tag_along 0.8.2 → 0.8.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -1,7 +1,6 @@
 rvm:
   - 1.9.3
   - 2.0.0
-bundler_args: --without development
 branches:
   only:
       - master

data/CHANGELOG

@@ -1,3 +1,5 @@
+0.8.3 -- corrected handling of depencencies
+
 0.8.2 -- bug fix where script would break on empty offset lists
 
 0.8.1 -- fixing tests

data/Gemfile

@@ -1,17 +1,4 @@
 source 'https://rubygems.org'
 
-gem 'json', '~> 1.7'
-
-group :development do
-  gem 'bundler', '~> 1.3'
-  gem 'debugger','~> 1.6'
-end
-
-group :test do
-  gem 'rake', '~> 10.1'
-  gem 'rspec', '~> 2.14'
-  gem 'rr', '~> 1.1'
-  gem 'coveralls', '~> 0.6'
-end
-  
+gemspec 
 

data/README.md

@@ -219,7 +219,7 @@ Copyright
 
 Authors: [Dmitry Mozzherin][12] 
 
-Copyright (c) 2013 Marine Biological Laboratory. See LICENSE for
+Copyright (c) 2013-2014 Marine Biological Laboratory. See LICENSE for
 further details.
 
 [1]: https://badge.fury.io/rb/tag_along.png

data/lib/tag_along/version.rb

@@ -1,3 +1,3 @@
 class TagAlong
-  VERSION = '0.8.2'
+  VERSION = '0.8.3'
 end

data/spec/files/clean.txt

@@ -0,0 +1,60 @@
+
+
+
+	
+ 		Temperature-Dependent Sex Determination in Reptiles
+	
+	
+		The sex of a reptile embryo partly results from the production of sex hormones during development, and one such process to produce those hormones depends on temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism’s genes alone determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. 
+Temperature-dependent sex determination (TSD), where the temperature of the embryo’s environment influences its sex development, is a widespread non-genetic process  of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.
+		One cause of TSD is the enzyme aromatase. Aromatase helps to convert sex steroids, a group of hormones that influence sex development and reproduction, from male sex hormones 
+		(androgens) to female sex hormones 
+		(estrogens). Individuals with low levels of aromatase during the thermosensitive period will develop male characteristics. High levels of aromatase activity increase the production of female hormones, resulting in the development of female characteristics. While aromatase activity remains low for much of development in individuals that exhibit TSD, during the thermosensitive period, variations in temperature increase the activity of aromatase. This increase in aromatase enables individuals to develop into males or females depending on the temperatures experienced. Although other environmental influences can have similar effects, temperature is the most wide-spread factor that alters aromatase activity and sex determination.
+		Madeline Charnier, at the University of Dakar, in Dakar, Senegal, first described vertebrate TSD in Senegal in 1966.  Charnier observed that temperature affected sex ratios, which are the number of females versus males in a population or a single clutch of eggs, of the rainbow Agama lizard, 
+		Agama agama. Charnier published her results in the meeting records of the local Society of Biology in West Africa, a journal with limited distribution, and her efforts were not widely recognized for several years.
+		In 1967, the book Sex Chromosomes and Sex-Linked Genes by Susumu Ohno, a researcher at the City of Hope National Medical Center, in Duarte, California, drew attention to the genetic mechanisms and evolution of sex determination. In the late 1970s, James J. Bull, a professor at the University of Texas at Austin, argued that Ohno’s publication treated TSD only as an aberrant imperfection in sex development, and scientists largely ignored TSD during the 1960s. In 1971 and 1972, Claude Pieau, a researcher at the Université Paris, in Paris, France, published findings on the effects of temperature on sex differentiation of the European pond turtle, 
+		Emys orbicularis, and on the Mediterranean tortoise, 
+		Testudo graeca. Although few previous studies had supported the theory in reptiles, Pieau proposed TSD as an alternative to genotypic sex determination. At this point, little evidence supported TSD as a possible mode of sex determination.
+		In 1974 researchers established the existence of genotypic sex determination among turtles, a result that weakened support for TSD in  reptiles and in vertebrates. When Bull and Eric Charnov, at the University of Utah, in Salt Lake City, Utah, proposed a model for the evolution of environmental sex determination in 1977, they only suggested applying the model to plants and invertebrates, and not to vertebrates. This evolutionary model, called the Charnov-Bull model, outlines the conditions under which the evolution of environmental sex determination occurs, and scientists later applied it to vertebrates with TSD. 
+		In 1979 Bull and Richard Vogt, a researcher at the Instituto Nactional de Pesquisas da Amazônia in Aleixo, Brazil, showed that TSD exists in some reptiles.  Bull and Vogt’s article, “Temperature-dependent Sex Determination in Turtles”, investigated the effects of temperature on the sex of hatchlings in five turtle species under controlled and natural field conditions. The results, which found evidence of TSD in four out of five species, confirmed that some vertebrate species exhibit TSD. As of 2004, sixty-five of seventy-nine tested species of turtles were found to exhibit TSD.
+		Following Bull and Vogt’s 1979 publication, TSD attracted more interest. Over the next two decades, scientists worked to test mechanisms of sex differentiation in more species and to pinpoint pivotal temperatures, which are species-specific temperature ranges in which males and females are produced in equal number. Pieau and his colleagues focused on defining the TSD thermosensitive period, or the time of development during which changes in temperature can alter sexual organ growth. 
+		Turtle species that display TSD are thought to follow one of two patterns of temperature dependence. In some species, low temperatures produce mainly females, and high temperatures produce mostly males. Other species show disproportionately high female production at both high and low temperatures, with intermediate temperatures causing mostly male development. 
+		In the 1990s, David Crews, a biologist at the University of Texas at Austin, and colleagues found that some environmental pollutants caused sex-altering effects in turtles and other reptiles. For instance, polychlorinated biphenyls (PCBs) are pollutants whose molecules are structurally similar to some estrogens. PCBs can act as an estrogen replacement, causing feminization of sex organs in growing reptiles. At certain levels of PCBs, the feminizing effects can override the influence of temperature, negating the effects of TSD in an organism.
+		 Scientists are still working to understand the evolution of TSD and the implications of climate change for species that exhibit this mechanism of sex determination. The consequences of TSD on fitness, or reproductive success, are largely unknown.  However, a 2008 publication by Daniel Warner, at Iowa State University, in Ames, Iowa, and Richard Shine, at the University of Sydney, in Sydney, Australia, titled, 
+“The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile”, posited that TSD maximizes reproductive success in some lizards. Warner and Shine used hormonal manipulations to produce males and females across a range of temperatures in a species with TSD. They did so to test the predictions of the Charnov-Bull model. Their results suggest that the temperatures an organism experiences during development significantly affect its reproductive success. Warner and Shine’s publication supports the Charnov-Bull model for evolution of TSD in lizards. The scope of the model for other reptiles, however, requires further research. 
+		
+		
+		Sources
+			
+				Bull, James. “Perspective on Sex Determination: Past and Future.” In Temperature-dependent Sex Determination in Vertebrates, eds. Nicole Valenzuela and Valentine Lance, 5–8. Washington: Smithsonian Books, 2004.
+			
+				Bull, James, and Richard Vogt. “Temperature-Dependent Sex Determination in Turtles.” Science 206 (1979): 1186–8.
+			
+				Bull, James. “Sex Determination in Reptiles.” The Quarterly Review of Biology 55 (1980): 3–21.
+			
+				Charnier, Madeline. “Action de la Temperature sur la Sex-Ratio chez l’Embryon d’Agama agama (Agamidae: Lacertilien)” [Action of Temperature on Sex Ratio in the Agama agama (Agamidae: Lacertilia) embryo]. C.R. Séances Société Biologie L’Ouest Africain [Records of Meetings of the Society of Biology of West Africa] 160 (1966): 620–22.
+			
+				Crews, David, Judith Bergeron, and John McLachlan. “The Role of Estrogen in Turtle Sex Determination and the Effect of PCBs.” Environmental Health Perspectives 103 (1995): 73–7.
+			
+				Ewert, Michael, Cory Etchberger, and Craig Nelson. “Turtle Sex-Determining Modes and TSD Patterns, and Some TSD Pattern Correlates.” In Temperature-dependent Sex Determination in Vertebrates, eds. Nicole Valenzuela and Valentine Lance, 21–32. Washington: Smithsonian Books, 2004.
+			
+				Ohno, Susumu. Sex Chromosomes and Sex-Linked Genes. Berlin: Springer-Verlag, 1967.
+			
+				Pieau, Claude. “Sur la Proportion Sexuelle chez les Embryons de Deux Cheloniens (Testudo graeca L. et Emys orbicularis L.) Issus d’Oeufs Incubes Artificiellement” [The Sexual Proportion of Embryos of Two Chelonians From Artificial Incubation of Eggs]. Comptes Rendus Academie des Sciences, Paris [Academy of Sciences Reports, Paris] 272 (1971): 3071–4.
+			
+				Pieau, Claude. “Effets de la Temperature sur le Developpement des Glandes Genitales chez les Embryons de Deux Cheloniens, Emys orbicularis L. et Testudo graeca L.” [Effects of Temperature on the Development of Glands in Embryo Genitals of Two Chelonians, Emys orbicularis and Testudo graeca]. Comptes Rendus Academie des Sciences, Paris [Academy of Sciences Reports, Paris] 274 (1972): 719–22.
+			
+				Pough, F. Harvey, Robin Andrews, John Cadle, Martha Crump, Alan Savitsky, and Kentwood Wells. Herpetology. New Jersey: Pearson Education, 2003.
+			
+				Pough, F. Harvey, Christine Janis, and John Heiser. Vertebrate Life. New Jersey: Prentice Hall, 1998. 
+			
+				Valenzuela, Nicole. “Temperature-Dependent Sex Determination.” In Reptilian Incubation: Environment, Evolution and Behaviour. Ed. Charles Deeming. Nottingham: Nottingham University Press. 2004.
+			
+				Viets, Brian, Alan Tousignant, Michael Ewert, Craig Nelson, and David Crews. “Temperature-Dependent Sex Determination in the Leopard Gecko, Eublepharis macularius.” Journal of Experimental Zoology 265 (1993): 679–83.
+			
+				Warner, Daniel, and Richard Shine. “The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile.” Nature Letters 451 (2008): 566–8.
+			
+		
+	
+
+	

data/spec/files/clean2.txt

@@ -0,0 +1,60 @@
+
+
+
+	
+ 		Temperature-Dependent Sex Determination in Reptiles
+	
+	
+		The sex of a reptile embryo partly results from the production of sex hormones during development, and one such process to produce those hormones depends on temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism’s genes alone determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. 
+Temperature-dependent sex determination (TSD), where the temperature of the embryo’s environment influences its sex development, is a widespread non-genetic process  of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.
+		One cause of TSD is the enzyme aromatase. Aromatase helps to convert sex steroids, a group of hormones that influence sex development and reproduction, from male sex hormones 
+		(androgens) to female sex hormones 
+		(estrogens). Individuals with low levels of aromatase during the thermosensitive period will develop male characteristics. High levels of aromatase activity increase the production of female hormones, resulting in the development of female characteristics. While aromatase activity remains low for much of development in individuals that exhibit TSD, during the thermosensitive period, variations in temperature increase the activity of aromatase. This increase in aromatase enables individuals to develop into males or females depending on the temperatures experienced. Although other environmental influences can have similar effects, temperature is the most wide-spread factor that alters aromatase activity and sex determination.
+		Madeline Charnier, at the University of Dakar, in Dakar, Senegal, first described vertebrate TSD in Senegal in 1966.  Charnier observed that temperature affected sex ratios, which are the number of females versus males in a population or a single clutch of eggs, of the rainbow Agama lizard, 
+		Agama agama. Charnier published her results in the meeting records of the local Society of Biology in West Africa, a journal with limited distribution, and her efforts were not widely recognized for several years.
+		In 1967, the book Sex Chromosomes and Sex-Linked Genes by Susumu Ohno, a researcher at the City of Hope National Medical Center, in Duarte, California, drew attention to the genetic mechanisms and evolution of sex determination. In the late 1970s, James J. Bull, a professor at the University of Texas at Austin, argued that Ohno’s publication treated TSD only as an aberrant imperfection in sex development, and scientists largely ignored TSD during the 1960s. In 1971 and 1972, Claude Pieau, a researcher at the Université Paris, in Paris, France, published findings on the effects of temperature on sex differentiation of the European pond turtle, 
+		Emys orbicularis, and on the Mediterranean tortoise, 
+		Testudo graeca. Although few previous studies had supported the theory in reptiles, Pieau proposed TSD as an alternative to genotypic sex determination. At this point, little evidence supported TSD as a possible mode of sex determination.
+		In 1974 researchers established the existence of genotypic sex determination among turtles, a result that weakened support for TSD in  reptiles and in vertebrates. When Bull and Eric Charnov, at the University of Utah, in Salt Lake City, Utah, proposed a model for the evolution of environmental sex determination in 1977, they only suggested applying the model to plants and invertebrates, and not to vertebrates. This evolutionary model, called the Charnov-Bull model, outlines the conditions under which the evolution of environmental sex determination occurs, and scientists later applied it to vertebrates with TSD. 
+		In 1979 Bull and Richard Vogt, a researcher at the Instituto Nactional de Pesquisas da Amazônia in Aleixo, Brazil, showed that TSD exists in some reptiles.  Bull and Vogt’s article, “Temperature-dependent Sex Determination in Turtles”, investigated the effects of temperature on the sex of hatchlings in five turtle species under controlled and natural field conditions. The results, which found evidence of TSD in four out of five species, confirmed that some vertebrate species exhibit TSD. As of 2004, sixty-five of seventy-nine tested species of turtles were found to exhibit TSD.
+		Following Bull and Vogt’s 1979 publication, TSD attracted more interest. Over the next two decades, scientists worked to test mechanisms of sex differentiation in more species and to pinpoint pivotal temperatures, which are species-specific temperature ranges in which males and females are produced in equal number. Pieau and his colleagues focused on defining the TSD thermosensitive period, or the time of development during which changes in temperature can alter sexual organ growth. 
+		Turtle species that display TSD are thought to follow one of two patterns of temperature dependence. In some species, low temperatures produce mainly females, and high temperatures produce mostly males. Other species show disproportionately high female production at both high and low temperatures, with intermediate temperatures causing mostly male development. 
+		In the 1990s, David Crews, a biologist at the University of Texas at Austin, and colleagues found that some environmental pollutants caused sex-altering effects in turtles and other reptiles. For instance, polychlorinated biphenyls (PCBs) are pollutants whose molecules are structurally similar to some estrogens. PCBs can act as an estrogen replacement, causing feminization of sex organs in growing reptiles. At certain levels of PCBs, the feminizing effects can override the influence of temperature, negating the effects of TSD in an organism.
+		 Scientists are still working to understand the evolution of TSD and the implications of climate change for species that exhibit this mechanism of sex determination. The consequences of TSD on fitness, or reproductive success, are largely unknown.  However, a 2008 publication by Daniel Warner, at Iowa State University, in Ames, Iowa, and Richard Shine, at the University of Sydney, in Sydney, Australia, titled, 
+“The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile”, posited that TSD maximizes reproductive success in some lizards. Warner and Shine used hormonal manipulations to produce males and females across a range of temperatures in a species with TSD. They did so to test the predictions of the Charnov-Bull model. Their results suggest that the temperatures an organism experiences during development significantly affect its reproductive success. Warner and Shine’s publication supports the Charnov-Bull model for evolution of TSD in lizards. The scope of the model for other reptiles, however, requires further research. 
+		
+		
+		Sources
+			
+				Bull, James. “Perspective on Sex Determination: Past and Future.” In Temperature-dependent Sex Determination in Vertebrates, eds. Nicole Valenzuela and Valentine Lance, 5–8. Washington: Smithsonian Books, 2004.
+			
+				Bull, James, and Richard Vogt. “Temperature-Dependent Sex Determination in Turtles.” Science 206 (1979): 1186–8.
+			
+				Bull, James. “Sex Determination in Reptiles.” The Quarterly Review of Biology 55 (1980): 3–21.
+			
+				Charnier, Madeline. “Action de la Temperature sur la Sex-Ratio chez l’Embryon d’Agama agama (Agamidae: Lacertilien)” [Action of Temperature on Sex Ratio in the Agama agama (Agamidae: Lacertilia) embryo]. C.R. Séances Société Biologie L’Ouest Africain [Records of Meetings of the Society of Biology of West Africa] 160 (1966): 620–22.
+			
+				Crews, David, Judith Bergeron, and John McLachlan. “The Role of Estrogen in Turtle Sex Determination and the Effect of PCBs.” Environmental Health Perspectives 103 (1995): 73–7.
+			
+				Ewert, Michael, Cory Etchberger, and Craig Nelson. “Turtle Sex-Determining Modes and TSD Patterns, and Some TSD Pattern Correlates.” In Temperature-dependent Sex Determination in Vertebrates, eds. Nicole Valenzuela and Valentine Lance, 21–32. Washington: Smithsonian Books, 2004.
+			
+				Ohno, Susumu. Sex Chromosomes and Sex-Linked Genes. Berlin: Springer-Verlag, 1967.
+			
+				Pieau, Claude. “Sur la Proportion Sexuelle chez les Embryons de Deux Cheloniens (Testudo graeca L. et Emys orbicularis L.) Issus d’Oeufs Incubes Artificiellement” [The Sexual Proportion of Embryos of Two Chelonians From Artificial Incubation of Eggs]. Comptes Rendus Academie des Sciences, Paris [Academy of Sciences Reports, Paris] 272 (1971): 3071–4.
+			
+				Pieau, Claude. “Effets de la Temperature sur le Developpement des Glandes Genitales chez les Embryons de Deux Cheloniens, Emys orbicularis L. et Testudo graeca L.” [Effects of Temperature on the Development of Glands in Embryo Genitals of Two Chelonians, Emys orbicularis and Testudo graeca]. Comptes Rendus Academie des Sciences, Paris [Academy of Sciences Reports, Paris] 274 (1972): 719–22.
+			
+				Pough, F. Harvey, Robin Andrews, John Cadle, Martha Crump, Alan Savitsky, and Kentwood Wells. Herpetology. New Jersey: Pearson Education, 2003.
+			
+				Pough, F. Harvey, Christine Janis, and John Heiser. Vertebrate Life. New Jersey: Prentice Hall, 1998. 
+			
+				Valenzuela, Nicole. “Temperature-Dependent Sex Determination.” In Reptilian Incubation: Environment, Evolution and Behaviour. Ed. Charles Deeming. Nottingham: Nottingham University Press. 2004.
+			
+				Viets, Brian, Alan Tousignant, Michael Ewert, Craig Nelson, and David Crews. “Temperature-Dependent Sex Determination in the Leopard Gecko, Eublepharis macularius.” Journal of Experimental Zoology 265 (1993): 679–83.
+			
+				Warner, Daniel, and Richard Shine. “The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile.” Nature Letters 451 (2008): 566–8.
+			
+		
+	
+
+	

data/spec/files/embryo129157.xhtml

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+	<head>
+ 		<title>Temperature-Dependent Sex Determination in Reptiles</title>
+	</head>
+	<body>
+		<p>The sex of a reptile embryo partly results from the production of sex hormones during development, and one such process to produce those hormones depends on temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism&rsquo;s genes alone determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. 
+Temperature-dependent sex determination (TSD), where the temperature of the embryo&rsquo;s environment influences its sex development, is a widespread non-genetic process  of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.</p>
+		<p>One cause of TSD is the enzyme aromatase. Aromatase helps to convert sex steroids, a group of hormones that influence sex development and reproduction, from male sex hormones 
+		(androgens) to female sex hormones 
+		(estrogens). Individuals with low levels of aromatase during the thermosensitive period will develop male characteristics. High levels of aromatase activity increase the production of female hormones, resulting in the development of female characteristics. While aromatase activity remains low for much of development in individuals that exhibit TSD, during the thermosensitive period, variations in temperature increase the activity of aromatase. This increase in aromatase enables individuals to develop into males or females depending on the temperatures experienced. Although other environmental influences can have similar effects, temperature is the most wide-spread factor that alters aromatase activity and sex determination.</p>
+		<p>Madeline Charnier, at the University of Dakar, in Dakar, Senegal, first described vertebrate TSD in Senegal in 1966.  Charnier observed that temperature affected sex ratios, which are the number of females versus males in a population or a single clutch of eggs, of the rainbow Agama lizard, 
+		<i><a href="http://eol.org/pages/815935/overview">Agama agama</a></i>. Charnier published her results in the meeting records of the local <i>Society of Biology</i> in West Africa, a journal with limited distribution, and her efforts were not widely recognized for several years.</p>
+		<p>In 1967, the book Sex Chromosomes and Sex-Linked Genes</i> by Susumu Ohno, a researcher at the City of Hope National Medical Center, in Duarte, California, drew attention to the genetic mechanisms and evolution of sex determination. In the late 1970s, James J. Bull, a professor at the University of Texas at Austin, argued that Ohno&rsquo;s publication treated TSD only as an aberrant imperfection in sex development, and scientists largely ignored TSD during the 1960s. In 1971 and 1972, Claude Pieau, a researcher at the Universit&eacute; Paris, in Paris, France, published findings on the effects of temperature on sex differentiation of the European pond turtle, 
+		<i><a href="http://eol.org/pages/1056912/overview">Emys orbicularis</a></i>, and on the Mediterranean tortoise, 
+		<i><a href="http://eol.org/pages/1055221/overview">Testudo graeca</a></i>. Although few previous studies had supported the theory in reptiles, Pieau proposed TSD as an alternative to genotypic sex determination. At this point, little evidence supported TSD as a possible mode of sex determination.</p>
+		<p>In 1974 researchers established the existence of genotypic sex determination among turtles, a result that weakened support for TSD in  reptiles and in vertebrates. When Bull and Eric Charnov, at the University of Utah, in Salt Lake City, Utah, proposed a model for the evolution of environmental sex determination in 1977, they only suggested applying the model to plants and invertebrates, and not to vertebrates. This evolutionary model, called the Charnov-Bull model, outlines the conditions under which the evolution of environmental sex determination occurs, and scientists later applied it to vertebrates with TSD. </p>
+		<p>In 1979 Bull and Richard Vogt, a researcher at the Instituto Nactional de Pesquisas da Amaz&ocirc;nia in Aleixo, Brazil, showed that TSD exists in some reptiles.  Bull and Vogt&rsquo;s article, &ldquo;Temperature-dependent Sex Determination in Turtles&rdquo;, investigated the effects of temperature on the sex of hatchlings in five turtle species under controlled and natural field conditions. The results, which found evidence of TSD in four out of five species, confirmed that some vertebrate species exhibit TSD. As of 2004, sixty-five of seventy-nine tested species of turtles were found to exhibit TSD.</p>
+		<p>Following Bull and Vogt&rsquo;s 1979 publication, TSD attracted more interest. Over the next two decades, scientists worked to test mechanisms of sex differentiation in more species and to pinpoint pivotal temperatures, which are species-specific temperature ranges in which males and females are produced in equal number. Pieau and his colleagues focused on defining the TSD thermosensitive period, or the time of development during which changes in temperature can alter sexual organ growth. </p>
+		<p>Turtle species that display TSD are thought to follow one of two patterns of temperature dependence. In some species, low temperatures produce mainly females, and high temperatures produce mostly males. Other species show disproportionately high female production at both high and low temperatures, with intermediate temperatures causing mostly male development. </p>
+		<p>In the 1990s, David Crews, a biologist at the University of Texas at Austin, and colleagues found that some environmental pollutants caused sex-altering effects in turtles and other reptiles. For instance, polychlorinated biphenyls (PCBs) are pollutants whose molecules are structurally similar to some estrogens. PCBs can act as an estrogen replacement, causing feminization of sex organs in growing reptiles. At certain levels of PCBs, the feminizing effects can override the influence of temperature, negating the effects of TSD in an organism.</p>
+		<p> Scientists are still working to understand the evolution of TSD and the implications of climate change for species that exhibit this mechanism of sex determination. The consequences of TSD on fitness, or reproductive success, are largely unknown.  However, a 2008 publication by Daniel Warner, at Iowa State University, in Ames, Iowa, and Richard Shine, at the University of Sydney, in Sydney, Australia, titled, 
+&ldquo;The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile&rdquo;, posited that TSD maximizes reproductive success in some lizards. Warner and Shine used hormonal manipulations to produce males and females across a range of temperatures in a species with TSD. They did so to test the predictions of the Charnov-Bull model. Their results suggest that the temperatures an organism experiences during development significantly affect its reproductive success. Warner and Shine&rsquo;s publication supports the Charnov-Bull model for evolution of TSD in lizards. The scope of the model for other reptiles, however, requires further research. </p>
+		
+		<div id="references">
+		<h2>Sources</h2>
+			<ol>
+				<li>Bull, James. &ldquo;Perspective on Sex Determination: Past and Future.&rdquo; In <i>Temperature-dependent Sex Determination in Vertebrates</i>, eds. Nicole Valenzuela and Valentine Lance, 5&ndash;8. Washington: Smithsonian Books, 2004.</li>
+			
+				<li>Bull, James, and Richard Vogt. &ldquo;Temperature-Dependent Sex Determination in Turtles.&rdquo; <i>Science</i> 206 (1979): 1186&ndash;8.</li>
+			
+				<li>Bull, James. &ldquo;Sex Determination in Reptiles.&rdquo; <i>The Quarterly Review of Biology </i>55 (1980): 3&ndash;21.</li>
+			
+				<li>Charnier, Madeline. &ldquo;Action de la Temperature sur la Sex-Ratio chez l&rsquo;Embryon d&rsquo;<i>Agama agama </i>(Agamidae: Lacertilien)&rdquo; [Action of Temperature on Sex Ratio in the <i>Agama agama </i>(Agamidae: Lacertilia) embryo]. <i>C.R. S&eacute;ances Soci&eacute;t&eacute; Biologie L&rsquo;Ouest Africain </i>[Records of Meetings of the Society of Biology of West Africa] 160 (1966): 620&ndash;22.</li>
+			
+				<li>Crews, David, Judith Bergeron, and John McLachlan. &ldquo;The Role of Estrogen in Turtle Sex Determination and the Effect of PCBs.&rdquo; <i>Environmental Health Perspectives </i>103 (1995): 73&ndash;7.</li>
+			
+				<li>Ewert, Michael, Cory Etchberger, and Craig Nelson. &ldquo;Turtle Sex-Determining Modes and TSD Patterns, and Some TSD Pattern Correlates<i>.</i>&rdquo; In <i>Temperature-dependent Sex Determination in Vertebrates</i>, eds. Nicole Valenzuela and Valentine Lance, 21&ndash;32. Washington: Smithsonian Books, 2004.</li>
+			
+				<li>Ohno, Susumu. <i>Sex Chromosomes and Sex-Linked Genes.</i> Berlin: Springer-Verlag, 1967.</li>
+			
+				<li>Pieau, Claude. &ldquo;Sur la Proportion Sexuelle chez les Embryons de Deux Cheloniens (Testudo graeca L. et Emys orbicularis L.) Issus d&rsquo;Oeufs Incubes Artificiellement&rdquo; [The Sexual Proportion of Embryos of Two Chelonians From Artificial Incubation of Eggs]. <i>Comptes Rendus Academie des Sciences, Paris</i> [Academy of Sciences Reports, Paris] 272 (1971): 3071&ndash;4.</li>
+			
+				<li>Pieau, Claude. &ldquo;Effets de la Temperature sur le Developpement des Glandes Genitales chez les Embryons de Deux Cheloniens, <i>Emys orbicularis</i> L. et <i>Testudo graeca</i> L.&rdquo; [Effects of Temperature on the Development of Glands in Embryo Genitals of Two Chelonians, <i>Emys orbicularis </i>and <i>Testudo graeca</i>]. <i>Comptes Rendus Academie des Sciences, Paris</i> [Academy of Sciences Reports, Paris] 274 (1972): 719&ndash;22.</li>
+			
+				<li>Pough, F. Harvey, Robin Andrews, John Cadle, Martha Crump, Alan Savitsky, and Kentwood Wells. <i>Herpetology.</i> New Jersey: Pearson Education, 2003.</li>
+			
+				<li>Pough, F. Harvey, Christine Janis, and John Heiser. <i>Vertebrate Life.</i> New Jersey: Prentice Hall, 1998. </li>
+			
+				<li>Valenzuela, Nicole. &ldquo;Temperature-Dependent Sex Determination.&rdquo; In <i>Reptilian Incubation: Environment, Evolution and Behaviour</i>. Ed. Charles Deeming. Nottingham: Nottingham University Press. 2004.</li>
+			
+				<li>Viets, Brian, Alan Tousignant, Michael Ewert, Craig Nelson, and David Crews. &ldquo;Temperature-Dependent Sex Determination in the Leopard Gecko, <i>Eublepharis macularius</i>.&rdquo; <i>Journal of Experimental Zoology</i> 265 (1993): 679&ndash;83.</li>
+			
+				<li>Warner, Daniel, and Richard Shine. &ldquo;The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile.&rdquo; <i>Nature Letters </i>451 (2008): 566&ndash;8.</li>
+			</ol>
+		</div>
+	</body>
+</html>
+	

data/spec/files/embryo129157.xhtml.json

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+    },
+    {
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data/spec/files/embryo129157.xhtml.tagged

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+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+	<head>
+ 		<title>Temperature-Dependent Sex Determination in Reptiles</title>
+	</head>
+	<body>
+		<p>The sex of a reptile embryo partly results from the production of sex hormones during development, and one such process to produce those hormones depends on temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism&rsquo;s genes alone determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. 
+Temperature-dependent sex determination (TSD), where the temperature of the embryo&rsquo;s environment influences its sex development, is a widespread non-genetic process  of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.</p>
+		<p>One cause of TSD is the enzyme aromatase. Aromatase helps to convert sex steroids, a group of hormones that influence sex development and reproduction, from male sex hormones 
+		(androgens) to female sex hormones 
+		(estrogens). Individuals with low levels of aromatase during the thermosensitive period will develop male characteristics. High levels of aromatase activity increase the production of female hormones, resulting in the development of female characteristics. While aromatase activity remains low for much of development in individuals that exhibit TSD, during the thermosensitive period, variations in temperature increase the activity of aromatase. This increase in aromatase enables individuals to develop into males or females depending on the temperatures experienced. Although other environmental influences can have similar effects, temperature is the most wide-spread factor that alters aromatase activity and sex determination.</p>
+		<p>Madeline Charnier, at the University of Dakar, in Dakar, Senegal, first described vertebrate TSD in Senegal in 1966.  Charnier observed that temperature affected sex ratios, which are the number of females versus males in a population or a single clutch of <a href="http://eol.org/pages/17789" class="resolved">eggs,</a> of the rainbow Agama lizard, 
+		<i><a href="http://eol.or<a href="http://eol.org/pages/815935" class="resolved">g/pages/815</a>935/overview">Agama agama</a></i>. Charnier published her results in the meeting records of the local <i>Society of Biology</i> in West Africa, a journal with limited distribution, and her efforts were not widely recognized for several years.</p>
+		<p>In 1967, the book Sex Chromosomes and Sex-Linked Genes</i> by Susumu Ohno, a researcher at the City of Hope National Medical Center, in Duarte, California, drew attention to the genetic mechanisms and evolution of sex determination. In the late 1970s, James J. Bull, a professor at the University of Texas at Austin, argued that Ohno&rsquo;s publication treated TSD only as an aberrant imperfection in sex development, and scientists largely ignored TSD during the 1960s. In 1971 and 1972, Claude Pieau, a researcher at the Universit&eacute; Paris, in Paris, France, published findings on the effects of temperature on sex differentia<a href="http://eol.org/pages/1056912" class="resolved">tion of the Euro</a>pean pond turtle, 
+		<i><a href="http://eol.org/pages/1056912/overview">Emys orbicularis</a<a href="http://eol.org/pages/1055221" class="resolved">></i>, and on the </a>Mediterranean tortoise, 
+		<i><a href="http://eol.org/pages/1055221/overview">Testudo graeca</a></i>. Although few previous studies had supported the theory in reptiles, Pieau proposed TSD as an alternative to genotypic sex determination. At this point, little evidence supported TSD as a possible mode of sex determination.</p>
+		<p>In 1974 researchers established the existence of genotypic sex determination among turtles, a result that weakened support for TSD in  reptiles and in vertebrates. When Bull and Eric Charnov, at the University of Utah, in Salt Lake City, Utah, proposed a model for the evolution of environmental sex determination in 1977, they only suggested applying the model to plants and invertebrates, and not to vertebrates. This evolutionary model, called the Charnov-Bull model, outlines the conditions under which the evolution of environmental sex determination occurs, and scientists later applied it to vertebrates with TSD. </p>
+		<p>In 1979 Bull and Richard Vogt, a re<a href="http://google.com?search=Pesquisas%20da#q=Pesquisas%20da" class="unresolved">searcher at </a>the Instituto Nactional de Pesquisas da Amaz&ocirc;nia in Aleixo, Brazil, showed that TSD exists in some reptiles.  Bull and Vogt&rsquo;s article, &ldquo;Temperature-dependent Sex Determination in Turtles&rdquo;, investigated the effects of temperature on the sex of hatchlings in five turtle species under controlled and natural field conditions. The results, which found evidence of TSD in four out of five species, confirmed that some vertebrate species exhibit TSD. As of 2004, sixty-five of seventy-nine tested species of turtles were found to exhibit TSD.</p>
+		<p>Following Bull and Vogt&rsquo;s 1979 publication, TSD attracted more interest. Over the next two decades, scientists worked to test mechanisms of sex differentiation in more species and to pinpoint pivotal temperatures, which are species-specific temperature ranges in which males and females are produced in equal number. Pieau and his colleagues focused on defining the TSD thermosensitive period, or the time of development during which changes in temperature can alter sexual organ growth. </p>
+		<p>Turtle species that display TSD are thought to follow one of two patterns of temperature dependence. In some species, low temperatures produce mainly females, and high temperatures produce mostly males. Other species show disproportionately high female production at both high and low temperatures, with intermediate temperatures causing mostly male development. </p>
+		<p>In the 1990s, David Crews, a biologist at the University of Texas at Austin, and colleagues found that some environmental pollutants caused sex-altering effects in turtles and other reptiles. For instance, polychlorinated biphenyls (PCBs) are pollutants whose molecules are structurally similar to some estrogens. PCBs can act as an estrogen replacement, causing feminization of sex organs in growing reptiles. At certain levels of PCBs, the feminizing effects can override the influence of temperature, negating the effects of TSD in an organism.</p>
+		<p> Scientists are still working to understand the evolution of TSD and the implications of climate change for species that exhibit this mechanism of sex determination. The consequences of TSD on fitness, or reproductive success, are largely unknown.  However, a 2008 publication by Daniel Warner, at Iowa State University, in Ames, Iowa, and Richard Shine, at the University of Sydney, in Sydney, Australia, titled, 
+&ldquo;The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile&rdquo;, posited that TSD maximizes reproductive success in some lizards. Warner and Shine used hormonal manipulations to produce males and females across a range of temperatures in a species with TSD. They did so to test the predictions of the Charnov-Bull model. Their results suggest that the temperatures an organism experiences during development significantly affect its reproductive success. Warner and Shine&rsquo;s publication supports the Charnov-Bull model for evolution of TSD in lizards. The scope of the model for other reptiles, however, requires further research. </p>
+		
+		<div id="references">
+		<h2>Sources</h2>
+			<ol>
+				<li>Bull, James. &ldquo;Perspective on Sex Determination: Past and Future.&rdquo; In <i>Temperature-dependent Sex Determination in Vertebrates</i>, eds. Nicole Valenzuela and Valentine Lance, 5&ndash;8. Washington: Smithsonian Books, 2004.</li>
+			
+				<li>Bull, James, and Richard Vogt. &ldquo;Temperature-Dependent Sex Determination in Turtles.&rdquo; <i>Science</i> 206 (1979): 1186&ndash;8.</li>
+			
+				<li>Bull, James. &ldquo;Sex Determination in Reptiles.&rdquo;<a href="http://eol.org/pages/1734" class="resolved"> <i>The Qu</a>arterly Review of Biology </i>55 (1980): 3&ndash;21.</li>
+			
+				<li<a href="http://eol.org/pages/815935" class="resolved">>Charnier, </a>Made<a href="http://eol.org/pages/1734" class="resolved">line. &ldq</a>uo;Ac<a href="http://eol.org/pages/2819161/names/synonyms" class="resolved">tion de la </a>Temperature sur la Sex-Ratio chez l&rsquo;Embryon d&rsquo;<i>Agama agama </i>(Agamidae: Lacertilien)&rdquo; [Action of Temperature on Sex Ratio in the <i>Agama agama </i>(Agamidae: Lacertilia) embryo]. <i>C.R. S&eacute;ances Soci&eacute;t&eacute; Biologie L&rsquo;Ouest Africain </i>[Records of Meetings of the Society of Biology of West Africa] 160 (1966): 620&ndash;22.</li>
+			
+				<li>Crews, David, Judith Bergeron, and John McLachlan. &ldquo;The Role of Estrogen in Turtle Sex Determination and the Effect of PCBs.&rdquo; <i>Environmental Health Perspectives </i>103 (1995): 73&ndash;7.</li>
+			
+				<li>Ewert, Michael, Cory Etchberger, and Craig Nelson. &ldquo;Turtle Sex-Determining Modes and TSD Patterns, and Some TSD Pattern Correlates<i>.</i>&rdquo; In <i>Temperature-dependent Sex Determination in Vertebrates</i>, eds. Nicole Valenzue<a href="http://eol.org/pages/1055221" class="resolved">la and Valentin</a>e Lance, 21<a href="http://eol.org/pages/1056912" class="resolved">&ndash;32. Washi</a>ngton: Smithsonian Books, 2004.</li>
+			
+				<li>Ohno, Susumu. <i>Sex Chromosomes and Sex-Linked Genes.</i> Berlin: Springer-Verlag, 1967.</li>
+			
+				<li>Pieau, Claude. &ldquo;Sur la Proportion Sexuelle chez les Embryons de Deux Cheloniens (Testudo graeca L. et Emys orbicularis L.) Issus d&rsquo;Oeufs Incubes Artificiellement&rd<a href="http://google.com?search=GENITALES#q=GENITALES" class="unresolved">quo; [The</a> Sexual Proportion of Embryos of Two Chelon<a href="http://eol.org/pages/1056912" class="resolved">ians From Artifi</a>cial Incubat<a href="http://eol.org/pages/1055221" class="resolved">ion of Eggs]. </a><i>Comptes Rendus Academie des Sciences, Paris</i> [Academy of Sciences Reports, Paris] 272 (1971): <a href="http://eol.org/pages/1056912" class="resolved">3071&ndash;4.</l</a>i>
+			
+				<li>Pieau,</a> Claude. &ldquo;Effets de la Temperature sur le Developpement des Glandes Genitales chez les Embryons de Deux Cheloniens, <i>Emys orbicularis</i> L. et <i>Testudo graeca</i> L.&rdquo; [Effects of Temperature on the Development of Glands in Embryo Genitals of Two Chelonians, <i>Emys orbicularis </i>and <i>Testudo graeca</i>]. <i>Comptes Rendus Academie des Sciences, Paris</i> [Academy of Sciences Reports, Paris] 274 (1972): 719&ndash;22.</li>
+			
+				<li>Pough, F. Harvey, Robin Andrews, John Cadle, Martha Crump, Alan Savitsky, and Kentwood Wells. <i>Herpetology.</i> New Jersey: Pearson Education, 2003.</li>
+			
+				<li>Pough, F. Harvey, Christine Janis, and John Heiser. <i>Vertebrate Life.</i> New Jersey: Prentice Hall, 1998. </li>
+			
+				<li>Valenzuela, Nicole. &ldquo;Temper<a href="http://eol.org/pages/790141" class="resolved">ature-Dependent Sex Dete</a>rmination.&rdquo; In <i>Reptilian Incubation: Environment, Evolution and Behaviour</i>. Ed. Charles Deeming. Nottingham: Nottingham University Press. 2004.</li>
+			
+				<li>Viets, Brian, Alan Tousignant, Michael Ewert, Craig Nelson, and David Crews. &ldquo;Temperature-Dependent Sex Determination in the Leopard Gecko, <i>Eublepharis macularius</i>.&rdquo; <i>Journal of Experimental Zoology</i> 265 (1993): 679&ndash;83.</li>
+			
+				<li>Warner, Daniel, and Richard Shine. &ldquo;The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile.&rdquo; <i>Nature Letters </i>451 (2008): 566&ndash;8.</li>
+			</ol>
+		</div>
+	</body>
+</html>
+	

data/spec/files/embryo129157.xhtml.txt

@@ -0,0 +1,60 @@
+
+
+
+	
+ 		Temperature-Dependent Sex Determination in Reptiles
+	
+	
+		The sex of a reptile embryo partly results from the production of sex hormones during development, and one such process to produce those hormones depends on temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism’s genes alone determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. 
+Temperature-dependent sex determination (TSD), where the temperature of the embryo’s environment influences its sex development, is a widespread non-genetic process  of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.
+		One cause of TSD is the enzyme aromatase. Aromatase helps to convert sex steroids, a group of hormones that influence sex development and reproduction, from male sex hormones 
+		(androgens) to female sex hormones 
+		(estrogens). Individuals with low levels of aromatase during the thermosensitive period will develop male characteristics. High levels of aromatase activity increase the production of female hormones, resulting in the development of female characteristics. While aromatase activity remains low for much of development in individuals that exhibit TSD, during the thermosensitive period, variations in temperature increase the activity of aromatase. This increase in aromatase enables individuals to develop into males or females depending on the temperatures experienced. Although other environmental influences can have similar effects, temperature is the most wide-spread factor that alters aromatase activity and sex determination.
+		Madeline Charnier, at the University of Dakar, in Dakar, Senegal, first described vertebrate TSD in Senegal in 1966.  Charnier observed that temperature affected sex ratios, which are the number of females versus males in a population or a single clutch of eggs, of the rainbow Agama lizard, 
+		Agama agama. Charnier published her results in the meeting records of the local Society of Biology in West Africa, a journal with limited distribution, and her efforts were not widely recognized for several years.
+		In 1967, the book Sex Chromosomes and Sex-Linked Genes by Susumu Ohno, a researcher at the City of Hope National Medical Center, in Duarte, California, drew attention to the genetic mechanisms and evolution of sex determination. In the late 1970s, James J. Bull, a professor at the University of Texas at Austin, argued that Ohno’s publication treated TSD only as an aberrant imperfection in sex development, and scientists largely ignored TSD during the 1960s. In 1971 and 1972, Claude Pieau, a researcher at the Université Paris, in Paris, France, published findings on the effects of temperature on sex differentiation of the European pond turtle, 
+		Emys orbicularis, and on the Mediterranean tortoise, 
+		Testudo graeca. Although few previous studies had supported the theory in reptiles, Pieau proposed TSD as an alternative to genotypic sex determination. At this point, little evidence supported TSD as a possible mode of sex determination.
+		In 1974 researchers established the existence of genotypic sex determination among turtles, a result that weakened support for TSD in  reptiles and in vertebrates. When Bull and Eric Charnov, at the University of Utah, in Salt Lake City, Utah, proposed a model for the evolution of environmental sex determination in 1977, they only suggested applying the model to plants and invertebrates, and not to vertebrates. This evolutionary model, called the Charnov-Bull model, outlines the conditions under which the evolution of environmental sex determination occurs, and scientists later applied it to vertebrates with TSD. 
+		In 1979 Bull and Richard Vogt, a researcher at the Instituto Nactional de Pesquisas da Amazônia in Aleixo, Brazil, showed that TSD exists in some reptiles.  Bull and Vogt’s article, “Temperature-dependent Sex Determination in Turtles”, investigated the effects of temperature on the sex of hatchlings in five turtle species under controlled and natural field conditions. The results, which found evidence of TSD in four out of five species, confirmed that some vertebrate species exhibit TSD. As of 2004, sixty-five of seventy-nine tested species of turtles were found to exhibit TSD.
+		Following Bull and Vogt’s 1979 publication, TSD attracted more interest. Over the next two decades, scientists worked to test mechanisms of sex differentiation in more species and to pinpoint pivotal temperatures, which are species-specific temperature ranges in which males and females are produced in equal number. Pieau and his colleagues focused on defining the TSD thermosensitive period, or the time of development during which changes in temperature can alter sexual organ growth. 
+		Turtle species that display TSD are thought to follow one of two patterns of temperature dependence. In some species, low temperatures produce mainly females, and high temperatures produce mostly males. Other species show disproportionately high female production at both high and low temperatures, with intermediate temperatures causing mostly male development. 
+		In the 1990s, David Crews, a biologist at the University of Texas at Austin, and colleagues found that some environmental pollutants caused sex-altering effects in turtles and other reptiles. For instance, polychlorinated biphenyls (PCBs) are pollutants whose molecules are structurally similar to some estrogens. PCBs can act as an estrogen replacement, causing feminization of sex organs in growing reptiles. At certain levels of PCBs, the feminizing effects can override the influence of temperature, negating the effects of TSD in an organism.
+		 Scientists are still working to understand the evolution of TSD and the implications of climate change for species that exhibit this mechanism of sex determination. The consequences of TSD on fitness, or reproductive success, are largely unknown.  However, a 2008 publication by Daniel Warner, at Iowa State University, in Ames, Iowa, and Richard Shine, at the University of Sydney, in Sydney, Australia, titled, 
+“The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile”, posited that TSD maximizes reproductive success in some lizards. Warner and Shine used hormonal manipulations to produce males and females across a range of temperatures in a species with TSD. They did so to test the predictions of the Charnov-Bull model. Their results suggest that the temperatures an organism experiences during development significantly affect its reproductive success. Warner and Shine’s publication supports the Charnov-Bull model for evolution of TSD in lizards. The scope of the model for other reptiles, however, requires further research. 
+		
+		
+		Sources
+			
+				Bull, James. “Perspective on Sex Determination: Past and Future.” In Temperature-dependent Sex Determination in Vertebrates, eds. Nicole Valenzuela and Valentine Lance, 5–8. Washington: Smithsonian Books, 2004.
+			
+				Bull, James, and Richard Vogt. “Temperature-Dependent Sex Determination in Turtles.” Science 206 (1979): 1186–8.
+			
+				Bull, James. “Sex Determination in Reptiles.” The Quarterly Review of Biology 55 (1980): 3–21.
+			
+				Charnier, Madeline. “Action de la Temperature sur la Sex-Ratio chez l’Embryon d’Agama agama (Agamidae: Lacertilien)” [Action of Temperature on Sex Ratio in the Agama agama (Agamidae: Lacertilia) embryo]. C.R. Séances Société Biologie L’Ouest Africain [Records of Meetings of the Society of Biology of West Africa] 160 (1966): 620–22.
+			
+				Crews, David, Judith Bergeron, and John McLachlan. “The Role of Estrogen in Turtle Sex Determination and the Effect of PCBs.” Environmental Health Perspectives 103 (1995): 73–7.
+			
+				Ewert, Michael, Cory Etchberger, and Craig Nelson. “Turtle Sex-Determining Modes and TSD Patterns, and Some TSD Pattern Correlates.” In Temperature-dependent Sex Determination in Vertebrates, eds. Nicole Valenzuela and Valentine Lance, 21–32. Washington: Smithsonian Books, 2004.
+			
+				Ohno, Susumu. Sex Chromosomes and Sex-Linked Genes. Berlin: Springer-Verlag, 1967.
+			
+				Pieau, Claude. “Sur la Proportion Sexuelle chez les Embryons de Deux Cheloniens (Testudo graeca L. et Emys orbicularis L.) Issus d’Oeufs Incubes Artificiellement” [The Sexual Proportion of Embryos of Two Chelonians From Artificial Incubation of Eggs]. Comptes Rendus Academie des Sciences, Paris [Academy of Sciences Reports, Paris] 272 (1971): 3071–4.
+			
+				Pieau, Claude. “Effets de la Temperature sur le Developpement des Glandes Genitales chez les Embryons de Deux Cheloniens, Emys orbicularis L. et Testudo graeca L.” [Effects of Temperature on the Development of Glands in Embryo Genitals of Two Chelonians, Emys orbicularis and Testudo graeca]. Comptes Rendus Academie des Sciences, Paris [Academy of Sciences Reports, Paris] 274 (1972): 719–22.
+			
+				Pough, F. Harvey, Robin Andrews, John Cadle, Martha Crump, Alan Savitsky, and Kentwood Wells. Herpetology. New Jersey: Pearson Education, 2003.
+			
+				Pough, F. Harvey, Christine Janis, and John Heiser. Vertebrate Life. New Jersey: Prentice Hall, 1998. 
+			
+				Valenzuela, Nicole. “Temperature-Dependent Sex Determination.” In Reptilian Incubation: Environment, Evolution and Behaviour. Ed. Charles Deeming. Nottingham: Nottingham University Press. 2004.
+			
+				Viets, Brian, Alan Tousignant, Michael Ewert, Craig Nelson, and David Crews. “Temperature-Dependent Sex Determination in the Leopard Gecko, Eublepharis macularius.” Journal of Experimental Zoology 265 (1993): 679–83.
+			
+				Warner, Daniel, and Richard Shine. “The Adaptive Significance of Temperature-Dependent Sex Determination in a Reptile.” Nature Letters 451 (2008): 566–8.
+			
+		
+	
+
+	

data/tag_along.gemspec

@@ -1,7 +1,5 @@
 # coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
-$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'tag_along/version'
+require File.expand_path('../lib/tag_along/version', __FILE__)
 
 Gem::Specification.new do |sp|
   sp.name          = 'tag_along'
@@ -21,4 +19,14 @@ Gem::Specification.new do |sp|
   sp.files         = `git ls-files`.split($/)
   sp.test_files    = sp.files.grep(%r{^(spec|features)/})
   sp.require_paths = ['lib']
+
+  sp.add_runtime_dependency 'json', '~> 1.7'
+
+  sp.add_development_dependency 'rake', '~> 10.1'
+  sp.add_development_dependency 'bundler', '~> 1.3'
+  sp.add_development_dependency 'rspec', '~> 2.14'
+  sp.add_development_dependency 'rr', '~> 1.1'
+  sp.add_development_dependency 'coveralls', '~> 0.7'
+  sp.add_development_dependency 'debugger', '~> 1.6'
+  
 end

metadata

@@ -1,15 +1,113 @@
 --- !ruby/object:Gem::Specification
 name: tag_along
 version: !ruby/object:Gem::Version
-  version: 0.8.2
+  version: 0.8.3
 platform: ruby
 authors:
 - Dmitry Mozzherin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-09 00:00:00.000000000 Z
-dependencies: []
+date: 2013-12-18 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '10.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '10.1'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.14'
+- !ruby/object:Gem::Dependency
+  name: rr
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: debugger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
 description: |-
   Tags a text with arbitrary tags
                             based on array of start/end offsets
@@ -31,6 +129,12 @@ files:
 - lib/tag_along/offsets.rb
 - lib/tag_along/tagged_text.rb
 - lib/tag_along/version.rb
+- spec/files/clean.txt
+- spec/files/clean2.txt
+- spec/files/embryo129157.xhtml
+- spec/files/embryo129157.xhtml.json
+- spec/files/embryo129157.xhtml.tagged
+- spec/files/embryo129157.xhtml.txt
 - spec/files/spec_data.json
 - spec/spec_helper.rb
 - spec/tag_along/offsets_spec.rb
@@ -64,6 +168,12 @@ summary: A user who runs a search tool on a text would find  multiple text fragm
   corresponding to the search. These fragments can be found again by storing their  start
   and end offsets. This gem places arbitrary markup tags surrounding the fragments.
 test_files:
+- spec/files/clean.txt
+- spec/files/clean2.txt
+- spec/files/embryo129157.xhtml
+- spec/files/embryo129157.xhtml.json
+- spec/files/embryo129157.xhtml.tagged
+- spec/files/embryo129157.xhtml.txt
 - spec/files/spec_data.json
 - spec/spec_helper.rb
 - spec/tag_along/offsets_spec.rb