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Posts

April 16, 2014

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2:00 PM | Self-Healing Composites- The Trick is Biology
Let’s face it, things wear out. Car tires go bye-bye, seals get worn, and Jets need constant upkeep to make sure that cracks in the fuselage [the main body of […]

Patrick J.F., Hart K.R., Krull B.P., Diesendruck C.E., Moore J.S., White S.R. & Sottos N.R. (2014). Continuous Self-Healing Life Cycle in Vascularized Structural Composites, Advanced Materials, n/a-n/a. DOI:

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1:37 PM | Video Tip of the Week: NaviCell for custom interaction maps for systems biology
The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a […]

Kuperstein I., Cohen D.P., Pook S., Viara E., Calzone L., Barillot E. & Zinovyev A. (2013). NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps, BMC Systems Biology, 7 (1) 100. DOI:

Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N. & Kitano H. (2008). CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, 96 (8) 1254-1265. DOI:

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1:17 PM | Journal Club: What’s old is new again: newly discovered songbird family is ancient
SUMMARY: Scientists analysing songbird DNA discovered that the spotted wren-babbler is neither a wren nor a wren-babbler, nor even a babbler. Instead, it represents an old evolutionary family that has no close living relatives. Spotted wren-babbler, Elachura formosa (previously Spelaeornis formosus). Image: Per Alström/SLU [doi:10.1098/rsbl.2013.1067]. A newly published study has uncovered a previously unknown family of songbirds that is represented by just one species. After analyzing one […]

Alström P., Hooper D.M., Liu Y., Olsson U., Mohan D., Gelang M., Hung L.M., Zhao J., Lei F. & Price T.D. & (2014). Discovery of a relict lineage and monotypic family of passerine birds, Biology Letters, 10 (3) DOI:

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1:17 PM | Journal Club: What’s old is new again: newly discovered songbird family is ancient
SUMMARY: Scientists analysing songbird DNA discovered that the spotted wren-babbler is neither a wren nor a wren-babbler, nor even a babbler. Instead, it represents an old evolutionary family that has no close living relatives. Spotted wren-babbler, Elachura formosa (previously Spelaeornis formosus). Image: Per Alström/SLU [doi:10.1098/rsbl.2013.1067]. A newly published study has uncovered a previously unknown family of songbirds that is represented by just one species. After analyzing one […]

Alström P., Hooper D.M., Liu Y., Olsson U., Mohan D., Gelang M., Hung L.M., Zhao J., Lei F. & Price T.D. & (2014). Discovery of a relict lineage and monotypic family of passerine birds, Biology Letters, 10 (3) DOI:

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12:30 PM | Does Animal-Assisted Therapy Help At-Risk Boys?
If existing behavioural programs aren’t working, can therapeutic sessions with a dog help boys who have problems at school?Photo: criben / ShutterstockA new paper by Abbey Schneider et al (2014) investigates the success of a program designed to help boys who are considered ‘at-risk’ – by matching them up with a specially trained dog and handler.In Colorado, a group of elementary schools take part in a program called the Human Animal Bond in Colorado (HABIC). It is […]

Schneider, A.A.,, Rosenberg, J., Baker, M., Melia, N., Granger, B. & Biringen, Z. (2014). Becoming relationally effective: High-risk boys in animal-assisted therapy, Human-Animal Interaction Bulletin, 2 (1) 1-18. Other: Link

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12:00 PM | Using Pain To Stop Pain
Biology concepts – desensitization, habituation, counter irritation, cautery, heat sensing, pain, chronic, acute, analgesiaGout usually attacks middle-aged men and the big toe joint is a favorite spot. But it can occur anywhere and in anyone. The accretions or urates build up and clog the joint, causng poor function and intense pain, painful enough that even the weight of a sheet on it at night is too much. Usually the acute attacks are far worse, and become less painful gouty arthritisas […]

Andreev YA, Kozlov SA, Korolkova YV, Dyachenko IA, Bondarenko DA, Skobtsov DI, Murashev AN, Kotova PD, Rogachevskaja OA, Kabanova NV & Kolesnikov SS (2013). Polypeptide modulators of TRPV1 produce analgesia without hyperthermia., Marine drugs, 11 (12) 5100-15. PMID:

Tobaldini G, de Siqueira BA, Lima MM, Tambeli CH & Fischer L (2014). Ascending nociceptive control contributes to the anti-nociceptive effect of acupuncture in a rat model of acute pain., The journal of pain : official journal of the American Pain Society, PMID:

Lee MG, Huh BK, Choi SS, Lee DK, Lim BG & Lee M (2012). The effect of epidural resiniferatoxin in the neuropathic pain rat model., Pain physician, 15 (4) 287-96. PMID:

Kelly S, Chapman RJ, Woodhams S, Sagar DR, Turner J, Burston JJ, Bullock C, Paton K, Huang J, Wong A & McWilliams DF (2013). Increased function of pronociceptive TRPV1 at the level of the joint in a rat model of osteoarthritis pain., Annals of the rheumatic diseases, PMID:

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10:13 AM | Tiger sharks: Each to their own diving depth
Despite some broad similarities, the diving behaviour of tiger sharks appears to vary greatly amongst individuals.  Tiger sharks (Galeocerdo cuvier) are one of the top predators in tropical and subtropical waters throughout the world. These large sharks are known to occupy both coastal and open seas, and can travel over both short and long distances. […]

Vaudo, J., Wetherbee, B., Harvey, G., Nemeth, R., Aming, C., Burnie, N., Howey-Jordan, L. & Shivji, M. (2014). Intraspecific variation in vertical habitat use by tiger sharks (Galeocerdo cuvier) in the western North Atlantic, Ecology and Evolution, DOI:

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5:54 AM | Joined by HDAC (inhibitors)
I'm treading quite carefully with this post which came about following my [non-expert] reading of the paper abstract from Anand Venkatraman and colleagues [1] on a potential downside to the use of HDAC (histone deacetylase) inhibitors for treating spinocerebellar ataxia type 1 (SCA1), a progressive disease affecting movement and other knock-on functions. This follows other work suggesting that certain HDAC inhibitors might offer some important new lines of investigation when it […]

Venkatraman A, Hu YS, Didonna A, Cvetanovic M, Krbanjevic A, Bilesimo P & Opal P (2014). The histone deacetylase HDAC3 is essential for Purkinje cell function, potentially complicating the use of HDAC inhibitors in SCA1., Human molecular genetics, PMID:

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1:36 AM | New Study Shows Surgical Checklists In Operating Rooms Are Less Effective Than Assumed
The patient has verified his or her identity, the surgical site, the type of procedure, and his or her consent. Check. The surgical site is marked on a patient if such marking is appropriate for the procedure. Check. The probe measuring blood oxygen content has been placed on the patient and is functioning. Check. All members of the surgical and anesthesia team are aware of whether the patient has a known allergy? Check. These were the first items on a... Read more

Urbach DR, Govindarajan A, Saskin R, Wilton AS & Baxter NN (2014). Introduction of surgical safety checklists in Ontario, Canada., The New England Journal of Medicine, 370 (11) 1029-38. PMID:

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1:36 AM | New Study Shows Surgical Checklists In Operating Rooms Are Less Effective Than Assumed
The patient has verified his or her identity, the surgical site, the type of procedure, and his or her consent. Check. The surgical site is marked on a patient if such marking is appropriate for the procedure. Check. The probe measuring blood oxygen content has been placed on the patient and is functioning. Check. All members of the surgical and anesthesia team are aware of whether the patient has a known allergy? Check. These were the first items on a... Read more

Urbach DR, Govindarajan A, Saskin R, Wilton AS & Baxter NN (2014). Introduction of surgical safety checklists in Ontario, Canada., The New England Journal of Medicine, 370 (11) 1029-38. PMID:

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1:32 AM | Stone Soup Eyes
Another installment from the Developmental Neurobiology Students at Reed College. Hope you enjoy! It’s not often that you get to recount the classic tale of Stone Soup when thinking about developmental biology, but that’s exactly what we did when discussing an almost classic 2011 Nature paper from Yoshiki Sasai’s group. In the story, a grumpy […]

Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K., Adachi, T. & Sasai, Y. (2011). Self-organizing optic-cup morphogenesis in three-dimensional culture, Nature, 472 (7341) 51-56. DOI:

Fuhrmann, S. (2010). Eye Morphogenesis and Patterning of the Optic Vesicle, Current Topics in Developmental Biology, DOI:

Nakano, T., Ando, S., Takata, N., Kawada, M., Muguruma, K., Sekiguchi, K., Saito, K., Yonemura, S., Eiraku, M. & Sasai, Y. & (2012). Self-Formation of Optic Cups and Storable Stratified Neural Retina from Human ESCs, Cell Stem Cell, 10 (6) 771-785. DOI:

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April 15, 2014

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10:21 PM | Hold the drill! Fracking emitting more methane than previously thought
As politically divisive as hydraulic fracturing is, we still need much more data to determine its environmental effects before deciding if it can be major source of energy during our transition away from fossil fuels.  Unfortunately, this lack of data … Continue reading →

Caulton, D., Shepson, P., Santoro, R., Sparks, J., Howarth, R., Ingraffea, A., Cambaliza, M., Sweeney, C., Karion, A., Davis, K. & Stirm, B. (2014). Toward a better understanding and quantification of methane emissions from shale gas development, Proceedings of the National Academy of Sciences, DOI:

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7:50 PM | Cheap, Abundant, Low-Toxic Photocatalyst Discovered
A research group at Japan Science and Technology Agency (JST) led by the principal researcher Hideki Abe and the senior researcher Naoto Umezawa at the NIMS’s Environmental Remediation Materials Unit discovered a new photocatalyst, Sn3O4, that uses sunlight to produce hydrogen from water. Read more »

Manikandan, M., Tanabe, T., Li, P., Ueda, S., Ramesh, G., Kodiyath, R., Wang, J., Hara, T., Dakshanamoorthy, A., Ishihara, S. & Ariga, K. (2014). Photocatalytic Water Splitting under Visible Light by Mixed-Valence Sn O , ACS Applied Materials & Interfaces, 6 (6) 3790-3793. DOI:

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5:32 PM | Quantum Dots Could Be Used to Make Efficient Solar Windows
A house window that doubles as a solar panel could be on the horizon, thanks to recent quantum-dot work by Los Alamos National Laboratory researchers in collaboration with scientists from University of Milano-Bicocca (UNIMIB), Italy. Read more »

Meinardi, F., Colombo, A., Velizhanin, K., Simonutti, R., Lorenzon, M., Beverina, L., Viswanatha, R., Klimov, V. & Brovelli, S. (2014). Large-area luminescent solar concentrators based on ‘Stokes-shift-engineered’ nanocrystals in a mass-polymerized PMMA matrix, Nature Photonics, DOI:

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5:14 PM | NBA and WNBA players perform differently with age
Life-history traits are often shaped by a balance between somatic maintenance and reproductive investment. That is, an individual wants their own cells to be active, but also needs to invest in making offspring. This tension between natural and sexual selection can generate age-related physiological trajectories that differ between organisms, environments and populations. In simpler terms, […]

Lailvaux S.P., Wilson R. & Kasumovic M.M. (2014). Trait comparison and sex-specific aging of performance in male and female professional basketball players, Evolution, DOI:

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5:00 PM | Penicillin 2.0 – Reviving an Old Winner
Penicillin, it was one of the great feats of science and has saved countless lives. Antibiotics have been fighting the war on infections since before most of us were even […]

Zhang J., Chen Y.P., Miller K.P., Ganewatta M.S., Bam M., Yan Y., Nagarkatti M., Decho A.W. & Tang C. (2014). Antimicrobial Metallopolymers and Their Bioconjugates with Conventional Antibiotics against Multidrug-Resistant Bacteria, Journal of the American Chemical Society, 136 (13) 4873-4876. DOI:

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2:00 PM | The perfect marriage of crystallography and mass spectrometry: PI3K
  Sorry for the cheesy title, but I’m getting married in a couple of weeks and it is all I can think about (oh, and science of course).  I have to admit that I chose a GREAT paper this time!: “Molecular determinants of PI3Kγ-mediated activation downstream of G-protein–coupled receptors” which was published last year in […]

Vadas O., Dbouk H.A., Shymanets A., Perisic O., Burke J.E., Abi Saab W.F., Khalil B.D., Harteneck C., Bresnick A.R. & Nurnberg B. & (2013). Molecular determinants of PI3K -mediated activation downstream of G-protein-coupled receptors (GPCRs), Proceedings of the National Academy of Sciences, 110 (47) 18862-18867. DOI:

Rommel C., Camps M. & Ji H. (2007). PI3Kδ and PI3Kγ: partners in crime in inflammation in rheumatoid arthritis and beyond?, Nature Reviews Immunology, 7 (3) 191-201. DOI:

Walker E.H., Perisic O., Ried C., Stephens L. & Williams R.L. Structural insights into phosphoinositide 3-kinase catalysis and signalling., Nature, PMID:

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2:51 AM | Disordered Eating and Athletic Performance: Where’s the Line?
If a person severely restricts his diet and exercises for hours each day, he has an eating disorder. If another does exactly the same but it is because she wants to make the lightweight rowing team (which has an upper weight limit), she’s a committed athlete. When the two overlap, and an athlete presents with eating disorder symptoms, how do we distinguish between the demands of the sport and the illness? I’ve been interested in the distinctions we make between disordered and […]

Werner, A., Thiel, A., Schneider, S., Mayer, J., Giel, K. & Zipfel, S. (2013). Weight-control behaviour and weight-concerns in young elite athletes – a systematic review, Journal of Eating Disorders, 1 (1) 18. DOI:

Martinsen, M., Bratland-Sanda, S., Eriksson, A. & Sundgot-Borgen, J. (2009). Dieting to win or to be thin? A study of dieting and disordered eating among adolescent elite athletes and non-athlete controls, British Journal of Sports Medicine, 44 (1) 70-76. DOI:

Rouveix M, Bouget M, Pannafieux C, Champely S & Filaire E (2007). Eating attitudes, body esteem, perfectionism and anxiety of judo athletes and nonathletes., International journal of sports medicine, 28 (4) 340-5. PMID:

Ferrand C, Magnan C & Philippe RA (2005). Body-esteem, body mass index, and risk for disordered eating among adolescents in synchronized swimming., Perceptual and motor skills, 101 (3) 877-84. PMID:

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April 14, 2014

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8:02 PM | Mosquito sperm need to smell to swim
You’ve probably had someone tell you, at some point in your life, that the sense of smell is the sense most tightly linked to memory. Now, scientists have found that at least for mosquitoes, the sense of smell is also linked to the ability of their sperm to swim. The research was published in February in … Continue reading →

Pitts RJ, Liu C, Zhou X, Malpartida JC & Zwiebel LJ (2014). Odorant receptor-mediated sperm activation in disease vector mosquitoes., Proceedings of the National Academy of Sciences of the United States of America, 111 (7) 2566-71. PMID:

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7:59 PM | Airborne Wind Turbines Have Significant Potential, Study Finds
Airborne wind turbines hovering high in the air and tethered to the ground, like kites, have the potential to generate huge amounts of electricity, based on a recent wind availability study led by the University of Delaware. Read more »

Archer, C., Delle Monache, L. & Rife, D. (2014). Airborne wind energy: Optimal locations and variability, Renewable Energy, 64 180-186. DOI:

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7:40 PM | Dual-Luciferase Imaging in vivo
We are used to seeing multicolored fluorescence images labeling either specific events or structures within cells. When compared to imaging with fluorescent methods, bioluminescence imaging methods provide the advantages of low background and subsequent higher signal to noise ratio—enhancing sensitivity. A key prerequisite for dual-imaging experiments is the ability to distinguish the signal from each […]

Stacer AC, Nyati S, Moudgil P, Iyengar R, Luker KE, Rehemtulla A & Luker GD (2013). NanoLuc reporter for dual luciferase imaging in living animals., Molecular imaging, 12 (7) 1-13. PMID:

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6:37 PM | Scientists Gain Insight Into High-Temperature Superconductivity
In a new study by the U.S. Department of Energy’s (DOE) Argonne National Laboratory, researchers have identified and solved at least one paradox in the behavior of high-temperature superconductors. The riddle involves a phenomenon called the “pseudogap,” a region of energy levels in which relatively few electrons are allowed to exist. Read more »

Mishra, V., Chatterjee, U., Campuzano, J. & Norman, M. (2014). Effect of the pseudogap on the transition temperature in the cuprates and implications for its origin, Nature Physics, DOI:

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5:10 PM | Does Access to Birth Control Reduce Poverty?
In American politics the proliferation of birth control is important because of how it affects the eternal resting place of our immortal souls. But believe it or not, there are also non-metaphysical policy consequences to increasing access to birth control. A new study by a pair of economists — Stephanie Browne of J.P. Morgan and […]

Browne, S. & LaLumia, S. (2014). The Effects of Contraception on Female Poverty, Journal of Policy Analysis and Management, DOI:

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4:50 PM | Silly Putty ingredient promotes stem cell growth
Researchers cultured stem cells on ultrafine carpets made of  microscopic posts of a key ingredient in Silly Putty. Credit: Ye Tao, Rose Anderson, Yubing Sun, Jianping FuThe sponginess of the environment where human embryonic stem cells are growing affects the type of specialized cells they eventually become, a new study shows.The researchers coaxed human embryonic stem cells to turn into working spinal cord cells more efficiently by growing the cells on a soft, ultrafine carpet made of a […]

Sun, Y., Yong, K., Villa-Diaz, L., Zhang, X., Chen, W., Philson, R., Weng, S., Xu, H., Krebsbach, P. & Fu, J. & (2014). Hippo/YAP-mediated rigidity-dependent motor neuron differentiation of human pluripotent stem cells, Nature Materials, DOI:

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2:00 PM | Phonology and the brain: it’s all in the features.
…and the vision that was planted in my brain still remains, . within the sound of silence. . (Simon and Garfunkel, The sound of silence 1964) […] Read more The post Phonology and the brain: it’s all in the features. appeared first on Mapping Ignorance. Related posts:Sesame Street and brain activity in children Reinforcement learning in the brain The (energetical) cost of having a brain

Mesgarani N., Cheung C., Johnson K. & Chang E.F. (2014). Phonetic Feature Encoding in Human Superior Temporal Gyrus, Science, 343 (6174) 1006-1010. DOI:

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10:04 AM | Interview with Beddington Medal winner William Razzell
Each year, the British Society for Developmental Biology (BSDB) awards the Beddington Medal to the best PhD thesis in developmental biology. This year’s award went to William Razzell, who completed his PhD in Paul Martin’s lab at the University of Bristol. At the BSDB Spring Meeting last month, Will presented his thesis studies of wound […]

Razzell, W., Wood, W. & Martin, P. (2014). Recapitulation of morphogenetic cell shape changes enables wound re-epithelialisation, Development, DOI:

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7:58 AM | Neurology of inflammatory bowel diseases
The paper by Ben-Or and colleagues [1] talking about a neurologic profile present in a small participant cohort of children and adolescents diagnosed with an inflammatory bowel disease (IBD) caught my eye recently. Their findings reporting that over two-thirds of their paediatric participant group diagnosed with IBD also "exhibited neurologic manifestations" provides some compelling preliminary evidence for further investigation in this area.Outside of reports of headache and dizziness, the […]

Ben-Or O, Zelnik N, Shaoul R, Pacht A & Lerner A (2014). The Neurologic Profile of Children and Adolescents With Inflammatory Bowel Disease., Journal of child neurology, PMID:

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3:45 AM | Big data, prediction, and scientism in the social sciences
Much of my undergrad was spent studying physics, and although I still think that a physics background is great for a theorists in any field, there are some downsides. For example, I used to make jokes like: “soft isn’t the opposite of hard sciences, easy is.” Thankfully, over the years I have started to slowly […]

Lazer, D., Kennedy, R., King, G. & Vespignani, A. (2014). Big data. The parable of Google Flu: traps in big data analysis., Science, 343 (6176) 1203-1205. PMID:

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April 13, 2014

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2:18 AM | Early brain development and heat shock proteins
The brain development of a fetus is really an amazing thing. The first sign of an incipient nervous system emerges during the third week of development; it is simply a thickened layer of tissue called the neural plate. After about 5 more days, the neural plate has formed an indentation called the neural groove, and the sides of the neural groove have curled up and begun to fuse together (see pic to the right). This will form the neural tube, which will eventually become the brain and spinal […]

Hashimoto-Torii, K., Torii, M., Fujimoto, M., Nakai, A., El Fatimy, R., Mezger, V., Ju, M., Ishii, S., Chao, S., Brennand, K. & Gage, F. (2014). Roles of Heat Shock Factor 1 in Neuronal Response to Fetal Environmental Risks and Its Relevance to Brain Disorders, Neuron, DOI:

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April 12, 2014

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5:06 PM | Polycystic Ovary Syndrome: Causes, Symptoms, and Home Remedies
Polycystic ovary syndrome (PCOS) is one of the most common causes of woman's infertility. It is a problem results from an imbalance of female sex hormones. It may cause irregular menstruation,... [[To read the full story, visit my website.]]

Pau CT, Keefe CC & Welt CK (2013). Cigarette smoking, nicotine levels and increased risk for metabolic syndrome in women with polycystic ovary syndrome., Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology, 29 (6) 551-5. PMID:

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