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A wake-up call on HIV/AIDS

Posted on Dec 11, 2014 9:54:33 AM


By Moss Stern

On November 24, 2014, the Centers for Disease Control and Prevention (CDC) published the results of a comprehensive 2011 study on HIV diagnosis and treatment showing that out of the estimated 1.2 million persons living with HIV in the United States in 2011, 86% had been diagnosed; 40% were engaged in HIV medical care; 37% were using antiretroviral therapy (ART); and 30% had achieved successful viral suppression. These statistics had remained relatively unchanged since 2009, and presumably have not improved substantially since.

That’s right: while people with HIV who are using ART can achieve a very low viral load, can look forward to a nearly normal life expectancy, and pose a very low risk for transmitting HIV to others, only 30% of infected Americans have attained successful suppression. The other 70% of infected Americans (839,336) have not been so fortunate.

Younger people are particularly at risk: the report noted that viral suppression was significantly less prevalent among persons aged 18–24 years (13%), 25–34 years (23%), and 35–44 years (27%) compared with those aged ≥65 years (37%). Meanwhile, according to the same report, nearly 50,000 persons in the U.S. become newly infected each year.

The authors of the CDC study concluded that significant improvements are still needed across the HIV care continuum, and that state and local health departments, community-based organizations, and health care providers all have essential roles to play in improving outcomes. They emphasized that the greatest opportunities lie in reducing the number of undiagnosed HIV infections, and increasing the percentage of infected persons who are actively engaged in care.

It is sometimes tempting to think that ever since the advent of ART, the HIV epidemic is under control. This is far from the case. It behooves every health professional to be aware that the battle still rages on, and that HIV education and engagement must remain a vital aspect of caring for every patient.


Top 5 mobile apps in Cardiology

Posted on Nov 21, 2014 5:30:00 AM

cardiology app search
by Moss Stern

There has been enthusiastic interest in our previous posts reviewing the top 20 apps across all of medicine as well as the top apps in Hematology and Oncology. This week, we turn our attention to our favorite apps in Cardiology. These apps represent valuable clinical reference sources, patient education tools, and calculators – all designed to make practice easier for busy cardiologists.

Look for more app highlights in other specialties coming soon...tell us what you think…and let us know if we've overlooked any apps that you find valuable!

1. 5 star user rating This app represents an extremely convenient and effective way for cardiologists to stay current. It includes informative and frequently updated news articles, summaries of both newer and older clinical trials, and a "radio station" that houses audio podcasts from the likes of Drs. Eric Topol and Paul Teirstein. The functionality is superb, the content is impressive, and the app is free. Highly recommended!

2. Cardiology Tool by Epocrates5 star user rating

Cardiology Tool by Epocrates Epocrates’ Cardiology Tool makes it simple to perform all of the most frequently used calculations in this specialty. Its design is clean, straightforward, and effective. Both residents and experienced practitioners will find it very helpful.

3. EP Mobile5 star user rating

EP Mobile A very well-designed toolkit for cardiac electrophysiology, this app is comprised of a variety of free-standing calculators, diagnostic algorithms, references and tools, and risk scores for various heart conditions. Judging from its many enthusiastic user reviews, EP Mobile has been eagerly embraced as a helpful mobile reference source by many clinicians who work with arrhythmia patients.

4. Heartpedia5 star user rating

Heartpedia Help your patients and their caregivers understand congenital heart defects and their treatment! This well-constructed app allows them to see a 3-D model of a normal heart, a heart that features a particular defect, and a repaired heart – and rotate each model to view it from every side. You can also select cross-sectional views; hide/show labels; pull up a condition’s signs and symptoms, diagnosis, and treatment; and watch videos that provide additional explanations and animations.

5. ECG Guide5 star user rating

ECG Guide This powerful app is a complete ECG textbook, collection of samples, self-assessment quiz, and interpretation tool in one source. It explains the basics of electrocardiography, the principles of interpretation, waves and segments, and the appearance of a normal ECG as well as of the full range of adult and pediatric conditions. 200 sample tracings allow comparison to those seen in practice, and practice quizzes test your skills. Finally, a built-in guide helps you systematically interpret any ECG by asking you questions about a patient's heart rate, P waves, QRS width, and other factors.

cardiology app center

Tags: Cardiology, Cardio, cardiology app

Recommended Mobile Apps in Oncology and Hematology

Posted on Oct 31, 2014 5:00:00 AM

by Moss Stern

Recently we brought you a list of the Top 20 Medical Apps Reviewed by MDLinx. Those apps were selected for their broad appeal across all medical specialties. The response to that post was very enthusiastic, so we've decided to explore some of the apps we like within individual specialties.

In this week's post, we will highlight the most promising apps in Oncology and Hematology. These apps offer valuable, on-the-go answers on overall topics in cancer…decision making in therapeutics…radiation oncology…blood cell morphology…and genetic targets for cancer treatment.

Look for more app highlights in other specialties coming soon…tell us what you think…and let us know if we've overlooked any apps that you find valuable!

1. CancerRx

CancerRx Clinical decision making in oncology is a challenge of monumental complexity, and while the ever-expanding scientific understanding of cancer genetics continually offers new hopes for more precisely targeted therapies, it also places an onus on clinicians to take these expanded options into consideration.

CancerRx is designed to guide therapeutic decision making in an algorithmic fashion. Focusing on lung cancer, melanoma, metastatic breast cancer, and colorectal cancer, it poses a series of questions to guide users to the best evidence-based therapy recommendations for each patient. All the user reviews have been highly positive, and clearly these reviewers have found it a very helpful clinical tool. As long as the developers continue updating the app with new information, it should continue to be, in the words of one user, "a life saver."

2. Cancer Management Handbook

Cancer Management Handbook An organized, easy-to-use format classifies cancers according to type and body area, and then provides concise summaries of epidemiology, etiology and risk factors, signs and symptoms, diagnosis, screening and surveillance, pathology, staging and prognosis, treatment, and suggested readings. Four appendices provide additional useful content such as the Karnofsky performance index and newly approved cancer agents. All of this serves as an accessible, multidisciplinary compendium of information that's ideal for clinicians, students, and even patients.

3. Rad Onc Resource

Rad Onc Resource This app is designed to help radiation oncologists make important calculations and clinical decisions. It allows users to calculate tissue tolerance for a variety of vulnerable areas using conventional fractionation or hypofractionation; estimate breast cancer recurrence risk and prostate risk; calculate biological effective dose; estimate mortality risk using the Schonberg Index; and also follow a link to the Radiation Oncology Wiki, a complete, open-source radiation oncology reference.

In addition, by signing in via email or Twitter, users can join a community of radiation oncologists, converse in a chat room, and exchange messages. This should make it easier to consult with colleagues and compare notes. Many users have rated Rad Onc Resource highly and have applauded its clinical utility. It appears to successfully fill an important need in the field.

4. Cancer.Net Mobile

Cancer.Net Mobile Upon being diagnosed with cancer, patients and their caregivers must quickly begin navigating a complex and unfamiliar terrain of issues and stressors. Cancer.Net Mobile is designed to serve as a resource for these individuals. A mobile version of ASCO's Cancer.Net website, it offers a wealth of information and advice on everything from managing one's cancer, side effects, and the costs of cancer, through emotional and physical dimensions, relationships, survivorship, and more.

The app also allows users to select their particular cancer type and then review the relevant statistics, risk factors, symptoms and signs, diagnostic process, staging, treatment, side effects, post-treatment monitoring, current research, and questions to ask. In addition, there are sections for writing down one's own questions for the doctor, recording what medications one is taking, recording one's symptoms, and reading an RSS feed from ASCO on a wide range of cancer topics.

While Cancer.Net Mobile can't begin to answer every conceivable question or address every patient's concerns, it will go a long way towards helping them prepare to face this difficult journey.

5. CellAtlas

CellAtlas Residents and medical students studying the basics of blood cell morphology will find this an efficient, portable learning tool. Concise, well-illustrated lectures walk users through the various types of hematopoiesis, the range of normal findings in peripheral blood, abnormal findings, and erythrocytes. Then, the “CellQuiz” part of the app challenges you to visually identify various types of blood cells as seen on microscope slides. It all adds up to a well-constructed, high-yield review of the subject matter.

6. My Cancer Genome

My Cancer Genome Individualized medicine holds great potential for genetically targeted treatments. The My Cancer Genome app was designed to help clinicians navigate the labyrinth of diseases, genes, variants, antineoplastic agents, and targets. The staff at are continuously updating and adding to this content, theoretically ensuring that users always have access to the most current information.

To find out about other Oncology mobile apps that we recommend, browse our Oncology App Center!

oncology app center

Tags: mobile apps, oncology apps

Top 20 Medical Apps Reviewed by MDLinx

Posted on Sep 30, 2014 9:26:00 AM

by Moss Stern

Here at MDLinx, we are excited by the possibilities afforded by mobile applications in healthcare. At their best, they enable clinicians to look up information more quickly and conveniently, perform calculations more easily, record data on the fly, and thus save precious time. Some also challenge clinicians’ clinical knowledge and skills, helping them become better practitioners. It is our privilege to review some of the latest and most useful medical apps, and recommend those that we think clinicians will find most helpful.

Here, we’ve compiled a list of our 20 favorite medical apps that have the broadest appeal. We hope you enjoy them!

1. Epocrates Clinical Reference

Epocrates Easy to navigate and quick to use, Epocrates may just be the gold standard every medical app should be measured against. A veritable “Swiss army knife” of indispensable tools, it offers drug information, a provider directory, calculators, and a myriad of tables organized by medical specialty. Drug information includes formulary coverage, alternative drugs, drug interactions, dosages, contraindications, pharmacology, safety information, and pill ID. DocAlert messages provide clinical alerts, government safety alerts, medically relevant tips on practice management, and guideline updates. A must-have.

2. Medscape from WebMD Clinical Reference

Medscape from WebM This app is a quick and efficient way to access medical information from It allows you to read the latest news across 30+ medical specialties; look up adult and pediatric drug dosing information in seconds; access 129 medical calculators covering formulas, scales, and classifications; and complete accredited CME/CE courses for professional development – all in one place.

3. Read: Personalized Medical & Scientific Journal Clinical Reference

Read: Personalized Medical & Scientific Journal Keeping up with your reading is a major challenge. So many articles, so little time! Read by QXMD allows you to keep up with your topics of interest in one app. Simply enter your specialty, areas of interest, and preferred medical and scientific journals, and it grabs the content relevant to those interests and sources and enables you to read it all in one place — with a very clean, intuitive user interface. Read succeeds admirably in consolidating the key medical news that you need. It is highly recommended.

4. Medication Guide Clinical Reference Medication Medication Guide lets you look up FDA monographs for any drug name; look up drugs by condition or class; search a database of side effects to see what drugs can cause them; check interactions; obtain pregnancy and breastfeeding safety information; look up dosages; and even search a database of symptoms. Its drug monographs include links to recent clinical trial results, FDA alerts, and other relevant news. It also lets you record what drugs you are taking and contains a pill identifier tool.

5. Diagnose Clinical Reference

Diagnose Determine the statistical probability, based on the available evidence, that a given patient has a particular ailment. You simply check whether they are positive or negative for a list of examination criteria and diagnostic tests, and it hands you a probability percentage at the end. The interface is simple and functional, and assuming the data are reliable, in theory this app should lead you to a higher degree of diagnostic certainty. The range of conditions is very extensive, from childhood otitis media and influenza to blunt intra-abdominal trauma, ectopic pregnancy, ACL knee injury, and malaria.

6. ICD 10 On the Go Medical Codes Clinical Reference

ICD 10 On the Go Medical Codes Distinctly easy to use, ICD 10 On the Go Medical Codes lets you look up diagnostic codes in seconds. You can star frequently-used diagnoses as "favorites" so as to find those codes even more rapidly. And you can email any code or print it out. It's hard to imagine a better app for quick ICD-10 lookup than this one. It is highly recommended.

7. LactMed Clinical Reference

LactMed To the extent that women and their doctors have reported on their experiences with drugs and breastfeeding, or that drug levels in maternal milk have been tested, or that anything else is known about various drugs' lactation safety, those data have made their way into the National Library of Medicine's Toxicology Data Network database, and thus into LactMed – probably the most complete and current mobile source of information on drugs' safety for breastfeeding mothers.

8. Wilderness First Aid App Clinical Reference

Wilderness First Aid App Wilderness excursions can lead you to places of exotic beauty...and sometimes serious danger. Whether you are kayaking, hiking, skiing, or otherwise enjoying the great outdoors, it’s best to be prepared for trouble. The Wilderness First Aid App is a good portable source on everything from altitude illness to frostbite, diabetic emergencies, head trauma, bites and stings, trauma, wound care, and much more. It could be a life saver for people with all levels of medical training. Hopefully you’ll never need to use it, but if you do, you’ll be glad to have it on your phone.

9. CDC Blast Injury Clinical Reference

CDC Blast Injury Blast injuries are unfortunately among the problems that all healthcare providers must be prepared to face. This app from the CDC equips you to understand and prepare for blast injuries and explosive events, and assess and treat explosive injuries to the head and torso, musculoskeletal trauma, and other blast-related conditions. CDC Blast Injury also works when Wi-Fi is even if your hospital or trauma center has lost power, you can still look up the answers you need.

10. Epocrates Bugs + Drugs Clinical Reference

Epocrates Bugs + Drugs This colorful app collects data from hospitals in your geographical region, to make you aware of how many cases of a given infectious agent ("bugs") have been reported within a particular time frame, and summarizes the various drugs you can use to treat these infections.

11. CDC Vaccine Schedules Clinical Reference

CDC Vaccine Schedules This app from the CDC provides at-a-glance access to recommended vaccination schedules for children, adolescents, and adults. You can also look up specific indications for different patient populations (pregnancy, immunocompromising conditions, HIV infection, heart disease, etc.), as well as contraindications for individual immunizations. CDC Vaccine Schedules is recommended to all healthcare providers who are responsible for keeping patients' immunizations up to date.

12. Medical Doctor: Reference Tool Clinical Reference

Medical Doctor: Reference Tool A surprisingly practical and well-organized collection of information that would be valuable to medical students and residents as well as nurses and physician assistants. Six sections cover H&P, Sounds, Lab Values, Pediatrics, Obstetrics, and Notes & Orders. Each section uses a series of tabs to efficiently convey a large amount of important clinical data. A succinct and accessible design makes it easy to prepare for rounds or look up quick answers in the clinical setting.

13. X-Anatomy Anatomy

X-Anatomy This app is a terrific tool for learning normal cross-sectional CT anatomy in the transverse plane. You can move a slider up and down to see all the structures visible within a particular cross-sectional view. By double-tapping on any area you can enlarge it, and if you tap on a structure, an identifying label appears – often accompanied by additional anatomy notes. X-Anatomy basically puts a powerful interactive CT simulation on your mobile device so you can study it at will. It is highly recommended to all medical professionals who need a strong working familiarity with cross-sectional anatomy.

14. Essential Anatomy 2 Anatomy

Essential Anatomy 2 This is a fully interactive, 3-dimensional anatomical model for learning and reference purposes. You can view any body system, rotate it in any direction, zoom in and out, hide and reveal structures as desired, and tap on individual structures to have them identified and explained. Given the decreased time and resources being devoted to cadaver dissection today, medical students need resources of this quality to supplement their study. Despite the glaring omission of the male and female reproductive systems, Essential Anatomy 3 is nonetheless a fascinating and enjoyable learning tool.

15. Skeleton System Pro III Anatomy

Skeleton System Pro III This app gives you a very detailed 3-D model of the human skeleton, with the ability to rotate every structure in any direction, zoom in to specific skeletal regions, view cross sections of certain structures, view/hide pins identifying specific features (and add your own), add and remove layers, locate structures based on an alphabetical index, and take quizzes. You can also draw on structures and write comments with your fingertip. This opens up great possibilities for instruction and patient education.

16. Clinical Sense Study Tool

Clinical Sense Clinical Sense tests your clinical decision making when faced with a variety of clinical situations. While each scenario goes by quickly, it still confronts you with several decisions that have significant implications for the care of the hypothetical patient. It's a good way to test your familiarity with a wide range of clinical practice guidelines having to do with conditions such as diabetes, heart disease, suspected breast cancer, and obstetrical emergencies. When you make a wrong decision, the scenarios end in various calamitous ways, and you are presented with an explanation of what you did incorrectly as well as references to standard sources in the literature.

17. Resuscitation! Study Tool

Resuscitation! Test your clinical decision-making skills in a variety of patient simulations. In each case, you are presented with data on a patient’s H&P, then asked to formulate possible diagnoses, choose tests, initiate interventions, and make decisions concerning patient disposition. At the end, you receive feedback on your decisions as well as your correct, neutral, and incorrect actions. This culminates in a numerical score, which you can use to compete with your friends.

18. Ward Round Study Tool

Ward Round A fun and challenging way to test your readiness for clinical rounds! Quick case simulations challenge you to interpret clinical information and make the right decisions. You get only 12 seconds to answer each question, and then receive immediate feedback on which answer was correct and why. At the end, you receive a percentage score based on how many questions you answered correctly. 12 seconds isn’t a lot of time to respond, but that is what makes Ward Round both entertaining and effective...because to get good scores, you really need to have the answers top-of-mind!

19. HealthTap for U.S. Doctors Telemedicine

HealthTap for U.S. Doctors This is a networking tool that has the potential to transform healthcare. It gives you a ready-made platform for practicing telemedicine, providing patients across geographies with paid video consultations at your own convenience, collaborating with fellow practitioners, and more. All physicians who have the time, passion, and energy to help more patients should consider joining; and the iOS and Android apps make it easy to interact with HealthTap on your mobile device.

20. SharePractice Social Media

SharePractice This social media app lets you see how highly your fellow users have rated various treatments on a five-star scale, add treatments and ratings of your own, and participate in discussions. It’s essentially a way of crowdsourcing clinical consults with your peers. If this app catches on, it could be a valuable source for reaching significant clinical consensus on various treatment options. And like other social media platforms, SharePractice allows you to invite your colleagues so you can contribute to its expansion.

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Genetics of the 2014 Ebola outbreak

Posted on Sep 23, 2014 8:34:12 AM

The Ebola virus can cause severe illness and death in people and other primates. The 2014 Ebola outbreak is the largest outbreak in history, with more than 3,600 infections and 1,800 deaths as of the end of August, according to the World Health Organization. The outbreak is the first in West Africa and the first to affect major cities.

Once Ebola virus has been transmitted from an animal host to a human, it can spread through person–to–person contact. Symptoms usually appear 2 to 21 days after exposure. Infection can cause fever, headache, body aches, weakness, stomach pain, and lack of appetite. Later symptoms include vomiting, diarrhea, rash, impaired kidney and liver function, and in some cases, internal and external bleeding (hemorrhage). There are no approved drugs for the disease, but prompt diagnosis and aggressive supportive care can improve survival.

To better understand this outbreak, an international team led by Dr. Pardis Sabeti at the Broad Institute and Harvard University collected virus samples from 78 patients living in Sierra Leone near the origin of the 2014 outbreak. The researchers used advanced technologies to quickly and accurately analyze the viral genomes. The work was funded in part by NIH’s Common Fund and National Institute of Allergy and Infectious Diseases (NIAID). The findings were published in Science on September 12, 2014.

The researchers sequenced 99 Ebola virus genomes in total, as some people were sampled more than once. The analysis revealed more than 300 genetic differences from viruses responsible for past outbreaks. The strain responsible for this outbreak appeared to diverge as early as 2004 from one found in Central Africa, indicating movement from Central to West Africa over the span of a decade.

The team also found more than 50 mutations that arose as the outbreak spread. They estimated that the first infection from an unknown source in late 2013 was followed by exclusive human–to–human transmissions. The virus was brought into Sierra Leone by 14 people who had been in nearby Guinea to attend the funeral of a traditional healer who had treated Ebola patients.

The team released all its sequence data as it was generated to aid in relief efforts and speed global research. “By making the data immediately available to the community, we hope to accelerate response efforts,” Sabeti says.

This study highlights the need for continued “genomic surveillance” to track and try to slow the evolution of this virus as the outbreak continues. Understanding the genetics of the virus will also help in the development of new and improved drugs and vaccines.

NIH has been playing a key role in investigating potential Ebola vaccines and medications. It recently announced the launch of an early–stage trial to begin human testing of a candidate vaccine.


Top news in Infectious Disease

Tags: Ebola

WHO calls for coordinated action to reduce suicides worldwide

Posted on Sep 6, 2014 7:28:37 AM

4 SEPTEMBER 2014  GENEVA – More than 800,000 people die by suicide every year – around one person every 40 seconds, according to WHO's first global report on suicide prevention, published today. Some 75% of suicides occur in low– and middle–income countries.

Pesticide poisoning, hanging, and firearms are among the most common methods of suicide globally. Evidence from Australia, Canada, Japan, New Zealand, the United States, and a number of European countries reveals that limiting access to these means can help prevent people dying by suicide. Another key to reducing deaths by suicide is a commitment by national governments to the establishment and implementation of a coordinated plan of action. Currently, only 28 countries are known to have national suicide prevention strategies.

Suicide is a global phenomenon

Suicide occurs all over the world and can take place at almost any age. Globally, suicide rates are highest in people aged 70 years and over. In some countries, however, the highest rates are found among the young. Notably, suicide is the second leading cause of death in 15–29 year–olds globally.

“This report is a call for action to address a large public health problem which has been shrouded in taboo for far too long,” said Dr. Margaret Chan, Director–General of WHO.

Generally, more men die by suicide than women. In richer countries, 3 times as many men die by suicide than women. Men aged 50 years and over are particularly vulnerable.

In low– and middle–income countries, young adults and elderly women have higher rates of suicide than their counterparts in high–income countries. Women over 70 years old are more than twice as likely to die by suicide than women aged 15–29 years.

Suicides are preventable

Reducing access to means of suicide is one way to reduce deaths. Other effective measures include responsible reporting of suicide in the media, such as avoiding language that sensationalizes suicide and avoiding explicit description of methods used, and early identification and management of mental and substance use disorders.

Follow–up care by health workers through regular contact, including by phone or home visits, for people who have attempted suicide, together with provision of community support, are essential, because people who have already attempted suicide are at the greatest risk of trying again.

“No matter where a country currently stands in suicide prevention,” said Dr. Alexandra Fleischmann, Scientist in the Department of Mental Health and Substance Abuse at WHO, “effective measures can be taken, even just starting at local level and on a small–scale.”

WHO recommends countries involve a range of government departments in developing a comprehensive coordinated response. High–level commitment is needed not just within the health sector, but also within education, employment, social welfare, and judicial departments.

“This report, the first WHO publication of its kind, presents a comprehensive overview of suicide, suicide attempts, and successful suicide prevention efforts worldwide. We know what works. Now is the time to act,” said Dr. Shekhar Saxena, Director of the Department of Mental Health and Substance Abuse at WHO.

The report’s launch comes just a week before World Suicide Prevention Day, observed on 10 September every year. The Day provides an opportunity for joint action to raise awareness about suicide and suicide prevention around the world.

In the WHO Mental Health Action Plan 2013–2020, WHO Member States have committed themselves to work towards the global target of reducing the suicide rate by 10% by 2020. WHO’s Mental Health Gap Action Programme includes suicide prevention as a priority and provides evidence–based technical guidance to expand service provision.

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Tags: suicide prevention, world health organization

Scientists looking across human, fly, and worm genomes find shared biology

Posted on Aug 28, 2014 7:01:45 AM


Researchers analyzing human, fly, and worm genomes have found that these species have a number of key genomic processes in common, reflecting their shared ancestry. The findings, appearing Aug. 28, 2014, in the journal Nature, offer insights into embryonic development, gene regulation and other biological processes vital to understanding human biology and disease.

The studies highlight the data generated by the modENCODE Project and the ENCODE Project, both supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health. Integrating data from the three species, the model organism ENCyclopedia Of DNA Elements (modENCODE) Consortium studied how gene expression patterns and regulatory proteins that help determine cell fate often share common features. Investigators also detailed the similar ways in which the three species use protein packaging to compact DNA into the cell nucleus and to regulate genome function by controlling access to DNA.

Launched in 2007, the goal of modENCODE is to create a comprehensive catalog of functional elements in the fruit fly and roundworm genomes for use by the research community. Such elements include genes that code for proteins, non–protein–coding genes and regulatory elements that control gene expression. The current work builds on initial catalogs published in 2010. The modENCODE projects complement the work being done by the ENCyclopedia Of DNA Elements (ENCODE) Project, which is building a comprehensive catalog of functional elements in the human and mouse genomes.

“The modENCODE investigators have provided a valuable resource for researchers worldwide,” said NHGRI Director Eric Green, MD, PhD. “The insights gained about the workings of model organisms’ genomes greatly help to inform our understanding of human biology.”

“One way to describe and understand the human genome is through comparative genomics and studying model organisms,” said Mark Gerstein, PhD, Albert L. Williams Professor of Biomedical Informatics at Yale University in New Haven, Connecticut, and the lead author on one of the papers. “The special thing about the worm and fly is that they are very distant from humans evolutionarily, so finding something conserved across all three — human, fly and worm — tells us it is a very ancient, fundamental process.”

In one study, scientists led by Dr. Gerstein and others, analyzed human, fly and worm transcriptomes, the collection of gene transcripts (or readouts) in a genome. They used large amounts of gene expression data generated in the ENCODE and modENCODE projects — including more than 67 billion gene sequence readouts — to discover gene expression patterns shared by all three species, particularly for developmental genes.

Investigators showed that the ways in which DNA is packaged in the cell are similar in many respects, and, in many cases, the species share programs for turning on and off genes in a coordinated manner. More specifically, they used gene expression patterns to match the stages of worm and fly development and found sets of genes that parallel each other in their usage. They also found the genes specifically expressed in the worm and fly embryos are re–expressed in the fly pupae, the stage between larva and adult.

The researchers found that in all three organisms, the gene expression levels for both protein–coding and non–protein–coding genes could be quantitatively predicted from chromatin features at the promoters of genes. A gene’s promoter tells the cell’s machinery where to begin copying DNA into RNA, which can be used to make proteins. DNA is packaged into chromatin in cells, and changes in this packaging can regulate gene function.

The latest medical news

Tags: Medical news, genomes

Gut microbiome analysis improved noninvasive colorectal cancer screening

Posted on Aug 23, 2014 8:37:56 AM

PHILADELPHIA — Analysis of the gut microbiome more successfully distinguished healthy individuals from those with precancerous adenomatous polyps and those with invasive colorectal cancer compared with assessment of clinical risk factors and fecal occult blood testing, according to data published in Cancer Prevention Research, a journal of the American Association for Cancer Research.


“A person’s gut microbiome is the collection of all the bacteria in their gut,” said Patrick D. Schloss, PhD, associate professor in the Department of Microbiology and Immunology at the University of Michigan in Ann Arbor. “The number of bacteria in the gut is huge; it outnumbers the number of cells in our bodies 10 to one, and the diversity of the bacteria present is critical to our health. By sequencing the V4 region of the 16S rRNA gene we were able to identify the bacteria present in each individual’s gut microbiome.

“We found that the composition of the gut microbiome allowed us to identify who in our study had precancerous adenomatous polyps and who had invasive colorectal cancer,” continued Schloss. “If our results are confirmed in larger groups of people, adding gut microbiome analysis to other fecal tests may provide an improved, noninvasive way to screen for colorectal cancer.”

By analyzing stool samples from 90 individuals—30 healthy individuals, 30 patients with precancerous adenomatous polyps, and 30 patients with invasive colorectal cancer—Schloss and his colleagues established that the composition of the gut microbiome was different for individuals in the three groups.

Using this information, they identified gut microbiome signatures for each group. Adding analysis of these signatures to assessment of age and race, which are clinical risk factors for precancerous adenomatous polyps, improved prediction of the presence of precancerous adenomatous polyps 4.5–fold. Adding analysis of the gut microbiome signatures to assessment of age, race, and body mass index (BMI), which are clinical risk factors of invasive colorectal cancer, improved prediction of the presence of invasive colorectal cancer 5.4–fold.

In addition, analysis of the gut microbiome signatures was better than fecal occult blood testing at distinguishing individuals with precancerous adenomatous polyps from those with invasive colorectal cancer (AUC=0.617 and AUC=0.952, respectively). Assessing BMI, fecal occult blood test results, and gut microbiome signatures together further improved the ability to distinguish between the two conditions (AUC=0.969).

“Our data show that gut microbiome analysis has the potential to be a new tool to noninvasively screen for colorectal cancer,” said Schloss. “We don’t think that this would ever replace other colorectal cancer screening approaches, rather we see it as complementary.

“The study involved not just microbiologists but also researchers skilled in statistics, genomics, and epidemiology,” continued Schloss. “Its success shows just how important interdisciplinary science is.”

source: American Association for Cancer Research News


Tags: colorectal cancer, polyps

World Humanitarian Day: WHO calls for protection of health workers in conflicts, disasters

Posted on Aug 19, 2014 7:18:11 AM

World Humanitarian Day

 As major emergencies around the globe increase in scale, complexity and frequency, the World Health Organization is calling for an end to the targeting of health workers in conflicts and other humanitarian crises, which represent a breach of the fundamental right to health.

World Humanitarian Day, celebrated every 19 August, WHO will draw attention to the continued trend of attacks on health care workers, hospitals, clinics and ambulances in Syria, Gaza, Central African Republic, Iraq, South Sudan and other areas.

Threats and harassment of health workers in West African countries have also been a worrying element of the Ebola Virus Disease outbreak. These professionals are taking personal risks to provide critical medical care, but have been threatened, shunned and stigmatized.

“Doctors, nurses and other health workers must be allowed to carry out their life–saving humanitarian work free of threat of violence and insecurity,” says Dr. Margaret Chan, WHO Director–General.

Dr. Richard Brennan, Director of WHO’s Department of Emergency Risk Management and Humanitarian Response, adds: “Assaults on health workers and facilities seriously affect access to health care, depriving patients of treatment and interrupting measures to prevent and control contagious diseases. WHO has a specific mandate to protect the human right to health, especially for people affected by humanitarian emergencies.”

While the adverse impacts of attacks on health care have been well documented in conflicts such as Syria and South Sudan, Gaza, health workers are also being prevented from carrying out their essential work outside of war–zones. In Pakistan and Nigeria, polio vaccinators, most of them female, have been specifically targeted.

As part of its lead role in coordinating the health response to international emergencies, WHO is working with partners to better document, prevent and respond to such incidents. Protecting those who care for the sick and vulnerable in the world’s most difficult circumstances is one of the most pressing responsibilities of the international community.



'Shape-shifting' material could help reconstruct faces

Posted on Aug 14, 2014 7:24:32 AM

surgery Researchers reported that they have developed a “self–fitting” material that expands with warm salt water to precisely fill bone defects, and also acts as a scaffold for new bone growth. The team described their approach in one of nearly 12,000 presentations at the 248th National Meeting & Exposition of the American Chemical Society (ACS).

To develop a material, Grunlan and her colleagues at Texas A&M University made a shape–memory polymer (SMP) that molds itself precisely to the shape of the bone defect without being brittle. It also supports the growth of new bone tissue. SMPs are materials whose geometry changes in response to heat. The team made a porous SMP foam by linking together molecules of poly(epsilon–caprolactone), an elastic, biodegradable substance that is already used in some medical implants. The resulting material resembled a stiff sponge, with many interconnected pores to allow bone cells to migrate in and grow.


Upon heating to 140 degrees Fahrenheit, the SMP becomes very soft and malleable. So, during surgery to repair a bone defect, a surgeon could warm the SMP to that temperature and fill in the defect with the softened material. Then, as the SMP is cooled to body temperature (98.6 degrees Fahrenheit), it would resume its former stiff texture and “lock” into place. The researchers also coated the SMPs with polydopamine, a sticky substance that helps lock the polymer into place by inducing formation of a mineral that is found in bone. It may also help osteoblasts, the cells that produce bone, to adhere and spread throughout the polymer. The SMP is biodegradable, so that eventually the scaffold will disappear, leaving only new bone tissue behind. more medical news articles

Tags: Surgery

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