bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bone morphogenetic protein expression in newborn rat kidneys after prenatal exposure to radiofrequency radiation
Authors: Pyrpasopoulou Athina , Kotoula Vassiliki , Cheva Angeliki , Hytiroglou Prodromos , Nikolakaki Eleni , Magras Ioannis N. , Xenos Thomas D. , Tsiboukis Theodoros D. , Karkavelas Georgios 
Published: March 2004

AbstractEffects of nonthermal radiofrequency radiation (RFR) of the global system of mobile communication (GSM) cellular phones have been as yet mostly studied at the molecular level in the context of cellular stress and proliferation, as well as neurotransmitter production and localization. In this study, a simulation model was designed for the exposure of pregnant rats to pulsed GSM‐like RFR (9.4 GHz), based on the different resonant frequencies of man and rat. The power density applied was 5 μW/cm2, in order to avoid thermal electromagnetic effects as much as possible. Pregnant rats were exposed to RFR during days 1–3 postcoitum (p.c.) (embryogenesis, pre‐implantation) and days 4–7 p.c. (early organogenesis, peri‐implantation). Relative expression and localization of bone morphogenetic proteins (BMP) and their receptors (BMPR), members of a molecular family currently considered as major endocrine and autocrine morphogens and known to be involved in renal development, were investigated in newborn kidneys from RFR exposed and sham irradiated (control) rats. Semi‐quantitative duplex RT‐PCR for BMP‐4, ‐7, BMPR‐IA, ‐IB, and ‐II showed increased BMP‐4 and BMPR‐IA, and decreased BMPR‐II relative expression in newborn kidneys. These changes were statistically significant for BMP‐4, BMPR‐IA, and ‐II after exposure on days 1–3 p.c. (P < .001 each), and for BMP‐4 and BMPR‐IA after exposure on days 4–7 p.c. (P < .001 and P = .005, respectively). Immunohistochemistry and in situ hybridization (ISH) showed aberrant expression and localization of these molecules at the histological level. Our findings suggest that GSM‐like RFR interferes with gene expression during early gestation and results in aberrations of BMP expression in the newborn. These molecular changes do not appear to affect renal organogenesis and may reflect a delay in the development of this organ. The differences of relative BMP expression after different time periods of exposure indicate the importance of timing for GSM‐like RFR effects on embryonic development. Bioelectromagnetics 25:216–227, 2004. © 2004 Wiley‐Liss, Inc.
Influence of anesthesia on ocular effects and temperature in rabbit eyes exposed to microwaves
Authors: Kojima Masami , Hata Ikuho , Wake Kanako , Watanabe So‐ichi , Yamanaka Yukio , Kamimura Yoshitsugu , Taki Masao , Sasaki Kazuyuki 
Published: March 2004

AbstractTo investigate the effect of systemic anesthesia on ocular effects and temperature in rabbit eyes exposed to microwaves, one eye each of 43 male pigmented rabbits (Dutch, 1.8–2.2 kg) was exposed at 2.45 GHz for 60–20 min (300 mW/cm2; 108 W/kg), either under anesthesia (ketamine hydrochloride (5 mg/kg) + xylazine (0.23 mg/kg)) or without anesthesia. Changes in the anterior segment were evaluated by image analysis utilizing a Scheimpflug camera, specular microscopy, and a laser flare cell meter. Temperatures within the eye were measured during microwave exposure by a Fluoroptic thermometer. The exposed eyes showed miosis, conjunctival congestion, corneal edema, and an increase in the light scattering of the anterior shallow cortex in the pupillary area of the lens. The group under systemic anesthesia showed much stronger symptoms than those treated without anesthesia. All of the anterior ocular changes disappeared within a week. The highest temperature during exposure was in the vitreous, followed by the anterior chamber, and the retrobulbar cavity of the orbit. The ocular temperatures of the rabbits under systemic anesthesia were 2–9 °C higher than those without anesthesia. Body temperature showed an increase of 1 °C during the exposure. Acute high intensity microwave exposure temporarily induced anterior segments inflammation and lens changes. The more pronounced ocular effects in the anesthetized rabbits were associated with the significantly higher ocular temperatures in the anesthetized animals. The influence of systemic anesthesia on ocular changes should be considered. Bioelectromagnetics 25:228–233, 2004. © 2004 Wiley‐Liss, Inc.
Brownian dynamics of interactions between glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) mutants and F‐actin
Authors: Waingeh Victor F. , Lowe Stephen L. , Thomasson Kathryn A. 
Published: March 2004

AbstractBrownian dynamics simulations of computer models of GAPDH mutants interacting with F‐actin emphasized the electrostatic nature of such interactions, and confirmed the importance of four previously identified lysine residues on the GAPDH structure (Ouporov, I.V.; Knull, H.R.; Lowe, S.L.; Thomasson, K.A. J Mol Recognit 2001, 14, 29–41) in these interactions. Mutants were GAPDH models in which one or more of the previously identified lysines had been replaced with alanine. Simulations showed reduced binding of these mutants to F‐actin compared to wild‐type GAPDH. Binding was significantly reduced by mutating the four lysines; the specific electrostatic interaction energy of the quadruple mutant was −7.3 ± 1.0 compared to −11.4 ± 0.5 kcal/mol for the wild enzyme. The BD simulations also reaffirmed the importance of quaternary structure for GAPDH binding F‐actin. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Molecular dynamics simulation study of oriented polyamine‐ and Na‐DNA: Sequence specific interactions and effects on DNA structure
Authors: Korolev Nikolay , Lyubartsev Alexander P. , Laaksonen Aatto , Nordenskiöld Lars 
Published: March 2004

AbstractMolecular dynamics (MD) computer simulations have been carried out on four systems that correspond to an infinite array of parallel ordered B‐DNA, mimicking the state in oriented DNA fibers and also being relevant for crystals of B‐DNA oligonucleotides. The systems were all comprised of a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charges. The sequence of the double helical DNA decamer was d(5′‐ATGCAGTCAG)×d(5′‐TGACTGCATC). The counterions were the two natural polyamines spermidine3+ (Spd3+) and putrescine2+ (Put2+), the synthetic polyamine diaminopropane2+ (DAP2+), and the simple monovalent cation Na+. This work compares the specific structures of the polyamine‐ and Na‐DNA systems and how they are affected by counterion interactions. It also describes sequence‐specific hydration and interaction of the cations with DNA. The local DNA structure is dependent on the nature of the counterion. Even the very similar polyamines, Put2+ and DAP2+, show clear differences in binding to DNA and in effect on hydration and local structure. Generally, the polyamines disorder the hydration of the DNA around their binding sites whereas Na+ being bound to DNA attracts and organizes water in its vicinity. Cation binding at the selected sites in the minor and in the major groove is compared for the different polyamines and Na+. We conclude that the synthetic polyamine (DAP2+) binds specifically to several structural and sequence‐specific motifs on B‐DNA, unlike the natural polyamines, Spd3+ and Put2+. This specificity of DAP2+ compared to the more dynamic behavior of Spd3+ and Put2+ may explain why the latter polyamines are naturally occurring in cells. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Cyclic peptide interleukin 5 antagonists mimic CD turn recognition epitope for receptor α
Authors: Ruchala Piotr , Varadi Gyorgyi , Ishino Tetsuya , Scibek Jeffery , Bhattacharya Madhushree , Urbina Cecilia , Ryk Donald Van , Uings Iain , Chaiken Irwin 
Published: March 2004

AbstractThe cyclic peptide AF17121 (Ac‐VDECWRIIASHTWFCAEE) that inhibits interleukin 5 (IL‐5) function and IL‐5 receptor α‐chain (IL‐5Rα) binding has been derived from recombinant random peptide library screening and follow‐up synthetic variation. To better understand the structural basis of its antagonist activity, AF17121 and a series of analogs of the parent peptide were prepared by solid phase peptide synthesis. Sequence variation was focused on the charged residues Asp2, Glu3, Arg6, Glu17, and Glu18. Two of those residues, Glu3 and Arg6, form an EXXR motif that was found to be common among library‐derived IL‐5 antagonists. The E and R in the EXXR motif have a proximity similar to charged residues in a previously identified receptor α binding region, the β‐strand between the C‐ and D‐helices of human IL‐5. Optical biosensor interaction kinetics and cell proliferation assays were used to evaluate the antagonist activities of the purified synthetic peptides, by measuring competition with the highly active single chain IL‐5. Analogs in which acidic residues (Asp2, Glu3, Glu17, and Glu18) were replaced individually by Ala retained substantial competition activity, with multiple replacements in these residues leading to fractional loss of potency at most. In contrast, R6A analogs had strongly reduced competition activity. The results reveal that the arginine residue is crucial for the IL‐5Rα binding of AF17121, while the acidic residues are not essential though likely complex‐stabilizing particularly in the Asp2–Glu3 region. By CD, AF17121 exhibited mostly disordered structure with evidence for a small β‐sheet content, and replacement of the arginine had no influence on the observed secondary structure of the peptides. The dominance of Arg6 in AF17121 activity corresponds to previous findings of dominance of the positive charge balance in the antiparallel β‐sheet of IL‐5 composed of 88EERRR92 in one strand of the CD turn region of IL‐5 and with Arg32 in the neighboring β‐strand. These results argue that AF17121 and related library‐derived peptides function by mimicking the CD turn receptor α recognition epitope in IL‐5 and open the way to small molecule antagonist design. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Determination of stress‐induced changes in plasma molecular species by two‐dimensional correlation Fourier transform infrared spectrometry
Authors: Petibois Cyril , Desbat Bernard , Déléris Gérard 
Published: March 2004

AbstractFor determining exercise‐induced changes in plasma molecular species, we investigated the feasibility of using two‐dimensional correlation spectra (2D‐COS) on 21 series of plasma samples obtained from progressive exercise tests. Intensities of 2D synchronous and asynchronous correlation peaks were compared to concentration evolutions of glucose, lactate, triglycerides (TG), glycerol, fatty acyl moieties, amino acids, proteins, and albumin [determined from plasma Fourier transform infrared (FTIR) spectra] and to performance and training levels of athletes. Synchronous 2D‐COS allowed us to determine the linear relationship between protein and fatty acid concentration evolutions as exercise intensity increased (ν1 − ν2; 2959 vs 1656 and 1543 cm−1). Asynchronous 2D‐COS allowed differentiation of fibrinolysis level in subjects during intense exercise, as well as parameters of fatty acid metabolism specifically related either to performance or to training levels. Furthermore, unexpected correlated evolutions of molecular species were highlighted by this method, showing that 2D spectrometry may also be used for experimental investigations on human physiology. This study has demonstrated that 2D‐COS may be used for the treatment of complex biological samples, such as plasma. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Study of protein aggregation using two‐dimensional correlation infrared spectroscopy and spectral simulations
Authors: Lefèvre Thierry , Arseneault Karin , Pézolet Michel 
Published: March 2004

AbstractTwo‐dimensional (2D) correlation spectroscopy establishes correlations between intensity variations in a series of spectra obtained by the application of an external perturbation. However, spectral effects (wavenumber shift or bandwidth change) are known to generate apparent asynchronisms in 2D maps. Surprisingly, spectral effects are often neglected in the literature when interpreting experimental maps, which can lead to erroneous conclusions. In an attempt to evaluate the contribution of these effects and that of true asynchronisms on 2D maps, the heat‐induced aggregation of glutamyl‐tRNA synthetase (GluRS) was studied as a typical example of the application of Fourier transform infrared (FTIR) spectroscopy in the amide I region. The data were compared with those obtained from a mutant protein that differs by one amino acid. To determine whether the aggregation mechanisms are identical for both proteins, the experimental 2D maps were compared to simulations based on curve fitting of the initial and final spectra of the series, which allows change in position and bandwidth of the components to be taken into account. Intermediate spectra were generated using a convenient function that mimics the spectral evolution. The speed and the delay of each component were controlled. Apart from the appearance of turns that occur for the mutant and not for GluRS, the aggregation mechanisms of both proteins seems to be essentially identical. In particular, the loss of α‐helices seems to be concomitant with the formation of intermolecular β‐sheets, whereas the loss of intramolecular β‐sheets is delayed. Since the experimental maps are satisfactorily simulated when almost all the components are in phase, it appears that many of the asynchronous features are mainly due to spectral effects. Thus, one has to be aware that true asynchronisms are not necessarily at the origin of peaks observed in asynchronous maps. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Population shift vs induced fit: The case of bovine seminal ribonuclease swapping dimer
Authors: Merlino Antonello , Vitagliano Luigi , Sica Filomena , Zagari Adriana , Mazzarella Lelio 
Published: March 2004

AbstractBovine seminal ribonuclease (BS‐RNase) is a unique member of the pancreatic‐like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N‐terminal segment (M×M BS‐RNase). In this article, the crystal structures of the ligand‐free M×M BS‐RNase and its complex with 2′‐deoxycitidylyl(3′,5′)‐2′‐deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand‐free form and the previously published sulfate‐bound structure reveals significant differences. In particular, the ligand‐free M×M BS‐RNase is closer to the structure of M×M BS‐RNase productive complexes than to the sulfate‐bound form. These results reveal that M×M BS‐RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N‐terminal helices. These findings have important implications to the ligand binding mechanism of M×M BS‐RNase. Indeed, a population shift rather than a substrate‐induced conformational transition may occur in the M×M BS‐RNase ligand binding process. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
An algebraic model of RNA duplex formation
Authors: Bashford J. D. , Jarvis P. D. 
Published: March 2004

AbstractWe propose a simple algebraic description of the two‐body interactions of bases in RNA thermodynamics showing in detail qualitative equivalence with conventional nearest‐neighbor models. The process of obtaining base content, polymer, and oligomer parameters is illustrated, and for duplexes containing Watson–Crick pairs, fits to oligonucleotide duplex heat‐of‐formation data are shown to be statistically equivalent to existing models. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Water‐mediated contacts in thetrp‐repressor operator complex recognition process
Authors: Wibowo Fajar R. , Rauch Christine , Trieb Michael , Wellenzohn Bernd , Liedl Klaus R. 
Published: March 2004

AbstractWater‐mediated contacts are known as an important recognition tool intrp‐repressor operator systems. One of these contacts involves two conserved base pairs (G6· C−6and A5· T−5) and three amino acids (Lys 72, Ile 79, and Ala 80). To investigate the nature of these contacts, we analyzed the X‐ray structure (PDB code: 1TRO) of thetrp‐repressor operator complex by means of molecular dynamics simulations. This X‐ray structure contains two dimers that exhibit structural differences. From these two different starting structures, two 10 ns molecular dynamics simulations have been performed. Both of our simulations show an increase of water molecules in the major groove at one side of the dimer, while the other side remains unchanged compared to the X‐ray structure. Though the maximum residence time of the concerned water molecules decreases with an increase of solvent at the interface, these water molecules continue to play an important role in mediating DNA–protein contacts. This is shown by new stable amino acids–DNA distances and a long water residence time compared to free DNA simulation. To maintain stability of the new contacts, the preferential water binding site on O6(G6) is extended. This extension agrees with mutation experiment data on A5and G6, which shows different relative affinity due to mutation on these bases [A. Joachimiak, T. E. Haran, P. B. Sigler,EMBOJournal 1994, Vol. 13, No. (2) pp. 367–372]. Due to the rearrangements in the system, the phosphate of the base G6is able to interconvert to the BIIsubstate, which is not observed on the other half side of the complex. The decrease of the number of hydrogen bonds between protein and DNA backbone could be the initial step of the dissociation process of the complex, or in other words an intermediate complex conformation of the association process. Thus, we surmise that these features show the importance of water‐mediated contacts in thetrp‐repressor operator recognition process. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Synthesis, conformation, and immunoreactivity of new carrier molecules based on repeated tuftsin‐like sequence
Authors: Mezö Gábor , Kalászi Adrián , Reményi Judit , Majer Zsuzsa , Hilbert Ágnes , Láng Orsolya , Köhidai László , Barna Krisztina , Gaál Dezsö , Hudecz Ferenc 
Published: March 2004

AbstractSequential oligopeptides based on a pentapeptide (TKPKG) derived from tuftsin with different lengths were synthesized by stepwise solid phase methodology. These highly soluble oligomers were nontoxic on mouse spleen cells, and other biological data suggested that tuftsin‐like properties were also presented. The (TKPKG)n (n=2,4,6,8) oligopeptides were not immunogenic; however, they increased sheep red blood cells (SRBC) antigen specific antibody response in mice, demonstrating their immunostimulatory effect. Chemotactic activity was also found on J774 monocyte cells, while MRC5 fibroblasts were chemotactically nonresponders to the tested forms of tuftsin. These oligomers showed unordered and flexible structure by CD measurements, confirmed by computer modeling studies indicating also a fairly good accessibility of the ϵ‐amino group of each lysine residue. Data suggest that these new oligotuftsin derivatives can be considered as promising carriers for synthetic vaccine. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Influence of laparoscopy on postoperative recurrence and survival in patients with ruptured hepatocellular carcinoma undergoing hepatic resection
Authors: Lang B H H , Poon R T P , Fan S T , Wong J 
Published: March 2004

AbstractBackgroundUse of laparoscopy in patients with gastrointestinal cancer has been associated with port-site and peritoneal tumour metastases. The effect of laparoscopy on tumour recurrence and long-term survival in patients undergoing resection of ruptured hepatocellular carcinoma (HCC) remains unknown.MethodsBetween June 1994 and December 2001, 59 patients with ruptured HCC underwent surgical exploration with a view to hepatic resection. Laparoscopy with laparoscopic ultrasonography was performed in 33 patients; the other 26 patients underwent exploratory laparotomy without laparoscopy. Perioperative and long-term outcomes were compared between the two groups.ResultsExploratory laparotomy was avoided in 12 of 13 patients with irresectable HCC who had a laparoscopy. The hospital stay of these 12 patients was significantly shorter than that of eight patients found to have irresectable HCC at exploratory laparotomy (median 11 versus 15 days; P = 0·043). Twenty patients had a laparoscopy followed by open resection of HCC, whereas 18 patients underwent laparotomy and resection without laparoscopy. There were no significant differences in disease-free (16 versus 19 per cent; P = 0·525) and overall (32 versus 48 per cent; P = 0·176) survival at 3 years between the two groups. The tumour recurrence pattern was similar between the two groups, and there were no port-site or wound metastases.ConclusionUse of diagnostic laparoscopy in patients with ruptured HCC helps avoid unnecessary exploratory laparotomy. The present data suggest that laparoscopy does not have an adverse effect on tumour recurrence or survival in patients who undergo resection.
Routine use of laparoscopic repair for perforated peptic ulcer
Authors: Siu W T , Chau C H , Law B K B , Tang C N , Ha P Y , Li M K W 
Published: March 2004

Abstract

Background
Laparoscopic repair of perforated peptic ulcer was reported in 1990 but has not gained wide acceptance. The aim of this study was to evaluate the safety and efficacy of laparoscopic repair for perforated peptic ulcer in routine clinical practice.

Methods
This was a prospective analysis of 172 patients who underwent laparoscopic repair of a perforated peptic ulcer between July 1997 and June 2003.

Results
One hundred and seventy-two patients of mean age 54 (range 14–93) years had perforated peptic ulcer diagnosed by laparoscopy. There were 172 duodenal ulcers, 22 prepyloric and 13 non-juxtapyloric gastric ulcers. One hundred and sixty-five patients underwent omental patch closure of perforations; there were six Pólya gastrectomies and one ulcerectomy. Thirty-seven patients (21·5 per cent) required conversion to laparotomy. The mean operating time was 64·8 (range 14–180) min. The median postoperative requirement for intramuscular pethidine was one dose. The median postoperative hospital stay was 6 days. Complications occurred in 28 patients (16·3 per cent) resulting in three reoperations. Six patients with intra-abdominal collections were managed by percutaneous drainage. Two patients who underwent conversion developed a wound infection. Fourteen patients (8·1 per cent) died, 11 of whom were American Society of Anesthesiologists grade III and IV.

Conclusion
Laparoscopic repair of perforated peptic ulcer is a safe emergency procedure in routine clinical practice for patients with perforated pyloroduodenal ulcer.