A resonant optical modulator comprises a transmission fiber-optic waveguide, a circumferential-mode optical resonator transverse-coupled thereto, a modulator optical component transverse-coupled to the circumferential-mode resonator, and a modulator control component. A control signal applied to the modulator optical component through the modulator control component alters the round-trip optical loss of the circumferential-mode resonator, thereby altering the transmission of a resonant optical signal through the transmission fiber-optic waveguide. The modulator optical element may comprise an open waveguide or a closed waveguide (i.e., resonator). The resonator round-trip optical loss may be altered by altering the optical absorption/scattering of the modulator optical component, by altering the amount of optical power transfer between the resonator and the modulator optical component, or by altering an optical resonance frequency of a resonant modulator optical component.

This application is related to subject matter disclosed in:                A1) U.S. provisional Application No. 60/111,484 entitled "An all-fiber-optic modulator" filed Dec. 7, 1998 in the names of Kerry J. Vahala and Amnon Yariv, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A2) U.S. Application No. 09/454,719, now U.S. Pat. No. 6,633,696 entitled "Resonant optical wave power control devices and methods" filed Dec. 7, 1999 in the names of Kerry J. Vahala and Amnon Yariv, said application being hereby incorporated by reference in its entirety as if fully set forth herein;        A3) U.S. provisional Application No.60/108,358 entitled "Dual tapered fiber-microsphere coupler" filed Nov. 13, 1998 in the names of Kerry J. Vahala and Ming Cai, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A4) U.S. Application No.09/440,311, now U.S. Pat. No. 6,580,851 entitled "Resonator fiber bi-directional coupler" filed Nov. 12, 1999 in the names of Kerry J. Vahala, Ming Cai, and Guido Hunziker, said application being hereby incorporated by reference in its entirety as if fully set forth herein;        A5) U.S. provisional Application No.60/183,499 entitled "Resonant optical power control devices and methods of fabrication thereof" filed Feb. 17, 2000 in the names of Peter C. Sercel and Kerry J. Vahala, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A6) U.S. provisional Application No.60/226,147 entitled "Fiber-optic waveguides for evanescent optical coupling and methods of fabrication and use thereof", filed Aug. 18, 2000 in the names of Peter C. Sercel, Guido Hunziker, and Robert B. Lee, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A7) U.S. provisional Application No. 60/170,074 entitled "Optical routing/switching based on control of waveguide-ring resonator coupling", filed Dec. 9, 1999 in the name of Amnon Yariv, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A8) U.S. Pat. No. 6,052,495 entitled "Resonator modulators and wavelength routing switches" issued Apr. 18, 2000 in the names of Brent E. Little, James S. Foresi, and Hermann A. Haus, said patent being hereby incorporated by reference in its entirety as if fully set forth herein;        A9) U.S. Pat. No. 6,101,300 entitled "High efficiency channel drop filter with absorption induced on/off switching and modulation" issued Aug. 8, 2000 in the names of Shanhui Fan, Pierre R. Villeneuve, John D. Joannopoulos, Brent E. Little, and Hermann A. Haus, said patent being hereby incorporated by reference in its entirety as if fully set forth herein;        Ab 10) U.S. Pat. No.5,926,496 entitled "Semiconductor micro-resonator device" issued Jul. 20, 1999 in the names of Seng-Tiong Ho and Deanna Rafizadeh, said patent being hereby incorporated by reference in its entirety as if fully set forth herein;        A11) U.S. Pat. No.6,009,115 entitled "Semiconductor micro-resonator device" issued Dec. 28, 1999 in the name of Seng-Tiong Ho, said patent being hereby incorporated by reference in its entirety as if fully set forth herein;        A12) U.S. provisional Application No.60/257,218 entitled"Wave guides and resonators for integrated optical devices and methods of fabrication and use thereof", filed Dec. 21, 2000 in the name of Oskar J. Painter, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A13) U.S. provisional Application No.60/257,248 entitled "Modulators for resonant optical power control devices and methods of fabrication and use thereof", filed Dec. 21, 2000 in the names of Oskar J. Painter, Kerry J. Vahala, Peter C. Sercel, and Guido Hunziker, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A14) U.S. provisional Application No.60/301,519 entitled "Waveguide-fiber Mach-Zender interferometer and methods of fabrication and use thereof", filed Jun. 27, 2001 in the names of Oskar J. Painter, David W. Vernooy, and Kerry J. Vahala, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A15) U.S. non-provisional Application No.09/788,303 entitled "Cylindrical processing of optical media", filed Feb. 16, 2001 in the names of Peter C. Sercel, Kerry J. Vahala, David W. Vernooy, and Guido Hunziker, said non-provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A16) U.S. non-provisional Application No.09/788,331 entitled "Fiber-ring optical resonators", filed Feb. 16, 2001 in the names of Peter C. Sercel, Kerry J. Vahala, David W. Vernooy, Guido Hunziker, and Robert B. Lee, said non-provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A17) U.S. non-provisional Application No.09/788,300 entitled "Resonant optical filters", filed Feb. 16, 2001 in the names of Kerry J. Vahala, Peter C. Sercel, David W. Vernooy, Oskar J. Painter, and Guido Hunziker, said non-provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A18) U.S. non-provisional Application No.09/788,301 entitled "Resonant optical power control device assemblies", filed Feb. 16, 2001 in the names of Peter C. Sercel, Kerry J. Vahala, David W. Vernooy, Guido Hunziker, Robert B. Lee, and Oskar J. Painter, said non-provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A19) U.S. provisional Application No. 60/333,236 entitled "Alignment apparatus and methods for transverse optical coupling", Docket No. CQC16P, filed Nov. 23, 2001 in the names of Charles I. Grosjean, Guido Hunziker, Paul M. Bridger, and Oskar J. Painter, said provisional application being hereby incorporated by reference in its entirety as if fully set forth herein;        A20) U.S. non-provisional Application No. 10/037,966, filed Dec. 21, 2001 entitled "Multi-layer dispersion-engineered waveguides and resonators", Docket No. CQC14NP, filed concurrently with the present application in the names of Oskar J. Painter, David W. Vernooy, and Kerry J. Vahala, said non-provisional application being hereby incorporated by reference in its entirety as if fully set forth herein.
This application is also related to subject matter disclosed in the following publications, each of said publications being hereby incorporated by reference in its entirety as if fully set forth herein:                P1) Ming Cai, Guido Hunziker, and Kerry Vahala, "Fiber-optic add-drop device based on a silica microsphere whispering gallery mode system", IEEE Photonics Technology Letters Vol. 11 686 (1999);        P2) J. C. Knight, G. Cheung, F. Jacques, and T. A. Birks, "Phased-matched excitation of whispering gallery-mode resonances by a fiber taper", Optics Letters Vol. 22 1129 (1997);        P3) R. D. Pechstedt, P. St. J. Russell, T. A. Birks, and F. D. Lloyd-Lucas, "Selective coupling of fiber modes with use of surface-guided Bloch modes supported by dielctric multilayer stacks", J. Opt. Soc. Am. A Vol. 12(12) 2655 (1995);        P4) R. D. Pechstedt, P. St. J. Russell, "Narrow-band in-line fiber filter using surface-guided Bloch modes supported by dielectric multilayer stacks", J. Lightwave Tech. Vol. 14(6) 1541 (1996);        P5) Hiroshi Wada, Takeshi Kamijoh, and Yoh Ogawa, "Direct bonding of InP to different materials for optical devices", Proceedings of the third international symposium on semiconductor wafer bonding: Physics and applications, Electrochemical Society Proceedings, Princeton N.J., Vol. 95-7, 579-591 (1995);        P6) R. H. Horng, D. S. Wuu, S. C. Wei, M. F. Huang, K. H. Chang, P. H. Liu, and K. C. Lin, "AlGaInP/AuBe/glass light emitting diodes fabricated by wafer-bonding technology", Appl. Phys. Letts. Vol. 75(2) 154 (1999);        P7) Y. Shi, C. Zheng, H. Zhang, J. H. Bechtel, L. R. Dalton, B. B. Robinson, W. Steier, "Low (sub-1-volt) halfwave voltage polymeric electro-optic modulators achieved by controlling chromophore shape", Science Vol. 288, 119 (2000);        P8) E. L. Wooten, K. M. Kissa, and A. Yi-Yan, "A review of lithium niobate modulators for fiber-optic communications systems", IEEE J. Selected Topics in Quantum Electronics, Vol. 6(1), 69 (2000);        P9) D. L. Huffaker, H. Deng, Q. Deng, and D. G. Deppe, "Ring and stripe oxide-confined vertical-cavity surface-emitting lasers", Appl. Phys. Lett., Vol. 69(23), 3477 (1996);        P10) Serpenguzel, S. Arnold, and G. Griffel, "Excitation of resonances of microspheres on an optical fiber", Opt. Lett. Vol. 20, 654 (1995);        P11) F. Treussart, N. Dubreil, J. C. Knight, V. Sandoghar, J. Hare, V. Lefevre-Seguin, J. M. Raimond, and S. Haroche, "Microlasers based on silica microspheres", Ann. Telecommun. Vol. 52, 557 (1997);        P12) M. L. Gorodetsky, A. A. Savchenkov, V. S. Ilchenko, "Ultimate Q of optical microsphere resonators", Optics Letters, Vol. 21, 453 (1996);        P13) Carl Arft, Diego R. Yankelovich, Andre Knoesen, Erji Mao, and James S. Harris Jr., "In-line fiber evanescent field electrooptic modulators", Journal of Nonlinear Optical Physics and Materials Vol. 9(1) 79 (2000);        P14) Pochi Yeh, Amnon Yariv, and Chi-Shain Hong, "Electromagnetic propagation in periodic stratified media. I. General theory", J. Optical Soc. Am., Vol. 67(4) 423 (1977);        P15) Ming Cai, Oskar Painter, and Kerry J. Vahala, "Observation of critical coupling in a fiber taper to a silica-microsphere whispering-gallery mode system", Physical Review Letters, Vol. 85(1) 74 (2000);        P16) M. Kondow, T. Kitatani, S. Nakatsuka, M. C. Larson, K. Nakahara, Y. Yazawa, M. Okai, and K. Uomi, "GaInNAs: A novel material for long-wavelength semiconductor lasers", IEEE Journal of Selected Topics in Quantum Electronics, Vol 3(3), 719 (1997);        P17) H. Saito, T. Makimoto, and N. Kobayashi, "MOVPE growth of strained InGaAsN/GaAs quantum wells", J. Crystal Growth, Vol. 195 416 (1998);        P18) W. G. Bi and C. W. Tu, "Bowing parameter of the band-gap energy of GaNxAs1−y". Appl. Phys. Lett. Vol. 70(12) 1608 (1997);        P19) H. P. Xin and C. W. Tu, "GaInNAs/GaAs multiple quantum wells grown by gas-source molecular beam epitaxy", Appl. Phys Lett. Vol. 72(19) 2442 (1998);        P20) B. Koley, F. G. Johnson, O. King, S. S. Saini, and M. Dagenais, "A method of highly efficient hydrolization oxidation of III-V semiconductor lattice matched to indium phosphide", Appl. Phys. Lett. Vol. 75(9) 1264 (1999);        P21) Z. J. Wang, S. -J. Chua, F. Zhou, W. Wang, and R. H. Wu, "Buried heterostructures InGaAsP/InP strain-compensated multiple quantum well laser with a native-oxidized InAlAs current blocking layer", Appl. Phys. Lett. Vol 73(26) 3803 (1998);        P22) N. Ohnoki, F. Koyama, and K. Iga, "Superlattice AlAs/AlInAs-oxide current aperture for long wavelength InP-based vertical-cavity surface-emitting laser structure", Appl. Phys. Lett. Vol. 73(22) 3262 (1998);        P23) N. Ohnoki, F. Koyama, and K. Iga, "Super-lattice AlAs/AlInAs for lateral-oxide current confinement in InP-based lasers", J. Crystal Growth Vol. 195 603 (1998);        P24) K. D. Choquette, K. M. Geib, C. I. H. Ashby, R. D. Twesten, 0. Blum, H. Q. Hou, D. M. Follstaedt, B. E. Hammons, D. Mathes, and R. Hull, "Advances in selective wet oxidation of AlGaAs alloys", IEEE Journal of Selected Topics in Quantum Electronics Vol. 3(3) 916(1997);        P25) M. H. MacDougal, P. D. Dapkus, "Wavelength shift of selectively oxidized AlxOy—AlGaAs—GaAs distributed Bragg reflectors", IEEE Photonics Tech. Lett. Vol. 9(7) 884 (1997);        P26) C. I. H. Ashby, M. M. Bridges, A. A. Alleman, B. E. Hammons, "Origin of the time dependence of wet oxidation of AlGaAs", Appl. Phys. Lett. Vol. 75(1) 73 (1999);        P27) P. Chavarkar, L. Zhao, S. Keller, A. Fisher, C. Zheng, J. S. Speck, and U. K. Mishra, "Strain relaxation of InxGa1−xAs during lateral oxidation of underlying AlAs layers", Appl. Phys. Lett. Vol. 75(15) 2253 (1999);        P28) R. L. Naone and L. A. Coldren, "Surface energy model for the thickness dependence of the lateral oxidation of AlAs", J. Appl. Phys. Vol. 82(5) 2277 (1997);        P29) M. H. MacDougalP. D. Dapkus, A. E. Bond, C. -K. Lin, and J. Geske, "Design and fabrication of VCSEL's with AlxOy-GaAs DBR's", IEEE Journal of Selected Topics in Quantum Electronics Vol. 3(3) 905 (1997);        P30) E. I. Chen, N. Holonyak, Jr., and M. J. Ries, "Planar disorder- and native-oxide-defined photopumped AlAs—Gas superlattice minidisk lasers", J. Appl. Phys. Vol. 79(11) 8204 (1996); and        P31) Y. Luo, D. C. Hall, L. Kou, L. Steingart, J. H. Jackson, O. Blum, and H. Hou, "Oxidized AlxGa1−xAs heterostructures planar waveguides", Appl. Phys. Lett. Vol. 75(20) 3078 (1999).
Optical fiber and propagation of high-data-rate optical pulse trains therethrough has become the technology of choice for high speed telecommunications. Wavelength division multiplexing (WDM) techniques are now commonly used to independently transmit a plurality of signals over a single optical fiber, independent data streams being carried by optical fields propagating through the optical fiber at a slightly differing optical carrier wavelengths (i.e., signal channels). WDM techniques include dense wavelength division multiplexing (DWDM) schemes, wherein the frequency spacing between adjacent signal channels may range from a few hundred GHz down to a few GHz. A propagating mode of a particular wavelength must be modulated, independently of other propagating wavelengths, in order to carry a signal. A signal carried by a particular wavelength channel must be independently accessible for routing from a particular source to a particular destination. These requirements have previously required complex and difficult-to-manufacture modulating and switching devices requiring extensive active alignment procedures during fabrication/assembly, and as a result are quite expensive. Such devices may require conversion of the optical signals to electronic signals and/or vice versa, which is quite power consuming and inefficient. In various of the patent applications cited above a new approach has been disclosed for controlling optical power transmitted through an optical fiber that relies on the use of resonant circumferential-mode optical resonators, or other optical resonators, for direct optical coupling to a propagating mode of an optical fiber resonant with the optical resonator, thereby enabling wavelength-specific modulation, switching, and routing of optical signals propagating through the optical fiber. A thorough discussion of the features and advantages of such optical power control devices and techniques, as well as methods of fabrication, may be found in these applications, already incorporated by reference herein.
One important element of these latter devices is optical coupling between a fiber-optic waveguide and a circumferential-mode optical resonator. The circumferential-mode optical resonator provides wavelength specificity, since only optical signals substantially resonant with the circumferential-mode optical resonator will be significantly affected by the device. A fiber-optic waveguide for transmitting the optical signal through the control device is typically provided with an transverse-coupling segment, where an evanescent portion of the optical signal extends beyond the waveguide and overlaps a portion of a circumferential optical mode of the circumferential-mode optical resonator, thereby optically coupling the circumferential-mode optical resonator and the fiber-optic waveguide. The transverse-coupling segment may take one of several forms, including an optical fiber taper, D-shaped optical fiber, an optical fiber with a saddle-shaped concavity in the cladding layer, and/or other functionally equivalent configurations. These are discussed in detail in various patent applications cited herein.
The circumferential-mode optical resonator structure may comprise a glass micro-sphere or micro-disk, a fiber-ring resonator, a semiconductor ring/waveguide, or other functionally equivalent structure, described in detail in various earlier-cited applications. A high-Q circumferential-mode optical resonator supports relatively narrow-linewidth resonant circumferential optical modes (i.e., having a linewidth consistent with typical linewidths of a WDM system, TDM system, or other optical data transmission system), which in an optical power control device may optically couple to optical signals of the fiber-optic waveguide of substantially resonant optical wavelength. The circumferential-mode optical resonator therefore provides the wavelength selectivity of the optical power control device. Non-resonant propagating optical signals pass by the circumferential-mode optical resonator relatively undisturbed, and are transmitted through the device. By controllably adjusting the loss per round trip experienced by the circumferential optical mode circulating about the circumferential-mode optical resonator, the optical power control device may function in either of two modes:                1) Switching the circumferential-mode optical resonator between an over-coupled condition (where the loss per round trip in the circumferential-mode optical resonator is small compared to the optical coupling between the fiber-optic waveguide and circumferential-mode optical resonator, and the transmission through the fiber-optic waveguide past the resonator is large) and the condition of critical coupling (at which the optical coupling of the fiber-optic waveguide and circumferential-mode optical resonator is substantially equal to the round trip loss of the circumferential-mode optical resonator, and substantially all of the optical power is dissipated by/from the circumferential-mode optical resonator resulting in near zero optical transmission through the fiber-optic waveguide past the circumferential-mode optical resonator); or        2) Switching states between the condition of critical coupling (near zero transmission through the fiber-optic waveguide) and a condition of under-coupling (where the loss per round trip in the circumferential-mode optical resonator is large compared to the optical coupling between the fiber-optic waveguide and circumferential-mode optical resonator, and the transmission through the fiber-optic waveguide past the circumferential-mode optical resonator is non-zero).
For each of these modes of operation, there are essentially two classes of mechanism by which one can introduce round trip loss to a circulating optical wave (i.e., resonant circumferential optical mode) in the circumferential-mode resonator. Either optical power of the circulating wave can be absorbed within the resonator, or it can be gated out of the circumferential-mode optical resonator into a second optical component, such as a second waveguide or second resonator. The gating may preferably be achieved by control of the optical coupling between the circumferential-mode optical resonator and the second optical component and functions rather like a trapdoor. These two general possibilities are both disclosed in several earlier-cited applications. The current disclosure describes such devices in greater detail, particularly optical loss components, elements, and/or transducers provided as a separate component to control optical loss from a circumferential-mode resonator by either of these means (as distinguished from designs in which the loss control component is an integral part of the circumferential-mode optical resonator structure).


The present invention is directed to methods and compositions for isolating template nucleic acids containing target sequences of interest, wherein those isolated template nucleic acids can be further assessed for information related to sequence and nucleic acid modifications.

The ability to understand the genetic code has yielded advances in countless areas. From the ability to diagnose disease to the ability to identify evolutionary connections and/or diversity, to the ability to manipulate the genetic framework in the development of new materials and compositions, this understanding has opened doors to advances that have benefited and will continue to benefit biomedical research.
Integral to these advances have been developments in technology directed to the reading and/or characterization of the genetic code. For example, development of nucleic acid sequencing technologies has allowed for the base by base identification of the nucleic acid sequences that make up the genetic code to the point that entire human genomes have been elucidated. Other advances include rapid array based technologies that allow reasonably facile identification of genetic patterns from patients or other biological samples.
One area of development in the analysis of the genetic code is the ability to assess the variety of modifications that can occur in nucleic acids. Such modifications include chemical modifications, variations in nucleic acid conformation or composition, interactions of an agent with a nucleic acid (e.g., bound to the nucleic acid), and other perturbations associated with the nucleic acid.
One challenge in assessing modifications of nucleic acids, particularly genomic DNA, is that many technologies rely on amplified samples for assessment of nucleic acids. However, many nucleic acid modifications (including, for example, methylation) are not retained through the amplification process. The inability to retain these modifications in amplified samples can further contribute to the difficulty of identifying the portions of a nucleic acid sample that contain modifications and separating those nucleic acids from those that do not contain such modifications.

Methods and compositions for isolating template nucleic acids


A machine classification learning method titled Generalized Reduced Error Logistic Regression (RELR) is presented. The method overcomes significant limitations in prior art logistic regression and other machine classification learning methods. The method is applicable to all current applications of logistic regression, but has significantly greater accuracy using smaller sample sizes and larger numbers of input variables than other machine classification learning methods including prior art logistic regression.

This invention relates to a method of classification through machine learning methodology that improves upon previous endeavors employing logistic regression. Automated classifications systems are an integral part of the fields of data mining and machine learning. Since the pioneering work of Luce (1959), there has been widespread use of logistic regression as an analytical engine to make classifying decisions. Examples of its application include predicting the probability that a person will get cancer given a list of their environmental risk factors and genes, predicting the probability that a person will vote Republican, Democratic or Green given their demographic profile, and predicting the probability that a high school student will rank in the bottom third, the middle third, or the upper third of their class given their socioeconomic and demographic profile. Logistic Regression has potential application to any scientific, engineering, social, medical, or business classification problem where target variable values can be formalized as binary, nominal, rank-ordered, or interval-categorized outcomes. More generally, Logistic Regression is a machine learning method that can be programmed into computers, robots and artificial intelligence agents for the same types of applications as Neural Networks, Random Forests, Support Vector Machines and other such machine learning methods, many of which are the subject of issued U.S. patents. Logistic Regression is an important and widely used analytical method in today's economy. Unlike most other machine learning methods, Logistic Regression is not a "black box" method. Instead, Logistic Regression is a transparent method that does not require elaborate visualization methods to understand how the classification works.
Prior art forms of logistic regression, along with other machine classification methods, have significant limitations with regard to their ability to handle errors such as sampling errors in small training sample sizes, over fitting error, and multicollinearity error related to highly correlated input variables. Many prior art logistic regression methods also do not handle high dimensional problems having very large numbers of variables effectively.
The present machine learning method is fundamentally different from prior art methods such as the one described in U.S. Pat. No. 7,222,127 (the '127 patent). For example, the method of the present invention is based upon reduced error logistic regression that can be shown to yield less error in machine learning applications with large numbers of multicollinear variables and a small number of observations, and the method of the present invention employs backward selection in its variable selection processing. The backward selection in the method of the present invention is based upon the magnitude of t values; this backward selection process starts with a very large number of variables and eliminates the least important variables based upon the magnitude of the t values until the best model is discovered as defined through a log likelihood function based upon probability of error that results from reduced error logistic regression. In contrast, the '127 patent employs additive or forward selection in its variable selection and further employs an arbitrary cost function in its objective function that is fundamentally different from that obtained through appropriately scaled symmetrical error modeling in the reduced error logistic regression method.
The present disclosure is directed to improvements in a method for Generalized Reduced Error Logistic Regression which overcomes significant limitations in prior art logistic regression. This prior art includes work by Golan et al. (1996) and early theoretical work disclosed by the Applicant in 2005 and 2006 that preceded what is currently known as Reduced Error Logistic Regression (RELR). The method of the present invention is applicable to all current applications of logistic regression. The present method effectively deals with error and dimensionality problems in logistic regression, and therefore has significantly greater reliability and validity using smaller sample sizes and potentially very high dimensionality in numbers of input variables. These are major advantages over prior art logistic regression methods. In addition, this improved method has an effective variable selection method and scales the model with an appropriate scale factor Ω that adjusts for total variable importance across variables to calculate more reliable and valid logit coefficient parameters generally. The present Generalized RELR method was not obvious or even possible given the Golan et al. (1996) work and the prior art theoretical work of the Applicant disclosed in 2005 and 2006. For example, the Golan et al. (1996) work does not include t values as measures that are inversely related to expected extreme error. In addition, the Golan et al. (1996) work and all such related work also have the same machine learning deficiencies as the early prior art theoretical work disclosed by the Applicant in 2005 and 2006. Once again, this prior art work of the Applicant had significant limitations and problems including lack of appropriate scaling and lack of variable selection that rendered it useless as a generalized machine learning method.
The present method is a continuation-in-part of U.S. patent application Ser. No. 11/904,542 also titled Generalized Reduced Error Logistic Regression Method. The major changes from the method described in this previous Ser. No. 11/904,542 application are:
1. The present application clears up ambiguities and errors in some of the formulas presented in application Ser. No. 11/904,542.
2. application Ser. No. 11/904,542 employed a t-value that required categorizing interval-category and ordinal dependent variables into binary dependent variables. The method of the present invention now uses a slightly different t-value measure than defined in application Ser. No. 11/904,542 that appears appropriate for all types of target variables and can give greater accuracy with interval or ordinal target variables. This is defined through Equations (5a) and (5b) and the description that follows these equations. This present t-value is analogous to the t-value used to test whether a Pearson correlation across independent observations is significantly different from zero. It differs from the previous one-sample t-value only because of a slightly different denominator to reflect differing estimates of degrees of freedom. We have found no evidence that this slightly different denominator in this measure in comparison to the one-sample t-value used in Ser. No. 11/904,542 has an effect on the accuracy, reliability or validity of models that do not have interval-category or ordinal dependent variables with the sample sizes that we typically employ with at least 40-50 target observations.
3. In contrast to the t-value formula in Ser. No. 11/904,542, the current t-value formula is affected by the number of independent observations. This differential treatment of completely independent vs. not completely independent observations in this current measure related to a t-value in Equations (5a) and (5b) was not adequately addressed in the Ser. No. 11/904,542 application, but is now handled with these changes.
4. The relative magnitude scaling factor Ω now is multiplied by 2 as shown in Equation (5b). This is because there are both positive and negative measures of expected error for each moment in the model. This doubling of the scale factor Ω reflects both positive and negative largest expected error measures proportional to the inverse of the t-value. The doubling of the scale makes mathematical sense because this is a relative magnitude scale, so it should be a sum of all t-values in the model, including those relating to both positive and negative expected error.
5. The method of the present invention now allows a user to control the speed of the variable selection phase through batch processing of the t-values. For models with very large numbers of observations and very large numbers of variables, this may yield an enormous savings in computational time, but will always give the exact same solutions as would be obtained without employing batch processing.
6. The method of the present invention now adds the ability to model patterns of missing vs. non-missing observations on input variables that have a structural relationship to the target variable.
7. The method of the present invention now allows for hierarchical rules for interactions to govern variable selection as is sometimes done in genomic models. This option is under user control, but is not arbitrary and is instead determined by unique features of an application.
8. The results chart now change slightly for RELR because of the use of appropriate McNemar statistics for dependent proportions and because of updated changes in software to reflect method changes. In addition, we found that we could get a better SVM model for the large sample political polling model (FIG. 3), so SVM fares better in these comparisons. Finally, in other comparative modeling approaches such as Neural Networks, we found that we were able to get slightly better models by changing certain parameters, so in these cases we report the best possible model for comparison. In other cases, the results change slightly as we discovered errors in our data processing. The results now clearly show that RELR specifically improves classification performance in a dataset with a relatively small sample size where sampling and multicollinearity error would be expected to be most pronounced as shown in FIG. 2.
9. Finally, the method of the present invention now specifies a measure of model performance that is used as a measure of the best model; such a measure was unspecified in the Ser. No. 11/904,542 application. This measure is the maximal Log Likelihood across the training observations. This measure of the best model is described through Equation (1a).

Generalized reduced error logistic regression method


Apparatus (10) for attaching an object (O) to a sidewall (S) of an aquarium (A). A magnet (18) is attached to an object to be placed inside the aquarium. A niche or pocket (14) is formed in the side (16) of the object which will abut the inside wall of the aquarium. The niche or pocket is sufficiently large to accommodate the magnet which is affixed in place by any suitable means. A second magnet (24) is positioned on the outside of the wall adjacent the object. The magnetic attraction between the two magnets serves to hold the object in place, even if the object is positioned below the waterline (L) in the aquarium.

This invention relates to aquariums for displaying or exhibiting fish, and more particularly, to a magnetic display apparatus by which rocks, tree limbs and other decorative artifacts can be attached to a sidewall of the aquarium.
Aquariums are generally four sided glass tanks which are filled with water and used to display fish, crustaceans, and other aquatic life. It is not uncommon for an aquarium to have rocks and rock formations, tree branches, and other decorative artifacts placed on the bottom of tank for the marine life to move around, through and about. If there is a substantial volume of this material, it will not only cover the bottom of the tank but do so to a depth that the material starts to cover the bottom portion of the sidewalls of the aquarium as well. It sometimes may be desirable, for the overall appearance of aquarium, to want to attach an object to the an inside wall of the tank at a level above that of the other material placed in the tank. Heretofore, that has been difficult to do. For example, an artifact could be taped or glued to the wall of the tank, but this requires draining the tank and refilling it. In addition, prolonged submersion in the water may cause the glue or tape to lose its adhesiveness, causing the object to dislodge. A hole could be drilled through the sidewall of the aquarium to allow the object to be set in place using a screw or the like. This again requires draining and refilling of the tank, in addition to providing a waterproof seal about the hole. If the object is later removed, the hole must be filled which may leave an unsightly appearance.
It would be beneficial therefore to provide apparatus which permits an object to be readily and removably attached to the inside wall of an aquarium, below the waterline, as well as to permit the object to be easily repositioned if so desired.


Apparatus for positioning at least one bracket element at a desired location proximate to at least one respective tooth of a subject include a support body supporting and integrally formed with at least one support arm. The support arm is arranged to locate a respective bracket element at a desired location with respect to a respective tooth. At least one locating element serves to locate the support body relative to at least one tooth of a subject.

In recent years, orthodontic treatments have become increasingly common for adults and children. Traditionally, orthodontic treatment comprises the fixing of dental bracket elements on a surface of a tooth by an orthodontist. The orthodontist chooses the location of each dental bracket on a tooth with an aim of achieving a desired movement of the respective tooth. A wire element, known as an arch wire, is threaded between adjacent dental brackets and secured at either end. Once tensioned, the arch wire provides a force causing the teeth to move.
A disadvantage of bracket and arch wire treatments is that they typically require brackets to be positioned and bonded by hand. Performing this correctly requires years of training, is extremely time consuming and, even when care is taken, can often result in incorrectly positioned brackets. This type of procedure is also usually outside the scope of a general dental practitioner and must be performed by a specialist orthodontist.
New types of treatment have become available, such as those that involve sequential removable aligners from companies such as Invisalign®. These treatments do not require an orthodontist to position any brackets and therefore general practitioner dentists can fit these treatment types for patients.
However, for many patients it is still beneficial to use a more traditional bracket and arch wire treatment because it can provide more precise control over tooth alignment and occlusion, larger tooth movements and rotations, and excellent tooth retention post-treatment.
One way of avoiding positioning brackets by hand is by providing a bonding tray, which is a tray shaped to conform to a surface of a patient's teeth and intended to locate bracket elements with respect to the teeth. In this technique, adhesive is applied to brackets and the brackets are friction fitted into the bonding tray. The tray is then fitted over a patient's teeth and the adhesive is cured, which bonds the brackets in place. Finally, the bonding tray is removed by peeling or pulling it away from the patient's teeth and brackets, leaving the brackets in place.
In order to be removable after bonding, bonding trays have to be made from a relatively soft material that allows them to be peeled or pulled away from the teeth. However, this can cause the trays to deform during positioning, meaning that the brackets are not held in position accurately. The action of peeling or pulling the bonding tray away from the teeth can also be problematic because it places a large force on the brackets that can lead to brackets detaching from the teeth.
The shape of bonding trays reduces access to the area where the teeth and brackets meet, making it harder to cure adhesives. Additionally, since adhesive must be applied to brackets before the bonding tray is positioned over the teeth, adhesive can be smeared over the surface of teeth during the subsequent positioning procedure.
Due to the different requirements in terms of their shape and mechanical properties, bonding trays and brackets are typically composed of different materials, manufactured using separate processes and must then be assembled by a lab or dental professional. This can make the manufacturing and fitting processes expensive and time consuming.
It is an aim of certain embodiments of the present invention to at least partly mitigate the above-mentioned problems.
It is an aim of certain embodiments of the present invention to provide an apparatus that improves the accuracy and speed with which bracket elements can be positioned with respect to a patient's teeth.

Method and apparatus for positioning a dental bracket element


Provided are methods and articles of manufacture for use in stem cell therapy, for the treatment of diseases or conditions of SCA. Particularly, the invention provides a method for treating SCA, comprising parenterally or locally administering an effective amount of stem cells as a unit dosage to a subject, wherein the administration is performed with one or more treatment cycles, wherein one treatment cycle comprises dosing three unit dosages each at a dosing interval of two to six weeks.

Ataxias are a clinically and genetically heterogeneous group of neurodegenerative diseases that variably affect the cerebellum, brainstem, and spinocerebellar tracts. Spinocerebellar ataxia (SCA) is progressive, degenerative, and fatal. SCA includes degeneration of neuronal tissues in which the main locus of pathological change exists in the nucleus or neural pathway of cerebellum, brain stem or spinal cord. The fetal conditions of SCA come from not only extensive neuron loss, but also bedridden and respiratory failure at the end-staged disease. The most common of SCA generic subtypes are poly-glutamine (polyQ) mediated SCA, i.e., SCA1, SCA2, SCA3, SCA6, SCA7 and SCA17.
U.S. Pat. No. 7,067,545 provides a method for treating spincerebellar degeneration which comprises administering to a patient with this disease an efficacious dose of one or more members selected from among D-cycloserine, D-serine esters, D-serine and salts thereof. U.S. Pat. No. 9,125,924 relates to a method of alleviating a sign or symptom of SCA by intravenously administering an aqueous formulation comprising trehalose.
However, there is no effective medical treatment or potential cure for SCA. Accordingly, there is a need for therapeutic methods for alleviating the signs and symptoms of SCA.

Therapy for polyglutamine (polyQ) diseases


A system and method are provided for automatically acquiring a serial data stream clock. The method receives a serial data stream with an unknown clock frequency and coarsely determines the clock frequency. The frequency is coarsely determined by (initially) selecting a high frequency first reference clock (Fref1), and counting the number of data transitions in a first time segment of the serial data stream at a plurality of sample frequencies equal to Fref1/n, where n is an integer≧1. The count for each sampling frequency is compared to the count for Fref1 (n=1). Next, the highest sampling frequency (n=x) is determined, which has a lower count than Fref1, and the coarse clock frequency is set to Fc1 =Fref1/(x−1).

1. Field of the Invention
This invention generally relates to digital communications and, more particularly, to a system and method for determining and acquiring the clock frequency of a serial data stream.
2. Description of the Related Art
Digital high-speed communications, either electrical or optical, such as those compliant with the Synchronous Optical Network (SONET) or Synchronous Digital Hierarchy (SDH) standards, are enabled using a serial data stream. To recover the serial data stream at a receiver, the clock frequency of the received data must first be detected. Typically, the approximate frequency of the serial data stream is known. One common method of providing a data clock is to use a phase-locked loop (PLL) with a voltage controlled oscillator (VCO) to acquire the frequency, and then the phase of the received data.
Voltage controlled ring oscillators are commonly used in monolithic clock data recovery (CDR) units, as they are easy to fabricate and provide reliable results. Voltage controlled ring oscillators can, and usually do exhibit a tuning range much wider than the closed loop PLL bandwidth of the circuits in which they operate.
Clock recovery phase-locked loops (PLLs) generally don't use phase-frequency detectors (PFDs) in the data path since the incoming data signal isn't deterministic. PFDs are more typically used in frequency synthesizers with periodic (deterministic) signals. Clock recovery PLLs use exclusive-OR (XOR)-based phase detectors to maintain quadrature phase alignment between the incoming data pattern and the re-timed pattern. XOR-based phase detectors have a limited frequency discrimination capability, generally restricting frequency offsets to less than the closed loop PLL bandwidth. This characteristic, coupled with the wide tuning range of the VCO, requires CDR circuits to depend upon an auxiliary frequency acquisition system.
There are two basic PLL frequency acquisition techniques. The first is a VCO sweep method. During an out-of-lock condition, auxiliary circuits cause the VCO frequency to slowly sweep across its tuning range in search of an input signal. The sweeping action is halted when a zero-beat note is detected, causing the PLL to lock to the input signal. The VCO sweep method is generally used in microwave frequency synthesis applications. The second type of acquisition aid, commonly found in clock recovery circuits, uses a PFD in combination with an XOR phase detector. When the PLL isn't locked to a data stream, the PLL switches over to a PFD that is driven by a stable reference clock source. The reference clock frequency is approximately equal to the data stream rate. Thus, the VCO frequency is held very close to the data rate. Keeping the VCO frequency in the proper range of operation facilitates acquisition of the serial data and maintains a stable downstream clock when serial data isn't present at the CDR input. When serial data is applied to the CDR, the XOR based phase detector replaces the PFD, and data re-timing resumes.
However, serial data streams may be clocked at a number of frequencies, depending upon the communication protocol. Due to the PLL constraints mentioned above, a typical receiver is designed to operate at one particular data clock rate. Thus, a conventional receiver necessarily has a limited use. Even if the frequency of use can be selected from a range of potential frequencies, the actual operating frequency that is selected must be pre-programmed.
It would be advantageous if a synchronous serial data stream receiver could be made to operate at a number of different clock rates, without the preliminary step of pre-programming the operating frequency.
It would be advantageous if a synchronous serial data stream receiver could automatically determine the frequency of a received data stream and supply an appropriate data clock to recover the signal.

System and method for automatic clock frequency acquisition


In aspects, embodiments of the present invention provide devices, systems and methods for managing cuttings formed during drilling of a subsea wellbore. By managing, it is meant the processing, storage, transportation and disposal of the cuttings. In an exemplary application, an offshore rig adapted to drill the wellbore uses one or more a selectively buoyant containers to transport the cuttings. The containers are positioned adjacent the offshore rig. In one arrangement, the containers are submerged to a selected depth below the water's surface. A transfer unit flows the cuttings from the offshore rig to the container via a conduit connected to the container.

1. Field of the Invention
This invention relates to devices and methods for the collection, storage and disposal of drill cuttings, particularly during offshore drilling operations.
2. Description of Related Art
During a drilling operation, drill cuttings and rock are scraped out of the formation being drilled by a drill bit. The cuttings are then circulated to the surface as drilling mud returns up the annulus of the wellbore. The cuttings are commonly separated from the drilling mud by devices such as shale shakers fitted on the drilling rig. The shakers capture the cuttings and large solids from the drilling fluid during the circulation thereof. A screen is fitted on each shale shaker of certain mesh size and is vibrated to facilitate separation of the majority of fluids from the solids.
Handling of the drill cuttings following separation is a significant problem, particularly in offshore drilling, where space on a drilling rig is limited. More generally, this limited space can create difficulties in conveying and storing other materials at the drilling rig.

Floatable drill cuttings bag and method and system for use in cuttings disposal


An algorithm for a (t.sub.1,t.sub.2)-detecting code, and a method and apparatus for decoding same, for detecting skewed transitions in a parallel asynchronous communication system without acknowledgement. Transitions sent at the same time in a parallel channel may arrive at different times, but the algorithm permits a limited degree of variation in transmission speeds between channels. A desired control operation will be initiated whenever a skewed transition occurs. The code will detect up to t.sub.1 or t.sub.2 skewed transitions. The values of t.sub.1 or t.sub.2 for the algorithm are preselected by the user. t.sub.1 is the maximum number of transitions that may be missing from a first transmitted codeword when a transition arrives from a second transmitted codeword, and t.sub.2 is the maximum number of transitions from the second codeword that may arrive before all transitions of the first codeword arrive.

If a communication system which consists of many parallel channels operates asynchronously and without acknowledgement, there is neither a clock signal received by the receiver nor an acknowledgement signal sent back to the transmitter. Each transmission consists of one or more transitions (i.e., "1" bits) which are transmitted at the same time. If the information bits from different channels do not arrive at the same time (e.g., because of a delay in one or more channels), the receiver may receive some "1" bits corresponding to a next transmission before the present transmission has been completed, a condition referred to as "skew".
A paper by T. Verhoeff entitled "Delay-insensitive Codes--An Overview", published in Distributed Computing, Vol. 3, pp. 1-8, 1988, suggests the use in a parallel asynchronous communication system of unordered vectors because they are "delay insensitive". However, the parallel asynchronous communication system he describes requires that an acknowledgement signal be sent by the receiver to the transmitter upon completion of each transmission; and he does not disclose or suggest the use of vectors with Hamming distance properties which are unordered.
To fully understand unordered codes, it is best to consider an example. For a binary vector u of length n, u=u.sub.1,u.sub.2, . . . , u.sub.n. The set of non-zero bits of vector u are hereafter referred to as the "support" of u. For instance, for n=6, if u=100101, the support of u is the set {1,4,6}. Two vectors u and v of length n are considered unordered when their supports are unordered as sets; i.e., neither of them contains the other. Thus, u=100101 and v=010101 are unordered because their corresponding supports are {1,4,6} and {2,4,6}. By contrast, the vector w=000101 which has a support of {4,6} would not be unordered relative to either u or v because its support {4,6} is a subset of the support of both u and v.
There is a need for a parallel asynchronous communication system which (1) does not require acknowledgement between the receiver and transmitter when a transmission is completed; (2) ensures that the receiver can correctly determine when each transmission is completed; (3) distinguishes between signal levels belonging to different transmissions; (4) decodes each transmission to identify when an error-free transmission has arrived; and (5) decodes the transmissions in such a manner as to detect (and, if desired, initiate a preselected control operation) if skew occurs as a result of mixing of transitions in successive transmissions.

Coding method for skewed transition detection in parallel asynchronous communication system

International Business Machines Corporation


The invention relates to a lamp with elongated housing, comprising elongated housing and at least a light-emitting unit arranged on the housing; each of the light-emitting unit comprising: light source arranged in the housing; fastening member arranged in the housing; mounting hole arranged on the outer wall of the housing; lamp holder arranged in the mounting hole and fastened to the fastening member; lens arranged in the lamp holder. In the present invention, each light source can be provided with a lamp holder, and the light emitted by each light source can be emitted through the lens on the corresponding lamp holder, so that the beam angle of each light source can be controlled in a small range to form a light spot.

For a lamp with an elongated housing, since the lamp has a small mounting space in its width direction, making the mounting structure unable to be provided, and the elongated housing of the lamp is generally thin in wall thickness, making it impossible to provide the threaded mounting hole on the elongated housing of the lamp, it is generally impossible to provide a lens on the light source for a lamp with an elongated housing. Therefore, for a lamp with an elongated housing, since there is no lens, the light emitted by the light source is dispersed, making it impossible to form light spot, so that a focused illumination cannot be formed on a certain area, and a certain area or an object cannot be under highlighted illumination.


An improved system for draining bunkers on golf courses and other sports playing areas, and for draining landscaped areas. A receptacle is positioned below the surface for receiving drain water and for discharging the water through an outlet. A perforated pipe water collection system can be attached to the receptacle to direct water to the receptacle interior space. A receptacle cover is removable to permit access to the receptacle interior space. The cover is sufficiently strong to support the overlying weight of people and equipment, and can have apertures for permitting water entry while resisting entry of sand and other solids into the interior space of the receptacle.

The invention relates to under-surface drain systems and particularly systems for bunkers in golf courses, drainage areas in sports fields, such as the areas along the sides of tennis courts, and football, baseball, and soccer fields; and landscape areas where under-surface drainage systems are required or preferred for consistent surface appearance and integrity.
A golf course imposes unique design requirements on turf systems and sand bunkers on the course. Bunkers are deliberately positioned to create artificial hazards for errant golf balls The bunkers are typically constructed as depressions having a clay base with sloped sidewalls rising upward to surrounding turf. The bunkers have specific peripheral configurations, depth, and sloped sides. Sand overlays the clay base or other base material to provide the playing surface for golf balls. The sand is typically groomed daily by hand or with motorized equipment to present an even surface to the golfers. Rakes and other equipment fluff the top surface of the sand to present the desired surface. A drainage system for bunkers should be located below the surface of the sand a sufficient distance to allow regular sand shots to be taken above the drainage system.
In wet climates, rainwater compacts the sand and mixes the sand with the underlying clay base. Clay particles or "fines" discolor the overlying sand and also alter the playing qualities of the bunker. Various efforts have been made to reduce the commingling of sand and clay particles and to prevent other contamination of the sand. As shown in U.S. Pat. No. 5,746,546 to Hubbs et al. (1998), fiber strands and water absorbent particles such as psyllium may be added to soil to improve the soil shear strength.
Other bunker systems use geotextile fabrics underlying the sand. Fabric liners do not easily retain the sand on the sloped sides and are subject to rupture and other failure. Such liners do not independently correct the problems associated with accumulation of rainwater in the bunkers.
Because the bunkers comprise depressions in the soil, rainwater collects in the bunkers and must be drained to another location. Perforated pipe has been installed in the bottom of bunkers to drain excess water to a water discharge line. Gravel has been packed around the exterior surface of the perforated drain pipe to form a French drain. Such systems eventually fail in wet climates because the clay linings are susceptible to erosion. Clay particles and other contaminants such as grass clippings pack around the perforated pipe to lower the fluid transmissivity of the gravel, and such particles further enter the pipe interior. Over time the accumulated intrusion clogs the pipe which requires new construction of the entire bunker. Such construction is not only expensive to accomplish but also disrupts the utility of the golf course during construction.
Landscape areas whether mulched; sand and stone; grass of various types; and flowerbeds should have unique under-surface design to preclude standing water in low areas. Standing water in low areas contributes to damage of living plants in landscaped areas and leaves residual flotsam, debris and watermarks which destroy and compromise the surface design and appearance.
Drain systems have been developed for other applications such as large playing fields. For example, U.S. Pat. No. 5,648,856 to Bohnhoff (1998) discloses a thermoplastic mat underlying the surface which facilitates capture of water within an inflatable container for redistribution to the turf surface. Bohnhoff further describes conventional perforated pipe networks and the problems associated with poor drainage. Large playing fields usually require drainage along the sides of the fields. The fields are usually rounded to drain toward the sides. These fields need a drainage system which is below the playing surface to avoid interference with the play of the game and support activities around the fields.
In bunkers having perforated pipe drains, clay fines inevitably pack off the pipe at the lowest point in the bunker. This occurrence causes excess water to pond at this position within the bunker, further accelerating deterioration of the bunker drainage system. A need exists for an improved bunker drainage system which facilitates water drainage from bunkers and facilitates maintenance operations, and for a water drainage system for other sports fields which can be located below the sports surface to avoid interference with play and field use above the drainage system.


The present invention provides a protein which catalyzes the synthesis of a dipeptide different from L-Ala-L-Ala, a process for producing the protein which catalyzes the synthesis of a dipeptide, a process for producing a dipeptide using the protein which catalyzes the synthesis of a dipeptide, and a process for producing the dipeptide using a culture of a microorganism producing the protein which catalyzes the synthesis of a dipeptide or the like as an enzyme source.

The present invention relates to a protein which catalyzes the synthesis of a dipeptide, a process for producing the protein which catalyzes the synthesis of a dipeptide, a process for producing a dipeptide using the protein which catalyzes the synthesis of a dipeptide, a microorganism or a transformant producing the protein which catalyzes the synthesis of a dipeptide, and a process for producing the dipeptide using such microorganism or transformant.
Chemical synthesis methods (liquid phase method and solid phase method), enzymatic synthesis methods and biological synthesis methods utilizing recombinant DNA techniques are available for large-scale peptide synthesis. Currently, the enzymatic synthesis methods and biological synthesis methods are employed for the synthesis of long-chain peptides longer than 50 residues, and the chemical synthesis methods and enzymatic synthesis methods are mainly employed for the synthesis of dipeptides.
In the synthesis of dipeptides by the chemical synthesis methods, however, operations such as introduction and removal of protective groups for functional groups are necessary, and racemates are also formed. The chemical synthesis methods are thus considered to be disadvantageous in respect of cost and efficiency. They are unfavorable also from the viewpoint of environmental hygiene because of the use of large amounts of organic solvents and the like.
As to the synthesis of dipeptides by the enzymatic methods, the following methods are known: a method utilizing reverse reaction of protease (J. Biol. Chem., 119, 707-720 (1937)); methods utilizing thermostable aminoacyl t-RNA synthetase (Japanese Published Unexamined Patent Application No. 146539/83, Japanese Published Unexamined Patent Application No. 209991/83, Japanese Published Unexamined Patent Application No. 209992/83, and Japanese Published Unexamined Patent Application No. 106298/84); and methods utilizing non-ribosome peptide synthetase (hereinafter referred to as NRPS) (Chem. Biol., 7, 373-384 (2000), FEBS Lett., 498, 42-45 (2001), U.S. Pat. No. 5,795,738 and U.S. Pat. No. 5,652,116).
However, the method utilizing reverse reaction of protease requires introduction and removal of protective groups for functional groups of amino acids used as substrates, which causes difficulties in raising the efficiency of peptide-forming reaction and in preventing peptide-degradating reaction. The methods utilizing thermostable aminoacyl t-RNA synthetase have the defects that the expression of the enzyme and the prevention of side reactions forming by-products other than the desired products are difficult. The methods utilizing NRPS are inefficient in that the expression of the enzyme by recombinant DNA techniques is difficult because of its large enzyme molecule size and that the supply of coenzyme 4′-phosphopantetheine is necessary.
On the other hand, there exist a group of peptide synthetases that have enzyme molecular weight lower than that of NRPS and do not require coenzyme 4′-phosphopantetheine; for example, γ-glutamylcysteine synthetase, glutathione synthetase, D-alanine-D-alanine (D-Ala-D-Ala) ligase, and poly-γ-glutamate synthetase. Most of these enzymes utilize D-amino acids as substrates or catalyze peptide bond formation at the γ-carboxyl group. Because of such properties, they can not be used for the synthesis of dipeptides by peptide bond formation at the α-carboxyl group of L-amino acid.
The only known example of an enzyme capable of dipeptide synthesis by the activity to form a peptide bond at the α-carboxyl group of L-amino acid is bacilysin (dipeptide antibiotic derived from a microorganism belonging to the genus Bacillus) synthetase. Bacilysin synthetase is known to have the activity to synthesize bacilysin [L-alanyl-L-anticapsin (L-Ala-L-anticapsin)] and L-alanyl-L-alanine (L-Ala-L-Ala), but there is no information about its activity to synthesize other peptides (J. Ind. Microbiol., 2, 201-208 (1987) and Enzyme. Microbial. Technol., 29, 400-406 (2001)).
As for the bacilysin biosynthetase genes in Bacillus subtilis 168 whose entire genome information has been clarified (Nature, 390, 249-256 (1997)), it is known that the productivity of bacilysin is increased by amplification of bacilysin operons containing ORFs ywfA-F (WO00/03009 pamphlet). However, it is not known whether an ORF encoding a protein having the activity to ligate two or more amino acids by peptide bond is contained in these ORFs, and if contained, which ORF encodes the protein.
An object of the present invention is to provide a protein which catalyzes the synthesis of a dipeptide which is different from L-Ala-L-Ala and for which no enzymatic synthesis method using peptide synthetase or the like has so far been proposed, and a protein for the synthesis of the dipeptide; DNA encoding the protein having the dipeptide-synthesizing activity; a recombinant DNA comprising the DNA; a transformant carrying the recombinant DNA; a process for producing the protein having the dipeptide-synthesizing activity; an enzymatic method for synthesizing the dipeptide using the protein having the dipeptide-synthesizing activity or the protein for the dipeptide synthesis; and a process for producing the dipeptide using, as an enzyme source, a culture of a microorganism having the ability to produce the protein having the dipeptide-synthesizing activity or the protein for the dipeptide synthesis, or the like.
An object of the present invention is to provide a protein which catalyzes the synthesis of a dipeptide which is different from L-Ala-L-Ala and for which no enzymatic synthesis method using peptide synthetase or the like has so far been proposed, and a protein for the synthesis of the dipeptide; DNA encoding the protein having the dipeptide-synthesizing activity; a recombinant DNA comprising the DNA; a transformant carrying the recombinant DNA; a process for producing the protein having the dipeptide-synthesizing activity; an enzymatic method for synthesizing the dipeptide using the protein having the dipeptide-synthesizing activity or the protein for the dipeptide synthesis; and a process for producing the dipeptide using, as an enzyme source, a culture of a microorganism having the ability to produce the protein having the dipeptide-synthesizing activity or the protein for the dipeptide synthesis, or the like.

This patent is subject to a terminal disclaimer.


An apparatus for automated examination of biological material (6) includes a microscope (8) with a cross table (9) with the biological material (6) being arranged on the cross table (9) between an object slide (1) or an analysis plate and a cover (4); a light source (15, 16); an evaluation unit; a device for automatic focusing (11); an image recording unit (17) for recording an image of the biological material (6) enlarged via of an object lens (10) of the microscope (8) and for transferring the image to the evaluation unit; and a biochip (2). Labeling (7) is provided on a surface of the biochip (2). Focusing is executable by targeted movement of the cross table (9) based on detection of the labeling (7), and a target interval is determinable by determination of a location and/or a position of the labeling, within which focusing of the biological material takes place.

The instant application should be granted the priority dates of Aug. 23, 2010, the filing date of the corresponding German patent application 102010035104.0, as well as Aug. 23, 2011, the filing date of the International patent application PCT/EP2011/004227.
The invention relates to a method as well as an apparatus for automated examination of biological material with a microscope, on the cross table of which the biological material is arranged between an object slide or an analysis plate and at least one cover, with at least one light source for exposure of the biological material as well as with an image recording unit recording at least one image of the biological material enlarged by means of the object lens of the microscope and transferring it to an evaluation unit. The technical solution described provides labeling, which is detectable by a device for automatic focusing of the biological material, wherein the focusing can be executed by targeted movement of the cross table taking the detection of the labeling as the basis.
In medical diagnostics, fluorescence microscopy represents a standard method for the examination of patient samples. In that, in this area, too, an attempt in respect of the further development of this technology consists in increasing the degree of automation in order to thus minimize the error probability and to improve the economic efficiency of microscopy.
In order to achieve an increase in the degree of automation at the laboratory, it is conceivable, on the one hand, to further automate the processing of the samples to be examined, in particular the dilution as well as the incubation steps, or, on the other hand, to design the process of the predominantly visual evaluation of the processed samples more effectively. The invention explained in more detail in the following lies in the field of sample evaluation or diagnostics, respectively, wherein also in respect of fluorescence microscopy it is already known in principle to generate digital image data of the samples to be examined and to transfer these to a data processing unit for the preparation of diagnostic findings, on which unit a special laboratory software is installed, and to evaluate the data in a computer-aided fashion.
With fluorescence microscopy at least partially automated in such manner, the generation and selection of high quality images is of outstanding significance, above all in order to be able to guarantee constantly high quality in the preparation of a laboratory result. A substantial quality feature of the recorded images ultimately is their sharpness, so that focusing of the biological material to be examined is of particular significance. For focusing of the biological material or the substrates, respectively, to be examined, usually a multitude of images is recorded at different levels, of which images those with low quality are discarded during the electronic evaluation.
In respect of automated focusing for microscopes, different technical solutions are known. In that, active autofocus systems, which are normally used in reflected-light microscopes, are characterized by the fact that using an auxiliary light source, a light spot or a marking is projected onto the surface of the sample to be examined or a cover slip covering the sample, then shape, position or size of the light spot are evaluated, and, on the basis of the evaluation, focusing on the sample or cover slip surface takes place. An active autofocus system designed in such manner is known, for example, from DE 34 46 727 C2, and is to enable fast automatic focusing.
In transmitted-light microscopes, passive autofocus systems are normally used instead of active ones. Passive autofocus systems, as, e.g., known from DE 34 39 304 C2, determine the focus level on the basis of a comparison of the recorded image data, i.e. the level, at which the sharpest image was recorded. Frequently, however, such systems are comparatively slow, since a multitude of search runs must be undertaken in order to achieve a satisfactory result.
A further special active autofocus system is known from DE 10 2010 035 104. In this printed publication, an apparatus for automatic focusing of weakly luminescent substrates is described, which is to guarantee fast image focusing. The comparatively fast focusing, on the one hand, is to increase the effectiveness of automatic microscopy and, on the other hand, minimize fading of the fluorescent dyes during focusing. The technical solution described is characterized by the fact that first, several recordings are undertaken in a transmitted-light mode, and therefrom the sharpest image is determined using known evaluation methods. Following switching-off of the transmitted-light source, the cross table of the microscope is moved to the focus level determined in the transmitted-light mode. In order to generate a fluorescence image, an excitation light source is then activated. Since, however, the fluorescence can vary at various levels in respect of the thickness of the substrate, it is necessary to still adjust the focus level in the fluorescence mode compared to the focus level determined in the transmitted-light mode on a regular basis. For determination of the exact focus level, however, due to the pre-focusing previously undertaken in the transmitted-light mode, only few images must be included in a comparatively small search area. The fluorescence images ultimately lying at the exact focus level are recorded by means of a digital camera and transferred to a data processing unit for the further preparation of diagnostic findings.
One objective of the further development of autofocus systems in fluorescence microscopy always is to minimize the time required for focusing or the number of images recorded during focusing and unusable for later examination of the substrate, respectively. For that, a further method for automatic focusing of a substrate in fluorescence microscopy is known from DE 101 00 247 A1, using which the object lens focus can be determined in a highly exact manner and still within a comparatively short period. In this case, an interference microscope is described, in which a surface of the object slide unit is provided with a coating detectable by light microscopy. The reflected light is detected by a detector, and on the basis of the detection signals, the phase position in the object area of the interference microscope is concluded. In this manner, it is finally possible to adjust the interference microscope in a suitable manner.
The microscopes with automatic or at least partially automated focusing previously described are frequently used to make special proteins visible by means of antibodies. In this manner, it is determined in which tissue a special protein exists and in which compartment of a cell it is located. Frequently, fixed tissue consisting of tissue sections is used for this antibody staining. Such tissue sections are generated by first preparing a frozen section of a healthy tissue and applying it to the surface of a glass slide, in particular an object slide or a cover slip. Subsequently, the tissue is thawed and dried. Normally, the tissue sections for the known test systems are attached to standard object slides, wherein for each tissue section, a separate standard object slide is used.
Beside the previously described possibility for examination of a patient sample using a tissue section arranged on a standard object slide, the so-called biochip technology of the company Euroimmun AG is known. Contrary to the conventional technology of indirect immunofluorescence, for which a tissue section is always attached to a standard object slide provided for the examination, this technology, due to a miniaturization of the samples to be examined, offers the possibility to standardize the determination of auto-antibodies and infection antibodies. In this manner, the work at the laboratory is facilitated and becomes more efficient.
The biochips of the company Euroimmun are comparatively small slides with biological material. In that, the effect is utilized, that very small tissue sections can be prepared and used for examination, provided that these are applied to a substrate carrying the section, and together with this substrate they are attached to an object slide or an analysis plate. While a standard cover slip is an about 100 μm to 200 μm thin, rectangular or round glass platelet, which usually has an area of 18×18 mm2, biochips are cover slip fragments coated with suitable biological material, which thus have a much smaller surface. Therefore, compared to standard cover slips, biochips are on the one hand characterized by a distinctly lower space requirement, and on the other hand, the amount of tissue required is considerably reduced.
For the manufacture of a biochip, first a frozen section of the required tissue is likewise applied to a standard cover slip, then partially thawed and dried. Subsequently, the cover slip with the tissue is fragmented by producing score lines in the area of the tissue section using a diamond tip or a laser, along which the coated cover slip is broken and thus divided into segments. In order to enable an improved, in particular more effective examination, the biochips are applied to suitable reaction fields of an object slide. In this connection, it is conceivable to provide a multitude of reaction fields for respective biochips on one object slide, wherein in one reaction field, more than one biochip, preferably with different tissues, may also be provided. In order to design the examination of a patient sample particularly effective, suitable BIOCHIP-Mosaiks™ are formed by providing a multitude of reaction fields with respective biochips on one object slide.
No matter, whether a tissue section located on a standard cover slip or a biochip or special BIOCHIP-Mosaiks™, respectively, is used for the examination of a patient sample, the basic course of sample processing, in particular dilution of the patient serum as well as incubation of the tissue section, as well as of the visual examination using a microscope is the same.
During processing of the sample, the tissue is incubated with diluted patient serum, which is to be examined for the presence of special antibodies, as well as a conjugate, which normally includes antibodies originating from an animal, which are marked with a fluorescent substance and directed against the antibodies suspected in the patient serum. If the patient serum has antibodies against the antigens of the tissue section, these antibodies bind to the tissue section and the fluorescently marked secondary antibodies bind to the human antibodies attached to the tissue section. Ultimately, the fluorescent dye bound to the respective tissue structures can be detected using a fluorescence microscope.
Prior to using the microscope, the incubated tissue section is coated with a mounting medium, like e.g. ph-buffered glycerin, and covered with a cover slip. The cover slip is arranged such that though it is located at a secure distance from the surface of the tissue section, viewing it with the microscope is still possible without any problem.
As already indicated, the objective for the further development of automatic apparatuses for the examination of patient samples principally consists in designing any procedural steps from receipt of the sample up to preparation of a laboratory result as efficient as possible, simultaneously eliminating possible sources of error as far as possible. Taking this general attempt of making laboratory work more effective and even more reliable as the basis, the present invention is based on the special object to further develop the technical solutions for automatic microscopy of biological material known from the state of the art such that automation of the microscopy of an object slide with biochips located thereon, in particular with BIOCHIP-Mosaiks, is possible in an advantageous manner. Above all, the process of focusing of the biological material arranged on the biochip(s) is to be realizable with comparatively simple means and simultaneously take place quickly as well as with high quality. The technical solution to be stated is to be easy to integrate into the known systems for automatic microscopy of biological material and represent an aid for the personnel working at the laboratory. A further object, on which the present invention is based, consists in minimizing the number of recordings made during focusing and not required later for image evaluation.

Method and apparatus for automatic focusing of substrates in flourescence microscopy

EUROIMMUN MEDIZINISCHE LABORDIAGNOSTIKA AG


A paintball gun loading device includes a gun body, a loading member and a funnel. The loading member comprises a fixture at an upper portion thereof. The fixture comprises a circular trough with a plurality of slots along the circular trough. A clamp sleeved on the circular trough is tightened with a quick-release rod and a nut to fasten the funnel in a different size.

1. Field of the Invention
This invention relates to a paintball gun loading device, and more particularly to a paintball gun able to replace with different sizes of funnels in a quick and easy manner.
2. Description of the Prior Art
There are various paintball guns on the market, and the loading methods are different with each other. One conventional paintball gun A, as shown in FIG. 5, comprises an opening A2 at the top of a barrel A1, and a pair of threaded holes A3 at respective sides of the opening A2. The threaded holes A3 are inserted with a pair of screws A4 to secure protruding plates B1 of a loading member B. The loading member B comprises a loading opening B2 on top thereof to connect with a fixing end C1 of a funnel C. This design allows the paintball to drop into the barrel A1 and wait for shooting. The connection between the loading member B and the gun A may cause loosening or misalignment, thus it has to be adjusted all the time.


A surface treated anode and a lithium battery using the same are provided. The surface treated anode includes a current collector, and an anode active material layer formed on the current collector. The anode active material layer is treated with an amine group containing compound.

1. Field of the Invention
Aspects of the present invention relate to a surface treated anode, and a lithium battery using the same.
2. Description of the Related Art
Various conventional techniques, proposing the use of lithium metals as anode active materials for lithium batteries, have been suggested. However, when lithium metals are used in lithium batteries, short circuits may occur, due to lithium dendrite formation, which can cause explosions. Thus, carbonaceous active materials have been widely used as anode materials, instead of lithium metals. Examples of such carbonaceous active materials include: crystalline carbon, such as, natural graphite and artificial graphite; and amorphous carbon, such as, soft carbon and hard carbon. However, although amorphous carbon has a high capacity, many of its charge/discharge reactions are irreversible. Since the theoretical capacity of crystalline carbon (including graphite) is relatively high, i.e., 372 mAh/g, crystalline carbon is widely used as an anode active material. Although the theoretical capacity of such graphite or carbon-based active materials (approximately 380 mAh/g) is relatively high, it is not high enough for future higher capacity lithium batteries.
To address these problems, research on metal-based and metalloid-based, anode active materials has been actively conducted. For example, research on lithium batteries using metals or metalloids, such as, aluminum, germanium, silicon, tin, zinc, lead, etc., as the anode active material, has been conducted. Such materials are known to have large capacities, high energy densities, and good insertion/extraction capabilities, as compared to carbon-based anode active materials. Thus, lithium batteries having large capacities and high energy densities can be prepared using these materials. For example, pure silicon is known to have a high theoretical capacity of 4017 mAh/g.
However, such materials have shorter life cycles than carbon-based materials, and thus, cannot be put to practical use. When inorganic particles, such as, silicon or tin are used as the anode active material, the volume of inorganic particles changes considerably during charge/discharge cycles. This may result in the degradation of an electronic conduction network between the active material particles, or may result in the detachment of an anode active material from an anode current collector. That is, the volume of an inorganic material, such as, silicon or tin, increases by about 300 to 400%, due to alloying with lithium during charging. The volume decreases during discharging, due to the extraction of lithium. Therefore, after repeated charge/discharge cycles, spaces may be generated between the active material particles, and electrical insulation may occur, thereby rapidly lowering the life cycle characteristics of these materials, and causing serious problems when using these materials in lithium batteries.
Recently, various attempts have been made to develop new active materials for secondary batteries, having increased theoretical capacities. One such attempt includes the use of high-capacity, composite, anode active materials, for example, silicon (Si)-carbon (C), or tin (Sn)-carbon (C). However, there may be several disadvantages in using such materials, such as, severe electrochemical irreversibility during charging and discharging. This may be caused by increases in the defects and the specific surface area of carbon, during a compounding process. In addition, the charge/discharge efficiency is lowered, due to weakened bonds between active material particles, which may be caused by the extreme expansion and contraction of the active materials.

Surface treated anode and lithium battery using the same