Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.Comment: 12 pages, 10 figure

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Analysis of Four Polymorphisms Located at the Promoter of the Estrogen Receptor Alpha ESR1 Gene in a Population With Gender Incongruence

[Abstract] Introduction: Gender incongruence defines a state in which individuals feel discrepancy between the sex assigned at birth and their gender. Some of these people make a social transition from male to female (transwomen) or from female to male (trans men). By contrast, the word cisgender describes a person whose gender identity is consistent with their sex assigned at birth. Aim: To analyze the implication of the estrogen receptor a gene (ESR1) in the genetic basis of gender incongruence. Main Outcome Measures: Polymorphisms rs9478245, rs3138774, rs2234693, rs9340799. Method: We carried out the analysis of 4 polymorphisms located at the promoter of the ESR1 gene (C1 ¼ rs9478245, C2 ¼ rs3138774, C3 ¼ rs2234693, and C4 ¼ rs9340799) in a population of 273 trans women, 226 trans men, and 537 cis gender controls. For SNP polymorphisms, the allele and genotype frequencies were analyzed by c2 test. The strength of the SNP associations with gender incongruence was measured by binary logistic regression. For the STR polymorphism, the mean number of repeats were analyzed by the ManneWhitney U test. Measurement of linkage disequilibrium and haplotype frequencies were also performed. Results: The C2 median repeats were shorter in the trans men population. Genotypes S/S and S/L for the C2 polymorphism were overrepresented in the trans men group (P ¼ .012 and P ¼ .003 respectively). We also found overtransmission of the A/A genotype (C4) in the trans men population (P ¼ .017), while the A/G genotype (C4) was subrepresented (P ¼ .009]. The analyzed polymorphisms were in linkage disequilibrium. In the trans men population, the T(C1)-L(C2)-C(C3)-A(C4) haplotype was overrepresented (P ¼ .019) while the T(C1)-L(C2)-C(C3)-G(C4) was subrepresented (P ¼ .005). Conclusion: The ESR1 is associated with gender incongruence in the trans men populationThis work was supported by grants: ED431B 019/02 (EP), PGC2018-094919-B-C21 (AG), PGC2018-094919-B-C22 (RF), and FPU 15/02558 (JCC)Xunta de Galicia; ED431B 019/0

Avoiding initiation of repair in L2 conversations-for-learning

Using audio-recorded data from second language (L2) English conversations-for-learning between an L2 user of English and a first language (L1) user of English (the researcher), this study analyzes cases in which the L1 user avoids initiation of repair. In each case, the L2 user appears to have misunderstood something said by the L1 user. Instead of initiating repair in next turn on the L2 user’s talk, or in third position on his own talk, the L1 user goes along, at least briefly, with the direction set by the L2 user. Often, the L1 user, sooner or later, returns to the misunderstood talk. Avoidance of repair initiation is one way in which the L1 user contributes to the construction of the L2 user as interactionally competent to participate in conversations-for-learning

Extraordinary Emergencies: Reproducing Moral Discourses of the Child in Institutional Interaction

This report uses audio recorded telephone calls and textual data from an emergency medical services call center to examine the interactional practices through which speakers produce what we call “extraordinary emergencies”, treating the events concerned as requiring moral, as well as medical, attention. Since one of the overarching institutional aims of emergency call centers is to facilitate the efficient provision of medical services, call-takers typically treat reported emergencies as routine events. However, in some instances speakers produce practices that do not contribute toward the institutional agenda of providing medical assistance, thereby treating them as extraordinary cases. These practices occurred recurrently in calls involving reports of emergencies relating to child sexuality, including sexual assaults against children and obstetric emergencies where the mother was particularly young. We discuss the implications of these findings for the situated reproduction of particular moral norms, especially with respect to the category of the child in society

How can I help you? User instructions in telephone calls

We a small corpus of instructions given in phone calls to customers who need support for programming their universal remote control, to make it suitable for their particular TV set VCR, Audio, etc. Typically, in these calls the operator or 'agent' coaches the client while the client is performing actions with the equipment (turning it on, pressing buttons and codes, directing it towards the TV, etc.). We compared these oral instructions with the concept of a 'streamlined step procedure' (Farkas, 1999) and other principles that are well-known from the literature about written instructions. Our conclusion is that many problems arise because the operator does not provide 'meta-communication' about the goals that have to be achieved, and because the feedback given by the client is neglected or misinterpreted