bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyclonal chemoprotection against temozolomide in a large-animal model of drug resistance gene therapy
Authors: Neff Tobias , Beard Brian C. , Peterson Laura J. , Anandakumar Ponni , Thompson Jesse , Kiem Hans-Peter 
Published: October 2004

AbstractIncorporation of drug resistance genes into gene vectors has 2 important roles in stem cell gene therapy: increasing the proportion of gene-corrected cells in vivo (ie, in vivo selection) and marrow protection to permit higher or more tightly spaced doses of chemotherapy in the treatment of malignant diseases. We studied in a clinically relevant canine model of gene therapy the P140K mutant of the drug resistance gene methylguanine methyltransferase (MGMT), which encodes a DNA-repair enzyme that confers resistance to the combination of the MGMT inhibitor O6-benzylguanine (O6BG) and nitrosourea drugs such as carmustine and methylating agents such as temozolomide. Two dogs received MGMT(P140K)–transduced autologous CD34+-selected cells. After stable engraftment, gene marking in granulocytes was between 3% and 16% in the 2 animals, respectively. Repeated administration of O6BG and temozolomide resulted in a multilineage increase in gene-modified repopulating cells with marking levels of greater than 98% in granulocytes. MGMT(P140K) overexpression prevented the substantial myelosuppression normally associated with this drug combination. Importantly, hematopoiesis remained polyclonal throughout the course of the study. Extrahematopoietic toxicity was minimal, and no signs of myelodysplasia or leukemia were detected. These large-animal data support the evaluation of MGMT(P140K) in conjunction with O6BG and temozolomide in clinical trials.
G-CSF and IL-8 for early diagnosis of sepsis in neonates and critically ill children – safety and cost effectiveness of a new laboratory prediction model: study protocol of a randomized controlled trial [ISRCTN91123847]
Authors: Horisberger Thomas , Harbarth Stephan , Nadal David , Baenziger Oskar , Fischer Joachim E 
Published: October 2004

Abstract
Introduction
Bacterial infection represents a serious risk in neonates and critically ill paediatric patients. Current clinical practice is characterized by frequent antibiotic treatment despite low incidence of true infection. However, some patients escape early diagnosis and progress to septic shock. Many new markers, including cytokines, have been suggested to improve decision making, but the clinical efficacy of these techniques remains uncertain. Therefore, we will test the clinical efficacy of a previously validated diagnostic strategy to reduce antibiotic usage and nosocomial infection related morbidity.

Methods
All patients admitted to the multidisciplinary neonatal and paediatric intensive care unit of a university children's hospital will be included. Patients will be allocated either to routine sepsis work up or to the intervention strategy with additional cytokine measurements. Physicians will be requested to estimate the pre-test probability of sepsis and pneumonia at initial suspicion. In the treatment arm, physicians will receive raw cytokine results, the likelihood ratio and the updated post-test probability. A high post-test probability will suggest that immediate initiation of antibiotic treatment is appropriate, whereas a low post-test probability will be supportive of watchful waiting or discontinuing prophylactic empirical therapy. Physicians may overrule the suggestions resulting from the post-test probability.

Conclusion
This trial will ascertain the clinical efficacy of introducing new diagnostic strategies consisting of pre-test probability estimate, novel laboratory markers, and computer-generated post-test probability in infectious disease work up in critically ill newborns and children.
Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum
Authors: Huang Jinling , Mullapudi Nandita , Lancto Cheryl A , Scott Marla , Abrahamsen Mitchell S , Kissinger Jessica C 
Published: October 2004

Abstract
Background
The apicomplexan parasite Cryptosporidium parvum is an emerging pathogen capable of causing illness in humans and other animals and death in immunocompromised individuals. No effective treatment is available and the genome sequence has recently been completed. This parasite differs from other apicomplexans in its lack of a plastid organelle, the apicoplast. Gene transfer, either intracellular from an endosymbiont/donor organelle or horizontal from another organism, can provide evidence of a previous endosymbiotic relationship and/or alter the genetic repertoire of the host organism. Given the importance of gene transfers in eukaryotic evolution and the potential implications for chemotherapy, it is important to identify the complement of transferred genes in Cryptosporidium.

Results
We have identified 31 genes of likely plastid/endosymbiont (n = 7) or prokaryotic (n = 24) origin using a phylogenomic approach. The findings support the hypothesis that Cryptosporidium evolved from a plastid-containing lineage and subsequently lost its apicoplast during evolution. Expression analyses of candidate genes of algal and eubacterial origin show that these genes are expressed and developmentally regulated during the life cycle of C. parvum.

Conclusions
Cryptosporidium is the recipient of a large number of transferred genes, many of which are not shared by other apicomplexan parasites. Genes transferred from distant phylogenetic sources, such as eubacteria, may be potential targets for therapeutic drugs owing to their phylogenetic distance or the lack of homologs in the host. The successful integration and expression of the transferred genes in this genome has changed the genetic and metabolic repertoire of the parasite.
Genomic Expansion Across the Albumin Gene Family on Human Chromosome 4q Is Directional
Authors: Nishio Hitomi , Hamdi Hamdi K. , Dugaiczyk Achilles 
Published: October 2004

AbstractThe albumin gene family arose in a series of duplication events which gave rise to symmetry in its structure. The four genes are tandemly linked on human chromosome 4q in the order: 5′ ALB-5′ AFP-5′ ALF-5′ DBP-centromere, and their introns display a symmetrical and repetitive pattern that is shared by members of the gene family. These repetitive motifs provide an internal reference, allowing observations of evolutionary changes within a single line (human) of evolutionary descent. The four genes and three intergenic regions between them increase in size as they get closer to the centromere. An invasion by multiple repetitive DNA elements may account, in part, for this expansion.
Plasmin Produces an E-Cadherin Fragment That Stimulates Cancer Cell Invasion
Authors: Ryniers Filip , Stove Christophe , Goethals Marc , Brackenier Liesbeth , Noë Veerle , Bracke Marc , Vandekerckhove Joël , Mareel Marc , Bruyneel Erik 
Published: October 2004

AbstractMatrix metalloproteases from the cell surface cleave an 80 kDa Ecadherin fragment (sECAD) that induces invasion of cancer cells into collagen type I and inhibits cellular aggregation. Conditioned media from MDCKts.srcCl2 cells at 40 C and 35 C, PCm.src5 and COLO-16 cells at 37 C contained spontaneously released sECAD; these 48 h old conditioned media were capable of inhibiting Ecadherin functions in a paracrine way. Here we show direct cleavage of the extracellular domain of Ecadherin by the serine protease plasmin. sECAD released by plasmin inhibits Ecadherin functions as evidenced by induction of invasion into collagen type I and inhibition of cellular aggregation. This functional inhibition by sECAD was reversed by aprotinin or by immunoadsorption on protein Sepharose 4 fast flow beads with antibodies against the extracellular part of Ecadherin. Our results demonstrate that plasmin produces extracellular Ecadherin fragments which regulate Ecadherin function in cells containing an intact Ecadherin/ catenin complex.
Interactions of Nitric Oxide and Peroxynitrite with Low-Density Lipoprotein
Authors: Rubbo H. , Trostchansky A. , Botti H. , Batthyány C. 
Published: October 2004

AbstractNitric oxide (NO) is a free radical species that diffuses and concentrates in the hydrophobic core of lowdensity lipoprotein (LDL) to serve as a potent inhibitor of lipid oxidation processes. Peroxynitrite (PN), the product of the diffusionlimited reaction between NO and superoxide (O2), represents a relevant mediator of oxidative modifications in LDL. The focus of this review is the analysis of interactions between NO and PN and its secondary reactions with oxygen radicals on LDL oxidation, which are relevant in the development of the early steps as well as progression of atherosclerosis. We propose that the balance between rates of PN and NO production, which greatly depends on oxidative stress processes within the vascular wall, will critically determine the final extent of oxidative LDL modifications leading or not to scavenger receptormediated LDL uptake and foam cell formation.
Analysis of the Structural Determinants for RNA Binding of the Human Protein AUF1/hnRNP D
Authors: Moraes Karen C.M. , Lee Wen Hwa , Kobarg Jörg 
Published: October 2004

AbstractThe protein AUF1/hnRNP D was one of the first factors identified that binds to the AUrich region of certain mRNAs and mediates their fast degradation. Here we describe experiments to address the structural determinants for the binding of AUF1 to the RNA by combining comparative molecular modeling with gel shift assays. From our model of the RNA binding region of AUF1 we predicted that it interacts with RNA predominantly through stacking interactions that do not provide basespecific recognition. Only two RNA positions bound by AUF1 show base preferences: one for pyrimidine bases and the second for a conserved adenine residue. Gel shift assays with a panel of RNA oligonucleotides largely confirmed these modelbased binding determinants. An alignment with proteins of the hnRNP family demonstrated that the amino acids involved in the stacking interactions are conserved whereas those that confer a basespecific recognition in AUF1 are variable.
Epoxysuccinyl Peptide-Derived Cathepsin B Inhibitors: Modulating Membrane Permeability by Conjugation with the C-Terminal Heptapeptide Segment of Penetratin
Authors: Schaschke Norbert , Deluca Dominga , Assfalg-Machleidt Irmgard , Höhneke Clara , Sommerhoff Christian P. , Machleidt Werner 
Published: October 2004

Abstract
Besides its physiological role in lysosomal protein
breakdown, extralysosomal cathepsin B has recently
been implicated in apoptotic cell death. Highly specific
irreversible cathepsin B inhibitors that are readily cellpermeant
should be useful tools to elucidate the effects
of cathepsin B in the cytosol. We have covalently
functionalised the poorly cellpermeant epoxysuccinyl
based cathepsin B inhibitor [RGlyGlyLeu(2S,
3S)tEpsLeuProOH; R=OMe] with the Cterminal
heptapeptide segment of penetratin (R=AhxArg
ArgNleLysTrpLysLysNH2). The high inhibitory potency
and selectivity for cathepsin B versus cathepsin
L of the parent compound was not affected by the conjugation
with the penetratin heptapeptide. The conjugate
was shown to efficiently penetrate into MCF-7
cells as an active inhibitor, thereby circumventing an
intracellular activation step that is required by other inhibitors,
such as the prodruglike epoxysuccinyl peptides
E64d and CA074Me.
Muscarinic Toxin-Like Proteins from Taiwan Banded Krait (Bungarus multicinctus) Venom: Purification, Characterization and Gene Organization
Authors: Chung C. , Wu B.-N. , Yang C.-C. , Chang L.-S. 
Published: October 2004

AbstractTwo novel proteins, BM8 and BM14, were isolated from Bungarus multicinctus (Taiwan banded krait) venom using the combination of chromatography on a SPSephadex C-25 column and a reversephase HPLC column. Both proteins contained 82 amino acid residues including 10 cysteine residues, but there were two amino acid substitutions at positions 37 and 38 (Glu37Ala38 in BM8; Lys37Lys38 in BM14). CD spectra and acrylamide quenching studies revealed that the gross conformation of BM8 and BM14 differed. In contrast to BM8, BM14 inhibited the binding of [3H]quinuclidinyl benzilate to the M2 muscarinic acetylcholine (mAchR) receptor subtype. Trinitrophenylation of Lys residues abolished the mAchRbinding activity of BM14, indicating that the Lys substitutions at positions 37 and 38 played a crucial role in the activity of BM14. The genomic DNA encoding the precursor of BM14 was amplified by PCR. The gene shared virtually identical structural organization with αneurotoxin and cardiotoxin genes. The intron sequences of these genes shared a sequence identity up to 84%, but the proteincoding regions were highly variable. These results suggest that BM8, BM14, neurotoxins and cardiotoxins may have originated from a common ancestor, and the evolution of snake venom proteins shows a tendency to diversify their functions.
An Efficient Method for the Preparation of Long Heteroduplex DNA as Substrate for Mismatch Repair by the Escherichia coli MutHLS System
Authors: Thomas E. , Pingoud A. , Friedhoff P. 
Published: October 2004

AbstractWe present a method that allows preparing long DNA containing defined mismatches without the use of gel electrophoretic or chromatographic purification steps. The preparation starts with the synthesis of two PCR products, which are identical except for those positions that will later form the mismatches. One of the PCR primers must be 5phosphorylated, such that in two separate reactions two PCR products are obtained, which are 5phosphorylated in one strand. After removal of the phosphorylated strands by λexonuclease, the resulting single strands are hybridized to form the mismatchcontaining heteroduplex. The application of this procedure is demonstrated for the analysis of the Escherichia coli MutHLS system.
Amylin-Induced Cytotoxicity Is Associated with Activation of Caspase-3 and MAP Kinases
Authors: Rumora L. , Hadzija M. , Bariic K. , Maysinger D. , Grubiic T. Zanic 
Published: October 2004

AbstractNanomolar concentrations of human amylin promote death of RINm5F cells in a time and concentrationdependent manner. Morphological changes of chromatin integrity suggest that cells are predominantly undergoing apoptosis. Human amylin induces significant activation of caspase-3 and strong and sustained phosphorylation of stressactivated protein kinases, cJun Nterminal kinase (JNK) and p38, that precedes cell death. Extracellular signalregulated kinase (ERK) activation was not concomitant with JNK and/or p38 activation. Activation of caspase-3 and mitogenactivated protein kinases (MAPKs) was detected by Western blot analysis. Addition of the MEK1 inhibitor PD 98059 had no effect on amylininduced apoptosis, suggesting that ERK activation does not play a role in this apoptotic scenario. A correlative inhibition of JNK activation by the immunosuppressive drug FK506, as well as a selective inhibition of p38 MAPK activation by SB 203580, significantly suppressed procaspase-3 processing and the extent of amylininduced cell death. Moreover, simultaneous pretreatment with both FK506 and SB 203580, or with the caspase-3 inhibitor AcDEVDCHO alone, almost completely abolished procaspase-3 processing and cell death. Thus, our results suggest that amylininduced apoptosis proceeds through sustained activation of JNK and p38 MAPK followed by caspase-3 activation.
Properties of Baculovirus Particles Displaying GFP Analyzed by Fluorescence Correlation Spectroscopy
Authors: Toivola J. , Ojala K. , Michel P.O. , Vuento M. , Oker-Blom C. 
Published: October 2004

Abstract
Recombinant baculovirus particles displaying green
fluorescent protein (GFP) fused to the major envelope
glycoprotein gp64 of the Autographa californica multicapsid
nucleopolyhedrovirus (AcMNPV) were characterized
by fluorescence correlation spectroscopy
(FCS). FCS detected Brownian motion of single, intact
recombinant baculovirus display particles with a diffusion
coefficient (D) of (2.89±0.74)10 8 cm2s 1 and
an apparent hydrodynamic radius of 83.35±21.22 nm.
In the presence of sodium dodecyl sulfate (SDS), Triton
X-100, and octylglucoside, the diffusion time was
reduced to the 0.2 ms range (D = 7.5710 7 cm2s 1),
showing that the fusion proteins were anchored in the
viral envelope. This allowed for a calculation of the
number of single gp64 fusion proteins incorporated in
the viral membrane. A mean value of 3.2 fluorescent
proteins per virus particle was obtained. Our results
show that FCS is the method of choice for studying
enveloped viruses such as a display virus with one
component being GFP.
Incorporation of 13C-Labeled Coniferyl Alcohol into Developing Ginkgo biloba L. Lignin Revealed by Analytical Pyrolysis and CuO Oxidation in Combination with Isotope Ratio Monitoring-Gas Chromatography-Mass Spectrometry
Authors: Eglinton T. I. , Goñi M. A. , Boon J. J. , Hage E. R. E. van der , Terashima N. , Xie Y. 
Published: October 2004

Summary
A suite of four samples of xylem tissue from Ginkgo (Ginkgo biloba L.) shoots grown in a medium containing
coniferin 13C-labeled at differing side-chain carbon atoms were studied using thermal and chemical
degradation methods in combination with molecular-level isotopic analyses. The aims of the study
were threefold: (1) to verify conclusions drawn from Nuclear Magnetic Resonance experiments previously
performed on the same tissue samples, (2) to investigate degradation mechanisms and (3) to quantify
the proportion of labeled material in each sample.
Isotopic analysis of specific degradation products revealed the presence of the label exclusively within
lignin-derived (phenolic) products and that the label is retained in its original position on the side-chain.
These two results clearly indicate that there is no “scrambling” of carbon atoms as a result of thermal
or chemical degradation, and thus lend strong support to analytical pyrolysis and chemolysis as
viable approaches for structural investigations of the lignin macromolecule. Indeed, the isotopic enrichment
of specific degradation products provides new evidence for certain types of linkages within the
lignin polymer.
The distribution and isotopic composition of the degradation products also strongly suggest an origin
from newly-formed lignin as opposed to DHP-type products or unreacted substrate. As such, the data
provides added confidence in the selective labeling approach for elucidation of the structure and biosynthesis
of lignin. Isotopic mass balance calculations reveal that certain pyrolysis and CuO oxidation products
show enhanced labeling which may be indicative of preferential incorporation of their specific precursors
into the growing lignin macromolecule or heterogeneous lignin deposition.
Atomic Force Microscopy (AFM) Investigation of Langmuir-Blodgett (LB) Films of Sugar Cane Bagasse Lignin
Authors: Constantino C. J. L. , Dhanabalan A. , Cotta M. A. , Pereira-da-Silva M. A. , Curvelo A. A. S. , Oliveira O. N. 
Published: October 2004

Summary
The morphological features of Langmuir-Blodgett (LB) films of pure lignin extracted from sugar cane
bagasse and composites of lignin and cadmium stearate have been investigated using atomic force
microscopy (AFM). Results indicated that despite the non-amphiphilic nature of lignin and associated
relatively poor stability and transferability of the lignin monolayer, the surface of the film is smooth at
the micron level and comparable to that of LB films from typical amphiphilic compounds. Distinct
domain structures from lignin and cadmium stearate could be visualized in the composite LB film
even in one monolayer thick LB films. The mean surface roughness increases with increasing numbers of
layers.
Monitoring of Lignin and Hemicelluloses in Spent Cooking Liquor during Kraft Delignification
Authors: Bikova T. , Klevinska V. , Treimanis A. 
Published: October 2004

Summary
A direct and rapid method for determining the average molecular weight (MW) and content of lignin and
hemicelluloses in spent cooking liquor by high performance size-exclusion chromatography (HPSEC)
using a cartridge glass column and 2.5 mM NaOH as an eluent was developed. A Uv290 detector in line
with a RI detector was applied to characterise lignin and hemicelluloses, respectively, from liquor during
the kraft cooking of grey and black alder wood. During the main delignification stage, the concentration
of high-MW wood components in liquor changed through the maximum. The MW values of hemicelluloses
in the liquor decreased to DPn = 30 ± 5 and DPw = 55 ± 5. The M̄
n and M̄
w of lignin in spent
kraft cooking liquor during the main and final delignification stages did not exceed 3000 and 5000, respectively.
Preparation of Wood with Thermoplastic Properties, Part 1. Classical Synthesis
Authors: Timar Maria Cristina , Mihai Maria Daniela , Maher Kevin , Irle Mark 
Published: October 2004

Summary
Aspen wood (Populus tremula) as sawdust was chemically modified through a two-step procedure: esterification
with maleic anhydride and subsequent oligoesterification with glycidyl methacrylate and maleic
anhydride. Chemical analyses and infra-red spectroscopy revealed the differences in the chemical
composition and structure of wood as a result of this treatment. These changes were also reflected by a
hygroscopicity test and thermal analyses such as thermogravimetry and thermomechanical analysis. The
esterified wood showed an increased hygroscopicity and a decreased thermal stability compared to
unmodified wood. In contrast, the oligoesterified wood demonstrated a reduced hygroscopicity and a
comparable thermal stability up to about 200°C. The thermomechanical analysis of oligoesterified wood
clearly showed a significant softening phenomenon in the range 80–140°C, a direct evidence of the thermoplastic
properties gained by this chemical modification.
Confirmation of the Presence of Formaldehyde and N-(Methylene)morpholinium Cations as Reactive Species in the Cellulose/NMMO/Water System by Trapping Reactions
Authors: Potthast A. , Rosenau T. , Kosma P. , Chen C.-L. , Gratzl J. S. 
Published: October 2004

Summary
The presence of formaldehyde (4) in solutions of cellulose in N-methylmorpholine-N-oxide (NMMO, 1)
has been shown by trapping formaldehyde as dimedone adduct 8 in a two-phase system. o-Dichlorobenzene
was used as an inert solvent to extract the trapping product as soon as it had formed.
Morpholine is a degradation product of NMMO and is always present in systems containing NMMO.
Formaldehyde can react with morpholine to form an intermediate carbenium-iminium ion, N-(methylene)
morpholinium (6). The occurrence of 6 in the system cellulose/NMMO was demonstrated by trapping
this intermediate in a Mannich type reaction with 2-acetonaphthone (9). Both formaldehyde and N-(methylene)morpholinium cations are highly reactive species readily undergoing further reactions with
nucleophiles. These processes might contribute to the observed discoloration of the reaction mixture, and
might also be responsible for the decomposition of NMMO that is inducible by carbenium-iminium ions.
Removal of Phenolic Hydroxyl Groups in Lignin Model Compounds and Its Effect on Photostability
Authors: Hu Thomas Q. , Cairns Graham R. , James Brian R. 
Published: October 2004

Summary
The phenolic hydroxyl groups in the lignin model compounds, 2-methoxy-4-propylphenol and 4-hydroxy-3-methoxyacetophenone, were removed by first converting the hydroxyl groups to the trifluoromethanesulfonates
(triflates) and then cleaving the triflate substituents via catalytic hydrogen transfer.
The products, 1-methoxy-3-propylbenzene and 3-methoxyacetophenone, were characterized by 1H and
13C NMR, mass spectrometry and elemental analyses. The effect of the removal of the phenolic groups
on the photostability of the model compounds was evaluated by impregnating the compounds into Whatman
filter paper sheets, and subjecting them to an accelerated yellowing experiment in a UV chamber.
The removal of the phenolic groups resulted in a significant yellowing inhibition, with a higher photostabilizing
effect than methylation or acetylation of the hydroxyl, particularly for the model compound
without an α-carbonyl group.