gebhart/patrepeval huggingface dataset:
Expression of Trophinin, Tastin, and Bystin by Trophoblast and Endometrial Cells in Human Placenta1 (1999)

Trophinin, tastin, and bystin comprise a complex mediating a unique homophilic cell adhesion between trophoblast and endometrial epithelial cells at their respective apical cell surfaces. In this study, we prepared mouse monoclonal antibodies specific to each of these molecules. The expression of these molecules in the human placenta was examined immunohistochemically using the antibodies. In placenta from the 6th week of pregnancy, trophinin and bystin were found in the cytoplasm of the syncytiotrophoblast in the chorionic villi, and in endometrial decidual cells at the utero placental interface. Tastin was exclusively present on the apical side of the syncytiotrophoblast. Tissue sections were also examined by in situ hybridization using RNA probes specific to each of these molecules. This analysis showed that trophoblast and endometrial epithelial cells at the utero placental interface express trophinin, tastin, and bystin. In wk 10 placenta, trophinin and bystin were found in the intravillous cytotrophoblast, while tastin was not found in the villi. After wk 10, levels of all three proteins decreased and then disappeared from placental villi.
Treatment plan evaluation for interstitial photodynamic therapy in a mouse model by Monte Carlo simulation with FullMonte (2015)

Monte Carlo (MC) simulation is recognized as the “gold standard” for biophotonic simulation, capturing all relevant physics and material properties at the perceived cost of high computing demands. Tetrahedral-mesh-based MC simulations particularly are attractive due to the ability to refine the mesh at will to conform to complicated geometries or user-defined resolution requirements. Since no approximations of material or light-source properties are required, MC methods are applicable to the broadest set of biophotonic simulation problems. MC methods also have other implementation features including inherent parallelism, and permit a continuously-variable quality-runtime tradeoff. We demonstrate here a complete MC-based prospective fluence dose evaluation system for interstitial PDT to generate dose-volume histograms on a tetrahedral mesh geometry description. To our knowledge, this is the first such system for general interstitial photodynamic therapy employing MC methods and is therefore applicable to a very broad cross-section of anatomy and material properties. We demonstrate that evaluation of dose-volume histograms is an effective variance-reduction scheme in its own right which greatly reduces the number of packets required and hence runtime required to achieve acceptable result confidence. We conclude that MC methods are feasible for general PDT treatment evaluation and planning, and considerably less costly than widely believed.
Dynamic group testing to control and monitor disease progression in a population (2022)

In this paper, we introduce a "discrete-time SIR stochastic block model" that also allows for group testing and interventions on a daily basis. Our model can be regarded as a discrete version of the well-known continuous-time SIR stochastic network model [1] and relies on a specific type of weighted graph to capture the underlying community spread. Given that infection model, we then formulate a dynamic group-testing problem by asking: (a) what is the minimum number of tests needed everyday to identify all infections? and (b) are there nonadaptive group testing strategies that achieve this with vanishing error probability? Our results show that one can leverage the knowledge of the community infection model to compute a lower bound on the number of tests and also inform nonadaptive group testing algorithms, so that they can achieve (almost) the same performance as complete individual testing with a much smaller number of tests. Moreover, these algorithms are order-optimal, under specific conditions.
Prism adaptation improves neglect-related motor perseveration (P5.175) (2015)

Prism adaptation may improve motor-intentional deficits in a patient with chronic post-stroke left spatial neglect. While performing four cancellation tasks, he displayed left-sided omissions and three types of motor perseverative errors: additional marks (AM), scribbles, and flying marks (FM). After two weeks of home-based Prism Adaptation therapy, our patient cancelled an average of 19.6[percnt] more targets on all four cancellation tasks and improved significantly on figure copying/drawing. Consistent with Gandola et al 2013 who showed that only AM and FM errors are related to neglect severity, we predicted that PAT would improve these perseverative errors, but have no effect on scribbles. A t-test evaluating percent changes in AM/FM Density (mean = -0.633, std. dev. = 0.243) and in Scribble Density (mean = -0.030, std. dev. = 0.220) showed a trend (one-tailed t(3)=-1.86, p=0.08), but did not reach significance. PAT did decrease the density of AM/FM errors by over 63.3[percnt]. AM and FM errors may be related to motor-intentional Aiming mechanisms, thereby making them more susceptible to prism therapy. Further research is needed to examine whether prism adaptation may be effective for all individuals with AM or FM motor perseverative errors, even if they do not meet the clinical criteria for spatial neglect.
Surface Crystal Growth of Perovskite Nanocrystals via Postsynthetic Lead(II) Bromide Treatment to Increase the Colloidal Stability and Efficiency of Light-Emitting Devices (2020)

The surface modification of metal halide perovskite nanocrystals (NCs) significantly impacts their optical properties and colloidal stability. This subsequently affects the performance of light-emitting devices (LEDs). Therefore, numerous surface passivation techniques like ligand exchange and metal halide doping have been explored to passivate the surface defects of perovskite NCs and obtain highly efficient LEDs. In this study, we demonstrated the postsynthetic metal halide doping treatment using lead(II) bromide (PbBr<sub>2</sub>) to passivate the surface defects of the CsPbBr<sub>3</sub> NCs at a moderate reaction temperature of 80 °C. The alkyl quaternary ammonium salt, didodecyldimethylammonium bromide (DC<sub>12</sub>AB), enabled the complete dissolution of PbBr<sub>2</sub> in a nonpolar solvent, toluene. Because of surface crystal growth, the particle sizes of the PbBr<sub>2</sub>-doped CsPbBr<sub>3</sub> NCs were higher than those of the as-synthesized CsPbBr<sub>3</sub> NCs. The photoluminescence quantum yield of the CsPbBr<sub>3</sub> NCs drastically increased from 26.8 to 83.9% after the PbBr<sub>2</sub> doping treatment. Moreover, the PbBr<sub>2</sub>-doped CsPbBr<sub>3</sub> NCs possessed long-term colloidal stability of more than 2 months that indicates the strong bonding between the NCs and ligands. We observed that the alkyl chain length of the quaternary alkyl ammonium salts affected the luminance and device stability during operations. In this study, a promising strategy was devised to achieve highly luminescent perovskite NCs with excellent colloidal stability that can enhance the performance of LEDs.
Improvement of butanol production in Clostridium acetobutylicum through enhancement of NAD(P)H availability (2018)

Clostridium acetobutylicum is a natural producer of butanol, butyrate, acetone and ethanol. The pattern of metabolites reflects the partitioning of redox equivalents between hydrogen and carbon metabolites. Here the exogenous genes of ferredoxin-NAD(P)<sup>+</sup> oxidoreductase (FdNR) and trans-enoyl-coenzyme reductase (TER) are introduced to three different Clostridium acetobutylicum strains to investigate the distribution of redox equivalents and butanol productivity. The FdNR improves NAD(P)H availability by capturing reducing power from ferredoxin. A butanol production of 9.01 g/L (36.9% higher than the control), and the highest ratios of butanol/acetate (7.02) and C<sub>4</sub>/C<sub>2</sub> (3.17) derived metabolites were obtained in the C acetobutylicum buk<sup>-</sup> strain expressing FdNR. While the TER functions as an NAD(P)H oxidase, butanol production was decreased in the C. acetobutylicum strains containing TER. The results illustrate that metabolic flux can be significantly changed and directed into butanol or butyrate due to enhancement of NAD(P)H availability by controlling electron flow through the ferredoxin node.
Detection and Quantification of Multi-Analyte Mixtures Using a Single Sensor and Multi-Stage Data-Weighted RLSE (2018)

This work reports the development and experimental verification of a sensor signal processing technique for online identification and quantification of aqueous mixtures of benzene, toluene, ethylbenzene, xylenes (BTEX) and 1, 2, 4-trimethylbenzene (TMB) at ppb concentrations using time-dependent frequency responses from a single polymer-coated shear-horizontal surface acoustic wave sensor. Signal processing based on multi-stage exponentially weighted recursive leastsquares estimation (EW-RLSE) is utilized for estimating the concentrations of the analytes in the mixture that are most likely to have produced a given sensor response. The initial stages of EW-RLSE are used to eliminate analyte(s) that are erroneously identified as present in the mixture; the final stage of EW-RLSE with the corresponding sensor response model representing the analyte(s) present in the mixture is used to obtain a more accurate quantification result of the analyte(s). The success of this method in identifying and quantifying analytes in real-time with high accuracy using the response of just a single sensor device demonstrates an effective, simpler, lower-cost alternative to a sensor array that includes the advantage of not requiring a complex training protocol.
Reduction of the Switching Field of TMR Devices. (2001)

Two types of laminated structures for free layers were investigated to avoid the increase in the switching field of the free layer caused by the reduction of the size of the TMR element. Laminated free layers of NiFe(5)/Ru(0.7)/NiFe(3) and NiFe(4)/Ta(3)/NiFe(4) showed a lower switching field than a single free layer of NiFe(8). The low switching field of the synthetic free layer is due to the decrease in the net moment, which results in a decrease of the demagnetizing field. In the case of the NiFe(4)/Ta(3)/NiFe(4) free layer, there is a possibility that magnetostatic coupling plays an important role in the decrease in the demagnetizing field.
Deconvolution of Combinatorial Libraries for Drug Discovery:  Theoretical Comparison of Pooling Strategies (1996)

Synthesis and testing of mixtures of compounds in a combinatorial library allow much greater throughput than synthesis and testing of individual compounds. When mixtures of compounds are screened, however, the possibility exists that the most active compound will not be identified. The specific strategies employed for pooling and deconvolution will affect the likelihood of success. We have used a nucleic acid hybridization example to develop a theoretical model of library deconvolution for a library of more than 250,000 compounds. This model was used to compare various strategies for pooling and deconvolution. Simulations were performed in the absence and presence of experimental error. We found iterative deconvolution to be most reliable when active molecules were assigned to the same subset in early rounds. Reliability was reduced only slightly when active molecules were assigned randomly to all subsets. Iterative deconvolution with as many as 65,536 compounds per subset did not drastically reduce the reliability compared to one-at-a-time testing. Pooling strategies compared using this theoretical model are compared experimentally in an accompanying paper.
Anomalous contrast in broadband THz near-field imaging of gold microstructures (2021)

THz scattering-type scanning near-field microscopy (s-SNOM) has become a powerful technique for measuring carrier dynamics in nanoscale materials and structures. Changes in a material's local THz reflection or transmission can be correlated to changes in electrical conductivity. Here, we perform tip-based THz nano-imaging of subwavelength gold nanostructures and demonstrate image contrast unrelated to any spatially varying material properties. We show that the specific physical configuration of the gold structures can have a strong influence on local excitations which can obscure the sample's true dielectric response, even in cases where the relevant structures are far outside of the spatial region probed by the AFM tip.
Secure Control in Partially Observable Environments to Satisfy LTL Specifications (2020)

This article studies the synthesis of control policies for an agent that has to satisfy a temporal logic specification in a partially observable environment, in the presence of an adversary. The interaction of the agent (defender) with the adversary is modeled as a partially observable stochastic game. The goal is to generate a defender policy to maximize satisfaction of a given temporal logic specification under any adversary policy. The search for policies is limited to the space of finite-state controllers, which leads to a tractable approach to determine policies. We relate the satisfaction of the specification to reaching (a subset of) recurrent states of a Markov chain. We present an algorithm to determine a set of defender and adversary finite-state controllers of fixed sizes that will satisfy the temporal logic specification and prove that it is sound. We then propose a value-iteration algorithm to maximize the probability of satisfying the temporal logic specification under finite-state controllers of fixed sizes. Finally, we extend this setting to the scenario where the size of the finite-state controller of the defender can be increased to improve the satisfaction probability. We illustrate our approach with an example.
Non-specular point reflections in GNSS bistatic radar (2006)

In this paper the impact of using different measurement platforms with different qualities is discussed. Data collected during three different measurement campaigns were used in this study. The dat ...
Oscillator Models in Unimolecular Reactions (1961)

The absolute reaction-rate theory for the unimolecular decomposition of isolated excited molecules is applied to two models. The first considers the molecule as a set of harmonic oscillators in which only a finite amount of energy may be stored in a particular degree of freedom. In the second model the spacing between adjacent levels is assumed to decrease exponentially. The first leads to a decrease in the lifetime above that calculated for the conventional harmonic oscillator model for short-lived molecules. The second produces an increase depending directly on the rate of change of the level spacing.
Vitamins, 5. Vitamin K (2011)

Abstract The article contains sections titled: 1. Introduction; History 2. Physical Properties 3. Chemical Properties 4. Occurrence 5. Biosynthesis 6. Chemical Synthesis 7. Analysis 8. Metabolism 9. Importance for the Organism 9.1. Function 9.2. Antagonists and Anticoagulants 9.3. Relative Activity 10. Deficiency Symptoms 10.1. Causes 10.2. Evaluation of Vitamin K Status 11. Requirement 12. Application 13. Tolerance 14. Trade Names and Economic Aspects
Genomic DNA isolation from amplified product for recursive genotyping of low-template DNA samples (2013)

Thesis (M.S.F.S.) PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
16.4 0.6-to-1.0V 279&#x03BC;m<sup>2</sup>, 0.92&#x03BC;W temperature sensor with less than &#x002B;3.2/-3.4&#x00B0;C error for on-chip dense thermal monitoring (2014)

On-chip temperature sensors are key building blocks for the thermal management of multi-core microprocessors. The sensors are embedded at multiple locations in a microprocessor and monitor temperatures that are used to manage the operation of the microprocessor under local and global thermal constraints. While existing sensors achieve impressive area and accuracy, emerging technology trends such as multi-core architectures, 3D integration, tri-gate devices, and low-voltage operation demand even better sensors with difficult-to-meet requirements. Those requirements are three-fold: 1) Sensors need to be area efficient. By increasing the number of cores and hot spots, there are more locations that require thermal monitoring. To reduce the overhead, the sensor footprint needs to be minimized. A compact footprint is further critical for design flexibility, as the exact sensor locations (e.g. near hot spots) are often only identified in later stages of the design process [1]. 2) Sensors need to have low calibration cost, while achieving sufficient accuracy. The requirements of <;8°C in absolute inaccuracy and <;3°C in relative inaccuracy have been outlined in [2]. 3) Finally, the sensors need better supply voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> ) scalability. Sub-1V operation for digital systems is being explored to reduce power. The conventional sensors often cannot operate below 1V, necessitating additional power distribution or regulation. Sub-1V scalability eliminates such overhead.
Quencher Effects at 22 nm Pattern Formation in Chemically Amplified Resists (2008)

The trade-off between line edge roughness (LER), sensitivity, and resolution is the most challenging issue associated with the development of resist processes for extreme ultraviolet (EUV) lithography. It has been reported that quenchers (basic compounds) affect the sensitivity, resolution, and extent of LER. However, the details are still unclear. In this study, the effects of quencher diffusion constants in 22 nm pattern formation were investigated by a simulation based on the reaction mechanism of chemically amplified EUV resists. For the suppression of line width expansion due to acid diffusion, mobile quenchers are effective. The quality of a latent image is also improved with the increase in diffusion constant. However, the high mobility of quenchers increases the pattern dependence of line width. The same order of diffusion constants for acids and quenchers are preferable for 22 nm fabrication.
Research Notes : United States : Inheritance of resistance to Phytophthora megasperma f. sp. glycinea in the soybean PI 92.718-2 (1987)

Phytophthora root rot, caused by Phytophthora megasperma f. sp. glycinea Kuan and Erwin, (Pmg) is one of the most serious diseases of soybeans when conditions are favorable (Kuan and Irwin, 1980). Resistance in soybeans to phytophthora root rot has been reported to be controlled by nine dominant genes (Layton et al., 1984). The cultivars 'Bombay' and 'OAC 211' also have been identified to carry one and two genes for Pmg resistance, respectively, although these genes have not been named (Moots et al., 1983). Twenty-four races of the pathogen have been identified (Keeling, 1984).
Fast cell search algorithm for system with coexisting cellular and hot-spot cells suitable for OFCDM forward link broadband wireless access (2004)

This paper proposes a new cell-specific scrambling code (CSSC) assignment method and a fast cell search algorithm in the forward link of orthogonal frequency and code division multiplexing (OFCDM) wireless access that are suited to a system of coexisting hot-spot and cellular cells. In the proposed method, one or some CSSC groups and thereby the CSSCs belonging to the CSSC groups are exclusively assigned to hot-spot cells. By detecting the best CSSC assigned to a hot-spot cell with higher priority than the cellular cells, the best cell including the hot-spot cell obtaining the minimum path loss can be detected far faster than by using the conventional cell search method, which is associated with uniform CSSC assignment. The computer simulation results elucidate that by applying the proposed cell search method together with the exclusive CSSC assignment to the hot-spot cells, the detection probability of the hot-spot cell of 0.7 is achieved after the cell search time of 1.7 msec at the average received signal energy of the common pilot channel (CPICH) per bit-to-background noise power spectrum density ratio of the cellular cell of E/sub b/N/sub 0/ = 9.9 dB at the cell boundary without notifying the user equipment of the CSSC information of the surrounding cells and when the transmission power ratio of the CPICH to the traffic channel (TCH) for a one-code channel is R/sub CPICH/ = 9 dB in a 20-cell layout model.
Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo (2023)

Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene <i>PTMA</i>, which encodes prothymosin α. This association was genome-wide significant (<i>P</i><sub>adjusted</sub> < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
Investigation of Fundamental Transport Mechanism of Product Water From Cathode Catalyst Layer in PEMFCs (2007)

Understanding how water produced in the cathode catalyst layer is removed during PEMFC operation can be critical for materials optimization and representative models. The present work combines in-situ and ex-situ experiments to determine the dominant water discharge mechanism when considering capillarity and vapor transport. Water flux of vapor driven by the thermal gradient in the cathode diffusion layer is shown to be sufficient to remove product water at high current densities with saturated gas in the gas delivery channels. The role of an intermediate microporous layer and its impact in vapor versus liquid transport is also considered. Through novel experimental techniques and capturing all key physical interactions it is concluded that vapor diffusion is the fundamental mechanism by which water is removed from the cathode catalyst layer.