Four small puzzles that Rosetta doesn't solve

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular "puzzles" should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special Collectio

Comparison of silicon oil removal with various viscosities after complex retinal detachment surgery

BACKGROUND: Despite the progress in vitreoretinal surgery and the importance of silicone oil as an adjunct for the treatment of complex forms of retinal detachment, controversy still surrounds the issue of selecting the proper oil viscosity for clinical use. Herein, we evaluate the outcomes of retinal detachment (RD) surgery after removing silicone oils of different viscosities. METHODS: In this retropsective cohort study, eighty-two eyes with surgically re-attached retinas, of which 53 were filled with 5000cs silicone oil and 29 with 1000cs silicone oil were enrolled. We evaluated the outcomes and complications following silicone oil removal. Final anatomic success (stable re-attachment), final visual acuity (VA) and intraocular pressure (IOP)were recorded and analysed. RESULTS: Of 82 eyes, 41 had proliferative vitreoretinopathy (PVR), 24 were associated with intraocular foreign bodies, 10 had endophthalmitis and 7 had proliferative diabetic retinopathy with tractional retinal detachment. Prior to silicone oil removal, the retina was attached in all eyes, 29% had VA ≥ 6/120 and 52% had IOP ≥ 21 mmHg. After silicone oil removal, the retina remained attached in 59(72%) of the eyes, 34% had VA ≥ 6/120 and 9% had IOP ≥ 21 mmHg. Comparing 1000cs and 5000cs silicone oil filled eyes, redetachment occurred more frequently in the latter group especially in cases with associated PVR. Final VA worse than 6/120 was associated with initial VA < 6/120 (OR = 32.2 95%CI 7.4–140.2) and use of 5000cs silicone oil (OR = 7.9 95%CI 1.9–32.2). No factor was significantly associated with final IOP ≥ 21 mmHg. CONCLUSION: In complicated retinal detachment surgery, use of 5000cs silicone oil may be associated with a poorer anatomic and visual outcome compared with 1000cs silicone oil. However there was no difference between the two viscosities in IOP elevation. A randomized controlled study is necessary to further evaluate such a possibility

Self-force: Computational Strategies

Building on substantial foundational progress in understanding the effect of a small body's self-field on its own motion, the past 15 years has seen the emergence of several strategies for explicitly computing self-field corrections to the equations of motion of a small, point-like charge. These approaches broadly fall into three categories: (i) mode-sum regularization, (ii) effective source approaches and (iii) worldline convolution methods. This paper reviews the various approaches and gives details of how each one is implemented in practice, highlighting some of the key features in each case.Comment: Synchronized with final published version. Review to appear in "Equations of Motion in Relativistic Gravity", published as part of the Springer "Fundamental Theories of Physics" series. D. Puetzfeld et al. (eds.), Equations of Motion in Relativistic Gravity, Fundamental Theories of Physics 179, Springer, 201

Activation of BMP-Smad1/5/8 Signaling Promotes Survival of Retinal Ganglion Cells after Damage In Vivo

While the essential role of bone morphogenetic protein (BMP) signaling in nervous system development is well established, its function in the adult CNS is poorly understood. We investigated the role of BMP signaling in the adult mouse retina following damage in vivo. Intravitreal injection of N-Methyl-D-aspartic acid (NMDA) induced extensive retinal ganglion cell death by 2 days. During this period, BMP2, -4 and -7 were upregulated, leading to phosphorylation of the downstream effector, Smad1/5/8 in the inner retina, including in retinal ganglion cells. Expression of Inhibitor of differentiation 1 (Id1; a known BMP-Smad1/5/8 target) was also upregulated in the retina. This activation of BMP-Smad1/5/8 signaling was also observed following light damage, suggesting that it is a general response to retinal injuries. Co-injection of BMP inhibitors with NMDA effectively blocked the damage-induced BMP-Smad1/5/8 activation and led to further cell death of retinal ganglion cells, when compared with NMDA injection alone. Moreover, treatment of the retina with exogenous BMP4 along with NMDA damage led to a significant rescue of retinal ganglion cells. These data demonstrate that BMP-Smad1/5/8 signaling is neuroprotective for retinal ganglion cells after damage, and suggest that stimulation of this pathway can serve as a potential target for neuroprotective therapies in retinal ganglion cell diseases, such as glaucoma

Year in review in Intensive Care Medicine 2010: I. Acute renal failure, outcome, risk assessment and ICU performance, sepsis, neuro intensive care and experimentals

SCOPUS: re.jinfo:eu-repo/semantics/publishe

SOSORT consensus paper: school screening for scoliosis. Where are we today?

This report is the SOSORT Consensus Paper on School Screening for Scoliosis discussed at the 4th International Conference on Conservative Management of Spinal Deformities, presented by SOSORT, on May 2007. The objectives were numerous, 1) the inclusion of the existing information on the issue, 2) the analysis and discussion of the responses by the meeting attendees to the twenty six questions of the questionnaire, 3) the impact of screening on frequency of surgical treatment and of its discontinuation, 4) the reasons why these programs must be continued, 5) the evolving aim of School Screening for Scoliosis and 6) recommendations for improvement of the procedure

CITRATE IN MINERALIZED TISSUES. VI. THE EFFECTS OF DIETARY REHABILITATION WITH CALCIUM OR WITH VITAMIN D, OR WITH CALCIUM AND VITAMIN D, IN RATS PREVIOUSLY MAINTAINED ON A DIET DEFICIENT IN BOTH CALCIUM AND VITAMIN D.

Fifty weanling hooded rats were maintained for 8 weeks on a diet low in calcium and vitamin D. Similar groups were then transferred to diets adequate in calcium, or adequate in vitamin D, or sufficient in both respects. They were continued on these diets and representatives were killed at intervals during the 35 day period. The concentrations of calcium, phosphorus, and citrate in blood and bone were determined. When the deficient animals were rehabilitated with vitamin D alone, the concentration of citrate in bone was increased before that in the serum. Rehabilitation with calcium alone caused an increase in the concentration of serum citrate before any increase was observed in the bone. When the animals were transferred to a diet containing adequate supplies of calcium and vitamin D, the effects of both factors were distinguished since they occurred at different times. The implications of these results in relation to the possible function of citrate in bone are discussed. © 1963

Relative levels of citric and lactic acids in certain mineralized tussues.

The citric acid and lactic acid contents of a number of mineralized tissues were estimated. Of the tissues examined the rat incisor was unique in that it was the only one in which the lactic acid content exceeded that of citric acid, the effect being largely due to the unusually low level of the latter. This observation may be related to the fact that the rat incisor is a continuously growing and metabolically active tissue. © 1963

Newer knowledge of non-collagenous protein in dentin and cortical bone matrix.

The current state of knowledge of the composition of the NCM components of bone and dentin has been summarized at the end of the appropriate sections. It is significant that increasing interest in the chemistry of hard tissue matrices has coincided with the development and refinement of a wide range of separation techniques, resulting in the isolation of an unexpectedly large number of components. The most sophisticated techniques, such as iso-electric focusing and isotachophoresis, give rise to discrete fractions often of very similar composition, particularly in terms of amino acid content. Such components might best be considered in groups, especially should such groups be identified in terms of common immunochemical properties. Dickson has used such an approach in a recent study of the proteins of sheep cortical bone. The Liverpool group has approached the problem on a broad front and thus directed attention to the number and diversity of NCM components, but it will be seen that those studies directed to the isolation of a specific component have invariably revealed the presence of several other fractions, set aside while attention was directed to the component under investigation. It is clear that the major proportion of bone and dentin NCM consists of glycoproteins of the less-acidic and anionic types. Several of the anionic components contain phosphate, levels being higher in those derived from dentin. Glycosaminoglycans, the first class of non-collagenous compounds to be identified in hard tissue matrices, are now known to comprise only about 5-7 per cent of the NCM. Precise details of the glycosaminoglycan fraction of human dentin and considerable information concerning that of bovine bone are now available. The major component in each tissue is chondroitin-4-sulfate, which exists in the form of proteoglycan, the protein moieties of those from bovine bone and human dentin being very different. Although greater interest is currently being shown in the glycoprotein fractions, several studies have been made of the calcium-binding properties of proteoglycan preparations and of individual glycosaminoglycans. Attempts to relate differences in chemical composition and properties to specific bone sites may not prove to be the best approach to the study of the precise chemistry of mineralization. It is clear, from the earlier work of Lindenbaum and Kuettner that mineralization takes place in a very narrow layer which will normally represent only a fraction of a typical zone prepared for analysis..