bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the mechanisms of the vertebrate circadian clock: zebrafish may light the way
Authors: Pando Matthew P. , Sassone‐Corsi Paolo 
Published: October 2004

AbstractMost organisms display oscillations of approximately 24 hours in their physiology. In higher organisms, these circadian oscillations in biochemical and physiological processes ultimately control complex behavioral rhythms that allow an organism to thrive in its natural habitat. Daily and seasonal light cycles are mainly responsible for keeping the circadian system properly aligned with the environment. The molecular mechanisms responsible for the control of the circadian clock have been explored in a number of systems. Interestingly, the circadian oscillations that are responsive to environmental stimuli are present very early during development. This review focuses on the advantages of using the zebrafish to study the development of the vertebrate circadian system and light‐dependent signaling to the clock. BioEssays 24:419–426, 2002. © 2002 Wiley Periodicals, Inc.
Binding modes of cyclic AMP and environments of tryptophan residues in 1:1 and 1:2 complexes of cyclic AMP receptor protein and cyclic AMP
Authors: Fujimoto Naoko , Toyama Akira , Takeuchi Hideo 
Published: October 2004

AbstractCyclic AMP (cAMP) receptor protein (CRP) forms 1:1 and 1:2 complexes with cAMP, and the former complex is considered to be the most active form of CRP in binding to specific DNA sequences and in modulating gene transcription by RNA polymerases. We examine the cAMP binding modes and structural changes of CRP upon cAMP binding by UV resonance Raman spectroscopy. The Raman spectra of CRP‐(cAMP)1 and CRP‐(cAMP)2 extracted from those of CRP–cAMP mixtures at varied mixing ratios clearly show that the hydrogen bonding state and the conformation of cAMP in both complexes in solution are very similar to those found in the X‐ray crystal structure of CRP‐(cAMP)2, which is evidence that the cAMP binding mode does not differ between the two complexes. The environmental hydrophobicity of Trp85 monitored by UV resonance Raman intensity shows a significant decrease upon binding of the first cAMP molecule, whereas no further change occurs in the second cAMP binding step. The environmental change of Trp85 suggests an opening of the cleft between the N‐terminal cAMP and C‐terminal DNA binding domains in the process of CRP activation by binding of a single cAMP molecule. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 186–196, 2002
Evidence for nonhydrogen bonded compound II in cyclic reaction of hemoglobin I from Lucina pectinata with hydrogen peroxide
Authors: De Jesús‐Bonilla Walleska , Ramírez‐Meléndez Eunice , Cerda José , López‐Garriga Juan 
Published: October 2004

AbstractStudies that elucidate the behavior of the hemoglobins (Hbs) and myoglobins upon reaction with hydrogen peroxide are essential to the development of oxygen carrier substitutes. Stopped‐flow kinetics and resonance Raman data show that the reaction between hydrogen peroxide and oxygenated and deoxygenated ferric Hb I (oxy‐ and deoxy‐HbI) from Lucina pectinata produce compound I and compound II ferryl species. The rate constants ratio (k23/k41) between the formation of compound II from compound I (k23) and the oxidation of the ferrous HbI (k41, i.e., 25 M−1 s−1) of 12 × 10−4 M suggests that HbI has a peroxidative capacity for removing H2O2 from solution. Resonance Raman presents the formation of both, met‐aquo‐HbI and compound II ferryl species in the cyclic reaction of HbI with H2O2. The ferric HbI species is maintained by the presence of H2O2; it can produce HbI compound I, or it can be reduced to a deoxy‐HbI derivative to form HbI compound II upon reaction with H2O2. The compound II ferryl vibration frequency appears at 805 and 769 cm−1 for HbIFeIV16O and HbIFeIV18O species, respectively. This ferryl mode indicates the absence of hydrogen bonding between the carbonyl group of the distal Q64 and the HbIFeIVO ferryl moiety. The observation suggests that both the trans‐ligand effect and the polarizabilty of the HbI heme pocket are responsible for the observed ferryl oxo vibrational energy. The vibrational mode also suggests that the carbonyl group of the distal Q64 is oriented toward the iron of the heme group, increasing the distal pocket electron density. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 67: 178–185, 2002
Excluded volume effects in gene stretching
Authors: Lam Pui‐Man 
Published: October 2004

AbstractWe investigate the effects excluded volume on the stretching of a single DNA in solution. We find that for small force F, the extension h is not linear in F but proportion to Fγ, with γ = (1 − ν)/ν, where ν is the well‐known universal correlation length exponent. A freely joint chain model with the segment length chosen to reproduce the small extension behavior gives excellent fit to the experimental data of λ‐phage DNA over the whole experimental range. We show that excluded volume effects are stronger in two dimensions and derive results in two dimensions that are different from the three‐dimensional results. This suggests experiments to be performed in these lower dimensions. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 57–62, 2002
Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution
Authors: Aita Takuyo , Hamamatsu Norio , Nomiya Yukiko , Uchiyama Hidefumi , Shibanaka Yasuhiko , Husimi Yuzuru 
Published: October 2004

AbstractWe present a method for analysis of a fitness landscape of a biopolymer with significantly epistatic sites. The analysis is based on a quasi‐additive fitness model. The fitness model is constructed with additive terms conducted by “site‐fitness” and epistatic terms conducted by “pair‐fitness,” where the site‐fitness is a fitness contribution from an independent residue and the pair‐fitness is a fitness contribution from a pair of epistatic residues. As a case study, we analyzed the sequence‐fitness data for 45 clones of thermostable prolyl endopeptidase mutants. They were generated by a mutation scrambling method, which can accumulate advantageous mutations. The fitness contributions from 14 single‐point mutations including E67Q and Q656R were identified by the analysis. As a result, we found that the fitness model with a significant epistatic term by a pair of the 67th site and 656th site was in good agreement with the experimental data and that the explored landscape in the binary 14‐dimensional sequence space is still a mountainous landscape with twin peaks. The validity was supported by the analysis of mutant fitness distributions derived from another mutation scrambling experiment and by (3D) structural data. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 95–105, 2002
Monte Carlo study of cycloamylose: Chain conformation, radius of gyration, and diffusion coefficient
Authors: Nakata Yasushi , Norisuye Takashi , Kitamura Shinichi 
Published: October 2004

AbstractCyclic (1 → 4)‐α‐D‐glucan chains with or without excluded volume have been collected from a huge number (about 107) of linear amylosic chains generated by the Monte Carlo method with a conformational energy map for maltose, and their mean‐square radii of gyration 〈S2〉 and translational diffusion coefficients D (based on the Kirkwood formula) have been computed as functions of x (the number of glucose residues in a range from 7 to 300) and the excluded‐volume strength represented by the effective hard‐core radius. Both 〈S2〉/x and D in the unperturbed state weakly oscillate for x < 30 and the helical nature of amylose appears more pronouncedly in cyclic chains than in linear chains. As x increases, these properties approach the values expected for Gaussian rings. Though excluded‐volume effects on them are always larger in cycloamylose than in the corresponding linear amylose, the ratios of 〈S2〉 and the hydrodynamic radius of the former to the respective properties of the latter in good solvents can be slightly lower than or comparable to the (asymptotic) Gaussian‐chain values when x is not sufficiently large. An interpolation expression is constructed for the relation between the gyration‐radius expansion factors for linear and cyclic chains from the present Monte Carlo data and the early proposed asymptotic relation with the aid of the first‐order perturbation theories. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 72–79, 2002
Strategies for manipulating the relative concentration of recombinant rotavirus structural proteins during simultaneous production by insect cells
Authors: Palomares Laura A. , López Susana , Ramírez Octavio T. 
Published: October 2004

AbstractAdequate production strategies of virus‐like particles are among the challenges that must be addressed before such complex multimeric structures find practical applications as vaccines. Attainment of the correct stoichiometric relation between proteins that constitute virus‐like particles should result in an increased productivity by maximizing the concentration of assembled proteins and preventing the accumulation of waste monomers. In this work, strategies for manipulating the relative concentration between two of the structural proteins that constitute rotavirus‐like particles (VP2 and VP6) were explored using the insect cell baculovirus expression vector system. It was shown that multiplicity of infection is a useful tool for manipulating protein production rates and maximum concentrations in cultures expressing one or two recombinant proteins. Thus, multiplicity of infection can be employed for improving production of rotavirus‐like particles. VP2 and VP6 production rates obtained during individual infections remained unchanged when both were simultaneously produced, indicating that such rates can be utilized for estimating protein concentrations during coexpression. Manipulation of the time of infection between the two recombinant baculoviruses, proposed here for the first time, also proved to be effective for controling the relative protein concentrations. The use of such sequential infections constituted an effective production alternative that does not require high amounts of virus stocks and is easy to implement. In addition to VP2 and VP6, kinetic parameters for the individual production of the other two proteins (VP4 and VP7) that constitute rotavirus‐like particles were also obtained. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 635–644, 2002.
A kinetic model for surfactant inhibition of pentachlorophenol biodegradation
Authors: Cort Todd L. , Bielefeldt Angela R. 
Published: October 2004

AbstractA kinetic model is used to describe the effect of the nonionic surfactant Tergitol NP‐10 (TNP10) on pentachlorophenol (PCP) biodegradation by Sphingomonas chlorophenolica sp. strain RA2. Different initial biomass to initial substrate ratios ranging from 13 to 418 were tested with 23 TNP10 concentrations ranging from 0 to 1500 mg/L. Tests were also conducted at 10°C and 20°C. No PCP biodegradation inhibition was observed at concentrations below the critical micelle concentration (CMC) of 50 mg/L. TNP10 concentrations above 100 to 200 mg/L were increasingly inhibitory to PCP biodegradation rates. This inhibition was best described by the Monod kinetic equation wherein the effect of TNP10 inhibition is reflected in the half‐saturation constant (Ks). The value of the Ks increased from between 1.5 and 13.5 mg/L with no surfactant present to 44 to 131 mg/L at 1000 mg/L TNP10. Using a standard competitive inhibition approach, the inhibition constant for TNP10 was approximately 100 mg/L at both 10°C and 20°C. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 606–616, 2002.
Measuring the pH environment of DNA delivered using nonviral vectors: Implications for lysosomal trafficking
Authors: Akinc Akin , Langer Robert 
Published: October 2004

AbstractThe degradation of DNA in lysosomes represents a major obstacle to efficient nonviral gene delivery. The rational design of vectors that overcome this obstacle requires a better understanding of the lysosomal barrier to gene delivery, which in turn requires a means to investigate this intermediate step. To this end, we developed a technique to measure the pH environment of delivered DNA, from which the degree to which vectors avoided trafficking to acidic Iysosomes could be determined. The measured average pH of DNA delivered using poly‐L‐lysine (PLL) polyplexes was 4.5, suggesting that PLL polyplexes were trafficked to acidic lysosomes. Other vectors could avoid or buffer the pH of Iysosomes as DNA delivered using Lipofectamine Plus, polyethylenimine (PEI), linear polyethylenimine (LPEI), and two degradable poly(β‐amino ester)s (poly‐1 and poly‐2) had average pH values of 7.1, 5.9, 5.0, 6.7, and 6.4, respectively. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 78: 503–508, 2002.
Microsurgical anatomy of the facial nerve trunk
Authors: Salame K. , Ouaknine G.E.R. , Arensburg B. , Rochkind S. 
Published: October 2004

AbstractDissection and manipulation of the facial nerve (FN) trunk between its exit from the cranial base through the stylomastoid foramen (SMF) and its bifurcation is a critical step in various otologic, plastic and neurosurgical procedures. This study demonstrates the anatomical relationships and variability of the FN trunk with emphasis on some important morphometric data, particularly with relevance to hypoglossal‐facial nerve anastomosis (HFA). Bilateral microsurgical dissection was performed on twenty‐three human cadavers fixed with formalin. The whole trunk of the FN was exposed, its diameter at the SMF and its length were measured, its branches were observed and the site of its bifurcation was determined. Anastomotic connections with other nerves and blood supply of the trunk were studied. The FN invariably emerged from the cranial base through the SMF. Its diameter upon its emergence from the foramen was 2.66 ± 0.55 mm. Two branches consistently originated from the trunk: the posterior auricular nerve and the nerve to the digastric muscle. Less consistent were the communicating branch with the glossopharyngeal nerve and the nerve to the stylohyoid muscle. The bifurcation of the FN occurred before its penetration into the parotid gland in 15% of cases and within the gland in 85%. The length of the FN trunk was 16.44 ± 3.2 mm. Anastomoses between the FN and other nerves were observed in one‐third of the dissections. The blood supply to the FN trunk was provided by the stylomastoid artery that was identified in 91% of cases. Understanding the microsurgical anatomy of the FN trunk is essential for performing any surgical procedure in the relevant region. Surgical implications of this study are presented with emphasis on HFA surgery. Clin. Anat. 15:93–99, 2002. © 2002 Wiley‐Liss, Inc.
Variability in human quadriceps muscles: Quantitative study and review of clinical literature
Authors: Willan P.L.T. , Ransome J.A. , Mahon M. 
Published: October 2004

AbstractKnowledge of variations in normal human thigh musculature is important for the interpretation of various clinical and biomedical investigations. In this study, cross‐sections from whole thighs of 34 cadavers were analyzed qualitatively and morphometrically. Sections were cut from right and left limbs at three levels in the region often used for muscle biopsy. Measurements were made of limb circumferences and cross‐sectional areas of the three vasti and of the femur, and of the extent of overlap and fusion between the vasti on the lateral aspect of the thigh. Limb circumference proved to be a good predictor of total cross‐sectional area of the quadriceps muscle. Large individual variations were found for most measurements but especially for the amount of fusion between the muscle bellies of vastus lateralis and vastus intermedius. Significant differences were found for most variables between the three levels, but there were few differences between sides except for the cross‐sectional area of vastus lateralis which was greater on the right at the most distal level. These variations in size and form of thigh musculature should be considered when interpreting data obtained from muscle biopsy, imaging, biomechanical, electromyographic, and functional studies of the human thigh. Review of the literature on variability of quadriceps muscle and its clinical relevance showed a diversity of approaches but insufficient definitive data suitable for interpreting functional outcomes in response to exercise or following surgery. Further work is suggested combining current anatomical datasets with advanced imaging techniques capable of determining muscle fiber orientation and fiber type composition, and including 3D reconstruction. Clin. Anat. 15:116–128, 2002. © 2002 Wiley‐Liss, Inc.
Intramuscular Martin‐Gruber anastomosis
Authors: Rodriguez‐Niedenführ Marc , Vazquez Teresa , Ferreira Bartolome , Parkin Ian , Nearn Lynette , Sañudo Jose R. 
Published: October 2004

AbstractThe incidence and morphology of the intramuscular Martin‐Gruber anastomosis are presented based on the study of 118 human cadavers (55 male, 63 female).The Martin‐Gruber anastomosis was found in 25 (21.2%) of the 118 cadavers. It occurred in 11 (20%) of the 55 male cadavers (4 bilateral, 7 unilateral; 5 left and 2 right) and in 14 (22.2%) of the 63 female cadavers (2 bilateral, 12 unilateral; 8 left and 4 right). Therefore, the Martin‐Gruber anastomosis was found in 31 (13.1%) of the 236 upper limbs. According to a recent classification (Rodríguez‐Niedenführ et al., 2000), pattern I was found in 29 cases (93.5%), corresponding to Type A in 13 (41.9%), Type B in 3 (9.7%) and Type C in 13 (41.9%), whereas pattern II was found in 2 cases (6.5%), both being a duplication of Type IC. Intramuscular Martin‐Gruber anastomosis was a single anastomosis that originated in all cases from the anterior interosseous nerve (pattern IC) and then passed through a muscle bundle of the flexor digitorum profundus and behind the ulnar artery to join the ulnar nerve as a single connecting branch. It did not send branches to the flexor digitorum profundus. This intramuscular course was observed in 3 of the 13 cases of Type C anastomosis (23.1%) or 3 cases out of 31 Martin‐Gruber anastomoses (10%). Clin. Anat. 15:135–138, 2002. © 2002 Wiley‐Liss, Inc.
Approach to the educational opportunities provided by variant anatomy, illustrated by discussion of a duplicated inferior vena cava
Authors: Zucconi William B. , Guelfguat Mark , Solounias Nikos 
Published: October 2004

AbstractVariant anatomy recognized during routine cadaveric dissection in the first year of medical school offers great learning potential by allowing students to gain enhanced understanding of an array of important subjects. It provides a framework for reviewing common morphology and embryogenesis of the structure in question, and through the help of appropriate faculty, yields insight into the potential medical, radiologic, and surgical implications. The frequency of clinically important anatomic variation is high enough to allow the gross anatomy laboratory to serve as an excellent teaching platform in this regard. Through anatomy, the student is introduced to the concept of patient individuality, and to the individualization of medical and surgical therapies. Recently, one of the variations encountered in our lab was a duplicated inferior vena cava. We describe our approach to such findings through a systematic discussion of the anatomy and embryology, as well as the radiologic and clinical correlates. Clin. Anat. 15:165–168, 2002. © 2002 Wiley‐Liss, Inc.
Endovascular treatment of the subclavian artery: Stent implantation with or without predilatation
Authors: Amor Max , Eid‐Lidt Guering , Chati Zukai , Wilentz James R. 
Published: October 2004

AbstractThe endovascular treatment of subclavian artery (SA) lesions is less invasive than open surgical repair, with a low rate of complications. We report our experience in 89 subclavian obstructive lesions (n = 86) treated with stenting: 76 (85.3%) stenoses and 13 (14.6%) total occlusions. The left side was most frequently involved (83.1%), localized at the prevertebral segment in 91%. Technical success was obtained in 83 (93.3%) cases, 100% in stenotic lesions and 53.8% in total occlusions. There were nine global complications (10.1%): five (5.6%) at site of puncture, two distal embolization (2.2%), and two (2.3%) major events. The long‐term follow‐up was 3.51 ± 1.98 years, during which time 13 (16.8%) restenoses and 2 (2.6%) reocclusions were noted. Subgroup analysis of patients with stenting after predilatation versus direct stenting technique showed in‐hospital complications only in the first group, with a restenosis rate of 28.5% vs. 4.7%, respectively (P = 0.003). We consider stenting for SA obstructive lesions the first therapeutic option. Cathet Cardiovasc Interv 2004;63:364–370. © 2004 Wiley‐Liss, Inc.
Initial clinical experience with intracardiac echocardiography in guiding balloon mitral valvuloplasty: Technique, safety, utility, and limitations
Authors: Green Nathan E. , Hansgen Adam R. , Carroll John D. 
Published: October 2004

AbstractThe objective of this study was to examine the feasibility and technique of intracardiac echocardiography during percutaneous balloon mitral valvuloplasty. Echocardiographic imaging is commonly used during mitral valvuloplasty. Intracardiac echocardiography is a newer technology that may provide superior imaging during complex valvular interventions. Intracardiac echocardiography and transthoracic echocardiography were performed in 19 patients undergoing percutaneous balloon mitral valvuloplasty. Intracardiac ultrasound images were obtained via the femoral vein in all patients. Imaging projections and catheter locations that were useful for the performance of mitral valvuloplasty were defined. Intracardiac echocardiography guided transseptal puncture, augmented the assessment of valve apparatus deformity, facilitated balloon positioning across the mitral valve, and permitted postprocedural valvular assessment including identification of mitral regurgitation with color Doppler. Intracardiac echocardiography provided essential imaging guidance and procedural monitoring during percutaneous mitral valvuloplasty. Cathet Cardiovasc Interv 2004;63:385–394. © 2004 Wiley‐Liss, Inc.
High‐output congestive heart failure successfully treated with transcatheter coil embolization of a large renal arteriovenous fistula
Authors: Bates Mark C. , Almehmi Ammar 
Published: October 2004

AbstractLeft heart catheterization was performed in response to progressive congestive heart failure of uncertain etiology in a 59‐year‐old male. The coronary arteries were normal but screening abdominal aortography revealed a large arterial venous communication between the left inferior segmental renal artery and the ipsilateral renal vein. The massive size and brisk flow patterns in the fistula presented technical challenges for transcatheter closure. The use of multiple Amplatz vascular obstructive devices (spiders) to create a matrix for securing subsequent coils in staged procedures and the patient's progress following successful closure are discussed. Cathet Cardiovasc Intervent 2004;63:373–376. © 2004 Wiley‐Liss, Inc.
Infective endocarditis after transcatheter closure of a patent foramen ovale
Authors: Calachanis Marco , Carrieri Luisella , Grimaldi Roberto , Veglio Franco , Orzan Fulvio 
Published: October 2004

AbstractInfection of devices for percutaneous transcatheter closure of atrial septal defects are exceedingly rare. Two cases of device‐associated endocarditis have been reported, which were both operated on. We describe the successful treatment with antibiotics of a device‐associated endocarditis. Catheter Cardiovasc Interv 2004;63:351–354. © 2004 Wiley‐Liss, Inc.