text:
Sushant Sundaresh (undergraduate) login: be131-10 Date submitted: 10.16.2009 HW4, RNA Folding Lab BioE131
2.1 in Methods in a sequence of the form
with xxxxxx... representing a 16-22nt sequence that is quasi-randomizable, as long as that sequence
maintains a specified bound secondary structure that masks the active ribozyme site.
the sequence structure noted is supposed to be "similar" but obviously it isn't even the right length. i've checked this
a few times, visually, so i think either i made a typographical mistake or its really just a rough specification for the
future structure of the randomized sequence. it doesnt need to be as exact.. and since the xxxx is a 16-22 nt region, it makes sense
that the length wouldn't be exact. its not a big deal for this hw, persay.
as I want to verify that when DNA-1 binds to those 16-22nt X's it will in fact
generate the correct stem-loop structure to "open" the active ribozyme cleavage site (which basically means RNAfold -C with those X's forced
non-bped, or x'ed) I ended up visually/physically copying down the 22nt XXX... sequence that is complementary to DNA-1 for this particular
YES-1 gate as I wanted the sequence as exact as possible for the folding analysis.
that said, here are the sequences/files that are relevant, with the added note that the sequence is 80nts long
and therefore is in proper fasta format.
file yes1.fasta
> yes1 hammerhead ribozyme apatamer (figure 2.a breaker paper)
file yes1_constrained.txt
so in the 'on' position (stem I, II, III properly formed)
the entire sequence except "AGCUCGUCACUGUCCAGGUUCA," the OBS sequence binding to DNA-1, or DNA-1's marker, is unconstrained,
with "AGCUCGUCACUGUCCAGGUUCA" being constrained to be unbound to anything else
in this sequence
(which in our case means bound to the DNA-1 oligonucleotide, and therefore theoretically in the "on" position)
in the 'off' position, the entire sequence is allowed to fold as it will, with, theoretically,
the minimum free energy (MFE) solution to the folding problem corresponding to a secondary structure that
blocks the formation of the II stem with the IV stem (which has the AGCUCGUCACUGUCCAGGUUCA sequence along with
other nts bound up in a stem that prevents the proper stem II formation, which in turn blocks the self-cleaving
I pasted these into a notepad file named yes1.fasta and yes1_constrained.txt in my ~/hw/hw4/ directory,
and (after installing the DART package and after Oscar wrote a .bashrc file referencing the
ihh/...install directory path to my main PATH variables) ran the bash commands that follow ($ represents command line prompt from
my hw/hw4 directory):
verifying "OFF position"
37C and ensuring with RNAheat that the structure
held for the range of 20-40C, specifically also at 23C. also, the second command converted (using an image converter in the DART package)
the yes1_ss.ps file to .pdf format, for later retrieval and visual comparison.
since RNAheat generates plots of specific heat and in this hw we care about structure,
I'm just testing at 23C and 30C as proof of concept.
$ cat yes1.fasta | RNAfold -T 23 > yes123C.fold
$ cat yes1.fasta | RNAfold -T 30 > yes130C.fold
$ cat yes1.fasta | RNAfold
and here are the relevant structures. no need for .ps or .pdf images here, those come later. this is just to show that the structures are not
significantly impacted in the given temperature range, 20-40C, as stated in the specs of the paper methodology. the last line ensures the yes1_ss.ps
file points to the default 37C representation.
Temperature Stability of OFF configuration
((((((((((((((((((((.(..(((.......))).)))))))).))))).....(((((....))))).)))))))) (-47.29)
((((((((((((((((((((.(..(((.......))).)))))))).))))).....(((((....))))).)))))))) (-41.06)
((((((((((((((((((((.(..(((.......))).)))))))).))))).....(((((....))))).)))))))) (-35.10)
and a quick visual screen confirms that there is no difference in the folded structure (unconstrained) at the three temperatures, spanning
approximately the 20-40C range specified in the paper.
alright, so now that temperature is no longer an issue for the off state, lets see what it actually looks like, its
visual secondary structure:
YES-1 37C OFF configuration
where in this image,
YES-1 Dotplot 37C OFF configuration
the "ghost" pixels represent lower probability base pairing events, presumably. the ones we care about are above the topleft-bottomright
line demarcation, in strong black.
all right, so these two together pretty much verify the actual structure predicted/verified in the P&B paper. let's go through the
structural elements one by one..
stem 1: clearly visible. this stem is the strong black downward-left diagonal line at the top right of the dotplot. stem 1 is supposed to be preserved in the off-configuration, to go by figure 2.a of the P&B paper.
stem 4: visible. easiest to find by viewing the bottom triangle (from bottom left to the main grey diagonal) and seeing the longest black upward-and-to-the-right diagonal trail, and finding its mirror image on the top-right to grey diagonal triangular region of the dotplot. this structure is smack in the 22nt OBS (oligonucleotide binding site) built in for DNA-1, which shows that without these nts being bound, the structure of the YES-1 gate is skewed by this OBS region forming a new stem, masking the stem II critical to ribozyme self-cleaving activity. it is interesting to note that there are other (one, mainly) somewhat high probability folds up and to the left of this one, but in any case, stem II is not one of them. contains an inner single nt A loop, which is weird (single nucleotide loops should be energetically unfavorable and rare) and two other seconardy loops further down the stem. the variants (differing probability stem IV structures) are described as "precluding" stem II formation in the paper.
stem 2: ghosts visible, probably not present. if this were really energetically favorable, there would have been a strong black down-left diagonal line slightly down and to the right of the stem 4 diagonal. in this case, there are some ghost pixels, which represent low probability events, and given the significance of the difference in coloring between the two (stem IV, stem II) I think the paper is valid in claiming the off configuration is valid.
stem 3: visible. this is, in the upper triangular region of the dotplot, the lowest-to-the-right corner diagonal (going down and to the left). it has few neighbors, mostly low probability ghost pixels. stem 3 is preserved, as stated in the paper, figure 2.a
accessibility of cleavage site based on lecture, though the stem II is a little more flexible in terms of nucleotide composition, stems I, II, and III must be formed to create the open loop around the cleavage site 'agccguagguugccc' or more specifically 'guag' between the 'g' and 'a' but clearly in this off configuration stem II has not formed at all, and from the structure image it seems like, as stated by P&B the core loop of the ribozyme has been severely curtailed, with some core loop nts being taken into stem IV. the cleavage site is not accessible, as our structures match the ones published in the papers pretty much exactly and their cleavage results with the off state (no effector) indicate lack of cleavage.
verifying "ON position"
AGCUCGUCACUGUCCAGGUUCA) cannot be bound in the resulting structure. by
specifying that the resultant structure leave those nts unbound, we approximate this RNA binding to DNA-1, and therefore unable
to utilize those 22nts in the creation of, say, a stem IV loop. that said.. plots! and bash commands. and analysis....
the following bash commands are basically word for word repeats of those described above, just with piped filenames changed. i'm not
repeating the usage descriptions. see above if necessary.
$ cat yes1.fasta yes1_constrained.txt | RNAfold -C > yes137C_ON.fold
pass constraint text file i.e. ...xxx...xx.. to RNAfold. constraint function described previously, above.
$ convert yes1_ss.ps yes1_37C_on.pdf
$ cat yes1.fasta yes1_constrained.txt | RNAfold -C -T 23 > yes123C_ON.fold
$ cat yes1.fasta yes1_constrained.txt | RNAfold -C -T 30 > yes130C_ON.fold
$ cat yes1.fasta yes1_constrained.txt | RNAfold -C -p -d2
$ convert yes1_dp.ps yes1_37C_on_dotplot.pdf
Temperature Stability of ON configuration
((((((((.......((((((...........................))))))...(((((....))))).)))))))) (-36.98)
((((((((.......((((((...........................))))))...(((((....))))).)))))))) (-32.67)
((((((((.......((((((...........................))))))...(((((....))))).)))))))) (-28.53)
visual check confirms that there are no structural differences for the minimum free energy (MFE) secondary structure
predicted by RNAfold under the given constraints (for the OBS sequence complementary to DNA-1) in the approximate range
of 20-40C, as given the by P&B paper specs under
Methods 2.1
see, this is even clearer:
((((((((.......((((((...........................))))))...(((((....))))).)))))))) (-36.98)
((((((((.......((((((...........................))))))...(((((....))))).)))))))) (-32.67)
((((((((.......((((((...........................))))))...(((((....))))).)))))))) (-28.53)
alright, so temperature dependence is not a problem in this case either. lets go through and check stems I, II, and III (don't want IV, but check also) in the predicted MFE secondary structures. dotplots and .ps images ahead:
YES-1 ON configuration 37C Secondary Structure
this image is obviously different-looking than the one presented in P&B's paper, as we just told RNAfold to constrain the OBS to NOT be bound, while
they either simulated its binding to DNA-1, the complement to the OBS described numerous times in this answer, OR just made a pretty image where they
showed DNA-1 bound reverse-complement style, linearly, to the 22nt OBS. in any case, semantics aside,
YES-1 ON configuration 37C Dotplot
stem I stem I forms as before, top left corner, extending diagonally down and to the left. strong, black, high probability in the MFE structure.
stem II this is the interesting part; stem II forms down and to the right slightly of the old stem IV in the off configuration. it is a simple 6bp down-left diagonal, strong and black, meaning high probability. there are the same spray of ghost pixels, or alternative far less probabilistic and energetically favorable base pairings, but only one even gets close to eye-level visible and that one is isolated and it is clear that the stem II loop is stable and highly favored. stem II definitely forms, stabilizing the core loop structure and enabling access to the cleavage site.
stem III forms as before, in the bottom right of the upper triangular region (above grey right-diagonal) strong black, high probability in MFE secondary structure. even fewer ghost pixels than last time. it seems like this already stable structure is further stabilized by the stem II loop formation and OBS binding to the DNA-1 oligonucleotide.
stem IV no sign of it. there are some ghost pixels where it used to be, but they are faint and they don't extend nearly as long diagonally.
accessibility of cleavage site the 'guag' site, between 'g' and 'a' as before. this time, stem loop II, necessary for cleavage, as described in lecture, is formed and core-loop stabilizing. plus core loop 2 seems more open. the cleavage site is exposed and all three required stems, I, II, and III, are properly bp'd and in the correct orientations (to judge by P&B's positive analysis of cleavage products when their same YES-1 structure was introduced to DNA-1 effector) to induce cleavage. the cleavage site is active and accessible, because stem loop II formed.
This is what I assume is meant by "of the form" in the previous hw question, as this is how P&B describe their general YES gate form in their Methods
This strategy, while missing a few details, is incredibly similar to the algorithm that P&B implemented in and described in their Methods section for optimizing random OBS sequence-based hammerhead ribozyme apatamer generation. So I am effectively running a GIVEN sequence against their algorithm to ensure it matches their standards. That is the point of this question as I see it.
I use the same stemI, II, III implies YES gate functionality (and therefore cleavage site accessibility) (verified via some cleavage-product isolation based study) rationale because your problem specifications describe a "YES gate of the
form given in the ... homework" which till this point has meant the YES-1 gate from the P&B paper, in figure 2.a.
Finally, the output: the truth table. The reason the P&B algorithm restarts its procedural generation of data each time a screen fails is because
the output from that particular YES gate is not predictable to within a certain degree of tolerance, over a given temperature range and with respect
to a given OBS. with that in mind, there is no reason that errors (input errors, etc.) OR failed screens should print truth tables. These would be meaningless.. all I could say is that 0-> 0,1 but without certainty as to when 0 or 1 is produced as Yes(0) or Yes(1). Therefore, I have opted to only print the truth table upon successful verification of the yes gate; see 1.11.
#!/usr/bin/perl -w
3 things, an RNA sequence (argument 1) and the coordinates [low, high] (two values, two arguments) inclusive bounds on the nucleotides that make up the OBS sequence.
obviously, depending on the length of the RNA sequence, the user might or might not want to type them into the STDIN, and from what I see a lot of these RNAfold Vienna package programs just take STDIN to allow people to pipe in data from their own text files. This program will act similarly; the user should be able to pipe in all the relevant input, as one RNA sequence file and two numerical integer values representing the OBS bounds.
Appropriate exceptions (die) calls will be made if, say, the RNA file is non-existent or unreadable, and if the bounds for the OBS are invalid (outside sequence length, below zero, etc.). Since I don't have to write this, let's just say this program takes DNA or RNA sequences of arbitrary length (though the longer it is, the longer this will take) in FASTA format sequences (parsers can be nicked from BioPerl and Cpan) and that sequences with thymines and no uracils will be transcribed into RNA (reverse complemented, lc($_) and =~ tr/t/u/ globally). If that isn't acceptable, I could also write this to simply do the transliteration after lower-casing, to preserve sequence order.
The program should also print a help message when called from the shell with a '-h' tag, providing a help message with valid user input before terminating.
All right, the code for this is would not be helpful in the slightest, its just a bunch of if, elsif calls and die calls when pre-conditions are not met. Administrative stuff out of the way. Now onto the hard part.. actually verifying, now that we know the input data is accurate.
GGGCGACCCUGAUGAGCUUGAGUUU AUCAGGCGAAACGGUGAAAGCCGUAGGUUGCCC <-- ribozyme stem I, II precursor, III, core loop, &cleavage site AGCUCGUCACUGUCCAGGUUCA <-- the specific sequence used in YES-1 for P&B NNNNNNNNNNNNNNNN[NNNNNN] <-- 16-22 nt randomized, given certain pre-conditions outlined belowI assume also that when items are piped through the standard input STDIN, if there are multiple files, the value of <> in each successive call is not 'undef' until all files have been exhausted. so I will use one while loop, with the obvious potential modification that if <> returns undef at the end of each file, I need to introduce trivial checks for that.
# a large part of the trickiness in parsing is due to the fact that the user will pipe in 1 argument file and 2 integer arguments to STDIN. how to #deal with that? i have to make a few assumptions about how such data is piped in, in lieu of actually writing the code, which I assume was not #intended for an exercise dealing with "code snippets" #the first 74-80 nt (16-22 nt OBS + 58 nt ribozyme stems + core elements) must be RNA elements. The reverse-complement case is a detail that is best left to actual implementation, it adds nothing to write in in here with the bigger-picture regex parsing design, etc. #the next non \s or \n element must be a number, as must the one after it. all other commands are ignored (or i could terminate. either way). my ($rnaSeq, $lowerOBSBound, $upperOBSBound); # boundTag lets us know whether there is invalid input of the form agagagaga 2 agagag $boundTag = 0; $startSequenceTag = 0; my $description; while (<>) { # want to maintain newlines, ensure proper, rigid formatting in this limited implementation. don't chomp. if (m/(>.*\n)/) { if ($startSequenceTag) {die "multiple fasta format files inputted on STDIN";} $startSequenceTag = 1; $description = $1; } # again, only dealing with RNA here, not DNA. that is a special case that can be implemented later if necessary. also not dealing with random # whitespace formatting. its easier to show the snippet this way, to not get bogged down in details. # for this small scale psuedo implementation, at least, the sequence is restricted to exactly what the YES gate is defined as in the P&B ==Methods== if (m/(GGGCGACCCUGAUGAGCUUGAGUUU[ACGU]{16,20}AUCAGGCGAAACGGUGAAAGCCGUAGGUUGCCC)/i) { # no description line or >.. invalid format. such error checks can be extended if (! $startSequenceTag) {die "invalid fasta format";} if ($rnaSeq) {die "multiple sequences in input. invalid. error. terminated.";} $rnaSeq .= $1; } else {die "invalid YES-gate; incorrect number of nucleotides";) #obviously I havent checked for the agagagaga2 case, but again, details. input errors are to be checked, but for the program outline it is useless. # also, I am assuming that piping opens files into the standard input with separating newlines or spaces, so this will work. the general idea is to # check for two integer arguments if (m/(\d+)[\s\n]*(\d+)/) { # if either are defined, then there were multiple bounds passed and we have an error. if ($lowerOBSBound || $upperOBSbound) {die "numerical arguments passed already.";} # if neither is defined but there is only one number.. we have a problem if ($1 || $2 && (! ($1 && $2))) {die "incorrect number of integer arguments passed.";} # now we're fine, basic errors checked $lowerOBSBound = $1; $upperOBSBound = $2; } # more error checking... etc. } # so now we have an rnaSeq scalar string with the give RNA sequence and the necessary OBS bounds. if ($lowerOBSBound > $upperOBSBound || $lowerOBSBound > length($rnaSeq) || $upperOBSBound > length($rnaSeq)) {die "invalid bounds";} # generate on state constraint strings, make actual method calling easier. $onStateConstraint = ""; for (my $i = 0; $i < $lowerOBSBound; $i+=1) { $onStateConstraint .= "."; } # i'm pretty sure these bounds are right.. for (my $i = 0; $i < $upperOBSBound-$lowerOBSBound; $i+=1) { $onStateConstraint .= "x"; } # again, pretty sure about my bounds, might need to add/subtract 1. basic idea gets through. for (my $i = 0; $i < length ($rnaSeq) - $upperOBSBound; $i += 1) { $onStateConstraint .= "."; } # internal error checking if (length ($onStateConstraint) != length ($offStateConstraint) && length ($onStateConstraint) != length ($rnaSeq)) {die "bounds wrong on constraint generation for loops.";} # now we can actually start following the rest of the P&B "check if a sequence is a valid YES-gate" algorithm
# 1.1 & 1.2 have been done for us as we are given a sequence with an OBS user-specified. #1.3 in Methods describes calculating the free energy at 37C of the proper SETSEQUENCE[16-20 nt OBS]SETSEQUENCE RNA using the partition function -p. #open a filehandle to an RNAfold program execution with tag -p (partition function & free energy calculation) with consistent energy functions (-d2) open RNAFOLD, "| RNAfold -p -d2 |"; $fastaRNA = ">myprog\n" . $rnaSeq; print RNAFOLD $fastaRNA;
# 1.4 make sure that nt 3-9 (numbering referenced to another paper, reference #52, in figure 1.a) # of the "hammerhead core" are base-paired in the off configuration. # now we have a filehandle to RNAfold which is printing to STDOUT that we can read via <RNAFOLD> and we can therefore parse the RNAFOLD output # to find the partition function's returned free energy value and store it to a special variable, $free energy. # furthermore, we have access to the dominant structures from the dot matrix for probabilities of pairing (the .ps file of the form myprog_dp.ps) # which we have to parse out of the STDOUT, as the -p -d2 option prints the dominant forms ((..))... form secondary structure to the STDOUT. # if we want to find out whether the necessary base-pairs are formed dominantly in the off state... we can easily parse this out of STDOUT. while (<RNAFOLD>) { if (m/>.*\n/) {break;} } my $energy; while (<RNAFOLD>) { # match to current structure (of the form ((((((...))) .... [energy value]. the digits it matches to are approximate form. for example, 2.3 matches, # but .3 doesnt. that is also a reasonably easy fix though, just more | or cases. $_ =~ m/(.*)\[([+-]\d+\.\d*)\]/i if (! $energy || $2 && $energy > $2) { $energy = $2; $mostProbableStructure = $1; # next line was one of most probable structures, or dominant OFF states } } # so just found the minimum energy, or dominant state, MFE secondary structure for the OFF configuration, now # 1.4 parse the necessary nts from $mostProbableStructure, 3-9 via the referenced numbering system, and see if they are ( < or { as opposed to . if # they are base-paired, move on. otherwise quit, the given sequence is not valid. (this code is not included.. but consider this pseudo-code) close RNAFOLD;
#1.5 use my $onStateConstraint string to set up ON configuration open RNAFOLD_On, "| RNAfold -p -C -d2 |"; # not entirely sure I can do this. but it waits for me to enter first a sequence then a constraint in the normal stdin prompt.. so maybe it works. print RNAFOLD_On $fastaRNA; print RNAFOLD_On $onStateConstraint;
# 1.6,1.7 then the same code above applies, with small changes as we are now looking for stems, so more than just 3-9 bps. # I won't rewrite the code, but just as we found the lowest energy structure and made sure that certain elements were # base paired in the final structure, in the ON configuration, we want to make sure that stem I, stem II, stem III are all basepaired accurately, and # furthermore we want to make sure that the cleavage site is NOT base paired. then we can move on. in the end, it boils down to the same type of # "extract energies, find minimum, extract dominant sequence, then check specific locations of known sequence for basepairing, related to stems, etc." close RNAFOLD_On;
# 1.8 now if the sequence has gotten this far we need to make sure that in the OFF state that if <30% or >70% of the OBS nts bp without an effector, # again, in the OFF state, then we have problems. assuming I saved the dominant, lowest energy structure, and since I still have the bounds on the OBS, # i can check the percentage that form base-pairs of some sort in the off state. lets still call it $mostProbableStructure.. assume in the 1.6,1.7 # setup I called the variable something different. $OBS_Struc_String = substr $mostProbableStructure, $lowerOBSBound, $upperOBSBound - $lowerOBSBound; @OBS_Structure = split (//, $OBS_Struc_String); $OBS_Length = @OBS_Structure + 0; $OBS_BPs = 0; for (my $i = 0; $i < $OBS_Length; $i+=1) { #i'm not including secondary base pair notation like { } | etc. though | is a type of constraint too... hm. well, again, this is just proof of #concept. if ($OBS_Structure[$i] =~ m/[\(\)]/) {$OBS_BPs++;} } $fract_OBSbps = $OBS_BPs / $OBS_Length; if ($fract_OBSbps < 0.3 || $fract_OBSbps > 0.7) {die "invalid YES-gate structure, too many OBS base pairs.";}
# 1.9 if the energy gap calculated between OFF and ON states ($energy and .. whatever I set it to in the referenced over 1.6,1.7 section) is # not between -6, -10 kcal / mol the sequence is invalid. the actual algorithm suggests going back to 1.1, but we just want to verify, not generate. # lets just assume I've set $energy_Off and $energy_On to the respective values. see the partial implementation of 1.4 for what a given $energy is # (dominant structure energy from -p -d2 RNAfold stdoutput. # assuming energy values from RNAfold given in standard units, kcal / mol if ($energy_On - $energy_Off < -10 || $energy_On - $energy_Off > -6) {die "energy gaps for OBS & RNA sequence are too high between ON and OFF";}
# 1.10 suggests running the program on RNAheat in 20-40C range, ensure that dominant off/on structures preserved in that range. # only problem is that RNAheat returns specific heats, not energys that I've previously calculated, and it doesn't as far as the # man page shows, have a -C function to allow me to specify the ON configuration. so I must have an older version than the one they used. # anyways, the other way to test the same stability vs. temperature is to iterate through and calculate/compare manually. # i am going to make use of $mostProbableStructure_Off and $mostProbableStructure_On which refer the respective variants of the $mostProbableStructure # generated in 1.4 $temp = 20; for (; $temp < 41; $temp +=1) { open RNA_1_10_Off, "| RNAfold -T $temp |"; # this is straight from 1.4, but in a final implementation, this would be properly modularized as a general "get most probable structure" subroutine print RNA_1_10_Off $fastaRNA; while (<RNA_1_10_Off>) { if (m/>.*\n/) {break;} } my $energy_Off; my $tempProb_Off; while (<RNA_1_10_Off>) { $_ =~ m/(.*)\[([+-]\d+\.\d*)\]/i if (! $energy_Off || $2 && $energy_Off > $2) { $energy_Off = $2; $tempProb_Off = $1; } } if ($tempProb_Off ne $mostProbableStructure_Off) {die "instable OFF state in varying temperature";} close RNA_1_10_Off; open RNA_1_10_On, "| RNAfold -C -T $temp |"; print RNA_1_10_On $fastaRNA; print RNA_1_10_On $onStateConstraint; while (<RNA_1_10_On>) { if (m/>.*\n/) {break;} } my $energy_On; my $tempProb_On; while (<RNA_1_10_On>) { $_ =~ m/(.*)\[([+-]\d+\.\d*)\]/i if (! $energy_On || $2 && $energy_On > $2) { $energy_On = $2; $tempProb_On = $1; } } if ($tempProb_On ne $mostProbableStructure_On) {die "instable ON state in varying temperature";} close RNA_1_10_On; }
# 1.11 if the ensemble diversity does not exceed 9 units for the OFF and ON states, it is a valid YES-gate structure. otherwise die, there is too # much secondary structure variability. # need -p and -d2 to get standard energy partition and to print ensemble diversity to stdout, so it can be parsed. open RNA_1_11_On, "| RNAfold -C -p -d2|"; print RNA_1_11_On $fastaRNA; print RNA_1_11_On $onStateConstraint; # we want to keep parsing till we get to a stage where we match to "ensemble diversity x.xx" where x are numbers. # i'm skewing the matching towards 2.3ish things again, vs. .3, which won't be caught, but again, its a matter of minutes # to add in the relevant other cases (i.e. 2.3, .3, 2., and such if Perl doubles are anything like Java doubles). # here it would unnecessary clutter the code, i just want the point to get across. $ens_On; while (<RNA_1_11_On>) { if ($_ =~ m/ensemble\sdiversity\s(\d+\.\d*)/) { $ens_On = $1; break; } } close RNA_1_11_On; open RNA_1_11_Off, "| RNAfold -p -d2|"; print RNA_1_11_Off $fastaRNA; $ens_Off; while (<RNA_1_11_Off>) { if ($_ =~ m/ensemble\sdiversity\s(\d+\.\d*)/) { $ens_Off = $1; break; } } close RNA_1_11_Off; # does not exceed is inclusive of the upper bound if (! ($ens_On <= 9 && $ens_Off <= 9)) {die "ensemble diversity too high, sequence too structurally variable.";} # else success, FINALLY print truth table (if there are errors, what is the use in printing? it isn't a truth table, and if the # rna structure has less than specified stability/specificity, there is no telling if there will be quantifiable, reproducible results # every time. # print to STDOUT $truthTable = "YES Gate Verified. For input A, YES(A) = A. Logic Function Confirmed\n"; $truthTable .= "A | YES(A)\n"; $truthTable .= "0 | 0\n"; $truthTable .= "1 | 1\n"; $truthTable .= "\n"; $truthTable .= "Program Terminated Successfully. Exit Code (0)\n"; print $truthTable;
# stage 2 screening as described in ==Methods== by P&B # is meant for generating distinct subsequences of OBS to generate variants of each OBS-YES-1 gate. if our sequence passes stage 1 testing, # as described in P&B ==Methods== then there are no more problems; we are not trying to procedurally generate new variants, we just wanted to verify # it was a valid Yes-Gate structure. If it passes the stage1 screens, for our purposes, it is.
# thus at this point, the problem is complete. in following 1.1 -> 1.11 of ==Methods== in the paper, if every time those # methods call for "returning to step 1.x," we ensure program termination, then we are effectively screening a given sequence from the user # against the criteria for valid Yes-Gate structure & stability -- verifying the structure of the sequence, with previous assumptions (stated above) # holding.
First things first: the sequences at Rfam do not include the species we were given as a homework problem. The closest to our particular species is a type I hammerhead ribozyme from the ==cf59== variety of the avocado viroid we are studying (cf39). therefore, this will be more comparative than definitive. i will try and get a range for how this particular variety folds in different temperatures, pick a somewhat representative one, and compare against the "structure" given in Rfam where here I take structure to mean the composite, aggregate structures composed in Rfam. Keep in mind that since cf39 and cf59 are different species, it is possible that there are significant structural differences. actually doing the structure prediction is exactly the same as in the first problem. i've copied the commands for ease of view. i won't bother with constraints, these aren't engineered apatamers.. and RNAheat is not useful here, I don't have any specific goal in mind. I just want a structure and a dotplot. i saved the hammerhead 70-186 nt fragment to a .fasta file straight from Pubmed, but changed the description tag so my filenames turned out nice. furthermore, since Rfold requires that even long sequences maintain single lines for a given sequence, without linebreaks, i needed to change the file from fasta formatting to single-line sequence. i didnt have to do this before since it was a (max) 80 nt file for the last few problems.
file hammerheadcf39.fasta
$ cat hammerheadcf39.fasta | RNAfold -p -d2 > hhcf39_37.txt
$ cat hammerheadcf39.fasta | RNAfold -p -d2 -T 23 > hh23.txt
$ cat hammerheadcf39.fasta | RNAfold -p -d2 -T 30 > hh30.txt
so.. first off. structures at different temperatures, ranging from 20-40C. is the predicted structure stable?
...........((((.((((.((....(((.(((.....(.(((((((...((((......)))))))))))).)))))).))))))))))....(((((.........)))))... (-38.65)
frequency of mfe structure in ensemble 0.00443165; ensemble diversity 26.38
...........((((.((((.((((....))))((.((((.(((((((...((((......)))))))))))..))..)).))))))))))....(((((.........)))))... (-31.28)
frequency of mfe structure in ensemble 0.00271294; ensemble diversity 24.74
...........((((.(((((((((....)))))....((.(((((((...((((......)))))))))))..)).......))))))))....(((((.........)))))... (-24.80)
frequency of mfe structure in ensemble 0.00435267; ensemble diversity 23.79
ensemble diversity seems to drop as we increase Temp from 23->37, so structural variability decreases over that temperature span, to judge by how
P&B described the term ensemble diversity.
...........((((.((((.((....(((.(((.....(.(((((((...((((......)))))))))))).)))))).))))))))))....(((((.........)))))... (-38.65)
...........((((.((((.((((....))))((.((((.(((((((...((((......)))))))))))..))..)).))))))))))....(((((.........)))))... (-31.28)
...........((((.(((((((((....)))))....((.(((((((...((((......)))))))))))..)).......))))))))....(((((.........)))))... (-24.80)
staring at these for a little while lets you see pretty quickly that the structure of the loops changes significantly with temperature. the general structure is preserved but I would estimate at least 7% of bp changes between 23->37C. Therefore, I think we should go with Temp = 23C just because the it is apparently the most stable of the lot (lowest energy kcal/mol) and in any case, this is comparative. the fact that there is such high ensemble diversity and the fact that the MFE structure changes so visibly over a 20C delta is weird but there's no reason that the structure hasn't evolved to be flexible. if it turns out that the 23C version has little in common with those secondary structures on Rfam, I can always re-analyze._$ cat hammerheadcf39.fasta | RNAfold -p -d2 -T 23 $ convert hhcf39_ss.ps hhcf39.pdf $ convert hhcf39_dp.ps hhcf39_dp.pdf In order from Left to Right: Hammerhead Ribozyme from Avocado Viroid genome nt 70-186, RNAfold -p -d2 -T [10, 16, 23, 30, 37, 47]
i did this many because i noticed the variability (extreme, in some cases) due to temperature. before we start comparing, we need to choose a particular temperature as our "baseline" structural value. I would say that as this is a plant viroid, its natural temperature of expression is around 10-25C tops. so something in the range of 16-23C would be acceptable. that said, to match up to anything Rfam has to offer we would also expect some sort of stem-based 5' 3' loose end interaction, but interestingly what we have here is more reminiscent of a quasi-loop closure.. which really means that the stem is farther up, and the 5' 3' non-paired ends are just unpaired, excess nucleotides. the other alternative is that this is a new structure that we haven't seen before but I just notice that the structure gets farther and farther from the ideal 3stem/coreloop/cleavage site set up the more extreme the temperatures get, and that there are recognizable elements of the ribozyme structure in this sequence, given appropriate temperature ranges. t = 16 has elements of an acceptable 3stem structure, though the core loop is tight, but one of its stems has a region (as do pretty much all the others) with many overlapping bases, which seems unlikely.. though it was clearly a low energy structure in comparison. the issue is that I feel like I am stretching the physical bounds to get a structural image in the form of that which we viewed in the earlier parts of the homework.
these in particular are interesting because I notice that at a reasonable temperature there are the exact three stems, core loop, etc. that I've grown to know and love. Of course, I know from the online pubmed citation that the 117bp sequence is from a viral RNA genome, which means reverse-complementing it is meaningless in this case. still.. its interesting, that a meaningless sequence would have an appropriate structure.
rotate the structure in your mind such that the leftmost stem out of the central core loop is pointing to the right. then the bottommost stem is pointing at an angle to the left, and the top stem, which branches on one line (once the stem stops being a double helix) to another stem/loop structure, is now actually on top of the core loop. this structure then corresponds to the stemI, II, III around the core loop that we've come to know and expect from standard hammerhead type1 ribozymes. i say type 1 specifically (though I have just shown through images that the loop numbering comes out right) because we now have a case where the ribozyme is composed of three stems, the top one of which (Stem I) is not closed, with 5' and 3' ends unpaired, in this case with one end extending to further structures of its own. lets take a look at what t=37C gives us in terms of structure and dotplot... get a better feel for these values. the fact that the ensemble diversity readings are so much higher than engineered varieties indicates that we should see either various strong overlapping enclosure diagonals or many weak ones. some setup where there are multiple close-MFE energy values. notice that in the dotplot there are way, way more ghost pixels than we've seen previously in the engineered ribozymes. this might in part be because of the higher temperatures, but I do notice that even with the reverse complemented version, which forms a similar structure around 23C, there is still a lot of noise. perhaps in part this is due to unknown ligands. perhaps although the structure we see is the most stable structure, there are more stable or more predictably stable (less ghost pixels, less alternative probable conformations altogether) due to interactions with unknown ligands. in any case, though there are varying spreads of ghost pixels it is clear from the bottom-triangular region (below grey line) that those most probable have in fact been selected for the resultant structure.
I am looking through Rfam Hammerhead Type-1 secondary structures' consensus sequences and secondary structure plots. I am not really considering specifically the closest relative on the list (assumed the cf59 species) because Rfam posts the secondary structure descriptions for the ribozyme family as a whole. Notice that the 'bpcons' notes only the 3 stems circling the core loop as having significantly conserved base pairing. in our particular case, in the rotated structure for cf39, stem II and stem I both have far more base pairs than noted in the consensus, but this might be because the bp_consensus is more of a minimal guideline than an upper bound. as another note, consider that the 'cov' plot shows that, again, the three stems are the most conserved sequences/base pairing regions of the entire structure, with "red" as a high covariance scaling color, all the stems are blue/green. the 'norm' view just confirms that type-1 hammerhead ribozymes have stem 2 and 3 closed, with stem 1 open, with dangling 5' and 3' ends. again, this seems more like a minimum bound than an upper bound, and it seems likely that the stem 1 structure in cf39, our sample, with the elongated end with its own stem/loop structure dangling, is legitimate, if not the most conserved structure. finally, we get to the 'cons' plot, describing sequence conservation. this comparison in general should be taken with a grain of salt; the cons plot is of a consensus sequence for the hammerhead type-1 ribozyme taken from the documented sequences in the RFam database. sequences do not need to have identity with the consensus to fall within the family declaration; structure determines function, and sequences are allowed to vary. what I do notice though is that from the sequences Rfam has noted, the core loop sequence is colored red, for the most part, indicating very little room or flexibility with respect to that core sequence. comparison to our predicted structure at 37C indicates that CUGA GAGC GAAAU, the darkest red/orange of the conserved sequences in the core loop ringed by the three stems, CUGC GC GAA are present in the loop structure, indicating one of two things: either 1 the loop structure as folded is in an inactive state, as its core loop is in part deviating from the identity consensus core loop 2 the core loop structure is in an active state as folded, it requires no extra ligand/it is not an apatamer setup, and the consensus is not as strict for functionality as I would have assumed. the first seems more likely; if structure determines function, and function is preserved evolutionarily, there should be a good reason why variants of this ribozyme across multiple species have the same consensus core loop. if our predicted structure at 37C (and mind you, the others are worse, without a core loop at all) does not generate a close enough (who defines close enough?) match to the consensus identity core loop sequence when its MFE structure is predicted alone, then maybe an external ligand is not being taken into account, preventing certain residues from base pairing and significantly altering the core loop structure. it seems unlikely that the stem structures would be significantly modified, but stem II is clearly capable of being played with, and it is quite a bit longer than expected, to judge by consensus minimum bounds. so the same OBS situation as in the first parts of the hw could apply, with stemII being stabilized by some external oligonucleotide or ligand, allowing a better core loop structure to form.
The cf39 avocado viroid hammerhead type-1 ribozyme deviates from the consensus identity sequences for all three stems and the core loop structure in its minimum free energy state of folding as predicted by RNAfold with partition option -p -d2 at the default 37C. However, at 37C (which might not be a reasonable physical temperature for a plant outside a greenhouse) it is clear from a pictorial representation of the secondary structure and the dotplot (with ghost pixels prevalent but not nearing the probability levels of the MFE structures) that the cf39 ribozyme is composed of three distinct stem loops, with the topmost one (read: stem I) containing the dangling 5' and 3' ends of the RNA sequence ,as required for a type-1 hammerhead ribozyme. Thus, the general structure is we would expect from comparison to the consensus structures on RFam are preserved without the actual consensus sequences being conserved, even partially in some stem cases, though with degeneracy obviously certain residues were conserved. The general feeling I get from this structure is that stem II, the bottommost stem in the picture above, pre-mental-rotation, is long, long enough to participate in the same sort of ligand/OBS response function as described in the Breaker paper. Perhaps the predicted RNAfold MFE structure is true in the "off" state, but for the cf39 type-1 hammerhead ribozyme to achieve cleavage, I feel like the core loop sequences must be better preserved, and that perhaps with additional constraints on the binding of the stemII structure it could be intuited which OBS/ligand binding induces proper stem II stability & core loop formation. the alternative is that perfect identity to the consensus core loop is not required for function and that this particular viroid ribozyme is just adapted to cleave with a longer stem II. perhaps the cleavage site is even different.. The conclusion is effectively that through consensus sequence/structure/bp models we can intuit that the general structure of cf39 preserves the type-1 hammerhead ribozyme prerequisites, but without further analysis of the situation it is unclear whether our particular MFE is in the OFF or ON configuration, or whether there is a difference between the two.. whether there are more favorable conditions that our particular phage has adapted to.
|2009-10-16 - 16:52
|2009-10-16 - 17:04
|2009-10-16 - 15:27
|2009-10-16 - 16:54
|2009-10-16 - 16:55
|2009-10-16 - 22:04
|2009-10-16 - 16:56
|2009-10-16 - 21:42
|2009-10-16 - 21:43
|2009-10-16 - 06:45
|yes1-off-37C secondary structure hw4 rna folding
|2009-10-16 - 07:14
|yes1 off 37C dotplot
|2009-10-16 - 08:14
|2009-10-16 - 08:14


text:
Got a question? Something on your mind? Talk to your community, directly.
by SalgiFoundation
by Dana-Farber
by Jackie DiNatale
by Kirley Masonry and Stove Emporium
by Valerie
by Debra Morais
by Outboard Exchange LLC
by American Heart Association
by Steve Hopkins
by Mike Seewald
by Impact Marketing
by Heather Hasso-Schlichting
by Kelly Noonan Funaro
by wendy
by Emina Zahirovic
by Dominic Amenta
by Boston University Athletics
by Diane McGee
by Kim Lipsy
by Regina Norfolk
by David Grossman
by Fran Witham
by Leaura Levine
by Sydney
by Scott Smith
by Theresa Freeman
Find your Patch
Start a Blog

subset: commoncrawl


text:
4071 Keokuk St, St Louis, MO | Directions 6311638.587562 -90.256826
Sat: 12pm-10pm, Sun: 12pm-8pm, Tue-Fri: 4pm-10pm
Neighborhoods: Dutchtown South, Saint Louis
Tasted like German Food – A friend of ours gave us a gift certificate to Grbic a year or two ago and we weren't sure what to think of going to a Bosnian restaurant. We finally decided to give it a try. The parking lot was packed and we later found out there was a huge party on the other side of the restaurant enjoying the food "family style". The rest of the restaurant was pretty filled at 8:45pm on a Sat. night. We liked the atmosphere, friendly and unique with the brick interior. All of the staff was extremely friendly despite them being very busy.
We started with the soup and salad. The soup special was Trhana and it was excellent. I could just sit and eat the soup and be satisfied It was a tomato based soup with tiny pieces of tender beef and the tiniest pieces of sourdough noodles. The Grbic salad was tasty and refreshing. My husband had the salmon and vegetable rice and I ordered the veal weiner schnitzel with spaetzles instead of the fries. I felt like it was just as good if not better than any German restaurant in town. The mushroom wine sauce was unique with a strong wine flavor. Delicious all around. We also ordered a side of veggies which was enough for both of us to share and were cooked to perfection with a light butter taste. Also, the bread was very fresh,which my husband used to sop up the soup and the wine sauce.
We would definitely drive from Maryland Heights to come back. Next time we'll bring our son who will also enjoy the chicken schnitzel. Hopefully we'll have room to try the apple strudel that looked delicious.
Authentic East European cuisine & decor – Having visited Europe & Yogoslavia numerous times, I know authentic East European cuisine, service and ambiance when I see it. Grbic has brought these fine dining qualities to St. Louis. It is totally worth finding this place in South City. I LOVE this place from the real-deal Bosnian dishes, to the real white linen napkins and table cloths (even at lunch) to the ceramic tile in the restrooms from floor to ceiling! Europeans follow much higher dining standards than typical American restaurants... they do things the right way from the start and are dedicated to the art of dining. Great place to hold a large party, wedding reception etc with the arched bricks, tile floor, wood carved central located bar. Spotless clean, nice staff OH, and Apple Strudel is like they make it in Vienna, Austria - so fine! I can't wait to go back again. Hope to see you there too!
Great food PLUS Great service from a staff that really cares... – Just have to tell someone what a great dinning experience we have every time at Grbic.
The place is spacious yet romantic with a lot of old world charm. Our neighbor, who is from Bosnia,
took us there the first time. I wasn't sure what "Bosnian" food even was. We all ordered something different and shared. i found my beloved German schnitzel and spazzle. Absolutely, every dish was succulent. The salad is tomatoes with cucumbers, onions, in oil and vinegar, like granny used to make and the gulasch soup was great. there were 4 of us and we had so much food, we had to move to an 8-top table!
But the best of all is the service you receive. (ask for Allen!) They all will make sure you are completely satisfied.
Delicious food and friendly surroundings provide an introductory lesson in Bosnian cuisine, even if the tutorial moves slowly. – The Scene
Grbic's large, two-room dining area is designed to evoke the feeling of an Eastern European country kitchen. Brick walls decorated with stone murals and quaint oil paintings, along with light, European balladry, inspire a tranquil, relaxed evening. Expect friendly and helpful servers, even though their graciousness lacks urgency.
The Food
One spoonful of the goulash, a hearty tomato broth thickened with meat and vegetables, sparks visions of the old country--even if you've never been there. Cauliflower schnitzel, similar to a cauliflower Parmesan, may be surprising and unfamiliar, but the light, crunchy batter and tangy tomato sauce quickly arouse a tasty recognition of the Italian version. The Grbic grill plate--a steak, veal, sausage and chicken sampler with a crisp, charbroiled flavor--exemplifies staples of Bosnian cuisine, even if the smallish portion feels slightly overpriced. For dessert, marvel at the wonderfully flaky crust of the honey-swirled baklava.
Sign in with Facebook Sign in with Facebook to see what your friends are up to!
Do you have a review of Grbic Restaurant on your blog? If you include the Citysearch image link (shown below) in your post, we'll automatically link to your review from the business profile page. Here's how our Linkback system works:
The Linkback system is free and automatic. It's really that easy.
To link to our business profile page, copy the html below to your web page.


text:
Important Info About Your Account
We're sorry. We cannot find a valid password which matches the E-mail address you've provided.
Cross Pendant in Sterling Silver with Stainless Steel Chain 24"
10k Yellow Gold Diamond-Cut Cross Pendant
Cross Pendant in 14k Gold
Crucifix Pendant in 14k Gold
You've just found the perfect accessory for today's edgy new look. Flash your name across this fabulous personalized pendant. 1 1/2" length. Specify name, from 1 to 9 letters. Sterling silver. Chain sold separately. Personalized items are not returnable, unless the mistake is our error.Item#


text:
Black Coat City, a new release of poetry from Miguel Jacq, explores the nature of anxiety, uncertainty and identity.
Comprised of 34 poems and two parts, this is a uniquely introspective journey through the fleeting thoughts of the individual; thoughts which bleed into the collective soul of a city of 'black coats' all grappling with identity, their strengths and their weaknesses.
No greater than a sum of their parts, society's cities endlessly battle the same demons as individuals, and must come to terms with themselves through experience and a continuous desire to self-improve.
Black Coat City is the first full-length collection of published poetry by Miguel Jacq. He lives in Melbourne, Australia.


text:
I gave ya some Rep Points and also +50 credits... and attached the EXE to your post as well. Thanks!
Thanks for this information. Now, to find out the best pieces to modify. Many possibilities come to mind.
I see that a lot of people are trying to view EXT3 formatted disk in Windows. Have you consider scp from YD5 to your Windows? that way, you don't have to bother moving disks around. It might be a bit slower, but will also work.
This is how I did a blu-ray dump because I didn't feel like hooking up an external drive, so I just mounted a windows share and copied it to their like this:
mkdir /mnt/share
mount //<shareip>/<sharename> /mnt/share -o username=user,password=xxx
dd if=/dev/cdrom of=/mnt/share/dump.iso


text:
Iodization of salt
Iodine deficiency is the main cause of preventable brain damage and reduced IQ in children worldwide. It also negatively affects women's health, as well as economic productivity and quality of life.
Most people need an additional source of iodine as it is found in relatively small amounts in the diet. WHO recommends universal salt iodization – the fortification with iodine of all salt used for human and animal consumption – as the main strategy for eliminating iodine deficiency.
The public health goals of reducing salt and increasing iodine intake through salt iodization are compatible as the concentration of iodine in salt can be adjusted as needed. Monitoring the levels of iodine in salt and the iodine status of the population are critical for ensuring that the population's needs are met and not exceeded.
WHO documents
GRC-approved guidelines
Status: not currently available
Other guidance documents
Recommended iodine levels in salt and guidelines for monitoring their adequacy and effectiveness
Publication date: 1996
Guidelines on food fortification with micronutrients
Publication date: 2006
Related Cochrane reviews
Other related systematic reviews
Fortified salt for preventing iodine deficiency disorders: a systematic review
Jiang T, Xue Q.
Chinese Journal of Evidence-Based Medicine, 2010, 7:857–861
Iodized salt for iodine deficiency disorders: a systematic review
Clar C et al.
Endocrinology & Metabolism Clinics of North America, 2002, 31(3):681–698 doi:10.1016/S0889-8529(02)00011-7


text: Haluška, Ján; Hutník, Ondrej The general Fubini theorem in complete bornological locally convex spaces. (English) Zbl 1198.46037 Banach J. Math. Anal. 4, No. 2, 53-74, electronic only (2010). This paper is a continuation of the authors' paper ["The Fubini theorem for bornological product measures", Results Math. 54, No. 1–2, 65–73 (2009; Zbl 1184.46043)]. Here, X,Y,Z are Hausdorff complete bornological locally convex spaces with filtering upwards bases of bornologies 𝒰,𝒲,𝒱, respectively; here, each U∈𝒰 is a closed, absolutely convex bounded subset of X and U⊃U 0 a fixed closed, absolutely convex bounded subset of X. The subspace of X generated by U, with Minkowski functional of U, is a Banach space X U . The topology of X is the inductive limit topology of the Banach spaces {X U :U∈𝒰}. Similar properties hold for the topologies of Y,Z arising from 𝒲,𝒱 respectively. L(X,Y) is the space of all continuous linear functions from X to Y; similarly for L(Y,Z) and L(X,Z). T,S are two sets, △ and ▽ are δ-rings on T and S, respectively, and m:△→L(X,Y) and n:▽→L(Y,Z) are two measures. With the help of (U,W,V)∈(𝒰,𝒲,𝒱), the authors reduce the study from complete bornological locally convex spaces X,Y,Z to the Banach spaces X U ,Y W ,Z V ,. Under certain conditions, an existence theorem for the product measure m⊗n:△⊗▽→L(X,Z) is proved. Then under certain conditions, a Fubini type theorem is proved for this product measure.Reviewer: Surjit Singh Khurana (Iowa City) MSC:46G10Vector-valued measures and integration28B05Vector-valued set functions, measures and integrals (measure theory)Keywords:Fubini theorem; bilinear integral; bornology; locally convex topological vector space; product measure; Dobrakov integral BibTeX EMIS EuDML


text:
phpMyAdmin is a tool intended to handle the administration of MySQL over the Web. It can create, rename, and drop databases, create/drop/alter tables, delete/edit/add fields, execute any SQL statement, manage keys on fields, create dumps of tables and databases, export/import CSV data, and administrate one single database and multiple MySQL servers.
LimeSurvey (formerly PHPSurveyor) is a Web application that interacts with MySQL, MSSQL, or Postgres to develop surveys, publish surveys, and collect responses to surveys. Once a survey has been created, data can be inserted into the survey either by a "pretty" public screen which presents each question one at a time, or by a quick and nasty data entry screen. It includes the capacity to generate individualized "tokens", so that invitations can be issued to participants. It also has the capacity to set conditions on whether questions will display (branching), numerous question types, and a basic statistics function.
XWiki is a WikiWiki clone written in Java that supports many popular features of other Wikis like the Wiki syntax, version control, attachments, security, and searching, but also many advanced features like templates, database and dynamic development using scripting languages (Velocity, Groovy, Ruby, Python, PHP, and more), an extension system and skinability, J2EE scalability, an XML/RPC remote API, statistics, RSS feeds, PDF exporting, WYSIWYG editing, an Office viewer and importer, and a lot more.
The WiKID Strong Authentication System is a highly scalable, secure two-factor authentication system. It is simple to implement and maintain, allows users to be validated automatically, requires no hardware tokens, has a simple API for application support (via Ruby, PHP, Java, COM, Python, etc.), supports multiple domains, and supports replication for fault tolerance and scalability. It also supports mutual /host and transaction authentication, wireless tokens only domains, locked tokens (to your PC), anti-keystroke logger keypad PIN entry, etc.
phpMyFAQ is a multilingual, completely database-driven FAQ system. It support various database systems and it also offers a content management system with a WYSIWYG editor, an image manager, flexible multi-group and multi-user support, a news system, user tracking, language modules, templates, PDF support, a backup system, Active Directory support, and an easy to use installation script.
Kronolith is the Horde calendar application. It provides a stable and featureful individual calendar system with integrated collaboration and scheduling features. It makes extensive use of the Horde Framework to provide integration with other applications. It implements a solid, stand-alone calendar system, allowing repeating events, all-day events, custom fields, keywords, shared calendars, iCalendar support, generation of free/busy information, and managing multiple users through Horde Authentication.
Piggydb is a flexible and scalable knowledge building platform that supports a heuristic or bottom-up approach to discover new concepts or ideas based on your input. You can begin with using it as a flexible outliner, diary or notebook, and as your database grows, Piggydb helps you to shape or elaborate your own knowledge. Piggydb is a Web application provided as a self-contained package that contains a Web server and database engine.
A library designed for MPEG TS and DVB PSI tables decoding and generation.
A library to solve the Schroedinger equation numerically.


text:
Investigate Identify
Researching and documenting the property's historical
significance, focusing on the availability of documentary
and physical evidence needed to justify reconstruction
of the non-surviving building.
Undertaking a reconstruction based on insufficient research,
so that, as a result, an historically inaccurate building
is created.
Reconstructing a building unnecessarily when an existing
building adequately reflects or explains the history
of the property, the historical event, or has the same
associative value.
Executing a design for the building that was never
constructed historically.
Investigating archeological resources to identify
and evaluate those features and artifacts which are
essential to the design and plan of the building.
Minimizing disturbance of terrain to reduce the
possibility of destroying archeological resources.
Failing to identify and evaluate archeological information
prior to reconstruction, or destroying extant historical
information not relevant to the reconstruction but that
should be preserved in place.
Introducing heavy machinery or equipment into areas
where it may disturb archeological resources.
Identifying, retaining, and preserving extant historic
features of the building and site, such as remnants
of a foundation, chimney, or walkway.
Beginning reconstruction work without first conducting
a detailed site investigation to physically substantiate
the documentary evidence.
Basing a reconstruction on conjectural designs or the
availability of different features from other historic
RESTORING- reconstructing


text:
Main Content
Start the summer off right with flawless style in the Harper hat from Brixton. It features embroidered brand graphics, a flat bill and an adjustable plastic snap strap.
- 60% Cotton/40% Polyester
- Structured fit
- Quality embroidery
- One size fits most
- Adjustable plastic snap strap
- Flat bill
- Five panels
- No eyelets
- Imported
Brixton Customers also liked:
Special event items are produced by manufacturers only after the outcome of a game or event. These are advanced sale items and will ship immediately after they are received in our warehouse.
Manufacturer direct items are shipped directly from the manufacturer. These items are not available for international or expedited shipping.
Customized items can be personalized with options such as your name, your favorite number, and/or designs. Some options may be limited by league rules.


text:
Work on planting and potting atop this organizational CASTLECREEK™ Garden Work Bench. Ideal for creating your own hanging baskets, repotting house plants, trimming bonsai and more! Do it all at waist-high level without taxing your back.
Order ONLINE Now!
CASTLECREEK™ Garden Work Bench
You qualify for a free gift. It will be added to your cart automatically.
Shop Similar Items
to find something that we have now or that can be backordered.
If you would like to be notified when we have this item available for sale, click
and enter your email address to receive an email notification.


text:
Fashion Pendant (3)
Solitaire (8)
Three Stone (1)
Cushion (1)
Heart (1)
Princess (2)
Round (8)
Certified (8)
Gold (8)
Platinum (4)
White (10)
Yellow (2)
Learn more about:
We want to hear from you! Customer Feedback Form
Receive a $50 Offer When You Sign Up for Email*
No Thank You
*Valid for new registrations only.
A welcome email will be sent with your offer information.
Privacy Policy


text:
Indiana University-Purdue University Financial Aid Terms and Condition.
Skip Links ↓
Student Loan Code of Conduct
Mon-Thurs 8 A.M.-6 P.M.
Fri- 9 A.M.-5 P.M.
260-481-6820Fax:email@example.com E. Coliseum Blvd.
Fort Wayne, IN, 46805
© 2014 Indiana University–Purdue University Fort Wayne (IPFW). All rights reserved. IPFW is an equal access/equal opportunity university.
If you have trouble accessing this page because of a disability, please email the Office of Institutional Equity at email@example.com.


text:
For the first time in 16 years, BOTH the Lady Cats and Bearcats were named the 2013 Class 3A District Basketball Champions. The Lady Cats will advance to Regionals in hopes on continuing on to Area play.
Bearcats go into District Playoffs with 16-4 record!
The Rattan Ram were recently named the 2013 Class 2A District Basketball Champions. They will continue forward to Regionals to compete for a chance to continue on to the Area competition.
February 1st our Bearcats traveled to Atoka to take on the Atoka Wampuscats, who we had already taken on and beat at home so they were looking for a bit of redemption on their home court. In the beginning it seemed Atoka was up to the challenge ending the first period four points ahead with a score of 11-15 Atoka. Sr. Guard Harlan House was the leader in stats for this game with 14 points, 4 rebounds, 3steals and 2 assists in the first half alone.
Jake Collins recently signed a letter of intent to play baseball at Eastern Oklahoma State College. Jake is the grandson of Kenneth & Royce Battles of Antlers and was recently name Oklahoma Baseball Coaches Association Player of the Year. Seated are his parents: Ed Collins & Tammy Collins. Standing is head coach Craig Price.
Hundreds of students from across the state recently competed in the 66th annual Southeast District Livestock Show at Eastern Oklahoma State College in Wilburton. The show is jointly sponsored by the Eastern Agriculture Division and the Wilburton Lions Club. There were 413 swine, 108 sheep, 159 goats and 124 cattle entered in the show.
On Tuesday, January 29th, our Bearcats traveled to Valliant to take on Coach Aaron Noel's Bulldogs, who we haven't been able to beat in nine years. Our Bearcats knew this game would be a tough one, especially on the Bulldogs homecoming night, and they were prepared to go hard all four quarters.
The Moyers Tigers were recently named the 2013 Coleman Tournament Champions!! WAY TO GO TIGERS!!!!!
"For the past few years Jamie and Alex have been strong leaders for Texas Zoom Gold, an Elite College Showcase team, they dominate the game in every area and I anticipate they will continue that in helping the Paris Lady Dragons. Paris Junior College has a great softball program and I am happy for them." – David Thompson, Head Coach Texas Zoom Gold


text:
- 4 Comments
Welcome to Ben's Bargains. Please Register, Sign in or Sign in with Facebook
Cannot check out.
gnuibe - TD is getting slammed because of the deals its been offering tonight.
Circuit city has it also
Good for purchases through 11/30, so if you're willing to take the chance they won't run out, you can wait to buy.
Already a member? Sign in below.
Registration takes seconds! Once registered you�ll have members only access to:


text:
Len: To be perfectly honest, it is a hard sell to get people to change. They don't feel comfortable making those changes. Doing business today is different than it was even four years ago. If you are not out there selling yourself, you are really missing the boat. People who have made changes are the ones who are successful. In the past year, (chamber) seminars, networking sessions have doubled in attendance. It is hard for people to leave the store. They think, "Who is going to run it if I am not there?" Well, who is going to run it if you have no traffic? Cut your hours and go to the place where you need to be.
Tribune: So, you say that business owners need to get out and sell themselves to grow business. How can they do that?
Len: If you think networking is going out and handing out cards, you are wrong. More important than handing out that card is that one person who you clicked with. It is sort of like a friend suggesting a restaurant. You are more likely to go to a place where the (employee or manager) left a good impression on someone. We have moved back to a personal way of marketing. That was the way that business did things 20 years ago. People did (networking) the natural way, like getting together at a place like Scoopers and talking or over at the Rotary club. They did it by developing relationships.
Tribune: What changes can managers make to grow help their business in the new year?
Len: You need to be in the business of providing service. Service is the key word. You have to do it 100 percent and treat each customer as an individual. The hard part is when you grow past 20 to 25 employees. Many business owners fail to communicate their vision to their employees. That person (employee) needs to develop a compassion for what they are doing. They are the front line of defense and that mentality is missing in business today. Business people have a tendency to worry about just today. But when market conditions change, are you ready for it?


text:
Wichita >Doctors > Sears Optical
7700 E Kellogg Towne East Shopping Center, Wichita, KS | Directions 6720737.67974 -97.248159
M-F 10am-7pm, Sa 10am-6pm, Su 11am-5pm
Editorial Review by Citysearch Editors – Value-minded company offers tires, DieHard batteries and auto accessories. Services include oil change, belt replacement, brake repair and more.
Sign in with Facebook Sign in with Facebook to see what your friends are up to!
Do you have a review of Sears Optical on your blog? If you include the Citysearch image link (shown below) in your post, we'll automatically link to your review from the business profile page. Here's how our Linkback system works:
The Linkback system is free and automatic. It's really that easy.
To link to our business profile page, copy the html below to your web page.


text:
Saturday, June 15, 2013, the weather could not be more perfect here at NHMS for the Moat Mountain Road Course Series race.
Shaun Buffington's car almost didn't start in time for today's race, but once the car started it was unstoppable. Shaun Buffington scored another road course win, and his teammate, Tom Gray, finished right behind him. Alex Vorrilas, sporting new graphics on his car, scored his second podium today, finishing third.
The legend cars will return to the Moat Mountain Road Course tomorrow at 11:20.
|Loudon Classic
|Sprint Cup Series Pole Day
|New England 200 (NNS)
|Camping World RV Sales 301
|Vintage Racing Celebration


text:
Need Help?
Find information on common issues.
Ask questions and find answers from other users.
Suggest a new site feature or improvement.
Check on status of your tickets.
Grid Appliance: a First-time User's Tutorial
Ranking is calculated from a formula comprised of user reviews and usage data. Learn more ›
08 Jan 2007 | Online Presentations | Contributor(s): David Wolinsky
This video shows step-by-step instructions on how to use the nanoHUB virtual machine Grid Appliance: from starting it up to running Rappture applications, accessing your nanoHUB files through WebDAV, and submitting jobs for remote execution using Condor.
Top 1 shown
nanoHUB.org, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.


text:
Delish Dish's Quickfire with Top Chef's Mark Simmons
While visiting Season Four contestant Mark Simmons at Double Crown restaurant in Manhattan, Delish Dish host Kiri challenges him to her favorite Quickfire. Can he create a fantastic meal in only one pot, and in only 45 minutes? Watch for yourself!
» More from Food Celebs & Shows - More
Post a Comment
When using Facebook Connect your image and name may display on Delish. All privacy settings are controlled by Facebook.


text:
Collier County Sheriff Kevin Rambosk filed for re-election Monday, rounding out a list of the same three candidates who ran against one another in 2008.
Rambosk, a Republican, will face off against private investigator Victor Ortino in the August primary election. Vincent "Vinny" Angiolillo, a local businessman, is running as an independent.
Rambosk took office in 2008 after winning about 75 percent of the vote, compared to Ortino's 20 percent and Angiolillo's 5 percent.
Rambosk said he would release details later this week about his campaign's vision for the future, which is meant to reinforce the agency's Community Safety Plan.
"It's a comprehensive plan with new ideas and new directions for keeping the community safe," he said.


text:
Projek Raw
The Montreal-based menswear label Projek Raw designs clothing for free-spirited young gents who live "by the pulse of the city." Inspired by classic American streetwear, this fashion upstart offers tailored lightweight jackets, distressed denim, plaid shirts, and graphic-print hoodies distinguished by bold patterns and modern, cutting-edge silhouettes. Relaxed jeans, Bermuda shorts, classic cotton Henleys, and quasi-futuristic pieces like the faux leather Moto Jacket blend downtown NYC chic with post-industrial ruggedness. Founded by Canadian clothier Robert Cohen and headed up by Cohen's son Dov and son-in-law Ariel Hassan, Projek Raw has become a favorite label among style-conscious twenty- and thirtysomething men since its 2001 debut.


text:
Contact Us
We love getting feedback from our readers - we'd love to hear what you liked or disliked, what you'd like to see in the future, or simply what you think of IntoMobile. No suggestion or critique is too small or overlooked.Contact Us
Sony Ericsson T707 is a stylish clamshell-shaped feature phone that the handset maker announced with tennis star and style icon Maria Sharapova, who also acts as a brand ambassador for the company. Features include a 2.2-inch QVGA screen, 3.2-megapixel camera, FM radio, music player and a memory expansion slot.


text:
This ergonomic, ADA-compliant Vault sink is handcrafted from durable stainless steel with bold, modern lines that bring contemporary style to your kitchen. A lowered divider in between the basins helps minimize splashing and provides convenient space to transfer heavy or bulky items. An engineered sound-absorption system significantly reduces disposal and dishwashing noise for a quieter kitchen environment. This dual-mount sink gives you the option of top- or under-mount installation. When installed in a top-mount application, Vault's ultra-flat, 1.25-mm-thick rim makes it easy to wipe from the counter directly into the sink.
Parts, Service & Support• Sink Clip Service Parts Interactive Diagram
Have a question or concern about this product? If you don't find your answer,
we're always here to help.
Call 1-800-4KOHLER (1-800-456-4537) or send us a question or request.
Height 6-5/16"
Length 33"
Width 22"
Template & Symbol Downloads
To open these downloads you will need specific programs such as Autocad.
Technical Information Downloads


text:
- SEC All-Freshman Team -- 2014
- SEC First-Year Academic Honor Roll -- 2013
- Since taking over the point guard reins, has piloted Tennessee to a 12-1 record in the last 13 games.
- Averaged 9.0 points and 2.7 rebounds per game, and shot 50.0 percent (12-24) through three games in SEC Tournament action.
- Recorded her 10th double-digit scoring outing this season against LSU in the SEC Tournament, notching 10 points.
- Filled in for Ariel Massengale against Texas A&M, stepping up to play all 40 minutes, scoring 10 points, including a perfect 4-4 from the FT line.
- Was instrumental in UT's 20-point win over Florida, dishing out a career-high eight assists.
- The first player off the bench in last three contests, Carter is 20-for-23 on free throws through five games this season as well as 7-for-10 (.700) on three-pointers
- Hit two three-pointers to help Tennessee to a total of eight vs. North Carolina and finished with 10 points vs. the Tar Heels
- Came off the bench at Middle Tennessee to sink the most threes on the team (2) and was a perfect 4-for-4 on free throws
- Was 2-for-4 on field goals against exhibition opponent Carson-Newman, with nine points, seven rebounds, two assists, three blocks and two steals.
- Played in seven games, starting the first five contests, in her first year at UT before redshirting due to injury.
- Became the 17th freshman to start her first career game as a Lady Vol, notching four points, two rebounds and two steals in 17 minutes against Chattanooga.
- Had four assists, four rebounds, three points and only one turnover during 36 minutes in a start at Georgia Tech that gave Holly Warlick her first victory as head coach.
- Led the Lady Vols to another key early-season road victory, going 4-5 from the arc and 4-4 from the line for a career-high 16 points in 28 minutes at Miami.
- Injured her right shoulder vs. Miami and later re-injured it vs. Middle Tennessee and North Carolina.
- Had surgery on that shoulder on Dec. 13 to repair a labral tear and missed remainder of the season.
- Member of the 2010 USA Youth Olympic Games Team that posted a 6-1 slate and captured the bronze medal in Singapore.
- Participated in the 2009 USA U16 National Team Trials.
- Played AAU ball for Georgia Elite.
- Ranked No. 21 on HoopGurlz Class of 2012 ESPNU 100 Rankings.
- Honored as a 2010 ESPN Rise Underclass All-American.
- Missed more than half of her senior season while recovering from a torn ACL in her left knee and played last few games of her career with a partially-separated shoulder.
- Had career highs of 31 points (2009) and 13 rebounds (2010).
- Averaged 14.8 points, 6.6 rebounds and 3.7 steals as a junior.
- Numbers included 17.6 points, 6.5 rebounds, 4.7 assists, 5.7 steals and 2.2 blocks as a sophomore.
- Georgia Sports Writers Association All-State First Team (2009, 2010, 2011), Honorable Mention (2012) and GSWA Player of the Year (2010, 2011).
- Georgia Athletic Coaches Association All-State (2009-12) and GACA Player of the Year in (2011).
- Atlanta Tip-Off Club All-Metro Team (2009, 2010, 2011, 2012).
- Atlanta Journal Constitution All-Gwinnett County First Team (2009, 2010, 2011) and Second Team (2012).
- 6AA All-Region (2009, 2010, 2011, 2012) and Region 6AA Player of the Year (2010, 2011).
- Led Buford to AA state titles from 2009-11 and a runner-up finish in 2012.
- Full name is Andraya Nichole "Draya" Carter.
- Born on Nov. 12, 1993, in Decatur, Ga., and signed with UT on her 18th birthday.
- Parents are Gary "Tyke" and Jessica Lhamon.
- Siblings include Alli, Zoey and Curt Lhamon and Chris and Shay Carter.
- Majoring in communication studies.
- Honor graduate from BHS.
- Has a pet snake named "Nothing."
- Twitter handle is @DrayaNichole.


text:
this wiki
If music bothers you, please check the bottom of the page to turn off
MarioWiki is a collaborative encyclopedia for everything related to the Mario series. There are 4,569 articles and growing since this wiki was founded in July 2007. The wiki format allows anyone to create or edit any article, so we can all work together to create a comprehensive database for the Mario series.
The MarioWiki community would love it if you'd join us in our Chat room for friendly conversation.
Attention! The Glitz Pit has been revived! Please vote on your character right away!
Attention! Puzzle Panic Fever is now in session! Have fun with solving word searches and other cool stuff!
Featured ArticleRosalina is a major, reoccurring character that first appeared in Super Mario Galaxy as the main supporting character. She lives at the Comet Observatory with the Lumas. Rosalina's role is small in Super Mario Galaxy 2 where she sends Mario letters with a familiar image on them. She also appears in the form of Cosmic Spirits that will often aid Mario on his quest. Rosalina makes her full game appearance after completing the Daredevil Comet of the Grandmaster Galaxy and appears in the second ending of the game.
Other Appearances
Since her appearances since the Super Mario Galaxy games, Rosalina has grew to be a popular character appearing in games outside the Galaxy series. Rosalina has appeared as a playable character in Mario Kart Wii for the first time. She reappears in Mario Kart 7 and even has her own course in Rosalina's Ice World. Rosalina will go on to being one of the five playable characters in Super Mario 3D World using powerups for the first time. Rosalina is even set to appear in Mario Kart 8 and Super Smash Bros. 3DS/Wii U.
Past Featured Articles... Super Mario Bros. 3... Antasma... Compat-I-Com... Bowser... Hotel Mario... Ludwig von Koopa... Luigi's Mansion: Dark Moon... Mario Kart 8... Super Mario 3D World... Super Mario 64... Mario and Luigi: Dream Team... Deanna Mustard...
Super Mario RPG: Legend of the Seven Stars Review
By Iphoneorange
Date: 04/17/2014 Rating: 9.5/10Grass Land and ends up in Dark Land (and all the worlds in between). The gameplay is a simple platformer. The player moves around world maps selecting levels, castles, Mushroom houses and even Hammer Brothers. The game stars Mario and his trusty, but clumsy brother Luigi. The levels are quite simple, but get quite hard extremely fast. The music is amazing. So many catchy tunes, that'll stick in your head for hours. The game has a fun multiplayer mode and many surprises, such as Mushroom houses, castles or other interesting things. Overall, I love this game and deeply recommend it. But if you're interested in buying a format of this game, I recommend the GBA remake over this one. Still, a classic no doubt.
9.5/10 By Iphoneorange
Past reviews... Super Mario 64(beta) Review... Donkey Kong Review... Luigi's Mansion Review... Super Mario 64 Review... Paper Mario Review...
Joke of the Month
Credit goes to Jeremy★VAL for such an amazing joke!
Part 1
Part 2
Also, suggest a joke!
See previous joke results here!
Remember: Choosing a number means something:
- 5 - I love it
- 4 - I like it
- 3 - Not bad
- 2 - Ehhh...
- 1 - Nah....
Before you hit the I don't get it button, read this so the joke would become clear to you. After reading, respond to the poll both above and below.
Part 1
- Rosalina threatens Bowser to turn him into stardust faster than the speed of sonic if he tries to kidnap her. Bowser tells her that he won't kidnap her and to take it easy.
Part 2
- Luigi describes Rosalina in her scary look that she is like King Boo, Bowser, and Daisy combined into the scariest living thing in the Mushroom Kingdom. Daisy overhears this and become raging mad at Luigi for adding her as one of the things he is scared of.
Featured MediaMario Kart 8 vs. N64's Rainbow Road(02:44)
Suggest a song/video at the Featured Media page.
Monthly Poll
What is your favorite phrase?
Also, suggest a poll!
Cleanup of the Month
Attention MarioWiki editors:
read more rules at the rules page.


text:
Not mass-produced — crafted with care.
Flat, Set of 6 — Save with this set, which includes a wide range of different sizes: 2, 4, 6, 8, 12, and 16.
Note — Brush sizes are not standardized. The length and width of a brush of a given shape and size varies considerably by manufacturer. Since fine art brushes are handmade, expect some variation even among brushes from a given manufacturer.
® Blick and Blick Studio are registered trademarks.


text:
I want to start by saying this: Just because YOU don't understand the Bible doesn't make the Bible wrong or God a liar. For some reason, atheists in particular, are drawn to the parts of the Bible they do not understand, and then finger-point like little children while whining away. What is worse, if YOU personally cannot give them an answer, then they conclude that THEY are right and YOU are wrong.
How ignorant and childish.
Just because you cannot give an answer to someone on any topic doesn't make your statement false. I can say with confidence that the speed of light is 186,000 miles per second, but if someone asks me to prove it I'm going to have to shrug. If they ask me how I know it is true, I'm going to have to point to a book somewhere. If they further challenge me to prove the book I didn't write true, I'm going to have to say "Go to the author." Atheists, however, do not want to go to the Author of the Bible, because they do not believe in God. So instead, they want you to speak for God, and are ready to pounce on you if you can't. "See! You can't prove it! It must not be true!" So, God is a liar because I cannot prove the Bible true?? Wow.
Well, the speed of light is still 186,000 miles per second, and it's not up to me to prove anything. So it is with questions about the Bible I may not fully understand. That we both, atheists and Christians alike, may not fully understand a particular passage of Scripture does not instantly make God a liar, or the Bible untrue, nor do I have to prove anything.
That said, Christians should feel free to stiff-arm the questions they do not understand for a while and say "Let me do some research on that and get back with you." Truth is, there is nothing to fear from such childish finger-pointing, and if you will put just a little time into some Bible study, looking at the context of the passage in its proper place and time, and really seek to gain a real understanding, then I believe you can have an answer.
Here is one particular passage that, for no good reason, has confused many. Again, atheists will finger-point like little children and ignore the vast majority of Scripture in an effort to hold YOU responsible for a Book you didn't write. I will simply let the question stand as written first and then give answer next week.
"Matthew 16:28, "Verily I say unto you, There be some standing here, which shall not taste of death, till they see the Son of man coming in his kingdom."
Mark 9:1, "And he said unto them, Verily I say unto you, That there be some of them that stand here, which shall not taste of death, till they have seen the kingdom of God come with power."
Luke 9:27, "But I tell you of a truth, there be some standing here, which shall not taste of death, till they see the kingdom of God."
Some means more than one. Jesus has not returned with all of his powers. Where are these men who were alive then and are still alive? Truth or lie: There are 2,000 year old men still wondering the earth who personally met Jesus."
See how the question is worded? He wants to draw an exact line with the words "truth or lie" and later he personally challenges me to give answer "Where are these 2,000 year old men?" as though I had them hidden somewhere in some secret undisclosed location or something. It's funny really, because the Bible answers this exact question.
I told him on February 21, 2012 that I would answer his question next week, and so I will. Meanwhile, until next week arrives, I wanted to allow this question to go to all of you out there.
The words were spoken by Christ. Christ has not yet come in His kingdom. There were some present when Jesus spoke that were not going to taste of death until such an event took place. The Bible is true. Jesus did not lie, and you CAN find the answer in the Bible. Well? What do you think?
As I told my atheist friend, I will answer this question next week, but for the next seven days, why don't you think this over, study it out, and see what you find. I'll give you a small hint: he didn't ask "Where is the 6,000 year old Christian?" or "Where is the 3,000 year old Christian?" but he could have.
- reposted from www.MenRising.com


text:
- Previous
- 1 of 6
- Next
- Previous
- 1 of 6
- Next
Related Stories for College basketball: FGCU men at USC Upstate
Comments on this photo » 0
Be the first to post a comment!
Want to participate in the conversation? Become a subscriber today. Subscribers can read and comment on any story, anytime. Non-subscribers will only be able to view comments on select stories.


text:
Existing Users -- Log Into Your Employer Folder
Log in to your Employer Folder account below.
If you forgot the password to your account or don't remember creating one, click here for help.
Job Seekers: Post a Resume
| Job Alerts | Job Seeker Folder
Employers: Post a Job | Search Resumes | Employer Log In
© 1998-2014. New Roads Media LLC. All Rights Reserved.
Site usage subject to Terms and Conditions. Read our Privacy Policy.


text:
CTL is a cross-platform control dispatching tool that makes it easy to automate any kind of distributed systems management or application provisioning task. Rather than writing complex and error-prone scripts that over utilize "for loops", CTL handles the network dispatching for you and allows you to focus on the actual management tasks you need to accomplish. In addition to being a dispatching tool, CTL comes with pre-built cross-platform utilities so you don't have to script actions like file distribution or process and port checking. You can also write your own custom utilities and share them with others in your organization. Custom utilities are defined in XML, and your scripting can be done in multiple scripting languages (Perl, Python, etc.), *nix shell, Windows batch, and/or Ant.
PrinterSetup is a flexible printer setup system. It is tailored to institutions with more than 20 deployed printers. It is designed to work with CUPS on Mac OS X. PrinterSetup is a component of PrintingWorks, a print accounting solution. There is limited documentation. Apple package deployment requires Mac OS X 10.3 or later, and is untested on earlier versions. Apple package development requires Mac OS X 10.5 or later and Xcode 3.0 or later.
The Open Vulnerability Assessment System (OpenVAS) scanner runs many network vulnerability tests (NVTs) against many target hosts and delivers the results. It uses a communication protocol to have client tools (graphical end-user or batched) connect to it, configure and execute a scan and finally receive the results for reporting. Tests are implemented in the form of plugins which need to be updated to cover recently identified security issues. The core component is a server with a set of network vulnerability tests (NVTs) to detect security problems in remote systems and applications. Additional components are: openvas-client to control the scanner, and openvas-manager and openvas-administrator to leverage OpenVAS to a comprehensive vulnerability management solution. OpenVAS is a fork of Nessus.
Pike ScriptRunner allows you to run scripts written in Pike under any FastCGI-enabled Web server. It provides request parsing and I/O handling, enabling you to get right to the task of writing your code. It is a dynamic object-oriented language with a C-like syntax and a number of features that make it desirable for rapid prototyping and deployment of Web applications.
Cassandra is a scientific data viewer based on VTK. Cassandra provides dynamic interaction with the VTK pipeline and enables the user to load plug-ins dynamically in order to perform specific tasks in data manipulation and visualisation. Cassandra is open and modular, and can easily be extended to new filters through a set of dynamically loadable plug-ins. A plug-in template is provided to help users to develop and share their own plug-ins. This approach allows users to perform complex filtering without any specific knowledge of VTK or C++.
Unity is a user-friendly development environment for designing and programming 3D games and a 3D game engine. Scripting is done using JavaScript, C#, or Boo via an embedded Mono run time. The resulting games can be deployed as stand-alone Mac OS X or Windows applications, Web plug-ins, or as Dashboard widgets. Unity is the tool that was used by Unity Technologies to create their game Gooball, which is available from Ambrosia Software.
PySL is a package that makes S-Lang functions and variables accessible via Python. It allows any S-Lang data type to move from S-Lang to Python scope and back. It also lets the user call any intrinsic or user-defined S-Lang function (including those defined by imported modules) from Python. All of this can be accomplished using a simple, module-like interface.
Bible study and concordance software.
A point of sales system for untamed managers.


text:
Canvas Frame
Material List
- Canvas, 11"x14"
- DCWV® Paper Pad – Blossom Song
- Acrylic Paint – Colors of Choice
- Ribbon – Color of Choice
- Gerber Daisy, 2
- Sticker – Circle
- Paintbrush
- Low Heat Glue Gun
- Terrifically Tacky Tape®
- Paper Trimmer
- Scissors
- Large Brad
- Wire Cutter
Project Instructions
Paint canvas as desired. Let dry.
Dry brush white paint around the edges. Let dry.
Choose two coordinating sheets of scrapbook paper from the paper pad. Cut one to 9"x12" and the other to 8½"x11½". Layer and attach to canvas with Terrifically Tacky Tape®.
Choose a third coordinating sheet of scrapbook paper from the paper pad and cut to 5"x7" and then cut a solid sheet to 4"x6".
Add to canvas.
Add photo.
Using Terrifically Tacky Tape®, adhere ribbon as shown.
Dissassemble two gerber daisies and combine two colors. Assemble back together using a large brad. Put a decorative sticker on the brad. Secure to canvas with glue.


text:
Center Companies
Companies in the ACCELERATION (Up and Running) Phase
VitalMed Management, LLC - VitalMed Management provides coordinated technology and management solutions for health care practices that will enable them to better serve patients while increasing efficiency and reducing costs.
Companies and/or Ideas in the CREATE (Venture Development) Phase
VINsage – A proprietary system for rapidly aging wine and liquor.
Joycehangers.com – Patented Barracuda Brackets used for making building bookshelves, TV stands and other furniture.
Potential student companies from the 2011/2012 Entrepreneurship Classes (BUDV310 and 410)
Ideas in the INNOVATE (Idea Development) Phase
Student Ideas from across all 3 schools at Siena.


text:
Journal of Pharmaceutical Sciences
- Print ISSN
- 0022-3549
- Electronic ISSN
- 1520-6017
- Impact factor
- 3.031
- Publisher
- wiley
- http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1520-6017
- Usage rank
- 141
- Article count
- 19316
- Free count
- 143
- Free percentage
- 0.00740319
- PDFs via platforms
- Proquest, Rcgp, Ingenta, Wiley, and CSA
Methyl-Beta-cyclodextrins: the role of number and types of substituents in solubilizing power.
Journal of Pharmaceutical Sciences 103(5):1443 (2014) PMID 24590624We compared various methylated β-CDs concerning their structure characterized by nuclear magnetic resonance spectroscopy, composition analyzed by HPLC and solubilizing capability by using model compounds such as cholesterol, fatty acids, furosemide, tamoxifen, and amiodarone. All the commercially av...
Oil-in-Oil-Emulsions with Enhanced Substantivity for the Treatment of Chronic Skin Diseases.
Journal of Pharmaceutical Sciences 103(5):1515 (2014) PMID 24634106We therefore developed oil-in-oil-emulsions that deliver the active pharmaceutical ingredient (API) to the skin over a prolonged period of time. In this study, we compare the permeation of the API from a conventional formulation to its permeation from an oil-in-oil-emulsion under infinite and finite...
Pretreatment with skin permeability enhancers: importance of duration and composition on the delivery of diclofenac sodium.
Journal of Pharmaceutical Sciences 103(5):1497 (2014) PMID 24644068The use of chemical penetration enhancers (CPEs) is one of the most common approaches to improve the dermal and transdermal delivery of drugs. However, often, incorporation of CPEs in the formulation poses compatibility and stability challenges. Moreover, incorporation of enhancers in the formulatio...
Toward an improved understanding of the precipitation behavior of weakly basic drugs from oral lipid-based formulations.
Journal of Pharmaceutical Sciences 103(4):1194 (2014) PMID 24515977These results suggested that in vitro conditions (dispersive versus digestive) largely influenced the solid-state properties of precipitating weak bases. Solid-state characterization of precipitated drugs under different experimental conditions should be routinely performed in formulation screening...
Overcoming Multidrug Resistance in 2D and 3D Culture Models by Controlled Drug Chitosan-Graft Poly(Caprolactone)-Based Nanoparticles.
Journal of Pharmaceutical Sciences 103(4):1064 (2014) PMID 24523221The principal limitations of chemotherapy are dose-limiting systemic toxicity and the development of multidrug-resistant phenotypes. The aim of this study was to investigate the efficiency of a new sustained drug delivery system based on chitosan and ε-caprolactone to overcome multidrug resistance i...
Determination of the optimal cell-penetrating peptide sequence for intestinal insulin delivery based on molecular orbital analysis with self...
Journal of Pharmaceutical Sciences 102(2):469 (2013) PMID 23160942We sought to determine the CPP that most effectively enhanced intestinal insulin absorption. An in situ loop absorption study using 26 penetratin analogues suggested that the chain length, hydrophobicity, and amphipathicity of the CPPs, as well as their basicity, contribute to their absorption-enhan...
Effects of submicron particles on formation of micron-sized particles during long-term storage of an interferon-beta-1a solution.
Journal of Pharmaceutical Sciences 102(2):347 (2013) PMID 23233283We present evidence that homogeneous submicron particles can influence the growth rate of larger particles upon long-term storage in a temperature-dependent manner. Interferon-beta-1a was thermally stressed at 50°C for 6 h and characterized using nanoparticle tracking analysis (NTA), microflow digi...
Solubility prediction of drugs in mixed solvents using partial solubility parameters
Journal of Pharmaceutical Sciences 100(10):4368 (2011) PMID 21630276Solubility of drugs in binary and ternary solvent mixtures composed of water and pharmaceutical cosolvents at different temperatures were predicted using the Jouyban-Acree model and a combination of partial solubility parameters as interaction descriptors in the solution. The general...
PhRMA CPCDC initiative on predictive models of human pharmacokinetics, part 1: Goals, properties of the PhRMA dataset, and comparison with l...
Journal of Pharmaceutical Sciences 100(10):4050 (2011) PMID 21523782This study is part of the Pharmaceutical Research and Manufacturers of America (PhRMA) initiative on predictive models of efficacy, safety, and compound properties. The overall goal of this part was to assess the predictability of human pharmacokinetics (PK) from preclinical data and...
PLGA microdevices for retinoids sustained release produced by supercritical emulsion extraction: Continuous versus batch operation layouts
Journal of Pharmaceutical Sciences 100(10):4357 (2011) PMID 21638283Retinyl acetate (RA) was selected as a model compound to be entrapped in poly(lactic-co-glycolic)acid (PLGA) microspheres using supercritical emulsion extraction (SEE). Several oil-in-water emulsions prepared using acetone and aqueous glycerol (80% glycerol, 20% water) were processed...