bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new dynamical layout algorithm for complex biochemical reaction networks
Authors: Wegner Katja , Kummer Ursula 
Published: August 2005

Abstract
Background
To study complex biochemical reaction networks in living cells researchers more and more rely on databases and computational methods. In order to facilitate computational approaches, visualisation techniques are highly important. Biochemical reaction networks, e.g. metabolic pathways are often depicted as graphs and these graphs should be drawn dynamically to provide flexibility in the context of different data. Conventional layout algorithms are not sufficient for every kind of pathway in biochemical research. This is mainly due to certain conventions to which biochemists/biologists are used to and which are not in accordance to conventional layout algorithms. A number of approaches has been developed to improve this situation. Some of these are used in the context of biochemical databases and make more or less use of the information in these databases to aid the layout process. However, visualisation becomes also more and more important in modelling and simulation tools which mostly do not offer additional connections to databases. Therefore, layout algorithms used in these tools have to work independently of any databases. In addition, all of the existing algorithms face some limitations with respect to the number of edge crossings when it comes to larger biochemical systems due to the interconnectivity of these. Last but not least, in some cases, biochemical conventions are not met properly.

Results
Out of these reasons we have developed a new algorithm which tackles these problems by reducing the number of edge crossings in complex systems, taking further biological conventions into account to identify and visualise cycles. Furthermore the algorithm is independent from database information in order to be easily adopted in any application. It can also be tested as part of the SimWiz package (free to download for academic users at [1]).

Conclusion
The new algorithm reduces the complexity of pathways, as well as edge crossings and edge length in the resulting graphical representation. It also considers existing and further biological conventions to create a drawing most biochemists are familiar with. A lot of examples can be found on [2].
Improved prediction of critical residues for protein function based on network and phylogenetic analyses
Authors: Thibert Boris , Bredesen Dale E , del Rio Gabriel 
Published: August 2005

Abstract
Background
Phylogenetic approaches are commonly used to predict which amino acid residues are critical to the function of a given protein. However, such approaches display inherent limitations, such as the requirement for identification of multiple homologues of the protein under consideration. Therefore, complementary or alternative approaches for the prediction of critical residues would be desirable. Network analyses have been used in the modelling of many complex biological systems, but only very recently have they been used to predict critical residues from a protein's three-dimensional structure. Here we compare a couple of phylogenetic approaches to several different network-based methods for the prediction of critical residues, and show that a combination of one phylogenetic method and one network-based method is superior to other methods previously employed.

Results
We associate a network with each member of a set of proteins for which the three-dimensional structure is known and the critical residues have been previously determined experimentally. We show that several network-based centrality measurements (connectivity, 2-connectivity, closeness centrality, betweenness and cluster coefficient) accurately detect residues critical for the protein's function. Phylogenetic approaches render predictions as reliable as the network-based measurements, although, interestingly, the two general approaches tend to predict different sets of critical residues. Hence we propose a hybrid method that is composed of one network-based calculation – the closeness centrality – and one phylogenetic approach – the Conseq server. This hybrid approach predicts critical residues more accurately than the other methods tested here.

Conclusion
We show that network analysis can be used to improve the prediction of amino acids critical for protein function, when utilized in combination with phylogenetic approaches. It is proposed that such improvement is due to the complementary nature of these approaches: network-based methods tend to predict as critical those residues that are highly connected and internal (i.e., non-surface), although some surface residues are indeed identified as critical by network analyses; whereas residues chosen by phylogenetic approaches display a lower overall probability of being surface inaccessible.
Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin
Authors: Hartwig Christine , Veske Andres , Krejcova Sarka , Rosenberger Georg , Finckh Ulrich 
Published: August 2005

Abstract

Background
Plexins, known to date as receptors of semaphorins, are implicated in semaphorin-mediated axon repulsion and growth cone collapse. However, subtype-specific functions of the majority of the nine members of the mammalian plexin family are largely unknown. In order to investigate functional properties of B-plexins, we analyzed the expression of human and murine plexin B3 and expressed full-length human plexins B2 (B2) and B3 (B3) in NIH-3T3 cells.

Results
Unexpectedly, B3 strongly and B2 moderately stimulate neurite outgrowth of primary murine cerebellar neurons. Both plexins mediate Ca2+/Mg2+-dependent cell aggregation due to homophilic trans-interaction, which is strong in the case of B3 and moderate for B2. Using different deletion constructs we show that the sema domain of B3 is essential for homophilic interaction. Using yeast two-hybrid analysis, we identified the neuron-specific and calmodulin-binding Ras-related GTPase Rin as an interaction partner of the intracellular part of B3, but not of B2. Rin, also known for its neurite outgrowth-inducing characteristics, co-localizes and co-immunoprecipitates with B3 in co-transfected COS-7 cells.

Conclusion
Our data suggest an involvement of homophilic interaction of B3 in semaphorin-independent signaling mechanisms positively influencing neuronal morphogenesis or function. Furthermore the neuron-specific small GTPase Rin is involved in downstream signaling of plexin B3.
Organic acid toxicity, tolerance, and production in Escherichia coli biorefining applications
Authors: Warnecke Tanya , Gill Ryan T 
Published: August 2005

AbstractOrganic acids are valuable platform chemicals for future biorefining applications. Such applications involve the conversion of low-cost renewable resources to platform sugars, which are then converted to platform chemicals by fermentation and further derivatized to large-volume chemicals through conventional catalytic routes. Organic acids are toxic to many of the microorganisms, such asEscherichia coli, proposed to serve as biorefining platform hosts at concentrations well below what is required for economical production. The toxicity is two-fold including not only pH based growth inhibition but also anion-specific effects on metabolism that also affect growth.E. colimaintain viability at very low pH through several different tolerance mechanisms including but not limited to the use of decarboxylation reactions that consume protons, ion transporters that remove protons, increased expression of known stress genes, and changing membrane composition. The focus of this mini-review is on organic acid toxicity and associated tolerance mechanisms as well as several examples of successful organic acid production processes forE. coli.
Teratogenicity of depleted uranium aerosols: A review from an epidemiological perspective
Authors: Hindin Rita , Brugge Doug , Panikkar Bindu 
Published: August 2005

Abstract

Background
Depleted uranium is being used increasingly often as a component of munitions in military conflicts. Military personnel, civilians and the DU munitions producers are being exposed to the DU aerosols that are generated.

Methods
We reviewed toxicological data on both natural and depleted uranium. We included peer reviewed studies and gray literature on birth malformations due to natural and depleted uranium. Our approach was to assess the "weight of evidence" with respect to teratogenicity of depleted uranium.

Results
Animal studies firmly support the possibility that DU is a teratogen. While the detailed pathways by which environmental DU can be internalized and reach reproductive cells are not yet fully elucidated, again, the evidence supports plausibility. To date, human epidemiological data include case examples, disease registry records, a case-control study and prospective longitudinal studies.

Discussion
The two most significant challenges to establishing a causal pathway between (human) parental DU exposure and the birth of offspring with defects are: i) distinguishing the role of DU from that of exposure to other potential teratogens; ii) documentation on the individual level of extent of parental DU exposure. Studies that use biomarkers, none yet reported, can help address the latter challenge. Thoughtful triangulation of the results of multiple studies (epidemiological and other) of DU teratogenicity contributes to disentangling the roles of various potentially teratogenic parental exposures. This paper is just such an endeavor.

Conclusion
In aggregate the human epidemiological evidence is consistent with increased risk of birth defects in offspring of persons exposed to DU.
Non-infected preterm parturition is related to increased concentrations of IL-6, IL-8 and MCP-1 in human cervix
Authors: Törnblom Susanne Abelin , Klimaviciute Aurelija , Byström Birgitta , Chromek Milan , Brauner Annelie , Ekman-Ordeberg Gunvor 
Published: August 2005

AbstractBackgroundHuman cervical ripening is an inflammatory process. In labour at term the mRNA-levels and protein concentrations for interleukin-6 (IL-6) and IL-8 in cervix significantly increase. The aim of this study was to investigate if there are differences in the inflammatory process of preterm and term cervical ripening.MethodsCervical biopsies from 50 singleton pregnant women without clinical signs of infection were allocated to four groups: preterm labour, term labour, preterm not in labour and term not in labour. The protein levels of IL-8, IL-6, monocyte chemotactic protein-1 (MCP-1), regulated upon activation normal t cells expressed and secreted (RANTES) and tumour necrosis factor-alpha (TNF-alpha) were quantified in tissue homogenates by ELISA or Immulite. The mRNA expression of IL-8, MCP-1 and RANTES was studied using RT-PCR. White blood cell count (WBC) and C-reactive protein (CRP) in the blood were determined. For determination of statistically significant differences between study groups Mann-Whitney U test or Kruskal-Wallis test were applied.ResultsProtein concentrations of IL-8, IL-6, and MCP-1 were significantly increased during labour compared to non-labouring groups, whereas no changes were observed for RANTES and TNF-alpha. The mRNA levels of representative cytokines such as IL-8 and MCP-1 increased significantly during labour whereas RANTES mRNA expression remained unchanged. WBC and CRP were significantly higher in the labouring groups as compared to groups not in labour. For neither of the analysed cytokines, WBC or CRP levels were there any changes between preterm and term respective groups.ConclusionOur findings indicate that non-infected preterm cervical ripening is an inflammatory process, just as cervical ripening at term, with cytokines as important mediators.
The SARS Coronavirus S Glycoprotein Receptor Binding Domain: Fine Mapping and Functional Characterization
Authors: Chakraborti Samitabh , Prabakaran Ponraj , Xiao Xiaodong , Dimitrov Dimiter S 
Published: August 2005

Abstract
The entry of the SARS coronavirus (SCV) into cells is initiated by binding of its spike envelope glycoprotein (S) to a receptor, ACE2. We and others identified the receptor-binding domain (RBD) by using S fragments of various lengths but all including the amino acid residue 318 and two other potential glycosylation sites. To further characterize the role of glycosylation and identify residues important for its function as an interacting partner of ACE2, we have cloned, expressed and characterized various soluble fragments of S containing RBD, and mutated all potential glycosylation sites and 32 other residues. The shortest of these fragments still able to bind the receptor ACE2 did not include residue 318 (which is a potential glycosylation site), but started at residue 319, and has only two potential glycosylation sites (residues 330 and 357). Mutation of each of these sites to either alanine or glutamine, as well as mutation of residue 318 to alanine in longer fragments resulted in the same decrease of molecular weight (by approximately 3 kDa) suggesting that all glycosylation sites are functional. Simultaneous mutation of all glycosylation sites resulted in lack of expression suggesting that at least one glycosylation site (any of the three) is required for expression. Glycosylation did not affect binding to ACE2. Alanine scanning mutagenesis of the fragment S319–518 resulted in the identification of ten residues (K390, R426, D429, T431, I455, N473, F483, Q492, Y494, R495) that significantly reduced binding to ACE2, and one residue (D393) that appears to increase binding. Mutation of residue T431 reduced binding by about 2-fold, and mutation of the other eight residues – by more than 10-fold. Analysis of these data and the mapping of these mutations on the recently determined crystal structure of a fragment containing the RBD complexed to ACE2 (Li, F, Li, W, Farzan, M, and Harrison, S. C., submitted) suggested the existence of two hot spots on the S RBD surface, R426 and N473, which are likely to contribute significant portion of the binding energy. The finding that most of the mutations (23 out of 34 including glycosylation sites) do not affect the RBD binding function indicates possible mechanisms for evasion of immune responses.
Surface Modification of Photoluminescent CdS Nanocrystals Inducing Spontaneous Phase Transfer Reaction
Authors: Kuwabata Susumu , Sato Keiichi , Hattori Shinya , Chiba Taeko , Ueda-Sarson Keiko , Tachibana Yasuhiro , Torimoto Tsukasa 
Published: August 2005

Abstract
A facile one-step method to modify the surface of luminescent CdS nanocrystals by alkylamines, without their luminescence intensity loss, was established. The interfacial modification inducing spontaneous transfer of the CdS from an aqueous to a non-polar organic phase was found to be controlled simply by choosing the alkyl group of the amine. Analysis of the absorption and emission spectra revealed the phase transfer yield of ca. 100%.
The First RuIIPdII2S3 Metallochelate Ring Formed on a [Ru(bpy)2]2+ Core
Authors: Yoshimura Takashi , Shinohara Atsushi , Hirotsu Masakazu , Konno Takumi 
Published: August 2005

Abstract
The 1:2 reaction of [RuCl2(bpy)2] (bpy = 2,2′-bipyridine) with [Pd(aet)2] (aet = 2-aminoethanethiolate) led to the formation of [Ru(bpy)2{Pd2(aet)3}{Pd(aet)2}]3+ ([1]3+), which was converted into [Ru(bpy)2{Pd2(aet)3}{Pd(aet)(2-aminoethanesulfenato)}]3+ ([1′]3+) and [Ru(bpy)2{Pd2(aet)3Cl}]2+ ([2]2+) having a six-membered RuPd2S3 metallochelate ring.
Bacterial contaminants and antibiotic prophylaxis in total hip arthroplasty
Authors: Al-Maiyah M. , Hill D. , Bajwa A. , Slater S. , Patil P. , Port A. , Gregg P. J. 
Published: August 2005

We have investigated the contaminating bacteria in primary hip arthroplasty and their sensitivity to the prophylactic antibiotics currently in use. Impressions (627) of the gloved hands of the surgical team in 50 total hip arthroplasties were obtained on blood agar. The gloves were changed after draping, at intervals of 20 minutes thereafter, and before using cement. Changes were also undertaken whenever a visible puncture was detected. The culture plates were incubated at 37°C for 48 hours. Isolates were identified and tested for sensitivity to flucloxacillin, which is a recognised indicator of sensitivity to cefuroxime. They were also tested against other agents depending upon their appearance on Gram staining. We found contamination in 57 (9%) impressions and 106 bacterial isolates. Coagulase-negative staphylococci were seen most frequently (68.9%), but we also isolated Micrococcus (12.3%), diphtheroids (9.4%), Staphylococcus aureus (6.6%) and Escherichia coli (0.9%). Of the coagulase-negative staphylococci, only 52.1% were sensitive to flucloxacillin and therefore to cefuroxime. We believe that it is now appropriate to review the relevance of prophylaxis with cefuroxime and to consider the use of other agents.
Impact loading of articular cartilage during transplantation of osteochondral autograft
Authors: Whiteside R. A. , Jakob R. P. , Wyss U. P. , Mainil-Varlet P. 
Published: August 2005

Surgical reconstruction of articular surfaces by transplantation of osteochondral autografts has shown considerable promise in the treatment of focal articular lesions. During mosaicplasty, each cylindrical osteochondral graft is centred over the recipient hole and delivered by impacting the articular surface. Impact loading of articular cartilage has been associated with structural damage, loss of the viability of chondrocytes and subsequent degeneration of the articular cartilage. We have examined the relationship between single-impact loading and chondrocyte death for the specific confined-compression boundary conditions of mosaicplasty and the effect of repetitive impact loading which occurs during implantation of the graft on the resulting viability of the chondrocytes. Fresh bovine and porcine femoral condyles were used in this experiment. The percentage of chondrocyte death was found to vary logarithmically with single-impact energy and was predicted more strongly by the mean force of the impact rather than by the number of impacts required during placement of the graft. The significance of these results in regard to the surgical technique and design features of instruments for osteochondral transplantation is discussed.
Suturing of lacerations of skeletal muscle
Authors: Kragh J. F. , Svoboda S. J. , Wenke J. C. , Ward J. A. , Walters T. J. 
Published: August 2005

Our aim was to compare the biomechanical properties of suturing methods to determine a better method for the repair of lacerated skeletal muscle. We tested Kessler stitches and the combination of Mason-Allen and perimeter stitches. Individual stitches were placed in the muscle belly of quadriceps femoris from a pig cadaver and were tensioned mechanically. The maximum loads and strains were measured and failure modes recorded. The mean load and strain for the Kessler stitches were significantly less than those for combination stitches. All five Kessler stitches tore out longitudinally from the muscle. All five combination stitches did not fail but successfully elongated. Our study has shown that the better method of repair for suturing muscle is the use of combination stitches.
Is there a place for shelf acetabuloplasty in the management of adult acetabular dysplasia?
Authors: Fawzy E. , Mandellos G. , De Steiger R. , McLardy-Smith P. , Benson M. K. D. , Murray D. 
Published: August 2005

We followed up 76 consecutive hips with symptomatic acetabular dysplasia treated by acetabular shelf augmentation for a mean period of 11 years. Survival analysis using conversion to hip replacement as an end-point was 86% at five years and 46% at ten years. Forty-four hips with slight or no narrowing of the joint space pre-operatively had a survival of 97% at five and 75% at ten years. This was significantly higher (p = 0.0007) than that of the 32 hips with moderate or severe narrowing of the joint-space, which was 76% at five and 22% at ten years. There was no significant relationship between survival and age (p = 0.37) or the pre- and post-operative centre-edge (p = 0.39) and acetabular angles (p = 0.85). Shelf acetabuloplasty is a reliable, safe procedure offering medium-term symptomatic relief for adults with acetabular dysplasia. The best results were achieved in patients with mild and moderate dysplasia of the hip with little arthritis.
The effect of recombinant human osteogenic protein-1 on allograft incorporation
Authors: Lietman S. A. , Inoue N. , Rafiee B. , Deitz L. W. , Chao E. Y. S. 
Published: August 2005

We used a canine intercalary bone defect model to determine the effects of recombinant human osteogenic protein 1 (rhOP-1) on allograft incorporation. The allograft was treated with an implant made up of rhOP-1 and type I collagen or with type I collagen alone. Radiographic analysis showed an increased volume of periosteal callus in both test groups compared with the control group at weeks 4, 6, 8 and 10. Mechanical testing after 12 weeks revealed increased maximal torque and stiffness in the rhOP-1 treated groups compared with the control group. These results indicate a benefit from the use of an rhOP-1 implant in the healing of bone allografts. The effect was independent of the position of the implant. There may be a beneficial clinical application for this treatment.
Cementless total hip arthroplasty using a threaded cup and a rectangular tapered stem
Authors: Pospischill M. , Knahr K. 
Published: August 2005

We carried out a clinical and radiological review of 103 cementless primary hip arthroplasties with a tapered rectangular grit-blasted titanium press-fit femoral component and a threaded conical titanium acetabular component at a mean follow-up of 14.4 years (10.2 to 17.1). The mean Harris hip score at the last follow-up was 89.2 (32 to 100). No early loosening and no fracture of the implant were found. One patient needed revision surgery because of a late deep infection. In 11 hips (10.7%), the reason for revision was progressive wear of the polyethylene liner. Exchange of the acetabular component because of aseptic loosening without detectable liner wear was carried out in three hips (2.9%). After 15 years the survivorship with aseptic loosening as the definition for failure was 95.6% for the acetabular component and 100% for the femoral component.
Displacement of the common peroneal nerve in posterolateral corner injuries of the knee
Authors: Bottomley N. , Williams A. , Birch R. , Noorani A. , Lewis A. , Lavelle J. 
Published: August 2005

We reviewed the relationship between the pattern of damage to the posterolateral corner of the knee and the position of the common peroneal nerve in 54 consecutive patients with posterolateral corner disruption requiring surgery. We found that 16 of the 18 patients with biceps avulsions or avulsion-fracture of the fibular head had a displaced common peroneal nerve. The nerve was pulled anteriorly with the biceps tendon. None of the 34 proximal injuries resulted in an abnormal nerve position. Whenever bone or soft-tissue avulsion from the fibular head is suspected, the surgeon should expect an abnormal position of the common peroneal nerve and appreciate the increased risk of iatrogenic damage.