Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences. For example, a score function can be determined based on information associated with the sequencing platform that can be used to analyze polymorphisms based on the base-call interpretation and/or alignment.

Currently, there likely exists efforts to develop a relatively inexpensive genome sequencing platform that can be of acceptable accuracy (e.g., about one base error in 10,000 base pairs (bps)) and relatively high-speed (e.g., a turn-around/processing time of less than one day). In order for the sequence reads obtained from such a sequencing platform to be useful in certain biomedical applications, they can usually have to be sufficiently long and accurate, which can thus enable sequence assembly and/or resequencing (e.g., through an alignment against a reference genome, where available). If the reads from a sequencing platform are shorter than certain thresholds, its utility in many biomedical applications can be limited even though the platform can provide a cost and/or throughput advantage. One way to improve the accuracy and/or length of sequence reads from such a platform can be through better statistical algorithms (and/or procedures) for base-calling and/or alignment than heretofore available.
If certain simplifying assumptions about genomes in a human population were to be true, then resequencing and/or alignment tasks can potentially often be made algorithmically trivial and, to some degree, capable of generating useful bio-medical information. For example, if it is possible to be reasonably assured of the correctness of the assembly of the reference genotype sequence (e.g., that the polymorphisms can be relatively rare and uniformly distributed, and that the populations can have very few admixtures of separate ancestries), then it can likely suffice to just position a massive number of short reads that can be aligned to a single (and/or a few, several, bunch, many, etc.) reference sequence(s), which can thus facilitate a relatively non-complicated technology to determine and/or study virtually any individual's genomic make-up.
In the absence of a genuine (acceptable) confidence in these underlying assumptions, there can be a need for, e.g., integrating multiple technologies that can be coupled to computational algorithms in order to accurately detect a wide class of polymorphisms (e.g., single nucleotide polymorphisms (SNPs), copy number variations (CNVs), structural variations (SVs), etc.), confidently characterize the detected polymorphisms, and/or assemble and align the reads to whole genome genotypic and/or haplotypic reference sequences, for example. In order for the relatively less expensive and high-throughput sequencing platforms to be of value to these applications, it can involve improving the statistical algorithms that can be used to interpret raw data from experiments into a base-by-base sequence. For example, in certain sequencing platforms, where the read-lengths may not be short (e.g., in a range from about 100 bps to about 1000 bps), these statistical algorithms can be useful in reducing the corresponding coverage and thus the associated cost.
Previously available sequencing platforms likely fall short of a scalable haplotypic whole-genome technology for which there appears to be a need. For example, such heretofore available technologies usually can generate relatively short genotypic reads (e.g., from about 35 bps to about 300 bps, without haplotypic and locational context), that can be corrupted by errors such as low-quality base-calls and/or compression of homopolymeric runs, and can frequently lack long-range contextual information aside from mate-pair data. These shortcomings can affect the yield and/or speed of the resulting technology and have a debilitating effect on the complexity of the base-calling, alignment and/or assembly algorithms and/or procedures.
To meet the challenges of long-range haplotypic analysis, there may be a need for, e.g., technology and/or algorithm design principles that can go beyond base-by-base reads and take into account the tractability of a computation that can be used to handle the resulting data. Otherwise, a cost improvement and/or throughput gain at the single-base level can be mis-utilized without the intended benefit, when used at the whole-genome level, for example. Sequencing technologies can typically be considered and/or thought of in terms of two extremes. For example, at one extreme can be technologies such as, e.g., Sanger sequencing, which can work by producing a correct index for every base, but can generally extend only over a short range. At the other extreme technologies may be provided that, similarly to many single-molecule and/or nanopore-based sequencers, can aim for (potentially) long reads, but can lack any location information, for example. These and related current and/or anticipated technologies can be generally categorized into three groups, e.g., (i) Short Reads-Low Throughput Technology (e.g. 454, Solexa, Solid, etc.), (ii) Shorter Reads-High Throughput Technology (e.g., Lab-on-chips, Illumina's Flowcell based systems, Raindance, etc.), and (iii) Long Reads and Contextual Reads Technology (e.g., PacificBio, NanoBioMatrix, Oxford Nanopore, Nanopore Sequencing, etc.).
Certain proposals for generating short sequence reads from genomes relatively quickly, inexpensively and in large amounts have likely led to commercial equipment that can be used accordingly. Before such proposals and associated equipment, dideoxynucleotide termination DNA sequencing technology, introduced by Fred Sanger in 1977 and known as the "Sanger Sequencing" technology, had likely been the routine procedure for large-scale sequencing. (See, e.g., Smith L. M. et al., Fluorescence Detection in Automated DNA Sequence Analysis, Nature, 321, 6071, 674-679 (1986)). Since its introduction in 1977, Sanger Sequencing technology has been improved upon, e.g., streamlined with better latency and higher throughput via improved, parallel and relatively rapid sorting of fragments using capillary gel electrophoresis, addressing some of the inherent limitations posed by Joule-heating during fragment separation using slab gels, for example. However, despite such improvements, at least two limitations can remain. For example, the upper limit of read-lengths can be about one Kb, and the reads can have no associated contextual information (e.g., chromosomal location and/or haplotypic disambiguation).
Several intensive parallel sequencing methods have been proposed to address some of these issues. However, while some of these proposed methods may provide lower latency and/or higher throughput at a relatively lower cost, such proposed methods may not have improved the read lengths nor provided for any contextual information. For example, one such massively parallel sequencing technology can be "Sequencing by Synthesis Pyrosequencing," (see, e.g., Nyren, P. et al., Solid Phase DNA minisequencing by an Enzymatic Luminometric Inorganic Pyrophosphate Detection Assay, Annal Biochem 208, 1, 171-175 (1993); Ronaghi, M. et al., PCR-Introduced Loop Structure as Primer in DNA sequencing, Biotechniques, 25, 5, 876-884 (1998); and Margulies, M. et al., Genome Sequencing in Micro-fabricated High-Density Picoliter Reactors, Nature, 437, 7057, 376-380 (2005). In addition, a goal of Pacific Bioscience can be to create a technology that can read up to about 5 Kb without increasing the associated cost. While such technology can potentially have a positive effect on certain approaches and algorithms, Pacific Biosciences' technology can provide only a limited improvement as it can still lack long-range information, for example.
In pyrosequencing procedures, which can include a sequencing-by-synthesis technology, upon nucleotide incorporation by the polymerase, the released pyrophosphate can be converted to adenosine triphosphate (ATP) by action of the enzyme sulfurylase using an energy source to convert luciferin to oxyluciferin and light. Because, in sequencing by synthesis, during each cycle, a single nucleotide species (e.g., A, T, C or G) can be used for querying, detection of the emitted light in each reaction cycle can provide the information as to which particular base (and how many) was incorporated in such reaction cycle. By combining the information from many successive cycles, it is possible to read a large number of sequences in parallel. These sequencing technologies can be found in certain applications, such as, e.g., SNP-calling, CNV-detection, serial analysis of gene expression (SAGE) profiling, cDNA sequencing, nucleasome positioning and metagenomics. However, such sequencing technologies can have certain shortcomings in various applications, including applications addressing population genomics, personal genomics and/or genomics-based individualized medicine, which can likely be due to associated length limitations and/or lack of contextual information.
For example, the pyrosequencing procedures can occur in the 454 GS-20 sequencing instruments (see, e.g., Margulies, M. et al., Genome Sequencing in Microfabricated Serial Analysis of Gene Expression High-Density Picolitre Reactors, Nature, 437, 7057, 376-380 (2005)). Such instrument can integrate and parallelize the process, e.g., from library construction to sequence detection, Starting with a genomic library of 500 bps-long fragments, the ends of such fragments can first be repaired, then ligated with 454-specific linkers, and then coupled to Sepharose beads with covalently linked complementary oligoes that can hybridize to the fragment library's ligated linkers, for example. The bead/DNA complexes can be emulsified in oil suspension containing aqueous PCR reagents in order for PCR amplifications to occur for each library-fragment producing many like PCR products attached to the same bead. Pyrosequencing reactions can then be performed on these PCR products simultaneously so long as sequence detection can be achieved reliably and synchronously. For example, the pyrosequencing reactions can be carried out on the beads once they are suitably arrayed on a PicoTiterPlate (PTP) device with sensors (e.g., fused optical fibers) designed on to them. It is possible to then deconvolve the optical data into about 400,000 sequencing reads of 500 bps reads (e.g., about 200 Mb of data in total), over the course of a few hours.
However, similarly to the other related technologies, 454-platform's read-length can be relatively short (e.g., only about 500 bps) and the 400,000 fragments can lack contextual information. In addition, because in each cycle there can be no unambiguous way of determining exactly how many bases get incorporated, if the genomic fragment has a run of a single nucleotide base, the 454-instrument cannot tell the run length, and thus cannot produce a compression of the homopolymeric run to a single base, for example.
In order to circumvent the problem of compression of homopolymeric runs, it is possible to utilize a more complex reversible dye-terminator chemistry, such as used in a platform by, e.g., Solexa, Ltd. Starting with a library of genomic fragments, which can then be linker ligated, they can be amplified in situ following hybridization to complementary oligoes covalently linked to a flow cell surface. For example, the fragments can then be amplified into clusters of PCR products, denatured, annealed with sequencing primers, and then read by a sequencing-by-synthesis approach to detect the 3′-blocked fluorescent-labeled nucleotide incorporated in a reaction cycle. Using this approach, a Solexa instrument can read about 60 million sequences, each can have a read-length of no larger than about 50 bps. Similarly to other technologies, the read-lengths from this technology can be relatively short and have no contextual information. Thus, despite being able to read almost 1× coverage of a genotypic human genome in a single run, these reads can fail to assemble and provide any meaningful information. Even in relatively simple resequencing applications, a lack of contextual information can pose significant difficulties/obstacles in placing the short sequence reads in the reference sequence efficiently and accurately.
In 454-, Solexa's technologies and other similar technologies, the problem that limits the length of the sequence reads (and/or accurate base calling) can be primarily due to, e.g., (i) unavoidable failure in synchronization among the relatively small number of like molecules being queried in parallel, and (ii) their inability to survive in toto until the completion of succession of the necessary read queries. For example, the first problem can manifest itself in terms of corruption due to lead and lag reads (increasing a structured noise), and the second problem can manifest itself in terms of loss of signal due to fading (decreasing the signal). The resulting loss/reduction in signal-to-noise ratio (SNR), which can deteriorate exponentially, can make it virtually impossible to read a sequence beyond a certain limited read-length. It is possible to facilitate the read-length of the Solexa technology by modeling these stochastic processes by a random-walk model whose parameters can be learned automatically from the reads of few calibrating DNA molecules. (See, e.g.; Erlich Y., et al., Alta-Cyclic: a self-optimizing base caller for next-generation sequencing" Nat Methods, 5, 8, 679-82 (2008)).
In addition to these two platforms, there can be other related technologies, such as ligation-based sequencing (e.g., building on genotyping methods used in ligation-chain-reaction (LCR) and oligonucleotide ligation assay (OLA)), sequencing by hybridization (e.g., a variant called single molecule approach to sequencing by hybridization (SMASH) which can replace array-based hybridization with hybridization to single molecules that can then be queried on a surface), sequencing with zero-mode waveguide, and nanopore sequencing approaches, for example. (See, e.g., Barany, F., The Ligase Chain Reaction in a PCR World, PCR Methods Appl., 1, 1, 5-16 (1991): Nickerson, D. A., et al., Automated DNA Diagnostics Using an ELISA-Based Oligonucleotide Ligation Assay, PNAS, 87, 22, 8923-8927 (1991); Drmanac, R., et al., DNA Sequence Determination by Hybridization: A Strategy for Efficient Large-Scale Sequencing, Science, 260, 5114, 1649-1652, (1993); Broude, N. E., et al., Enhanced DNA Sequencing by Hybridization, PNAS, 91, 8, 3072-3076 (1994); Levene, M. J., et al., Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations, Science, 299, 5607, 682-686 (2003); Fologea, D. et al., Detecting Single Stranded DNA with a Solid State Nanopore, Nano Letter, 5, 10, 1905-1909 (2005); and Meller, A., et al., Rapid Nanopore Discrimination Between Single Polynucleotide Molecules, PNAS, 97, 3, 1079-1084, (2000)).
With the particular successful completion of the human genome project (HGP), it likely has been generally assumed that, with access to a reference human genome sequence, it would be relatively easy to catalog individual genomic differences relative to the reference genome sequence. For example, it has been generally assumed that the remaining significant challenges would only be in terms of designing (i) inexpensive experimental setups targeting relatively few and manageably small regions of polymorphic sites (e.g., about 30,000 haplotype blocks each encompassing no more than about 10 haplotypes), and (ii) efficient algorithmic solutions for interpreting a massive amount of population-wide polymorphism data. However, several implicit assumptions and hitherto unknown facts can impede progress along this direction. For example, currently available reference genome sequences can generally provide only genotypic information and can remain to be validated as to its suitability in representing humans in a universal manner.
Additionally, the possible categories of dominant polymorphisms and their distributions likely have not been satisfactorily cataloged. Further, haplotype data from a population can likely only be collected in many non-contextual short-range fragments that can provide no meaningful long-range structural information. Moreover, such short-range data can likely have to be phased statistically from population-wide distributions and with an inferred (and/or assumed) distribution of recombination sites, which can differ significantly from the reality, for example.
In attempting to exacerbating these and other fundamental hurdles, it is possible to also encounter an added difficulty of dealing with relatively high intractable computational problems, which can arise from having to interpret non-contextual short-range data from many individuals and many subpopulations with unknown population stratification relative to a genotypic reference sequence. Certain developments can circumvent these difficulties by, e.g., focusing on every individual in a population one at a time and by reconstructing their haplotypic genome sequences relatively accurately (e.g., SMASH sequencing-by-hybridization technology). Such technologies can do so without the reference to other genome sequence(s) from another (e.g., in a trio or from a sibling) or many other individual(s) from a population.
For example, with the use of currently available non-contextual short-range sequencing platforms, it is possible to map the sequence reads to the reference genome using a relatively efficient and accurate sequence alignment algorithm under an assumption that reads will contain few localized polymorphisms and are nearly identical to their corresponding sequence in the reference genome. In practice, it is possible to use a low-coverage (e.g., about 2 or 3×) sequencing project to generate a sufficient number of reads to characterize a large number of positional variations on the target genome. However, the entire approach relies on the simplifying assumption that, although the "next-generation" sequencing technologies can be unsuitable for de novo genome sequencing, they can be adapted to genome resequencing, in which assumption as to how haplotypic ambiguities and structural variations can be suitably handled can be unclear.
Further, in studies based on a resequencing approach, it may have been assumed that it can be of no significance to ignore most of the different sequence variations that any individual carries, and that it can suffice to concentrate efforts on important common variations, such as those carried by a relatively large fraction (e.g., greater than or equal to about 5%) of individuals in a population, as only these are likely assumed to be disease associated. Following this reasoning, it is possible to first characterize the frequent genetic variations by short-range resequencing of a limited number of randomly selected individual(s) from populations and, using this information, from genome-wide genotyping, to determine allelic types for any previously characterized variation sites in the target genome(s). For example, this approach has been an integral component of the HapMap Project, which focuses on mapping common SNPs. (See, e.g., The International HapMap Consortium, The International HapMap Project, Nature, 426, 18, 789-796 (2003); and The International HapMap Consortium, A Haplotype Map of the Human Genome, Nature, 437, 27, 1299-1320 (2005)).
The HapMap project has been implemented in two primary phases. First, using the genomes of 269 individuals from different populations, about a million SNPs were mapped across the genome and later augmented with an additional 4.6 million SNPs. Second, using population-wide correlations among the SNPs, the sequences of SNP sites on the reference genomes were segmented into a relatively small number of combinations of alleles, with the relatively consecutive linkage-disequilibrium blocks assumed to be separated by recombination hotspots. The combinations are referred to as haplotypes and the segments as haplotype blocks. (See, e.g., M. Stephens and P. Donelly, A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data, American Journal of Human Genetics, 73, 5, 1162-1169 (2003).
One deficiency associated with HapMap project based technologies, however, can be that subsequent analyses on the population can be carried out using these inferred blocks independently of any validity as to whether the individual actually physically carries such haplotypes in their genome. Further, a problematic circularity reasoning can be associated with this process because the population, which can be used for haplotype inference, can then be analyzed by the same haplotypes used to understand population stratification, disease association and selection processes acting on these genomes, for example.
Another significant problem with these technologies can be the assumption that all sequence variations in the human genome are single nucleotide mutations. Indeed, this assumption has been challenged by the serendipitous detection of CNPs through array comparative genome hybridization (array-CGH) technologies. Initially, copy-number fluctuations in the genomic segments likely were assumed to be a hallmark of cancer genomes, to arise by somatic mutations, and implicitly to be so detrimental to the normal genomes that they were not expected to vary in the germ-line genomes. However, the technology that likely revealed these polymorphisms and can currently be used to study these variations, such as array-CGH, can be incapable of characterizing their exact long-range structural properties involving, e.g., chromosomal inversions, translocations, segmental deletions, segmental duplications and large-scale aneuploidy), and can thus be of limited utility. Moreover, these CNVs may not be detected or be positionally and/or haplotypically located by using conventional short-range non-contextual shotgun sequencing technologies, for example. (See, e.g., L. Feuk et al., Structural Variation in the Human Genome, Nature Review Genetics, 7, 2, 85-97 (2006); and J. Sebat et al., Large-Scale Copy Number Polymorphism in the Human Genome, Science, 305, 5683, 525-528 (2004)).
Despite the difficulties described above, which can significantly undermine the reliability of population-wide genomic studies in the short term, researchers have focused on the algorithms for interpreting the data from high-throughput short non-contextual sequence reads from recently developed (next-generation) sequencing platforms. For example, it can be preferable for these sequence reads to either be assembled into contiguous overlapping sequences encompassing the information contained in each haploid chromosome, or be aligned to a phylogenetically reasonably close haplotypic reference sequence. A capture-recapture based statistical analysis of the databases of known SNP and CNV polymorphisms can indicate that about a few thousand haplotypic whole-genome reference sequences of properly sampled individuals from a human population can suffice, as indicated by, e.g., I. Ionita-Laza, currently unpublished results. However, such resources having a sufficiently large number of reference sequences are likely unavailable. Rather, databases of SNPs and CNVs and a very small number of reference genotypic sequences are in existence. Thus, the currently available bioinformatics procedures can be limited in that they can work with this available data to interpret only short-read sequence data, for example.
Further exacerbating the problem can be that when the sequencing technology provides only short non-contextual genotypic reads, as can be the case with heretofore available sequencing platforms, unambiguous interpretation of the polymorphism information can become computationally demanding. For example, as the reads become shorter and/or the base-calling algorithms introduce further errors, it can become increasingly difficult to align a sequence read to a single genomic region unambiguously. Thus, even when data can be available for reference sequences and SNPs with a population-based phasing into haplotype blocks (e.g., each block supporting a small number of haplotypes), because a proper interpretation of the resequenced data can involve enforcing certain parsimony constraints, such as interpreting with minimal number of haplotype blocks or minimal number of additional recombination sites. The resulting formulation can typically involve computationally hard non-convex combinatorial optimization. Thus, what can be counterintuitive, as the depth of the reads increases, without providing accurate overlap and contextual information, the underlying computational problems can become increasingly more intractable unless other helpful heuristics are utilized. For example, computational intractability, which can be inherent to these problems, can be ameliorated through exploitation of the underlying probabilistic structures of the data. Although such analysis as described below, can provide an indication about the nature of and parameters involved in certain probabilistic 0-1 laws that can guide the design of a preferred strategy for data collection using multiple platforms, it is possible that the optimal designs have to be ultimately discovered using real genomes through large-scale simulation tools, for example.
While it is likely believed that the algorithms and the software that can be used to support this approach can present a more meaningful interpretation and thus be of potential benefit and value with respect to genomic biomarker discovery and associated development cost, these types of solutions can most likely be short-lived. This is because, for example, as the sequencing technologies improve to provide long-range contextual information together with longer read lengths, it is possible that the problem of aligning reads uniquely can unlikely remain a significant issue. However, it is likely that new algorithmic problems will arise and have to be addressed ab initio which did not exist in the simpler platforms, such as how to efficiently align longer reads or maps, how to detect and interpret structural variations that can now appear rampant in the human genome, and how to handle new sources of statistical errors (e.g., false-positive and false-negatives in detecting markers such as restriction or hybridization sites).
Yet another challenge can be, e.g., with respect to developing technology-agnostic procedures, is the use of scalable and accurate procedures for sequences, maps and whole-genomes alignment, which can involve parallelism, genome-structure based heuristics and probabilistic methods. While such a problem can be solved via a branch-and-bound strategy, any such solution is not likely to determine an optimal (preferred) result in a polynomial-based amount of time in the worst-case, especially when each sequence-read can have a relatively large number of ambiguous alignments). Other approaches can involve seeking approximate solutions using linear programming relaxation heuristics or specific Bayesian statistical methods that can assume certain priors. For example, such approaches can be achieved through model-base analysis of the sequencing data (See, e.g., Erlich Y., et al., supra.). However, as described in this reference, there can exist in, e.g., a Solexa sequencing platform, nonstationary noise factors which can accumulate throughout a run and thus reduce yield and accuracy for subsequent sequencing cycles, as well as other associated problems as described herein.
For example, one dominant noise factor can be phasing, which can be a well-known source of noise in many sequencing-by-synthesis platforms which use a cyclic reversible termination (CRT) process. CRT can repeat cycles of three steps, e.g., (i) extension of a nascent strand with addition of a single extension-blocked fluorophore-labeled nucleotide, (ii) imaging and (iii) removal of the block and fluorophore in preparation for the next synthesis cycle. In an idealized model, the nascent strands within a clonal DNA cluster can all be the same and remain perfectly synchronized, thus generating a strong coherent signal. Imperfections in the chemistry of CRT, however, can cause stochastic failures which in turn can cause nucleotide misincorporations and imperfect (e.g., suboptimal, less than preferred) block removal in a particular cycle. The resulting heterogeneity in nascent strand lengths can manifest itself in lagging (behind the dominant nascent strands) and leading (ahead of the dominant nascent strands) members within the cluster, which can thus degrade the signal with sequence-specific noise from neighboring positions, for example. The noise introduced in this manner can be nonstationary and structured, as it can depend on, e.g., the number of preceding cycles and base-composition in the neighborhood of the interrogated location. Another dominant noise factor can be fading, which can be an exponential decay in fluorescent signal intensity that can increase with the number of preceding cycles. A resulting degradation of signal-to-noise ratio can typically be attributed to a material loss during sequencing, for example. Yet another dominant noise factor can be a cycle-dependent change in fluorophore cross-talk, which can induce a significant bias toward certain base calls in later cycles. Indeed, individually and/or together, these noise factors can have a significant negative effect on the quality of the signal that can be produced by the sequencing machine.
Certain approaches have been described in an attempt to address these problems, such as described in, e.g., Erlich Y. et al., supra., although these approaches can have several limitations. For example, one such limitation can be, e.g., that Alta-Cyclic technologies can be slow, with the majority of the computation spent on sparse-matrix manipulation. Another limitation can be, e.g., that Alta-Cyclic technologies can produce only one solution, e.g., the MLE solution. Yet another problem can be, e.g., that Alta-Cyclic technologies can lack flexibility. The Alta-Cyclic based implementations can have require to be repeatedly rebuilt to create new models, with new families of parameters and new estimation routines, every time the sequencing platform makes even a small modification to the underlying chemistry and physical sensing, for example. Yet still another problem can be, e.g., that Alta-Cyclic technologies can not generalize to a large class of sequencing platforms even though these parameters may share many of the same structures. Alta-cyclic and related technologies can be too inflexible to allow extension of the method from Solexa to 454, which may not have cyclic reversible termination and resulting homopolymer errors, although 454 can have its own phasing, fading and cross talk errors. Yet still another problem associated with Alta-Cyclic technologies can be, e.g., that such method can not provide for relatively easy integration with other higher-level modules, such as, e.g., alignment, SNP-calling, overlap detection, layout-generation, consensus sequence generation, shotgun, map-based assembly, etc.).
Thus, it may be beneficial to address and/or overcome at least some of the deficiencies described herein above.

Method, computer-accessible medium and system for base-calling and alignment


A bed siderail has a vertical siderail extension, a horizontal siderail extension, or both. A bed siderail has dual vertical siderail extensions. A bed has gap fillers pivotally mounted to the headboard and/or footboard, either in the manner of a hinge, or by means of a dual axis pivot, to fill gaps between the headboard/footboard and a siderail. A bed siderail has pivotally mounted gap fillers directed toward the headboard, footboard, or an adjacent siderail. A bed has slidably mounted gap fillers. A bed siderail has pivotally mounted gap fillers, to fill a gap between the siderail and a mattress, the gap fillers being either gravity- or cam-activated, or being integrally formed in the siderail support arms. A bed siderail is rotatable from a deployed to a stowed position, and is simultaneously stowed close-into or underneath the bed frame.

1. Field of the Invention
The invention relates to a bed siderail. In one of its aspects, the invention relates to a bed siderail with vertical and/or horizontal extensions or gap fillers. In another aspect, the invention relates to a siderail retractable underneath a bed support frame. In another of its aspects, the invention relates to a siderail deployed to a position closely abutting a bed mattress.
2. Description of Related Art
Hospital beds are provided siderails to prevent a patient from falling out. Additional safeguards are sometimes desirable, providing siderails with greater coverage of the bedside, thereby reducing gaps between the siderails or the siderails and the headboard or footboard.
It would be advantageous to provide a siderail or bed and siderail assembly that reduces gaps, and increases safety.


A method to control the quality of a buried oxide region, and to substantially reduce or eliminate deep divots in SOI substrates is provided. Specifically, the inventive method includes the steps of implanting oxygen ions into a surface of a Si-containing substrate; and annealing the Si-containing substrate containing the implanted oxygen ion at a temperature of about 1300xc2x0 C. or above and in a chlorine-containing ambient so as to form a buried oxide region that electrically isolates a superficial Si-containing layer from a bottom Si-containing layer. The chlorine-containing ambient employed in the annealing step includes oxygen and a chlorine-containing carrier gas such as HCl, methylene chloride, trichloroethylene and trans 1,2-dichloroethane.

The present invention relates to silicon-on-insulator (SOI) substrates, and more particularly to a separation by implantation of oxygen (SIMOX) process in which internal thermal oxidation (ITOX) is sufficiently controlled so as to improve the circuit yield of the SOI substrate. The circuit yield can be increased in the present invention by improving the quality of the buried oxide (BOX) region and/or by decreasing the deep divot density.
During some SIMOX processes such as described, for example, in U.S. Pat. No. 5,930,643 to Sadana, et al., extensive internal thermal oxidation (ITOX) takes place in the oxygen implanted region of the Si-containing substrate during high-temperature (on the order of about 1300xc2x0 C. or higher) annealing in an oxidizing ambient.
FIG. 1 is a graph of ITOX thickness (xc3x85) vs. surface oxidation thickness (xc3x85) for typical SIMOX processes in which ITOX is occurring. Specifically, FIG. 1 shows how ITOX thickness depends on the surface oxide thickness formed during high-temperature annealing. As is shown, ITOX thickness increases with increasing surface oxide thickness.
Internal therm oxidation has both beneficial and detrimental effects on the quality of low-dose SIMOX processes. The beneficial effects that are obtained from ITOX include: (i) formation of a thermal oxide cap layer over the implanted oxide thereby increasing the overall thickness of the BOX region; (ii) improvement in the continuity of the BOX; and (iii) improvement in the electrical quality of the BOX region as measured by its breakdown field.
The detrimental effect of ITOX includes the formation of deep divots in the superficial Si layer (i.e., top Si layer that overlays the BOX region) of a SOI substrate which could be a device killer and impact circuit yield adversely.
The prior art SIMOX processes in which ITOX is a factor do not provide adequate control of this phenomena. Control of ITOX is important for various reasons. For example, the quality of the BOX region relates directly to the yield of microprocessors and memory devices such as dynamic random access memories (DRAMs) and static random access memories (SRAMs). Lowering the quality of the BOX region (i.e., lower the breakdown voltage) lowers the circuit yield. Similarly, the higher the deep divot density, the lower the circuit yield is. Both of these phenomena are directly related to ITOX which may occur during the high-temperature annealing step of conventional SIMOX processes.
In view of the above drawbacks with conventional SIMOX processes, there is a continued need for providing a new and improved SIMOX process in which ITOX is sufficiently controlled so as to improve the circuit yield of the SOI substrate.
One object of the present invention is to provide a SIMOX process in which ITOX is sufficiently controlled so as to be capable of adjusting the BOX thickness formed during the process.
Another object of the present invention is to provide a SIMOX process in which ITOX is sufficiently controlled so as to improve the quality of the BOX region.
A further object of the present invention is to provide a SIMOX process in which ITOX is sufficiently controlled so as to substantially decrease or eliminate the deep divot defects that are present in the top, i.e., superficial, Si-containing layer of a SOI substrate.
A yet further object of the present invention is to provide a SIMOX process in which no additional steps besides implanting and annealing are employed in forming a BOX region within a Si-containing substrate.
An even further object of the present invention is to provide a SIMOX process in which conventional ion implants are employed, and control of ITOX is achieved by changing the ambient employed during the annealing step.
These and other objects and advantages are achieved in the present invention by providing a SIMOX process in which ITOX is controlled by adding a chlorine-containing carrier gas to the annealing ambient during high-ternperature annealing.
Specifically, the present invention provides a method to control the quality of the BOX region formed during a SIMOX process, and to substantially reduce or eliminate deep divots in SOI substrates. The inventive method comprises the steps of:
implanting oxygen ions into a surface of a Si-containing substrate; and
annealing said Si-containing substrate containing said implanted oxygen ions at a temperature of about 1000xc2x0 C. or above and in a chlorine-containing ambient so as to form a buried oxide region that electrically isolates a superficial Si-containing layer from a bottom Si-containing layer.
The method of the present invention, which employs a chlorine-containing ambient during annealing, provides SOI substrates having a high quality (in terms of structural and electrical properties) BOX region and a superficial Si-containing layer that has a reduced number of divot defects present therein.
The term xe2x80x9chigh structural qualityxe2x80x9d is used herein to denote a SOI substrate which has little or no etch pitch density (less than about 1E5 cm2); little or no top or bottom superficial Si/buried oxide roughness (surface roughness of less than about 100 xc3x85 as measured by TEM (transmission electron microscopy); a low HF-defect density (less than about 1 cm2); and a low surface roughness (of about 6 xc3x85 root mean square).
The term xe2x80x9chigh electrical qualityxe2x80x9d is used herein to denote a structure wherein the buried oxide breakdown field is high (greater than about 5 megavolts per cm); the buried oxide minibreakdown voltage is high (greater than about 35 volts); the buried oxide leakage at a given voltage is low (less than about 1 nanoAmp); and the buried oxide short density is low (less than about 1 cmxe2x88x922).

Controlling internal thermal oxidation and eliminating deep divots in SIMOX by chlorine-based annealing

International Business Machines Corporation


A magneto-optic recording medium in which a vertically magnetized film on which magnetized domains are recorded by applying a light beam and an outer magnetic field is provided along a recording track and structure bands which do not contribute to read out of the magnetized domains are provided on both sides of the recording track so that the magnetization state of the magnetized domains recorded on the vertically magnetized film is read from an area limited by the width of the recording track. By scanning the magneto-optic recording medium along the recording track with a light beam having a diameter larger than the width of the recording track so as to heat an area larger than the width of the recording track to a temperature exceeding the curie temperature of the vertically magnetized film and also by applying a magnetic field in a predetermined direction to the area irradiated with the light beam, the magnetized domains are recorded in accordance with the direction of the applied magnetic field, and the magnetization state of the magnetized domains is read out only from the area limited by the width of the recording track through the magneto-optic effect.

The present invention relates to a magneto-optic recording/reproducing method and device and a magneto-optic recording medium used for them. More particularly, the present invention relates to a magneto-optic recording/reproducing method which is suitable to accurately demodulate data at a high speed by suppressing jitter due to "feather-shaped magnetic domains" which will be generated in performing overwrite through magnetic field modulation.
A magneto-optic disk has been identified as an optic disk which can rewrite information. The magneto-optic disk, using a vertically magnetized film as a recording film, forms recording domains through a thermomagnetic effect and reproduces them through a magneto-optic effect. More specifically, the recording domains are formed as follows. The temperature of the magnetized film is increased to its Curie temperature by irradiating a laser optical spot to remove the magnetization of the irradiated area, and in the cooling process an external magnetic field is applied to fix the vertical magnetization of the optical spot irradiated area in the direction of the magnetic field, thereby forming the recording (magnetized) domains.
The method for forming such magnetized domains includes two techniques. One is an optical modulation technique which, with an external magnetic field with a certain intensity applied in the direction opposite to the direction of initial magnetization of the vertically magnetized film, modulates the intensity of the laser optical spot in accordance with the data to be recorded. The other is a magnetic field modulation technique which, with the laser optical spot with a certain intensity applied to increase the temperature of the magnetized film to its Curie temperature or more, modulates the direction of the external magnetic field. For example, the technical Report at the Academic Society of Electronics, Information and Communication (DENSI JOHO TSUSIN GAKKAI GIJUTSU HOKOKU) MR 87-37 (1987), pages 13 to 20, discloses that a storage density of 0.6 .mu.m/bit is obtained at a scanning speed (linear velocity) of a laser light beam of 1.2 m/sec. through the magnetic field modulation technique.
However, this reference does not refer to the influence from the angular projections of the recorded magnetized domains and the change of the center position and width of the magnetized domains, and also does not entirely consider problems in the case of overwrite and reproduction at a high speed and with a high density.

Magneto-optic recording/reproducing method and device and magneto-optic recording medium used for them


A method for fabricating a CCD image sensor includes the steps of forming a P type well in a surface of a semiconductor substrate, forming a buried CCD (BCCD) in a surface of the P type well, forming an offset gate and a reset gate on the BCCD at a predetermined interval, forming a floating diffusion region in the BCCD between the offset gate and the reset gate, forming a mask layer on an entire surface of the semiconductor substrate to form a contact hole in the floating diffusion region, forming a metal layer on the entire surface of the semiconductor substrate including the contact hole, and selectively removing the metal layer on the mask layer together with the mask layer to form a floating gate in the contact hole.

1. Field of the Invention
The present invention relates to a charge coupled device (CCD), and more particularly, to a method for fabricating a CCD image sensor.
2. Discussion of the Related Art
Generally, a solid-state image sensor includes a plurality of photoelectric conversion regions, a plurality of vertical charge transfer regions, a horizontal charge transfer region, and a floating diffusion region. The photoelectric conversion regions are disposed at a predetermined interval in a matrix arrangement and convert an optical signal to an electrical signal to produce image charges. The vertical charge transfer regions are formed between the respective photoelectric conversion regions in vertical direction and transfer the image charges produced in the photoelectric conversion regions in vertical direction. The horizontal charge transfer region transfers the image charges transferred in the vertical direction in horizontal direction. The floating diffusion region senses the image charges transferred in the horizontal direction and outputs them to peripheral circuits.
FIG. 1a is a plan view of a conventional floating diffusion. FIG. 1b is a sectional view of a conventional floating diffusion taken along II--II line of FIG. 1a.
The floating diffusion FD is formed at the end of the horizontal charge transfer region and includes a P-well 12, a buried charge coupled device (BCCD) 13, an offset gate (OG) 14, a floating diffusion region 15, a reset drain region 16, a reset gate 17, and a charge detector. The P-well 12 is formed on a surface of an N type substrate 11. The BCCD 13 is formed in a surface of the P-well 12. The offset gate 14 is formed at a top portion of the end of the BCCD 13 and transfers charges transferred to the end of the BCCD 13. The floating diffusion region 15 is formed at the end of the BCCD 13 and senses the charges transferred through the offset gate 14. The reset drain region 16 is formed at one side of the floating diffusion region 15 and resets the sensed charges. The reset gate 17 is formed at a top portion between the floating diffusion region 15 and the reset drain region 16 and transfers the sensed charges to the reset drain region 16. The charge detector (not shown) is formed of transistors which are connected to a floating gate 18 of the floating diffusion region 15 to sense the charges.
In the aforementioned conventional floating diffusion, a current flows from the floating diffusion region 15 to the reset drain region 16 if a bias is applied to the reset gate 17 and the reset drain region 16.
A method for fabricating the conventional CCD image sensor will be described with reference to FIG. 2a to FIG. 2f.
FIG. 2a to FIG. 2f are sectional views illustrating fabricating process steps of a conventional CCD image sensor.
As illustrated in FIG. 2a, a P-well 22 is formed on a surface of an N type semiconductor substrate 21. Ions are implanted into a predetermined region of the P-well 22 to form a BCCD 23 which is used as a horizontal charge transfer channel.
A gate oxide film 24 and a nitride film 25 for a gate insulation are sequentially formed on an entire surface of the N type semiconductor substrate 21 including the BCCD 23. A polysilicon 26 is formed on the nitride film 25. A first photoresist 27 is deposited on the polysilicon 26 and patterned by exposure and developing processes.
As illustrated in FIG. 2b, the polysilicon 26 is selectively removed using the patterned first photoresist 27 as a mask to form an offset gate 26a and a reset gate 26b.
Subsequently, an oxide film 28 is formed on the entire surface of the N type semiconductor substrate including the offset gate 26a and the reset gate 26b. The oxide film 28 is selectively removed to remain at top portions and side portions of the offset gate 26a and the reset gate 26b.
As illustrated in FIG. 2c, a second photoresist 29 is deposited on the entire surface of the N type semiconductor substrate 21 including the oxide film 28 and patterned by exposure and developing processes.
The nitride film 25 is then selectively removed using the patterned second photoresist 29 as a mask to partially expose a surface of the gate oxide film 24.
Thereafter, impurity ions are implanted into the entire surface of the N type semiconductor substrate 21 using the patterned second photoresist 29 as a mask to form a floating diffusion region 30 for ohmic contact in a predetermined region of the BCCD 23.
As illustrated in FIG. 2d, the second photoresist 29 is removed. A third photoresist 31 is deposited on the entire surface of the N type semiconductor substrate 21 and patterned by exposure and developing processes.
Subsequently, the gate oxide film 24 is selectively removed using the patterned photoresist 31 as a mask to partially expose a surface of the floating diffusion region 30, so that a contact hole 32 is formed.
As illustrated in FIG. 2e, the third photoresist 31 is removed. A metal layer 33 is formed on the entire surface of the N type semiconductor substrate 21 including the contact hole 32. A fourth photoresist 34 is deposited on the metal layer 33 and then patterned by exposure and developing processes.
As illustrated in FIG. 2f, the metal layer 33 is patterned using the patterned fourth photoresist 34 as a mask to ohmic contact with the floating diffusion region 30. As a result, a floating gate 33a is formed. The floating gate 33a outputs image charges in the contact hole 32 and at a top portion of the nitride film 25 adjacent to the contact hole 32 to peripheral circuits (not shown).
Generally, overall charges produced by light can be expressed as Qsig=Cin*Vout, where Cin is overall capacitance applied to the floating diffusion region through a sensing amplifier and Vout is a sensing voltage in the floating diffusion region.
In addition, Vout=Qsig/Cin can be achieved by the above expression. In this case, the larger Cin is, the lower the sensing voltage of the floating diffusion region is.
The conventional method for fabricating a CCD has a problem.
That is, since the floating gate is widely formed around the contact hole including the contact hole to avoid misalignment of the floating gate which is used for ohmic contact with the floating diffusion region, parasitic capacitance occurs in the floating diffusion region. As a result, there results in limitation in increasing the sensing voltage of the floating diffusion.

Method for fabricating charge coupled device image sensor


A shelf management method and device are provided. The method comprises: controlling a conveying means to convey a first shelf to a workbench in a warehouse, the first shelf being a shelf in the warehouse; controlling, if the first shelf is one of high-frequency shelves, the conveying means to convey the first shelf to a first storage position in the warehouse, wherein the high-frequency shelves comprise a preset number of shelves subject to the highest numbers of deliveries in the warehouse; and controlling, if the first shelf is one of low-frequency shelves, the conveying means to convey the first shelf to a second storage position in the warehouse, wherein the low-frequency shelves comprise shelves other than the high-frequency shelves, and a distance between the first storage position and the workbench is less than a distance between the second storage position and the workbench. Efficiency of delivery can be improved.

A warehouse is a storage facility for stuffs. A warehouse includes a large number of shelves, trolleys and workbenches. A shelf bears various stuffs and can be conveyed, by a trolley, from a workbench for bale and delivery to a storage position of the warehouse where the shelf is typically arranged.
To deliver a stuff from the warehouse, the shelf bearing the stuff and storage position thereof are first to be determined. The shelf is conveyed by a trolley to the workbench from the storage position as determined. The stuff is then taken from the shelf, and baled on the workbench for delivery. The shelf is conveyed by the trolley back to the storage position after delivery.
In the implementation of the present application, applicant notes that the prior art has at least the following problem:
A shelf having stuffs frequently subject to deliveries may be remote from the workbench such that it may take a long time for the trolley to convey the shelf. Delivery efficiency is thus reduced.

Stock shelf management method and device


An information processing apparatus which causes a printing apparatus to print an image to which information is added, includes a causing unit for causing, when a setting is specified for adding information to an image and the information cannot be acquired from a router, the printing apparatus not to print the image, and for causing, when a setting is specified for adding information to an image and the information can be acquired from a router, the printing apparatus to print an image to which the acquired information is added.

1. Field of the Invention
The present invention relates to an information processing apparatus, a control method thereof, and a program.
2. Description of the Related Art
A function can be added to a printer driver installed in a host computer by additionally installing a function expansion module to the printer driver.
An example of the additional function is a copy-forgery-inhibited pattern function (e.g., refer to Japanese Patent Application Laid-Open No. 2001-197297). A copy-forgery-inhibited pattern image in an original document (i.e., a printed output from a printer) simply looks like a pattern or a background image to a viewer. However, when the original document is copied, a predetermined text or image becomes visualized. The copy-forgery-inhibited pattern thus prevents use of copy products.
Colors in the copy-forgery-inhibited pattern image and the text that becomes visualized when the original document is copied can be freely set in such a copy-forgery-inhibited pattern function added to the printer driver. Further, output date and time and information unique to a printing apparatus can also be set in the copy-forgery-inhibited pattern image.
However, according to conventional techniques, if the output date and time and the information unique to a printing apparatus cannot be acquired, there is no information to be embedded in the copy-forgery-inhibited pattern image. A copy-forgery-inhibited pattern image that has no embedded information thus becomes generated.
Such an issue is not limited to the copy-forgery-inhibited pattern image, and a similar issue occurs in a bar code, a two-dimensional code, and digital watermark.

Information processing apparatus, control method thereof, and program


The present invention introduces a novel design for active matrix displays, utilizing both organic light-emitting diode (OLED) and thin-film electroluminescent technologies. In a first aspect there is provided a top-emitting OLED, including an optical interference contrast-enhancing stack that is placed on the top of the driving thin-film transistor, and which extendes to the entire pixel area to cover the reflecting parts of the pixel. In a second aspect, there is provided a bottom-emitting OIED wherein an optical interference contrast-enhancing stack is placed right under the driving thin-film transistor and, separately between the organic stack and the top electrode, typically a cathode. The optical interference contrast-enhancing stack suppresses light reflection from the thin-film transistor and the upper electrode. In the top emitting design, the optical interference contrast-enhancing stack is placed on the top of the thin-film transistor source and drain electrodes as well as on the top of the opaque bottom electrode. A method of achieving substantial uniformity across a display having multiple areas of optical interference members is also provided.

Many display technologies are well known and such technologies are continuing to advance rapidly. For example, modem active matrix display technology can be incorporated into display devices that are relatively lightweight, thin, and which provide high resolution and richly coloured pictures for televisions, computer monitors, and more generally, for a wide variety of display devices that can be incorporated into appliances like personal digital assistants and cellular telephones. While current active matrix displays can be expensive, it is expected that further research will result in advances that will can reduce the costs of such displays and lead to overall greater usage of active matrix display devices.
Active matrix displays are proving to be superior in many ways to older display technologies such as cathode-ray tubes ("CRT"). However, the problem of "glare" off of active matrix displays is also a concern, just as with older CRTs. "Glare" can be defined as ambient light that is reflected off of the device and back towards the viewer, thereby reducing the contrast and overall performance of the display device.
Thus, it is also known to incorporate technology to reduce reflectance into displays and thereby improve their performance. In the case of active matrix displays (or indeed, any other type of pixellated display) it is known to use a black matrix of filtering material. The black matrix is mounted in a complementary fashion to the matrix of pixels in the display, such that the black matrix is a generally continuous filter that surrounds each pixel. Black matrices are described in a number of patents and patent applications, such as "Anti-reflector black matrix for use in display devices and method for preparation of same", EP 716 334 to Steigerwald ("Steigerwald #1"); "Transmissive Display Device Having Two Reflection Metallic Layers of Differing Reflectances", U.S. Pat. No. 6,067,131 to Sato ("Sato"); "Anti-reflector black matrix display devices comprising three layers of zinc oxide, molybdenum and zinc oxide", U.S. Pat. No. 5,570,212 to Steigerwald ("Steigerwald #2"); "Anti-reflector Black Matrix Having Successively A Chromium Oxide Layer, a Molybdenum Layer And a Second Chromium Oxide Layer", U.S. Pat. No. 5,566,011 to Steigerwald ("Steigerwald #3"); and, "Low Reflectance Shadow Mask", U.S. Pat. No. 5,808,714 to Rowlands et al. ("Rowlands"). One particular disadvantage to Steigerwald #1, Steigerwald #2 Steigerwald #3 and Rowlands is that they are confined to black matrix structures having specific sets of materials. A more general discussion of applying a black matrix as applied to a display having colour filters is found in U.S. Pat. No. 5,587,818 to Lee ("Lee").
However, such prior art black matrix structures are not always useful or practical to incorporate into display devices. For example, prior art black matrix structures are frequently formed as a separate unit from the display, thereby eventually requiring the assembly of the black matrix structure to the display structure, such as by mounting the black matrix structure to the front of the display.
It is also known to use optical interference to reduce reflectance in various thin film display technologies, such as electroluminescent devices ("ELD"s). For example, reducing reflectance of ambient light can be achieved by using additional thin film layers sandwiched between one or more layers of the ELD, which are configured to achieve destructive optical interference of the ambient light incident on the display, thereby substantially reducing reflected ambient light. Optical interference technology is discussed in detail in U.S. Pat. No. 5,049,780 to Dobrowolski et al., ("Dobrowolski") and U.S. Pat. No. 6,411,019 to Hofstra et al. ("Hofstra"). In addition, certain inventors of the present invention have also contemplated the use of the optical interference technology taught in Hofstra and Dobrowolski in conjunction with the bus lines that form the matrix surrounding each pixel in an active matrix display. See Canadian Patent Application 2,364,201 filed Dec. 12, 2001.
More recently, U.S. Pat. No. 6,429,451 to Hung ("Hung") has proposed another type of ambient light reducing layer also for incorporation into a pixel of the ELD.
However, notwithstanding the improvements provided by the prior art, it is now been discovered that the prior art does not provide ambient light reduction across all areas of the display, as is now offered by polarizers that are also used with prior art displays. Because polarizers can offer substantially uniform ambient light reduction across the entire viewable surface of the display, polarizers can be preferred over other prior art solutions that embed or otherwise incorporate the ambient light reduction means within the actual display structure. In order to obviate the need for polarizers and achieve the attendant advantages eliminating the post production costs associated with polarizers, it is desired to provide a means to substantially uniformly reduce ambient light reflection across the entire viewable surface of the display by means of embedding the contrast enhancement apparatus within the display.

OLED display with contrast enhancing interference members


There are provided a piezoelectric vibration module and a vibration generating apparatus including the same. The piezoelectric vibration module includes: a piezoelectric actuator including a piezoelectric element deformed in both a first direction and a second direction perpendicular to the first direction through the application of electrical power thereto; at least one first rod transferring deformation force of the piezoelectric actuator in the first direction; at least one second rod converting deformation force of the piezoelectric actuator in the second direction into deformation force in the first direction and transferring the converted deformation force; and a mass body connected to the first and second rods and disposed on the piezoelectric actuator so that displacement is generated in the first direction.

1. Field of the Invention
The present invention relates to a piezoelectric vibration module and a vibration generating apparatus including the same.
2. Description of the Related Art
A vibration generating apparatus, a component converting electrical energy into mechanical vibrations through the generation of electromagnetic force, is commonly mounted in a mobile phone to be used to silently notify a user of call reception by transferring vibrations thereto.
Meanwhile, in accordance with rapid growth in the mobile phone market and the trend for adding functionality to mobile phones, mobile phone components having a compact size and a high degree of quality have been required. In this situation, the demand for the development of a vibration generating apparatus having a novel structure capable of overcoming the disadvantages of existing vibration generating apparatuses, and having significantly improved quality with respect thereto, has increased.
In addition, as the release of smartphones has rapidly increased, a touchscreen scheme has been adopted therein, such that in addition to silently notifying a user of call reception, vibration generating apparatuses have been used in order to generate vibrations when the touchscreen is touched.
Degrees of performance required of the vibrations generated when the touchscreen is touched in particular, are as follows. First, since vibrations are generated more frequently in devices having touchscreens than in phones merely vibrating at the time of call reception, an operational lifespan of a vibration generating apparatus should be increased. Second, in order to improve user satisfaction when a user is provided with vibrations when the touchscreen is touched, a vibration response speed should be increased, in accordance with a speed at which the screen is touched.
In accordance to the demand for an increased operational lifespan and improved response times as described above, a linear vibrator has been currently used in the mobile phone including a touch screen.
The linear vibrator may linearly resonance-move a mover suspended from a spring due to electromagnetic force generated between a coil and a magnet using a mass body connected to an elastic member installed in the vibrator rather than using a principle of rotation of a motor to generate vibrations.
Alternatively, the linear vibrator may linearly resonance-move a mover through contraction and expansion of a piezoelectric element using the piezoelectric element as an actuator to generate vibrations.
Particularly, a vibration generating apparatus using the piezoelectric element is deformed when the piezoelectric element has power applied thereto. However, since a degree of deformation of the piezoelectric element is significantly low, it may be very difficult to utilize this deformation for vibrations.

Piezoelectric vibration module and vibration generating apparatus including the same


The blanketing valve has a diagnostic port to aid in analyzing the valve's operation. A pressure gauge is connectable or permanently connected to the diagnostic port. The diagnostic port measures the pressure above a main valve in a passageway connecting a pilot inlet chamber and a main valve piston chamber. This pressure controls the main valve and is an indicator of pilot valve action. Comparing this pressure to inlet pressure indicates pilot response and is a valuable aid in determining what problems may exist.

Tank blanketing is an effective way to prevent fires in storage tanks which contain flammable liquids. Tank blanketing prevents the formation of an explosive vapor/air mixture. A blanket or pad of inert gas in a vapor space inside a tank prevents atmospheric air from entering the tank. In addition to preventing outside air, which contains oxygen, moisture and other contaminants from entering the tank, the blanket also minimizes evaporation of the stored product to reduce product emission levels.
The inert gas, usually Nitrogen, is injected as necessary, into the vapor space in the tank to maintain an inert atmosphere. The blanket pressure is usually very low (less than 1 PSI).
The inert gas is admitted only during inbreathing cycles (vacuum cycles). An inbreathing cycle occurs when liquid is being withdrawn from a tank, or when vapors condense in a tank due to a decrease in temperature. The amount of inert gas required for a specific application is based on the maximum inbreathing demand under conditions of sudden cooling, caused by weather conditions, and the emptying rate of the tank.
Although Nitrogen is most commonly used, other gases, including natural gas, may be used in some applications. Depending upon the specific application, the selection of an inert gas for a particular process is based upon at least one of the following characteristics:
1. Non-flammable in the desired atmosphere PA1 2. Non-interacting with the tank liquid PA1 3. Chemically inactive PA1 4. Non-toxic PA1 5. Availability in large quantities PA1 6. Economic factors
In designing a tank blanketing system, several considerations are evaluated:
1. The tanks themselves as well as the piping, dikes, fittings, etc., should be designed and constructed in accordance with sound engineering principles.
2. Inert gas or tank blanketing equipment must be completely reliable and capable of maintaining an adequate supply of inert gas at all times. Equipment breakdown or equipment that is inadequately sized for the job will result in a higher oxygen concentration in the vapor space of the storage tank which would mix with the vapors resulting in a potentially flammable mixture.
3. The inert gas should be introduced into the tank so that it is distributed effectively.
4. Contamination of the inert gas from any source must be guarded against. Suitable devices should be employed to hold moisture to an absolute minimum.
A blanketing valve is used in tank blanketing applications to regulate the pressure of the inert gas layer on top of a tank liquid. The valve senses the pressure of the tank blanket and opens to allow flow in of more inert gas when pressure drops below a set pressure. The valve closes and stops flow when pressure builds back up to the set pressure in the tank.


A method of depositing a organosilicate dielectric layer exhibiting high adhesion strength to an underlying substrate disposed within a single processing chamber without plasma arcing. The method includes positioning a substrate within a processing chamber having a powered electrode, flowing an interface gas mixture into the processing chamber, the interface gas mixture comprising one or more organosilicon compounds and one or more oxidizing gases, depositing a silicon oxide layer on the substrate by varying process conditions, wherein DC bias of the powered electrode varies less than 60 volts.

1. Field of the Invention
Embodiments of the present invention generally relate to the fabrication of integrated circuits. More particularly, embodiments of the present invention relate to a method for depositing organosilicate layers on a substrate.
2. Description of the Related Art
In the manufacture of integrated circuits, plasma processes are increasingly being used to replace thermal processes. Plasma processing provides several advantages over thermal processing. For example, plasma enhanced chemical vapor deposition (PECVD) allows deposition processes to be performed at substantially lower temperatures than the temperatures required in analogous thermal processes. This is advantageous for processes with stringent thermal budget demands, such as in very large scale or ultra-large scale integrated circuit (VLSI or ULSI) device fabrication.
However, one problem that has been encountered with plasma processing in integrated circuit fabrication is device damage that occurs as a result of exposure of a device to non-uniform plasma conditions, such as electric field gradients caused by changing process conditions. While the susceptibility or degree of device damage typically depends at least partially on the stage of device fabrication and the type of device, many types and stages of devices can experience plasma-induced damage (PID). For example, a substrate that has a barrier layer or dielectric layer deposited thereon is more susceptible to PID due to the accumulation of surface charge, and a buildup of potential gradients during processing. Furthermore, as the size of devices become smaller and the dielectric layers become increasingly thinner, devices are becoming increasingly susceptible to PID.
In order to further reduce the size of devices on integrated circuits, it has become necessary to use conductive materials having low resistivity and to use insulators having low dielectric constants (low-k) to reduce the capacitive coupling between adjacent metal lines. Methods to form low-k dielectric layers include PECVD of organosilicate precursor gases to form organosilicate dielectric layers, such as carbon doped silicon oxide films. One challenge in this area has been to develop a carbon doped silicon oxide dielectric film that has a low k value, but also exhibits desirable adhesion properties to the underlying substrate or adjacent dielectric diffusion barrier layer materials which include silicon, silicon dioxide, silicon carbide, silicon nitride, oxygen-doped silicon carbide, titanium, titanium nitride, tantalum, tantalum nitride, tungsten, aluminum, copper, and combinations thereof. Inadequate adhesion may result in delamination of the low-k dielectric layer from the underlying substrate and potential failure of the device. One approach to enhancing adhesion of carbon doped silicon oxide films is inserting a thin silicon oxide film between the carbon doped silicon oxide layer and the underlying barrier layer. However, the thin silicon oxide layer must be a minor portion of the combined dielectric film to retain significant reduction in dielectric constant. Furthermore, the deposition of a thin silicon oxide layer prior to deposition of a carbon doped silicon oxide layer substantially increases processing time unless the layers are deposited sequentially in the same chamber. Sequential deposition has resulted in plasma arcing when the deposition conditions are changed. The plasma arcing damages the substrate surface and effectively negates any advantage in depositing the thin silicon oxide film and the carbon doped silicon oxide layer in the same chamber.
Therefore, there is a need for a process for depositing an organosilicate dielectric layer exhibiting high adhesion strength to an underlying substrate without plasma arcing.

Interface engineering to improve adhesion between low k stacks


A system for controlling an electric motor comprises, in one embodiment, an encoder; a central processor in communication with said encoder; a module processor in communication with said central processor; feedback circuitry in communication with said module processor, wherein said encoder is an electronic device that provides rotor and stator positional information to said central processor, and further comprising a user interface in communication with said central processor, wherein said user interface enables a user to select preferred operational parameters for an electric motor. Another embodiment comprises a method for controlling an electric motor, comprising: determining rotor position based on data received from an encoder; determining how to energize stator coils; directing a power module to provide appropriate current to appropriate coils; and monitoring rotor response, wherein determining how to energize stator coils comprises consulting a look-up table.

Conventional wisdom holds that electrical motors and generators are mature and that their efficiency can improve only incrementally. The truth is that these machines operate with 90–99% efficiency near their rated speed and load but with much lower efficiency when the speed or load varies from the rated values.
In a conventional electric motor, the maximum rotor speed and torque required by the application determine the key design parameters. The motor typically performs optimally only in a narrow speed-torque band centered close to the maximum steady-state speed and torque. Performance drops off when the motor must supply an intermittent burst, when the motor needs to deliver only a small fraction of its rated torque or power, or when it runs at low speed. Indeed, the specification sheets for power motors typically do not specify torque-efficiency performance for rotor speeds below about 1500 RPM, since motor performance degrades precipitously at those speeds.
Consequently, a diverse range of motor designs has evolved in the art, with each design optimized to serve a narrow set of applications. For example, a three-phase AC motor can drive a conveyor belt in a factory with close to 99% efficiency if the belt starts up once per shift and carries a nearly constant load. In practice, however, many applications require frequent starts and stops and encounter a wide range of loads. Therefore, a motor's efficiency rarely remains consistently high under real world operating conditions.
Use of electric motors to power electric vehicles (EVs) became somewhat more practical when engineers began replacing DC motors (which usually require brushes to make electrical contact with the spinning rotor) with three-phase AC motors. Since then, efforts have focused on improving the inverter that converts stored DC power into three-phase AC power to drive the motor. The inverter must also vary the frequency of the three-phase power to control the motor speed effectively. The Partnership for a Next Generation of Vehicles, a joint R&D effort between government and industry, has identified the inverter as a key technical obstacle to commercializing EVs at a reasonable price. The preferred motor design of the present invention eliminates the need for an external inverter—the inverter is integrated into individual coil modules.
In a conventional three-phase induction motor (3PIM), three sinusoidally varying currents 120° apart drive three electromagnets that comprise the stator, the part of the motor that remains fixed in place. Together these electromagnets create a strong primary magnetic field whose direction spins like the hour hand of a clock. This rotating field induces currents in the windings of the rotor (the part of the motor that spins) that in turn create a reactive magnetic field, which tries to align itself with the primary field by twisting the rotor. The rotor spins continuously, lagging behind the stator field. Each motor operates most efficiently at some design-specific combination of speed and torque that optimizes the rate at which the rotor slips a full rotation behind the stator field (the "slip rate"). Lower speeds induce a smaller secondary field and hence generate lower torque, in addition, at lower speeds the rotor slips more frequently, reducing energy transfer to the rotor and increasing dissipation (loss of energy as heat). A 3PIM becomes an adjustable speed drive motor with the addition of an inverter, an expensive power module that generates three-phase AC power with adjustable frequency and amplitude from a DC supply to vary the speed of the motor. Reducing the frequency allows the motor to start up more gently and efficiently but also reduces the torque supplied. In general, varying the amplitude and frequency of the power provides some flexibility to tune motor operation, but cannot overcome the limitations inherent in the 3PIM's fixed number of poles and the geometric factors that determine the ideal angular velocity of the rotor relative to the stator field precession.

Electronically controlled electric motor


A toothbrush handle includes a support structure formed of clarified polypropylene and a body formed of thermoplastic elastomer disposed on the support structure. The support structure includes a web having a thickness in a first direction orthogonal to an axis of the toothbrush handle of less than 2 millimeters and at least one rib depending from the web and having a thickness in a second direction, orthogonal to the axis and angled relative to the first direction, of less than about 2 millimeters. The body at least partially covers the web and the at least one rib. The handle has a light transmissivity of greater than 40% through a portion of the handle at which the body covers the web and the at least one rib.

Functionality and aesthetics play significant roles in driving consumer demand for manual toothbrushes. Clear, or transparent, toothbrushes, especially toothbrush handles, provide a unique and oftentimes desirable aesthetic. Conventional clear toothbrushes are generally made from polymers or acrylics that maintain clarity at standard toothbrush dimensions. However, those materials tend to be more expensive than polymers generally used in manual toothbrush manufacture and may slow manufacturing throughput. For example, copolyesters have been used to make clear toothbrushes, but such materials have many drawbacks over conventionally-used polymers. Notably, copolyesters take a relatively long time to cure, lengthening the production time. Moreover, copolyesters are generally more expensive than conventional materials.
Accordingly, there is a need in the art for a toothbrush with desirable aesthetics, such as a transparent or semi-transparent appearance, but that is readily manufactured.

Toothbrush with light transmissive handle


A method of measuring mechanical runout including: mounting a work piece on a rotatable mount, wherein the mount is configured to rotate the work piece; placing a displacement sensor at a known position adjacent a surface of the work piece, the displacement sensor being configured to measure a radial dimension of the work piece; attaching a removable angle indicator to the surface of the work piece; rotating the work piece while mounted on the mount and collecting rotational data of the rotational position of the work piece during the rotation; collecting displacement data from the displacement sensor as the work piece rotates, wherein the displacement data indicates a radial distance from a rotational axis of the work piece to the surface of the work piece at points on the surface as the surface rotates with respect to the displacement sensor; analyzing the displacement data to detect data representing the angle indicator on the surface of the work piece; correlating the displacement data with the rotational data, and determining displacements of points on the surface of the work piece based on the correlated displacement data.

The invention relates to measuring mechanical runout of a rotating work piece.
A uniform radius is desirable around the circumference of rotating work pieces such as the rotor work piece of a turbine. Knowing the shape of a work piece relative to ideal roundness may be used to compensate for or reduce vibration induced by rotation of the work piece. Measuring a radius at each circumference along the length of an entire work piece often requires a great deal of time and cost, primarily associated with labor.
"Runout", generally, is the amount of deviation from a desired rotation radius of a rotor during operation, and can be described in terms of mechanical runout and electrical runout. The mechanical runout of a rotor is the deviation from an ideal circular geometry of the rotor plane during rotation. Accurate measurement of the mechanical runout is necessary to be able to minimize the negative impact of these imperfections on performance, such as vibration of the rotor at operational speeds.
In addition to knowing generally the shape of the surface of a mechanical rotor and how far the rotor is from an ideal circular geometry, there is value in knowing the angular position of each piece of surface information relative to some reference point. Therefore, it is desirable to measure mechanical runout as a function of work piece angular position. Currently available options to accurately measure runout as a function of angular position require (1) a human to manually determine and measure an angular position; or (2) the use of phase reference probes.
Measurements taken at speeds of 15% or lower of rated speeds for the work piece in question are called "slow roll mechanical runout." The slow roll mechanical runout provides an indication as to whether the work piece will function properly during normal operation, as it is an indication of the irregularities in surface shape.
Currently, the runout is measured in one of a few ways: (1) a complete manual 12-point runout, (2) a semi-manual 12-point runout, (3) use of a high sample rate digital sensor, i.e., a CL profiler, or (4) use of phase reference indicators, which require additional instrumentation.
Other available runout measurement methods require additional instrumentation. Key phasors, encoders, magnets and magnetic field sensors are potential options. Some options, like phase reference probes, may require the work piece to be altered to create an intentionally-machined discontinuity, such as a slot or key way, to serve as a once-per-revolution indicator. Under this method, phase references probes are positioned over a machined discontinuity in the work piece and provide a once-per-turn reference pulse from which the phase angle of the vibration can be determined.

System and method for mechanical runout measurement