during uterine tumourigenesis either directly by activating c‐src and Akt and/or via cross‐talk with the canonical Wnt signalling pathway, as suggested by the increased expression of P‐GSK‐3β, DP‐β‐catenin, and increased nuclear localization of β‐catenin in human and MMTV‐CR‐1 mice leiomyosarcomas. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Pocket and antipocket conformations for the CH4@C84 endohedral fullerene
Authors: Rehaman Abdul , Gagliardi Laura , Pyykkö Pekka 
Published: October 2006

AbstractThe endohedral fullerene CH4@C84 has been studied using density functional theory (DFT) and second‐order Møller–Plesset perturbation theory (MP2). In addition to the structure with a CH bond of CH4 in a tetrahedral pocket conformation, we find an alternative minimum, very close in energy (6.3–9.5 kJ/mol higher according to the level of theory), with the methane inverted, which we call the antipocket conformation. Computed IR spectra are reported for CH4@C84 and also for the reference system CH4@C60. The calculated vibrational levels, in a harmonic approximation, reveal close‐lying translational, librational, and shell‐vibrational modes. The results are also presented for the isoelectronic species NH@C60. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Babel's tower revisited: a universal resource for cross-referencing across annotation databases
Authors: Drăghici Sorin , Sellamuthu Sivakumar , Khatri Purvesh 
Published: October 2006

Abstract
Motivation: Annotation databases are widely used as public repositories of biological knowledge. However, most of these resources have been developed by independent groups which used different designs and different identifiers for the same biological entities. As we show in this article, incoherent name spaces between various databases represent a serious impediment to using the existing annotations at their full potential. Navigating between various such name spaces by mapping IDs from one database to another is a very important issue which is not properly addressed at the moment.
Results: We have developed a web-based resource, Onto-Translate (OT), which effectively addresses this problem. OT is able to map onto each other different types of biological entities from the following annotation databases: Swiss-Prot, TrEMBL, NREF, PIR, Gene Ontology, KEGG, Entrez Gene, GenBank, GenPept, IMAGE, RefSeq, UniGene, OMIM, PDB, Eukaryotic Promoter Database, HUGO Gene Nomenclature Committee and NetAffx. Currently, OT is able to perform 462 types of mappings between 29 different types of IDs from 17 databases concerning 53 organisms. Among these, over 300 types of translations and 15 types of IDs are not currently supported by any other tool or resource. On average, OT is able to correctly map between 96 and 99% of the biological entities provided as input. In terms of speed, sets of ∼20 000 IDs can be translated in &lt;30 s, in most cases.
Availability: OT is a part of Onto-Tools, which is freely available at
Contact: sorin@wayne.edu
Adding sequence context to a Markov background model improves the identification of regulatory elements
Authors: Kim Nak-Kyeong , Tharakaraman Kannan , Spouge John L. 
Published: October 2006

Abstract
Motivation: Many computational methods for identifying regulatory elements use a likelihood ratio between motif and background models. Often, the methods use a background model of independent bases. At least two different Markov background models have been proposed with the aim of increasing the accuracy of predicting regulatory elements. Both Markov background models suffer theoretical drawbacks, so this article develops a third, context-dependent Markov background model from fundamental statistical principles.
Results: Datasets containing known regulatory elements in eukaryotes provided a basis for comparing the predictive accuracies of the different background models. Non-parametric statistical tests indicated that Markov models of order 3 constituted a statistically significant improvement over the background model of independent bases. Our model performed slightly better than the previous Markov background models. We also found that for discriminating between the predictive accuracies of competing background models, the correlation coefficient is a more sensitive measure than the performance coefficient.
Availability: Our C++ program is available at
Contact: spouge@ncbi.nlm.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
MUSA: a parameter free algorithm for the identification of biologically significant motifs
Authors: Mendes Nuno D. , Casimiro Ana C. , Santos Pedro M. , Sá-Correia Isabel , Oliveira Arlindo L. , Freitas Ana T. 
Published: October 2006

Abstract
Motivation: The ability to identify complex motifs, i.e. non-contiguous nucleotide sequences, is a key feature of modern motif finders. Addressing this problem is extremely important, not only because these motifs can accurately model biological phenomena but because its extraction is highly dependent upon the appropriate selection of numerous search parameters. Currently available combinatorial algorithms have proved to be highly efficient in exhaustively enumerating motifs (including complex motifs), which fulfill certain extraction criteria. However, one major problem with these methods is the large number of parameters that need to be specified.
Results: We propose a new algorithm, MUSA (Motif finding using an UnSupervised Approach), that can be used either to autonomously find over-represented complex motifs or to estimate search parameters for modern motif finders. This method relies on a biclustering algorithm that operates on a matrix of co-occurrences of small motifs. The performance of this method is independent of the composite structure of the motifs being sought, making few assumptions about their characteristics. The MUSA algorithm was applied to two datasets involving the bacterium Pseudomonas putida KT2440. The first one was composed of 70 σ54-dependent promoter sequences and the second dataset included 54 promoter sequences of up-regulated genes in response to phenol, as suggested by quantitative proteomics. The results obtained indicate that this approach is very effective at identifying complex motifs of biological significance.
Availability: The MUSA algorithm is available upon request from the authors, and will be made available via a Web based interface.
Contact: atf@inesc-id.pt
Supplementary information: An appendix is available at under ‘Papers on-line’.
Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays
Authors: Tembe Waibhav , Zavaljevski Nela , Bode Elizabeth , Chase Catherine , Geyer Jeanne , Wasieloski Leonard , Benson Gary , Reifman Jaques 
Published: October 2006

AbstractMotivation: Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify ‘DNA fingerprints’, i.e. oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computational identification of DNA fingerprints for design of microarray-based pathogen diagnostic assays. We provide a quantifiable definition of a DNA fingerprint stated both from a computational as well as an experimental point of view, and the analytical proof that all in silico fingerprints satisfying the stated definition are found using our approach.Results: The presented computational approach is implemented in an integrated high-performance computing (HPC) software tool for oligonucleotide fingerprint identification termed TOFI. We employed TOFI to identify in silico DNA fingerprints for several bacteria and plasmid sequences, which were then experimentally evaluated as potential probes for microarray-based diagnostic assays. Results and analysis of approximately 150 in silico DNA fingerprints for Yersinia pestis and 250 fingerprints for Francisella tularensis are presented.Availability: The implemented algorithm is available upon request.Contact: jaques.reifman@us.army.mil.
Non‐invasive evaluation of hair interior morphology by X‐ray microscope
Authors: KIM Beom Joon , KWON Oh Sang , PARK Won Seok , YOUN Hwa Shik , CHOI Chong Won , KIM Kyu Han , EUN Hee Chul 
Published: October 2006

ABSTRACTLots of trials have been performed to obtain better microscopic images of hair structure. Although scanning electron microscopy (SEM) and transmission electron microscopy (TEM) provide detailed images of hair, artificial processing may modify the original images during sample preparation. To overcome this limitation, we applied newly‐developed X‐ray microscopy with an 80–100 nm spatial resolution to produce a detailed view of the morphological change of hair interior. This X‐ray microscopy permits us to penetrate a hair shaft without any artificial change and also provides precise images of hair interior with fine resolution. We evaluated the interior morphological change of Japanese standard hair tress No. 8 by various treatments such as ultraviolet (UV) irradiation, heating, hair dyeing, decolorizing bleaching agents and permanent waving. Internal morphological images were relatively similar in both heated and UV‐irradiated hair. They revealed coarsening of cuticles and dehydration of cortex and medulla. When compared with TEM, X‐ray microscopy provides more intact images in the cuticle and may be a useful tool in observing fine cracks of hair cortex. Additionally, X‐ray images were intact and not influenced by any processing procedures. In observing the external and internal structure of hair, its resolution seems to be somewhat lesser than TEM and there are also several remaining weaknesses to be improved. Hopefully, forthcoming technology will solve these problems in the near future.
Case of acrodermatitis continua accompanied by psoriatic arthritis
Authors: JO Seong Jin , PARK Je Young , YOON Hyun Sun , YOUN Jai Il 
Published: October 2006

ABSTRACTAcrodermatitis continua of Hallopeau (ACH) is a rare chronic pustular eruption that predominantly involves the fingertips. The characterization of this disease has been confused. Some have considered it as a separate entity while others as a variant of pustular psoriasis. The presented patient simultaneously had ACH and joint lesions which were diagnosed as psoriatic arthritis. We believe that because ACH may be accompanied by psoriatic arthritis, as in this case, it could be evidence that it is a variant of psoriasis.
Urticarial vasculitis appearing in the progression of systemic sclerosis
Authors: KATO Yoko , AOKI Mikako , KAWANA Seiji 
Published: October 2006

ABSTRACTWe report a case of urticarial vasculitis that appeared during the course of limited cutaneous systemic sclerosis. The urticarial lesions responded to systemic administration of prednisolone. After the appearance of urticarial vasculitis, the progression of scleroderma in distal sites of her elbow and knee joint became apparent. We consider this case to be consistent with limited cutaneous systemic sclerosis. The patient started treatment with prednisolone and her edema as well as scleroderma softened gradually. We analyzed, by immunohistochemistry, the number of tryptase‐positive mast cells of this case in the lesions of urticarial vasculitis as well as systemic sclerosis. The number of tryptase‐positive mast cells in the lesions of urticarial vasculitis as well as systemic sclerosis was significantly increased compared to normal skin (P < 0.05 and P < 0.005, respectively). We demonstrate that, in the present case, mast cells might be involved in both courses of urticarial vasculitis and systemic sclerosis as a common factor.
Necrobiotic xanthogranuloma of the nose without paraproteinemia
Authors: KUNIKATA Nagisa , KIKUCHI Katsuko , HASHIMOTO Akira , TAGAMI Hachiro 
Published: October 2006

ABSTRACTWe report a 65‐year‐old Japanese woman who presented with a nodule on the nose near the left eye. Histological examination of the totally resected lesion revealed the typical features of necrobiotic xanthogranuloma (NXG). However, her laboratory investigation revealed no paraproteinemia. We believe that the present case represents a cutaneous variant of NXG without accompaniment of paraproteinemia or any systemic involvement.
The PKA‐CREB system encoded by the honeybee genome
Authors: Eisenhardt D. , Kühn C. , Leboulle G. 
Published: October 2006

AbstractThe cAMP‐dependent kinase (PKA) plays a crucial part in long‐term memory formation in the honeybee (Apis mellifera). One of the putative substrates of the PKA activity is the cAMP response element binding protein (CREB), a transcription factor in the bZIP protein family. We searched the honeybee genome to characterize genes from the CREB/CREM and the PKA families. We identified two genes that encode regulatory subunits and three genes encode catalytic subunits of PKA. Eight genes code for bZIP proteins, but only one gene was found that encodes a member of the CREB/CREM family. The phylogenetic relationship of these genes was analysed with their Drosophila and human counterparts.