How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories

Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no rigorous guarantees. Determining the amount of data needed to correctly reconstruct population histories is a major challenge. Using a variety of tools from information theory, the theory of extremal polynomials, and approximation theory, we prove new sharp information-theoretic lower bounds on the problem of reconstructing population structure -- the history of multiple subpopulations that merge, split and change sizes over time. Our lower bounds are exponential in the number of subpopulations, even when reconstructing recent histories. We demonstrate the sharpness of our lower bounds by providing algorithms for distinguishing and learning population histories with matching dependence on the number of subpopulations. Along the way and of independent interest, we essentially determine the optimal number of samples needed to learn an exponential mixture distribution information-theoretically, proving the upper bound by analyzing natural (and efficient) algorithms for this problem.Comment: 38 pages, Appeared in RECOMB 201

Ischemic Stroke Caused by Paradoxical Embolism After an Unsuccessful Transcatheter Atrial Septal Defect Closure Procedure: A Word of Caution

Transcatheter device closure of atrial septal defect (ASD) has become a well-accepted alternative to surgical repair. Serious complications of transcatheter ASD closure are rare, but when they occur, devastating consequences may result. Herein, we present the case of a 4-year-old girl who had an ischemic stroke caused by a presumptive paradoxical embolism after an unsuccessful transcatheter ASD procedure and in whom subsequent venous color Doppler showed deep venous thrombosis (DVT) of the right lower extremity. The risk factors that predisposed to paradoxical cerebral embolism and DVT in this patient are discussed, and the literature is reviewed

Bistability in Apoptosis by Receptor Clustering

Apoptosis is a highly regulated cell death mechanism involved in many physiological processes. A key component of extrinsically activated apoptosis is the death receptor Fas, which, on binding to its cognate ligand FasL, oligomerize to form the death-inducing signaling complex. Motivated by recent experimental data, we propose a mathematical model of death ligand-receptor dynamics where FasL acts as a clustering agent for Fas, which form locally stable signaling platforms through proximity-induced receptor interactions. Significantly, the model exhibits hysteresis, providing an upstream mechanism for bistability and robustness. At low receptor concentrations, the bistability is contingent on the trimerism of FasL. Moreover, irreversible bistability, representing a committed cell death decision, emerges at high concentrations, which may be achieved through receptor pre-association or localization onto membrane lipid rafts. Thus, our model provides a novel theory for these observed biological phenomena within the unified context of bistability. Importantly, as Fas interactions initiate the extrinsic apoptotic pathway, our model also suggests a mechanism by which cells may function as bistable life/death switches independently of any such dynamics in their downstream components. Our results highlight the role of death receptors in deciding cell fate and add to the signal processing capabilities attributed to receptor clustering.Comment: Accepted by PLoS Comput Bio

Chinese version of the Global Youth Tobacco Survey: cross-cultural instrument adaptation

<p>Abstract</p> <p>Background</p> <p>Tobacco smoking poses public health concerns because of its high risk for many chronic diseases. Most smokers begin using tobacco in their teens and recent reports indicate that smoking prevalence is climbing among youth. The Global Youth Tobacco Survey (GYTS) is a worldwide, school-based, tobacco-specific survey, but cross-cultural differences limit its effectiveness in international studies. Specifically, the GYTS assesses not only the prevalence of smoking, but also tobacco-related attitudes, school curricula, and advertisements, which are culturally influenced. Therefore, we conducted this study to develop a Chinese version of the GYTS for both national surveillance and international comparison.</p> <p>Methods</p> <p>The original English GYTS was translated and back translated using a cross-cultural adaptation process. The comprehensiveness and feasibility of using the Chinese-version GYTS were reviewed by a panel of 6 tobacco-control experts. The understandability and cultural relevance of the Chinese-version GYTS were discussed in a focus group of 5 schoolteachers and 8 students. The expert and focus group feedback was incorporated into a final Chinese version of the GYTS, which was administered to 382 students throughout Taiwan by multi-stage sampling from 10 randomly selected schools.</p> <p>Results</p> <p>The internal consistency (Cronbach's alpha) for the GYTS subscales (smoking susceptibility, attitude toward smoking, and media messages about smoking) ranged from 0.70 to 0.94. The internal logical agreement of responses ranged from 85.3 to 99.2%.</p> <p>Conclusion</p> <p>The Chinese version of the GYTS has good reliability and validity and can serve as the foundation for international comparison and tobacco control in Chinese-speaking communities.</p

A functional variant in promoter region of platelet-derived growth factor-D is probably associated with intracerebral hemorrhage

<p>Abstract</p> <p>Background</p> <p>Platelet-derived growth factor D (PDGF-D) plays an important role in angiogenesis, vessel remodeling, inflammation and repair in response to injury. We hypothesized that genetic variation in <it>PDGFD </it>gene might alter the susceptibility to stroke.</p> <p>Findings</p> <p>We determined the genotypes of a single nucleotide polymorphism (SNP) (-858A/C, rs3809021) in 1484 patients with stroke (654 cerebral thrombosis, 419 lacunar infarction, 411 intracerebral hemorrhage [ICH]) and 1528 control subjects from an unrelated Chinese Han population and followed the stroke patients up for a median of 4.5 years.</p> <p>The -858AA genotype showed significantly increased risk of ICH (dominant model: odds ratio [OR] 1.29, 95% confidence interval [CI] 1.00-1.68, <it>P </it>= 0.05; additive model: OR 1.24, 95% CI 1.01-1.52, <it>P </it>= 0.04) than wild-type genotype. Further analyses showed that -858AA genotype conferred about 2-fold increase in risk of non-hypertensive ICH (dominant model: OR 2.1, 95%CI 1.34-3.29, <it>P </it>= 0.001; additive model: OR 1.75, 95% CI 1.24-2.46, <it>P </it>= 0.001). After a median follow-up of 4.5 years, -858AA genotype was associated with a reduced risk of ICH recurrence (dominant model: adjusted hazard ratio [HR] 0.09, 95%CI 0.01-0.74, P = 0.025; additive model: HR 0.21, 95% CI 0.04-1.16, <it>P </it>= 0.073) in non-hypertensive patients.</p> <p>Conclusions</p> <p>The -858AA genotype is probably associated with risk for non-hypertensive ICH. Further studies should be conducted to reveal the role of PDGF-D at various stages of ICH development--beneficial, or deleterious.</p

SnO2Nanowire Arrays and Electrical Properties Synthesized by Fast Heating a Mixture of SnO2and CNTs Waste Soot

SnO2nanowire arrays were synthesized by fast heating a mixture of SnO2and the carbon nanotubes waste soot by high-frequency induction heating. The resultant SnO2nanowires possess diameters from 50 to 100 nm and lengths up to tens of mircrometers. The field-effect transistors based on single SnO2nanowire exhibit that as-synthesized nanowires have better transistor performance in terms of transconductance and on/off ratio. This work demonstrates a simple technique to the growth of nanomaterials for application in future nanoelectronic devices

Temperature Modulates Plant Defense Responses through NB-LRR Proteins

An elevated growth temperature often inhibits plant defense responses and renders plants more susceptible to pathogens. However, the molecular mechanisms underlying this modulation are unknown. To genetically dissect this regulation, we isolated mutants that retain disease resistance at a higher growth temperature in Arabidopsis. One such heat-stable mutant results from a point mutation in SNC1, a NB-LRR encoding gene similar to disease resistance (R) genes. Similar mutations introduced into a tobacco R gene, N, confer defense responses at elevated temperature. Thus R genes or R-like genes involved in recognition of pathogen effectors are likely the causal temperature-sensitive component in defense responses. This is further supported by snc1 intragenic suppressors that regained temperature sensitivity in defense responses. In addition, the SNC1 and N proteins had a reduction of nuclear accumulation at elevated temperature, which likely contributes to the inhibition of defense responses. These findings identify a plant temperature sensitive component in disease resistance and provide a potential means to generate plants adapting to a broader temperature range

Expression of Bmi-1 is a prognostic marker in bladder cancer

<p>Abstract</p> <p>Background</p> <p>The molecular mechanisms of the development and progression of bladder cancer are poorly understood. The objective of this study was to analyze the expression of Bmi-1 protein and its clinical significance in human bladder cancer.</p> <p>Methods</p> <p>We examined the expression of Bmi-1 mRNA and Bmi-1 protein by RT-PCR and Western blot, respectively in 14 paired bladder cancers and the adjacent normal tissues. The expression of Bmi-1 protein in 137 specimens of bladder cancer and 30 specimens of adjacent normal bladder tissue was determined by immunohistochemistry. Statistical analyses were applied to test the relationship between expression of Bmi-1, and clinicopathologic features and prognosis.</p> <p>Results</p> <p>Expression of Bmi-1 mRNA and protein was higher in bladder cancers than in the adjacent normal tissues in 14 paired samples (<it>P </it>< 0.01). By immunohistochemical examination, five of 30 adjacent normal bladder specimens (16.7%) versus 75 of 137 bladder cancers (54.3%) showed Bmi-1 protein expression (<it>P </it>< 0.05). Bmi-1 protein expression was intense in 20.6%, 54.3%, and 78.8% of tumors of histopathological stages G1, G2, and G3, respectively (<it>P </it>< 0.05). Expression of Bmi-1 protein was greater in invasive bladder cancers than in superficial bladder cancers (81.5% versus 32.5%, <it>P </it>< 0.05). In invasive bladder cancers, the expression of Bmi-1 protein in progression-free cancers was similar to that of cancers that have progressed (80.0% versus 82.4%, <it>P </it>> 0.5). In superficial bladder cancers, the expression of Bmi-1 protein in recurrent cases was higher than in recurrence-free cases (62.5% versus 13.7%, <it>P </it>< 0.05). Bmi-1 expression was positively correlated with tumor classification and TNM stage (<it>P </it>< 0.05), but not with tumor number (<it>P </it>> 0.05). Five-year survival in the group with higher Bmi-1 expression was 50.8%, while it was 78.5% in the group with lower Bmi-1 expression (<it>P </it>< 0.05). Patients with higher Bmi-1 expression had shorter survival time, whereas patients with lower Bmi-1 expression had longer survival time (<it>P </it>< 0.05).</p> <p>Conclusion</p> <p>Expression of Bmi-1 was greater in bladder cancers than in the adjacent normal tissues. The examination of Bmi-1 protein expression is potentially valuable in prognostic evaluation of bladder cancer.</p