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High throughput sequencing

Inductive matrix completion

Long intergenic non-coding RNAs

Long non-coding RNAs

Non-negative matrix factorization

Robust inductive matrix completion

Stable robust inductive matrix completion

Single nucleotide polymorphism

Transcriptor factor binding sites

Term frequency inverse document frequency

We express deepest gratitude to Dr. Kytai Nguyen in Bioeengineering Department at University of Texas at Arlington for the comments and feedback on our lincRNAs discovery results.

Funding

Not applicable.

Availability of data and materials

The ChIP-base dataset is available at Lakai Mens Griffinm Walnut Canvas Ae1dHlWgvM
. The Linc2GO dataset is available at: https://omictools.com/linc2go-tool . The SNP-lincRNA data can be found at: http://bioinfo.life.hust.edu.cn/lncRNASNP/ .

About this supplement

This article has been published as part of Volume 10 Supplement 5, 2017: Selected articles from the IEEE BIBM International Conference on Bioinformatics Biomedicine (BIBM) 2016: medical genomics. The full contents of the supplement are available online at https://bmcmedgenomics.biomedcentral.com/articles/supplements/volume-10-supplement-5 .

Authors’ contributions

AKB conceived the package and wrote the manuscript. DK and MK contributed to data analysis and programming for the experiment. CD contributed to the two-step algorithm to solve the proposed RIMC algorithm. JG provided overall supervision. All authors reviewed, edited and approved the final manuscript.

Ethics approval and consent to participate

All the datasets used in this study are from publicly available data repository. No patients samples were used or collected in this study.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( FRYE Womens Rachel TStrap Sandal Leopard72569 vJbwUZs7k
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( http://creativecommons.org/publicdomain/zero/1.0/ ) applies to the data made available in this article, unless otherwise stated.

Department of Computer Science and Engineering, University of Colorado Denver, Denver, USA
Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, USA
Department of Computer Science, University of Rio Grande Valley, Edinburg, USA
Department of Computer Science, Kennesaw State University, Marietta, USA
©The Author(s)2017

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On top of that, the CEO noted the company has enough space to detain 7000 more people than it is right now, which could mean another $60 million per year in revenue.

GEO Group investors who asked questions on the call were closely following the impact of Trump’s changes on the business, peppering the executives with questions about how policy changes could make the company more lucrative. Michael Kodesch, an analyst with Cannacord Genuity, asked what the company saw as “the new opportunity set” given Congressional budgeting.

“What we see is ICE beginning to implement their interior enforcement strategy,” said David Venturella, the company’s senior vice president of business development. “For the past 8 to 10 years, the focus has been on the border. I think everybody has seen the number of apprehensions and crossings going down, so Phase 2 of that strategy is to focus in the interior.

“We’ll start to see the benefits of that through increased apprehensions and increased detention in the interior part of the United States, not necessarily along the southern border,” he added….

“I think any enforcement by federal law enforcement agencies could generate more prosecution convictions and then eventual detention in the federal system,” Venturella said. “I think the attorney general’s recent announcement regarding the prosecution of criminal aliens would apply to all the federal agencies, so we will monitor the impact of that new policy directive. But certainly, any increase in law enforcement activity could generate additional apprehensions and then eventually detentions.”

The company, GEO Group, contracts with governments around the world to incarcerate 100,000 people, and its top executives expressed optimism on a public shareholder call on Tuesday about how Trump’s immigration crackdown will impact their business. It’s indicative of a cultural overhaul taking place under the Trump administration—where well-connected multi-national corporations are poised to see significant financial gains because of tougher immigration law enforcement.

GEO Group has close ties to Trump’s political circles. The company gave $250,000 to Trump’s inauguration, Clarks Womens Palma Trina Boot Dark Brown Nubuck LMrvWpZ77
A subsidiary of the company gave $225,000 to a super PAC helmed by the Mercer family. And Rebekah Mercer, hedge fund manager Robert Mercer’s daughter, is widely reported to be one of the most influential donors in Trump’s circle. And last October, the company retained two former aides to now-Attorney General Jeff Sessions to lobby the federal government on prison contracts, Salomon Womens Speedcross 3 Trail Running Shoe Bordeaux/Hot Pink/Lotus Pink omD44
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Beyond being politically connected, GEO Group is controversial. Immigrants’ rights groups have long criticized it and its biggest American counterpart, CoreCivic, for the way they treat detainees. And in February, a federal judge ruled that former detainees at one GEO immigrant detention center could direct a class-action lawsuit at the company for forcing them to work for little or no wages—which they allege violates the Trafficking Victims Protection Act. GEO strongly denies those allegations.

This page helps you design your Apache Beam pipeline. It includes information about how to determine your pipeline’s structure, how to choose which transforms to apply to your data, and how to determine your input and output methods.

Before reading this section, it is recommended that you become familiar with the information in the Beam programming guide .

What to consider when designing your pipeline

When designing your Beam pipeline, consider a few basic questions:

Where is your input data stored? What does your data look like? What do you want to do with your data? What does your output data look like, and where should it go?

The simplest pipelines represent a linear flow of operations, as shown in figure 1.

Figure 1: A linear pipeline.

However, your pipeline can be significantly more complex. A pipeline represents a Directed Acyclic Graph of steps. It can have multiple input sources, multiple output sinks, and its operations ( PTransform s) can both read and output multiple PCollection s. The following examples show some of the different shapes your pipeline can take.

It’s important to understand that transforms do not consume PCollection s; instead, they consider each individual element of a PCollection and create a new PCollection as output. This way, you can do different things to different elements in the same PCollection .

You can use the same PCollection as input for multiple transforms without consuming the input or altering it.

The pipeline in figure 2 is a branching pipeline. The pipeline reads its input (first names represented as strings) from a database table and creates a PCollection of table rows. Then, the pipeline applies multiple transforms to the same PCollection . Transform A extracts all the names in that PCollection that start with the letter ‘A’, and Transform B extracts all the names in that PCollection that start with the letter ‘B’. Both transforms A and B have the same input PCollection .

Figure 2: A branching pipeline. Two transforms are applied to a single PCollection of database table rows.

The following example code applies two transforms to a single input collection.

Another way to branch a pipeline is to have a single transform output to multiple PCollection s by using tagged outputs . Transforms that produce more than one output process each element of the input once, and output to zero or more PCollection s.

single

Figure 3 illustrates the same example described above, but with one transform that produces multiple outputs. Names that start with ‘A’ are added to the main output PCollection , and names that start with ‘B’ are added to an additional output PCollection .

There were 2 recommendations from the task force that might have provided a little, limited relief to citizens. However, even that was too much for COGCC and the industry allow. We are now left with rules that bear little resemblance to the original recommendations. As currently written, they will result in even more placement of wells next to our homes, schools and businesses. Cities and counties will have no power to stop them.

The day was spent with witnesses testifying. The commissioners sat with bored expressions on their faces and some spent the time on their phones and computers.

Industry and supporters spent their time raging against a sentence in the proposed rules which put a time limit on the how long the drilling and fracking processes can take.

The other side of the equation was the citizens and activist groups. There were many new activists at the meeting. (Every time a new area is fracked, more activists are born.) All of these new activists go through a stage, just as I did, hopeful that they can find the right words to reach those in power.

It was heart wrenching to watch people testify and pour out their hearts in a plea for mercy while I sat there with the knowledge that the game is already rigged against them.People came from across the state to tell their stories: Battlement Mesa, Paonia, Thornton, Wadley Farms, Greeley and Pleasant View. Boulder County and Adams County Commissioners came to plead for their citizens.

A few months ago several of us came to the realization that the COGCC doesn’t care and will never protect us. CAF staged a walk out at the stakeholders meeting in Greeley, letting them know we are aware that they don’t care.

So, I didn’t bother to prepare any remarks. I didn’t bore them further with tales of the latest health studies. I didn’t tell them about fear for my grandchildren.

The task force was a bust. We knew it would not give us any relief from the dangers of fracking. Our governor and the COGCC don’t care and won’t act to protect us.

Now we will take the next step. We will band together and get a ballot initiative on the ballot next fall. Then we will work with our partners to get it passed. It is time to send the fossil fuel industry into the fossil bin where it belongs. It is time for a renewable, sustainable future. We will build it together.

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24 Sep/15
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Comments made at EPA hearing on Methane Rules. September 23, 2015

As I was preparing for this I thought what should I tell the EPA?

I could tell you that methane is 86 times more potent than CO2 as a green house gas. But you already know that.

I could tell you that everyone touts the Colorado methane regulations, but the methane and other toxins in our air here have increased. But you already know that.

I could tell you that Methane and the other VOC’s from fracking are contributing to very high ozone here, so high that the American Lung Association gave us an F and you, the EPA have labeled us as a non attainment area. But you already know that.

I could tell you that methane is leaking not only from fracking extraction sites, but at every point along the way. But you already know that.

I could tell you that along with the methane spewing out of these wells it brings with it VOC’s that are dangerous to our health. But you already know that.

I could tell you that the amount of methane leaking is known to be vastly under estimated. But you already know that.

I could tell you that methane is going to drastically increase global warming which will adversely affect all parts of the world with sea level rise, droughts, wild fires, habitat destruction, and more frequent severe weather. But you already know that.

But Have you thought of the consequences of that?

I decided I would read you a poem by Drew Dellinger

When you turn a blind eye to fracking, you are participating in the war against the future of our children, which is being waged by the fossil fuel industry.

So here is what I will tell you. There is no need for new regulations. The President has the power and needs to have the courage to eliminate all new wells and should do so immediately. The EPA needs reclaim their power to enforce all the regulations that were ended with the Halliburton loophole. All current wells that are non compliant need to be closed if compliance isn’t met within a month. Enforcement of the Clean air, Clean water, RCRA and other regulations with severe immediate consequences must happen. This would have an immediate effect on our environmental degradation and on the US contribution to climate change. Don’t say it can’t be done. It can. Put people to work building an infrastructure for the future instead of export terminals for fossil fuels.

Tell President Obama and the head of the EPA: You KNOW. Now what will you do?

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24 Sep/15
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fracking Karen Dike

When I was trying to decide what to write for this occasion I saw another one of those commercials. You know the commercials? The ads that are from Noble or some other part of the industry. I thought: I know what I can do. I could do talk that is a version of 3 truths and a lie. 3 Truths and a Lie is an ice breaker game where you give three true facts about yourself and 1 lie. The rest of the team then decides what is true. Here’s my new game called: Many Lies and Little Truth. It should be a fun game. I will give you statements and you tell me truth or lie. Here we go. Yell out your answers.

By the way the punch line that those of us who are trying to stop fracking, get her goat, makes me feel a little crazy.

If you haven’t testified yet, go tell the EPA to listen to the truth, listen to scientists not industry lobbyists. Tell the EPA that fracking is never safe. The EPA needs to lead us to a future free from fossil fuel!

Let’s start with the commercial showing the cute woman who has an organic farm and raises goats and allows fracking on her land because it is so safe. Is fracking safe? Truth or lie? What I hear is that she does have an organic farm, does raise goats, she just leases her mineral rights that are not on her organic farm but allows the wells next to some other family.
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