gebhart/patrepeval huggingface dataset:
<title>Registration of CT and MR brain images using a combination of points and surfaces</title> (1995)

In this paper we present a hybrid registration technique that uses a weighted combination of several feature shapes, e.g. points and surfaces. The technique is a modification of Besl & McKay's iterative closest point (ICP) algorithm (IEEE Trans. Pattern Anal. Mach. Intell., 14:239-256, 1992). We use the technique to register x-ray computed tomography (CT) and T2-weighted magnetic resonance (MR) volume head images acquired from eleven patients that underwent craniotomies in a neurosurgical clinical trial. Each patient had five external markers attached to transcutaneous posts screwed into the outer table of the skull. We define registration error as the distance between corresponding marker positions after registration and transformation. The CT and MR images are registered using points (marker positions) only, surfaces only, and a weighted combination of points and surfaces. The CT surfaces are derived from contours corresponding to the inner surface of the skull. The MR surfaces are derived from contours corresponding to the cerebrospinal fluid (CSF)-dura interface. Registration using points and surfaces is more accurate than registration using only points or surfaces.
Measurement extents and sampling intervals for multiple-bounce SAR image formation (2004)

Recent analysis has resulted in an innovative technique for forming spotlight synthetic aperture radar (SAR) images without the multiple-bounce (MB) ghosting artifacts that arise in traditional methods. This paper develops expressions for the measurement extents and sampling intervals in both frequency and aperture angle, which are required for a desired image resolution and extent in terms of the down-range coordinate, the cross-range coordinate, and the multiple-bounce or "delay" coordinate. The resulting analysis is validated via simulated frequency response data that includes the effects of multiple-bounce scattering.
Electrochemical Detection of <i>Pseudomonas aeruginosa</i> in Polymicrobial Environments (2018)

Abstract A major cause of hospital‐acquired infections is Pseudomonas aeruginosa , a gram‐negative bacterial pathogen. This bacterium secretes a unique, redox‐active molecule known as pyocyanin that can serve as a useful biomarker for identification and detection of this opportunistic pathogen. This current study investigates the impact to pyocyanin production and ability to electrochemically distinguish pyocyanin when P. aeruginosa is co‐cultured with other bacterial pathogens. To accomplish this, P. aeruginosa was co‐cultured with up to four different clinically‐relevant bacteria typically found in a wound infection. P. aeruginosa ’s production of pyocyanin was electrochemically monitored over a three day period and the results demonstrated that pyocyanin can be readily measured and that there were no observed enhancements or inhibitory effects to the production of pyocyanin. This information is valuable in the development of this sensing platform for clinical point‐of‐care diagnostics, where polymicrobial growth at the site of infection is common.
Development of a POC Test for TB Based on Multiple Immunodominant Epitopes of M. tuberculosis Specific Cell-Wall Proteins (2014)

The need for an accurate, rapid, simple and affordable point-of-care (POC) test for Tuberculosis (TB) that can be implemented in microscopy centers and other peripheral health-care settings in the TB-endemic countries remains unmet. This manuscript describes preliminary results of a new prototype rapid lateral flow TB test based on detection of antibodies to immunodominant epitopes (peptides) derived from carefully selected, highly immunogenic M. tuberculosis cell-wall proteins. Peptide selection was initially based on recognition by antibodies in sera from TB patients but not in PPD-/PPD+/BCG-vaccinated individuals from TB-endemic settings. The peptides were conjugated to BSA; the purified peptide-BSA conjugates striped onto nitrocellulose membrane and adsorbed onto colloidal gold particles to devise the prototype test, and evaluated for reactivity with sera from 3 PPD-, 29 PPD+, 15 PPD-unknown healthy subjects, 10 patients with non-TB lung disease and 124 smear-positive TB patients. The assay parameters were adjusted to determine positive/negative status within 15 minutes via visual or instrumented assessment. There was minimal or no reactivity of sera from non-TB subjects with the striped BSA-peptides demonstrating the lack of anti-peptide antibodies in subjects with latent TB and/or BCG vaccination. Sera from most TB patients demonstrated reactivity with one or more peptides. The sensitivity of antibody detection ranged from 28-85% with the 9 BSA-peptides. Three peptides were further evaluated with sera from 400 subjects, including additional PPD-/PPD+/PPD-unknown healthy contacts, close hospital contacts and household contacts of untreated TB patients, patients with non-TB lung disease, and HIV+TB- patients. Combination of the 3 peptides provided sensitivity and specificity>90%. While the final fully optimized lateral flow POC test for TB is under development, these preliminary results demonstrate that an antibody-detection based rapid POC lateral flow test based on select combinations of immunodominant M. tb-specific epitopes may potentially replace microscopy for TB diagnosis in TB-endemic settings.
Antibody buffering of a ligand<i>in vivo</i> (2004)

Clearance is the practical limit on drug action. Here we propose a means of slowing clearance, thereby extending drug lifetime in vivo by "antibody buffering." In this process, a drug and an anti-drug antibody are coadministered. Most of the drug is bound to the antibody, preventing the drug from acting, but also preventing its elimination. A dynamic free drug pool is established by reversible dissociation from the antibody. The free drug is active and can be eliminated, but the free pool is constantly replenished by reequilibration from the antibody-drug complex, giving a long effective lifetime. Here we explore antibody buffering experimentally by using a model compound, 2-phenyloxazol-5-one-gamma-aminobutyrate (Ox), as a drug proxy. We show that antibody buffering can extend by an order of magnitude the plasma lifetime of Ox in rats, and that the steady-state Ox level depends on the molecular properties of the antibody used to buffer the Ox. In addition, the anti-Ox antibody can be recharged with drug in vivo to extend Ox lifetime without additional antibody administration, making this technique even more suitable for possible clinical application.
A novel approach to thermoelectrics materials research of skutterudites (2002)

In recent years, attention has been refocused on thermoelectric materials research because of the interesting crystal structure and transport properties of the skutterudite family of compounds. The interest in this material system arises from its marked reduction in lattice thermal conductivity where the voids in the crystal structure are filled with "guest" atoms. The disorder resulting from these atomic inclusions acts as an excellent phonon-scattering mechanism, although this mechanism(s) is not as yet totally understood. In this paper we introduce a novel synthesis approach for the continuing investigation of this interesting crystal system.
The Role of the Active Site Cysteine in Catalysis by Type 1 Iodothyronine Deiodinase* (1997)

Type 1 iodothyronine deiodinase (deiodinase 1) is a selenoenzyme that converts the prohormone T4 to the active thyroid hormone T3 by outer ring deiodination or to the inactive metabolite rT3 by inner ring deiodination. Although selenocysteine has been demonstrated to be essential for the biochemical profile of deiodinase 1, the role of a highly conserved, active site cysteine (C124 in rat deiodinase 1) has not been defined. The present studies examined the effects of a Cys124Ala mutation on rat deiodinase 1 enzymatic function and substrate affinity. At a constant 10-mM concentration of dithiothreitol (DTT), the C124A mutant demonstrated a 2-fold lower apparent maximal velocity (Vmax) and Km for rT3 (KmrT3) than the wild type for outer ring deiodination, whereas the Vmax/Km ratio was unchanged. Similarly, the apparent Vmax and KmT3 sulfate for inner ring deiodination were 2-fold lower in the C124A mutant relative to those in the wild type, with no change in the Vmax/Km ratio. The C124A mutant exhibited ping-pong kinetics in the presence of DTT, and substitution of the active site cysteine increased the KmDTT by 14-fold relative to that of the wild-type enzyme, with no significant effects on KmrT3 or Vmax. The C124A mutant was inhibited by propylthiouracil in an uncompetitive fashion and exhibited a 2-fold increase in K(i)propylthiouracil compared with that of the wild type. KmrT3 was also reduced for the C124A mutant when 5 mM reduced glutathione, a potential physiological monothiol cosubstrate, was used in outer ring deiodination assays. These results demonstrate that thiol cosubstrate interactions with C124 in type 1 deiodinase play an important role in enhancing catalytic efficiency for both outer and inner ring deiodination.
Accurate Differentiation Between Irritable Bowel Syndrome And Inflammatory Bowel Disease Using Novel Biomarkers from Peripheral Blood Specimens (2009)

Purpose: Accurate laboratory differentiation of Irritable Bowel Syndrome (IBS) from Inflammatory Bowel Disease (IBD) would have great clinical utility for primary care physicians and gastroenterologists. We describe here a gene expression biomarker set that distinguishes patients with IBS from patients with IBD. Methods: In an effort to discover a molecular profile diagnostic for differentiation of IBS from IBD we investigated 10 genes that were previously identified by application of Exagen's proprietary in silico data analysis engine1 CopernaTM to publicly available full-genome expression microarray data from 85 IBD patients and 42 normal controls2. The expression levels of those 10 discovery phase genes were assayed in a clinical study of independently ascertained, consecutively enrolled, prospective cohorts of 98 patients with IBS and 189 patients with IBD (91 with Ulcerative Colitis, 98 with Crohn's Disease). Each patient was diagnosed by a board-certified gastroenterologist; IBD was confirmed by biopsy and IBS met Rome I criteria. All protocols were IRB approved; informed consent was obtained and peripheral blood samples and clinical data were collected from all patients. Expression data was obtained from peripheral whole blood samples (with no mononuclear enrichment) by isolating total mRNAs, synthesizing cDNAs, and performing real-time quantitative PCR. Expression levels of the 10 candidate biomarker genes were assayed on each patient specimen and normalized to a within-patient reference gene. Results: An optimal scoring algorithm for classification of patients as IBS or IBD was derived based on 7 of the 10 tested genes (BLCAP, CALM3, GPX1, HIST1H2BK, PPP2R5A, RAP1A, UBE2G1). The classification of patients by clinical diagnosis and test result is given in Table 1. The diagnostic performance of the classification is summarized in Table 2.Table 1: Classification by 7-gene IBS/IBD differential biomarkerTable 2: Diagnostic performance of 7-gene IBS/IBD differential biomarkerConclusion: The genes identified as differentiating between IBS and IBD in this study have potential as a clinical laboratory diagnostic test.
CD4 mimetics sensitize HIV-1-infected cells to ADCC (2015)

HIV-1-infected cells presenting envelope glycoproteins (Env) in the CD4-bound conformation on their surface are preferentially targeted by antibody-dependent cell-mediated cytotoxicity (ADCC). HIV-1 has evolved a sophisticated mechanism to avoid exposure of ADCC-mediating Env epitopes by down-regulating CD4 and by limiting the overall amount of Env at the cell surface. Here we report that small-molecule CD4-mimetic compounds induce the CD4-bound conformation of Env, and thereby sensitize cells infected with primary HIV-1 isolates to ADCC mediated by antibodies present in sera, cervicovaginal lavages, and breast milk from HIV-1-infected individuals. Importantly, we identified one CD4 mimetic with the capacity to sensitize endogenously infected ex vivo-amplified primary CD4 T cells to ADCC killing mediated by autologous sera and effector cells. Thus, CD4 mimetics hold the promise of therapeutic utility in preventing and controlling HIV-1 infection.
Evolution Strategies for Robust Optimization (2006)

In this paper, we propose two evolutionary strategies for the optimization of problems with actuator noise as encountered in robust optimization, where the design or objective parameters are subject to noise: the ROSAES and the ROCSAES. Both algorithms use a control rule for increasing the population size when the residual error to the optimizer state has been reached. Theoretical analysis has previously shown that the residual error depends among other factors on the population size and on the variance of the noise. Furthermore, ROSAES exploits the similarity of the mutation term in evolutionary strategies and the additive noise term in the case of actuator noise. The population variance is controlled to guarantee that the realized noise level is adjusted correctly. Simulations are carried out on test functions and the results are analyzed with respect to the performance and the dependence of ROSAES and ROCSAES on newly introduced exogenous strategy parameters.
Fabrication of high frequency ultrasonic transducer arrays using physical vapor deposition [for in vivo imaging] (2003)

Creare is developing microfabrication techniques to manufacture low-cost, multi-dimensional ultrasonic transducer arrays with single- and multi-layer piezoelectric elements. The fabrication approach is scaleable for manufacturing arrays in the frequency range of 10-500 MHz in dense or sparse array designs. Our approach employs the following processes: (1) high-rate physical vapor deposition (sputtering) of high-quality piezoelectric films using reactive sputtering of a metallic target and (2) photolithography and masking to provide the interlayer electrodes. This transducer technology has the potential to provide new tools to the clinician which should enable higher resolution ultrasound imaging and miniaturization of ultrasound arrays for in vivo imaging.
Deep sequencing of phage-displayed peptide libraries reveals sequence motif that detects norovirus (2016)

Norovirus infections are the leading cause of non-bacterial gastroenteritis and result in about 21 million new cases and $2 billion in costs per year in the United States. Existing diagnostics have limited feasibility for point-of-care applications, so there is a clear need for more reliable, rapid, and simple-to-use diagnostic tools in order to contain outbreaks and prevent inappropriate treatments. In this study, a combination of phage display technology, deep sequencing and computational analysis was used to identify 12-mer peptides with specific binding to norovirus genotype GI.1 virus-like particles (VLPs). After biopanning, phage populations were sequenced and analyzed to identify a consensus peptide motif-YRSWXP. Two 12-mer peptides containing this sequence, NV-O-R5-3 and NV-O-R5-6, were further characterized to evaluate the motif's functional ability to detect VLPs and virus. Results indicated that these peptides effectively detect GI.1 VLPs in solid-phase peptide arrays, ELISAs and dot blots. Further, their specificity for the S-domain of the major capsid protein enables them to detect a wide range of GI and GII norovirus genotypes. Both peptides were able to detect virus in norovirus-positive clinical stool samples. Overall, the work reported here demonstrates the application of phage display coupled with next generation sequencing and computational analysis to uncover peptides with specific binding ability to a target protein for diagnostic applications. Further, the reagents characterized here can be integrated into existing diagnostic formats to detect clinically relevant genotypes of norovirus in stool.
Reduction of steelmaking slag using closed type DC arc furnace (2015)

The closed type DC arc furnace was investigated as a smelt reduction furnace for reducing steelmaking slag, especially molten hot slag. The reduction capability and its characteristics in DC arc fu ...
P‐1.8: External Compensation for TFT Vth&Mobility Using Linear Charge Sense Method in AMOLED Display (2018)

A new method for Sense and Calculate TFT characteristics is simulated with 3T1C structure of AMOLED display. By using data programming compensation, it can correct both Vth and Mobility. The proposed method uses Linear Charging Method which has faster charging speed than Source Follower Method. By increasing the Vgs of driving TFT, we can even reduce the charging time to 0.5ms. And fast charging make it possible to achieve real‐time detection in higher and higher resolution display. The principle of the method will be described in detail and giving out the simulation data. The experiments are carried out in a 31‐inch AMOLED panel.
Soft-feature decoding for speech recognition over wireless channels (2002)

A distributed automatic speech recognition (ASR) system is considered where features of the speech signal are extracted at the wireless terminal and transmitted to a centralized ASR server. An unequal error protection scheme is used for the quantized ASR feature stream. At the receiver, coherent demodulation is performed and the probability of error for each bit is computed using the max-log MAP algorithm. A 'soft-feature' decoding strategy is introduced at the ASR server that uses the marginal distribution of only the reliable features during likelihood computation. Alternatively, the confidence of each feature is computed from the bit error probabilities and each feature in the probability computation is weighted as a function of the feature confidence. The performance of the proposed soft-feature algorithms is evaluated over typical cellular wireless channels and it is shown to reduce ASR error rate by over 50% for certain channels at a small additional computational cost.
Down-regulation of the<i>IbEXP1</i>gene enhanced storage root development in sweetpotato (2012)

The role of an expansin gene (IbEXP1) in the formation of the storage root (SR) was investigated by expression pattern analysis and characterization of IbEXP1-antisense sweetpotato (Ipomoea batatas cv. Yulmi) plants in an attempt to elucidate the molecular mechanism underlying SR development in sweetpotato. The transcript level of IbEXP1 was high in the fibrous root (FR) and petiole at the FR stage, but decreased significantly at the young storage root (YSR) stage. IbEXP1-antisense plants cultured in vitro produced FRs which were both thicker and shorter than those of wild-type (WT) plants. Elongation growth of the epidermal cells was significantly reduced, and metaxylem and cambium cell proliferation was markedly enhanced in the FRs of IbEXP1-antisense plants, resulting in an earlier thickening growth in these plants relative to WT plants. There was a marked reduction in the lignification of the central stele of the FRs of the IbEXP1-antisense plants, suggesting that the FRs of the mutant plants possessed a higher potential than those of WT plants to develop into SRs. IbEXP1-antisense plants cultured in soil produced a larger number of SRs and, consequently, total SR weight per IbEXP1-antisense plant was greater than that per WT plant. These results demonstrate that SR development was accelerated in IbEXP1-antisense plants and suggest that IbEXP1 plays a negative role in the formation of SR by suppressing the proliferation of metaxylem and cambium cells to inhibit the initial thickening growth of SRs. IbEXP1 is the first sweetpotato gene whose role in SR development has been directly identified in soil-grown transgenic sweetpotato plants.
LPD-Net: 3D Point Cloud Learning for Large-Scale Place Recognition and Environment Analysis (2019)

Point cloud based place recognition is still an open issue due to the difficulty in extracting local features from the raw 3D point cloud and generating the global descriptor, and it's even harder in the large-scale dynamic environments. In this paper, we develop a novel deep neural network, named LPD-Net (Large-scale Place Description Network), which can extract discriminative and generalizable global descriptors from the raw 3D point cloud. Two modules, the adaptive local feature extraction module and the graph-based neighborhood aggregation module, are proposed, which contribute to extract the local structures and reveal the spatial distribution of local features in the large-scale point cloud, with an end-to-end manner. We implement the proposed global descriptor in solving point cloud based retrieval tasks to achieve the large-scale place recognition. Comparison results show that our LPD-Net is much better than PointNetVLAD and reaches the state-of-the-art. We also compare our LPD-Net with the vision-based solutions to show the robustness of our approach to different weather and light conditions.
Optical detection of intracellular cavitation during selective laser targeting of the retinal pigment epithelium: dependence of cell death mechanism on pulse duration (2007)

Selective laser targeting of the retinal pigment epithelium (RPE) is an attractive method for treating RPE-associated disorders. We are developing a method for optically detecting intracellular microcavitation that can potentially serve as an immediate feedback of the treatment outcome. Thermal denaturation or intracellular cavitation can kill RPE cells during selective targeting. We examined the cell damage mechanism for laser pulse durations from 1 to 40 micros ex vivo. Intracellular cavitation was detected as a transient increase in the backscattered treatment beam. Cavitation and cell death were correlated for individual cells after single-pulse irradiation. The threshold radiant exposures for cell death (ED(50,d)) and cavitation (ED(50,c)) increased with pulse duration and were approximately equal for pulses of up to 10 micros. For 20 micros, the ED(50,d) was about 10% lower than the ED(50,c); the difference increased with 40-micros pulses. Cells were killed predominantly by cavitation (up to 10-micros pulses); probability of thermally induced cell death without cavitation gradually increases with pulse duration. Threshold measurements are discussed by modeling the temperature distribution around laser-heated melanosomes and the scattering function from the resulting cavitation. Detection of intracellular cavitation is a highly sensitive method that can potentially provide real-time assessment of RPE damage during selective laser targeting.
Development of p-type Ion Implantation Technique for Realization of GaN Vertical MOSFETs (2023)

GaN has attracted attention as a semiconductor material for next-generation power switching devices. Vertical-type GaN devices with MOS gate driving are preferable for high-power switching applications. Due to recent advances in bulk GaN crystal growth [1], more studies are reporting vertical-type GaN devices with a breakdown voltage exceeding 1 kV on GaN substrates [2, 3]. However, these reports use an epitaxially grown p-type layer or fin-structure.
Synthesis of a porphyrin-labelled carboranyl phosphate diester: a potential new drug for boron neutron capture therapy of cancer (2002)

A boron-rich, water-soluble porphyrin conjugate was synthesized by coupling of two carboranyl alcohols with 2-chlorophenoxyphosphorus dichloride, followed by conjugation to an amine-functionalized tetraphenyl-porphyrin via an amide linkage.