Excitonic effects on coherent phonon dynamics in single wall carbon nanotubes

We discuss how excitons can affect the generation of coherent radial breathing modes in ultrafast spectroscopy of single wall carbon nanotubes. Photoexcited excitons can be localized spatially and give rise to a spatially distributed driving force in real space which involves many phonon wavevectors of the exciton-phonon interaction. The equation of motion for the coherent phonons is modeled phenomenologically by the Klein-Gordon equation, which we solve for the oscillation amplitudes as a function of space and time. By averaging the calculated amplitudes per nanotube length, we obtain time-dependent coherent phonon amplitudes that resemble the homogeneous oscillations that are observed in some pump-probe experiments. We interpret this result to mean that the experiments are only able to see a spatial average of coherent phonon oscillations over the wavelength of light in carbon nanotubes and the microscopic details are averaged out. Our interpretation is justified by calculating the time-dependent absorption spectra resulting from the macroscopic atomic displacements induced by the coherent phonon oscillations. The calculated coherent phonon spectra including excitonic effects show the experimentally observed symmetric peaks at the nanotube transition energies in contrast to the asymmetric peaks that would be obtained if excitonic effects were not included.Comment: submitted to Phys. Rev. B on 7 May 2013, revised on 17 July and 13 August 2013, published 30 August 201

Toenail Manganese: A Sensitive and Specific Biomarker of Exposure to Manganese in Career Welders

Manganese (Mn) is an essential trace metal. It is also a component of welding fume. Chronic inhalation of manganese from welding fume has been associated with decreased neurological function. Currently, there is not a universally recognized biomarker for Mn exposure; however, hair and toenails have shown promise. In a cohort of 45 male welders and 35 age-matched factory control subjects, we assessed the sensitivity and specificity of toenail Mn to distinguish occupationally exposed subjects from unexposed controls. Further we examined the exposure time window that best correlates with the proposed biomarker, and investigated if non-occupational exposure factors impacted toenail Mn concentrations. Toenail clippings were analyzed for Mn using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Exposure to respirable Mn-containing particles (<4 µm) was estimated using an exposure model that combines personal air monitoring, work history information, and dietary intake to estimate an individual's exposure to Mn from inhalation of welding fume. We assessed the group differences in toenail concentrations using a Student's t-test between welders and control subjects and performed a receiver operating characteristic (ROC) curve analysis to identify a threshold in toenail concentration that has the highest sensitivity and specificity in distinguishing welders from control subjects. Additionally, we performed mixed-model regressions to investigate the association between different exposure windows and toenail Mn concentrations. We observed that toenail Mn concentrations were significantly elevated among welders compared to control subjects (6.87 ± 2.56 versus 2.70 ± 1.70 µg g-1; P < 0.001). Our results show that using a toenail Mn concentration of 4.14 µg g-1 as cutoff allows for discriminating between controls and welders with 91% specificity and 94% sensitivity [area under curve (AUC) = 0.98]. Additionally, we found that a threshold of 4.66 µg g-1 toenail Mn concentration enables a 90% sensitive and 90% specific discrimination (AUC = 0.96) between subjects with average exposure above or below the American Conference of Governmental Industrial Hygienist (ACGIH) Threshold Limit Value (TLV) of 0.02 mg m-3 during the exposure window of 7-12 months prior to the nail being clipped. Investigating which exposure window was best reflected by toenail Mn reproduced the result from another study of toenail Mn being significantly (P < 0.001) associated with exposure 7-12 months prior to the nail being clipped. Lastly, we found that dietary intake, body mass index, age, smoking status, and ethnicity had no significant effect on toenail Mn concentrations. Our results suggest that toenail Mn is a sensitive, specific, and easy-to-acquire biomarker of Mn exposure, which is feasible to be used in an industrial welder population

Rapid annotation of seizures and interictal-ictal-injury continuum EEG patterns

Background: Manual annotation of seizures and interictal-ictal-injury continuum (IIIC) patterns in continuous EEG (cEEG) recorded from critically ill patients is a time-intensive process for clinicians and researchers. In this study, we evaluated the accuracy and efficiency of an automated clustering method to accelerate expert annotation of cEEG. New method: We learned a local dictionary from 97 ICU patients by applying k-medoids clustering to 592 features in the time and frequency domains. We utilized changepoint detection (CPD) to segment the cEEG recordings. We then computed a bag-of-words (BoW) representation for each segment. We further clustered the segments by affinity propagation. EEG experts scored the resulting clusters for each patient by labeling only the cluster medoids. We trained a random forest classifier to assess validity of the clusters. Results: Mean pairwise agreement of 62.6% using this automated method was not significantly different from interrater agreements using manual labeling (63.8%), demonstrating the validity of the method. We also found that it takes experts using our method 5.31 +/- 4.44 min to label the 30.19 +/- 3.84 h of cEEG data, more than 45 times faster than unaided manual review, demonstrating efficiency. Comparison with existing methods: Previous studies of EEG data labeling have generally yielded similar human expert interrater agreements, and lower agreements with automated methods. Conclusions: Our results suggest that long EEG recordings can be rapidly annotated by experts many times faster than unaided manual review through the use of an advanced clustering method

Real-Time Analysis of Individual Airborne Microparticles Using Laser Ablation Mass Spectroscopy and Genetically Trained Neural Networks

We are developing a method for analysis of airborne microparticles based on laser ablation of individual molecules in an ion trap mass spectrometer. Airborne particles enter the spectrometer through a differentially-pumped inlet, are detected by light scattered from two CW laser beams, and sampled by a pulsed excimer laser as they pass through the center of the ion trap electrodes. After the laser pulse, the stored ions are separated by conventional ion trap methods. The mass spectra are then analyzed using genetically-trained neural networks (NNs). A number of mass spectra are averaged to obtain training cases which contain a recognizable spectral signature. Averaged spectra for a bacteria and a non-bacteria are shown to the NNs, the response evaluated, and the weights of the connections between neurodes adjusted by a Genetic Algorithm (GA) such that the output from the NN ranges from 0 for non-bacteria to 1 for bacteria. This process is iterated until the population of the GA converges or satisfies predetermined stopping criteria. Using this type of bipolar training we have obtained generalizing NNs able to distinguish five new bacteria from five new non-bacteria, none of which were used in training the NN

Anthropogenics: Human Influence on Global and Genetic Homogenization of Parasite Populations

The distribution, abundance, and diversity of life on Earth have been greatly shaped by human activities. This includes the geographic expansion of parasites; however, measuring the extent to which humans have influenced the dissemination and population structure of parasites has been challenging. In-depth comparisons among parasite populations extending to landscape-level processes affecting disease emergence have remained elusive. New research methods have enhanced our capacity to discern human impact, where the tools of population genetics and molecular epidemiology have begun to shed light on our historical and ongoing influence. Only since the 1990s have parasitologists coupled morphological diagnosis, long considered the basis of surveillance and biodiversity studies, with state-of-the-art tools enabling variation to be examined among, and within, parasite populations. Prior to this time, populations were characterized only by phenotypic attributes such as virulence, infectivity, host range, and geographical location. The advent of genetic/molecular methodologies (multilocus allozyme electrophoresis, polymerase chain reaction–DNA [PCR-DNA] fragments analysis, DNA sequencing, DNA microsatellites, single nucleotide polymorphisms, etc.) have transformed our abilities to reveal variation among, and within, populations at local, regional, landscape, and global scales, and thereby enhanced our understanding of the biosphere. Numerous factors can affect population structure among parasites, e.g., evolutionary and ecological history, mode of reproduction and transmission, host dispersal, and life-cycle complexity. Although such influences can vary considerably among parasite taxa, anthropogenic factors are demonstrably perturbing parasite fauna. Minimal genetic structure among many geographically distinct (isolated) populations is a hallmark of human activity, hastened by geographic introductions, environmental perturbation, and global warming. Accelerating environmental change now plays a primary role in defining where hosts, parasites, and other pathogens occur. This review examines how anthropogenic factors serve as drivers of globalization and genetic homogenization of parasite populations and demonstrates the impact that human intervention has had on the global dissemination of parasites and the accompanying diseases

Erratum: Prolonged monitoring of cerebral blood flow and autoregulation with diffuse correlation spectroscopy in neurocritical care patients

Corrected disclosures for the article “Prolonged monitoring of cerebral blood flow and autoregulation with diffuse correlation spectroscopy in neurocritical care patients.” DOI: 10.1117/1.NPh.5.4.045005.Published versio

Genome-Wide Association of Implantable Cardioverter-Defibrillator Activation With Life-Threatening Arrhythmias

OBJECTIVES: To identify genetic factors that would be predictive of individuals who require an implantable cardioverter-defibrillator (ICD), we conducted a genome-wide association study among individuals with an ICD who experienced a life-threatening arrhythmia (LTA; cases) vs. those who did not over at least a 3-year period (controls). BACKGROUND: Most individuals that receive implantable cardioverter-defibrillators never experience a life-threatening arrhythmia. Genetic factors may help identify who is most at risk. METHODS: Patients with an ICD and extended follow-up were recruited from 34 clinical sites with the goal of oversampling those who had experienced LTA, with a cumulative 607 cases and 297 controls included in the analysis. A total of 1,006 Caucasian patients were enrolled during a time period of 13 months. Arrhythmia status of 904 patients could be confirmed and their genomic data were included in the analysis. In this cohort, there were 704 males, 200 females, and the average age was 73.3 years. We genotyped DNA samples using the Illumina Human660 W Genotyping BeadChip and tested for association between genotype at common variants and the phenotype of having an LTA. RESULTS AND CONCLUSIONS: We did not find any associations reaching genome-wide significance, with the strongest association at chromosome 13, rs11856574 at P = 5×10⁻⁶. Loci previously implicated in phenotypes such as QT interval (measure of the time between the start of the Q wave and the end of the T wave as measured by electrocardiogram) were not found to be significantly associated with having an LTA. Although powered to detect such associations, we did not find common genetic variants of large effect associated with having a LTA in those of European descent. This indicates that common gene variants cannot be used at this time to guide ICD risk-stratification. TRIAL REGISTRATION: ClinicalTrials.gov NCT00664807

Comparative Survival of Asian and White Metastatic Castration-Resistant Prostate Cancer Men Treated With Docetaxel

There are few data regarding disparities in overall survival (OS) between Asian and white men with metastatic castration-resistant prostate cancer (mCRPC). We compared OS of Asian and white mCRPC men treated in phase III clinical trials with docetaxel and prednisone (DP) or a DP-containing regimen. Individual participant data from 8820 men with mCRPC randomly assigned on nine phase III trials to receive DP or a DP-containing regimen were combined. Men enrolled in these trials had a diagnosis of prostate adenocarcinoma. The median overall survival was 18.8 months (95% confidence interval [CI] = 17.4 to 22.1 months) and 21.2 months (95% CI = 20.8 to 21.7 months) for Asian and white men, respectively. The pooled hazard ratio for death for Asian men compared with white men, adjusted for baseline prognostic factors, was 0.95 (95% CI = 0.84 to 1.09), indicating that Asian men were not at increased risk of death. This large analysis showed that Asian men did not have shorter OS duration than white men treated with docetaxel

A multi-site campaign to measure solar-like oscillations in Procyon. II. Mode frequencies

We have analyzed data from a multi-site campaign to observe oscillations in the F5 star Procyon. The data consist of high-precision velocities that we obtained over more than three weeks with eleven telescopes. A new method for adjusting the data weights allows us to suppress the sidelobes in the power spectrum. Stacking the power spectrum in a so-called echelle diagram reveals two clear ridges that we identify with even and odd values of the angular degree (l=0 and 2, and l=1 and 3, respectively). We interpret a strong, narrow peak at 446 muHz that lies close to the l=1 ridge as a mode with mixed character. We show that the frequencies of the ridge centroids and their separations are useful diagnostics for asteroseismology. In particular, variations in the large separation appear to indicate a glitch in the sound-speed profile at an acoustic depth of about 1000 s. We list frequencies for 55 modes extracted from the data spanning 20 radial orders, a range comparable to the best solar data, which will provide valuable constraints for theoretical models. A preliminary comparison with published models shows that the offset between observed and calculated frequencies for the radial modes is very different for Procyon than for the Sun and other cool stars. We find the mean lifetime of the modes in Procyon to be 1.29 +0.55/-0.49 days, which is significantly shorter than the 2-4 days seen in the Sun.Comment: accepted for publication in Ap

Hiding in plain sight: discovery and phylogeography of a cryptic species of Trichinella (Nematoda: Trichinellidae) in wolverine (Gulo gulo)

Understanding parasite diversity and distribution is essential in managing the potential impact of para- sitic diseases in animals and people. Imperfect diagnostic methods, however, may conceal cryptic species. Here, we report the discovery and phylogeography of a previously unrecognized species of Trichinella in wolverine (Gulo gulo) from northwestern Canada that was indistinguishable from T. nativa using the stan- dard multiplex PCR assay based on the expansion segment 5 (ESV) of ribosomal DNA. The novel genotype, designated as T13, was discovered when sequencing the mitochondrial genome. Phylogenetic analyses of the mitochondrial genome and of 15 concatenated single-copy orthologs of nuclear DNA indicated a com- mon ancestor for the encapsulated clade is shared by a subclade containing Trichinella spiralis and Trichinella nelsoni, and a subclade containing T13 and remaining taxa: T12 + (T2 + T6) + [(T5 + T9) + (T 3 + T8)]. Of 95 individual hosts from 12 species of mammalian carnivores from northwestern Canada from which larvae were identified as T. nativa on multiplex PCR, only wolverines were infected with T13 (14 of 42 individuals). These infections were single or mixed with T. nativa and/or T6. Visual examination and motility testing confirmed that T13 is encapsulated and likely freeze-tolerant. We developed a new Polymerase Chain Reaction-Restriction Fragment Length Polymorphism which unequivocally distinguishes between T13 and T. nativa. We propose Trichinella chanchalensis n. sp. for T13, based on significant genetic divergence from other species of Trichinella and broad-based sampling of the Trichinella genome. Exploration of Alaskan and Siberian isolates may contribute to further resolution of a phylogeo- graphically complex history for species of Trichinella across Beringia, including Trichinella chanchalensis n. sp. (T13