Developing a western Siberia reference site for tropospheric water vapour isotopologue observations obtained by different techniques (in situ and remote sensing)

Water stable isotopologues provide integrated tracers of the atmospheric water cycle, affected by changes in air mass origin, non-convective and convective processes and continental recycling. Novel remote sensing and in situ measuring techniques have recently offered opportunities for monitoring atmospheric water vapour isotopic composition. Recently developed infrared laser spectrometers allow for continuous in situ measurements of surface water vapour δD_v and δ¹⁸O_v. So far, very few intercomparisons of measurements conducted using different techniques have been achieved at a given location, due to difficulties intrinsic to the comparison of integrated with local measurements. Nudged simulations conducted with high-resolution isotopically enabled general circulation models (GCMs) provide a consistent framework for comparison with the different types of observations. Here, we compare simulations conducted with the ECHAM5-wiso model with two types of water vapour isotopic data obtained during summer 2012 at the forest site of Kourovka, western Siberia: hourly ground-based FTIR total atmospheric columnar δD_v amounts, and in situ hourly Picarro δD_v measurements. There is an excellent correlation between observed and predicted δD_v at surface while the comparison between water column values derived from the model compares well with FTIR estimates

Quantitative constraints on the atmospheric chemistry of nitrogen oxides: An analysis along chemical coordinates

In situ observations Of NO_2, NO, NO_y, ClONO_2, OH, O_3, aerosol surface area, spectrally resolved solar radiation, pressure and temperature obtained from the ER-2 aircraft during the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) experiments are used to examine the factors controlling the fast photochemistry connecting NO and NO_2 and the slower chemistry connecting NO_x and HNO_3. Our analysis uses “chemical coordinates” to examine gradients of the difference between a model and precisely calibrated measurements to provide a quantitative assessment of the accuracy of current photochemical models. The NO/NO_2 analysis suggests that reducing the activation energy for the NO+O_3 reaction by 1.7 kJ/mol will improve model representation of the temperature dependence of the NO/NO_2 ratio in the range 215–235 K. The NO_x/HNO_3 analysis shows that systematic errors in the relative rate coefficients used to describe NO_x loss by the reaction OH + NO_2 → HNO_3 and by the reaction set NO_2 + O_3 → NO_3; NO_2 + NO_3 → N_(2)O_5; N_(2)O_5 + H_(2)O → 2HNO_3 are in error by +8.4% (+30/−45%) (OH+NO_2 too fast) in models using the Jet Propulsion Laboratory 1997 recommendations [DeMore et al., 1997]. Models that use recommendations for OH+NO2 and OH+HNO_3 based on reanalysis of recent and past laboratory measurements are in error by 1.2% (+30/−45%) (OH+NO_2 too slow). The +30%/−45% error limit reflects systematic uncertainties, while the statistical uncertainty is 0.65%. This analysis also shows that the POLARIS observations only modestly constrain the relative rates of the major NO_x production reactions HNO3 + OH → H_(2)O + NO_3 and HNO_3 + hν → OH + NO_2. Even under the assumption that all other aspects of the model are perfect, the POLARIS observations only constrain the rate coefficient for OH+HNO_3 to a range of 65% around the currently recommended value

Higgs After the Discovery: A Status Report

Recently, the ATLAS and CMS collaborations have announced the discovery of a 125 GeV particle, commensurable with the Higgs boson. We analyze the 2011 and 2012 LHC and Tevatron Higgs data in the context of simplified new physics models, paying close attention to models which can enhance the diphoton rate and allow for a natural weak-scale theory. Combining the available LHC and Tevatron data in the ZZ* 4-lepton, WW* 2-lepton, diphoton, and b-bbar channels, we derive constraints on the effective low-energy theory of the Higgs boson. We map several simplified scenarios to the effective theory, capturing numerous new physics models such as supersymmetry, composite Higgs, dilaton. We further study models with extended Higgs sectors which can naturally enhance the diphoton rate. We find that the current Higgs data are consistent with the Standard Model Higgs boson and, consequently, the parameter space in all models which go beyond the Standard Model is highly constrained.Comment: 37 pages; v2: ATLAS dijet-tag diphoton channel added, dilaton and doublet-singlet bugs corrected, references added; v3: ATLAS WW channel included, comments and references adde

Inorganic chlorine partitioning in the summer lower stratosphere: Modeled and measured [ClONO_2]/[HCl] during POLARIS

We examine inorganic chlorine (Cl_y,) partitioning in the summer lower stratosphere using in situ ER-2 aircraft observations made during the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) campaign. New steady state and numerical models estimate [ClONO_2]/[HCl] using currently accepted photochemistry. These models are tightly constrained by observations with OH (parameterized as a function of solar zenith angle) substituting for modeled HO_2 chemistry. We find that inorganic chlorine photochemistry alone overestimates observed [ClONO_2]/[HCl] by approximately 55–60% at mid and high latitudes. On the basis of POLARIS studies of the inorganic chlorine budget, [ClO]/[ClONO_2], and an intercomparison with balloon observations, the most direct explanation for the model-measurement discrepancy in Cl_y, partitioning is an error in the reactions, rate constants, and measured species concentrations linking HCl and ClO (simulated [ClO]/[HCl] too high) in combination with a possible systematic error in the ER-2 ClONO_2 measurement (too low). The high precision of our simulation (±15% 1σ for [ClONO_2]/[HCl], which is compared with observations) increases confidence in the observations, photolysis calculations, and laboratory rate constants. These results, along with other findings, should lead to improvements in both the accuracy and precision of stratospheric photochemical models

Mathematical Properties of a New Levin-Type Sequence Transformation Introduced by \v{C}\'{\i}\v{z}ek, Zamastil, and Sk\'{a}la. I. Algebraic Theory

\v{C}\'{\i}\v{z}ek, Zamastil, and Sk\'{a}la [J. Math. Phys. \textbf{44}, 962 - 968 (2003)] introduced in connection with the summation of the divergent perturbation expansion of the hydrogen atom in an external magnetic field a new sequence transformation which uses as input data not only the elements of a sequence $\{s_n \}_{n=0}^{\infty}$ of partial sums, but also explicit estimates $\{\omega_n \}_{n=0}^{\infty}$ for the truncation errors. The explicit incorporation of the information contained in the truncation error estimates makes this and related transformations potentially much more powerful than for instance Pad\'{e} approximants. Special cases of the new transformation are sequence transformations introduced by Levin [Int. J. Comput. Math. B \textbf{3}, 371 - 388 (1973)] and Weniger [Comput. Phys. Rep. \textbf{10}, 189 - 371 (1989), Sections 7 -9; Numer. Algor. \textbf{3}, 477 - 486 (1992)] and also a variant of Richardson extrapolation [Phil. Trans. Roy. Soc. London A \textbf{226}, 299 - 349 (1927)]. The algebraic theory of these transformations - explicit expressions, recurrence formulas, explicit expressions in the case of special remainder estimates, and asymptotic order estimates satisfied by rational approximants to power series - is formulated in terms of hitherto unknown mathematical properties of the new transformation introduced by \v{C}\'{\i}\v{z}ek, Zamastil, and Sk\'{a}la. This leads to a considerable formal simplification and unification.Comment: 41 + ii pages, LaTeX2e, 0 figures. Submitted to Journal of Mathematical Physic

Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases

For the first time in Europe hundreds of rare disease (RD) experts team up to actively share and jointly analyse existing patient’s data. Solve-RD is a Horizon 2020-supported EU flagship project bringing together >300 clinicians, scientists, and patient representatives of 51 sites from 15 countries. Solve-RD is built upon a core group of four European Reference Networks (ERNs; ERN-ITHACA, ERN-RND, ERN-Euro NMD, ERN-GENTURIS) which annually see more than 270,000 RD patients with respective pathologies. The main ambition is to solve unsolved rare diseases for which a molecular cause is not yet known. This is achieved through an innovative clinical research environment that introduces novel ways to organise expertise and data. Two major approaches are being pursued (i) massive data re-analysis of >19,000 unsolved rare disease patients and (ii) novel combined -omics approaches. The minimum requirement to be eligible for the analysis activities is an inconclusive exome that can be shared with controlled access. The first preliminary data re-analysis has already diagnosed 255 cases form 8393 exomes/genome datasets. This unprecedented degree of collaboration focused on sharing of data and expertise shall identify many new disease genes and enable diagnosis of many so far undiagnosed patients from all over Europe

Comparison of modeled and observed values of NO_2 and JNO_2 during the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) mission

Stratospheric measurements of NO, NO_(2), O_(3), ClO, and HO_(2) were made during spring, early summer, and late summer in the Arctic region during 1997 as part of the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) field campaign. In the sunlit atmosphere, NO_(2) and NO are in steady state through NO2 photolysis and reactions involving O_(3), ClO, BrO, and HO_(2). By combining observations of O_(3), ClO, and HO_(2), observed and modeled values of the NO_(2) photolysis rate coefficient (JNO_(2)), and model estimates of BrO, several comparisons are made between steady state and measured values of both NO_(2) and JNO_(2). An apparent seasonal dependence in discrepancies between calculated and measured values was found; however, a source for this dependence could not be identified. Overall, the mean linear fits in the various comparisons show agreement within 19%, well within the combined uncertainties (±50 to 70%). These results suggest that photochemistry controlling the NO_(2)/NO abundance ratio is well represented throughout much of the sunlit lower stratosphere. A reduction in the uncertainty of laboratory determinations of the rate coefficient of NO + O_(3) → NO_(2) + O_(2) would aid future analyses of these or similar atmospheric observations

A guide to writing systematic reviews of rare disease treatments to generate FAIR-compliant datasets: Building a Treatabolome

Background: Rare diseases are individually rare but globally affect around 6% of the population, and in over 70% of cases are genetically determined. Their rarity translates into a delayed diagnosis, with 25% of patients waiting 5 to 30 years for one. It is essential to raise awareness of patients and clinicians of existing gene and variant-specific therapeutics at the time of diagnosis to avoid that treatment delays add up to the diagnostic odyssey of rare diseases' patients and their families. Aims: This paper aims to provide guidance and give detailed instructions on how to write homogeneous systematic reviews of rare diseases' treatments in a manner that allows the capture of the results in a computer-accessible form. The published results need to comply with the FAIR guiding principles for scientific data management and stewardship to facilitate the extraction of datasets that are easily transposable into machine-actionable information. The ultimate purpose is the creation of a database of rare disease treatments ("Treatabolome") at gene and variant levels as part of the H2020 research project Solve-RD. Results: Each systematic review follows a written protocol to address one or more rare diseases in which the authors are experts. The bibliographic search strategy requires detailed documentation to allow its replication. Data capture forms should be built to facilitate the filling of a data capture spreadsheet and to record the application of the inclusion and exclusion criteria to each search result. A PRISMA flowchart is required to provide an overview of the processes of search and selection of papers. A separate table condenses the data collected during the Systematic Review, appraised according to their level of evidence. Conclusions: This paper provides a template that includes the instructions for writing FAIR-compliant systematic reviews of rare diseases' treatments that enables the assembly of a Treatabolome database that complement existing diagnostic and management support tools with treatment awareness data

Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood

It has been known for over a decade that a majority of men who self report as members of the Jewish priesthood (Cohanim) carry a characteristic Y chromosome haplotype termed the Cohen Modal Haplotype (CMH). The CMH has since been used to trace putative Jewish ancestral origins of various populations. However, the limited number of binary and STR Y chromosome markers used previously did not provide the phylogenetic resolution needed to infer the number of independent paternal lineages that are encompassed within the Cohanim or their coalescence times. Accordingly, we have genotyped 75 binary markers and 12 Y-STRs in a sample of 215 Cohanim from diverse Jewish communities, 1,575 Jewish men from across the range of the Jewish Diaspora, and 2,099 non-Jewish men from the Near East, Europe, Central Asia, and India. While Cohanim from diverse backgrounds carry a total of 21 Y chromosome haplogroups, 5 haplogroups account for 79.5% of Cohanim Y chromosomes. The most frequent Cohanim lineage (46.1%) is marked by the recently reported P58 T->C mutation, which is prevalent in the Near East. Based on genotypes at 12 Y-STRs, we identify an extended CMH on the J-P58* background that predominates in both Ashkenazi and non-Ashkenazi Cohanim and is remarkably absent in non-Jews. The estimated divergence time of this lineage based on 17 STRs is 3,190 ± 1,090 years. Notably, the second most frequent Cohanim lineage (J-M410*, 14.4%) contains an extended modal haplotype that is also limited to Ashkenazi and non-Ashkenazi Cohanim and is estimated to be 4.2 ± 1.3 ky old. These results support the hypothesis of a common origin of the CMH in the Near East well before the dispersion of the Jewish people into separate communities, and indicate that the majority of contemporary Jewish priests descend from a limited number of paternal lineages

Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

Tracking of ancestral histone proteins over multiple generations of genome replication in yeast reveals that old histones move along genes from 3′ toward 5′ over time, and that maternal histones move up to around 400 bp during genomic replication