bluuebunny/crossref_metadata_2025 huggingface dataset:
The light‐sensitive photoprotein berovin from the bioluminescent ctenophore Beroe abyssicola: a novel type of Ca2+‐regulated photoprotein
Authors: Markova Svetlana V. , Burakova Ludmila P. , Golz Stefan , Malikova Natalia P. , Frank Ludmila A. , Vysotski Eugene S.
Published: January 2012

Light‐sensitive Ca2+‐regulated photoproteins are responsible for the bright bioluminescence of ctenophores. Using functional screening, four full‐size cDNA genes encoding the same 208‐amino‐acid polypeptide were isolated from two independent cDNA libraries prepared from two Beroe abyssicola specimens. Sequence analysis revealed three canonical EF‐hand calcium‐binding sites characteristic of Ca2+‐regulated photoproteins, but a very low degree of sequence identity (27–29%) with aequorin‐type photoproteins, despite functional similarities. Recombinant berovin was expressed in Escherichia coli cells, purified, converted to active photoprotein and characterized. Active berovin has absorption maxima at 280 and 437 nm. The Ca2+‐discharged protein loses visible absorption, but exhibits a new absorption maximum at 335 nm. The berovin bioluminescence is blue (λmax = 491 nm) and a change in pH over the range 6.0–9.5 has no significant effect on the light emission spectrum. By contrast, the fluorescence of Ca2+‐discharged protein (λex = 350 nm) is pH sensitive: at neutral pH the maximum is at 420 nm and at alkaline pH there are two maxima at 410 and 485 nm. Like native ctenophore photoproteins, recombinant berovin is also inactivated by light. The Ca2+ concentration–effect curve is a sigmoid with a slope on a log–log plot of ∼ 2.5. Although this curve for berovin is very similar to those obtained for obelin and aequorin, there are evident distinctions: berovin responds to calcium changes at lower concentrations than jellyfish photoproteins and its Ca2+‐independent luminescence is low. Recombinant berovin was successfully expressed in mammalian cells, thereby demonstrating potential for monitoring intracellular calcium.

Database
 The nucleotide sequences have been deposited in the GenBankTM/EBI Data Bank with accession numbers: apoberovin cDNA genes, JN673813 (BA1), JN673814 (BA2), JN673815 (BA3), JN673816 (BA4); fragment 18S rRNA, JN673817 (BA‐rRNA5).
In Silico Characterization of Atypical Kinase PFD0975w from Plasmodium Kinome: A Suitable Target For Drug Discovery
Authors: Trivedi Vishal , Nag Swagata
Published: January 2012

RIO‐2 kinase is known to regulate ribosome biogenesis and other cell cycle events. The 3D model of ATP bound and an unbound form of PFD0975w was generated using AfRIO‐2 crystal structure 1TQI, 1ZAO as template employing Modeller9v7 program. Structural characterization identified N‐terminal winged helix domain (1–84), C‐terminal kinase domain (148–275), and presence of other critical residues known for ATP binding and kinase activity. Using Q‐site and pocket finder, a number of well‐defined substrate (peptide) binding regions were identified in the catalytic core of the protein. The peptide binding regions were further validated by molecular modeling a non‐specific polyalanine peptide and a sequence‐specific peptide2 into these sites to generate a stable PFD0975w/peptide complexes. Peptide fits well into identified pocket on PFD0975w and makes extensive interaction with the protein residues. These newly identified peptide binding sites potentially give opportunity to design a specific inhibitor against PFD0975w. There are subtle but significant differences between Plasmodium falciparum and human RIO‐2 to exploit PFD0975w for drug development. In conclusion, our finding will let us to design effective chemotherapy against malaria parasite exploiting PFD0975w as a drug target.
Using Eye Tracking Technology to Determine the Most Effective Viewing Format and Content for Osteoporosis Prevention Print Advertisements
Authors: O'MALLEY DEBORAH , LATIMER AMY , BERENBAUM ERIN
Published: January 2012

In series of three experiments young women's attention patterns were analyzed using eye tracking to deteremine the most effective viewing format and message content for presenting osteoporosis prevention ads. In Experiment 1A ads including both images and text attracted more attention than the image‐only or text‐only formats, p < .01. Experiment 1B revealed that osteoporosis ads attract significantly less attention than fashion and beauty ads (p < .01) and exercise apparel ads (p < .01). The last experiment revealed that osteoporosis ads featuring exercise messages were more effective at capturing attention than those promoting increased calcium and vitamin D consumption (p < .01). These findings may inform the way in which future osteoporosis prevention ads are created.
Current protected sites do not allow the representation of endangered invertebrates: the Spanish case
Authors: HERNÁNDEZ‐MANRIQUE OLGA L. , NUMA CATHERINE , VERDÚ JOSE R. , GALANTE EDUARDO , LOBO JORGE M.
Published: January 2012

Abstract.  1. Using a recently created database representing the joint effort of around 100 invertebrate taxonomists, this study uses the information on 52 arthropoda and 27 mollusca species that are endangered and critically endangered to examine to what extent invertebrate species are represented in existing Spanish protected areas.

2. As distribution information is available at a 100 km2 resolution, we consider different area thresholds to judge cells as being protected.

3. Approximately 19% of the area represented by the grid cells with observed occurrences rates as extant protected reserves, and 36% is included within the Natura 2000 network.

4. If having 50% of the cell area as a Natura 2000 reserve is considered as sufficient to have effective protection, almost 68% of species and 32% of probable populations (contiguous cell groups) would be represented.

5. However, 77% of species and 94% of probable populations are not represented in the current protected reserves if we establish that at least 95% of each cell area should belong to a reserve to provide effective protection.

6. Thus, existing conservation strategies, which are based primarily on the protection of certain areas and vertebrate species, may be insufficient to ensure the conservation of invertebrate species.
Discovery of a Novel Circulating Biomarker in Patients with Abdominal Aortic Aneurysm: A Pilot Study Using a Proteomic Approach
Authors: Wallinder Jonas , Bergström Jörgen , Henriksson Anders E.
Published: January 2012

Abdominal aortic aneurysm (AAA) is a common condition with high mortality when ruptured. Most clinicians agree that small AAAs are best managed by ultrasonographic surveillance. However, it has been stated in recent reviews that a serum/plasma biomarker that predicts AAA rupture risk would be a powerful tool in stratifying patients with small AAA. Identification of such circulating biomarkers has been to date unsuccessful. In this study, we used a proteomic approach to find new, potential plasma AAA biomarker candidates. Prefractionated plasma samples were analyzed by two‐dimensional differential in‐gel electrophoresis to identify differentially expressed proteins between four patients with small AAA and four controls without aneurysm. Protein spots that differed significantly between patients and controls were selected and identified by mass spectrometry. Three protein spots had significantly different expression between patients and controls. The most interesting finding was that patients with small AAA had increased levels of the enzyme glycosylphosphatidylinositol‐specific phospholipase D (GPI‐PLD) compared with the controls without aneurysm. In conclusion, by using a proteomic approach, this pilot‐study provides evidence of GPI‐PLD as a novel potential plasma biomarker for AAA. Clin Trans Sci 2012; Volume 5: 56–59
Linkage Disequilibrium and Haplotype Analysis of COX‐2 and Risk of Colorectal Adenoma Development
Authors: Kwagyan John , Apprey Victor , Ashktorab Hassan
Published: January 2012

Single nucleotide polymorphisms (SNPs) in the promoter and untranslated region of cyclooxygenase (COX)‐2, an inducible enzyme responsible for the synthesis of prostaglandins, have been reported to modulate the risk for many human cancers. We performed comprehensive linkage disequilibrium (LD) and haplotype analyses of 13 single nucleotide polymorphisms of the COX‐2 gene and examined its susceptibility to adenoma development in 72 African American cases and 142 controls. Results revealed significant variation in LD patterns with consequence for adenoma development. Two distinct haplotype blocks were identified; one block covered the coding regions of exon 1, introns and a section of the 3′‐unstranslated region (3′‐UTR), whereas the second block resided solely in the 3′‐UTR region. A haplotype in block 1 increased the risk of adenoma development by threefold (odds ratio [OR]= 2.9, confidence interval [CI]= 1.8–3.7, P= 0.002). Regression analysis showed, increase in copies of minor alleles of 6,064(T>C) polymorphism associated with increased odds of adenoma development by 80% (OR = 1.80, CI = 1.09–3.21, P= 0.034), 10,848(G>A) by 84% (OR = 1.84, CI = 1.05–3.23, P= 0.034) and 10,935(A>G) by 32% (OR = 1.32, CI = 1.12–3.69, P= 0.036). These results support the hypothesis that COX‐2 gene might play a role in the etiology of colon cancer and warrant further investigation in other cancers. Besides, these variations should be taken into account for disease‐based association studies in which the COX‐2 polymorphism is considered as a candidate gene. Clin Trans Sci 2012; Volume 5: 60–64
Effects of Contact Interface Parameters on Vibration of Turbine Bladed Disks With Underplatform Dampers
Authors: Schwingshackl C. W. , Petrov E. P. , Ewins D. J.
Published: January 2012

The design of high cycle fatigue resistant bladed disks requires the ability to predict the expected damping of the structure in order to evaluate the dynamic behavior and ensure structural integrity. Highly sophisticated software codes are available today for this nonlinear analysis, but their correct use requires a good understanding of the correct model generation and the input parameters involved to ensure a reliable prediction of the blade behavior. The aim of the work described in this paper is to determine the suitability of current modeling approaches and to enhance the quality of the nonlinear modeling of turbine blades with underplatform dampers. This includes an investigation of a choice of the required input parameters, an evaluation of their best use in nonlinear friction analysis, and an assessment of the sensitivity of the response to variations in these parameters. Part of the problem is that the input parameters come with varying degrees of uncertainty because some are experimentally determined, others are derived from analysis, and a final set are often based on estimates from previous experience. In this investigation the model of a commercial turbine bladed disk with an underplatform damper is studied, and its first flap, first torsion, and first edgewise modes are considered for 6 EO and 36 EO excitation. The influence of different contact interface meshes on the results is investigated, together with several distributions of the static normal contact loads, to enhance the model setup and, hence, increase accuracy in the response predictions of the blade with an underplatform damper. A parametric analysis is carried out on the friction contact parameters and the correct setup of the nonlinear contact model to determine their influence on the dynamic response and to define the required accuracy of the input parameters.
Effective Stiffening and Damping Enhancement of Structures With Strongly Nonlinear Local Attachments
Authors: Sapsis Themistoklis P. , Dane Quinn D. , Vakakis Alexander F. , Bergman Lawrence A.
Published: January 2012

We study the stiffening and damping effects that local essentially nonlinear attachments can have on the dynamics of a primary linear structure. These local attachments can be designed to act as nonlinear energy sinks (NESs) of shock-induced energy by engaging in isolated resonance captures or resonance capture cascades with structural modes. After the introduction of the NESs, the effective stiffness and damping properties of the structure are characterized through appropriate measures, developed within this work, which are based on the energy contained within the modes of the primary structure. Three types of NESs are introduced in this work, and their effects on the stiffness and damping properties of the linear structure are studied via (local) instantaneous and (global) weighted-averaged effective stiffness and damping measures. Three different applications are considered and show that these attachments can drastically increase the effective damping properties of a two-degrees-of-freedom system and, to a lesser degree, the stiffening properties as well. An interesting finding reported herein is that the essentially nonlinear attachments can introduce significant nonlinear coupling between distinct structural modes, thus paving the way for nonlinear energy redistribution between structural modes. This feature, coupled with the well-established capacity of NESs to passively absorb and locally dissipate shock energy, can be used to create effective passive mitigation designs of structures under impulsive loads.
Towards a Generic Vehicle Model
Authors: Mikelsons Lars , Brandt Thorsten
Published: January 2012

Real-time control often requires process models that can be solved adequately fast on prescribed control hardware. One class of applications is model predictive control, which can be considered as one of the most powerful control techniques. However, for real-time control of systems with fast dynamics such as vehicles, appropriate models are necessary. Thus, on the one hand, the design process requires models of adequate complexity to cover all relevant effects, and, on the other hand, real-time control requires models with a limited number of computations. In this contribution, an approach for a generation of generic models of the dynamic of technical systems is presented. In this context generic is twofold. First, the model is dimensionless. In particular, the model is robust with respect to variations of the dimensionless parameters and can be easily projected onto a large variety of geometries. Second, equation-based reduction techniques are used to limit the number of necessary operations for a simulation. Hence, the models can be reduced for given controller hardware. As an application example, a standard vehicle model with nonlinear tire characteristics is used. Here the equation-based reduction techniques lead to a reduction of the required computations by a factor of five. In this case the maximum error compared to the reference model is smaller than 5%.
Dry Electrode Based Wearable Wireless Brain–Computer Interface System
Authors: Kai Guo , WeiHua Pei , Yu Wang , Bing Xu , Qiang Gui , Jian Liu , HongDa Chen
Published: January 2012

Brain–computer interface (BCI) technology is a key issue in neural engineering, which can manipulate machine by electroencephalography (EEG). An important question surrounding the use of the BCI is the design of a wearable electroencephalography recording and processing equipment. We report the design and fabrication of a novel system based on dry electrodes, in which skin preparation and application of electrolytic gel are not required. In this study, an EEG-based BCI system, which includes a wireless transmitter module and an receiver module was designed, EEG is acquired using dry electrodes, amplified and processed by an application-specific integrated circuit (ASIC), and transmitted to the receiver by RF chip. The BCI system can obtain the subject’s degree of concentration, and those trained subjects have the ability of controlling the machine by changing their EEG signals. A experiment that controlling a toy car using the BCI system is successfully performed. The wearable transmitter module weighs 39 g only and easy to wear. The transmitter consumes 60 mW of dc power and generates an output power of 0 dBm. The BCI system is suitable for long-term EEG monitoring in users’ daily life. This system is feasible for further extension.
Wnt/β-Catenin Signaling and AXIN1 Regulate Apoptosis Triggered by Inhibition of the Mutant Kinase BRAF
V600E
in Human Melanoma
Authors: Biechele Travis L. , Kulikauskas Rima M. , Toroni Rachel A. , Lucero Olivia M. , Swift Reyna D. , James Richard G. , Robin Nick C. , Dawson David W. , Moon Randall T. , Chien Andy J.
Published: January 2012

The functional crosstalk between Wnt/β-catenin and BRAF signaling may yield more effective therapies for treating melanoma.
A Dual Array-Based Approach to Assess the Abundance and Posttranslational Modification State of Signaling Proteins
Authors: Luckert Katrin , Gujral Taranjit S. , Chan Marina , Sevecka Mark , Joos Thomas O. , Sorger Peter K. , MacBeath Gavin , Pötz Oliver
Published: January 2012

Combining two strategies enables simultaneous quantification of multiple signaling proteins.
A Wnt-Bmp Feedback Circuit Controls Intertissue Signaling Dynamics in Tooth Organogenesis
Authors: O’Connell Daniel J. , Ho Joshua W. K. , Mammoto Tadanori , Turbe-Doan Annick , O’Connell Joyce T. , Haseley Psalm S. , Koo Samuel , Kamiya Nobuhiro , Ingber Donald E. , Park Peter J. , Maas Richard L.
Published: January 2012

Computational and genetic analyses reveal a key circuit involving Wnt and Bmp in developing teeth in mice.
Effect of pH on
In Vitro
Susceptibility of Candida glabrata and Candida albicans to 11 Antifungal Agents and Implications for Clinical Use
Authors: Danby Claire S. , Boikov Dina , Rautemaa-Richardson Rina , Sobel Jack D.
Published: January 2012

The treatment of vulvovaginal candidiasis (VVC) due to
Candida glabrata
is challenging, with limited therapeutic options. Unexplained disappointing clinical efficacy has been reported with systemic and topical azole antifungal agents in spite of
in vitro
susceptibility. Given that the vaginal pH of patients with VVC is unchanged at 4 to 4.5, we studied the effect of pH on the
in vitro
activity of 11 antifungal agents against 40
C. glabrata
isolates and compared activity against 15 fluconazole-sensitive and 10 reduced-fluconazole-susceptibility
C. albicans
strains.
In vitro
susceptibility to flucytosine, fluconazole, voriconazole, posaconazole, itraconazole, ketoconazole, clotrimazole, miconazole, ciclopirox olamine, amphotericin B, and caspofungin was determined using the CLSI method for yeast susceptibility testing. Test media were buffered to pHs of 7, 6, 5, and 4. Under conditions of reduced pH,
C. glabrata
isolates remained susceptible to caspofungin and flucytosine; however, there was a dramatic increase in the MIC
90
for amphotericin B and every azole drug tested. Although susceptible to other azole drugs tested at pH 7,
C. albicans
strains with reduced fluconazole susceptibility also demonstrated reduced susceptibility to amphotericin B and all azoles at pH 4. In contrast, fluconazole-sensitive
C. albicans
isolates remained susceptible at low pH to azoles, in keeping with clinical observations. In selecting agents for treatment of recurrent
C. glabrata
vaginitis, clinicians should recognize the limitations of
in vitro
susceptibility testing utilizing pH 7.0.
Nonthermal Atmospheric Plasma Rapidly Disinfects Multidrug-Resistant Microbes by Inducing Cell Surface Damage
Authors: Kvam Erik , Davis Brian , Mondello Frank , Garner Allen L.
Published: January 2012

Plasma, a unique state of matter with properties similar to those of ionized gas, is an effective biological disinfectant. However, the mechanism through which nonthermal or “cold” plasma inactivates microbes on surfaces is poorly understood, due in part to challenges associated with processing and analyzing live cells on surfaces rather than in aqueous solution. Here, we employ membrane adsorption techniques to visualize the cellular effects of plasma on representative clinical isolates of drug-resistant microbes. Through direct fluorescent imaging, we demonstrate that plasma rapidly inactivates planktonic cultures, with >5 log
10
kill in 30 s by damaging the cell surface in a time-dependent manner, resulting in a loss of membrane integrity, leakage of intracellular components (nucleic acid, protein, ATP), and ultimately focal dissolution of the cell surface with longer exposure time. This occurred with similar kinetic rates among methicillin-resistant
Staphylococcus aureus
(MRSA),
Pseudomonas aeruginosa
, and
Candida albicans
. We observed no correlative evidence that plasma induced widespread genomic damage or oxidative protein modification prior to the onset of membrane damage. Consistent with the notion that plasma is superficial, plasma-mediated sterilization was dramatically reduced when microbial cells were enveloped in aqueous buffer prior to treatment. These results support the use of nonthermal plasmas for disinfecting multidrug-resistant microbes in environmental settings and substantiate ongoing clinical applications for plasma devices.
In Vitro
Potential of Equine DEFA1 and eCATH1 as Alternative Antimicrobial Drugs in Rhodococcosis Treatment
Authors: Schlusselhuber Margot , Jung Sascha , Bruhn Oliver , Goux Didier , Leippe Matthias , Leclercq Roland , Laugier Claire , Grötzinger Joachim , Cauchard Julien
Published: January 2012

Rhodococcus equi
, the causal agent of rhodococcosis, is a severe pathogen of foals but also of immunodeficient humans, causing bronchopneumonia. The pathogen is often found together with
Klebsiella pneumoniae
or
Streptococcus zooepidemicus
in foals. Of great concern is the fact that some
R. equi
strains are already resistant to commonly used antibiotics. In the present study, we evaluated the
in vitro
potential of two equine antimicrobial peptides (AMPs), eCATH1 and DEFA1, as new drugs against
R. equi
and its associated pathogens. The peptides led to growth inhibition and death of
R. equi
and
S. zooepidemicus
at low micromolar concentrations. Moreover, eCATH1 was able to inhibit growth of
K. pneumoniae
. Both peptides caused rapid disruption of the
R. equi
membrane, leading to cell lysis. Interestingly, eCATH1 had a synergic effect together with rifampin. Furthermore, eCATH1 was not cytotoxic against mammalian cells at bacteriolytic concentrations and maintained its high killing activity even at physiological salt concentrations. Our data suggest that equine AMPs, especially eCATH1, may be promising candidates for alternative drugs to control
R. equi
in mono- and coinfections.
Voltammetric study of 2-guanidinobenzimidazole: Electrode mechanism and determination at mercury electrode
Authors: Skrzypek Sławomira , Mirceski Valentin , Smarzewska Sylwia , Guziejewski Dariusz , Ciesielski Witold
Published: January 2012

Although 2-guanidinobenzimidazole (GBI; CAS: 5418-95-1) is a compound of biological interest, generally there is a lack of electrochemical studies and the methods of its determination. The GBI behavior at a mercury electrode was analyzed under conditions of linear sweep voltammetry (LSV), differential pulse voltammetry (DPV), square-wave voltammetry (SWV) and square-wave stripping voltammetry (SWSV). Although GBI is electrochemically inactive at mercury electrode it adsorbs at the mercury surface and catalyzes effectively the hydrogen evolution reaction. Theoretical analysis of two possible pathways, according to which the GBI electrode mechanism can be explained, is performed. Simple analysis of peak current and potential with respect to available time window, i.e. change of frequency can be helpful in discerning the character of the recorded SW current. The established electrode mechanism is assumed to involve a preceding chemical reaction in which the adsorbed catalyst (GBIads) is protonated and the protonated form of the catalyst (GBIH+(ads)) is irreversibly reduced at potential about –1.18 V vs Ag|AgCl (citrate buffer pH 2.5). New methods of voltammetric determination of 2-guanidinobenzimidazole were developed. The detection and quantifications limits were found to be 1 × 10–7, 1 × 10–6 mol l–1 (SWV); 8 × 10–8, 9 × 10–7 mol l–1 (SWSV); 4 × 10–7, 2 × 10–6 mol l–1 (DPV) and 6 × 10–7, 3 × 10–6 mol l–1 (LSV), respectively.
Testing models of aquatic N2O flux for inland waters
Authors: Baulch Helen M. , Schiff Sherry L. , Maranger Roxane , Dillon Peter J.
Published: January 2012

The current Intergovernmental Panel on Climate Change (IPCC) method for tabulating agricultural nitrous oxide (N2O) emissions suggests that aquatic ecosystems may be important N2O sources. However, estimates are highly uncertain, and the method to estimate emissions is rarely tested. The default IPCC emission factor for groundwater and surface drainage (EF5-g; defined as N2O-N:nitrate-N) has been lowered recently. Our data support further reduction. Notably, we present the first EF5-gdata under ice, which reflects groundwater inputs not confounded by gas exchange. These under-ice data suggest an EF5-gof 0.13%, approximately half the current IPCC default value. Our data from the open-water season also suggest a reduction to 0.11% (based on annual means). The data highlight major problems with the IPCC method. EF5-gwas extremely variable, with the highest values observed in a stream that was a net sink of N2O. Testing the overall method for freshwater emissions is more problematic because of the multidecade transit time from headwaters in our study region to the Atlantic Ocean and limited information on emissions from lakes.
PaV1 infection in the Florida spiny lobster (Panulirus argus) fishery and its effects on trap function and disease transmission
Authors: Behringer Donald C. , Butler Mark J. , Moss Jessica , Shields Jeffrey D.
Published: January 2012

The Caribbean spiny lobster (Panulirus argus) supports the most economically valuable fishery in the Caribbean. In Florida, USA, the majority of the catch is landed in traps “baited” with live, sublegal-sized lobsters that attract other lobsters due to their social nature. This species is also commonly infected by the pathogenic virus Panulirus argus Virus 1 (PaV1). Here we describe a polymerase chain reaction (PCR) based assessment of the prevalence of PaV1 in the lobster fishery from the Florida Keys. We tested the effect of PaV1-infected lobsters in traps on catch and on transmission to other trapped, uninfected lobsters. We found that 11% of the lobsters caught in commercial traps were positive for the virus by PCR, but none of these animals showed visible signs of disease. We also tested whether healthy lobsters avoid diseased lobsters in traps. Traps into which we introduced an infected lobster caught significantly fewer lobsters than traps containing an uninfected lobster. Moreover, uninfected lobsters confined in traps with infected lobsters acquired significantly more PaV1 infections than those confined with uninfected lobsters. This study demonstrates the indirect effects that pathogens can have on fisheries and the unintended consequences of certain fishery practices on the epidemiology of a marine pathogen.
Trisomy greatly enhances interstitial crossing over in a translocation heterozygote of Secale
Authors: Sybenga J. , Verhaar H.M. , Botje D.G.A.
Published: January 2012

Chromosomal rearrangements, including reciprocal translocations, may prevent recombinational transfer of genes from a donor genotype to a recipient, especially when the gene is located in an interstitial segment. The effect of trisomy of chromosome arm 1RS on recombination was studied in translocation heterozygote T248W of rye ( Secale cereale ), involving chromosome arms 1RS and 6RS. (Pro)metaphase I configuration frequencies were analyzed. Crossing over, estimated as chiasma parameters, in five genetically different euploid heterozygotes was compared with those of 10 different single arm trisomics. The addition of 1RS greatly altered the crossing over pattern around the translocation break point, with a special increase in the interstitial segment of 6RS and adjoining regions, normally hardly accessible to recombination. Furthermore, there was considerable variation between plants of closely related genotypes. Heterogeneity widens the distribution of crossing overs, including segments normally not accessible to recombination, but decreases average recombination in other segments. The extra chromosome and abnormal segregants are eliminated by using the trisomic as the pollen parent.
Detection of interstitial telomeric sequences in the Arctic charr (Salvelinus alpinus) (Teleostei: Salmonidae)
Authors: Pomianowski K. , Jankun M. , Ocalewicz K.
Published: January 2012

Highly polymorphic Arctic charr ( Salvelinus alpinus Linnaeus, 1758) chromosomes were studied using conventional and molecular methods. The diploid chromosome number in the studied individuals was 2n = 81 or 2n = 82, with a fundamental arm number (NF) = 100. These differences are due to Robertsonian fusions. Interindividual variation in the number and size of DAPI and CMA3 positively stained chromatin sites was observed in studied specimens. In the case of two individuals, the subtelomeric region of the long arm (q) of the largest acrocentric chromosome (chromosome number 10) was positively stained by CMA3 fluorochrome. Both primed in situ labelling (PRINS) and fluorescence in situ hybridization (FISH) revealed that this CMA3-positive region was flanked by telomeric sequences. Previously, the subterminal position of interstitial telomeric sequences located in the vicinity of the CMA3-positive guanine-rich chromatin have been described in two other Salvelinus species, brook trout ( Salvelinus fontinalis ) and lake trout ( Salvelinus namaycush ). Moreover, multichromosomal location and variation in size of CMA3 bands have been observed in various Salvelinus taxa, including fishes with internally located telomeric sequences. These results suggest that relocation of CMA3-positive chromatin segments in these species may be facilitated by flanking interstitial telomeric sequences (ITSs).
Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice
Authors: Cheng Lirui , Wang Yun , Meng Lijun , Hu Xia , Cui Yanru , Sun Yong , Zhu Linghua , Ali Jauhar , Xu Jianlong , Li Zhikang
Published: January 2012

Effect of genetic background on detection of quantitative trait locus (QTL) governing salinity tolerance (ST) was studied using two sets of reciprocal introgression lines (ILs) derived from a cross between a moderately salinity tolerant japonica variety, Xiushui09 from China, and a drought tolerant but salinity susceptible indica breeding line, IR2061–520–6-9 from the Philippines. Salt toxicity symptoms (SST) on leaves, days to seedling survival (DSS), and sodium and potassium uptake by shoots were measured under salinity stress of 140 mmol/L of NaCl. A total of 47 QTLs, including 26 main-effect QTLs (M-QTLs) and 21 epistatic QTLs (E-QTLs), were identified from the two sets of reciprocal ILs. Among the 26 M-QTLs, only four (15.4%) were shared in the reciprocal backgrounds while no shared E-QTLs were detected, indicating that ST QTLs, especially E-QTLs, were very specific to the genetic background. Further, 78.6% of the M-QTLs for SST and DSS identified in the reciprocal ILs were also detected in the recombinant inbred lines (RILs) from the same cross, which clearly brings out the background effect on ST QTL detection and its utilization in ST breeding. The detection of ILs with various levels of pyramiding of nonallelic M-QTL alleles for ST from Xiushui09 into IR2061-520-6-9 allowed us to further improve the ST in rice.
Exploring polymorphisms and associations of the bovine MOGAT3 gene with growth traits
Authors: Sun Jiajie , Zhang Chunlei , Lan Xianyong , Lei Chuzhao , Chen Hong
Published: January 2012

Monoacylglycerol acyltransferase (MGAT3, also known as MOGAT3) catalyzes the synthesis of diacylglycerol (DAG) using 2-monoacylglycerol and fatty acyl coenzyme A. This enzymatic reaction is believed to be an essential and rate-limiting step for the absorption of dietary fat in the small intestine. However, similar research for the bovine MOGAT3 gene is lacking. Therefore, in this paper, polymorphisms of the bovine MOGAT3 gene were detected in 1145 individuals from five cattle breeds by DNA pooling, PCR–RFLP, and DNA sequencing methods. The results showed that 26 novel SNPs were identified, which included 16 mutations in the coding region and the others in the introns. Additionally, association analysis between two missense mutations, g.A229G and g.G1627A, and growth traits in Nanyang cattle up to 2 years of age and adult Qinchuan cattle was performed. The results indicated that polymorphisms were significantly associated with Nanyang cattle, but no convincing associations were observed for Qinchuan cattle for the studied traits.
Polycyclic aromatic hydrocarbon degrading gene islands in five pyrene-degradingMycobacteriumisolates from different geographic locations
Authors: Zhang Chun , Anderson Anne J.
Published: January 2012

Mycobacterium sp. strain KMS utilizes pyrene, a high-molecular weight polycyclic aromatic hydrocarbon (PAH), as a sole carbon source. Bioinformatic analysis of the genome of isolate KMS predicted 25 genes with the potential to encode 17 pyrene-induced proteins identified by proteomics; these genes were clustered on both the chromosome and a circular plasmid. RT-PCR analysis of total RNA isolated from KMS cells grown with or without pyrene showed that the presence of pyrene increased the transcript accumulation of 20 of the predicted chromosome- and plasmid-located genes encoding pyrene-induced proteins. The transcribed genes from both the chromosome and a circular plasmid were within larger regions containing genes required for PAH degradation constituting PAH-degrading gene islands. Genes encoding integrases and transposases were found within and outside the PAH-degrading gene islands. The lower GC content of the genes within the gene island (61%–64%) compared with the average genome content (68%) suggested that these mycobacteria initially acquired these genes by horizontal gene transfer. Synteny was detected for the PAH-degrading islands in the genomes of two additional Mycobacterium isolates from the same PAH-polluted site and of two other pyrene-degrading Mycobacterium from different sites in the United States of America. Consequently, the gene islands have been conserved from a common ancestral strain.
Effect of inter-renal aortic coarctation-induced hypertension on function and expression of vascular α1A- and α1D-adrenoceptors
Authors: López-Islas Inés , López-Sánchez Pedro , Ibarra Maximiliano , Gallardo-Ortiz Itzell A. , Terrón José A.
Published: January 2012

We investigated the effect of inter-renal aortic coarctation on the function and expression of vascular α1A- and α1D-adrenoceptors and plasma angiotensin II (ATII) in rats. Male Wistar rats, either sham operated (SO), or with aortic coarctation for 7 (AC7) and 14 days (AC14) were used for agonist-induced pressor responses in vehicle (physiological saline)- and antagonist-treated anesthetized animals, immunoblot analysis (α1A- and α1D-adrenoceptor in aorta and caudal arteries), and immunoassay (plasma ATII). The α1D-adrenoceptor antagonist, BMY-7378 (BMY) blocked noradrenaline-induced responses in the order SO > AC7 ≫ AC14; in contrast, the α1A-adrenoceptor antagonist RS-100329 (RS), produced a marginal shift to the right of the dose–response curve to noradrenaline, along with a strong decrease of the maximum pressor effect in the order SO > AC7 = AC14. The potency of the α1A-adrenoceptor agonist A-61603 increased in rats with AC14, and responses were inhibited by RS in the order AC14 > AC7 > SO. In aorta, α1D-adrenoceptor protein increased in AC7 and decreased in AC14; α1A-adrenoreceptor protein increased in the caudal artery of AC7 and returned to control values in AC14. Plasma ATII increased in AC7 and AC14, compared with SO rats. These results suggest an early and direct relationship between ATII and α1D-adrenoreceptors in the development of hypertension in this experimental model.
THE CATEGORY OF SIMULATIONS FOR WEIGHTED TREE AUTOMATA
Authors: ÉSIK ZOLTÁN , MALETTI ANDREAS
Published: January 2012

Simulations of weighted tree automata (wta) are considered. It is shown how such simulations can be decomposed into simpler functional and dual functional simulations also called forward and backward simulations. In addition, it is shown in several cases (fields, commutative rings, NOETHERIAN semirings, semiring of natural numbers) that all equivalent wta M and N can be joined by a finite chain of simulations. More precisely, in all mentioned cases there is a single wta that simulates both M and N. Those results immediately yield decidability of equivalence provided that the semiring is finitely (and effectively) presented.
OPTIMAL HYPER-MINIMIZATION
Authors: MALETTI ANDREAS , QUERNHEIM DANIEL
Published: January 2012

Minimal deterministic finite automata (DFAs) can be reduced further at the expense of a finite number of errors. Recently, such minimization algorithms have been improved to run in time O(n log n), where n is the number of states of the input DFA, by [GAWRYCHOWSKI and JEŻ: Hyper-minimisation made efficient. Proc. MFCS, LNCS 5734, 2009] and [HOLZER and MALETTI: An n log n algorithm for hyper-minimizing a (minimized) deterministic automaton. Theor. Comput. Sci. 411, 2010]. Both algorithms return a DFA that is as small as possible, while only committing a finite number of errors. These algorithms are further improved to return a DFA that commits the least number of errors at the expense of an increased (quadratic) run-time. This solves an open problem of [BADR, GEFFERT, and SHIPMAN: Hyper-minimizing minimized deterministic finite state automata. RAIRO Theor. Inf. Appl. 43, 2009]. In addition, an experimental study on random automata is performed and the effects of the existing algorithms and the new algorithm are reported.
TREE-BASED 2D INDEXING
Authors: ŽĎÁREK JAN , MELICHAR BOŘIVOJ
Published: January 2012

A new approach to the 2D pattern matching and specifically to 2D text indexing is proposed. A transformation of a 2D text into the form of a tree is presented. It preserves the context of each element of the 2D text. The tree can be linearised using the prefix notation into the form of a string (a linear text) and the pattern matching is performed in this text. Pushdown automata indexing the 2D text are constructed over the tree representation. They allow to search for 2D prefixes, 2D suffixes, and 2D factors of the 2D text in time proportional to the size of the representation of a 2D pattern. This result achieves the properties analogous to the results obtained in tree pattern matching and string indexing.
GOAL-ORIENTED PROCESSES WITH GPMN
Authors: JANDER KAI , BRAUBACH LARS , POKAHR ALEXANDER , LAMERSDORF WINFRIED , WACK KARL-JOSEF
Published: January 2012

Business process management is a challenging task that requires business processes being described, executed, monitored and continuously enhanced. This process management lifecycle requires business as well as IT people working together, whereby the view on business process is quite different on both sides. One important means for bridging the gap between both consists in having a modeling notation that can be easily understood but also has a precise semantics and can be used as a basis for workflow execution. Although existing approaches like BPMN and EPCs aim at being such as notation they are already very activity oriented and do not consider the underlying motivations of processes. Introducing the goal oriented process modeling notation (GPMN) a new language is presented that has the objective of bringing together both sides by establishing higher-level modeling concepts for workflows. This results in an increased intelligibility of workflow descriptions for business people and greater consideration for the way processes are described on the business side. The core idea of the approach consists in introducing different kinds of goals and goal relationships in addition to the established activity-centered behavior model. The applicability of the approach is further illustrated with an example workflow from Daimler AG.
INSTANCE MIGRATION BETWEEN ONTOLOGIES HAVING STRUCTURAL DIFFERENCES
Authors: DAVIDOVSKY MAXIM , ERMOLAYEV VADIM , TOLOK VYACHESLAV
Published: January 2012

Ontology instance migration is one of the complex and not fully solved problems in knowledge management. A solution is required when the ontology schema evolves in the life cycle and the assertions have to be transferred to the newer version. The problem may become more complex in distributed settings when, for example, several autonomous software entities use and exchange partial assertional knowledge in a domain that is formalized by different though semantically overlapping descriptive theories. Such an exchange is essentially the migration of the assertional part of an ontology to other ontologies belonging to or used by different entities. The paper presents our method and tool for migrating instances between the ontologies that have structurally different but semantically overlapping schemas. The approach is based on the use of the manually coded transformation rules describing the changes between the input and the output ontologies. The tool is implemented as a plug-in for the ProjectNavigator prototype software framework. The article also reports the results of our three evaluation experiments. In these experiments we evaluated the degree of complexity in the structural changes to which our approach remains valid. We also chose the ontology sets in one of the experiments to make the results comparable with the ontology alignment software. Finally we checked how well our approach scales with the increase of the quantity of the migrated ontology instances to the numbers that are characteristic to industrial ontologies. In our opinion the evaluation results are satisfactory and suggest some directions for the future work.
A SEMI-ANALYTICAL APPROACH TO PERTURBATIONS IN MUTATED HILLTOP INFLATION
Authors: PAL BARUN KUMAR , PAL SUPRATIK , BASU B.
Published: January 2012

We study cosmological perturbations and observational aspects for mutated hilltop model of inflation. Employing mostly analytical treatment, we evaluate observable parameters during inflation as well as post-inflationary perturbations. This further leads to exploring observational aspects related to cosmic microwave background (CMB) radiation. This semi-analytical treatment reduces complications related to numerical computation to some extent for studying the different phenomena related to CMB angular power spectrum for mutated hilltop inflation.
EXPERIMENTAL SEMIOTICS: AN ENGINE OF DISCOVERY FOR UNDERSTANDING HUMAN COMMUNICATION
Authors: GALANTUCCI BRUNO , ROBERTS GARETH
Published: January 2012

The recent growth of Experimental Semiotics (ES) offers us a new option to investigate human communication. We briefly introduce ES, presenting results from three themes of research which emerged within it. Then we illustrate the contribution ES can make to the investigation of human communication systems, particularly in comparison with the other existing options. This comparison highlights how ES can provide an engine of discovery for understanding human communication. In fact, in complementing the other options, ES offers us unique opportunities to test assumptions about communicative behavior, both through the experimenters' planned manipulations and through the unexpected behaviors humans exhibit in experimental settings. We provide three examples of such opportunities, one from each of the three research themes we present.
Vacuum Rabi Oscillation in Nonzero Temperature Open Cavity
Authors: Stefańska Patrycja , Wilczewski Marcin , Czachor Marek
Published: January 2012

Comparison of the theory of Rabi oscillations with experiment [M. Wilczewski and M. Czachor, Phys. Rev. A 79, 033836 (2009)] suggests that cavity lifetime parameters obtained in measurements with many photons may be much smaller than those applicable to almost vacuum states of light. In this context, we show that the conclusion remains unchanged even if one takes a more realistic description of the initial state of light in cavity.
COLLABORATIVE BEHAVIOUR OF SOFTWARE PRODUCT DEVELOPMENT TEAMS VARYING ON PRODUCT NEWNESS AS A SURROGATE MEASURE FOR INNOVATION
Authors: PUSHPA RANDHIR REGHUNATH , MATHEW MARY
Published: January 2012

Product development (PD) has traditionally been a collaborative effort with the PD team having to interact with various entities within and outside its boundary. Depending on the context and the kind of product being developed, teams typically interact with other teams, vendors, academic institutions and end users. This paper analyses the collaborative boundary crossing behaviour of software PD teams and the role of newness of product developed. The boundaries have been classified as horizontal, geographical and value-chain. Measurement was done with the help of two sets of questionnaires, one, to map the entities in the environment of the PD team and newness of the product developed, and the other, to measure collaborative boundary crossing behaviours of the team. The study showed that teams had low level of collaboration and the boundaries influenced collaboration behaviour. The newness of the product was also found to influence collaboration.
LEARNING ORIENTATION, INNOVATIVENESS AND FINANCIAL PERFORMANCE IN TRADITIONAL MANUFACTURING FIRMS: A HIGHER-ORDER STRUCTURAL EQUATION MODEL
Authors: NYBAKK ERLEND
Published: January 2012

This study examines the relationships among learning orientation, firm innovativeness and financial performance in the context of the Norwegian wood industry. A questionnaire-based survey was sent to the CEOs of firms in the wood industry in Norway (241 usable replies, response rate of 49 percent). Learning orientation and firm innovativeness were conceptualised and analysed as latent second-order constructs by using structural equation modelling. The findings show that learning orientation has a positive effect on firm innovativeness in the traditional manufacturing industry. In addition, learning orientation was found to positively affect financial performance via the full mediating effect of firm innovativeness. Furthermore, firm innovativeness was also found to have an independent positive effect on financial performance. No direct effect of learning orientation on financial performance was found. According to the data, firm age also does not appear to affect the relationship between learning orientation and firm innovativeness.
Local connections
Authors: Coughlan Tim , van der Linden Janet , Adams Anne
Published: January 2012

On Heritage aims to offer and promote a rich discussion at the intersection of art, performance, and culture that expands the boundaries of HCI while broadening our understanding of how things of the past come to matter in the present.

Elisa Giaccardi, Editor
"Towards more readable web: measuring readability of web pages based on link structure" by Adam Jatowt, Kouichi Akamatsu, Nimit Pattanasri, and Katsumi Tanaka with Ching-man Au Yeung as coordinator
Authors: Jatowt Adam , Akamatsu Kouichi , Pattanasri Nimit , Tanaka Katsumi
Published: January 2012

Although Web search engines have become information gateways to the Internet, search results often contain pages that are difficult to understand for non-expert users, especially when queries contain technical or rare terms. Readability indexes are well-known measures for estimating text comprehensibility. However, readability indexes are not sufficient for evaluating the comprehensibility of Web pages, as they are designed for general purpose texts. In this research, we investigate the relationship between links and readability of text extracted from Web pages for two datasets, namely English and Japanese pages. We then describe a link analysis algorithm for measuring comprehensibility of Web pages based on the TrustRank algorithm originally used for combating Web spam. Lastly, we report results of preliminary studies to measure the correlation between search rank and readability of Web search results.