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Archive for December, 2015

 

Multiple factors related to initial trial design may predict low patient accrual for cancer clinical trials

Reporter: Stephen J. Williams, Ph.D.

UPDATED 5/15/2019

A recently published paper in JCNI highlights results determining factors which may affect cancer trial patient accrual and the development of a predictive model of accrual issues based on those factors.

To hear a JCNI podcast on the paper click here

but below is a good posting from scienmag.com which describes their findings:

Factors predicting low patient accrual in cancer clinical trials

source: http://scienmag.com/factors-predicting-low-patient-accrual-in-cancer-clinical-trials/

Nearly one in four publicly sponsored cancer clinical trials fail to enroll enough participants to draw valid conclusions about treatments or techniques. Such trials represent a waste of scarce human and economic resources and contribute little to medical knowledge. Although many studies have investigated the perceived barriers to accrual from the patient or provider perspective, very few have taken a trial-level view and asked why certain trials are able to accrue patients faster than expected while others fail to attract even a fraction of the intended number of participants. According to a study published December 29 in the JNCI: Journal of the National Cancer Institute, a number of measurable trial characteristics are predictive of low patient accrual.

Caroline S. Bennette, M.P.H., Ph.D., of the Pharmaceutical Outcomes Research and Policy Program, University of Washington, Seattle, and colleagues from the University of Washington and the Fred Hutchinson Cancer Research Center analyzed information on 787 phase II/III clinical trials sponsored by the National Clinical Trials Network (NCTN; formerly the Cooperative Group Program) launched between 2000 and 2011. After excluding trials that closed because of toxicity or interim results, Bennette et al. found that 145 (18%) of NCTN trials closed with low accrual or were accruing at less than 50% of target accrual 3 years or more after opening.

The authors identified potential risk factors from the literature and interviews with clinical trial experts and found multiple trial-level factors that were associated with poor accrual to NCTN trials, such as increased competition for patients from currently ongoing trials, planning to enroll a higher proportion of the available patient population, and not evaluating a new investigational agent or targeted therapy. Bennette et al. then developed a multivariable prediction model of low accrual using 12 trial-level risk factors, which they reported had good agreement between predicted and observed risks of low accrual in a preliminary validation using 46 trials opened between 2012 and 2013.

The researchers conclude that “Systematically considering the overall influence of these factors could aid in the design and prioritization of future clinical trials…” and that this research provides a response to the recent directive from the Institute of Medicine to “improve selection, support, and completion of publicly funded cancer clinical trials.”

In an accompanying editorial, Derek Raghavan, M.D., Levine Cancer Institute, writes that the focus needs to be on getting more patients involved in trials, saying, “we should strive to improve trial enrollment, giving the associated potential for improved results. Whether the basis is incidental, because of case selection bias, or reflects the support available to trial patients has not been determined, but the fact remains that outcomes are better.”

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Contact info:

Article: Caroline S. Bennette, M.P.H., Ph.D., cb11@u.washington.edu

Editorial: Derek Raghavan, M.D., derek.raghavan@carolinashealthcare.org

Other investigators also feel that initial trial design is of UTMOST importance for other reasons, especially in the era of “precision” or “personalized” medicine and why the “basket trial” or one size fits all trial strategy is not always feasible.

In Why the Cancer Research Paradigm Must Transition to “N-of-1” Approach

Dr. Maurie Markman, MD gives insight into why the inital setup of a trial and the multi-center basket type of  accrual can be a problematic factor in obtaining meaningful cohorts of patients with the correct mutational spectrum.

The anticancer clinical research paradigm has rapidly evolved so that subject selection is increasingly based on the presence or absence of a particular molecular biomarker in the individual patient’s malignancy. Even where eligibility does not mandate the presence of specific biological features, tumor samples are commonly collected and an attempt is subsequently made to relate a particular outcome (eg, complete or partial objective response rate; progression-free or overall survival) to the individual cancer’s molecular characteristics.

One important result of this effort has been the recognition that there are an increasing number of patient subsets within what was previously—and incorrectly—considered a much larger homogenous patient population; for example, non–small cell lung cancer (NSCLC) versus EGFR-mutation–positive NSCLC. And, while it may still be possible to conduct phase III randomized trials involving a relatively limited percentage of patients within a large malignant entity, extensive and quite expensive effort may be required to complete this task. For example, the industry-sponsored phase III trial comparing first-line crizotinib with chemotherapy (pemetrexed plus either carboplatin or cisplatin) in ALK-rearrangement–positive NSCLC, which constitutes 3% to 5% of NSCLCs, required an international multicenter effort lasting 2.5 years to accrue the required number of research subjects.1

But what if an investigator, research team, or biotech company desired to examine the clinical utility of an antineoplastic in a patient population representing an even smaller proportion of patients with NSCLC such as in the 1% of the patient population with ROS1 abnormalities,2 or in a larger percentage of patients representing 4%-6% of patients with a less common tumor type such as ovarian cancer? How realistic is it that such a randomized trial could ever be conducted?

Further, considering the resources required to initiate and successfully conduct a multicenter international phase III registration study, it is more than likely that in the near future only the largest pharmaceutical companies will be in a position to definitively test the clinical utility of an antineoplastic in a given clinical situation.

One proposal to begin to explore the benefits of targeted antineoplastics in the setting of specific molecular abnormalities has been to develop a socalled “basket trial” where patients with different types of cancers with varying treatment histories may be permitted entry, assuming a well-defined molecular target is present within their cancer. Of interest, several pharmaceutical companies have initiated such clinical research efforts.

Yet although basket trials represent an important research advance, they may not provide the answer to the molecular complexities of cancer that many investigators believe they will. The research establishment will have to take another step toward innovation to “N-of-1” designs that truly explore the unique nature of each individual’s cancer.

Trial Illustrates Weaknesses

A recent report of the results of one multicenter basket trial focused on thoracic cancers demonstrates both the strengths but also a major fundamental weakness of the basket trial approach.3

However, the investigators were forced to conclude that despite accrual of more than 600 patients onto a study conducted at two centers over a period of approximately 2 years, “this basket trial design was not feasible for many of the arms with rare mutations.”3

They concluded that they needed a larger number of participating institutions and the ability to adapt the design for different drugs and mutations. So the question to be asked is as follows: Is the basket-type approach the only alternative to evaluate the clinical relevance of a targeted antineoplastic in the presence of a specific molecular abnormality?

Of course, the correct answer to this question is surely: No!

– See more at: http://www.onclive.com/publications/Oncology-live/2015/July-2015/Why-the-Cancer-Research-Paradigm-Must-Transition-to-N-of-1-Approach#sthash.kLGwNzi3.dpuf

The following is a video on the website ClinicalTrials.gov which is a one-stop service called EveryClinicalTrial to easily register new clinical trials and streamline the process:

 

UPDATED 5/15/2019

Another possible roadblock to patient accrual has always been the fragmentation of information concerning the availability of clinical trails and coordinating access among the various trial centers, as well as performing analytics on trial data to direct new therapeutic directions.  The NIH has attempted to circumvent this problem with the cancer trials webpage trials.gov however going through the vast number of trials, patient accrual requirements, and finding contact information is a daunting task.  However certain clinical trial marketplaces are now being developed which may ease access problems to clinical trials as well as data analytic issues, as highlighted by the Scientist.com article below:

Scientist.com Launches Trial Insights, A Transformative Clinical Trials Data Analytics Solution

The world’s largest online marketplace rolls out first original service, empowering researchers with on demand insights into clinical trials to help drive therapeutic decisions

SAN DIEGO–(BUSINESS WIRE)–Scientist.com, the online marketplace for outsourced research, announced today the launch of Trial Insights, a digital reporting solution that simplifies data produced through clinical trial, biomarker and medical diagnostic studies into an intuitive and user-friendly dashboard. The first of its kind, Trial Insights curates publicly available data nightly from information hubs such as clinicaltrials.gov and customizes it to fit a researcher or research organization’s specific project needs.

Trial Insights, new clinical trial reporting solution, allows researchers to keep track of the evolving landscape of drugs, diseases, sponsors, investigators and medical devices important to their work.

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“Trial Insights offers researchers an easy way to navigate the complexity of clinical trials information,” said Ron Ranauro, Founder of Incite Advisors. “Since Trial Insights’ content is digitally curated, researchers can continuously keep track of the evolving landscape of drugs, diseases, sponsors, investigators and medical devices important to their work.”

As the velocity, variety and veracity of data available on sites like clinicaltrials.gov continues to increase, the ability to curate it becomes more valuable to different audiences. With the advancement of personalized medicine, it is important to make the data accessible to the health care and patient communities. Information found on the Trial Insights platform can help guide decision making across the pharmaceutical, biotechnology and contract research organization industries as clinical trial data is a primary information source for competitive intelligence, research planning and clinical study planning.

“We are extremely excited to launch the first Scientist.com exclusive, original service offering to our clients in the life sciences,” said Mark Herbert, Scientist.com Chief Business Officer. “Our goal at Scientist.com is to help cure all diseases by 2050, and we believe solutions like Trial Insights, which greatly simplifies access to and reporting of clinical trial data, will get us one step closer to reaching that goal.”

source: https://www.businesswire.com/news/home/20190416005362/en/Scientist.com-Launches-Trial-Insights-Transformative-Clinical-Trials?utm_source=TrialIO+List

 

Other article on this Open Access Journal on Cancer Clinical Trial Design include:

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See the fireworks Leaders in Pharmaceutical Business Intelligence created by blogging on WordPress.com. Check out their 2015 annual report.

Source: See the #fireworks I created by blogging on #WordPressDotCom. My 2015 annual report.

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Circadian cycles shift as humans get older—sleep and body temperature patterns change, for instance. The rhythmic cycling of numerous genes’ expression in the brain also shifts as people age, researchers reported this week (December 21) inPNAS. The levels of many transcripts became less robust in their daily ups and downs, while another set of mRNAs emerged with a rhythmicity not seen in younger counterparts.

“You can imagine that things actually get weaker with age, but that things can get stronger with age is really exciting,” Doris Kretzschmar, a neuroscientist at the Oregon Institute of Occupational Health Sciences who was not involved in the study, told NPR’s Shots.

The researchers, led by Colleen McClung at the University of Pittsburgh School of Medicine in Pennsylvania, collected cortical tissue from people whose hour of death was known. Comparing gene expression levels between 31 subjects under 40 years old and 37 subjects over age 60, the researchers found 1,063 transcripts in one part of the prefrontal cortex that lost rhythmicity altogether in the older group. In this same part of the brain, 434 genes gained a rhythm that was not seen among younger individuals. In another part of the prefrontal cortex, 588 genes lost their daily cycling with age, while 533 became rhythmic.

It’s not clear what these changes in expression cycles might mean for health and aging. “Since depression is associated with accelerated molecular aging, and with disruptions in daily routines, these results also may shed light on molecular changes occurring in adults with depression,” coauthor Etienne Sibille of the University of Toronto said in a press release.

Sourced through Scoop.it from: www.the-scientist.com

See on Scoop.itCardiovascular and vascular imaging

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Century of PNAS

Century of PNAS

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

The Engineering of Biology and Medicine

SPECIAL FEATURE: INTRODUCTION  1915-2015

Mark E. Davisa,1 and Robert Langerb,1
a Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and b Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
http://www.pnas.org/content/112/47/14423.full.pdf

In celebration of the 100th Anniversary of PNAS, this Special Feature summarizes the enormous progress that has been made in the engineering of biology and medicine. In 1915, PNAS published articles, such as “A comparison of methods for determining the respiratory exchange of man,” by T. M. Carpenter (1), “The lymphocyte as a factor in natural and induced resistance to transplanted cancer,” by J. B. Murphy and J. J. Morton (2), and “Mechanism of protection against bacterial infection,” by C. G. Bull (3). It is fascinating to look back at these early studies and see how much progress has been made in the engineering of biology and medicine. Biology and medicine have been transformed from descriptive science and art to quantitative, mechanistic understandings of function, primarily because of the elucidation of biology at the molecular level. These advancements have led to the creation of new drugs, vaccines, devices, diagnostics, and imaging agents that significantly contribute to life saving and life extension. In this Special Feature, a variety of topics are presented to highlight the current state of the art and possible future scenarios for the engineering of biology and medicine. We thank PNAS for publishing together these state-of-the art reviews, as we feel that this Special Feature will provide a useful reference for those in field—as well as those out of field—who are seeking to understand where the engineering of biology and medicine is likely to be in the future.

 

1 Carpenter TM (1915) A comparison of methods for determining the respiratory exchange of man. Proc Natl Acad Sci USA 1(12):602–605.

2 Murphy JB, Morton JJ (1915) The lymphocyte as a factor in natural and induced resistance to transplanted cancer. Proc Natl Acad Sci USA 1(4): 435–437.

3 Bull CG (1915) Mechanism of protection against bacterial infection. Proc Natl Acad Sci USA 1(11):545–546.

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p53 tumor drug resistance mechanism target

Larry H Bernstein, MD, FCAP, Curator

LPBI

 

Biologists unravel drug-resistance mechanism in tumor cells

Targeting the RNA-binding protein that promotes resistance could lead to better cancer therapies.

 

P53, which helps healthy cells prevent genetic mutations, is missing from about half of all tumors. Researchers have found that a backup system takes over when p53 is disabled and encourages cancer cells to continue dividing. In the background of this illustration are crystal structures of p53 DNA-binding domains.

http://news.mit.edu/sites/mit.edu.newsoffice/files/styles/news_article_image_top_slideshow/public/images/2015/MIT-Cancer-Drug-Resistance_0.jpg

 

P53, which helps healthy cells prevent genetic mutations, is missing from about half of all tumors. Researchers have found that a backup system takes over when p53 is disabled and encourages cancer cells to continue dividing. In the background of this illustration are crystal structures of p53 DNA-binding domains.

Image: Jose-Luis Olivares/MIT (p53 illustration by Richard Wheeler/Wikimedia Commons)

About half of all tumors are missing a gene called p53, which helps healthy cells prevent genetic mutations. Many of these tumors develop resistance to chemotherapy drugs that kill cells by damaging their DNA.

MIT cancer biologists have now discovered how this happens: A backup system that takes over when p53 is disabled encourages cancer cells to continue dividing even when they have suffered extensive DNA damage. The researchers also discovered that an RNA-binding protein called hnRNPA0 is a key player in this pathway.

“I would argue that this particular RNA-binding protein is really what makes tumor cells resistant to being killed by chemotherapy when p53 is not around,” says Michael Yaffe, the David H. Koch Professor in Science, a member of the Koch Institute for Integrative Cancer Research, and the senior author of the study, which appears in the Oct. 22 issue of Cancer Cell.

The findings suggest that shutting off this backup system could make p53-deficient tumors much more susceptible to chemotherapy. It may also be possible to predict which patients are most likely to benefit from chemotherapy and which will not, by measuring how active this system is in patients’ tumors.

Rewired for resistance

In healthy cells, p53 oversees the cell division process, halting division if necessary to repair damaged DNA. If the damage is too great, p53 induces the cell to undergo programmed cell death.

In many cancer cells, if p53 is lost, cells undergo a rewiring process in which a backup system, known as the MK2 pathway, takes over part of p53’s function. The MK2 pathway allows cells to repair DNA damage and continue dividing, but does not force cells to undergo cell suicide if the damage is too great. This allows cancer cells to continue growing unchecked after chemotherapy treatment.

“It only rescues the bad parts of p53’s function, but it doesn’t rescue the part of p53’s function that you would want, which is killing the tumor cells,” says Yaffe, who first discovered this backup system in 2013.

In the new study, the researchers delved further into the pathway and found that the MK2 protein exerts control by activating the hnRNPA0 RNA-binding protein.

RNA-binding proteins are proteins that bind to RNA and help control many aspects of gene expression. For example, some RNA-binding proteins bind to messenger RNA (mRNA), which carries genetic information copied from DNA. This binding stabilizes the mRNA and helps it stick around longer so the protein it codes for will be produced in larger quantities.

“RNA-binding proteins, as a class, are becoming more appreciated as something that’s important for response to cancer therapy. But the mechanistic details of how those function at the molecular level are not known at all, apart from this one,” says Ian Cannell, a research scientist at the Koch Institute and the lead author of the Cancer Cell paper.

In this paper, Cannell found that hnRNPA0 takes charge at two different checkpoints in the cell division process. In healthy cells, these checkpoints allow the cell to pause to repair genetic abnormalities that may have been introduced during the copying of chromosomes.

One of these checkpoints, known as G2/M, is controlled by a protein called Gadd45, which is normally activated by p53. In lung cancer cells without p53, hnRNPA0 stabilizes mRNA coding for Gadd45. At another checkpoint called G1/S, p53 normally turns on a protein called p21. When p53 is missing, hnRNPA0 stabilizes mRNA for a protein called p27, a backup to p21. Together, Gadd45 and p27 help cancer cells to pause the cell cycle and repair DNA so they can continue dividing.

Personalized medicine

The researchers also found that measuring the levels of mRNA for Gadd45 and p27 could help predict patients’ response to chemotherapy. In a clinical trial of patients with stage 2 lung tumors, they found that patients who responded best had low levels of both of those mRNAs. Those with high levels did not benefit from chemotherapy.

“You could measure the RNAs that this pathway controls, in patient samples, and use that as a surrogate for the presence or absence of this pathway,” Yaffe says. “In this trial, it was very good at predicting which patients responded to chemotherapy and which patients didn’t.”

“The most exciting thing about this study is that it not only fills in gaps in our understanding of how p53-deficient lung cancer cells become resistant to chemotherapy, it also identifies actionable events to target and could help us to identify which patients will respond best to cisplatin, which is a very toxic and harsh drug,” says Daniel Durocher, a senior investigator at the Samuel Lunenfeld Research Institute of Mount Sinai Hospital in Toronto, who was not part of the research team.

The MK2 pathway could also be a good target for new drugs that could make tumors more susceptible to DNA-damaging chemotherapy drugs. Yaffe’s lab is now testing potential drugs in mice, including nanoparticle-based sponges that would soak up all of the RNA binding protein so it could no longer promote cell survival.

This work was supported in part by the Charles and Marjorie Holloway Foundation.

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PCT – The International Patent System

Curator: Yossi Mograbi

From: Yossi Mograbi <yossi@vit4pro.com>

Date: Wednesday, December 23, 2015 at 8:31 AM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>, Gerard Loiseau <gerard.loiseau@bluewin.ch>

Subject: IP

http://www.wipo.int/pct/en/

https://en.wikipedia.org/wiki/Patent_Cooperation_Treaty

http://www.wipo.int/wipo_magazine/en/2005/05/article_0006.html

http://www.bios.net/daisy/patentlens/2768.html

https://en.wikipedia.org/wiki/Patent_infringement

https://en.wikipedia.org/wiki/Composition_of_matter

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OpenAI: $1 Billion to Create Artificial Intelligence Without Profit Motive by Who is Who in the Silicon Valley

Reporter: Aviva Lev-Ari, PhD, RN

3.4.12

3.4.12   OpenAI: $1 Billion to Create Artificial Intelligence Without Profit Motive by Who is Who in the Silicon Valley, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 3: AI in Medicine

Silicon Valley Kingpins Commit $1 Billion to Create Artificial Intelligence Without Profit Motive

SOURCE

http://blogs.wsj.com/digits/2015/12/11/silicon-valley-kingpins-commit-1-billion-to-create-artificial-intelligence-without-profit-motive/

Elon Musk, head of electric (and increasingly autonomous) car maker Tesla, launched a non-profit artificial intelligence research firm on Dec. 11 with other Silicon Valley giants including Peter Thiel and Reid Hoffman,

The fledgling company has already attracted a handful of AI researchers. Ilya Sutskever left Google’s deep learning group to be the research director of OpenAI.

“I wish Ilya well in his new endeavor,” said Geoff Hinton, a leading AI researcher who works at Google. He declined to comment further, as did a Google spokesman.

A group of deep-pocketed Silicon Valley investors committed $1 billion to ensure that artificial intelligence serves societal needs rather than commercial interests.

The commitment announced on Friday will fund a non-profit research firm called OpenAI Inc., where researchers will be unencumbered by the pressures of for-profit companies and grant-writing duties of academia.

On its website, the group suggested that companies dedicated to pleasing shareholders should not be allowed to control the future of AI. “Our aim is to build value for everyone rather than shareholders,” the group said.

The announcement follows a string of moves on the part of commercial companies to make AI technology available on a noncommercial basis. Facebook Inc.FB +0.37%, Google, and International Business Machines Corp.IBM -0.21% recently donated portions of their formerly proprietary AI software through an open source license, which allows the technology to be freely used, shared, and modified.

At the same time, several funders of OpenAI have business interests in developing artificial intelligence. How OpenAI’s efforts would dovetail with their commercial priorities is not clear.

The group’s backers include A-list entrepreneurs including Tesla Motors Inc.TSLA +0.38% CEO Elon Musk, Y Combinator President Sam Altman, LinkedIn Corp.LNKD +0.03% co-founder Reid Hoffman, venture capitalist Peter Thiel and Jessica Livingston, a Y Combinator partner.

SOURCE

http://blogs.wsj.com/digits/2015/12/11/silicon-valley-kingpins-commit-1-billion-to-create-artificial-intelligence-without-profit-motive/

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New data published in Hepatology showed that beta-blockers lowered portal pressure in patients with clinically significant portal hypertension, suggesting they could prevent decompensation of cirrhosis in this patient population.

Sourced through Scoop.it from: www.healio.com

See on Scoop.itCardiovascular Disease: PHARMACO-THERAPY

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Beta-blocker use in ST-segment elevation myocardial infarction in the reperfusion era (GRACE). – PubMed – NCBI

Reporter: Aviva Lev-Ari, PhD, RN

 

Am J Med. 2014 Jun;127(6):503-11. doi: 10.1016/j.amjmed.2014.02.009. Epub 2014 Feb 18. Multicenter Study; Observational Study; Research Support, Non-U.S. Gov’t

Beta-blocker use in ST-segment elevation myocardial infarction in the reperfusion era (GRACE)

Affiliations 

Abstract

Background: Current guidelines recommend early oral beta-blocker administration in the management of acute coronary syndromes for patients who are not at high risk of complications.

Methods: Data from patients enrolled between 2000 and 2007 in the Global Registry of Acute Coronary Events (GRACE) were used to evaluate hospital outcomes in 3 cohorts of patients admitted with ST-elevation myocardial infarction, based on beta-blocker use (early [first 24 hours] intravenous (IV) [± oral], only early oral, or delayed [after first 24 hours]).

Results: Among 13,110 patients with ST-elevation myocardial infarction, 21% received any early IV beta-blockers, 65% received only early oral beta-blockers, and 14% received delayed (>24 hours) beta-blockers. Higher systolic blood pressure, higher heart rate, and chronic beta-blocker use were independent predictors of early beta-blocker use. Early beta-blocker use was less likely in older patients, patients with moderate to severe left ventricular dysfunction, and in those presenting with inferior myocardial infarction or Killip class II or III heart failure. IV beta-blocker use and delayed beta-blocker use were associated with higher rates of cardiogenic shock, sustained ventricular fibrillation/ventricular tachycardia, and acute heart failure, compared with oral beta-blocker use. In-hospital mortality was increased with IV beta-blocker use (propensity score adjusted odds ratio, 1.41; 95% confidence interval, 1.03-1.92) but significantly reduced with delayed beta-blocker administration (propensity adjusted odds ratio, 0.44; 95% confidence interval, 0.26-0.74).

Conclusions: Early beta-blocker use is common in patients presenting with ST-elevation myocardial infarction, with oral administration being the most prevalent. Oral beta-blockers were associated with a decrease in the risk of cardiogenic shock, ventricular arrhythmias, and acute heart failure. However, the early receipt of any form of beta-blockers was associated with an increase in hospital mortality.

Keywords: Clinical outcomes; Intravenous beta-blockers; Oral beta-blockers; ST-elevation myocardial infarction.

Sourced through Scoop.it from: www.ncbi.nlm.nih.gov

See on Scoop.itCardiovascular Disease: PHARMACO-THERAPY

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Medical Treatment for Angina

Reporter: Aviva Lev-Ari, PhD, RN

 

 

 

 

The medical treatment for angina and ischemia include drugs such as nitrates, beta blockers, calcium blockers and Ranexa, as well as non-drug therapy like exercise training and EECP.

Sourced through Scoop.it from: heartdisease.about.com

See on Scoop.itCardiovascular Disease: PHARMACO-THERAPY

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