bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of a deep-water wave with a vertical cylinder: effect of self-excited vibrations on quantitative flow patterns
Authors: OZGOREN M. , ROCKWELL D. 
Published: January 2007

Interaction of a deep-water wave with a cylinder gives rise to ordered patterns of the flow structure, which are quantitatively characterized using a technique of high-image-density particle image velocimetry. When the cylinder is stationary, the patterns of instantaneous flow structure take on increasingly complex forms for increasing Keulegan--Carpenter number KC. These patterns involve stacking of small-scale vorticity concentrations, as well as large-scale vortex shedding. The time-averaged consequence of these patterns involves, at sufficiently high KC, an array of vorticity concentrations about the cylinder.When the lightly damped cylinder is allowed to undergo bidirectional oscillations, the trajectories can be classified according to ranges of KC. At low values of KC, the trajectory is elliptical, and further increases of KC allow, first of all, both elliptical and in-line trajectories as possibilities, followed by predominantly in-line and figure-of-eight oscillations at the largest value of KC.Representations of the quantitative flow structure, in relation to the instantaneous cylinder position on its oscillation trajectory, show basic classes of patterns. When the trajectory is elliptical, layers of vorticity rotate about the cylinder surface, in accordance with rotation of the relative velocity vector of the wave motion with respect to the oscillating cylinder. Simultaneously, the patterns of streamline topology take the form of large-scale bubbles, which also rotate about the cylinder. When the cylinder trajectory is predominantly in-line with the wave motion, generic classes of vortex formation and shedding can be identified; they include sweeping of previously shed vorticity concentrations past the cylinder to the opposite side. Certain of these patterns are directly analogous to those from the stationary cylinder.
Structure of the human β‐ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase
Authors: Christensen Caspar Elo , Kragelund Birthe B. , von Wettstein‐Knowles Penny , Henriksen Anette 
Published: January 2007

AbstractTwo distinct ways of organizing fatty acid biosynthesis exist: the multifunctional type I fatty acid synthase (FAS) of mammals, fungi, and lower eukaryotes with activities residing on one or two polypeptides; and the dissociated type II FAS of prokaryotes, plastids, and mitochondria with individual activities encoded by discrete genes. The β‐ketoacyl [ACP] synthase (KAS) moiety of the mitochondrial FAS (mtKAS) is targeted by the antibiotic cerulenin and possibly by the other antibiotics inhibiting prokaryotic KASes: thiolactomycin, platensimycin, and the α‐methylene butyrolactone, C75. The high degree of structural similarity between mitochondrial and prokaryotic KASes complicates development of novel antibiotics targeting prokaryotic KAS without affecting KAS domains of cytoplasmic FAS. KASes catalyze the C2 fatty acid elongation reaction using either a Cys‐His‐His or Cys‐His‐Asn catalytic triad. Three KASes with different substrate specificities participate in synthesis of the C16 and C18 products of prokaryotic FAS. By comparison, mtKAS carries out all elongation reactions in the mitochondria. We present the X‐ray crystal structures of the Cys‐His‐His‐containing human mtKAS and its hexanoyl complex plus the hexanoyl complex of the plant mtKAS from Arabidopsis thaliana. The structures explain (1) the bimodal (C6 and C10–C12) substrate preferences leading to the C8 lipoic acid precursor and long chains for the membranes, respectively, and (2) the low cerulenin sensitivity of the human enzyme; and (3) reveal two different potential acyl‐binding‐pocket extensions. Rearrangements taking place in the active site, including subtle changes in the water network, indicate a change in cooperativity of the active‐site histidines upon primer binding.
Covalent heme attachment in Synechocystis hemoglobin is required to prevent ferrous heme dissociation
Authors: Hoy Julie A. , Smagghe Benoit J. , Halder Puspita , Hargrove Mark S. 
Published: January 2007

AbstractSynechocystis hemoglobin contains an unprecedented covalent bond between a nonaxial histidine side chain (H117) and the heme 2‐vinyl. This bond has been previously shown to stabilize the ferric protein against denaturation, and also to affect the kinetics of cyanide association. However, it is unclear why Synechocystis hemoglobin would require the additional degree of stabilization accompanying the His117–heme 2‐vinyl bond because it also displays endogenous bis‐histidyl axial heme coordination, which should greatly assist heme retention. Furthermore, the mechanism by which the His117–heme 2‐vinyl bond affects ligand binding has not been reported, nor has any investigation of the role of this bond on the structure and function of the protein in the ferrous oxidation state. Here we report an investigation of the role of the Synechocystis hemoglobin His117–heme 2‐vinyl bond on structure, heme coordination, exogenous ligand binding, and stability in both the ferrous and ferric oxidation states. Our results reveal that hexacoordinate Synechocystis hemoglobin lacking this bond is less stable in the ferrous oxidation state than the ferric, which is surprising in light of our understanding of pentacoordinate Hb stability, in which the ferric protein is always less stable. It is also demonstrated that removal of the His117–heme 2‐vinyl bond increases the affinity constant for intramolecular histidine coordination in the ferric oxidation state, thus presenting greater competition for the ligand binding site and lowering the observed rate and affinity constants for exogenous ligands.
Role of aspartate 400, arginine 262, and arginine 401 in the catalytic mechanism of human coproporphyrinogen oxidase
Authors: Stephenson Jason R. , Stacey Julie A. , Morgenthaler Justin B. , Friesen Jon A. , Lash Timothy D. , Jones Marjorie A. 
Published: January 2007

AbstractCoproporphyrinogen oxidase (CPO) is the sixth enzyme in the heme biosynthetic pathway, catalyzing two sequential oxidative decarboxylations of propionate moieties on coproporphyrinogen‐III forming protoporphyrinogen‐IX through a monovinyl intermediate, harderoporphyrinogen. Site‐directed mutagenesis studies were carried out on three invariant amino acids, aspartate 400, arginine 262, and arginine 401, to determine residue contribution to substrate binding and/or catalysis by human recombinant CPO. Kinetic analyses were performed on mutant enzymes incubated with three substrates, coproporphyrinogen‐III, harderoporphyrinogen, or mesoporphyrinogen‐VI, in order to determine catalytic ability to perform the first and/or second oxidative decarboxylation. When Asp400 was mutated to alanine no divinyl product was detected, but the production of a small amount of monovinyl product suggested the Km value for coproporphyrinogen‐III did not change significantly compared to the wild‐type enzyme. Upon mutation of Arg262 to alanine, CPO was again a poor catalyst for the production of a divinyl product, with a catalytic efficiency <0.01% compared to wild‐type, including a 15‐fold higher Km for coproporphyrinogen‐III. The efficiency of divinyl product formation for mutant enzyme Arg401Ala was ∼3% compared to wild‐type CPO, with a threefold increase in the Km value for coproporphyrinogen‐III. These data suggest Asp400, Arg262, and Arg401 are active site amino acids critical for substrate binding and/or catalysis. Possible roles for arginine 262 and 401 include coordination of carboxylate groups of coproporphyrinogen‐III, while aspartate 400 may initiate deprotonation of substrate, resulting in an oxidative decarboxylation.
Topical application of F991, an immunoglobulin free light chain antagonist, prevents development of contact sensitivity in mice
Authors: Van Houwelingen A. H. , Kaczynska K. , Kraneveld A. D. , Kool M. , Nijkamp F. P. , Redegeld F. A. 
Published: January 2007

SummaryBackground
Exposure to reactive chemicals or environmental allergens can lead to hypersensitivity reactions in the skin of predisposed people. Most of these reactions are of atopic origin, but a subgroup of patients exhibits skin hypersensitivity reactions without features of atopy.Objective
This study was undertaken to examine the effect of inhibiting the action of Ig‐free light chains in a murine model for non‐atopic skin hypersensitivity by dermal application of the free light chain antagonist F991.Methods
To study the efficacy of F991, BALB/c mice were either passively immunized with trinitrophenyl (TNP)‐specific immunoglobulin light chains (IgLC) and challenged with the hapten picryl chloride (PCl) or actively skin‐sensitized and challenged with dinitrofluorobenzene (DNFB). The effect of F991 or control treatment was investigated by measuring local edema formation and the production of pro‐inflammatory cytokines.Results
Passive immunization with TNP‐specific IgLC resulted in an increase in ear swelling 2 h after PCl challenge. F991 inhibited this enhanced ear swelling in a dose‐dependent manner when applied 4 h before the sensitization with IgLC. F991 also inhibited DNFB‐induced contact hypersensitivity reaction in the mouse skin 2 and 24 h after challenge when applied before challenge. Besides the prophylactic action, F991 when applied 2 h after DNFB‐challenge, it was also able to attenuate symptoms of the DNFB‐induced hypersensitivity reaction at 24 h after challenge. We showed that the beneficial effects of F991 are restricted to the side of application.Conclusion
F991 is able to effectively alleviate symptoms of contact sensitivity in mice. Our study suggests that local interference with IgLC‐induced allergic symptoms may be attractive in the treatment of hypersensitivity responses.
Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life‐history forms
Authors: ARAKI HITOSHI , WAPLES ROBIN S. , ARDREN WILLIAM R. , COOPER BECKY , BLOUIN MICHAEL S. 
Published: January 2007

AbstractThe effective population size is influenced by many biological factors in natural populations. To evaluate their relative importance, we estimated the effective number of breeders per year (Nb) and effective population size per generation (Ne) in anadromous steelhead trout (Oncorhynchus mykiss) in the Hood River, Oregon (USA). Using demographic data and genetic parentage analysis on an almost complete sample of all adults that returned to the river over 15 years (> 15 000 individuals), we estimated Nb for 13 run years and Ne for three entire generations. The results are as follows: (i) the ratio of Ne to the estimated census population size (N) was 0.17–0.40, with large variance in reproductive success among individuals being the primary cause of the reduction in Ne/N; (ii) fish from a traditional hatchery program (Htrad: nonlocal, multiple generations in a hatchery) had negative effects on Nb, not only by reducing mean reproductive success but also by increasing variance in reproductive success among breeding parents, whereas no sign of such effects was found in fish from supplementation hatchery programs (Hsupp: local, single generation in a hatchery); and (iii) Nb was relatively stable among run years, despite the widely fluctuating annual run sizes of anadromous adults. We found high levels of reproductive contribution of nonanadromous parents to anadromous offspring when anadromous run size is small, suggesting a genetic compensation between life‐history forms (anadromous and nonanadromous). This is the first study showing that reproductive interaction between different life‐history forms can buffer the genetic impact of fluctuating census size on Ne.
Hepatic Lipogenesis in Broiler Chickens with Different Fat Deposition during Embryonic Development
Authors: Zhao S. , Ma H. , Zou S. , Chen W. , Zhao R. 
Published: January 2007

SummaryIn order to identify the genes involved in the fatness variability, we studied the expression of several genes implicated in the hepatic lipid metabolism of broiler chickens with different fat deposition patterns during embryonic development. The mRNA expression of acetyl CoA carboxylase (ACC), fatty acid synthase (FAS), malic enzyme (ME) and apolipoprotein B100 (apoB100) genes were determined using reverse transcriptase‐polymerase chain reaction (RT‐PCR). Samples of livers were collected from Arbor Acres (AA) and Sanhuang (SH) chickens on day 9, 14 and 19 of embryonic development as well as at hatching. This study showed that hepatic triglyceride (TG) level was found to increase suddenly during day 14 of embryonic development, to gradually increase thereafter, and to remain relatively constant at hatching. FAS gene expression in AA and SH broilers occurred prior to hatching and at hatching. The gene was expressed more in the former breed. ACC gene expression was observed beginning at the earlier development stage of days 9. No breed difference was observed in ME and apoB gene expression. This study indicated that the expression of lipogenic enzyme genes of the liver in broiler chickens exhibited scheduling during embryogenesis. The ACC gene started to express earlier than the FAS gene during embryonic development. This suggested that embryonic liver synthesized fatty acid, and breed difference was noticed prior to hatching.
Dydrogesterone and norethisterone regulate expression of lipoprotein lipase and hormone‐sensitive lipase in human subcutaneous abdominal adipocytes
Authors: Palin S. L. , McTernan P. G. , McGee K. C. , Sturdee D. W. , Barnett A. H. , Kumar S. 
Published: January 2007

Aim:  In premenopausal women, hyperandrogenicity is associated with central obesity and an increased cardiovascular risk. The aim of this study was to investigate the effects of dydrogesterone (DYD) (a non‐androgenic progestogen) and norethisterone (NET) (an androgenic progestogen) on lipoprotein lipase (LPL), hormone‐sensitive lipase (HSL) and glycerol release in adipocytes isolated from subcutaneous abdominal adipose tissue.Methods:  Adipose tissue was obtained from 12 non‐diabetic women, mean age 51 years (range 37–78) and mean body mass index 25.4 kg/m2 (range 20.3–26.4). Adipocytes were treated with increasing doses of DYD and NET for 48 h prior to protein extraction. Effects on lipogenesis and lipolysis were assessed using western blotting to determine the expression of key enzymes, LPL (56 kDa) and HSL (84 kDa) respectively. Measurement of glycerol release into the medium provided an assessment of lipolytic activity.Results:  Expression of LPL was increased by DYD and NET (mean protein expression relative to control ± s.e.), with greatest effect at 10−8 M for DYD: 2.32 ± 0.51 (p < 0.01) and 10−8 M for NET: 2.06 ± 0.19 (p < 0.01). In contrast, HSL expression was reduced by all concentrations of DYD, with maximal effect at 10−9 M : 0.49 ± 0.02 (p < 0.001). NET reduced HSL expression at all concentrations from 10−9 M : 0.62 ± 0.06 (p < 0.001) to 10−7 M : 0.69 ± 0.08 (p < 0.001). Glycerol measurements supported the HSL expression studies although they were not statistically significant (p > 0.05).Conclusions:  DYD and NET significantly increased LPL expression relative to control, while significantly reducing HSL expression. At the concentrations studied, similar effects were observed with the androgenic NET and the non‐androgenic DYD despite differing effects on the lipid profile when taken orally in combination with oestrogen. Further work examining the effects of different progestogens on body fat distribution may enable progestogen use to be tailored to maximize benefits and minimize potential harm.
Up‐regulation of plasma membrane‐associated redox activities in neuronal cells lacking functional mitochondria
Authors: Hyun Dong‐Hoon , Hunt Nicole D. , Emerson Scott S. , Hernandez Joe O. , Mattson Mark P. , Cabo Rafael de 
Published: January 2007

AbstractMitochondria‐deficient cells (ρo cells) survive through enhanced glycolytic metabolism in the presence of pyruvate and uridine. The plasma membrane redox system (PMRS) contains several NAD(P)H‐related enzymes and plays a key role in maintaining the levels of NAD+/NADH and reduced coenzyme Q. In this study, ρo cells were used to investigate how the PMRS is regulated under conditions of mitochondrial dysfunction. ρo cells exhibited a lower oxygen consumption rate and higher levels of lactate than parental cells, and were more sensitive to glycolysis inhibitors (2‐deoxyglucose and iodoacetamide) than control cells. However, they were more resistant to H2O2, consistent with increased catalase activity and decreased oxidative damage (protein carbonyls and nitrotyrosine). PM‐associated redox enzyme activities were enhanced in ρo cells compared to those in control cells. Our data suggest that all PMRS enzymes and biomarkers tested are closely related to the ability of the PMs to maintain redox homeostasis. These results illustrate that an up‐regulated PM redox activity can protect cells from oxidative stress as a result of an improved antioxidant capacity, and suggest a mechanism by which neurons adapt to conditions of impaired mitochondrial function.
Adapting the voice‐centred relational method of data analysis: reading trainees’ accounts of their learning on a pilot programme for practitioners working with parents
Authors: Fairtlough Anna C. 
Published: January 2007

AbstractIn this paper, the author reflects on the process of analysing and interpreting what trainees said about their learning during an external evaluation of an innovative training programme for practitioners working in the emerging field of parenting education and support. Applying the ‘voice‐centred relational’ method of qualitative analysis to a training evaluation context, qualitative accounts from trainees were read through four different lenses: the plot and evaluator responses to the narrative; the voice of the ‘I’; relationships; and placing people within cultural contexts and social structures. The use of this framework is then illustrated by an analysis of an interview with one trainee. The importance of the evaluator being emotionally and intellectually reflexive and aware of the impact of the content and process of the learning on the trainees is stressed.
Older donor allografts are associated with poor patient survival after living donor liver transplantation for hepatitis B virus‐related liver diseases
Authors: Kim Do Young , Choi Moon Seok , Lee Joon Hyoek , Koh Kwang Cheol , Paik Seung Woon , Yoo Byung Chul , Joh Jae Won , Lee Suk Koo , Rhee Jong Chul 
Published: January 2007

AbstractBackground and Aims: The significance of donor age in living donor liver transplantation (LDLT) for hepatitis B virus (HBV) infection has not been fully evaluated.Methods: We analyzed the data of 136 patients who underwent LDLT for HBV‐related liver diseases from January 1999 to April 2004. The recipients were divided into an older donor group (donor age ≥40) and a younger donor group (donor age <40). Posttransplant clinical outcomes and survival were compared between two groups, and predictors of survival after LDLT were evaluated.Results: Baseline characteristics were not different between the two groups, except for more number of female donors and higher positive donor anti‐HBc rate in the older group. The frequencies of acute rejection and early mortality after transplantation were similar in the two groups. The long‐term survival rates for the older donor group were significantly lower than those of the younger donor group (1‐, 3‐, 5‐year survival rate=84%, 75%, 46% vs. 92%, 86%, and 83%, P=0.03). Multivariate analysis showed that older donor age was the only independent risk factor associated with survival after LDLT (HR=2.3; 95% CI=1.1–5.6, P=0.04).Conclusions: Our study suggests that older donor allografts would be associated with poor patient survival after LDLT for HBV‐related liver diseases.
Simultaneous concentration of platelets and marrow cells: A simple and useful technique to obtain source cells and growth factors for regenerative medicine
Authors: Nishimoto Soh , Oyama Tomoki , Matsuda Ken 
Published: January 2007

ABSTRACTPlatelet‐rich plasma (PRP) has attracted attention as a safe and cost‐effective source of growth factors that stimulate cells to regenerate tissue. Bone marrow aspirate was processed with the same protocol to obtain PRP from peripheral blood. This concentrate contained condensed nucleated bone marrow cells, which are useful for regenerative medicine, as well as condensed platelets. In PRP derived from bone marrow aspirate, the density of platelets and levels of growth factors (platelet‐derived growth factor and transforming growth factor‐β) were the same as in PRP derived from peripheral blood. Condensation of nucleated cells, especially small‐sized cells, was confirmed. With a simple and cost‐effective technique, source cells and growth factors can be obtained at the same time. This simultaneous concentration of platelets and bone marrow cells has great potential as a source of materials for regenerative medicine.
Clinical impact of FDG‐PET/CT in the planning of radiotherapy for early‐stage Hodgkin lymphoma
Authors: Hutchings Martin , Loft Annika , Hansen Mads , Berthelsen Anne Kiil , Specht Lena 
Published: January 2007

Abstract Background: Early‐stage Hodgkin lymphoma (HL) has excellent survival rates but carries a high risk of late treatment‐related adverse effects. Modern, individualised therapeutic strategies require an accurate determination of the extent of the disease. This study investigated the potential impact of 2‐[18F]‐fluoro‐2‐deoxy‐d‐glucose positron emission tomography/computerised tomogrpahy (FDG‐PET/CT) in the planning of involved field radiotherapy (IFRT). Patients and methods: Thirty patients received staging FDG‐PET/CT before therapy, and IFRT after a short course of ABVD (adriamycin, bleomycin, vinblastine, dacarbazine) chemotherapy. IFRT planning was performed using only the CT data from the FDG‐PET/CT scan. Later, the IFRT planning was performed anew using the FDG‐PET/CT data as basis for contouring. Results: In 20 out of 30 patients, the radiotherapy (RT) course was unaffected by the addition of FDG‐PET/CT. FDG‐PET/CT would have increased the irradiated volume in seven patients where the volume receiving a minimum of 90% of the target dose was increased by 8–87%. FDG‐PET/CT decreased the volume in two patients where the volume was reduced by 18% and 30%. Conclusions: When used for RT planning, FDG‐PET/CT results in larger IFRT treatment volumes. If FDG‐PET/CT is introduced to RT planning, the method should be accompanied by a change in RT treatment strategy, aiming at more targeted therapy in order to best avoid radiation to normal tissues.