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We report the properties of two new series of compounds that show the ferroelectric nematic phase in which the length of a terminal chain is varied. The longer the terminal chain, the weaker the dipole-dipole interactions of the molecules are along the director, and thus the lower the temperature at which the axially ferroelectric nematic phase is formed. For homologues of intermediate chain length, between the non-polar and ferroelectric nematic phases, there is a wide temperature range nematic phase with antiferroelectric character. The size of the antiparallel ferroelectric domains critically increases upon transition to the ferroelectric phase. In dielectric studies, both collective ("ferroelectric" and non-collective fluctuations are present, the "ferroelectric" mode softens weakly at the N-NX phase transition because the polar order in this phase is weak. The transition to the NF phase is characterized by a much stronger lowering of the mode relaxation frequency and an increase in its strength, typical critical behavior is observed.

A critical end point above which an isotropic phase continuously evolves into a polar (ferroelectric) nematic phase with an increasing electric field is found in a ferroelectric nematic liquid crystalline material. The critical end point is approximately 30 K above the zero-field transition temperature from the isotropic to nematic phase and at an electric field of the order of 10 V/micron. Such systems are interesting from the application point of view because a strong birefringence can be induced in a broad temperature range in an optically isotropic phase.

Elastic moduli of liquid crystals, known as Frank constants, are of quintessential importance for understanding fundamental properties of these materials and for the design of their applications. Although there are many methods to measure the Frank constants in the nematic phase, little is known about the elastic constants of the chiral version of the nematic, the so-called cholesteric liquid crystal, since the helicoidal structure of the cholesteric renders these methods inadequate. Here we present a technique to measure the bend modulus $K_{33}$ of cholesterics that is based on the electrically tunable reflection of light at an oblique helicoidal $Ch_{OH}$ cholesteric structure. $K_{33}$ is typically smaller than 0.6 pN, showing a non-monotonous temperature dependence with a slight increase near the transition to the twist-bend phase. $K_{33}$ depends strongly on the molecular composition. In particular, chiral mixtures that contain the flexible dimer 1'',7''-bis(4-cyanobiphenyl-4'-yl) heptane (CB7CB) and rod-like molecules such as pentylcyanobiphenyl (5CB) show a $K_{33}$ value that is 5 times smaller than $K_{33}$ of pure CB7CB or of mixtures of CB7CB with chiral dopants. Furthermore, $K_{33}$ in CB11CB doped with a chiral agent is noticeably smaller than $K_{33}$ in a similarly doped CB7CB which is explained by the longer flexible link in CB11CB. The proposed technique allows a direct in-situ determination of how the molecular composition, molecular structure and molecular chirality affect the elastic properties of chiral liquid crystals., Comment: 20 pages, 8 figures

We describe the interface between measure theoretic probability and causal inference by constructing causal models on probability spaces within the potential outcomes framework. We find that measure theory provides a precise and instructive language for causality and that consideration of the probability spaces underlying causal models offers clarity into central concepts of causal inference. By closely studying simple, instructive examples, we demonstrate insights into causal effects, causal interactions, matching procedures, and randomization. Additionally, we introduce a simple technique for visualizing causal models on probability spaces that is useful both for generating examples and developing causal intuition. Finally, we provide an axiomatic framework for causality and make initial steps towards a formal theory of general causal models.

In many biological materials with a hierarchical structure there is an intriguing and unique mechanism responsible for the 'propagation' of order from the molecular to the nano- or micro-scale level. Here we present a much simpler molecular system built of achiral mesogenic dimeric molecules that shows a similar complexity with four levels of structural chirality (i) layer chirality, (ii) helicity of a basic 4-layer repeating unit, (iii) a helix with a pitch of several layers and (iv) mesoscopic helical filaments. As seen in many biological systems, there is a coupling between chirality at different levels. The structures were identified by a combination of hard and soft x-ray diffraction measurements, optical studies and theoretical modelling.

The critical behavior at the transition from uniform nematic to twist-bend modulated nematic phase is revealed and shown to be well explained by the mean field approximation. The study was performed on a group of materials that exhibit an unusually broad temperature range of the nematic phase above the twist-bend modulated nematic phase, so the critical range in which the order parameter fluctuations are strong and can be experimentally observed is wide. The formation of instantaneous helices is observed already several degrees above the transition temperature, strongly influencing the birefringence of the system. The analysis of a critical part of the birefringence changes provides a set of critical exponents that are consistent with the mean field approximation, indicating a large correlation length of helical fluctuations in the nematic phase.

We synthesized the liquid crystal dimer and trimer members of a series of flexible linear oligomers and characterized their microscopic and nanoscopic properties using resonant soft x-ray scattering and a number of other experimental techniques. On the microscopic scale, the twist-bend phases of the dimer and trimer appear essentially identical. However, while the liquid crystal dimer exhibits a temperature-dependent variation of its twist-bend helical pitch varying from 100 - 170 {\AA} on heating, the trimer exhibits an essentially temperature-independent pitch of 66 {\AA}, significantly shorter than those reported for other twist-bend forming materials in the literature. We attribute this to a specific combination of intrinsic conformational bend of the trimer molecules and a sterically favorable intercalation of the trimers over a commensurate fraction (two-thirds) of the molecular length. We develop a geometric model of the twist-bend phase for these materials with the molecules arranging into helical chain structures, and we fully determine their respective geometric parameters., Comment: supplemental information included

A series of asymmetric dimers with an odd number of atoms in the spacer were found to form different types of twisted structures despite being achiral. The formation of a variety of helical structures is accompanied by a gradual freezing of molecular rotation. The tight pitch heliconical nematic (NTB) phase and heliconical tilted smectic C (SmCTB) phase are formed. In the lowest temperature smectic phase, HexI, the twist is expressed through the formation of hierarchical structure: nano-scale helices and mesoscopic helical filaments. The short pitch helical structure in smectic phases is confirmed by resonant x-ray measurements.

The summit of the Antarctic plateau, Dome A, is proving to be an excellent site for optical, NIR, and THz astronomical observations. GATTINI was a wide-field camera installed on the PLATO instrument module as part of the Chinese-led traverse to Dome A in January, 2009. We present here the measurements of sky brightness with the Gattini ultra-large field of view (90 deg x 90 deg) in the photometric B-, V-, and R-bands, cloud cover statistics measured during the 2009 winter season, and an estimate of the sky transparency. A cumulative probability distribution indicates that the darkest 10% of the nights at Dome A have sky brightness of S_B = 22.98, S_V = 21.86, and S_R = 21.68 mag arcsec^{-2}. These values were obtained around the year 2009 with minimum aurora, and they are comparable to the faintest sky brightness at Mauna Kea and the best sites of northern Chile. Since every filter includes strong auroral lines that effectively contaminate the sky brightness measurements, for instruments working around the auroral lines, either with custom filters or with high spectral resolution instruments, these values could be easily obtained on a more routine basis. In addition, we present example light curves for bright targets to emphasize the unprecedented observational window function available from this ground-based site. These light curves will be published in a future paper., Comment: 36 pages, 18 figure, submitted to AJ

We consider the problem of extracting a low-dimensional, linear latent variable structure from high-dimensional random variables. Specifically, we show that under mild conditions and when this structure manifests itself as a linear space that spans the conditional means, it is possible to consistently recover the structure using only information up to the second moments of these random variables. This finding, specialized to one-parameter exponential families whose variance function is quadratic in their means, allows for the derivation of an explicit estimator of such latent structure. This approach serves as a latent variable model estimator and as a tool for dimension reduction for a high-dimensional matrix of data composed of many related variables. Our theoretical results are verified by simulation studies and an application to genomic data.

Cholesteric liquid crystals with helicoidal molecular architecture are known for their ability to selectively reflect light with the wavelength that is determined by the periodicity of molecular orientations. Here we demonstrate that by using a cholesteric with oblique helicoidal(heliconical) structure, as opposed to the classic right-angle helicoid, one can vary the wavelength of selectively reflected light in a broad spectral range, from ultraviolet to visible and infrared (360-1520 nm for the same chemical composition) by simply adjusting the electric field applied parallel to the helicoidal axis. The effect exists in a wide temperature range (including the room temperatures) and thus can enable many applications that require dynamically controlled transmission and reflection of electromagnetic waves, from energy-saving smart windows to tunable organic lasers, reflective color display, and transparent see-through displays., Comment: 11 pages, 5figures

E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain families. Here we formally show that for "stratified" multiple hypothesis testing problems, controlling the local False Discovery Rate (lFDR) per stratum, or partition, yields the most predictions across the data at any given threshold on the FDR or E-value over all strata combined. For the important problem of protein domain prediction, a key step in characterizing protein structure, function and evolution, we show that stratifying statistical tests by domain family yields excellent results. We develop the first FDR-estimating algorithms for domain prediction, and evaluate how well thresholds based on q-values, E-values and lFDRs perform in domain prediction using five complementary approaches for estimating empirical FDRs in this context. We show that stratified q-value thresholds substantially outperform E-values. Contradicting our theoretical results, q-values also outperform lFDRs; however, our tests reveal a small but coherent subset of domain families, biased towards models for specific repetitive patterns, for which FDRs are greatly underestimated due to weaknesses in random sequence models. Usage of lFDR thresholds outperform q-values for the remaining families, which have as-expected noise, suggesting that further improvements in domain predictions can be achieved with improved modeling of random sequences. Overall, our theoretical and empirical findings suggest that the use of stratified q-values and lFDRs could result in improvements in a host of structured multiple hypothesis testing problems arising in bioinformatics, including genome-wide association studies, orthology prediction, motif scanning, and multi-microarray analyses., Comment: 31 pages, 8 figures, does not include supplementary files

We present spectral line images of [CI] 809 GHz, CO J=1-0 115 GHz and HI 1.4 GHz line emission, and calculate the corresponding C, CO and H column densities, for a sinuous, quiescent Giant Molecular Cloud about 5 kpc distant along the l=328{\deg} sightline (hereafter G328) in our Galaxy. The [CI] data comes from the High Elevation Antarctic Terahertz (HEAT) telescope, a new facility on the summit of the Antarctic plateau where the precipitable water vapor falls to the lowest values found on the surface of the Earth. The CO and HI datasets come from the Mopra and Parkes/ATCA telescopes, respectively. We identify a filamentary molecular cloud, ~75 x 5 pc long with mass ~4 x 10E4 Msun and a narrow velocity emission range of just 4 km/s. The morphology and kinematics of this filament are similar in CO, [CI] and HI, though in the latter appears as self-absorption. We calculate line fluxes and column densities for the three emitting species, which are broadly consistent with a PDR model for a GMC exposed to the average interstellar radiation field. The [C/CO] abundance ratio averaged through the filament is found to be approximately unity. The G328 filament is constrained to be cold (Tdust < 20K) by the lack of far-IR emission, to show no clear signs of star formation, and to only be mildly turbulent from the narrow line width. We suggest that it may represent a GMC shortly after formation, or perhaps still be in the process of formation., Comment: 29 pages, 5 figures. Accepted for publication in The Astrophysical Journal (2014)

Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that allow for complex population structure. We formulate two general probabilistic models, and we propose computationally efficient algorithms to estimate them. First, we show how principal component analysis (PCA) can be utilized to estimate a general model that includes the well-known Pritchard-Stephens-Donnelly mixed-membership model as a special case. Noting some drawbacks of this approach, we introduce a new "logistic factor analysis" (LFA) framework that seeks to directly model the logit transformation of probabilities underlying observed genotypes in terms of latent variables that capture population structure. We demonstrate these advances on data from the human genome diversity panel and 1000 genomes project, where we are able to identify SNPs that are highly differentiated with respect to structure while making minimal modeling assumptions., Comment: Wei Hao and Minsun Song contributed equally to this work

We present results from a season of observations with the Chinese Small Telescope ARray (CSTAR), obtained over 183 days of the 2010 Antarctic winter. We carried out high-cadence time-series aperture photometry of 20,000 stars with i<15.3 mag located in a 23 square-degree region centered on the south celestial pole. We identified 188 variable stars, including 67 new objects relative to our 2008 observations, thanks to broader synoptic coverage, a deeper magnitude limit and a larger field of view. We used the photometric data set to derive site statistics from Dome A. Based on two years of observations, we find that extinction due to clouds at this site is less than 0.1 and 0.4 mag during 45% and 75% of the dark time, respectively., Comment: Accepted for publication in the Astronomical Journal. Light curves and finding charts of all variable stars will be made available at http://casdc.china-vo.org/data/cstar

There are a number of well-established methods such as principal components analysis (PCA) for automatically capturing systematic variation due to latent variables in large-scale genomic data. PCA and related methods may directly provide a quantitative characterization of a complex biological variable that is otherwise difficult to precisely define or model. An unsolved problem in this context is how to systematically identify the genomic variables that are drivers of systematic variation captured by PCA. Principal components (and other estimates of systematic variation) are directly constructed from the genomic variables themselves, making measures of statistical significance artificially inflated when using conventional methods due to over-fitting. We introduce a new approach called the jackstraw that allows one to accurately identify genomic variables that are statistically significantly associated with any subset or linear combination of principal components (PCs). The proposed method can greatly simplify complex significance testing problems encountered in genomics and can be utilized to identify the genomic variables significantly associated with latent variables. Using simulation, we demonstrate that our method attains accurate measures of statistical significance over a range of relevant scenarios. We consider yeast cell-cycle gene expression data, and show that the proposed method can be used to straightforwardly identify statistically significant genes that are cell-cycle regulated. We also analyze gene expression data from post-trauma patients, allowing the gene expression data to provide a molecularly-driven phenotype. We find a greater enrichment for inflammatory-related gene sets compared to using a clinically defined phenotype. The proposed method provides a useful bridge between large-scale quantifications of systematic variation and gene-level significance analyses., Comment: 35 pages, 1 table, 6 main figures, 7 supplementary figures

Background: Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features for association with disease. We propose a new approach, called gene set bagging, for measuring the stability of ranking procedures using predefined gene sets. Gene set bagging involves resampling the original high-throughput data, performing gene-set analysis on the resampled data, and confirming that biological categories replicate. This procedure can be thought of as bootstrapping gene-set analysis and can be used to determine which are the most reproducible gene sets. Results: Here we apply this approach to two common genomics applications: gene expression and DNA methylation. Even with state-of-the-art statistical ranking procedures, significant categories in a gene set enrichment analysis may be unstable when subjected to resampling. Conclusions: We demonstrate that gene lists are not necessarily stable, and therefore additional steps like gene set bagging can improve biological inference of gene set analysis., Comment: 3 Figures

A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for determining the existence, strength, and type of relationship between high-resolution chromatin structure in terms of DNaseI hypersensitivity (DHS) and genome-wide gene expression levels in 20 diverse human cell lines. We show that ~25% of genes show cell-type specific expression explained by alterations in chromatin structure. We find that distal regions of chromatin structure (e.g., +/- 200kb) capture more genes with this relationship than local regions (e.g., +/- 2.5kb), yet the local regions show a more pronounced effect. By exploiting variation across cell-types, we were capable of pinpointing the most likely hypersensitive sites related to cell-type specific expression, which we show have a range of contextual usages. This quantitative framework is likely applicable to other settings aimed at relating continuous genomic measurements to gene expression variation., Comment: First version completed December 2010. Last modified August 2011. We remain in the submission and publication process, so the content of this manuscript may change in the future. With the recent publication of 30 ENCODE papers, we would like to share our related work with the research community. The Supplementary Information may be found among the source files, specifically in arxiv_SI.pdf

Dome A on the Antarctic plateau is likely one of the best observing sites on Earth thanks to the excellent atmospheric conditions present at the site during the long polar winter night. We present high-cadence time-series aperture photometry of 10,000 stars with i<14.5 mag located in a 23 square-degree region centered on the south celestial pole. The photometry was obtained with one of the CSTAR telescopes during 128 days of the 2008 Antarctic winter. We used this photometric data set to derive site statistics for Dome A and to search for variable stars. Thanks to the nearly-uninterrupted synoptic coverage, we find 6 times as many variables as previous surveys with similar magnitude limits. We detected 157 variable stars, of which 55% are unclassified, 27% are likely binaries and 17% are likely pulsating stars. The latter category includes delta Scuti, gamma Doradus and RR Lyrae variables. One variable may be a transiting exoplanet., Comment: Accepted for publication in the Astronomical Journal. PDF version with high-resolution figures available at http://faculty.physics.tamu.edu/lmacri/papers/wang11.pdf

A 'PILOT-Like Telescope' is likely to have differences in science goals to the original PILOT. Furthermore, our understanding of the environmental conditions at Dome C has changed significantly since the start of the PILOT design study in June 2007. Therefore, it is timely to re-examine some of the basic design decisions. We present here one alternative concept: a silicon-carbide, GLAO-assisted, three-mirror anastigmat, and possibly equatorial, PILOT-Like-Telescope., Comment: 4 pages. NOT published in "3rd ARENA Conference: An Astronomical Observatory at CONCORDIA (Dome C, Antarctica) L. Spinoglio and N. Epchtein (eds)", due to an error in compilation of the proceedings

The Antarctic plateau contains the best sites on earth for many forms of astronomy, but none of the existing bases was selected with astronomy as the primary motivation. In this article, we try to systematically compare the merits of potential observatory sites.We include South Pole, Domes A, C, and F, and also Ridge B (running northeast from Dome A), and what we call "Ridge A" (running southwest from Dome A). Our analysis combines satellite data, published results, and atmospheric models, to compare the boundary layer, weather, aurorae, airglow, precipitable water vapor, thermal sky emission, surface temperature, and the free atmosphere, at each site. We find that all Antarctic sites are likely to be compromised for optical work by airglow and aurorae. Of the sites with existing bases, Dome A is easily the best overall; but we find that Ridge A offers an even better site. We also find that Dome F is a remarkably good site. Dome C is less good as a thermal infrared or terahertz site, but would be able to take advantage of a predicted "OH hole" over Antarctica during spring., Comment: Revised version. 16 pages, 21 figures (22 in first version). Submitted to PASP 16/05/09, accepted 13/07/09; published 20/08/09

This white paper is submitted to the Astronomy and Astrophysics 2010 Decadal Survey (Astro2010)1 Committee on the State of the Profession to emphasize the potential of the Stratospheric Observatory for Infrared Astronomy (SOFIA) to contribute to the training of instrumentalists and observers, and to related technology developments. This potential goes beyond the primary mission of SOFIA, which is to carry out unique, high priority astronomical research. SOFIA is a Boeing 747SP aircraft with a 2.5 meter telescope. It will enable astronomical observations anywhere, any time, and at most wavelengths between 0.3 microns and 1.6 mm not accessible from ground-based observatories. These attributes, accruing from the mobility and flight altitude of SOFIA, guarantee a wealth of scientific return. Its instrument teams (nine in the first generation) and guest investigators will do suborbital astronomy in a shirt-sleeve environment. The project will invest $10M per year in science instrument development over a lifetime of 20 years. This, frequent flight opportunities, and operation that enables rapid changes of science instruments and hands-on in-flight access to the instruments, assure a unique and extensive potential - both for training young instrumentalists and for encouraging and deploying nascent technologies. Novel instruments covering optical, infrared, and submillimeter bands can be developed for and tested on SOFIA by their developers (including apprentices) for their own observations and for those of guest observers, to validate technologies and maximize observational effectiveness., Comment: 10 pages, no figures, White Paper for Astro 2010 Survey Committee on State of the Profession

This paper has been withdrawn., Comment: This paper has been withdrawn

The recent discovery of exceptional seeing conditions at Dome C, Antarctica, raises the possibility of constructing an optical observatory there with unique capabilities. However, little is known from an astronomer's perspective about the optical sky brightness and extinction at Antarctic sites. We review the contributions to sky brightness at high-latitude sites, and calculate the amount of usable dark time at Dome C. We also explore the implications of the limited sky coverage of high-latitude sites and review optical extinction data from the South Pole. Finally, we examine the proposal of Baldry and Bland-Hawthorn (2001) to extend the amount of usable dark time through the use of polarising filters., Comment: 18 pages, 7 figures, 5 tables, accepted for publication in the March 2006 issue of PASP