bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patients with adenosine deaminase deficiency surviving after hematopoietic stem cell transplantation are at high risk of CNS complications
Authors: Hönig Manfred , Albert Michael H. , Schulz Ansgar , Sparber-Sauer Monika , Schütz Catharina , Belohradsky Bernd , Güngör Tayfun , Rojewski Markus T. , Bode Harald , Pannicke Ulrich , Lippold Dominique , Schwarz Klaus , Debatin Klaus-Michael , Hershfield Michael S. , Friedrich Wilhelm 
Published: December 2006

AbstractAdenosine deaminase (ADA) deficiency is a systemic metabolic disease that causes an autosomal recessive variant of severe combined immunodeficiency (SCID) and less consistently other complications including neurologic abnormalities. Hematopoietic stem cell transplantation (HSCT) is able to correct the immunodeficiency, whereas control of nonimmunologic complications has not been extensively explored. We applied HSCT in 15 ADA-deficient patients consecutively treated at our institutions since 1982 and analyzed long-term outcome. Seven patients received transplants without conditioning from HLA-matched family donors (MFDs); the other 8 patients received conditioning and were given transplants either from HLA-mismatched family donors (MMFDs; n = 6) or from matched unrelated donors (MUDs; n = 2). At a mean follow-up period of 12 years (range, 4-22 years), 12 patients are alive with stable and complete immune reconstitution (7 of 7 after MFD, 4 of 6 after MMFD, and 1 of 2 after MUD transplantation). Six of 12 surviving patients show marked neurologic abnormalities, which include mental retardation, motor dysfunction, and sensorineural hearing deficit. We were unable to identify disease or transplantation-related factors correlating with this divergent neurologic outcome. The high rate of neurologic abnormalities observed in long-term surviving patients with ADA deficiency indicates that HSCT commonly fails to control CNS complications in this metabolic disease.
Identification of potential CepR regulated genes using a cep box motif-based search of the Burkholderia cenocepacia genome
Authors: Chambers Catherine E , Lutter Erika I , Visser Michelle B , Law Peggy PY , Sokol Pamela A 
Published: December 2006

Abstract

Background
The Burkholderia cenocepacia CepIR quorum sensing system has been shown to positively and negatively regulate genes involved in siderophore production, protease expression, motility, biofilm formation and virulence. In this study, two approaches were used to identify genes regulated by the CepIR quorum sensing system. Transposon mutagenesis was used to create lacZ promoter fusions in a cepI mutant that were screened for differential expression in the presence of N-acylhomoserine lactones. A bioinformatics approach was used to screen the B. cenocepacia J2315 genome for CepR binding site motifs.

Results
Four positively regulated and two negatively regulated genes were identified by transposon mutagenesis including genes potentially involved in iron transport and virulence. The promoter regions of selected CepR regulated genes and site directed mutagenesis of the cepI promoter were used to predict a consensus cep box sequence for CepR binding. The first-generation consensus sequence for the cep box was used to identify putative cep boxes in the genome sequence. Eight potential CepR regulated genes were chosen and the expression of their promoters analyzed. Six of the eight were shown to be regulated by CepR. A second generation motif was created from the promoters of these six genes in combination with the promoters of cepI, zmpA, and two of the CepR regulated genes identified by transposon mutagenesis. A search of the B. cenocepacia J2315 genome with the new motif identified 55 cep boxes in 65 promoter regions that may be regulated by CepR.

Conclusion
Using transposon mutagenesis and bioinformatics expression of twelve new genes have been determined to be regulated by the CepIR quorum sensing system. A cep box consensus sequence has been developed based on the predicted cep boxes of ten CepR regulated genes. This consensus cep box has led to the identification of over 50 new genes potentially regulated by the CepIR quorum sensing system.
Tissue microarray analysis reveals a tight correlation between protein expression pattern and progression of esophageal squamous cell carcinoma
Authors: Xue Li-yan , Hu Nan , Song Yong-mei , Zou Shuang-mei , Shou Jian-zhong , Qian Lu-xia , Ren Li-qun , Lin Dong-mei , Tong Tong , He Zu-gen , Zhan Qi-min , Taylor Philip R , Lu Ning 
Published: December 2006

Abstract

Background
The development of esophageal squamous cell carcinoma (ESCC) progresses a multistage process, collectively known as precursor lesions, also called dysplasia (DYS) and carcinoma in situ (CIS), subsequent invasive lesions and final metastasis. In this study, we are interested in investigating the expression of a variety of functional classes of proteins in ESCC and its precursor lesions and characterizing the correlation of these proteins with ESCC malignant progression.

Methods
Fas, FADD, caspase 8, CDC25B, fascin, CK14, CK4, annexin I, laminin-5γ2 and SPARC were analyzed using immunohistochemistry on tissue microarray containing 205 ESCC and 173 adjacent precursor lesions as well as corresponding normal mucosa. To confirm the immunohistochemical results, three proteins, fascin, CK14 and laminin-5γ2, which were overexpressed in ESCC on tissue microarray, were detected in 12 ESCC cell lines by Western blot assay.

Results
In ESCC and its precursor lesions, FADD, CDC25B, fascin, CK14, laminin-5γ2 and SPARC were overexpressed, while Fas, caspase 8, CK4 and annexin I were underexpressed. The abnormalities of these proteins could be classified into different groups in relation to the stages of ESCC development. They were "early" corresponding to mild and moderate DYS with overexpression of fascin, FADD and CDC25B and underexpression of Fas, caspase 8, CK4 and annexin I, "intermediate" to severe DYS and CIS with overexpression of FADD and CK14, and "late" to invasive lesions (ESCC) and to advanced pTNM stage ESCC lesions with overexpression of CK14, laminin-5γ2 and SPARC.

Conclusion
Analyzing the protein expression patterns of Fas, FADD, caspase 8, CDC25B, fascin, CK14, CK4, annexin I, laminin-5γ2 and SPARC would be valuable to develop rational strategies for early detection of lesions at risk in advance as well as for prevention and treatment of ESCC.
Multiplexed expression and screening for recombinant protein production in mammalian cells
Authors: Chapple Susan DJ , Crofts Anna M , Shadbolt S Paul , McCafferty John , Dyson Michael R 
Published: December 2006

Abstract

Background
A variety of approaches to understanding protein structure and function require production of recombinant protein. Mammalian based expression systems have advantages over bacterial systems for certain classes of protein but can be slower and more laborious. Thus the availability of a simple system for production and rapid screening of constructs or conditions for mammalian expression would be of great benefit. To this end we have coupled an efficient recombinant protein production system based on transient transfection in HEK-293 EBNA1 (HEK-293E) suspension cells with a dot blot method allowing pre-screening of proteins expressed in cells in a high throughput manner.

Results
A nested PCR approach was used to clone 21 extracellular domains of mouse receptors as CD4 fusions within a mammalian GATEWAY expression vector system. Following transient transfection, HEK-293E cells grown in 2 ml cultures in 24-deep well blocks showed similar growth kinetics, viability and recombinant protein expression profiles, to those grown in 50 ml shake flask cultures as judged by western blotting. Following optimisation, fluorescent dot blot analysis of transfection supernatants was shown to be a rapid method for analysing protein expression yielding similar results as western blot analysis. Addition of urea enhanced the binding of glycoproteins to a nitrocellulose membrane. A good correlation was observed between the results of a plate based small scale transient transfection dot blot pre-screen and successful purification of proteins expressed at the 50 ml scale.

Conclusion
The combination of small scale multi-well plate culture and dot blotting described here will allow the multiplex analysis of different mammalian expression experiments enabling a faster identification of high yield expression constructs or conditions prior to large scale protein production. The methods for parallel GATEWAY cloning and expression of multiple constructs in cell culture will also be useful for applications such as the generation of receptor protein microarrays.
Expression and function of the OX40/OX40L costimulatory pair during herpes stromal keratitis
Authors: Lepisto Andrew J , Xu Min , Yagita Hideo , Weinberg Andrew D , Hendricks Robert L 
Published: December 2006

AbstractHerpes stromal keratitis (HSK) is an immunopathological disease regulated by Th1 CD4 T cells, which require APC and costimulation within the infected cornea to mediate disease. Recent studies suggest the OX40:OX40 ligand (OX40L) interaction enhances effector cell cytokine secretion at inflammatory sites. OX40+ cells were detected in HSV-1-infected mouse corneas as early as 3 days postinfection (dpi), prior to the onset of HSK, and their frequency increased through 15 dpi, when all mice exhibited severe HSK. OX40L+ cells were first detected at 7 dpi, coincident with the initiation of HSK. It is interesting that the OX40L+ cells did not coexpress MHC Class II or the dendritic cell (DC) marker CD11c. Our findings demonstrate rapid infiltration of activated (OX40+) CD4+ T cells into HSV-1-infected corneas and expression of OX40L on MHC Class II-negative cells but surprisingly, not on MHC Class II+ CD11c+ DC, which are present in the infected corneas and required for HSK. Moreover, neither local nor systemic treatment of mice with a blocking antibody to OX40L or with a blocking fusion protein altered the course of HSK significantly, possibly as a result of a lack of OX40L expression on functional APC.
Estrogen selectively regulates chemokines in murine splenocytes
Authors: Lengi Andrea J , Phillips Rebecca A , Karpuzoglu Ebru , Ahmed S Ansar 
Published: December 2006

AbstractEstrogen has striking effects on immunity and inflammatory autoimmune conditions. One potential mechanism of estrogen-induced regulation of immunity and inflammatory autoimmune conditions is by altering the secretion of chemokines by lymphocytes, an aspect not well addressed thus far. We found that estrogen has marked, but differential, effects on the secretion of chemokines from activated splenocytes. Estrogen treatment significantly increased the secretion of MCP-1, MCP-5, eotaxin, and stromal cell-derived factor 1β from Con A-activated splenocytes when compared with placebo-treated controls, and it had no effects on the levels of RANTES, thymus and activation-regulated chemokine, and keratinocyte-derived chemokine (KC) at 24 h. A kinetic analysis showed that chemokines tended to increase with stimulation time, but only MCP-1 and MCP-5 showed a biological trend of increasing in splenocytes from estrogen-treated mice, and KC was decreased significantly in estrogen-treated splenocytes at 18 h. Estrogen did not affect the protein levels of chemokine receptors CCR1 or CCR2 at 24 h. Estrogen-induced alterations in the levels of MCP-1 and MCP-5 are mediated, in part, by IFN-γ, as estrogen treatment of IFN-γ null mice, unlike wild-type mice, did not up-regulate these chemokines. However, addition of recombinant IFN-γ resulted in markedly increased secretion of MCP-1 and MCP-5 only in the cells derived from estrogen-treated mice. These studies provide novel data indicating that estrogen may promote inflammatory conditions by altering the levels of chemokines, providing evidence for an additional mechanism by which estrogens can regulate inflammation.
Identification of Regions within the F Domain of the Human Estrogen Receptor α that Are Important for Modulating Transactivation and Protein-Protein Interactions
Authors: Koide Akiko , Zhao Changqing , Naganuma Misuzu , Abrams Judith , Deighton-Collins Sarah , Skafar Debra F. , Koide Shohei 
Published: December 2006

AbstractThe estrogen receptor (ER)α is a biologically and clinically important ligand-modulated transcription factor. The F domain of the ERα modulates its functions in a ligand-, promoter-, and cell-specific manner. To identify the region(s) responsible for these functions, we characterized the effects of serial truncations within the F domain. We found that truncating the last 16 residues of the F domain altered the activity of the human ERα (hERα) on an estrogen response element-driven promoter in response to estradiol or 4-hydroxytamoxifen (4-OHT), its sensitivity to overexpression of the coactivator steroid receptor coactivator-1 in mammalian cells, and its interaction with a receptor-interacting domain of the coactivator steroid receptor coactivator-1 or engineered proteins (“monobodies”) that specifically bind to ERα/ligand complexes in a yeast two-hybrid system. Most importantly, the ability of the ER to induce pS2 was reduced in MDA-MB-231 cells stably expressing this truncated ER vs. the wild-type ER. The region includes a distinctive segment (residues 579–584; LQKYYIT) having a high content of bulky and/or hydrophobic amino acids that was previously predicted to adopt a β-strand-like structure. As previously reported, removal of the entire F domain was necessary to eliminate the agonist activity of 4-OHT. In addition, mutation of the vicinal glycine residues between the ligand-binding domain and F domains specifically reduced the 4-OHT-dependent interactions of the hERα ligand-binding domain and F domains with monobodies. These results show that regions within the F domain of the hERα selectively modulate its activity and its interactions with other proteins.
Side Population Analysis Using a Violet-Excited Cell-Permeable DNA Binding Dye
Authors: Telford William G. , Bradford Jolene , Godfrey William , Robey Robert W. , Bates Susan E. 
Published: December 2006

Abstract
Hoechst 33342 side population (SP) analysis is a common method for identifying stem cells in mammalian hematopoietic and nonhematopoietic tissues. Although widely employed for stem cell analysis, this method requires an ultraviolet (UV) laser to excite Hoechst 33342. Flow cytometers equipped with UV sources are not common because of the cost of both the laser and optics that can transmit light UV light. Violet laser sources are inexpensive and are now common fixtures on flow cytometers, but have been previously shown to provide insufficient Hoechst dye excitation for consistent resolution of SP cells. One solution to this problem is to identify additional fluorescent substrates with the same pump specificity as Hoechst 33342, but with better violet excitation characteristics. DyeCycle Violet reagent has emission characteristics similar to those of Hoechst 33342, but with a longer wavelength excitation maxima (369 nm). When this dye is loaded into hematopoietic cells, a sharply resolved side population was also observed, similar in appearance to that seen with Hoechst 33342. Unlike Hoechst SP, DCV SP was similar in appearance with both violet and UV excitation. DCV SP could be inhibited fumitremorgin C, and showed the same membrane pump specificity as Hoechst 33342. Simultaneous immunophenotyping with stem cell markers in mouse bone marrow demonstrated that DCV SP was restricted to the stem cell lineage− Sca-1+ c-kit+ cells population, as is Hoechst SP. Pending confirmation by functional analysis of DCV SP cells, these results suggest that DCV efflux identified approximately the same stem cell population as did Hoechst 33342 efflux. Substituting DCV for Hoechst 33342 in the SP technique may, therefore, allow side population analysis on flow cytometers with violet lasers.
Disclosure of potential conflicts of interest is found at the end of this article.
Improved Human Embryonic Stem Cell Embryoid Body Homogeneity and Cardiomyocyte Differentiation from a Novel V-96 Plate Aggregation System Highlights Interline Variability
Authors: Burridge Paul W. , Anderson David , Priddle Helen , Barbadillo Muñoz Maria D. , Chamberlain Sarah , Allegrucci Cinzia , Young Lorraine E. , Denning Chris 
Published: December 2006

AbstractAlthough all human ESC (hESC) lines have similar morphology, express key pluripotency markers, and can differentiate toward primitive germ layers in vitro, the lineage-specific developmental potential may vary between individual lines. In the current study, four hESC lines were cultured in the same feeder-free conditions to provide a standardized platform for interline analysis. A high-throughput, forced-aggregation system involving centrifugation of defined numbers of hESCs in V-96 plates (V-96FA) was developed to examine formation, growth, and subsequent cardiomyocyte differentiation from &gt;22,000 EBs. Homogeneity of EBs formed by V-96FA in mouse embryo fibroblast-conditioned medium was significantly improved compared with formation in mass culture (p &lt; .02; Levene's test). V-96FA EB formation was successful in all four lines, although significant differences in EB growth were observed during the first 6 days of differentiation (p = .044 to .001; one-way analysis of variance [ANOVA]). Cardiomyocyte differentiation potential also varied; 9.5% ± 0.9%, 6.6% ± 2.4%, 5.2% ± 3.1%, and 1.6% ± 1.0% beating EBs were identified for HUES-7, NOTT2, NOTT1, and BG01, respectively (p = .008; one-way ANOVA). Formation of HUES-7 V-96FA EBs in defined medium containing activin A and basic fibroblast growth factor resulted in 23.6% ± 3.6% beating EBs, representing a 13.1-fold increase relative to mass culture (1.8% ± 0.7%), consistent with an observed 14.8-fold increase in MYH6 (αMHC) expression by real-time polymerase chain reaction. In contrast, no beating areas were derived from NOTT1-EBs and BG01-EBs formed in defined medium. Thus, the V-96FA system highlighted interline variability in EB growth and cardiomyocyte differentiation but, under the test conditions described, identified HUES-7 as a line that can respond to cardiomyogenic stimulation.Disclosure of potential conflicts of interest is found at the end of this article.
Nemaline myopathy caused by absence of α‐skeletal muscle actin
Authors: Nowak Kristen J. , Sewry Caroline A. , Navarro Carmen , Squier Waney , Reina Cristina , Ricoy Jose R. , Jayawant Sandeep S. , Childs Anne‐Marie , Dobbie J. Angus , Appleton Richard E. , Mountford Roger C. , Walker Kendall R. , Clement Sophie , Barois Annie , Muntoni Francesco , Romero Norma B. , Laing Nigel G. 
Published: December 2006

AbstractObjectiveTo investigate seven congenital myopathy patients from six families: one French Gypsy, one Spanish Gypsy, four British Pakistanis, and one British Indian. Three patients required mechanical ventilation from birth, five died before 22 months, one is ventilator‐dependent, but one, at 30 months, is sitting with minimal support. All parents were unaffected.MethodsThe α‐skeletal muscle actin gene (ACTA1) was sequenced. Available muscle biopsies were investigated by standard histological and electron microscopic techniques. The expression of various proteins was determined by immunohistochemistry, western blotting, or both.ResultsThree homozygous ACTA1 null mutations were identified: p.Arg41X in the French patient, p.Tyr364fsX in the Spanish patient, and p.Asp181fsX10 in all five British patients. An absence of α‐skeletal muscle actin protein but presence of α‐cardiac actin was shown in all muscle biopsies examined, with more α‐cardiac actin in the biopsy from the child with the greatest muscle function. Muscle biopsies from all patients exhibited nemaline bodies whereas three also contained zebra bodies.InterpretationThe seven patients have recessive nemaline myopathy caused by absence of α‐skeletal muscle actin. The level of retention of α‐cardiac actin, the skeletal muscle fetal actin isoform, may determine α‐skeletal muscle actin disease severity. This has implications for possible future therapy. Ann Neurol 2006
Simulation and Optimization of an Adiabatic Multi‐Bed Catalytic Reactor for the Oxidation of SO2
Authors: Nodehi A. , Mousavian M. A. 
Published: December 2006

AbstractA software package was developed for the simulation and optimization of a multi‐bed adiabatic reactor for the catalytic oxidation of SO2, using a heterogeneous plug flow model. The orthogonal collocation (OC) technique with up to eight collocation points was used for the solution of a nonlinear, two‐point boundary value differential equation for the catalyst particle, and it was shown that the use of the OC technique with two collocation points can describe the system well. Because of the nonlinear behavior of the effectiveness factor along the bed, optimal catalyst distribution between the beds and corresponding inlet temperatures were determined by two methods, including: the use of (1) intrinsic or (2) actual rate of reaction in the optimization criteria. The results showed that for the second case, the minimum amount of the catalyst can be reached at lower temperatures, the amount of catalyst required is always less, and the number of beds is greater than or equal to that of the first case.
A Highly Regular Hexapod Structure of Lead Sulfide: Solution Synthesis and Raman Spectroscopy
Authors: Zhang Ya‐Hui , Guo Lin , Yin Peng‐Gang , Zhang Rui , Zhang Qi , Yang Shi‐He 
Published: December 2006

AbstractA highly regular hexapod‐like structure of PbS with six symmetric arms has been synthesized by a simple and mild chemical solution route. The hexapod‐like PbS structure was characterized by X‐ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and high‐resolution TEM (HRTEM). The results show that each arm is perpendicular to the other four, and opposite to the last one. The arms are about 0.3–0.6 μm long, which have about 40–60 nm tips and 150–200 nm base. And the arm shows an icicle‐like structure and some clear steps, and grows along 〈100〉 directions. The most possible growth mechanism discussed herein is based on the characterization results. The Raman spectra of the hexapod‐like PbS structure were investigated. The results show that our products are sensitive to the laser and can be photodegraded easily.
Ludwig Pilgrim, a pioneer of colorimetry
Authors: Kuehni Rolf G. 
Published: December 2006

AbstractColorimetry derives from the early efforts of Newton, Young, Maxwell, and Helmholtz. In 1901 Pilgrim published a paper in which he quantitatively described a colorimetric system both in trichromatic as well as opponent color format. He appears to be the first to have offered a depiction of the cone‐shaped surface of spectral vectors in the space of color fundamentals. © 2006 Wiley Periodicals, Inc. Col Res Appl, 32, 5–10, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/col.20288
Texture transformations and orientational properties of lyotropic nematics in magnetic field
Authors: Nesrullajev Arif , Oktik Şener 
Published: December 2006

AbstractDynamics of changes of the morphological properties and processes of orientation in lyotropic nematic mesophases by application of external magnetic field have been investigated in detail. The dynamics of changes of the optical birefringence values in nematic‐calamitic mesophase vs. time has been determined. The optical mappings of nonequilibrium magnetically induced textures, which have been observed for this mesophase during orientational process, and changes of birefringence vs. time are presented. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)