InSiDDe: A server for designing artificial disordered proteins

InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E. coli at high levels without degradation when fused to a natural molecular recognition element (MoRE). In addition, the artificial fusion protein exhibited the expected behavior in terms of binding modulation of the specific partner recognized by the MoRE. To the best of our knowledge, InSiDDe is the first publicly available software for the design of intrinsically disordered protein (IDP) sequences. InSiDDE is publicly available online

Speeding up Cylindrical Algebraic Decomposition by Gr\"obner Bases

Gr\"obner Bases and Cylindrical Algebraic Decomposition are generally thought of as two, rather different, methods of looking at systems of equations and, in the case of Cylindrical Algebraic Decomposition, inequalities. However, even for a mixed system of equalities and inequalities, it is possible to apply Gr\"obner bases to the (conjoined) equalities before invoking CAD. We see that this is, quite often but not always, a beneficial preconditioning of the CAD problem. It is also possible to precondition the (conjoined) inequalities with respect to the equalities, and this can also be useful in many cases.Comment: To appear in Proc. CICM 2012, LNCS 736

Covariant localizations in the torus and the phase observables

We describe all the localization observables of a quantum particle in a one-dimensional box in terms of sequences of unit vectors in a Hilbert space. An alternative representation in terms of positive semidefinite complex matrices is furnished and the commutative localizations are singled out. As a consequence, we also get a vector sequence characterization of the covariant phase observables.Comment: 16 pages, no figure, Latex2

New technologies to improve root canal disinfection

Effective irrigant delivery and agitation are prerequisites to promote root canal disinfection and debris removal and improve successful endodontic treatment. This paper presents an overview of the currently available technologies to improve the cleaning of the endodontic space and their debridement efficacy. A PubMed electronic search was conducted with appropriate key words to identify the relevant literature on this topic. After retrieving the full-text articles, all the articles were reviewed and the most appropriate were included in this review. Several different systems of mechanical activation of irrigants to improve endodontic disinfection were analysed: manual agitation with gutta-percha cones, endodontic instruments or special brushes, vibrating systems activated by low-speed hand-pieces or by sonic or subsonic energy, use of ultrasonic or laser energy to mechanically activate the irrigants and apical negative pressure irrigation systems. Furthermore, this review aims to describe systems designed to improve the intracanal bacterial decontamination by a specific chemical action, such as ozone, direct laser action or light-activated disinfection. The ultrasonic activation of root canal irrigants and of sodium hypochlorite in particular still remains the gold standard to which all other systems of mechanical agitation analyzed in this article were compared. From this overview, it is evident that the use of different irrigation systems can provide several advantages in the clinical endodontic outcome and that integration of new technologies, coupled with enhanced techniques and materials, may help everyday clinical practice

Elemental Phosphorus: structural and superconducting phase diagram under pressure

Pressure-induced superconductivity and structural phase transitions in phosphorous (P) are studied by resistivity measurements under pressures up to 170 GPa and fully $ab-initio$ crystal structure and superconductivity calculations up to 350 GPa. Two distinct superconducting transition temperature (T$_{c}$) vs. pressure ($P$) trends at low pressure have been reported more than 30 years ago, and for the first time we are able to reproduce them and devise a consistent explanation founded on thermodynamically metastable phases of black-phosphorous. Our experimental and theoretical results form a single, consistent picture which not only provides a clear understanding of elemental P under pressure but also sheds light on the long-standing and unsolved $anomalous$ superconductivity trend. Moreover, at higher pressures we predict a similar scenario of multiple metastable structures which coexist beyond their thermodynamical stability range. Metastable phases of P experimentally accessible at pressures above 240 GPa should exhibit T$_{c}$'s as high as 15 K, i.e. three times larger than the predicted value for the ground-state crystal structure. We observe that all the metastable structures systematically exhibit larger transition temperatures than the ground-state ones, indicating that the exploration of metastable phases represents a promising route to design materials with improved superconducting properties.Comment: 14 pages, 4 figure

The response of the male freshwater goby to natural and synthetic male courtship sound playback following exposure to different female sexual sitimuli.

Among teleosts, field and laboratory experiments have shown the playback of male courtship sounds often elicits competitive courtship and sound emission in the territorial male. However, the importance of female stimulation for the male response to the sound is poorly understood. In this study, playback experiments with the freshwater goby, Padogobius martensii, examined the response of resident males (i.e. males individually housed within laboratory tanks for at least 5 days) to natural and synthetic male courtship sounds after exposure to chemical or visual stimuli from a ripe female. All playback tests consisted of one experimental (sound playback) and two control treatments, all of equal duration. Three experiments were conducted on a first group of 12 males using natural courtship sounds. Experiment 1 consisted of playing back the sound to a male that had not exposed to female stimulation for at least 24 hr. The same male was exposed to the “female pheromone” by dropping a few cm3 of female holding water into the male’s tank, just prior to playback (Experiment 2), or to the view of a live ripe female in a close-by tank, during playback (Experiment 3). The sound playback failed to elicit positive responses by males not exposed to female stimuli (Experiment 1), and did not increase courtship activity of the male in visual contact with the female (Experiment 3). However, it increased swimming activity and facilitated courtship and sound production in the male after an increase in sexual arousal by prior chemical stimulation (Experiment 2). In Experiment 4, the synthetic version of the courtship sound and one deprived of pulse-rate modulation and harmonic content (pure tone) were played back to 10 resident males following prior chemical stimulation. The synthetic courtship sound, but not the pure tone, was effective in eliciting positive responses by the sexually aroused male. Functional implications of the responses to the courtship sound for the territorial male are discussed. The results are relevant to the understanding of the role of sound communication and interception among gobies and to develop playback experiments in the field

High-spatial-resolution passive microwave sounding systems

During this period the emphasis was on the following: (1) further design, construction, and testing of the improved 54-GHz portion of the 54-118 GHz microwave temperature sounder (MTS) aircraft radiometer system in preparation for ER-2 observations in July 1991; and (2) final analysis and documentation of procedures for detecting and analyzing thermal waves in our 118-GHz MTS imagery. In addition, we have new unpublished measurements of dry-air attenuation at frequencies of 54 to 66 GHz and over a temperature range of 280K to 326K; these measurements should enable us to improve further our atmospheric transmittance models. It was further noted that the proposed SSMIS conical-scanning microwave spectrometer on the military DMSP Block 5D-3 spacecraft designed to measure stratospheric and mesospheric temperature profiles will be observing the Zeeman-split oxygen lines with sufficient spectral resolution that the changing Doppler shifts with view angle will substantially degrade the potential system performance unless remedied; this was briefly studied and documented

Coagulation disorders in coronavirus infected patients: COVID-19, SARS-CoV-1, MERS-CoV and lessons from the past

© 2020 Elsevier B.V. Coronavirus disease 2019 (COVID-19) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus strain disease, has recently emerged in China and rapidly spread worldwide. This novel strain is highly transmittable and severe disease has been reported in up to 16% of hospitalized cases. More than 600,000 cases have been confirmed and the number of deaths is constantly increasing. COVID-19 hospitalized patients, especially those suffering from severe respiratory or systemic manifestations, fall under the spectrum of the acutely ill medical population, which is at increased venous thromboembolism risk. Thrombotic complications seem to emerge as an important issue in patients infected with COVID-19. Preliminary reports on COVID-19 patients’ clinical and laboratory findings include thrombocytopenia, elevated D-dimer, prolonged prothrombin time, and disseminated intravascular coagulation. As the pandemic is spreading and the whole picture is yet unknown, we highlight the importance of coagulation disorders in COVID-19 infected patients and review relevant data of previous coronavirus epidemics caused by the severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and the Middle East Respiratory Syndrome coronavirus (MERS-CoV)