gebhart/patrepeval huggingface dataset:
Biosensor for Dengue Virus Detection:  Sensitive, Rapid, and Serotype Specific (2002)

A serotype-specific RNA biosensor was developed for the rapid detection of Dengue virus (serotypes 1-4) in blood samples. After RNA amplification, the biosensor allows the rapid detection of Dengue virus RNA in only 15 min. In addition, the biosensor is portable, inexpensive, and very easy to use, making it an ideal detection system for point-of-care and field applications. The biosensor is coupled to the isothermal nucleic acid sequence-based amplification (NASBA) technique with which small amounts of virus RNA are amplified using a simple water bath. During the NASBA reaction, a generic sequence is attached to all RNA molecules as described earlier (Wu, S. J.; Lee, E. M.; Putvatana, R.; Shurtliff, R. N.; Porter, K R.; Suharyono, W.; Watt, D. M.; King, C. C.; Murphy, G. S.; Hayes, C. G.; Romano, J. W. J. Clin. Microbiol. 2001, 39, 2794-2798.). It has been shown earlier that Dengue virus can be detected specifically using two DNA probes: a first probe hybridized with the attached generic sequence and, therefore, bound to every amplified RNA molecule; and a second probe either bound to all four Dengue virus serotypes or chosen to be specific for only one serotype. These probes were utilized in the biosensor described in this publication. For a generic Dengue virus biosensor, the second probe is complementary to a conserved region found in all Dengue serotypes. For identification of the individual Dengue virus serotypes, four serotype-specific probes were developed (Wu, S. J.; Lee, E. M.; Putvatana, R.; Shurtiff, R. N.; Porter, K. R.; Suharyono, W.; Watt, D. M.; King, C. C.; Murphy, G. S.; Hayes, C. G.; Romano, J. W. J. Clin. Microbiol. 2001, 39, 2794-2798.). The biosensor is a membrane-based DNA/RNA hybridization system using liposome amplification. The generic DNA probe (reporter probe) is coupled to the outside of dye-encapsulating liposomes. The conserved or Dengue serotype specific probes (capture probes) are immobilized on a polyethersulfone membrane strip. Liposomes are mixed with amplified target sequence and are then applied to the membrane. The mixture is allowed to migrate along the test strip, and the liposome-target sequence complexes are immobilized in the capture zone via hybridization of the capture probe with target sequence. The amount of liposomes present in the immobilized complex is directly proportional to the amount of target sequence present in the sample and can be quantified using a portable reflectometer. The different biosensor components have been optimized with respect to sensitivity and, foremost, specificity toward the different serotypes. An excellent correlation to a laboratory-based detection system was demonstrated. Finally, the assay was tested using a limited number of clinical human serum samples. Although Dengue serotypes 1, 2 and 4 were identified correctly, serotype 3 displayed low cross-reactivity with biosensors designed for detection of serotypes 1 and 4.
Concept Expansion Using Web Tables (2015)

We study the following problem: given the name of an ad-hoc concept as well as a few seed entities belonging to the concept, output all entities belonging to it. Since producing the exact set of entities is hard, we focus on returning a ranked list of entities. Previous approaches either use seed entities as the only input, or inherently require negative examples. They suffer from input ambiguity and semantic drift, or are not viable options for ad-hoc tail concepts. In this paper, we propose to leverage the millions of tables on the web for this problem. The core technical challenge is to identify the ``exclusive'' tables for a concept to prevent semantic drift; existing holistic ranking techniques like personalized PageRank are inadequate for this purpose. We develop novel probabilistic ranking methods that can model a new type of table-entity relationship. Experiments with real-life concepts show that our proposed solution is significantly more effective than applying state-of-the-art set expansion or holistic ranking techniques.
Direct Monitoring of Absorption in Solution by Cavity Ring-Down Spectroscopy (2002)

Cavity ring-down spectroscopy is applied to the liquid phase by placing the target solution directly into the optical cavity. We demonstrate that solutions in the cavity can be stirred and more importantly monitored in a flow. We report a minimum detectable absorption of 10(-6) cm(-1) for a range of organic solvents. This detection limit corresponds to picomolar concentrations for strong absorbers.
Generation of millijoule-level soft-x-ray laser pulses at a 4-Hz repetition rate in a highly saturated tabletop capillary discharge amplifier (1999)

Laser pulses with energies of as much as 1 mJ were generated at a wavelength of 46.9 nm by single-pass amplification in a 34.5 cm-long Ne-like Ar capillary discharge plasma. The large gain-length product of this plasma column allows for soft-x-ray amplification in a highly saturated regime, resulting in efficient energy extraction. Average laser output pulse energy of 0.88 mJ and peak power of 0.6 MW were obtained at a repetition rate of 4 Hz. With an estimated peak spectral brightness of approximately 1x10(23)photons /(s mm(2)mrad> (2)0.01% bandwidth) this tabletop laser is one of the brightest soft-x-ray sources to date.
Active probes and microfluidic ink delivery for Dip Pen Nanolithography (2004)

Dip Pen Nanolithography (DPN<sup>TM</sup>) is a scanning probe technique for nanoscale lithography: A sharp tip is coated with a functional molecule (the “ink”) and then brought into contact with a surface where it deposits ink via a water meniscus. The DPN process is a direct-write pattern transfer technique with nanometer resolution and is inherently general with respect to usable inks and substrates including biomolecules such as proteins and oligonucleotides. We present functional extensions of the basic DPN process by showing actuated multi-probes as well as microfluidic ink delivery. We present the fabrication process and characterization of such active probes that use the bimorph effect to induce deflection of individual cantilevers as well as the integration of these probes. We also developed the capability to write with multiple inks on the probe array permitting the fabrication of multi-component nanodevices in one writing session. For this purpose, we fabricate passive microfluidic devices and present microfluidic behavior and ink loading performance of these components.
How2Sketch: Generating Easy-To-Follow Tutorials for Sketching 3D Objects (2016)

Accurately drawing 3D objects is difficult for untrained individuals, as it requires an understanding of perspective and its effects on geometry and proportions. Step-by-step tutorials break the complex task of sketching an entire object down into easy-to-follow steps that even a novice can follow. However, creating such tutorials requires expert knowledge and is a time-consuming task. As a result, the availability of tutorials for a given object or viewpoint is limited. How2Sketch addresses this problem by automatically generating easy-to-follow tutorials for arbitrary 3D objects. Given a segmented 3D model and a camera viewpoint,it computes a sequence of steps for constructing a drawing scaffold comprised of geometric primitives, which helps the user draw the final contours in correct perspective and proportion. To make the drawing scaffold easy to construct, the algorithm solves for an ordering among the scaffolding primitives and explicitly makes small geometric modifications to the size and location of the object parts to simplify relative positioning. Technically, we formulate this scaffold construction as a single selection problem that simultaneously solves for the ordering and geometric changes of the primitives. We demonstrate our algorithm for generating tutorials on a variety of man-made objects and evaluate how easily the tutorials can be followed with a user study.
Isolation and characterization of monoclonal antibodies against human carbonic anhydrase-IX (2021)

The architectural complexity and heterogeneity of the tumor microenvironment (TME) remains a substantial obstacle in the successful treatment of cancer. Hypoxia, caused by insufficient oxygen supply, and acidosis, resulting from the expulsion of acidic metabolites, are prominent features of the TME. To mitigate the consequences of the hostile TME, cancer cells metabolically rewire themselves and express a series of specific transporters and enzymes instrumental to this adaptation. One of these proteins is carbonic anhydrase (CA)IX, a zinc-containing extracellular membrane bound enzyme that has been shown to play a critical role in the maintenance of a neutral intracellular pH (pH<sub>i</sub>), allowing tumor cells to survive and thrive in these harsh conditions. Although CAIX has been considered a promising cancer target, only two antibody-based therapeutics have been clinically tested so far. To fill this gap, we generated a series of novel monoclonal antibodies (mAbs) that specifically recognize the extracellular domain (ECD) of human CAIX. Here we describe the biophysical and functional properties of a set of antibodies against the CAIX ECD domain and their applicability as: 1) suitable for development as an antibody-drug-conjugate, 2) an inhibitor of CAIX enzyme activity, or 3) an imaging/detection antibody. The results presented here demonstrate the potential of these specific hCAIX mAbs for further development as novel cancer therapeutic and/or diagnostic tools.
Stringer Detection and Drilling System Significantly Reduces the Invisible Lost Time (ILT) Caused by Reaming (2023)

Abstract Drilling hard stringers that are erratically distributed in an underlying rather soft formation is challenging from different perspectives. An unforeseen change of the drilled formation from soft to hard and dense rock can cause impact damage to the bit, deflect the bottom-hole assembly (BHA), result in high bending loads, increase vibration, and cause wear/tear on BHA components. If not properly managed, this leads to non-productive time (NPT) and increased maintenance costs. Further, a deflection caused by a stringer away from the planned well path that is detected late results in high local doglegs (HLD) and requires time-consuming correction through reaming with invisible lost time (ILT). Recently, a stringer detection method based on vibrations, namely high-frequency torsional oscillations (HFTO), has been presented. A case study with 21 sections in the North Sea based on this solution is shown that demonstrates a reduction in ILT by 80%. The system is based on a timely and reliable detection of stringers, an optimized mud pulse telemetry scheme, and an automated advisory system. The downhole algorithm embedded in a measurement while drilling tool is consistently interpreting HFTO based on tangential acceleration and dynamic torsional torque measurement. By defining thresholds for the amplitude and the localization with respect to frequency content of HFTO, the algorithm results are translated into a binary value with 1 – stringer currently drilled or 0 - no stringer is drilled. The low bandwidth consuming 1-bit value and downhole measured bending moment are sent in 10 to 15 second intervals to the surface by mud pulse telemetry. Once the stringer is detected, the bending moment data is closely monitored to react correctly and efficiently to a stringer in different scenarios. This solution is discussed in a case study in Norway covering 21 sections with and without the system deployed. The offshore application is challenged by frequently occurring stringer layers and nodules of different geometry. Based on the stringer content, the reaming time has been typically high in this application. The system, however, enabled a timely detection of the stringers and an optimal stringer drilling enabled by the frequently sent bending moment information. Therefore, stringer drilling was done without having to pull off-bottom frequently and ream the transition area between soft and hard formation thereby saving time and reducing wear on the BHA and drill pipe, ultimately ending up with a smoother/straighter wellbore. By using the system, a faster reaction to any stringer and the use of appropriate parameters to avoid costly HLDs are achieved. The case study demonstrates a significant and consistent improvement in ILT. The reaming hours per 1000 m as a benchmark have been reduced from 2-5 hours without to 0.3-0.6 hours with the system resulting in an average saving of 12 hours per reservoir section.
Correlation of p34cdc2 cyclin-dependent kinase overexpression, CD44s downregulation, and HER-2/neu oncogene amplification with recurrence in prostatic adenocarcinomas. (1998)

This study showed that p34cdc2, CD44s, and HER-2/neu are variably expressed or amplified in prostatic carcinoma and that such alteration may affect tumor behavior. In addition, CDK overexpression and HER-2/neu amplification may be biologically related.
Nanowire Arrays: A Low‐Frequency Energy Harvester from Ultralong, Vertically Aligned BaTiO<sub>3</sub> Nanowire Arrays (Adv. Energy Mater. 11/2014) (2014)

Highly compliant ultralong (≈40 μm) vertically aligned BaTiO3 nanowire arrays, synthesized using a newly developed hydrothermal process, act as promising candidates for fabrication of low frequency energy harvesters, as demonstrated by Aneesh Koka and Henry A. Sodano in article number 1301660. This novel ultralong BaTiO3 nanowire array based energy harvester has several favorable attributes such as compact size, lowresonant frequency, and biocompatibility for its practical implementation in consumer electronics and biomedical applications.
Rate distortion-based motion estimation search ordering for rate-constrained successive elimination algorithms (2014)

In this paper, we propose a new class of search ordering algorithms to reduce the computational cost of motion estimation in video coding. We show that conventional search orderings, such as spiral search, can weaken the filtering criterion of rate-constrained successive elimination algorithms. Based on this new insight, we derive a new search ordering that takes into account the impact of the rate constraint. Our simulation results demonstrate that, on average, the amount of SAD operations required to encode the tested sequences, is reduced by 2.86%, when compared to the H.264 JM reference software's implementation of spiral search. For sequences with unpredictable motion, this reduction is greater than 5% and can exceed 10% when smaller block partitions are evaluated.
Homogeneous and Heterogeneous Feed-Forward XOR Physical Unclonable Functions (2020)

Physical unclonable functions (PUFs) are hardware security primitives that are used for device authentication and cryptographic key generation. Standard XOR PUFs typically contain multiple standard arbiter PUFs as components, and are more secure than standard arbiter PUFs or feed-forward (FF) arbiter PUFs (FF PUFs). This paper proposes design of feed-forward XOR PUFs (FFXOR PUFs) where each component PUF is a FF PUF. Various homogeneous and heterogeneous FFXOR PUFs are presented and evaluated in terms of four fundamental properties of PUFs: uniqueness, attack-resistance, reliability and randomness. Certain key issues pertaining to XOR PUFs such as their vulnerability to machine learning attacks and instability in responses are investigated. Other important challenges like the lack of uniqueness in FF PUFs and the asymmetry in FPGA arbiter PUFs are addressed and it is shown that FFXOR PUFs can naturally overcome these problems. It is shown that heterogeneous FFXOR PUFs (i.e., FFXOR PUFs with non-identical components) can be resilient to state-of-the-art machine learning attacks. We also present systematic reliability analysis of FFXOR PUFs and demonstrate that soft-response thresholding can be used as an effective countermeasure to overcome the degraded reliability bottleneck. Observations from simulations are further verified through hardware implementation of 64-bit FFXOR PUFs on Xilinx Artix-7 FPGA.
Elimination of Saturated Fatty Acids, Toxic Cyclic nonapeptide and Cyanogen Glycoside Components from Flax Seed Oil (2007)

Flax seed(Linseed, Linum usitatissimum L.) and its oil, a richest source of alpha-linolenic acid(ALA)(<TEX>${\omega}-3$</TEX>), contain saturated fatty acids, neurotoxic cyanogen glycosides and immuno-suppressive cyclic-nonapeptides. Present paper describes the development of two chemical processes, Process-A and -B, to remove saturated fatty acids and to destroy cyclic nonapeptides and cyanogen glycosides from flax seed oil. Process-A consists of three major steps, i.e., extraction of fatty acid mixture by alkaline saponification, removal of saturated fatty acid by urea-complexation, and triglyceride reconstruction of unsaturated fatty acid via fatty acyl-chloride activation using oxalyl chloride. Process-B consists of preparation of fatty acid ethyl ester by transesterification, elimination of saturated fatty acid ester by urea-complexation, and reconstruction of triglyceride by interesterification with glycerol-triacetate (triacetin). The destruction of lipophilic cyclic nonapeptide during saponification or transesterification processes could be demonstrated indirectly by the disappearance of antibacterial activity of bacitracin, an analogous cyclic-decapeptide. The cyanogen glycosides were found only in the dregs after hexane extraction, but not in the flax seed oil. The reconstructed triglyceride of flax seed oil, obtained by these two different pathways after elimination of saturated fatty acid and toxic components, showed agreeable properties as edible oil in terms of taste, acid value, iodine and peroxide value, glycerine content, and antioxidant activity.
A fast discrete S-transform for biomedical signal processing (2008)

Determining the frequency content of a signal is a basic operation in signal and image processing. The S-transform provides both the true frequency and globally referenced phase measurements characteristic of the Fourier transform and also generates local spectra, as does the wavelet transform. Due to this combination, the S-transform has been successfully demonstrated in a variety of biomedical signal and image processing tasks. However, the computational demands of the S-transform have limited its application in medicine to this point in time. This abstract introduces the fast S-transform, a more efficient discrete implementation of the classic S-transform with dramatically reduced computational requirements.
Successful Development and Implementation of Statistical Outlier Techniques on 90nm and 65nm Process Driver Devices (2006)

Burn-in and the concomitant post-burn-in retest are significant cost adders to the overall IC manufacturing and test process. Methods to reduce burn-in capacity are continually sought. Traditional outlier screens such as fixed-limit analyses with parametric or non-parametric statistics, when applied to the newest technologies, result in excessive Type I or II errors which cannot be tolerated. In this paper, we describe the results from applying statistical burn-in avoidance techniques using time-zero sort test responses to driver designs fabricated in 90nm and 65nm low leakage technologies and libraries
Tensile and forming properties of auxetic warp-knitted spacer fabrics (2016)

Poisson’s ratio (PR) is defined as the negative ratio between the lateral strain and the longitudinal strain of a material under tensile or compressive loading condition. Auxetic fabrics are those having a negative PR, which means that when their longitudinal strain is positive, their lateral strain is also positive, and vice versa. In this work, tensile and forming properties of auxetic warp-knitted spacer fabrics were investigated and compared with those of the conventional warp-knitted spacer fabrics. Both uniaxial tensile tests and hemispherical compression experiments were conducted, and the relationships of the tensile and forming properties with the auxetic effect were discussed in terms of different fabric structural parameters. The results show that the auxetic warp-knitted spacer fabrics have a prolonged low stress stage in the wale direction, indicating that they are more prone to undergo deformation along the wale direction, and fabric with a longer low stress stage has a better auxetic effect. The results also show that the formability of auxetic warp-knitted spacer fabrics is much better than that of conventional warp-knitted spacer fabrics, due to the much low forming energies required under hemispherical compression, which can be affected by many factors such as auxetic effect, fabric thickness and stiffness, yarn materials and the structure of the spacer layer. When all other parameters are similar, auxetic fabric with a better auxetic effect will have better formability. The study has provided useful information for the design and application of this type of nonconventional spacer fabrics.
Photochromic Polymer Composites for Two-Photon 3D Optical Data Storage (2007)

In this paper we demonstrate 3D two-photon recording and two-photon readout in photochromic polymer composites containing a mixture of 1,2-bis(2-methylbenzo[b]thiophen-3-yl)hexafluorocyclopentene (diarylethene 1) and fluorene derivatives 2,2‘-(9,9-didecyl-9H-fluorene-2,7-diyl)bis(ethene-2,1-diyl)bis(4,1-phenylene)) dibenzo[d]thiazole (2) or poly(9,9-didecyl-2,7-dipheylaminofluorene) (3). The recording mechanism in this system is based on two-photon excitation of the closed form of diarylethene 1 at 800 nm. The readout mechanism is based on the modulation of the emission intensity of fluorene derivatives 2 or 3 by the closed form of diarylethene 1 through Resonance Energy Transfer (RET). Föster distances (R0) and critical concentrations (A0) were calculated from the spectral overlap of the donor's emission (fluorene derivatives) and the acceptor's absorption (closed form of diarylethene 1) in solution and in polymer films of PMMA-co-VBP. This system was demonstrated to be suitable for recording data by two-photon excitation in thick storage media. The RET-based readout method proved to be essentially nondestructive (exhibiting a loss of the initial fluorescence emission less than 20% of the initial emission after 10 000 readout cycles), providing a solution to a long-standing challenge in photochromic optical data storage.