gebhart/patrepeval huggingface dataset:
Crystal structure and functional analysis of tetracenomycin ARO/CYC: Implications for cyclization specificity of aromatic polyketides (2008)

Polyketides are a class of natural products with highly diverse chemical structures and pharmaceutical activities. Polyketide cyclization, promoted by the aromatase/cyclase (ARO/CYC), helps diversify aromatic polyketides. How the ARO/CYC promotes highly specific cyclization is not well understood because of the lack of a first-ring ARO/CYC structure. The 1.9 A crystal structure of Tcm ARO/CYC reveals that the enzyme belongs to the Bet v1-like superfamily (or STAR domain family) with a helix-grip fold, and contains a highly conserved interior pocket. Docking, mutagenesis, and an in vivo assay show that the size, shape, and composition of the pocket are important to orient and specifically fold the polyketide chain for C9-C14 first-ring and C7-C16 second-ring cyclizations. Two pocket residues, R69 and Y35, were found to be essential for promoting first- and second-ring cyclization specificity. Different pocket residue mutations affected the polyketide product distribution. A mechanism is proposed based on the structure-mutation-docking results. These results strongly suggest that the regiospecific cyclizations of the first two rings and subsequent aromatizations take place in the interior pocket. The chemical insights gleaned from this work pave the foundation toward defining the molecular rules for the ARO/CYC cyclization specificity, whose rational control will be important for future endeavors in the engineered biosynthesis of novel anticancer and antibiotic aromatic polyketides.
Demosaicing for RGBZ sensor (2013)

In this paper, we proposed a new technique for demosaicing a unique RGBZ color-depth imaging sensor, which captures color and depth images simultaneously, with a specially designed color-filter-array (CFA) where two out of six RGB color rows are replaced by “Z” pixels that capture depth information but no color information. Therefore, in an RGBZ image, the red, green and blue colors are more sparsely sampled than in a standard Bayer image. Due to the missing rows in the data image, commonly used demosaicing algorithms for the standard Bayer CFA cannot be applied directly. To this end, our method first fills-in the missing rows to reconstruct a full Bayer CFA, followed by a color-selective adaptive demosaicing algorithm that interpolates missing color components. In the first step, unlike common bilinear interpolation approaches that tend to blur edges, our edge-based directional interpolation approach, derived from de-interlacing techniques, emphasizes reconstructing more straight and sharp edges with fewer artifacts and thereby preserves the vertical resolution in the reconstructed the image. In the second step, to avoid using the newly estimated pixels for demosaicing, the bilateral-filter-based approach interpolates the missing color samples based on weighted average of adaptively selected known pixels from the local neighborhoods. Tests show that the proposed method reconstructs full color images while preserving edges details, avoiding artifacts, and removing noise with high efficiency.
Thermal resistance of ultrasound probe cable (2017)

Ultrasound probe cable for 3D and 4D designs must efficiently dissipate the higher heat of probe head piezoelectric elements. A typical ultrasound probe cable consists of many micro-coaxial cables with an overall shield and jacket. By simply changing materials and termination methods, a significant reduction of heat can be transferred and dissipated through the cable. We will show our analysis of the ability of removing this heat through a redesigned thermal connection of the probe head to the shielding material.
Evidential Deep Learning to Quantify Classification Uncertainty (2018)

Deterministic neural nets have been shown to learn effective predictors on a wide range of machine learning problems. However, as the standard approach is to train the network to minimize a prediction loss, the resultant model remains ignorant to its prediction confidence. Orthogonally to Bayesian neural nets that indirectly infer prediction uncertainty through weight uncertainties, we propose explicit modeling of the same using the theory of subjective logic. By placing a Dirichlet distribution on the class probabilities, we treat predictions of a neural net as subjective opinions and learn the function that collects the evidence leading to these opinions by a deterministic neural net from data. The resultant predictor for a multi-class classification problem is another Dirichlet distribution whose parameters are set by the continuous output of a neural net. We provide a preliminary analysis on how the peculiarities of our new loss function drive improved uncertainty estimation. We observe that our method achieves unprecedented success on detection of out-of-distribution queries and endurance against adversarial perturbations.
Comparison Between Left Ventricular Electromechanical Mapping and Radionuclide Perfusion Imaging for Detection of Myocardial Viability (1998)

In patients with myocardial ischemia, LV mapping, compared with myocardial perfusion imaging, shows (1) mild reduction of endocardial voltage potentials and LS in segments with reversible perfusion defects and (2) profound electromechanical impairment in segments with fixed perfusion defects. Thus, such an LV mapping procedure may allow the detection on-line of myocardial viability in the catheterization laboratory.
Hydrogen peroxide release from mouse peritoneal macrophages: dependence on sequential activation and triggering. (1977)

Using a specific and sensitive fluorometric assay, the H2O2 release from as few as 2 X 10(5) mouse peritoneal macrophages could be detected continuously and quantitated. It is emphasized that the assay measured H2O2 release, not production. Induction of H2O2 release required sequential application of two stimuli: the administration of an activating agent to the mice from 4 days to 10 wk before all harvest, and the exposure of the cells in vitro to a triggering agent. BCG was most effective as an activating agent, resulting in peritoneal macrophages which could be triggered to release H2O2 almost as copiously (8 nmol/10(6) macrophages per 5 min) as mouse peritoneal PMN (9 NMOL/10(6) PMN per 5 min). Casein and C. parvum could also serve as activators, but thioglycollate and FCS were ineffective after single injections. PMA was a potent triggering agent, resulting in a maximal rate of H2O2 release after a latency of about 40 s for cells in suspension. Other triggering agents included the ionophore A23187, concanavalin A in the presence of cytochalasin B, and phagocytosis. H2O2 release could be attributed to macrophages and PMN in peritoneal cell suspensions or in preparations of adherent peritoneal cells, but not to lymphocytes. Indirect evidence suggested that the H2O2 detected was formed from superoxide anion. These observations appear to justify renewed interest in the idea that H2O2 may be important in macrohpage antimicrobial and antitumor mechanisms.
Ultrahigh relaxation oscillation frequency (up to 30 GHz) of highly <i>p</i>-doped GaAs/GaAlAs multiple quantum well lasers (1987)

We have demonstrated a relaxation oscillation frequency (fr) of up to 30 GHz in highly p-doped (Be=1×1019 cm−3) GaAs/GaAlAs multiple quantum well (MQW) lasers grown by molecular beam epitaxy. This is the highest fr achieved at room temperature for III-V semiconductor lasers. The high fr is attained by the large differential gain in the p-doped MQW structure having a low threshold electron density resulted from the excess hole density in addition to the quantum size effect.
Black-box hamiltonian simulation and unitary implementation (2012)

We present general methods for simulating black-box Hamiltonians using quantum walks. These techniques have two main applications: simulating sparse Hamiltonians and implementing black-box unitary operations. In particular, we give the best known simulation of sparse Hamiltonians with constant precision. Our method has complexity linear in both the sparseness D (the maximum number of nonzero elements in a column) and the evolution time t, whereas previous methods had complexity scaling as D4 and were superlinear in t. We also consider the task of implementing an arbitrary unitary operation given a black-box description of its matrix elements. Whereas standard methods for performing an explicitly specified N × N unitary operation use O(N2) elementary gates, we show that a black-box unitary can be performed with bounded error using O(N2/3(log logN)4/3) queries to its matrix elements. In fact, except for pathological cases, it appears that most unitaries can be performed with only O(√N) queries, which is optimal.
MR evaluation of vertebral metastases: T1-weighted, short-inversion-time inversion recovery, fast spin-echo, and inversion-recovery fast spin-echo sequences. (1995)

STIR was superior to both T1-weighted and FSE (with and without fat saturation) for detection of metastatic lesions, in terms of both percent contrast and contrast-to-noise ratio and visibility. IRFSE was equal to STIR for the detection of metastasis by both subjective and objective criteria. T1-weighted, FSE, and fat-saturated FSE sequences were superior to STIR and IRFSE in the detection of epidural metastatic disease. IRFSE provided faster scanning time, which could be translated into greater resolution.
The improved central decoder of a multiple description and distributed codec for videos (2010)

Multiple description coding (MDC) provides stable wireless multimedia communications with the help of multiple transmission paths, while distributed video coding (DVC) effectively shifts the encoder complexity to decoder for mobile media devices. We proposed to combine MDC with DVC, abbreviated as MDVC, to construct a reliable and efficient video codec system. To improve the codec performance, the DPCM prediction gain is exploited from the correlations among sub-video sequences inside the MDVC to increase the reconstructed video quality. In addition, a MDVC central decoder control method, operated dynamically at frame-level, is proposed to improve the adaptation capability, as compared to the current MDC central decoder that selects one best description for the output video. The intra-and inter-correlations among MDC descriptions were investigated to make this frame selection decision for the central decoder. Simulations showed that the proposed MDVC control method demonstrates higher average PSNR and lower PSNR variations of the output videos, with the help of DPCM prediction gain and the efficient central decoder control method that correctly selected high quality WZ frames for low quality key-frames.
Genertion Mean Analysis of Resistance to Race 3 of Soybean Cyst Nematode (1993)

The soybean cyst nematode (SCN) ( Heterodera glycines Ichinohe) is a serious pest of soybean [( Glycine max (L.) Merr.]. Most genetic studies of resistance in soybean to SCN have used qualitative models, although continuous distributions of phenotypes from zero to many cysts have been observed. We investigated the mode of inheritance for resistance to Race 3 of SCN by weighted least squares regression analysis of generation means for genetic models having additive and dominance parameters. Reaction to SCN was determined by counting the white females present on plant roots 30 d after inoculation. Four crosses, including one reciprocal, were made between resistant and susceptible genotypes. The ancestry of the resistant genotypes (‘A20’, ‘Jack’, and ‘Cordell’) traces to different sources of SCN resistance. Six generation means (P 1 , P 2 , F l , F 2 , BC p1 , and BC P2 ) in three of the crosses, and four in one (P l , P 2 , F 1 , F 2 ), were used to estimate the genetic effects contained in the means. The data were transformed for analysis because they were not normally distributed. The results indicated that an additive genetic model was sufficient to explain most of the genetic variation for resistance to Race 3 in each cross. Analysis of the pooled data from all crosses, however, indicated the presence of dominance effects as well. Recovery of parental phenotypes in the F 2 and backcross populations indicated that no more than four genes were involved in the inheritance of the trait. Estimates for broad sense heritabilities on single plant basis ranged from 0.48 to 0.81. The relatively high heritability and additive genetic control indicate that breeder should be able to select genotypes with an intermediate level of resistance.
Evidence for Aharonov-Bohm effect with magnetic field completely shielded from electron wave (1986)

Evidence for the Aharonov-Bohm effect was obtained with magnetic fields shielded from the electron wave. A toroidal ferromagnet was covered with a superconductor layer to confine the field, and further with a copper layer for complete shielding from the electron wave. The expected relative phase shift was detected with electron holography between two electron beams, one passing through the hole of the toroid, and the other passing outside. The experiment gave direct evidence for flux quantization also.
Optimal phase contrast in common-path interferometry (2001)

We have developed an analytical model for the design and optimization of common-path interferometers (CPI's) based on spatial filtering. We describe the mathematical analysis in detail and show how its application to the optimization of a range of different CPI's results in the development of a graphical framework to characterize quantitatively CPI performance. A detailed analytical treatment of the effect of curvature in the synthetic reference wave is undertaken. We show that it is possible to improve the linearity and fringe accuracy of certain standard interferometers by a modification of the Fourier filter, and we propose and analyze a dual CPI system for the unambiguous mapping of phase to intensity over the complete input phase range.
Type II Diabetes and Incidence of Estrogen Receptor Negative Breast Cancer in African American Women (2017)

White women with type II diabetes (T2D) have an estimated 20% increased risk of developing breast cancer. Little is known about associations by breast cancer subtype or among African American (AA) women, who are disproportionately affected by T2D and estrogen receptor negative (ER-) breast cancer. We assessed the relation of T2D to incidence of ER- and ER+ breast cancer in data from the Black Women's Health Study, a prospective cohort of AA women enrolled in 1995 and followed biennially. During 847,934 person-years of follow-up, there were 1,851 incident invasive breast cancers, including 914 ER+ and 468 ER- cases. Multivariable Cox proportional hazards models were used to compute HRs for breast cancer incidence associated with T2D relative to no T2D, controlling for body mass index (BMI) and other potential confounders. The HR for T2D relative to no T2D was 1.18 [95% confidence interval (CI) 1.00-1.40] for overall breast cancer incidence, with the increase accounted for by ER- cancer: HRs were 1.02 (95% CI, 0.80-1.31) for ER+ and 1.43 (95% CI, 1.03-2.00) for ER- cancer. The HR for T2D and ER- breast cancer was highest among nonobese women (1.92; 95% CI, 1.22-3.04). The findings suggest that AA women with T2D are at increased risk of developing ER- breast cancer and that poor metabolic health may be more important than obesity for this subtype. Given the high prevalence of T2D in AA women, the observed association could, in part, explain racial disparities in incidence of ER- breast cancer. <i>Cancer Res; 77(22); 6462-9. ©2017 AACR</i>.
Outpatient-based Subcutaneous Interleukin-2 Monotherapy in Advanced Renal Cell Carcinoma: an Update (1996)

To minimize interleukin-2-related toxicity while retaining its efficacy, a treatment schedule utilizing subcutaneous IL-2 was evaluated in a phase II setting. Eighty unselected, consecutive patients with metastatic or recurrent renal cell carcinoma (RCC), mean age 58 years (range, 21 to 76), received IL-2 on an outpatient basis, 5 days per week for 4 or 6 consecutive weeks. During the first 5-day cycle, a dose of 18 million IU IL-2 was administered once a day; during subsequent cycles the dose in the first two days was reduced to 9 million IU. Two 6-week or three 4-week courses were given maximally. Patients who had completed at least one full course were considered evaluable. To circumvent flu-like symptoms, all patients received a maximum oral dose of 3 g acetaminophen daily. Seventy-seven patients were assessable for response. Three (4%) complete responses (CR) and 6 (8%) partial responses (PR) were observed, and 44 (57%) patients had stable disease (SD). Response durations were 64, 29, 29+ months for the CR and 2, 6, 8, 11, 32, 47 months for the PR. The median length of survival of all patients was 12 months, whereas the median survival of responders and non-responders was 35+ and 10+ months, respectively (P < 0.001). Side effects included fever, chills, nausea, vomiting, and transient inflammation and induration at the injection sites. These complications were acceptable, even in the patients with concomitant disease, and completely disappeared after cessation of IL-2. Subcutaneous IL-2 mediates antitumor responses, has limited side effects and is also suitable for elderly RCC patients with concomitant disease.
Cellular Ceramics (2005)

Foreword by David J. Green. Preface. 1 Introduction. 1.1 Cellular Solids - Scaling of Properties. 1.2 Liquid Foams - Precursors for Solid Foams. 2 Manufacturing. 2.1 Ceramic Foams. 2.2 Honeycombs. 2.3 3D Periodic Strutures. 2.4 Connected Fibers: Fiber Felts and Mats. 2.5 Microcellular Ceramics from Wood. 2.6 Carbon Foams. 2.7 Glass Foams. 2.8 Hollow Spheres. 2.9 Cellular Concrete. 3 Structure. 3.1 Characterization of Structure and Morphology. 3.2 Modelling Structure-Property Relationships in Random Cellular Material. 4 Properties. 4.1 Mechanical Properties. 4.2 Permeability. 4.3 Thermal Properties. 4.4 Electrical Properties. 4.5 Acoustic Properties. 5 Applications. 5.1 Liquid Metal Filtration. 5.2 Gas (Particulate) Filtration. 5.3 Kiln Furnitures. 5.4 Heterogeneously Catalysed Processes with Porous Cellular Ceramic Monoliths. 5.5 Porous Burners. 5.6 Acoustic Transfer in Ceramic Surfac Burners. 5.6 Solar Radiation Conversion. 5.7 Biomedical Applications: Tissue Engineering. 5.9 Interpenetrating Composites. 5.10 Porous Media in Internal Combustion Engines. 5.11 Other Developments and Special Applications. Concluding Remarks.
Matrix metalloproteinase-2 is required for the switch to the angiogenic phenotype in a tumor model (2000)

Among the earliest and most important stages during tumorigenesis is the activation of the angiogenic process, an event that is termed the "switch to the angiogenic phenotype." We have developed an in vivo system that can reliably recapitulate the stages in tumor development that represent this transition. Using this model, we have harvested and studied tumor nodules that can be distinguished from each other on the basis of their degree of vascularization. Angiogenic tumor nodules were characterized by the presence of capillary vessels as determined by factor VIII immunohistochemistry, and both angiogenic and proteolytic activities in vitro. In contrast, preangiogenic nodules were devoid of microvessels and showed little angiogenic or proteolytic activity in vitro. Addition of a specific metalloproteinase inhibitor resulted in the abrogation of both angiogenic and proteolytic activities of the angiogenic nodules in vitro. Comparative substrate gel electrophoresis detected the presence of a prominent matrix metalloproteinase (MMP-2) in the angiogenic nodules when compared with the preangiogenic ones. Suppression of MMP-2 activity by antisense oligonucleotides in the vascular nodules resulted in the loss of angiogenic potential both in vitro and in vivo in the chick chorioallantoic membrane assay. Moreover, this suppression of MMP-2 activity in angiogenic nodules inhibited tumor growth in vivo by approximately 70%. These results strongly implicate the activity of MMP-2 as a requirement for the switch to the angiogenic phenotype and validate this model as a reliable and reproducible tool by which to study other cellular and biochemical factors involved in the acquisition of the angiogenic phenotype.
Regional Body Composition: Cross‐calibration of DXA Scanners—QDR4500W and Discovery Wi (2009)

Differences exist in body composition assessed by dual-energy X-ray absorptiometers (DXAs) between devices produced by different manufacturers and different models from the same manufacturer. Cross-calibration is needed to allow body composition results to be compared in multicenter trials or when scanners are replaced. The aim was to determine reproducibility and extent of agreement between two fan-beam DXA scanners (QDR4500W, Discovery Wi) for body composition of regional sites. The sample was: 39 women 50.6 +/- 9.6 years old with BMI 26.8 +/- 5.5 kg/m(2), body fat 33 +/- 7%. Four whole body scans (two on each device) were performed over 3 weeks. Major variables were fat mass, nonosseous lean mass, and bone mineral content (BMC) for the truncal and appendicular regions. Extent of agreement was assessed using Bland and Altman plots. Both devices demonstrated good precision with mean test-retest differences close to zero for fat mass, nonosseous lean mass, and BMC of the truncal and appendicular regions. Evaluation of interdevice agreement revealed significant differences for truncal and appendicular BMC, nonosseous lean mass, and fat mass. The greatest interdevice difference was for truncal fat mass (0.69 +/- 0.60 kg). Differences in truncal and appendicular fat mass increased in magnitude at higher mean values. Furthermore, differences in truncal and appendicular fat mass were strongly related to BMI (R = -0.61, R = -0.55, respectively). In conclusion, in vivo cross-calibration is important to ensure comparability of regional body composition data between scanners, especially for truncal fat mass and for subjects with higher BMI.
Woofer-tweeter deformable mirror control for closed-loop adaptive optics: theory and practice (2014)

Deformable mirrors with very high order correction generally have smaller dynamic range of motion than what is required to correct seeing over large aperture telescopes. As a result, systems will need to have an architecture that employs two deformable mirrors in series, one for the low-order but large excursion parts of the wavefront and one for the finer and smaller excursion components. The closed-loop control challenge is to a) keep the overall system stable, b) avoid the two mirrors using control energy to cancel each others correction, c) resolve actuator saturations stably, d) assure that on average the mirrors are each correcting their assigned region of spatial frequency space. We present the control architecture and techniques for assuring that it is linear and stable according to the above criteria. We derived the analytic forms for stability and performance and show results from simulations and on-sky testing using the new ShaneAO system on the Lick 3-meter telescope.
New Approach for the Removal of Metal Ions from Water:  Adsorption onto Aquatic Plants and Microwave Reaction for the Fabrication of Nanometals (2005)

We adsorb heavy metal ions such as Ag(+), Pb(2+), and Ru(3+) onto an aquatic plant and convert the adsorbed ions to the corresponding nanometallic particles by the polyol reaction carried out in a microwave oven.