Quantum engineering of atomic phase-shifts in optical clocks

Quantum engineering of time-separated Raman laser pulses in three-level systems is presented to produce an ultra-narrow optical transition in bosonic alkali-earth clocks free from light shifts and with a significantly reduced sensitivity to laser parameter fluctuations. Based on a quantum artificial complex-wave-function analytical model, and supported by a full density matrix simulation including a possible residual effect of spontaneous emission from the intermediate state, atomic phase-shifts associated to Ramsey and Hyper-Ramsey two-photon spectroscopy in optical clocks are derived. Various common-mode Raman frequency detunings are found where the frequency shifts from off-resonant states are canceled, while strongly reducing their uncertainties at the 10$^{-18}$ level of accuracy.Comment: accepted for publication in PR

Evolution of the Freshwater Sardinella, Sardinella Tawilis (Clupeiformes: Clupeidae), in Taal Lake, Philippines and Identification of iIts Marine Sister-Species, Sardinella Hualiensis

We identify the sister species of the world\u27s only freshwater sardinella, Sardinella tawilis (Herre, 1927) of Taal Lake, Philippines as the morphologically-similar marine Taiwanese sardinella Sardinella hualiensis (Chu and Tsai, 1958). Evidence of incomplete lineage sorting and a species tree derived from three mitochondrial genes and one nuclear gene indicate that S. tawilis diverged from S. hualiensis in the late Pleistocene. Neutrality tests, mismatch distribution analysis, sequence diversity indices, and species tree analysis indicate populations of both species have long been stable and that the divergence between these two lineages occurred prior to the putative 18th century formation of Taal Lake

Hidden Diversity in Sardines: Genetic and Morphological Evidence for Cryptic Species in the Goldstripe Sardinella, Sardinella gibbosa (Bleeker, 1849)

Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine

So, You Want to Use Next Generation Sequencing In Marine Systems? Insight from the Pan Pacific Advanced Studies Institute

The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled Genomic Applications to Marine Science and Resource Management in Southeast Asia was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions

So, You Want to Use Next-Generation Sequencing in Marine Systems? Insight from the Pan-Pacific Advanced Studies Institute

The emerging field of next-generation sequencing (NGS) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in Southeast Asia. The first Pan-Pacific Advanced Studies Institute (PacASI) entitled “Genomic Applications to Marine Science and Resource Management in Southeast Asia” was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGS in helping address the aforementioned challenges. Here we synthesize discussions held during the PacASI to provide perspectives and guidance to help scientists new to NGS choose among the variety of available advanced genomic methodologies specifically for marine science questions

Interleukin-6 gene (IL-6): a possible role in brain morphology in the healthy adult brain

Background: Cytokines such as interleukin 6 (IL-6) have been implicated in dual functions in neuropsychiatric disorders. Little is known about the genetic predisposition to neurodegenerative and neuroproliferative properties of cytokine genes. In this study the potential dual role of several IL-6 polymorphisms in brain morphology is investigated. Methodology: In a large sample of healthy individuals (N = 303), associations between genetic variants of IL-6 (rs1800795; rs1800796, rs2069833, rs2069840) and brain volume (gray matter volume) were analyzed using voxel-based morphometry (VBM). Selection of single nucleotide polymorphisms (SNPs) followed a tagging SNP approach (e.g., Stampa algorigthm), yielding a capture 97.08% of the variation in the IL-6 gene using four tagging SNPs. Principal findings/results: In a whole-brain analysis, the polymorphism rs1800795 (−174 C/G) showed a strong main effect of genotype (43 CC vs. 150 CG vs. 100 GG; x = 24, y = −10, z = −15; F(2,286) = 8.54, puncorrected = 0.0002; pAlphaSim-corrected = 0.002; cluster size k = 577) within the right hippocampus head. Homozygous carriers of the G-allele had significantly larger hippocampus gray matter volumes compared to heterozygous subjects. None of the other investigated SNPs showed a significant association with grey matter volume in whole-brain analyses. Conclusions/significance: These findings suggest a possible neuroprotective role of the G-allele of the SNP rs1800795 on hippocampal volumes. Studies on the role of this SNP in psychiatric populations and especially in those with an affected hippocampus (e.g., by maltreatment, stress) are warranted.Bernhard T Baune, Carsten Konrad, Dominik Grotegerd, Thomas Suslow, Eva Birosova, Patricia Ohrmann, Jochen Bauer, Volker Arolt, Walter Heindel, Katharina Domschke, Sonja Schöning, Astrid V Rauch, Christina Uhlmann, Harald Kugel and Udo Dannlowsk

Oynophagia in patients after dental extraction: surface electromyography study

OBJECTIVES: Surface electromyographic (sEMG) studies were performed on 40 adult patients following extraction of lower third and second molars to research the approach and limitations of sEMG evaluation of their odynophagia complaints. METHODS: Parameters evaluated during swallowing and drinking include the timing, number of swallows per 100 cc of water, and range (amplitude) of EMG activity of m. masseter, infrahyoid and submental-submandibular group. The above mentioned variables (mean + standard deviation) were measured for the group of dental patients (n = 40) and control group of healthy adults (n = 40). RESULTS: The duration of swallows and drinking in all tests showed increase in dental patients' group, in which this tendency is statistically significant. There was no statistically significant difference between male and female adults' duration and amplitude of muscle activity during continuous drinking in both groups (p = 0.05). The mean of electric activity (in μV) of m. masseter was significantly lower in the dental patients' group in comparison with control group. The electric activity of submental-submandimular and infrahyoid muscle groups was the same in both groups. CONCLUSION: Surface EMG of swallowing is a simple and reliable noninvasive method for evaluation of odynophagia/dysphagia complaints following dental extraction with low level of discomfort of the examination. The surface EMG studies prove that dysphagia following dental extraction and molar surgery has oral origin, does not affect pharingeal segment and submental-submandibular muscle group. This type of dysphagia has clear EMG signs: increased duration of single swallow, longer drinking time, low range of electric activity of m. masseter, normal range of activity of submental-submandibular muscle group, and the "dry swalow" aftereffect. The data can be used for evaluation of complaints and symptoms, as well as for comparison purposes in pre- and postoperative stages and in EMG monitoring during treatment of post-surgical oral cavity discomfort and dysphagia

In-Silico Patterning of Vascular Mesenchymal Cells in Three Dimensions

Cells organize in complex three-dimensional patterns by interacting with proteins along with the surrounding extracellular matrix. This organization provides the mechanical and chemical cues that ultimately influence a cell's differentiation and function. Here, we computationally investigate the pattern formation process of vascular mesenchymal cells arising from their interaction with Bone Morphogenic Protein-2 (BMP-2) and its inhibitor, Matrix Gla Protein (MGP). Using a first-principles approach, we derive a reaction-diffusion model based on the biochemical interactions of BMP-2, MGP and cells. Simulations of the model exhibit a wide variety of three-dimensional patterns not observed in a two-dimensional analysis. We demonstrate the emergence of three types of patterns: spheres, tubes, and sheets, and show that the patterns can be tuned by modifying parameters in the model such as the degradation rates of proteins and chemotactic coefficient of cells. Our model may be useful for improved engineering of three-dimensional tissue structures as well as for understanding three dimensional microenvironments in developmental processes.National Institutes of Health (U.S.) (GM69811)United States. Dept. of Energy (DOE CSGF fellowship