gebhart/patrepeval huggingface dataset:
Final Technique Report of SMIRTP (2018)

Positron emission tomography (PET) imaging agents play significantly roles in detection and management of diseases. There are urgent needs to increase output and translate probes more rapidly for clinical use. Moreover, there is a crucial lack of trained radiochemists and nuclear medicine physician scientists to meet the increasing demand of developing novel PET imaging probes for clinical use. With strong support and commitment from Office of Science, Department of Energy, coupled with an expanding interest in the benefits of molecular and biomedical imaging, Stanford Molecular Imaging Research and Training Program (SMIRT) has advanced generalizable strategies to develop PET agents and multimodality radiotracers that can target most cell surface receptors. These radioactive imaging agents have been based on novel protein scaffolds such as knottins and Affibodies, and newly developed gold nanoparticles and organic nanoparticles. The projects yielded several new classes of knottin-based imaging probes that target αvb6, αvb3, EGFR, melanin, etc. as single or multimodal imaging agents. More importantly, the projects firmly established the development of knottins based PET probes as a generalizable approach for many tumor targets. Three novel PET probes have been successfully developed from research lab and translated into pilot clinical patient imaging studies during the course of the funding period. We also increased the number of trained radiochemists/nuclear medicine physician-scientists and provided them with comprehensive training regarding probe development and the clinical translational process. The research opportunities of this SMIRT engaged trainees in cutting-edge projects with experienced mentors and improve cross-training between radiochemists and nuclear medicine physicians. The training enabled an overall understanding of the complete probe development and clinical translation process, and encouraged trainees to pursue rewarding careers in radionuclide based imaging.
Development of a Flavor Profile of `Gala' Apples Using OSME Sensory Technique (1995)

`Gala' is an early season apple variety that has a distinctive aroma and flavor. Studies were conducted to identify volatile compounds that contribute to `Gala' aroma. `Gala' apples were harvested at optimum maturity in a commercial orchard. Volatile compounds were trapped on activated charcoal using dynamic headspace sampling and eluted with carbon disulfide. Odor profiles of the samples were determined using OSME, a method developed at Oregon State Univ. that combines gas chromatography and olfactometry with a time-intensity scale. Three trained panelists described odor characteristics of compounds eluted through a sniff port of a gas chromatograph. Compounds were identified by matching Kovats indices with those of standards and also by mass spectrometry. Butyl acetate, 2-methyl butyl acetate, and pentyl acetate were characteristic of `Gala' apple. Methyl-2-methyl butyrate, ethyl-2-methyl butyrate, pentyl acetate, and butyl-2-methyl butyrate carried apple-like descriptors.
Requirement of the Pseudomonas aeruginosa CbrA Sensor Kinase for Full Virulence in a Murine Acute Lung Infection Model (2013)

Pseudomonas aeruginosa is an opportunistic pathogen that is a major cause of respiratory tract and other nosocomial infections. The sensor kinase CbrA is a central regulator of carbon and nitrogen metabolism and in vitro also regulates virulence-related processes in P. aeruginosa. Here, we investigated the role of CbrA in two murine models of infection. In both peritoneal infections in leukopenic mice and lung infection models, the cbrA mutant was less virulent since substantially larger numbers of cbrA mutant bacteria were required to cause the same level of infection as wild-type or complemented bacteria. In contrast, in the chronic rat lung model the cbrA mutant grew and persisted as well as the wild type, indicating that the decrease of in vivo virulence of the cbrA mutant did not result from growth deficiencies on particular carbon substrates observed in vitro. In addition, a mutant in the cognate response regulator CbrB showed no defect in virulence in the peritoneal infection model, ruling out the involvement of certain alterations of virulence properties in the cbrA mutant including defective swarming motility, increased biofilm formation, and cytotoxicity, since these alterations are controlled through CbrB. Further investigations indicated that the mutant was more susceptible to uptake by phagocytes in vitro, resulting in greater overall bacterial killing. Consistent with the virulence defect, it took a smaller number of Dictyostelium discoideum amoebae to kill the cbrA mutant than to kill the wild type. Transcriptional analysis of the cbrA mutant during D. discoideum infection led to the conclusion that CbrA played an important role in the iron metabolism, protection of P. aeruginosa against oxidative stress, and the regulation of certain virulence factors.
State of zirconium and aluminum ions on silica gel surfaces modified by small amount of ZrO/sub 2/ and Al/sub 2/O/sub 3/: IR spectroscopy in diffusely scattered light (1987)

The state of zirconium and aluminum ions on silica gel surfaces modified by small additions of ZrO/sub 2/ and Al/sub 2/O/sub 3/ has been studied by IR spectroscopy in diffusely scattered light. Molecular hydrogen adsorbed at 77/sup 0/K was used as criterion for low-coordinated ions. It was shown that small amount of ZrO/sub 2/ are located mainly on the carrier surface, whereas a significant fraction of aluminum exists in a state inaccessible for adsorption of test molecules. Silica gel modified by ZrO/sub 2/ and Al/sub 2/O/sub 3/ is characterized by Lewis acid centers that form at low treating temperatures (> 470/sup 0/K for ZrO/sub 2/-SiO/sub 2/, and > 670/sup 0/K for Al/sub 2/O/sub 3/-SiO/sub 3/).
Correction of Penile Curvatures Caused by Unsuccessful Hypospadias Repair Using the Scrotal Septum Pedicled Skin Tube Principle Combined with Corporoplasty and a Modified Meatoglanuloplasty (1989)

Scrotal septum pedicled skin tube urethroplasty combined with a modified meatoglanuloplasty and corporoplsty were used in 2 adults. They had three previous hypospadias repair attempts in their childhood, leaving them with a meatus near the glans but with severe ventral penile curvature. Scrotal septum pedicled skin flaps used for the repair, by providing natural vascularization and offering more flexibility, allow the surgeon to reconstruct long urethral defects. The cosmetic and functional results of this combined technique are satisfactory. This principle can also be applied in adult hypospadias cases with deficient preputium in which the midanterior scrotum contains a shiny non-hair-bearing skin.
Agrin--A Bridge Between the Nervous and Immune Systems (2001)

Molecular mechanisms of osteogenesis and antibacterial activity of Cu-bearing Ti alloy in a bone defect model with infection in vivo,
Supplementary Figure 3C-3F from Discovery and Characterization of Novel Mutant FLT3 Kinase Inhibitors (2023)

Supplementary Figure 3C-3F from Discovery and Characterization of Novel Mutant FLT3 Kinase Inhibitors
Adjacent Track Interference in Heat-Assisted Magnetic Recording: Impact and Implications (2019)

Some aspects of the challenges to high track density heat-assisted magnetic recording (HAMR) are addressed with a focus on track interferences (adjacent as well as non-nearest neighbor erasure). Comparisons with corresponding conventional perpendicular magnetic recording (PMR) parameters are also made. Adjacent and non-nearest neighbor track erasure data from functional HAMR and PMR drives and simulation data of signal-to-noise ratio loss in HAMR are also presented.
SU‐E‐I‐54: Volumetric Breast Density: Comparison of Estimates From Tomosynthesis Reconstructions with Mammography (2014)

Purpose: To measure the volumetric breast density (VBD) from digital breast tomosynthesis (DBT) reconstructions and compare with estimates from mammography. Methods: A kernel‐based fuzzy c‐means algorithm developed to segment DBT reconstructed slices to provide anatomic priors for near‐infrared spectroscopy (NIRS) in a multimodality NIRS/DBT clinical‐prototype imaging system was used to quantitate VBD. The VBD was determined from 17 DBT reconstructions of 11 breasts from 9 subjects (6 subjects—unilateral 2‐view, 1 subject—unilateral craniocaudal (CC) view, 2 subjects—bilateral CC view) who underwent multimodality NIRS/DBT imaging. VBD from mammography (Quantra, Hologic Inc.) matched for subject, breast laterality and view was used for comparison. To account for differences in compressed breast thickness (T) between the modalities, the metric normalized VBD (nVBD = VBD/T) was considered. Results: All data satisfied normality assumption (Shapiro‐Wilks, p&gt;0.06). Pearson's correlation (r) and paired t‐tests were used for analysis. The normalized VBD (nVBD) was statistically correlated (r=0.66, p&lt;0.01) between the two modalities, but the VBD was not (r=0.47, p=0.06), as the compressed breast thickness (p=0.01, difference=6.6+/−9.8 mm) and the total breast volume (p&lt;0.01, difference=183+/−169 cc) were higher with mammography than with clinical‐prototype NIRS‐coupled DBT system, while the fibroglandular volume was not different (p=0.21). The intra‐modality nVBD assessed between 2‐views of the same breast (n=6) were better correlated (r=0.86, p=0.03) in DBT than in mammography (r=0.57, p=0.24). Conclusion: Normalized VBD (nVBD) could be a better metric when compressed breast thickness differs between the modalities. nVBD estimated from DBT is better correlated between 2‐views of the same breast than mammography and could improve the consistency in the estimate. The algorithm, in addition to providing anatomic priors for NIRS reconstruction, may also be suitable for breast density estimation. Ability to use DBT reconstructions could facilitate widespread adaptation. Future studies will investigate VBD from images acquired on a combined mammography/DBT system. This work was supported in parts by National Institutes of Health (NIH) grants R01CA139449 and R21CA176470. The contents are solely the responsibility of the authors and do not represent the official views of the NIH or the National Cancer Institute.
Provider backbone transport (2006)

The article consists of a Powerpoint presentation on provider backbone transport. The topics discussed include: Ethernet switches; Ethernet standards; telecommunications infrastructure; packet services; MPLS; IEEE 802.1ah hierarchy; MAC-in-MAC hierarchy and carrier networking technology.
Design framework for multifunctional additive manufacturing: Coupled optimization strategy for structures with embedded functional systems (2017)

The driver for this research is the development of multi-material additive manufacturing processes that provide the potential for multi-functional parts to be manufactured in a single operation. In order to exploit the potential benefits of this emergent technology, new design, analysis and optimization methods are needed. This paper presents a method that enables in the optimization of a multifunctional part by coupling both the system and structural design aspects. This is achieved by incorporating the effects of a system, comprised of a number of connected functional components, on the structural response of a part within a structural topology optimization procedure. The potential of the proposed method is demonstrated by performing a coupled optimization on a cantilever plate with integrated components and circuitry. The results demonstrate that the method is capable of designing an optimized multifunctional part in which both the structural and system requirements are considered.
Interferon Alpha, GM-CSF-Activated T Cells, and IL-6 in Renal Cell Carcinoma (2001)

Treatment of renal cell carcinoma (RCC) has historically involved surgical removal of the primary tumor when localized, but when presented with metastatic disease the options have been limited. Approximately 30% of patients present with metastatic disease implicating a generally poor prognosis. The most significant advances have occurred in the area of immunotherapy as treatment for metastatic disease. This is because RCC is generally resistant to chemotherapy and radiation. One of the major successes of immunotherapy has been with interleukin-2 (IL-2). Initial IL-2 therapy proved difficult due to the significant administrative and side effect problems that occurred. This led to numerous variations in dose scheduling and delivery to identify an optimal beneficial way of administering IL-2. In addition, investigation also led to other immunotherapy agents such as interferon and cellular therapy.
Long-Term Integrity of Waste Package Final Closure for HLW Geological Disposal, (II) Applicability of TIG Welding Method to Overpack Final Closure (2005)

Overpack, a high-level radioactive waste package for geological disposal, seals vitrified waste and in line with Japan's waste management program is required to isolate it from contact with groundwater for 1,000 years. In this study, TIG (Tungsten Inert Gas) welding method, a typical arc welding method and widely used in various industries, was examined for its applicability to seal a carbon steel overpack lid with a thickness of 190 mm. Welding conditions and welding parameters were examined for multi-layer welding in a narrow gap for four different groove depths. Weld joint tests were conducted and weld flaws, macro- and microstructure, and mechanical properties were assessed within tentatively applied criteria for weld joints. Measurement and numerical calculation for residual stress were also conducted and the tendency of residual stress distribution was discussed. These test results were compared with the basic requirements of the welding method for overpack which were pointed out in our first report. It is assessed that the TIG welding method has the potential to provide the necessary requirements to complete the final closure of overpack with a maximum thickness of 190 mm.
The case for simple, visible cache coherency (2008)

The shared memory research community has proposed many complex communication protocols that aim to eliminate specific performance bottlenecks, while still providing an easy-to-use communication interface. Although tailored protocols can eliminate some bottlenecks that arise in real applications, removing the cause of the bottleneck through software optimizations and bug fixes is cheaper to implement, faster to fix (once found), and requires no additional support by the hardware beyond a simple shared memory interface. In fact, in our experience, the choice of coherence protocol is much less important than providing an efficient hardware feedback that indentifies the source of the problem. Future cache-coherence research should focus efforts on illuminating memory system behavior, providing smarter tools to identify bottlenecks, and helping to eliminate them through software optimizations.
Efficient recovery of variational quantum algorithms landscapes using classical signal processing (2022)

We employ spectral analysis and compressed sensing to identify settings where a variational algorithm's cost function can be recovered purely classically or with minimal quantum computer access. We present theoretical and numerical evidence supporting the viability of sparse recovery techniques. To demonstrate this approach, we use basis pursuit denoising to efficiently recover simulated Quantum Approximate Optimization Algorithm (QAOA) instances of large system size from very few samples. Our results indicate that sparse recovery can enable a more efficient use and distribution of quantum resources in the optimisation of variational algorithms.
Lytic polysaccharide monooxygenase (LPMO) mediated production of ultra-fine cellulose nanofibres from delignified softwood fibres (2019)

An environmentally friendly, energy-efficient method for cellulose nanofibre (CNF) production from softwood holocellulose utilising oxidative enzymes, lytic polysaccharide monooxygenases (LPMOs).
Hypertriglyceridemia is Frequent in Endometrial Cancer Survivors (2013)

Our report highlights the importance of the relationship between endometrial cancer and lipid metabolism, which may aid in preventing cerebrovascular or cardiovascular diseases due to dyslipidemia and improving the quality of life in endometrial cancer survivors.
Fidelity of Eucaryotic DNA Polymerase δ Holoenzyme fromSchizosaccharomyces pombe (2000)

The fidelity of Schizosaccharomyces pombe DNA polymerase delta was measured in the presence or absence of its processivity subunits, proliferating cell nuclear antigen (PCNA) sliding clamp and replication factor C (RFC) clamp-loading complex, using a synthetic 30-mer primer/100-mer template. Synthesis by pol delta alone was distributive. Processive synthesis occurred in the presence of PCNA, RFC, and Escherichia coli single strand DNA-binding protein (SSB) and required the presence of ATP. "Passive" self-loading of PCNA onto DNA takes place in the absence of RFC, in an ATP-independent reaction, which was strongly inhibited by SSB. The nucleotide substitution error rate for pol delta holoenzyme (HE) (pol delta + PCNA + RFC) was 4.6 x 10(-4) for T.G mispairs, 5.3 x 10(-5) for G.G mispairs, and 4.5 x 10(-6) for A.G mispairs. The T.G misincorporation frequency for pol delta without the accessory proteins was unchanged. The fidelity of pol delta HE was between 1 and 2 orders of magnitude lower than that measured for the E. coli pol III HE at the same template position. This relatively low fidelity was caused by inefficient proofreading by the S. pombe polymerase-associated proofreading exonuclease. The S. pombe 3'-exonuclease activity was also extremely inefficient in excising primer-3'-terminal mismatches in the absence of dNTP substrates and in hydrolyzing single-stranded DNA. A comparison of pol delta HE with E. coli pol IIIalpha HE (lacking the proofreading exonuclease subunit) showed that both holoenzymes exhibit similar error rates for each mispair.
VersaPower: Power estimation for diverse FPGA architectures (2012)

This paper presents VersaPower, a tool capable of modelling the power usage of many different field programmable gate array (FPGA) architectures.The latest release of the academic FPGA CAD tool, Versatile Place and Route 6.0 (VPR), supports new architecture features such as fracturable look-up tables and complex logic blocks. Past FPGA power models do not support these new features. VersaPower is designed to work closely with VPR to provide power estimation for any architecture supported by this new CAD flow. This allows researchers to investigate the effects on power usage of both new FPGA architectures, as well as new CAD algorithms. VersaPower is designed to operate with modern CMOS technologies, and is validated against SPICE using 22 nm, 45 nm and 130 nm technologies. Results show that for common architectures, roughly 60% HDL of power consumption is due to the routing fabric, 30% from logic blocks and 10% from the clock network. Architectures ODN supporting fracturable LUTs require 5-10% more power, as each CLB has additional I/O pins, increasing the sizes of local interconnect crossbars and connection boxes.
Single input state, single-mode fiber-based polarization-sensitive optical frequency domain imaging by eigenpolarization referencing (2015)

Fiber-based polarization-sensitive optical frequency domain imaging is more challenging than free-space implementations. Using multiple input states, fiber-based systems provide sample birefringence information with the benefit of a flexible sample arm but come at the cost of increased system and acquisition complexity, and either reduce acquisition speed or require increased acquisition bandwidth. Here we show that with the calibration of a single polarization state, fiber-based configurations can approach the conceptual simplicity of traditional free-space configurations. We remotely control the polarization state of the light incident at the sample using the eigenpolarization states of a wave plate as a reference, and determine the Jones matrix of the output fiber. We demonstrate this method for polarization-sensitive imaging of biological samples.
Algebraic Dynamic Multilevel (ADM) Method for Immiscible Multiphase Flow in Heterogeneous Porous Media with Capillarity (2016)

An algebraic dynamic multilevel method (ADM) is developed for fully-implicit (FIM) simulations of multiphase flow in heterogeneous porous media with strong non-linear physics. The fine-scale resolution is defined based on the heterogeneous geological one. Then, ADM constructs a space-time adaptive FIM system on a dynamically defined multilevel nested grid. The multilevel resolution is defined using an error estimate criterion, aiming to minimize the accuracy-cost trade-off. ADM is algebraically described by employing sequences of adaptive multilevel restriction and prolongation operators. Finite-volume conservative restriction operators are considered whereas different choices for prolongation operators are employed for different unknowns. The ADM method is applied to challenging heterogeneous test cases with strong nonlinear heterogeneous capillary effects. It is illustrated that ADM provides accurate solution by employing only a fraction of the total number of fine-scale grid cells. ADM is an important advancement for multiscale methods because it solves for all coupled unknowns (here, both pressure and saturation) simultaneously on arbitrary adaptive multilevel grids. At the same time, it is a significant step forward in the application of dynamic local grid refinement techniques to heterogeneous formations without relying on upscaled coarse-scale quantities.
Ablation and thermal effects in treatment of hard and soft materials and biotissues using ultrafast-laser pulse-train bursts (2012)

Abstract Ultrafast laser pulses (≤1 ps) are qualitatively different in the nature of their interaction with materials, including biotissues, as compared to nanosecond or longer pulses. This can confer pronounced advantages in outcomes for tissue therapy or laser surgery. At the same time, there are distinct limitations of their strong-field mode of interaction. As an alternative, it is shown here that ultrafast laser pulses delivered in a pulse-train burst mode of radiant exposure can access new degrees of control of the interaction process and of the heat left behind in tissues. Using a laser system that delivers 1 ps pulses in 20 μs pulse-train bursts at 133 MHz repetition rates, a range of heat and energy-transfer effects on hard and soft tissue have been studied. The ablation of tooth dentin and enamel under various conditions, to assess the ablation rate and characterize chemical changes that occur, are reported. This is compared to ablation in agar gels, useful live-cell-culture phantom of soft tissues, and presenting different mechanical strength. Study of aspects of the optical science of laser-tissue interaction promises to make qualitative improvements to medical treatments using lasers as cutting and ablative tools.
A Measurement System for the Analysis of the Response of the Human Eye to the Light Flicker (2007)

The response of the human eye to flicker depends on the type of lamp used. Standard flickermeters measure the voltage across the lamp and assumes a 60-W incandescent lamp as a light source. When a different lamp is the light flicker source, standard flickermeters give erroneous results. This paper presents a dynamic model of the eye-brain response to flicker. The model is based on the analysis of the light emitted by the lamp. A suitable measurement system has been developed, and three different kinds of lamps have been considered. Experimental results show how the emitted light spectra and the human eye response to different colors combined to determine the level of annoyance. The uncertainty affecting such results, which arises from the hardware of the developed system, has been also estimated.