gebhart/patrepeval huggingface dataset:
Clinical stage T1c prostate cancer: Pathologic outcomes following radical prostatectomy in black and white men (2002)

BACKGROUND The incidence of prostate cancer in black men is 50% to 70% higher than among age-matched white men. Black men have a twofold higher mortality rate and overall tend to have higher serum prostate-specific antigen (PSA) levels than white men. To determine whether racial differences exist in men whose prostate cancer was diagnosed based solely on an elevated serum PSA level, we compared clinical and pathologic features in black and white men undergoing radical prostatectomy (RP) for clinical stage T1c prostate cancer. METHODS We used a prospectively collected database to identify all men undergoing RP for clinical T1c prostate cancer between July 1995 and October 2000. A total of 129 consecutive men (56 black men and 73 white men) were compared for age at diagnosis, serum PSA level, biopsy Gleason score, pathologic stage, RP specimen Gleason score, incidence of lymph node metastasis, and incidence of positive surgical margins. RESULTS Statistically significant differences were not found by race in patients' ages, serum PSA levels, biopsy Gleason score, pathologic stage, incidence of lymph node metastases, or incidence of positive surgical margins. The RP specimen Gleason score was more heterogeneous in black men than white men (P = 0.02). CONCLUSIONS Racial differences in the incidence and mortality rate of prostate cancer are well known, but differences in the clinical and pathologic features between black and white men with prostate cancer identified solely based on an elevated serum PSA level with negative results on digital rectal examination (clinical stage T1c ) have been poorly studied. Our results suggest that men with clinical stage T1c prostate cancer have similar clinical and pathologic findings regardless of race. These results suggest that early-detection programs using serum PSA testing for prostate cancer in black men potentially can result in improvements in prostate cancer outcomes in this high-risk group. Prostate 50: 236–240, 2002. © 2002 Wiley-Liss, Inc.
Comparison of the lymphatic transport of a lipophilic drug from vehicles containing α-tocopherol and/or triglycerides in rats (2001)

The applicability of alpha-tocopherol as a lymphotropic carrier for a highly lipophilic drug has been evaluated. Transport to the intestinal lymph of the highly lipophilic model drug, Lu28-179, in rats after administration to the stomach in an alpha-tocopherol emulsion was compared with lymphatic transport after administration of a sesame oil emulsion and an alpha-tocopherol/sesame oil emulsion. Lymphatic transport of the triglycerides and of alpha-tocopherol was determined. A conscious rat model was used, and the mesenteric lymph was collected. There was no significant difference between the cumulative masses of triglyceride from the two emulsions containing triglyceride 24 h after administration. Administration of an alpha-tocopherol emulsion seemed to induce mobilization of endogenous triglyceride. The lymphatic transport of alpha-tocopherol was less than 1 mg 24 h after administration of both emulsions containing alpha-tocopherol. The absorption of Lu28-179 from the alpha-tocopherol emulsion was very low, with a lymphatic recovery of 0.05%. When administered in an alpha-tocopherol/sesame oil emulsion, the recovery of Lu28-179 increased sevenfold to 0.35%. However, after administration of Lu28-179 in a sesame oil emulsion, the lymphatic recovery increased a further 13-fold to 4.5%. In conclusion, the study showed that alpha-tocopherol did not promote lymphatic absorption of Lu28-179 and thus was not a good lymphotropic carrier, as compared with sesame oil. Alpha-tocopherol in combination with sesame oil was not a good lymphotropic carrier either. The non-absorbed alpha-tocopherol fraction in the intestine might be able to prevent the absorption of Lu28-179.
The use of high‐energy irradiation in an investigation of the mechanism and kinetics of emulsion polymerization (1961)

Abstract The emulsion polymerization of styrene initiated by γ‐rays was studied using competitive particle growth and conventional techniques. With γ‐rays, the rate of free‐radical generation is independent of temperature, and the absorption of energy is uniform throughout the system. From the competitive growth experiments, the particle growth rates were similar to those of persulfate ion‐initiated systems and quite different from those of benzoyl peroxide‐initiated systems. From the conventional experiments, the number of particles increased approximately as the square of the emulsifier concentration for both γ‐ray and persulfate ion‐initiated polymerizations. With γ‐rays, the number of particles decreased with increasing temperature; the opposite was observed for persulfate. This may be explained by the relative rates of free‐radical generation of each system; for γ‐rays this rate is independent of temperature, while for persulfate, the activation energy for initiator decomposition is greater than that for polymerization propagation. For the γ‐ray system, the calculated values of k p increased with increasing particle size; the activation energy was 7.2 (σ = 0.59) kcal./mole. The calculated values of k t at 50°C. were 10 4 –10 5 l./mole/sec.
A New Lattice Representation and Sub-Optimal Decoding for ATSC 3.0 MIMO (2018)

This paper presents a new lattice representation for ATSC 3.0 MIMO which transforms 2×2 complex channel model into 4×4 real-valued linear system. It provides a better understanding of the ATSC 3.0 MIMO precoding and allows the design of simple decoding algorithms. Based on the new lattice representation, a new maximum-likelihood (ML) decoding algorithm is derived. Also, a sub-optimal decoding algorithm based on successive interference cancellation is proposed. The simulation results show that the new ML decoding achieves similar performance to the conventional ML decoder. Furthermore, the sub-optimal decoding algorithm can significantly reduce the decoding complexity.
Optical and Radio Seamless MIMO Transmission with 20-Gbaud QPSK (2012)

MIMO radio transmission seamlessly converted from an optical DP-QPSK signal is performed with a polarization-diversity digital coherent detection technique. Obtained total capacity of radio transmission is achieved 74.4 Gb/s with 7% FEC overhead.
Lateral migration of living cells in inertial microfluidic systems explored by fully three-dimensional numerical simulation (2013)

The effects of cell size and deformability on the lateral migration and deformation of living cells flowing through a rectangular microchannel has been numerically investigated and compared with the inertial-microfluidics data on detection and separation of cells. The results of this work indicate that the cells move closer to the centerline if they are bigger and/or more deformable and that their equilibrium position is largely determined by the solvent (cytosol) viscosity, which is much less than the polymer (cytoskeleton) viscosity measured in most rheological systems. Simulations also suggest that decreasing channel dimensions leads to larger differences in equilibrium position for particles of different viscoelastic properties, giving design guidance for the next generation of microfluidic cell separation chips.
Polarized Infrared Absorption Spectrum of Matrix-Isolated Methylperoxyl Radicals, CH3OO X 2A‘ ‘ (2001)

We have used a tandem pair of supersonic nozzles to produce clean samples of CH3OO radicals in cryogenic matrices. One hyperthermal nozzle decomposes azomethane (CH3NNCH3) to generate intense pulses of CH3 radicals, while the second nozzle alternately fires a burst of O2/Ar at the 20 K matrix. The CH3/O2/20 K argon radical sandwich acts to produce target methylperoxyl radicals: CH3 + O2 → CH3OO. The absorption spectra of the radicals are monitored with a Fourier transform infrared spectrometer. We report 10 of the 12 fundamental infrared bands of the methylperoxyl radical CH3OO, X̃ 2A‘ ‘, in an argon matrix at 20 K. The experimental frequencies (cm-1) and polarizations follow: the a‘ modes are 3032, 2957, 1448, 1410, 1180, 1109, 902, 492, while the a‘‘ modes are 3024 and 1434. We cannot detect the asymmetric CH3 rocking mode, ν11, nor the torsion, ν12. The infrared spectra of CH318O18O, 13CH3OO, and CD3OO have been measured as well in order to determine the isotopic shifts. The experimental frequencies, {ν}, for the methylperoxyl radicals are compared to harmonic frequencies, {ω}, resulting from a UB3LYP/6-311G(d,p) electronic structure calculation. Linear dichroism spectra were measured with photooriented radical samples in order to establish the experimental polarizations of most vibrational bands. The methylperoxyl radical matrix frequencies listed above are within ±2% of the gas-phase vibrational frequencies. A final set of vibrational frequencies for the CH3OO radical are recommended. See also http://ellison.colorado.edu/methylperoxyl.
Stereotyped synaptic connectivity is restored during circuit repair in the adult mammalian retina (2018)

Proper function of the central nervous system (CNS) depends on the specificity of synaptic connections between cells of various types. Cellular and molecular mechanisms responsible for the establishment and refinement of these connections during development are the subject of an active area of research [1-6]. However, it is unknown if the adult mammalian CNS can form new type-selective synapses following neural injury or disease. Here, we assess whether selective synaptic connections can be reestablished after circuit disruption in the adult mammalian retina. The stereotyped circuitry at the first synapse in the retina, as well as the relatively short distances new neurites must travel compared to other areas of the CNS, make the retina well suited to probing for synaptic specificity during circuit reassembly. Selective connections between short-wavelength sensitive cone photoreceptors (S-cones) and S-cone bipolar cells provides the foundation of the primordial blue-yellow&amp;nbsp;vision, common to all mammals [7-18]. We&amp;nbsp;take advantage of the ground squirrel retina, which has a one-to-one S-cone-to-S-cone-bipolar-cell&amp;nbsp;connection, to test if this connectivity can be&amp;nbsp;reestablished following local photoreceptor loss [8, 19]. We find that after in&amp;nbsp;vivo selective photoreceptor ablation, deafferented S-cone bipolar cells expand their dendritic trees. The new dendrites randomly explore the proper synaptic layer, bypass medium-wavelength sensitive cone photoreceptors (M-cones), and selectively synapse with S-cones. However, non-connected dendrites are not pruned back to resemble unperturbed S-cone bipolar cells. We show, for the first time, that circuit repair in the adult mammalian retina can recreate stereotypic selective wiring.
Quantum coherence in Fe 8 molecular nanomagnets (1999)

International audience
Monitoring Translation Activity of mRNA-Loaded Nanoparticles in Mice (2018)

Targeting mRNA to eukaryotic cells is an emerging technology for basic research and provides broad applications in cancer immunotherapy, vaccine development, protein replacement, and in vivo genome editing. Although a plethora of nanoparticles for efficient mRNA delivery exists, in vivo mRNA targeting to specific organs, tissue compartments, and cells remains a major challenge. For this reason, methods for reporting the in vivo targeting specificity of different mRNA nanoparticle formats will be crucial. Here, we describe a straightforward method for monitoring the in vivo targeting efficiency of mRNA-loaded nanoparticles in mice. To achieve accurate mRNA delivery readouts, we loaded lipoplex nanoparticles with Cre-recombinase-encoding mRNA and injected these into commonly used Cre reporter mouse strains. Our results show that this approach provides readouts that accurately report the targeting efficacy of mRNA into organs, tissue structures, and single cells as a function of the used mRNA delivery system. The method described here establishes a versatile basis for determining in vivo mRNA targeting profiles and can be systematically applied for testing and improving mRNA packaging formats.
Optimal coil design for well-logging applications (2002)

Transmitting and receiving antennas used in many well-logging tools are made up of ferrite-backed coils wound on a metallic cylinder. A critical requirement in the design of these coils is to produce a desired spatial variation of the magnetic field. In some other applications, MRI for instance, in addition to a specified spatial variation, it is also desirable to have low inductance (L) of coils to reduce switching time constants that depend on L/R where R is the coil resistance. In well-logging tools, it is often required to have uniformity of electromagnetic field along the axial direction over a specified range at a given radial distance from the tool-face. This requirement is met by placing several coils along the length of the tool. In this paper we discuss an application of genetic algorithms to determine coil position and the direction of current. A combination of FEM and superposition method is used to solve the forward problem. Numerical and experimental results are presented.
Distribution of tccP in Clinical Enterohemorrhagic and Enteropathogenic Escherichia coli Isolates (2005)

Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) are diarrheagenic pathogens that colonize the gut through the formation of attaching and effacing lesions, which depend on the translocation of effector proteins via a locus of enterocyte effacement-encoded type III secretion system. Recently, two effector proteins, EspJ and TccP, which are encoded by adjacent genes on prophage CP-933U in EHEC O157:H7, have been identified. TccP consists of a unique N-terminus region and several proline-rich domains. In this project we determined the distribution of tccP in O157:H7, in non-O157 EHEC, and in typical and atypical EPEC isolates. All the EHEC O157:H7 strains tested were tccP(+). Unexpectedly, tccP was also found in non-O157 EHEC, and in typical and atypical EPEC isolates, particularly in strains belonging to serogroups O26 (EHEC), O119 (typical EPEC), and O55 (atypical EPEC). We recorded some variation in the length of tccP, which reflects diversity in the number of the proline-rich repeats. These results show the existence of a class of "attaching and effacing" pathogens which express a combination of EPEC and EHEC virulence determinants.
Screening procedure for complementation-dependent mutants of vesicular stomatitis virus (1975)

To isolate new types of vesicular stomatitis virus (VSV) mutants, a four-stage screen was developed which identifies and characterizes mutants capable of complementing the defect in the VSV temperature-sensitive mutant tsG11. Two types of mutants of VSV, Indiana serotype, have been found by using the screen; they are new temperature-sensitive mutants which are, of necessity, not in complementation group I and mutants which do not produce plaques under conditions of single infection at 31 C (the normal permissive temperature) and are, therefore, called complementation-dependent mutants. The newly isolated, temperature-sensitive mutants fall into three complementation groups, two of which are congruent with known complementation groups; the newly identified group extends to six the number of complementation groups of VSV Indiana. The nature of the complementation-dependent mutants has not been established, but one was shown to not contain a significant deletion in its nucleic acid.
The effect of hearing aid dynamic range compression on speech intelligibility in a realistic virtual sound environment (2022)

Measures of "aided" speech intelligibility (SI) for listeners wearing hearing aids (HAs) are commonly obtained using rather artificial acoustic stimuli and spatial configurations compared to those encountered in everyday complex listening scenarios. In the present study, the effect of hearing aid dynamic range compression (DRC) on SI was investigated in simulated real-world acoustic conditions. A spatialized version of the Danish Hearing In Noise Test was employed inside a loudspeaker-based virtual sound environment to present spatialized target speech in background noise consisting of either spatial recordings of two real-world sound scenarios or quadraphonic, artificial speech-shaped noise (SSN). Unaided performance was compared with results obtained with a basic HA simulator employing fast-acting DRC. Speech reception thresholds (SRTs) with and without DRC were found to be significantly higher in the conditions with real-world background noise than in the condition with artificial SSN. Improvements in SRTs caused by the HA were only significant in conditions with real-world background noise and were related to differences in the output signal-to-noise ratio of the HA signal processing between the real-world versus artificial conditions. The results may be valuable for the design, development, and evaluation of HA signal processing strategies in realistic, but controlled, acoustic settings.
Dehydrogenation of propane in the presence of CO2 on Cr(3%)/SiO2 catalyst under supercritical conditions (2020)

The propane dehydrogenation reaction was carried out in the presence of CO2 on a Cr(3%)/SiO2 catalyst under supercritical conditions. Dependences of the propane conversion, product selectivity, and olefin productivity on the C3H8:CO2 ratio and reagent consumption were revealed. It was found that the application of supercritical conditions resulted in the increase in propylene productivity by a factor of three and overall olefin productivity by a factor of five as compared to a conventional reaction in the gas phase.
Self-assembled quantum dot-based swept laser source for optical coherence tomography applications (2012)

In this work the use of two identical QD SOAs to enhance the performance of swept laser system for OCT applications is discussed, resulting in an increase in bandwidth up to 94nm. The combination of GaAs based QD SOAs and InP based QW SOAs for realizing broad bandwidth sources for OCT system is described. For the swept laser source a 154nm spectral bandwidth from 1193nm to 1347nm and an average power of 8mW is obtained and for the filtered ASE source a 225 nm bandwidth is demonstrated.
Manuscript: The National Implications of Adding Sewer CH4 and Methanol-Derived CO2 to Wastewater Treatment and Conveyance GHG Inventories (2017)

Sewer methane (CH4) and methanol carbon dioxide (CO2) have been poorly covered in greenhouse-gas (GHG) emissions protocols. Sewer CH4 in the developed world has been formally discounted by the IPCC (2006) and this approach has been adopted by all other protocols to date. Methanol, which is derived from natural gas and its conversion to CO2 therefore represents an anthropogenic emissions source, had been ignored until ICLEI's US Protocol published their methodology WW.9 in 2012. This paper normalizes estimate for these two “new” GHG sources within the context of DC Water's (Washington, DC) Blue Plains Advanced Wastewater Treatment Plant's (AWTP) GHG inventory. These DC Water data are then used to estimate the national significance of these new sources.
Testing the role of predicted gene knockouts in human anthropometric trait variation (2016)

Although the role of complete gene inactivation by two loss-of-function mutations inherited in trans is well-established in recessive Mendelian diseases, we have not yet explored how such gene knockouts (KOs) could influence complex human phenotypes. Here, we developed a statistical framework to test the association between gene KOs and quantitative human traits. Our method is flexible, publicly available, and compatible with common genotype format files (e.g. PLINK and vcf). We characterized gene KOs in 4498 participants from the NHLBI Exome Sequence Project (ESP) sequenced at high coverage (>100×), 1976 French Canadians from the Montreal Heart Institute Biobank sequenced at low coverage (5.7×), and >100 000 participants from the Genetic Investigation of ANthropometric Traits (GIANT) Consortium genotyped on an exome array. We tested associations between gene KOs and three anthropometric traits: body mass index (BMI), height and BMI-adjusted waist-to-hip ratio (WHR). Despite our large sample size and multiple datasets available, we could not detect robust associations between specific gene KOs and quantitative anthropometric traits. Our results highlight several limitations and challenges for future gene KO studies in humans, in particular when there is no prior knowledge on the phenotypes that might be affected by the tested gene KOs. They also suggest that gene KOs identified with current DNA sequencing methodologies probably do not strongly influence normal variation in BMI, height, and WHR in the general human population.
Data Supplement from Downregulation of MHC-I Expression Is Prevalent but Reversible in Merkel Cell Carcinoma (2023)

&lt;p&gt;Allred proportion (ranging from 0-5) and intensity (ranging from 0-3) scores for each tumor. The median score among triplicate TMA cores and reviewers was utilized. Most MCC tumors with an Allred score of 7 continued to express MHC class I in all tumor cells, however the intensity of expression was significantly reduced as compared to those with an Allred score of 8.&lt;/p&gt;
Focus-and-Expand: Training Guidance Through Gradual Manipulation of Input Features (2020)

We present a simple and intuitive Focus-and-eXpand (\fax) method to guide the training process of a neural network towards a specific solution. Optimizing a neural network is a highly non-convex problem. Typically, the space of solutions is large, with numerous possible local minima, where reaching a specific minimum depends on many factors. In many cases, however, a solution which considers specific aspects, or features, of the input is desired. For example, in the presence of bias, a solution that disregards the biased feature is a more robust and accurate one. Drawing inspiration from Parameter Continuation methods, we propose steering the training process to consider specific features in the input more than others, through gradual shifts in the input domain. \fax extracts a subset of features from each input data-point, and exposes the learner to these features first, Focusing the solution on them. Then, by using a blending/mixing parameter $α$ it gradually eXpands the learning process to include all features of the input. This process encourages the consideration of the desired features more than others. Though not restricted to this field, we quantitatively evaluate the effectiveness of our approach on various Computer Vision tasks, and achieve state-of-the-art bias removal, improvements to an established augmentation method, and two examples of improvements to image classification tasks. Through these few examples we demonstrate the impact this approach potentially carries for a wide variety of problems, which stand to gain from understanding the solution landscape.