Description of W.H.O.I. rock dredge samples : volume 3

This report is Volume III of DESCRIPTIONS OF WHOI ROCK DREDGE SAMPLES. This series represents a major effort to catalog the rock dredge samples in the WHOI Sea Floor Samples collection, and to disseminate this information throughout the scientific community. Volume III contains sample descriptions and station data for the dredge stations from five cruises during the period September 1978 through December 1980. The material in this and subsequent volumes of rock descriptions was largely prepared onboard ship by the participating scientists. Volumes I and II are now being prepared by the WHOI Curatorial staff, and describe material in the rock collection obtained prior to 1978. Volume III is being printed prior to volumes I and II because of the excellent documentation of the samples represented in this volume, and because more effort remains in documenting the samples obtained on some of the older cruises. We expect that volumes I and II will be printed and distributed with in the next year.Prepared for the National Science Foundation under Grant OCE 78-25231

Possible link between Earth's rotation rate and oxygenation

The biotic and abiotic controls on major shifts in atmospheric oxygen and the persistence of low-oxygen periods over a majority of Earth’s history remain under debate. Explanations of Earth’s stepwise pattern of oxygenation have mostly neglected the effect of changing diel illumination dynamics linked to daylength, which has increased through geological time due to Earth’s rotational deceleration caused by tidal friction. Here we used microsensor measurements and dynamic modelling of interfacial solute fluxes in cyanobacterial mats to investigate the effect of changing daylength on Precambrian benthic ecosystems. Simulated increases in daylength across Earth’s historical range boosted the diel benthic oxygen export, even when the gross photosynthetic production remained constant. This fundamental relationship between net productivity and daylength emerges from the interaction of diffusive mass transfer and diel illumination dynamics, and is amplified by metabolic regulation and microbial behaviour. We found that the resultant daylength-driven surplus organic carbon burial could have shaped the increase in atmospheric oxygen that occurred during the Great and Neoproterozoic Oxidation Events. Our suggested mechanism, which links the coinciding increases in daylength and atmospheric oxygen via enhanced net productivity, reveals a possible contribution of planetary mechanics to the evolution of Earth’s biology and geochemistry

Enantiomerically pure β-phenylalanine analogues from α–β-phenylalanine mixtures in a single reactive extraction step

An efficient and selective method for the extraction of α-amino acids in preference over their β-isomers using PdCl2(PPh3)2 was discovered, which enables the separation of product mixtures obtained in the enantioselective enzymatic formation of β-amino acids.

Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

High-throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double-digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high-throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/136081/1/Nazareno et al. 2017a.pdfDescription of Nazareno et al. 2017a.pdf : Main articl

Comparison of a combined quantum mechanics/interatomic potential function approach with its periodic quantum-mechanical limit: Proton siting and ammonia adsorption in zeolite chabazite

Published versio

Interrogation of caesium atoms in a fountain clock by a femtosecond laser microwave oscillator

A caesium fountain clock is operated utilizing a microwave oscillator that derives its frequency stability from a stable laser by means of a fiber-laser femtosecond frequency comb. This oscillator is based on the technology developed for optical clocks and replaces the quartz based microwave oscillator commonly used in fountain clocks. As a result, a significant decrease of the frequency instability of the fountain clock is obtained, reaching 0.74E-14 at 100 s averaging time. We could demonstrate that for a significant range of detected atom numbers the instability is limited by quantum projection noise only, and that for the current status of this fountain clock the new microwave source poses no limit on the achievable frequency instability.Comment: 4 pages, 4 figure

Sympathetic Cooling of Mixed Species Two-Ion Crystals for Precision Spectroscopy

Sympathetic cooling of trapped ions has become an indispensable tool for quantum information processing and precision spectroscopy. In the simplest situation a single Doppler-cooled ion sympathetically cools another ion which typically has a different mass. We analytically investigate the effect of the mass ratio of such an ion crystal on the achievable temperature limit in the presence of external heating. As an example, we show that cooling of a single Al+ with Be+, Mg+ and Ca+ ions provides similar results for heating rates typically observed in ion traps, whereas cooling ions with a larger mass perform worse. Furthermore, we present numerical simulation results of the rethermalisation dynamics after a background gas collision for the Al+/Ca+ crystal for different cooling laser configurations.Comment: Made Graphics black & white print compatible, clarified abstract and summar

Early Contrast Enhancement: a novel Magnetic Resonance Imaging biomarker of pleural malignancy

Introduction: Pleural Malignancy (PM) is often occult on subjective radiological assessment. We sought to define a novel, semi-objective Magnetic Resonance Imaging (MRI) biomarker of PM, targeted to increased tumour microvessel density (MVD) and applicable to minimal pleural thickening. Materials and methods: 60 consecutive patients with suspected PM underwent contrast-enhanced 3-T MRI then pleural biopsy. In 58/60, parietal pleura signal intensity (SI) was measured in multiple regions of interest (ROI) at multiple time-points, generating ROI SI/time curves and Mean SI gradient (MSIG: SI increment/time). The diagnostic performance of Early Contrast Enhancement (ECE; which was defined as a SI peak in at least one ROI at or before 4.5 min) was compared with subjective MRI and Computed Tomography (CT) morphology results. MSIG was correlated against tumour MVD (based on Factor VIII immunostain) in 31 patients with Mesothelioma. Results: 71% (41/58) patients had PM. Pleural thickening was <10 mm in 49/58 (84%). ECE sensitivity was 83% (95% CI 61–94%), specificity 83% (95% CI 68–91%), positive predictive value 68% (95% CI 47–84%), negative predictive value 92% (78–97%). ECE performance was similar or superior to subjective CT and MRI. MSIG correlated with MVD (r = 0.4258, p = .02). Discussion: ECE is a semi-objective, perfusion-based biomarker of PM, measurable in minimal pleural thickening. Further studies are warranted

Unloading work of breathing during high-frequency oscillatory ventilation: a bench study

INTRODUCTION: With the 3100B high-frequency oscillatory ventilator (SensorMedics, Yorba Linda, CA, USA), patients' spontaneous breathing efforts result in a high level of imposed work of breathing (WOB). Therefore, spontaneous breathing often has to be suppressed during high-frequency oscillatory ventilation (HFOV). A demand-flow system was designed to reduce imposed WOB. METHODS: An external gas flow controller (demand-flow system) accommodates the ventilator fresh gas flow during spontaneous breathing simulation. A control algorithm detects breathing effort and regulates the demand-flow valve. The effectiveness of this system has been evaluated in a bench test. The Campbell diagram and pressure time product (PTP) are used to quantify the imposed workload. RESULTS: Using the demand-flow system, imposed WOB is considerably reduced. The demand-flow system reduces inspiratory imposed WOB by 30% to 56% and inspiratory imposed PTP by 38% to 59% compared to continuous fresh gas flow. Expiratory imposed WOB was decreased as well by 12% to 49%. In simulations of shallow to normal breathing for an adult, imposed WOB is 0.5 J l(-1 )at maximum. Fluctuations in mean airway pressure on account of spontaneous breathing are markedly reduced. CONCLUSION: The use of the demand-flow system during HFOV results in a reduction of both imposed WOB and fluctuation in mean airway pressure. The level of imposed WOB was reduced to the physiological range of WOB. Potentially, this makes maintenance of spontaneous breathing during HFOV possible and easier in a clinical setting. Early initiation of HFOV seems more possible with this system and the possibility of weaning of patients directly on a high-frequency oscillatory ventilator is not excluded either