gebhart/patrepeval huggingface dataset:
Design and control considerations for safe needle steering in brain tissue (2012)

This paper presents a preliminary investigation of numerous design and control parameters of bevel-tipped needles with regard to their effect on safety of brain tissue during insertion. The needle is designed for use with a control method developed in our laboratory that provides proportional control of path curvature via duty-cycled rotation. Parameters investigated include needle radius, bevel angle, bevel tip fillet radius, insertion velocity, and rotational velocity. Design parameters are investigated in terms of their effect on stress, strain, and strain rate of brain tissue. Based on the effects of the preliminary investigation, a safe needle design is selected and demonstrated in a three-dimensional simulation of closed-loop control of needle steering via duty-cycled rotation in a deep brain stimulation application.
Binary copper oxide semiconductors: From materials towards devices (2012)

Abstract Copper‐oxide compound semiconductors provide a unique possibility to tune the optical and electronic properties from insulating to metallic conduction, from bandgap energies of 2.1 eV to the infrared at 1.40 eV, i.e., right into the middle of the efficiency maximum for solar‐cell applications. Three distinctly different phases, Cu 2 O, Cu 4 O 3 , and CuO, of this binary semiconductor can be prepared by thin‐film deposition techniques, which differ in the oxidation state of copper. Their material properties as far as they are known by experiment or predicted by theory are reviewed. They are supplemented by new experimental results from thin‐film growth and characterization, both will be critically discussed and summarized. With respect to devices the focus is on solar‐cell performances based on Cu 2 O. It is demonstrated by photoelectron spectroscopy (XPS) that the heterojunction system p‐Cu 2 O/n‐AlGaN is much more promising for the application as efficient solar cells than that of p‐Cu 2 O/n‐ZnO heterojunction devices that have been favored up to now.
Human Pose and Seat Occupancy Classification with Commercial MMWave WiFi (2020)

Our previous studies introduced a mid-grained intermediate-level channel measurement – spatial beam signal-to-noise ratios (SNRs) that are inherently available and defined in the 60-GHz IEEE 802.11ad/ay standards – for the fingerprinting-based indoor localization. In this paper, we take one step further to use the mid-grained channel measurement for human monitoring applications including human pose and seat occupancy classifications. The effectiveness of the mid-grained channel measurement is validated by an in-house experimental dataset that includes 5 separate data collection sessions using classical classification methods and modern deep neural networks. Our preliminary result shows that mmWave beam SNRs are capable of delivering high classification accuracy above 90%.
Hierarchical Bayes Models for the Progression of HIV Infection Using Longitudinal CD4 T-Cell Numbers (1992)

Abstract Taking the absolute number of CD4 T-cells as a marker of disease progression for persons infected with the human immunodeficiency virus (HIV), we model longitudinal series of such counts for a sample of 327 subjects in the San Francisco Men's Health Study (Waves 1–8, excluding zidovudine cases). We conduct a fully Bayesian analysis of these data. We employ individual level nonlinear models incorporating such critical features as incomplete and unbalanced data, population covariates (age at study entry and an indicator of self-reported herpes simplex virus infection), unobserved random change points, heterogeneous variances, and errors in variables. We construct prior distributions using results of previously published work from several different sources and data from HIV-negative men in this study. We also develop an approach to Bayesian model choice and individual prediction. Our analysis provides marginal posterior distributions for all population parameters in our model for this cohort. Using an inverse prediction approach, we also develop the posterior distributions of time for CD4 T-cell number to reach a specified level.
AEROSOL DRUG DELIVERY FOR LUNG ON A CHIP (2011)

Animal models for drug toxicity and efficacy are expensive and often do not accurately reflect the human response, resulting in wasteful clinical trials and ineffective drug development. Expanding human cell culture systems to microenvironments that mimic in vivo organ-level function may increase human relevance and translation of products to patients. Here we present a method of delivering aerosolized drug to a previously described biomimetic microfluidic device or ‘Lung-on-a-Chip” that reproduces the alveolar-capillary interface of the human lung under physiologically relevant cyclic mechanical strain and flow conditions (Huh et al., Science 2010; 328:1662-1668). We demonstrate the first reported deposition of aerosol into a microfluidic channel using a commercial nebulizer as a source of aerosol. This method should enable toxicity and efficacy testing of pulmonary drugs in a human-relevant in vitro system.
Correlating electrochemical properties with structure on the mesoscale (2013)

The integration of inorg. nanocrystals as building units into mesoscale architectures yields materials whose structure is controllable on at., nano, and meso length scales providing a foundation for understanding how system-level functional properties emerge. We assembly nanocrystals into thin film electrodes by chem. displacing the insulating org. ligands coating their surfaces to leave exposed coordination sites at which block copolymer templating agents dynamically adsorb [1]. Through selection of the nanocrystal and polymer building blocks, the crystallite size and shape, the mesopore dimensions, and the inorg. wall thickness are all tunable. As a result, electrochem. properties can be correlated with structure on multiple length scales to det. design rules for high performance electrodes. In one example, the shape and size of anatase titania nanocrystals are correlated with performance characteristics of lithium ion battery electrodes. Nanorod-based mesoporous films are found to exhibit minimal loss in charge capacity out to at least 1000 cycles.[1] R. Buonsanti, et al. Nano Lett. 12 (2012), 3872.
2,4,5-Trichlorophenol Degradation Using a Novel TiO2-Coated Biofilm Carrier: Roles of Adsorption, Photocatalysis, and Biodegradation (2011)

Intimate coupling of photocatalysis and biodegradation (ICPB) offers potential for degrading biorecalcitrant and toxic organic compounds. This study reports on a novel sponge-type, TiO(2)-coated biofilm carrier that showed significant adherence of TiO(2) and ability to accumulate biomass in its interior. This carrier was tested for ICPB in a continuous-flow photocatalytic circulating-bed biofilm reactor (PCBBR) to mineralize 2,4,5-trichlorophenol (TCP), which is biorecalcitrant. Four mechanisms possibly acting in ICPB were tested separately: TCP adsorption to the carrier, UV photolysis, UV photocatalysis, and biodegradation by biofilm inside the carrier. The carrier exhibited strong TCP adsorption that followed a Freundlich isotherm with an exponent near 2. Whereas UV photolysis was negligible, photocatalysis produced TCP-degradation products that could be mineralized, and the strong adsorption of TCP to the carrier enhanced biodegradation by relieving toxicity. Validating the ICPB concept, biofilm was protected inside the carriers, although biomass originally on the outer surface of the carriers was eliminated. ICPB significantly lowered the diversity of the bacterial community, but five genera known to biodegrade chlorinated phenols (Ralstonia, Bradyrhizobium, Methylobacterium, Cupriavidus, and Pandoraea) were markedly enriched.
Low Temperature Strength and Notch Sensitivity of Glass Mat Polypropylene (1997)

Literature on the effects of lowered temperature on the toughness of random short fiber composites have neither offered a clear trend nor explained the mechanisms of failure. In this work, unnotched and notched strengths at room temperature and −30°C of two glass mat polypropylenes with different fiber architectures are investigated. Observations are explained based on models for Young's modulus and notch sensitivity. Increases in strength and stiffness with lowered temperature are caused by increased matrix modulus and yield stress. Fiber bridging operating in a damage zone of substantial length was the major toughening mechanism and forms the basis for the modeling approach for notch sensitivity. Increased notch toughness at low temperature is caused by increased work of fracture in the damage zone. The increased matrix modulus and yield stress lead to an increased toughening efficiency of short fibers.
Preparation of (Triphenylphosphoranylidene)‐Ketene from (Methoxycarbonylmethylene)‐Triphenylphosphorane (2005)

Abstract (Triphenylphosphoranylidene)ketene (Methoxycarbonylmethylene)triphenylphosphorane Hexamethyldisilazane Sodium amide
Cement properties with embedded sensors for wellbore integrity monitoring (2020)

There is a need for embedded sensor technologies to monitor wellbore integrity in real-time for carbon storage and geothermal applications. Emerging sensing technologies such as optical fiber sensors and wireless sensors have been studied for physical parameter monitoring (e.g. temperature, vibration, and strain) and chemical parameter monitoring (e.g. pH, CO<sub>2</sub>, corrosion) to monitor structural health of the wellbore. The desirable sensors need to be able to withstand the harsh environments relevant for carbon storage and geothermal wellbores, and they must not inadvertently cause potential sources of wellbore failures. Therefore, we investigated the cement properties with embedded sensors to compare with baseline cement properties, including porosity, permeability, mechanical properties (e.g. Young’s modulus, Poisson’s Ratio, etc), and 3D computed tomography (CT) scans. The sensor devices (optical fiber sensors [OFS] and wireless chip sensors) were embedded in cement cores under wellbore relevant conditions. Then, the cement samples were examined using AutoLab 1500, nitrogen permeability testing, helium porosity testing, and 3D CT scanners. Results show that the cement samples with embedded sensor devices had a slight increase in porosity of 1.5% to 3.6% compared to the blank cement samples. Permeability slightly increased by 0.001 mD with embedded chip sensors. The embedded chip sensors did not significantly change the cement mechanical properties; whereas, the embedded OFS prototypes improved the cement mechanical strengths, e.g. increasing the Young’s modulus by as much as 10% and the bulk modulus by up to 25.5%. CT scans confirmed the proper embedding and good bonding between sensor devices and cement.
Whole Genomes Define Concordance of Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer (2017)

ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among solid malignancies and improved therapeutic strategies are needed to improve outcomes. Patient-derived xenografts (PDX) and patient-derived organoids (PDO) serve as promising tools to identify new drugs with therapeutic potential in PDAC. For these preclinical disease models to be effective, they should both recapitulate the molecular heterogeneity of PDAC and validate patient-specific therapeutic sensitivities. To date however, deep characterization of PDAC PDX and PDO models and comparison with matched human tumour remains largely unaddressed at the whole genome level. We conducted a comprehensive assessment of the genetic landscape of 16 whole-genome pairs of tumours and matched PDX, from primary PDAC and liver metastasis, including a unique cohort of 5 ‘trios’ of matched primary tumour, PDX, and PDO. We developed a new pipeline to score concordance between PDAC models and their paired human tumours for genomic events, including mutations, structural variations, and copy number variations. Comparison of genomic events in the tumours and matched disease models displayed single-gene concordance across major PDAC driver genes, and genome-wide similarities of copy number changes. Genome-wide and chromosome-centric analysis of structural variation (SV) events revealed high variability across tumours and disease models, but also highlighted previously unrecognized concordance across chromosomes that demonstrate clustered SV events. Our approach and results demonstrate that PDX and PDO recapitulate PDAC tumourigenesis with respect to simple somatic mutations and copy number changes, and capture major SV events that are found in both resected and metastatic tumours.
Organic-Acid-Assisted Fabrication of Low-Cost Li-Rich Cathode Material (Li[Li1/6Fe1/6Ni1/6Mn1/2]O2) for Lithium–Ion Battery (2014)

A novel Li-rich cathode Li[Li1/6Fe1/6Ni1/6Mn1/2]O2 (0.4Li2MnO3-0.6LiFe1/3Ni1/3Mn1/3O2) was synthesized by a sol-gel method, which uses citric acid (SC), tartaric acid (ST), or adipic acid (SA) as a chelating agent. The structural, morphological, and electrochemical properties of the prepared samples were characterized by various methods. X-ray diffraction showed that single-phase materials are formed mainly with typical α-NaFeO2 layered structure (R3̅m), and the SC sample has the lowest Li/Ni cation disorder. The morphological study indicated homogeneous primary particles in good distribution size (100 nm) with small aggregates. The Fe, Ni, and Mn valences were determined by X-ray absorption near-edge structure analysis. In coin cell tests, the initial reversible discharge capacity of an SA electrode was 289.7 mAh g(-1) at the 0.1C rate in the 1.5-4.8 V voltage range, while an SC electrode showed a better cycling stability with relatively high capacity retention. At the 2C rate, the SC electrode can deliver a discharge capacity of 150 mAh g(-1) after 50 cycles. Differential capacity vs voltage curves were employed to further investigate the electrochemical reactions and the structural change process during cycling. This low-cost, Fe-based compound prepared by the sol-gel method has the potential to be used as the high capacity cathode material for Li-ion batteries.
IRREVERSIBLE OXIDATION OF PORPHYRINATO COBALT(II)(TPPCo) AND THE EFFECT OF FLUORINE-CONTAINING POLYMERS ON THE LIFETIME OF TPPCo COMPLEX MEMBRANES. (2003)

The oxidizing process and the oxygen-binding lifetime of 5,10,15,20-tetra( o -pivalamidophenyl)-porphyrinato cobalt(II) (TPPCo) complexed with poly(vinylimidazole- co -fluoropentyl methacrylate) (PFIm) were studied,and the mechanism and dynamics of irreversible oxidation of TPPCo were discussed.The TPPCo displayed a reversible change in the UV-visible absorption spectrum from the deoxy form ( λ max = 530?nm ) to the oxygen-binding one ( λ max = 548?nm ) with an isosbestic point at 538 nm,in response to the partial oxygen pressure of the atmosphere.But the active TPPCo complex in the membrane was slowly changed,via the irreversible oxidation reaction in the open atmosphere,to the TPPCo(Ⅲ) complex without the oxygen-binding ability,which could be monitored by the UV-visible absorption at λ max = 548?nm.In the solid membrane state, water molecules in air may attack the TPPCo-bound dioxygen to yield a hydrodioxy radical and TPPCo(Ⅲ),which is the main reason that diminishes the oxygen-binding ability of the TPPCo complex and that of the membrane.The half-lifetime ( τ ) of the TPPCo complex as an oxygen carrier was measured by allowing the TPPCo-PFIm membrane to stand in dry air (environmental humidity 10%),in laboratory air (humidity ca. 50%),and in a water vapor atmosphere (humidity 95%) at room temperature,respectively.The decrease course of the active TPPCo complex approximately follows the first-order kinetics and gives the t values.The τ value of the PFIm-TPPCo complexed membrane was as long as ca. 250 days even in the water vapor-saturated atmosphere.Under the same laboratory air condition,the lifetime of the PFIm-TPPCo membrane was much longer ( ca. 13 times) than that of the reference non-fluoro membrane such as the membrane of TPPCo complexed with poly(octyl methacrylate- co -vinylimidazole).The hydrophobic property of the PFIm polymer is considered to suppress the irreversible oxidation of the active TPPCo carriers caused by water molecules and to significantly prolong the operational lifetime of the TPPCo complex membrane.
SCRF/Monte Carlo Study of Solvent Effects on a Polar [2+2] Cycloaddition (1996)

Solvent effects on the polar [2+2] cycloaddition of 1,1-dicyanoethylene (DCNE) and methyl vinyl ether (MVE) have been studied using ab initio self-consistent reaction field (SCRF) and Monte Carlo (MC) statistical mechanics calculations. Emphasis is placed on the dependence of transition-state structure and energetics on solvation and on the impact of using different charge sets and geometries from the SCRF calculations in the MC simulations. The ab initio calculations were performed with dielectric constants ε of 1.0, 2.23 (CCl4), and 35.94 (CH3CN) with the 6-31G* basis set at the Hartree−Fock (HF) level and incorporating electron correlation through MP2 and Becke3LYP density functional methods. Computed dipole moments of 10−17 D for the transition structures overlap estimates based on the solvent effects observed by Steiner and Huisgen. However, the mechanistic picture that emerges is medium dependent. In the gas phase and nonpolar solvent, the results here indicate a concerted (single barrier) process with no intermediate, while at ε = 35.94, an anti zwitterion is formed and then is transformed to the product. With the Onsager and SCIPCM SCRF calculations, the activation energy is computed to be lowered by 10−13 kcal/mol in going from CCl4 to CH3CN, which overestimates observed effects for such reactions. Five sets of charges and geometries from the ab initio calculations were tested in MC free energy perturbation (FEP) simulations using 260 explicit carbon tetrachloride and acetonitrile molecules in periodic cells. The resultant predicted solvent effects of 7−20 kcal/mol on the free energy of activation are also greater than the observed ca. 5 kcal/mol. The best results are obtained using the charges and geometries from Becke3LYP/6-31G* gas-phase (ε = 1) calculations.
Analysis of Closed‐Loop Concepts (2003)

This chapter contains sections titled: Generalized Feedback Signalling Design Analysis of SNR Gain of the Co-phase Algorithm Analysis of SNR Gain of the Order and Co-phase Algorithm SNR Gain in Multipath Rayleigh Fading Channels Errors in Feedback Signalling Feedback Latency Bit-error Probability Transmit Weight Generation for the Order and Co-phase Algorithm SNR Gain in Correlated Rayleigh Fading Channels Summary
Insulin-Like Growth Factor-I Resistance* (1998)

I. Introduction II. The IGFs and Their Receptors III. Genetically Engineered Mouse Models IV. Malnutrition V. Conditions Associated with Genetic IGF-I Resistance in Humans A. African Efe Pygmies B. Leprechaunism and other genetic disorders associated with severe insulin resistance C. Deletions of the distal arm of chromosome 15 D. Rare examples of “idiopathic” short stature associated with elevated circulating levels of IGF-I VI. Conditions Associated with Acquired IGF-I Resistance in Humans A. HIV-1 infection B. Chronic renal insufficiency C. Mauriac syndrome VII. Conclusions
Optimized monotonic convex pair potentials stabilize low-coordinated crystals (2011)

We have previously used inverse statistical-mechanical methods to optimize isotropic pair interactions with multiple extrema to yield low-coordinated crystal classical ground states (e.g., honeycomb and diamond structures) in d-dimensional Euclidean space d. Here we demonstrate the counterintuitive result that no extrema are required to produce such low-coordinated classical ground states. Specifically, we show that monotonic convex pair potentials can be optimized to yield classical ground states that are the square and honeycomb crystals in 2 over a non-zero number density range. Such interactions may be feasible to achieve experimentally using colloids and polymers.
SNR enhancement in radial SSFP imaging using partial k-space averaging (2005)

The steady-state free precessing (SSFP) sequences, widely used in MRI today, acquire data only during a short fraction of the repetition time (TR). Thus, they exhibit a poor scan efficiency. In this paper, a novel approach to extending the acquisition window for a given TR without considerably modifying the basic sequence is explored for radial SSFP sequences. The additional data are primarily employed to increase the signal-to-noise ratio, rather than to improve the temporal resolution of the imaging. The approach is analyzed regarding its effect on the image SNR (signal to noise ratio) and the reconstruction algorithm. Results are presented for phantom experiments and cardiac functions studies. The gain in SNR is most notable in rapid imaging, since SNR enhancement for a constant repetition time may be used to compensate for the increase in noise resulting from angular undersampling.
Fast live simultaneous multiwavelength four-dimensional optical microscopy (2010)

Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000× below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.
Hepatic Nucleases (1975)

In the large granule fraction of rat liver, the density distribution of inhibitor‐sensitive neutral ribonuclease is similar to that for acid hydrolases and its density distribution is similarly modified by Triton WR‐1339 accumulation in lysosomes. Particulate neutral ribonuclease is latent; the enzyme is unmasked by very low digitonin concentrations or hypoosmotic shock. These observations demonstrate that the bulk of liver neutral ribonuclease is associated with the lysosomal system. In view of the neutral pH optimum of the enzyme and of some particularities of its distribution in fractionation experiments, the possibility of an extrahepatic origin of neutral ribonuclease has been investigated. After partial pancreatectomy, a significant decrease is observed in both plasma and liver neutral ribonuclease. The effect is specific, for it does not occur for other lysosomal enzymes. Also, labelled bovine pancreatic ribonuclease, when injected intravenously, is taken up by the liver. The sedimentable labelled enzyme has a density distribution similar to the distribution of other foreign proteins, horseradish peroxidase or yeast invertase. These results are explained by the uptake of plasmatic neutral ribonuclease from pancreatic origin by the liver.