gebhart/patrepeval huggingface dataset:
867. Spliceosome Mediated RNA Trans-Splicing To Increase Blood Levels of Apolipoprotein A-I and High Density Lipoproteins (2006)

Low levels of high density lipoprotein (HDL) represent an important predictor of cardiovascular disease risk1,2. An increase of 1mg/dl in HDL correlates with a risk reduction of cardiovascular disease of 2–3%3. We have adapted spliceosome mediated RNA trans-splicing technology (SMaRT™) to trans-splice the sequences of wild type human apolipoprotein A-I (apoA-I) into the highly abundant albumin pre-mRNA in hepatocytes with the objective of transiently increasing blood levels of HDL. ApoA-I is the major protein component of HDL. We targeted a pre-trans-splicing molecule (PTM) to bind to specific sequences in the first intron of mouse albumin pre-mRNA. The bound PTM will then trans-splice, inserting sequences for human ApoA-I into intron 1 of albumin pre-mRNA. With trans-splicing, apoA-I would be made in hepatocytes, the same cells that naturally synthesize apoA-I. Mincircle plasmids encoding this PTM were hydrodynamically injected into the tail vein of C57Bl/6 mice. Trans-spliced product was detected within 48 hours of injection which resulted in an increase of 20–25 mg/dl HDL in independent experiments. These increases persisted for at least 8 weeks when the studies were terminated; the trans-spliced product could be detected for at least 10 weeks after injection. In a separate study, 10, 25 or 70 ug minicrcle PTM was administered to mice. Plasmids were re-administered eight weeks after the first injection. Following re-administration, apoA-I blood levels increased 3–5x in a dose response fashion, suggesting the absence of immunogenic response to either the transgene or the minicircle plasmid. Since intron sequences are not well conserved among species, a PTM was developed to target intron 1 of human albumin. In comparative studies with in vitro model systems, the PTM targeting the human albumin transcript was approximately 3x more efficient in trans-splicing than its mouse counterpart. In addition, the level of human albumin pre-mRNA was 1.6x that of its mouse counterpart. These results demonstrate that targeting highly abundant transcripts, such as albumin, might be appropriate for in vivo synthesis of therapeutic proteins for the treatment of cardiovascular disease. Literature cited: Brewer, H.B. Amer. Heart J.148:514-S15-S-18, 2004. Castelli, W.P. Can. J. Cardiol. 4 (Suppl A): 5–10A, 1988. Olsson, A.G. et al. Eur Heart J. 26: 890–896, 2005. I have company stock options.
Geometric calibration of multi-projector systems on general display-surfaces (2008)

Multi-projector systems provide scalability for low-cost, high-resolution display needed for many applications including data visualization, telepresence, and ambient or immersive displays. But geometric calibration of the systems is a great challenge, and for many display configurations, existing camera-based techniques are unsatisfactory. A simple, non-parametric robust technique exists for single-camera calibration, but it doesn't scale to high-resolution displays. Scalability can be gained with a parametric model, but general approaches have tended to compromise robustness or accuracy. Special-purpose models have improved the situation, but at the cost of flexibility. We describe a hybrid calibration framework that combines the robustness of non-parametric calibration with the scalability of parametric calibration. 
Each parametric calibration technique has a hybrid cousin. The parametric model is fit just as before, but it is not directly used by the rendering algorithm. Instead, the rendering algorithm resembles a non-parametric renderer–it corrects the rendered output using an interpolated lookup table of correspondences between projector framebuffers and a common space. But the space isn't the camera's image; rather it consists of the screen points reconstructed according to the parametric model. 
By structuring the correspondences and lookup table in a particular way, we are able to ensure that parametric model-fitting error does not hurt the calibration's registration accuracy. We achieve accurate calibration with a general parametric model. Projectors are not modelled, and their radial distortion is corrected implicitly. Multiple cameras are supported. The calibration supports headtracked immersive rendering. 
A number of related and ancillary research contributions are described in this dissertation, including an analysis of resolution loss in two-pass rendering, together with a technique for preventing the loss by dividing the display surface into clusters based on surface normal. Also techniques are described which improve the reliability of the structure from motion estimation needed for calibration. Other contributions include work in precision feature localization and uncertainty estimation, and a technique for calibrating radial distortion using any number of cameras and without knowledge or assumptions about scene structure. 
We believe that this work provides key contributions towards robust, hassle-free strong geometric calibration of wide-area, heterogeneous multi-projector environments. 
Keywords: Projector-Camera Systems, Camera Calibration, Feature Matching, Multi-View Geometry, 3D Reconstruction .
Cutaneous Patches to Monitor Myoelectric Activity of the Gastrointestinal Tract in Postoperative Pediatric Patients (2019)

Measuring myoelectric intestinal activity continuously using a wireless patch system is feasible in a wide age range of pediatric patients. The increase in activity over time correlated well with the patients' return of bowel function. More studies are planned to determine if this technology can predict return of bowel function or differentiate between physiologic ileus and pathologic conditions.
18.4: <i>Distinguished Student Paper</i> : Two‐Color‐Field Sequential Method for Color‐Filter‐Free MVA‐LCDs (2009)

Abstract A novel displaying method, two‐color‐field driving scheme, was proposed for field‐sequential‐color LCDs without color filters. The least number of fields alleviated the demand for fast response LC modes in sequential‐type LCDs. The proposed method reproduced full color images with acceptable colorimetric reproduction accuracy, average ΔE 00ave <3. Furthermore, less chrominance difference between the two fields was beneficial to suppress color break‐up.
Rule-Based Data-Driven Analytics for Wide-Area Fault Detection Using Synchrophasor Data (2016)

Synchrophasor technology, also known as wide-area monitoring system technology, utilizes phasor measurement unit (PMU) to monitor real-time system data, which can provide unique insights into the operation of a power grid. In this paper, a rule-based data-driven analytics method for wide-area fault detection in a power system using synchrophasor data is proposed. As a data-driven approach, this method relies on rules created using PMU measurement data, and does not require knowledge of the power system's topology and model. It can detect fault location (bus and line) and fault type for a particular fault event. Three common types of short circuit faults in a power grid, single-line-to-ground, line-to-line, and three-phase faults, can be identified using the proposed method. Fault thresholds used in rules are determined based on theoretical values and recorded PMU data during fault events in Bonneville power administration (BPA)'s large power grid. The proposed method is validated by comparing with the recorded field data for fault events provided by BPA. It is found that it can effectively detect most faults with a great accuracy. It has been developed into a software program, and can be readily used by utility companies.
Design and fabrication of double chirped mirrors (2005)

We present an analytic design method for the reproducible fabrication of double-chirped mirrors to achieve simultaneously a high reflectivity and dispersion compensation over an extended bandwidth compared with those of standard quarter-wave Bragg mirrors. The mirrors are fabricated by ion beam sputtering. Use of these mirrors in a Ti:sapphire laser leads to 6.5-fs pulses directly out of the laser. The method can also be applied to the design of chirped-fiber gratings and general optical filters.  1997 Optical Society of America Short-pulse generation has advanced to a degree where the bandwidth of standard Bragg mirrors composed of SiO2yTiO2 layer pairs limits the pulse width of ultrashort pulsed lasers. Chirped mirrors 1 overcome the bandwidth limitation and provide simultaneously a means for compensation of the group-delay dispersion in the laser. However, so far the chirped-mirror design has been done by computer optimization, 1 because a simple chirping of the center wavelength of the Bragg mirror is not enough. 2 Chirping would introduce oscillations in the group delay for longer wavelengths, which penetrate deeper into the mirror. The oscillations are due to an effective Gire‐Tournois interferometer. The interferometer is created by partial reflection from the front section of the mirror, which acts as a transmission grating, and the reflection at the back of the mirror, which acts as a Bragg reflector. We present an analytic design for chirped mirrors based on coupled-mode and transmission-line theory. The cause of the oscillations in the group-delay dispersion is identified as an impedance-matching problem. We solve this problem by slowly tapering the impedance, which is shown to be equivalent to a chirp in the thickness of the high-index layer in addition to the chirp of the center wavelength of the Bragg mirror.
Dynamic regulation of microRNA networks in the brainstem underlie hypertension development (686.22) (2014)

This study aims to elucidate the mechanisms by which microRNAs (miRNA) regulate autonomic control networks driving hypertension development. Using a high‐throughput assay for 419 miRNAs in the Spontaneously Hypertensive Rat (SHR) and Wistar‐Kyoto (WKY) control at three key stages of hypertension development, significant differences appear in 23 miRNAs of the nucleus tractus solitarius (NTS) and rostral ventrolateral medulla (RVLM). Alterations were stage‐ and region‐dependent, with significant differences occurring at mid‐stage in NTS vs early‐stage in RVLM. 96 gene targets corresponding to catecholaminergic processes and neuromodulation were predicted using the miRWALK database and tested using high‐throughput qPCR. Using correlational relationships between miRNAs and mRNAs, we observed a double‐negative regulatory motif, which appears prevalent throughout the data. This motif consists of a miRNA down‐regulating a negative regulator of a pro‐hypertensive signaling pathway like Angiontensin II signaling or leukotriene‐based inflammation. We demonstrated for the first time that the broad concordance of microRNA dynamics and target gene expression compose a regulatory network in the brainstem underlying hypertension. Grant Funding Source : Supported by NIGMS R01 GM083108, NHLBI R01 HL111621
Fecal Cyclooxygenase 2 Plus Matrix Metalloproteinase 7 mRNA Assays as a Marker for Colorectal Cancer Screening (2009)

We previously reported that fecal cyclooxygenase 2 (COX-2) mRNA assay, detecting COX-2 mRNA in feces, is useful for identifying subjects with colorectal cancer (CRC). To further improve the sensitivity, we evaluated the usefulness of the combination of COX-2 mRNA and matrix metalloproteinase 7 (MMP-7) mRNA assays as a marker of CRC. The study cohort included 62 patients with CRC and 29 control patients without colorectal neoplasia. RNA was isolated from routinely collected fecal samples. The expression levels of COX-2 and MMP-7 mRNAs were determined by nested reverse transcription-PCR. PCR conditions were optimized where the specificity of fecal COX-2 and MMP-7 mRNA assay result in 100%. The sensitivity of each fecal assay was 87% [95% confidence interval (95% CI), 76-94%] and 65% (95% CI, 51-76%) for CRC, respectively. The sensitivity of fecal RNA test (either marker being positive) was high for CRC (90%; 95% CI, 80-96%). The sensitivity of the fecal RNA test was also high (93%; 95% CI, 80-98%) in patients with stage I or II who are often cured by surgical resection. The fecal RNA test using COX-2 and MMP-7 mRNAs improved the sensitivity to detect CRC without decreasing the specificity. These results suggest that the fecal RNA test would be a promising approach for CRC screening, although larger clinical investigations are indicated.
Synchronization Performance of the Precision Time Protocol (2007)

This paper analyzes the factors that affect the synchronization performance in using the precision time protocol (FTP). We first study the influence of jitter under the assumption of no frequency drifts. Then we study the influence of frequency drift in the absence of jitter. The analytic formulas provide a theoretical ground for the understanding of simulation results as well as guidelines for choosing both system and control parameters when applying FTP.
Solid State Gas Microsensors for Environmental and Industrial Monitoring (1999)

We describe solid state gas microsensor array technology for real-time, low-cost environmental and industrial monitoring. The four-element, surface-micromachined arrays are designed in CMOS technology and consist of multiple platforms called 'microhotplates.' Each microhotplate can be individually addressed, and includes functionality for rapid control and measurement of sensor temperature and gas-induced changes in a sensing film's electrical properties. The array elements can be tuned for specific analytes, by choice of sensing material and the temperature-programs applied, in order to better meet the needs of a particular application. Tin oxide was used as the base sensing material for microhotplates used in these studies. Tin oxide is grown selectively on each individual element within the arrays using a chemical vapor deposition process involving thermal decomposition of tetramethyltin in an argon and oxygen ambient. Catalytic additives, such as Pt, Pd and Cu are surface-dispersed to make the films more selective and sensitive. Detection capabilities for the low power microhotplate sensing technology are being established for target analytes in ambients that are relevant to process control, environmental measurements, and vapor-related remediation studies. We describe the use of these micromachined arrays to detect approximately ppm levels of methanol, benzene and hydrogen in ambient air and to produce analyte-specific signatures using temperature programs, T(t).© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Fabrication and commercialization of scalpel masks (1998)

SCALPEL masks have been fabricated for use in the Proof-of- Lithography system and to demonstrate the feasibility of having them produced by a commercial blank manufacturer and optical mask shops. Masks blanks are formed from 100 mm diameter silicon wafers. A 100-150 nm thick SiN<SUB>x</SUB> layer is LPCVD deposited onto the wafers followed by magnetron sputter deposition of a thin Cr/W metal layer which is used as the scatterer layer for the mask>the mask is supported by an underlying network of struts which are arranged to be compatible with the step and scan writing strategy of the exposure tool and to provide robustness to the mask. Crystallographic wet etching of the silicon wafer forms membranes and struts. To date over 300 mask blanks have been formed and yield data as a function of the thickness of the silicon nitride membrane has been quantified. Recent developments in the mask blank formation process include the production of blanks by MCNC who serve as a commercial source of SCALPEL mask blanks. They have successfully delivered 36 blanks that exhibit equivalent properties to those produced at Lucent. Mask patterning has been performed at the commercial optical mask shops of PHOTRONICS and DUPONT. In this investigation a MEBES exposure system has been used to write patterns. The resist used is ZEP-520 and development and pattern transfer processes are performed in the STEAG-Hammatech spray/spin processing tool. Metrology is performed using a KMS 310 RT optical microscope. Pattern placement accuracy is measured on the LMS 2020 system without modification. The masks are inspected for defects using the optical based KLA 300 series inspection system in a die to die mode and in transmission. Results to date suggest feasibility of producing SCALPEL masks by a commercial blank supplier and by merchant optical mask shops.
Small Molecules in Development for the Treatment of Spinal Muscular Atrophy (2016)

Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease resulting from pathologically low levels of survival motor neuron (SMN) protein. The majority of mRNA from the SMN2 allele undergoes alternative splicing and excludes critical codons, causing an SMN protein deficiency. While there is currently no FDA-approved treatment for SMA, early therapeutic efforts have focused on testing repurposed drugs such as phenylbutyrate (2), valproic acid (3), riluzole (6), hydroxyurea (7), and albuterol (9), none of which has demonstrated clinical effectiveness. More recently, clinical trials have focused on novel small-molecule compounds identified from high-throughput screening and medicinal chemistry optimization such as olesoxime (11), CK-2127107, RG7800, LMI070, and RG3039 (17). In this paper, we review both repurposed drugs and small-molecule compounds discovered following medicinal chemistry optimization for the potential treatment of SMA.
Rule-based construction of matching processes (2011)

Semi-automatic schema matching systems have been developed to compute mapping suggestions that can be corrected by a user. However, constructing and tuning match strategies still requires a high manual effort. We therefore propose a self-configuring schema matching system that is able to automatically adapt to the given mapping problem at hand. Our approach is based on analyzing the input schemas as well as intermediate match results. A variety of matching rules use the analysis results to automatically construct and adapt an underlying matching process for a given match task. The evaluation shows that our system is able to robustly return good quality mappings across different mapping problems and domains.
Research on Maintenance of Driver's Arousal Level Using Steady Running Noise (2011)

In order to prevent a driver from dozing as the result of a low arousal state, the authors generated wake-up sounds by processing the pressure, tonal quality, and rhythm of the steady running noise generated by a car. In this paper, the authors evaluated wake-up sounds in a real environment where music or a radio is being played. The results showed that playing music can generate a transient arousal state. Moreover, playing wake-up sounds along with music can maintain the arousal state for a longer period than playing music alone. In addition, the authors focused on the habituation to wake-up sounds, generated wake-up sounds that made habituation more difficult, and evaluated the sounds’ effectiveness for arousal maintenance. The results showed that the wake-up sounds that prevented habituation could maintain the arousal state for a longer period than the wake-up sounds that did not prevent habituation.
Response of Merkel Cell Polyomavirus-Positive Merkel Cell Carcinoma Xenografts to a Survivin Inhibitor (2013)

Merkel cell carcinoma (MCC) is a neuroendocrine skin cancer associated with high mortality. Merkel cell polyomavirus (MCV), discovered in 2008, is associated with ~80% of MCC. The MCV large tumor (LT) oncoprotein upregulates the cellular oncoprotein survivin through its conserved retinoblastoma protein-binding motif. We confirm here that YM155, a survivin suppressor, is cytotoxic to MCV-positive MCC cells in vitro at nanomolar levels. Mouse survival was significantly improved for NOD-Scid-Gamma mice treated with YM155 in a dose and duration dependent manner for 3 of 4 MCV-positive MCC xenografts. One MCV-positive MCC xenograft (MS-1) failed to significantly respond to YM155, which corresponds with in vitro dose-response activity. Combination treatment of YM155 with other chemotherapeutics resulted in additive but not synergistic cell killing of MCC cell lines in vitro. These results suggest that survivin targeting is a promising therapeutic approach for most but not all MCV-positive MCCs.
Complement peptide C3a inhibits IgEmediated triggering of rat mucosal mast cells (1995)

The relationship between mast cells' secretory response to stimulation via their type 1 Fc epsilon receptors (Fc epsilon RI) and that provided by the C3a fragment of the complement system was investigated in the rat mucosal-type mast cell line RBL-2H3. These cells are known to be unresponsive to the so-called 'peptidergic' stimulus provided by cationic agents, such as anaphylatoxins, neuropeptides or polyamines. We now observed that C3a effectively inhibits the Fc epsilon RI clustering induced secretion of RBL-2H3 cells. This inhibition is dose-dependent and takes place at a C3a concentration range of 0.4-12.5 nM, i.e. at least three orders of magnitude lower than those where this anaphylatoxin exerts its secretory stimulus to 'serosal' mast cells. In order to identify where C3a interferes in the Fc epsilon RI coupling cascade, we have studied its effect on the cells' protein phosphorylation pattern, hydrolysis of phosphatidyl inositides, transient rise in free cytosolic Ca2+ ion concentration and Ca2+ uptake. All these processes were found to be inhibited by a similar C3a concentration range.
Space-time super-resolution (2005)

We propose a method for constructing a video sequence of high space-time resolution by combining information from multiple low-resolution video sequences of the same dynamic scene. Super-resolution is performed simultaneously in time and in space. By "temporal super-resolution," we mean recovering rapid dynamic events that occur faster than regular frame-rate. Such dynamic events are not visible (or else are observed incorrectly) in any of the input sequences, even if these are played in "slow-motion." The spatial and temporal dimensions are very different in nature, yet are interrelated. This leads to interesting visual trade-offs in time and space and to new video applications. These include: 1) treatment of spatial artifacts (e.g., motion-blur) by increasing the temporal resolution and 2) combination of input sequences of different space-time resolutions (e.g., NTSC, PAL, and even high quality still images) to generate a high quality video sequence. We further analyze and compare characteristics of temporal super-resolution to those of spatial super-resolution. These include: How many video cameras are needed to obtain increased resolution? What is the upper bound on resolution improvement via super-resolution? What is the temporal analogue to the spatial "ringing" effect?
Three-dimensional modeling of DCIR and identification of new drugs blocking HIV-1 attachment and propagation (2012)

The HIV-1 pandemic continues to expand while no effective vaccine is yet available. Finding new therapeutic targets and drugs is therefore crucial. We have previously shown that the dendritic cell immunoreceptor (DCIR), a C-type lectin receptor expressed in dendritic cells (DCs), acts as an attachment factor for HIV-1 to DCs and contributes to HIV-1 transmission to CD4+ T lymphocytes (CD4TL). Directly involved in HIV-1 infection, DCIR is expressed in apoptotic or infected CD4TL and promotes trans-infection to bystander cells. The aim of the present study is to characterize the extracellular domain of DCIR and to test chemical inhibitors of HIV-1 attachment thereto.