Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1

Epileptic encephalopathies are a devastating group of epilepsies with poor prognosis, of which the majority are of unknown etiology. We perform targeted massively parallel resequencing of 19 known and 46 candidate genes for epileptic encephalopathy in 500 affected individuals (cases) to identify new genes involved and to investigate the phenotypic spectrum associated with mutations in known genes. Overall, we identified pathogenic mutations in 10% of our cohort. Six of the 46 candidate genes had 1 or more pathogenic variants, collectively accounting for 3% of our cohort. We show that de novo CHD2 and SYNGAP1 mutations are new causes of epileptic encephalopathies, accounting for 1.2% and 1% of cases, respectively. We also expand the phenotypic spectra explained by SCN1A, SCN2A and SCN8A mutations. To our knowledge, this is the largest cohort of cases with epileptic encephalopathies to undergo targeted resequencing. Implementation of this rapid and efficient method will change diagnosis and understanding of the molecular etiologies of these disorders.

Widespread plasticity in CTCF occupancy linked to DNA methylation

CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environments. Here we analyze genome-wide occupancy patterns of CTCF by ChIP-seq in 19 diverse human cell types, including normal primary cells and immortal lines. We observed highly reproducible yet surprisingly plastic genomic binding landscapes, indicative of strong cell-selective regulation of CTCF occupancy. Comparison with massively parallel bisulfite sequencing data indicates that 41% of variable CTCF binding is linked to differential DNA methylation, concentrated at two critical positions within the CTCF recognition sequence. Unexpectedly, CTCF binding patterns were markedly different in normal versus immortal cells, with the latter showing widespread disruption of CTCF binding associated with increased methylation. Strikingly, this disruption is accompanied by up-regulation of CTCF expression, with the result that both normal and immortal cells maintain the same average number of CTCF occupancy sites genome-wide. These results reveal a tight linkage between DNA methylation and the global occupancy patterns of a major sequence-specific regulatory factor.

The accessible chromatin landscape of the human genome

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.

An expansive human regulatory lexicon encoded in transcription factor footprints

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.

Search for low-mass dark-sector Higgs bosons

Recent astrophysical and terrestrial experiments have motivated the proposal of a dark sector with GeV-scale gauge boson force carriers and new Higgs bosons. We present a search for a dark Higgs boson using 516 fb(-1) of data collected with the BABAR detector. We do not observe a significant signal and we set 90% confidence level upper limits on the product of the standard model-dark-sector mixing angle and the dark-sector coupling constant.

Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR

Globin gene switching is a complex, highly regulated process allowing expression of distinct globin genes at specific developmental stages. Here, for the first time, we have characterized all of the zebrafish globins based on the completed genomic sequence. Two distinct chromosomal loci, termed major (chromosome 3) and minor (chromosome 12), harbor the globin genes containing α/β pairs in a 5'-3' to 3'-5' orientation. Both these loci share synteny with the mammalian α-globin locus. Zebrafish globin expression was assayed during development and demonstrated two globin switches, similar to human development. A conserved regulatory element, the locus control region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks and GATA1 binding sites. Surprisingly, the position of these sites with relation to the globin genes is evolutionarily conserved, despite a lack of overall sequence conservation. Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture. Functional homology to the mammalian α-LCR MCS-R2 region was confirmed by robust and specific reporter expression in erythrocytes of transgenic zebrafish. Our studies provide a comprehensive characterization of the zebrafish globin loci and clarify the regulation of globin switching.

Search for hadronic decays of a light Higgs boson in the radiative decay Υ→γA0

We search for hadronic decays of a light Higgs boson (A(0)) produced in radiative decays of an Υ(2S) or Υ(3S) meson, Υ→γA(0). The data have been recorded by the BABAR experiment at the Υ(3S) and Υ(2S) center-of-mass energies and include (121.3±1.2)×10(6) Υ(3S) and (98.3±0.9)×10(6) Υ(2S) mesons. No significant signal is observed. We set 90% confidence level upper limits on the product branching fractions B(Υ(nS)→γA(0))B(A(0)→hadrons) (n=2 or 3) that range from 1×10(-6) for an A(0) mass of 0.3 GeV/c(2) to 8×10(-5) at 7 GeV/c(2).

Observation of the decay B- → D(s)((*)+) K- ℓ- ν(ℓ)

We report the observation of the decay B- → D(s)((*)+) K- ℓ- ν(ℓ) based on 342  fb(-1) of data collected at the Υ(4S) resonance with the BABAR detector at the PEP-II e+ e- storage rings at SLAC. A simultaneous fit to three D(s)(+) decay chains is performed to extract the signal yield from measurements of the squared missing mass in the B meson decay. We observe the decay B- → D(s)((*)+) K- ℓ- ν(ℓ) with a significance greater than 5 standard deviations (including systematic uncertainties) and measure its branching fraction to be B(B- → D(s)((*)+) K- ℓ- ν(ℓ)) = [6.13(-1.03)(+1.04)(stat)±0.43(syst)±0.51(B(D(s)))]×10(-4), where the last error reflects the limited knowledge of the D(s) branching fractions.

Search for production of invisible final states in single-photon decays of Υ(1S)

We search for single-photon decays of the Υ(1S) resonance, Υ → γ + invisible, where the invisible state is either a particle of definite mass, such as a light Higgs boson A⁰, or a pair of dark matter particles, χχ. Both A⁰ and χ are assumed to have zero spin. We tag Υ(1S) decays with a dipion transition Υ(2S) → π⁺π⁻Υ(1S) and look for events with a single energetic photon and significant missing energy. We find no evidence for such processes in the mass range m(A⁰) ≤ 9.2 GeV and m(χ) ≤ 4.5 GeV in the sample of 98 × 10⁶ Υ(2S) decays collected with the BABAR detector and set stringent limits on new physics models that contain light dark matter states.

Development of a compact fast CCD camera and resonant soft x-ray scattering endstation for time-resolved pump-probe experiments

The designs of a compact, fast CCD (cFCCD) camera, together with a resonant soft x-ray scattering endstation, are presented. The cFCCD camera consists of a highly parallel, custom, thick, high-resistivity CCD, readout by a custom 16-channel application specific integrated circuit to reach the maximum readout rate of 200 frames per second. The camera is mounted on a virtual-axis flip stage inside the RSXS chamber. When this flip stage is coupled to a differentially pumped rotary seal, the detector assembly can rotate about 100°/360° in the vertical/horizontal scattering planes. With a six-degrees-of-freedom cryogenic sample goniometer, this endstation has the capability to detect the superlattice reflections from the electronic orderings showing up in the lower hemisphere. The complete system has been tested at the Advanced Light Source, Lawrence Berkeley National Laboratory, and has been used in multiple experiments at the Linac Coherent Light Source, SLAC National Accelerator Laboratory.

Search for f(J)(2220) in radiative J/ψ decays

We present a search for f(J)(2220) production in radiative J/ψ→γf(J)(2220) decays using 460  fb⁻¹ of data collected with the BABAR detector at the SLAC PEP-II e(+)e⁻ collider. The f(J)(2220) is searched for in the decays to K(+)K⁻ and K(S)⁰K(S)⁰. No evidence of this resonance is observed, and 90% confidence level upper limits on the product of the branching fractions for J/ψ→γf(J)(2220) and f(J)(2220)→K(+)K⁻(K(S)⁰K(S)⁰) as a function of spin and helicity are set at the level of 10⁻⁵, below the central values reported by the Mark III experiment.

Economic evaluations of HIV treatment and health research with people diagnosed with HIV infection and co-occurring mental health and substance use disorders

This paper describes the research challenges involved in measuring costs in economic evaluations of patients who are coping simultaneously with HIV/AIDS and co-occurring mental health and substance abuse disorders-especially in multi-site studies. We describe the general issues that arise in measuring costs for this population and suggest some operational solutions for their resolution, drawing from our experience in a recent multi-site health services research study focused on this population. We show that while reliance on patient self-report data may be unavoidable to provide a common denominator in multi-site studies, there are also some practical ways of improving the accuracy of such data and the cost estimates that result from them. We also provide readers with a means for securing the data collection instruments developed for the cost component of this study in the hope that these may serve as templates for researchers doing similar work.

Evidence for direct CP violation in the measurement of the Cabbibo-Kobayashi-Maskawa angle γ with B∓ → D(*)K(*)∓ decays

We report the measurement of the Cabibbo-Kobayashi-Maskawa CP-violating angle γ through a Dalitz plot analysis of neutral D-meson decays to K(S)(0) π+ π- and K(S)(0) K+ K- produced in the processes B∓ → DK∓, B∓ D* K∓ with D* → Dπ(0), Dγ, and B∓ → DK*∓ with K*∓ → K(S)(0) π∓, using 468 million BB pairs collected by the BABAR detector at the PEP-II asymmetric-energy e+ e- collider at SLAC. We measure γ = (68 ± 14 ± 4 ± 3)° (modulo 180°), where the first error is statistical, the second is the experimental systematic uncertainty, and the third reflects the uncertainty in the description of the neutral D decay amplitudes. This result is inconsistent with γ = 0 (no direct CP violation) with a significance of 3.5 standard deviations.

Measurement of D0-D0 mixing parameters using D0 → K(S)(0)π+ π- and D0 → K(S)(0)K+ K- decays

We report a direct measurement of D0-D0 mixing parameters through a time-dependent amplitude analysis of the Dalitz plots of D(0) → K(S)(0) π+ π- and, for the first time, D0 → K(S)(0)K+ K- decays. The low-momentum pion π(s)(+) in the decay D*+ → D0 π(s)(+) identifies the flavor of the neutral D meson at its production. Using 468.5 fb(-1) of e+ e- colliding-beam data recorded near square root(s)=10.6 GeV by the BABAR detector at the PEP-II asymmetric-energy collider at SLAC, we measure the mixing parameters x = [1.6 ± 2.3(stat) ± 1.2(syst) ± 0.8(model)] × 10(-3), and y = [5.7 ± 2.0(stat) ± 1.3(syst) ± 0.7(model)] × 10(-3). These results provide the best measurement to date of x and y. The knowledge of the value of x, in particular, is crucial for understanding the origin of mixing.

Measurements of charged current lepton universality and |Vus| using tau lepton decays to e- ν(e) ν(τ), μ- ν(μ) ν(τ), π- ν(τ), and K- ν(τ)

Using 467  fb(-1) of e+e- annihilation data collected with the BABAR detector, we measure (B(τ- → μ- ν(μ) ν(τ)))/(B(τ- → e- ν(e) ν(τ))) =(0.9796±0.0016±0.0036), (B(τ- → π- ν(τ)))/(B(τ- → e- ν(e) ν(τ))) = (0.5945±0.0014±0.0061), and (B(τ- → K- ν(τ)))/(B(τ- → e- ν(e) ν(τ))) = (0.03882±0.00032±0.00057), where the uncertainties are statistical and systematic, respectively. From these precision τ measurements, we test the standard model assumption of μ-e and τ-μ charge current lepton universality and provide determinations of |Vus| experimentally independent of the decay of a kaon.

Test of lepton universality in Υ(1S) decays at BABAR

The ratio R(τμ)(Υ(1S))=Γ(Υ(1S)→τ+ τ-)/Γ(Υ(1S)→μ+ μ-) is measured using a sample of (121.8±1.2)×10(6)Υ(3S) events recorded by the BABAR detector. This measurement is intended as a test of lepton universality and as a search for a possible light pseudoscalar Higgs boson. In the standard model (SM) this ratio is expected to be close to 1. Any significant deviations would violate lepton universality and could be introduced by the coupling to a light pseudoscalar Higgs boson. The analysis studies the decays Υ(3S)→Υ(1S)π+ π-, Υ(1S)→l+ l-, where l=μ, τ. The result, R(τμ)(Υ(1S))=1.005±0.013(stat)±0.022(syst), shows no deviation from the expected SM value, while improving the precision with respect to previous measurements.

Search for charged lepton flavor violation in narrow upsilon decays

Charged-lepton flavor-violating processes are unobservable in the standard model, but they are predicted to be enhanced in several extensions to the standard model, including supersymmetry and models with leptoquarks or compositeness. We present a search for such processes in a sample of 99x10(6)Upsilon(2S) decays and 117x10(6)Upsilon(3S) decays collected with the BABAR detector. We place upper limits on the branching fractions B(Upsilon(nS)-->e(+/-)tau(-/+)) and B(Upsilon(nS)-->mu(+/-)tau(-/+)) (n=2,3) at the 10(-6) level and use these results to place lower limits of order 1 TeV on the mass scale of charged-lepton flavor-violating effective operators.