bluuebunny/crossref_metadata_2025_split huggingface dataset:
YAKUSA: A fast structural database scanning method
Authors: Carpentier Mathilde , Brouillet Sophie , Pothier Joël 
Published: July 2005

AbstractYAKUSA is a program designed for rapid scanning of a structural database with a query protein structure. It searches for the longest common substructures called SHSPs (structural high‐scoring pairs) existing between a query structure and every structure in the structural database. It makes use of protein backbone internal coordinates (α angles) in order to describe protein structures as sequences of symbols. The structural similarities are established in 5 steps, the first 3 being analogous to those used in BLAST: (1) building up a deterministic finite automaton describing all patterns identical or similar to those in the query structure; (2) searching for all these patterns in every structure in the database; (3) extending the patterns to longer matching substructures (i.e., SHSPs); (4) selecting compatible SHSPs for each query–database structure pair; and (5) ranking the query–database structure pairs using 3 scores based on SHSP similarity, on SHSP probabilities, and on spatial compatibility of SHSPs. Structural fragment probabilities are estimated according to a mixture transition distribution model, which is an approximation of a high‐order Markov chain model. With regard to sensitivity and selectivity of the structural matches, YAKUSA compares well to the best related programs, although it is by far faster: A typical database scan takes about 40 s CPU time on a desktop personal computer. It has also been implemented on a Web server for real‐time searches. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Novel cyclic azo‐bridged analogs of gonadotropin‐releasing hormone
Authors: Fridkin Gil , Rahimipour Shai , Ben‐Aroya Nurit , Kapitkovsky Aviva , Di‐Segni Susanna , Rosenberg Masha , Kustanovich Irina , Koch Yitzhak , Gilon Chaim , Fridkin Mati 
Published: August 2005

AbstractFive linear analogs of GnRH containing a p‐aminophenylalanine (Pap) residue in their sequence and their six corresponding azo‐bridged cyclic derivatives were synthesized. The precyclic peptides were prepared on solid‐support, while azo‐cyclization was performed in solution by diazotization of the p‐aminophenylalanine residue followed by intramolecular coupling of the formed diazo salt with either tyrosine or histidine side chains present in the sequence. All peptides were examined for their binding ability to the GnRH receptor expressed on rat pituitary membranes and for their LH‐release activity from dispersed rat pituitary cells. Linear analogs 1 i.e [Pap5] GnRH and 3, i.e. [Tyr3, Pap5] GnRH, were found to bind to the GnRH receptors only slightly less avidly than native GnRH. Their cyclization, however, led to a marked reduction in the binding capacity, i.e. from IC50 of 10−9 M to the 10−7 M range, and in biopotency, i.e. LH‐release. All other linear and cyclic peptides were found to bind selectively to the GnRH receptor only in the low µM range. Only peptide 1 was found comparable to native GnRH in respect to LH‐release activity and thus may potentially be a good agonist of the parent peptide. Peptides 1–4, the most potent GnRH receptor binders, were examined for their conformational properties using CD. Cyclic‐azo peptides 2 and 4 were further evaluated by NMR spectroscopy in solution combined with molecular modeling. The structural information obtained explains in part the GnRH‐like biological activity observed. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.
Antibacterial peptides and proteins with multiple cellular targets
Authors: Otvos Laszlo 
Published: August 2005

AbstractNative antimicrobial peptides and proteins represent bridges between innate and adaptive immunity in mammals. On the one hand they possess direct bacterial killing properties, partly by disintegrating bacterial membranes, and some also by inhibiting functions of intracellular biopolymers. On the other, native antimicrobial peptides and proteins upregulate the host defense as chemoattractants or by various additional immunostimulatory effects. Structure‐activity relationship studies indicate that residues responsible for the activities on bacterial membranes or for the secondary functions do not perfectly overlap. In reality, in spite of the relatively short size (18–20 amino acid residues) of some of these molecules, the functional domains can frequently be separated, with the cell‐penetrating fragments located at the C‐termini and the protein binding domains found upstream. As a cumulative effect, multifunctional and target‐specific (agonist or antagonist) antimicrobial peptides and proteins interfere with more than one bacterial function at low concentrations, eliminating toxicity concerns of the earlier generations of antibacterial peptides observed in the clinical setting. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.
Purification, characterization and molecular cloning of glycosylphosphatidylinositol-anchored arginine-specific ADP-ribosyltransferases from chicken
Authors: Terashima Masaharu , Osago Harumi , Hara Nobumasa , Tanigawa Yoshinori , Shimoyama Makoto , Tsuchiya Mikako 
Published: July 2005

Mono-ADP-ribosylation is a post-translational modification that regulates the functions of target proteins or peptides by attaching an ADP-ribose moiety. Here we report the purification, molecular cloning, characterization and tissue-specific distribution of novel arginine-specific Arts (ADP-ribosyltransferases) from chicken. Arts were detected in various chicken tissues as GPI (glycosylphosphatidylinositol)-anchored forms, and purified from the lung membrane fraction. By molecular cloning based on the partial amino acid sequence using 5′- and 3′-RACE (rapid amplification of cDNA ends), two full-length cDNAs of chicken GPI-anchored Arts, cgArt1 (chicken GPI-anchored Art1) and cgArt2, were obtained. The cDNA of cgArt1 encoded a novel polypeptide of 298 amino acids which shows a high degree of identity with cgArt2 (82.9%), Art6.1 (50.2%) and rabbit Art1 (42.1%). In contrast, the nucleotide sequence of cgArt2 was identical with that of Art7 cloned previously from chicken erythroblasts. cgArt1 and cgArt2 proteins expressed in DT40 cells were shown to be GPI-anchored Arts with a molecular mass of 45 kDa, and these Arts showed different enzymatic properties from the soluble chicken Art, Art6.1. RNase protection assays and real-time quantitative PCR revealed distinct expression patterns of the two Arts; cgArt1 was expressed predominantly in the lung, spleen and bone marrow, followed by the heart, kidney and muscle, while cgArt2 was expressed only in the heart and skeletal muscle. Thus GPI-anchored Arts encoded by the genes cgArt1 and cgArt2 are expressed extensively in chicken tissues. It may be worthwhile determining the functional roles of ADP-ribosylation in each tissue.
A study of the horseradish peroxidase catalytic site by FTIR spectroscopy
Authors: Ingledew W.J. , Rich P.R. 
Published: August 2005

Vibrational changes in the catalytic site of horseradish peroxidase were investigated by FTIR (Fourier-transform infrared) spectroscopy in the 1000–2500 cm−1 range. Difference spectra were generated by photolysis of the haemII-CO compound at different pH/pD values. The spectra report on the fine structure around the catalytic site and show vibrational changes of protein backbone, amino acid residues and cofactors. Assignments of the FTIR vibrations can be made based upon known crystal structures, comparisons with absorption frequencies and extinction coefficients of model amino acids and cofactors, effects of H2O/2H2O exchange and changes of pH/pD. Concomitant with the photolysis of the CO ligand are changes due to haem and protein vibrations, predominant among which are arginine and histidine residue vibrations.
S -Ketamine Anesthesia Increases Cerebral Blood Flow in Excess of the Metabolic Needs in Humans
Authors: Långsjö Jaakko W. , Maksimow Anu , Salmi Elina , Kaisti Kaike , Aalto Sargo , Oikonen Vesa , Hinkka Susanna , Aantaa Riku , Sipilä Hannu , Viljanen Tapio , Parkkola Riitta , Scheinin Harry 
Published: July 2005

Background
Animal studies have demonstrated neuroprotective properties of S-ketamine, but its effects on cerebral blood flow (CBF), metabolic rate of oxygen (CMRO2), and glucose metabolic rate (GMR) have not been comprehensively studied in humans.

Methods
Positron emission tomography was used to quantify CBF and CMRO2 in eight healthy male volunteers awake and during S-ketamine infusion targeted to subanesthetic (150 ng/ml) and anesthetic (1,500-2,000 ng/ml) concentrations. In addition, subjects' GMRs were assessed awake and during anesthesia. Whole brain estimates for cerebral blood volume were obtained using kinetic modeling.

Results
The mean +/- SD serum S-ketamine concentration was 159 +/- 21 ng/ml at the subanesthetic and 1,959 +/- 442 ng/ml at the anesthetic levels. The total S-ketamine dose was 10.4 mg/kg. S-ketamine increased heart rate (maximally by 43.5%) and mean blood pressure (maximally by 27.0%) in a concentration-dependent manner (P = 0.001 for both). Subanesthetic S-ketamine increased whole brain CBF by 13.7% (P = 0.035). The greatest regional CBF increase was detected in the anterior cingulate (31.6%; P = 0.010). No changes were detected in CMRO2. Anesthetic S-ketamine increased whole brain CBF by 36.4% (P = 0.006) but had no effect on whole brain CMRO2 or GMR. Regionally, CBF was increased in nearly all brain structures studied (greatest increase in the insula 86.5%; P < 0.001), whereas CMRO2 increased only in the frontal cortex (by 15.7%; P = 0.007) and GMR increased only in the thalamus (by 11.7%; P = 0.010). Cerebral blood volume was increased by 51.9% (P = 0.011) during anesthesia.

Conclusions
S-ketamine-induced CBF increases exceeded the minor changes in CMRO2 and GMR during anesthesia.
Role of Adenosine Receptors in Volatile Anesthetic Preconditioning against Neutrophil-induced Contractile Dysfunction in Isolated Rat Hearts
Authors: Hu Guochang , Salem M Ramez , Crystal George J. 
Published: July 2005

Background
The authors tested the hypothesis that adenosine receptors in polymorphonuclear neutrophils and the heart mediate the preconditioning effects of volatile anesthetics against neutrophil-induced contractile dysfunction.

Methods
Studies were conducted in buffer-perfused and paced isolated rat hearts. Left ventricular developed pressure served as index of contractility. Neutrophils and platelet-activating factor were added to perfusate for 10 min followed by 30 min of recovery. The effect of selective pretreatment of the neutrophils and the hearts with 1.0 minimum alveolar concentration isoflurane or sevoflurane on the neutrophil-induced contractile dysfunction was assessed. Studies were performed in the absence and presence of the nonselective adenosine receptor antagonist 8-phenyltheophylline (10 microM). Neutrophil retention was determined from difference between those administered and collected in coronary effluent and from myeloperoxidase concentration in myocardial samples. Superoxide production of neutrophils was measured by spectrophotometry.

Results
Under control conditions (no anesthetic pretreatment), activated neutrophils caused marked and persistent reductions in left ventricular developed pressure, associated with increases in neutrophil retention and myeloperoxidase activity. Pretreatment of the neutrophils or the heart with either isoflurane or sevoflurane abolished these effects. Pretreatment of the neutrophils also reduced the platelet-activating factor-induced increase in superoxide production by 29 and 33%, respectively. 8-Phenyltheophylline blunted the effects of anesthetic pretreatment of the neutrophils, whereas it did not alter the effects of anesthetic pretreatment of the heart.

Conclusion
An activation of adenosine receptors in neutrophils, but not in the heart, plays a role in the preconditioning effects of volatile anesthetics against neutrophil-induced contractile dysfunction.
Propofol Inhibits Long-term Potentiation but Not Long-term Depression in Rat Hippocampal Slices
Authors: Nagashima Kimimoto , Zorumski Charles F. , Izumi Yukitoshi 
Published: July 2005

Background
Although propofol is known to produce amnesia when used for anesthesia, mechanisms underlying its effects on memory are poorly understood. The current study was designed to examine the effects of propofol on forms of synaptic plasticity thought to contribute to memory processing.

Methods
Extracellular excitatory postsynaptic potentials were recorded from the CA1 region of rat hippocampal slices. Long-term potentiation (LTP) was induced using theta-burst stimulation (10 bursts of 4 pulses at 100 Hz, applied at 5 Hz) of the Schaffer-collateral pathway, while low-frequency stimulation (1 Hz x 900 pulses) was delivered to induce long-term depression. The authors also used higher-frequency stimulation (10 bursts of 4 pulses at 200 Hz, applied at 5 Hz) in the presence of MK-801 to examine the effects of propofol on an N-methyl-D-aspartate receptor-independent form of LTP.

Results
At 30 microM, propofol inhibited LTP induction produced by theta-burst stimulation but had less effect on LTP maintenance. Similarly, when LTP was induced by 200-Hz stimulation in the presence of MK-801, propofol also blocked LTP induction. Propofol did not block LTP induction in the presence of picrotoxin, a specific antagonist of gamma-aminobutyric acid type A receptors, suggesting that modulation of gamma-aminobutyric acid type A receptors participates in propofol-mediated LTP inhibition. Propofol did not inhibit long-term depression.

Conclusions
Propofol inhibits LTP induction through modulation of gamma-aminobutyric acid type A receptors but not via inhibition of N-methyl-D-aspartate receptors. However, other factors also possibly contribute to propofol-mediated LTP inhibition.
Overlapping Induction of Anesthesia
Authors: Hanss Robert , Buttgereit Björn , Tonner Peter H. , Bein Berthold , Schleppers Andreas , Steinfath Markus , Scholz Jens , Bauer Martin 
Published: July 2005

Background
Overlapping induction (OI), i.e., induction of anesthesia with an additional team while the previous patient is still in the operating room (OR), was investigated.

Methods
The study period was 60 days in two followed by three ORs during surgical Block Time (7:30 am until 3:00 pm). Patients were admitted the day before surgery and were thus available and did not have surgery that day unless there was a time reduction. Facilities were already constructed. Number of cases, Nonsurgical Time (Skin Suture Finish until next Procedure Start Time), Turnover Time, and Anesthesia Control Time plus Turnover Time were studied. In addition, economic benefit was calculated.

Results
Three hundred thirty-five cases were studied. Using OI, the time of care of regularly scheduled cases was shortened, and the number of cases performed within OR Block Time increased (151 to 184 cases; P < 0.05). Nonsurgical Time (in h:min) decreased (1:08 +/- 0:26 to 0:57 +/- 0:18; P < 0.001), Turnover Time decreased (0:38 +/- 0:24 to 0:25 +/- 0:15; P < 0.05), and Anesthesia Control Time plus Turnover Time decreased (0:43 +/- 0:23 to 0:28 +/- 0:18; P < 0.001). Subgroup analysis showed a significant benefit of OI only in three ORs. In three ORs, economic benefit can be gained at a case mix index greater than 0.3 besides additional costs.

Conclusions
Overlapping induction increased productivity and profit despite the expense of additional staff. Subgroup analysis emphasizes the importance of the number of ORs involved in OI.
Serum homocysteine, folate and risk of stroke: Kuopio Ischaemic Heart Disease Risk Factor (KIHD) Study
Authors: Virtanen Jyrki K. , Voutilainen Sari , Happonen Pertti , Alfthan Georg , Kaikkonen Jari , Mursu Jaakko , Rissanen Tiina H. , Kaplan George A. , Korhonen Maarit J. , Sivenius Juhani , Salonen Jukka T. 
Published: August 2005

Background Homocysteine and folate have been suggested to have opposite effects on the risk of stroke, although the results are controversial. Design and methods The purpose of this study was to assess the effects of serum total homocysteine (tHcy) and serum folate levels on the risk of stroke in a prospective cohort study. The subjects were 1015 men aged 46–64 years and free of prior stroke, examined in 1991–1993 in the Kuopio Ischaemic Heart Disease Risk Factor (KIHD) Study. Results At baseline the mean serum tHcy concentration was 10.9 μmol/l (SD 3.4). During an average follow-up time of 9.6 years, 49 men experienced a stroke, of which 34 were ischaemic. In Cox proportional hazards models, men in the highest tHcy third had a risk factor-adjusted hazard rate ratio (RR) of 2.77 [95% confidence interval (CI): 1.23–6.24] for any stroke and 2.61 (95% CI: 1.02–6.71) for ischaemic stroke, compared with men in the lowest third. The mean baseline serum folate concentration was 10.4 nmol/l (SD 4.1). Men in the highest third of serum folate (> 11.2 nmol/l) had an adjusted RR for any stroke of 0.35 (95% CI: 0.14–0.87) and for ischaemic stroke of 0.40 (95% CI: 0.15–1.09), compared with men in the lowest third. Conclusion Elevated serum tHcy is associated with increased risk of all strokes and ischaemic strokes in middle-aged eastern Finnish men free of prior stroke. On the other hand, high serum folate concentration may protect against stroke.
Exercise training in chronic heart failure: correlation between reduced local inflammation and improved oxidative capacity in the skeletal muscle
Authors: Gielen Stephan , Adams Volker , Linke Axel , Erbs Sandra , Möbius-Winkler Sven , Schubert Andreas , Schuler Gerhard , Hambrecht Rainer 
Published: August 2005

Background Chronic heart failure (CHF) is accompanied by an inflammatory activation which occurs both systemically and in the skeletal muscle. Exercise training has been shown to reduce the local expression of cytokines and inducible nitric oxide synthase (iNOS) in muscle biopsies of CHF patients. INOS-derived NO can inhibit oxidative phosphorylation and contribute to skeletal muscle dysfunction in CHF. Design To investigate the correlation between changes in local iNOS expression associated with regular exercise and changes in aerobic enzyme activities in the skeletal muscle of patients with CHF. Twenty male CHF patients [ejection fraction 25% (SE 2), age 54 (SE 2) years] were randomized to a training ( n = 10) or a control group (C, n = 10). Methods At baseline and after 6 months skeletal muscle iNOS expression was measured by real-time polymerase chain reaction. INOS protein and protein nitrosylation were assessed by immunohistochemistry. Cytochrome c oxidase (COX) activity was quantified electrochemically using the Clark oxygen electrode. Results Exercise training led to a 27% increase in cytochrome c oxidase activity [from 21.8 (SE 3.2) to 27.7 (SE 3.5) nmol O2/mg per min, P=0.02 versus baseline]. Changes in iNOS expression and iNOS protein content were inversely correlated with changes in COX-activity ( r= −0.60, P=0.01; r= −0.71, P<0.001). Conclusions The inverse correlation between iNOS expression/iNOS protein content and COX-activity indicates that local anti-inflammatory effects may contribute to improved muscular oxidative metabolism.
Internet development and connectivity in Nigeria
Authors: Adomi Esharenana E. 
Published: August 2005

PurposeTo describe internet development and connectivity in Nigeria.Design/methodology/approachReviews the history of the internet in Africa, particularly in Nigeria, and surveys its current status.FindingsRecommendations are given on how use of the internet can be developed in Nigeria.Originality/valueIt will assist relevant authorities and stakeholders in Nigeria and in other developing countries to gain insights on how to improve internet connectivity. It also provides insights into the problems of developing countries for those from the developed world.
Some lessons learned from post‐earthquake damage survey of structures in Bam, Iran earthquake of 2003
Authors: Mehrabian Ali , Haldar Achintya 
Published: August 2005

PurposeSome lessons learned from post‐earthquake damage survey of structures affected by the Bam earthquake of December 26, 2003 in Iran are encapsulated in this paper. The Bam earthquake caused catastrophic structural damage in the region.Design/methodology/approachA method similar to that of rapid evaluation procedure (REP), recommended by the Applied Technology Council (ATC‐20) in the USA, was used for damage survey.FindingsBam represents a typical ancient city in many countries around the world. Most of the structures in the region are made of adobe, unreinforced masonry, steel, and unreinforced/reinforced concrete. Some of the main types of structural damage, their causes, and potential remedial measures are characterized with an emphasis on the very basic fundamental principles of earthquake‐resistant design.Practical implicationsThe research reported has considerable implications for other seismic‐affected regions of the world.Originality/valueA first hand‐account of the catastrophic damage caused by this natural disaster and the implications for future design and construction in seismic‐affected areas.
An improvement in instructional quality: can evaluation of teaching effectiveness make a difference?
Authors: Waithanji Ngware Moses , Ndirangu Mwangi 
Published: August 2005

PurposeTo report study findings on teaching effectiveness and feedback mechanisms in Kenyan universities, which can guide management in developing a comprehensive quality control policy.Design/methodology/approachThe study adopted an exploratory descriptive design. Three public and two private universities were randomly selected to participate in the study. A random sampling procedure was also used to select 79 respondents to participate in the research. A questionnaire administered in all participating universities was the main instrument for data collection.FindingsThere was no clear university policy on the evaluation of teaching effectiveness, despite its importance in quality control. Student evaluation of teaching effectiveness (SETE) was found to be unreliable, although widely used where evaluation existed, without other evaluation support systems. Feedback from the evaluation, though crucial in professional improvement, was not made available to the respondents.Research limitations/implicationsThe study examined the evaluation of teaching effectiveness from the lecturers' perspectives. Further research may provide insights into the contribution of SETE to teaching effectiveness from the students' standpoint.Practical implicationsUse of a variety of evaluation tools (e.g. self, peer) rather than relying solely on SETE is necessary. Comprehensive and usable information may be provided for effective teaching. Universities should provide clear policy guidelines on quality control for faculties to develop multiple teaching effectiveness evaluation instruments.Originality/valueTeaching evaluation is important in order to bring about an improvement in areas such as student achievement, and use of public funds or educational materials. The findings provide critical information for management decision making to assist universities to translate the resources at their disposal into learning outcomes.