A Second Look at String-Inspired Models for Proton-Proton Scattering via Pomeron Exchange

We re-examine a string dual model for elastic proton-proton scattering via Pomeron exchange. We argue that the method of "Reggeizing" a propagator to take into account an entire trajectory of exchanged particles can be generalized, in particular by modifying the value of the mass-shell parameter in the model. We then fit the generalized model to scattering data at large s and small t. The fitting results are inconclusive, but suggest that a better fit might be obtained by allowing the mass-shell to vary. The model fits the data equally well (roughly) for a wide range of values of the mass-shell parameter, but the other fitting parameters (the slope and intercept of the Regge trajectory, and the coupling constant and dipole mass from the proton-proton-glueball coupling) are then inconsistent with what we expect. On the other hand, using the traditional method of Reggeization generates a weaker fit, but the other parameters obtain more physically reasonable values. In analyzing the fitting results, we also found that our model is more consistent with the sqrt(s) = 1800 GeV coming from the E710 experiment than that coming from the CDF experiment, and that our model has the greatest discrepancy with the data in the range 0.5 GeV^2 < |t| < 0.6 GeV^2, suggesting that the transition from soft Pomeron to hard Pomeron may occur closer to t = -0.5 GeV^2 rather than t = -0.6 GeV^2 as previously thought.Comment: 16 pages, 7 figures, 2 table

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-6

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>ryp sequences and human, and as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for (), () and (F); red for human (); brown for () and green for (). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. The results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-8

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>ains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for (), () and (F); red for human (); brown for () and green for (). Most sequence IDs are from the Swiss-Prot database but there are also NCBI database accession numbers used (beginning 'NP'). Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support. Dashed lines show phylogenetic relationships as indicated in an initial tree from an ungapped alignment. Each clade was analysed separately to obtain robust phylogenetic analysis and these were then combined to show the whole PPM family

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-2

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>d as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for (), () and (F); red for human (); brown for () and green for (). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-9

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>ifferent families: S/T Phosphatases, Protein tyrosine phosphatases, Dual-specificity phosphatases and PTEN/MTM lipid phosphatases. Phosphatase complements are shown for , , , in comparison with those for the Human [24, 26, 29, 128], [129, 130] and [76, 131] genomes. ACR2/cdc25-like are included in the DSP group

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-7

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>tase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for (Tc), (Tb) and (LmjF); red for human (Hs); brown for S. cerevisiae (Sc) and green for A. thaliana (At). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences and systematic IDs for the parasites. Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support. The symbol '+' marks kinetoplastid sequences with catalytic mutations (listed in Additional file )

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-5

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>man, and as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for (), () and (F); red for human (); brown for () and green for (). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. The results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-1

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p>sphatase subfamilies. PTP, protein tyrosine phosphatase; DSP, dual-specificity phosphatase (crossed means pseudophosphatase); kinase, protein kinase domain (crossed means pseudokinase); TPR, Tetratricopeptide repeat; LRR, Leucine rich repeat; CaLB, Calcium lipid binding; GRAM, glucosyltransferases, Rab-like GTPases activators and myotubularins domain (plasma membrane protein-binding domain); FYVE, Fab1p/YOTB, Vac1p/EEA1 (PI3P binding domain); EF-hand, calcium binding domain; S/T phosphatase, serine/threonine phosphatase catalytic domain; FCP, CTD protein phosphatase. Note that many InterPro domains are variations representing the same biological function and sometimes they overlap. Only one domain is represented for these regions in this figure. Numbers of each domain type are listed for the kinetoplastids and '-' shows where one of the parasites lacks a particular architecture. ACR2/cdc25-like are included in the DSP group

The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains-4

<p><b>Copyright information:</b></p><p>Taken from "The TriTryp Phosphatome: analysis of the protein phosphatase catalytic domains"</p><p>http://www.biomedcentral.com/1471-2164/8/434</p><p>BMC Genomics 2007;8():434-434.</p><p>Published online 26 Nov 2007</p><p>PMCID:PMC2175518.</p><p></p> essential conserved residues for catalysis marked above. Analysis of the both kinase domains from the three kinatases is shown underneath. Fully conserved motifs are boxed in black and conserved residues from partially conserved regions are in bold type

File_S1_Celegans_N2_to_CB4856_lastz_alignment.txt

LASTZ alignments between C. elegans N2 (WormBase version WS230) and C. elegans Hawaiian CB4856 (Genbank accession: JZEW00000000