gebhart/patrepeval huggingface dataset:
Deep learning image reconstruction method for limited-angle ultrasound tomography in prostate cancer (2019)

Problem: The gold standard for prostate cancer diagnosis is B-mode transrectal ultrasound-guided systematic core needle biopsy. However, cancer is indistinguishable under ultrasound and thus additional costly imaging methods are necessary to perform targeted biopsies. Speed of sound is a potential biomarker for prostate cancer and has the potential to be measured using ultrasound tomography. Given the physical constraints of the prostate’s anatomy, this work explores a simulation study using deep learning for limited-angle ultrasound tomography to reconstruct speed of sound. Methods: A deep learning-based image reconstruction framework is used to address the limited-angle ultrasound tomography problem. The training data is generated using the k-wave acoustic simulation package. The general network structure is composed of a series of dense fully-connected layers followed by an encoder and a decoder network. The basic idea behind this neural network is to encode a time of flight map into a lower dimension representation that can then be decoded into a speed of sound image. Results and Conclusions: We show that limited-angle UST is feasible in simulation using an auto-encoder-like DL framework. There was a mean absolute error of 7.5 ± 8.1 m/s with a maximum absolute error of 139.3 m/s. Future validation on experimental data will further assess their ability in improving limited-angle ultrasound tomography.
ChemInform Abstract: Electronic Absorption Spectra of Binuclear Rhodium(I) Isocyanide Complexes. Comparison of Ground‐State and dσ* → pσ Excited‐State Bond Energies. (1989)

Abstract The polarized single‐crystal absorption spectra of the complexes (I) are measured and analyzed.
Protection scheme for passive optical networks shared between a fixed and a mobile operator (2012)

A protection scheme for passive optical networks (PONs) is proposed. It supports partial protection, relevant when reusing existing PON infrastructure for LTE-Advanced mobile network backhaul. We provide a protection level and cost analysis.
Metabolic Activation of Benzo(a)pyrene in SENCAR and BALB/c Mouse Embryo Cell Cultures (1986)

The metabolism and DNA binding of benzo(a)pyrene [B(a)P] were compared in early passage mouse embryo cell cultures prepared from SENCAR mice, a strain especially susceptible to two-stage tumorigenesis, and BALB/c mice, a strain relatively resistant to two-stage tumorigenesis. Cultures from both strains metabolized similar amounts of B(a)P; however, the proportion of water-soluble metabolites formed was higher in the BALB/c cultures than in the SENCAR cultures. The major metabolites formed in cultures from both strains were B(a)P-9,10-diol, B(a)P-7,8-diol and the glucuronic acid conjugate of 3-hydroxy-B(a)P. The level of binding of B(a)P to DNA was greater in the SENCAR mouse embryo cell cultures than in the BALB/c cultures after 5, 24, and 48 hr exposure. The major B(a)P-DNA adduct formed in B(a)P-treated cultures from both strains was the adduct formed by reaction of (+)anti-B(a)P-7,8-diol-9,10-epoxide [anti-B(a)PDE, the isomer with the epoxide and the benzylic hydroxyl on opposite faces of the molecule] with the exocyclic amino group of deoxyguanosine. Immobilized boronate chromatography followed by high-performance liquid chromatography demonstrated the presence of small amounts of syn-B(a)PDE (the isomer with the epoxide and benzylic hydroxyl on the same face of the molecule)-DNA adducts. The proportions of these amounts were similar in cultures from both strains. The results suggest that SENCAR mouse embryo cell cultures may convert less B(a)P to water-soluble metabolites and more to DNA-binding metabolites than BALB/c mouse embryo cells.(ABSTRACT TRUNCATED AT 250 WORDS)
A Cost-Effectiveness Analysis of Alternative Disease Management Strategies in Patients with Crohn's Disease Treated with Azathioprine or 6-Mercaptopurine (2005)

The addition of alternative strategies to CC may improve AZA outcomes and reduce the total cost of care for steroid treated chronically active CD patients, with TPMT being more beneficial for initial response to treatment and MM being more beneficial for sustained response to treatment.
Site-directed deletions of Abelson murine leukemia virus define 3' sequences essential for transformation and lethality (1983)

Abelson murine leukemia virus (A-MuLV) encodes a single protein with tyrosine kinase activity that can transform fibroblast cell lines in vitro and lymphoid target cells in vitro and in vivo. Expression of kinase-active A-MuLV protein can result in a deleterious effect on transformed fibroblast populations, leading to cell death or selection for nonlethal mutants of the virus. These mutants retain expression of the kinase activity but have lost large portions of the carboxy terminus of the Abelson protein. To more precisely map the sequences involved in this lethal effect, we have isolated a series of site-directed deletions from a DNA clone of the P160 wild-type strain of A-MuLV. In addition, a number of unexpected, spontaneous deletions occurring during transfection of NIH 3T3 cells were isolated. These deletions result in expression of carboxy-terminal truncated forms of the A-MuLV protein ranging from 130,000 to 84,000 in molecular weight. Analysis of the transforming and lethal activities of each mutant recovered in its RNA viral form shows that the transformation-essential and lethal-essential sequences do not overlap. These data and our previous work suggest that a function carried by the carboxy-terminal region of the A-MuLV protein acts in cis with the kinase-essential region to mediate the lethal effect.
Selection of Optimal Modulation Frequencies in Multi-Frequency DOT (2006)

Use of multi-frequency DOT for reconstruction of optical properties is investigated. Choosing appropriate frequency values by considering system noise and using multi-parameter Tikhonov regularization, improvement is demonstrated using phantom data with multi-frequency reconstruction.
Enhancing Gas-Reservoir Characterization by Integrating a Reliable Formation-Testing Permeability Method Into the Workflow (2011)

Abstract Permeability is one of the most important parameters in determining the productivity index and potential reserves of a producing interval. Very few instruments, however, are available for use on discovery and appraisal wells that can make this measurement. Although cores can be used, this process always leaves some uncertainty concerning the in-situ permeability and its variation across the interval. Moreover, the results are often not available as they are needed to assist in decision making. Nuclear magnetic resonance (NMR) logging tools can provide a continuous log of permeability; however, a core study is typically needed to calibrate the log. Formation testers can determine the mobility (permeability/viscosity), but the viscosity must be estimated to determine the permeability. This paper presents methods for estimating the viscosity and then deriving permeability from the analysis of formation tester pretests. The required viscosity estimate could be obtained by considering the properties of the mud system used when drilling, given that pretest’s radius of investigation is limited to the invaded zone surrounding the wellbore. The fluid occupying the pore space in this region must be considered as mud filtrate, especially in permeable zones that are of greatest potential. After obtaining the viscosity estimate and expressing the results of the formation pretest analysis in terms of permeability, we are able to validate them by comparing them with the actual core data. We can also use them to quantify the total reservoir flow capacity (kh) by calibrating the NMR permeability log or by up-scaling the results obtained at several depth points across the zone. Total reservoir-flow capacity (kh) can then be used to accurately forecast production capacity. In addition, this result could already compare or be validated with the total kh result obtained from a long extended drill-stem test (DST) or production test in each zone if they are performed. In this paper, we address the steps involved in this process; field examples are included to validate all of these approaches. The primary goal of this study is to increase the use and confidence of the formation tester’s results.
Synthesis and Structure−Activity Relationship of Novel 6-Aryl-1,4- dihydrobenzo[d][1,3]oxazine-2-thiones as Progesterone Receptor Modulators Leading to the Potent and Selective Nonsteroidal Progesterone Receptor Agonist Tanaproget (2005)

Tanaproget represents a potential first-in-class nonsteroidal PR agonist for contraception with improved safety and side effect profiles versus currently available steroidal oral contraceptives. Additional SAR, biological activity, and structural information from a tanaproget/hPR-LBD (hPR-LBD = human progesterone receptor ligand binding domain) cocrystal structure will also be presented.
Shut-Down of Type IX Protein Secretion Alters the Host Immune Response to Tannerella forsythia and Porphyromonas gingivalis (2022)

<i>Tannerella forsythia</i> and <i>Porphyromonas gingivalis</i> target distinct virulence factors bearing a structurally conserved C-terminal domain (CTD) to the type IX protein secretion system (T9SS). The T9SS comprises an outer membrane translocation complex which works in concert with a signal peptidase for CTD cleavage. Among prominent T9SS cargo linked to periodontal diseases are the TfsA and TfsB components of <i>T. forsythia's</i> cell surface (S-) layer, the bacterium's BspA surface antigen and a set of cysteine proteinases (gingipains) from <i>P. gingivalis</i>. To assess the overall role of the bacterial T9SS in the host response, human macrophages and human gingival fibroblasts were stimulated with <i>T. forsythia</i> and <i>P. gingivalis</i> wild-type bacteria and T9SS signal peptidase-deficient mutants defective in protein secretion, respectively. The immunostimulatory potential of these bacteria was compared by analyzing the mRNA expression levels of the pro-inflammatory mediators IL-6, IL-8, MCP-1 and TNF-α by qPCR and by measuring the production of the corresponding proteins by ELISA. Shot-gun proteomics analysis of <i>T. forsythia</i> and <i>P. gingivalis</i> outer membrane preparations confirmed that several CTD-bearing virulence factors which interact with the human immune system were depleted from the signal peptidase mutants, supportive of effective T9SS shut-down. Three and, more profoundly, 16 hours post stimulation, the <i>T. forsythia</i> T9SS mutant induced significantly less production of cytokines and the chemokine in human cells compared to the corresponding parent strain, while the opposite was observed for the <i>P. gingivalis</i> T9SS mutant. Our data indicate that T9SS shut-down translates into an altered inflammatory response in periodontal pathogens. Thus, the T9SS as a potential novel target for periodontal therapy needs further evaluation.
Immolation of p-Aminobenzyl Ether Linker and Payload Potency and Stability Determine the Cell-Killing Activity of Antibody–Drug Conjugates with Phenol-Containing Payloads (2018)

The valine-citrulline (Val-Cit) dipeptide and p-aminobenzyl (PAB) spacer have been commonly used as a cleavable self-immolating linker in ADC design including in the clinically approved ADC, brentuximab vedotin (Adcetris). When the same linker was used to connect to the phenol of the cyclopropabenzindolone (CBI) (P1), the resulting ADC1 showed loss of potency in CD22 target-expressing cancer cell lines (e.g., BJAB, WSU-DLCL2). In comparison, the conjugate (ADC2) of a cyclopropapyrroloindolone (CPI) (P2) was potent despite the two corresponding free drugs having similar picomolar cell-killing activity. Although the corresponding spirocyclization products of P1 and P2, responsible for DNA alkylation, are a prominent component in buffer, the linker immolation was slow when the PAB was connected as an ether (PABE) to the phenol in P1 compared to that in P2. Additional immolation studies with two other PABE-linked substituted phenol compounds showed that electron-withdrawing groups accelerated the immolation to release an acidic phenol-containing payload (to delocalize the negative charge on the anticipated anionic phenol oxygen during immolation). In contrast, efficient immolation of LD4 did not result in an active ADC4 because the payload (P4) had a low potency to kill cells. In addition, nonimmolation of LD5 did not affect the cell-killing potency of its ADC5 since immolation is not required for DNA alkylation by the center-linked pyrrolobenzodiazepine. Therefore, careful evaluation needs to be conducted when the Val-Cit-PAB linker is used to connect antibodies to a phenol-containing drug as the linker immolation, as well as payload potency and stability, affects the cell-killing activity of an ADC.
Navigation Strategies for Exploring Indoor Environments (2002)

In this paper, we investigate safe and efficient map-building strategies for a mobile robot with imperfect control and sensing. In the implementation, a robot equipped with a range sensor builds apolygonal map (layout) of a previously unknown indoor environment. The robot explores the environment and builds the map concurrently by patching together the local models acquired by the sensor into a global map. A well-studied and related problem is the simultaneous localization and mapping (SLAM) problem, where the goal is to integrate the information collected during navigation into the most accurate map possible. However, SLAM does not address the sensor-placement portion of the map-building task. That is, given the map built so far, where should the robot go next? This is the main question addressed in this paper. Concretely, an algorithm is proposed to guide the robot through a series of “good” positions, where “good” refers to the expected amount and quality of the information that will be revealed at each new location. This is similar to the next-best-view (NBV) problem studied in computer vision and graphics. However, in mobile robotics the problem is complicated by several issues, two of which are particularly crucial. One is to achieve safe navigation despite an incomplete knowledge of the environment and sensor limitations (e.g., in range and incidence). The other issue is the need to ensure sufficient overlap between each new local model and the current map, in order to allow registration of successive views under positioning uncertainties inherent to mobile robots. To address both issues in a coherent framework, in this paper we introduce the concept of a safe region, defined as the largest region that is guaranteed to be free of obstacles given the sensor readings made so far. The construction of a safe region takes sensor limitations into account. In this paper we also describe an NBV algorithm that uses the safe-region concept to select the next robot position at each step. The new position is chosen within the safe region in order to maximize the expected gain of information under the constraint that the local model at this new position must have a minimal overlap with the current global map. In the future, NBV and SLAM algorithms should reinforce each other. While a SLAM algorithm builds a map by making the best use of the available sensory data, an NBV algorithm, such as that proposed here, guides the navigation of the robot through positions selected to provide the best sensory inputs.
Expression of Dog Microdystrophin in Mouse and Dog Muscles by Gene Therapy (2020)

Duchenne muscular dystrophy (DMD) is characterized by the absence of dystrophin. Several previous studies demonstrated the feasibility of delivering microdystrophin complementary DNA (cDNA) into mouse and normal nonhuman primate muscles by ex vivo gene therapy. However, these animal models do not reproduce completely the human DMD phenotype, while the dystrophic dog model does. To progress toward the use of the best animal model of DMD, a dog microdystrophin was transduced into human and dystrophic dog muscle precursor cells (MPCs) with a lentivirus before their transplantation into mouse muscles. One month following MPC transplantation, myofibers expressing the dog microdystrophin were observed. We also used another approach to introduce this transgene into myofibers, i.e., the electrotransfer of a plasmid coding for the dog microdystrophin. The plasmid was injected into mouse and dog muscles, and brief electric pulses were applied in the region of injection. Two weeks later, the transgene was detected in both animals. Therefore, ex vivo gene therapy and electrotransfer are two possible methods to introduce a truncated version of dystrophin into myofibers of animal models and eventually into myofibers of DMD patients.
Nod1 acts as an intracellular receptor to stimulate chemokine production and neutrophil recruitment in vivo (2006)

Nod1 is a member of family of intracellular proteins that mediate host recognition of bacterial peptidoglycan. To characterize immune responses mediated by Nod1, synthetic ligand compounds possessing enhanced ability to stimulate Nod1 were developed to study the function of Nod1. Stimulation of epithelial cells with Nod1 stimulatory molecules induced chemokines and other proinflammatory molecules that are important for innate immune responses and recruitment of acute inflammatory cells. Administration of Nod1 ligands into mice induced chemokines and recruitment of acute inflammatory cells, an activity that was abolished in Nod1-null mice. Microarray analysis revealed that Nod1 stimulation induces a restricted number of genes in intestinal epithelial cells compared with that induced by tumor necrosis factor (TNF) alpha. Nod1 stimulation did not induce TNFalpha, interleukin 12, and interferon gamma, suggesting that the primary role of Nod1 is to induce the recruitment of immune cells. These results indicate that Nod1 functions as a pathogen recognition molecule to induce expression of molecules involved in the early stages of the innate immune response.
Immunological properties of subcellular rat lymphocyte preparations. Primary allogeneic stimulation in vitro by fractions containing Ia (RT1-B), but not RT1-A antigens. (1980)

Rat thymocyte membrane fractions have been prepared which exhibit strain-specific primary mixed-lymphocyte reaction (MLR)-stimulating and Ia (RT1-B) antigenic properties. These preparations lack the antigenicity of classical, serologically-defined RT1-A (Ag-B) antigens, as defined by in vitro serologic assays. Furthermore, after immunization of allogeneic hosts, specific anti-Ia and MLR-blocking antibodies, but not anti-AgB, alloantibodies are elaborated. Thymidine suicide experiments show that the same clones respond to whole cells and the fragments made from those cells, and the response segregates appropriately in F2 progeny as a major histocompatibility complex (RT1)-linked phenomenon. Hence, it is possible to generate Ia-related allogeneic helper signals in primary, as well as secondary, in vitro responses, using subcellular membrane fragments that have restricted expression of RT1-B-, but not RT1-A-, encoded antigens.
High-Capacity and High-Spectral-Efficiency Seamless Fiber-Wireless System for High-Speed Trains (2016)

We propose a dual-hop network to high-speed trains by using a seamless fiber-millimeter-wave system for backhaul transmission and a high-speed in-train network. Transmission of a 64-QAM OFDM signal over the cascaded system is successfully confirmed.
Pesticide Detection With A Direct Optical Immunoprobe (2005)

SUMMARY An approach for the detection of pesticides in water based on antibodies and optical detection is described. Sdective detection of the analyte is achieved by pesticide specific antibodies in a competitive test scheme. Unoccupied antibodies from the test mixture bind at the surface of an optical transducer. The amount of antibodies bound is inversdy related to the concentration of analyte in the sample. The time resolved detection of them binding process is based on white light reflectometry or evanescent field refractometry. Test midpoints at O.5ppb have been achieved, putting the EU drinking water limit (0. lppb) within reach.
DOP033 Severely active ulcerative colitis is associated with high baseline infliximab clearance, reduced serum half-life and worse endoscopic outcomes (2017)

Background: Therapeutic drug monitoring is a useful tool to optimize infliximab (IFX) therapy in clinical practice. The relationship between IFX concentration and change from baseline in endoscopic disease activity during induction and maintenance therapy is unknown. Methods: Data from the randomized controlled ACT-1 and -2 trials encompassing 484 patients with ulcerative colitis treated with IFX therapy were analyzed. A two-compartment population pharmacokinetic model was used to estimate IFX clearance (CL) at baseline. The Mayo endoscopic score (MES; range 0–3, with 3 representing most severe inflammation) was available at Week (W) 0, W8 and W30. A test for a linear trend between mean baseline IFX CL and MES (0–3) at W8 was performed. A concentration-effect curve was established by sorting all patients from low to high IFX concentration at specific time points with corresponding change in MES from W0 to W8 (ΔMES8) and from W0 to W30 (ΔMES30). Receiver operating curve (ROC) analysis was performed to identify IFX concentration cut-points with combined maximal sensitivity and specificity that corresponded to a MES of 0–1 or 0. Patients with missing data at W8 and/or W30 were considered treatment failures. Results: A linear relationship was observed between baseline IFX CL and MES at W8 (p<0.001). Concurrently, approximate median baseline IFX half-life was significantly shorter in patients with W8 MES ≥2 vs W8 MES <2 (12 vs 15 days, respectively, p<0.001). In patients with higher IFX exposure during induction and maintenance therapy, ΔMES8 and ΔMES30 was greater (Fig. 1A and 1B, respectively). Figure 1. IFX concentration-effect curve. Each point is the median of ≥40 IFX concentrations at specified time-points, stratified in ascending order with corresponding change (Δ) in MES (with standard deviation) from (A) Week 0 to 8 and (B) Week 0 to 30. IFX cut-points of 26 ug/mL at W2, 11 ug/mL at W6 and 35 ug/mL at W8 correlated with W8 MES <2, and 5.0 ug/mL at W14 and 2.3 ug/mL at W30 correlated with W30 MES <2 (Table 1). Table 1. Association between IFX cut-points and endoscopic outcomes Conclusions: Ulcerative colitis patients with high baseline IFX CL may benefit from accelerated dosing during induction treatment to achieve drug exposure above the cut-points associated with short- and long-term mucosal healing.
Simulation, modeling, and testing embedded RF capacitors in low temperature cofired ceramic (2002)

Accurate circuit simulation models for embedded RF passive components in low temperature cofired ceramic (LTCC) provide a way to efficiently design high performance RF modules. This paper compares EM simulation results with lab measurement data for a set of embedded LTCC capacitors. Equivalent circuits based on EM simulation and measurement data describe all the important component properties including primary capacitance value, port parasitic capacitances, Q values as a function of frequency, and resonant frequencies. Models built from equivalent circuits accurately represent the performance of embedded RF module passive components when used with circuit simulation tools during RF module design. These models can also be used during IC design to simulate circuit operation in the RF module environment.