Causal Inference by Stochastic Complexity

The algorithmic Markov condition states that the most likely causal direction between two random variables X and Y can be identified as that direction with the lowest Kolmogorov complexity. Due to the halting problem, however, this notion is not computable. We hence propose to do causal inference by stochastic complexity. That is, we propose to approximate Kolmogorov complexity via the Minimum Description Length (MDL) principle, using a score that is mini-max optimal with regard to the model class under consideration. This means that even in an adversarial setting, such as when the true distribution is not in this class, we still obtain the optimal encoding for the data relative to the class. We instantiate this framework, which we call CISC, for pairs of univariate discrete variables, using the class of multinomial distributions. Experiments show that CISC is highly accurate on synthetic, benchmark, as well as real-world data, outperforming the state of the art by a margin, and scales extremely well with regard to sample and domain sizes

Potential of model predictive control of a polder water system including pumps, weirs and gates

This work presents an assessment of the potential of model predictive control (MPC) of a Dutch polder system. The system drains to the Linge river and includes 13 weirs, 4 hydraulic gates and 4 large pumping stations each equipped with multiple pumps, managed by the Water Board Rivierenland. The management of the system must comply with several goals: keep the water levels within the bounds of safety, pump out the excess water at minimum cost or CO2 emission, but always have enough water for irrigation and shipping. To achieve these goals there are weirs regulating the water level in different pools, pumping stations to pump water in and out and gates to let water in and out by free flow when possible. These pumping stations consume large amounts of energy. We propose multi-objective mixed-integer optimization by using goal programming to prioritize different operational objectives. For the control of the pumps mixed-integer optimization is used, which makes it possible to not only model the energy consumption of the pumps while in operation, but also to model if the pumps are turned on or off. The control system is implemented using RTC-Tools, an open-source software tool to implement MPC. It is demonstrated that the proposed control system implementation can comply with the operational goals of the water board: keeping the water levels within the bounds while reducing the operational costs. The proposed control system has been tested numerically on data from the year 2013, and it is shown that it highly outperforms the current operation.</p

Erratum to: Localization of Fatty Acyl and Double Bond Positions in Phosphatidylcholines Using a Dual Stage CID Fragmentation Coupled with Ion Mobility Mass Spectrometry.

A high content molecular fragmentation for the analysis of phosphatidylcholines (PC) was achieved utilizing a two-stage [trap (first generation fragmentation) and transfer (second generation fragmentation)] collision-induced dissociation (CID) in combination with travelling-wave ion mobility spectrometry (TWIMS). The novel aspects of this work reside in the fact that a TWIMS arrangement was used to obtain a high level structural information including location of fatty acyl substituents and double bonds for PCs in plasma, and the presence of alkali metal adduct ions such as [M + Li](+) was not required to obtain double bond positions. Elemental compositions for fragment ions were confirmed by accurate mass measurements. A very specific first generation fragment ion m/z 577 (M-phosphoryl choline) from the PC [16:0/18:1 (9Z)] was produced, which by further CID generated acylium ions containing either the fatty acyl 16:0 (C(15)H(31)CO(+), m/z 239) or 18:1 (9Z) (C(17)H(33)CO(+), m/z 265) substituent. Subsequent water loss from these acylium ions was key in producing hydrocarbon fragment ions mainly from the α-proximal position of the carbonyl group such as the hydrocarbon ion m/z 67 (+H(2)C-HC = CH-CH = CH(2)). Formation of these ions was of important significance for determining double bonds in the fatty acyl chains. In addition to this, and with the aid of (13)C labeled lyso-phosphatidylcholine (LPC) 18:1 (9Z) in the ω-position (methyl) TAP fragmentation produced the ion at m/z 57. And was proven to be derived from the α-proximal (carboxylate) or distant ω-position (methyl) in the LPC. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13361-011-0172-2) contains supplementary material, which is available to authorized users

Social Change and Betty Friedan's The Feminine Mystique: A Study of the Charismatic Author-Leader

In this thesis I explore the significance of the publication of Betty Friedan's The Feminine Mystique (1963) to the emergence of the second wave Women's Liberation Movement in the US in the late 1960s. To this end, I deploy key concepts provided through social movement theory (eg collective identity, collective action frames, social problem construction). I also incorporate Max Weber and Antonio Gramsci's insights on the indispensable role played by leaders who demonstrate a clear and effective political will. Weber's three part model of pure charisma is used as a general template for understanding the impact of Friedan's text. I critique aspects of Weber's theory of charisma, in particular his failure to appreciate that the written word can mark the initial emergence phase of charisma rather than its routinisation. I augment Weber's insights on charismatic leadership by attending to Gramsci's emphasis on the necessity of winning the 'war of ideas' that must be waged at the level of civil society within advanced capitalist societies. I examine Gramsci's understanding of the power available to the organic intellectual who is aligned with the interests of subaltern groups and who succeeds in revealing the hegemonic commitments of accepted 'common sense'. In the latter part of this thesis, I apply these many useful concepts to my case study analysis of Betty Friedan's The Feminine Mystique. I argue that Friedan's accessible, middlebrow text gave birth to a new discursive politics which was critically important not only for older women, but for a younger generation of more radicalised women. I emphasise how Friedan's text mounted a concerted attack on the discursive construction of femininity under patriarchal capitalism. I question Friedan's diagnostic claim that the problems American women faced were adequately captured by the terminology of the trapped housewife syndrome. I conclude by arguing that social movement researchers have to date failed to appreciate the leadership potential of the charismatic author-leader who succeeds in addressing and offering a solution to a pressing social problem through the medium of a best-selling, middlebrow text

Иберийско-кавказское языкознание N42

Analytical BioScience

Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining

Classical non-homologous end-joining (cNHEJ) is the dominant pathway used by human cells to repair DNA double-strand breaks (DSBs) and maintain genome stability. Here the authors show that PARP1-driven chromatin expansion allows the recruitment of ZNF384, which in turn recruits Ku70/Ku80 to facilitate cNHEJ.DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damage as they can lead to mutations and chromosomal rearrangements, which underlie cancer development. Classical non-homologous end-joining (cNHEJ) is the dominant pathway for DSB repair in human cells, involving the DNA-binding proteins XRCC6 (Ku70) and XRCC5 (Ku80). Other DNA-binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair, but their role in cNHEJ remained elusive. Here we show that ZNF384, a member of the C2H2 family of ZnF proteins, binds DNA ends in vitro and is recruited to DSBs in vivo. ZNF384 recruitment requires the poly(ADP-ribosyl) polymerase 1 (PARP1)-dependent expansion of damaged chromatin, followed by binding of its C2H2 motifs to the exposed DNA. Moreover, ZNF384 interacts with Ku70/Ku80 via its N-terminus, thereby promoting Ku70/Ku80 assembly and the accrual of downstream cNHEJ factors, including APLF and XRCC4/LIG4, for efficient repair at DSBs. Altogether, our data suggest that ZNF384 acts as a 'Ku-adaptor' that binds damaged DNA and Ku70/Ku80 to facilitate the build-up of a cNHEJ repairosome, highlighting a role for ZNF384 in DSB repair and genome maintenance.Cancer Signaling networks and Molecular Therapeutic

Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLF AD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLF AD-histone octamer complex shows that APLF AD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLF AD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted