bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composition of the blood sampled from surgical drainage after joint arthroplasty: quality of return
Authors: Sinardi Daniele , Marino Anatonella , Chillemi Sergio , Irrera Massimo , Labruto Guglielmo , Mondello Epifanio 
Published: January 2005

BACKGROUND:  The quality of blood obtained with a device for postoperative blood drainage and autotransfusion (Bellovac‐ABT, Astra Tech AB) was investigated in 50 patients who underwent total hip replacement (THR) or total knee replacement (TKR) surgeries.STUDY DESIGN AND METHODS:  The Bellovac‐ABT drainage set was inserted and blood collection began after skin closure (THR) or 15 minutes after tourniquet deflation (TKR). A collecting bag stayed in place for less than 6 hours. The product was then returned after sedimentation and discard of supernatant, without anticoagulants.RESULTS:  Blood returned with the Bellovac‐ABT had optimal hemoglobin levels and red blood cell (RBC) counts; the low platelet count reduced the risk of disseminated intravascular coagulation. Inertia of materials maintained acceptable values of C‐reactive protein, whereas cytokines and complement split products rose rapidly. Higher concentrations of adenosine triphosphate and 2,3‐diphosphoglycerate than in circulating blood suggested a normal RBC metabolism. No adverse reactions were observed in any participants.CONCLUSION:  Because of its simplicity and safety, the Bellovac‐ABT autologous blood transfusion system is recommended in THR or TKR without joint infection or malignancy.
Low propidium iodide intensity in flow cytometric white blood cell counting as a marker of cell destruction?
Authors: Wagner Thomas , Guber Sylvia E. , Stubenrauch Maria‐Luise , Lanzer Gerhard , Neumueller Josef 
Published: January 2005

BACKGROUND:  Residual white blood cells (WBC) in filtered blood products were investigated with flow cytometry. Frequently two distinct populations with different propidium iodide (PI) intensities can be found. The aim of this study was to specify a population with low PI intensity and discuss it as a marker of ongoing cell destruction and their possible impact on cytomegalovirus safety.STUDY DESIGN AND METHODS:  Buffy coat–depleted red blood cells were filtered with an in‐line filtration set (LCR5, MacoPharma) after 4 hours (LCR5/4 hr) and 16 hours (LCR5/16 hr) of storage, and whole blood was filtered with a whole‐blood filtration set (LST1, MacoPharma [LST1/4 hr]). The population with low PI intensity was sorted with a flow cytometer and prepared for transmission electron microscopy.RESULTS:  The absolute count obtained in the low‐PI‐intensity area before filtration was significantly different comparing LCR5/4 hr (11.5 × 106 ± 6.84 × 106 and 0.12 × 106 ± 0.1 × 106/unit) and LCR5/16 hr (69.3 ± 42.12 and 0.06 ± 0.05; p < 0.002). By use of LST1/4 hr no difference was found compared to LCR5/4 hr after filtration (0.12 ± 0.09 vs. 0.12 ± 0.1), but a significant difference was found when comparing the results before filtration (1.25 ± 0.41 vs. 11.5 ± 6.84; p < 0.02). Electron microscopy revealed that the sorted population consisted of predominantly cell and nuclear fragments.CONCLUSIONS:  Events found in the low‐PI‐intensity area are not WBCs but partially degraded DNA coming from ongoing cell destruction during extended storage. Our results provide evidence that the absolute count of events found in the low‐PI‐intensity area can be used as a semiquantitative marker of WBC destruction.
Combined Inactivation and Expression Strategy To Study Gene Function under Physiological Conditions: Application to Identification of NewEscherichia coliAdhesins
Authors: Roux Agnès , Beloin Christophe , Ghigo Jean-Marc 
Published: January 2005

ABSTRACTIn bacteria, whereas disruption methods have been improved recently, the use of plasmid complementation strategies are still subject to limitations, such as cloning difficulties, nonphysiological levels of gene expression, or a requirement for antibiotics as plasmid selection pressure. Moreover, because of the pleiotropic modifications of cell physiology often induced by plasmid-based complementation, these strategies may introduce biases when biological process such as adhesion or biofilm formation are studied. We developed a plasmid-free approach that combines the lambda-red linear DNA recombination method with site-directed insertion of a repression and expression (RExBAD) cassette which places a functional pBAD promoter upstream of a target gene. We showed that this method permits both inactivation and modulation of mostEscherichia coligene expression, including expression of toxin and essential genes. We used this strategy to study adhesion and bacterial biofilms by placing the RExBAD cassette in front of thetraoperon, encoding the DNA transfer and pilus genes on the F conjugative plasmid, and in front offlu, the antigen 43 (Ag43) autotransporter adhesin-encoding gene. In silico analysis revealed the existence of 10 genes with homology to the Ag43 gene that were good candidates for genes that encode putative new adhesins inE. coli. We used the RExBAD strategy to study these genes and demonstrated that induction of expression of four of them is associated with adhesion ofE. colito abiotic surfaces. The potential use of the RExBAD approach to study the function of cryptic or uncharacterized genes in large-scale postgenomic functional analyses is discussed.
The
Enterococcus faecalis
SigV Protein Is an Extracytoplasmic Function Sigma Factor Contributing to Survival following Heat, Acid, and Ethanol Treatments
Authors: Benachour Abdellah , Muller Cécile , Dabrowski-Coton Monika , Le Breton Yoann , Giard Jean-Christophe , Rincé Alain , Auffray Yanick , Hartke Axel 
Published: January 2005

ABSTRACT

Analysis of the genome sequence of
Enterococcus faecalis
allowed the identification of two genes whose protein products showed 33 and 34% identity with those of
sigV
and
yrhM
of
Bacillus subtilis
, respectively. These genes, named
sigV
and
rsiV
, are predicted to encode members of the extracytoplasmic function subfamily of eubacterial RNA polymerase sigma and anti-sigma factors, respectively. This group of sigma factors has been shown to regulate gene expression in response to stress conditions.
sigV
and
rsiV
were shown to be under the control of the same promoter. The transcriptional start site was determined, and the 1.5-kb mRNA transcript was shown to be overexpressed under glucose and complete starvation, as well as under physicochemical treatments. Three mutants, affected in
sigV
,
rsiV
, and both genes, were constructed by double-crossover recombination within the genome of
E
.
faecalis
strain JH2-2. Compared with the wild type and the
rsiV
mutant, the
sigV
mutants were more susceptible to heat shock, acid, and ethanol treatments and displayed decreased survival during long-term starvation. A nisin-inducible
sigV
gene construction used in complementation assays restored the wild phenotype of the
sigV
mutants, confirming the involvement of SigV in the heat shock, ethanol, and acid stress responses. Northern blot analysis carried out with the three mutant strains revealed the inhibition of
sigV
expression by the related anti-sigma factor gene
rsiV
. In addition, putative candidates of the
sigV
regulon determined by computer search for the
sigV
promoter sequence were analyzed.
Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in
Anabaena
sp. Strain PCC 7120
Authors: Huang Guocun , Fan Qing , Lechno-Yossef Sigal , Wojciuch Elizabeth , Wolk C. Peter , Kaneko Takakazu , Tabata Satoshi 
Published: January 2005

ABSTRACT

As demonstrated with
alr2835
(
hepA
) and
alr2834
(
hepC
) mutants, heterocysts of
Anabaena
sp. strain PCC 7120, a filamentous cyanobacterium, must have an envelope polysaccharide layer (the Hep
+
phenotype) to fix dinitrogen in an oxygen-containing milieu (the Fox
+
phenotype). Transpositions presumptively responsible for a Fox
−
phenotype were localized in open reading frames (ORFs) near
hepA
and
hepC
. A mutation in each of nine of these ORFs was complemented by a clone bearing only that single, intact ORF. Heterocysts of the nine mutants were found to lack an envelope polysaccharide layer. Complementation of mutations in
alr2832
and
alr2840
may have resulted from recombination. However,
alr2825
,
alr2827
,
alr2831
,
alr2833
,
alr2837
,
alr2839
, and
alr2841
, like
hepA
and
hepC
, are required for a Hep
+
Fox
+
phenotype.
Genome-Wide Expression Analysis Indicates that FNR ofEscherichia coliK-12 Regulates a Large Number of Genes of Unknown Function
Authors: Kang Yisheng , Weber K. Derek , Qiu Yu , Kiley Patricia J. , Blattner Frederick R. 
Published: January 2005

ABSTRACTThe major regulator controlling the physiological switch between aerobic and anaerobic growth conditions inEscherichia coliis the DNA binding protein FNR. To identify genes controlled by FNR, we used Affymetrix Antisense GeneChips to compare global gene expression profiles from isogenic MG1655 wild-type and Δfnrstrains grown in glucose minimal media under aerobic or anaerobic conditions. We found that 297 genes contained within 184 operons were regulated by FNR and/or by O2levels. The expression of many genes known to be involved in anaerobic respiration and fermentation was increased under anaerobic growth conditions, while that of genes involved in aerobic respiration and the tricarboxylic acid cycle were repressed as expected. The expression of nine operons associated with acid resistance was also increased under anaerobic growth conditions, which may reflect the production of acidic fermentation products. Ninety-one genes with no presently defined function were also altered in expression, including seven of the most highly anaerobically induced genes, six of which we found to be directly regulated by FNR. Classification of the 297 genes into eight groups byk-means clustering analysis indicated that genes with common gene expression patterns also had a strong functional relationship, providing clues for studying the function of unknown genes in each group. Six of the eight groups showed regulation by FNR; while some expression groups represent genes that are simply activated or repressed by FNR, others, such as those encoding functions for chemotaxis and motility, showed a more complex pattern of regulation. A computer search for FNR DNA binding sites within predicted promoter regions identified 63 new sites for 54 genes. We suggest thatE. coliMG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized.
Sinorhizobium meliloti dctA
Mutants with Partial Ability To Transport Dicarboxylic Acids
Authors: Yurgel Svetlana N. , Kahn Michael L. 
Published: January 2005

ABSTRACT

Sinorhizobium meliloti dctA
encodes a transport protein needed for a successful nitrogen-fixing symbiosis between the bacteria and alfalfa. Using the toxicity of the DctA substrate fluoroorotic acid as a selective agent in an iterated selection procedure, four independent
S. meliloti dctA
mutants were isolated that retained some ability to transport dicarboxylates. Two mutations were located in a region called motif B located in a predicted transmembrane helix of the protein that has been shown in other members of the glutamate transporter family to be involved in cation binding. A G114D mutation was located in the third transmembrane helix, which had not previously been directly implicated in transport. Multiple sequence alignment of more than 60 members of the glutamate transporter family revealed a glycine at this position in nearly all members of the family. The fourth mutant was able to transport succinate at almost wild-type levels but was impaired in malate and fumarate transport. It contains two mutations: one in a periplasmic domain and the other predicted to be in the cytoplasm. Separation of the mutations showed that each contributed to the altered substrate preference.
dctA
deletion mutants that contain the mutant
dctA
alleles on a plasmid can proceed further in symbiotic development than null mutants of
dctA
, but none of the plasmids could support symbiotic nitrogen fixation, although they can transport dicarboxylates, some at relatively high levels.
Characterization of a Truncated Lipoarabinomannan from the Actinomycete
Turicella otitidis
Authors: Gilleron Martine , Garton Natalie J. , Nigou Jérôme , Brando Thérèse , Puzo Germain , Sutcliffe Iain C. 
Published: January 2005

ABSTRACT

Lipoarabinomannan (LAM) lipoglycans have been characterized from a range of mycolic acid-containing actinomycetes and from the amycolate actinomycete
Amycolatopsis sulphurea
. To further understand the structural diversity of this family, we have characterized the lipoglycan of the otic commensal
Turicella otitidis
.
T. otitidis
LAM (TotLAM) has been determined to consist of a mannosyl phosphatidylinositol anchor unit carrying an (α 1→6)-linked mannan core and substituted with terminal-arabinosyl branches. Thus, TotLAM has a novel truncated LAM structure. Using the human monocytic THP-1 cell line, it was found that TotLAM exhibited only minimal ability to induce tumor necrosis factor alpha. These findings contribute further to our understanding of actinomycete LAM diversity and allow further speculation as to the correlation between LAM structure and the immunomodulatory activities of these lipoglycans.
The magnitude and breadth of hepatitis C virus–specific CD8+ T cells depend on absolute CD4+ T-cell count in individuals coinfected with HIV-1
Authors: Kim Arthur Y. , Lauer Georg M. , Ouchi Kei , Addo Marylyn M. , Lucas Michaela , Wiesch Julian Schulze zur , Timm Joerg , Boczanowski Melinda , Duncan Jared E. , Wurcel Alysse G. , Casson Deborah , Chung Raymond T. , Draenert Rika , Klenerman Paul , Walker Bruce D. 
Published: January 2005

AbstractCD8+ T-cell responses are an essential antiviral host defense in persistent viral infections, and their sustained effectiveness is thought to be critically dependent on CD4+ T-helper cells. To determine the relationship between HIV-1–induced CD4+ T-cell depletion and hepatitis C virus (HCV)–specific CD8+ T-cell responses during viral persistence, we studied 103 persons positive for HCV, 74 coinfected with HIV-1. CD8+ T-cell responses to the entire HCV polyprotein were determined by using an interferon-γ enzyme-linked immunospot (ELISpot) assay. Although HIV-1 infection by itself was not associated with a diminished HCV-specific response, HIV-1–associated CD4+ depletion was associated with significantly lower HCV-specific CD8+ T cells (R = 0.48, P &lt; .0001). In contrast, declining CD4+ counts over the same range were not associated with diminished Epstein-Barr virus (EBV)– (R = 0.19, P = .31) or HIV-1–specific (R = –0.13, P = .60) CD8+ T-cell responses in persons infected with all viruses. These data indicate that frequencies of circulating HCV-specific CD8+ T-cell responses are sensitive to absolute CD4+ T-cell counts and provide a possible explanation for the accelerated HCV disease course in persons coinfected with HIV-1 and HCV.
Cross-recognition of human alloantigen by cytomegalovirus glycoprotein-specific CD4+ cytotoxic T lymphocytes: implications for graft-versus-host disease
Authors: Elkington Rebecca , Khanna Rajiv 
Published: January 2005

AbstractPresence of the HLA-DR7 allele in patients who receive transplants has been proposed as a risk factor for human cytomegalovirus (HCMV)–associated complications; however, the precise mechanism of this increased risk remains unresolved. Here we show that HLA-DR7–restricted HCMV-specific CD4+ cytotoxic T lymphocytes (CTLs) can display an unusual dual specificity toward a glycoprotein-B (gB) epitope and the alloantigen HLA-DR4. However, no HLA-DR4–specific alloreactivity was observed when the gB-specific CTLs were generated from virus carriers expressing both HLA-DR7 and DR4 alleles. This most likely demonstrates the clonal inactivation of potentially self-reactive T cells in humans. Fine specificity analysis showed that gB-specific CTLs from HLA-DR7+/DR4- individuals displayed a distinct pattern of recognition when compared with CTLs from HLA-DR7+/DR4+ individuals, presumably evading an area of the epitope that mimics a structure presented on HLA-DR4. These data illustrate a possible mechanism for the clinical association between HCMV and graft-versus-host disease.
Identification of a human mutation of DMT1 in a patient with microcytic anemia and iron overload
Authors: Mims Martha P. , Guan Yongli , Pospisilova Dagmar , Priwitzerova Monika , Indrak Karel , Ponka Prem , Divoky Vladimir , Prchal Josef T. 
Published: January 2005

Abstract
Divalent metal transporter 1 (DMT1) is a transmembrane protein crucial for duodenal iron absorption and erythroid iron transport. DMT1 function has been elucidated largely in studies of the mk mouse and the Belgrade rat, which have an identical single nucleotide mutation of this gene that affects protein processing, stability, and function. These animals exhibit hypochromic microcytic anemia due to impaired intestinal iron absorption, and defective iron utilization in red cell precursors. We report here the first human mutation of DMT1 identified in a female with severe hypochromic microcytic anemia and iron overload. This homozygous mutation in the ultimate nucleotide of exon 12 codes for a conservative E399D amino acid substitution; however, its pre-dominant effect is preferential skipping of exon 12 during processing of pre–messenger RNA (mRNA). The lack of full-length mRNA would predict deficient iron absorption in the intestine and deficient iron utilization in erythroid precursors; however, unlike the animal models of DMT1 mutation, the patient is iron overloaded. This does not appear to be due to up-regulation of total DMT1 mRNA. DMT1 protein is easily detectable by immunoblotting in the patient's duodenum, but it is unclear whether the protein is properly processed or targeted.
The effect of first-line imatinib interim therapy on the outcome of allogeneic stem cell transplantation in adults with newly diagnosed Philadelphia chromosome–positive acute lymphoblastic leukemia
Authors: Lee Seok , Kim Yoo-Jin , Min Chang-Ki , Kim Hee-Je , Eom Ki-Sung , Kim Dong-Wook , Lee Jong-Wook , Min Woo-Sung , Kim Chun-Choo 
Published: January 2005

AbstractPreviously, we suggested that imatinib incorporation into conventional chemotherapy as an alternative (imatinib interim therapy) might be a useful strategy for bridging the time to allogeneic stem cell transplantation (SCT) for newly diagnosed Philadelphia chromosome–positive acute lymphoblastic leukemia (Ph+ ALL). Here, we provide an updated report on this strategy in 29 patients. At the time of enrollment, 23 patients (79.3%) achieved complete remission (CR). After the first imatinib cycle, the median breakpoint cluster region–Abelson oncogene locus (BCR-ABL)/ABL ratios decreased by 0.77 log in 25 (86.2%) responders, and their BCR-ABL/ABL ratios decreased further by 0.34 log after the second imatinib cycle, which included 7 molecular CR. One patient (4.3%) relapsed during the imatinib therapy. The remaining 3 patients were primarily refractory to both imatinib and chemotherapy. Twenty-five (86.2%) of the 29 patients received transplants in first CR. With a median follow-up duration of 25 months after SCT, the 3-year estimated probabilities of relapse, nonrelapse mortality, disease-free survival, and overall survival were 3.8%, 18.7%, 78.1%, and 78.1%, respectively. In comparison to our historical control data, first-line imatinib interim therapy appears to provide a good quality of CR and a survival advantage for patients with Ph+ ALL. Further long-term follow-up is needed to validate the results of this study.
Modelling the correlation between the activities of adjacent genes in drosophila
Authors: Thygesen Helene H , Zwinderman Aeilko H 
Published: January 2005

Abstract
Background
Correlation between the expression levels of genes which are located close to each other on the genome has been found in various organisms, including yeast, drosophila and humans. Since such a correlation could be explained by several biochemical, evolutionary, genetic and technological factors, there is a need for statistical models that correspond to specific biological models for the correlation structure.

Results
We modelled the pairwise correlation between the expressions of the genes in a Drosophila microarray experiment as a normal mixture under Fisher's z-transform, and fitted the model to the correlations of expressions of adjacent as well as non-adjacent genes. We also analyzed simulated data for comparison. The model provided a good fit to the data. Further, correlation between the activities of two genes could, in most cases, be attributed to either of two factors: the two genes both being active in the same age group (adult or embryo), or the two genes being in proximity of each other on the chromosome. The interaction between these two factors was weak.

Conclusions
Correlation between the activities of adjacent genes is higher than between non-adjacent genes. In the data we analyzed, this appeared, for the most part, to be a constant effect that applied to all pairs of adjacent genes.
Genome-scale analysis of positional clustering of mouse testis-specific genes
Authors: Li Quan , Lee Bernett TK , Zhang Louxin 
Published: January 2005

Abstract
Background
Genes are not randomly distributed on a chromosome as they were thought even after removal of tandem repeats. The positional clustering of co-expressed genes is known in prokaryotes and recently reported in several eukaryotic organisms such as Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens. In order to further investigate the mode of tissue-specific gene clustering in higher eukaryotes, we have performed a genome-scale analysis of positional clustering of the mouse testis-specific genes.

Results
Our computational analysis shows that a large proportion of testis-specific genes are clustered in groups of 2 to 5 genes in the mouse genome. The number of clusters is much higher than expected by chance even after removal of tandem repeats.

Conclusion
Our result suggests that testis-specific genes tend to cluster on the mouse chromosomes. This provides another piece of evidence for the hypothesis that clusters of tissue-specific genes do exist.
Upregulated expression of human neutrophil peptides 1, 2 and 3 (HNP 1-3) in colon cancer serum and tumours: a biomarker study
Authors: Albrethsen Jakob , Bøgebo Rikke , Gammeltoft Steen , Olsen Jesper , Winther Benny , Raskov Hans 
Published: January 2005

Abstract
Background
Molecular markers for localized colon tumours and for prognosis following therapy are needed. Proteomics research is currently producing numerous biomarker studies with clinical potential. We investigate the protein composition of plasma and of tumour extracts with the aim of identifying biomarkers for colon cancer.

Methods
By Surface Enhanced Laser Desorption/Ionisation – Time Of Flight / Mass spectrometry (SELDI-TOF/MS) we compare the protein profiles of colon cancer serum with serum from healthy individuals and the protein profiles of colon tumours with normal colon tissue. By size exclusion chromatography, we investigate the binding of HNP 1-3 to high mass plasma proteins. By microflow we investigate the effect of HNP 1-3 on mammalian cells.

Results
Human Neutrophil Peptides -1, -2 and -3 (HNP 1-3), also known as alfa-defensin-1, -2 and -3, are present in elevated concentrations in serum from colon cancer patients and in protein extracts from colon tumours. A fraction of HNP 1-3 in serum is bound to unidentified high mass plasma proteins. HNP 1-3 purified from colon tumours are lethal to mammalian cells.

Conclusions
HNP 1-3 may serve as blood markers for colon cancer in combination with other diagnostic tools. We propose that HNP 1-3 are carried into the bloodstream by attaching to high mass plasma proteins in the tumour microenvironment. We discuss the effect of HNP 1-3 on tumour progression.