Joint Maximum Likelihood of Phylogeny and Ancestral States Is Not Consistent.

Maximum likelihood estimation in phylogenetics requires a means of handling unknown ancestral states. Classical maximum likelihood averages over these unknown intermediate states, leading to provably consistent estimation of the topology and continuous model parameters. Recently, a computationally efficient approach has been proposed to jointly maximize over these unknown states and phylogenetic parameters. Although this method of joint maximum likelihood estimation can obtain estimates more quickly, its properties as an estimator are not yet clear. In this article, we show that this method of jointly estimating phylogenetic parameters along with ancestral states is not consistent in general. We find a sizeable region of parameter space that generates data on a four-taxon tree for which this joint method estimates the internal branch length to be exactly zero, even in the limit of infinite-length sequences. More generally, we show that this joint method only estimates branch lengths correctly on a set of measure zero. We show empirically that branch length estimates are systematically biased downward, even for short branches.

Survival analysis of DNA mutation motifs with penalized proportional hazards.

Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved binding, though mutations are not distributed uniformly across sequence sites. Immunologists observe this nonuniformity to be consistent with "mutation motifs", which are short DNA subsequences that affect how likely a given site is to experience a mutation. Quantifying the effect of motifs on mutation rates is challenging: a large number of possible motifs makes this statistical problem high dimensional, while the unobserved history of the mutation process leads to a nontrivial missing data problem. We introduce an ℓ 1-penalized proportional hazards model to infer mutation motifs and their effects. In order to estimate model parameters, our method uses a Monte Carlo EM algorithm to marginalize over the unknown ordering of mutations. We show that our method performs better on simulated data compared to current methods and leads to more parsimonious models. The application of proportional hazards to mutation processes is, to our knowledge, novel and formalizes the current methods in a statistical framework that can be easily extended to analyze the effect of other biological features on mutation rates.

Nonclinical Safety Assessment of CFZ533, a Fc-Silent Anti-CD40 Antibody, in Cynomolgus Monkeys.

CFZ533 is a pathway blocking, nondepleting anti-CD40 antibody that is in clinical development for inhibition of transplant organ rejection and therapy for autoimmune diseases. A 26-week GLP toxicity study in sexually mature Cynomolgus monkeys was conducted in order to support chronic application of CFZ533. CFZ533 was subcutaneously administered at doses up to 150 mg/kg/week and was safe and generally well tolerated. CFZ533 showed no adverse effects for cardiovascular, respiratory, and neurobehavioral endpoints, and no changes were observed for blood lymphocyte and platelet counts or blood coagulation markers. In line with the nondepleting nature of CFZ533, CD20+ B cells in the blood were only marginally reduced. A complete suppression of germinal center (GC) development in lymph nodes and spleen was the most prominent result of post-mortem histological investigations. This was corroborated by an abrogated T-dependent antibody response (TDAR) to the antigen Keyhole Limpet Hemocyanin (KLH) as well as an absence of anti-drug antibodies (ADAs) in the absence of B cell depletion as seen with immunophenotyping and histology. When serum levels of CFZ533 in recovery animals dropped levels necessary for full CD40 occupancy on B cells, all animals were able to mount a TDAR to KLH. All histological changes also reverted to normal appearance after recovery. In summary, CFZ533 was shown to be well tolerated and safe in the 26-week toxicity study with a distinct pharmacodynamic profile in histology and immune function.

Long bonds and short barriers: ionization and isomerization of alkyl nitriles.

Ab initio molecular orbital calculations demonstrate that ionizing alkyl nitriles produces a dramatic geometry change involving lengthening of a C-CH(2)CN bond. The experimental determination of the adiabatic ionization energy of these species is thus very difficult. In addition, there are generally low barriers for 1,2-H shift reactions in the molecular ions leading to RCHCHN(+*) and RCHCNH(+*) isomers, which makes generating pure ionized alkyl nitrile in a mass spectrometer a challenge. Threshold photoelectron spectroscopy and threshold photoelecton photoion coincidence spectroscopy were employed to study the ionization and dissociation of two alkyl nitriles, in particular, pentanenitrile and 2,2-dimethylpropanenitrile. Threshold ionization is shown to result not in the respective molecular ions, but rather in isomeric forms, resulting in dissociation thresholds that lie below the calculated adiabatic ionization energies of the two molecules. Appearance energies for all observed fragment ions are reported and compared to available literature values. Charge separation in the dissociation of doubly ionized 2,2-dimethylpropanenitrile is observed as fragment-ion time-of-flight peak broadening at high photon energies.

Does tetrahydrofuran ring open upon ionization and dissociation? A TPES and TPEPICO investigation.

The threshold photoelectron spectrum (TPES) of tetrahydrofuran (THF) is compared to that of the unsaturated furan molecule. In general, there is a similarity in the orbital ionization profile for the two species, though unlike furan, THF exhibits (modest) vibrational detail only in the (9b)(-1) X (2)B band. An adiabatic ionization energy of 9.445 +/- 0.010 eV has been derived from the onset of the TPES spectrum. Threshold photoelectron photoion coincidence spectroscopy was used to explore the loss of a hydrogen atom from ionized THF over the photon energy range of 9.9-10.4 eV. RRKM fitting of the resulting breakdown curves yields an E(0) of 0.85 +/- 0.03 eV (82 +/- 3 kJ mol(-1)) (AE = 10.30 +/- 0.04 eV). If the G3 IE of 9.48 eV is used to convert the experimental data from photon energy to THF ion internal energy, E(0) = 0.81 +/- 0.01 eV (78 +/- 1 kJ mol(-1)). The latter value is closer to the G3 E(0) of 72 kJ mol(-1) for the formation of the cyclic ion 1. A variety of ring-opening reactions were also probed at the B3-LYP/6-31+G(d) and G3 levels of theory. The distonic isomer (*)CH(2)CH(2)CH(2)OCH(2)(+) lies 70 kJ mol(-1) higher than ionized THF, which places it within 1 kJ mol(-1) of the threshold for the dissociation to 1. All of the probed H-loss products from the distonic isomer (which includes singlet and triplet species) lie significantly higher in energy than ion 1, eliminating the possibility that ionized THF dissociates to m/z 71 via a ring-opening reaction in the present experiment. The derived Delta(double dagger)S value for the dissociation, 8 +/- 5 J K(-1) mol(-1), is also consistent with the formation of 1. The experimentally derived E(0) values can be used to derive the Delta(f)H(o)(0) for ion 1. Together with the Delta(f)H(o)(0) values for the THF ion (752.0 +/- 2 kJ mol(-1), derived from the neutral Delta(f)H(o)(0) of -154.9 +/- 0.7 kJ mol(-1) and experimental IE of 9.445 +/- 0.010 eV) and H atom (218.5 kJ mol(-1)) our E(0) of 82 +/- 3 kJ mol(-1) yields a Delta(f)H(o)(0) for ion 1 of 620 +/- 4 kJ mol(-1) (Delta(f)H(o)(298) = 594 +/- 4 kJ mol(-1)), in good agreement with the G3 Delta(f)H(o)(0) of 621 kJ mol(-1). Appearance energies for all fragment ions up to photon energies of 34 eV are also reported and discussed in comparison with the available literature.

Nitro-nitrite isomerization and transition state switching in the dissociation of ionized nitromethane: a threshold photoelectron-photoion coincidence spectroscopy study.

Threshold photoelectron-photoion coincidence (TPEPICO) spectroscopy has been employed to investigate the competition between bond cleavage and rearrangement reactions in the dissociation of ionized nitromethane, 1. Modeling TPEPICO breakdown diagrams with a combination of RRKM theory and ab initio calculations at the G3 level of theory allowed the derivation of the activation energy for the isomerisation of 1 to ionized methyl nitrite, 2, 82 kJ mol(-1). In addition, evidence was found for a transition state switch in the bond cleavage reaction in 1 leading to CH(3)(*) + NO(2)(+). As internal energy increases, the effective transition state for this reaction becomes tighter (i.e. is characterized by a lower entropy of activation, Delta(double dagger)S). Fitted thresholds for NO(+) and CH(2)OHO(+) ions, originating from the isomeric methyl nitrite ion, are consistent with G3 level ab initio calculations.

Methyl t-butyl ether and methyl trimethylsilyl ether ions dissociate near their ionization thresholds: a TPES, TPEPICO, RRKM, and G3 investigation.

The threshold photoelectron spectra and threshold photoelectron photoion coincidence (TPEPICO) mass spectra of methyl t-butyl ether, (CH(3))(3)COCH(3) (MTBE), and methyl trimethylsilyl ether, (CH(3))(3)SiOCH(3) (MTMSE), have been measured using synchrotron radiation. The effect of silicon substitution on the unimolecular dissociation processes and the threshold photoelectron spectrum has been investigated. Both molecular ions dissociate at low internal energies. For ionized MTBE, the parent ion is no longer observed at an internal energy of only 0.2 eV. For this reason, it was not possible to fit the TPEPICO data to extract reliable thermochemical information. G3 level calculations place the molecular ion 5 kJ mol(-1) above the lowest-energy dissociation products, (CH(3))(2)COCH(3)(+) + (*)CH(3), suggesting the participation of an isomer, potentially the distonic ion (*)CH(2)(CH(3))(2)CO(+)(H)CH(3), in the dissociation. However, the calculations are not considered accurate enough to reliably determine the role this isomer plays, if any. RRKM modeling of the threshold region of the TPEPICO breakdown curves for ionized MTMSE leads to an E(0) for methyl loss of 63 +/- 2 kJ mol(-1), in good agreement with the G3 value of 66 kJ mol(-1). The resulting Delta(f)H(0) for (CH(3))(2)SiOCH(3)(+) of 384 +/- 10 kJ mol(-1) (Delta(f)H(298) = 361 +/- 10 kJ mol(-1)) is 28 kJ mol(-1) lower than the G3 value of 412 kJ mol(-1) due to the G3 Delta(f)H(0) for neutral MTMSE being 16 kJ mol(-1) higher than the previously reported value and the fact that the experimental IE(a) is 6 kJ mol(-1) lower than the G3 estimate. Appearance energy values for higher-energy fragmentation channels up to 36 (for MTBE) and 32 eV (for MTMSE) are reported and compared to literature values. An investigation of fragment ion peak broadening at high internal energy indicated that the two doubly charged molecular ions are not stable on the microsecond time scale. Each was found to dissociate into two singly charged ions along one or more neutral species.

Three products are better than two: entropic advantages in the competing dissociation reactions of ionized azo-t-butane.

Ionized azo-t-butane (m/z 142) undergoes three dissociation reactions: competitive cleavage of the N-C bond to form (1) the t-butyl cation ((CH(3))(3)C(+), m/z 57) plus a neutral that is nominally (CH(3))(3)CN(2)(*) (85 Da); (2) m/z 85 cation, (CH(3))(3)CN(2)(+), plus the neutral t-butyl radical; and (3) a minor rearrangement reaction leading to ionized butene. The competition between channels (1) and (2) is governed by both energetic and entropic considerations as the 85 Da neutral lies in a 1 kJ mol(-1) potential energy well and when formed dissociates into the t-butyl radical and N(2). This gives channel 1 an entropic advantage over channel 2, as long as the transition states for these processes reside close to products, a conclusion supported by threshold photoelectron photoion coincidence spectroscopy, tandem mass spectrometry, and ab initio calculations.

Ionized o-, m-, and p-difluorobenzene dissociate through ring-opened intermediates: a TPEPICO investigation.

Threshold photoelectron photoion coincidence (TPEPICO) experiments have shown that o-, m-, and p-difluorobenzene ions dissociate via a common, ring-opened intermediate and not via ionized p-difluorobenzene. Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental breakdown curves yields activation energies for the initial isomerization of 4.48 +/- 0.05, 4.55 +/- 0.05, and 4.68 +/- 0.05 eV for o-, m-, and p-difluorobenzene, respectively. These values place each ion at a similar absolute energy and thus similar transition states. A large positive DeltaS(double dagger) for each ion (ca 100 J K(-1) mol(-1)) suggests a ring-opened structure for these transition states.

Thermochemistry of N-N containing ions: a threshold photoelectron photoion coincidence spectroscopy study of ionized methyl- and tetramethylhydrazine.

The unimolecular dissociation reactions of the methylhydrazine (MH) and tetramethylhydrazine (TMH) radical cations have been investigated using tandem mass spectrometry and threshold photoelectron photoion coincidence spectroscopy in the photon energy ranges 9.60-31.95 eV (for the MH ion) and 7.74-29.94 eV (for the TMH ion). Methylhydrazine ions (CH3NHNH2(+*)) have three low-energy dissociation channels: hydrogen atom loss to form CH2NHNH2(+) (m/z 45), loss of a methyl radical to form NHNH2(+) (m/z 31), and loss of methane to form the fragment ion m/z 30, N2H2(+*). Tetramethylhydrazine ions only exhibit two dissociation reactions near threshold: that of methyl radical loss to form (CH3)2NNCH3(+) (m/z 73) and of methane loss to form the fragment ion m/z 72 with the empirical formula C3H8N2(+*). The experimental breakdown curves were modeled with Rice-Ramsperger-Kassel-Marcus theory, and it was found that, particularly for methyl radical loss, variational transition state theory was needed to obtain satisfactory fits to the data. The 0 K enthalpies of formation (delta(f)H0) for all fragment ions (m/z 73, m/z 72, m/z 45, m/z 31, and m/z 30) have been determined from the 0 K activation energies (E0) obtained from the fitting procedure: delta(f)H0[(CH3)2NNCH3(+)] = 833 +/- 5 kJ mol(-1), delta(f)H0 [C3H8N2(+*)] = 1064 +/- 5 kJ mol(-1), delta(f)H0[CH2NHNH2(+)] = 862 +/- 5 kJ mol(-1), delta(f)H0[NHNH2(+)] = 959 +/- 5 kJ mol(-1), and delta(f)H0[N2H2(+*)] = 1155 +/- 5 kJ mol(-1). The breakdown curves have been measured from threshold up to h nu approximately 32 eV for both hydrazine ions. As the photon energy increases, other dissociation products are observed and their appearance energies are reported.

Morphological study into the temperature dependence of solid ammonia under astrochemical conditions using vacuum ultraviolet and Fourier-transform infrared spectroscopy.

The authors present the results of a morphological study of solid ammonia using both Fourier-transform infrared and vacuum ultraviolet (VUV) spectroscopy. Dramatic changes in the VUV and infrared spectra at temperatures between 65 and 85 K provide a deeper insight into the structure of ammonia ice particularly with the observation of an exciton transition at 194 nm (6.39 eV) in the VUV spectrum, revealing a structure that is composed of crystallites. A complementary structure is observed in the IR spectrum at 1100 cm(-1) which is assigned to the symmetric deformation of ammonia molecules at the surfaces of the crystallites. Such spectral signatures may be used to identify the environment within which the ammonia ice is formed and provide a new route for obtaining information on the physical and chemical conditions occurring within the interstellar medium, on the surfaces of planetary bodies, and in Kuiper belt objects.

Entropy effects in the fragmentation of 1,1-dimethylhydrazine ions.

The 1,1-dimethylhydrazine ion ((CH3)2NNH2+*) has two low-energy dissociation channels, the loss of a hydrogen atom to form the fragment ion m/z 59, (CH3)(CH2)NNH2+, and the loss of a methyl radical to form the fragment ion m/z 45, the methylhydrazyl cation, CH3NNH2+. The dissociation of the 1,1-dimethylhydrazine ion has been investigated using threshold photoelectron-photoion coincidence (TPEPICO) spectroscopy, in the photon energy range 8.25-31 eV, and tandem mass spectrometry. Theoretical breakdown curves have been obtained from a variational transition state theory (VTST) modeling of the two reaction channels and compared to those obtained from experiment. Seven transition states have been found at the B3-LYP/6-31+G(d) level of theory for the methyl radical loss channel in the internal energy range of 2.32-3.56 eV. The methyl loss channel transition states are found at R(N-C) = 4.265, 4.065, 3.965, 3.165, 2.765, 2.665, and 2.565 A over this internal energy range. Three transition states have been found for the hydrogen atom loss channel: R(H-C) = 2.298, 2.198, and 2.098 A. The DeltaS++(45) value, at an internal energy of 2.32 eV and a bond distance of R(N-C) = 4.265 A, is 65 J K-1 mol-1. As the internal energy increases to 3.56 eV the variational transition state moves to lower R value so that at R(N-C) = 2.565 A, the DeltaS++ decreases to 29 J K-1 mol-1. For the hydrogen atom loss channel the variation in DeltaS++ is less than that for the methyl loss channel. To obtain agreement with the experimental breakdown curves, DeltaS++(59) = 26-16 J K-1 mol-1 over the studied internal energy range. The 0 K enthalpies of formation (DeltafH0) for the two fragment ions m/z 45 and m/z 59 have been calculated from the 0 K activation energies (E0) obtained from the fitting procedure: DeltafH0[CH3NNH2+] = 906 +/- 6 kJ mol-1 and DeltafH0[(CH3)(CH2)NNH2+] = 822 +/- 7 kJ mol-1. The calculated G3 values are DeltafH0[CH3NNH2+] = 911 kJ mol-1 and DeltafH0[(CH3)(CH2)NNH2+] = 825 kJ mol-1. In addition to the two low-energy dissociation products, 21 other fragment ions have been observed in the dissociation of the 1,1-dimethylhydrazine ion as the photon energy was increased. Their appearance energies are reported.

VUV spectroscopy and photo-processing of astrochemical ices: an experimental study.

In order to understand much of the chemistry that underpins astronomical phenomena (e.g. star and planet formation) it is essential to probe the physico-chemistry of ice surfaces under astronomical conditions. The physical properties and chemical reactivity of such icy surfaces depends upon its morphology. Thus it is necessary to explore how the morphology of astrochemical ices is influenced by their local environment (e.g. temperature and pressure) and the mechanisms by which they are processed. In this paper we report the results of a series of experiments to explore the morphology of a variety of molecular ices using VUV spectroscopy. Spectral signatures are found that may allow the morphology of such ices to be identified.

A photoelectron and TPEPICO investigation of the acetone radical cation.

The valence shell photoelectron spectrum, threshold photoelectron spectrum, and threshold photoelectron photoion coincidence (TPEPICO) mass spectra of acetone have been measured using synchrotron radiation. New vibrational progressions have been observed and assigned in the X 2B2 state photoelectron bands of acetone-h6 and acetone-d6, and the influence of resonant autoionization on the threshold electron yield has been investigated. The dissociation thresholds for fragment ions up to 31 eV have been measured and compared to previous values. In addition, kinetic modeling of the threshold region for CH3* and CH4 loss leads to new values of 78 +/- 2 kJ mol(-1) and 75 +/- 2 kJ mol(-1), respectively, for the 0 K activation energies for these two processes. The result for the methyl loss channel is in reasonable agreement with, but slightly lower than, that of 83 +/- 1 kJ mol(-1) derived in a recent TPEPICO study by Fogleman et al. The modeling accounts for both low-energy dissociation channels at two different ion residence times in the mass spectrometer. Moreover, the effects of the ro-vibrational population distribution, the electron transmission efficiency, and the monochromator band-pass are included. The present activation energies yield a Delta(f)H298 for CH3CO+ of 655 +/- 3 kJ mol(-1), which is 4 kJ mol(-1) lower than that reported by Fogleman et al. The present Delta(f)H298 for CH3CO+ can be combined with the Delta(f)H298 for CH2CO (-47.5 +/- 1.6 kJ mol(-1)) and H+ (1530 kJ mol(-1)) to yield a 298 K proton affinity for ketene of 828 +/- 4 kJ mol(-1), in good agreement with the value (825 kJ mol(-1)) calculated at the G2 level of theory. The measured activation energy for CH4 loss leads to a Delta(f)H298 (CH2CO+*) of 873 +/- 3 kJ mol(-1).

Threshold-photoelectron spectroscopic study of methyl-substituted hydrazine compounds.

The valence shell electronic structures of methylhydrazine (CH(3)NHNH(2)), 1,1-dimethylhydrazine ((CH(3))(2)NNH(2)) and tetramethylhydrazine ((CH(3))(4)N(2)) have been studied by recording threshold and conventional (kinetic energy resolved) photoelectron spectra. Ab initio calculations have been performed on ammonia and the three methyl substituted hydrazines, with the structures being optimized at the B3-LYP/6-31+G(d) level of theory. The ionization energies of the valence molecular orbitals were calculated using the Green's function method, allowing the photoelectron bands to be assigned to specific molecular orbitals. The ground-state adiabatic and vertical ionization energies, as determined from the threshold photoelectron spectra, were IE(a) = 8.02 +/- 0.16 eV and IE(v) = 9.36 +/- 0.02 eV for methylhydrazine, IE(a) = 7.78 +/- 0.16 eV and IE(v) = 8.86 +/- 0.01 eV for 1,1-dimethylhydrazine and IE(a) = 7.26 +/- 0.16 eV and IE(v) = 8.38 +/- 0.01 eV for tetramethylhydrazine. Due to the large geometry change that occurs upon ionization, these IE(a) values are all higher than the true thresholds. New features have been observed in the inner valence region and these have been compared with similar structure in the spectrum of hydrazine. The effect of resonant autoionization on the threshold photoelectron yield is discussed. New heats of formation (Delta(f)H) are proposed for the three hydrazines on the basis of G3 calculations: 107, 94, and 95 kJ/mol for methylhydrazine, 1,1-dimethyhydrazine and tetramethylhydrazine, respectively. The previously reported Delta(f)H for tetramethylhydrazine is shown to be erroneous.