bluuebunny/crossref_metadata_2025 huggingface dataset:
Some 3‐connected 4‐edge‐critical non‐Hamiltonian graphs
Authors: Yuansheng Yang , Chengye Zhao , Xiaohui Lin , Yongsong Jiang , Xin Hao
Published: August 2005

Let γ(G) be the domination number of graph G, thus a graph G is k‐edge‐critical if γ (G) = k, and for every nonadjacent pair of vertices u and υ, γ(G + uυ) = k−1. In Chapter 16 of the book “Domination in Graphs—Advanced Topics,” D. Sumner cites a conjecture of E. Wojcicka under the form “3‐connected 4‐critical graphs are Hamiltonian and perhaps, in general (i.e., for any k ≥ 4), (k−1)‐connected, k‐edge‐critical graphs are Hamiltonian.” In this paper, we prove that the conjecture is not true for k = 4 by constructing a class of 3‐connected 4‐edge‐critical non‐Hamiltonian graphs. © 2005 Wiley Periodicals, Inc.
Osteology and skeletal development of Phyllomedusa vaillanti (Anura: Hylidae: Phyllomedusinae) and a comparison of this arboreal species with a terrestrial member of the genus
Authors: Sheil Christopher A. , Alamillo Hugo
Published: August 2005

Few descriptions of skeletal development and morphology exist for neobatrachians, despite their abundance and diversity. Herein, the adult morphologies of Phyllomedusa vaillanti and P. atelopoides are described and compared and the ontogeny of the larval skeleton of P. vaillanti is described and compared with those of Hyla lanciformis (the only hylid for which a detailed cranial and postcranial osteological ontogenesis has been described) and P. trinitatis (the only other member of this genus for which the larval skeleton has been described). These descriptions and comparisons are made on the basis of cleared and double‐stained, dry skeletal, and alcohol‐preserved specimens. In P. vaillanti, the first elements that ossify are the neural arches of the presacral vertebrae (Gosner Stage 34), followed by the parasphenoid, occipital condyles, exoccipitals, and prootics at Stage 38; many elements of the postcranial skeleton ossify contemporaneously with the first cranial elements. Major modifications of the chondrocranium begin at Stage 44. In adults, the skulls of P. vaillanti and P. atelopoides do not seem atypical of hylid frogs, and their elements are gracile and unornamented. Although P. atelopoides is a terrestrial species, the morphology of its hands and feet does not seem to differ dramatically from that of other phyllomedusines, which are arboreal; however, the relative lengths of the appendages and vertebral column are shorter and more robust than those of all other Phyllomedusa. J. Morphol. © 2005 Wiley‐Liss, Inc.
Protein Folding with a Reduced Model and Inaccurate Short‐Range Restraints
Authors: Plewczynska Dorota , Kolinski Andrzej
Published: August 2005

Summary: A reduced high‐coordination lattice protein model and the Replica Exchange Monte Carlo sampling were employed in de novo folding simulations of a set of representative small proteins. Three distinct situations were analyzed. In the first series of simulations, the folding was controlled purely by the generic force field of the model. In the second, a bias was introduced towards the theoretically predicted secondary structure. Finally, we superimposed soft restraints towards the native‐like local conformation of the backbone. The short‐range restraints used in these simulations are based on approximate values of ϕ and ψ dihedral angles, which may simulate restraints derived from inaccurate experimental measurements. Incorporating such data into the reduced model required developing a procedure, which transforms the ϕ and ψ coordinates into coordinates of the protein alpha carbon trace. It has been shown that such limited data are sufficient for de novo determination of three‐dimensional structures of small and topologically not too complex proteins.

Protein folding based on secondary structure prediction and simulated torsion angles data.

magnified image

Protein folding based on secondary structure prediction and simulated torsion angles data.
Experimentally produced diploid〈‐〉triploid mouse chimaeras develop up to adulthood
Authors: Suwińska Aneta , Ożdżeński Wacław , Waksmundzka Małgorzata , Tarkowski Andrzej K.
Published: August 2005

Spontaneous diploid〈‐〉triploid chimaeras occur sporadically in various mammalian species including man, but so far have never been produced experimentally. In order to get a deeper insight into the developmental consequences of this anomaly, we have developed two procedures that enabled for the first time to produce routinely diploid〈‐〉triploid embryos, foetuses, and animals in the mouse. These procedures are: (1) aggregation of cleaving diploid embryos with triploid embryos produced by suppression of the second polar body in zygotes, and (2) fusion of a haploid karyoplast with one blastomere of the two‐cell diploid embryos. The first procedure yielded 23 living and 6 dead postimplantation embryos and foetuses (age: 8th–19th day) out of which 22 were chimaeric. In addition, three chimaeric neonates reached adulthood. Two animals were fertile, and one—an overt chimaera—was an infertile male. The rate of postimplantation development of aggregation chimaeras was normal or only slightly retarded, and with one exception the foetuses were morphologically normal. Generally, the highest contribution of the 3n component in extra‐embryonic structures was noted in the yolk sac, and usually it was higher than its contribution to the organs of the body. Chimaerism was most often noted in the liver, the heart, the intestine, and the lungs. Participation of triploid cells to all tissues studied, both in the body and in extra‐embryonic structures, appeared to decrease slightly as development progressed. The second procedure yielded 10 foetuses and 6 adults. Three foetuses were chimaeric. Six fertile adults were probably nonchimaeras: the triploid component was absent in the coat and in the blood. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Estimation of peroneal and tibial afferent activity from a multichannel cuff placed on the sciatic nerve
Authors: Cheng Hang‐Shing , Ju Ming‐Shaung , Lin Chou‐Ching K.
Published: August 2005

The afferent signals recorded with a multi‐electrode cuff on the sciatic nerve were employed to investigate the possibility of extracting components ascending from the peroneal and tibial nerves. Two methods, an inverse regression model and principal component method, were studied. The parameters of inverse regression model, determined by data collected in semistatic conditions, were validated by data collected in dynamic conditions. The results showed that the regression model, which used only two channels of the sciatic recordings, was sufficient to separate the distal afferent components. The model, at the expense of requiring distal branch recordings for estimating model parameters, yielded better separation than the principal component method. In conclusion, peroneal and tibial afferent activity can be estimated from the sciatic nerve: the principal component method is suitable for applications focused on acquiring afferent information, whereas the inverse regression model is better for applications in which stimulations will be applied to the branches. The estimation technique provides a powerful tool for in vivo investigation of sensory information transmitted in a peripheral nerve and facilitates implementation of advanced functional neuromuscular stimulation systems. Muscle Nerve, 2005
Wide diameter and minimum length of disjoint Menger path systems
Authors: Kojima Toru
Published: August 2005

Let k be a positive integer and let G be a graph with at least k + 1 vertices. For two distinct vertices x,y of G, the k‐wide distance dk(x,y) between x and y is the minimum integer l such that there exist k internally disjoint (x,y)‐paths whose lengths are at most l. We define dk(x,x) = 0. The k‐wide diameter dk(G) of G is the maximum value of the k‐wide distances between two vertices of G. Let X,Y be k‐subsets of V(G). We define mk(X,Y) to be the minimum integer l such that there exist k vertex‐disjoint (X,Y)‐paths of length at most l, and we define mk(G) to be the maximum value of mk(X,Y) over all k‐subsets X,Y of V(G). We study relationships between dk(G) and mk(G). Among other results, we show that if k ≥ 2 and G is a k‐connected graph, then

© 2005 Wiley Periodicals, Inc. NETWORKS, Vol. 46(3), 136–141 2005
Minimum path bases and relevant paths
Authors: Gleiss Petra M. , Leydold Josef , Stadler Peter F.
Published: August 2005

Given an undirected graph G(V,E) and a vertex subset U ⊆ V the U‐space is the vector space over GF(2) spanned by the paths with end‐points in U and the cycles in G(V,E). We extend Vismara's algorithm to the computation of the union of all minimum length bases of the U‐space. Although the size distribution of subgraphs is the same in all minimum length bases, the number of cycles and paths may differ. © 2005 Wiley Periodicals, Inc. NETWORKS, Vol. 46(3), 119–123 2005
Maximizing fundraising's strategic contribution
Authors: Falk Stephen C.
Published: August 2005

Discover the key issues affecting the nonprofit health care organization as it integrates philanthropy into its strategic plan.
Integrating fundraising into finance
Authors: Costa Nick G.
Published: August 2005

It is not uncommon to hear of differences between the development office and the hospital's finance department. Differences arise due to different goals, audiences, needs, and measurement tools.
Successful strategies for effective stewardship
Authors: Metrick L. Alayne
Published: August 2005

Effective stewardship is one of the best ways to reduce donor attrition, increase revenue, and decrease costs. It is a powerful element in winning and retaining donors who have the continued ability to make major gifts.
Physician fundraising: Evolution, not revolution
Authors: Hook Mara , Mapp Jerry
Published: August 2005

Health care organizations must create a culture of philanthropy that includes physicians.
Performance benchmarking: Lessons on using performance benchmarks to maximize fundraising results
Authors: Smith Stuart R.
Published: August 2005

Benchmarking should not be viewed as a number or a goal to be achieved. The value of benchmarking is its use as a management tool to improve fund‐raising performance.
Sudden scrutiny of hospital billing and collections: Managing the oppositional crisis
Authors: Chern Mary Anne
Published: August 2005

With the recent scrutiny of hospital pricing and collections and hospital billing problems, it is imperative that development officers retain the public trust. What effective tactics and lessons can be learned from outside the hospital industry?
Strain rate sensitivity of Cu after severe plastic deformation by multiple compression
Authors: Li Y. J. , Blum W.
Published: August 2005

Coarse‐grained Cu99.99 was prestrained by εpre in multiple compression in three orthogonal directions at room temperature. While the flow stress σ saturates at εpre ≈ 2, the strain rate sensitivity of σ at 318 K increases by a factor of ≈ 2.7 from εpre = 2 to 7. This increase is attributed to decrease of grain size and corresponding increase in fraction of high‐angle grain boundaries. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Method of travel time estimation for wide‐area traffic information service
Authors: Yamane Ken'Ichiro , Yokota Takayoshi , Fushiki Takumi
Published: August 2005

An effective means of ameliorating highway traffic congestion, which has become increasingly severe in recent years, is to provide the traffic information to the road users in real time. In order to make the traffic information service more effective to the users, the area covered by information provision and the accuracy of the information provided are of the greatest importance. From such a viewpoint, a method of travel time estimation which aims at enlargement of the service area and accuracy improvement and stabilization of the provided information is considered. The method tries to utilize in a sophisticated and effective way the data obtained by ultrasonic vehicle detectors and infrared beacons, which are expected to find the widest use in Japan. The method is applied to a real VICS system for ordinary roads, and the accuracy of the provided information is evaluated. © 2005 Wiley Periodicals, Inc. Syst Comp Jpn, 36(11): 82–92, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ scj.20242
Structured program induction from behavioral traces
Authors: Ichise Ryutaro , Shapiro Daniel , Langley Pat
Published: August 2005

This paper addresses the problem of learning control skills from observation. In particular, we show how to infer a hierarchical, reactive program that reproduces and explains the observed actions of other agents, specifically the elements that are shared across multiple individuals. We infer these programs using a three‐stage process that learns flat unordered rules, combines these rules into a classification hierarchy, and finally translates this structure into a hierarchical reactive program. The resulting program is concise and easy to understand. This makes it possible to view program induction as a practical technique for knowledge acquisition. © 2005 Wiley Periodicals, Inc. Syst Comp Jpn, 36(11): 49–59, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20312
Separation of position and direction information of robots by a product model of self‐organizing map and neural gas
Authors: Date Akira , Kurata Koji
Published: August 2005

This paper proposes a neural network model which receives visual inputs from a robot moving freely in a room, and extracts its position and direction information separately. The model has three‐dimensional structure in which two‐dimensional neural fields (unit planes) are arranged in a toroidal form. The learning algorithm takes a form of neural gas in each unit plane and self‐organizing map (SOM) in the toroidal direction. It is shown by computer simulation that position and view direction of the robot can be extracted from visual inputs, and the effectiveness of the learning algorithm is verified. © 2005 Wiley Periodicals, Inc. Syst Comp Jpn, 36(11): 1–11, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20349
Umbilical Pilonidal Sinus Disease: Predisposing Factors and Treatment
Authors: Eryilmaz Ramazan , Sahin Mustafa , Okan Ismail , Alimoglu Orhan , Somay Adnan
Published: August 2005

Pilonidal sinus disease is a common problem of sacrococcygeal region. However, it is also observed in the periumbilical area. There are only a few reports about umbilical pilonidal sinus in the literature. In this study, 26 patients (24 men (92 %), 2 women (8 %) with a mean age of 22 years) with umbilical pilonidal sinus disease were included. Predisposing factors, patient characteristics, treatment modalities, and their results have been studied. Male sex, young age, hairiness, deep navel, and poor personal hygiene were found to be predisposing factors. Twenty‐five patients were treated conservatively. However, two patients failed to respond to conservative treatment. Those patients underwent surgery where umbilectomy was carried out without reconstruction. One patient was also operated on for the preoperative misdiagnosis of irreducible umbilical hernia. Patients were followed for 14–96 months. We recommend conservative treatment in patients with umbilical pilonidal sinus. Surgery should be performed in recurrent cases resistant to conservative treatment. The importance of differential diagnosis of umbilical pilonidal sinus from other umbilical pathologies is also emphasized.
The relationship between salinity, suspended particulate matter and water clarity in aquatic systems
Authors: Håkanson Lars
Published: August 2005

This work presents and recommends 1) an empirically based new model quantifying the relationship between salinity, suspended particulate matter (SPM) and water clarity (as given by the Secchi depth) and (2) an empirical model for oxygen saturation in the deep‐water zone for coastal areas (O2Sat in %). This paper also discusses the many and important roles that SPM plays in aquatic ecosystems and presents comparisons between SPM concentrations in lakes, rivers and coastal areas. Such comparative studies are very informative but not so common. The empirical O2Sat model explains (statistically) 80% of the variability in mean O2Sat values among 23 Baltic coastal areas. The model is based on data on sedimentation of SPM, the percentage of ET areas (areas where erosion and transportation of fine sediments occur), the theoretical deep‐water retention time and the mean coastal depth. These two new models have been incorporated into an existing dynamic model for SPM in coastal areas that quantifies all important fluxes of SPM into, within and from coastal areas, such as river inflow, primary production, resuspension, sedimentation, mixing, mineralisation and the SPM exchange between the given coastal area and the sea (or adjacent coastal areas). The modified dynamic SPM model with these two new sub‐models has been validated (blind tested) with very good results; the model predictions for Secchi depth, O2Sat and sedimentation are within the uncertainty bands of the empirical data.
2.45 GHz radiofrequency fields alter gene expression in cultured human cells
Authors: Lee Sanggyu , Johnson Debra , Dunbar K. , Dong Hui , Ge Xijin , Kim Yeong C. , Wing Claudia , Jayathilaka Nimanthi , Emmanuel Nimmi , Zhou Chenn Q. , Gerber Howard L. , Tseng Charles C. , Wang San Ming
Published: August 2005

The biological effect of radiofrequency (RF) fields remains controversial. We address this issue by examining whether RF fields can cause changes in gene expression. We used the pulsed RF fields at a frequency of 2.45 GHz that is commonly used in telecommunication to expose cultured human HL‐60 cells. We used the serial analysis of gene expression (SAGE) method to measure the RF effect on gene expression at the genome level. We observed that 221 genes altered their expression after a 2‐h exposure. The number of affected genes increased to 759 after a 6‐h exposure. Functional classification of the affected genes reveals that apoptosis‐related genes were among the upregulated ones and the cell cycle genes among the downregulated ones. We observed no significant increase in the expression of heat shock genes. These results indicate that the RF fields at 2.45 GHz can alter gene expression in cultured human cells through non‐thermal mechanism.
Molecular evolution and multilocus sequence typing of 145 strains of SARS‐CoV
Authors: Wang Zhi-Gang , Zheng Zhi-Hua , Shang Lei , Li Lan-Juan , Cong Li-Ming , Feng Ming-Guang , Luo Yun , Cheng Su-Yun , Zhang Yan-Jun , Ru Miao-Gui , Wang Zan-Xin , Bao Qi-Yu
Published: August 2005

In this study, we have identified 876 polymorphism sites in 145 complete or partial genomes of SARS‐CoV available in the NCBI GenBank. One hundred and seventy‐four of these sites existed in two or more SARS‐CoV genome sequences. According to the sequence polymorphism, all SARS‐CoVs can be divided into three groups: (I) group 1, animal‐origin viruses (such as SARS‐CoV SZ1, SZ3, SZ13 and SZ16); (II) group 2, all viruses with clinical origin during first epidemic; and (III) group 3, SARS‐CoV GD03T0013. According to 10 special loci, group 2 again can be divided into genotypes C and T, which can be further divided into sub‐genotypes C1–C4 and T1–T4. Positive Darwinian selections were identified between any pair of these three groups. Genotype C gives neutral selection. Genotype T, however, shows negative selection. By comparing the death rates of SARS patients in the different regions, it was found that the death rate caused by the viruses of the genotype C was lower than that of the genotype T. SARS‐CoVs might originate from an unknown ancestor.
North Wales randomized controlled trial of cognitive behaviour therapy for acute schizophrenia spectrum disorders: two-year follow-up and economic evaluation
Authors: STARTUP MIKE , JACKSON MIKE C. , EVANS KEITH E. , BENDIX SUE
Published: August 2005

Background. There is good evidence now that cognitive behaviour therapy (CBT) is effective in the treatment of people suffering from schizophrenia. There is also some evidence that the benefits of CBT persist after the end of treatment and that the direct costs of providing CBT as an adjunct to standard care are no higher than the direct costs of standard care alone. The aims of the present study were to discover if the benefits of CBT for acute schizophrenia which were found 1 year after index admission persist for another year, and to evaluate the comparative costs of providing CBT.

Method. Consecutive admissions meeting criteria were recruited. After screening, 43 were assigned at random to a treatment-as-usual (TAU) control group and 47 were assigned to TAU plus CBT. Patients (73% of original) were rated on symptoms and social functioning 2 years after index admission. An evaluation of the direct costs of services was also completed.

Results. The CBT group had maintained its advantage over the TAU group on negative symptoms and social functioning but had lost the advantage it previously enjoyed in positive symptoms. The difference between groups in total direct costs over the 2 years was not statistically significant despite the cost of providing CBT.

Conclusions. Some of the benefits of CBT for patients suffering acute psychotic episodes persist for 2 years. After the end of regular treatment, CBT should probably be targeted on the appearance of early signs of relapse to forestall the re-emergence of positive symptoms.
PARVOVIRUS B19 INFECTION IN PREGNANCY
Authors: COHEN BERNARD J , KUMAR SAILESH
Published: August 2005

Parvoviruses are widespread in nature, with a diversity of virus types affecting many animal species, usually in a species-specific manner. Some members of the parvovirus family give rise to asymptomatic infections but others are highly pathogenic, causing disease not only in adults but also in the young, the newborn and in the fetus. Parvoviruses of animals have for long been regarded as agents of reproductive failure and parvovirus B19 was recognised as a cause of fetal loss in humans in the 1980s. Moreover, following the control of congenital rubella by pre-pubertal and child vaccination, parvovirus B19 infection has emerged as probably the leading cause of viral embryopathy. This review will focus on the laboratory diagnosis of parvovirus B19 infection following exposure in pregnancy. The indications for testing maternal and fetal samples and the interpretation of test results will be discussed and a section is included on clinical management of the infection in pregnancy. The obstetric outcome in pregnant women who seroconvert will be reviewed.
Upper ocean heat and freshwater budgets in the eastern Pacific warm pool
Authors: Wijesekera Hemantha W. , Rudnick Daniel L. , Paulson Clayton A. , Pierce Stephen D. , Pegau W. Scott , Mickett John , Gregg Michael C.
Published: August 2005

This study focuses on upper ocean budgets of heat and freshwater, which yield estimates of net surface heat flux and rainfall minus evaporation. The budgets are based on a 19 day ship survey conducted as part of the Eastern Pacific Investigation of Climate Processes in the Coupled Ocean‐Atmosphere System 2001 in September 2001. Underway measurements included temperature and salinity sections from an undulating platform, SeaSoar, and horizontal currents from an acoustic Doppler current profiler along a 146 × 146 km survey pattern centered near 10°N, 95°W in the eastern Pacific warm pool. Additional measurements from a second ship at the center of the survey pattern included radar backscatter from rainfall, air‐sea fluxes, and vertical profiles of temperature, salinity, microstructure, and horizontal velocity. Satellite measurements of surface height, temperature, and rainfall were also analyzed. The heat budget of 20 and 25 m surface layers indicated that storage, advection, turbulent transport, and penetrative solar radiation were all significant components of the heat budget with a net surface cooling of 41 W m−2 estimated as a residual, which agreed with atmospheric measurements (30 W m−2). The precipitation rate from the freshwater budget was 29 mm d−1, which was in excellent agreement with in situ measurements on both ships and in good agreement with satellite estimates for the same period. Lateral transports of heat and salt were influenced by an anticyclonic eddy in the survey area, and it is suggested that anticyclonic eddies, which form near the Central American coast, may carry anomalously warm sea surface temperature toward the west and become preferential sites for heavy rainfall.
Predicting southern African summer rainfall using a combination of MOS and perfect prognosis
Authors: Landman Willem A. , Goddard Lisa
Published: August 2005

A statistical‐dynamical approach to probabilistic precipitation forecasts of southern African summer rainfall is described and validated. An ensemble of seasonal precipitation and circulation fields is obtained from the ECHAM4.5 atmospheric general circulation model (AGCM). Model output statistics (MOS) then spatially recalibrate the AGCM fields relative to observations. Although the MOS equations are built using the simulation data, in which observed SSTs force the AGCM, the same set of equations can be applied to the predicted data, in which predicted SSTs force the AGCM. The use of prediction data in a set of equations developed for simulations, assumes that the AGCM forecast skill approximates its simulation skill and that the systematic biases of the AGCM do not change in a prediction setting; this assumption is analogous to a perfect prognosis (PP) approach. Probabilistic forecast skill is assessed using this MOS‐PP‐recalibration scheme for 3 equi‐probable categories using a 3‐year‐out cross‐validation approach. High skill scores are found over the north‐eastern interior of the region, with marginal skill over the remainder of the austral summer rainfall regions. When skill is assessed for only the wettest and driest of the years, high skill appears over most of the region.
Variations of N+/O+ in the ring current during magnetic storms
Authors: Liu W. L. , Fu S. Y. , Zong Q.‐G. , Pu Z. Y. , Yang J. , Ruan P.
Published: August 2005

Based on the energetic particle measurements obtained by CRRES/MICS, variations of the third most important ion species, N+, in the ring current region have been investigated in detail. The ratio of N+/O+ during geomagnetic quiet times is found to be about 0.314 ± 0.043 and decreases with enhanced solar radiation, as indicated by the F10.7 index. Through a statistic study, the ratio of N+/O+ has been demonstrated to decrease with enhanced geomagnetic activity for strong storms, whereas for small storms, there is no obvious correlation found for this ratio. It is worthy to note that not all the values during active times are higher than those at quiet times. The quite different ratios of N+/O+ (up to 50%) in the ring current region found between quiet and storm times in this paper, together with the different combination rates of atomic oxygen and nitrogen, suggest that the ionospheric nitrogen ions may play a crucial role during some magnetic storms and should have a strong impact on the magnetic storm simulation works on the build‐up and/or decay processes of the ring current.
Recent increase in summertime extreme wave heights in the western North Pacific
Authors: Sasaki W. , Iwasaki S. I. , Matsuura T. , Iizuka S.
Published: August 2005

Recent increase in summertime extreme wave heights (H10, June–August average of the highest 10% of significant wave heights at each month) in the western North Pacific is found by applying an empirical orthogonal function analysis to H10 derived from 3rd–generation wave model forced by 6‐hourly sea surface wind fields of NCEP‐NCAR reanalysis over the period 1980–2004. The leading principal component of H10 demonstrates that the highest four years of H10 during 1980–2004 occurred in the last 10 years. It is found that the recent increase in H10 corresponds to the recent increase in total duration of intense tropical cyclones (ITC, with central pressure below 980 hPa) in the western North Pacific. Time series of the total duration of ITC reveals that the highest three years of the total duration of ITC during the last three decades occurred in the last 10 years.
Morphometry of network and nonnetwork space of basins
Authors: Chockalingam L. , Daya Sagar B. S.
Published: August 2005

Morphometric analysis of channel network of a basin provides several scale‐ independent measures. To better characterize basin morphology, one requires, besides channel morphometric properties, scale‐independent but shape‐dependent measures to record the sensitive differences in the morphological organization of nonnetwork spaces. These spaces are planar forms of hillslopes or the retained portion after subtracting the channel network from the basin space. The principal aim of this paper is to focus on explaining the importance of alternative scale‐independent but shape‐dependent measures of nonnetwork spaces of basins. Toward this goal, we explore how mathematical morphology‐based decomposition procedures can be used to derive basic measures required to quantify estimates, such as dimensionless power laws, that are useful to express the importance of characteristics of nonnetwork spaces via decomposition rules. We demonstrate our results through characterization of nonnetwork spaces of eight subbasins of the Gunung Ledang region of peninsular Malaysia. We decompose the nonnetwork spaces of eight fourth‐order basins in a two‐dimensional discrete space into simple nonoverlapping disks (NODs) of various sizes by employing morphological transformations. Furthermore, we show relationships between the dimensions estimated via morphometries of the network and their corresponding nonnetwork spaces. This study can be extended to characterize hillslope morphologies, where decomposition of three‐dimensional hillslopes needs to be addressed.
Imaging Visual Recognition Memory Network by PET in the Baboon: Perirhinal Cortex Heterogeneity and Plasticity after Perirhinal Lesion
Authors: Rauchs Géraldine , Blaizot Xavier , Giffard Cyrille , Baron Jean-Claude , Insausti Ricardo , Chavoix Chantal
Published: August 2005

We recently mapped the visual recognition memory network in the behaving baboon using a positron emission tomography (PET) activation paradigm with 18F-fluoro-deoxyglucose during a visual delayed matching-to-sample task. This study confirmed the key role of the perirhinal cortex and documented an unexpected left-sided advantage. Specific contribution of each subdivision of the perirhinal cortex has, however, never been investigated. Furthermore, although alteration to the perirhinal cortex has been implicated in several brain disorders, putative plasticity within the entire brain network after perirhinal damage remains largely unknown. To confirm our previous data and to investigate these latter issues, we used our PET activation paradigm on a second healthy baboon before and after 16 months after bilateral excitotoxic lesions of the perirhinal cortex. Activation common to our two healthy baboons occurred only in the left rostroventral perirhinal cortex (i.e., areas 36pm and rostral 36r) and insular cortex. Although histologic analysis disclosed that the perirhinal lesions achieved in the present baboon were essentially caudal to this preoperatively activated area, memory performance was severely impaired. Concomitant with this long-lasting cognitive deficit, changes in the neural network implicated in the task were observed, involving disappearance of the preoperative activations and appearance of a significant activation of the frontal and occipital cortices. However, different activation patterns were found in the first and last eight postoperative months. These findings highlight the functional heterogeneity of the perirhinal cortex and evidence progressive plasticity after perirhinal cortex damage.
Activation of RelA homodimers by tumour necrosis factor α: a possible transcriptional activator in human vascular endothelial cells
Authors: Marui Nobuyuki , Medford Russell M. , Ahmad Mushtaq
Published: August 2005

In vascular endothelial cells, cytokines induce genes that are expressed in inflammatory lesions partly through the activation of transcription factor NF-κB (nuclear factor-κB). Among the members of the NF-κB/rel protein family, homodimers of the RelA subunit of NF-κB can also function as strong transactivators when expressed in cells. However, the functional role of endogenous RelA homodimers has not been clearly elucidated. We investigated whether RelA homodimers are induced in cytokine-treated vascular endothelial cells. Gel mobility-shift and supershift assays revealed that a cytokine TNFα (tumour necrosis factor α) activated both NF-κB1/RelA heterodimers and RelA homodimers that bound to a canonical κB sequence, IgκB (immunoglobulin κB), in SV40 (simian virus 40) immortalized HMEC-1 (human dermal microvascular endothelial cell line 1). In HMEC-1 and HUVEC (human umbilical-vein endothelial cells), TNFα also induced RelA homodimers that bound to the sequence 65-2κB, which specifically binds to RelA homodimers but not to NF-κB1/RelA heterodimers in vitro. Deoxycholic acid, a detergent that can dissociate the NF-κB–IκB complex (where IκB stands for inhibitory κB), induced the binding of the RelA homodimers to 65-2κB from the cytosolic fraction of resting HMEC-1. Furthermore, TNFα induced the transcriptional activity of a reporter gene that was driven by 65-2κB in HMEC-1. These results suggest that in addition to NF-κB1/RelA heterodimers, TNFα also induces RelA homodimers that are functionally active. Thus RelA homodimers may actively participate in cytokine regulation of gene expression in human vascular endothelial cells.
A high-throughput fluorescence polarization assay specific to the CD4 binding site of HIV-1 glycoproteins based on a fluorescein-labelled CD4 mimic
Authors: Stricher François , Martin Loïc , Barthe Philippe , Pogenberg Vivian , Mechulam Alain , Menez André , Roumestand Christian , Veas Francisco , Royer Catherine , Vita Claudio
Published: August 2005

The three-dimensional structure of CD4M33, a mimic of the host-cell receptor-antigen CD4 and a powerful inhibitor of CD4–gp120 (viral envelope glycoprotein 120) interaction and HIV-1 entry into cells [Martin, Stricher, Misse, Sironi, Pugniere, Barthe, Prado-Gotor, Freulon, Magne, Roumestand et al. (2003) Nat. Biotechnol. 21, 71–76], was solved by 1H-NMR and its structure was modelled in its complex with gp120. In this complex, CD4M33 binds in a CD4-like mode and inserts its unnatural and prominent Bip23 (biphenylalanine-23) side-chain into the gp120 interior ‘Phe43 cavity’, thus filling its volume. CD4M33 was specifically labelled with fluorescein and shown by fluorescence anisotropy to bind to different gp120 glycoproteins with dissociation constants in the nanomolar range. Fluorescent CD4M33 was also used in a miniaturized 384-well-plate assay to study direct binding to a large panel of gp120 glycoproteins and in a competition assay to study binding of CD4 or other ligands targeting the CD4 binding site of gp120. Furthermore, by using the fluorescently labelled CD4M33 and the [Phe23]M33 mutant, which possesses a natural Phe23 residue and thus cannot penetrate the gp120 Phe43 cavity, we show that a recently discovered small-molecule-entry inhibitor, BMS-378806, does not target the CD4 binding site nor the Phe43 cavity of gp120. The fluorescently labelled CD4M33 mimic, its mutants and their derivatives represent useful tools with which to discover new molecules which target the CD4 binding site and/or the Phe43 cavity of gp120 glycoproteins in a high-throughput fluorescence-polarization assay and to characterize their mechanism of action.
Hepatocyte growth factor is a preferred in vitro substrate for human hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers
Authors: Herter Sylvia , Piper Derek E. , Aaron Wade , Gabriele Timothy , Cutler Gene , Cao Ping , Bhatt Ami S. , Choe Youngchool , Craik Charles S. , Walker Nigel , Meininger David , Hoey Timothy , Austin Richard J.
Published: August 2005

Hepsin is a membrane-anchored, trypsin-like serine protease with prominent expression in the human liver and tumours of the prostate and ovaries. To better understand the biological functions of hepsin, we identified macromolecular substrates employing a tetrapeptide PS-SCL (positional scanning-synthetic combinatorial library) screen that rapidly determines the P1–P4 substrate specificity. Hepsin exhibited strong preference at the P1 position for arginine over lysine, and favoured threonine, leucine or asparagine at the P2, glutamine or lysine at the P3, and proline or lysine at the P4 position. The relative activity of hepsin toward individual AMC (7-amino-4-methylcoumarin)-tetrapeptides was generally consistent with the overall peptide profiling results derived from the PC-SCL screen. The most active tetrapeptide substrate Ac (acetyl)-KQLR-AMC matched with the activation cleavage site of the hepatocyte growth factor precursor sc-HGF (single-chain HGF), KQLR↓VVNG (where ↓ denotes the cleavage site), as identified by a database analysis of trypsin-like precursors. X-ray crystallographic studies with KQLR chloromethylketone showed that the KQLR peptide fits well into the substrate-binding cleft of hepsin. This hepsin-processed HGF induced c-Met receptor tyrosine phosphorylation in SKOV-3 ovarian cancer cells, indicating that the hepsin-cleaved HGF is biologically active. Activation cleavage site mutants of sc-HGF with predicted non-preferred sequences, DPGR↓VVNG or KQLQ↓VVNG, were not processed, illustrating that the P4–P1 residues can be important determinants for substrate specificity. In addition to finding macromolecular hepsin substrates, the extracellular inhibitors of the HGF activator, HAI-1 and HAI-2, were potent inhibitors of hepsin activity (IC50 4±0.2 nM and 12±0.5 nM respectively). Together, our findings suggest that the HGF precursor is a potential in vivo substrate for hepsin in tumours, where hepsin expression is dysregulated and may influence tumorigenesis through inappropriate activation and/or regulation of HGF receptor (c-Met) functions.
Activation of hepatocyte growth factor by urokinase-type plasminogen activator is ionic strength-dependent
Authors: Mars Wendy M. , Jo Minji , Gonias Steven L.
Published: August 2005

The hepatocyte growth factor (HGF) is a multifunctional cytokine that is produced as latent scHGF (single chain HGF). Various proteases reportedly cleave scHGF to generate the active two-chain form (HGF), including u-PA (urokinase-type plasminogen activator), t-PA (tissue-type plasminogen activator), kallikrein, Factor XIa, Factor XIIa, HGF activator and matriptase. Considerable evidence indicates that, in vivo, u-PA activates scHGF in the liver; however, the in vivo results have not been uniformly supported by in vitro experiments. We now report that cleavage of scHGF by high-molecular-mass u-PA (abbreviated u-PA throughout) is sensitive to ionic strength. scHGF cleavage by u-PA was accelerated as the ionic strength was decreased. This result was equivalent irrespective of whether the predominant anion was chloride or acetate. Lmw-u-PA (low-molecular-mass u-PA) was ineffective at cleaving scHGF, regardless of ionic strength. Although scHGF shares homology with plasminogen, EACA (ϵ-amino-caproic acid) did not regulate u-PA-mediated scHGF cleavage. Soluble HGF receptor (MET) and soluble u-PAR (u-PA receptor) inhibited the scHGF cleavage. These results support a model in which the ability of u-PA to activate scHGF in vivo may be highly dependent on local conditions within the extracellular space.
Autosomal dominant retinitis pigmentosa mutations in inosine 5′-monophosphate dehydrogenase type I disrupt nucleic acid binding
Authors: Mortimer Sarah E. , Hedstrom Lizbeth
Published: August 2005

Two mutations of IMPDH1 (inosine 5′-monophosphate dehydrogenase type I), R224P and D226N, have recently been found to cause adRP (autosomal dominant retinitis pigmentosa). IMPDH1 catalyses the rate-limiting step in guanine nucleotide biosynthesis and also binds single-stranded nucleic acids. In the present paper, we report the biochemical characterization of the adRP-linked mutations, R224P and D226N, and a potentially pathogenic mutation, V268I. The adRP-linked mutations have no effect on enzyme activity, protein stability or protein aggregation. These results suggest strongly that the mutations do not affect enzyme activity in vivo and thus do not perturb the guanine nucleotide pool. The R224P mutation changes the distribution of enzyme between the nucleus and cytoplasm. This effect was not observed with the D226N mutation, so the relevance of this observation to disease is unclear. In contrast, both mutations decrease the affinity of nucleic acid binding and both fail to co-immunoprecipitate RNA. These observations suggest that nucleic acid binding provides a functional assay for adRP pathogenicity. The putative adRP-linked mutation V268I also disrupts nucleic acid binding, which suggests that this mutation is indeed pathogenic.
The spot 14 protein inhibits growth and induces differentiation and cell death of human MCF-7 breast cancer cells
Authors: Sanchez-Rodriguez Jinny , Kaninda-Tshilumbu John P. , Santos Angel , Perez-Castillo Ana
Published: August 2005

The S14 (spot 14) gene encodes a protein that is predominantly expressed in lipogenic tissues, such as the liver, white and brown adipose tissues and the lactating mammary glands. Accumulated evidence suggests that S14 could play an important role in the induction of lipogenic enzymes. In humans, the S14 locus resides in the chromosome region 11q13, which is frequently amplified in breast tumours, and as a result, it has been suggested that this protein could play a role in the metabolism and growth of these kinds of tumours. In the present study, we have examined the effects of S14 overexpression in MCF-7 human breast cancer cells. We found that S14 causes (i) an inhibition of cell proliferation and of anchorage-independent growth, (ii) a marked reduction in the number of viable cells and (iii) the induction of differentiation and cell death of these cells. The inhibition of cell growth was associated with a decrease in the expression of cyclin D1 and a reduction of cyclin D1 promoter activity. Increased expression of S14 also caused the accumulation of cytochrome c in the cytosol and loss of mitochondrial membrane potential. These findings suggest that S14 may function as an important modulator of tumorigenesis in human breast by decreasing cell growth and inducing cell death and differentiation.
Ca2+ accumulation into acidic organelles mediated by Ca2+- and vacuolar H+-ATPases in human platelets
Authors: López José J. , Camello-Almaraz Cristina , Pariente José A. , Salido Ginés M. , Rosado Juan A.
Published: August 2005

Most physiological agonists increase cytosolic free [Ca2+]c (cytosolic free Ca2+ concentration) to regulate a variety of cellular processes. How different stimuli evoke distinct spatiotemporal Ca2+ responses remains unclear, and the presence of separate intracellular Ca2+ stores might be of great functional relevance. Ca2+ accumulation into intracellular compartments mainly depends on the activity of Ca2+- and H+-ATPases. Platelets present two separate Ca2+ stores differentiated by the distinct sensitivity to thapsigargin and TBHQ [2,5-di-(t-butyl)-1,4-hydroquinone]. Although one store has long been identified as the dense tubular system, the nature of the TBHQ-sensitive store remains uncertain. Treatment of platelets with GPN (glycylphenylalanine-2-naphthylamide) impaired Ca2+ release by TBHQ and reduced that evoked by thrombin. In contrast, GPN did not modify Ca2+ mobilization stimulated by ADP or AVP ([arginine]vasopressin). Treatment with nigericin, a proton carrier, and bafilomycin A1, an inhibitor of the vacuolar H+-ATPase, to dissipate the proton gradient into acidic organelles induces a transient increase in [Ca2+]c that was abolished by previous treatment with the SERCA (sarcoplasmic/endoplasmic-reticulum Ca2+-ATPase) 3 inhibitor TBHQ. Depleted acidic stores after nigericin or bafilomycin A1 were refilled by SERCA 3. Thrombin, but not ADP or AVP, reduces the rise in [Ca2+]c evoked by nigericin and bafilomycin A1. Our results indicate that the TBHQ-sensitive store in human platelets is an acidic organelle whose Ca2+ accumulation is regulated by both Ca2+- and vacuolar H+-ATPases.
Characterization of a recombinant type II 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Helicobacter pylori
Authors: Webby Celia J. , Patchett Mark L. , Parker Emily J.
Published: August 2005

DAH7P (3-Deoxy-D-arabino-heptulosonate 7-phosphate) synthase catalyses the condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) as the first committed step in the biosynthesis of aromatic compounds in plants and micro-organisms. Previous work has identified two families of DAH7P synthases based on sequence similarity and molecular mass, with the majority of the mechanistic and structural studies being carried out on the type I paralogues from Escherichia coli. Whereas a number of organisms possess genes encoding both type I and type II DAH7P synthases, the pathogen Helicobacter pylori has only a single, type II, enzyme. Recombinant DAH7P synthase from H. pylori was partially solubilized by co-expression with chaperonins GroEL/GroES in E. coli, and purified to homogeneity. The enzyme reaction follows an ordered sequential mechanism with the following kinetic parameters: Km (PEP), 3 μM; Km (E4P), 6 μM; and kcat, 3.3 s−1. The enzyme reaction involves interaction of the si face of PEP with the re face of E4P. H. pylori DAH7P synthase is not inhibited by phenylalanine, tyrosine, tryptophan or chorismate. EDTA inactivates the enzyme, and activity is restored by a range of bivalent metal ions, including (in order of decreasing effectiveness) Co2+, Mn2+, Ca2+, Mg2+, Cu2+ and Zn2+. Analysis of type II DAH7P synthase sequences reveals several highly conserved motifs, and comparison with the type I enzymes suggests that catalysis by these two enzyme types occurs on a similar active-site scaffold and that the two DAH7P synthase families may indeed be distantly related.
Crystal structure of levansucrase from the Gram-negative bacterium Gluconacetobacter diazotrophicus
Authors: Martínez-Fleites Carlos , Ortíz-Lombardía Miguel , Pons Tirso , Tarbouriech Nicolas , Taylor Edward J. , Arrieta Juan G. , Hernández Lázaro , Davies Gideon J.
Published: August 2005

The endophytic Gram-negative bacterium Gluconacetobacter diazotrophicus SRT4 secretes a constitutively expressed levansucrase (LsdA, EC 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. The enzyme is included in GH (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. The three-dimensional structure of LsdA has been determined by X-ray crystallography at a resolution of 2.5 Å (1 Å=0.1 nm). The structure was solved by molecular replacement using the homologous Bacillus subtilis (Bs) levansucrase (Protein Data Bank accession code 1OYG) as a search model. LsdA displays a five-bladed β-propeller architecture, where the catalytic residues that are responsible for sucrose hydrolysis are perfectly superimposable with the equivalent residues of the Bs homologue. The comparison of both structures, the mutagenesis data and the analysis of GH68 family multiple sequences alignment show a strong conservation of the sucrose hydrolytic machinery among levansucrases and also a structural equivalence of the Bs levansucrase Ca2+-binding site to the LsdA Cys339–Cys395 disulphide bridge, suggesting similar fold-stabilizing roles. Despite the strong conservation of the sucrose-recognition site observed in LsdA, Bs levansucrase and GH32 family Thermotoga maritima invertase, structural differences appear around residues involved in the transfructosylation reaction.