Tables with colspan (1723)

A large number of similarities are found. Species differences are highlighted in bold. NA, not applicable; ND, not done.

Exon junction array results assessing splicing changes in the hippocampus after pilocarpine seizure, compared to sham controls. The total number of alternative exons identified from the brains of pilocarpine treated animals from which RNA was analyzed by genome-wide exon junction arrays is shown. The data in is organized as a function of differing stringency thresholds (as previously described: ΔI, a measure of the inclusion of exons in sham relative to pilocarpine treated animals; ΔI was determined using the ASPIRE algorithm (Ule et al., 2005b) and ΔI t-test using ASPIRE2 (Licatalosi et al., 2008)). Each data point represents analysis of all results from three pairs of biological replicates. Validated refers to independent qRT-PCR validation (see Supplementary file 1) of selected transcripts from total.

The improvement of model fit by inclusion of phylogenetic random effect was calculated as the difference in AIC (ΔAIC) between the GLMM (with phylogenetic random effect) and a GLM as ΔAIC = AIC(GLMM)-AIC(GLM). p(THR) was binomially distributed assuming species that were CR, EN or VU were threatened (1) and LC species were not (0). We present ΔAIC for two other threat classifications, assuming: THR also includes NT species, or THR was a continuous categorical variable ranging from LC = 0 to CR = 5.

Shown are the appropriate culture and methanol and water volumes used in the ‘cold’ methanol quenching procedure for cells prior to RNA and intracellular metabolite extraction.

With each parameter the range used in the best fit search is indicated.

WT: wild-type plants.

With each parameter the range used in the best fit search is indicated.

For monotherapy, we assume that 50 point mutations (n = 50) can in principle confer resistance to the drug. With dual therapy, we assume that 50 point mutations can in principle confer resistance to each drug individually (n₁ = n₂ = 50). Two scenarios are modeled: in the first, there is one mutation that can in principle confer resistance to both drugs (i.e., cross-resistance, n₁₂ = 1). In the other case, there are no possible mutations that can confer resistance to both drugs (n₁₂ = 0). Parameter values: birth rate, b = 0.14, death rate, d = 0.13, death rate for sensitive cells during treatment, d′ = 0.17, point mutation rate u = 10⁻⁹.

Colon: colonic adenocarcinoma; Rectal: rectal adenocarcinoma; Pancreas: pancreatic ductal adenocarcinoma.

Sidechains coordinating the Ca²⁺ ion in EF hands 1 and 2 were implemented as distance restraints.

χ¹ angles were obtained from PREDITOR (Berjanskii et al., 2006), and ϕ and ψ angles were calculated using TALOS+ (Shen et al., 2009).

The r.m.s differences (Hz) between the experimental RDC data and back-calculated RDCs from the 10 lowest energy structures were obtained by SVD fitting using the program PALES (Zweckstetter and Bax, 2000).

The pairwise RMSD for residues 421-486 and structure quality factor were generated using the Protein Structure Validation Software suite v1.4 (Bhattacharya et al., 2007).

The Ramachandran statistics were evaluated for residues 422-486 with PROCHECK (Laskowski et al., 1996).

Data were collected from single crystals.

Values in parentheses are for highest-resolution shell.

The Student’s T-test and p-value are based on the comparison to Aβ fiber alone.

Mann–Whitney test for pre-MBT vs MBT zygotic transcript size: p<10⁻²⁰.

Fisher test for pre-MBT vs MBT zygotic: p<0.0003.

Fisher test for pre-MBT vs MBT zygotic: p<10⁻²³.

Table 1 shows average center frequency of low frequency peak at∼6–10 Hz, if present, across all channels for Subjects 1 in relation to time off zolpidem prior to 1 hr baseline EEG measurements and clock time of each dose. In both patients, shorter zolpidem dosing intervals are associated with higher center frequencies across posterior but not anterior EEG channels. Similarly, an increased standard deviation of the measurement is observed as interval between doses is shorter for the posterior EEG channel measurements. Of note, for both subjects, anterior EEG channel pre-zolpidem dose baselines revealed a consistent∼7.4 Hz average center frequency with a small standard deviation. The consistency of these findings despite the wide difference in their underlying etiologies of injury support the proposed common cellular and circuit mechanism; the correspondence of the∼7.4 Hz peak and intrinsic oscillation frequency of neocortical Layer V cells (Silva et al., 1991) also support this model.

Table 2 shows average center frequency of low frequency peak at∼6–10 Hz, if present, across all channels for Subjects 2 in relation to time off zolpidem prior to 1 hr baseline EEG measurements and clock time of each dose. In both patients, shorter zolpidem dosing intervals are associated with higher center frequencies across posterior but not anterior EEG channels. Similarly, an increased standard deviation of the measurement is observed as interval between doses is shorten for the posterior EEG channel measurements. Of note, for both subjects, anterior EEG channel pre-zolpidem dose baselines revealed a consistent∼7.4 Hz average center frequency with a small standard deviation. The consistency of these findings despite the wide difference in their underlying etiologies of injury support the proposed common cellular and circuit mechanism; the correspondence of the∼7.4 Hz peak and intrinsic oscillation frequency of neocortical Layer V cells (Silva et al., 1991) also support this model. Of note as an outlier is the second baseline for this subject which is the only measurement early in the morning (8:30) suggesting a possible interaction with diurnal activity of the brain arousal system, however, insufficient data is available to establish this linkage.

Phenotypes, stages of observation and penetrances of Megf8^−/− mutants are listed. V1 refers to the ophthalmic branch of the trigeminal nerve. Bmp loss-of-function lines known to display similar phenotypes are noted.

By Fisher′s exact test there is a significant absence of tryptic-like cleavages in the 16 rapidly cleaved peptides (p=0.005).

all children show motor delay due to vestibular defects.

The mutational spectrum of the population is inferred based on the genetic alterations observed in the subset of strains sequenced.

IM, Intradermal melanocytic nevus. C, Compound nevus. LJ, Lentigenous juctional nevus. Samples highlighted in gray indicate C-to-G mutation during melanoma progression.

Solubility is based on the estimated final yield of the purified protein per liter of bacterial culture. +++: >5 mg/L; ++: 1–5mg/L; +: <1 mg/L.

Activity: N, no activity; P, partial activity; Y, activity close to wild-type.

q = number of queens examined; w = number of workers examined. Generic placement of Brachyponera lutea and Neoponera apicalis reflects the new reclassification of species within the former paraphyletic genus Pachycondyla (Schmidt CA, Shattuck SO, The higher classification of the ant subfamily Ponerinae [Hymenoptera: Formicidae], with a review of ponerine ecology and behavior. Under review).

Information on museum holdings and voucher codes for queens and workers. ABS, Archbold Biological Station; ALWC, Alexander Wild Collection; AMNH, American Museum of Natural History; ANIC, Australian National Insect Collection; BMNH, British Museum of Natural History; CASC, California Academy of Science; DADC, David A. Donoso Collection; JTLC, Jack Longino Collection; MCZ, Museum of Comparative Zoology (Harvard); MIZA, Museo del Instituto de. Zoología Agrícola (Venezuela); MNHN, Muséum national d’Histoire naturelle; MSNG, Natural History Museum, Genoa; MZSP, Museu de Zoologia Universidade de São Paulo; RAJC, Robert Johnson Collection; RAKC, Roberto Keller Collection; UCDC; University of California Davis.

^† denotes extinct taxa.

Number of ORFs overlapping with ORFs and various classes of ncRNAs, with various minimum size cut-offs for the overlapping region.

Totals are given for ORFs overlapping with ncRNAs and with unstable ncRNAs, including a percentage of overlapping ncRNAs that are unstable.

ncRNA: non-protein coding RNA; ORF: optical reading frame; XUT: Xrn1-sensitive unstable transcript (degraded in cytoplasm); CUT: cryptic unstable transcript (degraded by nuclear exosome); SUT: stable unannotated transcript (not known to be degraded).

OR = odds ratio

Abbreviations: t7, t9: 7 or 9 amino acid terminal truncations; aid: ABA interaction domain; cd: catalytic domain; ed, m: enhanced dimerization or monomeric variant

Alignments to the profile with more than three positions greater than three standard deviations from the mean of the profile position or with a maximum position less than the smallest maximum position within the profile (186) were excluded (filters). Pearson correlation coefficients are shown.

Only jackknife results for the centromere deleted from the model are shown.

Multiple high-scoring centromere hits above the first false positive (FP) one or two base pairs apart.

Cen4 (111 bp) was not included in the model.

Single base-pair cleavage peak at a site of anomalously low nucleosome occupancy.

Medians are based on all alignments for all 16 chromosomes, whether or not they passed the filters.

Transition rates between different flagellar waveforms: normal (CCW), semi-coiled and curly-1 (both CW). Data from wild-type cells (N = 52 cells, 203 tumbles). Values are mean ± SEM.

For MNase-seq, the experiment was performed and processed in pair-end. For nucleosome density, tags were not elongated but connected and the indicated sequence average length is withdrawn by our analysis pipeline using the pair-end information. For midpoints analyses, elongation does not apply and data treatment is indicated earlier in ‘Materials and methods–Processing of sequenced tags’.