Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence

BACKGROUND: Previous studies have suggested that recent segmental duplications, which are often involved in chromosome rearrangements underlying genomic disease, account for some 5% of the human genome. We have developed rapid computational heuristics based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies. RESULTS: Our analysis of the June 2002 public human genome assembly revealed that 107.4 of 3,043.1 megabases (Mb) (3.53%) of sequence contained segmental duplications, each with size equal or more than 5 kb and 90% identity. We have also detected that 38.9 Mb (1.28%) of sequence within this assembly is likely to be involved in sequence misassignment errors. Furthermore, we have identified a significant subset (199,965 of 2,327,473 or 8.6%) of single-nucleotide polymorphisms (SNPs) in the public databases that are not true SNPs but are potential paralogous sequence variants. CONCLUSION: Using two distinct computational approaches, we have identified most of the sequences in the human genome that have undergone recent segmental duplications. Near-identical segmental duplications present a major challenge to the completion of the human genome sequence. Potential sequence misassignments detected in this study would require additional efforts to resolve

Zee model and phenomenology of lepton sector

The virtual effects of the Zee charged scalar boson on the lepton-family-number (LFN) violating processes are studied. We obtain the constraints on the individual Yukawa coupling constants of the Zee boson to leptons. Using these constraints, we predict the upper bounds on the muonium-antimuonium conversion probability, the branching fractions of the LFN violating decays such as $\tau \to e\gamma$, $\tau \to \mu\gamma$, $\tau^- \to \mu^+e^-e^-$ and $\tau \to e^+\mu^-\mu^-$. The contribution of the Zee boson to the muon anomalous magnetic moment is also consideredComment: 13pages, 2figures, Latex; Notes added, two references adde

Supersymmetry in the shadow of photini

Additional neutral gauge fermions -- "photini" -- arise in string compactifications as superpartners of U(1) gauge fields. Unlike their vector counterparts, the photini can acquire weak-scale masses from soft SUSY breaking and lead to observable signatures at the LHC through mass mixing with the bino. In this work we investigate the collider consequences of adding photini to the neutralino sector of the MSSM. Relatively large mixing of one or more photini with the bino can lead to prompt decays of the lightest ordinary supersymmetric particle; these extra cascades transfer most of the energy of SUSY decay chains into Standard Model particles, diminishing the power of missing energy as an experimental handle for signal discrimination. We demonstrate that the missing energy in SUSY events with photini is reduced dramatically for supersymmetric spectra with MSSM neutralinos near the weak scale, and study the effects on limits set by the leading hadronic SUSY searches at ATLAS and CMS. We find that in the presence of even one light photino the limits on squark masses from hadronic searches can be reduced by 400 GeV, with comparable (though more modest) reduction of gluino mass limits. We also consider potential discovery channels such as dilepton and multilepton searches, which remain sensitive to SUSY spectra with photini and can provide an unexpected route to the discovery of supersymmetry. Although presented in the context of photini, our results apply in general to theories in which additional light neutral fermions mix with MSSM gauginos.Comment: 23 pages, 8 figures, references adde

N-of-1 randomized trials for psychological and health behavior outcomes: a systematic review protocol

Background Randomized controlled trials are the sine qua non of causal inference; however, heterogeneity of treatment effects for many chronic conditions and for many symptoms often limits their utility. Single-patient studies in which patients select a treatment after trying a randomized sequence of treatments (i.e., multiple crossover trials) offer an alternative to traditional randomized controlled trials by providing scientifically valid results in a practical manner that can be used by patients and their providers to decide upon their personally optimal treatment. Although N-of-1 trials have been used in the medical literature, their use for interventions that consist of psychological or health behavior outcomes is unknown. This systematic review thus aims to describe the interventions and outcomes and assess the quality of N-of-1 trials for psychological or health behavior outcomes. Methods/Design Electronic databases (Ovid MEDLINE, EMBASE, CINAHL, PsycINFO, and the six databases in the Cochrane Library) will be searched using all relevant subject headings and free-text terms to represent N-of-1 trials and psychological or behavioral interventions. Full text review and bibliography searching will be conducted. Unpublished studies will be sought by searching trial registries and contacting authors of included studies. Eligibility criteria are the following: population, all human participants for whom N-of-1 trials with psychological or health behavior outcomes have been conducted; interventions, all interventions for which N-of-1 trials have been conducted; comparison, placebo or active treatment control; and outcome, psychological and health behavior outcomes including self-perceived disease severity and psychological phenomena such as mood and affect. Studies that do not contain sufficient trial detail, describe only design or statistical analytic issues in N-of-1 trials without presentation of an N-of-1 trial itself, and/or are not written in the English language are ineligible. Screening, data extraction, and quality assessment will be conducted by two independent reviewers with disagreements resolved through discussion. Discussion This systematic review will describe the interventions and outcomes and assess the quality of N-of-1 trials for psychological or health behavior outcomes. The results will clarify the use of this research methodology in the health psychology and behavioral medicine literature and may pave the way for additional N-of-1 trials to be conducted

Probing anomalous top quark interactions at the Fermilab Tevatron Collider

We study the effects of dimension-six operators contributing to the $gt\bar t$ vertex in top quark pair production at the Tevatron collider. We derive both the limits from Run 1 data and the potential bounds from future runs (Run 2 and 3). Although the current constraints are not very strong, the future runs are quite effective in probing these operators. We investigate the possibility of disentangling different operators with the $t\bar t$ invariant mass distribution and the top quark polarization asymmetry. We also study the effects of a different set of operators contributing to single top production via the $Wt\bar b$ coupling. We derive the current and potential future bounds on these anomalous operators and find that the upgraded Tevatron can improve the existing constraints from $R_b$ for one of the operators.Comment: 20 pages, 2 figures, REVTEX, some clarifying remarks adde

R-parity violation and top quark polarization at the Fermilab Tevatron collider

The lepton or baryon number violating top quark interactions in the supersymmetric standard model with R parity violation contribute to the process d dbar to t tbar at the tree level via the t- or u-channel sfermion exchange. Since these interactions are chiral, they induce polarization to the top quark in the t tbar events at hadron colliders. We show in this article that the polarization can be a useful observable for probing these interactions at the upgraded Fermilab Tevatron collider, because the polarization is expected to be very small in the standard model.Comment: 15 pages, 5 figure

‘Caution! The Bread is Poisoned’: The Hong Kong Mass Poisoning of January 1857

This article examines the Hong Kong mass poisoning of 15 January 1857, in which bread from a Chinese bakery that supplied the colonial community was adulterated with arsenic. Even though there is a wealth of printed and manuscript documentation available many vital aspects of the poisoning remain unclear. What kind of incident was it: an act of terrorism and attempted mass murder, a war crime, a criminal conspiracy, an act of commercial sabotage, an accident or even an imagined or imaginary event? Throughout, our focus remains firmly fixed on the central act of the poisoning itself and on what it reveals about the precarious nature of early colonial Hong Kong. Interpretations have swarmed over the available ‘facts'. Equally ironic is what happened to the afterlife of how the event was understood. This article seeks to rescue the Hong Kong poisoning from being a freakish and isolated footnote of only local interest. Accepting this historical verdict would be a mistake as it is of significance not only at a local level, but geopolitically in Britain and across the empire

Quantum dot-doped porous silicon metal–semiconductor metal photodetector

In this paper, we report on the enhancement of spectral photoresponsivity of porous silicon metal–semiconductor metal (PS-MSM) photodetector embedded with colloidal quantum dots (QDs) inside the pore layer. The detection efficiency of QDs/PS hybrid-MSM photodetector was enhanced by five times larger than that of the undoped PS-MSM photodetector. The bandgap alignment between PS (approximately 1.77 eV) and QDs (approximately 1.91 eV) facilitates the photoinduced electron transfer from QDs to PS whereby enhancing the photoresponsivity. We also showed that the photoresponsitivity of QD/PS hybrid-MSM photodetector depends on the number of layer coatings of QDs and the pore sizes of PS.Published versio

Physical inactivity is a strong risk factor for stroke in the oldest old: Findings from a multi-ethnic population (the Northern Manhattan Study)

Background The fastest growing segment of the population is those age ≥80 who have the highest stroke incidence. Risk factor management is complicated by polypharmacy-related adverse events. Aims To characterize the impact of physical inactivity for stroke by age in a multi-ethnic prospective cohort study (NOMAS, n = 3298). Methods Leisure time physical activity was assessed by a validated questionnaire and our primary exposure was physical inactivity (PI). Participants were followed annually for incident stroke. We fit Cox-proportional hazard models to calculate hazard ratios and 95% confidence intervals (HR 95% CI) for the association of PI and other risk factors with risk of stroke including two-way interaction terms between the primary exposures and age (<80 vs. ≥80). Results The mean age was 69 ± 10.3 years and 562 (17%) were ≥80 at enrolment. PI was common in the cohort (40.8%). Over a median of 14 years, we found 391 strokes. We found a significant interaction of age ≥80 on the risk of stroke with PI (p = 0.03). In stratified models, PI versus any activity (adjusted HR 1.60, 95%CI 1.05–2.42) was associated with an increased risk of stroke among those ≥80. Conclusion Physical inactivity is a treatable risk factor for stroke among those older than age 80. Improving activity may reduce the risk of stroke in this segment of the population