gebhart/patrepeval huggingface dataset:
Identification of Linear Epitopes in Bacillus anthracis Protective Antigen Bound by Neutralizing Antibodies (2009)

Protective antigen (PA), the binding subunit of anthrax toxin, is the major component in the current anthrax vaccine, but the fine antigenic structure of PA is not well defined. To identify linear neutralizing epitopes of PA, 145 overlapping peptides covering the entire sequence of the protein were synthesized. Six monoclonal antibodies (mAbs) and antisera from mice specific for PA were tested for their reactivity to the peptides by enzyme-linked immunosorbent assays. Three major linear immunodominant B-cell epitopes were mapped to residues Leu(156) to Ser(170), Val(196) to Ile(210), and Ser(312) to Asn(326) of the PA protein. Two mAbs with toxin-neutralizing activity recognized two different epitopes in close proximity to the furin cleavage site in domain 1. The three-dimensional complex structure of PA and its neutralizing mAbs 7.5G and 19D9 were modeled using the molecular docking method providing models for the interacting epitope and paratope residues. For both mAbs, LeTx neutralization was associated with interference with furin cleavage, but they differed in effectiveness depending on whether they bound on the N- or C-terminal aspect of the cleaved products. The two peptides containing these epitopes that include amino acids Leu(156)-Ser(170) and Val(196)-Ile(210) were immunogenic and elicited neutralizing antibody responses to PA. These results identify the first linear neutralizing epitopes of PA and show that peptides containing epitope sequences can elicit neutralizing antibody responses, a finding that could be exploited for vaccine design.
Near-field optical microscopy with a vibrating probe in aqueous solution (2001)

We show that with an appropriately configured scanning quartz pipette coated with aluminum, a near-field scanning optical microscope (NSOM) can be constructed to operate in aqueous solution for applications in biology. Many of the technical limitations associated with a scanning pipette were circumvented by introducing a small modulation of the distance between the pipette and the sample. We show that this ac method allows the pipette to be positioned very close to the sample surface and is robust in obtaining reproducible NSOM images in solution. This approach is also compatible with fluorescence imaging and fluorescence resonance energy transfer, and should further facilitate the use of NSOM in various areas of cell biology where high resolution is considered to be critical.
Dual-mode, Fluxgate-Induction Sensor for UXO Detection and Discrimination (2010)

Abstract We describe an innovative, dual-mode, fluxgate-induction sensor (FIS) that combines a DC magnetometer and an electromagnetic (EM) sensor. This sensor will enable one-pass unexploded ordnance (UXO) detection and discrimination using the joint measurements. The FIS is based on a 5-inch long, high-permeability magnetic core and a sensing coil that are shared by both EM and magnetic (MAG) modes. This integration makes the sensor very compact and removes the potential crosstalk problem of the core material of one sensor dominating the response of the other. A prototype receiver was developed and true serial, dual-mode operation demonstrated. The FIS achieved sensitivities of 1 nT rms in MAG mode and 0.2 pT/√Hz at 1 kHz in EM mode, which compare favorably to existing commercial instruments. Triaxial dipole modeling confirms that three-component EM data are better for shape characterization than one (vertical) component. Assuming axisymmetry, inversions of three-component EM measurements of 22 cylindrical and disk-shaped targets yielded 100% correct classification of UXO-like objects (cylinders) and 38% misclassification of disks as cylinders. Degraded classification performance with increasing vertical distance may be caused by the small cross-sectional area of the FIS; an array will provide better field sampling. Triaxial dipole modeling of the MAG data confirmed its utility for detecting deeper targets using only the vertical component. Based on these results, the FIS is ready for field demonstration and validation.
Fabrication of FePt nanoparticles for self-organized magnetic array (2003)

A self-organized array of magnetic nanoparticles can be potentially used to increase the storage density in magnetic recording. One challenge in this approach is to obtain long-range order assemblies of the nanoparticles. One method to solve this problem is to pattern a substrate having circumferential patterns, whose dimensions are within the coherent length of the self-organized array. By patterning the disk into topographically confined circumferential patterns with such dimensions, thermally stable magnetic nanoparticles may be used to fabricate magnetic recording disks. The circumferential patterns in this case are formed on the disk substrate with dimensions of 100–500 nm and depths of 5–20 nm, prepared by electron beam lithography and reactive ion etching techniques. The monodispersed FePt nanoparticles were synthesized by thermal decomposition of iron pentacarbonyl and reduction of platinum salt simultaneously in the presence of surfactant molecules, achieving a size distribution of 3.15±0.20 nm. Our initial experimental results showed that the monodispersed FePt nanoparticles were successfully deposited into the circumferential patterns and they self-organized into a superlattice. The self-assembly of the FePt nanoparticles in the circumferential pattern strongly relied on the line edge roughness (LER) of the circumferential pattern. This suggests that we need to fabricate the circumferential pattern with LER at the length scales of approximate an individual nanoparticle size 3–4 nm in order to improve the assembly quality further. This is another challenge for today’s advanced lithography and etching processes.
Fabry-Perot fiber sensors with reproducible displacement sensitivities (2011)

An all-silica design and silicate bonding are used to demonstrate a Fabry-Perot acoustic fiber sensor for large-scale array applications with a high sensitivity, high thermal stability, and excellent reproducibility in displacement sensitivity (±0.6 dB).
Glassy steel optimized for glass-forming ability and toughness (2009)

An alloy development strategy coupled with toughness assessments and ultrasonic measurements is implemented to design a series of iron-based glass-forming alloys that demonstrate improved glass-forming ability and toughness. The combination of good glass-forming ability and high toughness demonstrated by the present alloys is uncommon in Fe-based systems, and is attributed to the ability of these compositions to form stable glass configurations associated with low activation barriers for shear flow, which tend to promote plastic flow and give rise to a toughness higher than other known Fe-based bulk-glass-forming systems.
Spatially mapping of tracheal ciliary beat frequency using real time phase resolved Doppler spectrally encoded interferometric microscopy (Conference Presentation) (2019)

Ciliary motion in the upper airway is the primary mechanism by which the body transports foreign particulate out of the respiratory system in order to maintain proper respiratory function. The ciliary beating frequency (CBF) is often disrupted with the onset of disease as well as other conditions, such as changes in temperature or in response to drug administration. Current imaging of ciliary motion relies on microscopy and high speed cameras, which cannot be easily adapted to in-vivo imaging. M-mode optical coherence tomography (OCT) imaging is capable of visualization of ciliary activity, and phase-resolved Doppler (PRD) algorithm can be integrated to measure the ciliary beating direction and amplitude with nanometer sensitivity. However, since ciliary activity naturally happens on the tissue surface, enface imaging modalities should be more suitable than cross-sectional ones such as OCT. We report on the development of a spectrally encoded interferometric microscopy (SEIM) system using a phase-resolved Doppler (PRD) algorithm to measure and map the ciliary beating frequency within an en face region. This novel high speed, high resolution system allows for visualization of both temporal and spatial ciliary motion patterns with nanometer sensitivity. Rabbit tracheal CBF ranging from 9 to 13 Hz have been observed under different temperature conditions, and the effects of using lidocaine and albuterol have also been measured. This study is the stepping stone to in-vivo studies and the translation of imaging spatial CBF in clinics.
A monomeric von Willebrand factor fragment, Leu-504--Lys-728, inhibits von Willebrand factor interaction with glycoprotein Ib-IX [corrected] (1992)

von Willebrand factor interaction with glycoprotein Ib alpha (GPIb alpha) plays a critical role in the initial phase of platelet adhesion at high shear rates, and it may also play a role in platelet thrombus formation in partially occluded arteries. Previous studies have indicated that two peptides, Cys-474--Pro-488 (peptide 153) and Ser-692--Pro-708 (peptide 154), inhibit von Willebrand factor--GPIb alpha interaction. We have expressed a recombinant fragment of von Willebrand factor, Leu-504--Lys-728 [corrected], with a single intrachain disulfide bond linking residues Cys-509--Cys-695 and examined its ability to inhibit von Willebrand factor--GPIb alpha interactions and platelet adhesion at high shear forces. This recombinant fragment, named VCL, inhibits ristocetin-induced, botrocetin-induced, and asialo-von Willebrand factor-induced platelet aggregation and binding to platelets at an IC50 = 0.011-0.260 microM, significantly lower than the IC50 of peptide 153 or 154, IC50 = 86-700 microM. Peptides 153 and 154 did not result in any inhibition of platelet adhesion (IC50 greater than 500 microM). In contrast, VCL inhibited 50% of platelet adhesion at 0.94 microM and at 7.6 microM inhibited greater than 80% of platelet adhesion to human umbilical artery subendothelium at high shear forces. VCL inhibited the contact and spreading of platelets and also caused a marked decrease in thrombus formation. These studies indicate that VCL may be an effective antithrombotic agent in preventing arterial thrombus formation in areas of high shear force.
Precision blood flow measurements in vascular networks with conservation constraints (2018)

In-vivo blood flow measurement, either catheter based or derived from medical images, has become increasingly used for clinical decision making. Most methods focus on a single vascular segment, catheter or simulations, due to mechanical and computational complexity. Accuracy of blood flow measurements in vascular segments are improved by considering the constraint of blood flow conservation across the whole network. Image derived blood flow measurements for individual vessels are made with a variety of techniques including ultrasound, MR, 2D DSA, and 4D-DSA. Time resolved DSA (4D) volumes are derived from 3D-DSA acquisitions and offer one such environment to measure the blood flow and respective measurement uncertainty in a vascular network automatically without user intervention. Vessel segmentation in the static DSA volume allows a mathematical description of the vessel connectivity and flow propagation direction. By constraining the allowable values of flow afforded by the measurement uncertainty and enforcing flow conservation at each junction, a reduction in the effective number of degrees of freedom in the vascular network can be made. This refines the overall measurement uncertainty in each vessel segment and provides a more robust measure of flow. Evaluations are performed with a simulated vascular network and with arterial segments in canine subjects and human renal 4D-DSA datasets. Results show a 30% reduction in flow uncertainty from a renal arterial case and a 2.5-fold improvement in flow uncertainty in some canine vessels. This method of flow uncertainty reduction may provide a more quantitative approach to treatment planning and evaluation in interventional radiology.
Self-Injection-Locked AIA Radar Sensor Using PLL Demodulator for N oncontact Vital Sign Detection (2018)

In this paper, a new self-injection-Iocked radar sensor with a self-oscillating active-integrated-antenna (AIA) and a phase-locked-loop demodulator is presented for noncontact vital sign detection. The AIA is developed to simultaneously radiate the radio-frequency signal and receive the back-scattered injection signal, which is phase-modulated by the chest movement of the human subject. According to the injection-locking theory, the oscillation frequency of the AIA will be shifted by injecting a signal with a phase variation, which amounts to the frequency modulation. Hence, the vital sign can be demodulated by a PLL demodulator. The developed radar sensor has been experimentally verified as the human subject is located at the distances of 1.5 m away from the radar sensor.
Phosphite ester compositions for PVC compounds (2002)

Abstract The activity of various structural classes of liquid organophosphite esters has been examined in flexible PVC applications. Blends of the most active phosphites have been developed as alternative heat stabilizers for PVC. These new phosphite mixtures eliminate the dependence of compounders upon mixed‐metal stabilizer systems based on heavy metals such as barium and cadmium. Static oven aging tests showed the superior performance of these blends compared to that of traditional mixed‐metal stabilizers.
Prostate cancer detection from multi-institution multiparametric MRIs using deep convolutional neural networks (2018)

Multiparametric magnetic resonance imaging (mpMRI) of the prostate aids in early diagnosis of prostate cancer, but is difficult to interpret and subject to interreader variability. Our objective is to generate probability maps, overlaid on original mpMRI images to help radiologists identify where a cancer is suspected as a computer-aided diagnostic (CAD). We optimized the holistically nested edge detection (HED) deep convolutional neural network. Our dataset contains T2, apparent diffusion coefficient, and high <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>b</mml:mi></mml:mrow> </mml:math> -value images from 186 patients across six institutions worldwide: 92 with an endorectal coil (ERC) and 94 without. Ground-truth was based on tumor segmentations manually drawn by expert radiologists based on histologic evidence of cancer. The training set consisted of 120 patients and the validation set and test set included 19 and 47, respectively. Slice-level probability maps are evaluated at the lesion level of analysis. The best model: HED using <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>5</mml:mn> <mml:mo>×</mml:mo> <mml:mn>5</mml:mn></mml:mrow> </mml:math> convolutional kernels, batch normalization, and optimized using Adam. This CAD performed significantly better ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>p</mml:mi> <mml:mo><</mml:mo> <mml:mn>0.001</mml:mn></mml:mrow> </mml:math> ) in the peripheral zone ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>AUC</mml:mi> <mml:mo>=</mml:mo> <mml:mn>0.94</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.01</mml:mn></mml:mrow> </mml:math> ) than the transition zone. It outperforms a previous CAD from our group in a head-to-head comparison on the same ERC-only test cases ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>AUC</mml:mi> <mml:mo>=</mml:mo> <mml:mn>0.97</mml:mn> <mml:mo>±</mml:mo> <mml:mn>0.01</mml:mn></mml:mrow> </mml:math> ; <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>p</mml:mi> <mml:mo><</mml:mo> <mml:mn>0.001</mml:mn></mml:mrow> </mml:math> ). Our CAD establishes a state-of-the-art performance for predicting prostate cancer lesions on mpMRIs.
Mass Spectrometric Analysis of Protein Markers for Ovarian Cancer (2004)

Ovarian cancer is the fifth leading cause of death from cancer in women and is the leading cause of gynecologic death in developed countries. Although the overall 5-year survival rate of patients with ovarian cancer is only 25%, the survival rate of patients diagnosed with early-stage ovarian cancer (I/IIa) approaches 90% (1). Therefore, a noninvasive diagnostic test that can detect early-stage ovarian cancer would be highly desirable, particularly if it could be coupled to a second, noninvasive diagnostic test such as transvaginal ultrasound. In a recently completed multiinstitutional protein expression profiling study encompassing 503 women from four institutions, we developed a three-marker panel that could distinguish women with early-stage ovarian cancer from healthy controls with higher diagnostic accuracy than could CA125 (area under the curve, 92% vs 77%) (2). Purification and identification of the three markers revealed that they were a truncated form of transthyretin, full-length apolipoprotein A1, and an internal fragment of inter-α-trypsin inhibitor heavy chain 4 (ITIH4).

Transthyretin is known to be cysteinylated and glutathionylated in addition to being truncated (3). ITIH4 is cleaved at multiple sites, generating numerous cleavage products (4). Conventional immunoassays generally cannot simultaneously distinguish or quantify multiple posttranslationally modified forms of a protein or its isoforms. Mass spectrometry (MS)-based assays have the advantage of being able to do so, but are often not considered to be quantitative. Because of the chromatographic nature of the ProteinChip® array surface, surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-MS has the advantage of being quantitative (5). When immunocapture is coupled with SELDI-TOF-MS, a single immunoassay can quantify multiple forms of an analyte. The immunocapture can be performed directly on the ProteinChip array surface (by use of a reactive surface array) or on beads coated with antibody. In the latter case, the bound material is eluted onto ProteinChip arrays.

Several antibodies to …
Dissociation of Locomotor Activation and Suppression of Food Intake Induced by CRF in CRFR1-Deficient Mice (2000)

Corticotropin-releasing factor (CRF) systems are involved in locomotor and feeding behaviors. Two distinct CRF receptor subtypes, CRFR1 and CRFR2, are thought to mediate CRF actions in the central nervous system. However, the role for each receptor in locomotor activity and feeding remains to be determined. Using CRFR1 null mutant mice, the present study examined the functional significance of this receptor in ambulation and feeding. CRF treatment of wild-type mice resulted in increased levels of locomotion whereas no change was observed in CRFR1-deficient mice as compared to vehicle-treated mutant mice. In contrast, CRF decreased food-water intake in both wild type and CRFR1-deficient mice equally. These results support an important role for CRFR1 in mediating CRF-induced locomotor activation, whereas other receptor subtypes, likely CRFR2, may mediate the appetite-suppressing effects of CRF-like peptides.
Document classification using a finite mixture model (1997)

We propose a new method of classifying documents into categories. We define for each category a finite mixture model based on soft clustering of words. We treat the problem of classifying documents as that of conducting statistical hypothesis testing over finite mixture models, and employ the EM algorithm to efficiently estimate parameters in a finite mixture model. Experimental results indicate that our method outperforms existing methods.
Phase‐based regional oxygen metabolism (PROM) using MRI (2011)

Venous oxygen saturation (Y(v) ) in cerebral veins and the cerebral metabolic rate of oxygen (CMRO(2)) are important indicators for brain function and disease. Although MRI has been used for global measurements of these parameters, currently there is no recognized technique to quantify regional Y(v) and CMRO(2) using noninvasive imaging. This article proposes a technique to quantify CMRO(2) from independent MRI estimates of Y(v) and cerebral blood flow. The approach uses standard gradient-echo and arterial spin labeling acquisitions to make these measurements. Using MR susceptometry on gradient-echo phase images, Y(v) was quantified for candidate vein segments in gray matter that approximate a long cylinder parallel to the main magnetic field. Local cerebral blood flow for the identified vessel was determined from a corresponding region in the arterial spin labeling perfusion map. Fick's principle of arteriovenous difference was then used to quantify CMRO(2) locally around each vessel. Application of this method in young, healthy subjects provided gray matter averages of 59.6% ± 2.3% for Y(v), 51.7 ± 6.4 mL/100 g/min for cerebral blood flow, and 158 ± 18 μmol/100 g/min for CMRO(2) (mean ± SD, n = 12), which is consistent with values previously reported by positron emission tomography and MRI.
Practical guidance for dosing and switching from paliperidone palmitate 1 monthly to 3 monthly formulation in schizophrenia (2015)

ClinicalTrials.gov identifier: NCT01559272 and NCT01529515.
Regulation of the Mouse Cartilage-derived Retinoic Acid-sensitive Protein Gene by the Transcription Factor AP-2 (1998)

The expression of cartilage-derived retinoic acid-sensitive protein (CD-RAP) is initiated at the beginning of chondrogenesis and continues throughout the cartilage development. In chondrocytes, CD-RAP is down-regulated by retinoic acid. To understand the molecular mechanism underlying this regulation and the cell-specific expression, the deletion constructs of the mouse CD-RAP promoter were transfected into chondrocytes and a melanoma cell line. The results revealed a domain that demonstrated high levels of expression specifically in chondrocytes. In this functional domain, we show that a cis-acting element, 5'-GCCTGAGGC-3', binds to the trans-acting factor protein AP-2. Mutation of the AP-2 site on the CD-RAP promoter led to decreased transcription in C5.18 chondrocytes, indicating that this site may act as an activator of transcription. In contrast, increased concentration of AP-2, stimulated by retinoic acid, led to decreased transcription of the CD-RAP promoter, an effect that was abolished by mutation of the AP-2 binding site. The effect of AP-2 was further examined by co-transfection of C5.18 and HepG2 cells with the CD-RAP promoter constructs and an AP-2 expression plasmid. In a dose-dependent manner, cotransfection with AP-2 elevated and then decreased CD-RAP promoter activity. Taken together, these results suggest that AP-2 is involved in the biphasic regulation of CD-RAP transcription.