clarifier 0.0.1

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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.idea
+pkg
+

data/CHANGELOG.md

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+# 0.0.1 / 2014-03-04
+* [FEATURE] Initial Release

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in clarifier.gemspec
+gemspec
+

data/Gemfile.lock

@@ -0,0 +1,23 @@
+PATH
+  remote: .
+  specs:
+    clarifier (0.0.1)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    metaclass (0.0.4)
+    minitest (5.0.8)
+    mocha (1.0.0)
+      metaclass (~> 0.0.1)
+    rake (10.1.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.5)
+  clarifier!
+  minitest (~> 5.0.8)
+  mocha
+  rake

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2014 Rob Styles
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,29 @@
+# Clarifier
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'clarifier'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install clarifier
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it ( http://github.com/meducation/clarifier/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

@@ -0,0 +1,9 @@
+require "bundler/gem_tasks"
+require 'rake/testtask'
+
+task :test do
+  $LOAD_PATH.unshift('lib', 'test')
+  Dir.glob('./test/**/*_test.rb') { |f| require f }
+end
+
+task default: :test

data/clarifier.gemspec

@@ -0,0 +1,25 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'clarifier/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'clarifier'
+  spec.version       = Clarifier::VERSION
+  spec.authors       = ['Rob Styles']
+  spec.email         = ['rob.styles@dynamicorange.com']
+  spec.summary       = 'Clarifier is a stopwords library for removing common words from text'
+  spec.description   = 'Clarifier is a stopwords library for removing common words from text'
+  spec.homepage      = 'http://github.com/meducation/clarifier'
+  spec.license       = 'MIT'
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.add_development_dependency 'bundler', '~> 1.5'
+  spec.add_development_dependency 'rake'
+  spec.add_development_dependency 'mocha'
+  spec.add_development_dependency 'minitest', '~> 5.0.8'
+end

data/lib/clarifier/stop_words.rb

@@ -0,0 +1,61 @@
+module Clarifier
+  class StopWords
+
+    attr_accessor :stopwords
+
+    @@lists = {}
+
+    def self.lists
+      @@lists
+    end
+
+    def initialize(desired_stopwords = nil)
+      if desired_stopwords.kind_of?(Array)
+        @stopwords = desired_stopwords
+      elsif @@lists[desired_stopwords]
+        @stopwords = @@lists[desired_stopwords]
+      else
+        @stopwords = @@lists[:en_gb_basic]
+      end
+    end
+
+    def clarify(input)
+      new_string = input.dup
+      #new_string.downcase!
+      #new_string.gsub!(/[[:punct:]]/, ' ')
+      #new_string.gsub!(/\s+/, ' ')
+
+      @stopwords.each do |word|
+        new_string.sub!(/^#{word}\s/i, '') #beginning
+        new_string.gsub!(/\s#{word}\s/i, ' ') #middle
+        new_string.sub!(/\s#{word}$/i, '') #end
+      end
+
+      #new_string.gsub!(/\s+/, ' ')
+
+      new_string
+    end
+
+    def train(docs, threshold = 0.8)
+      word_counts = {}
+      docs.each do |doc|
+        words = doc.split
+        words.uniq!
+        words.each do |word|
+          word_counts[word] ||= 0
+          word_counts[word] += 1
+        end
+      end
+      word_counts.each do |word,count|
+        if count.to_f / docs.length >= threshold
+          @stopwords << word
+        end
+      end
+    end
+
+  end
+end
+
+
+
+

data/lib/clarifier/version.rb

@@ -0,0 +1,3 @@
+module Clarifier
+  VERSION = "0.0.1"
+end

data/lib/clarifier/word_lists/en_gb_basic.rb

@@ -0,0 +1 @@
+Clarifier::StopWords.lists[:en_gb_basic] = %w(a able about across after all almost also am among an and any are as at be because been but by can cannot could dear did do does either else ever every for from get got had has have he her hers him his how however i if in into is it its just least let like likely may me might most must my neither no nor not of off often on only or other our own rather said say says she should since so some than that the their them then there these they this tis to too twas us wants was we were what when where which while who whom why will with would yet you your)

data/lib/clarifier/word_lists/en_gb_mysql.rb

@@ -0,0 +1 @@
+Clarifier::StopWords.lists[:en_gb_mysql] = %w(a's able about above according accordingly across actually after afterwards again against ain't all allow allows almost alone along already also although always am among amongst an and another any anybody anyhow anyone anything anyway anyways anywhere apart appear appreciate appropriate are aren't around as aside ask asking associated at available away awfully be became because become becomes becoming been before beforehand behind being believe below beside besides best better between beyond both brief but by c'mon c's came can can't cannot cant cause causes certain certainly changes clearly co com come comes concerning consequently consider considering contain containing contains corresponding could couldn't course currently definitely described despite did didn't different do does doesn't doing don't done down downwards during each edu eg eight either else elsewhere enough entirely especially et etc even ever every everybody everyone everything everywhere ex exactly example except far few fifth first five followed following follows for former formerly forth four from further furthermore get gets getting given gives go goes going gone got gotten greetings had hadn't happens hardly has hasn't have haven't having he he's hello help hence her here here's hereafter hereby herein hereupon hers herself hi him himself his hither hopefully how howbeit however i'd i'll i'm i've ie if ignored immediate in inasmuch inc indeed indicate indicated indicates inner insofar instead into inward is isn't it it'd it'll it's its itself just keep keeps kept know known knows last lately later latter latterly least less lest let let's like liked likely little look looking looks ltd mainly many may maybe me mean meanwhile merely might more moreover most mostly much must my myself name namely nd near nearly necessary need needs neither never nevertheless new next nine no nobody non none noone nor normally not nothing novel now nowhere obviously of off often oh ok okay old on once one ones only onto or other others otherwise ought our ours ourselves out outside over overall own particular particularly per perhaps placed please plus possible presumably probably provides que quite qv rather rd re really reasonably regarding regardless regards relatively respectively right said same saw say saying says second secondly see seeing seem seemed seeming seems seen self selves sensible sent serious seriously seven several shall she should shouldn't since six so some somebody somehow someone something sometime sometimes somewhat somewhere soon sorry specified specify specifying still sub such sup sure t's take taken tell tends th than thank thanks thanx that that's thats the their theirs them themselves then thence there there's thereafter thereby therefore therein theres thereupon these they they'd they'll they're they've think third this thorough thoroughly those though three through throughout thru thus to together too took toward towards tried tries truly try trying twice two un under unfortunately unless unlikely until unto up upon us use used useful uses using usually value various very via viz vs want wants was wasn't way we we'd we'll we're we've welcome well went were weren't what what's whatever when whence whenever where where's whereafter whereas whereby wherein whereupon wherever whether which while whither who who's whoever whole whom whose why will willing wish with within without won't wonder would wouldn't yes yet you you'd you'll you're you've your yours yourself yourselves zero)

data/lib/clarifier.rb

@@ -0,0 +1,9 @@
+require 'clarifier/version'
+require 'clarifier/stop_words'
+
+require 'clarifier/word_lists/en_gb_basic'
+require 'clarifier/word_lists/en_gb_mysql'
+
+module Clarifier
+
+end

data/test/stop_words_test.rb

@@ -0,0 +1,52 @@
+require_relative 'test_helper'
+require_relative 'test_docs'
+
+module Clarifier
+
+  class ClarifierStopWordsTest < Minitest::Test
+
+    def test_use_default_english_stopword_set
+      sw = Clarifier::StopWords.new
+      input = 'The quick brown fox jumped over the lazy dog.'
+      expected = 'quick brown fox jumped over lazy dog.'
+      assert_equal expected, sw.clarify(input)
+    end
+
+    def test_use_the_selected_stopword_list
+      skip
+    end
+
+    def test_use_an_array_of_stopwords_if_provided
+      sw = Clarifier::StopWords.new(%w(quick brown lazy))
+      input = 'The quick brown fox jumped over the lazy dog.'
+      expected = 'The fox jumped over the dog.'
+      assert_equal expected, sw.clarify(input)
+    end
+
+    def test_use_an_empty_array_of_stopwords_if_provided
+      sw = Clarifier::StopWords.new([])
+      input = 'The quick brown fox jumped over the lazy dog.'
+      expected = 'The quick brown fox jumped over the lazy dog.'
+      assert_equal expected, sw.clarify(input)
+    end
+
+    def test_derive_a_stopword_list_from_a_document_set
+      sw = Clarifier::StopWords.new([])
+      sw.train(StopWordsTestDocs.docs)
+      expected = %w(we are to the for a of and then is at one time with this that have here or in which can by you it these when on so your has be not if more some as there they)
+      assert_equal expected, sw.stopwords
+    end
+
+    def test_derive_a_stopword_list_from_a_document_set_with_a_threshold
+      sw = Clarifier::StopWords.new([])
+      sw.train(StopWordsTestDocs.docs, 0.2)
+      expected = %w(today we are going to discuss about the heart disease first for a run of concept and then we'll see what is between but at actually three concepts number one should special type whole time with people magic this an class workers that have up infection mission let's take our book bad give here or really back in which end bikini can inside them does especially by let me tell you particular produced who it don't know occurs because these dot part i when grow on its free political so hard out air your into that's true indeed talking right now has be across done must not go girl did if more supreme some over pretty friend like as bed system next their it's working think will start doesn't off there area present from good they stop him those diagram news red blood cell size cells regular he caused either environment two examples even pick way his side years easy however test many again chronic body were peers six having work tonight defined high loss jeans term process involves nothing help yeah get put world getting I'm waking doing us how lives living I do arm almost things same such close life hands you're just possible they're gonna happen down choose other rest changed tend little bit want car look mom looking kids kinda each she's got leg trying very quickly thing anything sorta yet case use only nineteen seventy medical been school medicine center health access patients proud last we're near new eighty nine group question towards complicated sometimes called able consistent too goes different both say he's all bodies physiology personal eyes no person until past within conditions would point come levels identify essential court well state act another against sort own view i'll refer make important under sir challenge face understanding uh... might began critical much sixty minutes sells understand week talk study hopefully lecture why won't live long without normal kidney chapter gross aspects differences fluid thought talked was created lot quite means show may block blue box around you'll remember low cast nerve signal four cardiac muscle contract yes action brains am could knowing always keep difficult general excess somehow sure left ask after pass basically said involved my young become fine spreading I'll through change maybe okay research most where buildings sections example find terrible cold coast something seeing moving mention boy fibers clearly underneath nuclei middle better try nice ah... took closely also bridge jason contraction ever ice had top trailer behind press didn't realize later seven brain hook surgery spinal cord)
+      assert_equal expected, sw.stopwords
+    end
+
+    def test_incrementally_derive_a_stopword_list_from_docs
+      skip
+    end
+
+  end
+end

data/test/test_docs.rb

@@ -0,0 +1,29 @@
+module Clarifier
+  class StopWordsTestDocs
+
+    def self.docs
+      @@docs
+    end
+
+    @@docs = [
+      "today we are going to discuss about the\nrheumatic fever aromatic heart disease first for a run of the concept of\nrheumatic fever and then we'll see what is the relationship between the\ndramatically but at the dramatic heart disease actually a total of three concepts number one one of the nation should bolster special\ntype of strip the whole time the relationship with the american\npeople and one of the nation triple rheumatic\nfever vedra magic card disease this is an art class today of workers that we have to run up one of the pump sexual relationship\nbetween streptococcal infection with the dramatic p one and one of the mission\ntrip a dramatic puma with the magic heart disease let's take a symbol of our book bad give the trend here or really happened back in this boson dissolved rourke nationals is a special labeled the kiosks which end of the end up francs japan subjugated vehicles up argument and cancels this special mobile bikini which can\ninside of the provided to them this is a struggle mark at this trip but what does further especially by bob strip the\nlogos let me tell you word of this particular produced a book organized trample who cried strip of august deductible it becomes which brook we don't know link occurs reproduces a strong hypothesis because these trickle piper diehl strong modest sensors for deals dot model for\nthe part of this is and by that this tropical i have begun when the\ndefense belonging to the lens feared plans for you grow big villains alluding cargo back on its free this subclasses fired up became political stripper pole quiet apartment with special papal somewhat carbohydrates so hard and lust and walked out wider\nair solved the stripper pole quiet rebecca lands for your classified dot batavia into that's true indeed cd so and so forth this particular between every time\ntalking right now this has to be stripped of across it has\nto be done with ridiculous it must not go blonde girl of must did not book nasrin grow up a let and if you have to be a few more\nroom and then extramarital jen supreme into some strain build some special strands over a big the chance for some pretty list pneumatic feeding less force that the sponsor and lots this particular streptococcal infection and a sore throat farm friend jake s bus like this then what really happens as you know bed did that give you have to be\nattacked by the macrophages and macrophages women it up the advent of the british dot and prevent buildup on the on system next fall's here is your mildred\nbarker this is not community partner decisions on their part of me it's on\nthe old system nam actually working couples addicted to\nit protect them because i think it will\nstart producing damaging debt and that doesn't know that information\noff dot friends and traditional defenses there\nnationally in europe though that macrophages that the media that particular date of the bihac area\nand present the evidence of macrophages so that from your system is that right and working together good men videos and they did that the vendor development so stop him communes of some of those foggy",
+
+      "if you can drop this diagram you can classify news based on red blood\ncell size anemic red blood cells are your small\nregular large small so he needs are caused by\neither the environment two genes environmental examples include if you don't even know firing or pick\nyou way genes include a bad palestinian here\ntoons large selling his are caused by the environment vitamin deficiency greedy in a drug side effects atlantis\nshows small or large in years identification is easy however if the\ntest shows regular size cells there are many more choices so we will\ncategorize these choices into bad red blood cell birth por las and subdivided categories into\nagain environment for Jeep pencil birth due to\nthe environment includes chronic disease exhausting your\nbody were a plastic immediately continue with their peers for bonior genetically that celebrate the knees are\ncaused by the bag at six the enzyme having steers\nremembrance then apply kind aids work hooky not necessarily tonight defined categories high cell loss\nsubdivided into environment in jeans environmentally acute\nhemorrhage the term for sale in the meaning of self genetic process involves\nsickle cells nothing can drive this time you have a\nframework to secede more theory into words help help support the hippocratic",
+
+      "yeah stir know here wake up in the morning you get dressed\nput on your shoes you head out into the world a the plan on coming back getting undressed going to bed I'm waking up doing it again and that\nanticipation that rhythm helps give us the structure to how we organize ourselves in our\nlives in gives a measure predictability living in\nNew York City as I do arm it's almost as if with so many\npeople doing so many things I A at the same time in such close\nquarters it's almost like life is dealing you\nextra hands added that Dec you're never it's just juxtapositions are are possible that\njust that on arm you don't think they're gonna happen\nand you never think you're going to be the\nguy who's walking down the street and because you choose to go down one\nside or the other the rest of your life is changed forever\ncom and one one tonight I'm riding the\nUptown local train I get on a tend to be a little bit vigilant when I get on her somewhere\ndon't and I want the people zoning out with\nheadphones or a book and they get on the car and I\nlook in a a I noticed this couple mom college-age student looking kids kinda girl in there sit next to each\nother and she's got her leg draped over his knee in there arm doing have this little contraption\nin there trying these not and they're doing it with one hand they\ndoing it left-handed and right-handed very quickly and then chill hand the\nthing to him and he'll do it never seen anything like this it's almost like\nthey're practicing magic tricks and a and at the next stop a guy get on the\ncar and he has this a sorta visiting professor look to him\nyet overstuffed leather satchel and its rectangular file case in a laptop",
+
+      "this program is a presentation of you\nseek levy for educational and non-commercial\nuse only to the university of california davis\nhouses since nineteen seventy three continuing\nmedical education has been a interval part educational\nmission u_c_ davis school of medicine and medical center the center for health and technology sixteen increases access to health education and\npromotes interaction patients other health care here patients and enrich school nurse alumni association dot\nshared bioethics at u_c_ davis and the topic that we will be\nconsidering is proud of options of last resort recent developments and emerging trends nothing to disclose simulation to this\npresentation the relief of pain and suffering is the essence palliative care we're going to be looking at the physician's responsibility to patients who are at or near the end end of their life and in the seminal article in the new\nengland journal in nineteen eighty nine a distinguished group of physicians\nposed the fundamental question what is the\nphysician's responsibility towards hopelessly ill patients we're going to look at some very\ncomplicated issue such as is there such a thing as intractable\npain or suffering at the end of life and can we be so bold as to actually distinguish between physical and psychological shel or sometimes called existential suffering\nat the end of life and if we're able to do that in a conscientious and consistent way ought we to be responding too goes different forms of suffering in different ways out both literally and figuratively one can\nsay that the physician eric cassell has written the book on suffering and there are two statements that he's\nmade on this subject that i think we should begin with first of all he notes transiently bodies do not suffer suffer and the implication of that is if we\nfocus obsessively on the physiology of the and we miss the personal engagement with\nthe patient then we cannot even recognize eyes let alone begin to treat suffering he goes on to say that the essence of\nsuffering is that it it curves when there is no\nimpending destruction of the person perceived or experienced and suffering continues until his past or the integrity of the person can be\nrestored and some of the matter this is from his definitive nineteen ninety-one work the nature of suffering and the goals of\nmedicine so the overarching ethical question with\nwhich we will grapple in this presentation is what what\nmeasures fall within the range of ethically acceptable palette of options of last resort with which conditions can respond to the suffering of patience at the end of life and i would say as an additional point we're not just talking about palliative medicine experts or hospice\npositions we're talking about the responsibility\nof all physicians who are likely to come into contact with\npatients who are at or near the end of the airline there are some learning objectives for\nthis presentation which i will review it this time at the end of the session you should be\nable to distinguish among the varieties of euthanasia and their respective levels of ethical\nacceptance identify the essential elements of notions as the doctrine of double a fact slippery slope arguments and discuss their relevance to end of life care you should be able to explain the\nholdings in the u_s_ supreme court indeed a definitive cases on physician-assisted\nsuicide quill and barco and their implications for physician assisted suicide or as some\nchoose to characterize it path physician-assisted dying as well as palliative sedation you should be able to state the requirements of the oregon\ndeath with dignity act and the significance of another u_s_\nsupreme court ruling in the case of gonzalez against oregon be able to describe the nature of the\ndata on the ten years sort of experience that we have with your even death with dignity act defined powder sedation and delineate\nthe guidelines for providing it and analyzed from unethical and a\nprofessional perspective your own view of the legitimate parameters for care of patients with intractable\nsuffering at the end of life article is i cited previously i'll refer to again because they and a very concise and didactic fashion make two important statements first the proper dose of pain medication is the dose that is sufficient to relieve pain and suffering and secondly to allow a patient to experience under arable pain or suffering is unethical medical practice returning to erica cells clinics are suffering and goals of\nmedicine heat essentially issues sir more of an indictment in just a\nchallenge medical colleagues he says the test of a\nsystem of medicine tributes adequacy in the face of suffering modern medicine he charges fails that test indeed goes on to say the central\nassumptions on which twentieth-century medicine is\nfound provide no basis for an understanding of suffering uh... what might he mean by that this is simply a reiteration of what i'd\nbegan with reiterated because of its critical\nimportance and relevance to much of what i will be saying in the next sixty minutes who sells is if we're to understand",
+
+      "this week we're going to talk about reno\nphysiology cell reno is active ny physiology that study of the uh... the function of kidneys and we're gonna talk mainly about how\nthey work when they're working correctly and what pontoons they perform in uh...\nin the body and are you probably know that their important but hopefully by the end lecture today\ndon't know exactly why they are so important for your overall a state of\nhelp and uh... and you you'd you won't live\nvery long without near normal kidney function and their the reading on this is chapter\nnine section we'll talk about the biomedical\nengineering innovation that over the last up if you're sixty\nyears or so it's really changed ob changed out the quality and duration\nof life for patients that have kidney disease and that kidney dialysis or renal dialysis so we'll talk about\nthat on thursday afternoon so this is just in an outline of the\nthings are going to cover uh... during that during the lecture\ntoday and on thursday we're going to talk about search\nsyringes gross aspects of the urinary system the kidney the bladder and the tubes that connects that these\nthings i'll talk a little bit about the\ndifferences between plasma plasma is the fluid circulates in your body and we thought about circulation of\nfluids in the body the week before spring break we talked about the heart and the blood\nvessels and uh... and the blood and so that main fluid of interest there was\nplasma this this fluid that blood cells circulated the main fluid will be interested in in\nreopens the ology as urine and this is a fluid that's produced by\nthe kidneys stored in the bladder next created from the body as one of the primary mechanisms that\nyour body has for getting rid of waste and regulating the composition of fluids\nlike plasma uh... and what up like a little bit more about that in just a second opted to deter understand how it works\nwill talk about the anatomy of the kidney on the gross level and on the\nmicroscopic level has an amazingly sophisticated\norganization which is critical for its function so if you understand the anatomy of that i can you understand a lot about\nhow it works and then we'll talk about specifics\nabout how you're in is created in the kidney and processed and and\num... it turns out that all of these processes are important for maintaining your health and as i\nmentioned we'll talk lastly about about dialysis which is a uh... extraordinarily effective but not quite perfect means uh... for for ab keeping people that\nhave kidney failure in good health so show you a picture like this may be\nexactly this picture a picture like this before but this is sort of a a aid at block diagram r engineering\nview of the human body and so you can see the outside world is\nthe things that surround this red and blue label box and the inside of the body is inside we talked last time we were here we\ntalked about the circulatory system and so this mechanism\nfor circulating fluids around in the body and we talked about how that works and why that's so\nimportant you'll remember that when we talked\nabout dud nervous system which which controls a lot of body\nfunctions we talked about both in the nervous system in the\ncardiovascular system how important certain tie-ins were for the function of those cells in\nparticular we talked about sodium and potassium sodium and potassium which are present\nin the case of sodium at high concentration outside of sells low\nconcentration inside cast in the reverse high concentration\ninside low concentration outside in order to those cells to function for a nerve sell to send a signal down\nan exxon or four cardiac muscle cell to contract those concentrations of ian's have to be\npresent and they have to be the way that i described you have to\nhave height extracellular sodium low intercellular it high intracellular potassium low\nextracellular so yes your cellular potassium levels are not\ncorrect you can't make an action potential in\nthe way that we described before part doesn't the brains can send signals so all of that busy elegy we talked\nabout in the nervous system and the heart depends on having i am concentrations in your body at the\ncorrect level so how is that maintained well one way\nyou could make a good think about it you have a box like this if this is your\nbody you can think about maintaining it by\njust knowing exactly how much sodium and potassium to eat everyday so you always\nkeep the right now you're going to lose some you lose some\nfluids so if you knew exactly how much to eat you could regulate concentration that\nway but that would be that's difficult to do right and we can you know we don't\ndo that we eat and general excess sodium and excess potassium so somehow our body is keeping these concentrations\nat the right level how does it do that well that's really the main function of\nthe kidney the main function the kidney is two\ncents how much sodium and potassium there is\nin your body and then to extract the amount that's\nnot needed in order to maintain the levels at the\nconstant concentration that's needed so was the main function of the urinary",
+
+      "this is a recording with them sure 20 chapter 14 principles diseases and bikini Salado vocabulary just left you for you to memorize and\nvery little concept concepts be a\nstraightforward and easy to follow ask our lease you are\nresponsible for knowing on different returns and concepts and examples giving fillets start lecture with technologies so pathogens like a lot of passage in\nsame class especially after many pass on the bacteria work that causes disease and vices have disease what is a passing pathogens basie me disease-causing Michael waking Sams apology is basically be scientific study disease which involves a number of things 10 which is the stadium cause the disease which is basically etiology etiology basically study after kaise have a\ndisease and is very important to know which or did them how I just the Zipcars said the CDC which is the Center for\nDisease Control a cell very involved in understanding\nthe disease process me and tiny learn how to control the\ndisease my understand young G oMG pasala G\nawesome involves pathogenesis which is demanding\nwhich disease develops and sausage important\nto understand this process to become you understand how disease on develops\nand what causes it hands your should be which them fine me who do its progression or stop spreading mythology us involves\na structural and functional changes has caused by the disease and disease\naffects on the body cell any action if the Beijing I'll station after body by pathogenic microorganisms East me that Mike organism econ through your skin into your body tree on to tissues mmm you system and or it said stars2 attach and stock market\nprice passed a cop car compensation question\nnow on actions to disease disease occurs\nwhen the infection resulting change from the\nhealthy state body you get sick OMS anything best I'm different any pathological changes\nthat snap theological physiological term usually means-testing normal condition\nphysiological mom now not all infections to see because your body is able to you overcome them action with it system and sometimes me having action without any detectable\ndiseases me that's no some sometimes the disease\nselfless past organisms multiplying you systems\nthat enable to to detected and say you won't be able\nto to see the disease take one to maybe\nsometimes me okay wife to my knowledge and she cast member we talked about the\nnormal flora or otherwise no nasty normal microbiota body be so basically Michael organisms have he established itself has this living inside body and it's\nreally not Heisey any harm to your body said no disease\nand no I'm done and normal conditions not to by conditions way system is compromised so on animals that are born laboratory I'm doing research sure that\nthese animals if it's sort of like do precondition\ngerm-free conditions in a laboratory discovered that his\nhappy animals mice I not sick they don't have bacteria James disbelieve that surging germ-free US lashing yet your own I'm proud to be blowing most youu Michael items when it passes through now special now China and how acquires microorganism spacey backpack on the female side is normal flower flies usually composed of Lactobacillus where\nspecies jeans back and so when the baby goes to\nthe first now it's working acquire some organisms I'm body sometimes I acquires some group just now swallow excess test this is Nash action more as to be with at this is asking quoting or buildings to quienes Mike Williams this way persist said sections this this is Ashley boosting betos system expose them to the microorganism sway awesome\nintroducing microorganism she hmmm be example said E-coli equalizing John happy of testings lives in Preston E-coli gets into them intestine\nconsumption food products or basically im nonlethal except now let me go back comment on me stacked born in laboratories tag Jim free on these I they don't get sick find area it sounds terrible Miami don't get sick however be having underdeveloped system and said would be get cold be would be I exposed to my quickness MZ batching won't do any harm to normal mice these mice get sick ride St haven't I'm develop first now chancy for a chancy microbiota be semi quaking means maybe eyes and should tying disappear so be so do like museum you know basically on both surfaces you body well inside mining your body I'm suggesting I basting said now scheme on my testing systems transient because we're you wash of way widest you we are close where you take off the coast up against\nsomething I'm you moved to my quaking washing handsome my point much touch something Houston\nyou introduce a microorganism on again I'm seeing of questions feasting each\nyou actually moving my question is am yasser Justin reintroducing my quaking my chin testing yes me the same principle so microorganism now absolutely\nessential for most because again of things in life laboratory passing mention in the year\non my stacked boy and a job for you my environment I'm do\nhaving underdeveloped and developing system do\nget sick life exposure to my quickness and\nstacked usually not highs is games now there something known past",
+      "this is is going to be a terrific case this is what i love when you see a\nwhole bunch of things in use little algorithms to quickly\nidentify what you're at this movie is called muscle there are three kinds of muscle\nhistologically there is muscle without strays shins so\nthat's called smooth muscle there are two types of muscle with strange chins and if the fibers are arranged parallel their car that's called skeletal or\nvoluntary striated muscle the striated muscle has fibers which\nintern connect with each other as a mesh that's\ncalled cardiac muscle in this field we have all three kinds of\nmuscle let's go to the first one on the left and let's assume that up a little bit and you could quickly see i hope that's these fibers here are clearly striated in addition they are arranged very longitudinally\nleg logs underneath the steps fireplace in addition you could see that the nuclei at all out\nto get the periphery so this is classical voluntary skeletal strated muscle technically if you cut one of these nuclei change in\nchile uh... with respect to the fiber it might\nlook like it was in the middle of the fiber but in reality that's just a geometric\narafat in true voluntary skeletal strated muscle the nuclear all at the periphery you can identify destroying shins better from doing longitudinal cuts with respect to the axis of the fiber you can identify where the nuclei are\nbetter by doing across or axial sections with respect to it this as classical striated skeletal muscle let's move on to the next piece of\ntissue here are muscle fibers in which you can\nclearly see there are no stratagene ds and in addition denuclearize are kinda like cigar shaped if you cut them longitudinally they look\na little bit like bent cigars if you happen to cut them more transversely\nwhat you see here they look around so once again it's a geometric\nphenomenon the if you were looking at nd smooth\nmuscle fibers which have been cut transfers for their longitudinal axis don't look like they're around if you cut them longitudinal because they're longitudinal access they\nwill look like a little cigars are very very spends lee quite frankly you can have a very hard\ntime differentiating this from connective tissue perhaps dense regular\nor irregular connective tissue but if you get a trite chrome stain be cytoplasm of the fibroblasts mt collagen fibres\nstay very clearly blue or greenish blue i want to try to come staying where a\nsmooth muscle would not pick up the greenish at all let's keep on moving away now from these\nnice smooth muscle fibers and grow and to our\nthird type of muscle which we are going to be seeing very\nvery soon an sure we have just landed ah... and\nthe uh... coast here in which there to see some muscle fibers now in which it i think you will unpaid meant it's a\nlittle bit more difficult to see the strangeness on this perhaps i could convince you very soon then it took let's go to a different area maybe we'll\nsee some strangulation spinner perhaps i could convince you then if you look very closely let's hear\nor perhaps here former political another place if you can see a\ngood just take a quick visit to another place if you look perhaps hopefully i can convince you that these are\nstraying shins are also blush two things separates us from skeletal voluntary striated muscle whereas i think i could convince you\nthat may be sir some strange names the nuclei are clearly within the center\nof the flavor like here but here is like here click here like\npractically everywhere and in addition the fibers are not\nstepped up nicely leg logs on the fireplace they've ranch and thirdly you'll have it and abundance of areas in which you can see little lines in the middle of to connecting fibers\nlike perhaps here like certainly here like certainly hear and these are your\nintercalated disks so cardiac muscle is also striated not nicely australia skeletal muscle but\nit has the nuclei in the middle of the fiber it hasn't urkel ada desks defy bridge bridge to connect with the\njason fibers because the method of contraction is not linear it's in\nmultiple dimensions and last but not least the fiber is not quite anesthetic is the osco skeletal muscle voluntary strated\nfiber they're a little bit smaller so there we are all three types of muscle and one nice\nslide and i hope that home i can convince you that there is no\npossible way you could ever confuse striated from skeletal from cardiac muscle for the rest of your life and i thank you very much",
+
+      "jason china create images that that make\npeople stop and think high also try to challenge myself to do\nthings that doctors say they're not possible i was very alive and new york city in the coffin for life in the coffin and bay probe nineteen ninety nine for a\nweek live there did nothing but water and it ended up being so much fun that i decided i could pursue doing more of these things the next one\nis i froze myself from block of ice for three days and three nights in new york\ncity that one was way more difficult than i\nhad expected the one after that i stood on top of our\nhundred foot trailer for thirty six hours began to hulu snake so hard with\nthe buildings that were behind we started to look like the animal hairs some excellent to london in london i live from glass box for\nforty four days with nothing but water it was for me one of the of the most\ndifficult things i've ever done but it was also the most beautiful there were some of the skeptics\nespecially the press in london they started flying cheeseburgers on\nhelicopters were on my boxes sampling so i felt very valid had one bit no internal medicine\nactually used the research society's my next pursuit was i want to see how\nlong it could go without breathing mcallen act to survive with nothing\nrunning for mayor i didn't realize that it would become\nthe most amazing journey of my life is a young magician i was obsessed with to being in his\nunderwater challenges so i began early on competing against\nthe other kids seeing how long extender water where they went up and down to\nbriefly on five times listed under a one breast by the time i was a teenager i was able\nto hold my breath for three minutes and thirty seconds i would later find out that was who'd\nbeen his personal record in nineteen eighty seven when i heard of\nthe story about a boy that fell through ice and was trapped\nunder a river he was underneath not breathing for forty\nfive minutes when the rescue workers came they were\nsuffocated him and there was no brain damage his core temperature had dropped two\nseventy seven degrees as a magician i think everything is\npossible and i think if something is done by one\nperson that can be done by others i started to think if the boy could\nsurvive without breathing for that longer must\nbe a way that i could do it so i'm out of the the top neurosurgeon and i asked him how long is it possible\nto go if everything like how long could i go without air and he said to me that anything over six\nminutes you have a serious risk of hypoxic so i took that as a challenge basically my first try uh... i figured that i could do\nsomething similar and i created a water tank and i filled\nit with ice and freezing cold water and i stayed inside of that water tank\nopen-minded temp my court until it starts have\ndropped and i was shivering in my first attempt\nto hold my breath i couldn't even last a minute surreal as i was completely not going to\nwork so i want to talk to a doctor friend past him how could i got how could i do that i\nwanna hold my breath for really long time how could be done and it's a very very your magician create the illusion of not breathing\nit'll be much easier so he came up with this idea of creating a real breather with the ceo to scrubber which is basically ah... to from homedepot with balloons dot take to it that he thought we could put inside of me and somehow a group of us circulate pierre marie breeze with this thing and me that this is a little hard tillotson purposes that attempt so that clearly wasn't going to war then i actually started thinking about liquid breathing there's a chemical that's called per\nflew brown and it's so high in oxygen levels of\ninterior could breathe it so i got my hands on my chemical filled\nthe sync up with it and stuffed my face in the sink and\ntried to breathe better which is really a shame possible it's basically like trying to breathe as a doctor said while having an\nelephant standing on your chest so bad idea disappeared then i started thinking would it be possible to hook up a\nheart-lung bypassed machine and have a surgery where it was a two\nbillion smile artery and then appear to not breathe while they were oxygen into\nmy blood which was another insane i_v_f_\nobviously then i thought about the craziest idea\nof all the ideas to actually do it taxi try to hold my breath past the\npoint adopters would consider u brenda so started researching internet pearl divers you know because i go down",
+
+      "another example of the only person\ndeserves a lot of the is our schedules are so he's got a significant dent in\ngeneral and the generational change for partially c_-four donna she's seven his final choruses grey stripe the white is normal spinal fluid you can\nsee within the spinal cord behind the c_-five original bodies got significant\nabnormal signal consistent with my own leisure or starring the spinal cord as a\nresult of chronic depression unperfor sections which is fine aboard as his kidney beans\nrestructure and then the why expired representing the mynameisamy this final receive what we want to demonstrate is not always refer to as an inbred\nreplacement historic places morally we tap on a person's embroidery ass\nreflex we have some contraction of muscle were\nnow armed forces well in his case not only do we have burglary alice contract as we see here but we also have a biceps\nuh... reflection as well so the requested\nspreading all the way through the arm assigned hyperplasia and if you look closely louis that he\nhas involuntary finger contraction is well where his fingers tend to contract\nagain associated with involuntary hype a reflexive reflexes\nbeyond what we normally see as a result of spinal cord hyperactivity",
+
+      "his surge in the house because I'm going to the new hoodie and\na lecture the cool I his schooling go walkabout the so it's a shocking I people whom you know the boys as you go\nto you reared but this is good stuff and bono's and okay should loss thought that we had a some you as a nice long line in as Utah's you you know when you has a on you know it are you to you mister you a Moses you here Houlihans all services right okay so I know complete his and him a message hebrew he worked here who much limited good yet contacted me okay israel's rustlers to okay for you to liaise called through you okay right let's get cracking to becoming quite\ndone isn't a problem think shop tonight tonight we're going to do a and and cranial nerves I thing after many years be in your size\nin the brainstem anatomically is very complicated so\nmight like joel is actually find ultra simple it like my great friend\nTerry pop music say how simple and animated missing a\nlot of stuff but I think they want to try and concentrate on all the aspects trailer sleeping on the\nyeah I the past the brains and terrible\nincluding okay I'm anything at all some more clinical stuff towards the end got\ntime remarkably and when ice ask highest you can sometimes a.m. can\nyou tell me the I'm Nixle is that you well k give me three parts of the brain\nstem this is sorta silence I meticulously we're not little I'm not many run phones thing and really gross babysit yeah I restaurant I so you in desperation my eye Commission 3 I use will call homie were who is involved\nin this always be one year's I so reunite them\nsaid goodness what what a slut said the\nSaugus I just or that he didn't he said many of my\npeers all done through this so i hook so no joke actually as well so we took me to bring the polls in the\nmiddle and where you actually that he wouldn't all about this is to know realize that\nthe cerebellum roofs the political get this point to it so here's the full\nbench cool and serve the like this and 12 surgery\non this Paul I have two numbers very cool in there and when I when I i time removing it you\nmight want to mention lost over child years to grow in this\nregion midline cerebellum call it was cool the builders and okay no so-called I was fiscal I'm to school this sorry and served this and grossed you and your client you searching on us to the so when I missus I'll saw what are you doing your\nshouldn't to this is scary new research cool stuff\nthe brainstem okay let's pass on a bit more so this is\nbecause it brings and we've got in and we'll the midbrain pons a little and when we\nlook at a the brainstem from from from the bank\nthis is the a ventral from the front surface over the reins them we see for this is\nhow close as you know the optic nerve differences\nis to the Jews England to gain it comes as no surprising that\ninto me that pituitary tumor is good Press either on\nan optic nerve possibly even if it goes back is only ok\ntrack but everybody knows the press is only up to china's in and\nwe'll talk a little bit about that later okay we talk a bit about vision enemy man in this the polls reaches its\ncourse anything's bridge across it I suppose and the last two lecture we were talking\nabout the parameter tracked and I said someone thought these\nlike pyramids and I don't think they look tall through\nthis but that's what they are and so the\ncorticospinal fibers at on news a prominent tracked and\nthat's what we talked about and last time look up close them into\nlittle reason to the top with the spinal cord and we should also we look plus almost\never inside because they are here this and\ntime gone by wonderful medical to school Frank netter\nis too low to show the cranial nerve nuclei ancestry or Catherine we will let and moving on the right we should\nremember reasons the enormous length all the time general do this\nwhich will come to you and make sure all to it's it's pretty"
+    ]
+  end
+end

data/test/test_helper.rb

@@ -0,0 +1,11 @@
+gem "minitest"
+require "minitest/autorun"
+require "minitest/pride"
+require "minitest/mock"
+require "mocha/setup"
+
+lib = File.expand_path('../../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+require "Clarifier"
+

metadata

@@ -0,0 +1,119 @@
+--- !ruby/object:Gem::Specification
+name: clarifier
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Rob Styles
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-03-04 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.5'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: mocha
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 5.0.8
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 5.0.8
+description: Clarifier is a stopwords library for removing common words from text
+email:
+- rob.styles@dynamicorange.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- CHANGELOG.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- clarifier.gemspec
+- lib/clarifier.rb
+- lib/clarifier/stop_words.rb
+- lib/clarifier/version.rb
+- lib/clarifier/word_lists/en_gb_basic.rb
+- lib/clarifier/word_lists/en_gb_mysql.rb
+- test/stop_words_test.rb
+- test/test_docs.rb
+- test/test_helper.rb
+homepage: http://github.com/meducation/clarifier
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: Clarifier is a stopwords library for removing common words from text
+test_files:
+- test/stop_words_test.rb
+- test/test_docs.rb
+- test/test_helper.rb