A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

Psychopolitics: Peter Sedgwick’s legacy for mental health movements

This paper re-considers the relevance of Peter Sedgwick's Psychopolitics (1982) for a politics of mental health. Psychopolitics offered an indictment of ‘anti-psychiatry’ the failure of which, Sedgwick argued, lay in its deconstruction of the category of ‘mental illness’, a gesture that resulted in a politics of nihilism. ‘The radical who is only a radical nihilist’, Sedgwick observed, ‘is for all practical purposes the most adamant of conservatives’. Sedgwick argued, rather, that the concept of ‘mental illness’ could be a truly critical concept if it was deployed ‘to make demands upon the health service facilities of the society in which we live’. The paper contextualizes Psychopolitics within the ‘crisis tendencies’ of its time, surveying the shifting welfare landscape of the subsequent 25 years alongside Sedgwick's continuing relevance. It considers the dilemma that the discourse of ‘mental illness’ – Sedgwick's critical concept – has fallen out of favour with radical mental health movements yet remains paradigmatic within psychiatry itself. Finally, the paper endorses a contemporary perspective that, while necessarily updating Psychopolitics, remains nonetheless ‘Sedgwickian’

"Meaning" as a sociological concept: A review of the modeling, mapping, and simulation of the communication of knowledge and meaning

The development of discursive knowledge presumes the communication of meaning as analytically different from the communication of information. Knowledge can then be considered as a meaning which makes a difference. Whereas the communication of information is studied in the information sciences and scientometrics, the communication of meaning has been central to Luhmann's attempts to make the theory of autopoiesis relevant for sociology. Analytical techniques such as semantic maps and the simulation of anticipatory systems enable us to operationalize the distinctions which Luhmann proposed as relevant to the elaboration of Husserl's "horizons of meaning" in empirical research: interactions among communications, the organization of meaning in instantiations, and the self-organization of interhuman communication in terms of symbolically generalized media such as truth, love, and power. Horizons of meaning, however, remain uncertain orders of expectations, and one should caution against reification from the meta-biological perspective of systems theory

Surface pretreatments for medical application of adhesion

Medical implants and prostheses (artificial hips, tendono- and ligament plasties) usually are multi-component systems that may be machined from one of three material classes: metals, plastics and ceramics. Typically, the body-sided bonding element is bone. The purpose of this contribution is to describe developments carried out to optimize the techniques , connecting prosthesis to bone, to be joined by an adhesive bone cement at their interface. Although bonding of organic polymers to inorganic or organic surfaces and to bone has a long history, there remains a serious obstacle in realizing long-term high-bonding strengths in the in vivo body environment of ever present high humidity. Therefore, different pretreatments, individually adapted to the actual combination of materials, are needed to assure long term adhesive strength and stability against hydrolysis. This pretreatment for metal alloys may be silica layering; for PE-plastics, a specific plasma activation; and for bone, amphiphilic layering systems such that the hydrophilic properties of bone become better adapted to the hydrophobic properties of the bone cement. Amphiphilic layering systems are related to those developed in dentistry for dentine bonding. Specific pretreatment can significantly increase bond strengths, particularly after long term immersion in water under conditions similar to those in the human body. The bond strength between bone and plastic for example can be increased by a factor approaching 50 (pealing work increasing from 30 N/m to 1500 N/m). This review article summarizes the multi-disciplined subject of adhesion and adhesives, considering the technology involved in the formation and mechanical performance of adhesives joints inside the human body

Sociological and Communication-Theoretical Perspectives on the Commercialization of the Sciences

Both self-organization and organization are important for the further development of the sciences: the two dynamics condition and enable each other. Commercial and public considerations can interact and "interpenetrate" in historical organization; different codes of communication are then "recombined." However, self-organization in the symbolically generalized codes of communication can be expected to operate at the global level. The Triple Helix model allows for both a neo-institutional appreciation in terms of historical networks of university-industry-government relations and a neo-evolutionary interpretation in terms of three functions: (i) novelty production, (i) wealth generation, and (iii) political control. Using this model, one can appreciate both subdynamics. The mutual information in three dimensions enables us to measure the trade-off between organization and self-organization as a possible synergy. The question of optimization between commercial and public interests in the different sciences can thus be made empirical.Comment: Science & Education (forthcoming

Assessing Syndromic Surveillance of Cardiovascular Outcomes from Emergency Department Chief Complaint Data in New York City

Prospective syndromic surveillance of emergency department visits has been used for near-real time tracking of communicable diseases to detect outbreaks or other unexpected disease clusters. The utility of syndromic surveillance for tracking cardiovascular events, which may be influenced by environmental factors and influenza, has not been evaluated. We developed and evaluated a method for tracking cardiovascular events using emergency department free-text chief complaints.There were three phases to our analysis. First we applied text processing algorithms based on sensitivity, specificity, and positive predictive value to chief complaint data reported by 11 New York City emergency departments for which ICD-9 discharge diagnosis codes were available. Second, the same algorithms were applied to data reported by a larger sample of 50 New York City emergency departments for which discharge diagnosis was unavailable. From this more complete data, we evaluated the consistency of temporal variation of cardiovascular syndromic events and hospitalizations from 76 New York City hospitals. Finally, we examined associations between particulate matter ≤2.5 µm (PM(2.5)), syndromic events, and hospitalizations. Sensitivity and positive predictive value were low for syndromic events, while specificity was high. Utilizing the larger sample of emergency departments, a strong day of week pattern and weak seasonal trend were observed for syndromic events and hospitalizations. These time-series were highly correlated after removing the day-of-week, holiday, and seasonal trends. The estimated percent excess risks in the cold season (October to March) were 1.9% (95% confidence interval (CI): 0.6, 3.2), 2.1% (95% CI: 0.9, 3.3), and 1.8% (95%CI: 0.5, 3.0) per same-day 10 µg/m(3) increase in PM(2.5) for cardiac-only syndromic data, cardiovascular syndromic data, and hospitalizations, respectively.Near real-time emergency department chief complaint data may be useful for timely surveillance of cardiovascular morbidity related to ambient air pollution and other environmental events

In Vivo Analysis of the Role of O-Glycosylations of Von Willebrand Factor

The objective of this project was to study the function of O-glycosylations in von Willebrand factor (VWF) life cycle. In total, 14 different murine Vwf cDNAs mutated on one or several O-glycosylations sites were generated: 9 individual mutants, 2 doublets, 2 clusters and 1 mutant with all 9 murine glycosylation sites mutated (Del-O-Gly). We expressed each mutated cDNA in VWF deficient-mice by hydrodynamic injection. An immunosorbent assay with Peanut Agglutinin (PNA) was used to verify the O-glycosylation status. Wild-type (WT) VWF expressed by hepatocytes after hydrodynamic injection was able to bind PNA with slightly higher affinity than endothelial-derived VWF. In contrast, the Del-O-Gly VWF mutant did not bind PNA, demonstrating removal of O-linked glycans. All mutants displayed a normal multimeric pattern. Two mutants, Del-O-Gly and T1255A/T1256A, led to expression levels 50% lower than those induced by WT VWF and their half-life in vivo was significantly reduced. When testing the capacity of each mutant to correct the bleeding time of VWF-deficient mice, we found that S1486A, T1255A, T1256A and the doublet T1255A/T1256A were unable to do so. In conclusion we have shown that O-glycosylations are dispensable for normal VWF multimerization and biosynthesis. It also appears that some O-glycosylation sites, particularly the T1255 and T1256 residues, are involved in the maintenance of VWF plasma levels and are essential for normal haemostasis. As for the S1486 residue, it seems to be important for platelet binding as demonstrated in vitro using perfusion experiments

Decision-Making and Depressive Symptomatology

Difficulty making decisions is a core symptom of depressive illness, but the nature of these difficulties has not been well characterized. The two studies presented herein use the same hypothetical scenarios that call for a decision. In Study 1, participants were asked to make and explain their decisions in a free-response format, as well as to describe their prior experiences with similar situations. The results suggest that those with more depressive symptoms make decisions that are less likely to further their interests. We also identified several interesting associations between features of decision-making and the presence of depressive symptoms. In Study 2, participants were guided through their decisions with simple decision tools to investigate whether the association between depressive symptoms and poor decisions is better accounted for by failure to use of good decision-making strategies, or by other factors, such as differences in priorities or goals. With this minimal intervention the quality of decisions no longer declined significantly as a function of depressive symptom severity. Moreover, few associations between depressive symptom severity and decision-related goals and priorities were evident, suggesting that the previously-exposed difficulties of depressed individuals with decision-making were largely the result of their failure to use effective decision-making techniques

A seesaw model for intermolecular gating in the kinesin motor protein

Recent structural observations of kinesin-1, the founding member of the kinesin group of motor proteins, have led to substantial gains in our understanding of this molecular machine. Kinesin-1, similar to many kinesin family members, assembles to form homodimers that use alternating ATPase cycles of the catalytic motor domains, or “heads”, to proceed unidirectionally along its partner filament (the microtubule) via a hand-over-hand mechanism. Cryo-electron microscopy has now revealed 8-Å resolution, 3D reconstructions of kinesin-1•microtubule complexes for all three of this motor’s principal nucleotide-state intermediates (ADP-bound, no-nucleotide, and ATP analog), the first time filament co-complexes of any cytoskeletal motor have been visualized at this level of detail. These reconstructions comprehensively describe nucleotide-dependent changes in a monomeric head domain at the secondary structure level, and this information has been combined with atomic-resolution crystallography data to synthesize an atomic-level "seesaw" mechanism describing how microtubules activate kinesin’s ATP-sensing machinery. The new structural information revises or replaces key details of earlier models of kinesin’s ATPase cycle that were based principally on crystal structures of free kinesin, and demonstrates that high-resolution characterization of the kinesin–microtubule complex is essential for understanding the structural basis of the cycle. I discuss the broader implications of the seesaw mechanism within the cycle of a fully functional kinesin dimer and show how the seesaw can account for two types of "gating" that keep the ATPase cycles of the two heads out of sync during processive movement