bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating prior information via shrinkage: a combined analysis of genome‐wide location data and gene expression data
Authors: Xie Yang , Pan Wei , Jeong Kyeong S. , Khodursky Arkady 
Published: September 2006

AbstractTranscriptional control is a critical step in regulation of gene expression. Understanding such a control on a genomic level involves deciphering the mechanisms and structures of regulatory programmes and networks. A difficulty arises due to the weak signal and high noise in various sources of data while most current approaches are limited to analysis of a single source of data. A natural alternative is to improve statistical efficiency and power by a combined analysis of multiple sources of data. Here we propose a shrinkage method to combine genome‐wide location data and gene expression data to detect the binding sites or target genes of a transcription factor. Specifically, a prior ‘non‐target’ gene list is generated by analysing the expression data, and then this information is incorporated into the subsequent binding data analysis via a shrinkage method. There is a Bayesian justification for this shrinkage method. Both simulated and real data were used to evaluate the proposed method and compare it with analysing binding data alone. In simulation studies, the proposed method gives higher sensitivity and lower false discovery rate (FDR) in detecting the target genes. In real data example, the proposed method can reduce the estimated FDR and increase the power to detect the previously known target genes of a broad transcription regulator, leucine responsive regulatory protein (Lrp) inEscherichia coli. This method can also be used to incorporate other information, such as gene ontology (GO), to microarray data analysis to detect differentially expressed genes. Copyright © 2006 John Wiley & Sons, Ltd.
Twin reversed arterial perfusion: fetoscopic laser coagulation of placental anastomoses or the umbilical cord
Authors: Hecher K. , Lewi L. , Gratacos E. , Huber A. , Ville Y. , Deprest J. 
Published: September 2006

AbstractObjectiveTo assess the feasibility and outcome of fetoscopic laser coagulation in pregnancies with twin reversed arterial perfusion (TRAP) sequence.MethodsIn a prospective multicenter study, percutaneous fetoscopic laser coagulation of placental anastomoses (n = 18) or the umbilical cord of the acardiac twin (n = 42) was performed in 60 consecutive pregnancies at a median gestational age of 18.3 (range, 14.3–24.7) weeks under local or locoregional anesthesia.ResultsVascular coagulation with arrest of blood flow was achieved in 82% (49/60) of cases by laser alone and in a further 15% (9/60) by laser coagulation in combination with bipolar forceps. The overall survival rate of the pump twin was 80% (48/60). Median gestational age at delivery was 37.4 (range, 23.7–41.4) weeks and the median interval between the procedure and delivery was 18.2 (range, 1.1–25.7) weeks. Median birth weight was 2720 (range, 540–3840) g. Preterm premature rupture of membranes before 34 weeks' gestation occurred in 18% (11/60) at a median of 62 (range, 1–102) days after the procedure. However, only two (3%) women delivered within 28 days of the procedure.ConclusionsFetoscopic laser coagulation of placental vascular anastomoses or the umbilical cord of the acardiac twin is an effective treatment of TRAP sequence, with a survival rate of 80%, and 67% of pregnancies with surviving pump twins going beyond 36 weeks' gestation without further complications. Copyright © 2006 ISUOG. Published by John Wiley & Sons, Ltd.
Analysis of a biphase mark protocol with U
ppaal
and PVS
Authors: Vaandrager F. W. , de Groot A. L. 
Published: September 2006

Abstract

The biphase mark protocol is a convention for representing both a string of bits and clock edges in a square wave. The protocol is frequently used for communication at the physical level of the ISO/OSI hierarchy, and is implemented on microcontrollers such as the Intel 82530 Serial Communications Controller. An important property of the protocol is that bit strings of arbitrary length can be transmitted reliably, despite differences in the clock rates of sender and receiver (drift), variations of the clock rates (jitter), and distortion of the signal after generation of an edge. In this article, we show how the protocol can be modelled naturally in terms of timed automata. We use the model checker
Uppaal
to derive the maximal tolerances on the clock rates, for different instances of the protocol, and to support the general parametric verification that we formalized using the proof assistant PVS. Based on the derived parameter constraints we propose instances of BMP that are correct (at least in our model) but have a faster bit rate than the instances that are commonly implemented in hardware.
Copepods associated with Phallusia mamillata and Ciona intestinalis (Tunicata) in the area of Taranto (Ionian Sea, southern Italy)
Authors: Pastore Michele 
Published: September 2006

Commensal and parasitic copepods (Arthropoda: Crustacea: Copepoda) of two common species of sea squirts, Phallusia mamillata and Ciona intestinalis have been investigated in the sea of Taranto (southern Italy).A total of 2590 specimens of copepods were collected (five families, eight genera and 13 species). The sex ratio on 2582 specimens was 1228 males (47·56%) to 1354 females (52·44%).The species were identified by the hosts in which they were found, their sex ratio host by host, and the specific variability and affinity analysis by means of the Sørensen index and the diversity index by means of the Shannon application.Some species of copepods have been found for the first time as in Ciona intestinalis (Hermannella rostrata) and in Phallusia mamillata (Notodelphys canui, Doropygus pulex, Pachypygus gibber, Notopterophorus auritus, Lichomolgus albens, Hersiliodes latericia). The association Notodelphys canui–Doropygus pulex—Notopterophorus auritu–Lichomolgus albens is noted for the first time in the Mediterranean Sea.
Aggressiveness, not impulsiveness or hostility, distinguishes suicide attempters with major depression
Authors: KEILP JOHN G. , GORLYN MARIANNE , OQUENDO MARIA A. , BRODSKY BETH , ELLIS STEVEN P. , STANLEY BARBARA , JOHN MANN J. 
Published: September 2006

Background. Impulsiveness, hostility and aggressiveness are traits associated with suicidal behavior, but also with borderline personality disorder (BPD). The presence of large numbers of BPD subjects in past attempter samples may distort the relative importance of each of these traits to predicting suicidal behavior, and lead to prospective, biological and genetic models that systematically misclassify certain subpopulations of suicidal individuals.Method. Two hundred and seventy-five subjects with major depressive disorder (MDD), including 87 with co-morbid BPD (69 past suicide attempters, 18 non-attempters) and 188 without BPD (76 attempters, 112 non-attempters) completed standard impulsiveness, hostility and aggressiveness ratings. Differences between past suicide attempters and non-attempters were examined with the sample stratified by BPD status.Results. As expected, BPD subjects scored significantly higher than non-BPD subjects on all three trait measures. Stratifying by BPD status, however, eliminated attempter/non-attempter differences in impulsiveness and hostility in both patient subgroups. Past suicide attempters in each of the two subgroups of patients were only distinguished by higher levels of aggressiveness.Conclusions. Once BPD is accounted for, a history of aggressive behavior appears to be the distinguishing trait characteristic of suicide attempters with major depression, rather than global personality dimensions such as impulsiveness or hostility. Aggressiveness, and not these related traits, may be the ideal target for behavioral, genetic and biological research on suicidal behavior, as well as for the clinical assessment of suicide risk.
Contour tracking of an unknown planar object by regulating force for mobile robot navigation
Authors: Jung Seul , Jeon Poongwoo , Hsia T. C. 
Published: September 2006

SUMMARYIn this paper, a novel contour-tracking control method of an unknown planar object by lateral force regulation for wheeled mobile robot navigation is presented. The robot is required to follow the contour of an unknown object toward the goal position. Based on mobile robot dynamic equations, a force-control algorithm is proposed to maintain constant contact with a planar object. Measured contact force from an object is used not only to regulate a contact force in a lateral direction, but also to control the orientation angle of the robot to avoid collision with an object. Simulation and experiment of contour-tracking tasks of a wheeled mobile robot are conducted. Experimental results show that the contact force is well-regulated, and the robot arrives at the goal position successfully.
Molecular evidence for infection by HTLV-2 among individuals with negative serological screening tests for HTLV antibodies
Authors: ISHAK R. , VALLINOTO A. C. R. , AZEVEDO V. N. , VICENTE A. C. P. , HALL W. W. , ISHAK M. O. G. 
Published: September 2006

SUMMARYPrevious serological studies on the Arara do Laranjal Indian group revealed extensive HTLV-2 infections. A collection of 97 new samples from the Arara were found repeatedly negative using three different commercial enzyme immunoassays. Eight samples that exhibited optical density readings close to the cut-off value were re-evaluated using Western blot (GeneLab 2.4, Singapore) assay. One sample was found to be non-reactive, five exhibited indeterminate patterns, one was classified as HTLV, and one was confirmed as HTLV-2. Peripheral blood mononuclear cell DNA of the eight samples were subjected to nested PCR and restriction fragment length polymorphism (RFLP) analysis of thepXandenvregions, and nucleotide sequencing of the 5′-LTRregion. All produced amplification products ofpX, butenvcould be amplified in only one sample with the commonly used primers. RFLP analysis of thepXregion usingTaqI confirmed HTLV-2 infection. Nucleotide sequencing of the 5′-LTRregion was performed in three samples (HTLV-2, HTLV and indeterminate based on Western blot pattern). Phylogenetic analysis of a 449-nt fragment using the Neighbour-Joining method clearly demonstrated that the three samples clustered within the HTLV-2c molecular subtype. The present study confirms the wide dissemination of the HTLV-2c subtype among linguistically and culturally distinct Amazonian Indian groups, and emphasizes the unique occurrence of infection by this subtype in Brazil. Moreover, it emphasizes the limitation of employing the present serological screening assays in blood banks, epidemiological studies, and the importance of molecular assays in the confirmatory procedures for the primary detection of HTLV-2 infections.
Arabidopsis SPO11‐2 functions with SPO11‐1 in meiotic recombination
Authors: Stacey Nicola J. , Kuromori Takashi , Azumi Yoshitaka , Roberts Gethin , Breuer Christian , Wada Takuji , Maxwell Anthony , Roberts Keith , Sugimoto‐Shirasu Keiko 
Published: September 2006

SummaryThe Spo11 protein is a eukaryotic homologue of the archaeal DNA topoisomerase VIA subunit (topo VIA). In archaea it is involved, together with its B subunit (topo VIB), in DNA replication. However, most eukaryotes, including yeasts, insects and vertebrates, instead have a single gene for Spo11/topo VIA and no homologues for topo VIB. In these organisms, Spo11 mediates DNA double‐strand breaks that initiate meiotic recombination. Many plant species, in contrast to other eukaryotes, have three homologues for Spo11/topo VIA and one for topo VIB. The homologues in Arabidopsis, AtSPO11‐1, AtSPO11‐2 and AtSPO11‐3, all share 20–30% sequence similarity with other Spo11/topo VIA proteins, but their functional relationship during meiosis or other processes is not well understood. Previous genetic evidence suggests that AtSPO11‐1 is a true orthologue of Spo11 in other eukaryotes and is required for meiotic recombination, whereas AtSPO11‐3 is involved in DNA endo‐reduplication as a part of the topo VI complex. In this study, we show that plants homozygous for atspo11‐2 exhibit a severe sterility phenotype. Both male and female meiosis are severely disrupted in the atspo11‐2 mutant, and this is associated with severe defects in synapsis during the first meiotic division and reduced meiotic recombination. Further genetic analysis revealed that AtSPO11‐1 and AtSPO11‐2 genetically interact, i.e. plants heterozygous for both atspo11‐1 and atspo11‐2 are also sterile, suggesting that AtSPO11‐1 and AtSPO11‐2 have largely overlapping functions. Thus, the three Arabidopsis Spo11 homologues appear to function in two discrete processes, i.e. AtSPO11‐1 and AtSPO11‐2 in meiotic recombination and AtSPO11‐3 in DNA replication.
Plastidial phosphorylase is required for normal starch synthesis in Chlamydomonas reinhardtii
Authors: Dauvillée David , Chochois Vincent , Steup Martin , Haebel Sophie , Eckermann Nora , Ritte Gerhard , Ral Jean‐Philippe , Colleoni Christophe , Hicks Glenn , Wattebled Fabrice , Deschamps Philippe , D'Hulst Christophe , Liénard Luc , Cournac Laurent , Putaux Jean‐Luc , Dupeyre Danielle , Ball Steven G. 
Published: September 2006

SummaryAmong the three distinct starch phosphorylase activities detected in Chlamydomonas reinhardtii, two distinct plastidial enzymes (PhoA and PhoB) are documented while a single extraplastidial form (PhoC) displays a higher affinity for glycogen as in vascular plants. The two plastidial phosphorylases are shown to function as homodimers containing two 91‐kDa (PhoA) subunits and two 110‐kDa (PhoB) subunits. Both lack the typical 80‐amino‐acid insertion found in the higher plant plastidial forms. PhoB is exquisitely sensitive to inhibition by ADP‐glucose and has a low affinity for malto‐oligosaccharides. PhoA is more similar to the higher plant plastidial phosphorylases: it is moderately sensitive to ADP‐glucose inhibition and has a high affinity for unbranched malto‐oligosaccharides. Molecular analysis establishes that STA4 encodes PhoB. Chlamydomonas reinhardtii strains carrying mutations at the STA4 locus display a significant decrease in amounts of starch during storage that correlates with the accumulation of abnormally shaped granules containing a modified amylopectin structure and a high amylose content. The wild‐type phenotype could be rescued by reintroduction of the cloned wild‐type genomic DNA, thereby demonstrating the involvement of phosphorylase in storage starch synthesis.
Defects in electronics and their significance for structural integrity
Authors: PLUMBRIDGE W. J. 
Published: September 2006

ABSTRACTWith Electronics likely to become a major area of interest to structural integrity practitioners, the paper aims to introduce the field from a structural integrity perspective. The Industry is presently facing two major challenges: continued miniaturisation and the implementation of lead‐free technology associated with interconnections. Following a consideration of the background of both aspects, a brief outline of typical components and production processes is presented. Attention is then focussed upon possible defects that may arise during manufacture, and under the, often, complex conditions of service. Comparisons are drawn with more traditional applications of structural integrity, and the fresh challenges associated with the utilisation of a new generation of solder alloys, and with micro and near‐nano dimensions, are introduced.
The development of area discrimination and its implications for number representation in infancy
Authors: Brannon Elizabeth M. , Lutz Donna , Cordes Sara 
Published: September 2006

Abstract This paper investigates the ability of infants to attend to continuous stimulus variables and how this capacity relates to the representation of number. We examined the change in area needed by 6‐month‐old infants to detect a difference in the size of a single element (Elmo face). Infants successfully discriminated a 1:4, 1:3 and 1:2 change in the area of the Elmo face but failed to discriminate a 2:3 change. In addition, the novelty preference was linearly related to the ratio difference between the novel and familiar area. Results suggest that Weber's Law holds for area discriminations in infancy and also reveal that at 6 months of age infants are equally sensitive to number, time and area.
The application of social cognitive theory to web‐based learning through NetPorts
Authors: Wang Shu‐Ling , Lin Sunny S. J. 
Published: September 2006

AbstractAlthough the Web allows for flexible learning, research has found that online students tend to lack focus, willingness to participate, confidence, and discipline. This study thus attempts to promote Web‐based self‐regulated learning from the social cognitive perspective, which emphasizes the interactions among personal, behavioral, and environmental influences.This study has identified the most significant factors for personal, behavioral, and environmental influences in the social cognitive model of self‐regulated learning, and also applied this model to the development of the NetPorts web‐based learning system. NetPorts, in turn, allows us to empirically analyze the interactions between the aforementioned factors. Our Web‐based findings support the social cognitive view of self‐regulated learning: students who hold higher levels of motivation apply more effective strategies, and respond more appropriately to environmental demands, in the Web‐based learning environment. These findings also further validate the application of the social cognitive model to Web‐based learning through the NetPorts.
Providing hearing‐impaired students with learning care after classes through smart phones and the GPRS network
Authors: Liu Chen‐Chung , Hong Yi‐Ching 
Published: September 2006

AbstractAlthough computers and network technology have been widely utilised to assist students learn, few technical supports have been developed to help hearing‐impaired students learn in Taiwan. A significant challenge for teachers is to provide after‐class learning care and assistance to hearing‐impaired students that sustain their motivation to participate in continuous learning activities. However, lacking an effective communication channel, teachers cannot easily provide after‐class learning care or instruction to sustain student motivation. This study developed a learning support system to provide after‐class learning care through smart phones and the General Packet Radio Service (GPRS) network. Student reactions identified effective strategies regarding student–teacher interaction while teachers utilised the wireless network and handheld devices to provide learning support. Questionnaire results demonstrated that most students and their parents considered student–teacher interaction and strategies through GPRS and smart phones effective in improving student learning at home.
DY‐9760e, a Novel Calmodulin Inhibitor, Exhibits Cardioprotective Effects in the Ischemic Heart
Authors: Fukunaga Kohji , Han Feng , Shioda Norifumi , Moriguchi Shigeki , Kasahara Jiro , Shirasaki Yasufumi 
Published: September 2006

ABSTRACTDY‐9760e (3‐[2‐[4‐(3‐chloro‐2‐methylphenyl)‐1‐piperazinyl]ethyl]‐5,6‐dimethoxy‐1‐(4‐imidazolylmethyl)‐1H‐indazole dihydrochloride‐3.5 hydrate) inhibits Ca2+/CaM‐dependent nitric oxide synthase (NOS), thereby inhibiting nitric oxide (NO) production. In cardiomyocytes from ischemic rat heart NO and superoxide levels are increased causing protein tyrosine nitration. In hearts subjected to ischemia/reperfusion DY‐9760e totally abolishes protein tyrosine nitration. Notably, DY‐9760e also inhibits calpain and cas‐pase‐3 activation that occurs prior to apoptosis in cardiomyocytes. In ischemic hearts fodrin is the substrate for calpain. DY‐9760e inhibits fodrin breakdown in the peri‐infarct area rather than in the infarct core. In the ischemic rat brain DY‐9760e inhibits caspase‐3‐induced proteolysis of calpastatin, an endogenous calpain inhibitor, suggesting that crosstalk between calpain and caspase‐3 is mediated by calpastatin breakdown. Thus, DY‐9760e rescues neurons and cardiomyocytes from ischemic injury by inhibiting crosstalk between calpain and caspase‐3 as well as protein tyrosine nitration.
Pharmacologic Profile and Therapeutic Potential of NCX 4016, a Nitric Oxide‐releasing Aspirin, for Cardiovascular Disorders
Authors: Gresele Paolo , Momi Stefania 
Published: September 2006

ABSTRACTNCX 4016, 2‐(acetyloxy)benzoic acid 3‐[(nitrooxy)methyl]phenyl ester, is a new molecule in which a nitric oxide (NO)‐releasing moiety is covalently linked to aspirin. After enzymatic metabolism, NCX 4016 releases both components.In vitroand in some animal models, these components exert their pharmacologic effects simultaneously. Nitric oxide (NO) is a small gaseous molecule that exerts several activities which may prevent atherothrombotic disorders. Moreover, it displays a protective activity on the gastric mucosa.NCX 4016 has been shown to inhibit platelet activationin vitromore effectively than aspirin, to inhibit smooth muscle cell proliferation, to exert an endothelial cell protective activity and to suppress the function of several inflammatory cells potentially involved in atherothrombosis.In animal models, NCX 4016 protected from platelet thromboembolism, prevented restenosis in atherosclerosis‐prone animals, protected the heart from ischemia/reperfusion injury, and induced neoangiogenesis in critically ischemic limbs. Moreover, it displayed little or no gastric toxicity and appeared to protect stomach from noxious stimuli, including aspirin.NCX 4016 has been evaluated in healthy volunteers and found to inhibit platelet cyclo‐oxygenase‐1 (COX‐1) similarly to or slightly less than aspirin, to raise the circulating levels of NO‐degradation products, and to have little or no gastric toxicity in short term studies. In particular, in phase II studies, NCX 4016 had favorable effects on effort‐induced endothelial dysfunction in intermittent claudication and on platelet‐activation parameters elicited by short‐term hyperglycemia in type II diabetics. In patients with type II diabetes the effects of NCX 4016 on microalbuminuria and on some hemodynamic parameters were promising. The pharmacokinetics ofin vivoaspirin‐ and NO‐ released by NCX 4016, as well as the bioavailability of the two molecules, were not yet adequately studied. Also, the long‐term tolerability of NCX 4016, as well as its possible effectiveness in preventing ischemic cardiovascular events and progression of atherosclerosis, should be explored.
Cardiovascular Therapeutic Aspects of Soluble Epoxide Hydrolase Inhibitors
Authors: Imig John D. 
Published: September 2006

ABSTRACTSoluble epoxide hydrolase (sEH) is an enzyme responsible for the conversion of lipid epoxides to diols by the addition of water. Biological actions on the cardiovascular system that are attributed to epoxides include vasodilation, antiinflammatory actions and vascular smooth muscle cell antimigratory actions. Conversion of arachidonic acid epoxides to diols by sEH diminishes the beneficial cardiovascular properties of these epoxyeicosano‐ids. Cardiovascular diseases in animal models and humans have been associated with decreased epoxygenase activity or increased sEH activity and these changes are responsible for the progression of the disease state. More recently, sEH gene polymorphisms in the human population have been associated with increased risk for cardiovascular diseases. Thus the biological actions of epoxyeicosanoids and the sEH enzyme are ideal therapeutic targets for cardiovascular diseases. The rapid development of 1,3‐disubstituted urea based sEH inhibitors over the past five years has resulted in a number of studies demonstrating cardiovascular protection. sEH inhibitors have antihypertensive and antiinflammatory actions and have been demonstrated to decrease cerebral ischemic and renal injury in rat models of hypertension. These findings of beneficial actions in animal models of disease position the sEH enzyme as a promising therapeutic target for cardiovascular diseases.