ProbCD: enrichment analysis accounting for categorization uncertainty

As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for
the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation

Are language production problems apparent in adults who no longer meet diagnostic criteria for attention-deficit/hyperactivity disorder?

In this study, we examined sentence production in a sample of adults (N = 21) who had had attention-deficit/hyperactivity disorder (ADHD) as children, but as adults no longer met DSM-IV diagnostic criteria (APA, 2000). This “remitted” group was assessed on a sentence production task. On each trial, participants saw two objects and a verb. Their task was to construct a sentence using the objects as arguments of the verb. Results showed more ungrammatical and disfluent utterances with one particular type of verb (i.e., participle). In a second set of analyses, we compared the remitted group to both control participants and a “persistent” group, who had ADHD as children and as adults. Results showed that remitters were more likely to produce ungrammatical utterances and to make repair disfluencies compared to controls, and they patterned more similarly to ADHD participants. Conclusions focus on language output in remitted ADHD, and the role of executive functions in language production

Testing the Gaussian expansion method in exactly solvable matrix models

The Gaussian expansion has been developed since early 80s as a powerful analytical method, which enables nonperturbative studies of various systems using `perturbative' calculations. Recently the method has been used to suggest that 4d space-time is generated dynamically in a matrix model formulation of superstring theory. Here we clarify the nature of the method by applying it to exactly solvable one-matrix models with various kinds of potential including the ones unbounded from below and of the double-well type. We also formulate a prescription to include a linear term in the Gaussian action in a way consistent with the loop expansion, and test it in some concrete examples. We discuss a case where we obtain two distinct plateaus in the parameter space of the Gaussian action, corresponding to different large-N solutions. This clarifies the situation encountered in the dynamical determination of the space-time dimensionality in the previous works.Comment: 30 pages, 15 figures, LaTeX; added references for section

Speaker- versus listener-oriented disfluency: A re-examination of arguments and assumptions from autism spectrum disorder

We re-evaluate conclusions about disfluency production in high-functioning forms of autism spectrum disorder (HFA). Previous studies examined individuals with HFA to address a theoretical question regarding speaker- and listener-oriented disfluencies. Individuals with HFA tend to be self-centric and have poor pragmatic language skills, and should be less likely to produce listener-oriented disfluency. However, previous studies did not account for individual differences variables that affect disfluency. We show that both matched and unmatched controls produce fewer repairs than individuals with HFA. For silent pauses, there was no difference between matched controls and HFA, but both groups produced more than unmatched controls. These results identify limitations in prior research and shed light on the relationship between autism spectrum disorders and disfluent speech

Talampanel reduces the level of motoneuronal calcium in transgenic mutant SOD1 mice only if applied presymptomatically

We tested the efficacy of treatment with talampanel in a mutant SOD1 mouse model of ALS by measuring intracellular calcium levels and loss of spinal motor neurons. We intended to mimic the clinical study; hence, treatment was started when the clinical symptoms were already present. The data were compared with the results of similar treatment started at a presymptomatic stage. Transgenic and wild-type mice were treated either with talampanel or with vehicle, starting in pre-symptomatic or symptomatic stages. The density of motor neurons was determined by the physical disector, and their intracellular calcium level was assayed electron microscopically. Results showed that motor neurons in the SOD1 mice exhibited an elevated calcium level, which could be reduced, but not restored, with talampanel only when the treatment was started presymptomatically. Treatment in either presymptomatic or symptomatic stages failed to rescue the motor neurons. We conclude that talampanel reduces motoneuronal calcium in a mouse model of ALS, but its efficacy declines as the disease progresses, suggesting that medication initiation in the earlier stages of the disease might be more effective

Detection of CN gas in Interstellar Object 2I/Borisov

The detection of Interstellar Objects passing through the Solar System offers the promise of constraining the physical and chemical processes involved in planetary formation in other extrasolar systems. While the effect of outgassing by 1I/2017 U1 ('Oumuamua) was dynamically observed, no direct detection of the ejected material was made. The discovery of the active interstellar comet 2I/Borisov means spectroscopic investigations of the sublimated ices is possible for this object. We report the first detection of gas emitted by an interstellar comet via the near-UV emission of CN from 2I/Borisov at a heliocentric distance of $r$ = 2.7 au on 2019 September 20. The production rate was found to be Q(CN) = $(3.7\pm0.4)\times10^{24}$ s$^{-1}$, using a simple Haser model with an outflow velocity of 0.5 km s$^{-1}$. No other emission was detected, with an upper limit to the production rate of C$_2$ of $4\times10^{24}$ s$^{-1}$. The spectral reflectance slope of the dust coma over $3900$ \AA\ $< \lambda< 6000$ \AA \ is steeper than at longer wavelengths, as found for other comets. Broad band $R_c$ photometry on 2019 September 19 gave a dust production rate of $Af\rho=143\pm10$ cm. Modelling of the observed gas and dust production rates constrains the nuclear radius to $0.7-3.3$ km assuming reasonable nuclear properties. Overall, we find the gas, dust and nuclear properties for the first active Interstellar Object are similar to normal Solar System comets.Comment: 9 pages, 4 figures, accepted for publication in ApJ

Spectroscopy around 36^{36}Ca

Expérience GANILInternational audienceAn experiment was performed to study excited states in neutron-deficient nuclei around Ca. A one-neutron knockout reaction was used to produce $^{36}$Ca ions from a $^{37}$Ca secondary beam, and in-beam $\gamma$-rays were measured. The $2^+$ energy in $^{36}$Ca is compared to the mirror nucleus $^{36}$S to deduce information on the isospin dependence of the nuclear force near the proton drip line. The energy of the first excited $2^+$ state in $^{36}$Ca and the cross section for the 1-neutron knock-out reaction from $^{37}$Ca at $\sim$ 45 · AMeV were obtained. Furthermore, for two other $T_z$ = −2 nuclei, $^{28}$S and $^{32}$Ar, the de-excitation of the first $2^+$ state has been observed

Probing exotic phenomena at the interface of nuclear and particle physics with the electric dipole moments of diamagnetic atoms: A unique window to hadronic and semi-leptonic CP violation

The current status of electric dipole moments of diamagnetic atoms which involves the synergy between atomic experiments and three different theoretical areas -- particle, nuclear and atomic is reviewed. Various models of particle physics that predict CP violation, which is necessary for the existence of such electric dipole moments, are presented. These include the standard model of particle physics and various extensions of it. Effective hadron level combined charge conjugation (C) and parity (P) symmetry violating interactions are derived taking into consideration different ways in which a nucleon interacts with other nucleons as well as with electrons. Nuclear structure calculations of the CP-odd nuclear Schiff moment are discussed using the shell model and other theoretical approaches. Results of the calculations of atomic electric dipole moments due to the interaction of the nuclear Schiff moment with the electrons and the P and time-reversal (T) symmetry violating tensor-pseudotensor electron-nucleus are elucidated using different relativistic many-body theories. The principles of the measurement of the electric dipole moments of diamagnetic atoms are outlined. Upper limits for the nuclear Schiff moment and tensor-pseudotensor coupling constant are obtained combining the results of atomic experiments and relativistic many-body theories. The coefficients for the different sources of CP violation have been estimated at the elementary particle level for all the diamagnetic atoms of current experimental interest and their implications for physics beyond the standard model is discussed. Possible improvements of the current results of the measurements as well as quantum chromodynamics, nuclear and atomic calculations are suggested.Comment: 46 pages, 19 tables and 16 figures. A review article accepted for EPJ