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Big Data

Name Investigator Tech ID Licensing Manager Name Micensing Manager Email Description Tags
Fast Dynamic Parallel Approximate Neighbor Search Data Structure Using Space Filling Curves Piyush Kumar 16-096 Matthieu Dumont mfdumont@fsu.edu <p>The nearest neighbor search (NNS) is a technique that is used in computing to optimize the amount of time it takes to accurately locate one data point in relation to another data point in a dataset that is organized so that distances between points are measured in Euclidian space. Increasingly, NNS computation is becoming a key sub-task in many algorithms and applications that are used to process, organize, cluster, learn, and understand massive data sets, such as those used in the automotive, aerospace, and geographic information system (GIS) industries.</p> <h2>The Problem:</h2> <p>The NNS algorithm works well for small data sets, but it is too time-consuming to implement with large data sets. The approximate nearest neighbor (ANN) search, an alternative to NNS, improves search time and saves memory by estimating the nearest neighbor, without guaranteeing that the actual nearest neighbor will be returned in every case. Two limitations of this method are that it is difficult to make an ANN algorithm dynamic (i.e., allows for insertions and deletions in the data structure) or to parallelize it (i.e., use multiple processors to speed up queries).</p> <h2>The Solution:</h2> <p>Dr. Kumar and his research team are developing a novel, practical, and theoretically-sound method that will solve the NNS problem in lower dimensional spaces. Specifically, the researchers are creating an approximate k-nearest neighbor algorithm, based on Morton Sorting of points, to create a software library for approximate nearest neighbor searches for Euclidian spaces. The library will use multi-core machines efficiently (parallel) and enable the insertion and deletion of points at run time (dynamic). This new algorithm delivers the search results with expected logarithmic query times that are competitive with or exceed Mount’s approximate nearest neighbor (ANN) search.</p> <h2>Advantages:</h2> <ul> <li>Speed on multicore machines</li> <li><span>Minimum spanning tree computation</span></li> </ul>
A Novel, Screening Assay for Colon and Rectum Cancer, based on a Antibody Specific for a Phosphorylated-Mcm2 at Serine 53 (Mcm2-S53P) Daniel Kaplan 16-093 Brent Edington bedington@fsu.edu <p>Approximately 4.5 percent of men and women will be diagnosed with colon and rectum cancer at some point during their lifetime, based on 2010-2012 data. The earlier colon and rectum cancer is caught, the better chance a person has of surviving five years after being diagnosed. Stool testing is likely to be particularly valuable, because it represents a non-invasive method for screening all of the colon and rectum, without the need for bowel preparation. The Mcm2 protein, a component of the DNA replication apparatus, is currently being developed for its use as an early marker of colorectal cancer in cells from stool washings. Mcm2 is a subunit of the replication fork helicase, the macromolecular assembly that unwinds DNA at a replication fork.</p> <p>Mcm2 lacks specificity because it is present in all stages of the cell cyle. The present invention identifies a novel post-translational modification of Mcm2, wherein the serine 53 residue is phosphorylated (Mcm2-S53P). This technology shows that the human Mcm2-S53P modification is an improved cancer marker compared to human Mcm2, and provides an improved screening array for cancer and other diseases of cell proliferation.</p> <h2>Advantages:</h2> <ul> <li>Higher sensitivity than other currently used markers of cell entry</li> </ul>
Novel Concept and Method for Developing and Screening ADHD Therapeutics Pradeep G. Bhide 15-138 Brent Edington bedington@fsu.edu <p>Attention Deficit Hyperactivity Disorder (ADHD) represents a conglomeration of multiple symptoms including inattention, hyperactivity, impulsivity and deficits in working memory. The proposed research shows that a prenatal nicotine exposure mouse model of ADHD displays each one of these symptoms, and that each symptom may have a distinct neurobiological basis. Moreover, the research using this mouse model suggests that improvement can be achieved in each symptom using a drug or a combination of drugs that selectively target specific neurobiological mechanism(s) underlying the symptom(s). However, at the present time, treatment for ADHD is not directed at tackling specific symptom domains or specific neurobiological mechanisms underlying such symptom domains. Development of drugs to target specific symptom domains or mechanisms is hampered by the lack of animal models that display the entire range of ADHD symptom domains, and in which each symptom domain and neurobiological mechanism can be assayed separately. Our mouse model of prenatal nicotine exposure fills this technological gap. Therefore, we advance the novel concept that drugs to selectively tackle each ADHD symptom domain can be screened using our mouse model. The significance of this concept is that efficacy of novel drugs can be evaluated against one or more specific ADHD symptom domains and their underlying neurobiological mechanisms.</p>
Genome Capture and Sequencing to Determine Genome-Wide Copy Number Variation David Gilbert 14-102 Brent Edington bedington@fsu.edu <p>The present invention provides a means to determine the copy number of genomic segments distributed throughout a genome at considerably reduced time and expense vs. whole-genome sequencing. We have developed a solution-based sequence capture method enabling the capture of an equal amount of sequence space every 10 kilo bases to achieve even coverage of the genome. This reduces the sequence space by approximately 99 percent and ensures the sequencing of genomic information at evenly spaced locations across the genome, providing resolution close to the spacing of the probes. The technology measures replication timing and copy number variation (CNV) in human pediatric acute lymphocytic leukemia samples, but it will be broadly applicable to any CNV application.  </p>
Fingerprint for Cell Identity and Pluripotency David Gilbert 12-028 Brent Edington bedington@my.fsu.edu <p>At Florida State University, we have developed a method to identify sets of regions that replicate at unique times in any given cell type (replication timing fingerprints) using pluripotent stem cells as an example, and show that genes in the pluripotency fingerprint belong to a class previously shown to be resistant to reprogramming in induced pluripotent stem cells (iPSCs), identifying potential new target genes for more efficient iPSC production. We propose that the order in which DNA is replicated (replication timing) provides a novel means for classifying cell types, and can reveal cell type specific features of genome organization.</p> <p>A major advantage of our fingerprinting method is in selection of a minimal set of regions that allow for classification with a straightforward PCR-based timing assay and a reasonably small set of primers, particularly if only cell-type specific regions are examined. Our results suggest that a standard set of 20 fingerprint loci can be effective for classification, but the number of regions queried can be adjusted based on the confidence level required. The sole requirement for replication profiling is the collection of a sufficient number of proliferating cells for sorting on a flow cytometer. Consistently, just as replication fingerprints can be generated for particular cell types or general categories of cells, features of replication profiles allow for the creation of disease-specific fingerprints, which may be valuable for prognosis. We have also identified regions that may undergo important organizational changes upon differentiation.</p>
Liposome Micro- and Nano-Arrays for Molecular Screens in Cell Culture Dr. Lenhert 11-191 Brent Edington bedington@fsu.edu <p>The proposed invention describes the use of surface supported liposome arrays as a platform for screening of molecular libraries in cell culture models. Drug candidates encapsulated into surface supported liposomes are arrayed on a surface to form lipid multilayer arrays. The surface has been functionalized to ensure liposome uptake by the cells. Cells are cultured on these arrays and their response to the liposomes are monitored optically. Multiple liposome compositions and different lipids or other additives printed onto the same surface can be simultaneously screened. The drugs that are and are not working can be determined by their position on the surface.</p> <p>Contrarily to actual small molecule microarrays for drug screening strategies our invention does not require to covalently attach to a surface, and cells can be grown on the surface. Covalent attachment of the small molecule on the surface prevents internalization of the compounds, limiting the types of tests that can be carried out. Furthermore, the number of molecules that a single cell can see is limited by the surface it contacts. Diffusion of small molecules from array sources, such as gels has also been used for screening, although molecular diffusion limits applicability of those methods. Using surface supported lipid multilayers encapsulating drug candidates solves these problems.</p> <h2>Applications:</h2> <ul> <li>Screening of delivery systems, particularly for lipophilic drug candidates</li> <li>Drug resistance cell screening, where cells from biopsies are cultured ex situ</li> </ul>
Method to Increase Dynamic Range of Segmented Non-Linear Devices Kurtis Johnson 10-048 Robby Freeborn-Scott cfreebornscott@fsu.edu <p>The present invention describes a method to increase the dynamic range of a solid-state monolithic device such as a silicon photomultiplier (SiPM). In this method, the incoming flux of photons is rendered non-uniform allowing a significant increase in the useful dynamic range achieved. The desired distortion of the incoming flux can be obtained in a variety of ways. These include simple non-focused lenses, prisms, interference films, mirrors, and attenuating films. Virtually any device which distorts the incoming flux will increase the dynamic range of the SiPM and combinations may be used to tailor the response to a desired application.</p> <p>In addition to silicon photomultiplier, the present inventive method can be applied to a wide range of non-linear detectors, sensors, or transducers. This invention enables an inexpensive jump in dynamic range which otherwise would only be attained by awaiting a new round of silicon chip production and masking.</p>
Pressure Sensors including an Ionic Conduction Sensing Mechanism Dr. Liu 08-132 Abby Queale aqueale@fsu.edu <p>The present invention describes thin film sensors for detecting the presence, intensity, and/or location of a compressive force, or pressure based on ionic conduction variation as the sensing principle. Upon wisely choosing soft materials-- elastomer-like polymer and polymeric gel electrolytes/polymer electrolytes in combination with appropriate patterning, the present invention offers low pressure level sensing and mapping capability with enhanced sensitivity. The sensor includes a plurality of conducting elements spaced apart from each other and at least one deformable electrolyte bridge contacting each of the conducting elements at one or more contact points having an aggregate contact area. Upon formation of an ionic circuit between two of the conducting elements, a first resistivity between the two conducting element exists. Upon application of a compressive force on the at least one deformable electrolyte bridge directed toward at least one of the conducting elements, the aggregate contact area increases such that a second resistivity between the two conducting elements exists. The difference between the first and second resistivity can be correlated with the pressure or mechanical displacement to be measured.</p> <h2>Applications:</h2> <ul> <li>This invention has numerous potential application in pressure sensing and mapping, e.g., seat occupancy detection for the automobile industry, tactile feedback for robots to sense and respond to environments, rehabilitation progress monitoring of a patient for the medical industry, biting force mapping in dentistry application, or measuring force on golf club grips.</li> </ul>
The Lookahead Instruction Fetch Engine (LIFE) Dr. David Whalley 08-033 Dr. Matthieu Dumont mfdumont@fsu.edu <p>The Lookahead Instruction Fetch Engine (LIFE) provides a mechanism to guarantee instruction fetch behavior in order to avoid access to fetch-associated structures, including the level one instruction cache (Ll IC), instruction translation look aside buffer (ITLB), branch predictor (BP), branch target buffer (BTB), and return address stack (RAS). Systems and methods may be provided for lookahead instruction fetching for processors. The systems and methods may include an L1 instruction cache, where the L1 instruction cache may include a plurality of lines of data, where each line of data may include one or more instructions. The systems and methods may also include a tagless hit instruction cache, where the tagless hit instruction cache may store a subset of the lines of data in the L1 instruction cache, where instructions in the lines of data stored in the tagless hit instruction cache may be stored with metadata indicative of whether a next instruction is guaranteed to reside in the tagless hit instruction cache, where an instruction fetcher may be arranged to have direct access to the L1 instruction cache and the tagless hit instruction cache, and where the tagless hit instruction cache may be arranged to have direct access to the L1 instruction cache.</p> <p>LIFE can both reduce energy consumption and power requirements with no or negligible impact on application execution times. It can be used to reduce energy consumption in embedded processors to extend battery life. It can be used to decrease power requirements of general purpose processors to help address heat issues. LIFE, unlike most energy saving features, does not come at the cost of increased execution time. It will result in a significant improvement over the state of the art and will extend the life of batteries making mobile computing more practical. Finally, it will allow general-purpose processors to run at a faster clock rate with similar heat being generated.</p>
Lipid Multi-Layer Gratings for Semi-Synthetic Quorum Sensors Dr. Lenhert 11-067 Brent Edington bedington@fsu.edu <p>The present invention provides a device comprising: a substrate, and a quorum sensor array on the substrate. The quorum sensor array comprises quorum sensors releasing signal molecules in response to one or more environmental signals being sense by the quorum sensors to thereby amplify the one or more environmental signals by causing a signal chain reaction in neighboring quorum sensors of the quorum sensor array, and wherein each of the quorum sensors comprises a lipid multi-layer structure.</p> <p>The present invention provides a method comprising the following steps: (a) detecting with a camera one or more light intensities of light scattered by one or more iridescent microstructures of a sample, and (b) determining a height of each of the one or more iridescent microstructures of the sample based on one or more light intensities detected in step (a) and a calibration profile for the camera, wherein the calibration profile is based on light intensities detected by the camera for light scattered one or more patterned arrays of standard iridescent microstructures of a calibration standard, and wherein each of the patterned arrays of iridescent microstructures comprises iridescent microstructures having the same shape and two or more different heights.</p>
A Robust Method to Measure the Temporal Order of Replication of all Chromosome Segments in a Cell Dr. Gilbert 12-102 Brent Edington bedington@fsu.edu <p>Cancers have unique replication timing fingerprints that hold great promise as a novel genre of biomarkers, and despite the heterogeneity in different individual cancers, each cancer more closely resemble their tissue of origin than they do other tissue types. This phenomenon demonstrates the great promise of replication timing profiling to determine tissue of origin for metastatic cancers.</p> <p><span style="font-family: inherit; font-size: 0.875rem; line-height: 1.4;"></span>There are many biomarkers on the market for cancer and most involve tests for chromosome abnormalities while some involve gene expression tests. Currently biomarkers are only partially effective at diagnosis. Our technology provides a completely novel genre of biomarkers that cannot be detected by any other existing method.</p> <p>This technology can provide a completely novel type of tissue of origin test, and queries the entire genome simultaneously and therefore is more comprehensive.</p>
Photosynthetic Transcription Factors that Determine Bundle Cell Fate and Function Hongchang Cui 13-087 Brent Edington bedington@fsu.edu <p>Photosynthesis is one of the most important reactions on the earth because its products are the ultimate energy source for all living organisms and the food of the human beings. Depending on the number of carbon atoms in the initial organic compound made in photosynthesis, plants can be grouped into C3 or C4 plants. C4 plants are evolved from C3 plants, but they have several features that make them much more efficient photosynthetically than C3 plants:</p> <ol> <li>The enzyme for C02 fixation, called PEP carboxylase, is not inhibited by oxygen. In contrast, the C02 fixation enzyme in C3 plants, called RUBICO carboxylase, has an oxygenase activity, which reverses the photosynthetic reaction. The oxygenase activity is favored at high light and high temperature, making C3 plants perform even worse in warm area where crop yield potential is high.</li> <li>C02 fixation occurs in the mesophyll cells, whereas C3-type photosynthesis is performed in the bundle sheath (BS) cells, which surround the vascular tissue, using the C02 concentrated by and supplied from mesophyll cells.</li> <li>There are more vascular bundles (veins), hence more BS cells, and a greater number of channels between BS and mesophyll cells, which ensures rapid transport between these two cell types. C4 plants are also efficient in water utilization. Because many important crops are C3 plants, such as rice and wheats, huge resources have been invested to introduce C4 photosynthesis into C3 plants. Although BS cells are also present in C3 plants, they generally contribute little to photosynthesis and this cell type has therefore become a primary target for C3-to-C4 bioengineering. Despite extensive research, until now the mechanism that controls BS cell fate is still unknown.</li> </ol> <p>Our work identified three transcription factors (SCR, SCL23 and SHR) that are required for BS cell fate specification in Arabidopsis, a model C3 plant. SCR and SCL23 are both expressed specifically in BS cells. Though they act redundantly in determining the BS cell fate, they have distinct functions. Because similar genes are present in other plant species, including rice and maize, which is a C4 plant, we believe that similar mechanisms control BSC cell fate determination in all C3 and C4 plants. These bundle sheath cell determinants offer a novel and powerful tool for the C3-to-C4 engineering, which is regarded as a key solution to the demand for food and biomass by a rapidly growing world population.</p>
System and Method of Probabilistic Passwords Cracking Dr. Sudhir Aggarwal 11-189 Dr. Matthieu Dumont mfdumont@fsu.edu <p>Professor Aggarwal and his team have created a  system and method of probabilistic passwords cracking.</p> <p>This technology is a novel password cracking system that generates password structures in highest probability order. Our program, called UnLock, automatically creates a probabilistic context-free grammar (CFG) based upon a training set of previously disclosed passwords.</p> <p>This CFG then allows to generate word-mangling rules, and from them, password guesses to be used in password cracking attacks.</p> <h2>Advantages:</h2> <ul> <li>Effectiveness demonstrated on real password sets</li> <li>Technology capable to crack 36% to 93% more passwords than John the Ripper, a publicly available standard password cracking program.</li> <li>Tested in digital forensic missions</li> </ul>
System and Methods for Analyzing and Modifying Passwords Dr. Sudhir Aggarwal 12-044 Dr. Matthieu Dumont mfdumont@ufl.edu <p>Professor Aggarwal's team developed a system for analyzing and modifying passwords in a manner that provides a user with a strong and usable/memorable password. The user would propose a password that has relevance and can be remembered. The invention would evaluate the password to ascertain its strength. The evaluation is based on a probabilistic password cracking system that is trained on sets of revealed passwords and that can generate password guesses in highest probability order. If the user's proposed password is strong enough, the proposed password is accepted. If the user's proposed password is not strong enough, the system will reject it. If the proposed password is rejected, the system modifies the password and suggests one or more stronger passwords. The modified passwords would have limited modifications to the proposed password. Thus, the user has a tested strong and memorable password.</p>
Sub-seasonal Forecasts of Winter Storms and Cold Air Outbreaks Dr. Ming Cai 16-090 Dr. Matthieu Dumont mfdumont@fsu.edu <p style="font-size: 18px;" class="font_8"> </p> <p class="lead">"Our technology is a dynamics-statistics hybrid model to forecast continental-scale cold air outbreaks 20-50 days in advance beyond the 2-week limit of predictability for weather."</p> <p style="font-size: 18px;" class="font_8"> </p> <p style="font-size: 18px;" class="font_8"><span style="font-size: 18px;">Professor Cai's team has developed a technology that allows them to make Sub-seasonal forecasts for cold air outbreaks in winter season. These forecasts are made on the basis of the relationship of the atmospheric mass circulation intensity and cold air outbreaks. The atmospheric poleward mass circulation aloft into the polar region, including the stratospheric component, is coupled with the equatorward mass circulation out of the polar region in the lower troposphere. The strengthening of the later is responsible for cold air outbreaks in mid-latitudes.</span></p> <p style="font-size: 18px;" class="font_8"><span style="font-size: 18px;">Due to the inherent predictability limit of 1-2 weeks for numerical weather forecasts, operational numerical weather forecast models no longer have useful forecast skill for weather forecasts beyond a lead time of about 10 days. Recently, the research carried out by Professor Cai and his team shows that operational numerical weather forecast models do possess useful skill for atmospheric anomalies over the polar stratosphere in cold seasons owing the models' ability to capture the poleward mass circulation into the polar stratosphere.</span></p> <p style="font-size: 18px;" class="font_8"><span style="font-size: 18px;">They calculate the stratospheric mass transport into the polar region from forecast outputs of the US NOAA NCEP's operational CFSv2 model and use it as our forecasts for the strength of the atmospheric mass circulation. The anomalous strengthening of it is indicative of the high probability of occurrence of cold air outbreaks in mid-latitudes.They further derive a set of forecasted indices describing a state of stratospheric mass circulation to obtain detailed spatial pattern and intensity of the associated cold air outbreak events. </span></p> <p style="font-size: 18px;" class="font_8"><span style="font-size: 18px;">Because cold air outbreak events are accompanied with development of low and high pressure systems and frontal circulations, our forecasts of cold air outbreaks are also indicative of snow, frozen rain, high wind, icy/freezing and other winter storm related hazards besides a large area of below-normal cold temperatures.</span></p> <p><a href="http://www.amccao.com/">Forecast website: http://www.amccao.com/</a></p> <p><a href="https://weather.com/news/weather/news/snow-siberia-russia-united-states-cold">Professor Cai in the news</a></p> <p> </p>
Systems and Methods for Improving Processor Efficiency Dr. David Whalley 13-101 Dr. Matthieu Dumont mfdumont@ufl.edu <p>Dr. Whalley's team has created  a data cache systems designed to enhance energy efficiency and performance of computing systems. A data filter cache herein may be designed to store a portion of data stored in a level one (L1) data cache. The data filter cache may reside between the L1 data cache and a register file in the primary compute unit. The data filter cache may therefore be accessed before the L1 data cache when a request for data is received and processed. Upon a data filter cache hit, access to the L1 data cache may be avoided. The smaller data filter cache may therefore be accessed earlier in the pipeline than the larger L1 data cache to promote improved energy utilization and performance. The data filter cache may also be accessed speculatively based on various conditions to increase the chances of having a data filter cache hit.</p> <p>Furthermore,  tagless access buffers (TABs) can optimize energy efficiency in various computing systems. Candidate memory references in an L1 data cache may be identified and stored in the TAB. Various techniques may be implemented for identifying the candidate references and allocating the references into the TAB. Groups of memory references may also be allocate to a single TAB entry or may be allocated to an extra TAB entry (such that two lines in the TAB may be used to store L1 data cache lines), for example, when a strided access pattern spans two consecutive L1 data cache lines. Certain other embodiments are related to data filter cache and multi-issue tagless hit instruction cache (TH-IC) techniques.</p>
System and method for Generating a Benchmark Dataset for Real noise Reduction Evaluation Dr. Adrian Barbu 15-046 Dr. Matthieu Dumont mfdumont@fsu.edu <p>Often images taken with smartphones or point-and-shoot digital cameras come out noisy due to lack of sufficient lighting. This low-light noise problem is widespread, being present in all of the smartphones in the world, more than 1 billion total. This problem generates in consumers disappointment and frustration with the quality of the images taken in low light. While a number of commercial denoising packages are already available on the market, the majority of them are trained on images corrupted by artificial noise, rather than trained on real low-light noisy images. Since artificial noise has different characteristics than real noise, these packages do not perform as well as a denoising algorithm trained on images corrupted by real noise as we have created.</p> <p>                We have developed a fully automatic state of the art algorithm (RENOIR) for denoising smartphone and digital camera images which have low-light noise problems. The RENOIR algorithm could be either; be sold directly to the public as a standalone application or could be licensed to smartphone or digital camera manufacturers to be embedded in their devices.</p> <p> </p>
Intelligent Wi-Fi Packet Relay Protocol Dr. Zhenghao Zhang 13-089 Dr. Matthieu Dumont mfdumont@fsu.edu <p>L2Relay is a novel packet relay protocol for Wi-Fi networks that can improve the performance and extend the range of the network. A device running L2Relay is referred to as a relayer, which overhears the packet transmissions and retransmits a packet on behalf of the Access Point (AP) or the node if no acknowledgement is overheard. L2Relay is ubiquitously compatible with all Wi-Fi devices. L2Relay is designed to be a layer 2 solution that has direct control over many layer 2 functionalities such as carrier sense. Unique problems are solved in the design of L2Relay including link measurement, rate adaptation, and relayer selection. L2Relay was implemented in the OpenFWWF platform and compared against the baseline without a relayer as well as a commercial Wi-Fi range extender. The results show that L2Relay outperforms both compared schemes.</p>