Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin.

Lysine specific demethylase-1 (LSD1/KDM1A) in complex with its corepressor protein CoREST is a promising target for epigenetic drugs. No therapeutic that targets LSD1/CoREST, however, has been reported to date. Recently, extended molecular dynamics (MD) simulations indicated that LSD1/CoREST nanoscale clamp dynamics is regulated by substrate binding and highlighted key hinge points of this large-scale motion as well as the relevance of local residue dynamics. Prompted by the urgent need for new molecular probes and inhibitors to understand LSD1/CoREST interactions with small-molecules, peptides, protein partners, and chromatin, we undertake here a configurational ensemble approach to expand LSD1/CoREST druggability. The independent algorithms FTMap and SiteMap and our newly developed Druggable Site Visualizer (DSV) software tool were used to predict and inspect favorable binding sites. We find that the hinge points revealed by MD simulations at the SANT2/Tower interface, at the SWIRM/AOD interface, and at the AOD/Tower interface are new targets for the discovery of molecular probes to block association of LSD1/CoREST with chromatin or protein partners. A fourth region was also predicted from simulated configurational ensembles and was experimentally validated to have strong binding propensity. The observation that this prediction would be prevented when using only the X-ray structures available (including the X-ray structure bound to the same peptide) underscores the relevance of protein dynamics in protein interactions. A fifth region was highlighted corresponding to a small pocket on the AOD domain. This study sets the basis for future virtual screening campaigns targeting the five novel regions reported herein and for the design of LSD1/CoREST mutants to probe LSD1/CoREST binding with chromatin and various protein partners

A study of the perceived risks, benefits and barriers to the use of SDD in adult critical care units (the SuDDICU study)

Peer reviewedPublisher PD

An Action-Based Approach to Presence: Foundations and Methods

This chapter presents an action-based approach to presence. It starts by briefly describing the theoretical and empirical foundations of this approach, formalized into three key notions of place/space, action and mediation. In the light of these notions, some common assumptions about presence are then questioned: assuming a neat distinction between virtual and real environments, taking for granted the contours of the mediated environment and considering presence as a purely personal state. Some possible research topics opened up by adopting action as a unit of analysis are illustrated. Finally, a case study on driving as a form of mediated presence is discussed, to provocatively illustrate the flexibility of this approach as a unified framework for presence in digital and physical environment

Laboratory comparison of aging characteristics of warm mix asphalts involving natural and synthetic water containing additives

When comparing the aging characteristics of hot and warm mix asphalts from a technical point of view, it can intuitively be expected that a warm mix asphalt would be less subjected to aging-induced failures due to lower application temperatures. Since the side effects of warm asphalt technology should be investigated distinctly. This study addresses the aging investigation of properties of bituminous mixtures containing two (i.e., natural and synthetic zeolite) water based additives available on the market. Within the scope of this study, short- and long-term aging conditions were simulated on mixtures containing various contents of additives as well as on control specimens. The aging indices were determined based on the hardness ratio employing indirect tensile strength values in order to investigate the aging induced failures betide by time. Aging indices showed that the specimens with water containing additives demonstrate relatively better resistance against hardening than conventional hot mix asphalt specimens

Relativistic ejecta from XRF 060218 and the rate of cosmic explosions

Over the last decade, long-duration gamma-ray bursts (GRBs) including the subclass of X-ray flashes (XRFs) have been revealed to be a rare variety of Type Ibc supernova (SN). While all these events result from the death of massive stars, the electromagnetic luminosities of GRBs and XRFs exceed those of ordinary Type Ibc SNe by many orders of magnitude. The essential physical process that causes a dying star to produce a GRB or XRF, and not just an SN, remains the crucial open question. Here we present radio and X-ray observations of XRF 060218 (associated with SN 2006aj), the second nearest GRB identified to-date, which allow us to measure its total energy and place it in the larger context of cosmic explosions. We show that this event is 100 times less energetic but ten times more common than cosmological GRBs. Moreover, it is distinguished from ordinary Type Ibc SNe by the presence of 10^48 erg coupled to mildly-relativistic ejecta, along with a central engine (an accretion-fed, rapidly rotating compact source) which produces X-rays for weeks after the explosion. This suggests that the production of relativistic ejecta is the key physical distinction between GRBs/XRFs and ordinary SNe, while the nature of the central engine (black hole or magnetar) may distinguish typical bursts from low-luminosity, spherical events like XRF 060218.Comment: To appear in Nature on August 31 2006 (15 pages, 3 figures, 1 table, including Supplementary Information

A Relativistic Type Ibc Supernova Without a Detected Gamma-ray Burst

Long duration gamma-ray bursts (GRBs) mark the explosive death of some massive stars and are a rare sub-class of Type Ibc supernovae (SNe Ibc). They are distinguished by the production of an energetic and collimated relativistic outflow powered by a central engine (an accreting black hole or neutron star). Observationally, this outflow is manifested in the pulse of gamma-rays and a long-lived radio afterglow. To date, central engine-driven SNe have been discovered exclusively through their gamma-ray emission, yet it is expected that a larger population goes undetected due to limited satellite sensitivity or beaming of the collimated emission away from our line-of-sight. In this framework, the recovery of undetected GRBs may be possible through radio searches for SNe Ibc with relativistic outflows. Here we report the discovery of luminous radio emission from the seemingly ordinary Type Ibc SN 2009bb, which requires a substantial relativistic outflow powered by a central engine. The lack of a coincident GRB makes SN 2009bb the first engine-driven SN discovered without a detected gamma-ray signal. A comparison with our extensive radio survey of SNe Ibc reveals that the fraction harboring central engines is low, ~1 percent, measured independently from, but consistent with, the inferred rate of nearby GRBs. Our study demonstrates that upcoming optical and radio surveys will soon rival gamma-ray satellites in pinpointing the nearest engine-driven SNe. A similar result for a different supernova is reported independently.Comment: To appear in Nature on Jan 28 2010. Embargoed for discussion in the press until 13:00 US Eastern Time on Jan 27 (Accepted version, 27 pages, Manuscript and Suppl. Info.

Lemierre's syndrome due to Klebsiella pneumoniae in a 63-year-old man with diabetes: a case report

<p>Abstract</p> <p>Introduction</p> <p>Lemierre's syndrome was originally documented to be caused by <it>Fusobacterium necrophorum</it>. It is a very rare condition with a prevalence of one to 14.4 instances per million. Its presentation is varied, not only in composition but also in the infecting organism. Treatment with anticoagulants has been controversial and applied only on a case-by-case basis.</p> <p>Case presentation</p> <p>A 63-year-old Saudi man who had had uncontrolled diabetes mellitus for 47 years presented to our facility with a five-day history of swelling on the right side of his neck and fever. The swelling progressively increased in size and was associated with pain, dysphagia, odynophagia, change of voice ('hot potato voice'), and reduced appetite. Abscess content culture and sensitivity testing revealed <it>Klebsiella pneumoniae</it>. However, blood culture results were repeatedly negative. The abscess was incised and drained without any complication. Our patient was treated with clindamycin and cefuroxime. Warfarin was also administered concurrently for six weeks, for an isolated internal jugular vein thrombosis (IJV), with complete resolution of the thrombus. Normoglycemia was achieved and our patient was discharged after complete wound healing and the return of his biochemical parameters to normal.</p> <p>Conclusions</p> <p>Only two cases of Lemierre's syndrome in patients with diabetes due to <it>K. pneumoniae </it>have been reported previously. A review of the literature suggested that an association exists between deep neck infections due to <it>K. pneumoniae </it>and diabetes mellitus. The reasons for this association are still not clear. This poses a question as to whether diabetes mellitus specifically predisposes these patients to infection with this organism. It is suggested that clinicians should consider infectious agents other than <it>F. necrophorum </it>in the causation of Lemierre's syndrome, especially in patients with diabetes.</p

Bardet-Biedl syndrome with end-stage kidney disease in a four-year-old Romanian boy: a case report

<p>Abstract</p> <p>Background</p> <p>Bardet-Biedl syndrome is a significant genetic cause of chronic kidney disease in children. Kidney abnormalities are a major cause of morbidity and mortality in Bardet-Biedl syndrome, but the onset of end-stage renal disease at an early age and continuous ambulatory peritoneal dialysis, however, are not commonly mentioned in the literature.</p> <p>Case presentation</p> <p>We present the case of a four-year-old Romanian boy who presented to our department with 'febrile seizures'. After an initial evaluation, we diagnosed our patient as having hypertension, severe anemia and end-stage renal disease. He met the major and minor criteria for the diagnosis of Bardet-Biedl syndrome and underwent continuous ambulatory peritoneal dialysis.</p> <p>Conclusions</p> <p>Close follow-up for renal involvement in patients with Bardet-Biedl syndrome and Alström syndrome from an early age is highly recommended to prevent end-stage renal disease and so renal replacement therapy can be started immediately.</p

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package