gebhart/patrepeval huggingface dataset:
Histotripsy-induced cavitation cloud initiation thresholds in tissues of different mechanical properties (2014)

Histotripsy is an ultrasound ablation method that depends on the initiation and maintenance of a cavitation bubble cloud to fractionate soft tissue. This paper studies how tissue properties impact the pressure threshold to initiate the cavitation bubble cloud. Our previous study showed that shock scattering off one or more initial bubbles, expanded to sufficient size in the focus, plays an important role in initiating a dense cavitation cloud. In this process, the shock scattering causes the positive pressure phase to be inverted, resulting in a scattered wave that has the opposite polarity of the incident shock. The inverted shock is superimposed on the incident negative pressure phase to form extremely high negative pressures, resulting in a dense cavitation cloud growing toward the transducer. We hypothesize that increased tissue stiffness impedes the expansion of initial bubbles, reducing the scattered tensile pressure, and thus requiring higher initial intensities for cloud initiation. To test this hypothesis, 5-cycle histotripsy pulses at pulse repetition frequencies (PRFs) of 10, 100, or 1000 Hz were applied by a 1-MHz transducer focused inside mechanically tunable tissue-mimicking agarose phantoms and various ex vivo porcine tissues covering a range of Young's moduli. The threshold to initiate a cavitation cloud and resulting bubble expansion were recorded using acoustic backscatter detection and optical imaging. In both phantoms and ex vivo tissue, results demonstrated a higher cavitation cloud initiation threshold for tissues of higher Young's modulus. Results also demonstrated a decrease in bubble expansion in phantoms of higher Young's modulus. These results support our hypothesis, improve our understanding of the effect of histotripsy in tissues with different mechanical properties, and provide a rational basis to tailor acoustic parameters for fractionation of specific tissues.
Unsupervised Learning of the Morphology of a Natural Language (2001)

This study reports the results of using minimum description length (MDL) analysis to model unsupervised learning of the morphological segmentation of European languages, using corpora ranging in size from 5,000 words to 500,000 words. We develop a set of heuristics that rapidly develop a probabilistic morphological grammar, and use MDL as our primary tool to determine whether the modifications proposed by the heuristics will be adopted or not. The resulting grammar matches well the analysis that would be developed by a human morphologist. In the final section, we discuss the relationship of this style of MDL grammatical analysis to the notion of evaluation metric in early generative grammar.
Microstructured magnetic tunnel junctions (invited) (1997)

We have used a simple self-aligned process to fabricate magnetic tunnel junctions down to submicron sizes. Optical and electron-beam lithographies were used to cover a range of areas spanning five orders of magnitude. The bottom magnetic electrodes (Co or permalloy) in our junctions were exchange biased by an antiferromagnetic layer (MnFe). The top electrodes were made of soft magnetic materials (Co or permalloy). We have consistently obtained large magnetoresistance ratios (15%–22%) at room temperature and in fields of a few tens of Oe. The shape of the field response of the magnetoresistance was varied from smooth to highly hysteretic by adjusting the shape anisotropy of one junction electrode.
A Rotationally Asymmetric Reluctance Machine With Improved Torque Density (2013)

Reluctance machines (RM) have desirable features including low rotor and no-load rotational losses. In this paper, a new type of RM is introduced, namely the asymmetrical RM. This machine has higher torque density than a conventional RM and is useful in situations where low rotor and no-load rotational losses are desirable. A design model for the new type of machine is presented and validated using finite-element analysis. The machine is compared to other machine types by comparing Pareto-optimal fronts of loss versus electromagnetic mass for a given torque.
Two dimensional hard x-ray nanofocusing with crossed multilayer Laue lenses (2011)

Hard x-ray microscopy with nanometer resolution will open frontiers in the study of materials and devices, environmental sciences, and life sciences by utilizing the unique characterization capabilities of x-rays. Here we report two-dimensional nanofocusing by multilayer Laue lenses (MLLs), a type of diffractive optics that is in principle capable of focusing x-rays to 1 nm. We demonstrate focusing to a 25 × 27 nm(2) FWHM spot with an efficiency of 2% at a photon energy of 12 keV, and to a 25 × 40 nm(2) FWHM spot with an efficiency of 17% at a photon energy of 19.5 keV.
Adaptive Estimation of the Engine Friction Torque (2006)

Errors in an estimate of friction torque in modern spark ignition automotive engines have a direct impact on driveability performance of a vehicle and necessitate a development of real-time algorithms for adaptation of the friction torque. The friction torque in the engine control unit is presented as a look-up table with two input variables (engine speed and indicated engine torque). Algorithms proposed in this paper estimate the friction torque during engine start and idle. Newton’s second law for rotational dynamics is used as a reference model during engine start. The friction torque is estimated via a deviation from the reference model. The values of the friction torque at the nodes of the look-up table are updated, if new measured data of the friction torque is available. New recursive and computationally efficient algorithms are developed for adaptation of the nodes of the look-up tables. The algorithms are tested on a Volvo vehicle equipped with a six cylinder prototype engine.
Liquid Crystals with Patterned Molecular Orientation as an Electrolytic Active Medium (2015)

Transport of fluids and particles at the microscale is an important theme both in fundamental and applied science. One of the most successful approaches is to use an electric field, which requires the system to carry or induce electric charges. We describe a versatile approach to generate electrokinetic flows by using a liquid crystal (LC) with surface-patterned molecular orientation as an electrolyte. The surface patterning is produced by photo-alignment. In the presence of an electric field, the spatially varying orientation induces space charges that trigger flows of the LC. The active patterned LC electrolyte converts the electric energy into the LC flows and transport of embedded particles of any type (fluid, solid, gaseous) along a predesigned trajectory, posing no limitation on the electric nature (charge, polarizability) of these particles and interfaces. The patterned LC electrolyte exhibits a quadratic field dependence of the flow velocities; it induces persistent vortices of controllable rotation speed and direction that are quintessential for micro- and nanoscale mixing applications.
The insulin A-chain epitope recognized by human T cells is posttranslationally modified (2005)

The autoimmune process that destroys the insulin-producing pancreatic beta cells in type 1 diabetes (T1D) is targeted at insulin and its precursor, proinsulin. T cells that recognize the proximal A-chain of human insulin were identified recently in the pancreatic lymph nodes of subjects who had T1D. To investigate the specificity of proinsulin-specific T cells in T1D, we isolated human CD4(+) T cell clones to proinsulin from the blood of a donor who had T1D. The clones recognized a naturally processed, HLA DR4-restricted epitope within the first 13 amino acids of the A-chain (A1-13) of human insulin. T cell recognition was dependent on the formation of a vicinal disulfide bond between adjacent cysteine residues at A6 and A7, which did not alter binding of the peptide to HLA DR4. CD4(+) T cell clones that recognized this epitope were isolated from an HLA DR4(+) child with autoantibodies to insulin, and therefore, at risk for T1D, but not from two healthy HLA DR4(+) donors. We define for the first time a novel posttranslational modification that is required for T cell recognition of the insulin A-chain in T1D.
Inductively Coupled Circuits with Spin Wave Bus for Information Processing (2008)

We describe a new approach to logic devices interconnection by the inductive coupling via a ferromagnetic film.The information among the distant devices is transmitted in a wireless manner via a magnetic field produced by spin waves propagating in the ferromagnetic film, referred to as the spin wave bus.As an alternative approach to the transistor-based architecture, logic circuits with spin wave bus do not use charge as an information carrier.A bit of information can be encoded into the phase or the amplitude of the spin wave signal.We present experimental data demonstrating inductive coupling through the 100nm thick NiFe and CoFe films at room temperature.The performance of logic circuits with spin wave bus is illustrated by numerical modeling based on the experimental data.Potentially, logic circuits with spin wave bus may resolve the interconnect problem and provide "wireless" read-in and read-out.Another expected
Ab Initio Atomic Polarizability Tensors for Organic Molecules (2001)

A recently developed method for deriving anisotropic atomic dipole polarizability tensors has been employed to derive these terms for each of the atoms in seven families of organic compounds: alcohols, alkanes, amides, amines, carboxylic acids, sulfur compounds, and benzene rings. The procedure uses fits to ab initio quantum mechanically computed molecular polarizability data to determine effective atomic polarizability tensor parameters. A new representation is described which uses bond increments, a property of the bonds rather than simply the atomic types, for polarizability components both parallel and perpendicular to the bonds. It is shown to give excellent results as gauged by its reproduction of the exact ab initio polarizabilities. We examine the accuracy of the ab initio isotropic polarizabilities compared to experiment and present a simple scaling procedure for the former. The isotropic approximations to the full anisotropic atomic polarizabilities are compared for differing atom types and bonding environments. The resulting molecular isotropic polarizabilities are also compared where possible with experiment. The present model consistently predicts both experimental isotropic molecular polarizabilities and empirically derived atomic parametrizations precisely within a few percent.
Fast sequencing of oligosaccharides: the reagent-array analysis method. (1992)

A method of oligosaccharide analysis involving controlled fragmentation resulting from enzymatic digestion is presented. The principle involves generating a set of fragments from the original oligosaccharides, characterizing them in terms of their hydrodynamic volumes, determining their molar proportions, and identifying the oligosaccharides by comparison with a computer-generated data base. Experimentally, this technique involves incubation of aliquots of a sample with a set of defined mixtures of exoglycosidases followed by pooling of the products and a single analysis on the product pool. This method has several practical advantages over current techniques, including speed and the ability to use smaller amounts of starting material. The detection of the intensity-versus-hydrodynamic volume profile is limited only by the specific activity of the labeling method. The ability to perform the enzyme digestions is limited by the individual Km values of the enzymes.
First-in-humans uPAR PET imaging in cancer (2015)

174 Objectives The urokinase-type plasminogen activator receptor (uPAR) represents a prognostic biomarker in common cancer types e.g. breast and prostate cancer. Immunohistochemically evaluations show that high expression of uPAR is associated with poor prognosis. Our objective was to perform a first-in-humans PET study with 64Cu-DOTA-AE105, an uPAR-specific PET ligand, in cancer patients. Methods 10 patients with one of the following cancer types were included: breast (n=3), prostate (n=4) and urothelial cancer (n=3). Each patient was PET/CT scanned 1, 3 and 24 hrs p.i. of 64Cu-DOTA-AE105. Images were analyzed for visible tumor uptake. SUVs were obtained from all lesions by manually drawing VOIs in the malignant tissue. Results are given as SUVmean, SUVmax and tumor to organ ratios. Surgical tumor specimens (n=7) were obtained for ex vivo target analysis. Results Both primary tumors and metastases were visually detectable. The highest tumor uptake 1 hr p.i. was found in prostate cancer (SUVmean 2.65±0.38; SUVmax 9.59±2.06) followed by urothelial cancer (SUVmean 2.45±2.0; SUVmax 4.56 ±1.99) and breast cancer (SUVmean 1.24±0.15; SUVmax 3.56±0.60). Tumor to organ ratios were as follows tumor-liver, tumor-kidney, tumor-blood, tumor-muscle: Prostate: 2.42, 2.58, 5.12 and 15.22. Urothelial: 0.88, 0.97, 2.60 and 11.90. Breast: 0.91, 0.96, 1.65 and, 8.91. Immunohistochemistry confirmed uPAR expression. Conclusions This is the first human study to demonstrate PET images of uPAR expression. A favorable biodistribution and high tumor-to-organ ratio were found already 1 hr p.i. The study supports clinical use of 64Cu-DOTA-AE105 for PET imaging of uPAR expression potentially identifying aggressive tumor phenotypes.
Evaluation of the protective effects of zinc butyrate in IPEC-J2 cells and grower pigs under heat stress1 (2019)

Heat stress (HS) is a major environmental stressor primarily affecting swine performance through negative effects on intestinal health. Zinc and butyric acid supplementation help maintain intestinal integrity and barrier function, and has been shown to be beneficial to swine during stress conditions. We tested a novel formulation of zinc butyrate (ZnB) to study whether it has protective effects toward swine using pig intestinal epithelial cells (IPEC-J2) and in a grower swine HS trial. IPEC-J2 cells were grown either under an inflammatory challenge (<i>Escherichia coli</i> lipopolysaccharide) or HS (41.5 °C for 48 h) using Transwell plates. The tight junction integrity of the cells under various treatments, including ZnB, zinc sulfate, and calcium butyrate, was followed over a period of 36 to 48 h by measuring transepithelial electrical resistance (TER). During inflammatory challenge, ZnB-treated cells had the greatest TER (<i>P</i> < 0.05) at 36 h. When the cells were exposed to HS at 41.5 °C, ZnB-treated cells had similar TER to the cells incubated at 37.0 °C, indicating significant protection against HS. In the swine trial (two dietary treatments, control and an encapsulated form of 40% zinc butyrate [E-ZnB] in hydrogenated palm oil pearls, 12 pigs per treatment), grower gilts (35 ± 1 kg) were supplemented with E-ZnB for 24 d before being subjected to biphasic HS for 7 d, 30 to 32 °C for 8 h and 28 °C for 16 h, for a total duration of 56 h of HS. At the end of the HS phase, half the pigs were euthanized from each treatment (<i>n</i> = 6 per treatment), and growth performance was calculated. During the HS phase, average daily gain (ADG; 0.53 vs. 0.79 kg) and gain-to-feed ratio (G:F; 0.33 vs. 0.43) were greater in the E-ZnB group (<i>P</i> < 0.05). Although in vivo intestinal permeability increased during the HS phase (<i>P</i> < 0.05), no differences were observed in the present study for the intestinal health parameters measured including TER, villus height:crypt depth ratio, and in vivo and ex vivo intestinal permeability between the two treatment groups. In conclusion, results presented here demonstrate that E-ZnB supplementation during HS improves ADG and G:F in grower pigs. Although we could not measure any differences, the mode of action of butyric acid and zinc suggests that the performance improvements are related to improved intestinal health.
Conformationally Defined 6-<i>s</i>-<i>trans</i>-Retinoic Acid Analogs. 3. Structure−Activity Relationships for Nuclear Receptor Binding, Transcriptional Activity, and Cancer Chemopreventive Activity (1996)

We recently demonstrated that conformationally defined 6-s-trans-retinoic acid (RA) analogs were effective in the prevention of skin papillomas (Vaezi et al. J. Med. Chem. 1994, 37, 4499-4507) and selective agonists for nuclear receptor binding and activation (Alam et al. J. Med. Chem. 1995, 38, 2302-2310). In order to probe important structure-activity relationships, we evaluated a homologous series of four 6-s-trans-retinoids that are 8-(2'-cyclohexen-1'-ylidene)-3,7-dimethyl-2,4,6-octatrienoic acids with different substituents at 2' (R2) and 3' (R1) positions on the cyclohexene ring. UAB1 (R1 = R2 = H), UAB4 (R1 = R2 = Me), UAB7 (R1 = Me, R2 = iPr), and UAB8 (R1 = Et, R2 = iPr) contain alkyl R groups that mimic, to different extents, portions of the trimethylcyclohexenyl ring of RA. Both 9Z- and all-E-isomers of these retinoids were evaluated in binding assays for cellular retinoic acid-binding proteins (CRABP-I and CRABP-II), a nuclear retinoic acid receptor (RAR alpha), and a nuclear retinoid X receptor (RXR alpha). The all-E-isomers of UAB retinoids bound tightly to CRABPs and RAR alpha, the binding affinity of the all-E-isomer increased systematically from UAB1 to UAB8, and binding for the latter was comparable to that of all-E-RA. In contrast to RA, the (9Z)-UAB retinoids were at least 200-fold less active than the all-E-isomers in binding to RAR alpha. The (9Z)-UAB isomers exhibited increasingly stronger binding to RXR alpha, and (9Z)-UAB8 was nearly as effective as (9Z)-RA in binding affinity. The retinoids were also evaluated in gene expression assays mediated by RAR alpha and RXR alpha homodimers or RAR alpha/RXR alpha heterodimers. Consistent with the binding affinities, the (all-E)-UAB retinoids activated gene transciption mediated by RAR alpha homodimers or RAR alpha/RXR alpha heterodimers, while the (9Z)-UAB isomers activated only the RXR alpha homodimer-mediated transcription. The all-E- and 9Z-isomers of the UAB retinoids were further evaluated for their capacity to prevent the induction of mouse skin papillomas. When compared to RA, only the (all-E)-UAB retinoids containing bulky R1 and R2 groups were effective in this chemoprevention assay. (9Z)-RA displayed equal capacity as RA to prevent papillomas, while the 9Z-isomers of the UAB retinoids were much less effective. Taken together, these studies demonstrate that the cyclohexenyl ring substituents of 6-s-trans-UAB retinoids are important for their biological activities and that the chemopreventive effect of the all-E-isomers of these retinoids correlates well with their capacity to bind to RARs and activate RAR/RXR-mediated transcription.
Myotonic dystrophy type 2 (2003)

DM2 is present in a large number of families of northern European ancestry. Clinically, DM2 resembles adult-onset DM1, with myotonia, muscular dystrophy, cataracts, diabetes, testicular failure, hypogammaglobulinemia, and cardiac conduction defects. An important distinction is the lack of a congenital form of DM2. The clinical and molecular parallels between DM1 and DM2 indicate that the multisystemic features common to both diseases are caused by CUG or CCUG expansions expressed at the RNA level.
Optically pumped dynamic nuclear hyperpolarization in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mmultiscripts><mml:mi mathvariant="normal">C</mml:mi><mml:mprescripts/><mml:none/><mml:mn>13</mml:mn></mml:mmultiscripts></mml:math>-enriched diamond (2019)

We investigate nuclear spin hyperpolarization from optically polarized nitrogen vacancy centers in isotopically enriched diamonds with $^{13}\mathrm{C}$ concentrations up to 100%. $^{13}\mathrm{C}$ enrichment leads to a nitrogen vacancy electron spin resonance with a complex hyperfine structure and dynamic nuclear polarization enhancement profile. We show that strongly coupled $^{13}\mathrm{C}$ spins in the first shell surrounding a nitrogen vacancy center generate resolved hyperfine splittings, but do not act as an intermediary in the transfer of hyperpolarization of bulk nuclear spins. High levels of $^{13}\mathrm{C}$ enrichment are desirable to increase the efficiency of hyperpolarization for magnetic resonance signal enhancement, imaging contrast agents, and as a platform for quantum sensing and many-body physics.
Prenatal Diagnosis of Fragile X Syndrome by Direct Detection of the Unstable DNA Sequence (1991)

FRAGILE X syndrome is the most common form of familial mental retardation.1 Its prenatal diagnosis has relied on cytogenetic detection of the fragile X chromosome in cultured amniotic fluid, chorionic-villus cells, or fetal blood obtained by cordocentesis. The rate of misdiagnosis is about 5 percent and is due to rare false positive and more frequent false negative diagnoses.2 A molecular-genetic approach using DNA polymorphisms linked to the fragile site is feasible for diagnosis, but the results are probabilistic rather than absolutely diagnostic.3 , 4 The fragile X syndrome has recently been shown to be characterized by an unstable DNA sequence that can . . .
Watermarking-based copyright protection of sequential functions (2003)

Watermarking is proposed as a means to protect intellectual property contents of electronic systems from copyright infringement. The technique consists of implanting indelible stamps in the circuit's inner structure, while not disrupting its functionality or degrading its performance. In this paper a novel method is proposed for the creation of watermarks in regular sequential functions operating on finite input/output sets. This is an important class of circuits, as it is the basis of most digital controllers. Algorithms are proposed for implanting and detecting watermarks so as to minimize implementation overhead for a specified level of robustness.
Low drive field amplitude for improved image resolution in magnetic particle imaging (2015)

To balance resolution, signal-to-noise ratio, specific absorption rate, and magnetostimulation requirements, the drive field can be a low amplitude and high frequency. Continued research into how the MPI drive field affects relaxation and its adverse effects will be crucial for developing new nanoparticles tailored to the unique physics of MPI. Moreover, this theory informs researchers how to design scanning sequences to minimize relaxation-induced blurring for better spatial resolution or to exploit relaxation-induced blurring for MPI with molecular contrast.
Rhodanine Derivatives as Selective Protease Inhibitors Against Bacterial Toxins (2008)

In this study, we analyzed a series of rhodanine derivatives, as potential inhibitors of bacterial toxins, namely the proteases anthrax lethal factor and the botulinum neurotoxin type A. Conducting an extensive structure-activity relationship study on rhodanine derivatives, we profiled their selectivity against the two bacterial toxins and two related human metalloproteases using in vitro assays. In addition, we examined initial in vitro ADME-Tox properties of selected compounds and their ability to protect lethal factor-induced cell death of macrophages. These data allowed the selection of one additional drug candidate for which preliminary in vivo efficacy studies against anthrax spores were conducted. Integration of these results with our structure-activity relationship studies provides a framework for the development of potential drug candidates against anthrax and botulinum.