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« Oct. 30 Nov. 1 » Wednesday, October 31, 2007
Strong in class
Oct. 31, 2007 in Sports on Page C4 INDIANAPOLIS – Nearly every main demographic group of top college athletes exceeds the graduation rate for its student-body counterparts. According to federal graduation rates released Tuesday by the NCAA, 63 …
Unsettled Seattle starts
Oct. 31, 2007 in Sports on Page C6 SEATTLE – Kevin Durant's much anticipated regular-season debut won't be overshadowed by the SuperSonics' impending departure from Seattle. At least not tonight.
Seattle U, Kentucky meet again
Oct. 31, 2007 in Sports on Page C6 SEATTLE – Joe Callero never shies away from striking up a conversation. So a few years ago while in Las Vegas, the Seattle University coach walked up to then-Kentucky coach …
Boras blows hot air during endless 'treatises'
Oct. 31, 2007 in Sports on Page C7 Scott Boras is a lot easier to take if you understand that the guys across the table from him are just as full of it as he is. They just …
Getting leg up
Oct. 31, 2007 in Sports on Page C7 HAMPTON, Ga. – Dario Franchitti may have bolstered his cred with the good ol' boys by getting penalized for rough driving. He still has a long way to go before …
Nuts about Green Bluff
Oct. 31, 2007 in Food on Page D1 When families pack into the car and head up to Green Bluff this time of year, they're usually on the prowl for apples, pumpkins or gourds. But there's another kind …
Creativity can transform leftover treats
Oct. 31, 2007 in Food on Page D1 Need help eating your (or your kid's) share of this year's payload of Halloween candy? You're probably not alone. Americans readily shell out some $2 billion a year for all …
A toast to Arbor Crest's 25th
Oct. 31, 2007 in Food on Page D1 Arbor Crest is celebrating its 25th anniversary this year, a landmark event for any Washington winery. Perhaps more importantly, it is one of a growing number that have passed winemaking …
Fresh sheet : Grub Rustlers put to the test
Oct. 31, 2007 in Food on Page D1 While you were sleeping this weekend, The Grub Rustlers were stoking the smoker fires at the Jack Daniel's World Championship Invitational Barbecue in Lynchburg, Tenn. The Sandpoint team won an …
People: It's time to say goodbye, Dolly
Oct. 31, 2007 in Features on Page D2 Dolly Parton says she feels like a part of her died along with her old duet partner, Porter Wagoner. But she's grateful that she was able to spend a few …
Hints from Heloise
Oct. 31, 2007 in Features on Page D2 Dear Readers: Do you wind up with leftover cooked vegetables at the end of the week? Here are some delicious ideas for leftover vegetables: "Think of them as the original …
Oct. 31, 2007 in Features on Page D2 For 10-31-2007
Carolyn Hax: If bored, time to examine life
Oct. 31, 2007 in Features on Page D2 Carolyn: I find myself in another futureless relationship, just passing the time until being single seems more enticing than dating this person. At which point, we'll break up. A month …
Culinary calendar
Oct. 31, 2007 in Food on Page D3 Epicurean Delight, Spokane's Ultimate Culinary Gala - The 26th annual event features the most exquisite restaurants, paired with the finest wineries and microbreweries of the Inland Northwest. Proceeds from this …
Keep comments simple in divorce cases
Oct. 31, 2007 in Features on Page D7 Dear Miss Manners: Two of my colleagues have divorced their spouses and are now dating one another. While speculation has circulated about them dating for the past year or so, …
Veggies retain fresh flavor in Glad steaming bags
Oct. 31, 2007 in Food on Page D7 Food panel tasters are always suspicious when vegetables and fruits land on their plates. Taste testing new food products from the grocery store often means picking through the latest processed …


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Median Salary by Job
26 E Main St
Norton, MA 02766
Wheaton College, Massachusetts, Wheaton College
Private School, Liberal Arts
76 %
13 %
40 %
16 %
Wheaton alumni find work in an assortment of industries including the health care industry, the engineering services industry, and the scholarship trusts industry. The retail industry registers as the most common industry among alumni. Former Wheaton graduates bring in $49K on average.
The Wheaton alumni who make the most are Administrative Assistants; they report a median pay of $39K.
The most popular destination for former Wheaton students is Boston, Mass. Wheaton grads also flock to Providence, R.I., which is home to salaries significantly above average (median pay is around $95K). On the other hand, Wheaton alumni who end up in Alexandria, Va. receive the lowest median salary of $38K. Alumni express interest in New York, N.Y. and Cambridge, Mass. as well.
A B.A. in Communication leads to the highest pay for Wheaton grads ($69K on average per year). A B.A. in Anthropology is less advantageous in terms of earnings; alums with this degree are the lowest earners with a median annual pay of about $38K.
Financial Reporting is a popular skill among Wheaton alumni, with nearly one in eight grads reporting using it on the job. Wheaton College grads who have experience with Financial Reporting can expect to make 49 percent more than other alumni (approximately $74K on average). Microsoft Excel, Accounts Payable, and Event Planning are among other dominant skills.
The larger part of respondents report receiving paid vacation days, but just one in three grads are paid for sick leave. A large number of grads plan for retirement by taking advantage of a company-sponsored 401(k) program. Most respondents enjoy benefits like health insurance, while a majority of the survey participants receive dental plans, too. Wheaton College graduates also take advantage of life insurance, tuition reimbursement, 403(b), and a casual working environment.
Pine Manor College grads report the most similar salaries to Wheaton alums, earning around $49K on average. Wellesley College, College of the Holy Cross, and Gordon College are also similar to Wheaton.
68 %
32 %
$33,719 - $65,066
$33,621 - $56,627
|Extremely satisfied
Rated 5 out of 5
based on 5 votes.
Obama Will Expand Overtime to 40 Percent of Salaried American Workers
Yesterday, President Obama announced a rule change that will expand time-and-half eligibility to around 5 million Americans. By raising the overtime t...>
How the Supreme Court Ruling on Same-Sex Marriage Could Affect Employee Benefits
On Friday, the Supreme Court handed down its decision in Obergefell v. Hodges, effectively legalizing gay marriage in the 13 states in which it wasn't...>
Rushed and Rude: The High Cost of Busyness
Discretionary time for adults feels like a thing of the past. How often are most of us able to wake up and decide what to do today? Almost never. It c...>
Tell us about your current job and your skillset, and we'll let you know how much employers are paying in your area.

subset: commoncrawl


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Stock Photo:
paintball shooter aiming the gun
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High quality images curated from over 150 countries.
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BS1 BALTIC STATES & Helsinki TOURSEARCH TOUR
Lithuania, Latvia, Estonia, Finland
Vilnius walking tour; Hill of Crosses: compelling memorial; Cosmopolitan Riga; Tallinn: one of Europe's best preserved old towns; Helsinki: 'Daughter of the Baltic'
Tour Map
*The red tour trail on the map does not represent the actual travel path.
Hotel List
The following is a list of sample hotels at some locations included on this tour. The hotels shown here are meant to provide a general sense of the standard of hotel we usually aim for; they are not necessarily confirmed for your chosen departure.
Hotel Congress
Location: Vilnius
Country: Lithuania
The hotel Congress, situated in the very centre of Vilnius, is the ideal place for business travellers and tourists. As ... of the oldest hotels of Vilnius, it was constructed on the banks of the Neris river, next to the legendary Bridge Zaliasis ("Green Bridge") dating back to the 16th century. The hotel is contiguous to the Old Town which can be admired through the bedrooms windows.
Read More.
Click here to visit hotel website
Hotel Vecriga
Location: Riga
Country: Latvia
With only 14 rooms, this hotel is suitable for our smaller groups. In the very centre of Old City is ... one of the coziest Riga hotels – Vecriga (in translation: Old Riga). Construction of the building began in the 15th century. Every room has a mini bar, telephone, TV.
Read More.
Click here to visit hotel website
Reval Central
Location: Tallinn
Country: Estonia
All Hotel Central's guestrooms offer multi-channel and pay TV, free WiFi Internet and blackout curtains. Each room has a minibar, ... and direct-dial telephone. Modern decor with the comforts of home.
Read More.
Click here to visit hotel website
Radisson Blu Helsinki
Location: Helsinki
Country: Finland
This stunning hotel in Helsinki sits in the city's heart, where its striking exterior serves as an architectural landmark in ... skyline. With proximity to transport and attractions, the city centre hotel allows guests to easily explore sites like Tennispalatsi Culture Centre and Ateneum Art Museum. The 262 rooms are both comfortable and stylish, and delectable on-site dining options are also available. The hotel houses the city's most renowned event facilities, which include 13 conference and banquet rooms for up to 300 guests. A special Brain Box breakout room is designed to elevate efficiency and encourage creativity.
Read More.
Click here to visit hotel website
Sokos Presidentti
Location: Helsinki
Country: Finland
Recently completely refurbished, Sokos Hotel Presidentti is located next to the Kamppi mall, in the heart of Helsinki, next to ... wealth of culture attractions and the best shopping in town.The extensive refurbishing of rooms and restaurant facilities was completed in the spring of 2007.
Read More.
Click here to visit hotel website
DURATION9 days
TOUR STARTVilnius
TOUR ENDHelsinki


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The Top 10 In Action Sports
01Brick By Brick: Camping Lego Style
02Booze and Bikes: 14 Tours That Let Combine Two of the Best Things in the World
03Who Needs Hollywood? These Incredible Videos Were All Filmed on the Simplest Cameras
04Sam Pilgrim vs. The World: The Champion Aiming To Reclaim His Crown In A New Era Of Biking
05Eccentric Adventures Episode 2: Britain's Most Brutal Illegal Event is All About Cheese
06A Journey Into Darkness: We Went Mountain Biking in the Abandoned Mines of Slovenia
07After the Apocalypse: Inside The World's Most Breathtaking Ghost Towns
08Debate: Let's Stop Hating On Parents Who Want To Raise Adventurous Kids
09Guns, Roses, And Eating Insects: Adventure Cycling in Vietnam
10From Intense Trails to Intensive Care: Dicing with Death In a Mountain Biking Paradise
Back Down Under - Trailer
A Motocross video by dailybrand - 5,685 views
You have all seen JDR Motorsports mini web-series "Coming to America" that followed their efforts in the US earlier this year and now JDR take you back to where it all started for them. "Back Down Under" follows the Australian team as the take on the first rounds of the Australian outdoor series... This is the first taste of whats to come!
What Do You Think?
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Lacoste Essential Deodorant Stick
We're sorry, this item has sold out. However, we have found some other items you may like. You can find those listed at right.
Infused with Lacoste's Essential, this deodorant features a unique fragrance with energetic top notes of tangerine, bergamot, tomato leaves and cassis. Use alone or layer it with other Lacoste Essential products for an even more fragrant experience.
Shipping & Returns
Shipping your purchase is easy on belk.com. Depending on the destination of your package, you can expect it to arrive within 4-7 business days. Shipping Information
Returns are easy on belk.com. Easy returns
More from: Lacoste


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Al Braunworth Photographer
calendehenModel Female Northfield, Minnesota, US
Mayhem # 3323247
About MeI love getting to work with all different types of people and challenge myself to learn something new at every shoot. I've been modeling for about 6 months now and I'm signed with 3 agencies. I enjoy lots of different types of modeling and working to create new ideas. I do paid work only and the best way to contact me is through Facebook.
Al Braunworth Photographer
Robert Evans 101 Photographer
Epic Win Photographer
DMRosemark Photographer
Supreme Images Photographer
Mark Steensgard Photographer
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About This Listing
My beautiful house is available for you. My name is Veronica. I'm from Chile and I've been living in Tokyo for nearly twenty years. I am fluent in Spanish, English and Japanese. I know Tokyo like the back of my hand and I can tell you about all the cool amazing places in Japan that few people know.
I have a spacious, modern, western style house with 4 bedrooms, including one large traditional Japanese style tatami room in central Tokyo minutes walk from Nakano Fujimichou station on the convenient Marunouchi subway line. The house has a lovely garden at the front with parking and two toilets, one large bathroom and a new fully equipped kitchen with an oven and dishwasher.
The communal living spaces are immaculate and comfortable. The living room has two sofas, coffee table, HD TV, cable, DVD player and of course wifi throughout.
Space where guests can cook their own meals
Towels, bed sheets, soap, and toilet paper
Space where guests can cook their own meals
Towels, bed sheets, soap, and toilet paper
Central heating or a heater in the listing
In the building, free or for a fee
In the building, free or for a fee
Continuous access in the listing
Breakfast is provided.
The listing can accommodate a gathering of 25 or more attendees
Easy access to the building and listing for guests in wheelchairs
Private or Shared
Free, in the building or nearby
Posted emergency information and resources
The Space
The house is 160 square meters. The room is 15 sq meters facing south into the sunny and spacious garden.
With a Japanese touch in.
Antique furniture and decoration.
Guest Access
The nearest station is 5 minutes walk from the house
and in the same location there are Japanese, Italian, Chinese,Indian,Korean BBQ and Thai restaurants,Bar,Sushi Restaurant,Drug store,Post office and 24 hours supermarket with ATM .Every think you need is walking distance from the House.
Interaction with Guests
I am out of the house all day but in the morning and night, love to speak and explain the best way to get around in Tokyo.
Also every Saturday and Thursday is a great flea market very near to the house.
The Neighborhood
Is a residential area surrounded by many Japanese Temple,very quiet and beautiful in the centre of this city.
Getting Around
Have a convenient metro Line Marounouchi 5 minutes from the house.Parking include.
You can be in Shinjuku in 8 min. 15 to Shibuya 21 to Roppongi.Marounuchi line is a easy and with many transfer to other lines like JR Yamanote Oedo/Ginza/Hibiya/Fukuntoshi etc.
Other Things to Note
Also I can pick you up by car to the near Narita express or any hotel in Shinjuku if you prefer come by bus from the Airport out of charge.Pick up by car from Haneda if you have a late arrival for an extra fee
Haneda 8,000 Narita 20,000.
Smoking is not allowed at the house however you may smoke outside the house in my lovely front garden.
No party'(website hidden) shoes in the house
60 Reviews
Veronica's place was the best place I stayed in during my Japan trip.
The room is gorgeous and comfortable. The house is beautifully decorated and very clean and tidy.
I had a fabulous time getting to know Veronica, she's very friendly and accommodating. After chatting for a couple of hours, Veronica gave me brilliant directions to the Shinjuku night life including recommendations of which places were better than others.
I was sad to leave as I believe she had many more suggestions for me, I hope to one day return to Japan and I will be sure to ask Veronica if I can stay over again!
The room was so nice!
Small little garden was cute!
And not far from the station :-)
Veronica was responded very quickly to all our questions. She arrived at the house shortly after we arrived to set up a futon for our son. She provided directions with pictures. Neighborhood was quiet.
Veronica was there to greet us when we arrived. She showed us around and was very friendly and informative. She answered our questions where to find vegan food in the area, and advised what to say/ask when in a restaurant. She even lent us an English/Japanese dictionary. Her place was exactly as pictured and described in the listing. The room was very clean and tidy. We had a great time. I would stay in her place when I visit Tokyo again.
Veronica was extremely kind and welcoming! She gave us lots of tips on where to go and what to make sure we saw! All her help was great. Our room on the main floor was very spacious and private. We felt very at home. Close proximity to the train was awesome. Would definitely stay here again!!
Veronica was super friendly and very knowledgable about things to do in tokyo (and the rest of japan). House was easy to find from the directions. Its close to one of the main subway lines so no problems getting in to central tokyo. A great place to stay and i will visit again if i come back to tokyo.
We were very happy with our accommodations at Veronica's. Everything well organized, the location in Tokyo was close enough to the action, along with being in a peaceful, pleasant neighborhood. We found the deco beautiful with a cosy atmosphere. Veronica's husband greeted us right away, we will definitely stay again if we get back to Tokyo.
This host has 159 reviews for other properties.View Other Reviews
About the Host, Veronica
My name is Veronica. I'm from Chile and I've been living in Tokyo for nearly 28 years. I am fluent in Spanish, English and Japanese. I know Tokyo like the back of my hand and I can tell you about all the cool amazing places in Japan that few people know.
I be happy to be your host!!!


text:
There are currently 394 users online. 168 members and 226 guests
Most users ever online was 947, 12-07-2013 at 00:35.
Nice TR and even better looking camp.
Thanks for posting.
Got the same one, only used it a couple times. I haven't had a problem but it does kinda block the wind.rustyshack11 Today, 12:04
Yeah, if it wasn't for that whole getting laid thing it might work.rustyshack11 Today, 12:02
Finding suitable spots to hang hammocks is going to be interesting at both shelters. At each shelter four hammocks can
no the suspension and the tarps are as from Clark
Reason for selling have a 250 and a 270 with underquilts so im covered as there are only 2 of
Ok, I'm good! I can lave pretty much anytime Friday. If anyone is interested a ride from Columbus, let me know. Not a lot of room in the Wrangler (I removedHobopelican Today, 12:00
I swatted a few flies off of her ears during the hot part of the day when we were hiking, but they weren't bad and didn't seem to bother her. I was surprisedcricky101 Today, 11:57
How to make a diagonal seam?
1) Down a "cold one"
2) Try to make a straight seam
Yep, that should do it.


text: Music Articles The Girlish Voice Of Blossom Dearie August 25, 1992 Blossom Dearie — that's her real name — has been a fixture on the New York nightclub scene for decades. The singer and pianist is known for her quiet voice, unusual choice of material and jazz-influenced style of singing. Listen Loading… 7:38 Playlist Download Embed Embed Close embed modal <iframe src="http://www.npr.org/player/embed/100441748/100424477" width="100%" height="290" frameborder="0" scrolling="no">


text:
Santa Fe, NMUSA 87501
July 24, 2011
I have been kayaking for about 30+ years I live in T or C . I also hike, climb, mountianbike, and sail. Email [masked] or call me at 5o[masked] I am looking forward the kayaking with this group.
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Existing statistical methods for tiling array transcriptome data either focus on transcript discovery in one biological or experimental condition or on the detection of differential expression between two conditions. Increasingly often, however, biologists are interested in time-course studies, studies with more than two conditions or even multiple-factor studies. As these studies are currently analyzed with the traditional microarray analysis techniques, they do not exploit the genome-wide nature of tiling array data to its full potential.
We present an R Bioconductor package, waveTiling, which implements a wavelet-based model for analyzing transcriptome data and extends it towards more complex experimental designs. With waveTiling the user is able to discover (1) group-wise expressed regions, (2) differentially expressed regions between any two groups in single-factor studies and in (3) multifactorial designs. Moreover, for time-course experiments it is also possible to detect (4) linear time effects and (5) a circadian rhythm of transcripts. By considering the expression values of the individual tiling probes as a function of genomic position, effect regions can be detected regardless of existing annotation. Three case studies with different experimental set-ups illustrate the use and the flexibility of the model-based transcriptome analysis.
The waveTiling package provides the user with a convenient tool for the analysis of tiling array trancriptome data for a multitude of experimental set-ups. Regardless of the study design, the probe-wise analysis allows for the detection of transcriptional effects in both exonic, intronic and intergenic regions, without prior consultation of existing annotation.
In the last few years tiling microarrays have become a well-established tool for whole-genome transcriptome analysis. They have shown to be very useful for exploring and unraveling the complex genome-wide trancriptional landscape of higher organisms, in which not only protein coding genes, but also non-coding RNAs play an important role [1-4]. The methods that have been developed for transcriptome analysis with tiling arrays either focus on segmentation and transcript discovery within a single biological condition [5-8], or on the detection of differential expression between two distinct conditions [9,10]. Recently, the focus in tiling array studies has shifted towards more complex experimental designs, such as studies with more than two conditions [11] and studies with several experimental factors [12]. Furthermore, it is recognized that expression is a dynamic rather than a static phenomenon. Hence, more and more time-course experiments are designed to provide insights into the whole-genome transcript regulation of species during different developmental stages or external periodic changes in the environment [13,14].
Currently, most tiling array transcriptome analysis pipelines start with summarization of the probe-level data. This can be done by constructing probesets from the groups of probes that map to known annotated genes, (e.g. [11,15]). Hereby unannotated regions are disregarded. In [12,13,16] a sliding window-based approach is adopted, combined with a thresholding rule for selecting transcriptional units, whereas in [14] segments with piece-wise constant intensity levels are constructed first [17]. After the summarization a statistical test or a more heuristic analysis technique is conducted on the summarized expression values of the transcriptional units. In current time-course and single-factor studies this is merely done by directly applying traditional microarray analysis methods, such as a pairwise moderated t-test (Limma) [18] conducted in [11] or a permutated t-test (SAM) [19] conducted in [16]. Other studies adopt ad-hoc approaches to filter the genes or transcriptional units of interest. Transcriptional units in a time-course experiment, for example, can be filtered based on thresholding the amplitude of the signal [20]. In an alternative approach the correlations between temporal expression patterns are explored and a clustering is performed of genomic regions based on expression profiles in different gene classes showing expression at different time-points [21]. The tests reported in [13] and [14] on the other hand are less ad hoc, but very specific for the periodic time-course design apparent in these studies [22-24]. The aforementioned methods either lack flexibility by only focusing on one specific experimental design, or they first summarize probes to probesets based on existing annotation, hence not exploiting the genome-wide nature of the data to the full extent.
Here, we present waveTiling, a R Bioconductor package for transcriptome analysis of tiling arrays with flexible designs. The package is based on and provides an extension to a recently introduced wavelet-based functional model for transcriptome analysis [25]. While the methodology in [25] was initially developed to conduct the simultaneous tasks of transcript discovery and detection of differential expression, their framework can be easily extended by adapting the model design matrix. After modeling the specific effect function of interest, probe-wise inference can be conducted for detecting affected regions. The probe-wise analysis allows for the detection of transcriptional units in both exonic, intronic and intergenic regions, without prior consultation of existing annotation. Currently, waveTiling provides a standard analysis flow for transcriptome analysis on single-factor experiments with two or more biological conditions, the detection of linear and quadratic effects and circadian rhythms in time-course experiments, and the analysis of two-factor experiments, while more experienced users can also specify customized designs. Furthermore, it generates along-genome plots and contains functions to easily extract the detected genes and unannotated regions. The Implementation section gives an overview of the main functionalities of the waveTiling package and describes the model for the different designs, as well as the associated inference procedures. In Results and Discussion we illustrate the use of the package and the model on three different case studies with very distinct experimental designs.
The waveTiling package is an add-on package to the Bioconductor project [26] written in the programming language and statistical environment R [27]. It provides all the tools necessary to conduct a full analysis of tiling microarray experiments for flexible designs based on the recently introduced wavelet-based functional model for trancriptome analysis [25]. The package uses the standard Bioconductor S4-class data structures making it fully compatible with existing packages. The data is imported with the aid of the oligo-package [28] and the resulting object inherits from TilingFeatureSet, which is specifically designed for representing tiling array data and in turn extends ExpressionSet. Existing instance methods from oligo and other Bioconductor packages supporting this structure are therefore applicable as well. Before starting the analysis the probes can be remapped to the existing annotation. Moreover, probes that contain duplicated sequences for perfect match and mismatch probes or for probes on different strands can be filtered because they are deemed unreliable due to cross-hybridization effects. The main transcriptome analysis consists of two consecutive steps: (1) fitting the wavelet-based functional model to the data, and (2) model-based inference to identify transcriptionally affected regions. The fitted model is stored in a WfmFit-class object. Depending on the design of the study a WfmFitFactor (factorial design), WfmFitTime (time-course design), WfmFitCircadian (circadian rhythm design) or WfmFitCustom (custom design) subclass is used. Part of the code for fitting the model is implemented in C to speed up computation. In the second step, different inference procedures can be conducted depending on the research question. The inference procedure that can be conducted depends on the WfmFit-subclass. The results are stored as a WfmInf -class object. There are 3 main subclasses: WfmInfCompare which contains the results of a pairwise comparison between two groups or time points; WfmInfMeans with the results of transcript discovery for each individual group or time point; and WfmInfEffects which contains results with linear or quadratic time effects for time-course designs and circadian rhythm effects for circadian designs. All transcriptionally affected regions can be extracted from the WfmInf -class objects and are stored as IRanges-class objects [29]. The model fitting and inference steps are described in more detail in the Statistical Methods part.
The results can be visually explored by means of a general plot function. The implementation is based on the GenomeGraphs package [30]. For any genomic region the fitted expression values and transcriptionally affected regions can be plotted along the genomic coordinate. Furthermore, two functions are available for further post-processing of the results. Provided a suitable annotation file is given, the transcriptionally affected regions are mapped against the existing annotation. The first function outputs the genes that are transcriptionally affected, while the second function provides a list of the detected unannotated regions. The output of both functions is a list of GRanges-class objects [31].
Statistical Methods
We start by presenting an overview of the basic model introduced by [25]. Subsequently, we show how we accomodate for several sampling schemes in time-course experiments or other experiments with more flexible designs.
Basic wavelet-based model for transcriptome analysis
We consider the functional model designed for the detection of (differentially) expressed regions in experiments with two biological conditions. It is given by [25]
with i=1,..N, Yi(t) the measured log2-transformed expression values for the probe with position t (t=1,..T) on array i (i=1,..N). T is the number of probes that are more or less equally spaced along the genomic position of the chromosome, and N=N1 + N2 is the number of tiling arrays in the experiment, with N1 the number for biological condition 1, say C1, and N2 the number for biological condition 2, say C2. Further, X1,i is a dummy variable which is 1 for C1and −1 for C2, and Ei(t) is a zero mean error term. It is assumed that Ei(1),..Ei(T) are jointly MVN(0Σε). Here, MVN(μΣ) denotes the density function of a multivariate normal distribution with mean μ and variance-covariance matrix Σ.
The model can also be written as
In this model, Yis an N×Tmatrix of measured log2-transformed expression values, containing the elements Yi(t) for the probe with genomic position t (t=1,.,T) on array i (i=1,..,N). Further, E is an N×T error matrix containing the errors terms Ei(t) for probe position t on array i. The N×2 design matrix Xis constructed as
where the upper row represents the dummy coding for the N1 arrays in C1 and the lower row the dummy coding for the N2 arrays in C2. The 2×T effect function matrix B contains the probe-wise effect functions β1(t) and β2(t) on the respective rows. Column 1 of Xwill be used to find regions with a mean expression level above some threshold, whereas the coding in column 2 allows for assessing differential expression between the two conditions. Note that the coding in Ximplies that two effect functions are estimated orthogonally for a balanced study design. This can be seen from
Before estimating the effect functions, the expression data are projected onto the wavelet space by using the discrete wavelet transform (DWT). This linear projection can be written as the matrix multiplication D=YWT, where W is an orthogonal DWT matrix. This allows us to rewrite model (2) in the wavelet space as
where the rows of the N×Tmatrix Dcontain the wavelet coefficients for each array, double-indexed by location k=1,..Kj and scale j=0,..J. The 2×T and N×T matrices B∗ and E∗ contain the wavelet coefficients for the effect functions and the error terms, respectively. By putting a normal prior on the effect functions in the wavelet space, this model can also be written as
where is the element of B∗ corresponding to scale j and location k and m=1,2. In (4) N(μσ2) denotes the density function of a normal distribution with mean μand variance σ2. The smoothing parameters τm(jk) and the error variances are estimated by marginal maximum likelihood using a Gauss-Seidel algorithm. The estimated induce a regularization of the wavelet coefficients of the effect functions. When backtransforming the modified coefficients to the original data space, this leads to a denoised expression signal whereby the main features are retained. The method has proven to be very fast which is essential when analyzing large datasets. For more details, see [25].
Wavelet-based models for transcriptome analysis in more flexible designs
To extend the modeling framework reviewed in the previous section and to make it suitable for the analysis of tiling array data with more flexible designs, the design matrix X needs to be adapted in an appropriate way. Firstly, the adaptation must enable the model to answer the specific research questions provoked by the experimental design. Secondly, it must allow us to use the same fast algorithms introduced in [25]. This second argument comes down to the preservation of the orthogonality of X. In the first part of this section we focus on general time-course designs and single-factor designs for more than 2 groups. The second part aims at specific time-course designs for assessing circadian rhythms in the transcriptome. The section concludes with looking specifically at non-orthogonal designs, typically encountered in multi-factor studies.
General time-course designs
In tiling array time-course experiments one is often interested in the detection of differentially expressed regions between any two different time points. An additional concern might be to detect significant effects of transcriptional activity in time, e.g. linearly increasing or decreasing transcriptional expression of certain regions. These two possible research aims can be dealt with by considering a functional relationship of the designed time points described by orthogonal polynomials. This approach has also been used in quantitative trait associated expression studies based on traditional microarrays [32]. In that paper the functional relationship with phenotype is considered instead of with time.
Consider a time-course experiment with whole-genome expression levels measured at q time points. Let N be the total number of arrays used in the experiment. The number of arrays used for each time point is represented by N1,…,Nq, with N1 + … + Nq=N. In this exposition we only consider balanced designs, i.e. N1=…=Nq, with equidistant time points. However, it is rather straightforward to obtain orthogonal polynomials when dealing with non-balanced and non-equidistance designs. A simple procedure is discussed in [33]. The design matrix X in model (2) now has dimensions N×qand can be written as
where are the N1,…,Nq-valued vectors that correspond with the q respective designed time points in the experiment. In (5) each function ψj(x) is a polynomial of degree j, with j=0,…,q−1, and is orthogonal to ψk(x) (k=0,…,q−1) if j≠k. Note that each 1 in the first column of X can also be seen as ψ0(Xi) ( ). The orthogonality of Xis clear from
With this design matrix a q×Nmatrix B with the q effect functions is associated. The first row of Bcorresponds with an overall mean expression level over all time points, while row 2 until q are associated with a linear, quadratic, cubic,…,(q−1)-th order polynomial effect respectively between the different time points. The fitted expression levels for each time point are obtained by a linear combination of all effect functions in accordance with model (2). This allows for a straightforward comparison between any two time points. When combining several effect functions, it may be desirable to induce the same amount of smoothing for each of them. This implies the estimation of one general smoothing parameter τ(jk), instead of a separate τm(jk) for each effect function (m=1,..q). To retain the fast algorithms of [25], however, the diagonal elements of XTXneed to be identical in this case. This can be obtained by normalizing each column vector of X to give the normalized design matrix X″. This leads to the property
where Iq is an q×q identity matrix. For this orthonormal design matrix X″it can be shown that the common smoothing parameter can be estimated by
Although design matrix (5) can also be used for non-ordered single factor studies, one may choose to use a design matrix specifically constructed for unordered factors, e.g. a Helmert contrast design matrix. Helmert contrasts are basically designed to compare the mean expression at a specific time point with the overall mean over all preceding time points. The main reason why we use them here, however, is that they also lead to estimation orthogonalities for the effect functions. This is seen from
Just like for the polynomials, the design matrix Xbased on Helmert contrasts still needs to be normalized if the same smoothing for all factor effects is desired.
Designs for circadian rhythms
Suppose now that we are interested in the detection of a certain circadian rhythm in the transcriptome of an organism, based on an equally spaced time-course experiment. A natural way to model the circular effect is to construct X by means of Fourier basis functions, instead of polynomial basis functions. The design matrix is then given by
Again the separate effect functions can be estimated orthogonally, which is seen from
To estimate a common smoothing parameter for inducing the same amount of smoothing for all effect functions, X can again be normalized as described previously.
Non-orthogonal designs
Design matrices for two- or multiple-factor designs are typically non-orthogonal. Using these in the wavelet-based model would imply that the fast algorithms presented in [25] would have to be adapted. This would lead to undesirably increased computation time during parameter estimation. A solution to this problem is to apply the Gram-Schmidt process to orthogonalize Xand subsequently estimate the model parameters based on the orthogonalized design matrix. The Gram-Schmidt orthogonalization comes down to a QR-decomposition [34] of X into an upper-triangular matrix Xtri and an orthogonal matrix Xorth, which is now used to fit the model. Afterwards, the estimated parameters have to be transformed back to obtain the parameter values for the original X. This is possible by premultiplying them with . Similar to single-factor and time-course designs, the coding of the initial design matrix X still determines how the parameters can be interpreted, and may thus be constructed according to the specific research interest.
Statistical inference: detection of transcriptional effect regions
Depending on the study design and the aim of the analysis, either the parameters themselves or a function of the parameters are used to detect transcriptional effect regions. In both instances, the effect of interest can be represented by . For general time-course designs one can be interested in detecting genomic regions that show a linear or a quadratic trend in time. In this situation is just the effect function β(t) that corresponds with either the linear polynomial term ψ1(X) or the quadratic polynomial term ψ2(X) in (5). On the other hand, if interest lies in the detection of differentially expressed regions between different time points, inference is performed on each row of a matrix ZXB, where Z is a contrast matrix indicating the specific time points to be contrasted. Hence, each row of ZXB corresponds with one of the possible pairwise comparisons between two time points and gives rise to an effect function for each desired comparison. In circadian rhythm designs the sine and the cosine effect functions are combined to give the amplitude A(t) of the circadian rhythm per probe position, i.e.
Based on the size of A(t) circadian effect regions can be detected. In the case of non-orthogonal designs in multiple-factor studies, there are several possibilities for the choice of , depending on the aim of the analysis. The idea remains the same, however.
For each genomic location t, is compared to a certain threshold value δwhich can be chosen freely by the biological researcher. A Bayesian FDR procedure [35] is adopted to evaluate statistical significance. This may be written as
It basically involves the calculation of a probability mass from a univariate normally distributed random variable if contains only one β(t), or from a multivariate normally distributed random variable if contains a linear combination of β(t)'s [25]. The variance-covariance matrix is readily available if Xis orthogonal. For non-orthogonal designs it can be calculated by
For the circadian rhythms design however, this approach is not possible because of the non-linear dependence of A(t) on the β(t)'s. In this case FDRF(t) can be approximated by simulation. In each simulation step we sample from the normal sine and cosine effect functions and calculate Asim(t). FDRF(t) is now given by the proportion of simulations for which Asim(t)<δ. Specifically for differential expression, (13) is used to detect overexpression at probe t, while for detecting underexpression at probe t we use
Results and discussion
The use and flexibility of the waveTiling package is illustrated in three case studies for transcriptome analysis with different experimental set-ups.
Case study 1: Time-course experiment
The first data set consists of a tiling array expression study for identifying the molecular events associated with early leaf development of the plant species Arabisopsis thaliana[11]. Unraveling the underlying mechanisms of on one hand the transition from cell division to cell expansion and on the other hand the transition from non-photosynthetic to photosynthetic leaves, was the focus of this study. Trancriptome analysis for six developmental time points (day 8 to day 13) was conducted with AGRONOMICS1 tiling arrays [36], with three biological replicates per time point. Primarily, the researchers were focusing on the detection of differentially expressed regions between any two pairs of developmental time points. This specific study design, however, also allows for the detection of expression regions that change linearly over time. The functions and code used for this case study are described in more detail in the package vignette (see Additional file 1).
Additional file 1. waveTiling package vignette.Package vignette containing detailed information on how to perform a transcriptome analysis using a wavelet-based functional model with the waveTiling package. The data set of case study 1 (leaf development data) is used in the vignette.
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Pairwise comparison
Figure 1 gives an example of a genomic region on chromosome 1 of Arabidopsis thaliana found to be differentially expressed between different time points. The threshold value used here was |log2(1.2)|. For the most significant time point pairs the detected regions clearly resemble the exons of gene AT1G04350, encoding a putative 2-oxoglutarate-dependent dioxygenase (Figure 1).
Figure 1. Pairwise day-to-day differentially expressed genomic region. Fitted differential expression effect for the genomic region of gene AT1G04350 on the forward strand of chromosome 1 between selected pairs of developmental time points varying from day 8 (D8) to day 13 (D13). The grey rectangles indicate the detected regions showing a significant differential expression effect. The different replicates are indicated by ∘, + and , while the different days are represented by different colors: black (D8), red (D9), green (D10), blue (D11), cyan (D12) and magenta (D13).
We evaluate the regions detected by the wavelet-based analysis against the genes produced by the well-established and often used RMA method [37]. This is done by comparing the results of a gene set enrichment analysis based on both methods. By mapping the genomic regions found by the wavelet-based method to the Arabidopsis thaliana TAIR9 annotation [38], a list of genes is created for this method. Only genes that showed an overlap of at least 15% with the detected regions were retained. The enrichment analysis as performed with Plaza [39] revealed a strong overlap in the processes detected by both methods. A total of 483 enrichments were identified using both genesets of which 360 common enrichments were shared. The RMA gene list had 75 specific enrichments, while the wavelet-based gene list had 48.
The enrichment analyses revealed a high similarity of genes in common by the two methods for identifying differentially expressed regions of the genome that have previously been annotated. However, we could also discover non-annotated regions that were differentially expressed. We identified a total of 109 unannotated and differentially expressed regions in the genome with a length of at least 200 bp. Selected regions were validated with qRT-PCR to confirm these findings. These regions were chosen based on the following criteria:
1. Region was not in or near an exon or promoter from an annotated gene.
2. Longer regions containing more differentially expressed probes were preferentially selected.
3. Regions showing homogeneous probe directionality (all probes going in the same direction) across the entire region of differential expression were preferentially selected.
Using these criteria 12 regions were selected and qRT-PCR analysis was performed (see Additional file 2: Table S1). Of the 12 regions, 11 could be confirmed to contain differentially expressed transcripts during the time-course analysis. Only 1 region had no detectable transcriptional products. Log fold changes were calculated for confirming the expression and differential expression, as well as the directionality of the differential expression. From this analysis 9 of the 11 regions showed the same log fold change directionality as previously identified from the tiling arrays, and 2 regions showed opposite log fold change directionality. However, these 2 regions had the lowest log fold changes in the wavelet-based analysis. More details about the methods of enrichment and qRT-PCR analysis can be found in Additional file 2.
Additional file 2. Methods for biological validation.Detailed information about the gene set enrichment and qRT-PCR analysis for case study 1 (leaf development data).
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Linear and quadratic time effects
In addition to a pairwise comparison analysis, the wavelet-based functional model using the orthogonal polynomial design matrix is also useful for detecting genes with linear and quadratic expression patterns over time. In fact, the estimated parameters now give direct interpretations in terms of the different order time effects. Figure 2 gives some example plots of genes from the forward strand of chromosome 1 with a clear linear or quadratic time effect. From the plots, it is clear that the fitted probe-wise log2 intensities at the different time points (orange lines) are squeezed to some extent towards the mean fitted log2 intensities over all probes in the whole detected region at these time points (purple line). The main reason for this is that in the wavelet domain strength is borrowed from the neighboring probes in the genomic region to provide a more reliable estimate for each probe-wise effect.
Figure 2. Gene-wise linear and quadratic effects of transcription levels. Example plot for two genes showing a linearly increasing (A) and decreasing (B) mean log2 intensity level as a function of the 6 days in the time-course. These genes map to two of the top detected regions with a linear time effect for the forward strand of chromosome 1. The mean of the linear time effect parameter estimates corresponding with the probes in these regions are 1.08 and -1.16 respectively. Plots C and D give two examples of genes with a strong quadratic effect on the forward strand of chromosome 1. The dotted black lines represent the mean observed log2 expression for the probes over the three biological replicates at the different time points. The dotted grey line is the mean observed log2 expression over all the probes in the region. The orange lines are the probe-wise fitted log2 expression values when only considering the intercept and the linear time effect in the model for the two upper-part genes, and considering the intercept, the linear and the quadratic time effect in the model for the two lower-part genes. The purple line gives the corresponding mean fitted log2 expression values at the different time points over all the probes in the region.
For two of the genes shown in Figure 2 a more detailed visualization is given of the fitted linear or quadratic time effect along the genomic coordinate of chromosome 1. Figure 3 shows the regions with significant decreasing linear time effects overlapping with gene AT1G62500, encoding a putative lipid transfer protein, while Figure 4 shows those regions with a significant quadratic time effect overlapping with gene AT1G16410, encoding a cytochrome P450. It is also possible to look at the fitted log2 intensities at the different time points. This means that we are still able to perform transcript discovery at each time point separately. Figure 5 gives the corresponding plots for the linearly decreasing gene AT1G62500. The trend apparent in the example plots of Figure 2 is also clear from this figure. The grey rectangles in Figure 5 indicate the discovered regions with mean log2 intensities significantly above a certain threshold chosen according to the procedure described in [25]. This illustrates that for the discussed models, it is possible to simultaneously detect differentially affected regions between groups as well as transcriptionally active regions for each group - in this case for each day - separately.
Figure 3. Genomic region with a linear time effect. Fitted linear time effect for the genomic region of gene AT1G62500 on the forward strand of chromosome 1. The different replicates are indicated by ∘, + and , while the different days are represented by different colors: black (D8), red (D9), green (D10), blue (D11), cyan (D12) and magenta (D13). The grey rectangles indicate the detected regions showing a significant linear time effect, while the black line corresponds with the coefficient function of the linear effect. The negative sign of the coefficients implies a decreasing effect over time. More specifically, the effect at probe t is .
Figure 4. Genomic region with a quadratic time effect. Fitted quadratic time effect for the genomic region of gene AT1G16410 on the forward strand of chromosome 1. The different replicates are indicated by ∘, + and , while the different days are represented by different colors: black (D8), red (D9), green (D10), blue (D11), cyan (D12) and magenta (D13). The grey rectangles indicate the detected regions showing a significant quadratic time effect.
Figure 5. Day-by-day expression levels for a genomic region show the linear effect. Fitted log2 intensities per time point of the genomic region of gene AT1G62500 on the forward strand of chromosome 1. The different replicates are indicated by ∘, + and , while the different days are represented by different colors: black (D8), red (D9), green (D10), blue (D11), cyan (D12) and magenta (D13). The grey rectangles indicate the detected regions showing a significant mean expression. The decreasing trend of the fitted log2 intensities over the different time points exemplified in Figures 2 and 3 is clearly apparent in this figure.
Case study 2: Circadian rhythms
The second case study concerns an expression analysis to examine circadian rhythms in Arabisopsis thaliana[13]. It is known that photosynthetic organisms anticipate changes in the daily environment with an internal oscillator, called the circadian clock. The aim of the study was to explore the genome-wide extent of the rhythmic expression patterns governed by this oscillator. In this experiment, 12 samples were collected from Arabidopsis thaliana seedlings that were placed under a 12 h light / 12 h dark cycles regime. Every 4 hours 2 samples were taken and hybridized to the Affymetrix AtTile 1.0F and 1.0R tiling arrays. More information about the experiment can be found in [13].
Figure 6 shows an example of the model fit for gene AT2G46830 with a clear strong circadian effect. This gene has been previously described and is known under the name CIRCADIAN CLOCK ASSOCIATED1 (CCA1). Besides the circadian effects, no other time-dependent effects are considered in the model. Therefore, the fitted log2 intensities for time points at identical moments in the 24h day/night cycle always coincide. This strong circadian effect is confirmed by Figure 7, which shows the fitted effect for the genomic region of CCA1. This effect corresponds with the amplitude of the circadian rhythm, , as estimated by the model.
Figure 6. Gene-wise circadian effect of transcription levels. Example plot for gene AT2G46830, better known as CIRCADIAN CLOCK ASSOCIATED1, showing a clear circadian rhythm effect of the mean log2 intensity level over the 48h time course. The dotted black lines represent the observed log2 expression for the probes at the different time points. The dotted grey line is the mean observed log2 expression over all the probes in the region. The orange lines are the probe-wise fitted log2 expression values, while the purple line gives the corresponding mean fitted log2 expression values at the different time points over all the probes in the region.
Figure 7. Genomic region with a circadian effect. Fitted circadian effect for the genomic region of gene AT2G46830 on the forward strand of chromosome 2. On the Y -axis the amplitude of the circadian rhythm is given. The grey rectangles indicate the detected regions showing a significant circadian effect. The different replicates are indicated by ∘ and , while the different samples in the 12 h light / 12 h dark cycles regime are represented by different colorsl.
The performance of the wavelet-based method for circadian rhythms is further tested by examining some specific circadian clock associated genes on the forward strand of the Arabidopsis thaliana genome [40]. The genes that we consider here were also reported in [13]. The results are shown in Table 1. All genes show a considerable overlap with the genomic regions for which a circadian effect was detected significantly above the threshold value log2(1.1), except TIME FOR COFFEE (AT3G22380). They also have a quite high maximum estimated effect or amplitude size, except TIME FOR COFFEE and ZEITLUPE (AT5G57360). These latter two genes are the only genes from the list that do not fall within the top 20 genes with the strongest estimated circadian effect for their corresponding chromosome. The gene TIME FOR COFFEE is known as a clock gene that does not cycle at the transcriptional level [41]. Hence, it is as expected that both the overlap between detected region and gene annotation, and the effect size are very small. The gene ZEITLUPE is reported as having weak rhythms at the transcriptional level [40]. This is confirmed by the low maximum effect size, while still showing a considerable overlap of the significant region with the existing annotation. The results of Table 1 are thus completely in line with what was expected from literature.
Table 1. Circadian effect for 9 genes put forward in the Hazen study
Case study 3: Non-orthogonal two-factor design
The third data set is used to illustrate the analysis of a two-factor design tiling array experiment. The data are taken from a study of the genome-wide analysis of endogenous abscisic acid (ABA)-mediated transcription in dry and imbibed seeds of Arabidopsis thaliana[12]. ABA is a phytohormone that is important for the induction and maintenance of seed dormancy. To understand how endogenous ABA regulates the transcriptome in seeds, whole-genome expression analyses were conducted in two ABA metabolism mutants, an ABA-deficient mutant (aba2) and an ABA over-accumulation mutant (cyp707a1a2a3 triple mutant), and compared to a wild type. This is the first factor in the design. Since endogenous levels of ABA often change drastically during seed imbibition [12], these experiments were done both for dry and for 24-h imbibed seeds. This is the second factor in the design. For each design point, three biological replicates were hybridized using the Affymetrix AtTile 1.0F and 1.0R tiling arrays, resulting in 18 samples. For this case, model (2) can be written as
where imbibed=1 if the seed was imbibed and imbibed=0 if the seed was dry, mutant1=1 for the aba2-mutant and mutant1=0 otherwise, and mutant2=1 for the cyp707a1a2a3 triple mutant and mutant2=0 otherwise. This model specification implies that the design matrix X used for this model is
Column 1 of Xcorresponds with an overall mean expression level over all samples. The main imbibition effect is coded in column 2. Note that this corresponds with the imbibition effect for wild types, which is the reference species. Columns 3 and 4 are associated with the main ABA mutation effects, whereas columns 5 and 6 allow to examine an interaction effect between imbibition and ABA mutation statuses. Figure 8 shows two examples plots for representing the model fit for the genes AT1G69530, encoding an expansin, and AT1G61520, encoding a chlorophyll a/b binding protein, on the forward strand of chromosome 1. Table 2 gives the associated gene-wise mean parameter estimates for these genes. The left panel plot of Figure 8 suggests a larger mean expression level of gene AT1G69530 for imbibed seeds compared to dry seeds. The increase in mean expression level, however, is larger for wild types than for ABA-related mutants. The increase in mean expression level between imbibed seeds compared to dry seeds is given by for wild types, while for aba2 mutants this increase is given by and for cyp707a1a2a3 triple mutants by . On the right panel of Figure 8 we see an increased mean expression level of gene AT1G61520 for aba2 mutants as compared to wild types and cyp707a1a2a3 triple mutants. In addition, this increase is much stronger for imbibed seeds.
Figure 8. Gene-wise main and interaction effects of transcription levels for a two-factor model. Interaction plots for genes AT1G69530 (A) and AT1G61520 (B). The black lines represent the observed log2 expression for the probes at the different combinations of the two factor levels. The dotted grey line is corresponding the mean observed log2 expression over all the probes in the region. The orange lines are the probe-wise fitted log2 expression values, while the purple line gives the corresponding mean fitted log2 expression values for all the probes in the region.
Table 2. Two-factor model gene-wise effects
In this paper, we have described the R package waveTiling for model-based analysis of tiling array expression studies with flexible designs. It implements the recently proposed wavelet-based model for transcriptome analysis [25] and extends its applicability towards more complex experimental set-ups. Unlike most currently applied methods, transcriptional activity is modeled at probe-level instead of gene- or exon-level. This probe-wise analysis allows for the detection of transcriptional units in both exonic, intronic and intergenic regions, without prior consultation of existing annotation. By appropriate adaptations of the basic model design matrix it becomes possible to easily analyze the transcriptome for single-factor experiments with more than two biological conditions, to detect linear and quadratic time effects or a circadian rhythm effect in time-course experiments, and to even conduct two- or multiple-factor studies. The package's use and flexibility are illustrated with three case studies on the reference plant Arabidopsis thaliana. These cases show the potential of the package and method to cope with a multitude of study designs and associated specific research questions and still provide reliable results. The waveTiling package will be freely available as part of the Bioconductor project.
Availability and requirements
• Project name: waveTiling
• Project home page: http://r-forge.r-project.org/projects/wavetiling/
• Operating system(s): Platform independent
• Programming language: R
• Other requirements: R >= 2.14
• License: GNU GPL
• Any restrictions to use by non-academics: None
Competing interests
The authors declare that they have no competing interests.
Author's contributions
KDB and LC conceived the study and developed the model. KDB implemented the model, conducted the case studies and statistical analyses and wrote the manuscript. PP helped in the design and implementation of the package. MA conducted the biological validation experiments and analyses and helped write the manuscript. OT and CC took part in several discussions related to the model. DI took part in several discussions regarding the biological data. All authors read and approved the final manuscript.
Part of this research was supported by IAP research network grant no. P6/03 of the Belgian government (Belgian Science Policy) and Ghent University (Multidisciplinary Research Partnership "Bioinformatics: from nucleotides to networks").
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text:
An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates
Article first published online: 22 AUG 2012
DOI: 10.1111/j.1461-0248.2012.01855.x
© 2012 Blackwell Publishing Ltd/CNRS
Ecology Letters
Volume 15, Issue 11, pages 1318–1325, November 2012
Additional Information
How to Cite
Ecology Letters (2012) 15: 1318–1325
Publication History
- Issue published online: 1 OCT 2012
- Article first published online: 22 AUG 2012
- Manuscript Accepted: 24 JUL 2012
- Manuscript Revised: 19 JUL 2012
- Manuscript Revised: 1 JUL 2012
- Manuscript Revised: 1 MAY 2012
- Manuscript Received: 26 MAR 2012
- Biodiversity;
- biogeography;
- nearctic region;
- neotropical region;
- niche evolution;
- tropical niche conservatism
The Tropical Niche Conservatism hypothesis is a leading explanation for why biodiversity increases towards the equator. The model suggests that most lineages have tropical origins, with few dispersing into temperate regions. However, biotas are comprised of lineages with differing geographical origins, thus it is unclear whether lineages that originated on different continents will exhibit similar patterns of niche conservatism. Here, we summarised biogeographical patterns of New World vertebrates and compared species diversity patterns between families that originated in North and South America. Overall, families with southern origins exhibit niche conservatism with many lineages restricted to the Neotropics, whereas many northern-origin families are distributed across the Neotropics and the Nearctic. Consequently, northern lineages have contributed to high tropical biodiversity, but southern lineages have contributed relatively little to temperate biodiversity in North America. The asymmetry in niche conservatism between northern and southern lineages is an important contributor to the biodiversity gradient.


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Originally written on The Penalty Flag | Last updated 5/18/12
The Seattle Seahawks proved last year its defense is solid, allowing 19.7 points per game and just over 320 yards per game, good for seventh and ninth best, respectively, in the NFL. The offense hampered the team, however, and the Hawks placed 28th in yards per game and 22nd in passing yards per game. Aside from Marshawn Lynch,
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text: Lathrop & Gage L.C. is a full-service law firm with 280 attorneys in 10 offices across the country. The firm has a regional, national and international practice in business and tort litigation, intellectual property, government relations, corporate, environmental, labor and employment, health care, real estate, financial institutions, tax, – more... wealth strategies, and bankruptcy and creditors' rights. – less – More from ZoomInfo »


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Analyst and programmer
Russia - Last active: 26 days ago - Tests: 47 - Portfolio: 7
Expert in VBA/Excel/Visual Basic 6/SQL, interested in Cuda, Python. Have some C++ and ASM experience. I'll be glad to help with: Optimization and automating of business-processes. Developing of decision support systems, E-commerce systems, including data interchange between Ebay/Amazon/SmugMug/ custom CRM systems. Web scraping/crawling, automated retrieval of weakly-structured data. Implementing methods of artificial intelligence (expert systems, artificial neural networks, genetic algorithms),data mining. Natural language processing tasks (intellectual textual search, natural language generation, etc). Imitational modeling (especially financial models, gaming), prediction of complex systems. Distributed applications, high performance computing (scientific computations), cloud computing (Azure/Amazon). Software reverse engineering.
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Finance & Accounting Expert
India - Last active: 2 days ago - Tests: 8 - Portfolio: 6
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India - Last active: 2 days ago - Tests: 16
1. I am a Chartered Accountant (equivalent to CPA in US) from India. 2. I have worked as Assistant Manager/ Finance Analyst in Closing and Reporting/ Financial Planning and analysis Profiles, in KPO Company in India. 3. Excellent communications skills as I have travelled across UK and US for Transition of Accounting work. 4. I have expert knowledge in Excel. Automated several routine works to ensure 100% accuracy and save manual hours which are costly. 5. I have expert knowledge of Technical Analysis of Forex, Stock Markets, Gold, and Oil. 6. Financial Modelling in Excel. 7. Equity research reports and equity valuation models on UK and US stocks. 8. Financial projections and proforma for start-ups. 9. Merger & Acquisition Models. 10. Analysis of financial statements. 11. Credit analysis of borrowers for financial institutions and banks. 12. Financial evaluation of projects in infrastructure based on cash flows, NPV, IRR, Sensitivity Analysis. 13. Business valuation. 14. Options, Futures and Derivatives. 15. Writing articles and blogs on stock markets, currency markets, economy and financial markets. 16. Collection of financial data from various sources such as annual report of companies, websites and SEC filings etc. 17. Statistical analysis. Besides I am Native Hindi speaker, Passion of Teaching Vedic Maths, Hindi, Sanskrit. Have got a team of people to do Data entry work under my supervision. Kindly see my work experience both at Odesk (online job world) and My Resume (Offline Job world).
Excel expert
Slovakia - Last active: 22 days ago - Tests: 7
Hello! I can help you transform your data into meaningfull and insightful information. I can prepare templates / tools for collecting, recording information, and of course, most importantly -- report against that information. My major field of expertise is spreadsheets (MS Excel in particular) and, to a lesser extent, databases -- MS Access and Myslq. I have a university background in Finance. I work as a financial controller for a conglomerate. I am interested in providing customized, Excel based solutions also by VBA automation.
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United Kingdom - Last active: 3 days ago - Tests: 7 - Portfolio: 2
My objective is to provide strategic insights to customer requests and quality solutions. I have over 7 years' experience in the commercial real estate and marketing industry as an reporting analyst, marketer and report writer. I have handled multiple projects related to portfolio analysis, lease administration and property management, demographic analysis, feasibility reporting, payroll reporting, report, journal and article writing, copywriting for commercial and residential real estate and survey creation and execution. I have strong experience with primary (telephone, focus Groups, interviews) and secondary (desktop) research experience and successfully continue to meet lead generation targets. I am able to think outside of the box, have strong attention to detail, excellent report writing and project management skills. I have experience in Google Earth and MapInfo GIS demographic profiling. Experienced in demographic data extraction from ABS and US Census Bureau and US Labor of Statistics. Experience with real estate comps programs including Costar, RP Data, Residex, Prospectnow, REIS, FlexMLS, Zillow, Trulia, Craigslist. Some experience with Project Management Tools (TeamWork, Evernote, Asana) Cloud storage devices, CRM tools (Insightly, HighRise, Sales Force), Accounting Software (JDE, Quickbooks, MYOB) and Property Management Software (Yardi, Buildium).
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Spain - Last active: 2 days ago - Tests: 6
I am a former Trader and Multi Asset Structurer (Forex, Interest Rates) at HSBC. I am also the CEO and Founder of a new social ticketing platform: www.togenit.com 5 Stars Odesk Freelancer able to maximize your Quality / Cost ratio and Save your Time. My expertise includes Financial Markets (forex, interest rates, credit bonds), Economics and Venture Strategy. I am also passionate about finance & business related writing: http://seekingalpha.com/article/2823146-safety-and-quality-to-beat-deflation-in-2015 http://seekingalpha.com/article/2816776-is-the-aussie-going-down-in-2015 http://moneytransfercomparison.com/ I speak English, French & Spanish. Proven Professional expertise in my field, so high value and quality guaranteed !
Grant Writing, Funds Development and Business Plan 4+ yrs
United States - Last active: 1 month ago - Tests: 3 - Portfolio: 2
Rushelli Luna brings the tools nonprofits need to execute their mission of raising funds for causes that matter to our communities. She offers services that give nonprofits the edge they need to effectively generate funds and get the community involved. Through effective researching, networking and proposal writing, Rushelli can manage budget and increase funds available for your programs. Her mission is to provide invaluable services to nonprofit organizations so that they can make a difference in our world. Rushelli Luna is an incredible leader who advocates for the causes that your organization is passionate about through critical thinking, ingenious researching and outstanding assistance. Specialty Services Business Consultation Grant Funding Consultation Business Plan Writing Grant Writing Program Development Budget Planning Cover Letter and Resume Writing Report Writing
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Bangladesh - Last active: 21 hours ago - Tests: 12 - Portfolio: 50
I am professional Graphics Designer and have two years of Practical Working experience on a Event Management firm. Now I work as a freelance designer. I have graduated on Economics from the University of Dhaka. Currently I am working with the Central Bank of Bangladesh. Previously I worked in leading Commercial Bank in Bangladesh. So, I have a lot experience on Data Management and Report Creation on Financial sector. I also occasionally write on the Financial Dailies of Bangladesh, so I have some writing experience too.
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Associated with: The Alpha Team
Business Plan, Financial Modeling in Excel, Bookkeeper and accountant
Pakistan - Last active: 21 hours ago - Tests: 12 - Portfolio: 2
I am ACCA (Association of Chartered Certified Accountants). Over the years i have developed myself as expert in all Accounting Module Software like Quickbooks, MYOB, Quicken, MS Office and MS Excel 2007 using charts, formulas and pivot table. Furthermore, i have been writing business plans for newly startup businesses. Moreover i have command over MS Excel financial modeling spreadsheets like for costing, Discounted CashFlows (for appraising investments) , Budgeting and forecasting, Variance Analysis. Futhermore i am owner of urbookkeeper ( just google it to know about it further !) My expertise and services includes.. Business Plan Writing (Including Marketing Plan and Financial Projections). Financial Modeling in Excel. Initial Accounts setup in any Accounting Software. Transaction Accounting. Online Bookkeeping. Accounts Payable Management. Accounts Receivable Management. General Ledger Accounting and Maintenance. Reconciliations of Accounts. Financial Statement Preparations. Interpretations of Financial Statements. Reporting of Financial Statements and Evaluation of Business. Payroll Services. Financial and Non- Financial Analysis of Financial Statements. Investment Appraisal. I am fluent in written and spoken English. I believe in quality work, quick turnaround and the right kind of price. Moreover, I am quick in communicating through emails, skype, gtalk and phone.
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Associated with: Rascons Financial Services
Financial Professional & MBA Grad
United States - Last active: 1 month ago - Tests: 17 - Portfolio: 11
PLEASE NOTE: At this time, I am only opening to working with clients on hourly (not fixed price) projects that meet or exceed my minimum $27.78 all-in hourly rate (net of 10% fees) and have an established history on oDesk/Upwork (which is open to interpretation, but generally either (i) 1-year of active history on the platform or (ii) 10+ completed contracts with favorable reviews). **Top 1% on Business Concepts (U.S.) test - Brainbench **Top 1% on Management Skills test - oDesk **4th out of 1050+ test takers in Day Trading test - oDesk **12th of 8700+ test takers in Business Writing Skills Certification - oDesk Are you looking for an experienced and reliable business professional with a strong track record in financial analysis, business consulting, and market research to provide consistent, best-in-class support to your important project or assignment? As a demanding client who rightfully expects quality work, rest assured that in hiring me you will receive high quality deliverables, executed on-time, with open communication throughout at a mutually-acceptable negotiable rate. I am a financial professional with over 10 years of progressive experience with financial institutions, Fortune 500 companies, and other reputable organizations. Furthermore I completed an honors undergraduate degree in economics from a top liberal art college in New York and hold an MBA in Finance. I look forward to advising my clients in accounting, finance, business plans, and business advisory services. I am eager to bring value to my clients, and thank you in advance for giving me the opportunity to work with you.
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Associated with: MBAFINANCE2010.COM


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