Bookmarked An information-based sequence distance and its application to whole mitochondrial genome phylogeny. by M. Li, J. H. Badger, X. Chen, S. Kwong, P. Kearney, H. Zhang (Bioinformatics. 2001 Feb;17(2):149-54.)

MOTIVATION: Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance.

RESULTS: We establish the mathematical foundations of our distance and illustrate its use by constructing a phylogeny of the Eutherian orders using complete unaligned mitochondrial genomes. This phylogeny is consistent with the commonly accepted one for the Eutherians. A second, larger mammalian dataset is also analyzed, yielding a phylogeny generally consistent with the commonly accepted one for the mammals.

AVAILABILITY: The program to estimate our sequence distance, is available at http://www.cs.cityu.edu.hk/~cssamk/gencomp/GenCompress1.htm. The distance matrices used to generate our phylogenies are available at http://www.math.uwaterloo.ca/~mli/distance.html.

PMID: 11238070

Bookmarked Measuring the similarity of protein structures by means of the universal similarity metric. by N. Krasnogor, D. A. PeltaN. Krasnogor, D. A. Pelta (Bioinformatics. 2004 May 1;20(7):1015-21. Epub 2004 Jan 29.)

MOTIVATION: As an increasing number of protein structures become available, the need for algorithms that can quantify the similarity between protein structures increases as well. Thus, the comparison of proteins' structures, and their clustering accordingly to a given similarity measure, is at the core of today's biomedical research. In this paper, we show how an algorithmic information theory inspired Universal Similarity Metric (USM) can be used to calculate similarities between protein pairs. The method, besides being theoretically supported, is surprisingly simple to implement and computationally efficient.

RESULTS: Structural similarity between proteins in four different datasets was measured using the USM. The sample employed represented alpha, beta, alpha-beta, tim-barrel, globins and serpine protein types. The use of the proposed metric allows for a correct measurement of similarity and classification of the proteins in the four datasets.

AVAILABILITY: All the scripts and programs used for the preparation of this paper are available at http://www.cs.nott.ac.uk/~nxk/USM/protocol.html. In that web-page the reader will find a brief description on how to use the various scripts and programs.

PMID: 14751983 DOI: 10.1093/bioinformatics/bth031

Bookmarked Information theory in living systems, methods, applications, and challenges. by R. A. Gatenby, B. R. FriedenR. A. Gatenby, B. R. Frieden (Bull Math Biol. 2007 Feb;69(2):635-57. Epub 2006 Nov 3.)

Living systems are distinguished in nature by their ability to maintain stable, ordered states far from equilibrium. This is despite constant buffeting by thermodynamic forces that, if unopposed, will inevitably increase disorder. Cells maintain a steep transmembrane entropy gradient by continuous application of information that permits cellular components to carry out highly specific tasks that import energy and export entropy. Thus, the study of information storage, flow and utilization is critical for understanding first principles that govern the dynamics of life. Initial biological applications of information theory (IT) used Shannon's methods to measure the information content in strings of monomers such as genes, RNA, and proteins. Recent work has used bioinformatic and dynamical systems to provide remarkable insights into the topology and dynamics of intracellular information networks. Novel applications of Fisher-, Shannon-, and Kullback-Leibler informations are promoting increased understanding of the mechanisms by which genetic information is converted to work and order. Insights into evolution may be gained by analysis of the the fitness contributions from specific segments of genetic information as well as the optimization process in which the fitness are constrained by the substrate cost for its storage and utilization. Recent IT applications have recognized the possible role of nontraditional information storage structures including lipids and ion gradients as well as information transmission by molecular flux across cell membranes. Many fascinating challenges remain, including defining the intercellular information dynamics of multicellular organisms and the role of disordered information storage and flow in disease.

PMID: 17083004 DOI: 10.1007/s11538-006-9141-5

In Law Schools, Grades Go Up, Just Like That

Bookmarked In Law Schools, Grades Go Up, Just Like That (New York Times)
In the last two years, at least 10 law schools have made their grading systems more lenient to give their students a better chance in a soft job market.

Is GPA tampering and grade inflation going too far with changes like this?

First U.S. stem cells transplanted into spinal cord | CNN.com

Bookmarked First U.S. stem cells transplanted into spinal cord by Miriam Falco, CNN Medical News Managing Editor (cnn.com)
For the first time in the United States, stem cells have been directly injected into the spinal cord of a patient, researchers announced Thursday.
A recent article announcing the first stem cells being transplanted into a human patient in the United States. I worked with the researchers and surgeon in this experiment and built the microinjectors that were used in the lead up experiments as well as for this first patient.
Bookmarked The structure of degradable quantum channels by Toby S. Cubitt, Mary Beth Ruskai, Graeme Smith (Journal of Mathematical Physics 49, 102104 (2008))
Degradable quantum channels are among the only channels whose quantum and private classical capacities are known. As such, determining the structure of these channels is a pressing open question in quantum information theory. We give a comprehensive review of what is currently known about the structure of degradable quantum channels, including a number of new results as well as alternate proofs of some known results. In the case of qubits, we provide a complete characterization of all degradable channels with two dimensional output, give a new proof that a qubit channel with two Kraus operators is either degradable or anti-degradable, and present a complete description of anti-degradable unital qubit channels with a new proof. For higher output dimensions we explore the relationship between the output and environment dimensions (dB and dE, respectively) of degradable channels. For several broad classes of channels we show that they can be modeled with an environment that is “small” in the sense of ΦC. Such channels include all those with qubit or qutrit output, those that map some pure state to an output with full rank, and all those which can be represented using simultaneously diagonal Kraus operators, even in a non-orthogonal basis. Perhaps surprisingly, we also present examples of degradable channels with “large” environments, in the sense that the minimal dimension dE>dB. Indeed, one can have dE>14d2B. These examples can also be used to give a negative answer to the question of whether additivity of the coherent information is helpful for establishing additivity for the Holevo capacity of a pair of channels. In the case of channels with diagonal Kraus operators, we describe the subclasses that are complements of entanglement breaking channels. We also obtain a number of results for channels in the convex hull of conjugations with generalized Pauli matrices. However, a number of open questions remain about these channels and the more general case of random unitary channels.
Alternate version on arXiv: https://arxiv.org/abs/0802.1360 
Bookmarked Automated on-chip rapid microscopy, phenotyping and sorting of C. elegans. by Kwanghun Chung, Matthew M. Crane, Hang Lu (Nature Methods [22 Jun 2008, 5(7):637-643])
Microscopy, phenotyping and visual screens are frequently applied to model organisms in combination with genetics. Although widely used, these techniques for multicellular organisms have mostly remained manual and low-throughput. Here we report the complete automation of sample handling, high-resolution microscopy, phenotyping and sorting of Caenorhabditis elegans. The engineered microfluidic system, coupled with customized software, has enabled high-throughput, high-resolution microscopy and sorting with no human intervention and may be combined with any microscopy setup. The microchip is capable of robust local temperature control, self-regulated sample-loading and automatic sample-positioning, while the integrated software performs imaging and classification of worms based on morphological and intensity features. We demonstrate the ability to perform sensitive and quantitative screens based on cellular and subcellular phenotypes with over 95% accuracy per round and a rate of several hundred worms per hour. Screening time can be reduced by orders of magnitude; moreover, screening is completely automated.
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Related: https://www.news.gatech.edu/2008/06/23/automated-microfluidic-device-reduces-time-screen-small-organisms

Bookmarked High fertilization and implantation rates after intracytoplasmic sperm injection. by Van Steirteghem AC , Nagy Z, Joris H, Liu J, Staessen C, Smitz J, Wisanto A, Devroey P. (Hum. Reprod., Vol. 8, No. 7. (1 July 1993), pp. 1061-1066)
Previously reported better fertilization rate after intracytoplasmic single sperm injection (ICSI) than after subzonal insemination of several spermatozoa was confirmed in a controlled comparison of the two procedures in 11 patients. Intracytoplasmic sperm injection was carried out in 150 consecutive treatment cycles of 150 infertile couples, who had failed to have fertilized oocytes after standard in-vitro fertilization (IVF) procedures or who were not accepted for IVF because not enough motile spermatozoa were present in the ejaculate. A single spermatozoon was injected into the ooplasm of 1409 metaphase II oocytes. Only 117 oocytes (8.3%) were damaged by the procedure and 830 oocytes (64.2% of the successfully injected oocytes) had two distinct pronuclei the morning after the injection procedure. The fertilization rate was not influenced by semen characteristics. After 24 h of further in-vitro culture, 71.2% of these oocytes developed into embryos, which were transferred or cryopreserved. Only 15 patients did not have embryos replaced. Three-quarters of the transfers were triple-embryo transfers. High pregnancy rates were noticed since 67 pregnancies were achieved, of which 53 were clinical, i.e. a total and clinical pregnancy rate of 44.7% and 35.3% per started cycle and 49.6% and 39.2% per embryo transfer. A total of 237 supernumerary embryos were cryopreserved in 71 treatment cycles.