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Results 1 to 10 of 14
Thread: Start high, build slow HP tweak
Sunday, 8th July, 2012, 07:17 AM #1
Novice (Lvl 1)
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Start high, build slow HP tweak
I was considering using a variation on HP progression for my up coming PF Campaign but i realise it will alter the game balance a fair bit so was looking for educated guesses or actual experience of the affects on a game.
I like that 4E PCs start with more HP and you can throw a tougher encounter at the party straight away, instead of sending tiny groups or individuals at them. BUt i don't like that a PC at higher level can basically fall off a clif and walk away from it (when rolling damage dice only and not giving PCs narratively accurate injuries).
So i was thinking of running an HP system which give the PCs a max dice plus their con stat as starting HP but only gives con bonus plus a very small dice or set value at each level.
That would be something like: 1 HP + con bonus for mages (and anyone using D6s), 2 HP + con bonus for Rouge/Cleric or 3 + con bonus for fighter types. Or: D2+con bonus for mages, D3 + con bonus for clerics and D4 + con bonus for fighters.
The good thing is that a DM can match the party against, probably, twice as many monsters of CR1 or less straight away and have dramatic battles right away (cause i don't think 4 PCs fighting 3-4 Orcs is very impressive).
But it will probably mean that as the PCs level they will not stay even with the CR of monsters. Which means that either monsters HP could be lowered a bit or a lower CR encounter would match them, in turn saving higher CR creatures for even higher charcter levels. I'd lean towards the second option.
Allowing the PCs to gain +1 to 2 stats each 4 levels, more like 4E could help to make them maintain parity with CR and allow a PC to be more diversely developed.
It might mean magic item distribution and treasure allocation should be altered a bit too.
Has anyone tried this or have enough experience with the game to have an idea how it would play out?
Some how a slower HP proggrassion strikes me as leading to more tense combats and a more agreeable game style (for me atleast).
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Sunday, 8th July, 2012, 10:12 AM #2
Magsman (Lvl 14)
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I'd wager giving average HP (ie half of their HD) per level would suit your fancy. A 10th level barbarian with a 20 CON would have (6+5)*10 or 110 HP versus a possible max of (12+5)*10 or 170.
Sunday, 8th July, 2012, 10:39 AM #3
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A quarter of an HD was more what i was thinking but it's worth knowing that it's within the bounds of posibility and bad luck just rolling the dice normally.
But if a player was to 'roll badly' every level till X, how far behind the power curve would it put them? And how far behind would a party of such poor rollers be?
Sunday, 8th July, 2012, 04:30 PM #4
Waghalter (Lvl 7)
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It seems reasonable to say hit points would need to fall across the board. It's hardly fair to keep that Adult Red Dragon at 212 hp when its L14 opponents (its CR) have their own hp so markedly reduced. Its d12's should be reduced to 3 per die just like the PC's.
But it will still have well over 100 hp. Why? It has a 23 CON. This system will massively increase the desirability of CON - instead of a boost, a 16 CON now doubles a warrior's hp per level and quadruples them for a wizard. And bigger monsters tend to massive CON, so they still stay well ahead on the curve. Toughness becomes a much more desirable feat as well, adding a much greater percentage of hp.
Since we're reducing hp but not damage, Blasting becomes a much more viable choice for spellcasters, and criticals are way more beneficial (or dangerous, depending on which end of the weapon you're on).
Undoubtedly, it changes the balance of the game, and will change a lot of things not obvious on first glance.
I also note you're comparing to 4e (more hp at the outset), but you're only reducing hp growth, not increasing starting hp, which are already max die + CON bonus.
Sunday, 8th July, 2012, 10:23 PM #5
Minor Trickster (Lvl 4)
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At higher levels, it will change a lot of things. N'raac listed several. Others include:
The symbol and power word spells often have a hit point limit. They either need to have that revised downward, or the spells become more powerful.
Healing takes less resources. If it currently takes 5 cure criticals wounds to bring the tank from 1 hp to full health, now it probably only takes 3 or 4.
If you do not also scale down damage, the time between uninjured and dead decreases notably. A power attacking Storm Giant (CR 13) does 4d6+33 with three attacks, average 57 points of damage per hit. A 13th level fighter with a con of 16 currently has 10+12*5.5+13*3=115 hp. Under the proposed rules, he has 10+16+12*(3+3)=96 hp. Instead of two hits leaving him at about 0, two hits now leave him at -20. The gap will get worse as you go to higher levels. By 20th level, you are about 40 hit points behind the nominal values.
OTOH, I've just shown that at 13th level, the fighter has about the hit points you currently expect for a rogue with a similar con score. So the world is more dangerous, but not on the level of front line characters dropping after half the hits.
I think this is a viable option. It makes the lower levels safer and the higher levels more dangerous. Characters with con penalties are probably not viable, since con is now a much more important part of your total hit points.
Sunday, 8th July, 2012, 11:11 PM #6
Waghalter (Lvl 7)
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All good points.
The characters all lose 2.5 hp per level beyond first, offsetting the difference between CON and CON bonus.
So what does that Dragon receive instead of his standard 212? 3 x 17 = 51 + 16x6 = 96 + 23 = 170? Does it now get the first d12 maxed out, or get 4 per die rather than 3 (where does the d12 sit?) for another 17 hp? Does it get CON added direct to its first hit die, or reduce the above by 17 hp?
The PC has more hp - does his Orc opponent also add his full CON, or only his bonus, to his 1 hit die?
Changes to the opponents also impact the balance.
Sunday, 8th July, 2012, 11:15 PM #7
Gallant (Lvl 3)
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I'm just going to throw this out there before a bunch of work is done that maybe doesn't need to be. The two drives behind this are 1} desire for beefier opponents at low-level and 2} desire for falling off a cliff to be fatal even at high level.
First up, take a look at the wiki for free fall. You'll discover that apparently (a few) human beings have survived falls from thousands of feet up, let alone the 200 that PFRPG falling damage caps out at. So... the premise that heroic and amazing adventurers might survive falling off a cliff isn't nearly as ridiculous as it seems.
Speaking of ridiculous, we're talking about a game where these very same characters get hit in the face with axes, regularly. Dragons breathe fire on the, they're struck by lightning bolts, they're poisoned frequently, swallowed whole by monsters, and get stabbed by assassins. If surviving one "hit" from a warhammer is acceptable to you, why isn't a little... falling?
Second, it seems to me that the easiest method is to adjust the goal-post, not the entire game. Say... make falling damage above 5 dice switch to d8s. Above 10 dice switches to d10s. Above 15 dice switches to d12s. Net effect is that at 200 feet of falling, you're looking at 130 damage on average instead of 70. Not good enough? Remove the 200ft cap. And maybe throw a multiplier on... every time you increase the dice size, double the rolled damage. So when you shift to d8s, double the result. When you shift to d10s, quadruple the result. When you shift to d12s, do eight times the rolled damage. This is all way easier than futzing with PC hit points, upon which the entire mathematical game structure hangs. Damage dealt by spells, hit points monsters have, availability of damage-increasing effects like bane weapons... it's all depending on hit points as a foundation for scaling.
Third, low-level survivability is easy. Go ahead, give your PCs double their hit die at 1st or something. If you leave that be, over time that boost will become statistically insignificant. A barbarian with 24+ConBonus+FavoredClass hit points at first is doing just fine.
All I'm saying is... if your problem is that you need to get a light bulb out of its socket, don't hold it still and rotate the universe around it.
Monday, 9th July, 2012, 12:26 AM #8
Grandfather of Assassins (Lvl 19)
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I wanted beefier first level PCs, too, but for a different reason. Namely, I wanted a campaign where all new characters came it at first level, and that new players would have a first level character kicking around with those who had a few levels under their belt.
As a disclaimer, I run an E6 game, so that the PCs "max out" at level 6. So there is that.
Anyways, in my campaign, PCs start out with their constitution score in hit points, plus HALF of their hit die. At each subsequent level, they roll their hit die, though this is not modified by their constitution modifier.
Instead, a character's constitution modifier only applies to the minimums and ceilings of their rolls. A character with a +2 modifier will bump any roll of 1 or 2 up to a 3, because that would normally be the smallest number of hit points he would get when progressing... but if he had a d8 hit die, he would not gain more than 8 HP any particular level. Likewise, characters with con penalties wouldn't apply the modifier unless they rolled higher than they could normally achieve.
The end result? Those with lower hit dice see a bonus, and those with a higher hit die wind up seeing a slight drop at the higher levels. It also gets rid of making con an absolutely necessary stat, while still making it quite useful.
Wik: Solving internet arguments since 1983.
Monday, 9th July, 2012, 01:44 AM #9
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Thanks for the interesting comments everyone.
I'll address a few points in order, hopefully don't miss anythign important.
N'raac; I imagine that changing the HP of every monster to be an arduous task that's best avoided. My thought was that it would be simpler to consider the PCs (of 14th lvl, eg.) to be of a lower level for the CR on the monsters (ie. CR 10).
That way they will fight 'less powerful' monsters longer and there is no hassle with gimping monsters HP. Likewise they wouldn't be increased for their first HD either. The monsters stay the same but are effectively higher CR.
Udalrich; those are things i'm particularly interested in as the effect could be quite dramatic and unbalancing. As long as the PC classes stay relatively balanced then it doesn't matter as much if the balance between PCs and monsters shift as you can change their CRs, as i said above.
Anguish; The point was not really to make falling more deadly, that could be easily aachieved by telling a player whose character has fallen 200 feet that their spine, pelvis, a couple of leg bones and a couple of arms and ribs are broken and they can't move because of the pain, oh yeah, now the scavengers at the bottom of the cliff are coming for a bite.
The idea was to make everything more dangerous or more accurately, the PCs less bullet proof. All those things you mentioned that PCs can get away with now, i would like to see them less able to get away with. A lightning bolt should be deadly at any level as should repeated whacks with a warhammer or being eaten whole.
So what you and Udalrich mention about extra damage weapons and spells, is it going to upset the balance between melee classes and magic classes? (I know it will, but will it be by a game breakable amount?)
The goal is to encourage creativity when approaching situations and encounters. They PCs could still win a straight up fight be dealing damage if they're lucky but is it worth the risk of dieing, which is a higher risk now?
And yes, some people have been lucky enough to survive falls from crazy heights (parachutes failing, etc) and other deadly injuries but those situations would have extraordinary circumstances contributing. A fall into a swamp would be much less dangerous (just the fall) than one onto concrete or rocks, for example.
Wik; i saw your method in another thread. It's quite similar but i don't actually want to make Con less important, but i realise this could make it much more important which i also don't want. I think all the stats should be equally important, even though they aren't. With low HP Str and Dex for attacks and AC is still important, as are the magic affecting mental stats.
I'm not planning on doing E6 but i do like the idea. If i had plenty of time to play and players keen to give everything a try i'd give it a go.
Monday, 9th July, 2012, 10:37 AM #10
Myrmidon (Lvl 10)
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I also don't think it'd be much fun to fight less powerful monsters for longer in a regular game.
Note that limiting a rules change to PCs conjures huge hassles at least on par with the 'change every monster stat block' approach: what about NPCs, which might be cohorts or followers or otherwise allied to the PCs? What about NPC opponents, who are suddenly even worse for their CR? What about summoning/animal companions/necromancy, which explicitly uses monster stat blocks (now powerful, high-HP creatures do the heroes' work, which is too dangerous for the heroes themselves?!)? What about temporary HP - which become much more useful to PCs than they are to monsters? What about fast healing or regeneration abilities, magical healing, DR, etc., which are all available to PCs and suddenly take on a whole new meaning?
Bottom line: the balance of the whole game is altered if you make changes to a fundamental stat like HP. You won't see the end to the repercussions of such a houserule. Note that I'm not saying it's a terrible idea - but your game won't be the same, in many many regards.
If you want certain effects to be deadly at any levels, I'd do changes to those effects specifically, not introduce an across-the-board change to a fundamental stat. I'd also think long and hard about which effects I'd like to increase in potency. I'd ask questions like "Is this effect available to PCs? At what level? What monsters/NPCs have access to it? What is immune/resistant to it?" etc.
If you want a system where warhammer hits, lightning bolts and long falls are deadly at all levels, I can only give the following counsel: don't play D&D. In fact, don't play a game which uses HP to model injury. Play some wound- or consequence-based system instead. Hârnmaster, for example, might see a veteran of twenty years with super-high sword skill be stabbed once by a 16-year-old with a rusty dagger and succumb to the wound's bleeding, or later to shock, or still later to infection.
One final thing: do your players feel the same way as you? If not, leave well enough alone. If yes, on the other hand, why not ask their opinions on the kind of houserule you want to use?

subset: commoncrawl


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Gobby is a free collaborative editor supporting multiple documents in one session and a multi-user chat. It runs on Microsoft Windows, Mac OS X, Linux and other Unix-like platforms.
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Seriously, Apollo? Yuck. OS X is *nix, embrace it. X11 comes with the system!
I would love to see a 'native' Cocoa port of Gobby, but I'd rather see them develop the software better first, and muck around with improving ports later.
geeze man, apollo wasn't around. X11 has been around for a long time now, and it runs on linux and mac. Whats ur problem? Afraid of a little *nix culture?
Geez, another X11 app? Why don't they just build this in Apollo?


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Papillomaviruses are small DNA viruses that persistently infect and replicate in stratified cutaneous and mucosal epithelia. Each papillomavirus type is species-specific and has a tropism for certain types of epithelia. In most cases, the resulting papillomas are benign, but infection with certain papillomavirus types can lead to the development of carcinomas.
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Dr. McBride received a B.Sc.(with Honors) in molecular biology from the University of Glasgow, Scotland, and a Ph.D. in biochemistry from the Imperial Cancer Research Fund and Imperial College, London, studying Epstein-Barr virus. She began working on human and other papillomaviruses as a postdoctoral fellow in the National Cancer Institute and joined NIAID in 1994. She became a senior investigator in the Laboratory of Viral Diseases in 2000.
Moon-Kyoo Jang, Staff ScientistKoenraad van Doorslaer, Postdoctoral FellowCaleb McKinney, Postdoctoral FellowWesley Stepp, Predoctoral FellowKatharine Dolley, Post-baccalaureate FellowDan Chen, Biologist
Jang MK, Shen K, McBride AA. Papillomavirus genomes associate with BRD4 to replicate at fragile sites in the host genome. PLoS Pathog. 2014 May 15;10(5):e1004117.
Chapman S, McDermott DH, Shen K, Jang MK, McBride AA. The effect of Rho kinase inhibition on long-term keratinocyte proliferation is rapid and conditional. Stem Cell Res Ther. 2014 Apr 28;5(2):60.
Sakakibara N, Chen D, Jang MK, Kang DW, Luecke HF, Wu SY, Chiang CM, McBride AA. Brd4 is displaced from HPV replication factories as they expand and amplify viral DNA. PLoS Pathog. 2013;9(11):e1003777.
Stepp WH, Meyers JM, McBride AA. Sp100 provides intrinsic immunity against human papillomavirus infection. MBio. 2013 Nov 5;4(6):e00845-13.
Sakakibara N, Chen D, McBride AA. Papillomaviruses use recombination-dependent replication to vegetatively amplify their genomes in differentiated cells. PLoS Pathog. 2013;9(7):e1003321.
Van Doorslaer K, Tan Q, Xirasagar S, Bandaru S, Gopalan V, Mohamoud Y, Huyen Y, McBride AA. The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D571-8.
Visit PubMed for a complete publication listing.
In collaboration with the NIAID Office of Cyber Infrastructure and Computational Biology, Bioinformatics and Computational Biosciences Branch, we established the PapillomaVirus Episteme (PaVE) to provide information and bioinformatics resources to the scientific community for research on the Papillomaviridae. The goal of PaVE is to provide an HPV sequence database and tools that will accelerate scientific progress and ultimately our understanding, detection, diagnosis, and treatment of diseases caused by papillomaviruses. Find out more about the PaVE animal papillomavirus and human papillomavirus (HPV) sequence database.
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You can stay warm if you keep your cool
|On a recent trip up Mount Greylock in western Mass, my climbing companion Sweep Voll found she was overdressed despite subs-zero temperatures, and had to remove some layers. Keeping cool helps you stay warm. (Tim Jones/EasternSlopes.com photo)
"What would you recommend for the ideal, close-to-skin layer clothing for winter hiking and running. I've tried a broad range of all of the stay-dry, thermal stuff, but, no matter what, I wind up soaked and cold. A short hike on the day after Christmas up Red Hill in Moultonboro was not fun. On the way down, I was freezing. I would appreciate your ideas on clothing that truly keeps one warm upon exertion."
I wish there was some magic answer, some miracle baselayer that would keep him warm and dry no matter what. But, if such a miracle garment exists, I've never found it.
The problem comes when you combine high aerobic activity (climbing a mountain, for example), with continued exposure to the cold after you've gotten all sweaty and stopped the real exertion.
Some people would say the answer is to never exercise so hard that you actually sweat ... but what fun is that? Human beings simply feel and function better when we work our bodies more.
The bad news for Chris is, his problem is not in his choice of baselayer, but in what he expects it to accomplish. There's no baselayer I know of that will keep you comfortable in cold weather if you work so hard you get completely soaked in sweat, then stop exercising.
So, the real trick is to not get soaked in the first place, and that means — you guessed it — dressing in layers and actively adjusting those layers to match your exertion level and the ambient temperature so you sweat as little as possible. You are still going to sweat, but good moisture management can keep you from getting completely soaked.
Here's the drill:
1) make sure the layer next to your skin is as light as possible; its only job is to allow moisture to move through rapidly.
2) Start cold. Wear just enough layers that, when you start, your fingers, ears and toes should feel noticeably cold. Not frostbite cold, but not "comfortable" either.
3) Once you are moving, start paying attention. If you warm up quickly, it's time to shed a layer, FAST! You want to stay on the edge of "too cold" as long as possible. "Comfortable" is too warm.
4) At some point your body is fully warmed up and putting out maximum heat. For most of us, that's about 20 to 30 minutes after starting to exercise. Then, if you are still "too cold" add a light layer. But you'll be surprised at how often you end up wearing nothing more than your ultralight base layer even when it's really cold.
5) Windchill can complicate things. Some of the new baselayers designed for cross country ski racing and cold weather cycling have wind-proof panels in specific areas. But it's often easiest to throw on a breathable shell layer to protect from wind (and snow and snow falling from trees in the wind). Just make sure it's a shell; no lining, no insulation.
6) If you can't control your sweating, the only solution is to carry a change of clothes in a daypack. When you stop exercising, immediately take off your baselayer and don't put a new one on until you start to feel chilled. Only then put on enough new, dry layers to keep you warm. If you put on a fresh shirt while you are still sweating, you've defeated the whole purpose.
I know it sounds odd, but, sometimes, you really do need to keep cool to stay warm. Life isn't a spectator sport. Get out and enjoy!
There are two schools of thought on baselayers. One prefers fabrics that stretch and cling tightly to the body, arguing that these help draw the moisture off the skin more quickly. The other camp argues for looser fit, claiming the movement between skin and garment helps get rid of moisture. I'm firmly in the "clingy" camp, but urge you to experiment for yourself.
The other factor is the neck. For active outdoor sports, nothing beats a quarter — or, better yet, half-zip long-sleeve T-neck. Pulling down that zipper lets you quickly vent a lot of heat and moisture, while zipping it up helps keep you warm when needed.
Then comes material. The real choices are synthetic polyester fabrics or Merino wool. Both work, -if you keep cool and don't oversweat in them.
I use both synthetics and wool almost interchangeably, but, personally, the more I use the new Merino wool underwear (and socks), the more I like it, with one exception. If you are really going all out aerobically, the modern synthetics have a slight edge over wool at keeping you dry-and warm.
Thermal In Action
I've climbed on two different mountains this winter, Monadnock in southwestern New Hampshire and Greylock in western Mass.
On Monadnock, the temperature was in the 20s. I started off with a wool zipneck, a light fleece over it, and a hat and lightweight gloves. On the bottom, I had ultralight synthetic longies under light nylon pants. The fleece and the hat came off as the trail started to steepen. Shortly after that, I rolled up my sleeves and pulled down the half-zip.
I kept the gloves on the entire journey. Turning around just below the summit, I put the fleece and hat back on and descended in comfort.
A week later, on Greylock, it was four below zero. I wore the same wool zipneck and fleece, with a thin quilted vest between. Again the fleece came off quickly, and I eventually unzipped the vest and the zip neck.
At the top, I put the fleece back on, added a down "puffy" jacket with a shell over it and a warmer hat, all of which kept me warm on the windy descent.
Tim Jones writes about outdoor sports and travel. Email: firstname.lastname@example.com.
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The Evolution of Facebook Features [INFOGRAPHIC]
GroSocial and Reid Johns created this infographic. Fantastic timeline of data to use for research.
Melissa Fach
Melissa is the owner of SEO Aware, LLC. She is a consultant and trainer helping companies make the most of their content marketing and SEO. She specializes is the Psychology behind blogging and content marketing. Melissa is also an associate on the Community team at Moz, an associate and writer at CopyPress and an editor at Authority Labs. She is a self-proclaimed Star Wars and Internet geek and volunteers with big cats at BigCatHabitat.org.
Latest posts by Melissa Fach (see all)
- Please Welcome the New Editor of SEJ, John Rampton - February 27, 2013
- You Can Be a Hero on New Year's! - December 31, 2012
- I'm Back… Let's Make SEJ a Better Place - December 18, 2012


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Whole Genome Shotgun Assembly
From ArachneWiki
Whole Genome Shotgun Assembly (often called simply Whole Genome Assembly or WGA) is the task of sequencing the entire genome of an organism by ordering and orienting reads. Reads are small snippets of DNA that come from random locations in the genome; they are typically found through paired-end sequencing of inserts. The inserts range in size from a few thousand base pairs up to 200,000 bp and are created by any of several sequencing methods.
Arachne approaches the task of WGA by organizing reads into successively larger assembly objects. Reads are combined into contigs, so called because they consist of many reads aligned together to create a contiguous sequence of base pairs. These are then used to make supercontigs, which consist of many contigs separated by gaps of estimated sizes. In practice, genomes are always sequenced to high levels of coverage, allowing for overlaps and redundancy checks. It is not at all uncommon to amass tens of millions of reads before attempting whole genome assembly.
Challenges to WGA
Whole genome assembly is akin to solving an enormous one-dimensional jigsaw puzzle. The biological and stochastic nature of the problem leads to some special difficulties, listed below. In the jigsaw puzzle analogy, random chance represents missing pieces. Cloning bias represents a tendency of some regions of the puzzle to resist being cut. Sequencing errors represent miscut pieces. Redundancy represents a repetitive pattern in the puzzle, so that a piece can fit in multiple places and distinct pieces may appear identical. Polymorphism represents two slightly different puzzles superimposed on each other.
Random chance
Unless the coverage is effectively infinite, some regions will simply not be represented. This leads to gaps in the assembly.
Cloning bias
Cloning bias is a tendency of certain regions of the genome to be cloned less often than others during sequencing, and thus less likely to be sequenced. This results in a lower expected read coverage in these regions, which magnifies the gap-producing effects of random chance. To get enough data to sequence these regions, a higher overall coverage is needed. The most prominent cause of cloning bias is AT-richness, which affects cloning rates in the Sanger sequencing process. In 454 sequencing process, another kind of cloning bias causes homopolymers to be counted incorrectly.
Sequencing errors
- Main article: Sequencing error
- Main article: Chimerism
There are many different sequencing methods, but none of them are perfect; they all call bases incorrectly from time to time. These mis-calls are called sequencing errors. Fortunately, the chance of a sequencing error is usually known and quantifiable. The quality score is a measure of confidence that a base has been called correctly.
A related problem is chimerism: the occurrence of paired production reads with an inaccurate link between them. Chimerism is a form of poor data quality; Arachne discards chimeric reads when it detects them.
- Main article: Repeat
Every genome has repeats: sequences that appear in more than one place. Repeats can look dramatically different from genome to genome, in terms of length, identity, and extent. While tame genomes contain almost no repeat sequences, others can be made up of repeats on more than half of the genome - and these are copies at high-identity. One common form of redundancy is segmental duplication. Repeats are also likely to appear in highly AT-rich or GC-rich genomes, for the simple statistical reason that these genomes contain less variety.
Repeats (or clusters thereof) begin to pose a problem for the assembly process when they are at least as long as the smallest insert size and identical at high rates (99% and up). It is not clear if some repetitive genomes can be assembled correctly at all; in any case, there are ways to at least ameliorate the problem.
- Main article: Polymorphism
Most organisms are diploid, meaning they have two complete pairs of chromosomes, one from the mother and one from the father. The two chromosomes are similar but, unless there is no variation in the gene pool, not identical. (Some species are effectively haploid; see mouse.) The reads in a library can come from either chromosome in a pair, and therefore, they might not match up even if they are taken from the exact same spot in the genome. Such genomes are said to be polymorphic.
Polymorphic genomes can pose a major problem to genome assembly. Do two reads come from polymorphic versions of the same region, or do they come from different copies of a repeat? What to do about indels -- sequences that exist in one chromosome but not in the other? What if some stretches are inverted relative to each other? When is it better to assemble both haplotypes together, and when should they be split apart into two separate assemblies?
Special Types of WGA
Assisted assembly
- Main article: Assisted assembly
Assisted assembly is the process of using an already-sequenced genome (a reference genome) as a reference for improving an assembly. Assisted assembly is a useful alternative to de novo assembly in the case of low-coverage assemblies. The main module that performs assisted assembly is AssistMain.
Hybrid assembly
- Main article: Hybrid assembly
Sanger sequencing is just one method of obtaining snippets of DNA sequence. Other promising technologies are emerging, and you may find yourself with a mix of data from Sanger and other sequencing methods. Arachne allows you to build hybrid assemblies.


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|Reno, NV worksite
Reno, Nevada is a Worksite of the Exotic and Invasive Weeds Research Unit located at the Western Regional Research Center in Albany, California. The Reno worksite focusses on integrated weed control and revegetation of temperate desert rangelands.
Directions to the Reno, NV worksite (link to Google Maps).


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Online shopping a boon to delivery companies
Companies that deliver packages are seeing a record number of deliveries this holiday season.
Thank online shopping.
"E-commerce is just blowing things away," said Shaman Smith, senior manager of the FedEx Station in San Diego. "This year is projected to be the biggest and e-commerce is fueling that for us. You can call us Santa's little helpers at this time of year."
IBM Benchmark, which tracks cybersales, reported a 30.3 percent increase in shopping online on Cyber Monday, the digital version of Black Friday. Online sales make up about 10 percent of holiday shopping and continues to grow each year, according to the experts.
FedEx, the United States Postal Service and the United Parcel Service (UPS) are seeing more packages than ever before this season. The Post Office reports a decrease in letters and cards, chalking it up to digital greetings and texting but the number of boxes is on the rise due to overall online shopping.
Monday marked FedEx's peak day of the holiday season - with a record 19 million packages moved. The Post Office forecasts its busiest day will be Dec. 17 and UPS is preparing for Dec. 20.
Get it there by Dec. 24 with these deadlines:
Ground shipping, Dec. 17
2Day Air, Dec. 20
Express Air, Dec. 22
U.S. Postal Service:
Express mail international is Today, Dec. 11
Parcel post domestic, Dec. 14
First class mail for cards and letters, Dec. 20
Priority mail packages, Dec. 21
Express mail packages, Dec. 22
Military APO and FPO addresses:
Express mail for letters, cards and packages, Dec. 17
Three day select shipping, Dec. 19
2nd Day Air, Dec. 20
Next Day Air, Dec. 21
The crush for FedEx is driven by vendors shipping to retailers, online shoppers receiving packages and parcels being sent to Military installations. Closer to the holiday the rush is boosted by those sending cards, letters and gifts to friends and family in the mail.
At the San Diego FedEx hub Monday 185 employees, including 128 couriers, were in full swing processing holiday packages that are flown in from across the country and internationally.
"The rest of the year is practice for this," Smith said.
Each morning before dawn a slew of 53-foot tractor trailers roll in from the airport carrying tons of weight in packages - some as small as a ring box and others as big as carpet rolls. The packages are placed on a conveyor belt and sent along to workers who label, sort, stack and deliver. Within two hours the drivers are loaded and on their way.
Greg Adame assessed a stack of boxes set to go in his truck on the company's busiest day for delivery around Point Loma.
"It's fun, especially when you have residential and you see the kids," he said about delivering during the holiday season. "They see you as Santa's helpers."
Packing Tips
- Select a box strong enough to hold and protect the contents
- If re-using a mailing box be sure it is sturdy, without markings and remove old labels
- Cushion items with bubble wrap or foam peanuts. You can also use real air-popped popcorn - do not salt or butter - which works just as well as foam. Be careful with packing items in newspaper because it may bleed ink on certain items.
- If packing glass, stuff the inside of the item such as a vase with filler and remove glass from frames and pack separately in the same box.
- Take batteries out of devices and pack with the item.
- Be sure to include the to and from information with full, accurate and legible addresses. It doesn't hurt to stick an additional label inside the package just in case.
- Use clear tape intended for packaging.
Source: U.S. Post Office
By the numbers
Did you know: It's the busiest time of the year for those delivering holiday goodness across the country and the world, here are some mind-boggling numbers:
• 19 million: the number of packages moved Monday, FedEx's busiest day of the season
•90,000: the number of packages processed Monday in San Diego County at four hubs, up from 60,000 to 65,000 on a regular day
•180: the number of deliveries made Monday by FedEx drivers, up from 120 during a non-Holiday period
•280 million: the number of packages expected to be delivered this season, up 13 percent from the prior year.
U.S. Post Office
•2 million: the number of letters and cards expected to be delivered on the Post Office's busiest day, Dec. 17, nearly triple what it processes on a daily basis.
•22.1 million: the number of holiday letters and cards expected to be delivered this season, down from 25.7 million last year
•5.9 million: the number of packages forecast for delivery by Christmas, up from 4.69 last year
•28 million: the number estimated for delivery on UPS's peak day, Dec. 20, accounting for 80 percent more volume than normal and up from 27 million last year on the busiest day.
•527 million: the number of packages expected to be delivered, up from 480 million last year.


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RENO, Nev. — The Battle Born Dirtbag Geocaching Society is proud to join KNPB, Channel 5 Public Broadcasting and the University of Nevada, Reno BalloonSAT Program for an inaugural event showcasing the sport of geocaching.
The idea is a collective effort to take geocaching to new heights and push the boundaries of creative and extreme geocaching. In keeping with that goal, attendees will help launch a high-altitude balloon and payload dubbed "Project Explorer" containing a geocache, global positioning system tracking devices, and video/still cameras, into the Earth's stratosphere exceeding 100,000-feet in altitude and have it safely return. Upon return to Earth, the landing location will become a permanent placement of a new geocache container on Geocaching.com. This is a family friendly event to promote both geocaching and science/engineering.
Launch is scheduled for Sept. 29, 9 a.m. outside the Palmer Engineering Building on the University of Nevada, Reno campus. The public is invited to arrive as early as 8 a.m. to witness the activities involved making this launch possible. The location and details are subject to change due to possible changing weather conditions. Those interested can find current launch information at http://coord.info/GC3V7R0.
Members from the UNR BalloonSat Program will provide a short presentation about the equipment and logistics used in the launch, and members from the BBDGS will present the basics of geocaching and advantages of a quality geocache. After the launch attendees will track the ascent and decent of the payload to its landing zone. A recovery team will be dispatched to recover the equipment and geocache. All are invited to join the recovery outing, however, the landing area may be very rough and difficult terrain and may not be suitable for all attendees. All participants will do so at their own risk.
Geocaching is a high-tech treasure hunting game played throughout the world by adventure seekers equipped with GPS devices. The basic idea is to locate hidden containers, called geocaches, outdoors and then share your experiences online.
The Battle Born Dirtbag Geocaching Society, the Nevada chapter of the Dirtbag Geocaching Society, was formed in 2011 in an effort to promote quality geocaches while using exceptional technical processes and unusual ideas to magnify the sport of geocaching.
The event is provided at no cost to attendees and the public is encouraged to attend.
For further information visit www.dirtbaggeocachingsociety.com, www.facebook.com/battleborndgs and www.geocaching.com.


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Moderator: Cydisc
-Scorecards will be purchased for $5 from Josh Lyster. The $5 will go towards paying for your spot in the tournament should you make one of the top 10 spots. Any extra cash leftover will be used to fundraise for the new pro tee pad on hole 4 at carrol marty.
-You can "buy back in" for $10 if you aren't happy with your rounds.
-If you do buy back in your scores will be averaged. This means that when you buy in you MUST play both courses again (ie if you don't throw well at one of the courses you can't just buy back in to play that course.) You must play both again.
Sidearm wrote:Locals only?
Cydisc wrote:This weekend is probably the only time I'll have to get my rounds in. I imagine somebody will be out to play with, right?
This will mark the first time I'll have thrown a frisbee since mid-December, so it will be interesting to say the least.
smalls51691 wrote:i will probably be there and it will be the first time i have thrown since mid september... since i had surgery in the begining of november
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The Summit Tigers boys' basketball team clung to its lead at the end of its non-conference game with Buena Vista Tuesday for a 55-51 win.
After Markeith McDonald and Cayman Lee got into foul trouble in the first quarter, the Tigers' lead turned into a deficit in the second, requiring a halftime game plan for how to get the two key players back into the game to help defend and put points on the board.
"Markeith is an important cog on our offense in a half-court or three-quarter-court trap. ... We use him to attack the back guy. That was our problem the second quarter - we didn't have him in that position," head coach Phil Tronsrue said.
Once the team left the locker room, it took control of the court, stopping Buena Vista's momentum to gain the lead and not let go. It came down to making free throws as the Demons were forced to foul to regain possession, and the TIgers didn't disappoint.
Coy Coker finished the night with 14 points, sinking two three-pointers and hitting four of eight from the free throw line. The point guard also had eight rebounds, two assists and four steals. Garret Tousey and McDonald each contributed nine points, while Max Ortiz sank two three-pointers to lend a hand to the team.
Tronsrue said his team showed poise and discipline in a tough game.
"We've been starting out good, but then we crumble, or we don't handle the pressure of fighting back once we lost the lead," he said. "We handled that situation a whole lot better (Tuesday) night."
The Tigers bump to 4-13 on the season (3-9 in the Western Slope conference). At 7 p.m. Friday, they play Rifle in a must-win game to have a chance at making the playoffs. If the team splits with Rifle, Summit gives itself a better chance of landing a seed, as many of the teams are locked up in ties right now. The Tigers have fewer games to play and more losses to make up for.
Meanwhile, the girls' team lost another one on the road. The Lady Demons defeated Summit 67-30, putting them at 1-16 overall.
Another win, another step toward the playoffs.
Summit High's hockey team broke through a Battle Mountain barrier Monday night to tally both another win and vengeance on the team that crushed it, 7-2, in the early season.
The 3-1 win sends Summit on its way toward its final three games in the hunt for a playoff seed.
"Hopefully we're starting to hit a stride a little bit and starting to understand a few things. It's too bad it took until Game (16) to start to figure it out," head coach Chris Ruhly said.
The fact that the team took on its rival (based on proximity) and knowing playoffs are at stake may have spurred the team into action, the coach said.
Though the first period's play was below average, allowing Battle Mountain's Bjorn Bredeson the only goal in the period, things picked up from there, Ruhly said. Travis Potts scored on an assist from Peter Grotemeyer, and then the third period sealed the deal. Simo Korpela skated the puck from end to end, making a few "nice" plays along the way before taking a hard shot to beat the goaltender. Then, Jack Nevicosi put his body in the way of a Battle Mountain shot, putting the puck to ice and he skated it to an empty net to score.
"It was probably one of the best periods we've played all season," Ruhly said about the third. "The energy was high, the intensity was there."
It was also a night Ruhly's team played for a full 51 minutes, he said.
This weekend will be a test of the team's fate. On Friday, it travels to Standley Lake, which is a top team in the conference. On Saturday, the Tigers face off against Aspen for their final home game of the season and senior night.
"This weekend is going to be a big test for us. It's going to come down to playing hard for 51 minutes, mistake-free hockey," Ruhly said, adding that if the Tigers tally wins this weekend, a playoff seed might come down to who wins the Steamboat contest next week.


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Share Photo
In this image provided by the family, Sarai Sierra is shown in an undated family photo, in New York. Sierra has reportedly gone missing during a trip to Turkey. She last contacted her family, Monday, Jan. 21, 2013, the day she was to fly from Istanbul to New York. (AP Photo/Family Photo)


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SANTA CLARA -- Although Vernon Davis' on-field production has been relatively quiet, his one catch in Saturday night's win should serve as reassurance that he remains a capable catalyst.
Davis produced a 44-yard reception late in the third quarter, setting up Frank Gore's 2-yard touchdown run that pushed the 49ers lead to 38-24 in an eventual 45-31 win over the Packers.
"It made me feel I'm unstoppable," Davis said.
Davis didn't catch any of the four other passes in which he was targeted and has only seven receptions over the past seven games.
His confidence is unshaken, nor is his politcally correct team-first attitude. "I've just got to take advantage of my opportunities," Davis said. "We're winning and that's a great thing."
Davis is well aware that his counterpart Sunday is arguably the league's greatest tight end in history, that being Tony Gonzalez.
"He's done a lot for the tight end position," Davis said. "I'm very thankful to have someone like that to look up to, and he's set the bar very high."
Davis place a new pair of red headphones in all of his teammates' lockers Thursday, as supplied by Beats By Dr. Dre.
For more on the 49ers, see Cam Inman's Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.


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Rehabilitation is an essential phase of cancer care and should be considered from the time of diagnosis in a complete and comprehensive treatment plan. Surgical resections often create large defects accompanied by dysfunction and disfigurement, and radiation therapy produces significant morbidity and unique tissue-management problems. Speech, swallowing, control of saliva, and mastication can all be adversely affected. If these cosmetic and functional impairments are not corrected or minimized, the patient may be unable to resume a normal working and social life.
The primary objective of rehabilitation is the restoration of appearance and function. How successfully this is accomplished, depends upon both the judgment and skill of the therapist, and the post-treatment anatomic, physiologic, and psychological makeup of the patient.
Rehabilitation of the head and neck cancer patient requires a team approach, which includes many specialists. In addition to the surgeon, the dental oncologist and the prosthetic doctor, there are many other individuals involved as part of the restorative team. The clinical social worker sees the patient at the time of diagnosis, during primary cancer treatment, and during the long period of rehabilitation, to the help patient understand the process of treatment and to mobilize resources to cope with the situation. Nurses can provide support and comfort for the patient, give instruction on the care of the surgical defect or tracheostomy, and arrange for visiting nurse support when the patient returns home. As there may be conditions which alter eating habits, or skills, dietitians advise patients on obtaining proper nutrition. Occupational and physical therapists help retrain altered muscular systems, and the speech pathologist can help patients to adapt speech mechanisms to prosthetic appliances, and altered physiology. Dental hygienists provide prophylaxis and oral-health-care instruction.
Most tumors of the paranasal sinus, palatal epithelium, or minor salivary glands require surgical removal of a portion of the upper jaw, This is either a partial or total maxillectomy. A radical maxillectomy entails surgical resection of the entire maxilla to the midline. This is accomplished by an insicion through the cheek and the upper lip, allowing the tissue to be folded (reflected) back for access to the maxilla. A partial maxillectomy is less encompassing, and may be performed without the reflection of these external tissues (transorally). The amount of soft palate included in these resections varies, and depends on the need to obtain tumor-free margins (edges of the incision).
Defects created by surgery to remove cancerous tissues of the hard or soft palate may produce a variety of problems. For instance, hypernasality could make speech unintelligible. Chewing (mastication) may be difficult, particularly for the patient without natural teeth (edentulous patient). Because denture-bearing tissue surfaces are lost, it is difficult for the denture to seal completely around the edges, a key factor in holding it securely in place. Swallowing likely will become awkward, since food and liquid may be forced up into the nasal cavity and out the nose. The nasal mucous membranes become dried out (desiccated) by abnormal exposure to the oral environment, causing chronic irritation. Nasal and sinus secretions may collect in the defect area. Facial disfigurement can result from lack of midface bony support for the facial soft tissues, or the necessary surgical damage to a branch of the facial nerve. In some cases, extensive tumor invasion requires surgical removal of the eye.
Rehabilitation after surgical resection of the hard or soft palate is best accomplished prosthodontically. Customarily, a temporary prosthesis, known as an immediate surgical obturator, is placed at the time of surgery. This will provide closure of the surgical defect. During the healing period, this prosthesis is recontoured (relined) periodically to compensate for tissue changes which occur as a normal part of the healing process. When these tissues become well healed and dimensionally stable (usually 3 to 4 months after surgery), the final prosthesis is made.
The purpose of an obturator prostheses is to restore the physical separation between the oral and nasal cavities, thereby restoring speech and swallowing to normal, and to provide support to the lip and cheek. Inadequate retention of the obturator compromises stability. The remaining teeth, therefore, become extremely valuable in providing support, retention, and stability for these restorations.
It is essential that the prosthodontist examine and consult with the patient before surgery. The sequence of treatment should be explained to the patient, and diagnostic casts and appropriate radiographs should be obtained. With this information, the prosthodontist is ready to consult with the surgeon about the design and fabrication of the surgical obturator. Modifications in the surgical plan that may improve the prosthetic prognosis without adversely affecting tumor removal should be discussed at this time.
Immediate or early coverage of a palatal defect with an obturator is important. The obturator provides a matrix upon which the surgical packing can be placed, minimizes contamination of the wound in the immediate postoperative period, and enables the patient to speak and swallow effectively immediately after surgery.
In order to fabricate the prostheses, a stone model is made of the maxillary arch and the anterior portion of the soft palate. The obturator's size is determined by the surgical boundaries of the resection, as indicated by the surgeon. In the patient who still has natural teeth, those in the path of the surgical resection are removed from the model. The obturator can now be made before the surgery, using self-curing plastics, and be ready for immediate insertion afterwards. If necessary, this first obturator can be altered at surgery by trimming it's size, or by adding a temporary denture reline material. After surgery the prosthesis is wired to remaining teeth, alveolar ridge, or other available structures.
After the surgical packing is removed the prosthesis is recontoured with a temporary denture reline material. As healing progresses, the obturator is periodically relined and extended further into the defect, adaptation is improved, and anterior teeth are added as necessary to improve speech and esthetics. Three to five months after surgery, when healing and the related tissue changes are essentially complete, the final prosthesis is begun. Patients without natural teeth (edentulous) to use as fixation points for the obturator, often require a longer period of healing because the defect must be engaged more aggressively to maximize stability, support, and retention.
Defects of the hard palate can be restored effectively with a denture prosthesis. Natural teeth greatly improve denture retention and stability of a maxillary prosthesis. When the denture is properly extended, speech, swallowing, mastication, and facial contour restoration can be accomplished. In it's final contour, the obturator should extend maximally along the lateral wall of the defect. This high lateral extension not only increases retention and lateral stability, but also provides support for the lip and cheek. In some patients, extensions across the nasal aperture may be necessary to provide acceptable retention.
The placement of osseointegrated implants (More on dental implants) into the remaining bony structures, dramatically improves the function of an obturator prosthesis, particularly for edentulous patients. Implants can be placed, either during the surgical procedure to remove the malignant tissues, or at some appropriate time thereafter. These implants will allow mechanical attachment of the denture prosthesis to them, adding significant stability. For instance, implants may be splinted together with a bar in the mouth that mates to female snaps in the base of the denture, allowing the denture to be "clipped" in and out of the mouth. In patients with some remaining natural teeth, implants may still be used to augment the retention provided by these teeth. When the prosthesis is inserted and attached to the fixed implants, speech and swallowing are restored to normal limits. The tissue side of most prostheses require relining/recontouring within the first year because of slow, but continuous changes of the tissues on the periphery of the surgical defect.
Defects of the soft palate and velopharyngeal complex require different and more complex prosthetic treatment. Closure normally occurs when the soft palate comes into contact with the contracting lateral and posterior walls of the nasopharynx. When a portion of the soft palate or lateral pharyngeal wall is surgically removed, or when the soft palate is perforated, scarred, or neurologically impaired, complete closure cannot occur. Speech becomes hypernasal, and nominal swallowing is not possible. With a pharyngeal obturator, the patient may be able to re-establish this closing. A properly designed obturator will not interfere with breathing, impinge upon soft tissues during postural movements, or hamper the tongue during swallowing and speech.
The soft palate obturator remains in a fixed position in the nasopharynx and does not attempt to duplicate normal movements of the soft palate. The tissue side of the obturator remains level with the hard palate contour. During breathing and the production of nasal speech sounds, the space around the obturator reflects the potential for muscular contraction. During swallowing and the production of other speech sounds, this muscular network moves into contact with the stationary plastic obturator, establishing closure. A correctly constructed obturator will usually result in the return of normal speech and swallowing.
Disabilities resulting from tongue and mandibular resections include impaired speech articulation, difficulty swallowing, deviation of the mandible during functional movements, poor control of salivary secretions, and often cosmetic disfigurement. Consequently, these patients seldom return to presurgical levels of social function.
Advanced tumors of the anterior two thirds of the tongue and floor of the mouth often require extensive resection of bone and soft tissue. The loss of large portions of the tongue prevents appropriate "valving" and/or interaction with the other oral structures. This loss of mobility combined with the loss of motor and sensory innervation leads to misarticulation of many speech sounds. Deglutition is less impaired, and most patients learn to swallow fairly efficiently. Tongue function is less affected if the resected portion is restored with either myocutaneous or free flaps. The myocutaneous flap restores bulk, prevents deviation of the mandible, and permits the reconstructed tongue to articulate more effectively with the palatal structures. Myocutaneous flaps, however, can become scarred and immobile. In contrast, tongues reconstructed with free flaps have the potential of supporting near normal speech and are less likely to become heavily scarred and immobile.
If much of the mandible is segmented and removed, the remaining functional mandibular segment will be retruded and deviated towards the surgical side at the vertical dimension of rest. When the jaw is opened this deviation increases. These factors, combined with impaired tongue function, may prevent effective mastication. The severity and permanence of mandibular deviation varies; some patients attend an acceptable intocclusal relationship without adjunctive therapy.
Resections of the tongue and mandible often obliterate portions of the lingual and buccal sulci so that a means of collecting and channeling secretions posteriorly no longer exists. In addition, the motor and sensory innervation of the lower lip on the resected side is often lost, impairing speech, eating, and control of saliva.
When removal of tumors in the anterior floor of the mouth requires that the mandible be resected anteriorly, and when mandibular continuity is not restored, the two remaining posterior fragments are pulled medially by the residual mylohoid muscles and superiorly by the muscles of mastication. Severe disfigurement and dysfunction result. Free flaps from the fibula can be used immediately to restore the lost hard and soft tissues, and most patients emerge with excellent function and acceptable appearance.
The nature and degree of the disabilities secondary to impaired tongue function after resection of lesions in the anterior floor of the mouth are proportional to the amount of tissue resected and to the nature of surgical closure. In most cases, motor control is unimpaired and the functional deficits depend on the degree of tongue mobility.
If the surgical wound is closed primarily (primary closure) by suturing the edges of the wound together, the functional disabilities are compounded. The introduction of the myocutaneous flap in the late 1970s ameliorated some of the disabilities, and improved tongue mobility resulted in acceptable speech, swallowing and saliva control. The advantage of free-tissue transfers (free flaps) over musculocutaneous flaps is the improved blood supply, enhancing wound healing and flap survival. The fibula is the preferred donor site unless the soft-tissue deficit is unusually large. The osteotomized fibula provides sufficient length and bulk and bone. Osseointegrated implants can be placed to retain and support prosthesis.
Vestibuloplasty and tongue release are of particular value when mandibular continuity has been maintained or restored. The creation of vestibules enables the patient to pool saliva more efficiently and allows for extension of denture flanges resulting in improved stability and retention . Creation of an attached keratinized mucosa on the ridge surface with either a skin graft or a palatal graft provides additional stability for a partial or complete denture. The patient's appearance may also be improved because a prosthodontic restoration can now be molded to provide contour and support for the lower lip and cheek portions of the resected area. Improvement of speech is less noticeable in patients who lack tongue mobility.
Surgically repairing mandibular discontinuity defects results in more normal mandibular movement patterns that enable an edentulous patient to exert force on both sides of the dental arch. This increases the stability of complete dentures. In dentulous patients a properly reconstructed mandible restores dental occlusion to normal and will partially alleviate deviation of the mandible.Free bone grafts. Reconstruction after extensive resection of oral malignancies with free grafts is difficult because of the lack of sufficient soft tissue to receive the graft, the decreased vascularity of the tissue bed secondary to radiation therapy and/or radical neck dissection, and the difficulty in achieving proper fixation of the graft during the healing period. The primary goals are to restore facial form, mandibular continuity and, in selected patients, appropriate volume and quality of bone should be provided for the placement of osseointegrated implants.
Autogenous graft sources for resected bone include iliac crest, rib, and clavicle. Most commonly the defects are restored either with particulate autogenous marrow housed in metal tray or with a block bone, both usually obtained from the iliac crest. The use of myocutaneous flaps for closure of the initial wound facilitates free-bone grafting of continuity defects by enhancing the volume and vascularity of the recipient soft tissue.
Free vascularized flaps. A major advance in mandibular reconstruction has been the development of improved techniques in microvascular surgery, which allow for composite grafting of large volumes of tissue. In microvascular surgery, which allow for composite grafting of large volumes of tissue. In microvascular free-tissue transfer (free flaps), bone, muscle, connective tissue, and skin can be autogenously grafted and remain viable. The grafting can be accomplished simultaneously with resection of the tumor, with excellent results.
Numerous donor sites have been used. The radial forearm is favored for reconstruction of most extensive soft-tissue defects such as the tonsillar, partial-glossectomy, and floor-of-mouth defects. The composite fibula flap is the preffered donor site for most complex oro-facial-mandibular defects. Multiple osteotomies may be performed without devascularizing the bone segments to replicate the contour of the replaced mandible. Fibular thickness makes it an excellent recipient of osseointegrated implants.
Even following successful reconstruction, functional deficits (deglutition, speech articulation, mastication efficiency) remain because of compromised motor and sensory control, inadequate tissue contour, and inadequate bulk of key tissues. Mastication efficiency is primarily dependent upon the quality of tongue function and the presence of a reasonable occlusal table adjacent to the sensate, functioning portion of the residual or reconstructed tongue. Articulation of speech is dependent upon tongue mobility and the presence of adequate tongue bulk. Patients with hemiglossectomy defects can learn to articulate and swallow effectively, if they can elevate their reconstructed tongue to interact with the palatal vault and maxillary dentition. More on dysphagia, speech, and eating issues.
If the reconstructed tongue does not possess the ability to elevate sufficiently to interact with the palatal structures, an acrylic resin template is made to engage the palatal contours and/or maxillary dentition. Their surfaces can be modified with modeling plastic or tissue-conditioning material and eventually processed into acrylic resin.
With the development of free flaps, there has been an increased success in surgically reconstructing the tongue in total glossectomy patients. When these flaps are used, bulk should be limited, allowing room for total restoration of the mandibular dentition with a prosthesis. Palatal speech and swallowing aids may be quite useful in selected patients.
When mandibular continuity is not restored, correction of mandibular deviation includes inter-maxillary fixation, and mandibularly based or palatally based guidance restorations. The method of choice should be combined with well-organized mandibular exercise program.
Mandibular guidance therapy begins when the immediate postsurgical sequelae have subsided, usually in 2 to 3 weeks. Upon maximum opening, the mandible is displaced by hand as forcefully as possible towards the nonsurgical side. These movements tend to lessen scar contracture, reduce trismus, and improve maxillomandibular relationships. The earlier mandibular guidance therapy is initiated, the more successful the result. Unfortunately, those patients suffering the most severe mandibular deviations (because of extensive soft-tissue loss, tight wound closure, radiation therapy, and/or radical neck dissection) are most susceptible to postsurgical complications that delay mandibular guidance therapy.
If the mandible can be manipulated into an acceptable maxillomandibular relationship, but the patient lacks the neuromuscular control to bring the mandible into occlusion, a cast mandibular resection prosthesis is appropriate. This prosthesis consists of a removal partial denture framework with a metal flange extending 7 to 10 mm laterally and superiorly on the buccal aspect of the bicuspids and molars on the unresected side. This flange engages the maxillary teeth during mandibular closure, thereby directing the mandible into an appropriate intercuspal position. The partial denture framework must be stable and retentive to counteract the lateral forces generated on the flange during closure. The guidance flange is constructed of cast chrome-cobalt metal. Modifications can be made with acrylic resin.
A second design confines the guidance ramp and index to a maxillary prosthesis. This form of guidance prosthesis is indicated when severe deviation prevents manipulation of the mandible into acceptable occlusal contact. Maxillary guidance ramps are more adjustable than mandibular guidance ramps. They are usually constructed of acrylic resin with either cast or wrought-wire retainers, since they usually serve only temporarily until an acceptable occlusion can be established.
The success of mandibular guidance therapy depends on the nature of the surgical defect, early initiation, and cooperation of the patient. Patients with extensive posterior base of tongue lesions, radical neck dissection, and radiation therapy are often unable to achieve functional intercuspal relationships. Mandibular guidance therapy is most successful when the resection involves minimal soft-tissue removal, or when defects are replaced with myocutaneous or fee flaps. Following mandibular guidance therapy, occlusal equilibration or selective crown placement may be required to achieve optimal interocclusal relationships.
The outcome of removable prostheses for patients with resections of the tongue and mandible depends upon the function of the residual tongue. In some patients with poor tongue function, only appearance and oral competence can be improved, while in others with good tongue function, mastication is a reasonable objective.
The usual principles of partial denture design and fabrication should be followed. Major connectors should be rigid; occlusal rests must be direct occlusal forces along the long axis of teeth; guiding planes should be employed to provide stability and bracing; retention must be within the limits of physiologic tolerance of the periodontal ligament of the abutment teeth; and maximum support should be gained from adjacent soft tissues. Retainers, minor connectors, and proximal plates should be designed so that they do not subject the remaining teeth to excessive lateral forces during function.
In patients with lateral discontinuity defects, it may not be possible to design a framework with retainers that disengage during function because of the altered patterns of force upon the prosthesis. Viewed from the frontal plane, the arc of closure of the mandible is angular rather than vertical, with forces of occlusion as the force of contracture on the unresected side is increased. The location of the fulcrum line of a partial denture is not easily determined because of the difficulty in predicting movement patterns of the prosthesis during function. The forces of occlusion are unilateral, so the axis of rotation (fulcrum line) of the partial denture deviates from the norm. By placing the occlusal rest on the mesial of the bicuspid that disengages during expression of an occlusal load in the distal extension area. However, a retainer can not be positioned in a retentive area on the opposite cuspid that disengages during occlusal function. Consequently, this retainer must either be placed on the height of contour, or it must be flexible so that an occlusal load will not subject the cupid to undue stress. All partial denture frameworks should be phsysiologically relieved.
After the partial denture casting has been fabricated, verified, and adjusted, an altered cast impression is obtained of the edentulous areas. Particular attention should be paid to the lingual extension on the unresected side, especially the polished surfaces, which provides additional retention and stability. Maximum extension of the denture base is always attempted. Coverage of the buccal shelf on the unresected side is essential to maximize support. Centric relation records are made and occlusal schemes developed that are consistent with the unilateral mandibular movement patterns of mandibulectomy patients.
Dentures for edentulous patients with discontinuity defects of the mandible may provide esthetic improvement by replacing teeth and improving lip and cheek contours, but unless the patient has extraordinary tongue control, mastication is generally not possible. A number of factors affect the patient's ability to function with resection dentures (1) stability, support, and retention of the mandibular denture are compromised; (2) quality and quantity of saliva; (3) the angular pathway of mandibular closure, which induces lateral forces upon dentures, tending to dislodge them; (4) abnormal maxillomandibular relationships that may prevent ideal placement of the denture teeth over their supporting structures; and (5) impairment of motor and/or sensory control of the tongue, lip, and cheek, limiting the ability to control dentures during function. Implant-assisted resection dentures can overcome many of these difficulties, particularly those associated with compromised retention, stability, or support.
The status of the remaining tongue is probably the most important prognostic factor. If motor and/or sensory control are not significantly impaired, and the tongue can be moved in several directions, resection denture stabilization and control of the food bolus during function become possible. Paradoxically, immobility of the tongue often permits a more aggressive extension of the lingual flange on the nonsurgical side, aiding stability and retention. The position of the tongue is also an important prosthodontic prognosticator relative to obtaining a peripheral seal.
Mandibular resections extending to the midline have a poor prosthetic prognosis. If the resection is limited to the ramus-molar or cuspid regions anteriorly, the prosthetic prognosis is more favorable. In some of these patients remmants of the masseter or medial pterygoid muscle may remain attatched to the mandible, enabling the development of bilaterally balanced occlusion. These patients demonstrate more-normal envelopes of motion, and near-normal ridge relationships, allowing for more favorable distribution of forces during mastication and swallowing.
Following impressions, centric and lateral registrations and occlusal schemes should take into consideration the altered pattern of mandibular movements. Denture extensions can be verified with a disclosing wax, and excessive tissue displacement eliminated with the aid of pressure indicating paste.
Patients with reasonable tongue bulk and mobility and with motor and sensory innervation intact on at least one side gain the most from implant-retained overlay prostheses. The tongue, then, is no longer required to control the denture, so it functions mainly to manipulate the food bolus during mastication and swallowing. If the patient's speech is intelligible, the prognosis for effective bolus manipulation with an implant-retained prosthesis is good.k j
In mandibular resection patients, if implants are to be placed into the mandible to retain and support an overlay prosthesis, consideration should be given to placing implants in the opposing maxilla. The unilateral occlusal forces and increased lateral forces generated during the chewing cycle tend to dislodge the upper denture. In addition, xerostomia may compromise the peripheral seal. Therefore, implants should be considered if the retention and stability of a conventional maxillary denture is marginal.
In most patients, the only implant sites available in the edentulous resected mandible are located in the symphyseal region. A minimum of two implants should be placed. However, more are desirable, if space allows, mainly for stability.
Implant success rates in bone grafts used to restore mandibular continuity defects have been encouraging. Free bone grafts demonstrate a homogenous calcification pattern that results in an excellent bone-implant interface, particularly with fibula free flaps. To date, of the 54 implants that have been placed at the University of California, Los Angeles, (UCLA) in fibula free flaps, 46 are in function; 2 have been buried because of improper positioning or angulation; 3 have failed; and 3 have not yet been placed into function.
Surgical reconstruction and prosthodontic restoration both have limitations. The surgeon is limited by the availability of tissue, damage to the local vascular bed, and the need for periodic visual inspection of an oncologic defect. The prosthodontist is limited by the materials available for facial restoration, movable tissue beds, difficulties in retaining large prostheses, and a patient's willingness to accept the result. The method of facial restoration should be considered before surgery and patients should participate in the decision making process with realistic expectations.
Surgical reconstruction of small facial defects is preferable. However, it is difficult for the surgeon to contour a facial component that is as effective in appearance as a well-made prosthesis. Osseointegrated implants in facial defects have changed patient perceptions about facial prostheses because of the retention achieved. Additionally, when a large resection is necessary and recurrence of tumor is realistic, it is advantageous to be able to monitor the surgical site closely, which a prosthesis permits. Even when surgical reconstruction is deemed possible, most surgeons prefer to wait at least one year before surgical construction. Also, surgical restoration of large defects is technically difficult and requires multiple procedures and hospitalizations, which may be further complicated if radiotherapy has been included.
The challenge to the prosthodontist is to fabricate an esthetically pleasing restoration. A conspicuous prosthesis may produce more anxiety and permit less social readjustment than a simple face bandage or eye patch. The most critical periods is the first 2 to 3 days after delivery. The patient must understand that a prosthesis has two different roles: for family, close friends, or business associates, it can only cosmetically replace the tissues excised; for the public at large, it generally provides enough concealment to render the reconstructed defect inconspicuous.
Current materials all possess some undesirable characteristics. The materials most often used are the new silicone elastomers, which have achieved wide clinical acceptance. Adhesives are used to retain facial restorations. A major development has been the use of osseointegrated implants, resulting in extremely well-retained prostheses that permit vigorous physical activities.
A presurgical moulage can be very helpful, especially if a total rhinectomy or total auriculectomy is anticipated. Impressions of the defect are usually obtained with elastic impression materials, taking care not to displace the tissues being recorded. The contours of the prostheses are sculptured in wax, both on the cast and on the patient. Surface characteristics, appropriate contour, coloration, and margin placement are equally important factors. Processing the materials is complicated and requires special instrumentation. Special flasks are necessary for processing large prostheses.
Basic skin tones should be developed into a shade guide for each material. The base shade selected should be slightly lighter than the lightest skin tones of the patient, because as color is added the prosthesis will darken. Intrinsic coloration is long-lasting and is therefore preferred over trinsic application.
When the integrity of the oral cavity has been destroyed, food and air escape during swallowing; speech is often unintelligible; and saliva control is difficult. Additionally, it is extremely hard to adapt the margins of the prosthesis to maintain tissue contact during facial and mandibular movements. Retention of maxillary teeth or a portion of the hard palate improves the prosthetic prognosis. Placement of implants, as well as skin grafts to decrease tissue contraction and to create undercut areas for retention, also improve the prosthetic prognosis.
Patients will experience less depression if as many functions as possible are restored immediately after surgery with a temporary prosthesis. These functions include swallowing food (thereby eliminating the need for a nasogastric tube or gastrostomy), controlling saliva, and speaking. The oral portion of the temporary prosthesis is constructed of acrylic resin and formed so that contact is established with healthy tissues adjacent to the defect. Functional contact with the remaining portions of the lips allows the patient to effectively seal the oral cavity. Tissue-bearing surfaces of the prosthesis are relined with temporary denture reliner at frequent intervals to accommodate tissue changes.
In constructing a definitive midface prosthesis, a custom tray is used for the master impression. Movable portions of the defect are recorded with a thermoplastic material. Record bases are fabricated, and centric relation records enable casts to be mounted on an articulator. Osseointegrated implants, eyeglass frames, adhesives, straps, teeth, and engagement of defect undercuts supply retention. The finished restoration usually provides the patient with acceptable appearance and function.
The use of osseointegrated implants has significantly improved patient acceptance. The retention provided by implants makes it possible to fabricate large prostheses that rest on movable tissues. This enables the prosthodontist to fabricate thinner margins, which enhance esthetics by blending and moving more effectively with mobile tissues. Other benefits include elimination of the occasional skin reactions to skin adhesives, ease and enhanced accuracy of prosthesis placement improved patient comfort, and decreased daily maintenance, which also increases the life span of the facial prosthesis.
The implants must be positioned within the confines of the proposed facial prosthesis. In most patients it is desirable to sculpt a wax replica of the future prosthesis and to use this replica to fabricate a surgical template. This template is sterilized and used as a guide during surgery to ensure proper implant position and angulation.
The number and arrangement of implants and possible bone sites are determined. In most acquired defects, radiographic studies are not necessary. In large extensive defects, CT scans and three-dimensional models may be useful in evaluating potential bone sites and important adjacent structures. The health of soft tissues circumscribing osseointegrated implants is easier to maintain if these tissues are thin (less than 5mm in thickness) and attached to underlying periosteum. If the skin contains hair follicles or scar tissue from past reconstructive procedures, these tissues should be removed and placed with skin grafts.
Craniofacial implant fixtures are fabricated from pure titanium. They are available either 3 or 4-mm lengths, with a 5-mm diameter flange. The short lengths are designed to permit placement in areas with limited available bone. The flange facilitates initial stabilization of the implant and prevents penetration into interior components.
For ear defects, two or three implants are positioned posteriorly and superiorly to the ear canal. For nasal defects, the preferred fixture location is the anterior portion of the floor of the nose. Care should be taken to avoid the roots of the teeth in this area. For orbital defects, the preferred location is the lateral portion of the superior orbital rim.
Several attachment systems have been used to connect the facial prosthesis to the implants, such as bar-clips, magnets, and O-ring types. For auricular and nasal prostheses we prefer the bar-clip systems because they provide superior retention. We prefer magnetic retention for orbital prosthesis, because the ease of insertion of magnetically retained prostheses outweighs the possibilities of magnet corrosion and decreased retention over time.
The retentive system is designed to fit within the contours of the facial prosthesis as an acrylic resin substructure. It should posses sufficient surface area so that the bond between the substructure and the silicone prosthesis will not fail during insertion or removal of the prosthesis.
Success rates for auricular sites have exceeded 95% in most studies and few complications have been encountered. Success rates of the floor-of-nose sites are between 85 and 90% and are about the same as oral implants placed in the premaxillary segment. Of 130 fixtures inserted at UCLA, only 2 of 83 floor-of-nose and mastoid implants were lost; however, there were 19 of 47 frontal bone failures. Success rates are diminished if implant sites have been irradiated previously.
The risk of developing an osteoradionecrosis is minimal in patients who have been edentulous for some time before undergoing head and neck radiation therapy. The risk of bone necrosis increases in those patients who have teeth removed just before or after radiotherapy. More on osteoradionecrosis (ORN).
Empirical recommended insertion times have ranged up to three years. In our study of 92 patients who were edentulous before the onset of cancer, prostheses were inserted, on an average, 15 months after radiation was completed; 45 patients received dentures within 6 months. None of the 92 developed a denture-related osteoradionecrosis. This data and our clinical experience indicate that dentures can be fabricated soon after completion of radiation therapy in most patients. If the radiation fields cover little of the mandibular denture-bearing surface, dentures can be inserted as soon as the mucositis resolves. An irregular mandibular ridge, especially in a patient whose mandible was wholly within the radiation field, may prompt the clinician to defer dentures indefinitely.
In summary, for edentulous patients who were experienced denture wearers before radiotherapy, there is little risk of developing significant complications from wearing dentures. For those who had teeth extracted within the radiation field before radiotherapy and were not experienced denture wearers, the risk of bone necrosis is higher. Therefore, placement of dentures depends upon patient needs, the status of the mucosal and bony wearing surfaces, and the amount and fields of radiation. Some patients in this group may never be candidates for complete dentures.
Boggy mucosa with prominent telangiectasia and fibrosis implies that prosthodontic restorations will be poorly tolerated, and mucosal integrity is at risk. In the case of floor-of-mouth lesions, it may be prudent to somewhat limit extension of the mandibular-lingual flange. Scar tissue is most unyielding, and the slightest overextention can result in a mucosal perforation and perhaps lead to bone or soft-tissue necrosis.
Excessive trismus is occasionally observed in patients whose radiation field includes the temporo-mandibular joint and muscles of mastication. If there is trismus, it may be necessary to reduce the vertical dimension of occlusion. This will make intake of food easier and may reduce the forces exerted on the supporting mucosa during closure. Xerostomia and viscous saliva compromise retetntion as well as increase friction at the denture mucosa interface, causing mucosal irritation. Here the use of a denture adhesive powder is recommended to facilitate retention. Patients with mandibular ridges having severe bilater undercuts, mandibular tori, or excessive ridge resorption with little attached mucosa are poor candidates for complete dentures after radiation therapy.
Conventional border molding using a custom tray and modeling plastic is advocated. If xerostomia is particularly profound, a thin coating of petroleum may be applied over the soft modeling plastic to prevent its sticking to dry mucosa. Displacement of the tissues of the floor of the mouth in an attempt to obtain peripheral seal is not advocated. Efforts in developing the lingual flange should be directed toward gaining stability and support rather than retention. The elastic impression materials are most suitable in refining the impression.
The completed impressions are boxed and poured in dental stone. Conventional record bases are prepared and used to determine the vertical dimension of occlusion. The usual methods of determining vertical dimension (phonetics, closest speaking distance, swallowing, neuromuscular perception, and recording vertical dimension at rest) and centric relation apply. Wax, plaster, and zinc oxide paste are suitable media for obtaining the final registrations. Graphic recording devices can likewise be employed successfully.
On a theoretical basis, we favor monoplane occlusal schemes with bilateral balance obtained with posteriorly situated balancing ramps. In arranging posterior teeth, there should be proper buccal horizantal overlap to avoid tongue and cheek biting. When using anatomic posterior teeth, bilateral balance during function is mandatory.
Eliminate occlusal discrepancies before removing processed dentures from their casts. Pressure-indicating paste is used to identify areas of excessive pressure, and disclosing wax is useful in verifying extension of denture flanges. Remount on a suitable articulator with new maxillomandibular records taken at the time of delivery. Instructions are provided about removing dentures if soreness develops, limiting denture use initially during mastication, and not wearing them during sleeping hours. During the first week, 24- and 48- hour recall appointments are recommended. Commercial denture cleansers are effective tools for removing plaque deposits and food particles from denture surfaces. Careful follow-up is essential for denture adjustments and to minimize necrosis and infections.