bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explorative Multivariate Analyses of 16S rRNA Gene Data from Microbial Communities in Modified-Atmosphere-Packed Salmon and Coalfish
Authors: Rudi Knut , Maugesten Tove , Hannevik Sigrun E. , Nissen Hilde 
Published: August 2004

ABSTRACT

Modified-atmosphere packaging (MAP) of foods in combination with low-temperature storage extends product shelf life by limiting microbial growth. We investigated the microbial biodiversity of MAP salmon and coalfish by using an explorative approach and analyzing both the total amounts of bacteria and the microbial group composition (both aerobic and anaerobic bacteria). Real-time PCR analyses revealed a surprisingly large difference in the microbial loads for the different fish samples. The microbial composition was determined by examining partial 16S rRNA gene sequences from 180 bacterial isolates, as well as by performing terminal restriction fragment length polymorphism analysis and cloning 92 sequences from PCR products of DNA directly retrieved from the fish matrix. Twenty different bacterial groups were identified. Partial least-squares (PLS) regression was used to relate the major groups of bacteria identified to the fish matrix and storage time. A strong association of coalfish with
Photobacterium phosphoreum
was observed.
Brochothrix
spp. and
Carnobacterium
spp., on the other hand, were associated with salmon. These bacteria dominated the fish matrixes after a storage period. Twelve
Carnobacterium
isolates were identified as either
Carnobacterium piscicola
(five isolates) or
Carnobacterium divergens
(seven isolates), while the eight
Brochothrix
isolates were identified as
Brochothrix thermosphacta
by full-length 16S rRNA gene sequencing. Principal-component analyses and PLS analysis of the growth characteristics (with 49 different substrates) showed that
C. piscicola
had distinct substrate requirements, while the requirements of
B. thermosphacta
and
C. piscicola
were quite divergent. In conclusion, our explorative multivariate approach gave a picture of the total microbial biodiversity in MAP fish that was more comprehensive than the picture that could be obtained previously. Such information is crucial in controlled food production when, for example, the hazard analysis of critical control points principle is used.
Strategy for Cloning Large Gene Assemblages as Illustrated Using the Phenylacetate and Polyhydroxyalkanoate Gene Clusters
Authors: García Belén , Olivera Elías R. , Sandoval Ángel , Arias-Barrau Elsa , Arias Sagrario , Naharro Germán , Luengo José M. 
Published: August 2004

ABSTRACT

We report an easy procedure for isolating chromosome-clustered genes. By following this methodology, the entire set of genes belonging to the phenylacetic acid (PhAc; 18-kb) pathway as well as those required for the synthesis and mobilization of different polyhydroxyalkanoates (PHAs; 6.4 kb) in
Pseudomonas putida
U were recovered directly from the bacterial chromosome and cloned into a plasmid for the first time. The transformation of different bacteria with these genetic constructions conferred on them the ability to either degrade PhAc or synthesize bioplastics (PHAs).
Nisin-Controlled Production of Pediocin PA-1 and Colicin V in Nisin- and Non-Nisin-Producing
Lactococcus lactis
Strains
Authors: Horn Nikki , Fernández Antonio , Dodd Helen M. , Gasson Michael J. , Rodríguez Juan M. 
Published: August 2004

ABSTRACT

The introduction of chimeric genes encoding the fusion leader of lactococcin A-propediocin PA-1 or procolicin V under the control of the inducible
nisA
promoter and the lactococcin A-dedicated secretion genes (
lcnCD
) into
Lactococcus lactis
strains, including a nisin producer, expressing the two component regulator NisRK led to the production or pediocin PA-1 or colicin V, respectively.
Nisin-Producing
Lactococcus lactis
Strains Isolated from Human Milk
Authors: Beasley Shea S. , Saris Per E. J. 
Published: August 2004

ABSTRACT

Characterization by partial 16S rRNA gene sequencing, ribotyping, and green fluorescent protein-based nisin bioassay revealed that 6 of 20 human milk samples contained nisin-producing
Lactococcus lactis
bacteria. This suggests that the history of humans consuming nisin is older than the tradition of consuming fermented milk products.
Immunodominant T-cell epitopes in the factor VIII C2 domain are located within an inhibitory antibody binding site
Authors: Okita David , Diethelm-Okita Brenda , Conti-Fine Bianca , Pratt Kathleen , Qian Jiahua , Ellaban Ekram , Scott David 
Published: August 2004

SummaryFormation of inhibitor antibodies to factor VIII (FVIII) is a major complication of FVIII replacement therapy for hemophilia A patients, and it occurs through a T-cell dependent process. The C2 domain of FVIII contains epitopes that are recognized by antibody inhibitors. We have examined regions of the C2 domain that form epitopes for T cells in mice congenitally deficient in FVIII. We obtained CD4+ T cells from mice immunized by intravenous infusion of therapeutic doses of recombinant human FVIII (rFVIII), or by subcutaneous injections of rFVIII or recombinant human C2 domain in adjuvant. In all cases, the T cells recognized most strongly and consistently two overlapping peptides that spanned residues 2191 to 2220 of the C2 domain. Analysis of the crystal structure of human factor VIII C2 bound to a human monoclonal antibody, BO2C11, showed these residues also constitute part of a human alloimmune B-cell epitope (Spiegel et al., Blood 2001; 98: 13-19).This region includes one of the “hydrophobic spike” protrusions, consisting of M2199 and F2200, as well as the basic residues R2215 and R2220. These residues contribute to membrane binding and to association with von Willebrand factor (vWF).These findings suggest that a major T-cell epitope in the C2 domain recognized by hemophilic mice is located within the same region that binds to inhibitors, vWF, and activated membranes.
The effect of vascular smooth muscle cell-targeted expression of tissue factor pathway inhibitor in a murine model of arterial thrombosis
Authors: Pan Shuchong , Kleppe Laurel , Witt Tyra , Mueske Cheryl , Simari Robert 
Published: August 2004

SummaryTissue factor pathway inhibitor (TFPI) is a Kunitz-type protease inhibitor that regulates the extrinsic pathway of coagulation by inhibiting the factor VIIa/tissue factor (TF) catalytic complex. TFPI is expressed by both endothelial and smooth muscle cells in the vasculature and circulates at low levels. The role of local vascular TFPI in thrombosis and the development of vascular disease is unknown. To establish an experimental animal model to directly modulate smooth muscle cell-derived TFPI on the development of arterial thrombosis, transgenic mice in which a cDNA encoding murine TFPI is expressed from the murine SM22α promoter were generated. Expression of transgenic mRNA was 4-fold higher than the level of endogenous TFPI mRNA in arteries from transgenic mice. In situ hybridization confirmed that expression of the transgene was limited to medial vascular smooth muscle cells. Vascular TFPI activity was increased to 2 to 3-fold in carotid homogenates. There was no difference in plasma TFPI levels or hemostatic measures (PT, aPTT and tail vein bleeding times) between these mice and their wildtype littermates. In a ferric chloride-induced model of carotid thrombosis, homozygotic transgenic mice demonstrated resistance to thrombotic occlusion compared to wildtype littermates. In transgenic mice 22% occluded within 30 minutes of application while 84% of wild type mice occluded within the same time frame (p <0.01). Heterozygotic transgenic mice had an intermediate thrombotic phenotype. Taken together, these data indicated that local VSMC-specific TFPI overexpression attenuated ferric chloride-induced thrombosis without systemic or hemostatic effects. Furthermore, this transgenic mouse model should prove useful for studying the role of TFPI in the development and progression of vascular disease.
Effects of heparin and low-molecular-weight heparins on bone mechanical properties in rats
Authors: Janiec Waldemar , Śliwiński Leszek , Folwarczna Joanna 
Published: August 2004

SummaryLong-term administration of heparin can be associated with development of osteoporosis. The present study was carried out to compare the effects of standard heparin and two low-molecular-weight heparins (nadroparin and enoxaparin) on bone mechanical properties in rats. The experiment was conducted on 3-month-old female Wistar rats. Standard heparin was administered in doses of 1000 or 2000 IU/kg sc daily, nadroparin and enoxaparin were administered in doses of 1000 or 2000 anti-Xa IU/kg sc daily, for 28 days. Bone mass, length, diameter, mineral content and mechanical properties of the whole femur (extrinsic stiffness, ultimate and breaking load, deformation caused by the applied load) and the femoral neck (load at fracture) were examined. Standard heparin (2000 IU/kg sc daily) weakened the femoral neck. Enoxaparin and the higher doses of standard heparin and nadroparin induced similar unfavourable changes in mechanical properties of the whole femur; the changes were noticeable the most after administration of enoxaparin.
Prevention of central venous line-related thrombosis by continuous infusion of low-dose unfractionated heparin, in patients with haemato-oncological disease
Authors: Ben Othman Tarek , Kammoun Leïla , Chelli Mouna , Ben Romdhane Neïla , Kriaa Azza , Ladeb Saloua , Torjman Lamia , Lakhal Amel , Achour Wafa , Ben Hassen Assia , Hsaïri Mohamed , Ladeb Fethi , Ben Abdeladhim Abdeladhim , Abdelkefi Abderrahman 
Published: August 2004

SummaryWe have conducted a prospective randomized controlled trial to evaluate the role of low-dose unfractionated heparin prophylaxis in preventing central venous line-related thrombosis in patients with haemato-oncological disease. Patients were randomly assigned to receive either prophylactic intravenous unfractionated heparin (continuous infusion of 100 IU/kg/daily) or 50 ml/daily of normal saline solution as a continuous infusion. CVLs were externalized, non tunneled, double lumen catheters. All CVLs were placed percutaneously by the same physician in the subclavian vein. Upper limb veins were systematically examined by ultrasonography just before, or < 24 hours after, catheter removal, and in case of clinical signs of thrombosis. One hundred and twenty-eight CVLs were inserted. Catheterrelated thrombosis occurred in 1.5% of the catheters inserted in patients of the heparin group, and in 12.6% in the control group (p = 0.03). No other risk factors were found for the development of catheter-related thrombosis. Two and three patients experienced severe bleeding in the heparin group, and in the control group, respectively (p = 0.18). There were no other side-effects clearly ascribable to the use of unfractionated heparin. This is the first prospective, randomized study, which shows that low-dose of unfractionated heparin is safe and effective to prevent catheter-related thrombosis in patients with haemato-oncological disease.
Paracetamol (acetaminophen) warfarin interaction: NAPQI, the toxic metabolite of paracetamol, is an inhibitor of enzymes in the vitamin K cycle
Authors: Soute Berry , Vervoort Lily , Claessens Jolanda , Thijssen Henk 
Published: August 2004

SummaryParacetamol (acetaminophen) is generally considered to be the analgesic of choice for patients undergoing oral anticoagulant therapy. Occasionally, however, interactions have been reported with therapeutic doses of the analgesic, e.g. if the drug is taken for a longer period of time. The mechanism of this interaction is not clearly understood. We investigated the effects of paracetamol and its toxic metabolite N-acetyl-para-benzoquinoneimine (NAPQI) on in vitro vitamin K-dependent γ-carboxylase (VKD-carb) and vitamin K epoxide reductase (VKOR) activities. Paracetamol had no effect in either enzymatic reactions. NAPQI, on the other hand, appeared to interfere with VKD-carb activity via two mechanisms; 1) oxidation of the cofactor vitamin K-hydroquinone, 2) inactivation of the enzyme. The inactivation, in micromolar ranges, is not reversible and may be the result of covalent binding of NAPQI with functional amino acids. NAPQI also inhibited VKOR, but at higher concentrations. Unexpectedly, N-acetylcysteine was found to inhibit VKOR activity at concentrations that are obtained during rescue therapy of paracetamol intoxication. We conclude that, the potentiation of the oral anticoagulant effect by paracetamol is likely to result from NAPQI-induced inhibition of enzymes of the vitamin K cycle, particularly VKD-carb.
A case series of 72 neonates with renal vein thrombosis
Authors: Kuhle Stefan , Massicotte Patti , Chan Anthony , Mitchell Lesley 
Published: August 2004

SummaryNeonatal renal vein thrombosis (RVT) is a well-recognized clinical entity which is associated with serious morbidity. However, current information regarding RVT has been restricted to case reports and small case series. In this study, it was our objective to describe patient demographics, clinical presentation, location and risk factors of RVT. For our study design, we looked at a case series of 72 neonates with RVT referred to the 1-800-NO-CLOTS consultation service between 9/1996 and 8/2001. Data on age, gender, associated conditions, prothrombotic disorders, family history, location of the thrombosis, diagnostic techniques, and treatment were prospectively recorded using a standardized form. Our results show that RVT affected males (65%, CI 52-76%) significantly more often than females (35%, CI 24-48%). Median age at presentation was 2 days (0-21 days). RVT was unilateral in 72% (left side: 67%, CI 49-81%; right side: 33%, CI 19-51%), and bilateral in 28%. The majority (83%) had at least one associated condition: Prematurity (54%), central venous lines (17%), a diabetic mother (13%), asphyxia (6%), infections (6%). Prothrombotic testing was performed in 21 neonates. Activated protein C resistance was found in 8 children (38%), other defects in three. This is the largest case series of neonatal RVT to date. Data from the study show that i) male infants are affected twice as often as females and ii) there appears to be a left-sided predominance of neonatal RVT. Neonatal RVT is only infrequently associated with the presence of a catheter as compared to thrombosis at other sites. The majority of infants have associated conditions with prematurity being most frequent. A small subset of neonates were screened for prothrombotic abnormalities and 50% of the children screened were positive.
The use of rFVIIa in non-haemophilia bleeding conditions in paediatrics
Authors: Mathew Prasad 
Published: August 2004

SummaryFrom its original envisioned use in patients with hemophilia and inhibitors, recombinant factor VIIa has been increasingly used in a variety of non-hemophilia bleeding/hemorrhagic situations with great efficacy. Most of the reported work has been in adult patients. This paper sets out to review its use in the pediatric non-hemophilia patients and the varied conditions it has been tried and used. Most of the published literature has shown that this agent is efficacious, safe and can be used as an adjunctive measure in the achievement of hemostasis. However, most of the published work is mainly anecdotal, case reports or small series. Randomized trials in children are eagerly awaited.
Incidence of post-thrombotic syndrome in patients with previous pulmonary embolism
Authors: Rossi Vincenza , Ricchio Roberto , Greco Antonio , Bloise Antonio , Daniele Filomena , Greco Francesco , Noto Alfonso , Bova Carlo 
Published: August 2004

SummaryThere is little information available about the true incidence of post-thrombotic syndrome (PTS) after pulmonary embolism (PE). The aim of this study was to investigate the incidence of PTS in patients with previous pulmonary embolism without concomitant ultrasonographically-detectable deep vein thrombosis (DVT). A retrospective cohort study was conducted at a single tertiary care centre, Cosenza, Italy. Forty-seven consecutive patients with proved PE without DVT within the previous 2 to 6 years, 45 patients with previous DVT in the same years, and 45 patients with diseases unrelated to venous thrombo-embolism (VTE) underwent a blind assessment for PTS using a clinical score. Two of 47 (4.2%, 95%CI: 0.01-9.9) patients with PE, 2 of 45 (4.4%, 95%CI: 0.01-10.4) patients with diseases unrelated to VTE, and 23 of 45 (53.3%, 95%CI: 38.7-67.9) patients with DVT showed signs and symptoms of PTS. The difference between the first two groups was not statistically significant (p = 0.7). In conclusion, the incidence of PTS after pulmonary embolism without DVT is low, and no different from that of patients without previous VTE.
Differential effects of heparin and low molecular weight heparin on osteoblastogenesis and adipogenesis in vitro
Authors: Osip Stephanie , Butcher Martin , Young Edward , Yang Lufang , Shaughnessy Stephen 
Published: August 2004

SummaryWe have previously demonstrated that heparin produces cancellous bone loss in rats due in part to a decrease in the number of osteoblasts lining the trabecular bone surface. In the present study, we use a stromal-derived cell culture system together with measurements of alkaline phosphatase (ALP) activity, to compare the effects of heparin and the low molecular weight heparin (LMWH), Fragmin, on osteoblast differentiation in vitro. In addition, we examined the possibility that both heparin and LMWH can induce adipogenesis in our stromal cell culture system. Both heparin and LMWH were found to produce a statistically significant (P <0.01) and concentration-dependent decrease in the number of osteoblasts while increasing the number of adipocytes. When the effects of gravimetrically equivalent amounts of heparin and LMWH were compared, heparin had a 4-fold greater effect than LMWH. In contrast to heparin, N-desulfated heparin was found to have minimal effects on both osteoblast and adipocyte differentiation indicating that the heparin effect is not only chain-length dependent but also charge-dependent. The observation that LMWH has less of an effect on bone formation than heparin is compatible with the results of clinical trials indicating that LMWH produces less bone loss after long-term administration.
Mouse models of thrombosis: thrombomodulin
Authors: Weiler Hartmut 
Published: August 2004

SummaryThis review describes animal models of TM-deficiency that cause thrombosis in mice. Thrombomodulin (TM) is a key component of the protein C anticoagulant pathway by facilitating the activation of protein C by thrombin. In addition, TM integrates fibrinolytic and anti-inflammatory responses in a manner that is in part independent of protein C and thrombin. A series of genetically modified mouse strains is available in which the various and distinct functions of TM have been altered by means of site-directed mutagenesis of the TM gene locus (Thbd). The focus of the current review is the pathological activation of the hemostatic mechanism in mice with altered TM function (the pathologic activation of the hemostatic mechanism). The analysis of these mouse models has revealed novel and in part organ-specific functions of TM, most notably in the vascular bed of the placenta. In these mouse models, the severity and phenotypic expression of thrombosis is highly variable and is dependent on interaction with secondary genetic or environmental modifiers. The mutant mouse strains replicate important aspects of thrombophilia and thrombosis in humans, and provide a valuable resource to validate existing, and develop novel concepts of disease mechanisms in human patients.
Role of tissue factor in haemostasis, thrombosis, angiogenesis and inflammation: lessons from low tissue factor mice
Authors: Pawlinski Rafal , Pedersen Brian , Erlich Jonathan , Mackman Nigel 
Published: August 2004

SummaryTissue factor (TF) contributes to a variety of biological processes by generating coagulation proteases and by the activation of protease activated receptors (PARs). Studies, using low TF mice, have provided us with novel insights into the role of TF in tissue-specific haemostasis. Low TF mice exhibit defects in the uterus, placenta, heart and lung, which are all tissues that normally express high levels of TF. We propose that these observed defects are primarily due to a reduction in the level of TF to below a critical threshold that is required to maintain adequate haemostasis. Nevertheless, a reduction in TF:FVIIa-dependent signaling may also reduce cell survival and/or compromise the integrity of the vasculature in these organs. Low TF mice are also a useful tool to study the role of TF and the coagulation cascade in other processes, such as thrombosis, inflammation and angiogenesis.
Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays
Authors: Lu Chao 
Published: July 2004

Abstract
Background
Normalization is an important step for microarray data analysis to minimize biological and technical variations. Choosing a suitable approach can be critical. The default method in GeneChip expression microarray uses a constant factor, the scaling factor (SF), for every gene on an array. The SF is obtained from a trimmed average signal of the array after excluding the 2% of the probe sets with the highest and the lowest values.

Results
Among the 76 U34A GeneChip experiments, the total signals on each array showed 25.8% variations in terms of the coefficient of variation, although all microarrays were hybridized with the same amount of biotin-labeled cRNA. The 2% of the probe sets with the highest signals that were normally excluded from SF calculation accounted for 34% to 54% of the total signals (40.7% ± 4.4%, mean ± sd). In comparison with normalization factors obtained from the median signal or from the mean of the log transformed signal, SF showed the greatest variation. The normalization factors obtained from log transformed signals showed least variation.

Conclusions
Eliminating 40% of the signal data during SF calculation failed to show any benefit. Normalization factors obtained with log transformed signals performed the best. Thus, it is suggested to use the mean of the logarithm transformed data for normalization, rather than the arithmetic mean of signals in GeneChip gene expression microarrays.